Thank you for your report! :sparkles:

To reproduce the issue can you please provide the following additional information about your system:

Which exact PIConGPU version did you use? Did you apply modifications?
compiler (gnu, intel, ...) and version (e.g., g++ --version or $CXX --version) did you load modules?
cmake version (cmake --version)
operating system / system name (e.g., Hypnos (HZDR), Ubuntu 14.04)
short example scripts and example data to reproduce the issue

ax3l on 21 Apr 2017

From a first guess into the blue it looks to me like Freetype (a library for wring text in libpng which we don't necessarily need) was available during the compile of PNGwriter but is not available any more while building PIConGPU

ax3l on 21 Apr 2017

My system is ubuntu 16.04
cmake version is 3.5.1
g++ version is 4.9.3
I tried to install Freetype and configured again
Here is the terminal showed:

cmake command: cmake -DCUDA_ARCH=sm_20 -DCMAKE_INSTALL_PREFIX=/home/lai/paramSets/case001 -DPIC_EXTENSION_PATH=/home/lai/paramSets/case001 /home/lai/src/picongpu
-- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum required is "5.5")
-- Compiling as C++11...
-- Debug version
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- program_options
-- regex
-- filesystem
-- system
-- thread
-- math_tr1
-- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum required is "5.0")
-- Boost version: 1.57.0
-- Found CUDA: /usr/local/cuda (found version "8.0")
-- Could NOT find NVML (missing: NVML_LIBRARY)
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- program_options
-- Found 'adios_config': /usr/bin/adios_config
-- The directory provided by 'adios_config -d' does not exist:
-- Could NOT find ADIOS (missing: ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.10.0")
-- libSplash supports PARALLEL output
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
PNGwriter_LIBRARIES
linked by target "picongpu" in directory /home/lai/src/picongpu/src/picongpu

-- Configuring incomplete, errors occurred!
See also "/home/lai/build/CMakeFiles/CMakeOutput.log".
See also "/home/lai/build/CMakeFiles/CMakeError.log".

Is the NVML a part of CUDA toolkit?
And how to completely install ADIOS and PNGwriter?
Sorry about many questions. I am a beginner in linux.

8i161029 on 21 Apr 2017

Thanks for the update!

Is the NVML a part of CUDA toolkit?

Yes it should since CUDA 8.0 but is optional. The actual error you get starts with the line CMake Error: ... for png.

And how to completely install ADIOS [...]?

ADIOS is optional, either. You can use it instead of libSplash (HDF5) but it's also not the problem you face here.

I tried to install Freetype and configured again. And how to completely install [...] PNGwriter?

Where did you install Freetype? In $HOME/src/freetype? It's not necessary, but if you do make sure to point to it properly via environment vars:

export PNGWRITER_ROOT=$HOME/src/pngwriter
export FREETYPE_DIR=$HOME/src/freetype
export LD_LIBRARY_PATH=$PNGWRITER_ROOT/lib:$FREETYPE_DIR/lib:$LD_LIBRARY_PATH

Last question:

Which exact PIConGPU version did you use? Did you apply modifications?

ax3l on 21 Apr 2017

It looks to me you are running an old version of PIConGPU (which?) which produces a confusing error message on an outdated version of PNGwriter (instead of saying it can't be used/is outdated).

The problem might be that your PNGwriter version is simply outdated (which version of PNGwriter do you use?).

ax3l on 21 Apr 2017

I got PNGwriter and PIConGPU by the commands in install.md:

git clone https://github.com/pngwriter/pngwriter.git
git clone https://github.com/ComputationalRadiationPhysics/picongpu.git $PICHOME/src/picongpu

Did I install an old version?

As for Freetype, when I reboot ubuntu the launcher and menu disappeared.
I tried to open CompizConfig Settings Manager with $ ccsm, but there was

ImportError: /usr/lib/x86_64-linux-gnu/libharfbuzz.so.0: undefined symbol: FT_Reference_Face

I found FT_Reference_Face is a part of Freetype. So I tried to uninstall Freetype and did $ccsm again.
Then the problem solved. So I don't have Freetype now.

8i161029 on 21 Apr 2017

Wonderful! Yes, we don't need freetype so you are good to go now! :)

Feel free to open further issues if you encounter any other troubles.

ax3l on 21 Apr 2017

Sorry...the above problem solved is launcher and menu disappeared in desktop.
I still have the same problem configuring case001.

8i161029 on 21 Apr 2017

Ah, you are running on a plain desktop environment with a single GPU?

Usually running an X-Server and CUDA at the same time is not the greatest combination since both require a lot a GPU memory (especially PIConGPU does take all that is free) and in old X-Server/CUDA combinations the maximum runtime of kernels is limited by the x-server.

You could do the following things:

shut down your window managers and X11 during the run and/or
reserve more GPU memory for your Desktop/X11 reservedGpuMemorySize in our memory.param

What kind of GPU are you using? The default examples without modification might be a bit memory hungry (since we work on Tesla Server GPUs). So you might want to reduce simulation size and number of particles per cell a little.

ax3l on 24 Apr 2017

Since you deinstalled freetype now, remove your install of PNGwriter and install it again to solve that issue.

ax3l on 24 Apr 2017

@8i161029 did you make progress by re-installing PNGwriter with your new environment?

ax3l on 27 Apr 2017

otherwise just remove PNGwriter and continue without it, writing HDF5 will be good enough

ax3l on 27 Apr 2017

I removed the following directories : /$HOME/lib/pngwriter , /$HOME/src/pngwriter, and /$HOME/pngwriter
Then configured again, but the terminal still showed the same message.
Did I remove all the pngwriter? Or how to completely remove?

8i161029 on 29 Apr 2017

And during installing pngwriter, terminal showed that could not found freetype.
Is freetype necessary to install pngwriter?
Last week I installed freetype and then my desktop disappeared, so I uninstalled it.
If it is necessary, how to install it without problem?
Thanks!

8i161029 on 29 Apr 2017

I removed the following directories : /$HOME/lib/pngwriter and /$HOME/pngwriter
and configured again, but the terminal still showed the same message.
Did I remove all the pngwriter? Or how to completely remove?

If you followed our guide, $HOME/lib/pngwriter is the only install. Your PIConGPU configure call should now show pngwriter as not found (but that is not an error) and you should be able to continue. Can you paste it's output here?

And during installing pngwriter, terminal showed that could not found freetype.
Is freetype necessary to install pngwriter?
Thanks!

No, it's not necessary.

ax3l on 29 Apr 2017

Here is the output:

cmake command: cmake -DCUDA_ARCH=sm_20 -DCMAKE_INSTALL_PREFIX=/home/lai/paramSets/case001 -DPIC_EXTENSION_PATH=/home/lai/paramSets/case001 /home/lai/src/picongpu
-- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum required is "5.5")
-- Compiling as C++11...
-- Debug version
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- program_options
-- regex
-- filesystem
-- system
-- thread
-- math_tr1
-- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum required is "5.0")
-- Boost version: 1.57.0
-- Found CUDA: /usr/local/cuda (found version "8.0")
-- Could NOT find NVML (missing: NVML_LIBRARY)
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- program_options
-- Found 'adios_config': /usr/bin/adios_config
-- The directory provided by 'adios_config -d' does not exist:
-- Could NOT find ADIOS (missing: ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.10.0")
-- libSplash supports PARALLEL output
-- Could NOT find Freetype (missing: FREETYPE_LIBRARY FREETYPE_INCLUDE_DIRS)
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
PNGwriter_LIBRARIES
linked by target "picongpu" in directory /home/lai/src/picongpu/src/picongpu

-- Configuring incomplete, errors occurred!
See also "/home/lai/build/CMakeFiles/CMakeOutput.log".
See also "/home/lai/build/CMakeFiles/CMakeError.log".

8i161029 on 29 Apr 2017

Can you please post the output of:

echo $PNGWRITER_ROOT
ls $PNGWRITER_ROOT
ls $PNGWRITER_ROOT/lib*

echo $CMAKE_PREFIX_PATH

ax3l on 1 May 2017

Here is the output:

echo $PNGWRITER_ROOT
/home/lai/lib/pngwriter

ls $PNGWRITER_ROOT
CHANGELOG.md examples lib make.include.linux src
CMakeLists.txt fonts Makefile make.include.osx tests
doc include make.include README.md

ls $PNGWRITER_ROOT/lib*
libpngwriter.a libpngwriter.so

echo $CMAKE_PREFIX_PATH

Output of the command "echo $CMAKE_PREFIX_PATH" is empty.
Thanks.

8i161029 on 2 May 2017

the install in $PNGWRITER_ROOT is broken as it also contains the sources.

ls $PNGWRITER_ROOT should only show lib/ and include/.

Please remove the install

rm -rf $PNGWRITER_ROOT

and if you try to install PNGwriter again check the source out in $HOME/src/pngwriter, build it in $HOME/build and install it to $PNGWRITER_ROOT which is $HOME/lib/pngwriter.

ax3l on 2 May 2017

I used the "rm -rf $PNGWRITER_ROOT" and configured, but failed.
So I installed PNGwriter again. Here is the log:

lai@lai-G56JR:~/build$ cmake -DCMAKE_INSTALL_PREFIX=$HOME/lib/pngwriter ~/src/pngwriter
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found suitable version "1.2.54", minimum required is "1.2.9") 
-- Could NOT find Freetype (missing:  FREETYPE_LIBRARY FREETYPE_INCLUDE_DIRS) 
-- Configuring done
-- Generating done
-- Build files have been written to: /home/lai/build
lai@lai-G56JR:~/build$ make install
Scanning dependencies of target pngwriter
[  6%] Building CXX object CMakeFiles/pngwriter.dir/src/pngwriter.cc.o
[ 13%] Linking CXX shared library libpngwriter.so
[ 20%] Built target pngwriter
Scanning dependencies of target pngwriter_static
[ 26%] Building CXX object CMakeFiles/pngwriter_static.dir/src/pngwriter.cc.o
[ 33%] Linking CXX static library libpngwriter.a
[ 33%] Built target pngwriter_static
Scanning dependencies of target pngtest
[ 40%] Building CXX object CMakeFiles/pngtest.dir/examples/pngtest.cc.o
[ 46%] Linking CXX executable pngtest
[ 46%] Built target pngtest
Scanning dependencies of target lyapunov
[ 53%] Building CXX object CMakeFiles/lyapunov.dir/examples/lyapunov.cc.o
[ 60%] Linking CXX executable lyapunov
[ 60%] Built target lyapunov
Scanning dependencies of target diamond
[ 66%] Building CXX object CMakeFiles/diamond.dir/tests/diamond.cc.o
[ 73%] Linking CXX executable diamond
[ 73%] Built target diamond
Scanning dependencies of target blackwhite
[ 80%] Building CXX object CMakeFiles/blackwhite.dir/tests/blackwhite.cc.o
[ 86%] Linking CXX executable blackwhite
[ 86%] Built target blackwhite
Scanning dependencies of target readwrite
[ 93%] Building CXX object CMakeFiles/readwrite.dir/tests/readwrite.cc.o
[100%] Linking CXX executable readwrite
[100%] Built target readwrite
Linking CXX shared library CMakeFiles/CMakeRelink.dir/libpngwriter.so
Install the project...
-- Install configuration: ""
-- Installing: /home/lai/lib/pngwriter/lib/libpngwriter.so
-- Installing: /home/lai/lib/pngwriter/lib/libpngwriter.a
-- Installing: /home/lai/lib/pngwriter/include/pngwriter.h

Then I configured again, but it still had an error.
I build PNGwriter in $HOME/build, and also configure case001 in $HOME/build.
Is this a problem I do both things in the same directory?
Did I do anything wrong? Teach me please.
Thank you.

8i161029 on 5 May 2017

Is this a problem I do both things in the same directory?

Yes it might be. Did you clean this temporary build directory in between?
Just run

lai@lai-G56JR:~/build$ rm -rf ../build/*

before running pic-configure

ax3l on 5 May 2017

Oh no I never cleaned build directory before I install these optional libraries...
I only deleted CMakeCache.txt when I met "the source ... does not match the source ... used to generate cache.
I may have to remove these libraries and reinstall them.
So before I need to do things in the build directory I should clean the build directory.
I ran ~/build$ rm -rf ../build/* and configured. Here is the output:

cmake command: cmake -DCUDA_ARCH=sm_20 -DCMAKE_INSTALL_PREFIX=/home/lai/paramSets/case001 -DPIC_EXTENSION_PATH=/home/lai/paramSets/case001 /home/lai/src/picongpu
-- The C compiler identification is GNU 4.9.3
-- The CXX compiler identification is GNU 4.9.3
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum required is "5.5")
-- Compiling as C++11...
-- Debug version
-- Found MPI_C: /usr/local/openmpi/lib/libmpi.so
-- Found MPI_CXX: /usr/local/openmpi/lib/libmpi.so
-- Found ZLIB: /usr/local/lib/libz.so (found version "1.2.11")
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- program_options
-- regex
-- filesystem
-- system
-- thread
-- math_tr1
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum required is "5.0")
-- Boost version: 1.57.0
-- Using mallocMC from thirdParty/ directory
-- Boost version: 1.57.0
-- Found mallocMC: /home/lai/src/picongpu/thirdParty/mallocMC/src (found suitable version "2.2.0", minimum required is "2.2.0")
-- Found CUDA: /usr/local/cuda (found version "8.0")
-- Could NOT find NVML (missing: NVML_LIBRARY)
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- program_options
-- Found 'adios_config': /usr/bin/adios_config
-- The directory provided by 'adios_config -d' does not exist:
-- Could NOT find ADIOS (missing: ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.10.0")
-- Found HDF5: /home/lai/lib/hdf5/lib/libhdf5.so;/usr/local/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.8.14")
-- libSplash supports PARALLEL output
-- Found Splash: /home/lai/lib/splash/lib/libsplash.a;/home/lai/lib/hdf5/lib/libhdf5.so;/usr/local/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/local/openmpi/lib/libmpi.so;/usr/local/openmpi/lib/libmpi.so (found suitable version "1.6.0", minimum required is "1.6.0")
-- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found suitable version "1.2.54", minimum required is "1.2.9")
-- Could NOT find Freetype (missing: FREETYPE_LIBRARY FREETYPE_INCLUDE_DIRS)
-- Found PNGwriter: PNGwriter_LIBRARIES-NOTFOUND;/usr/lib/x86_64-linux-gnu/libpng.so;/usr/local/lib/libz.so (found suitable version "0.5.6", minimum required is "0.5.6")
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
PNGwriter_LIBRARIES
linked by target "picongpu" in directory /home/lai/src/picongpu/src/picongpu
-- Configuring incomplete, errors occurred!
See also "/home/lai/build/CMakeFiles/CMakeOutput.log".
See also "/home/lai/build/CMakeFiles/CMakeError.log".

Please teach me the next step I need to do. Should I install the libraries again?
Thank you!

8i161029 on 6 May 2017

That's the right way to build two independent projects with cmake (removing all temporary build artifacts) but still did not solve your problem.

Let us circumvent it the hard way now: edit $PICSRC/src/picongpu/CMakeLists.txt can comment out this line but suffixing a #:

# find PNGwriter installation
# find_package(PNGwriter 0.5.6)

You will then not be able to use the png plugin for previews, but HDF5 or ADIOS output is more useful anyway.

Update: a cleaner way disabling a "wrongly found" plugin would be by passing -c"-DCMAKE_DISABLE_FIND_PACKAGE_PNGwriter=TRUE" as an option to your configure call:

# PIConGPU <0.3.0
$PICSRC/configure -c"-DCMAKE_DISABLE_FIND_PACKAGE_PNGwriter=TRUE" ~/paramSets/case001

# PIConGPU >= 0.3.0
pic-configure -c"-DCMAKE_DISABLE_FIND_PACKAGE_PNGwriter=TRUE" ~/paramSets/case001

ax3l on 7 May 2017

I entered $PICSRC/configure -c"-DCMAKE_DISABLE_FIND_PACKAGE_PNGwriter=TRUE" ~/paramSets/case001
and here is the out put:

cmake command: cmake -DCUDA_ARCH=sm_20 -DCMAKE_INSTALL_PREFIX=/home/lai/paramSets/case001 -DPIC_EXTENSION_PATH=/home/lai/paramSets/case001 -DCMAKE_DISABLE_FIND_PACKAGE_PNGwriter=TRUE /home/lai/src/picongpu
-- The C compiler identification is GNU 4.9.3
-- The CXX compiler identification is GNU 4.9.3
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum required is "5.5")
-- Compiling as C++11...
-- Debug version
-- Found MPI_C: /usr/local/openmpi/lib/libmpi.so
-- Found MPI_CXX: /usr/local/openmpi/lib/libmpi.so
-- Found ZLIB: /usr/local/lib/libz.so (found version "1.2.11")
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- program_options
-- regex
-- filesystem
-- system
-- thread
-- math_tr1
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum required is "5.0")
-- Boost version: 1.57.0
-- Using mallocMC from thirdParty/ directory
-- Boost version: 1.57.0
-- Found mallocMC: /home/lai/src/picongpu/thirdParty/mallocMC/src (found suitable version "2.2.0", minimum required is "2.2.0")
-- Found CUDA: /usr/local/cuda (found version "8.0")
-- Could NOT find NVML (missing: NVML_LIBRARY)
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- program_options
-- Found 'adios_config': /usr/bin/adios_config
-- The directory provided by 'adios_config -d' does not exist:
-- Could NOT find ADIOS (missing: ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.10.0")
-- Found HDF5: /home/lai/lib/hdf5/lib/libhdf5.so;/usr/local/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.8.14")
-- libSplash supports PARALLEL output
-- Found Splash: /home/lai/lib/splash/lib/libsplash.a;/home/lai/lib/hdf5/lib/libhdf5.so;/usr/local/lib/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/local/openmpi/lib/libmpi.so;/usr/local/openmpi/lib/libmpi.so (found suitable version "1.6.0", minimum required is "1.6.0")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/lai/build

I thought the previous problem was solved. Then I entered make
But there was another error. Here is log. It is a little bit long:

[ 8%] Building NVCC (Device) object build_picongpu/CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
/home/lai/boost_1_57_0/boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp(75): warning: variable "tmp" was set but never used
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp(53): warning: "boost::mpl::aux::type_wrapper operator/(const boost::mpl::m_item &, boost::mpl::aux::type_wrapper )" declares a non-template function -- add <> to refer to a template instance
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper> operator|(const boost::mpl::m_item &, boost::mpl::next::type *)" declares a non-template function -- add <> to refer to a template instance
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp(55): warning: "char (&operator||(const boost::mpl::m_item &, boost::mpl::aux::type_wrapper *))[boost::mpl::next::type::value]" declares a non-template function -- add <> to refer to a template instance
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp(69): warning: "boost::mpl::aux::type_wrapper operator/(const boost::mpl::m_mask &, boost::mpl::aux::type_wrapper *)" declares a non-template function -- add <> to refer to a template instance
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp(70): warning: "boost::mpl::aux::type_wrapper operator|(const boost::mpl::m_mask &, boost::mpl::x_order_impl::type *)" declares a non-template function -- add <> to refer to a template instance
/home/lai/boost_1_57_0/boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp(75): warning: variable "tmp" was set but never used
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp(53): warning: "boost::mpl::aux::type_wrapper operator/(const boost::mpl::m_item &, boost::mpl::aux::type_wrapper *)" declares a non-template function -- add <> to refer to a template instance
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper> operator|(const boost::mpl::m_item &, boost::mpl::next::type *)" declares a non-template function -- add <> to refer to a template instance
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp(55): warning: "char (&operator||(const boost::mpl::m_item &, boost::mpl::aux::type_wrapper *))[boost::mpl::next::type::value]" declares a non-template function -- add <> to refer to a template instance
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp(69): warning: "boost::mpl::aux::type_wrapper operator/(const boost::mpl::m_mask &, boost::mpl::aux::type_wrapper *)" declares a non-template function -- add <> to refer to a template instance
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp(70): warning: "boost::mpl::aux::type_wrapper operator|(const boost::mpl::m_mask &, boost::mpl::x_order_impl::type *)" declares a non-template function -- add <> to refer to a template instance
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp:53:109: warning: friend declaration ‘boost::mpl::aux::type_wrapper boost::mpl::operator/(const boost::mpl::m_item&, boost::mpl::aux::type_wrapper)’ declares a non-template function [-Wnon-template-friend]
BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper, VALUE_BY_KEY, m_item, aux::type_wrapper* );
^
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp:53:109: note: (if this is not what you intended, make sure the function template has already been declared and add <> after the function name here)
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp:54:90: warning: friend declaration ‘boost::mpl::aux::type_wrapper > boost::mpl::operator|(const boost::mpl::m_item&, boost::mpl::m_item::order)’ declares a non-template function [-Wnon-template-friend]
BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper, ITEM_BY_ORDER, m_item, order );
^
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp:55:85: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::m_item&, boost::mpl::aux::type_wrapper))[boost::mpl::m_item::order:: value]’ declares a non-template function [-Wnon-template-friend]
BOOST_MPL_AUX_MAP_OVERLOAD( order_tag_, ORDER_BY_KEY, m_item, aux::type_wrapper );
^
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp:69:121: warning: friend declaration ‘boost::mpl::aux::type_wrapper boost::mpl::operator/(const boost::mpl::m_mask&, boost::mpl::aux::type_wrapper)’ declares a non-template function [-Wnon-template-friend]
BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper, VALUE_BY_KEY, m_mask, aux::type_wrapper );
^
/home/lai/boost_1_57_0/boost/mpl/map/aux_/item.hpp:70:94: warning: friend declaration ‘boost::mpl::aux::type_wrapper boost::mpl::operator|(const boost::mpl::m_mask&, boost::mpl::m_mask::key_order_)’ declares a non-template function [-Wnon-template-friend]
BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper, ITEM_BY_ORDER, m_mask, key_order_ );
^
Scanning dependencies of target picongpu
[ 16%] Building CXX object build_picongpu/CMakeFiles/picongpu.dir/particlePatches.cpp.o
[ 25%] Building CXX object build_picongpu/CMakeFiles/picongpu.dir/patchReader.cpp.o
[ 33%] Building CXX object build_picongpu/CMakeFiles/picongpu.dir/ArgsParser.cpp.o
[ 41%] Building CXX object build_picongpu/CMakeFiles/picongpu.dir/stringHelpers.cpp.o
[ 50%] Linking CXX executable picongpu
/usr/bin/ld: warning: libmpi.so.12, needed by /home/lai/lib/hdf5/lib/libhdf5.so, may conflict with libmpi.so.20
/home/lai/lib/splash/lib/libsplash.a(SerialDataCollector.cpp.o): In function MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)': SerialDataCollector.cpp:(.text._ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb[_ZN3MPI2Op4InitEPFvPKvPviRKNS_8DatatypeEEb]+0x16): undefined reference toompi_mpi_cxx_op_intercept'
/home/lai/lib/splash/lib/libsplash.a(SerialDataCollector.cpp.o): In function MPI::Intracomm::Create_graph(int, int const*, int const*, bool) const': SerialDataCollector.cpp:(.text._ZNK3MPI9Intracomm12Create_graphEiPKiS2_b[_ZNK3MPI9Intracomm12Create_graphEiPKiS2_b]+0x38): undefined reference toMPI::Comm::Comm()'
/home/lai/lib/splash/lib/libsplash.a(SerialDataCollector.cpp.o): In function MPI::Graphcomm::Clone() const': SerialDataCollector.cpp:(.text._ZNK3MPI9Graphcomm5CloneEv[_ZNK3MPI9Graphcomm5CloneEv]+0x35): undefined reference toMPI::Comm::Comm()'
/home/lai/lib/splash/lib/libsplash.a(SerialDataCollector.cpp.o): In function MPI::Cartcomm::Clone() const': SerialDataCollector.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[_ZNK3MPI8Cartcomm5CloneEv]+0x35): undefined reference toMPI::Comm::Comm()'
/home/lai/lib/splash/lib/libsplash.a(SerialDataCollector.cpp.o): In function MPI::Intercomm::Merge(bool) const': SerialDataCollector.cpp:(.text._ZNK3MPI9Intercomm5MergeEb[_ZNK3MPI9Intercomm5MergeEb]+0x35): undefined reference toMPI::Comm::Comm()'
/home/lai/lib/splash/lib/libsplash.a(SerialDataCollector.cpp.o): In function MPI::Intracomm::Create(MPI::Group const&) const': SerialDataCollector.cpp:(.text._ZNK3MPI9Intracomm6CreateERKNS_5GroupE[_ZNK3MPI9Intracomm6CreateERKNS_5GroupE]+0x37): undefined reference toMPI::Comm::Comm()'
/home/lai/lib/splash/lib/libsplash.a(SerialDataCollector.cpp.o):SerialDataCollector.cpp:(.text._ZNK3MPI9Intracomm5SplitEii[_ZNK3MPI9Intracomm5SplitEii]+0x36): more undefined references to MPI::Comm::Comm()' follow /home/lai/lib/splash/lib/libsplash.a(SerialDataCollector.cpp.o):(.rodata._ZTVN3MPI8DatatypeE[_ZTVN3MPI8DatatypeE]+0x78): undefined reference toMPI::Datatype::Free()'
/home/lai/lib/splash/lib/libsplash.a(SerialDataCollector.cpp.o):(.rodata._ZTVN3MPI3WinE[_ZTVN3MPI3WinE]+0x48): undefined reference to `MPI::Win::Free()'
collect2: error: ld returned 1 exit status
build_picongpu/CMakeFiles/picongpu.dir/build.make:215: recipe for target 'build_picongpu/picongpu' failed
make[2]: * [build_picongpu/picongpu] Error 1
CMakeFiles/Makefile2:90: recipe for target 'build_picongpu/CMakeFiles/picongpu.dir/all' failed
make[1]: [build_picongpu/CMakeFiles/picongpu.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make: ** [all] Error 2

I think the error maybe start from [ 50%] Linking executable picongpu.
Did anything I wrongly install? Or I didn't install something necessary.
Thank you for help me a lot.

8i161029 on 10 May 2017

ok we are getting there ;)

it looks to me like something is wrong with your HDF5 install. Did you take care to --enable-parallel --enable-shared in HDF5 configure?

On ubuntu, just remove $HOME/lib/hdf5 (and unset the environment hints in bash for HDF5), apt-get install libopenmpi-dev libhdf5-openmpi-dev and compile & install libSplash again.

ax3l on 11 May 2017

Thank you! I think I installed successfully.
Here is log:

-- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum required is "5.5")
-- Compiling as C++11...
-- Debug version
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- program_options
-- regex
-- filesystem
-- system
-- thread
-- math_tr1
-- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum required is "5.0")
-- Boost version: 1.57.0
-- Found CUDA: /usr/local/cuda (found version "8.0")
-- Could NOT find NVML (missing: NVML_LIBRARY)
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- program_options
-- Found 'adios_config': /usr/bin/adios_config
-- The directory provided by 'adios_config -d' does not exist:
-- Could NOT find ADIOS (missing: ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.10.0")
-- libSplash supports PARALLEL output
-- Configuring done
-- Generating done
-- Build files have been written to: /home/lai/build
[ 8%] Linking CXX executable picongpu
/usr/bin/ld: warning: libmpi.so.12, needed by /usr/lib/x86_64-linux-gnu/hdf5/openmpi/lib/libhdf5.so, may conflict with libmpi.so.20
[ 50%] Built target picongpu
[ 58%] Linking CXX executable cuda_memtest
[ 83%] Built target cuda_memtest
[100%] Built target mpiInfo
Install the project...
-- Install configuration: ""
-- Installing: /home/lai/paramSets/case001/bin/picongpu
-- Set runtime path of "/home/lai/paramSets/case001/bin/picongpu" to ""
-- Up-to-date: /home/lai/paramSets/case001/bin
-- Installing: /home/lai/paramSets/case001/bin/cuda_memtest.sh
-- Installing: /home/lai/paramSets/case001/bin/cuda_memtest
-- Set runtime path of "/home/lai/paramSets/case001/bin/cuda_memtest" to ""
-- Installing: /home/lai/paramSets/case001/bin/mpiInfo
-- Set runtime path of "/home/lai/paramSets/case001/bin/mpiInfo" to ""

I moved to next step "Run". I entered tbg -s qsub -c submit/0016gpus.cfg -t submit/hypnos/k20_profile.tpl $PICHOME/runs/testBatch01
and here is the output:

The given tpl file "submit/hypnos/k20_profile.tpl" does not exist (-t|--tpl).

Maybe I lost some files. How to solve it?
I noticed that there is "( Again, do NOT use your home $HOME/runs - change this path!)" in install guide.
My path $PICHOME is $HOME. Do I need to change it?
Thank you!

8i161029 on 11 May 2017

Great, the install worked out! :sparkles:

Just continue reading the manual in-order: https://picongpu.readthedocs.io/en/dev/usage/tbg.html#usage

What you need is the right runtime configuration file in -c for your desktop, I guess you have one GPU, (or adjust an existing one to use one GPU) and the right template in -t which is in your case either mpirun or mpiexec running simply in your bash.

It then looks something like this on a desktop:

tbg -s bash -c submit/0001gpu.cfg -t submit/bash/bash_mpirun.tpl

ax3l on 11 May 2017

Hi @8i161029 ,
I suspect you ran tbg not from within /home/lai/paramSets/case001. Is this correct?
In /home/lai/paramSets/case001 there should be a submit directory which includes *.cfg files and directories with *.tpl files.

Furthermore I assume you are not running picongpu on the hypnos cluster at HZDR in Germany. Thus hypnos/k20_profile.tpl will not create a correct submit file for your cluster, but for the hynos cluster at HZDR.

[EDIT:] only valid on compute clusters [EDIT END]
In order to create a submit file for your cluster, please adjust a *.tpl file accordingly.
For details please see: https://picongpu.readthedocs.io/en/dev/usage/tbg.html
You can find several examples for various clusters for both PBS and slurm in the submit directory. It is probably best to adjust a similar .tbg to your needs.

[EDIT:] this is better described by @ax3l above [EDIT END]
To avoid an inital *.tbg file generation for the first runs on your cluster you could also use the bash *.tbg: bash_mpiexec.tpl. This creates a simulation directory and a shell script. By allocating node (with GPUs) interactively on your cluster, you can then just execute the script.

PrometheusPi on 11 May 2017

Is that I need to modify this order tbg -s qsub -c submit/0016gpus.cfg -t submit/hypnos/k20_profile.tpl $PICHOME/runs/testBatch01?
But I can see 0016gpus.cfg and k20_profile.tpl in $HOME/paramSets/case001/submit.
Here is ls $HOME/paramSets/case001/submit output:

0001gpus.cfg bash joker-tud openib.conf taurus-tud
0008gpus.cfg cuda.filter judge-fzj pizdaint-cscs titan-ornl
0016gpus.cfg davinci-rice keeneland-gt scorep.filter
0032gpus.cfg hypnos-hzdr lawrencium-lbnl submitAction.sh

output of ls $HOME/paramSets/case001/submit/bash:

bash_mpiexec.tpl bash_mpirun.tpl

and ls $HOME/paramSets/case001/submit/hypnos-hzdr

fermi_profile.tpl k20_vampir_profile.tpl picongpu.profile.example
k20_autoWait_profile.tpl k20_wait_profile.tpl
k20_profile.tpl k80_profile.tpl

I tried ~/paramSets/case001$ tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpirun.tpl $HOME/runs/testBatch01

Here is the output:

tbg/submit.start: line 32: ( TBG_tasks + TBG_gpusPerNode -1 ) / TBG_gpusPerNode: division by 0 (error token is "TBG_gpusPerNode")
Running program...
tbg/submit.start: line 41: /home/lai/picongpu.profile: No such file or directory
Data for JOB [2846,1] offset 0
======================== JOB MAP ========================
Data for node: lai-G56JR Num slots: 4 Max slots: 0 Num procs: 1
Process OMPI jobid: [2846,1] App: 0 Process rank: 0
=============================================================
mpiInfo: error while loading shared libraries: libmpi.so.20: cannot open shared object file: No such file or directory
ERROR: Invalid option:2
cuda_memtest crash: see file /home/lai/runs/testBatch01/simOutput/cuda_memtest_lai-G56JR_.err

Primary job terminated normally, but 1 process returned

a non-zero exit code.. Per user-direction, the job has been aborted.

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[2846,1],0]

Exit code: 1

Primary job terminated normally, but 1 process returned

a non-zero exit code.. Per user-direction, the job has been aborted.

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[2816,1],0]

Exit code: 1

It looked like I was wrong. Please teach me.
Thank you!

8i161029 on 11 May 2017

Great, don't worry. Just take the template file submit/bash/bash_mpirun.tpl and comment out line 41 with a prefix of an #, which tries to load your environment by "sourcing" $HOME/picongpu.profile (similar to what a .bashrc files is used for, just manually and application specific).

The picongpu.profile file is described in the manual and we usually use it to load a software environment on HPC systems. In your desktop-case just remove that a $HOME/picongpu.profile file is required (as written in the paragraph above) or create an empty one with:

touch $HOME/picongpu.profile

ax3l on 11 May 2017

I added an # in front of . ~/picongpu.profile in submit/bash/bash_mpirun.tpl.
Then deleted $HOME/runs/testBatch01 and tried again.
But it was the same result.
I found

mpiInfo: error while loading shared libraries: libmpi.so.20: cannot open shared object file: No such file or directory
ERROR: Invalid option:2
cuda_memtest crash: see file /home/lai/runs/testBatch01/simOutput/cuda_memtest_lai-G56JR_.err

in the output. What is the problem? I commented out a wrong line?
Thank you.

8i161029 on 11 May 2017

Let's reduce the template even more, but first do a simple test.

What does a

cd $HOME/paramSets/case001
ldd ./bin/picongpu
mpirun -n 1 ./bin/picongpu -s 10 -d 1 1 1 -g 64 64 64

output for you?

ax3l on 11 May 2017

output of ldd ./bin/picongpu:

linux-vdso.so.1 => (0x00007ffce8b1e000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007efee3b12000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007efee390e000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007efee3705000)
libmpi.so.20 => not found
libz.so.1 => /usr/local/lib/libz.so.1 (0x00007efee34e9000)
libboost_program_options.so.1.57.0 => not found
libboost_regex.so.1.57.0 => not found
libboost_filesystem.so.1.57.0 => not found
libboost_system.so.1.57.0 => not found
libboost_math_tr1.so.1.57.0 => not found
libhdf5_openmpi.so.10 => /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.10 (0x00007efee3038000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007efee2d2f000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007efee29ad000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007efee278a000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007efee2574000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007efee21ab000)
/lib64/ld-linux-x86-64.so.2 (0x0000562256015000)
libsz.so.2 => /usr/lib/x86_64-linux-gnu/libsz.so.2 (0x00007efee1fa7000)
libmpi.so.12 => /usr/lib/libmpi.so.12 (0x00007efee1cd1000)
libaec.so.0 => /usr/lib/x86_64-linux-gnu/libaec.so.0 (0x00007efee1ac8000)
libibverbs.so.1 => /usr/lib/libibverbs.so.1 (0x00007efee18b9000)
libopen-rte.so.12 => /usr/lib/libopen-rte.so.12 (0x00007efee163f000)
libopen-pal.so.13 => /usr/lib/libopen-pal.so.13 (0x00007efee13a1000)
libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 (0x00007efee1167000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007efee0f64000)
libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x00007efee0d58000)
libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007efee0b4e000)

and mpirun -n 1 ./bin/picongpu -s 10 -d 1 1 1 -g 64 64 64:

> ./bin/picongpu: error while loading shared libraries: libmpi.so.20: cannot open shared object file: No such file or directory

Primary job terminated normally, but 1 process returned

a non-zero exit code.. Per user-direction, the job has been aborted.

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[27383,1],0]

Exit code: 127

8i161029 on 11 May 2017

Looks like your mpi library was not found!

Can you search for it via

locate libmpi.so
find /usr/lib -name "libmpi.so*"

?

Also, I prepared a simplified .tpl file for you.

ax3l on 11 May 2017

Actually, it looks like you compiled against two different MPI installations:

output of ldd ./bin/picongpu:
...
libmpi.so.20 => not found
...
libhdf5_openmpi.so.10 => /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.10 (0x00007efee3038000)
...
libmpi.so.12 => /usr/lib/libmpi.so.12 (0x00007efee1cd1000)
...

