Installation with Conda. fatal error: cblas.h: No such file or directory #300

ruanyyyyyyy · 2021-01-19T02:09:27Z

Describe the bug
I use the installation with Conda way and follow the instructions.
conda install mkl mkl-include -c intel
conda install pytorch -c pytorch
git clone https://github.com/StanfordVL/MinkowskiEngine.git
cd MinkowskiEngine
python setup.py install --blas=mkl

fatal error: cblas.h: No such file or directory
#include <cblas.h>
^~~~~~~~~
compilation terminated.

To Reproduce
python setup.py install --blas=mkl

Desktop (please complete the following information):

OS: Ubuntu 18.04
Python version: 3.8.5
CUDA version: 10.2
NVIDIA Driver version: 440.64.00
Minkowski Engine version 0.5.0

Additional context
Maybe sudo apt install libopenblas-dev would solve this? But I do not have permissions to usesudo command.

The text was updated successfully, but these errors were encountered:

chrischoy · 2021-01-19T02:52:48Z

Could you try the conda blas?

conda install -c conda-forge blas openblas

ruanyyyyyyy · 2021-01-19T05:25:41Z

Sorry. But I still get the same error.

chrischoy · 2021-01-19T08:06:04Z

Sorry, the header is in the dev repo

conda install -c anaconda openblas-devel

ruanyyyyyyy · 2021-01-20T04:23:21Z

Thanks for your suggestion. I tried a lot today but it still failed. The results of conda list show that openblas-devel 0.3.2 is installed. Then after python setup.py install --blas=mkl, fatal error: cblas.h: No such file or directory and a new error appeared.

ninja: build stopped: subcommand failed.
Traceback (most recent call last):
  File "/home/xxx/miniconda3/envs/py3-mink/lib/python3.7/site-packages/torch/utils/cpp_extension.py", line 1522, in _run_ninja_build
    env=env)
  File "/home/xxx/miniconda3/envs/py3-mink/lib/python3.7/subprocess.py", line 512, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['ninja', '-v', '-j', '12']' returned non-zero exit status 1.

I'd appreciate it if you could tell me what goes wrong in the installation process.

chrischoy · 2021-01-20T05:26:23Z

Please follow the instruction exactly.

Start from a fresh environment and install requirements.

conda create -n py3.8-mink-issue-300 python=3.8
conda activate py3.8-mink-issue-300
conda install pytorch -c pytorch  # should be installed first
conda install openblas-devel -c anaconda

After this, make sure that you can find cblas.h. ${CONDA_PREFIX} is an environment variable automatically set by conda, so run the command as is without modification.
```
find ${CONDA_PREFIX}/include -name "cblas.h"
```
This SHOULD return something like
```
/home/chrischoy/anaconda3/envs/py3.8-mink-issue-300/include/cblas.h
```

Finally, install MinkowskiEngine. Choose either method you like

3.1 Pip installation

 pip install -U git+https://github.com/NVIDIA/MinkowskiEngine -v --no-deps --install-option="--blas_include_dirs=${CONDA_PREFIX}/include"  --install-option="--blas=openblas"

3.2 setup.py installation

 cd MinkowskiEngine
 git pull
 python setup.py install --blas_include_dirs=${CONDA_PREFIX}/include --blas=openblas

ruanyyyyyyy · 2021-01-20T07:34:18Z

Thanks for the reply! Step 1 and step 2 work well. cblas.h can be found. For step 3, both methods failed. Here is the output.

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `sinhq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `erfcq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `acosq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `tanq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `jnq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `strtoflt128@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `atan2q@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `nanq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `expq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `cexpq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `atanq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `atanhq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `lroundq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `truncq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `csinq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `csqrtq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `coshq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `ynq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `ccosq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `asinq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `quadmath_snprintf@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `tanhq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `clogq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `roundq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `fmodq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `copysignq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `fabsq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `sqrtq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `log10q@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `cosq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `asinhq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `logq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `acoshq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `sinq@QUADMATH_1.0'
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat/ld: /home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/./libgfortran.so.5: undefined reference to `cabsq@QUADMATH_1.0'
collect2: error: ld returned 1 exit status

