undefined symbol: cblas_sgemm_alloc

Question

undefined symbol: cblas_sgemm_alloc

zergrisk1 opened this issue 2 years ago · comments

When I tried python setup.py build_ext --inplace,It fails with the error:
Traceback (most recent call last): File "setup.py", line 7, in <module> from torch.utils.cpp_extension import BuildExtension, CppExtension, CUDAExtension File "/home/baichenghuan/anaconda3/envs/mesh_funcspace/lib/python3.6/site-packages/torch/__init__.py", line 84, in <module> from torch._C import * ImportError: /home/baichenghuan/anaconda3/envs/mesh_funcspace/lib/python3.6/site-packages/torch/lib/libmkldnn.so.0: undefined symbol: cblas_sgemm_alloc
How to solve it?

백승환 · Answer 1 · Tue Aug 02 2022 01:50:31 GMT+0800 (China Standard Time)

I also triedconda install mkl -c anaconda and conda update -n base -c defaults conda but didn't work.

jiyoonshincml · Answer 2 · Wed Aug 10 2022 12:06:13 GMT+0800 (China Standard Time)

I had the same problem, and solved it by installing torch 1.0.1 !

백승환 · Answer 3 · Wed Aug 10 2022 16:14:05 GMT+0800 (China Standard Time)

Oh it finally works !Thanks a lot !

Munga · Answer 4 · Thu Aug 18 2022 20:35:31 GMT+0800 (China Standard Time)

HI, I also add the same issue, but after installing torch 1.0.1, when I run python setup.py build_ext --inplace it throws this error. Currently I am unable to solve it

building 'im2mesh.utils.libkdtree.pykdtree.kdtree' extension
gcc -pthread -B /home/alphaar/anaconda3/envs/mesh_funcspace/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/alphaar/anaconda3/envs/mesh_funcspace/include/python3.6m -c im2mesh/utils/libkdtree/pykdtree/kdtree.c -o build/temp.linux-x86_64-3.6/im2mesh/utils/libkdtree/pykdtree/kdtree.o -std=c99 -O3 -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=kdtree -D_GLIBCXX_USE_CXX11_ABI=0
im2mesh/utils/libkdtree/pykdtree/kdtree.c:525:10: fatal error: numpy/arrayobject.h: No such file or directory
525 | #include "numpy/arrayobject.h"
| ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command 'gcc' failed with exit status 1

jiyoonshincml · Answer 5 · Fri Aug 19 2022 09:07:28 GMT+0800 (China Standard Time)

Try sudo apt-get install python-numpy

aalibasic · Answer 6 · Fri Sep 02 2022 22:07:26 GMT+0800 (China Standard Time)

HI, I also add the same issue, but after installing torch 1.0.1, when I run python setup.py build_ext --inplace it throws this error. Currently I am unable to solve it

building 'im2mesh.utils.libkdtree.pykdtree.kdtree' extension gcc -pthread -B /home/alphaar/anaconda3/envs/mesh_funcspace/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/alphaar/anaconda3/envs/mesh_funcspace/include/python3.6m -c im2mesh/utils/libkdtree/pykdtree/kdtree.c -o build/temp.linux-x86_64-3.6/im2mesh/utils/libkdtree/pykdtree/kdtree.o -std=c99 -O3 -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=kdtree -D_GLIBCXX_USE_CXX11_ABI=0 im2mesh/utils/libkdtree/pykdtree/kdtree.c:525:10: fatal error: numpy/arrayobject.h: No such file or directory 525 | #include "numpy/arrayobject.h" | ^~~~~~~~~~~~~~~~~~~~~ compilation terminated. error: command 'gcc' failed with exit status 1

Did you figure this one out.

Munga · Answer 7 · Fri Sep 02 2022 22:10:02 GMT+0800 (China Standard Time)

Thanks, @jiyoonshincml it worked with your suggestion!

xiaoyang-RL9 · Answer 8 · Fri Sep 23 2022 22:42:00 GMT+0800 (China Standard Time)

another method is useful:
conda install mkl=2018 -c anaconda

Bohan Liu · Answer 9 · Wed Nov 02 2022 10:09:46 GMT+0800 (China Standard Time)

HI, I also add the same issue, but after installing torch 1.0.1, when I run python setup.py build_ext --inplace it throws this error. Currently I am unable to solve it
building 'im2mesh.utils.libkdtree.pykdtree.kdtree' extension gcc -pthread -B /home/alphaar/anaconda3/envs/mesh_funcspace/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/alphaar/anaconda3/envs/mesh_funcspace/include/python3.6m -c im2mesh/utils/libkdtree/pykdtree/kdtree.c -o build/temp.linux-x86_64-3.6/im2mesh/utils/libkdtree/pykdtree/kdtree.o -std=c99 -O3 -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=kdtree -D_GLIBCXX_USE_CXX11_ABI=0 im2mesh/utils/libkdtree/pykdtree/kdtree.c:525:10: fatal error: numpy/arrayobject.h: No such file or directory 525 | #include "numpy/arrayobject.h" | ^~~~~~~~~~~~~~~~~~~~~ compilation terminated. error: command 'gcc' failed with exit status 1

Did you figure this one out.

I solved by following the top answer: https://stackoverflow.com/questions/14657375/cython-fatal-error-numpy-arrayobject-h-no-such-file-or-directory
there is a comment that:

Or, if you use cythonize() to make the ext_modules list,
include_dirs can be passed to setup()

follow that I add 'include_dirs' to setup, then it works