And above during compile:

/usr/bin/ld: warning: libmpi.so.12, needed by /usr/lib/x86_64-linux-gnu/hdf5/openmpi/lib/libhdf5.so, may conflict with libmpi.so.20

ax3l on 11 May 2017

Oh no maybe I wrongly install mpi...
output of locate libmpi.so :

/etc/alternatives/libmpi.so
/home/lai/openmpi-2.1.0/ompi/.libs/libmpi.so
/home/lai/openmpi-2.1.0/ompi/.libs/libmpi.so.20
/home/lai/openmpi-2.1.0/ompi/.libs/libmpi.so.20.10.0
/home/lai/openmpi-2.1.0/ompi/.libs/libmpi.so.20.10.0T
/usr/lib/libmpi.so
/usr/lib/libmpi.so.12
/usr/lib/libmpi.so.12.0.2
/usr/lib/openmpi/lib/libmpi.so
/usr/lib/openmpi/lib/libmpi.so.12.0.2
/usr/local/openmpi/lib/libmpi.so
/usr/local/openmpi/lib/libmpi.so.20
/usr/local/openmpi/lib/libmpi.so.20.10.0

find /usr/lib -name "libmpi.so*":

/usr/lib/libmpi.so.12.0.2
/usr/lib/libmpi.so
/usr/lib/openmpi/lib/libmpi.so.12.0.2
/usr/lib/openmpi/lib/libmpi.so
/usr/lib/libmpi.so.12

8i161029 on 11 May 2017

👍1

ah yes, just get rid of your additional MPI installation in your $HOME :-)

rm -rf $HOME/openmpi-2.1.0
# and to be sure, rebuild also the software that depends on MPI
rm -rf $HOME/lib/hdf5
rm -rf $HOME/lib/splash

then

take/keep the system MPI and system paralle HDF5 (see apt-get install libopenmpi-dev libhdf5-openmpi-dev from above)
reinstall libSplash
rebuild picongpu
mpirun it again

ax3l on 11 May 2017

I did following things:

rm -rf $HOME/openmpi-2.1.0
rm -rf $HOME/lib/hdf5
rm -rf $HOME/lib/splash
reinstall libSplash
reinstall HDF5
rebuild picongpu
Then did ~/paramSets/case001$ tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpirun.tpl $HOME/runs/testBatch01
Here is output:

tbg/submit.start: line 32: ( TBG_tasks + TBG_gpusPerNode -1 ) / TBG_gpusPerNode: division by 0 (error token is "TBG_gpusPerNode")
Running program...
Data for JOB [18798,1] offset 0
======================== JOB MAP ========================
Data for node: lai-G56JR Num slots: 4 Max slots: 0 Num procs: 1
Process OMPI jobid: [18798,1] App: 0 Process rank: 0
=============================================================
mpiInfo: error while loading shared libraries: libmpi.so.20: cannot open shared object file: No such file or directory
ERROR: Invalid option:2

cuda_memtest crash: see file /home/lai/runs/testBatch01/simOutput/cuda_memtest_lai-G56JR_.err

Primary job terminated normally, but 1 process returned

a non-zero exit code.. Per user-direction, the job has been aborted.

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[18798,1],0]

Exit code: 1

Primary job terminated normally, but 1 process returned

a non-zero exit code.. Per user-direction, the job has been aborted.

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[19089,1],0]

Exit code: 1

I entered locate libmpi.so:

/etc/alternatives/libmpi.so
/usr/lib/libmpi.so
/usr/lib/libmpi.so.12
/usr/lib/libmpi.so.12.0.2
/usr/lib/openmpi/lib/libmpi.so
/usr/lib/openmpi/lib/libmpi.so.12.0.2
/usr/local/openmpi/lib/libmpi.so
/usr/local/openmpi/lib/libmpi.so.20
/usr/local/openmpi/lib/libmpi.so.20.10.0

and find /usr/lib -name "libmpi.so*":

/usr/lib/libmpi.so.12.0.2
/usr/lib/libmpi.so
/usr/lib/openmpi/lib/libmpi.so.12.0.2
/usr/lib/openmpi/lib/libmpi.so
/usr/lib/libmpi.so.12

I see there are some openmpi files still in /usr/local/openmpi and /usr/lib .
Should I delete them? But I notice that libmpi.so.20 is a part of openmpi.
What should I do?
Thank you.

8i161029 on 11 May 2017

Somehow you have ~~openmpi 1.X~~ mpich and openmpi 2 installed alongside.

also don't install HDF5 from source, use the package from apt-get install and only build libSplash on top of both.

ax3l on 11 May 2017

Do I still have two versions of openmpi after I used rm -rf $HOME/openmpi-2.1.0?
And how to install HDF5 from apt-get install? I tried sudo apt-get install HDF5 but unable to locate.
Also what does it mean "build libSplash on top of both"?
Sorry for many questions and thank you for helping me.

8i161029 on 11 May 2017

Do I still have two versions of openmpi after I used rm -rf $HOME/openmpi-2.1.0?

yes, you somehow have an mpi in /usr/lib/ and in /usr/lib/openmpi/lib/

And how to install HDF5 from apt-get install? I tried sudo apt-get install HDF5 but unable to locate.

See above: sudo apt-get install libopenmpi-dev libhdf5-openmpi-dev
(Ubuntu package index)

Also what does it mean "build libSplash on top of both"?

Use apt-get to install MPI and HDF5 with MPI (parallel) support via apt-get as in the line above and only build libSplash (which depends on both) from source.

Sorry for many questions and thank you for helping me.

No problem, you are welcome!

ax3l on 12 May 2017

@8i161029 I won't be online for a week to help you further. My idea would be to try to get rid of the install of MPI in /usr/lib/libmpi.so*, maybe check what mpi packages you have installed with apt list --installed | grep mpi. Are there more then one?

In case it does not work for you to make sure always the same MPI version is used on your system, I would recommend installing nvidia docker to get a clean environment to work with. I have drafted an example in this thread and can guide you through it in 10 days from now in case you have any trouble.

Alternatively, the package manager spack can install and manage all PIConGPU dependencies for you. Anyways, both approaches require you to either learn how to use docker or spack.

ax3l on 12 May 2017

Thank you for your patient help! I deeply appreciate that.
I will try the method you recommended. Thank you very much!

8i161029 on 12 May 2017

👍1

Can you post the output of apt list --installed | grep mpi please?

ax3l on 12 May 2017

ok, here is the output:

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
compiz/xenial-updates,xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 all [installed]
compiz-core/xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 amd64 [installed]
compiz-gnome/xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 amd64 [installed]
compiz-plugins-default/xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 amd64 [installed]
compizconfig-settings-manager/xenial-updates,xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 all [installed]
libcompizconfig0/xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 amd64 [installed]
libexempi3/xenial,now 2.2.2-2 amd64 [installed]
libhdf5-openmpi-10/xenial,now 1.8.16+docs-4ubuntu1 amd64 [installed,automatic]
libhdf5-openmpi-dev/xenial,now 1.8.16+docs-4ubuntu1 amd64 [installed]
libmpich-dev/xenial,now 3.2-6build1 amd64 [installed,automatic]
libmpich12/xenial,now 3.2-6build1 amd64 [installed,automatic]
libopenmpi-dev/xenial,now 1.10.2-8ubuntu1 amd64 [installed]
libopenmpi1.10/xenial,now 1.10.2-8ubuntu1 amd64 [installed,automatic]
mpich/xenial,now 3.2-6build1 amd64 [installed]
openmpi-bin/xenial,now 1.10.2-8ubuntu1 amd64 [installed]
openmpi-common/xenial,xenial,now 1.10.2-8ubuntu1 all [installed,automatic]
python-compizconfig/xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 amd64 [installed,automatic]

8i161029 on 12 May 2017

Ok, just de-install mpich, this is the second MPI installation you are seeing, but you only need one:

sudo apt-get remove libmpich-dev libmpich12 mpich

then build libSplash and PIConGPU again

ax3l on 12 May 2017

Hi, I did sudo apt-get remove libmpich-dev libmpich12 mpich, rebuild libSplash and PIConGPU.
Then ran again. But it was still an error. Here is output:

lai@lai-G56JR:~/paramSets/case001$ tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpirun.tpl $HOME/runs/testBatch01
tbg/submit.start: line 32: ( TBG_tasks + TBG_gpusPerNode -1 ) / TBG_gpusPerNode: division by 0 (error token is "TBG_gpusPerNode")
Running program...
Data for JOB [7202,1] offset 0

======================== JOB MAP ========================

Data for node: lai-G56JR Num slots: 4 Max slots: 0 Num procs: 1
Process OMPI jobid: [7202,1] App: 0 Process rank: 0

===========================================================
mpiInfo: error while loading shared libraries: libmpi.so.20: cannot open shared object file: No such file or directory
ERROR: Invalid option:2

cuda_memtest crash: see file /home/lai/runs/testBatch01/simOutput/cuda_memtest_lai-G56JR_.err

Primary job terminated normally, but 1 process returned

a non-zero exit code.. Per user-direction, the job has been aborted.

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[7202,1],0]

Exit code: 1

Primary job terminated normally, but 1 process returned

a non-zero exit code.. Per user-direction, the job has been aborted.

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[7252,1],0]

Exit code: 1

I checked installation of MPI:
locate libmpi.so:

/etc/alternatives/libmpi.so
/usr/lib/libmpi.so
/usr/lib/libmpi.so.12
/usr/lib/libmpi.so.12.0.2
/usr/lib/openmpi/lib/libmpi.so
/usr/lib/openmpi/lib/libmpi.so.12.0.2
/usr/local/openmpi/lib/libmpi.so
/usr/local/openmpi/lib/libmpi.so.20
/usr/local/openmpi/lib/libmpi.so.20.10.0

find /usr/lib -name "libmpi.so*":

/usr/lib/libmpi.so.12.0.2
/usr/lib/libmpi.so
/usr/lib/openmpi/lib/libmpi.so.12.0.2
/usr/lib/openmpi/lib/libmpi.so
/usr/lib/libmpi.so.12

and apt list --installed | grep mpi:

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
compiz/xenial-updates,xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 all [installed]
compiz-core/xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 amd64 [installed]
compiz-gnome/xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 amd64 [installed]
compiz-plugins-default/xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 amd64 [installed]
compizconfig-settings-manager/xenial-updates,xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 all [installed]
libcompizconfig0/xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 amd64 [installed]
libexempi3/xenial,now 2.2.2-2 amd64 [installed]
libhdf5-openmpi-10/xenial,now 1.8.16+docs-4ubuntu1 amd64 [installed,automatic]
libhdf5-openmpi-dev/xenial,now 1.8.16+docs-4ubuntu1 amd64 [installed]
libopenmpi-dev/xenial,now 1.10.2-8ubuntu1 amd64 [installed]
libopenmpi1.10/xenial,now 1.10.2-8ubuntu1 amd64 [installed,automatic]
openmpi-bin/xenial,now 1.10.2-8ubuntu1 amd64 [installed]
openmpi-common/xenial,xenial,now 1.10.2-8ubuntu1 all [installed,automatic]
python-compizconfig/xenial-updates,now 1:0.9.12.2+16.04.20160823-0ubuntu1 amd64 [installed,automatic]

I can see libmpi.so.20 in /usr/local/openmpi/lib but not in /usr/lib.
Is it because of this so terminal can not find libmpi.so.20?
How to let libmpi.so.20 be found?
Thank you!

8i161029 on 25 May 2017

Looks OK so far, can you show your cfg file please? Looks like you entered a GPU dimension (-d) with zero.

ax3l on 25 May 2017

I used the 0001gpus.cfg from case001/submit.
Maybe I should try another cfg file?
In submit there are 0001gpus.cfg, 0008gpus.cfg, 0016gpus.cfg, and 0032gpus.cfg.
Which file should I use?
Thank you!

8i161029 on 25 May 2017

Ah sorry, it's in the .tpl file. Can you please check the file submit/bash/bash_mpirun.tpl in your parameter set and see if TBG_gpusPerNode correctly is set to 1?

ax3l on 27 May 2017

I check the bash_mpirun.tpl . Here is the content:

 .TBG_author=${MY_NAME:+--author \"${MY_NAME}\"}

# 4 gpus per node if we need more than 4 gpus else same count as TBG_tasks
.TBG_gpusPerNode=`if [ $TBG_tasks -gt 4 ] ; then echo 4; else echo $TBG_tasks; fi`

#number of cores per parallel node / default is 2 cores per gpu on k20 queue
TBG_coresPerNode="$(( TBG_gpusPerNode * 2 ))"

# use ceil to caculate nodes
TBG_nodes="$(( ( TBG_tasks + TBG_gpusPerNode -1 ) / TBG_gpusPerNode))"
## end calculations ##


echo 'Running program...'

cd !TBG_dstPath

export MODULES_NO_OUTPUT=1
#. ~/picongpu.profile
unset MODULES_NO_OUTPUT

#set user rights to u=rwx;g=r-x;o=---
umask 0027

mkdir simOutput 2> /dev/null
cd simOutput

mpirun --display-map -am !TBG_dstPath/tbg/openib.conf --mca mpi_leave_pinned 0 -x LD_LIBRARY_PATH -npernode !TBG_gpusPerNode -n !TBG_tasks !TBG_dstPath/picongpu/bin/cuda_memtest.sh

if [ $? -eq 0 ] ; then
  mpirun  -tag-output --display-map -am !TBG_dstPath/tbg/openib.conf --mca mpi_leave_pinned 0 -x LD_LIBRARY_PATH -npernode !TBG_gpusPerNode -n !TBG_tasks !TBG_dstPath/picongpu/bin/picongpu !TBG_author !TBG_programParams | tee output
fi

mpirun -npernode !TBG_gpusPerNode -n !TBG_tasks killall -9 picongpu 2>/dev/null || true

Sorry I don't know how to well present this on github...I only copy and paste.

8i161029 on 2 Jun 2017

Besides, last few months I tried to build PIConGPU in my pc for practice.
From this month I can try to build PIConGPU in the server in our lab.
It is Tesla k80 and OS is centOS7.
I make a check for MPI. Here is the log:
locate libmpi.so:

/opt/mpich-3.2_install/lib/.libs/libmpi.so
/opt/mpich-3.2_install/lib/.libs/libmpi.so.12
/opt/mpich-3.2_install/lib/.libs/libmpi.so.12.1.0
/opt/mpich_by_gcc4/lib/libmpi.so
/opt/mpich_by_gcc4/lib/libmpi.so.12
/opt/mpich_by_gcc4/lib/libmpi.so.12.1.0
/usr/lib/mpich-3.2/lib/libmpi.so.12
/usr/lib/mpich-3.2/lib/libmpi.so.12.1.0
/usr/lib64/mpich-3.2/lib/libmpi.so.12
/usr/lib64/mpich-3.2/lib/libmpi.so.12.1.0
/usr/lib64/openmpi/lib/libmpi.so
/usr/lib64/openmpi/lib/libmpi.so.12
/usr/lib64/openmpi/lib/libmpi.so.12.0.3
/usr/local/lib/libmpi.so
/usr/local/lib/libmpi.so.12
/usr/local/lib/libmpi.so.12.1.0

find /usr/lib -name "libmpi.so*":

/usr/lib/mpich-3.2/lib/libmpi.so.12
/usr/lib/mpich-3.2/lib/libmpi.so.12.1.0

Are there any problems with MPI installation?
And are install steps the same as I did on Ubuntu16.04?
Thank you!

8i161029 on 2 Jun 2017

For the bash_mpirun.tpl file: I guess you only have 1 GPU? In that case, set it accordingly in TBG_gpusPerNode (to 1) :-)

Your .cfg file is unchanged? (Can you post it?)

For the new system: ideally, let us discuss one issue per GitHub issue / thread so we don't mix up things. But so far, this system looks ok! Take care to link only against one version of MPI, maybe you want to deinstall the OpenMPI on it and only keep mpich 3 (or vice versa). Be aware that on this machine, a K80 is used which exposes to the user as if it would be 2 GPUs :)

ax3l on 7 Jun 2017

I am building PIConGPU in the new system now.
I try to completely build it.
When I was installing ADIOS, here was an error :

/usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[3]: * [adios_list_methods] Error 1

Maybe I don't have some libraries. Could this error be solved?
I hope I can completely build it. So I want to install all libraries if I can.

As for previous PIConGPU installation in my PC,
my PC is repairing... so I maybe start that in 5 days.

Thank you!

8i161029 on 29 Jun 2017

So far so excellent!

For a PC version, just use libSplash (HDF5) instead of ADIOS, they have the same features.

For older versions of adios, there has been the bug you reported when building it, try writing

LDFLAGS="-pthread" CFLAGS="-fPIC" ./configure ...

to fix this. (but as I said, libSplash/HDF5 is enough)

ax3l on 30 Jun 2017

Thank you! I installed ADIOS successfully.
Then I try to install splash2txt . Here is the log:

[81i61029@messi build]$ cmake -DCMAKE_INSTALL_PREFIX=$PICSRC/src/tools/bin $PICSRC/src/tools/splash2txt
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Setting build type to 'Debug' as none was specified.
-- Building Debug
-- Found MPI_C: /usr/local/lib/libmpi.so
-- Found MPI_CXX: /usr/local/lib/libmpicxx.so;/usr/local/lib/libmpi.so
-- Found HDF5: /home/81i61029/lib/hdf5/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so
-- libSplash supports PARALLEL output
-- Found Splash: /home/81i61029/lib/splash/lib/libsplash.a;/home/81i61029/lib/hdf5/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/local/lib/libmpi.so;/usr/local/lib/libmpicxx.so;/usr/local/lib/libmpi.so (found suitable version "1.6.0", minimum required is "1.6.0")
-- libSplash compiler definitions: -D_LARGEFILE_SOURCE;-D_LARGEFILE64_SOURCE;-D_BSD_SOURCE;-DENABLE_HDF5=1
-- Found 'adios_config': /home/81i61029/lib/adios/bin/adios_config
-- ADIOS linker flags (unparsed): -L/home/81i61029/lib/adios/lib -ladios -L/usr/lib64 -lz -pthread -lm
-- Found adios in /home/81i61029/lib/adios/lib/libadios.a
-- Found z in /usr/lib64/libz.so
-- Found m in /usr/lib64/libm.so
-- Found ADIOS: /home/81i61029/lib/adios/lib/libadios.a;/usr/lib64/libz.so;/usr/lib64/libm.so (found suitable version "1.10.0", minimum required is "1.10.0")
-- Boost version: 1.64.0
-- Found the following Boost libraries:
-- program_options
-- regex
-- Configuring done
-- Generating done
-- Build files have been written to: /home/81i61029/build

Then I entered make. However, there were 2 errors:

[81i61029@messi build]$ make
Scanning dependencies of target splash2txt
[ 33%] Building CXX object CMakeFiles/splash2txt.dir/splash2txt.cpp.o
/home/81i61029/src/picongpu/src/tools/splash2txt/splash2txt.cpp:221:5: warning:identifier ‘nullptr’ is a keyword in C++11 [-Wc++0x-compat]
ITools tools = nullptr;
^
/home/81i61029/src/picongpu/src/tools/splash2txt/splash2txt.cpp: In function ‘int main(int, char)’:
/home/81i61029/src/picongpu/src/tools/splash2txt/splash2txt.cpp:221:21: error: nullptr’ was not declared in this scope
ITools *tools = nullptr;
^
make[2]: * [CMakeFiles/splash2txt.dir/splash2txt.cpp.o] Error 1
make[1]: [CMakeFiles/splash2txt.dir/all] Error 2
make: * [all] Error 2

Could you please help me fixing this?
Thank you!

8i161029 on 6 Jul 2017

In addition, I have some questions about steps of testing case001.
Are the steps:

clone $HOME/src/picongpu/examples/LaserWakefield to $HOME/paramSets/case001
cd $HOME/paramSets/case001
pic-configure $HOME/paramSets/case001
make
make -j install

Do I need to move to $HOME/build to do any steps?
Besides, what is $SCRATCH mentioned in USAGE.rst? And how to get it?
And after step 5, is that I should try this command tbg -s qsub -c submit/0016gpus.cfg -t submit/hypnos/k20_profile.tpl $PICHOME/runs/testBatch01 ?
Methods in USAGE.rst are a little different from previous guide install.md so I am confused.

Sorry about many questions. Thank you very much!

8i161029 on 6 Jul 2017

you can skip splash2txt - the tool is outdated and will probably be removed soon or replaced by a general openPMD script #1544

ax3l on 6 Jul 2017

your steps are nearly correct, but you don't run pic-configure inside your input files but in a temporary build directory.

Do I need to move to $HOME/build to do any steps?

Yes, instead of 2. do: cd $HOME/build

See this section of our manual for the full details.

Besides, what is $SCRATCH mentioned in USAGE.rst? And how to get it?

Since a few weeks, that's also explained in the link above in the first section :)

[...] Second, decide where to store your output of simulations which needs to be placed on a high-bandwidth, large-storage file system which we will refer to as $SCRATCH.

For a first test you can also use your home directory $HOME as simulation directory $SCRATCH.

Sorry about many questions. Thank you very much!

Don't worry, that's normal. The files you mention are also actually part of our manual which you can find in its full glory under https://picongpu.readthedocs.io . The best thing might be if you read the first two chapters INSTALLATION and USAGE page by page.

And after step 5, is that I should try this command

The tool tbg is the last step which copies your input and executables to an output directory ("scratch") where it is then executed. You need to adjust it's parameters to only take one GPU (.cfg file) if you are running locally.

But before you get there, you will adjust your .cfg file accordingly (see the manual first). The final command will then likely look like:

#  interactive      use one GPU            run with mpirun         output directory
tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpirun.tpl $HOME/runs/lwfa_001

ax3l on 6 Jul 2017

Hello, I have some questions.
I found that the version of GCC in this server is 4.8.5. But my CUDA is version 8.0, so I need GCC version >5.
Then I installed GCC-6.3.0 in $HOME/lib/gcc-6.3.0.
However, I have problem setting environment variable...
I already set this line in .bash_profile:

PATH=$HOME/lib/gcc-6.3.0/bin:$PATH:HOME/.local/bin:$HOME/bin

I check gcc --version and c++ --version
Here are the output:

gcc (GCC) 6.3.0
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

c++ (GCC) 6.3.0
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

But as I configured case001, output showed that:

cmake command: cmake -DCUDA_ARCH=20 -DCMAKE_INSTALL_PREFIX=/home/81i61029/paramSets/case001 -DPIC_EXTENSION_PATH=/home/81i61029/paramSets/case001 /home/81i61029/src/picongpu/src/picongpu
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
.
.
.

C compiler is still GNU 4.8.5.
I think I set the path wrongly.
Could you please teach me how to set up GCC environment variable?

Besides, I see many " Cmake warning" in configure output. Such like:

Cmake warning at /opt/cmake-3.8.0 - rc2/Modules/FindBoost . cmake : 761 (message):
Imported targets not available for Boost version 106400
Call Stack (most recent call first) :
/opt/cmake-3.8.0 - rc2/Modules/FindBoost . cmake : 865 (_Boost_COMPONENT_DEPENDENCIES)
/opt/cmake-3.8.0-rc2/Modules/FindBoost.cmake:1456 (_Boost_MISSING_DEPENDENCIES)
CMakeLists.txt:152 (find_package)

Is this matter? Any problems between Cmake and Boost?
Although that Cmake warning, configuring is completed.
Maybe it is normal.
I think I am getting there. Thank you for your help!

8i161029 on 14 Jul 2017

I found that the version of GCC in this server is 4.8.5. But my CUDA is version 8.0, so I need GCC version >5.

That's not fully correct. CUDA 8.0 supports GCC up to 5.X (not at least GCC 5).
The PIConGPU requirements are noted in our INSTALL.rst files (see the online version here) which are GCC 4.9-5.X.

So yes, at least for PIConGPU 0.3.0 (latest release) GCC 4.8 is too old and 6.X is too new (due to CUDA 8.0 limitations).

C compiler is still GNU 4.8.5. I think I set the path wrongly.

Just export the variables CC and CXX in your picongpu.profile. If you change compilers, make sure all your dependencies are build with the same compiler to avoid ABI conflicts such as symbol mismatches.

For example:

export CC=$HOME/lib/gcc-6.3.0/bin/gcc
export CXX=$HOME/lib/gcc-6.3.0/bin/g++

CMake should then report the correct compiler choice :)

ax3l on 17 Jul 2017

Imported targets not available for Boost version 106400

this just means your CMake is too old (or your boost version is too new). Just use Boost 1.61.0 instead, for example in case it causes troubles :)
Those are "just" cmake hints chaining boost-internal dependencies together for some compiled boost libs, but usually it should still work since we request boost components rather explicitly in our CMakeLists.txt.

ax3l on 17 Jul 2017

Hello, I did locate picongpu.profile and here is the output:

/home/81i61029/src/picongpu/src/picongpu/submit/hypnos-hzdr/picongpu.profile.example
/home/81i61029/src/picongpu/src/picongpu/submit/lawrencium-lbnl/picongpu.profile.example
/home/81i61029/src/picongpu/src/picongpu/submit/pizdaint-cscs/picongpu.profile.example
/home/81i61029/src/picongpu/src/picongpu/submit/taurus-tud/picongpu.profile.example
/home/81i61029/src/picongpu/src/picongpu/submit/titan-ornl/picongpu.profile.example

I am not sure which picongpu.profile should I edit.
I edited ...hypnos-hzdr/picongpu.profile.example and configured. But GNU was still 4.8.5.
Could you please teach me which file should I edit? Thank you very much!

8i161029 on 19 Jul 2017

The picongpu.profile script is a bash script that sets up your (bash) environment, such as paths to installed dependencies, LD_LIBRARY_PATH, etc. See this chapter of the manual.

We usually place it in $HOME/ and source it

. $HOME/picongpu.profile

first after opening a terminal or connecting to a machine.

This is just a way to avoid placing all modifications of a specific software (such as PIConGPU) in your $HOME/.profile (or $HOME/.bashrc) since they might influence other installed software.

ax3l on 19 Jul 2017

Thank you!
Can I just add export CC=$HOME/lib/gcc-6.3.0/bin/gcc and export CXX=$HOME/lib/gcc-6.3.0/bin/g++
in ~/.bash_profile? Since this user home folder only installed PIConGPU. I set all the environment variables in this file.
If picongpu.profile is necessary, is that I should clone ...hypnos-hzdr/picongpu.profile.example to $HOME and save as picongpu.profile then edit it and source it?

I tried add that two export commands in ~/.bash_profile and configured. Output showed that GNU is 6.3.0 and configured successfully.
Then I make. Here is the error:

[81i61029@messi build]$ make
Scanning dependencies of target picongpu-hostonly
[ 5%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
g++: error: _LARGEFILE_SOURCE: No such file or directory
g++: error: _LARGEFILE64_SOURCE: No such file or directory
g++: error: _BSD_SOURCE: No such file or directory
make[2]: * [CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o] Error 1
make[1]: [CMakeFiles/picongpu-hostonly.dir/all] Error 2
make: ** [all] Error 2

g++ --version is:

g++ (GCC) 6.3.0
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Maybe I wrongly installed gcc-6.3.0.
I list my step to install gcc:

sudo yum install libmpc-devel mpfr-devel gmp-devel
wget http://mirrors.concertpass.com/gcc/releases/gcc-6.3.0/gcc-6.3.0.tar.bz2
tar jxvf gcc-6.3.0.tar.bz2
cd gcc-6.3.0
contrib/download_prerequisites
mkdir ../gcc-build
cd ../gcc-build
../gcc-6.3.0/configure -v --enable-languages=c,c++ --disable-multilib --prefix=$HOME/lib/gcc-6.3.0
make -j
mkdir $HOME/lib/gcc-6.3.0
make install
add PATH=$HOME/lib/gcc-6.3.0/bin:$PATH:HOME/.local/bin:$HOME/bin in ~/.bash_profile

Could you please teach me where is the problem? So sorry to keep bothering you.
I am so thankful for your help.

8i161029 on 19 Jul 2017

Yes, you can also take the vars from one of the example profiles and put them directly in to your .bashrc or .profile.

Output showed that GNU is 6.3.0 [...]

Please stay with GCC 5.X since CUDA 8 does not support GCC >5: see my comment above

Note: You need to set and source your picongpu.profile (or .bashrc) variables before building the dependencies of PIConGPU, so all libs are build with the same compiler.

Side note for an alternative install method: if you can install nvidia-docker on your machine, the setup can be as easy as:

nvidia-docker run -it ax3l/picongpu

ax3l on 19 Jul 2017

I have installed gcc-5.2.0 in /usr/local/bin:
g++ --version:

g++ (GCC) 5.2.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

c++ --version:

c++ (GCC) 5.2.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

And also cloned ...hypnos-hzdr/picongpu.profile.example to $HOME and save as picongpu.profile
Already added the two export commands:
export CC=/usr/local/bin/gcc
export CXX=/usr/local/bin/g++

in picongpu.profile then sourced it. (Soured ~/.bash_profile too since environment variables in it)

Output of configure showed that GNU is 5.2.0 and configured down.
But as I entered make there was still errors:

Scanning dependencies of target picongpu-hostonly
[ 5%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
g++: error: _LARGEFILE_SOURCE: No such file or directory
g++: error: _LARGEFILE64_SOURCE: No such file or directory
g++: error: _BSD_SOURCE: No such file or directory
make[2]: * [CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o] Error 1
make[1]: [CMakeFiles/picongpu-hostonly.dir/all] Error 2
make: ** [all] Error 2

I check cmake --version:

cmake version 3.8.0-rc2
CMake suite maintained and supported by Kitware (kitware.com/cmake).

and cc --version:

cc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-11)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Is it the problem that cc is still GCC-4.8.5?
how to change it?
Thank you!

8i161029 on 20 Jul 2017

I am not sure how to control the cc/c++ links on RHEL, on debian/ubuntu they are just links to /etc/alteratives/cc|c++ which in turn are links to the actual compiler that the package system uses. Those are not the same as the CXX/CC environment vars that control CMake, and your CMake output looks fine to me.

The problems seems to be more in the g++ error you get

g++: error: _LARGEFILE_SOURCE: No such file or directory

Did you recompile the dependencies, such as Boost, with GCC 5.2? Alternatively, it could indicate a broken install of g++ or unmatching std libs.

If you are having trouble to get a clean environment on your desktop, there are two alternatives I can recommend you to get an install done:

use our nvidia-docker image

or

install spack, setup a GCC 5.X compiler with it and install all dependencies:

spack install cmake
spack install cuda
spack install [email protected]
spack install [email protected]
spack install [email protected]
spack install [email protected]
spack install [email protected] ^hdf5~fortran

ax3l on 21 Jul 2017

Thank you!
Maybe I reinstall Boost and try again? What else libraries are dependencies?
If this method does not work, I will try to install spack as you suggested.

8i161029 on 21 Jul 2017

Sounds good!
All software in INSTALL.rst are dependencies :)

ax3l on 21 Jul 2017

Hi. I thought there are many people work on this machine and the environment is complicated.
So I installed spack. As I wanted to setup a GCC 5.4.0 compiler with it, I made a check:
spack compiler info [email protected] :

spack compiler info [email protected]
[email protected]:
paths:
cc = /home/81i61029/lib/gcc-5.4.0/bin/gcc
cxx = /home/81i61029/lib/gcc-5.4.0/bin/g++
f77 = None
fc = None
modules = []
operating system = centos7

And I also checked original gcc in this machine:
spack compiler info [email protected]:

[email protected]:
paths:
cc = /usr/bin/gcc
cxx = /usr/bin/g++
f77 = /usr/bin/gfortran
fc = /usr/bin/gfortran
modules = []
operating system = centos7

I found that GCC-5.4.0 compiler doesn't support Fortran. Does it matter?
How to set it? Thank you!

8i161029 on 26 Jul 2017

👍1

When compiling your own gcc, make sure you add --enable-languages=c,c++,fortran on the configure command to also build gfortran. You will need it for compiling openmpi (unfortunately).

here is an example:

configure CFLAGS="-fPIC" CXXFLAGS="-fPIC" \
    --prefix=$gccDir \
    --build=x86_64-linux-gnu --enable-languages=c,c++,fortran \
--enable-shared --disable-multilib

then just add it properly to spack as you tried above, you will now also have gfortran for [email protected] :)

ax3l on 26 Jul 2017

I reinstall GCC-5.4.0 and configured as your example(only changed prefix to $HOME/lib/gcc-5.4.0).
I made a check:
spack compiler info [email protected]:

spack compiler info [email protected]
[email protected]:
paths:
cc = /home/81i61029/lib/gcc-5.4.0/bin/gcc
cxx = /home/81i61029/lib/gcc-5.4.0/bin/g++
f77 = None
fc = None
modules = []
operating system = centos7

I found it still did not support Fortran. I thought maybe I need to set it.
I entered spack config edit compilers
and changed f77 and fc path to /home/81i61029/lib/gcc-5.4.0/bin/gfortran.
now the output of spack compiler info [email protected] is :

[email protected]:
paths:
cc = /home/81i61029/lib/gcc-5.4.0/bin/gcc
cxx = /home/81i61029/lib/gcc-5.4.0/bin/g++
f77 = /home/81i61029/lib/gcc-5.4.0/bin/gfortran
fc = /home/81i61029/lib/gcc-5.4.0/bin/gfortran
modules = []
operating system = centos7

Can I make this change? I am afraid that this change is wrong.
If it is ok, I can install all dependencies. Right?
Thank you!

8i161029 on 26 Jul 2017

Besides, after install these libraries, how to run PIConGPU on spack? Are there any user manuals?
Could you please teach me or give me some links?
Thank you very much!

8i161029 on 26 Jul 2017

In order to run PIConGPU with dependencies installed via spack, first set up spack. You already set your compilers in $HOME/.spack/compilers.yaml and do additionally add the following:

modules:
  enable::
    - lmod
  lmod:
    core_compilers:
      - '[email protected]'
    hash_length: 0
    gcc:
      environment:
        set:
          CC: gcc
          CXX: g++
          FC: gfortran
          F90: gfortran
          F77: gfortran
    openmpi:
      environment:
        set:
          OMPI_MCA_mpi_leave_pinned: '0'

to $HOME/.spack/modules.yaml.

Now install lmod so you can use the generated packages easily.

Install Dependencies

This part is still a bit verbose and will soon become shorter. But don't despair, you only need to do it once :)

Now run the following once (for install):

spack install cmake
spack install cuda
spack install [email protected]
spack install [email protected]
spack install [email protected]
spack install [email protected]
spack install [email protected] ^hdf5~fortran

This command will take a while and installs all dependencies from source.

The last step is to create a $HOME/picongpu.profile file with the following content (please adjust the first three lines as necessary with your paths and the other lines as you need it, e.g. to add your name to the meta data of generated output):

# Modules #####################################################################
#
. /usr/share/lmod/5.8/init/bash
. $HOME/src/spack/share/spack/setup-env.sh
export MODULEPATH=$HOME/src/spack/share/spack/lmod/linux-centos7-x86_64/Core

# Core Dependencies (based on gcc 5.4.0)
module load cmake
module load boost
module load cuda
module load openmpi

# Plugins (optional)
module load zlib libpng freetype pngwriter
module load hdf5 libsplash

# either use libSplash or ADIOS for file I/O
#module load adios

# Environment #################################################################
#
export PICSRC=/home/`whoami`/src/picongpu
export PIC_PROFILE=$(cd $(dirname $BASH_SOURCE) && pwd)"/"$(basename $BASH_SOURCE)

# send me mails on job (b)egin, (e)nd, (a)bortion or (n)o mail
export MY_MAILNOTIFY="n"
export MY_MAIL="[email protected]"
export MY_NAME="$(whoami) <$MY_MAIL>"

export PATH=$PATH:$PICSRC
export PATH=$PATH:$PICSRC/src/splash2txt/build
export PATH=$PATH:$PICSRC/src/tools/bin

export PYTHONPATH=$PICSRC/src/tools/lib/python:$PYTHONPATH

# "tbg" default options #######################################################
#   - interactive (bash + mpiexec)
export TBG_SUBMIT="bash"
export TBG_TPLFILE="etc/picongpu/bash/bash_mpiexec.tpl"

Using PIConGPU

Open a new terminal and run . ~/picongpu.profile once.
You can now use PIConGPU with all it's environment as described here: https://picongpu.readthedocs.io/en/latest/usage/basics.html

ax3l on 31 Jul 2017

Thank you for your response!
My compilers.yaml is in $HOME/.spack/linux/compilers.yaml and I cannot find modules.yaml
Here is the output of find .spack :

[81i61029@messi ~]$ find $HOME/.spack
/home/81i61029/.spack
/home/81i61029/.spack/cache
/home/81i61029/.spack/cache/providers
/home/81i61029/.spack/cache/providers/.builtin-index.yaml.lock
/home/81i61029/.spack/cache/providers/builtin-index.yaml
/home/81i61029/.spack/linux
/home/81i61029/.spack/linux/compilers.yaml

Can I create a modules.yaml in /home/81i61029/.spack/linux ?

And is the installation status of my GCC-5.4.0 okay? Because I made some change in compilers.yaml.
output of spack compiler info [email protected] :

[email protected]:
paths:
cc = /home/81i61029/lib/gcc-5.4.0/bin/gcc
cxx = /home/81i61029/lib/gcc-5.4.0/bin/g++
f77 = /home/81i61029/lib/gcc-5.4.0/bin/gfortran
fc = /home/81i61029/lib/gcc-5.4.0/bin/gfortran
modules = []
operating system = centos7

Thank you!

8i161029 on 31 Jul 2017

Yes just go ahead and create it :)

Your compilers.yaml looks good, otherwise we will know as soon as soon as openmpi compiles.

ax3l on 31 Jul 2017

Hi, I met some questions while installing lmod.

I met errors when I using Luarocks :

[81i61029@messi ~]$ luarocks install luaposix
Installing https://luarocks.org/luaposix-34.0.1-3.src.rock
Error: LuaRocks 2.4.1 bug (please report at https://github.com/keplerproject/luarocks/issues).
...61029/lib/luarocks/share/lua/5.1/luarocks/fs/lua.lua:784: attempt to call field 'mkdtemp' (a nil value)
stack traceback:
...61029/lib/luarocks/share/lua/5.1/luarocks/fs/lua.lua:784: in function 'make_temp_dir'
...i61029/lib/luarocks/share/lua/5.1/luarocks/fetch.lua:74: in function 'fetch_url_at_temp_dir'
...i61029/lib/luarocks/share/lua/5.1/luarocks/fetch.lua:142: in function 'fetch_and_unpack_rock'
...i61029/lib/luarocks/share/lua/5.1/luarocks/build.lua:358: in function <...i61029/lib/luarocks/share/lua/5.1/luarocks/build.lua:352>
(tail call): ?
...i61029/lib/luarocks/share/lua/5.1/luarocks/build.lua:407: in function <...i61029/lib/luarocks/share/lua/5.1/luarocks/build.lua:396>
(tail call): ?
(tail call): ?
(tail call): ?
[C]: in function 'xpcall'
...lib/luarocks/share/lua/5.1/luarocks/command_line.lua:180: in function 'run_command'
...cks/lib/luarocks/rocks/luarocks/2.4.1-1/bin/luarocks:33: in main chunk
[C]: ?

