Openpmd-api: Problem with installing new openPMD-api-dev version

[KseniaBastrakova]

Describe the bug
Where I tried to install openPMD-api from pip installing via pip install git+https://github.com/openPMD/openPMD-api.git@dev or from source, I got the error:

Linking CXX shared library ../lib.linux-x86_64-3.6/libopenPMD.ADIOS1.Serial.so
/usr/bin/ld: /usr/local/lib/libadios_nompi.a(libadios_nompi_a-adios.o): relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC

To Reproduce

pip install git+https://github.com/openPMD/openPMD-api.git@dev

Software Environment
I use lastest pip 19.1.1, ADIOS 1.13.1, and latest openPMD-api-dev (d0fa923)

[ax3l]

Hi Ksenia,

thank you for the report!
How did you install ADIOS1? Looks to me like it lacks the -fPIC flag. This is how you need to install ADIOS1 if you build it from source: install example

[KseniaBastrakova]

Thanks, Axel
yes, I have installed ADIOS1. at least everything worked with my previous version openPMD-api(d68e9fc2) maybe, I should reinstall ADIOS1 and it will be helpful?

[ax3l]

Yes, if you installed ADIOS1 yourself make sure to add -fPIC to the configuration step as linked above:

curl -Lo adios-1.13.1.tar.gz http://users.nccs.gov/~pnorbert/adios-1.13.1.tar.gz
tar -xzf adios-1.13.1.tar.gz
cd adios-1.13.1
CFLAGS="-fPIC" ./configure --enable-static --enable-shared --prefix=$HOME/sw/adios \
  --with-mpi=$MPI_ROOT --with-zlib=$HOME/sw/zlib --with-blosc=$HOME/sw/c-blosc
make
make install

# note: assumes you set MPI_ROOT and installed zlib and c-blosc in $HOME/sw first

Environment hints after install:

export ADIOS_ROOT=$HOME/sw/adios
export PATH=$ADIOS_ROOT/bin:$PATH
export LD_LIBRARY_PATH=$ADIOS_ROOT/lib:$LD_LIBRARY_PATH

[ax3l]

Hi Ksenia,

I just released a 0.10.2-alpha release #637 that also contains the fix from #635 to aide you.
You can just install the pre-compiled python wheel as usual via

python3 -m pip install --upgrade openpmd-api

that contains the ADIOS1 backend (and HDF5 and ADIOS2) compiled-in :)

[KseniaBastrakova]

Hi, Axel, new release helped me, now I installed openPMD-api successfuly, thank you.

[ax3l]

Awesome, please do not hesitate to tell how this works for you with regards to the read issue you experienced earlier.