Incubator-mxnet: Failed to build mxnet from source

[shroudie]

Description

Hello all, I was trying to build mxnet from source (for tensorrt support), but errors occurred during build process.

Error Message

Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_4bef8 && [1/2] Building C object CMakeFiles/cmTC_4bef8.dir/src.c.o
[2/2] Linking C executable cmTC_4bef8
FAILED: cmTC_4bef8
: && /usr/bin/cc -Wall -Wno-sign-compare -O3 -DCMAKE_HAVE_LIBC_PTHREAD CMakeFiles/cmTC_4bef8.dir/src.c.o -o cmTC_4bef8 && :
CMakeFiles/cmTC_4bef8.dir/src.c.o: In function main': src.c:(.text.startup+0x23): undefined reference topthread_create'
src.c:(.text.startup+0x2c): undefined reference to pthread_detach' src.c:(.text.startup+0x35): undefined reference topthread_cancel'
src.c:(.text.startup+0x40): undefined reference to pthread_join' src.c:(.text.startup+0x4b): undefined reference topthread_atfork'
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.

Source file was:

include

void* test_func(void* data)
{
return data;
}

int main(void)
{
pthread_t thread;
pthread_create(&thread, NULL, test_func, NULL);
pthread_detach(thread);
pthread_cancel(thread);
pthread_join(thread, NULL);
pthread_atfork(NULL, NULL, NULL);
pthread_exit(NULL);

return 0;
}

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_3f333 && [1/2] Building C object CMakeFiles/cmTC_3f333.dir/CheckFunctionExists.c.o
[2/2] Linking C executable cmTC_3f333
FAILED: cmTC_3f333
: && /usr/bin/cc -Wall -Wno-sign-compare -O3 -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTC_3f333.dir/CheckFunctionExists.c.o -o cmTC_3f333 -lpthreads && :
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.

Determining if the OPENBLAS_USE64BITINT exist failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_d0797 && [1/2] Building C object CMakeFiles/cmTC_d0797.dir/CheckSymbolExists.c.o
FAILED: CMakeFiles/cmTC_d0797.dir/CheckSymbolExists.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -fPIE -o CMakeFiles/cmTC_d0797.dir/CheckSymbolExists.c.o -c CheckSymbolExists.c
CheckSymbolExists.c: In function ‘main’:
CheckSymbolExists.c:8:19: error: ‘OPENBLAS_USE64BITINT’ undeclared (first use in this function); did you mean ‘OPENBLAS___64BIT__’?
return ((int*)(&OPENBLAS_USE64BITINT))[argc];
^~~~~~~~
OPENBLAS___64BIT__
CheckSymbolExists.c:8:19: note: each undeclared identifier is reported only once for each function it appears in
ninja: build stopped: subcommand failed.

File /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */

include

int main(int argc, char** argv)
{
(void)argv;

ifndef OPENBLAS_USE64BITINT

return ((int*)(&OPENBLAS_USE64BITINT))[argc];

else

(void)argc;
return 0;

endif

}
Performing C SOURCE FILE Test LIBOMP_HAVE_WNO_UNUSED_LOCAL_TYPEDEF_FLAG failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_df535 && [1/2] Building C object CMakeFiles/cmTC_df535.dir/src.c.o
FAILED: CMakeFiles/cmTC_df535.dir/src.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -DLIBOMP_HAVE_WNO_UNUSED_LOCAL_TYPEDEF_FLAG -fPIE -Wunused-local-typedef -o CMakeFiles/cmTC_df535.dir/src.c.o -c src.c
cc: error: unrecognized command line option '-Wunused-local-typedef'; did you mean '-Wunused-local-typedefs'?
ninja: build stopped: subcommand failed.

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test LIBOMP_HAVE_WNO_COVERED_SWITCH_DEFAULT_FLAG failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_9e84d && [1/2] Building C object CMakeFiles/cmTC_9e84d.dir/src.c.o
FAILED: CMakeFiles/cmTC_9e84d.dir/src.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -DLIBOMP_HAVE_WNO_COVERED_SWITCH_DEFAULT_FLAG -fPIE -Wcovered-switch-default -o CMakeFiles/cmTC_9e84d.dir/src.c.o -c src.c
cc: error: unrecognized command line option '-Wcovered-switch-default'; did you mean '-Wno-switch-default'?
ninja: build stopped: subcommand failed.