Please teach me how to fix this.

Maybe I can install lua Filesystem (lfs) and luaposix by using Package Manager to avoid this problem.
Could you please teach me how to get lua Filesystem (lfs) and luaposix by using Package Manager in CentOS?
Thank you!

8i161029 on 3 Aug 2017

Huh! Please report that bug with your operating system in https://github.com/keplerproject/luarocks/issues as the error states (or https://github.com/TACC/Lmod)

In the meantime, let us use "simple" environment modules.

sudo yum install environment-modules

Set

modules:
  tcl:
    hash_length: 0
    gcc:
      environment:
        set:
          CC: gcc
          CXX: g++
          FC: gfortran
          F90: gfortran
          F77: gfortran
    openmpi:
      environment:
        set:
          OMPI_MCA_mpi_leave_pinned: '0'

to $HOME/.spack/modules.yaml.

The first lines of your $HOME/picongpu.profile now need to read:

# Modules #####################################################################
#
. /usr/share/modules/init/bash
. $HOME/src/spack/share/spack/setup-env.sh
export MODULEPATH=$HOME/src/spack/share/spack/modules/linux-centos7-x86_64

ax3l on 4 Aug 2017

Thank you for your response!
May I ask a question?
Without this line

core_compilers:
- '[email protected]'

in the amended modules.yaml, does spack still use gcc-5.4.0?
During installing dependencies, I saw all dependencies installed in original compiler gcc-4.4.7.
For example:

[81i61029@messi ~]$ spack install [email protected]
==> zlib is already installed in /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/zlib-1.2.11-m6bccmouozijnhr2kkbobyxlvzp3f6dg
==> [email protected] : marking the package explicit

And in /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64 I can only see gcc-4.4.7
Is it normal? Should I also find gcc-5.4.0 in this directory?

Thank you!

8i161029 on 7 Aug 2017

I tried to change command: spack install [email protected] %[email protected].
Now I can see folder gcc-5.4.0 in /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64
and folder zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6 in gcc-5.4.0.
Should I make this change to all dependencies? After this does spack use gcc-5.4.0?
Thank you!

8i161029 on 7 Aug 2017

👍1

Yes, that's the right way to do it!

In order to spare always typing %[email protected], just set this compiler as your default compiler in a new file in $HOME/packages.yaml:

packages:
  all:
    compiler: [[email protected]]

You can also keep the other compiler included but with less priority:

packages:
  all:
    compiler: [[email protected], [email protected]]

The file in modules.yaml was a setting for lmod, which would have organized the compiled libs in a hierarchy "compiler -> MPI -> ..." for you. If you are using environment modules instead the module load might become a bit more longish but we will manage that or use or spack load instead.

ax3l on 7 Aug 2017

I met trouble during install dependencies after I changed default compiler.
I could not find packages.yaml in $HOME
So I added [email protected] in $HOME/lib/spack/etc/spack/defaults/packages.yaml in front of original line.
Here is the packages.yaml:

packages:
all:
compiler: [[email protected], gcc, intel, pgi, clang, xl, nag]
providers:
awk: [gawk]
blas: [openblas]
daal: [intel-parallel-studio+daal]
elf: [elfutils]
golang: [gcc]
ipp: [intel-parallel-studio+ipp]
lapack: [openblas]
mkl: [intel-parallel-studio+mkl]
mpe: [mpe2]
mpi: [openmpi, mpich]
opencl: [pocl]
openfoam: [openfoam-com, openfoam-org, foam-extend]
pil: [py-pillow]
scalapack: [netlib-scalapack]

Then I installed cmake, here is error:

==> Error: ProcessError: Command exited with status 11:
'./bootstrap' '--prefix=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy' '--parallel=64' '--no-system-jsoncpp' '--no-system-libs' '--no-qt-gui' '--' '-DCMAKE_USE_OPENSSL=ON'
/home/81i61029/lib/spack/var/spack/repos/builtin/packages/cmake/package.py:128, in install:
93 def install(self, spec, prefix):
94 # Consistency check
95 self.validate(spec)
96
97 options = [
98 '--prefix={0}'.format(prefix),
99 '--parallel={0}'.format(make_jobs)]
100 if spec.satisfies("@3.2:"):
101 options.append(
102 # jsoncpp requires CMake to build
103 # use CMake-provided library to avoid circular dependency
104 '--no-system-jsoncpp'
105 )
106
107 if '+ownlibs' in spec:
108 # Build and link to the CMake-provided third-party libraries
109 options.append('--no-system-libs')
110 else:
111 # Build and link to the Spack-installed third-party libraries
112 options.append('--system-libs')
113
114 if '+qt' in spec:
115 options.append('--qt-gui')
116 else:
117 options.append('--no-qt-gui')
118
119 if '+doc' in spec:
120 options.append('--sphinx-html')
121 options.append('--sphinx-man')
122
123 if '+openssl' in spec:
124 options.append('--')
125 options.append('-DCMAKE_USE_OPENSSL=ON')
126
127 bootstrap = Executable('./bootstrap')

128 bootstrap(*options)
129
130 make()
131 if self.run_tests:
132 make('test') # some tests fail, takes forever
133 make('install')
See build log for details:
/tmp/81i61029/spack-stage/spack-stage-kV8UBz/cmake-3.8.1/spack-build.out

Is that I shouldn't change $HOME/lib/spack/etc/spack/defaults/packages.yaml?
should I create a packages.yaml in $HOME?
Thank you!

update: I did things I mentioned above. But it is still the same situation.

8i161029 on 7 Aug 2017

No, don't adjust the $HOME/lib/spack/etc/spack/defaults/packages.yaml. Just add the lines to a new file in your $HOME/.spack/ dir.

ax3l on 7 Aug 2017

what's the output of /tmp/81i61029/spack-stage/spack-stage-kV8UBz/cmake-3.8.1/spack-build.out ? looks like building cmake 3.8.1 with gcc 5.4.0 seems to fail o.0

ax3l on 7 Aug 2017

If you already have an external cmake on your system and it's new enough, you can also just take that version. CMake is only needed as a tool.

Assuming your system already has a recent binary, say CMake 3.8.1 in /usr, then just add to your $HOME/.spack/packages.yaml:

packages:
  all:
    compiler: [[email protected], [email protected]]
  cmake:
    paths:
      [email protected]%[email protected] arch=linux-centos7-x86_64: /usr
    buildable: False

ax3l on 7 Aug 2017

If that fails, we just go with [email protected] instead (compile from source, the rest is the same).

ax3l on 7 Aug 2017

Oh no. I created a new file packages.yaml in $HOME/.spack/linux.
Then install cmake again. The output is the same.
I am afraid that my wrongly installed gcc-5.4.0 before. So I reinstall [email protected] by spack.
Now my [email protected] is in $HOME/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr
Output of spack compiler info [email protected]:

[email protected]:
paths:
cc = /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gcc
cxx = /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++
f77 = /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gfortran
fc = /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gfortran
modules = []
operating system = centos7

I tried to install cuda. And it was successful.
My problem now is I cannot install cmake by spack with [email protected].

8i161029 on 7 Aug 2017

Oh sorry I miss your message.
Here is the output of /tmp/81i61029/spack-stage/spack-stage-kV8UBz/cmake-3.8.1/spack-build.out

==> './bootstrap' '--prefix=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy' '--parallel=64' '--no-system-jsoncpp' '--no-system-libs' '--no-qt-gui' '--' '-DCMAKE_USE_OPENSSL=ON'
---------------------------------------------
CMake 3.8.1, Copyright 2000-2017 Kitware, Inc. and Contributors
C compiler on this system is: /home/81i61029/lib/spack/lib/spack/env/gcc/gcc
C++ compiler on this system is: /home/81i61029/lib/spack/lib/spack/env/gcc/g++
Makefile processor on this system is: gmake
/home/81i61029/lib/spack/lib/spack/env/gcc/g++ is GNU compiler
/home/81i61029/lib/spack/lib/spack/env/gcc/g++ has setenv
/home/81i61029/lib/spack/lib/spack/env/gcc/g++ has unsetenv
/home/81i61029/lib/spack/lib/spack/env/gcc/g++ does not have environ in stdlib.h
/home/81i61029/lib/spack/lib/spack/env/gcc/g++ has stl wstring
/home/81i61029/lib/spack/lib/spack/env/gcc/g++ has
---------------------------------------------
gmake: cmake' is up to date. /tmp/81i61029/spack-stage/spack-stage-kV8UBz/cmake-3.8.1/Bootstrap.cmk/cmake: /lib64/libstdc++.so.6: versionGLIBCXX_3.4.20' not found (required by /tmp/81i61029/spack-stage/spack-stage-kV8UBz/cmake-3.8.1/Bootstrap.cmk/cmake)
/tmp/81i61029/spack-stage/spack-stage-kV8UBz/cmake-3.8.1/Bootstrap.cmk/cmake: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /tmp/81i61029/spack-stage/spack-stage-kV8UBz/cmake-3.8.1/Bootstrap.cmk/cmake)
---------------------------------------------

8i161029 on 7 Aug 2017

With spack, the best thing is to install a compiler externally before starting with it.
This can be done either manually, via system package manager or via a second spack instance, see this link: http://spack.readthedocs.io/en/latest/getting_started.html#build-your-own-compiler

ax3l on 7 Aug 2017

I tried to verify your problem with gcc 5.4.0 and cmake 3.8.1 and could not reproduce it. Seems really like your gcc 5.4.0 was not installed properly? Did you bootstrap it (make bootstrap)? It looks like it is still using the wrong libstdc++ of your system

ax3l on 7 Aug 2017

Your spack compiler info [email protected]: looks wrong. It points to 4.4.7 paths instead of your install for gcc 5.4.

Can you post your $HOME/spack/compilers.yaml again, please? Make sure there are not several of those in your $HOME/.spack subfolders

ax3l on 7 Aug 2017

Ok, thank you!
I think I wrongly installed GCC again...
Now I try to reinstall gcc 5.4.0 with second spack instance.
Is that I need to install a new spack and get [email protected] by it, then dospack compiler find on original spack?

8i161029 on 7 Aug 2017

When in doubt, please also read the getting started sections of spack very carefully again, just to make sure you did not miss a step and understand what I am posting :)

ax3l on 7 Aug 2017

This short getting started section in the spack manual also tells you, that you can just add the new compiler like this:

spack compiler find /home/81i61029/lib/spack-tools/opt/...path...to...gcc5.4.0

while $HOME/lib/spack-tools is the second spack instance that you use solely for installing gcc 5.4.0

ax3l on 7 Aug 2017

Thank you a lot! I am installing gcc 5.4.0 by second spack instance.
May I ask what is the function of make bootstrap? I never did it while I install gcc-5.4.0.

Now my steps to install a new [email protected] are:

get another spack in $HOME/spack-tools
use the new spack to do spack install [email protected]
back to the original spack and do spack compiler find $HOME/spack-tools/spack/opt/...path...to...gcc5.4.0

Are there any things need to do but I forget?

8i161029 on 7 Aug 2017

Thank you a lot! I am installing gcc 5.4.0 by second spack instance.

that sounds good!

Are there any things need to do but I forget?

yes, please do not forget to replace the ...path...to...gcc5.4.0 in the path in step 3 :)

May I ask what is the function make bootstrap? I never did it while I install gcc-5.4.0.

You won't need that now, but usually one installs gcc similar to this and could add make bootstrap before make install to build the compiler again with itself to get rid of all external dependencies...

ax3l on 7 Aug 2017

So if I install [email protected] by second spack, I don't need to worry about bootstrap?
Because I see the error start from ./bootstrap while I install cmake in my comment above.

After I installed [email protected] by second spack, do I need to delete the

[email protected]:
paths:
cc = /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gcc
cxx = /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++
f77 = /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gfortran
fc = /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gfortran
modules = []
operating system = centos7

in compilers.yaml? Or just do the command spack compiler find?
Thank you!

8i161029 on 7 Aug 2017

So if I install [email protected] by second spack, I don't need to worry about bootstrap?

exactly.

After I installed [email protected] by second spack, do I need to delete the ...

yes, just remove the $HOME/.spack/compilers.yaml to start clean and then run the spack compiler find ... which will add it again and properly formatted for you.

ax3l on 7 Aug 2017

I finally installed cmake successfully !

First, After installing new [email protected], I did spack install cmake.
But it failed... so I check what happened. And I found there are many lines of Warning: Module file already exists : skipping creation and some errors mentioned about the directory dotkit
So I moved to the directories modules and dotkit in $HOME/lib/spack/share/spack/ and deleted all files in these two directories.
Then I also removed the directory $HOME/lib/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7
Eventually I entered spack install cmake, and it was successful !
I don't know which move I did that made me finish it. Just let you know I did these things.

Thank you!

update: All dependencies installed successfully! I will set picongpu.profile tomorrow.
Thank you a lot!

8i161029 on 7 Aug 2017

🎉2 👍1

Hello, I am setting picongpu.profile.
My spack is installed in $HOME/lib/spack. I did following changes:

change first three lines to:

. /usr/share/modules/init/bash
. $HOME/lib/spack/share/spack/setup-env.sh
export MODULEPATH=$HOME/lib/spack/share/spack/modules/linux-centos7-x86_64
change export PICSRC=/home/'whoami'/src/picongpu to:

export PICSRC=/home/81i61029/src/picongpu

I have some questions:

Do I need to revise this line? :
export PIC_PROFILE=$(cd $(dirname $BASH_SOURCE) && pwd)"/"$(basename $BASH_SOURCE)
and how to change it?
For this three lines:

export MY_MAILNOTIFY="n"
export MY_MAIL="[email protected]"
export MY_NAME="$(whoami) <$MY_MAIL>"

I'm not sure how to revise these.
Are these correct? :

export MY_MAILNOTIFY="n"
export [email protected]
export MY_NAME=$(81i61029) <$MY_MAIL>

Should I keep the sign " in these three lines?
Are there any lines I should revise but I miss?

Thank you!

8i161029 on 8 Aug 2017

Well done!

change first three lines to:

all right! module av should now show you available packages after sourcing the profile via . $HOME/picongpu.profile

change export PICSRC=/home/whoami/src/picongpu to:

ok, but you could have kept it that way since $(whoami) evaluates to your username 81i61029

Do I need to revise this line? : export PIC_PROFILE

no, keep it as it is, it just finds out the path to the profile

For this three lines: export MY_MAILNOTIFY ...

Keep MY_MAILNOTIFY on "n" (for no) since that only works on clusters with batch systems (mail on job start/end).
change MY_MAIL="..." to your e-mail
change the $(whoami) part in MY_NAME to your first and second name ... or artists name... or whatever you would use in a scientific publication as author name :)

this will make sure created files (HDF5, PNG, etc.) will have your name in the meta data

Should I keep the sign " in these three lines?

yes, the "" are escaping simple bash strings and are needed

ax3l on 8 Aug 2017

Thank you!
I recovered the whoami , revised the three lines about email and my name.
Here is my picongpu.profile :

# Modules #####################################################################
#
. /usr/share/modules/init/bash
. $HOME/lib/spack/share/spack/setup-env.sh
export MODULEPATH=$HOME/lib/spack/share/spack/modules/linux-centos7-x86_64

# Core Dependencies (based on gcc 5.4.0)
module load cmake
module load boost
module load cuda
module load openmpi

# Plugins (optional)
module load zlib libpng freetype pngwriter
module load hdf5 libsplash

# either use libSplash or ADIOS for file I/O
#module load adios

# Environment #################################################################
#
export PICSRC=/home/'whoami'/src/picongpu
export PIC_PROFILE=$(cd $(dirname $BASH_SOURCE) && pwd)"/"$(basename $BASH_SOURCE)

# send me mails on job (b)egin, (e)nd, (a)bortion or (n)o mail
export MY_MAILNOTIFY="n"
export MY_MAIL="[email protected]"
export MY_NAME="Po-Ting, Lai <$MY_MAIL>"

export PATH=$PATH:$PICSRC
export PATH=$PATH:$PICSRC/src/splash2txt/build
export PATH=$PATH:$PICSRC/src/tools/bin

export PYTHONPATH=$PICSRC/src/tools/lib/python:$PYTHONPATH

# "tbg" default options #######################################################
#   - interactive (bash + mpiexec)
export TBG_SUBMIT="bash"
export TBG_TPLFILE="etc/picongpu/bash/bash_mpiexec.tpl"

Is it ok?
Are there any examinations I can do to check all things I need are all right?
Or I just start to run case001?
Thank you!

8i161029 on 8 Aug 2017

I sourced it: . ~/picongpu.profile
and here is the output:

[81i61029@messi ~]$ . ~/picongpu.profile
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'cmake'
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'boost'
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'cuda'
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'openmpi'
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'zlib'
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'libpng'
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'freetype'
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'pngwriter'
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'hdf5'
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'libsplash'

I checked the directory $HOME/lib/spack/share/spack/modules/linux-centos7-x86_64
found these dependencies are named like cmake-3.8.1-gcc-5.4.0
So I revised picongpu.profile :

# Modules #####################################################################
#
. /usr/share/Modules/init/bash
. $HOME/lib/spack/share/spack/setup-env.sh
export MODULEPATH=$HOME/lib/spack/share/spack/modules/linux-centos7-x86_64

# Core Dependencies (based on gcc 5.4.0)
module load cmake-3.8.1-gcc-5.4.0
module load boost-1.61.0-gcc-5.4.0
module load cuda-8.0.61-gcc-5.4.0
module load openmpi-2.1.1-gcc-5.4.0

# Plugins (optional)
module load zlib-1.2.11-gcc-5.4.0 libpng-1.6.29-gcc-5.4.0 freetype-2.7.1-gcc-5.4.0 pngwriter-0.6.0-gcc-5.4.0
module load hdf5-1.10.1-gcc-5.4.0 libsplash-1.6.0-gcc-5.4.0

# either use libSplash or ADIOS for file I/O
#module load adios

# Environment #################################################################
#
export PICSRC=/home/81i61029/src/picongpu
export PIC_PROFILE=$(cd $(dirname $BASH_SOURCE) && pwd)"/"$(basename $BASH_SOURCE)

# send me mails on job (b)egin, (e)nd, (a)bortion or (n)o mail
export MY_MAILNOTIFY="n"
export MY_MAIL="[email protected]"
export MY_NAME="Po-Ting, Lai <$MY_MAIL>"

export PATH=$PATH:$PICSRC
export PATH=$PATH:$PICSRC/src/splash2txt/build
export PATH=$PATH:$PICSRC/src/tools/bin

export PYTHONPATH=$PICSRC/src/tools/lib/python:$PYTHONPATH

# "tbg" default options #######################################################
#   - interactive (bash + mpiexec)
export TBG_SUBMIT="bash"
export TBG_TPLFILE="etc/picongpu/bash/bash_mpiexec.tpl"

Then did . ~/picongpu.profile. Nothing showed up.
I think maybe I finish it...?
Here is the output of module av :

------ /home/81i61029/lib/spack/share/spack/modules/linux-centos7-x86_64 -------
boost-1.61.0-gcc-5.4.0        libtool-2.4.6-gcc-5.4.0
bzip2-1.0.6-gcc-5.4.0         libxml2-2.9.4-gcc-5.4.0
cmake-3.8.1-gcc-5.4.0         m4-1.4.18-gcc-5.4.0
cuda-8.0.61-gcc-5.4.0         ncurses-6.0-gcc-5.4.0
freetype-2.7.1-gcc-5.4.0      openmpi-2.1.1-gcc-5.4.0
hdf5-1.10.1-gcc-5.4.0         openssl-1.0.2k-gcc-5.4.0
hwloc-1.11.7-gcc-5.4.0        pkg-config-0.29.2-gcc-5.4.0
libpciaccess-0.13.5-gcc-5.4.0 pngwriter-0.6.0-gcc-5.4.0
libpng-1.6.29-gcc-5.4.0       util-macros-1.19.1-gcc-5.4.0
libsigsegv-2.11-gcc-5.4.0     xz-5.2.3-gcc-5.4.0
libsplash-1.6.0-gcc-5.4.0     zlib-1.2.11-gcc-5.4.0

Does it mean everything all right?
Thank you!

8i161029 on 8 Aug 2017

I configured LWFA. Although it was done, I found GNU is 4.8.5.
Can I add something in picongpu.profile to let module uses GCC-5.4.0?
What should I add? Can I add this line?

export PATH=$PATH:$HOME/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin

Thank you!

update: I tried this method, and I failed...

8i161029 on 8 Aug 2017

I made links for all modules in $HOME/spack-tools/spack/share/spack/modules/linux-centos7-x86_64
Putting them in $HOME/lib/spack/share/modules/linux-centos7-x86_64.
Adding module load gcc-5.4.0-gcc-4.4.7 in picongpu.profile and source it.
The output of module av:

------ /home/81i61029/lib/spack/share/spack/modules/linux-centos7-x86_64 -------
autoconf-2.69-gcc-4.4.7       libtool-2.4.6-gcc-4.4.7
automake-1.15-gcc-4.4.7       libtool-2.4.6-gcc-5.4.0
binutils-2.28-gcc-4.4.7       libxml2-2.9.4-gcc-4.4.7
bison-3.0.4-gcc-4.4.7         libxml2-2.9.4-gcc-5.4.0
boost-1.61.0-gcc-5.4.0        m4-1.4.18-gcc-4.4.7
bzip2-1.0.6-gcc-4.4.7         m4-1.4.18-gcc-5.4.0
bzip2-1.0.6-gcc-5.4.0         mpc-1.0.3-gcc-4.4.7
cmake-3.8.1-gcc-5.4.0         mpfr-3.1.5-gcc-4.4.7
cuda-8.0.61-gcc-5.4.0         ncurses-6.0-gcc-4.4.7
flex-2.6.4-gcc-4.4.7          ncurses-6.0-gcc-5.4.0
freetype-2.7.1-gcc-5.4.0      openmpi-2.1.1-gcc-5.4.0
gcc-5.4.0-gcc-4.4.7           openssl-1.0.2k-gcc-5.4.0
gettext-0.19.8.1-gcc-4.4.7    pkg-config-0.29.2-gcc-4.4.7
gmp-6.1.2-gcc-4.4.7           pkg-config-0.29.2-gcc-5.4.0
hdf5-1.10.1-gcc-5.4.0         pngwriter-0.6.0-gcc-5.4.0
help2man-1.47.4-gcc-4.4.7     tar-1.29-gcc-4.4.7
hwloc-1.11.7-gcc-5.4.0        util-macros-1.19.1-gcc-5.4.0
isl-0.14-gcc-4.4.7            xz-5.2.3-gcc-4.4.7
libpciaccess-0.13.5-gcc-5.4.0 xz-5.2.3-gcc-5.4.0
libpng-1.6.29-gcc-5.4.0       zip-3.0-gcc-4.4.7
libsigsegv-2.11-gcc-4.4.7     zlib-1.2.11-gcc-4.4.7
libsigsegv-2.11-gcc-5.4.0     zlib-1.2.11-gcc-5.4.0
libsplash-1.6.0-gcc-5.4.0

Then I configured:

[81i61029@messi build]$ pic-configure $HOME/picInputs/myLWFA
cmake command: cmake -DCUDA_ARCH=20 -DCMAKE_INSTALL_PREFIX=/home/81i61029/picInputs/myLWFA -DPIC_EXTENSION_PATH=/home/81i61029/picInputs/myLWFA   /home/81i61029/src/picongpu/src/picongpu
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gcc
-- Check for working C compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++
-- Check for working CXX compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "7.5") 
-- Found MPI_C: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so  
-- Found MPI_CXX: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so  
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   filesystem
--   system
--   math_tr1
-- Boost: Disable template aliases
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "5.0") 
-- Boost version: 1.61.0
-- Using mallocMC from thirdParty/ directory
-- Boost version: 1.61.0
-- Found mallocMC: /home/81i61029/src/picongpu/thirdParty/mallocMC/src (found suitable version "2.2.0", minimum required is "2.2.0")  
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "7.5") 
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "5.0") 
-- Boost version: 1.61.0
-- Found ZLIB: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so (found version "1.2.11") 
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   program_options
--   regex
--   filesystem
--   system
--   thread
--   math_tr1
--   serialization
--   chrono
--   date_time
--   atomic
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found version "8.0") 
-- Could NOT find NVML (missing:  NVML_LIBRARY) 
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   program_options
-- Can NOT find 'adios_config' - set ADIOS_ROOT or check your PATH
-- Could NOT find ADIOS (missing:  ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.10.0")
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.1") found components:  C 
-- libSplash supports PARALLEL output
-- Found Splash: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libsplash-1.6.0-up4oyugd7bmmbjd6wmbvxwciuvsfos2g/lib/libsplash.a;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so (found suitable version "1.6.0", minimum required is "1.6.0") 
-- Found PNG: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng.so (found suitable version "1.6.29", minimum required is "1.2.9") 
-- Found Freetype: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so (found version "2.7.1") 
-- Found PNGwriter: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/lib/libpngwriter.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so (found suitable version "0.6.0", minimum required is "0.5.6") 
-- Could NOT find ISAAC - set ISAAC_DIR or check your CMAKE_PREFIX_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/81i61029/build

I see some lines show up many times. Is it normal?
Finally, I installed:

[81i61029@messi build]$ make -j install
Scanning dependencies of target picongpu-hostonly
Scanning dependencies of target mpiInfo
[  5%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_cuda_memtest.cu.o
[ 11%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 17%] Building CXX object build_mpiInfo/CMakeFiles/mpiInfo.dir/main.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 29%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 35%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 41%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 47%] Linking CXX executable mpiInfo
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::typed_value<bool, char>::name() const':
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `main':
main.cpp:(.text.startup+0x5a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/mpiInfo.dir/main.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
collect2: error: ld returned 1 exit status
make[2]: *** [build_mpiInfo/mpiInfo] Error 1
make[1]: *** [build_mpiInfo/CMakeFiles/mpiInfo.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Scanning dependencies of target cuda_memtest
[ 52%] Building CXX object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/misc.cpp.o
[ 58%] Linking CXX static library libpicongpu-hostonly.a
[ 58%] Built target picongpu-hostonly
[ 64%] Linking CXX executable cuda_memtest
[ 64%] Built target cuda_memtest
make: *** [all] Error 2

The error information is the same as GNU is 4.8.5.
Could this method work(make link for gcc-5.4.0's modules)?
Could you please teach me how to correct it?
Thank you!

8i161029 on 8 Aug 2017

Hi,

above was a typo in whoami: you used ' instead of the small `

alternative:

export PICSRC=/home/$(whoami)/src/picongpu

ax3l on 9 Aug 2017

I checked the directory $HOME/lib/spack/share/spack/modules/linux-centos7-x86_64
found these dependencies are named like cmake-3.8.1-gcc-5.4.0
...
Adding module load gcc-5.4.0-gcc-4.4.7 in picongpu.profile and source it.

yes, brilliant! both are correct!

ax3l on 9 Aug 2017

Boost issue

It looks to me that although we are compiling with GCC 5.4.0, boost was compiled with -std=c++98.

Can you please try the following?
```bash

incase the module is still loaded

module unload boost-1.61.0-gcc-5.4.0

spack uninstall boost %[email protected]

... yes ...

spack install boost %[email protected] cppflags="-std=c++11"
````

Then open a new terminal, source $HOME/picongpu.profile again and try again to compile the example.

ax3l on 9 Aug 2017

Thank you!
I corrected the typo, now the line of whoami is:

export PICSRC=/home/$(whoami)/src/picongpu

For Boost issue,
Is that I do:

module unload boost-1.61.0-gcc-5.4.0

spack uninstall boost %[email protected]
spack install boost %[email protected] cppflags="-std=c++11"

on my currently terminal.
Then open a new terminal, do source $HOME/picongpu.profile?
Thank you!

8i161029 on 9 Aug 2017

Well done!

Yes, just:

Then open a new terminal, source $HOME/picongpu.profile again and try again to compile the example.

ax3l on 9 Aug 2017

Hello, I found if do spack install boost %[email protected] cppflags="-std=c++11",
spack will install [email protected].
So I deleted [email protected]
and changed the command to spack install [email protected] %[email protected] cppflags="-std=c++11".

Then source $HOME/picongpu.profile again and compile. But still could not make it.
Here is output:

[81i61029@messi build]$ make -j install
Scanning dependencies of target picongpu-hostonly
[  5%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_cuda_memtest.cu.o
[ 11%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o
Scanning dependencies of target mpiInfo
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 17%] Building CXX object build_mpiInfo/CMakeFiles/mpiInfo.dir/main.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 29%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 35%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 41%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 47%] Linking CXX executable mpiInfo
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::typed_value<bool, char>::name() const':
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `main':
main.cpp:(.text.startup+0x5a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/mpiInfo.dir/main.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
collect2: error: ld returned 1 exit status
make[2]: *** [build_mpiInfo/mpiInfo] Error 1
make[1]: *** [build_mpiInfo/CMakeFiles/mpiInfo.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 52%] Linking CXX static library libpicongpu-hostonly.a
[ 52%] Built target picongpu-hostonly
Scanning dependencies of target cuda_memtest
[ 58%] Building CXX object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/misc.cpp.o
[ 64%] Linking CXX executable cuda_memtest
[ 64%] Built target cuda_memtest
make: *** [all] Error 2

Maybe some dependencies also need to reinstall?
Thank you!

8i161029 on 9 Aug 2017

👍1

That's fine, both versions would work.

Did you open a new terminal before you sourced the picongpu.profile?

Inside build:

To be sure, also rm -rf ../build/* and pic-configure again.
What is the output of cmake -LA . | grep -i "boost"?

ax3l on 9 Aug 2017

Yes I opened a new terminal then sourced picongpu.profile.
And also do rm -rf ../build/* before configure.
Here is the output of cmake -LA . | grep -i "boost" :

[81i61029@messi build]$ cmake -LA . | grep -i "boost"
-- Boost version: 1.61.0
-- Found the following Boost libraries:
-- Boost: Disable template aliases
-- Boost version: 1.61.0
-- Boost version: 1.61.0
-- Boost version: 1.61.0
-- Found the following Boost libraries:
-- Boost version: 1.61.0
-- Found the following Boost libraries:
Boost_ATOMIC_LIBRARY_DEBUG:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboos_atomic-mt.so
Boost_ATOMIC_LIBRARY_RELEASE:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_atomic-mt.so
Boost_CHRONO_LIBRARY_DEBUG:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboos_chrono-mt.so
Boost_CHRONO_LIBRARY_RELEASE:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_chrono-mt.so
Boost_DATE_TIME_LIBRARY_DEBUG:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_date_time-mt.so
Boost_DATE_TIME_LIBRARY_RELEASE:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/liboost_date_time-mt.so
Boost_DIR:PATH=Boost_DIR-NOTFOUND
Boost_FILESYSTEM_LIBRARY_DEBUG:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_filesystem-mt.so
Boost_FILESYSTEM_LIBRARY_RELEASE:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_filesystem-mt.so
Boost_INCLUDE_DIR:PATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include
Boost_LIBRARY_DIR_DEBUG:PATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib
Boost_LIBRARY_DIR_RELEASE:PATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib
Boost_MATH_TR1_LIBRARY_DEBUG:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_math_tr1-mt.so
Boost_MATH_TR1_LIBRARY_RELEASE:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_math_tr1-mt.so
Boost_PROGRAM_OPTIONS_LIBRARY_DEBUG:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_program_options-mt.so
Boost_PROGRAM_OPTIONS_LIBRARY_RELEASE:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_program_options-mt.so
Boost_REGEX_LIBRARY_DEBUG:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_regex-mt.so
Boost_REGEX_LIBRARY_RELEASE:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_regex-mt.so
Boost_SERIALIZATION_LIBRARY_DEBUG:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_serialization-mt.so
Boost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_serialization-mt.so
Boost_SYSTEM_LIBRARY_DEBUG:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboos_system-mt.so
Boost_SYSTEM_LIBRARY_RELEASE:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_system-mt.so
Boost_THREAD_LIBRARY_DEBUG:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboos_thread-mt.so
Boost_THREAD_LIBRARY_RELEASE:FILEPATH=/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/lib/libboost_thread-mt.so

8i161029 on 9 Aug 2017

👍1

Ah, I catched why... It's a problem in mpiInfo.
We will provide a patch in the next hours, stay tuned!

ax3l on 9 Aug 2017

Sure! Thank you very much for your patient!

8i161029 on 9 Aug 2017

Sure thing, thank you for your patience, too!

ax3l on 9 Aug 2017

👍1

Does adding those lines

###############################################################################
# Language Flags
###############################################################################

# enforce C++11
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
set(CMAKE_CXX_STANDARD 11)

in $PICSRC/src/mpiInfo/CMakeLists.txt after line 48 fix it for you?

ax3l on 9 Aug 2017

add those lines in front of this part?

################################################################################
# Warnings
################################################################################

set(CMAKE_CXX_FLAGS_DEFAULT "-Wall")

8i161029 on 9 Aug 2017

just before that block starts

ax3l on 9 Aug 2017

ok, here is my src/mpiInfo/CMakeLists.txt :

#
# Copyright 2013-2017 Axel Huebl, Rene Widera, Felix Schmitt
#
# This file is part of mpiInfo.
#
# mpiInfo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# mpiInfo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with mpiInfo.
# If not, see <http://www.gnu.org/licenses/>.
#

################################################################################
# Required cmake version
################################################################################

cmake_minimum_required(VERSION 2.8.12.2)


################################################################################
# Project
################################################################################

project(mpiInfo)

if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
    set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}" CACHE PATH "install prefix" FORCE)
endif(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)

# set helper pathes to find libraries and packages
# Add specific hints
list(APPEND CMAKE_PREFIX_PATH "$ENV{MPI_ROOT}")
list(APPEND CMAKE_PREFIX_PATH "$ENV{BOOST_ROOT}")
# Add from environment after specific env vars
list(APPEND CMAKE_PREFIX_PATH "$ENV{CMAKE_PREFIX_PATH}")
# Last add generic system path to the end (as last fallback)
list(APPEND "/usr/lib/x86_64-linux-gnu/")


###############################################################################
# Language Flags
###############################################################################

# enforce C++11
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
set(CMAKE_CXX_STANDARD 11)

################################################################################
# Warnings
################################################################################

set(CMAKE_CXX_FLAGS_DEFAULT "-Wall")


################################################################################
# Find MPI
################################################################################

find_package(MPI REQUIRED)
include_directories(SYSTEM ${MPI_C_INCLUDE_PATH})
set(LIBS ${LIBS} ${MPI_C_LIBRARIES})

# bullxmpi fails if it can not find its c++ counter part
if(MPI_CXX_FOUND)
    set(LIBS ${LIBS} ${MPI_CXX_LIBRARIES})
endif(MPI_CXX_FOUND)


################################################################################
# Find Boost
################################################################################

find_package(Boost REQUIRED COMPONENTS program_options)
include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
set(LIBS ${LIBS} ${Boost_LIBRARIES})


################################################################################
# Compile & Link mpiInfo
################################################################################

add_executable(mpiInfo
    main.cpp
)

target_link_libraries(mpiInfo ${LIBS})


################################################################################
# Install mpiInfo
################################################################################

install(TARGETS mpiInfo
         RUNTIME DESTINATION bin)

I opened a new terminal and sourced picongpu.profile.
Here is the output of compile:

[81i61029@messi build]$ make -j
Scanning dependencies of target picongpu-hostonly
[  5%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_cuda_memtest.cu.o
Scanning dependencies of target mpiInfo
[ 11%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 17%] Building CXX object build_mpiInfo/CMakeFiles/mpiInfo.dir/main.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 29%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 35%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 41%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 47%] Linking CXX executable mpiInfo
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::typed_value<bool, char>::name() const':
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `main':
main.cpp:(.text.startup+0x5a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/mpiInfo.dir/main.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
collect2: error: ld returned 1 exit status
make[2]: *** [build_mpiInfo/mpiInfo] Error 1
make[1]: *** [build_mpiInfo/CMakeFiles/mpiInfo.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 52%] Linking CXX static library libpicongpu-hostonly.a
Scanning dependencies of target cuda_memtest
[ 52%] Built target picongpu-hostonly
[ 58%] Building CXX object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/misc.cpp.o
[ 64%] Linking CXX executable cuda_memtest
[ 64%] Built target cuda_memtest
make: *** [all] Error 2

It still failed...