Using BLAS=mkl
Using the default compiler
running install
running bdist_egg
running egg_info
writing MinkowskiEngine.egg-info/PKG-INFO
writing dependency_links to MinkowskiEngine.egg-info/dependency_links.txt
writing requirements to MinkowskiEngine.egg-info/requires.txt
writing top-level names to MinkowskiEngine.egg-info/top_level.txt
reading manifest file 'MinkowskiEngine.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'MinkowskiEngine.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiNetwork.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/__init__.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiCommon.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiInterpolation.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiSparseTensor.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiOps.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiNonlinearity.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiUnion.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiPooling.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiFunctional.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiTensor.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiCoordinateManager.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/sparse_matrix_functions.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiConvolution.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiNormalization.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiTensorField.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiPruning.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiBroadcast.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiChannelwiseConvolution.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiKernelGenerator.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/diagnostics.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
creating build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/init.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/__init__.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/collation.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/gradcheck.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/coords.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/quantization.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
creating build/lib.linux-x86_64-3.8/MinkowskiEngine/modules
copying ./MinkowskiEngine/modules/__init__.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/modules
copying ./MinkowskiEngine/modules/senet_block.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/modules
copying ./MinkowskiEngine/modules/resnet_block.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/modules
running build_ext
building 'MinkowskiEngineBackend._C' extension
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/pybind
Emitting ninja build file /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/build.ninja...
Compiling objects...
Using envvar MAX_JOBS (12) as the number of workers...
[1/20] c++ -MMD -MF /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.o.d -pthread -B /home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.cpp -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.o -fopenmp -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
FAILED: /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.o
c++ -MMD -MF /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.o.d -pthread -B /home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.cpp -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.o -fopenmp -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /project/6049211/yuer/MinkowskiEngine/src/math_functions.hpp:30:0,
                 from /project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.cpp:25:
/project/6049211/yuer/MinkowskiEngine/src/mkl_alternate.hpp:35:10: fatal error: cblas.h: No such file or directory
 #include <cblas.h>
          ^~~~~~~~~
compilation terminated.
[2/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/pooling_avg_kernel.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/pooling_avg_kernel.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
FAILED: /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/pooling_avg_kernel.o
/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/pooling_avg_kernel.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/pooling_avg_kernel.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
In file included from /project/6049211/yuer/MinkowskiEngine/src/math_functions.cuh:30:0,
                 from /project/6049211/yuer/MinkowskiEngine/src/pooling_avg_kernel.cuh:35,
                 from /project/6049211/yuer/MinkowskiEngine/src/pooling_avg_kernel.cu:44:
/project/6049211/yuer/MinkowskiEngine/src/mkl_alternate.hpp:35:10: fatal error: cblas.h: No such file or directory
 #include <cblas.h>
          ^~~~~~~~~
compilation terminated.

(...... same error repeated until [11/20])

[11/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(201): here
            instantiation of "minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>> minkowski::detail::kernel_map_functor<coordinate_type, TemplatedAllocator, minkowski::CoordinateMapGPU, minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>>>::operator()(const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, minkowski::CUDAKernelMapMode::Mode, minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cpp(630): here
            instantiation of "const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map_type &minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map(const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, minkowski::RegionType::Type, const at::Tensor &, __nv_bool, __nv_bool) [with coordinate_type=int32_t, coordinate_field_type=float, TemplatedAllocator=minkowski::detail::default_allocator, CoordinateMapType=minkowski::CoordinateMapGPU]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(383): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(201): here
            instantiation of "minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>> minkowski::detail::kernel_map_functor<coordinate_type, TemplatedAllocator, minkowski::CoordinateMapGPU, minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>>>::operator()(const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, minkowski::CUDAKernelMapMode::Mode, minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cpp(630): here
            instantiation of "const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map_type &minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map(const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, minkowski::RegionType::Type, const at::Tensor &, __nv_bool, __nv_bool) [with coordinate_type=int32_t, coordinate_field_type=float, TemplatedAllocator=minkowski::detail::default_allocator, CoordinateMapType=minkowski::CoordinateMapGPU]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(383): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(201): here
            instantiation of "minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>> minkowski::detail::kernel_map_functor<coordinate_type, TemplatedAllocator, minkowski::CoordinateMapGPU, minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>>>::operator()(const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, minkowski::CUDAKernelMapMode::Mode, minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cpp(630): here
            instantiation of "const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map_type &minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map(const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, minkowski::RegionType::Type, const at::Tensor &, __nv_bool, __nv_bool) [with coordinate_type=int32_t, coordinate_field_type=float, TemplatedAllocator=minkowski::detail::default_allocator, CoordinateMapType=minkowski::CoordinateMapGPU]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(383): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(201): here
            instantiation of "minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>> minkowski::detail::kernel_map_functor<coordinate_type, TemplatedAllocator, minkowski::CoordinateMapGPU, minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>>>::operator()(const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, minkowski::CUDAKernelMapMode::Mode, minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cpp(630): here
            instantiation of "const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map_type &minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map(const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, minkowski::RegionType::Type, const at::Tensor &, __nv_bool, __nv_bool) [with coordinate_type=int32_t, coordinate_field_type=float, TemplatedAllocator=minkowski::detail::default_allocator, CoordinateMapType=minkowski::CoordinateMapGPU]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(383): here