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test LIBOMP_HAVE_WNO_DEPRECATED_REGISTER_FLAG failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_507ea && [1/2] Building C object CMakeFiles/cmTC_507ea.dir/src.c.o
FAILED: CMakeFiles/cmTC_507ea.dir/src.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -DLIBOMP_HAVE_WNO_DEPRECATED_REGISTER_FLAG -fPIE -Wdeprecated-register -o CMakeFiles/cmTC_507ea.dir/src.c.o -c src.c
cc: error: unrecognized command line option '-Wdeprecated-register'; did you mean '-frename-registers'?
ninja: build stopped: subcommand failed.

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test LIBOMP_HAVE_WNO_GNU_ANONYMOUS_STRUCT_FLAG failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_eadb2 && [1/2] Building C object CMakeFiles/cmTC_eadb2.dir/src.c.o
FAILED: CMakeFiles/cmTC_eadb2.dir/src.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -DLIBOMP_HAVE_WNO_GNU_ANONYMOUS_STRUCT_FLAG -fPIE -Wgnu-anonymous-struct -o CMakeFiles/cmTC_eadb2.dir/src.c.o -c src.c
cc: error: unrecognized command line option '-Wgnu-anonymous-struct'
ninja: build stopped: subcommand failed.

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test LIBOMP_HAVE_WNO_SELF_ASSIGN_FLAG failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_9923d && [1/2] Building C object CMakeFiles/cmTC_9923d.dir/src.c.o
FAILED: CMakeFiles/cmTC_9923d.dir/src.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -DLIBOMP_HAVE_WNO_SELF_ASSIGN_FLAG -fPIE -Wself-assign -o CMakeFiles/cmTC_9923d.dir/src.c.o -c src.c
cc: error: unrecognized command line option '-Wself-assign'; did you mean '-Wcast-align'?
ninja: build stopped: subcommand failed.

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test LIBOMP_HAVE_WNO_VLA_EXTENSION_FLAG failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_43847 && [1/2] Building C object CMakeFiles/cmTC_43847.dir/src.c.o
FAILED: CMakeFiles/cmTC_43847.dir/src.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -DLIBOMP_HAVE_WNO_VLA_EXTENSION_FLAG -fPIE -Wvla-extension -o CMakeFiles/cmTC_43847.dir/src.c.o -c src.c
cc: error: unrecognized command line option '-Wvla-extension'; did you mean '-fms-extensions'?
ninja: build stopped: subcommand failed.

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test LIBOMP_HAVE_WNO_FORMAT_PEDANTIC_FLAG failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_b1681 && [1/2] Building C object CMakeFiles/cmTC_b1681.dir/src.c.o
FAILED: CMakeFiles/cmTC_b1681.dir/src.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -DLIBOMP_HAVE_WNO_FORMAT_PEDANTIC_FLAG -fPIE -Wformat-pedantic -o CMakeFiles/cmTC_b1681.dir/src.c.o -c src.c
cc: error: unrecognized command line option '-Wformat-pedantic'; did you mean '-Wno-pedantic'?
ninja: build stopped: subcommand failed.

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test LIBOMP_HAVE_MMIC_FLAG failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_0792e && [1/2] Building C object CMakeFiles/cmTC_0792e.dir/src.c.o
FAILED: CMakeFiles/cmTC_0792e.dir/src.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -DLIBOMP_HAVE_MMIC_FLAG -mmic -fPIE -mmic -o CMakeFiles/cmTC_0792e.dir/src.c.o -c src.c
cc: error: unrecognized command line option '-mmic'; did you mean '-fpic'?
cc: error: unrecognized command line option '-mmic'; did you mean '-fpic'?
ninja: build stopped: subcommand failed.