8i161029 on 9 Aug 2017

👍1

weird, I use the same gcc version in my docker images...

can you post the output of make VERBOSE=ON please?

ax3l on 9 Aug 2017

👍1

Wow it is very long.
here is the output:

[81i61029@messi build]$ make VERBOSE=ON
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -H/home/81i61029/src/picongpu/src/picongpu -B/home/81i61029/build --check-build-system CMakeFiles/Makefile.cmake 0
Re-run cmake file: Makefile older than: build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o.depend
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "7.5") 
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   filesystem
--   system
--   math_tr1
-- Boost: Disable template aliases
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "5.0") 
-- Boost version: 1.61.0
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "7.5") 
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "5.0") 
-- Boost version: 1.61.0
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   program_options
--   regex
--   filesystem
--   system
--   thread
--   math_tr1
--   serialization
--   chrono
--   date_time
--   atomic
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found version "8.0") 
-- Could NOT find NVML (missing:  NVML_LIBRARY) 
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   program_options
-- Can NOT find 'adios_config' - set ADIOS_ROOT or check your PATH
-- Could NOT find ADIOS (missing:  ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.10.0")
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- libSplash supports PARALLEL output
-- Could NOT find ISAAC - set ISAAC_DIR or check your CMAKE_PREFIX_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/81i61029/build
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -E cmake_progress_start /home/81i61029/build/CMakeFiles /home/81i61029/build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory `/home/81i61029/build'
make -f CMakeFiles/picongpu-hostonly.dir/build.make CMakeFiles/picongpu-hostonly.dir/depend
make[2]: Entering directory `/home/81i61029/build'
cd /home/81i61029/build && /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -E cmake_depends "Unix Makefiles" /home/81i61029/src/picongpu/src/picongpu /home/81i61029/src/picongpu/src/picongpu /home/81i61029/build /home/81i61029/build /home/81i61029/build/CMakeFiles/picongpu-hostonly.dir/DependInfo.cmake --color=
make[2]: Leaving directory `/home/81i61029/build'
make -f CMakeFiles/picongpu-hostonly.dir/build.make CMakeFiles/picongpu-hostonly.dir/build
make[2]: Entering directory `/home/81i61029/build'
make[2]: Nothing to be done for `CMakeFiles/picongpu-hostonly.dir/build'.
make[2]: Leaving directory `/home/81i61029/build'
[ 29%] Built target picongpu-hostonly
make -f CMakeFiles/picongpu.dir/build.make CMakeFiles/picongpu.dir/depend
make[2]: Entering directory `/home/81i61029/build'
[ 35%] Building NVCC (Device) object CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o
cd /home/81i61029/build/CMakeFiles/picongpu.dir && /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -E make_directory /home/81i61029/build/CMakeFiles/picongpu.dir//.
cd /home/81i61029/build/CMakeFiles/picongpu.dir && /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -D verbose:BOOL=ON -D build_configuration:STRING=Release -D generated_file:STRING=/home/81i61029/build/CMakeFiles/picongpu.dir//./picongpu_generated_main.cu.o -D generated_cubin_file:STRING=/home/81i61029/build/CMakeFiles/picongpu.dir//./picongpu_generated_main.cu.o.cubin.txt -P /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.Release.cmake
-- Removing /home/81i61029/build/CMakeFiles/picongpu.dir//./picongpu_generated_main.cu.o
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -E remove /home/81i61029/build/CMakeFiles/picongpu.dir//./picongpu_generated_main.cu.o
-- Generating dependency file: /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.NVCC-depend
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk/bin/nvcc -M -D__CUDACC__ /home/81i61029/src/picongpu/src/picongpu/main.cu -o /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.NVCC-depend -ccbin /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gcc -m64 --std c++11 -DPMACC_CUDA_COMPILER_CLANG=0 -DBOOST_RESULT_OF_USE_TR1_WITH_DECLTYPE_FALLBACK -DBOOST_NO_CXX11_TEMPLATE_ALIASES -DPMACC_VERBOSE_LVL=0 -DPIC_VERBOSE_LVL=1 -DENABLE_HDF5=1 -DPIC_ENABLE_PNG=1 -Xcompiler ,\"-fopenmp\",\"-fopenmp\",\"-Wall\",\"-Wno-unknown-pragmas\",\"-Wextra\",\"-Wno-unused-parameter\",\"-Wno-unused-local-typedefs\",\"-O3\",\"-DNDEBUG\" --generate-code arch=compute_20,code=sm_20 --generate-code arch=compute_20,code=compute_20 --use_fast_math --ftz=false -DNVCC -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk/include -I/home/81i61029/picInputs/myLWFA/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include -I/home/81i61029/src/picongpu/thirdParty/mallocMC/src/include -I/home/81i61029/src/picongpu/src/libPMacc/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libsplash-1.6.0-up4oyugd7bmmbjd6wmbvxwciuvsfos2g/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/include/freetype2 -I/home/81i61029/src/picongpu/src/picongpu/include
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
-- Generating temporary cmake readable file: /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.depend.tmp
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -D input_file:FILEPATH=/home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.NVCC-depend -D output_file:FILEPATH=/home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.depend.tmp -D verbose=ON -P /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/share/cmake-3.8/Modules/FindCUDA/make2cmake.cmake
-- Copy if different /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.depend.tmp to /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.depend
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -E copy_if_different /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.depend.tmp /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.depend
-- Removing /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.depend.tmp and /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.NVCC-depend
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -E remove /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.depend.tmp /home/81i61029/build/CMakeFiles/picongpu.dir//picongpu_generated_main.cu.o.NVCC-depend
-- Generating /home/81i61029/build/CMakeFiles/picongpu.dir//./picongpu_generated_main.cu.o
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk/bin/nvcc /home/81i61029/src/picongpu/src/picongpu/main.cu -c -o /home/81i61029/build/CMakeFiles/picongpu.dir//./picongpu_generated_main.cu.o -ccbin /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gcc -m64 --std c++11 -DPMACC_CUDA_COMPILER_CLANG=0 -DBOOST_RESULT_OF_USE_TR1_WITH_DECLTYPE_FALLBACK -DBOOST_NO_CXX11_TEMPLATE_ALIASES -DPMACC_VERBOSE_LVL=0 -DPIC_VERBOSE_LVL=1 -DENABLE_HDF5=1 -DPIC_ENABLE_PNG=1 -Xcompiler ,\"-fopenmp\",\"-fopenmp\",\"-Wall\",\"-Wno-unknown-pragmas\",\"-Wextra\",\"-Wno-unused-parameter\",\"-Wno-unused-local-typedefs\",\"-O3\",\"-DNDEBUG\" --generate-code arch=compute_20,code=sm_20 --generate-code arch=compute_20,code=compute_20 --use_fast_math --ftz=false -DNVCC -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk/include -I/home/81i61029/picInputs/myLWFA/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include -I/home/81i61029/src/picongpu/thirdParty/mallocMC/src/include -I/home/81i61029/src/picongpu/src/libPMacc/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libsplash-1.6.0-up4oyugd7bmmbjd6wmbvxwciuvsfos2g/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/include/freetype2 -I/home/81i61029/src/picongpu/src/picongpu/include
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp(75): warning: variable "tmp" was set but never used

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp(146): warning: variable "dt_old" was declared but never referenced
          detected during:
            instantiation of "boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type boost::numeric::odeint::default_step_adjuster<Value, Time>::increase_step(boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type, boost::numeric::odeint::default_step_adjuster<Value, Time>::value_type, int) const [with Value=picongpu::float_64, Time=picongpu::float_64]" 
(778): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, const StateIn &, const DerivIn &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, StateOut &, DerivOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateIn=boost::array<picongpu::float_64, 1UL>, DerivIn=boost::array<picongpu::float_64, 1UL>, StateOut=boost::array<picongpu::float_64, 1UL>, DerivOut=boost::array<picongpu::float_64, 1UL>]" 
(716): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, DerivInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>, DerivInOut=boost::array<picongpu::float_64, 1UL>]" 
(899): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step_v1(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
(617): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp(103): here
            instantiation of "size_t boost::numeric::odeint::detail::integrate_adaptive(Stepper, System, State &, Time &, Time, Time &, Observer, boost::numeric::odeint::controlled_stepper_tag) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp(45): here
            instantiation of "size_t boost::numeric::odeint::integrate_adaptive(Stepper, System, State &, Time, Time, Time, Observer) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/numeric/odeint/integrate/integrate.hpp(48): here
            instantiation of "boost::enable_if<has_value_type<State, mpl_::bool_<false>>::type, size_t>::type boost::numeric::odeint::integrate(System, State &, Time, Time, Time, Observer) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/numeric/odeint/integrate/integrate.hpp(68): here
            instantiation of "size_t boost::numeric::odeint::integrate(System, State &, Time, Time, Time) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64]" 
/home/81i61029/src/picongpu/src/picongpu/include/particles/bremsstrahlung/PhotonEmissionAngle.hpp(169): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/core/swap.hpp(36): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "void boost_swap_impl::swap_impl(T &, T &) [with T=std::__cxx11::string]" 
(56): here
            instantiation of "void boost::swap(T1 &, T2 &) [with T1=std::__cxx11::string, T2=std::__cxx11::string]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/property_tree/detail/ptree_implementation.hpp(214): here
            instantiation of "void boost::property_tree::basic_ptree<Key, Data, KeyCompare>::swap(boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/property_tree/detail/ptree_implementation.hpp(201): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::operator=(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/property_tree/detail/ptree_implementation.hpp(644): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/property_tree/detail/ptree_implementation.hpp(848): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &, Translator) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t, Translator=boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, size_t>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/property_tree/detail/ptree_implementation.hpp(860): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t]" 
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp(94): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp(75): warning: variable "tmp" was set but never used

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/get_pointer.hpp:48:46: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                              ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/detail/shared_count.hpp:402:19: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                   ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/shared_ptr.hpp:255:64: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/shared_ptr.hpp:454:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/shared_ptr.hpp:467:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/shared_ptr.hpp:544:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/shared_ptr.hpp:553:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/shared_ptr.hpp:555:32: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp: At global scope:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp:54:109: warning: friend declaration ‘boost::mpl::aux::type_wrapper<Key> boost::mpl::operator/(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp:54:109: note: (if this is not what you intended, make sure the function template has already been declared and add <> after the function name here) 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp:55:90: warning: friend declaration ‘boost::mpl::aux::type_wrapper<boost::mpl::pair<T1, T2> > boost::mpl::operator|(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::m_item<Key, T, Base>::order*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp:56:85: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::m_item<Key, T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( order_tag_, ORDER_BY_KEY, m_item, aux::type_wrapper<Key>* );
                                                                                     ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp:71:121: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator/(const boost::mpl::m_mask<Key, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/map/aux_/item.hpp:72:94: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator|(const boost::mpl::m_mask<Key, Base>&, boost::mpl::m_mask<Key, Base>::key_order_*)’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper<void_>, ITEM_BY_ORDER, m_mask, key_order_* );
                                                                                              ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp:47:83: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::s_item<T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_SET_OVERLOAD( order_tag_, ORDER_BY_KEY, s_item, aux::type_wrapper<T>* );
                                                                                   ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp:48:97: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp:63:98: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_mask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[2]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/mpl/set/aux_/item.hpp:77:99: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_unmask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/smart_ptr/scoped_ptr.hpp:74:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                          ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const ctor_args_list&, const allocator_type&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::ctor_args_list = boost::tuples::cons<boost::tuples::null_type, boost::tuples::cons<boost::tuples::tuple<boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, boost::tuples::null_type> >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::allocator_type = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/property_tree/detail/ptree_implementation.hpp:179:87:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree() [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:89:29:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/multi_index_container.hpp:175:100: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/multi_index_container.hpp:175:100: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/multi_index_container.hpp:160:10: warning:   when initialized here [-Wreorder]
   explicit multi_index_container(
          ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/property_tree/detail/ptree_implementation.hpp:191:145:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/stl_pair.h:133:78:   required from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, const _T2&) [with _U1 = std::__cxx11::basic_string<char>&; <template-parameter-2-2> = void; _T1 = const std::__cxx11::basic_string<char>; _T2 = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/property_tree/detail/ptree_implementation.hpp:646:8:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const path_type&, const self_type&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/property_tree/detail/ptree_implementation.hpp:848:30:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&, Translator) [with Type = long unsigned int; Translator = boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/property_tree/detail/ptree_implementation.hpp:859:11:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&) [with Type = long unsigned int; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:94:32:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/multi_index_container.hpp:262:86: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/multi_index_container.hpp:262:86: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include/boost/multi_index_container.hpp:261:1: warning:   when initialized here [-Wreorder]
   multi_index_container(
 ^
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Dependee "/home/81i61029/build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/home/81i61029/build/CMakeFiles/picongpu.dir/depend.internal".
Scanning dependencies of target picongpu
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[ 41%] Building CXX object CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++  -DBOOST_NO_CXX11_TEMPLATE_ALIASES -DBOOST_RESULT_OF_USE_TR1_WITH_DECLTYPE_FALLBACK -DENABLE_HDF5=1 -DPIC_ENABLE_PNG=1 -DPIC_VERBOSE_LVL=1 -DPMACC_CUDA_COMPILER_CLANG=0 -DPMACC_VERBOSE_LVL=0 -I/home/81i61029/picInputs/myLWFA/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include -isystem /home/81i61029/src/picongpu/thirdParty/mallocMC/src/include -isystem /home/81i61029/src/picongpu/src/libPMacc/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libsplash-1.6.0-up4oyugd7bmmbjd6wmbvxwciuvsfos2g/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/include/freetype2 -I/home/81i61029/src/picongpu/src/picongpu/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk/include  -std=c++11 -fopenmp -fopenmp -Wall -Wno-unknown-pragmas -Wextra -Wno-unused-parameter -Wno-unused-local-typedefs -O3 -DNDEBUG   -std=c++11 -o CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o -c /home/81i61029/src/picongpu/src/picongpu/include/ArgsParser.cpp
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/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++  -DBOOST_NO_CXX11_TEMPLATE_ALIASES -DBOOST_RESULT_OF_USE_TR1_WITH_DECLTYPE_FALLBACK -DENABLE_HDF5=1 -DPIC_ENABLE_PNG=1 -DPIC_VERBOSE_LVL=1 -DPMACC_CUDA_COMPILER_CLANG=0 -DPMACC_VERBOSE_LVL=0 -I/home/81i61029/picInputs/myLWFA/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.61.0-utp5zzdwiup74ar6wqudb5dham2vnhud/include -isystem /home/81i61029/src/picongpu/thirdParty/mallocMC/src/include -isystem /home/81i61029/src/picongpu/src/libPMacc/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libsplash-1.6.0-up4oyugd7bmmbjd6wmbvxwciuvsfos2g/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/include -isystem /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/include/freetype2 -I/home/81i61029/src/picongpu/src/picongpu/include -I/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk/include  -std=c++11 -fopenmp -fopenmp -Wall -Wno-unknown-pragmas -Wextra -Wno-unused-parameter -Wno-unused-local-typedefs -O3 -DNDEBUG   -std=c++11 -o CMakeFiles/picongpu.dir/include/plugins/common/particlePatches.cpp.o -c /home/81i61029/src/picongpu/src/picongpu/include/plugins/common/particlePatches.cpp
[ 52%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/stringHelpers.cpp.o
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[ 58%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
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CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `picongpu::ArgsParser::parse(int, char**)':
ArgsParser.cpp:(.text+0x48c): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
ArgsParser.cpp:(.text+0x90a): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::typed_value<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, char>::name() const':
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `void boost::program_options::validate<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, int)':
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0xa5): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x479): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::checkpointTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text+0x2847): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::restoreTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text+0xa0cf): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, float*, long) [clone .constprop.1917]':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text+0x12073): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long) [clone .constprop.1926]':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text+0x122cd): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned int*, long) [clone .constprop.1927]':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text+0x1242e): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106100::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::unwind_extra_block(bool)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb[_ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb]+0x2c): undefined reference to `boost::re_detail_106100::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x21): undefined reference to `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x39): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<unsigned int, char>::name() const':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIjcE4nameEv[_ZNK5boost15program_options11typed_valueIjcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<double, char>::name() const':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameEv[_ZNK5boost15program_options11typed_valueIdcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<float, char>::name() const':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIfcE4nameEv[_ZNK5boost15program_options11typed_valueIfcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<int, char>::name() const':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIicE4nameEv[_ZNK5boost15program_options11typed_valueIicE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv]+0x1d): more undefined references to `boost::program_options::arg[abi:cxx11]' follow
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::SimulationStarter<picongpu::InitialiserController, picongpu::PluginController, picongpu::MySimulation>::parseConfigs(int, char**)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x87): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x155): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x225): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x331): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::re_detail_106100::raise_error<boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > >(boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::error_type)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10610011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xa2): undefined reference to `boost::re_detail_106100::raise_runtime_error(std::runtime_error const&)'
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10610011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xc0): undefined reference to `boost::re_detail_106100::get_default_error_string(boost::regex_constants::error_type)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > boost::re_detail_106100::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::re_detail_106100::re_set_long<unsigned int> const*, boost::re_detail_106100::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10610016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x151): undefined reference to `boost::re_detail_106100::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const'
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10610016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x4e5): undefined reference to `boost::re_detail_106100::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106100::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::extend_stack()':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv[_ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv]+0x18): undefined reference to `boost::re_detail_106100::get_mem_block()'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106100::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_prefix()':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv[_ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv]+0x14c): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<unsigned int, std::allocator<unsigned int> >*, int)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned short, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned short*, long)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x3eb): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<double, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x52f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<int, std::allocator<int> >*, int)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<float, std::allocator<float> >*, int)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x28f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106100::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::find_imp()':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0xa): undefined reference to `boost::re_detail_106100::get_mem_block()'
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x151): undefined reference to `boost::re_detail_106100::verify_options(unsigned int, boost::regex_constants::_match_flags)'
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x190): undefined reference to `boost::re_detail_106100::put_mem_block(void*)'
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x32d): undefined reference to `boost::re_detail_106100::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `bool boost::regex_search<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >&, boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >)':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_[_ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_]+0xf3): undefined reference to `boost::re_detail_106100::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106100::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_match()':
tmpxft_0000aa39_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv[_ZN5boost16re_detail_10610012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv]+0x230): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIdcEE[_ZTVN5boost15program_options11typed_valueIdcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIjcEE[_ZTVN5boost15program_options11typed_valueIjcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[_ZTVN5boost15program_options11typed_valueIicEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIfcEE[_ZTVN5boost15program_options11typed_valueIfcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE]+0x40): more undefined references to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' follow
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make[2]: *** [picongpu] Error 1
make[2]: Leaving directory `/home/81i61029/build'
make[1]: *** [CMakeFiles/picongpu.dir/all] Error 2
make[1]: Leaving directory `/home/81i61029/build'
make: *** [all] Error 2

8i161029 on 9 Aug 2017

weird, still looks to me like boost is not build with ./b2 cxxflags="-std=c++11"

ax3l on 9 Aug 2017

Does the zlib installation effect boost?
I remembered when I accidentally installed the boost1.63, spack also installed another version of zlib.
So maybe I reinstall zlib and boost again?

8i161029 on 9 Aug 2017

In principle it could, but this error is quite directly stating the missing C++11 ABI in boost program options itself. We can have a look tomorrow again, I am already out of office for today. Maybe we patch spack to add the cxxflags to boost's ./b2 compiler call.

ax3l on 9 Aug 2017

Thank you! I found something strange just a moment ago.
I did the method I mentioned above, and there are some problems.
After spack install [email protected] %[email protected] cppflags="-std=c++11",
spack will install a new zlib-1.2.11. So now there are two zlib folder in $HOME/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0
But module of zlib inside $HOME/lib/spack/share/spack/modules still link to the old zilb-1.2.11.

Maybe it is the reason why boost still isn't build with c++11?

So I deleted two zlib and their dependencies and tried to reinstall them:

[81i61029@messi ~]$ spack uninstall --dependents --all  zlib %[email protected]

Then I opened a new terminal, installed boost with this command again:

spack install [email protected] %[email protected] cppflags="-std=c++11"

spack then installed boost and zlib. Next, I wanted to install cmake but didn't want it install another zlib.
I tried both commands:

spack install cmake %[email protected] ^zlib-1.2.11 %[email protected]

and

spack install cmake %[email protected] cppflags="-std=c++11" ^zlib-1.2.11 %[email protected]

But here is the output shows:

[81i61029@messi ~]$ spack install cmake %[email protected] ^zlib-1.2.11 %[email protected]
==> Error: cmake does not depend on 11

[81i61029@messi ~]$ spack install cmake %[email protected] cppflags="-std=c++11" ^zlib-1.2.11 %[email protected]
==> Error: cmake does not depend on 11

I cannot build boost and cmake with the same zlib.
If I just did spack install cmake, spack will install another zlib, and the module of zlib is link to the one with c++11.
I don't know whether it can work or not.
Any methods to solve this problem?
We try it tomorrow. Thank you for your help today!

8i161029 on 9 Aug 2017

So now there are two zlib folder in $HOME/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0

That's normal, since spack can build several variants of the same package and encodes their "specification" in a hash.

you can either spack uninstall the other version as above or select the one you want with spack load zlib %[email protected] (instead of module load zlib-...) which takes the same syntax as the spack install command took.

I cannot build boost and cmake with the same zlib.

Don't worry about that now, spack finds a matching version for you.

Boost Problem

First spack uninstall boost again in all variants you installed.

Can you now edit the "boost package file" inside $HOME/lib/spack/var/spack/repos/builtin/packages/boost/package.py?
It should contain the line:

threadingOpts = self.determine_b2_options(spec, b2_options)

Can you extend it to read the following, please?

threadingOpts = self.determine_b2_options(spec, b2_options)

b2_options.append('cxxflags="-std=c++11"')

then spack install boost %[email protected] again.

Last but not least test again the PIConGPU build: new terminal, source ~/picongpu.profile, cd build, rm -rf ../build/*, pic-configure ..., make install

ax3l on 10 Aug 2017

Thank you!
Please wait a second, I need to install the dependencies I removed yesterday...

8i161029 on 10 Aug 2017

This is the block of threadingOpts = self.determine_b2_options(spec, b2_options) in my boost/package.py

threadingOpts = self.determine_b2_options(spec, b2_options)

        b2('--clean')

Is that I change it to this? Delete the line b2('--clean')?

threadingOpts = self.determine_b2_options(spec, b2_options)

b2_options.append('cxxflags="-std=c++11"')

8i161029 on 10 Aug 2017

Do not delete any line, just add b2_options.append('cxxflags="-std=c++11"') after threadingOpts = self.determine_b2_options(spec, b2_options) as you wrote

ax3l on 10 Aug 2017

It failed...
Output of configure:

[81i61029@messi build]$ pic-configure $HOME/picInputs/myLWFA
cmake command: cmake -DCUDA_ARCH=20 -DCMAKE_INSTALL_PREFIX=/home/81i61029/picInputs/myLWFA -DPIC_EXTENSION_PATH=/home/81i61029/picInputs/myLWFA   /home/81i61029/src/picongpu/src/picongpu
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gcc
-- Check for working C compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++
-- Check for working CXX compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "7.5") 
-- Found MPI_C: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so  
-- Found MPI_CXX: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so  
-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   filesystem
--   system
--   math_tr1
-- Boost: Disable template aliases
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "5.0") 
-- Boost version: 1.63.0
-- Using mallocMC from thirdParty/ directory
-- Boost version: 1.63.0
-- Found mallocMC: /home/81i61029/src/picongpu/thirdParty/mallocMC/src (found suitable version "2.2.0", minimum required is "2.2.0")  
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "7.5") 
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "5.0") 
-- Boost version: 1.63.0
-- Found ZLIB: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so (found version "1.2.11") 
-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   program_options
--   regex
--   filesystem
--   system
--   thread
--   math_tr1
--   serialization
--   chrono
--   date_time
--   atomic
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found version "8.0") 
-- Could NOT find NVML (missing:  NVML_LIBRARY) 
-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   program_options
-- Can NOT find 'adios_config' - set ADIOS_ROOT or check your PATH
-- Could NOT find ADIOS (missing:  ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.10.0")
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.1") found components:  C 
-- libSplash supports PARALLEL output
-- Found Splash: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libsplash-1.6.0-up4oyugd7bmmbjd6wmbvxwciuvsfos2g/lib/libsplash.a;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so (found suitable version "1.6.0", minimum required is "1.6.0") 
-- Found PNG: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng.so (found suitable version "1.6.29", minimum required is "1.2.9") 
-- Found Freetype: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so (found version "2.7.1") 
-- Found PNGwriter: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/lib/libpngwriter.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so (found suitable version "0.6.0", minimum required is "0.5.6") 
-- Could NOT find ISAAC - set ISAAC_DIR or check your CMAKE_PREFIX_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/81i61029/build

output of make install:

[81i61029@messi build]$ make install
Scanning dependencies of target picongpu-hostonly
[  5%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 11%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 17%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
[ 29%] Linking CXX static library libpicongpu-hostonly.a
[ 29%] Built target picongpu-hostonly
[ 35%] Building NVCC (Device) object CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp(146): warning: variable "dt_old" was declared but never referenced
          detected during:
            instantiation of "boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type boost::numeric::odeint::default_step_adjuster<Value, Time>::increase_step(boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type, boost::numeric::odeint::default_step_adjuster<Value, Time>::value_type, int) const [with Value=picongpu::float_64, Time=picongpu::float_64]" 
(778): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, const StateIn &, const DerivIn &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, StateOut &, DerivOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateIn=boost::array<picongpu::float_64, 1UL>, DerivIn=boost::array<picongpu::float_64, 1UL>, StateOut=boost::array<picongpu::float_64, 1UL>, DerivOut=boost::array<picongpu::float_64, 1UL>]" 
(716): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, DerivInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>, DerivInOut=boost::array<picongpu::float_64, 1UL>]" 
(899): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step_v1(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
(617): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp(103): here
            instantiation of "size_t boost::numeric::odeint::detail::integrate_adaptive(Stepper, System, State &, Time &, Time, Time &, Observer, boost::numeric::odeint::controlled_stepper_tag) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp(45): here
            instantiation of "size_t boost::numeric::odeint::integrate_adaptive(Stepper, System, State &, Time, Time, Time, Observer) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(48): here
            instantiation of "boost::enable_if<has_value_type<State, mpl_::bool_<false>>::type, size_t>::type boost::numeric::odeint::integrate(System, State &, Time, Time, Time, Observer) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(68): here
            instantiation of "size_t boost::numeric::odeint::integrate(System, State &, Time, Time, Time) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64]" 
/home/81i61029/src/picongpu/src/picongpu/include/particles/bremsstrahlung/PhotonEmissionAngle.hpp(169): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/core/swap.hpp(36): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "void boost_swap_impl::swap_impl(T &, T &) [with T=std::__cxx11::string]" 
(56): here
            instantiation of "void boost::swap(T1 &, T2 &) [with T1=std::__cxx11::string, T2=std::__cxx11::string]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(214): here
            instantiation of "void boost::property_tree::basic_ptree<Key, Data, KeyCompare>::swap(boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(201): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::operator=(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(644): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(848): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &, Translator) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t, Translator=boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, size_t>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(860): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t]" 
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp(94): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/get_pointer.hpp:48:46: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                              ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/detail/shared_count.hpp:402:19: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                   ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:255:64: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:454:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:467:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:544:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:553:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:555:32: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp: At global scope:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: warning: friend declaration ‘boost::mpl::aux::type_wrapper<Key> boost::mpl::operator/(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: note: (if this is not what you intended, make sure the function template has already been declared and add <> after the function name here) 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:55:90: warning: friend declaration ‘boost::mpl::aux::type_wrapper<boost::mpl::pair<T1, T2> > boost::mpl::operator|(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::m_item<Key, T, Base>::order*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:56:85: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::m_item<Key, T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( order_tag_, ORDER_BY_KEY, m_item, aux::type_wrapper<Key>* );
                                                                                     ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:71:121: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator/(const boost::mpl::m_mask<Key, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:72:94: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator|(const boost::mpl::m_mask<Key, Base>&, boost::mpl::m_mask<Key, Base>::key_order_*)’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper<void_>, ITEM_BY_ORDER, m_mask, key_order_* );
                                                                                              ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:47:83: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::s_item<T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_SET_OVERLOAD( order_tag_, ORDER_BY_KEY, s_item, aux::type_wrapper<T>* );
                                                                                   ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:48:97: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:63:98: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_mask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[2]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:77:99: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_unmask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/scoped_ptr.hpp:74:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                          ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const ctor_args_list&, const allocator_type&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::ctor_args_list = boost::tuples::cons<boost::tuples::null_type, boost::tuples::cons<boost::tuples::tuple<boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, boost::tuples::null_type> >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::allocator_type = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:179:87:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree() [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:89:29:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:160:10: warning:   when initialized here [-Wreorder]
   explicit multi_index_container(
          ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:191:145:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/stl_pair.h:133:78:   required from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, const _T2&) [with _U1 = std::__cxx11::basic_string<char>&; <template-parameter-2-2> = void; _T1 = const std::__cxx11::basic_string<char>; _T2 = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:646:8:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const path_type&, const self_type&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:848:30:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&, Translator) [with Type = long unsigned int; Translator = boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:859:11:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&) [with Type = long unsigned int; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:94:32:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:261:1: warning:   when initialized here [-Wreorder]
   multi_index_container(
 ^
Scanning dependencies of target picongpu
[ 41%] Building CXX object CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o
[ 47%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/particlePatches.cpp.o
[ 52%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/stringHelpers.cpp.o
[ 58%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
[ 64%] Linking CXX executable picongpu
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `picongpu::ArgsParser::parse(int, char**)':
ArgsParser.cpp:(.text+0x48c): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
ArgsParser.cpp:(.text+0x90a): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::typed_value<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, char>::name() const':
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `void boost::program_options::validate<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, int)':
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0xa5): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x479): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::checkpointTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text+0x2727): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::restoreTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text+0x9f6f): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, float*, long) [clone .constprop.1916]':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text+0x11ed3): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long) [clone .constprop.1925]':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text+0x1212d): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned int*, long) [clone .constprop.1926]':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text+0x1228e): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::unwind_extra_block(bool)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb]+0x2c): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x21): undefined reference to `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x39): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<unsigned int, char>::name() const':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIjcE4nameEv[_ZNK5boost15program_options11typed_valueIjcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<double, char>::name() const':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameEv[_ZNK5boost15program_options11typed_valueIdcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<float, char>::name() const':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIfcE4nameEv[_ZNK5boost15program_options11typed_valueIfcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<int, char>::name() const':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIicE4nameEv[_ZNK5boost15program_options11typed_valueIicE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv]+0x1d): more undefined references to `boost::program_options::arg[abi:cxx11]' follow
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::SimulationStarter<picongpu::InitialiserController, picongpu::PluginController, picongpu::MySimulation>::parseConfigs(int, char**)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x86): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x14f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x21a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x30f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::re_detail_106300::raise_error<boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > >(boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::error_type)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xa2): undefined reference to `boost::re_detail_106300::raise_runtime_error(std::runtime_error const&)'
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xc0): undefined reference to `boost::re_detail_106300::get_default_error_string(boost::regex_constants::error_type)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > boost::re_detail_106300::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::re_detail_106300::re_set_long<unsigned int> const*, boost::re_detail_106300::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x151): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const'
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x4e5): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::extend_stack()':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv]+0x18): undefined reference to `boost::re_detail_106300::get_mem_block()'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_prefix()':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv]+0x14c): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<unsigned int, std::allocator<unsigned int> >*, int)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned short, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned short*, long)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x3eb): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<double, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x52f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<int, std::allocator<int> >*, int)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<float, std::allocator<float> >*, int)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x28f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::find_imp()':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0xa): undefined reference to `boost::re_detail_106300::get_mem_block()'
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x138): undefined reference to `boost::re_detail_106300::verify_options(unsigned int, boost::regex_constants::_match_flags)'
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x17f): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x2cd): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `bool boost::regex_search<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >&, boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >)':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_[_ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_]+0xf3): undefined reference to `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_match()':
tmpxft_0000ea62_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv]+0x210): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIdcEE[_ZTVN5boost15program_options11typed_valueIdcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIjcEE[_ZTVN5boost15program_options11typed_valueIjcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[_ZTVN5boost15program_options11typed_valueIicEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIfcEE[_ZTVN5boost15program_options11typed_valueIfcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE]+0x40): more undefined references to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' follow
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make[2]: *** [picongpu] Error 1
make[1]: *** [CMakeFiles/picongpu.dir/all] Error 2
make: *** [all] Error 2

8i161029 on 10 Aug 2017

ok, I think we need neither of the patches in mpiInfo nor in spack's boost package.

The most likely reason is that you have a second install of boost in your system (e.g. under /usr) that is accidentally taken during the link step. Weirdly, the cmake output does not link with absolute paths as it usually does.

ax3l on 10 Aug 2017

What does locate libboost_program_options.so output?

ax3l on 10 Aug 2017

oh I indeed have another boost in $HOME/lib/boost.
I also have other dependencies in $HOME/lib, they are built at the first time I tried to run PIConGPU without spack.
locate libboost_program_options.so:

[81i61029@messi ~]$ locate libboost_program_options.so
/home/81i61029/Downloads/boost_1_64_0/bin.v2/libs/program_options/build/gcc-4.8.5/release/threading-multi/libboost_program_options.so.1.64.0
/home/81i61029/Downloads/boost_1_64_0/stage/lib/libboost_program_options.so
/home/81i61029/Downloads/boost_1_64_0/stage/lib/libboost_program_options.so.1.64.0
/home/81i61029/lib/boost/lib/libboost_program_options.so
/home/81i61029/lib/boost/lib/libboost_program_options.so.1.64.0
/opt/matlab_2016a/bin/glnxa64/libboost_program_options.so.1.56.0
/usr/lib64/libboost_program_options.so
/usr/lib64/libboost_program_options.so.1.53.0

8i161029 on 10 Aug 2017

The ones that cause our trouble are in /usr/lib64/.

Try the following to link properly: edit the file $PICSRC/src/picongpu/CMakeLists.txt and add

cmake_policy(SET CMP0060 NEW)

in line 31 just before

project(PIConGPU)

ax3l on 10 Aug 2017

Here is my $PICSRC/src/picongpu/CMakeLists.txt:

...
################################################################################
# Project
################################################################################

cmake_policy(SET CMP0060 NEW)

project(PIConGPU)

if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
    set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}" CACHE PATH "install prefix" FORCE)
endif(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)

# set helper pathes to find libraries and packages
# Add specific hints
...

I opened new terminal, sourced picongpu.profile, clean the build folder, configured, and make install:

[81i61029@messi build]$ make install
Scanning dependencies of target picongpu-hostonly
[  5%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 11%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 17%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
[ 29%] Linking CXX static library libpicongpu-hostonly.a
[ 29%] Built target picongpu-hostonly
[ 35%] Building NVCC (Device) object CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp(146): warning: variable "dt_old" was declared but never referenced
          detected during:
            instantiation of "boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type boost::numeric::odeint::default_step_adjuster<Value, Time>::increase_step(boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type, boost::numeric::odeint::default_step_adjuster<Value, Time>::value_type, int) const [with Value=picongpu::float_64, Time=picongpu::float_64]" 
(778): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, const StateIn &, const DerivIn &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, StateOut &, DerivOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateIn=boost::array<picongpu::float_64, 1UL>, DerivIn=boost::array<picongpu::float_64, 1UL>, StateOut=boost::array<picongpu::float_64, 1UL>, DerivOut=boost::array<picongpu::float_64, 1UL>]" 
(716): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, DerivInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>, DerivInOut=boost::array<picongpu::float_64, 1UL>]" 
(899): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step_v1(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
(617): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp(103): here
            instantiation of "size_t boost::numeric::odeint::detail::integrate_adaptive(Stepper, System, State &, Time &, Time, Time &, Observer, boost::numeric::odeint::controlled_stepper_tag) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp(45): here
            instantiation of "size_t boost::numeric::odeint::integrate_adaptive(Stepper, System, State &, Time, Time, Time, Observer) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(48): here
            instantiation of "boost::enable_if<has_value_type<State, mpl_::bool_<false>>::type, size_t>::type boost::numeric::odeint::integrate(System, State &, Time, Time, Time, Observer) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(68): here
            instantiation of "size_t boost::numeric::odeint::integrate(System, State &, Time, Time, Time) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64]" 
/home/81i61029/src/picongpu/src/picongpu/include/particles/bremsstrahlung/PhotonEmissionAngle.hpp(169): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/core/swap.hpp(36): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "void boost_swap_impl::swap_impl(T &, T &) [with T=std::__cxx11::string]" 
(56): here
            instantiation of "void boost::swap(T1 &, T2 &) [with T1=std::__cxx11::string, T2=std::__cxx11::string]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(214): here
            instantiation of "void boost::property_tree::basic_ptree<Key, Data, KeyCompare>::swap(boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(201): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::operator=(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(644): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(848): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &, Translator) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t, Translator=boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, size_t>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(860): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t]" 
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp(94): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/get_pointer.hpp:48:46: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                              ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/detail/shared_count.hpp:402:19: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                   ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:255:64: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:454:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:467:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:544:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:553:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:555:32: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp: At global scope:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: warning: friend declaration ‘boost::mpl::aux::type_wrapper<Key> boost::mpl::operator/(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: note: (if this is not what you intended, make sure the function template has already been declared and add <> after the function name here) 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:55:90: warning: friend declaration ‘boost::mpl::aux::type_wrapper<boost::mpl::pair<T1, T2> > boost::mpl::operator|(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::m_item<Key, T, Base>::order*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:56:85: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::m_item<Key, T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( order_tag_, ORDER_BY_KEY, m_item, aux::type_wrapper<Key>* );
                                                                                     ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:71:121: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator/(const boost::mpl::m_mask<Key, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:72:94: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator|(const boost::mpl::m_mask<Key, Base>&, boost::mpl::m_mask<Key, Base>::key_order_*)’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper<void_>, ITEM_BY_ORDER, m_mask, key_order_* );
                                                                                              ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:47:83: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::s_item<T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_SET_OVERLOAD( order_tag_, ORDER_BY_KEY, s_item, aux::type_wrapper<T>* );
                                                                                   ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:48:97: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:63:98: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_mask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[2]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:77:99: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_unmask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/scoped_ptr.hpp:74:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                          ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const ctor_args_list&, const allocator_type&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::ctor_args_list = boost::tuples::cons<boost::tuples::null_type, boost::tuples::cons<boost::tuples::tuple<boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, boost::tuples::null_type> >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::allocator_type = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:179:87:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree() [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:89:29:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:160:10: warning:   when initialized here [-Wreorder]
   explicit multi_index_container(
          ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:191:145:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/stl_pair.h:133:78:   required from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, const _T2&) [with _U1 = std::__cxx11::basic_string<char>&; <template-parameter-2-2> = void; _T1 = const std::__cxx11::basic_string<char>; _T2 = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:646:8:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const path_type&, const self_type&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:848:30:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&, Translator) [with Type = long unsigned int; Translator = boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:859:11:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&) [with Type = long unsigned int; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:94:32:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:261:1: warning:   when initialized here [-Wreorder]
   multi_index_container(
 ^
Scanning dependencies of target picongpu
[ 41%] Building CXX object CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o
[ 47%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/particlePatches.cpp.o
[ 52%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/stringHelpers.cpp.o
[ 58%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
[ 64%] Linking CXX executable picongpu
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `picongpu::ArgsParser::parse(int, char**)':
ArgsParser.cpp:(.text+0x48c): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
ArgsParser.cpp:(.text+0x90a): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::typed_value<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, char>::name() const':
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `void boost::program_options::validate<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, int)':
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0xa5): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x479): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::checkpointTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text+0x2727): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::restoreTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text+0x9f6f): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, float*, long) [clone .constprop.1916]':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text+0x11ed3): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long) [clone .constprop.1925]':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text+0x1212d): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned int*, long) [clone .constprop.1926]':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text+0x1228e): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::unwind_extra_block(bool)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb]+0x2c): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x21): undefined reference to `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x39): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<unsigned int, char>::name() const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIjcE4nameEv[_ZNK5boost15program_options11typed_valueIjcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<double, char>::name() const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameEv[_ZNK5boost15program_options11typed_valueIdcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<float, char>::name() const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIfcE4nameEv[_ZNK5boost15program_options11typed_valueIfcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<int, char>::name() const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIicE4nameEv[_ZNK5boost15program_options11typed_valueIicE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv]+0x1d): more undefined references to `boost::program_options::arg[abi:cxx11]' follow
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::SimulationStarter<picongpu::InitialiserController, picongpu::PluginController, picongpu::MySimulation>::parseConfigs(int, char**)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x86): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x14f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x21a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x30f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::re_detail_106300::raise_error<boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > >(boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::error_type)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xa2): undefined reference to `boost::re_detail_106300::raise_runtime_error(std::runtime_error const&)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xc0): undefined reference to `boost::re_detail_106300::get_default_error_string(boost::regex_constants::error_type)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > boost::re_detail_106300::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::re_detail_106300::re_set_long<unsigned int> const*, boost::re_detail_106300::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x151): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x4e5): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::extend_stack()':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv]+0x18): undefined reference to `boost::re_detail_106300::get_mem_block()'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_prefix()':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv]+0x14c): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<unsigned int, std::allocator<unsigned int> >*, int)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned short, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned short*, long)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x3eb): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<double, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x52f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<int, std::allocator<int> >*, int)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<float, std::allocator<float> >*, int)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x28f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::find_imp()':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0xa): undefined reference to `boost::re_detail_106300::get_mem_block()'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x138): undefined reference to `boost::re_detail_106300::verify_options(unsigned int, boost::regex_constants::_match_flags)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x17f): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x2cd): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `bool boost::regex_search<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >&, boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_[_ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_]+0xf3): undefined reference to `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_match()':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv]+0x210): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIdcEE[_ZTVN5boost15program_options11typed_valueIdcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIjcEE[_ZTVN5boost15program_options11typed_valueIjcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[_ZTVN5boost15program_options11typed_valueIicEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIfcEE[_ZTVN5boost15program_options11typed_valueIfcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE]+0x40): more undefined references to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' follow
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make[2]: *** [picongpu] Error 1
make[1]: *** [CMakeFiles/picongpu.dir/all] Error 2
make: *** [all] Error 2

8i161029 on 10 Aug 2017

👍1

ok, can you attach the output of make VERBOSE=ON again so we see if we successfully influenced the linker flags? (you can also upload it as text in a .txt file)

ax3l on 10 Aug 2017

ok. Do I need to clean the build folder to do make VERBOSE=ON?
Here is the output without cleaning the build folder.
picongpu.txt

8i161029 on 10 Aug 2017

It will mess if I open this file in windows...
So I still attach the output on this comment.