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

[12/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(601): here
            instantiation of "minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::self_type minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_region(minkowski::cpu_kernel_region<coordinate_type> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_type &) const [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(2137): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(601): here
            instantiation of "minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::self_type minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_region(minkowski::cpu_kernel_region<coordinate_type> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_type &) const [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(2137): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(601): here
            instantiation of "minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::self_type minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_region(minkowski::cpu_kernel_region<coordinate_type> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_type &) const [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(2137): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(601): here
            instantiation of "minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::self_type minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_region(minkowski::cpu_kernel_region<coordinate_type> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_type &) const [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(2137): here

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

ninja: build stopped: subcommand failed.
Traceback (most recent call last):
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 1533, in _run_ninja_build
    subprocess.run(
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/subprocess.py", line 512, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ninja', '-v', '-j', '12']' returned non-zero exit status 1.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "setup.py", line 313, in <module>
    setup(
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/__init__.py", line 163, in setup
    return distutils.core.setup(**attrs)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/install.py", line 109, in do_egg_install
    self.run_command('bdist_egg')
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/bdist_egg.py", line 175, in run
    cmd = self.call_command('install_lib', warn_dir=0)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/bdist_egg.py", line 161, in call_command
    self.run_command(cmdname)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/install_lib.py", line 11, in run
    self.build()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/command/install_lib.py", line 107, in build
    self.run_command('build_ext')
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/build_ext.py", line 87, in run
    _build_ext.run(self)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/command/build_ext.py", line 340, in run
    self.build_extensions()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 670, in build_extensions
    build_ext.build_extensions(self)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/command/build_ext.py", line 449, in build_extensions
    self._build_extensions_serial()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/command/build_ext.py", line 474, in _build_extensions_serial
    self.build_extension(ext)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/build_ext.py", line 208, in build_extension
    _build_ext.build_extension(self, ext)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/command/build_ext.py", line 528, in build_extension
    objects = self.compiler.compile(sources,
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 491, in unix_wrap_ninja_compile
    _write_ninja_file_and_compile_objects(
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 1250, in _write_ninja_file_and_compile_objects
    _run_ninja_build(
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 1555, in _run_ninja_build
    raise RuntimeError(message) from e
RuntimeError: Error compiling objects for extension

chrischoy · 2021-01-20T08:13:18Z

I don't see the ${CONDA_PREFIX}/include anywhere in the include directories. You seemed to not include the blas include dirs.
You should follow the command exactly without modifying or removing the --blas_include_dirs. If you did, then the log should include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include which I don't see anywhere.
Please paste the command that you ran as well in the comment.

This is the compilation command you ran

[1/20] c++ -MMD -MF /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.o.d -pthread -B /home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.cpp -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.o -fopenmp -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14

If you just follow the command python setup.py install --blas_include_dirs=${CONDA_PREFIX}/include, there should be an include path -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include in the compilation command, which I don't see.

ruanyyyyyyy · 2021-01-20T08:30:37Z

Thanks! But I don't think I removed that option. Here is my command history. I just copied and pasted that command.