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test LIBOMP_HAVE_M32_FLAG failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_8e862 && [1/2] Building C object CMakeFiles/cmTC_8e862.dir/src.c.o
[2/2] Linking C executable cmTC_8e862
FAILED: cmTC_8e862
: && /usr/bin/cc -Wall -Wno-sign-compare -O3 -DLIBOMP_HAVE_M32_FLAG -m32 CMakeFiles/cmTC_8e862.dir/src.c.o -o cmTC_8e862 && :
/usr/bin/ld: cannot find Scrt1.o: No such file or directory
/usr/bin/ld: cannot find crti.o: No such file or directory
/usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/7/libgcc.a when searching for -lgcc
/usr/bin/ld: cannot find -lgcc
/usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/7/libgcc.a when searching for -lgcc
/usr/bin/ld: cannot find -lgcc
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.

Source file was:
int main(void) { return 0; }
Determining if files windows.h;psapi.h exist failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_056e1 && [1/2] Building C object CMakeFiles/cmTC_056e1.dir/LIBOMP_HAVE_PSAPI_H.c.o
FAILED: CMakeFiles/cmTC_056e1.dir/LIBOMP_HAVE_PSAPI_H.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -fPIE -o CMakeFiles/cmTC_056e1.dir/LIBOMP_HAVE_PSAPI_H.c.o -c /home/shunfan/Documents/mxnet/build/CMakeFiles/CheckIncludeFiles/LIBOMP_HAVE_PSAPI_H.c
/home/shunfan/Documents/mxnet/build/CMakeFiles/CheckIncludeFiles/LIBOMP_HAVE_PSAPI_H.c:2:10: fatal error: windows.h: No such file or directory
#include
^~~
compilation terminated.
ninja: build stopped: subcommand failed.

Source:
/* */

include

include

int main(void){return 0;}

Determining if the function EnumProcessModules exists in the psapi failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_1b5a9 && [1/2] Building C object CMakeFiles/cmTC_1b5a9.dir/CheckFunctionExists.c.o
[2/2] Linking C executable cmTC_1b5a9
FAILED: cmTC_1b5a9
: && /usr/bin/cc -Wall -Wno-sign-compare -O3 -DCHECK_FUNCTION_EXISTS=EnumProcessModules CMakeFiles/cmTC_1b5a9.dir/CheckFunctionExists.c.o -o cmTC_1b5a9 -lpsapi && :
/usr/bin/ld: cannot find -lpsapi
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.

Determining if the function __atomic_load_1 exists failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_79cae && [1/2] Building C object CMakeFiles/cmTC_79cae.dir/CheckFunctionExists.c.o
:0:23: warning: conflicting types for built-in function ‘__atomic_load_1’ [-Wbuiltin-declaration-mismatch]
/usr/local/share/cmake-3.18/Modules/CheckFunctionExists.c:7:3: note: in expansion of macro ‘CHECK_FUNCTION_EXISTS’
CHECK_FUNCTION_EXISTS(void);
^~~~~
[2/2] Linking C executable cmTC_79cae
FAILED: cmTC_79cae
: && /usr/bin/cc -Wall -Wno-sign-compare -O3 -DCHECK_FUNCTION_EXISTS=__atomic_load_1 -rdynamic CMakeFiles/cmTC_79cae.dir/CheckFunctionExists.c.o -o cmTC_79cae && :
CMakeFiles/cmTC_79cae.dir/CheckFunctionExists.c.o: In function main': CheckFunctionExists.c:(.text.startup+0xc): undefined reference to__atomic_load_1'
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.

Determining if the fopen64 exist failed with the following output:
Change Dir: /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/ninja cmTC_33bc3 && [1/2] Building C object CMakeFiles/cmTC_33bc3.dir/CheckSymbolExists.c.o
FAILED: CMakeFiles/cmTC_33bc3.dir/CheckSymbolExists.c.o
/usr/bin/cc -Wall -Wno-sign-compare -O3 -fopenmp -fPIE -o CMakeFiles/cmTC_33bc3.dir/CheckSymbolExists.c.o -c CheckSymbolExists.c
CheckSymbolExists.c: In function ‘main’:
CheckSymbolExists.c:8:19: error: ‘fopen64’ undeclared (first use in this function); did you mean ‘fopen’?
return ((int*)(&fopen64))[argc];
^~~
fopen
CheckSymbolExists.c:8:19: note: each undeclared identifier is reported only once for each function it appears in
ninja: build stopped: subcommand failed.