[81i61029@messi build]$ make VERBOSE=ON
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -H/home/81i61029/src/picongpu/src/picongpu -B/home/81i61029/build --check-build-system CMakeFiles/Makefile.cmake 0
Re-run cmake file: Makefile older than: CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o.depend
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "7.5") 
-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   filesystem
--   system
--   math_tr1
-- Boost: Disable template aliases
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "5.0") 
-- Boost version: 1.63.0
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "7.5") 
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "5.0") 
-- Boost version: 1.63.0
-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   program_options
--   regex
--   filesystem
--   system
--   thread
--   math_tr1
--   serialization
--   chrono
--   date_time
--   atomic
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found version "8.0") 
-- Could NOT find NVML (missing:  NVML_LIBRARY) 
-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   program_options
-- Can NOT find 'adios_config' - set ADIOS_ROOT or check your PATH
-- Could NOT find ADIOS (missing:  ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.10.0")
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- libSplash supports PARALLEL output
-- Could NOT find ISAAC - set ISAAC_DIR or check your CMAKE_PREFIX_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/81i61029/build
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -E cmake_progress_start /home/81i61029/build/CMakeFiles /home/81i61029/build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory `/home/81i61029/build'
make -f CMakeFiles/picongpu-hostonly.dir/build.make CMakeFiles/picongpu-hostonly.dir/depend
make[2]: Entering directory `/home/81i61029/build'
cd /home/81i61029/build && /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -E cmake_depends "Unix Makefiles" /home/81i61029/src/picongpu/src/picongpu /home/81i61029/src/picongpu/src/picongpu /home/81i61029/build /home/81i61029/build /home/81i61029/build/CMakeFiles/picongpu-hostonly.dir/DependInfo.cmake --color=
make[2]: Leaving directory `/home/81i61029/build'
make -f CMakeFiles/picongpu-hostonly.dir/build.make CMakeFiles/picongpu-hostonly.dir/build
make[2]: Entering directory `/home/81i61029/build'
make[2]: Nothing to be done for `CMakeFiles/picongpu-hostonly.dir/build'.
make[2]: Leaving directory `/home/81i61029/build'
[ 29%] Built target picongpu-hostonly
make -f CMakeFiles/picongpu.dir/build.make CMakeFiles/picongpu.dir/depend
make[2]: Entering directory `/home/81i61029/build'
cd /home/81i61029/build && /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -E cmake_depends "Unix Makefiles" /home/81i61029/src/picongpu/src/picongpu /home/81i61029/src/picongpu/src/picongpu /home/81i61029/build /home/81i61029/build /home/81i61029/build/CMakeFiles/picongpu.dir/DependInfo.cmake --color=
make[2]: Leaving directory `/home/81i61029/build'
make -f CMakeFiles/picongpu.dir/build.make CMakeFiles/picongpu.dir/build
make[2]: Entering directory `/home/81i61029/build'
[ 35%] Linking CXX executable picongpu
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cmake-3.8.1-ankgfj3uhenjmia46zyod2a3a5rvehcy/bin/cmake -E cmake_link_script CMakeFiles/picongpu.dir/link.txt --verbose=ON
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++   -std=c++11 -fopenmp -fopenmp -Wall -Wno-unknown-pragmas -Wextra -Wno-unused-parameter -Wno-unused-local-typedefs -O3 -DNDEBUG  -rdynamic CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o CMakeFiles/picongpu.dir/include/plugins/common/particlePatches.cpp.o CMakeFiles/picongpu.dir/include/plugins/common/stringHelpers.cpp.o CMakeFiles/picongpu.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o  -o picongpu -Wl,-Bstatic -lcudart_static -Wl,-Bdynamic -lpthread -ldl -lrt -Wl,-Bstatic -lcudart_static -Wl,-Bdynamic -lpthread -ldl -lrt -lmpi -lmpi_cxx -lmpi -lboost_filesystem-mt -lboost_system-mt -lboost_math_tr1-mt -lmpi -lpthread -lz -lboost_program_options-mt -lboost_regex-mt -lboost_filesystem-mt -lboost_system-mt -lboost_thread-mt -lboost_math_tr1-mt -lboost_serialization-mt -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -Wl,-Bstatic -lsplash -Wl,-Bdynamic -lhdf5 -lz -ldl -lm -lmpi -lmpi_cxx -lmpi -lpngwriter -lpng -lz -lfreetype libpicongpu-hostonly.a -lm -Wl,-Bstatic -lcudart_static -Wl,-Bdynamic -lpthread -ldl -lrt -lmpi -lmpi_cxx -lboost_filesystem-mt -lboost_system-mt -lboost_math_tr1-mt -lboost_program_options-mt -lboost_regex-mt -lboost_thread-mt -lboost_serialization-mt -lboost_chrono-mt -lboost_date_time-mt -lboost_atomic-mt -Wl,-Bstatic -lsplash -Wl,-Bdynamic -lhdf5 -ldl -lm -lpngwriter -lpng -lfreetype -lm 
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `picongpu::ArgsParser::parse(int, char**)':
ArgsParser.cpp:(.text+0x48c): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
ArgsParser.cpp:(.text+0x90a): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::typed_value<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, char>::name() const':
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `void boost::program_options::validate<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, int)':
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0xa5): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x479): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::checkpointTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text+0x2727): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::restoreTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text+0x9f6f): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, float*, long) [clone .constprop.1916]':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text+0x11ed3): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long) [clone .constprop.1925]':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text+0x1212d): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned int*, long) [clone .constprop.1926]':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text+0x1228e): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::unwind_extra_block(bool)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb]+0x2c): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x21): undefined reference to `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x39): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<unsigned int, char>::name() const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIjcE4nameEv[_ZNK5boost15program_options11typed_valueIjcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<double, char>::name() const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameEv[_ZNK5boost15program_options11typed_valueIdcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<float, char>::name() const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIfcE4nameEv[_ZNK5boost15program_options11typed_valueIfcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<int, char>::name() const':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIicE4nameEv[_ZNK5boost15program_options11typed_valueIicE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv]+0x1d): more undefined references to `boost::program_options::arg[abi:cxx11]' follow
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::SimulationStarter<picongpu::InitialiserController, picongpu::PluginController, picongpu::MySimulation>::parseConfigs(int, char**)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x86): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x14f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x21a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x30f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::re_detail_106300::raise_error<boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > >(boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::error_type)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xa2): undefined reference to `boost::re_detail_106300::raise_runtime_error(std::runtime_error const&)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xc0): undefined reference to `boost::re_detail_106300::get_default_error_string(boost::regex_constants::error_type)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > boost::re_detail_106300::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::re_detail_106300::re_set_long<unsigned int> const*, boost::re_detail_106300::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x151): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x4e5): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::extend_stack()':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv]+0x18): undefined reference to `boost::re_detail_106300::get_mem_block()'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_prefix()':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv]+0x14c): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<unsigned int, std::allocator<unsigned int> >*, int)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned short, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned short*, long)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x3eb): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<double, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x52f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<int, std::allocator<int> >*, int)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<float, std::allocator<float> >*, int)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x28f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::find_imp()':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0xa): undefined reference to `boost::re_detail_106300::get_mem_block()'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x138): undefined reference to `boost::re_detail_106300::verify_options(unsigned int, boost::regex_constants::_match_flags)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x17f): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x2cd): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `bool boost::regex_search<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >&, boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >)':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_[_ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_]+0xf3): undefined reference to `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_match()':
tmpxft_0000f91b_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv]+0x210): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIdcEE[_ZTVN5boost15program_options11typed_valueIdcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIjcEE[_ZTVN5boost15program_options11typed_valueIjcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[_ZTVN5boost15program_options11typed_valueIicEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIfcEE[_ZTVN5boost15program_options11typed_valueIfcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE]+0x40): more undefined references to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' follow
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make[2]: *** [picongpu] Error 1
make[2]: Leaving directory `/home/81i61029/build'
make[1]: *** [CMakeFiles/picongpu.dir/all] Error 2
make[1]: Leaving directory `/home/81i61029/build'
make: *** [all] Error 2
[81i61029@messi build]$

8i161029 on 10 Aug 2017

Hm, it still did not link the libs with absolute paths...

ax3l on 10 Aug 2017

Maybe I delete other boost in system? The user of boost is only me.
Could you teach me how to find those files and removed them?

8i161029 on 10 Aug 2017

Can you also add set(Boost_NO_SYSTEM_PATHS ON) to the same file? Just as an additional line.

ax3l on 10 Aug 2017

Sorry... where should I add it?

Add it after the line of cmake_policy(SET CMP0060 NEW)?

8i161029 on 10 Aug 2017

👍1

I added it after the line of cmake_policy(SET CMP0060 NEW).
But it failed...

[81i61029@messi build]$ make -j install
Scanning dependencies of target picongpu-hostonly
Scanning dependencies of target mpiInfo
[  5%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_cuda_memtest.cu.o
[ 11%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 17%] Building CXX object build_mpiInfo/CMakeFiles/mpiInfo.dir/main.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 29%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 35%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 41%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 47%] Linking CXX executable mpiInfo
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::typed_value<bool, char>::name() const':
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `main':
main.cpp:(.text.startup+0x5a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/mpiInfo.dir/main.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
collect2: error: ld returned 1 exit status
make[2]: *** [build_mpiInfo/mpiInfo] Error 1
make[1]: *** [build_mpiInfo/CMakeFiles/mpiInfo.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 52%] Linking CXX static library libpicongpu-hostonly.a
[ 52%] Built target picongpu-hostonly
Scanning dependencies of target cuda_memtest
[ 58%] Building CXX object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/misc.cpp.o
[ 64%] Linking CXX executable cuda_memtest
[ 64%] Built target cuda_memtest
make: *** [all] Error 2

8i161029 on 10 Aug 2017

Wuhu, it worked!

Now just add the same line, set(Boost_NO_SYSTEM_PATHS ON) to src/mpiInfo/CMakeLists.txt.

Alternatively, adding the same option to pic-configure spares you the adjustment of the source code:

pic-configure -c "-DBoost_NO_SYSTEM_PATHS=ON" $HOME/picInputs/myLWFA

ax3l on 10 Aug 2017

Well...I added it at this place:

################################################################################
# Project
################################################################################
set(Boost_NO_SYSTEM_PATHS ON)

project(mpiInfo)

if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
    set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}" CACHE PATH "install prefix" FORCE)
endif(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)

# set helper pathes to find libraries and packages
# Add specific hints

and it failed...
Then I tried pic-configure -c "-DBoost_NO_SYSTEM_PATHS=ON" $HOME/picInputs/myLWFA
and install. Still failed...

[81i61029@messi build]$ make -j install
Scanning dependencies of target picongpu-hostonly
[  5%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o
[ 11%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_cuda_memtest.cu.o
Scanning dependencies of target mpiInfo
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 17%] Building CXX object build_mpiInfo/CMakeFiles/mpiInfo.dir/main.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 29%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 35%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 41%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 47%] Linking CXX executable mpiInfo
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::typed_value<bool, char>::name() const':
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
main.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE4nameEv[_ZNK5boost15program_options11typed_valueIbcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
main.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/mpiInfo.dir/main.cpp.o: In function `main':
main.cpp:(.text.startup+0x5a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/mpiInfo.dir/main.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
collect2: error: ld returned 1 exit status
make[2]: *** [build_mpiInfo/mpiInfo] Error 1
make[1]: *** [build_mpiInfo/CMakeFiles/mpiInfo.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Scanning dependencies of target cuda_memtest
[ 52%] Building CXX object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/misc.cpp.o
[ 58%] Linking CXX static library libpicongpu-hostonly.a
[ 58%] Built target picongpu-hostonly
[ 64%] Linking CXX executable cuda_memtest
[ 64%] Built target cuda_memtest
make: *** [all] Error 2
[81i61029@messi build]$

8i161029 on 10 Aug 2017

And if you also add cmake_policy(SET CMP0060 NEW) to mpiInfo?

ax3l on 10 Aug 2017

It is longer than before! (100%)
But still have error:

[81i61029@messi build]$ make -j install
Scanning dependencies of target picongpu-hostonly
[  5%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o
[ 11%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_cuda_memtest.cu.o
Scanning dependencies of target mpiInfo
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 17%] Building CXX object build_mpiInfo/CMakeFiles/mpiInfo.dir/main.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 29%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 35%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 41%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 47%] Linking CXX executable mpiInfo
[ 47%] Built target mpiInfo
Scanning dependencies of target cuda_memtest
[ 52%] Linking CXX static library libpicongpu-hostonly.a
[ 58%] Building CXX object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/misc.cpp.o
[ 58%] Built target picongpu-hostonly
[ 64%] Building NVCC (Device) object CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 70%] Linking CXX executable cuda_memtest
[ 70%] Built target cuda_memtest
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp(146): warning: variable "dt_old" was declared but never referenced
          detected during:
            instantiation of "boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type boost::numeric::odeint::default_step_adjuster<Value, Time>::increase_step(boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type, boost::numeric::odeint::default_step_adjuster<Value, Time>::value_type, int) const [with Value=picongpu::float_64, Time=picongpu::float_64]" 
(778): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, const StateIn &, const DerivIn &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, StateOut &, DerivOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateIn=boost::array<picongpu::float_64, 1UL>, DerivIn=boost::array<picongpu::float_64, 1UL>, StateOut=boost::array<picongpu::float_64, 1UL>, DerivOut=boost::array<picongpu::float_64, 1UL>]" 
(716): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, DerivInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>, DerivInOut=boost::array<picongpu::float_64, 1UL>]" 
(899): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step_v1(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
(617): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp(103): here
            instantiation of "size_t boost::numeric::odeint::detail::integrate_adaptive(Stepper, System, State &, Time &, Time, Time &, Observer, boost::numeric::odeint::controlled_stepper_tag) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp(45): here
            instantiation of "size_t boost::numeric::odeint::integrate_adaptive(Stepper, System, State &, Time, Time, Time, Observer) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(48): here
            instantiation of "boost::enable_if<has_value_type<State, mpl_::bool_<false>>::type, size_t>::type boost::numeric::odeint::integrate(System, State &, Time, Time, Time, Observer) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(68): here
            instantiation of "size_t boost::numeric::odeint::integrate(System, State &, Time, Time, Time) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64]" 
/home/81i61029/src/picongpu/src/picongpu/include/particles/bremsstrahlung/PhotonEmissionAngle.hpp(169): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/core/swap.hpp(36): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "void boost_swap_impl::swap_impl(T &, T &) [with T=std::__cxx11::string]" 
(56): here
            instantiation of "void boost::swap(T1 &, T2 &) [with T1=std::__cxx11::string, T2=std::__cxx11::string]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(214): here
            instantiation of "void boost::property_tree::basic_ptree<Key, Data, KeyCompare>::swap(boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(201): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::operator=(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(644): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(848): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &, Translator) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t, Translator=boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, size_t>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(860): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t]" 
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp(94): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/get_pointer.hpp:48:46: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                              ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/detail/shared_count.hpp:402:19: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                   ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:255:64: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:454:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:467:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:544:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:553:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:555:32: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp: At global scope:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: warning: friend declaration ‘boost::mpl::aux::type_wrapper<Key> boost::mpl::operator/(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: note: (if this is not what you intended, make sure the function template has already been declared and add <> after the function name here) 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:55:90: warning: friend declaration ‘boost::mpl::aux::type_wrapper<boost::mpl::pair<T1, T2> > boost::mpl::operator|(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::m_item<Key, T, Base>::order*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:56:85: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::m_item<Key, T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( order_tag_, ORDER_BY_KEY, m_item, aux::type_wrapper<Key>* );
                                                                                     ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:71:121: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator/(const boost::mpl::m_mask<Key, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:72:94: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator|(const boost::mpl::m_mask<Key, Base>&, boost::mpl::m_mask<Key, Base>::key_order_*)’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper<void_>, ITEM_BY_ORDER, m_mask, key_order_* );
                                                                                              ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:47:83: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::s_item<T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_SET_OVERLOAD( order_tag_, ORDER_BY_KEY, s_item, aux::type_wrapper<T>* );
                                                                                   ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:48:97: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:63:98: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_mask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[2]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:77:99: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_unmask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/scoped_ptr.hpp:74:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                          ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const ctor_args_list&, const allocator_type&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::ctor_args_list = boost::tuples::cons<boost::tuples::null_type, boost::tuples::cons<boost::tuples::tuple<boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, boost::tuples::null_type> >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::allocator_type = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:179:87:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree() [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:89:29:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:160:10: warning:   when initialized here [-Wreorder]
   explicit multi_index_container(
          ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:191:145:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/stl_pair.h:133:78:   required from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, const _T2&) [with _U1 = std::__cxx11::basic_string<char>&; <template-parameter-2-2> = void; _T1 = const std::__cxx11::basic_string<char>; _T2 = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:646:8:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const path_type&, const self_type&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:848:30:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&, Translator) [with Type = long unsigned int; Translator = boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:859:11:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&) [with Type = long unsigned int; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:94:32:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:261:1: warning:   when initialized here [-Wreorder]
   multi_index_container(
 ^
Scanning dependencies of target picongpu
[ 76%] Building CXX object CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o
[ 82%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/particlePatches.cpp.o
[ 88%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/stringHelpers.cpp.o
[ 94%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
[100%] Linking CXX executable picongpu
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `picongpu::ArgsParser::parse(int, char**)':
ArgsParser.cpp:(.text+0x48c): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
ArgsParser.cpp:(.text+0x90a): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::typed_value<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, char>::name() const':
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `void boost::program_options::validate<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, int)':
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0xa5): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x479): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::checkpointTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text+0x2727): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::restoreTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text+0x9f6f): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, float*, long) [clone .constprop.1916]':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text+0x11ed3): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long) [clone .constprop.1925]':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text+0x1212d): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned int*, long) [clone .constprop.1926]':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text+0x1228e): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::unwind_extra_block(bool)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb]+0x2c): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x21): undefined reference to `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x39): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<unsigned int, char>::name() const':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIjcE4nameEv[_ZNK5boost15program_options11typed_valueIjcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<double, char>::name() const':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameEv[_ZNK5boost15program_options11typed_valueIdcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<float, char>::name() const':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIfcE4nameEv[_ZNK5boost15program_options11typed_valueIfcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<int, char>::name() const':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIicE4nameEv[_ZNK5boost15program_options11typed_valueIicE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv]+0x1d): more undefined references to `boost::program_options::arg[abi:cxx11]' follow
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::SimulationStarter<picongpu::InitialiserController, picongpu::PluginController, picongpu::MySimulation>::parseConfigs(int, char**)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x86): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x14f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x21a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x30f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::re_detail_106300::raise_error<boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > >(boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::error_type)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xa2): undefined reference to `boost::re_detail_106300::raise_runtime_error(std::runtime_error const&)'
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xc0): undefined reference to `boost::re_detail_106300::get_default_error_string(boost::regex_constants::error_type)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > boost::re_detail_106300::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::re_detail_106300::re_set_long<unsigned int> const*, boost::re_detail_106300::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x151): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const'
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x4e5): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::extend_stack()':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv]+0x18): undefined reference to `boost::re_detail_106300::get_mem_block()'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_prefix()':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv]+0x14c): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<unsigned int, std::allocator<unsigned int> >*, int)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned short, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned short*, long)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x3eb): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<double, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x52f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<int, std::allocator<int> >*, int)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<float, std::allocator<float> >*, int)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x28f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::find_imp()':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0xa): undefined reference to `boost::re_detail_106300::get_mem_block()'
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x138): undefined reference to `boost::re_detail_106300::verify_options(unsigned int, boost::regex_constants::_match_flags)'
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x17f): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x2cd): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `bool boost::regex_search<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >&, boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >)':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_[_ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_]+0xf3): undefined reference to `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_match()':
tmpxft_00000f2f_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv]+0x210): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIdcEE[_ZTVN5boost15program_options11typed_valueIdcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIjcEE[_ZTVN5boost15program_options11typed_valueIjcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[_ZTVN5boost15program_options11typed_valueIicEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIfcEE[_ZTVN5boost15program_options11typed_valueIfcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE]+0x40): more undefined references to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' follow
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make[2]: *** [picongpu] Error 1
make[1]: *** [CMakeFiles/picongpu.dir/all] Error 2
make: *** [all] Error 2

8i161029 on 10 Aug 2017

Weird.

What does

objdump -p /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so | grep SONAME

objdump -p /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so.1.63.0 | grep SONAME

output?

If you add this to PIConGPU CMakeLists.txt (somewhere after the project(...) line):

message("CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES: ${CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES}")

what does it output during pic-configure?

ax3l on 10 Aug 2017

objdump -p /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so | grep SONAME:

  SONAME               libboost_program_options.so.1.63.0

objdump -p /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so.1.63.0 | grep SONAME:

 SONAME               libboost_program_options.so.1.63.0

I put it here:

################################################################################
# Project
################################################################################

cmake_policy(SET CMP0060 NEW)

set(Boost_NO_SYSTEM_PATHS ON)

project(PIConGPU)

message("CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES: ${CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES}")

if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
    set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}" CACHE PATH "install prefix" FORCE)
endif(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)

# set helper pathes to find libraries and packages
# Add specific hints

the optput of configure:

[81i61029@messi ~]$ pic-configure $HOME/picInputs/myLWFA
cmake command: cmake -DCUDA_ARCH=20 -DCMAKE_INSTALL_PREFIX=/home/81i61029/picInputs/myLWFA -DPIC_EXTENSION_PATH=/home/81i61029/picInputs/myLWFA   /home/81i61029/src/picongpu/src/picongpu
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gcc
-- Check for working C compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++
-- Check for working CXX compiler: /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES: /lib;/lib32;/lib64;/usr/lib;/usr/lib32;/usr/lib64
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "7.5") 
-- Found MPI_C: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so  
-- Found MPI_CXX: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so  
-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   filesystem
--   system
--   math_tr1
-- Boost: Disable template aliases
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "5.0") 
-- Boost version: 1.63.0
-- Using mallocMC from thirdParty/ directory
-- Boost version: 1.63.0
-- Found mallocMC: /home/81i61029/src/picongpu/thirdParty/mallocMC/src (found suitable version "2.2.0", minimum required is "2.2.0")  
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "7.5") 
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found suitable version "8.0", minimum required is "5.0") 
-- Boost version: 1.63.0
-- Found ZLIB: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so (found version "1.2.11") 
-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   program_options
--   regex
--   filesystem
--   system
--   thread
--   math_tr1
--   serialization
--   chrono
--   date_time
--   atomic
-- Found CUDA: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cuda-8.0.61-trcvvggws37ule6li2tykglffdj3gjzk (found version "8.0") 
-- Could NOT find NVML (missing:  NVML_LIBRARY) 
-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   program_options
-- Can NOT find 'adios_config' - set ADIOS_ROOT or check your PATH
-- Could NOT find ADIOS (missing:  ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.10.0")
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.1") found components:  C 
-- libSplash supports PARALLEL output
-- Found Splash: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libsplash-1.6.0-up4oyugd7bmmbjd6wmbvxwciuvsfos2g/lib/libsplash.a;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so (found suitable version "1.6.0", minimum required is "1.6.0") 
-- Found PNG: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng.so (found suitable version "1.6.29", minimum required is "1.2.9") 
-- Found Freetype: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so (found version "2.7.1") 
-- Found PNGwriter: /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/lib/libpngwriter.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so;/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so (found suitable version "0.6.0", minimum required is "0.5.6") 
-- Could NOT find ISAAC - set ISAAC_DIR or check your CMAKE_PREFIX_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/81i61029

8i161029 on 10 Aug 2017

👍1

OH... I forgot cd build to do configure...

8i161029 on 10 Aug 2017

For your own home, you can already remove:

rm -rf /home/81i61029/Downloads/boost_1_64_0
rm -rf /home/81i61029/lib/boost/

What does

nm /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so.1.63.0 | grep validate

output?

You could also try

cd ~/build
rm -rf ../build/*
# pic-configure  ...

CXXFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0" make -j install

ax3l on 10 Aug 2017

output:

[81i61029@messi ~]$ nm /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so.1.63.0 | grep validate
000000000005e120 T _ZN5boost15program_options8validateERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS9_EEPbi
000000000005df60 T _ZN5boost15program_options8validateERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS9_EEPS9_i
000000000005e320 T _ZN5boost15program_options8validateERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIwSt11char_traitsIwESaIwEEESaIS9_EEPbi
000000000005dff0 T _ZN5boost15program_options8validateERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIwSt11char_traitsIwESaIwEEESaIS9_EEPNS5_IcS6_IcESaIcEEEi

output of CXXFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0" make -j install

[81i61029@messi build]$ CXXFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0" make -j install
[  5%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_cuda_memtest.cu.o
Scanning dependencies of target picongpu-hostonly
[ 11%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o
Scanning dependencies of target mpiInfo
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 17%] Building CXX object build_mpiInfo/CMakeFiles/mpiInfo.dir/main.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 29%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 35%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 41%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 47%] Linking CXX executable mpiInfo
[ 47%] Built target mpiInfo
[ 52%] Linking CXX static library libpicongpu-hostonly.a
[ 52%] Built target picongpu-hostonly
Scanning dependencies of target cuda_memtest
[ 58%] Building NVCC (Device) object CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 64%] Building CXX object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/misc.cpp.o
[ 70%] Linking CXX executable cuda_memtest
[ 70%] Built target cuda_memtest
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp(146): warning: variable "dt_old" was declared but never referenced
          detected during:
            instantiation of "boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type boost::numeric::odeint::default_step_adjuster<Value, Time>::increase_step(boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type, boost::numeric::odeint::default_step_adjuster<Value, Time>::value_type, int) const [with Value=picongpu::float_64, Time=picongpu::float_64]" 
(778): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, const StateIn &, const DerivIn &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, StateOut &, DerivOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateIn=boost::array<picongpu::float_64, 1UL>, DerivIn=boost::array<picongpu::float_64, 1UL>, StateOut=boost::array<picongpu::float_64, 1UL>, DerivOut=boost::array<picongpu::float_64, 1UL>]" 
(716): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, DerivInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>, DerivInOut=boost::array<picongpu::float_64, 1UL>]" 
(899): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step_v1(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
(617): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp(103): here
            instantiation of "size_t boost::numeric::odeint::detail::integrate_adaptive(Stepper, System, State &, Time &, Time, Time &, Observer, boost::numeric::odeint::controlled_stepper_tag) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp(45): here
            instantiation of "size_t boost::numeric::odeint::integrate_adaptive(Stepper, System, State &, Time, Time, Time, Observer) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(48): here
            instantiation of "boost::enable_if<has_value_type<State, mpl_::bool_<false>>::type, size_t>::type boost::numeric::odeint::integrate(System, State &, Time, Time, Time, Observer) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(68): here
            instantiation of "size_t boost::numeric::odeint::integrate(System, State &, Time, Time, Time) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64]" 
/home/81i61029/src/picongpu/src/picongpu/include/particles/bremsstrahlung/PhotonEmissionAngle.hpp(169): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/core/swap.hpp(36): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "void boost_swap_impl::swap_impl(T &, T &) [with T=std::__cxx11::string]" 
(56): here
            instantiation of "void boost::swap(T1 &, T2 &) [with T1=std::__cxx11::string, T2=std::__cxx11::string]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(214): here
            instantiation of "void boost::property_tree::basic_ptree<Key, Data, KeyCompare>::swap(boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(201): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::operator=(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(644): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(848): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &, Translator) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t, Translator=boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, size_t>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(860): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t]" 
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp(94): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/get_pointer.hpp:48:46: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                              ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/detail/shared_count.hpp:402:19: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                   ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:255:64: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:454:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:467:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:544:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:553:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:555:32: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp: At global scope:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: warning: friend declaration ‘boost::mpl::aux::type_wrapper<Key> boost::mpl::operator/(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: note: (if this is not what you intended, make sure the function template has already been declared and add <> after the function name here) 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:55:90: warning: friend declaration ‘boost::mpl::aux::type_wrapper<boost::mpl::pair<T1, T2> > boost::mpl::operator|(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::m_item<Key, T, Base>::order*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:56:85: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::m_item<Key, T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( order_tag_, ORDER_BY_KEY, m_item, aux::type_wrapper<Key>* );
                                                                                     ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:71:121: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator/(const boost::mpl::m_mask<Key, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:72:94: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator|(const boost::mpl::m_mask<Key, Base>&, boost::mpl::m_mask<Key, Base>::key_order_*)’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper<void_>, ITEM_BY_ORDER, m_mask, key_order_* );
                                                                                              ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:47:83: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::s_item<T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_SET_OVERLOAD( order_tag_, ORDER_BY_KEY, s_item, aux::type_wrapper<T>* );
                                                                                   ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:48:97: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:63:98: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_mask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[2]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:77:99: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_unmask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/scoped_ptr.hpp:74:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                          ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const ctor_args_list&, const allocator_type&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::ctor_args_list = boost::tuples::cons<boost::tuples::null_type, boost::tuples::cons<boost::tuples::tuple<boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, boost::tuples::null_type> >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::allocator_type = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:179:87:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree() [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:89:29:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:160:10: warning:   when initialized here [-Wreorder]
   explicit multi_index_container(
          ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:191:145:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/stl_pair.h:133:78:   required from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, const _T2&) [with _U1 = std::__cxx11::basic_string<char>&; <template-parameter-2-2> = void; _T1 = const std::__cxx11::basic_string<char>; _T2 = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:646:8:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const path_type&, const self_type&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:848:30:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&, Translator) [with Type = long unsigned int; Translator = boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:859:11:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&) [with Type = long unsigned int; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:94:32:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:261:1: warning:   when initialized here [-Wreorder]
   multi_index_container(
 ^
Scanning dependencies of target picongpu
[ 76%] Building CXX object CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o
[ 82%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/stringHelpers.cpp.o
[ 88%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/particlePatches.cpp.o
[ 94%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
[100%] Linking CXX executable picongpu
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `picongpu::ArgsParser::parse(int, char**)':
ArgsParser.cpp:(.text+0x48c): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
ArgsParser.cpp:(.text+0x90a): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::typed_value<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, char>::name() const':
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `void boost::program_options::validate<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, int)':
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0xa5): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x479): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::checkpointTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text+0x2727): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::restoreTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text+0x9f6f): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, float*, long) [clone .constprop.1916]':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text+0x11ed3): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long) [clone .constprop.1925]':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text+0x1212d): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned int*, long) [clone .constprop.1926]':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text+0x1228e): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::unwind_extra_block(bool)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb]+0x2c): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x21): undefined reference to `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x39): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<unsigned int, char>::name() const':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIjcE4nameEv[_ZNK5boost15program_options11typed_valueIjcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<double, char>::name() const':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameEv[_ZNK5boost15program_options11typed_valueIdcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<float, char>::name() const':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIfcE4nameEv[_ZNK5boost15program_options11typed_valueIfcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<int, char>::name() const':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIicE4nameEv[_ZNK5boost15program_options11typed_valueIicE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv]+0x1d): more undefined references to `boost::program_options::arg[abi:cxx11]' follow
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::SimulationStarter<picongpu::InitialiserController, picongpu::PluginController, picongpu::MySimulation>::parseConfigs(int, char**)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x86): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x14f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x21a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x30f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::re_detail_106300::raise_error<boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > >(boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::error_type)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xa2): undefined reference to `boost::re_detail_106300::raise_runtime_error(std::runtime_error const&)'
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xc0): undefined reference to `boost::re_detail_106300::get_default_error_string(boost::regex_constants::error_type)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > boost::re_detail_106300::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::re_detail_106300::re_set_long<unsigned int> const*, boost::re_detail_106300::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x151): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const'
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x4e5): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::extend_stack()':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv]+0x18): undefined reference to `boost::re_detail_106300::get_mem_block()'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_prefix()':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv]+0x14c): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<unsigned int, std::allocator<unsigned int> >*, int)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned short, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned short*, long)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x3eb): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<double, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x52f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<int, std::allocator<int> >*, int)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<float, std::allocator<float> >*, int)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x28f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::find_imp()':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0xa): undefined reference to `boost::re_detail_106300::get_mem_block()'
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x138): undefined reference to `boost::re_detail_106300::verify_options(unsigned int, boost::regex_constants::_match_flags)'
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x17f): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x2cd): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `bool boost::regex_search<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >&, boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >)':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_[_ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_]+0xf3): undefined reference to `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_match()':
tmpxft_00001bfb_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv]+0x210): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIdcEE[_ZTVN5boost15program_options11typed_valueIdcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIjcEE[_ZTVN5boost15program_options11typed_valueIjcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[_ZTVN5boost15program_options11typed_valueIicEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIfcEE[_ZTVN5boost15program_options11typed_valueIfcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE]+0x40): more undefined references to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' follow
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make[2]: *** [picongpu] Error 1
make[1]: *** [CMakeFiles/picongpu.dir/all] Error 2
make: *** [all] Error 2

8i161029 on 10 Aug 2017

Ok still the same.

Maybe we can trick cmake not to use the system libraries via:

LDFLAGS="-L/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib" make -j install

ax3l on 10 Aug 2017

Still didn't work...