973  conda create -n py3.8-mink-issue-300 python=3.8
  974  conda activate py3.8-mink-issue-300
  975  conda install pytorch -c pytorch
  976  conda install openblas-devel -c anaconda
  977  find ${CONDA_PREFIX}/include -name "cblas.h"
  978  pip install -U git+https://github.com/NVIDIA/MinkowskiEngine -v --no-deps --install-option="--blas_include_dirs=${CONDA_PREFIX}/include"
  979  cd MinkowskiEngine
  980  git pull
  981  python setup.py install --blas_include_dirs=${CONDA_PREFIX}/include
  982  gcc --version
  983  g++ --version
  984  find ${CONDA_PREFIX}/include -name "cblas.h"
  985  python setup.py install --blas_include_dirs=${CONDA_PREFIX}/include
  986  exit

chrischoy · 2021-01-20T09:02:00Z

Ah sorry, my bad, since blas was not supplied to the setup, it didn't trigger the blas include dirs to be added to the compilation.

Please try this again with --blas=openblas

python setup.py install --blas_include_dirs=${CONDA_PREFIX}/include --blas=openblas

ruanyyyyyyy · 2021-01-20T09:26:38Z

Thanks for your quick reply! Unfortunately, the error seems related to gcc now?

WARNING: Skipping MinkowskiEngine as it is not installed.
--------------------------------
| CUDA compilation set         |
--------------------------------

Using BLAS=openblas
Using the default compiler
running install
running bdist_egg
running egg_info
writing MinkowskiEngine.egg-info/PKG-INFO
writing dependency_links to MinkowskiEngine.egg-info/dependency_links.txt
writing requirements to MinkowskiEngine.egg-info/requires.txt
writing top-level names to MinkowskiEngine.egg-info/top_level.txt
reading manifest file 'MinkowskiEngine.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'MinkowskiEngine.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiNetwork.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/__init__.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiCommon.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiInterpolation.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiSparseTensor.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiOps.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiNonlinearity.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiUnion.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiPooling.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiFunctional.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiTensor.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiCoordinateManager.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/sparse_matrix_functions.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiConvolution.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiNormalization.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiTensorField.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiPruning.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiBroadcast.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiChannelwiseConvolution.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/MinkowskiKernelGenerator.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
copying ./MinkowskiEngine/diagnostics.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine
creating build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/init.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/__init__.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/collation.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/gradcheck.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/coords.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
copying ./MinkowskiEngine/utils/quantization.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/utils
creating build/lib.linux-x86_64-3.8/MinkowskiEngine/modules
copying ./MinkowskiEngine/modules/__init__.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/modules
copying ./MinkowskiEngine/modules/senet_block.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/modules
copying ./MinkowskiEngine/modules/resnet_block.py -> build/lib.linux-x86_64-3.8/MinkowskiEngine/modules
running build_ext
building 'MinkowskiEngineBackend._C' extension
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src
creating /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/pybind
Emitting ninja build file /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/build.ninja...
Compiling objects...
Using envvar MAX_JOBS (12) as the number of workers...
[1/20] c++ -MMD -MF /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.o.d -pthread -B /home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.cpp -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/math_functions_cpu.o -fopenmp -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
[2/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/math_functions_gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/math_functions_gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
[3/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/pooling_avg_kernel.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/pooling_avg_kernel.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/project/6049211/yuer/MinkowskiEngine/src/pooling_avg_kernel.cu(137): warning: variable "is_int64" was declared but never referenced

[4/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/pooling_max_kernel.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/pooling_max_kernel.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
[5/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/broadcast_kernel.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/broadcast_kernel.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
[6/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/convolution_kernel.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/convolution_kernel.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/project/6049211/yuer/MinkowskiEngine/src/convolution_kernel.cu(334): warning: integer conversion resulted in a change of sign

/project/6049211/yuer/MinkowskiEngine/src/convolution_kernel.cu(571): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/project/6049211/yuer/MinkowskiEngine/src/convolution_kernel.cu(334): warning: integer conversion resulted in a change of sign

/project/6049211/yuer/MinkowskiEngine/src/convolution_kernel.cu(571): warning: integer conversion resulted in a change of sign

[7/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/convolution_transpose_gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/convolution_transpose_gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

[8/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/local_pooling_transpose_gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/local_pooling_transpose_gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

[9/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/global_pooling_gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/global_pooling_gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

[10/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/project/6049211/yuer/MinkowskiEngine/src/gpu.cu(118): warning: function "minkowski::format_size" was declared but never referenced