File /home/shunfan/Documents/mxnet/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */

include

int main(int argc, char** argv)
{
(void)argv;

ifndef fopen64

return ((int*)(&fopen64))[argc];

else

(void)argc;
return 0;

endif

}

To Reproduce

cmake -DUSE_CUDA=1 -DUSE_TENSORRT=1 -G Ninja ..

Environment

----------Python Info----------
Version : 3.6.9
Compiler : GCC 8.4.0
Build : ('default', 'Oct 8 2020 12:12:24')
Arch : ('64bit', 'ELF')
------------Pip Info-----------
Version : 20.2.4
Directory : ~/.local/lib/python3.6/site-packages/pip
----------MXNet Info-----------
No MXNet installed.
----------System Info----------
Platform : Linux-5.4.0-56-generic-x86_64-with-Ubuntu-18.04-bionic
system : Linux
node : shunfan-pc
release : 5.4.0-56-generic
version : #62~18.04.1-Ubuntu SMP Tue Nov 24 10:07:50 UTC 2020
----------Hardware Info----------
machine : x86_64
processor : x86_64
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 6
On-line CPU(s) list: 0-5
Thread(s) per core: 1
Core(s) per socket: 6
Socket(s): 1
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 158
Model name: Intel(R) Core(TM) i5-9400F CPU @ 2.90GHz
Stepping: 10
CPU MHz: 3999.147
CPU max MHz: 4100.0000
CPU min MHz: 800.0000
BogoMIPS: 5799.77
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 9216K
NUMA node0 CPU(s): 0-5

[leezu]

Please provide the build configuration log.

cc @Zha0q1 due to the CheckSymbolExists.c:8:19: error: ‘OPENBLAS_USE64BITINT’ undeclared (first use in this function); did you mean ‘OPENBLAS___64BIT__’? above

[shroudie]

Please provide the build configuration log.

cc @Zha0q1 due to the CheckSymbolExists.c:8:19: error: ‘OPENBLAS_USE64BITINT’ undeclared (first use in this function); did you mean ‘OPENBLAS___64BIT__’? above

Were you talking about CMakeOutput.log? It is quite long, I've uploaded to Drive and shared with this link. Thanks,

[leezu]

I mean the output of the cmake command prior to running make or ninja. Sorry for the confusion

[shroudie]

I mean the output of the cmake command prior to running make or ninja. Sorry for the confusion

Thanks for the help. All I did was:

cp config/linux_gpu.cmake config.cmake

mkdir build && cd build

cmake -DUSE_CUDA=1 -DUSE_TENSORRT=1 ..

[leezu]

Yes, please provide the output of cmake -DUSE_CUDA=1 -DUSE_TENSORRT=1 .. with an empty build directory

[shroudie]

cmake -DUSE_CUDA=1 -DUSE_TENSORRT=1 ..

Hi, I shared a file of full output in here, thanks!

[leezu]

You can see that -- Configuring incomplete, errors occurred!.

Please install gfortran, for example via sudo apt install gfortran as the /usr/lib/x86_64-linux-gnu/libopenblas.a uses the libgfortran.

cc @mseth10 do you think we should detect libgfortran even if gfortran compiler is not present?

[mseth10]

We didn't have to install gfortran separately before. But now with @Zha0q1 's recent commit on statically linking openblas, we have to install it separately. @Zha0q1 can you update the build instructions with this update?

[shroudie]

It is all working fine now, thanks a lot!

[Zha0q1]

Please provide the build configuration log.

cc @Zha0q1 due to the CheckSymbolExists.c:8:19: error: ‘OPENBLAS_USE64BITINT’ undeclared (first use in this function); did you mean ‘OPENBLAS___64BIT__’? above

I think this is how cmake checks if a symbol exists. It tries to compile some dummy project and see it it succeeds

[Zha0q1]

I will update the build from source doc in instruct the user to install gfortran then