[81i61029@messi build]$ LDFLAGS="-L/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib" make -j install
Scanning dependencies of target picongpu-hostonly
[  5%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_cuda_memtest.cu.o
Scanning dependencies of target mpiInfo
[ 11%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 17%] Building CXX object build_mpiInfo/CMakeFiles/mpiInfo.dir/main.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 29%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 35%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 41%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 47%] Linking CXX executable mpiInfo
[ 47%] Built target mpiInfo
[ 52%] Linking CXX static library libpicongpu-hostonly.a
[ 52%] Built target picongpu-hostonly
[ 58%] Building NVCC (Device) object CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
Scanning dependencies of target cuda_memtest
[ 64%] Building CXX object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/misc.cpp.o
[ 70%] Linking CXX executable cuda_memtest
[ 70%] Built target cuda_memtest
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp(146): warning: variable "dt_old" was declared but never referenced
          detected during:
            instantiation of "boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type boost::numeric::odeint::default_step_adjuster<Value, Time>::increase_step(boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type, boost::numeric::odeint::default_step_adjuster<Value, Time>::value_type, int) const [with Value=picongpu::float_64, Time=picongpu::float_64]" 
(778): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, const StateIn &, const DerivIn &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, StateOut &, DerivOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateIn=boost::array<picongpu::float_64, 1UL>, DerivIn=boost::array<picongpu::float_64, 1UL>, StateOut=boost::array<picongpu::float_64, 1UL>, DerivOut=boost::array<picongpu::float_64, 1UL>]" 
(716): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, DerivInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>, DerivInOut=boost::array<picongpu::float_64, 1UL>]" 
(899): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step_v1(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
(617): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp(103): here
            instantiation of "size_t boost::numeric::odeint::detail::integrate_adaptive(Stepper, System, State &, Time &, Time, Time &, Observer, boost::numeric::odeint::controlled_stepper_tag) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp(45): here
            instantiation of "size_t boost::numeric::odeint::integrate_adaptive(Stepper, System, State &, Time, Time, Time, Observer) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(48): here
            instantiation of "boost::enable_if<has_value_type<State, mpl_::bool_<false>>::type, size_t>::type boost::numeric::odeint::integrate(System, State &, Time, Time, Time, Observer) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(68): here
            instantiation of "size_t boost::numeric::odeint::integrate(System, State &, Time, Time, Time) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64]" 
/home/81i61029/src/picongpu/src/picongpu/include/particles/bremsstrahlung/PhotonEmissionAngle.hpp(169): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/core/swap.hpp(36): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "void boost_swap_impl::swap_impl(T &, T &) [with T=std::__cxx11::string]" 
(56): here
            instantiation of "void boost::swap(T1 &, T2 &) [with T1=std::__cxx11::string, T2=std::__cxx11::string]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(214): here
            instantiation of "void boost::property_tree::basic_ptree<Key, Data, KeyCompare>::swap(boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(201): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::operator=(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(644): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(848): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &, Translator) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t, Translator=boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, size_t>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(860): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t]" 
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp(94): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/get_pointer.hpp:48:46: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                              ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/detail/shared_count.hpp:402:19: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                   ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:255:64: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:454:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:467:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:544:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:553:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:555:32: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp: At global scope:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: warning: friend declaration ‘boost::mpl::aux::type_wrapper<Key> boost::mpl::operator/(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: note: (if this is not what you intended, make sure the function template has already been declared and add <> after the function name here) 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:55:90: warning: friend declaration ‘boost::mpl::aux::type_wrapper<boost::mpl::pair<T1, T2> > boost::mpl::operator|(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::m_item<Key, T, Base>::order*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:56:85: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::m_item<Key, T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( order_tag_, ORDER_BY_KEY, m_item, aux::type_wrapper<Key>* );
                                                                                     ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:71:121: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator/(const boost::mpl::m_mask<Key, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:72:94: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator|(const boost::mpl::m_mask<Key, Base>&, boost::mpl::m_mask<Key, Base>::key_order_*)’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper<void_>, ITEM_BY_ORDER, m_mask, key_order_* );
                                                                                              ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:47:83: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::s_item<T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_SET_OVERLOAD( order_tag_, ORDER_BY_KEY, s_item, aux::type_wrapper<T>* );
                                                                                   ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:48:97: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:63:98: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_mask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[2]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:77:99: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_unmask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/scoped_ptr.hpp:74:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                          ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const ctor_args_list&, const allocator_type&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::ctor_args_list = boost::tuples::cons<boost::tuples::null_type, boost::tuples::cons<boost::tuples::tuple<boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, boost::tuples::null_type> >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::allocator_type = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:179:87:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree() [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:89:29:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:160:10: warning:   when initialized here [-Wreorder]
   explicit multi_index_container(
          ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:191:145:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/stl_pair.h:133:78:   required from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, const _T2&) [with _U1 = std::__cxx11::basic_string<char>&; <template-parameter-2-2> = void; _T1 = const std::__cxx11::basic_string<char>; _T2 = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:646:8:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const path_type&, const self_type&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:848:30:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&, Translator) [with Type = long unsigned int; Translator = boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:859:11:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&) [with Type = long unsigned int; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:94:32:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:261:1: warning:   when initialized here [-Wreorder]
   multi_index_container(
 ^
Scanning dependencies of target picongpu
[ 76%] Building CXX object CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o
[ 82%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/particlePatches.cpp.o
[ 88%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/stringHelpers.cpp.o
[ 94%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
[100%] Linking CXX executable picongpu
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `picongpu::ArgsParser::parse(int, char**)':
ArgsParser.cpp:(.text+0x48c): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
ArgsParser.cpp:(.text+0x90a): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::typed_value<std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, char>::name() const':
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x22): undefined reference to `boost::program_options::arg[abi:cxx11]'
ArgsParser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x28): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x46): undefined reference to `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char const* const*)':
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x298): undefined reference to `boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ArgsParser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x327): undefined reference to `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o: In function `void boost::program_options::validate<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >*, int)':
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0xa5): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
ArgsParser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x479): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::checkpointTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text+0x2727): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::restoreTxtFile(std::basic_ofstream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text+0x9f6f): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::detail::copy_option, boost::system::error_code*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, float*, long) [clone .constprop.1916]':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text+0x11ed3): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long) [clone .constprop.1925]':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text+0x1212d): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned int*, long) [clone .constprop.1926]':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text+0x1228e): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::unwind_extra_block(bool)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE18unwind_extra_blockEb]+0x2c): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x21): undefined reference to `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x39): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() const':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<unsigned int, char>::name() const':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIjcE4nameEv[_ZNK5boost15program_options11typed_valueIjcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<double, char>::name() const':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameEv[_ZNK5boost15program_options11typed_valueIdcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<float, char>::name() const':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIfcE4nameEv[_ZNK5boost15program_options11typed_valueIfcE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::program_options::typed_value<int, char>::name() const':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueIicE4nameEv[_ZNK5boost15program_options11typed_valueIicE4nameEv]+0x1d): undefined reference to `boost::program_options::arg[abi:cxx11]'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorIjSaIjEEcE4nameEv]+0x1d): more undefined references to `boost::program_options::arg[abi:cxx11]' follow
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `picongpu::SimulationStarter<picongpu::InitialiserController, picongpu::PluginController, picongpu::MySimulation>::parseConfigs(int, char**)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x86): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x14f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x21a): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc[_ZN8picongpu17SimulationStarterINS_21InitialiserControllerENS_16PluginControllerENS_12MySimulationEE12parseConfigsEiPPc]+0x30f): undefined reference to `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::re_detail_106300::raise_error<boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > >(boost::regex_traits_wrapper<boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::error_type)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xa2): undefined reference to `boost::re_detail_106300::raise_runtime_error(std::runtime_error const&)'
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE[_ZN5boost16re_detail_10630011raise_errorINS_20regex_traits_wrapperINS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEEEvRKT_NS_15regex_constants10error_typeE]+0xc0): undefined reference to `boost::re_detail_106300::get_default_error_string(boost::regex_constants::error_type)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > boost::re_detail_106300::re_is_set_member<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> >, unsigned int>(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::re_detail_106300::re_set_long<unsigned int> const*, boost::re_detail_106300::regex_data<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, bool)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x151): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform_primary(char const*, char const*) const'
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost16re_detail_10630016re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x4e5): undefined reference to `boost::re_detail_106300::cpp_regex_traits_implementation<char>::transform(char const*, char const*) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::extend_stack()':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12extend_stackEv]+0x18): undefined reference to `boost::re_detail_106300::get_mem_block()'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_prefix()':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE12match_prefixEv]+0x14c): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<unsigned int, std::allocator<unsigned int> >*, int)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIjcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<unsigned short, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned short*, long)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateItcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x3eb): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<double, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x52f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<int, std::allocator<int> >*, int)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x27f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `void boost::program_options::validate<float, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<float, std::allocator<float> >*, int)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIfcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x28f): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::find_imp()':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0xa): undefined reference to `boost::re_detail_106300::get_mem_block()'
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x138): undefined reference to `boost::re_detail_106300::verify_options(unsigned int, boost::regex_constants::_match_flags)'
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x17f): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE8find_impEv]+0x2cd): undefined reference to `boost::re_detail_106300::put_mem_block(void*)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `bool boost::regex_search<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, char, boost::regex_traits<char, boost::cpp_regex_traits<char> > >(__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >&, boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags, __gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >)':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_[_ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_]+0xf3): undefined reference to `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char, boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&, boost::regex_constants::_match_flags)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o: In function `boost::re_detail_106300::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_match()':
tmpxft_00002033_00000000-4_main.cudafe1.cpp:(.text._ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv[_ZN5boost16re_detail_10630012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv]+0x210): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIdcEE[_ZTVN5boost15program_options11typed_valueIdcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIiSaIiEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIjcEE[_ZTVN5boost15program_options11typed_valueIjcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[_ZTVN5boost15program_options11typed_valueIicEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIfcEE[_ZTVN5boost15program_options11typed_valueIfcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x40): undefined reference to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIjSaIjEEcEE]+0x40): more undefined references to `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' follow
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make[2]: *** [picongpu] Error 1
make[1]: *** [CMakeFiles/picongpu.dir/all] Error 2
make: *** [all] Error 2

8i161029 on 10 Aug 2017

In $PICSRC/src/picongpu/CMakeLists.txt is are the lines

find_package(Boost 1.57.0 REQUIRED COMPONENTS program_options regex filesystem
                                              system thread math_tr1
                                              serialization)
include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
set(LIBS ${LIBS} ${Boost_LIBRARIES})

Can you change them to:

find_package(Boost 1.57.0 REQUIRED COMPONENTS program_options regex filesystem
                                              system thread math_tr1
                                              serialization)
message(STATUS "BOOST INCLUDE++++: ${Boost_INCLUDE_DIRS}")
message(STATUS "BOOST LIBS++++: ${Boost_LIBRARIES}")
set(LIBS ${LIBS} Boost::program_options Boost::regex Boost::filesystem Boost::system Boost::thread Boost::math_tr1 Boost::serialization)

then clean the build dir and re-try?

ax3l on 10 Aug 2017

In src/mpiInfo/CMakeLists.txt it would be:

find_package(Boost REQUIRED COMPONENTS program_options)
include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
set(LIBS ${LIBS} ${Boost_LIBRARIES})

replaced with

find_package(Boost REQUIRED COMPONENTS program_options)
message(STATUS "BOOST INCLUDE++++: ${Boost_INCLUDE_DIRS}")
message(STATUS "BOOST LIBS++++: ${Boost_LIBRARIES}")
set(LIBS ${LIBS} Boost::program_options)

ax3l on 10 Aug 2017

some outputs after [100%] are gone.

[81i61029@messi build]$ make -j install
[  5%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_cuda_memtest.cu.o
Scanning dependencies of target picongpu-hostonly
Scanning dependencies of target mpiInfo
[ 11%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 17%] Building CXX object build_mpiInfo/CMakeFiles/mpiInfo.dir/main.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 29%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 35%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 41%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 47%] Linking CXX executable mpiInfo
[ 47%] Built target mpiInfo
[ 52%] Linking CXX static library libpicongpu-hostonly.a
[ 52%] Built target picongpu-hostonly
[ 58%] Building NVCC (Device) object CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
Scanning dependencies of target cuda_memtest
[ 64%] Building CXX object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/misc.cpp.o
[ 70%] Linking CXX executable cuda_memtest
[ 70%] Built target cuda_memtest
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp(146): warning: variable "dt_old" was declared but never referenced
          detected during:
            instantiation of "boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type boost::numeric::odeint::default_step_adjuster<Value, Time>::increase_step(boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type, boost::numeric::odeint::default_step_adjuster<Value, Time>::value_type, int) const [with Value=picongpu::float_64, Time=picongpu::float_64]" 
(778): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, const StateIn &, const DerivIn &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, StateOut &, DerivOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateIn=boost::array<picongpu::float_64, 1UL>, DerivIn=boost::array<picongpu::float_64, 1UL>, StateOut=boost::array<picongpu::float_64, 1UL>, DerivOut=boost::array<picongpu::float_64, 1UL>]" 
(716): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, DerivInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>, DerivInOut=boost::array<picongpu::float_64, 1UL>]" 
(899): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step_v1(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
(617): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp(103): here
            instantiation of "size_t boost::numeric::odeint::detail::integrate_adaptive(Stepper, System, State &, Time &, Time, Time &, Observer, boost::numeric::odeint::controlled_stepper_tag) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp(45): here
            instantiation of "size_t boost::numeric::odeint::integrate_adaptive(Stepper, System, State &, Time, Time, Time, Observer) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(48): here
            instantiation of "boost::enable_if<has_value_type<State, mpl_::bool_<false>>::type, size_t>::type boost::numeric::odeint::integrate(System, State &, Time, Time, Time, Observer) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(68): here
            instantiation of "size_t boost::numeric::odeint::integrate(System, State &, Time, Time, Time) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64]" 
/home/81i61029/src/picongpu/src/picongpu/include/particles/bremsstrahlung/PhotonEmissionAngle.hpp(169): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/core/swap.hpp(36): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "void boost_swap_impl::swap_impl(T &, T &) [with T=std::__cxx11::string]" 
(56): here
            instantiation of "void boost::swap(T1 &, T2 &) [with T1=std::__cxx11::string, T2=std::__cxx11::string]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(214): here
            instantiation of "void boost::property_tree::basic_ptree<Key, Data, KeyCompare>::swap(boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(201): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::operator=(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(644): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(848): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &, Translator) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t, Translator=boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, size_t>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(860): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t]" 
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp(94): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/get_pointer.hpp:48:46: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                              ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/detail/shared_count.hpp:402:19: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                   ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:255:64: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:454:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:467:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:544:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:553:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:555:32: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp: At global scope:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: warning: friend declaration ‘boost::mpl::aux::type_wrapper<Key> boost::mpl::operator/(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: note: (if this is not what you intended, make sure the function template has already been declared and add <> after the function name here) 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:55:90: warning: friend declaration ‘boost::mpl::aux::type_wrapper<boost::mpl::pair<T1, T2> > boost::mpl::operator|(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::m_item<Key, T, Base>::order*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:56:85: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::m_item<Key, T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( order_tag_, ORDER_BY_KEY, m_item, aux::type_wrapper<Key>* );
                                                                                     ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:71:121: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator/(const boost::mpl::m_mask<Key, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:72:94: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator|(const boost::mpl::m_mask<Key, Base>&, boost::mpl::m_mask<Key, Base>::key_order_*)’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper<void_>, ITEM_BY_ORDER, m_mask, key_order_* );
                                                                                              ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:47:83: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::s_item<T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_SET_OVERLOAD( order_tag_, ORDER_BY_KEY, s_item, aux::type_wrapper<T>* );
                                                                                   ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:48:97: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:63:98: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_mask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[2]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:77:99: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_unmask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/scoped_ptr.hpp:74:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                          ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const ctor_args_list&, const allocator_type&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::ctor_args_list = boost::tuples::cons<boost::tuples::null_type, boost::tuples::cons<boost::tuples::tuple<boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, boost::tuples::null_type> >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::allocator_type = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:179:87:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree() [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:89:29:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:160:10: warning:   when initialized here [-Wreorder]
   explicit multi_index_container(
          ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:191:145:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/stl_pair.h:133:78:   required from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, const _T2&) [with _U1 = std::__cxx11::basic_string<char>&; <template-parameter-2-2> = void; _T1 = const std::__cxx11::basic_string<char>; _T2 = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:646:8:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const path_type&, const self_type&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:848:30:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&, Translator) [with Type = long unsigned int; Translator = boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:859:11:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&) [with Type = long unsigned int; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:94:32:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:261:1: warning:   when initialized here [-Wreorder]
   multi_index_container(
 ^
Scanning dependencies of target picongpu
[ 76%] Building CXX object CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o
[ 82%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/stringHelpers.cpp.o
[ 88%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/particlePatches.cpp.o
[ 94%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
[100%] Linking CXX executable picongpu
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
make[2]: *** [picongpu] Error 1
make[1]: *** [CMakeFiles/picongpu.dir/all] Error 2
make: *** [all] Error 2

8i161029 on 10 Aug 2017

Excuse me, may I ask a question: What does this line mean?

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'

Is it because of the problem in boost?
I found some bug report of libpng-1.6.29: libpng/bugs/264/
Thank you.
I am really thankful for your patient help today!

8i161029 on 10 Aug 2017

@8i161029 that is very good news, our work-around worked!
The problem on your system seems to be that you have a lot of default libs installed in /usr and your cmake does for some reasons try to link relative instead of using absolute paths in the most cases.

We apply the same refactoring there in src/picongpu/CMakeLists.txt:

################################################################################
# Find zlib
################################################################################

find_package(ZLIB REQUIRED)
include_directories(SYSTEM ${ZLIB_INCLUDE_DIRS})
set(LIBS ${LIBS} ${ZLIB_LIBRARIES})

to

################################################################################
# Find zlib
################################################################################

find_package(ZLIB REQUIRED)
set(LIBS ${LIBS} ZLIB::ZLIB)

ax3l on 11 Aug 2017

What does this line mean?

This line means: during the linking step with libzlib.so (short and with implicit paths: -lzlib) the symbol inflateValidate@ZLIB_1.2.9 was not properly found but is required by the libpng16.so (which in turn is used in PNGwriter which in turn is used in PIConGPU for the optional png plugin). This can be simply caused by not linking the righ libzlib.so, as it happened to our boost dependency.

The change I proposed changes string-list based linking of libraries to a more modern way of expressing dependencies in CMake, which seems to be more robust in your environment.

ax3l on 11 Aug 2017

It works!
Here is the output:

[81i61029@messi build]$ make -j install
Scanning dependencies of target picongpu-hostonly
[  5%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_cuda_memtest.cu.o
[ 11%] Building NVCC (Device) object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/cuda_memtest_generated_tests.cu.o
Scanning dependencies of target mpiInfo
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 17%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/ArgsParser.cpp.o
[ 23%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/particlePatches.cpp.o
[ 29%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/common/stringHelpers.cpp.o
[ 35%] Building CXX object CMakeFiles/picongpu-hostonly.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 41%] Building CXX object build_mpiInfo/CMakeFiles/mpiInfo.dir/main.cpp.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 47%] Linking CXX static library libpicongpu-hostonly.a
[ 47%] Built target picongpu-hostonly
[ 52%] Building NVCC (Device) object CMakeFiles/picongpu.dir/picongpu_generated_main.cu.o
[ 58%] Linking CXX executable mpiInfo
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
[ 58%] Built target mpiInfo
Scanning dependencies of target cuda_memtest
[ 64%] Building CXX object build_cuda_memtest/CMakeFiles/cuda_memtest.dir/misc.cpp.o
[ 70%] Linking CXX executable cuda_memtest
[ 70%] Built target cuda_memtest
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/stepper/controlled_runge_kutta.hpp(146): warning: variable "dt_old" was declared but never referenced
          detected during:
            instantiation of "boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type boost::numeric::odeint::default_step_adjuster<Value, Time>::increase_step(boost::numeric::odeint::default_step_adjuster<Value, Time>::time_type, boost::numeric::odeint::default_step_adjuster<Value, Time>::value_type, int) const [with Value=picongpu::float_64, Time=picongpu::float_64]" 
(778): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, const StateIn &, const DerivIn &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, StateOut &, DerivOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateIn=boost::array<picongpu::float_64, 1UL>, DerivIn=boost::array<picongpu::float_64, 1UL>, StateOut=boost::array<picongpu::float_64, 1UL>, DerivOut=boost::array<picongpu::float_64, 1UL>]" 
(716): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, DerivInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>, DerivInOut=boost::array<picongpu::float_64, 1UL>]" 
(899): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step_v1(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
(617): here
            instantiation of "boost::numeric::odeint::controlled_step_result boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::try_step(System, StateInOut &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &, boost::numeric::odeint::controlled_runge_kutta<ErrorStepper, ErrorChecker, StepAdjuster, Resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>::time_type &) [with ErrorStepper=boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, ErrorChecker=boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, StepAdjuster=boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, Resizer=boost::numeric::odeint::initially_resizer, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, StateInOut=boost::array<picongpu::float_64, 1UL>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/detail/integrate_adaptive.hpp(103): here
            instantiation of "size_t boost::numeric::odeint::detail::integrate_adaptive(Stepper, System, State &, Time &, Time, Time &, Observer, boost::numeric::odeint::controlled_stepper_tag) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate_adaptive.hpp(45): here
            instantiation of "size_t boost::numeric::odeint::integrate_adaptive(Stepper, System, State &, Time, Time, Time, Observer) [with Stepper=boost::numeric::odeint::controlled_runge_kutta<boost::numeric::odeint::runge_kutta_dopri5<boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::array<picongpu::float_64, 1UL>, picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations, boost::numeric::odeint::initially_resizer>, boost::numeric::odeint::default_error_checker<picongpu::float_64, boost::numeric::odeint::array_algebra, boost::numeric::odeint::default_operations>, boost::numeric::odeint::default_step_adjuster<picongpu::float_64, picongpu::float_64>, boost::numeric::odeint::initially_resizer, boost::numeric::odeint::explicit_error_stepper_fsal_tag>, System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(48): here
            instantiation of "boost::enable_if<has_value_type<State, mpl_::bool_<false>>::type, size_t>::type boost::numeric::odeint::integrate(System, State &, Time, Time, Time, Observer) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64, Observer=boost::numeric::odeint::null_observer]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/numeric/odeint/integrate/integrate.hpp(68): here
            instantiation of "size_t boost::numeric::odeint::integrate(System, State &, Time, Time, Time) [with System=picongpu::particles::bremsstrahlung::GetPhotonAngle::Probability, State=boost::array<picongpu::float_64, 1UL>, Time=picongpu::float_64]" 
/home/81i61029/src/picongpu/src/picongpu/include/particles/bremsstrahlung/PhotonEmissionAngle.hpp(169): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/core/swap.hpp(36): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "void boost_swap_impl::swap_impl(T &, T &) [with T=std::__cxx11::string]" 
(56): here
            instantiation of "void boost::swap(T1 &, T2 &) [with T1=std::__cxx11::string, T2=std::__cxx11::string]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(214): here
            instantiation of "void boost::property_tree::basic_ptree<Key, Data, KeyCompare>::swap(boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(201): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::operator=(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(644): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(848): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &, Translator) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t, Translator=boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, size_t>]" 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp(860): here
            instantiation of "boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type &boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type &, const Type &) [with Key=std::__cxx11::string, Data=std::__cxx11::string, KeyCompare=std::less<std::__cxx11::string>, Type=size_t]" 
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp(94): here

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(47): warning: "char (&operator||(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(48): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_item<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(63): warning: "boost::mpl::aux::yes_tag operator%(const boost::mpl::s_mask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp(77): warning: "boost::mpl::aux::no_tag operator%(const boost::mpl::s_unmask<T, Base> &, boost::mpl::aux::type_wrapper<T> *)" declares a non-template function -- add <> to refer to a template instance

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/get_pointer.hpp:48:46: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                              ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/detail/shared_count.hpp:402:19: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                   ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:255:64: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:454:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:467:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                 ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:544:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:553:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/shared_ptr.hpp:555:32: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp: At global scope:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: warning: friend declaration ‘boost::mpl::aux::type_wrapper<Key> boost::mpl::operator/(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:54:109: note: (if this is not what you intended, make sure the function template has already been declared and add <> after the function name here) 
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:55:90: warning: friend declaration ‘boost::mpl::aux::type_wrapper<boost::mpl::pair<T1, T2> > boost::mpl::operator|(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::m_item<Key, T, Base>::order*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:56:85: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::m_item<Key, T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::m_item<Key, T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( order_tag_, ORDER_BY_KEY, m_item, aux::type_wrapper<Key>* );
                                                                                     ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:71:121: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator/(const boost::mpl::m_mask<Key, Base>&, boost::mpl::aux::type_wrapper<T>*)’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/map/aux_/item.hpp:72:94: warning: friend declaration ‘boost::mpl::aux::type_wrapper<mpl_::void_> boost::mpl::operator|(const boost::mpl::m_mask<Key, Base>&, boost::mpl::m_mask<Key, Base>::key_order_*)’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_MAP_OVERLOAD( aux::type_wrapper<void_>, ITEM_BY_ORDER, m_mask, key_order_* );
                                                                                              ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:47:83: warning: friend declaration ‘char (& boost::mpl::operator||(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[boost::mpl::s_item<T, Base>::order:: value]’ declares a non-template function [-Wnon-template-friend]
     BOOST_MPL_AUX_SET_OVERLOAD( order_tag_, ORDER_BY_KEY, s_item, aux::type_wrapper<T>* );
                                                                                   ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:48:97: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_item<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:63:98: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_mask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[2]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/mpl/set/aux_/item.hpp:77:99: warning: friend declaration ‘char (& boost::mpl::operator%(const boost::mpl::s_unmask<T, Base>&, boost::mpl::aux::type_wrapper<T>*))[1]’ declares a non-template function [-Wnon-template-friend]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/smart_ptr/scoped_ptr.hpp:74:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                          ^
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/unique_ptr.h:49:25: note: declared here
   template<typename> class auto_ptr;
                         ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const ctor_args_list&, const allocator_type&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::ctor_args_list = boost::tuples::cons<boost::tuples::null_type, boost::tuples::cons<boost::tuples::tuple<boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, boost::tuples::null_type> >; boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::allocator_type = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:179:87:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree() [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:89:29:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:175:100: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:160:10: warning:   when initialized here [-Wreorder]
   explicit multi_index_container(
          ^
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp: In instantiation of ‘boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>::multi_index_container(const boost::multi_index::multi_index_container<Value, IndexSpecifierList, Allocator>&) [with Value = std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; IndexSpecifierList = boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>; Allocator = std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > >]’:
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:191:145:   required from ‘boost::property_tree::basic_ptree<Key, Data, KeyCompare>::basic_ptree(const boost::property_tree::basic_ptree<Key, Data, KeyCompare>&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >]’
/home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/include/c++/5.4.0/bits/stl_pair.h:133:78:   required from ‘constexpr std::pair<_T1, _T2>::pair(_U1&&, const _T2&) [with _U1 = std::__cxx11::basic_string<char>&; <template-parameter-2-2> = void; _T1 = const std::__cxx11::basic_string<char>; _T2 = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:646:8:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put_child(const path_type&, const self_type&) [with Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::self_type = boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:848:30:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&, Translator) [with Type = long unsigned int; Translator = boost::property_tree::stream_translator<char, std::char_traits<char>, std::allocator<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/property_tree/detail/ptree_implementation.hpp:859:11:   required from ‘boost::property_tree::basic_ptree<K, D, C>& boost::property_tree::basic_ptree<Key, Data, KeyCompare>::put(const path_type&, const Type&) [with Type = long unsigned int; Key = std::__cxx11::basic_string<char>; Data = std::__cxx11::basic_string<char>; KeyCompare = std::less<std::__cxx11::basic_string<char> >; boost::property_tree::basic_ptree<Key, Data, KeyCompare>::path_type = boost::property_tree::string_path<std::__cxx11::basic_string<char>, boost::property_tree::id_translator<std::__cxx11::basic_string<char> > >]’
/home/81i61029/src/picongpu/src/picongpu/include/plugins/ResourceLog.hpp:94:32:   required from here
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning: base ‘boost::multi_index::detail::sequenced_index<boost::multi_index::detail::nth_layer<1, std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, boost::multi_index::indexed_by<boost::multi_index::sequenced<boost::multi_index::tag<> >, boost::multi_index::ordered_non_unique<boost::multi_index::tag<boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >::subs::by_name, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, boost::multi_index::member<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, const std::__cxx11::basic_string<char>, &std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::first>, std::less<std::__cxx11::basic_string<char> > >, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > >, boost::mpl::vector0<> >’ will be initialized after [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:262:86: warning:   base ‘boost::base_from_member<std::allocator<boost::multi_index::detail::sequenced_index_node<boost::multi_index::detail::ordered_index_node<boost::multi_index::detail::null_augment_policy, boost::multi_index::detail::index_node_base<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, boost::property_tree::basic_ptree<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > > > > > > >, 0>’ [-Wreorder]
/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/include/boost/multi_index_container.hpp:261:1: warning:   when initialized here [-Wreorder]
   multi_index_container(
 ^
Scanning dependencies of target picongpu
[ 76%] Building CXX object CMakeFiles/picongpu.dir/include/ArgsParser.cpp.o
[ 82%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/particlePatches.cpp.o
[ 88%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/common/stringHelpers.cpp.o
[ 94%] Building CXX object CMakeFiles/picongpu.dir/include/plugins/hdf5/openPMD/patchReader.cpp.o
[100%] Linking CXX executable picongpu
[100%] Built target picongpu
Install the project...
-- Install configuration: "Release"
-- Installing: /home/81i61029/picInputs/myLWFA/bin/picongpu
-- Up-to-date: /home/81i61029/picInputs/myLWFA/bin
-- Installing: /home/81i61029/picInputs/myLWFA/bin/cuda_memtest.sh
-- Installing: /home/81i61029/picInputs/myLWFA/bin/cuda_memtest
-- Installing: /home/81i61029/picInputs/myLWFA/bin/mpiInfo

I can move to next step right?
Thank you!

8i161029 on 11 Aug 2017

👍2

Yay, we made it! Well done! 🎉

Yes, just go on in the manual (release 0.3.0), chapter Usage :)

ax3l on 11 Aug 2017

Hello, I used this command:

tbg -s qsub -c $HOME/picInputs/myLWFA/submit/0001gpus.cfg -t $HOME/picInputs/myLWFA/submit/hypnos-hzdr/k80_profile.tpl $HOME/runs/lwfa_001

and here is the output:

[81i61029@messi myLWFA]$ tbg -s qsub -c $HOME/picInputs/myLWFA/submit/0001gpus.cfg -t $HOME/picInputs/myLWFA/submit/hypnos-hzdr/k80_profile.tpl $HOME/runs/lwfa_001
qsub: submit error (Unknown queue MSG=requested queue not found)

Our machine is Tesla k80.
Did I choose the correct .cfg and .tpl file?
Thank you!

8i161029 on 11 Aug 2017

The tbg tool provides a mean to copy and submit a simulation task for you, portable to any system, cluster or being used interactively. (Please see the link for its documentation.)

In your case, you just want to run locally one one K80, right?
(This means you can use up to two GPUs since a K80 exposes itself as two GPUs)

Just do

tbg -s bash -c $HOME/picInputs/myLWFA/submit/0001gpus.cfg -t $HOME/picInputs/myLWFA/submit/bash/bash_mpiexec.tpl $HOME/runs/lwfa_002

instead.

ax3l on 11 Aug 2017

Thank you! But there is error in cuda_memtest as output points:

[81i61029@messi myLWFA]$ tbg -s bash -c $HOME/picInputs/myLWFA/submit/0001gpus.cfg -t $HOME/picInputs/myLWFA/submit/bash/bash_mpiexec.tpl $HOME/runs/lwfa_002
Running program...
 Data for JOB [17538,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
    Process OMPI jobid: [17538,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
[08/11/2017 17:55:57][messi][0]:ERROR: CUDA error: CUDA driver version is insufficient for CUDA runtime version, line 279, file /home/81i61029/src/picongpu/thirdParty/cuda_memtest/cuda_memtest.cu
cuda_memtest crash: see file /home/81i61029/runs/lwfa_002/simOutput/cuda_memtest_messi_0.err
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[17538,1],0]
  Exit code:    1
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpiexec command
      line parameter option (remember that mpiexec interprets the first
      unrecognized command line token as the executable).

Node:       messi
Executable: LIBRARY_PATH
--------------------------------------------------------------------------
32 total processes failed to start

8i161029 on 11 Aug 2017

cuda_memtest crash: see file /home/81i61029/runs/lwfa_002/simOutput/cuda_memtest_messi_0.err

just open this file with a text editor and see what it says. maybe someone else used the GPU already?

32 total processes failed to start

Are you sure your 0001gpus.cfg is only requesting 1 GPU (-d 1 1 1 devices)?

You can alternatively take the mpirun file: -t $HOME/picInputs/myLWFA/submit/bash/bash_mpirun.tpl

ax3l on 11 Aug 2017

Thank you!
This is the file says:

[08/11/2017 17:55:57][messi][0]:Running cuda memtest, version 1.2.3
[08/11/2017 17:55:57][messi][0]:ERROR: CUDA error: CUDA driver version is insufficient for CUDA runtime version, line 279, file /home/81i61029/src/picongpu/thirdParty/cuda_memtest/cuda_memtest.cu

Does it says CUDA driver version is wrong?

here is the 0001gpus.cfg:

#################################
## Section: Required Variables ##
#################################

TBG_wallTime="1:00:00"

TBG_gpu_x=1
TBG_gpu_y=1
TBG_gpu_z=1

TBG_gridSize="-g 128 256 128"
TBG_steps="-s 1024"

#################################
## Section: Optional Variables ##
#################################

# png image output (electron density)
TBG_pngYX="--e_png.period 64 --e_png.axis yx --e_png.slicePoint 0.5 --e_png.folder pngElectronsYX"

TBG_plugins="!TBG_pngYX                    \
             --e_macroParticlesCount.period 100"


#################################
## Section: Program Parameters ##
#################################

TBG_devices="-d !TBG_gpu_x !TBG_gpu_y !TBG_gpu_z"

TBG_programParams="!TBG_devices      \
                   !TBG_gridSize     \
                   !TBG_steps        \
                   !TBG_plugins"

# TOTAL number of GPUs
TBG_tasks="$(( TBG_gpu_x * TBG_gpu_y * TBG_gpu_z ))"

"$TBG_cfgPath"/submitAction.sh

I did not make any change in it.

For mpirun file, does you mean -t $HOME/picInputs/myLWFA/submit/bash/bash_mpirun.tpl?

8i161029 on 11 Aug 2017

I tried tbg -s bash -c $HOME/picInputs/myLWFA/submit/0001gpus.cfg -t $HOME/picInputs/myLWFA/submit/bash/bash_mpirun.tpl $HOME/runs/lwfa_003
But it still doesn't start programming...

[81i61029@messi myLWFA]$ tbg -s bash -c $HOME/picInputs/myLWFA/submit/0001gpus.cfg -t $HOME/picInputs/myLWFA/submit/bash/bash_mpirun.tpl $HOME/runs/lwfa_003
Running program...
 Data for JOB [44796,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
    Process OMPI jobid: [44796,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
[08/11/2017 19:56:52][messi][0]:ERROR: CUDA error: CUDA driver version is insufficient for CUDA runtime version, line 279, file /home/81i61029/src/picongpu/thirdParty/cuda_memtest/cuda_memtest.cu
cuda_memtest crash: see file /home/81i61029/runs/lwfa_003/simOutput/cuda_memtest_messi_0.err
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[44796,1],0]
  Exit code:    1
--------------------------------------------------------------------------
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[44782,1],0]
  Exit code:    1
--------------------------------------------------------------------------

Is there anything wrong in CUDA?
Thank you!

8i161029 on 11 Aug 2017

Does it says CUDA driver version is wrong?

Oh that's simple!
You compiled with CUDA 8.0 but your Nvidia drivers are too old.

Just update the nvidia GPU drivers on your system! You probably need driver 375.26 or any newer one. See the output of nvidia-smi to find you which one is used right now.

ax3l on 11 Aug 2017

Thank you!
I have been looked for answer for a while.
I also tried to check nvidia driver, but the command nvidia-smi showed bash: nvidia-smi: command not found...
And there is not nvidia directory in /proc...
My teacher says this machine is nvidia Tesla k80. But there is nothing about nvidia in it.
It's so weird...
I can only get information from this command:

[81i61029@messi ~]$ lspci  -v -s  $(lspci | grep ' VGA ' | cut -d" " -f 1)
09:00.0 VGA compatible controller: ASPEED Technology, Inc. ASPEED Graphics Family (rev 30) (prog-if 00 [VGA controller])
    Subsystem: Super Micro Computer Inc Device 0844
    Flags: bus master, medium devsel, latency 0, IRQ 18, NUMA node 0
    Memory at c6000000 (32-bit, non-prefetchable) [size=16M]
    Memory at c7000000 (32-bit, non-prefetchable) [size=128K]
    I/O ports at 5000 [size=128]
    Expansion ROM at <unassigned> [disabled]
    Capabilities: <access denied>
    Kernel driver in use: ast
    Kernel modules: ast

8i161029 on 11 Aug 2017

I think this machine never installed nvidia driver...
I will ask users in our group and update situation as soon as possible.
I am very grateful for your help this week! Thank you very much!

8i161029 on 11 Aug 2017

👍1

Ah, you have no CUDA drivers installed yet at all. You will need them to do anything useful with a plugged-in K80 :)

Just download the latest CUDA version from here: https://developer.nvidia.com/cuda-downloads and download it including the SDK to /usr or /usr/local as it suggests (needs root permissions).

Yes, best is to synchronize with the other users, that step will install a proprietary kernel module.

ax3l on 11 Aug 2017

Thank you too for your patience, I am glad we solved the install issues and you can soon be computing!

ax3l on 11 Aug 2017

🎉1

Sorry...I need your help again...
These days I reviewed how I installed PIConGPU.
I found when I installed spack, I forgot to do spack install libelf at the beginning.
I thought it maybe the reason why cmake couldn't find the correct library.
So I did spack install libelf on spack both in $HOME/spack-tools and $HOME/lib/spack.
Now I try to run example,output shows this information:

[81i61029@messi ~]$ tbg -s bash -c $HOME/picInputs/myLWFA/submit/0001gpus.cfg -t $HOME/picInputs/myLWFA/submit/bash/bash_mpirun.tpl $HOME/runs/lwfa_004
cp: cannot stat ‘/home/81i61029/bin’: No such file or directory
cp: cannot stat ‘/home/81i61029/include’: No such file or directory
cp: cannot stat ‘/home/81i61029/submit’: No such file or directory
Running program...
no binary 'cuda_memtest' available, skip GPU memory test
 Data for JOB [25743,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
    Process OMPI jobid: [25743,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: /home/81i61029/runs/lwfa_004/picongpu/bin/picongpu
Node: messi

while attempting to start process rank 0.
--------------------------------------------------------------------------
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[27509,1],0]
  Exit code:    1
--------------------------------------------------------------------------

I uninstall libelf, but it is no help.
I think I accidentally changed the path...
Sorry...could you please help me to correct it?
Thank you!