[11/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/broadcast_gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/broadcast_gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

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/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

[13/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/convolution_gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/convolution_gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

[14/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/interpolation_gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/interpolation_gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

[15/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/pruning_gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/pruning_gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

[16/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(201): here
            instantiation of "minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>> minkowski::detail::kernel_map_functor<coordinate_type, TemplatedAllocator, minkowski::CoordinateMapGPU, minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>>>::operator()(const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, minkowski::CUDAKernelMapMode::Mode, minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cpp(630): here
            instantiation of "const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map_type &minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map(const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, minkowski::RegionType::Type, const at::Tensor &, __nv_bool, __nv_bool) [with coordinate_type=int32_t, coordinate_field_type=float, TemplatedAllocator=minkowski::detail::default_allocator, CoordinateMapType=minkowski::CoordinateMapGPU]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(383): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(201): here
            instantiation of "minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>> minkowski::detail::kernel_map_functor<coordinate_type, TemplatedAllocator, minkowski::CoordinateMapGPU, minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>>>::operator()(const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, minkowski::CUDAKernelMapMode::Mode, minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cpp(630): here
            instantiation of "const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map_type &minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map(const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, minkowski::RegionType::Type, const at::Tensor &, __nv_bool, __nv_bool) [with coordinate_type=int32_t, coordinate_field_type=float, TemplatedAllocator=minkowski::detail::default_allocator, CoordinateMapType=minkowski::CoordinateMapGPU]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(383): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(201): here
            instantiation of "minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>> minkowski::detail::kernel_map_functor<coordinate_type, TemplatedAllocator, minkowski::CoordinateMapGPU, minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>>>::operator()(const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, minkowski::CUDAKernelMapMode::Mode, minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cpp(630): here
            instantiation of "const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map_type &minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map(const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, minkowski::RegionType::Type, const at::Tensor &, __nv_bool, __nv_bool) [with coordinate_type=int32_t, coordinate_field_type=float, TemplatedAllocator=minkowski::detail::default_allocator, CoordinateMapType=minkowski::CoordinateMapGPU]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(383): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(201): here
            instantiation of "minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>> minkowski::detail::kernel_map_functor<coordinate_type, TemplatedAllocator, minkowski::CoordinateMapGPU, minkowski::gpu_kernel_map<minkowski::type_wrapper<uint32_t, int32_t, float>::index_type, TemplatedAllocator<char>>>::operator()(const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator> &, minkowski::CUDAKernelMapMode::Mode, minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cpp(630): here
            instantiation of "const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map_type &minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::kernel_map(const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapKey *, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, const minkowski::CoordinateMapManager<coordinate_type, coordinate_field_type, TemplatedAllocator, CoordinateMapType>::stride_type &, minkowski::RegionType::Type, const at::Tensor &, __nv_bool, __nv_bool) [with coordinate_type=int32_t, coordinate_field_type=float, TemplatedAllocator=minkowski::detail::default_allocator, CoordinateMapType=minkowski::CoordinateMapGPU]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_manager.cu(383): here

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

[17/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(601): here
            instantiation of "minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::self_type minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_region(minkowski::cpu_kernel_region<coordinate_type> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_type &) const [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(2137): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(601): here
            instantiation of "minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::self_type minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_region(minkowski::cpu_kernel_region<coordinate_type> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_type &) const [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(2137): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(601): here
            instantiation of "minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::self_type minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_region(minkowski::cpu_kernel_region<coordinate_type> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_type &) const [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(2137): here

/project/6049211/yuer/MinkowskiEngine/src/kernel_region.hpp(392): warning: calling a __host__ function from a __host__ __device__ function is not allowed
          detected during:
            instantiation of "minkowski::gpu_kernel_region<coordinate_type>::gpu_kernel_region(const minkowski::cpu_kernel_region<coordinate_type> &) [with coordinate_type=int32_t]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(601): here
            instantiation of "minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::self_type minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_region(minkowski::cpu_kernel_region<coordinate_type> &, const minkowski::CoordinateMapGPU<coordinate_type, TemplatedAllocator>::stride_type &) const [with coordinate_type=int32_t, TemplatedAllocator=minkowski::detail::default_allocator]"
/project/6049211/yuer/MinkowskiEngine/src/coordinate_map_gpu.cu(2137): here

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

[18/20] c++ -MMD -MF /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/quantization.o.d -pthread -B /home/yuer/miniconda3/envs/py3.8-mink-issue-300/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/quantization.cpp -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/quantization.o -fopenmp -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
[19/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/spmm.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/spmm.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
FAILED: /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/spmm.o
/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/src/spmm.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/project/6049211/yuer/MinkowskiEngine/src/spmm.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/project/6049211/yuer/MinkowskiEngine/src/spmm.cu(70): warning: variable "is_int64" was declared but never referenced

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/project/6049211/yuer/MinkowskiEngine/src/spmm.cu: In instantiation of ‘minkowski::coo_spmm(const at::Tensor&, const at::Tensor&, const at::Tensor&, int64_t, int64_t, const at::Tensor&, int64_t)::<lambda()>::<lambda()> [with th_int_type = int]’:
/project/6049211/yuer/MinkowskiEngine/src/spmm.cu:177:3871:   required from ‘struct minkowski::coo_spmm(const at::Tensor&, const at::Tensor&, const at::Tensor&, int64_t, int64_t, const at::Tensor&, int64_t)::<lambda()> [with th_int_type = int]::<lambda()>’
/project/6049211/yuer/MinkowskiEngine/src/spmm.cu:177:0:   required from ‘minkowski::coo_spmm(const at::Tensor&, const at::Tensor&, const at::Tensor&, int64_t, int64_t, const at::Tensor&, int64_t)::<lambda()> [with th_int_type = int]’
/project/6049211/yuer/MinkowskiEngine/src/spmm.cu:177:3871:   required from ‘struct minkowski::coo_spmm(const at::Tensor&, const at::Tensor&, const at::Tensor&, int64_t, int64_t, const at::Tensor&, int64_t) [with th_int_type = int; int64_t = long int]::<lambda()>’
/project/6049211/yuer/MinkowskiEngine/src/spmm.cu:177:0:   required from ‘at::Tensor minkowski::coo_spmm(const at::Tensor&, const at::Tensor&, const at::Tensor&, int64_t, int64_t, const at::Tensor&, int64_t) [with th_int_type = int; int64_t = long int]’
/project/6049211/yuer/MinkowskiEngine/src/spmm.cu:288:204:   required from here
/project/6049211/yuer/MinkowskiEngine/src/spmm.cu:177:624: internal compiler error: in maybe_undo_parenthesized_ref, at cp/semantics.c:1705
   AT_DISPATCH_FLOATING_TYPES(vals.scalar_type(), "coo_spmm", [&] {
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ^
Please submit a full bug report,
with preprocessed source if appropriate.
See <https://gcc.gnu.org/bugs/> for instructions.
[20/20] /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/bin/nvcc -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/torch/csrc/api/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/TH -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/THC -I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/10.2.89/include -I/project/6049211/yuer/MinkowskiEngine/src -I/project/6049211/yuer/MinkowskiEngine/src/3rdparty -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include -I/home/yuer/miniconda3/envs/py3.8-mink-issue-300/include/python3.8 -c -c /project/6049211/yuer/MinkowskiEngine/pybind/minkowski.cu -o /project/6049211/yuer/MinkowskiEngine/build/temp.linux-x86_64-3.8/pybind/minkowski.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options ''"'"'-fPIC'"'"'' --expt-relaxed-constexpr --expt-extended-lambda -O3 -DTORCH_API_INCLUDE_EXTENSION_H '-DPYBIND11_COMPILER_TYPE="_gcc"' '-DPYBIND11_STDLIB="_libstdcpp"' '-DPYBIND11_BUILD_ABI="_cxxabi1011"' -DTORCH_EXTENSION_NAME=_C -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_60,code=sm_60 -std=c++14
/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/boxing/impl/boxing.h(100): warning: integer conversion resulted in a change of sign