8i161029 on 14 Aug 2017

I found when I installed spack, I forgot to do spack install libelf at the beginning.

that is no problem, that is just an example of theirs ;)

Now I try to run example,output shows this information: [...]

That's just wrong usage of tbg :)
In order to submit a simulation, first go in its input (parameter) directory and submit with tbg from there.

In your case:

cd $HOME/picInputs/myLWFA/

tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpirun.tpl $HOME/runs/lwfa_005

That's all! 💃

ax3l on 14 Aug 2017

OH! Sorry about that... I was too nervous to remember to move to myLWFA...

By the way, I edit a PIConGPU installation guide in traditional Chinese(used in Taiwan).
Here you are:
PIConGPU Installation via spack 安裝指南.pdf
Please feel free to provide it to any users speaking Chinese.
Thank you!

8i161029 on 14 Aug 2017

🎉1 👍1

Wow, awesome thank you!

A little feedback on the manual (from what I can read ^^):

instead of mkdir spack-tools && cd spack-tools ... you can just run:
- git clone https://github.com/llnl/spack.git spack-tools
- export PATH=$HOME/spack-tools/bin:$PATH
- export SPACK_ROOT=$HOME/spack-tools
- ...
you don't need to run $ spack install libelf
you don't need to run $ spack spec netcdf

Here is a reviewed version of your pdf, do you want to update it slightly? :)
PIConGPU.Installation.via.spack.cn-reviewed.pdf

ax3l on 15 Aug 2017

Thank you for your feedback! I will update it as you suggested.

Besides, in step4.,
I want to make links for module files of GCC-5.4.0 and it's dependencies, putting them in the $HOME/lib/spack modules directory.
But I only know click on the right button of mouse → make link,
and put the links in the $HOME/lib/.... one by one.
Are there any convenient commands can do these things simultaneously?
Thank you!

8i161029 on 15 Aug 2017

Also for the line of tbg, Can I use the command like this? :

$ tbg -s bash -c /submit/0001gpus.cfg -t /submit/bash/bash_mpiexec.tpl $HOME/runs/lwfa_001

8i161029 on 15 Aug 2017

Hm, I am not sure if it's a good idea to hard-line the gcc from spack-tools/...

I would just set MODULEPATH for the second spack instance, as you do in your picongpu.profile.

Isn't this enough to make module load available in your case?

Also for the line of tbg, Can I use the command like this? :

close. without the slashes, these are relative paths:

$ cd $HOME/picInputs/myLWFA/
$ tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpiexec.tpl $HOME/runs/lwfa_001

ax3l on 15 Aug 2017

In my system,
MODULEPATH in picongpu.profile is =$HOME/lib/spack/share/spack/modules/linux-centos7-x86_64
But modules of gcc-5.4.0 are in $HOME/spack-tools/spack/share/spack/modules/linux-centos7-x86_64
So I tried the method I mentioned above, and module gcc-5.4.0 worked.
If I don't want to make link for gcc, how can I set the MODULEPATH?
Add another line like this in picongpu.profile? :

MODULEPATH=$HOME/spack-tools/spack/share/spack/modules/linux-centos7-x86_64

8i161029 on 15 Aug 2017

You can just concat it with a colon (:) in picongpu.profile.

export MODULEPATH=$HOME/lib/spack/share/spack/modules/linux-centos7-x86_64:$HOME/spack-tools/share/spack/modules/linux-centos7-x86_64

ax3l on 15 Aug 2017

Thank you!
I will modify the manual as you suggested.
Please wait a second.

8i161029 on 15 Aug 2017

Ok! Here is the modified manual:
PIConGPU-0.3.0 Installation via spack 安裝指南.pdf

Hope this will be helpful to you. :)
Thank you!

8i161029 on 15 Aug 2017

🎉1 👍1

Awesome, thank you!

If you haven't done so already, please make sure to subscribe to our user mailing list for announcements about new releases and potential fixes! Subscribe (select "Feed" on bottom left)

Since we are an open source project and due to its nature can not guess our user base, please make sure to cite PIConGPU and the version you used in your publications (papers, posters, talks, etc.).

Btw, for which institute do you work and are you trying to use PIConGPU for something specific that you can tell us?

Feel free to open new issues if something arises on the way!

ax3l on 15 Aug 2017

I am a senior of Department of Engineering and System Science at National Tsing Hua University in Taiwan.
My group is Photon Source and Radiation Application Group.
My teacher wants to do simulation via PIConGPU so as to replace Vorpal.
PIConGPU is my first project on Linux, it's the reason why I bother you for 4 months...
Very grateful for your help these months!
I will introduce PIConGPU to everyone!

8i161029 on 15 Aug 2017

❤1

That sounds great, thank you!

Very grateful for your help these months! I will introduce PIConGPU to everyone!

Jippey! 💃

Thank you too, you did very well! You also provided important feedback and we will make the next PIConGPU release even easier to use and install - I am already working on it.

Fell free to write us on GitHub anytime! ✨

ax3l on 15 Aug 2017

😄1

Hello! I found some typos in the manual.
In picongpu.profile part:
zilb1.2.11-gcc-5.4.0 → zlib-1.2.11-gcc-5.4.0 and freetype2.7.1-gcc-5.4.0 → freetype-2.7.1-gcc-5.4.0
Here is the revised manual:
PIConGPU-0.3.0 Installation via spack 安裝指南.pdf

Thank you!

8i161029 on 15 Aug 2017

👍1

I just remembered that in your picongpu.profile you can also use spack load ... instead of module load ....

The spack load command has the same syntax as the spack install command which makes it easier to type. For example spack load boost for the first matching boost or spack load [email protected] %[email protected] for a specific boost version that was further build with gcc 5.4.0

ax3l on 17 Aug 2017

I see. Thank you!

Because an user of our server needs to run some simulations these two weeks, I can not install NVIDIA driver for two weeks.
Once I can try to run PIConGPU, I will inform you.
Besides, a member in our group is following my pdf to build PIConGPU, I will also inform you if we finish it.
Thank you. :)

8i161029 on 17 Aug 2017

👍1

Sounds great! :)

Since it falls into that period: I won't be reachable in the last week of August and the first of September if anything comes up. Just open new issues for new questions or problems and others will help you as well during that time.

ax3l on 18 Aug 2017

👍1

Hello, I need your help again...
Last week I tried to install NVIDIA driver. And I met troubles...
I followed this page(it's Chinese), driver version is 384.66.
After I installed driver successfully, I rebooted, then the graphical mode is gone...
I used VNC connection, after login it will show this:
https://imgur.com/96pXy7l
Now I can SSH to this machine, nvidia-smi shows this:

[81i61029@messi ~]$ nvidia-smi
Fri Sep 15 23:51:40 2017
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 384.66                 Driver Version: 384.66                    |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  Tesla K80           Off  | 00000000:06:00.0 Off |                    0 |
| N/A   43C    P0    59W / 149W |      0MiB / 11439MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+
|   1  Tesla K80           Off  | 00000000:07:00.0 Off |                    0 |
| N/A   33C    P0    75W / 149W |      0MiB / 11439MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+
|   2  Tesla K80           Off  | 00000000:0A:00.0 Off |                    0 |
| N/A   44C    P0    58W / 149W |      0MiB / 11439MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+
|   3  Tesla K80           Off  | 00000000:0B:00.0 Off |                    0 |
| N/A   34C    P0    76W / 149W |      0MiB / 11439MiB |     94%      Default |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID  Type  Process name                               Usage      |
|=============================================================================|
|  No running processes found                                                 |
+-----------------------------------------------------------------------------+

I left a comment in that page, the author said maybe the graphical desktop is set to be opened by Tesla k80. But the monitor is connected to the motherboard.

Could you please let me know how you set your k80 as well as nvidia driver?
If it is convenient for you, could you please give me some guides to correct it?
Thank you very much! And sorry to bother you all the times!

8i161029 on 15 Sep 2017

Hi,

don't worry, that's a common issue people face when switching graphic card drivers.

First things first: since you can already SSH into the machine: you don't need X11 and can already compile & run PIConGPU on it ;)

I left a comment in that page, the author said maybe the graphical desktop is set to be opened by Tesla k80. But the monitor is connected to the motherboard.

From the nvidia-smi output, the driver seems to be installed successfully. The remaining issue might just be, that your X11 config is messed up for your desktop.

You can first check /var/log/Xorg.0.log for any obvious errors. You should also make sure the previous driver, probably the open source nouveau driver, is properly blacklisted so only the nvidia one is used.
I also found a couple of centos 7 threads that might help:

Do you have an additional on-board graphics card? maybe an intel one? https://www.dedoimedo.com/computers/centos-7-nvidia.html
https://www.centos.org/forums/viewtopic.php?t=61162

ax3l on 18 Sep 2017

Thank you very much!
I will look for more information to solve the desktop issue these days.
Besides, I tried to run the LWFA example.
Here is the output:

[81i61029@messi myLWFA]$ tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpirun.tpl $HOME/runs/lwfa_010
Running program...
 Data for JOB [48383,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
        Process OMPI jobid: [48383,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
 Data for JOB [48280,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
        Process OMPI jobid: [48280,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | Sliding Window is OFF
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | Courant c*dt <= 1.00229 ? 1
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | species e: omega_p * dt <= 0.1 ? 0.0247974
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | y-cells per wavelength: 18.0587
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | macro particles per gpu: 8388608
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | typical macro particle weighting: 6955.06
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_SPEED 2.99792e+08
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_TIME 1.39e-16
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_LENGTH 4.16712e-08
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_MASS 6.33563e-27
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_CHARGE 1.11432e-15
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_EFIELD 1.22627e+13
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_BFIELD 40903.8
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_ENERGY 5.69418e-10
[1,0]<stdout>:initialization time: 33sec 767msec = 33 sec
[1,0]<stdout>:  0 % =        0 | time elapsed:            29sec 499msec | avg time per step:   0msec
[1,0]<stdout>:[messi:04083] *** Process received signal ***
[1,0]<stdout>:[messi:04083] Signal: Segmentation fault (11)
[1,0]<stdout>:[messi:04083] Signal code:  (128)
[1,0]<stdout>:[messi:04083] Failing at address: (nil)
[1,0]<stdout>:[messi:04083] [ 0] [1,0]<stdout>:/lib64/libpthread.so.0(+0xf370[1,0]<stdout>:)[0x7f507f2cc370]
[1,0]<stdout>:[messi:04083] [ 1] [1,0]<stdout>:/lib64/libboost_filesystem-mt.so.1.53.0(+0xe22b[1,0]<stdout>:)[0x7f507e69022b]
[1,0]<stdout>:[messi:04083] [ 2] /lib64/libboost_filesystem-mt.so.1.53.0(_ZNK5boost10filesystem4path17m_parent_path_endEv+0x15)[0x[1,0]<stdout>:7f507e6906a5]
[1,0]<stdout>:[messi:04083] [1,0]<stdout>:[ 3] /lib64/libboost_filesystem-mt.so.1.53.0([1,0]<stdout>:_ZNK5boost10filesystem4path11parent_pathEv+0x2c)[1,0]<stdout>:[0x7f507e69223c]
[1,0]<stdout>:[messi:04083] [ 4] /lib64/libboost_filesystem-mt.so.1.53.0(_ZN5boost10filesystem6detail18create_directoriesERKNS0_4pathEPNS_6system10error_codeE+0x5d)[0x7f507e68c48d]
[1,0]<stdout>:[messi:04083] [ 5] [1,0]<stdout>:/home/81i61029/runs/lwfa_010/picongpu/bin/picongpu(_ZNK5PMacc10FilesystemILj3EE30createDirectoryWithPermissionsENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x[1,0]<stdout>:69)[0x68a109]
[1,0]<stdout>:[messi:04083] [1,0]<stdout>:[ 6] [1,0]<stdout>:/home/81i61029/runs/lwfa_010/picongpu/bin/picongpu(_ZN8picongpu10PngCreator11createImageIN5PMacc7DataBoxINS2_10PitchedBoxINS2_4math6VectorIfLi3ENS5_16StandardAccessorENS5_17StandardNavigatorENS5_6detail17Vector_componentsEEELj2EEEEEEEvT_NS2_9DataSpaceILj2EEE13MessageHeader[1,0]<stdout>:+0x848)[0x695338[1,0]<stdout>:]
[1,0]<stdout>:[messi:04083] [ 7] [1,0]<stdout>:/home/81i61029/runs/lwfa_010/picongpu/bin/picongpu(_ZN5boost6detail11thread_dataINS_3_bi6bind_tIvNS_4_mfi3mf3IvN8picongpu10PngCreatorEN5PMacc7DataBoxINS8_10PitchedBoxINS8_4math6VectorIfLi3ENSB_16StandardAccessorENSB_17StandardNavigatorENSB_6detail17Vector_componentsEEELj2EEEEENS8_9DataSpaceILj2EEE13MessageHeaderEENS2_5list4INS2_5valueIPS7_EENSP_ISJ_EENSP_ISL_EENSP_ISM_EEEEEEE3runEv+0x[1,0]<stdout>:a9)[0x75c259]
[1,0]<stdout>:[messi:04083] [ 8] [1,0]<stdout>:/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_thread.so.1.63.0(+0x[1,0]<stdout>:1340d)[0x7f507d48340d[1,0]<stdout>:]
[1,0]<stdout>:[messi:04083] [ 9] [1,0]<stdout>:/lib64/libpthread.so.0(+0x7dc5[1,0]<stdout>:)[0x7f507f2c4dc5]
[1,0]<stdout>:[messi:04083] [10] [1,0]<stdout>:/lib64/libc.so.6(clone+0x[1,0]<stdout>:6d)[0x7f507af5076d]
[1,0]<stdout>:[messi:04083] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node messi exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[41781,1],0]
  Exit code:    1
--------------------------------------------------------------------------
[81i61029@messi myLWFA]$

I think the GPU driver issue is solved.
Could you please teach me what does the error message mean?
Thank you!

8i161029 on 18 Sep 2017

Looks like it is taking the wrong runtime libs, what is in you $HOME/picongpu.profile ?

ax3l on 18 Sep 2017

Here is my picongpu.profile:

# Modules #####################################################################
#
. /usr/share/modules/init/bash
. $HOME/lib/spack/share/spack/setup-env.sh
export MODULEPATH=$HOME/spack/share/spack/modules/linux-centos7-x86_64:$HOME/spacktools/share/spack/modules/linux-centos7-x86_64
# Core Dependencies (based on gcc 5.4.0)
module load gcc-5.4.0-4.4.7
module load cmake-3.8.1-gcc-5.4.0
module load boost-1.63.0-gcc-5.4.0
module load cuda-8.0.61-gcc-5.4.0
module load openmpi-2.1.1-gcc-5.4.0
# Plugins (optional)
module load zlib-1.2.11-gcc-5.4.0 libpng-1.6.29-gcc-5.4.0 freetype-2.7.1-gcc-5.4.0
pngwriter-0.6.0-gcc-5.4.0
module load hdf5-1.10.1-gcc5.4.0 libsplash-1.6.0-gcc-5.4.0


# either use libSplash or ADIOS for file I/O
#module load adios

# Environment #################################################################
#
export PICSRC=/home/$(whoami)/src/picongpu
export PIC_PROFILE=$(cd $(dirname $BASH_SOURCE) && pwd)"/"$(basename $BASH_SOURCE)

# send me mails on job (b)egin, (e)nd, (a)bortion or (n)o mail
export MY_MAILNOTIFY="n"
export MY_MAIL="[email protected]"
export MY_NAME="Po-Ting, Lai <$MY_MAIL>"

export PATH=$PATH:$PICSRC
export PATH=$PATH:$PICSRC/src/splash2txt/build
export PATH=$PATH:$PICSRC/src/tools/bin

export PYTHONPATH=$PICSRC/src/tools/lib/python:$PYTHONPATH

# "tbg" default options #######################################################
#   - interactive (bash + mpiexec)
export TBG_SUBMIT="bash"
export TBG_TPLFILE="etc/picongpu/bash/bash_mpiexec.tpl"

Thank you.

8i161029 on 18 Sep 2017

Is that because last line in picongpu.profile links to bash_mpiexec.tpl, but I use mpirun.tpl in my command?
Do I need to change my command?
Thank you.

8i161029 on 18 Sep 2017

No, the last line is just a default if you don't specify any.

What does an
. $HOME/picongpu.profile
ldd bin/picongpu

Reveil when you are inside your input set?

ax3l on 18 Sep 2017

output of ldd bin/picongpu:

[81i61029@messi myLWFA]$ .  $HOME/picongpu.profile
[81i61029@messi myLWFA]$ ldd bin/picongpu
        linux-vdso.so.1 =>  (0x00007ffdd9758000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f078096e000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f078076a000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f0780562000)
        libmpi.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so.20 (0x00007f0780164000)
        libmpi_cxx.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so.20 (0x00007f077ff49000)
        libboost_filesystem-mt.so.1.53.0 => /lib64/libboost_filesystem-mt.so.1.53.0 (0x00007f077fd32000)
        libboost_system-mt.so.1.53.0 => /lib64/libboost_system-mt.so.1.53.0 (0x00007f077fb2d000)
        libboost_math_tr1-mt.so.1.53.0 => /lib64/libboost_math_tr1-mt.so.1.53.0 (0x00007f077f8ef000)
        libz.so.1 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so.1 (0x00007f077f6d1000)
        libboost_program_options.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so.1.63.0 (0x00007f077f44e000)
        libboost_regex.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_regex.so.1.63.0 (0x00007f077f162000)
        libboost_filesystem.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_filesystem.so.1.63.0 (0x00007f077ef48000)
        libboost_system.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_system.so.1.63.0 (0x00007f077ed44000)
        libboost_thread.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_thread.so.1.63.0 (0x00007f077eb1c000)
        libboost_math_tr1.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_math_tr1.so.1.63.0 (0x00007f077e8cf000)
        libboost_serialization.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_serialization.so.1.63.0 (0x00007f077e68e000)
        libhdf5.so.101 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so.101 (0x00007f077e0af000)
        libpngwriter.so => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/lib/libpngwriter.so (0x00007f077de94000)
        libpng15.so.15 => /lib64/libpng15.so.15 (0x00007f077dc69000)
        libfreetype.so.6 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so.6 (0x00007f077d993000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f077d690000)
        libboost_chrono.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_chrono.so.1.63.0 (0x00007f077d489000)
        libboost_date_time.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_date_time.so.1.63.0 (0x00007f077d277000)
        libboost_atomic.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_atomic.so.1.63.0 (0x00007f077d075000)
        libstdc++.so.6 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libstdc++.so.6 (0x00007f077ccfb000)
        libgomp.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libgomp.so.1 (0x00007f077cad8000)
        libgcc_s.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libgcc_s.so.1 (0x00007f077c8c1000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f077c500000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f0780bad000)
        libopen-rte.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libopen-rte.so.20 (0x00007f077c202000)
        libopen-pal.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libopen-pal.so.20 (0x00007f077bebd000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00007f077bcba000)
        libhwloc.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hwloc-1.11.7-znn4k7zfj4x2jizkhs5q7ysifffjd33p/lib/libhwloc.so.5 (0x00007f077ba6f000)
        libpciaccess.so.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpciaccess-0.13.5-nqj66marqppz7b6cqk3lj7lhgtyr6ysm/lib/libpciaccess.so.0 (0x00007f077b864000)
        libxml2.so.2 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libxml2-2.9.4-jj3guvl5civei5atlkimcrjg6ctpukc6/lib/libxml2.so.2 (0x00007f077b49b000)
        liblzma.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/xz-5.2.3-ehlxwhosxgdfbduwx3nk5zzxmo4qhmaq/lib/liblzma.so.5 (0x00007f077b267000)
        libpng16.so.16 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16 (0x00007f077b024000)
        libbz2.so.1.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/bzip2-1.0.6-egkg2fbrcljkai2d23pgrq7wzeg2k5p5/lib/libbz2.so.1.0 (0x00007f077ae13000)

Thank you.

8i161029 on 18 Sep 2017

oh, three boost libraries still link the wrong (/lib64) install: filesystem, system and math. It's even linked twice! And we don't even support Boost 1.53.0 in this release o.0

As a real hacky work-around for your system, can you try to add

set(Boost_USE_MULTITHREADED OFF)

before the line

find_package(Boost # ....

in src/picongpu/CMakeLists.txt? (Then re-compile and pls post the output of ldd again.)

ax3l on 22 Sep 2017

note to myself: this is likely caused by mallocMC since it does not use boost targets as we do yet.

ax3l on 22 Sep 2017

@8i161029 an easier work-around for your system will be: open thirdParty/cmake-modules/FindmallocMC.cmake and change

find_package(Boost 1.48.0 REQUIRED)

to

find_package(Boost 1.57.0 REQUIRED)

ax3l on 22 Sep 2017

Thank you!
I did the changes you suggested in src/picongpu/CMakeLists.txt and thirdParty/cmake-modules/FindmallocMC.cmake.

part Find Boost in src/picongpu/CMakeLists.txt:

################################################################################
# Find Boost
################################################################################

set(Boost_USE_MULTITHREADED OFF)

find_package(Boost 1.57.0 REQUIRED COMPONENTS program_options regex filesystem
                                              system thread math_tr1
                                              serialization)
message(STATUS "BOOST INCLUDE++++: ${Boost_INCLUDE_DIRS}")
message(STATUS "BOOST LIBS++++: ${Boost_LIBRARIES}")
set(LIBS ${LIBS} Boost::boost Boost::program_options Boost::regex Boost::filesystem Boost::system Boost::thread Boost::math_tr1 Boost::serialization)

part #dependencies in picongpu/src/thirdParty/cmake-modules/FindmallocMC.cmake:

# Required cmake version ######################################################
#
cmake_minimum_required(VERSION 2.8.12.2)


# dependencies ################################################################
#
find_package(CUDA 5.0 REQUIRED)
find_package(Boost 1.57.0 REQUIRED)

Here is the output of ldd bin/picongpu:

[81i61029@messi myLWFA]$ ldd bin/picongpu
        linux-vdso.so.1 =>  (0x00007ffea4fe3000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe11799d000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007fe117799000)
        librt.so.1 => /lib64/librt.so.1 (0x00007fe117591000)
        libmpi.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so.20 (0x00007fe117193000)
        libmpi_cxx.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so.20 (0x00007fe116f78000)
        libboost_filesystem-mt.so.1.53.0 => /lib64/libboost_filesystem-mt.so.1.53.0 (0x00007fe116d61000)
        libboost_system-mt.so.1.53.0 => /lib64/libboost_system-mt.so.1.53.0 (0x00007fe116b5c000)
        libboost_math_tr1-mt.so.1.53.0 => /lib64/libboost_math_tr1-mt.so.1.53.0 (0x00007fe11691e000)
        libz.so.1 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so.1 (0x00007fe116700000)
        libboost_program_options.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so.1.63.0 (0x00007fe11647d000)
        libboost_regex.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_regex.so.1.63.0 (0x00007fe116191000)
        libboost_filesystem.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_filesystem.so.1.63.0 (0x00007fe115f77000)
        libboost_system.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_system.so.1.63.0 (0x00007fe115d73000)
        libboost_thread.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_thread.so.1.63.0 (0x00007fe115b4b000)
        libboost_math_tr1.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_math_tr1.so.1.63.0 (0x00007fe1158fe000)
        libboost_serialization.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_serialization.so.1.63.0 (0x00007fe1156bd000)
        libhdf5.so.101 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so.101 (0x00007fe1150de000)
        libpngwriter.so => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/lib/libpngwriter.so (0x00007fe114ec3000)
        libpng15.so.15 => /lib64/libpng15.so.15 (0x00007fe114c98000)
        libfreetype.so.6 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so.6 (0x00007fe1149c2000)
        libm.so.6 => /lib64/libm.so.6 (0x00007fe1146bf000)
        libboost_chrono.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_chrono.so.1.63.0 (0x00007fe1144b8000)
        libboost_date_time.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_date_time.so.1.63.0 (0x00007fe1142a6000)
        libboost_atomic.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_atomic.so.1.63.0 (0x00007fe1140a4000)
        libstdc++.so.6 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libstdc++.so.6 (0x00007fe113d2a000)
        libgomp.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libgomp.so.1 (0x00007fe113b07000)
        libgcc_s.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libgcc_s.so.1 (0x00007fe1138f0000)
        libc.so.6 => /lib64/libc.so.6 (0x00007fe11352f000)
        /lib64/ld-linux-x86-64.so.2 (0x00007fe117bdc000)
        libopen-rte.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libopen-rte.so.20 (0x00007fe113231000)
        libopen-pal.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libopen-pal.so.20 (0x00007fe112eec000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00007fe112ce9000)
        libhwloc.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hwloc-1.11.7-znn4k7zfj4x2jizkhs5q7ysifffjd33p/lib/libhwloc.so.5 (0x00007fe112a9e000)
        libpciaccess.so.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpciaccess-0.13.5-nqj66marqppz7b6cqk3lj7lhgtyr6ysm/lib/libpciaccess.so.0 (0x00007fe112893000)
        libxml2.so.2 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libxml2-2.9.4-jj3guvl5civei5atlkimcrjg6ctpukc6/lib/libxml2.so.2 (0x00007fe1124ca000)
        liblzma.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/xz-5.2.3-ehlxwhosxgdfbduwx3nk5zzxmo4qhmaq/lib/liblzma.so.5 (0x00007fe112296000)
        libpng16.so.16 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16 (0x00007fe112053000)
        libbz2.so.1.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/bzip2-1.0.6-egkg2fbrcljkai2d23pgrq7wzeg2k5p5/lib/libbz2.so.1.0 (0x00007fe111e42000)
[81i61029@messi myLWFA]$

I can still find some lib64 in this output, maybe it doesn't work?

Then I configured, installed, and tried to run the example:

[81i61029@messi myLWFA]$ tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpiexec.tpl $HOME/runs/lwfa_001
Running program...
 Data for JOB [13431,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
        Process OMPI jobid: [13431,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../                                                          ../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
--------------------------------------------------------------------------
mpiexec was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpiexec command
      line parameter option (remember that mpiexec interprets the first
      unrecognized command line token as the executable).

Node:       messi
Executable: LIBRARY_PATH
--------------------------------------------------------------------------
32 total processes failed to start
--------------------------------------------------------------------------
mpiexec was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpiexec command
      line parameter option (remember that mpiexec interprets the first
      unrecognized command line token as the executable).

Node:       messi
Executable: LIBRARY_PATH
--------------------------------------------------------------------------
32 total processes failed to start
[81i61029@messi myLWFA]$

The message is different.
Could you please help me correct it?
Thank you!

8i161029 on 25 Sep 2017

That looks so far ok.
Can you just remove the

-x LIBRARY_PATH

From submit/bash/bash_mpiexec.tpl ?

ax3l on 25 Sep 2017

Here is my submit/bash/bash_mpiexec.tpl:

[81i61029@messi bash]$ vim bash_mpiexec.tpl
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with PIConGPU.
# If not, see <http://www.gnu.org/licenses/>.
#

##calculations will be performed by tbg##

# settings that can be controlled by environment variables before submit
.TBG_author=${MY_NAME:+--author \"${MY_NAME}\"}
.TBG_profile=${PIC_PROFILE:-"~/picongpu.profile"}

# 4 gpus per node if we need more than 4 gpus else same count as TBG_tasks
.TBG_gpusPerNode=$(if [ $TBG_tasks -gt 4 ] ; then echo 4; else echo $TBG_tasks; fi)

## end calculations ##


echo 'Running program...'

cd !TBG_dstPath

export MODULES_NO_OUTPUT=1
. !TBG_profile
unset MODULES_NO_OUTPUT

#set user rights to u=rwx;g=r-x;o=---
umask 0027

mkdir simOutput 2> /dev/null
cd simOutput

# test if cuda_memtest binary is available
if [ -f !TBG_dstPath/picongpu/bin/cuda_memtest ] ; then
  mpiexec --prefix $MPI_ROOT -tag-output --display-map -x LIBRARY_PATH -x LD_LIBRARY_PATH -am !TBG_dstPath/tbg/openib.conf --mca mpi_leave_pinned 0 -npernode !TBG_gpusPerNode -n !TBG_tasks !TBG_dstPath/picongpu/bin/cuda_memtest.sh
else
  echo "no binary 'cuda_memtest' available, skip GPU memory test" >&2
fi

if [ $? -eq 0 ] ; then
  mpiexec --prefix $MPI_ROOT -x LIBRARY_PATH -x LD_LIBRARY_PATH -tag-output --display-map -am !TBG_dstPath/tbg/openib.conf --mca mpi_leave_pinned 0 -npernode !TBG_gpusPerNode -n !TBG_tasks !TBG_dstPath/picongpu/bin/picongpu !TBG_author !TBG_programParams | tee output
fi

mpiexec --prefix $MPI_ROOT -x LIBRARY_PATH -x LD_LIBRARY_PATH -npernode !TBG_gpusPerNode -n !TBG_tasks killall -9 picongpu 2>/dev/null || true

There are three -x LIBRARY_PATH in this file.
Do I need to remove them all?
Thank you!

8i161029 on 25 Sep 2017

Yes, all three of them please :)

ax3l on 25 Sep 2017

here is the output:

[81i61029@messi myLWFA]$ tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpiexec.tpl $HOME/runs/lwfa_002
Running program...
 Data for JOB [8100,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
        Process OMPI jobid: [8100,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
--------------------------------------------------------------------------
mpiexec was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpiexec command
      line parameter option (remember that mpiexec interprets the first
      unrecognized command line token as the executable).

Node:       messi
Executable: LD_LIBRARY_PATH
--------------------------------------------------------------------------
32 total processes failed to start
--------------------------------------------------------------------------
mpiexec was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpiexec command
      line parameter option (remember that mpiexec interprets the first
      unrecognized command line token as the executable).

Node:       messi
Executable: LD_LIBRARY_PATH
--------------------------------------------------------------------------
32 total processes failed to start
[81i61029@messi myLWFA]$

Is that mean I need to remove -x LD_LIBRARY_PATH too?
Thank you.

8i161029 on 25 Sep 2017

Ok let's try.

ax3l on 25 Sep 2017

Here is the output:

[81i61029@messi myLWFA]$ tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpiexec.tpl $HOME/runs/lwfa_003
Running program...
 Data for JOB [31359,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
        Process OMPI jobid: [31359,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
 Data for JOB [31251,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
        Process OMPI jobid: [31251,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
PIConGPUVerbose PHYSICS(1) | Sliding Window is OFF
PIConGPUVerbose PHYSICS(1) | Courant c*dt <= 1.00229 ? 1
PIConGPUVerbose PHYSICS(1) | species e: omega_p * dt <= 0.1 ? 0.0247974
PIConGPUVerbose PHYSICS(1) | y-cells per wavelength: 18.0587
PIConGPUVerbose PHYSICS(1) | macro particles per gpu: 8388608
PIConGPUVerbose PHYSICS(1) | typical macro particle weighting: 6955.06
PIConGPUVerbose PHYSICS(1) | UNIT_SPEED 2.99792e+08
PIConGPUVerbose PHYSICS(1) | UNIT_TIME 1.39e-16
PIConGPUVerbose PHYSICS(1) | UNIT_LENGTH 4.16712e-08
PIConGPUVerbose PHYSICS(1) | UNIT_MASS 6.33563e-27
PIConGPUVerbose PHYSICS(1) | UNIT_CHARGE 1.11432e-15
PIConGPUVerbose PHYSICS(1) | UNIT_EFIELD 1.22627e+13
PIConGPUVerbose PHYSICS(1) | UNIT_BFIELD 40903.8
PIConGPUVerbose PHYSICS(1) | UNIT_ENERGY 5.69418e-10
initialization time: 33sec 442msec = 33 sec
  0 % =        0 | time elapsed:            29sec 481msec | avg time per step:   0msec
[messi:51564] *** Process received signal ***
[messi:51564] Signal: Segmentation fault (11)
[messi:51564] Signal code:  (128)
[messi:51564] Failing at address: (nil)
[messi:51564] [ 0] /lib64/libpthread.so.0(+0xf370)[0x7ffba856b370]
[messi:51564] [ 1] /lib64/libboost_filesystem-mt.so.1.53.0(+0xe22b)[0x7ffba792f22b]
[messi:51564] [ 2] /lib64/libboost_filesystem-mt.so.1.53.0(_ZNK5boost10filesystem4path17m_parent_path_endEv+0x15)[0x7ffba792f6a5]
[messi:51564] [ 3] /lib64/libboost_filesystem-mt.so.1.53.0(_ZNK5boost10filesystem4path11parent_pathEv+0x2c)[0x7ffba793123c]
[messi:51564] [ 4] /lib64/libboost_filesystem-mt.so.1.53.0(_ZN5boost10filesystem6detail18create_directoriesERKNS0_4pathEPNS_6system10error_codeE+0x5d)[0x7ffba792b48d]
[messi:51564] [ 5] /home/81i61029/runs/lwfa_003/picongpu/bin/picongpu(_ZNK5PMacc10FilesystemILj3EE30createDirectoryWithPermissionsENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x69)[0x68a109]
[messi:51564] [ 6] /home/81i61029/runs/lwfa_003/picongpu/bin/picongpu(_ZN8picongpu10PngCreator11createImageIN5PMacc7DataBoxINS2_10PitchedBoxINS2_4math6VectorIfLi3ENS5_16StandardAccessorENS5_17StandardNavigatorENS5_6detail17Vector_componentsEEELj2EEEEEEEvT_NS2_9DataSpaceILj2EEE13MessageHeader+0x848)[0x695338]
[messi:51564] [ 7] /home/81i61029/runs/lwfa_003/picongpu/bin/picongpu(_ZN5boost6detail11thread_dataINS_3_bi6bind_tIvNS_4_mfi3mf3IvN8picongpu10PngCreatorEN5PMacc7DataBoxINS8_10PitchedBoxINS8_4math6VectorIfLi3ENSB_16StandardAccessorENSB_17StandardNavigatorENSB_6detail17Vector_componentsEEELj2EEEEENS8_9DataSpaceILj2EEE13MessageHeaderEENS2_5list4INS2_5valueIPS7_EENSP_ISJ_EENSP_ISL_EENSP_ISM_EEEEEEE3runEv+0xa9)[0x75c259]
[messi:51564] [ 8] /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_thread.so.1.63.0(+0x1340d)[0x7ffba672240d]
[messi:51564] [ 9] /lib64/libpthread.so.0(+0x7dc5)[0x7ffba8563dc5]
[messi:51564] [10] /lib64/libc.so.6(clone+0x6d)[0x7ffba41ef76d]
[messi:51564] *** End of error message ***
--------------------------------------------------------------------------
mpiexec noticed that process rank 0 with PID 0 on node messi exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec was unable to find the specified executable file, and therefore
did not launch the job.  This error was first reported for process
rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpiexec command
      line parameter option (remember that mpiexec interprets the first
      unrecognized command line token as the executable).

Node:       messi
Executable: 1
--------------------------------------------------------------------------
32 total processes failed to start
[81i61029@messi myLWFA]$

Thank you.

8i161029 on 25 Sep 2017

Can you just try the mpirun template (tpl) instead?

ax3l on 25 Sep 2017

ok, here is the output of tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpirun.tpl $HOME/runs/lwfa_004 :

[81i61029@messi myLWFA]$ tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpirun.tpl $HOME/runs/lwfa_004
Running program...
 Data for JOB [20691,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
        Process OMPI jobid: [20691,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../                                                          ../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
 Data for JOB [22385,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
        Process OMPI jobid: [22385,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../                                                          ../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | Sliding Window is OFF
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | Courant c*dt <= 1.00229 ? 1
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | species e: omega_p * dt <= 0.1 ? 0.0247974
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | y-cells per wavelength: 18.0587
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | macro particles per gpu: 8388608
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | typical macro particle weighting: 6955.06
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_SPEED 2.99792e+08
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_TIME 1.39e-16
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_LENGTH 4.16712e-08
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_MASS 6.33563e-27
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_CHARGE 1.11432e-15
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_EFIELD 1.22627e+13
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_BFIELD 40903.8
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_ENERGY 5.69418e-10
[1,0]<stdout>:initialization time: 15sec 976msec = 15 sec
[1,0]<stdout>:  0 % =        0 | time elapsed:            29sec 472msec | avg time per step:   0msec
[1,0]<stdout>:[messi:58378] *** Process received signal ***
[1,0]<stdout>:[messi:58378] Signal: Segmentation fault (11)
[1,0]<stdout>:[messi:58378] Signal code:  (128)
[1,0]<stdout>:[messi:58378] Failing at address: (nil)
[1,0]<stdout>:[messi:58378] [ 0] [1,0]<stdout>:/lib64/libpthread.so.0(+0xf370[1,0]<stdout>:)[0x7fa051d53370]
[1,0]<stdout>:[messi:58378] [1,0]<stdout>:[ 1] /lib64/libboost_filesystem-mt.so.1.53.0([1,0]<stdout>:+0xe22b)[1,0]<stdout>:[0x7fa05111722b]
[1,0]<stdout>:[messi:58378] [1,0]<stdout>:[ 2] /lib64/libboost_filesystem-mt.so.1.53.0(_ZNK5boost10filesystem4path17m_parent_path_endEv[1,0]<stdout>:+0x15)[0x7fa0511176a5[1,0]<stdout>:]
[1,0]<stdout>:[messi:58378] [ 3] [1,0]<stdout>:/lib64/libboost_filesystem-mt.so.1.53.0(_ZNK5boost10filesystem4path11parent_pathEv[1,0]<stdout>:+0x2c)[0x7fa05111923c[1,0]<stdout>:]
[1,0]<stdout>:[messi:58378] [ 4] [1,0]<stdout>:/lib64/libboost_filesystem-mt.so.1.53.0(_ZN5boost10filesystem6detail18create_directoriesERKNS0_4pathEPNS_6system10error_codeE+0x5d)[0x[1,0]<stdout>:7fa05111348d]
[1,0]<stdout>:[messi:58378] [1,0]<stdout>:[ 5] [1,0]<stdout>:/home/81i61029/runs/lwfa_004/picongpu/bin/picongpu(_ZNK5PMacc10FilesystemILj3EE30createDirectoryWithPermissionsENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[1,0]<stdout>:+0x69)[0x[1,0]<stdout>:68a109]
[1,0]<stdout>:[messi:58378] [ 6] [1,0]<stdout>:/home/81i61029/runs/lwfa_004/picongpu/bin/picongpu(_ZN8picongpu10PngCreator11createImageIN5PMacc7DataBoxINS2_10PitchedBoxINS2_4math6VectorIfLi3ENS5_16StandardAccessorENS5_17StandardNavigatorENS5_6detail17Vector_componentsEEELj2EEEEEEEvT_NS2_9DataSpaceILj2EEE13MessageHeader[1,0]<stdout>:+0x848)[0x695338]
[1,0]<stdout>:[messi:58378] [ 7] [1,0]<stdout>:/home/81i61029/runs/lwfa_004/picongpu/bin/picongpu(_ZN5boost6detail11thread_dataINS_3_bi6bind_tIvNS_4_mfi3mf3IvN8picongpu10PngCreatorEN5PMacc7DataBoxINS8_10PitchedBoxINS8_4math6VectorIfLi3ENSB_16StandardAccessorENSB_17StandardNavigatorENSB_6detail17Vector_componentsEEELj2EEEEENS8_9DataSpaceILj2EEE13MessageHeaderEENS2_5list4INS2_5valueIPS7_EENSP_ISJ_EENSP_ISL_EENSP_ISM_EEEEEEE3runEv[1,0]<stdout>:+0xa9)[0x[1,0]<stdout>:75c259]
[1,0]<stdout>:[messi:58378] [1,0]<stdout>:[ 8] [1,0]<stdout>:/home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_thread.so.1.63.0(+0x[1,0]<stdout>:1340d)[0x7fa04ff0a40d]
[1,0]<stdout>:[messi:58378] [ 9] /lib64/libpthread.so.0([1,0]<stdout>:+0x7dc5)[0x[1,0]<stdout>:7fa051d4bdc5]
[1,0]<stdout>:[messi:58378] [1,0]<stdout>:[10] [1,0]<stdout>:/lib64/libc.so.6(clone+0x[1,0]<stdout>:6d)[0x7fa04d9d776d[1,0]<stdout>:]
[1,0]<stdout>:[messi:58378] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node messi exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[22351,1],0]
  Exit code:    1
--------------------------------------------------------------------------
[81i61029@messi myLWFA]$

Does the program still link to wrong libraries in /lib64?
Is it make the program fail?
Thank you.

8i161029 on 25 Sep 2017

the mpirun template seems to work for you.

looking at your previous output of ldd: did you re-compile after you changed the cmake files?

ax3l on 25 Sep 2017

Yes, I configured and installed the example again after I changed src/picongpu/CMakeLists.txt and thirdParty/cmake-modules/FindmallocMC.cmake.

8i161029 on 25 Sep 2017

All right, then let us add the option described here, too - so we exclude the multithreaded libs that are installed in the system paths.

set(Boost_USE_MULTITHREADED OFF)

before the line

find_package(Boost # ....

I currently can't spot where they are pulled in from.

ax3l on 25 Sep 2017

It's fine. You can put aside my problem if you are busy.
I am very thankful for your help.
Environment of this machine is so complicated...

8i161029 on 25 Sep 2017

Did adding set(Boost_USE_MULTITHREADED OFF) and re-compiling change anything? (ldd output, tbg execution).

ax3l on 25 Sep 2017

Uh, can you please also add 1.57.0 to the find_package call in src/mpiInfo/CMakeLists.txt ?

ax3l on 25 Sep 2017

I add 1.57.0 in here:

################################################################################
# Find Boost
################################################################################

find_package(Boost 1.57.0 REQUIRED COMPONENTS program_options)
include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
set(LIBS ${LIBS} ${Boost_LIBRARIES})

Then configured and installed.
Here is the output of ldd:

[81i61029@messi myLWFA]$ ldd bin/picongpu
        linux-vdso.so.1 =>  (0x00007ffd3e39d000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f052a2c1000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f052a0bd000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f0529eb5000)
        libmpi.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so.20 (0x00007f0529ab7000)
        libmpi_cxx.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so.20 (0x00007f052989c000)
        libboost_filesystem-mt.so.1.53.0 => /lib64/libboost_filesystem-mt.so.1.53.0 (0x00007f0529685000)
        libboost_system-mt.so.1.53.0 => /lib64/libboost_system-mt.so.1.53.0 (0x00007f0529480000)
        libboost_math_tr1-mt.so.1.53.0 => /lib64/libboost_math_tr1-mt.so.1.53.0 (0x00007f0529242000)
        libz.so.1 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so.1 (0x00007f0529024000)
        libboost_program_options.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so.1.63.0 (0x00007f0528da1000)
        libboost_regex.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_regex.so.1.63.0 (0x00007f0528ab5000)
        libboost_filesystem.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_filesystem.so.1.63.0 (0x00007f052889b000)
        libboost_system.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_system.so.1.63.0 (0x00007f0528697000)
        libboost_thread.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_thread.so.1.63.0 (0x00007f052846f000)
        libboost_math_tr1.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_math_tr1.so.1.63.0 (0x00007f0528222000)
        libboost_serialization.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_serialization.so.1.63.0 (0x00007f0527fe1000)
        libhdf5.so.101 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so.101 (0x00007f0527a02000)
        libpngwriter.so => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/lib/libpngwriter.so (0x00007f05277e7000)
        libpng15.so.15 => /lib64/libpng15.so.15 (0x00007f05275bc000)
        libfreetype.so.6 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so.6 (0x00007f05272e6000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f0526fe3000)
        libboost_chrono.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_chrono.so.1.63.0 (0x00007f0526ddc000)
        libboost_date_time.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_date_time.so.1.63.0 (0x00007f0526bca000)
        libboost_atomic.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_atomic.so.1.63.0 (0x00007f05269c8000)
        libstdc++.so.6 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libstdc++.so.6 (0x00007f052664e000)
        libgomp.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libgomp.so.1 (0x00007f052642b000)
        libgcc_s.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libgcc_s.so.1 (0x00007f0526214000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f0525e53000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f052a500000)
        libopen-rte.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libopen-rte.so.20 (0x00007f0525b55000)
        libopen-pal.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libopen-pal.so.20 (0x00007f0525810000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00007f052560d000)
        libhwloc.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hwloc-1.11.7-znn4k7zfj4x2jizkhs5q7ysifffjd33p/lib/libhwloc.so.5 (0x00007f05253c2000)
        libpciaccess.so.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpciaccess-0.13.5-nqj66marqppz7b6cqk3lj7lhgtyr6ysm/lib/libpciaccess.so.0 (0x00007f05251b7000)
        libxml2.so.2 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libxml2-2.9.4-jj3guvl5civei5atlkimcrjg6ctpukc6/lib/libxml2.so.2 (0x00007f0524dee000)
        liblzma.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/xz-5.2.3-ehlxwhosxgdfbduwx3nk5zzxmo4qhmaq/lib/liblzma.so.5 (0x00007f0524bba000)
        libpng16.so.16 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16 (0x00007f0524977000)
        libbz2.so.1.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/bzip2-1.0.6-egkg2fbrcljkai2d23pgrq7wzeg2k5p5/lib/libbz2.so.1.0 (0x00007f0524766000)
[81i61029@messi myLWFA]$

I think it is still the same...

8i161029 on 25 Sep 2017

thanks, let's change it further to

find_package(Boost 1.57.0 REQUIRED COMPONENTS program_options)
if(TARGET Boost::boost)
    set(LIBS ${LIBS} Boost::boost Boost::program_options)
else()
    include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
    set(LIBS ${LIBS} ${Boost_LIBRARIES})
endif()

ax3l on 25 Sep 2017

Is it I need to change this block

################################################################################
# Find Boost
################################################################################

find_package(Boost 1.57.0 REQUIRED COMPONENTS program_options)
message(STATUS "BOOST INCLUDE++++: ${Boost_INCLUDE_DIRS}")
message(STATUS "BOOST LIBS++++: ${Boost_LIBRARIES}")
set(LIBS ${LIBS} Boost::program_options)

to

################################################################################
# Find Boost
################################################################################

find_package(Boost 1.57.0 REQUIRED COMPONENTS program_options)
if(TARGET Boost::boost)
    set(LIBS ${LIBS} Boost::boost Boost::program_options)
else()
    include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
    set(LIBS ${LIBS} ${Boost_LIBRARIES})
endif()

right? Thank you.

8i161029 on 25 Sep 2017

I changed src/mpiInfo/CMakeLists.txt as above.
and recompiled, here is the ldd output:

[81i61029@messi myLWFA]$ ldd bin/picongpu
        linux-vdso.so.1 =>  (0x00007fff7073a000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007faa5f7e7000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007faa5f5e3000)
        librt.so.1 => /lib64/librt.so.1 (0x00007faa5f3db000)
        libmpi.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so.20 (0x00007faa5efdd000)
        libmpi_cxx.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so.20 (0x00007faa5edc2000)
        libboost_filesystem-mt.so.1.53.0 => /lib64/libboost_filesystem-mt.so.1.53.0 (0x00007faa5ebab000)
        libboost_system-mt.so.1.53.0 => /lib64/libboost_system-mt.so.1.53.0 (0x00007faa5e9a6000)
        libboost_math_tr1-mt.so.1.53.0 => /lib64/libboost_math_tr1-mt.so.1.53.0 (0x00007faa5e768000)
        libz.so.1 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so.1 (0x00007faa5e54a000)
        libboost_program_options.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so.1.63.0 (0x00007faa5e2c7000)
        libboost_regex.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_regex.so.1.63.0 (0x00007faa5dfdb000)
        libboost_filesystem.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_filesystem.so.1.63.0 (0x00007faa5ddc1000)
        libboost_system.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_system.so.1.63.0 (0x00007faa5dbbd000)
        libboost_thread.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_thread.so.1.63.0 (0x00007faa5d995000)
        libboost_math_tr1.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_math_tr1.so.1.63.0 (0x00007faa5d748000)
        libboost_serialization.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_serialization.so.1.63.0 (0x00007faa5d507000)
        libhdf5.so.101 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so.101 (0x00007faa5cf28000)
        libpngwriter.so => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/lib/libpngwriter.so (0x00007faa5cd0d000)
        libpng15.so.15 => /lib64/libpng15.so.15 (0x00007faa5cae2000)
        libfreetype.so.6 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so.6 (0x00007faa5c80c000)
        libm.so.6 => /lib64/libm.so.6 (0x00007faa5c509000)
        libboost_chrono.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_chrono.so.1.63.0 (0x00007faa5c302000)
        libboost_date_time.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_date_time.so.1.63.0 (0x00007faa5c0f0000)
        libboost_atomic.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_atomic.so.1.63.0 (0x00007faa5beee000)
        libstdc++.so.6 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libstdc++.so.6 (0x00007faa5bb74000)
        libgomp.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libgomp.so.1 (0x00007faa5b951000)
        libgcc_s.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libgcc_s.so.1 (0x00007faa5b73a000)
        libc.so.6 => /lib64/libc.so.6 (0x00007faa5b379000)
        /lib64/ld-linux-x86-64.so.2 (0x00007faa5fa26000)
        libopen-rte.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libopen-rte.so.20 (0x00007faa5b07b000)
        libopen-pal.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libopen-pal.so.20 (0x00007faa5ad36000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00007faa5ab33000)
        libhwloc.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hwloc-1.11.7-znn4k7zfj4x2jizkhs5q7ysifffjd33p/lib/libhwloc.so.5 (0x00007faa5a8e8000)
        libpciaccess.so.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpciaccess-0.13.5-nqj66marqppz7b6cqk3lj7lhgtyr6ysm/lib/libpciaccess.so.0 (0x00007faa5a6dd000)
        libxml2.so.2 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libxml2-2.9.4-jj3guvl5civei5atlkimcrjg6ctpukc6/lib/libxml2.so.2 (0x00007faa5a314000)
        liblzma.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/xz-5.2.3-ehlxwhosxgdfbduwx3nk5zzxmo4qhmaq/lib/liblzma.so.5 (0x00007faa5a0e0000)
        libpng16.so.16 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16 (0x00007faa59e9d000)
        libbz2.so.1.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/bzip2-1.0.6-egkg2fbrcljkai2d23pgrq7wzeg2k5p5/lib/libbz2.so.1.0 (0x00007faa59c8c000)
[81i61029@messi myLWFA]$

There are still some wrong libraries, so weird...

8i161029 on 25 Sep 2017

Let's try to avoid the sytem paths with -DBoost_NO_SYSTEM_PATHS=ON in CMake.

At the place where you already have your Boost_USE_MULTITHREADED add:

set(Boost_NO_SYSTEM_PATHS ON)

in src/picongpu/CMakeLists.txt

ax3l on 5 Oct 2017

You can also add this during pic-configure via:

$PICSRC/configure -c"-DCMAKE_DISABLE_FIND_PACKAGE_PNGwriter=TRUE -DBoost_NO_SYSTEM_PATHS=ON" ~/paramSets/case001

ax3l on 5 Oct 2017

Thank you!

I add set(Boost_NO_SYSTEM_PATHS ON) in here in src/picongpu/CMakeLists.txt:

################################################################################
# Find Boost
################################################################################

set(Boost_USE_MULTITHREADED OFF)

set(Boost_NO_SYSTEM_PATHS ON)

find_package(Boost 1.57.0 REQUIRED COMPONENTS program_options regex filesystem
                                              system thread math_tr1
                                              serialization)
message(STATUS "BOOST INCLUDE++++: ${Boost_INCLUDE_DIRS}")
message(STATUS "BOOST LIBS++++: ${Boost_LIBRARIES}")
set(LIBS ${LIBS} Boost::boost Boost::program_options Boost::regex Boost::filesystem Boost::system Boost::thread Boost::math_tr1 Boost::serialization)

################################################################################

Then configured with this command:

pic-configure -c"-DCMAKE_DISABLE_FIND_PACKAGE_PNGwriter=TRUE -DBoost_NO_SYSTEM_PATHS=ON"  $HOME/picInputs/myLWFA

But there are still some libraries of boost-1.53.0 in output of ldd bin/picongpu:

[81i61029@messi myLWFA]$ ldd bin/picongpu
        linux-vdso.so.1 =>  (0x00007ffe5b5d1000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f095cded000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f095cbe9000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f095c9e1000)
        libmpi.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7                                                          jukee/lib/libmpi.so.20 (0x00007f095c5e3000)
        libmpi_cxx.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23as                                                          lgt7jukee/lib/libmpi_cxx.so.20 (0x00007f095c3c8000)
        libboost_filesystem-mt.so.1.53.0 => /lib64/libboost_filesystem-mt.so.1.53.0 (0x00007f095c1b1000)
        libboost_system-mt.so.1.53.0 => /lib64/libboost_system-mt.so.1.53.0 (0x00007f095bfac000)
        libboost_math_tr1-mt.so.1.53.0 => /lib64/libboost_math_tr1-mt.so.1.53.0 (0x00007f095bd6e000)
        libz.so.1 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6                                                          /lib/libz.so.1 (0x00007f095bb50000)
        libboost_program_options.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mk                                                          p6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so.1.63.0 (0x00007f095b8cd000)
        libboost_regex.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2                                                          asfnoat7oordwxtq/lib/libboost_regex.so.1.63.0 (0x00007f095b5e1000)
        libboost_filesystem.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5s                                                          zuac2asfnoat7oordwxtq/lib/libboost_filesystem.so.1.63.0 (0x00007f095b3c7000)
        libboost_system.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac                                                          2asfnoat7oordwxtq/lib/libboost_system.so.1.63.0 (0x00007f095b1c3000)
        libboost_thread.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac                                                          2asfnoat7oordwxtq/lib/libboost_thread.so.1.63.0 (0x00007f095af9b000)
        libboost_math_tr1.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szu                                                          ac2asfnoat7oordwxtq/lib/libboost_math_tr1.so.1.63.0 (0x00007f095ad4e000)
        libboost_serialization.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6                                                          l5szuac2asfnoat7oordwxtq/lib/libboost_serialization.so.1.63.0 (0x00007f095ab0d000)
        libhdf5.so.101 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkv                                                          tmn2p/lib/libhdf5.so.101 (0x00007f095a52e000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f095a22c000)
        libboost_chrono.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac                                                          2asfnoat7oordwxtq/lib/libboost_chrono.so.1.63.0 (0x00007f095a024000)
        libboost_date_time.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5sz                                                          uac2asfnoat7oordwxtq/lib/libboost_date_time.so.1.63.0 (0x00007f0959e13000)
        libboost_atomic.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac                                                          2asfnoat7oordwxtq/lib/libboost_atomic.so.1.63.0 (0x00007f0959c10000)
        libstdc++.so.6 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcacl                                                          giko7zdjurr/lib64/libstdc++.so.6 (0x00007f0959896000)
        libgomp.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgi                                                          ko7zdjurr/lib64/libgomp.so.1 (0x00007f0959673000)
        libgcc_s.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclg                                                          iko7zdjurr/lib64/libgcc_s.so.1 (0x00007f095945c000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f095909b000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f095d02c000)
        libopen-rte.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23a                                                          slgt7jukee/lib/libopen-rte.so.20 (0x00007f0958d9d000)
        libopen-pal.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23a                                                          slgt7jukee/lib/libopen-pal.so.20 (0x00007f0958a58000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00007f0958855000)
        libhwloc.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hwloc-1.11.7-znn4k7zfj4x2jizkhs5q7ysifff                                                          jd33p/lib/libhwloc.so.5 (0x00007f095860a000)
        libpciaccess.so.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpciaccess-0.13.5-nqj66marqppz7b6c                                                          qk3lj7lhgtyr6ysm/lib/libpciaccess.so.0 (0x00007f09583ff000)
        libxml2.so.2 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libxml2-2.9.4-jj3guvl5civei5atlkimcrjg6ct                                                          pukc6/lib/libxml2.so.2 (0x00007f0958036000)
        liblzma.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/xz-5.2.3-ehlxwhosxgdfbduwx3nk5zzxmo4qhmaq                                                          /lib/liblzma.so.5 (0x00007f0957e02000)

Did I add at a wrong place?
And do I need to add something in src/mpiInfo/CMakeLists.txt?
Thank you!

8i161029 on 5 Oct 2017

You did it all right, sorry for that.

Can you make sure your Boost section in src/libPMacc/PMaccConfig.cmake also reads:

find_package(Boost 1.62.0 REQUIRED COMPONENTS filesystem system math_tr1)
if(TARGET Boost::filesystem)
     set(PMacc_LIBRARIES ${PMacc_LIBRARIES} Boost::boost Boost::filesystem
                                            Boost::system Boost::math_tr1)
else()
     set(PMacc_INCLUDE_DIRS ${PMacc_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS})
     set(PMacc_LIBRARIES ${PMacc_LIBRARIES} ${Boost_LIBRARIES})
endif()

It has the combination of components that might be pulled in wrongly.

ax3l on 6 Oct 2017

Thank you!
Here is that section in src/libPMacc/PMaccConfig.cmake:

################################################################################
# Find Boost
################################################################################

find_package(Boost 1.57.0 REQUIRED COMPONENTS filesystem system math_tr1)
set(PMacc_INCLUDE_DIRS ${PMacc_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS})
set(PMacc_LIBRARIES ${PMacc_LIBRARIES} ${Boost_LIBRARIES})

# Boost 1.55 added support for a define that makes result_of look for
# the result<> template and falls back to decltype if none is found. This is
# great for the transition from the "wrong" usage to the "correct" one as
set(PMacc_DEFINITIONS ${PMacc_DEFINITIONS} -DBOOST_RESULT_OF_USE_TR1_WITH_DECLTYPE_FALLBACK)

# Boost >= 1.60.0 and CUDA != 7.5 failed when used with C++11
# seen with boost 1.60.0 - 1.62.0 (atm latest) and CUDA 7.0, 8.0 (atm latest)
# CUDA 7.5 works without a workaround
if( (Boost_VERSION GREATER 105999) AND
    (NOT CUDA_VERSION VERSION_EQUAL 7.5) )
    # Boost Bug https://svn.boost.org/trac/boost/ticket/11897
    message(STATUS "Boost: Disable template aliases")
    set(PMacc_DEFINITIONS ${PMacc_DEFINITIONS} -DBOOST_NO_CXX11_TEMPLATE_ALIASES)
endif()

if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_NO_VARIADIC_TEMPLATES")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_NO_CXX11_VARIADIC_TEMPLATES")
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_NO_FENV_H")
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
    # suppress boost error
    # 'no member named "impl" in "boost::detail::thread_move_t<boost::detail::nullary_function<void ()> >"'
    # in 'boost/thread/detail/nullary_function.hpp'
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_NO_CXX11_SMART_PTR")
endif()

# Boost 1.64.0 is broken with CUDA 8.0 (nvcc) and C++11
#   https://github.com/ComputationalRadiationPhysics/picongpu/issues/2048
#   fixed in CUDA 9.0 (ticket 1928813)
if( ("${PMACC_CUDA_COMPILER}" STREQUAL "nvcc") AND
    (Boost_VERSION EQUAL 106400) AND
    (CUDA_VERSION VERSION_EQUAL 8.0) )
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_NO_CXX11_NOEXCEPT")
endif()

Is it I need to change the first three lines to this?

find_package(Boost 1.62.0 REQUIRED COMPONENTS filesystem system math_tr1)
if(TARGET Boost::filesystem)
     set(PMacc_LIBRARIES ${PMacc_LIBRARIES} Boost::boost Boost::filesystem
                                            Boost::system Boost::math_tr1)
else()
     set(PMacc_INCLUDE_DIRS ${PMacc_INCLUDE_DIRS} ${Boost_INCLUDE_DIRS})
     set(PMacc_LIBRARIES ${PMacc_LIBRARIES} ${Boost_LIBRARIES})
endif()

Boost version in this system is 1.63.0.
Thank you.

8i161029 on 6 Oct 2017

Is it I need to change the first three lines to this?

yes, the first three lines need to be replaced :)

ax3l on 6 Oct 2017

Thank you!
Here is the output of ldd after replaced those lines:

[81i61029@messi myLWFA]$ ldd bin/picongpu
        linux-vdso.so.1 =>  (0x00007ffc12bce000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f4251b63000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f425195f000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f4251757000)
        libmpi.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi.so.20 (0x00007f4251359000)
        libmpi_cxx.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libmpi_cxx.so.20 (0x00007f425113e000)
        libboost_filesystem.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_filesystem.so.1.63.0 (0x00007f4250f24000)
        libboost_system.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_system.so.1.63.0 (0x00007f4250d20000)
        libboost_math_tr1.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_math_tr1.so.1.63.0 (0x00007f4250ad2000)
        libz.so.1 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/zlib-1.2.11-ec535e2ikkpl7hd4y454t3yydjqorja6/lib/libz.so.1 (0x00007f42508b4000)
        libboost_program_options.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_program_options.so.1.63.0 (0x00007f4250631000)
        libboost_regex.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_regex.so.1.63.0 (0x00007f4250345000)
        libboost_thread.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_thread.so.1.63.0 (0x00007f425011d000)
        libboost_serialization.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_serialization.so.1.63.0 (0x00007f424fedd000)
        libhdf5.so.101 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hdf5-1.10.1-qqufijyfulmm6fg67htzfxubkkvtmn2p/lib/libhdf5.so.101 (0x00007f424f8fd000)
        libpngwriter.so => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/pngwriter-0.6.0-aa6low7xf7cpmmdc6kptjpv5jmvsuwi2/lib/libpngwriter.so (0x00007f424f6e3000)
        libpng15.so.15 => /lib64/libpng15.so.15 (0x00007f424f4b8000)
        libfreetype.so.6 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/freetype-2.7.1-p3vfcosafs2w3ziksjhwgzgc66uya2nu/lib/libfreetype.so.6 (0x00007f424f1e1000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f424eedf000)
        libboost_chrono.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_chrono.so.1.63.0 (0x00007f424ecd7000)
        libboost_date_time.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_date_time.so.1.63.0 (0x00007f424eac6000)
        libboost_atomic.so.1.63.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/boost-1.63.0-4sy7mkp6l5szuac2asfnoat7oordwxtq/lib/libboost_atomic.so.1.63.0 (0x00007f424e8c4000)
        libstdc++.so.6 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libstdc++.so.6 (0x00007f424e549000)
        libgomp.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libgomp.so.1 (0x00007f424e327000)
        libgcc_s.so.1 => /home/81i61029/spack-tools/spack/opt/spack/linux-centos7-x86_64/gcc-4.4.7/gcc-5.4.0-32u3h5tpy7z5xpznwcaclgiko7zdjurr/lib64/libgcc_s.so.1 (0x00007f424e10f000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f424dd4e000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f4251da2000)
        libopen-rte.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libopen-rte.so.20 (0x00007f424da51000)
        libopen-pal.so.20 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/openmpi-2.1.1-nyahmy4og22jb6xzbmb23aslgt7jukee/lib/libopen-pal.so.20 (0x00007f424d70c000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00007f424d508000)
        libhwloc.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/hwloc-1.11.7-znn4k7zfj4x2jizkhs5q7ysifffjd33p/lib/libhwloc.so.5 (0x00007f424d2be000)
        libpciaccess.so.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpciaccess-0.13.5-nqj66marqppz7b6cqk3lj7lhgtyr6ysm/lib/libpciaccess.so.0 (0x00007f424d0b2000)
        libxml2.so.2 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libxml2-2.9.4-jj3guvl5civei5atlkimcrjg6ctpukc6/lib/libxml2.so.2 (0x00007f424ccea000)
        liblzma.so.5 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/xz-5.2.3-ehlxwhosxgdfbduwx3nk5zzxmo4qhmaq/lib/liblzma.so.5 (0x00007f424cab6000)
        libpng16.so.16 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/libpng-1.6.29-66se2vm7alaemgyac4h7qy5n2zhow7bu/lib/libpng16.so.16 (0x00007f424c873000)
        libbz2.so.1.0 => /home/81i61029/lib/spack/opt/spack/linux-centos7-x86_64/gcc-5.4.0/bzip2-1.0.6-egkg2fbrcljkai2d23pgrq7wzeg2k5p5/lib/libbz2.so.1.0 (0x00007f424c662000)

Boost-1.53.0 does not show up anymore in this output!
But there are still some libraries from /lib64.
Is it normal?

I configured with the original command:

pic-configure $HOME/picInputs/myLWFA

Thank you.

8i161029 on 6 Oct 2017

🎉1

I tried to run the example, here is the output:

[81i61029@messi myLWFA]$ tbg -s bash -c submit/0001gpus.cfg -t submit/bash/bash_mpirun.tpl $HOME/runs/lwfa_001
Running program...
 Data for JOB [43985,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
        Process OMPI jobid: [43985,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
 Data for JOB [43933,1] offset 0

 ========================   JOB MAP   ========================

 Data for node: messi   Num slots: 32   Max slots: 0    Num procs: 1
        Process OMPI jobid: [43933,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]]:[BB/../../../../../../../../../../../../../../..][../../../../../../../../../../../../../../../..]

 =============================================================
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | Sliding Window is OFF
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | Courant c*dt <= 1.00229 ? 1
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | species e: omega_p * dt <= 0.1 ? 0.0247974
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | y-cells per wavelength: 18.0587
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | macro particles per gpu: 8388608
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | typical macro particle weighting: 6955.06
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_SPEED 2.99792e+08
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_TIME 1.39e-16
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_LENGTH 4.16712e-08
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_MASS 6.33563e-27
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_CHARGE 1.11432e-15
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_EFIELD 1.22627e+13
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_BFIELD 40903.8
[1,0]<stdout>:PIConGPUVerbose PHYSICS(1) | UNIT_ENERGY 5.69418e-10
[1,0]<stdout>:initialization time: 33sec 503msec = 33 sec
[1,0]<stdout>:  0 % =        0 | time elapsed:            29sec 486msec | avg time per step:   0msec
[1,0]<stdout>:  4 % =       51 | time elapsed:            31sec 297msec | avg time per step:  35msec
[1,0]<stdout>:  9 % =      102 | time elapsed:            33sec 174msec | avg time per step:  36msec
[1,0]<stdout>: 14 % =      153 | time elapsed:            35sec 225msec | avg time per step:  40msec
[1,0]<stdout>: 19 % =      204 | time elapsed:            37sec 521msec | avg time per step:  44msec
[1,0]<stdout>: 24 % =      255 | time elapsed:            40sec 112msec | avg time per step:  50msec
[1,0]<stdout>: 29 % =      306 | time elapsed:            43sec  16msec | avg time per step:  56msec
[1,0]<stdout>: 34 % =      357 | time elapsed:            46sec 121msec | avg time per step:  60msec
[1,0]<stdout>: 39 % =      408 | time elapsed:            49sec 438msec | avg time per step:  64msec
[1,0]<stdout>: 44 % =      459 | time elapsed:            52sec 924msec | avg time per step:  68msec
[1,0]<stdout>: 49 % =      510 | time elapsed:            56sec 571msec | avg time per step:  71msec
[1,0]<stdout>: 54 % =      561 | time elapsed:       1min  0sec 353msec | avg time per step:  74msec
[1,0]<stdout>: 59 % =      612 | time elapsed:       1min  4sec 207msec | avg time per step:  75msec
[1,0]<stdout>: 64 % =      663 | time elapsed:       1min  8sec   5msec | avg time per step:  74msec
[1,0]<stdout>: 69 % =      714 | time elapsed:       1min 11sec 635msec | avg time per step:  70msec
[1,0]<stdout>: 74 % =      765 | time elapsed:       1min 15sec 183msec | avg time per step:  69msec
[1,0]<stdout>: 79 % =      816 | time elapsed:       1min 18sec 766msec | avg time per step:  70msec
[1,0]<stdout>: 84 % =      867 | time elapsed:       1min 22sec 329msec | avg time per step:  69msec
[1,0]<stdout>: 89 % =      918 | time elapsed:       1min 25sec 767msec | avg time per step:  67msec
[1,0]<stdout>: 94 % =      969 | time elapsed:       1min 29sec  77msec | avg time per step:  64msec
[1,0]<stdout>: 99 % =     1020 | time elapsed:       1min 32sec 386msec | avg time per step:  64msec
[1,0]<stdout>:calculation  simulation time:  1min 32sec 651msec = 92 sec
[1,0]<stdout>:full simulation time:  2min  6sec 384msec = 126 sec
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[43587,1],0]
  Exit code:    1
--------------------------------------------------------------------------

Does the program run successfully?
Are there any problems in MPI?
Thank you.

8i161029 on 6 Oct 2017

Hurray, success!
Everything just worked as expected! Yay! ✨ 🚀

The first mpi output on top is just from our --display-map and the last is from a call to killall for hanging processes in batch systems. You can actually remove that last line in submit/bash/bash_mpirun.tpl to get rid of it.

ax3l on 6 Oct 2017

Thank you! Finally!
May I ask a question just to confirm?
What does the last part in output mean:

Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[43587,1],0]
  Exit code:    1
--------------------------------------------------------------------------

I see the job has been aborted so I guess the program is failed. But it successes.
Why does the output show this?
Does it matter?
Thank you.

8i161029 on 6 Oct 2017

👍1

Those lines are confusing and signal that a second mpirun, that is called to clean up hanging processes, did not find any (aka: everything was ok). I just added a PR to fix that mess in #2295

You can just remove this line:
https://github.com/ComputationalRadiationPhysics/picongpu/blob/0.3.0/src/picongpu/submit/bash/bash_mpirun.tpl#L58

in submit/bash/bash_mpirun.tpl to get rid of it already.

ax3l on 6 Oct 2017

👍1

Wonderful, Thank you!
You are very patient,
from the beginning I tried to install PIConGPU in my own pc's ubuntu system
to the centOS system in the server in my lab, and from installation issue to how to run an example.
You teach me step by step, even a Linux beginner as I can finish it.
I am very grateful for your help.
I am excited that I can use PIConGPU from now on! :)

8i161029 on 6 Oct 2017

🎉1 👍1

Thank you, you are a very patient and fast learning user as well!

I used the chance to make our installs more robust and add more automation for the upcoming 0.4.0 release.

I am excited that I can use PIConGPU from now on! :)

We are as well! Enjoy! ✨

ax3l on 6 Oct 2017

🎉1

Hello, May I ask a question?
I want to dump data as hdf5, so I added this line in 0001gpus.cfg file:

TBG_hdf5="--hdf5.period 100 --hdf5.file simData"

But after recompiling and running the example again, I still couldn't find .h5 files in $HOME/runs/.../simoutput.
Is it the right method to dump data as hdf5?
Thank you.

8i161029 on 10 Oct 2017

You should find the files under simOutput/h5/ by default :)

ax3l on 11 Oct 2017

Thank you.
But I cannot find directory h5 in simOutput...

[81i61029@messi lwfa_003]$ cd simOutput
[81i61029@messi simOutput]$ ls
e_macroParticlesCount.dat  output  pngElectronsYX

8i161029 on 11 Oct 2017

This is my 0001gpus.cfg :

#################################
## Section: Required Variables ##
#################################

TBG_wallTime="1:00:00"

TBG_gpu_x=1
TBG_gpu_y=1
TBG_gpu_z=1

TBG_gridSize="-g 128 256 128"
TBG_steps="-s 1024"

#################################
## Section: Optional Variables ##
#################################

# Dump simulation data (fields and particles) to HDF5 files using libSplash.
# Data is dumped every .period steps to the fileset .file.
TBG_hdf5="--hdf5.period 100 --hdf5.file simData"

# png image output (electron density)
TBG_pngYX="--e_png.period 64 --e_png.axis yx --e_png.slicePoint 0.5 --e_png.folder pngElectronsYX"

TBG_plugins="!TBG_pngYX                    \
             --e_macroParticlesCount.period 100"


#################################
## Section: Program Parameters ##
#################################

TBG_devices="-d !TBG_gpu_x !TBG_gpu_y !TBG_gpu_z"

TBG_programParams="!TBG_devices      \
                   !TBG_gridSize     \
                   !TBG_steps        \
                   !TBG_plugins"

# TOTAL number of GPUs
TBG_tasks="$(( TBG_gpu_x * TBG_gpu_y * TBG_gpu_z ))"

"$TBG_cfgPath"/submitAction.sh

I only added this section

# Dump simulation data (fields and particles) to HDF5 files using libSplash.
# Data is dumped every .period steps to the fileset .file.
TBG_hdf5="--hdf5.period 100 --hdf5.file simData"

Do I need to add other sections?

8i161029 on 11 Oct 2017

👍1

Ah, I see.

The .cfg file is in principle a standard bash script. That means intermediate variables that you define need to be used.

In your example, you defined TBG_hdf5="..." but did not add it to the TBG_plugins list (which is then in turn used in the TBG_programParams which are passed to PIConGPU.

Just change:

TBG_plugins="!TBG_pngYX                    \
             --e_macroParticlesCount.period 100"

to

TBG_plugins="!TBG_pngYX                    \
             !TBG_hdf5                     \
             --e_macroParticlesCount.period 100"

to truly enable the HDF5 plugin :)

ax3l on 11 Oct 2017

of course you could also do directly

TBG_plugins="!TBG_pngYX                    \
             --hdf5.period 100 --hdf5.file simData \
             --e_macroParticlesCount.period 100"

but that is less well organized when a lot of plugins come into play ;-)

ax3l on 11 Oct 2017

I see. Thank you!
I have a question just to confirm,
Is changing .cfg file enough to dump data as hdf5?
Do I need to create a output.param?
Thank you.

8i161029 on 11 Oct 2017

Oh! I find h5 files!
Thank you very much!

8i161029 on 11 Oct 2017

🎉1

Picongpu: Having trouble configuring case001

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Here is the output:

a non-zero exit code.. Per user-direction, the job has been aborted.

Exit code: 1

a non-zero exit code.. Per user-direction, the job has been aborted.

Exit code: 1

> ./bin/picongpu: error while loading shared libraries: libmpi.so.20: cannot open shared object file: No such file or directory

a non-zero exit code.. Per user-direction, the job has been aborted.

Exit code: 127

cuda_memtest crash: see file /home/lai/runs/testBatch01/simOutput/cuda_memtest_lai-G56JR_.err

a non-zero exit code.. Per user-direction, the job has been aborted.

Exit code: 1

a non-zero exit code.. Per user-direction, the job has been aborted.

Exit code: 1

cuda_memtest crash: see file /home/lai/runs/testBatch01/simOutput/cuda_memtest_lai-G56JR_.err

a non-zero exit code.. Per user-direction, the job has been aborted.

Exit code: 1

a non-zero exit code.. Per user-direction, the job has been aborted.

Exit code: 1

Install Dependencies

Using PIConGPU

Boost issue

incase the module is still loaded

... yes ...

Boost Problem

Related issues