/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/include/ATen/core/op_registration/op_whitelist.h(39): warning: integer conversion resulted in a change of sign

ninja: build stopped: subcommand failed.
Traceback (most recent call last):
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 1533, in _run_ninja_build
    subprocess.run(
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/subprocess.py", line 512, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ninja', '-v', '-j', '12']' returned non-zero exit status 1.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "setup.py", line 313, in <module>
    setup(
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/__init__.py", line 163, in setup
    return distutils.core.setup(**attrs)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/install.py", line 109, in do_egg_install
    self.run_command('bdist_egg')
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/bdist_egg.py", line 175, in run
    cmd = self.call_command('install_lib', warn_dir=0)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/bdist_egg.py", line 161, in call_command
    self.run_command(cmdname)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/install_lib.py", line 11, in run
    self.build()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/command/install_lib.py", line 107, in build
    self.run_command('build_ext')
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/build_ext.py", line 87, in run
    _build_ext.run(self)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/command/build_ext.py", line 340, in run
    self.build_extensions()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 670, in build_extensions
    build_ext.build_extensions(self)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/command/build_ext.py", line 449, in build_extensions
    self._build_extensions_serial()
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/command/build_ext.py", line 474, in _build_extensions_serial
    self.build_extension(ext)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/setuptools/command/build_ext.py", line 208, in build_extension
    _build_ext.build_extension(self, ext)
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/distutils/command/build_ext.py", line 528, in build_extension
    objects = self.compiler.compile(sources,
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 491, in unix_wrap_ninja_compile
    _write_ninja_file_and_compile_objects(
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 1250, in _write_ninja_file_and_compile_objects
    _run_ninja_build(
  File "/home/yuer/miniconda3/envs/py3.8-mink-issue-300/lib/python3.8/site-packages/torch/utils/cpp_extension.py", line 1555, in _run_ninja_build
    raise RuntimeError(message) from e
RuntimeError: Error compiling objects for extension

chrischoy · 2021-01-20T10:22:39Z

Related to #286 (comment)

This is a GCC bug https://gcc.gnu.org/bugzilla/show_bug.cgi?id=83204

The simplest solution is to install CUDA 11.1 and GCC 9, but since you don't have sudo, you have these options.

Compile g++-7 from sources and compile MinkowskiEngine with GCC >= 7.4 and CUDA 10.2
Ask admin to install CUDA 11.1 and GCC-9
Use the docker nvcr.io/nvidia/pytorch:20.10-py3 which is known to work out of box with MinkowskiEngine.

ruanyyyyyyy · 2021-01-21T06:44:12Z

Thanks for your patience! I tried again today and choose to email the admin now. Hope this can be solved soon!

chrischoy · 2021-03-21T07:56:32Z

Closing the issue.

For those who looking for the solution for <cblas.h>: No such file or directory error, install blas with

sudo apt install libopenblas-dev

as shown in the README installation section https://github.com/NVIDIA/MinkowskiEngine#pip

serser · 2022-05-08T16:23:31Z

Same with CentOS, I installed openblas with yum install openblas.x86_64 openblas-devel.x86_64 and rpm -ql openblas-devel.x86_64 gives

/usr/include/openblas
/usr/include/openblas/cblas.h
/usr/include/openblas/f77blas.h
/usr/include/openblas/lapacke.h
/usr/include/openblas/lapacke_config.h
/usr/include/openblas/lapacke_mangling.h
/usr/include/openblas/lapacke_utils.h
/usr/include/openblas/openblas_config.h
/usr/lib64/libopenblas.so
/usr/lib64/libopenblas64.so
/usr/lib64/libopenblas64_.so
/usr/lib64/libopenblaso.so
/usr/lib64/libopenblaso64.so
/usr/lib64/libopenblaso64_.so
/usr/lib64/libopenblasp.so
/usr/lib64/libopenblasp64.so
/usr/lib64/libopenblasp64_.so

My install command is python setup.py install --blas_include_dirs=/usr/include/openblas:${CONDA_PREFIX}/include: --blas=openblas. Do I need upgrade gcc to gcc7?

serser · 2022-05-08T16:47:20Z

I checkout to v0.4.3 and didpython setup.py install --blas=openblas --blas_include_dirs=/usr/include/openblas and passed through.

chrischoy closed this as completed Mar 21, 2021

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Installation with Conda. fatal error: cblas.h: No such file or directory #300

Installation with Conda. fatal error: cblas.h: No such file or directory #300

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Installation with Conda. fatal error: cblas.h: No such file or directory #300

Installation with Conda. fatal error: cblas.h: No such file or directory #300

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