ERROR: Could not build wheels for pytigre, which is required to install pyproject.toml-based projects
6ABCD0 opened this issue · 7 comments
Expected Behavior
When I try to run：pip install .
it appears：
error: subprocess-exited-with-error
× Building wheel for pytigre (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [37 lines of output]
which: no nvcc in (/tmp/pip-build-env-sf042_vp/overlay/bin:/tmp/pip-build-env-sf042_vp/normal/bin:/users/psi/wxie/anaconda3/envs/NeRP/bin:/users/psi/wxie/anaconda3/condabin:/users/psi/wxie/anaconda3/bin:/users/psi/wxie/.vscode-server/bin/b3e4e68a0bc097f0ae7907b217c1119af9e03435/bin/remote-cli:/users/psi/wxie/anaconda3/bin:/users/psi/wxie/anaconda3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/freeware/bin/gnu-tools:/freeware/bin:/software/bin)
running bdist_wheel
running build
running build_py
file tigre/py.py (for module tigre.py) not found
running egg_info
writing pytigre.egg-info/PKG-INFO
writing dependency_links to pytigre.egg-info/dependency_links.txt
writing requirements to pytigre.egg-info/requires.txt
writing top-level names to pytigre.egg-info/top_level.txt
file tigre/py.py (for module tigre.py) not found
reading manifest file 'pytigre.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.ipynb' under directory 'tigre/demos'
warning: no files found matching '*.mat' under directory 'tigre/demos'
adding license file 'LICENSE'
writing manifest file 'pytigre.egg-info/SOURCES.txt'
file tigre/py.py (for module tigre.py) not found
running build_ext
Compiling tigre/utilities/cuda_interface/_Ax.pyx because it depends on /tmp/pip-build-env-sf042_vp/overlay/lib/python3.7/site-packages/Cython/Includes/libc/string.pxd.
[1/1] Cythonizing tigre/utilities/cuda_interface/_Ax.pyx
building '_Ax' extension
gcc -pthread -B /users/psi/wxie/anaconda3/envs/NeRP/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DIS_FOR_PYTIGRE -I/tmp/pip-build-env-sf042_vp/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/local/cuda/include -I../Common/CUDA/ -I/users/psi/wxie/anaconda3/envs/NeRP/include/python3.7m -c ../Common/CUDA/GpuIds.cpp -o build/temp.linux-x86_64-cpython-37/../Common/CUDA/GpuIds.o -std=c++11
cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
../Common/CUDA/GpuIds.cpp: In member function ‘void GpuIds::SetAllGpus(int)’:
../Common/CUDA/GpuIds.cpp:44:21: warning: ignoring return value of ‘void* malloc(size_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
44 | (int*)malloc(iTotalDeviceCount*sizeof(int));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/cuda/bin/nvcc -DIS_FOR_PYTIGRE -I/tmp/pip-build-env-sf042_vp/overlay/lib/python3.7/site-packages/numpy/core/include -I/usr/local/cuda/include -I../Common/CUDA/ -I/users/psi/wxie/anaconda3/envs/NeRP/include/python3.7m -c ../Common/CUDA/Siddon_projection.cu -o build/temp.linux-x86_64-cpython-37/../Common/CUDA/Siddon_projection.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options '-fPIC' -gencode=arch=compute_90,code=sm_90 -gencode=arch=compute_87,code=sm_87 -gencode=arch=compute_86,code=sm_86 -gencode=arch=compute_80,code=sm_80 -gencode=arch=compute_75,code=sm_75 -gencode=arch=compute_70,code=sm_70 -gencode=arch=compute_61,code=sm_61 -gencode=arch=compute_60,code=sm_60 -gencode=arch=compute_52,code=sm_52 -gencode=arch=compute_70,code=compute_70 --ptxas-options=-v -c --default-stream=per-thread -std=c++11
In file included from /usr/local/cuda/include/cuda_runtime.h:82,
from <command-line>:
/usr/local/cuda/include/crt/host_config.h:143:2: error: #error -- unsupported GNU version! gcc versions later than 12 are not supported! The nvcc flag '-allow-unsupported-compiler' can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.
143 | #error -- unsupported GNU version! gcc versions later than 12 are not supported! The nvcc flag '-allow-unsupported-compiler' can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.
| ^~~~~
/tmp/pip-build-env-sf042_vp/overlay/lib/python3.7/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /esat/vauxite/wxie/naf_cbct/TIGRE/Python/tigre/utilities/cuda_interface/_Ax.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
error: command '/usr/local/cuda/bin/nvcc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pytigre
Failed to build pytigre
ERROR: Could not build wheels for pytigre, which is required to install pyproject.toml-based projects
Specifications
- python version: 3.7.4
- OS: Linux version 6.5.6-200.fc38.x86_64 (mockbuild@39479204bd704ee0abe1946d2acfd6e6) (gcc (GCC) 13.2.1 20230728 (Red Hat 13.2.1-1), GNU ld version 2.39-9.fc38) # 1 SMP PREEMPT_DYNAMIC Fri Oct 6 19:02:35 UTC 2023
- nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Tue_Aug_15_22:02:13_PDT_2023
Cuda compilation tools, release 12.2, V12.2.140
Build cuda_12.2.r12.2/compiler.33191640_0
It appears that your installed CUDA version is incompatible with your installed GCC version, as the error message suggests:
error: #error -- unsupported GNU version! gcc versions later than 12 are not supported! The nvcc flag '-allow-unsupported-compiler' can be used to override this version check; however, using an unsupported host compiler may cause compilation failure or incorrect run time execution. Use at your own risk.
You need to find a gcc that is compatible with your CUDA version, otherwise you won't be able to compile anything CUDA. This is unfortunately not something we can control from TIGRE, NVIDIA keeps changing which GCCs they accept in every version, its hard to keep track.
Thanks so much for your help! I changed a machine and I fix it! The example.py and d01_CreateGeometry.py was run smoothly. But when I try to run d02_SampleData.py. I appears:
/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/matplotlib/animation.py:888: UserWarning: Animation was deleted without rendering anything. This is most likely not intended. To prevent deletion, assign the Animation to a variable, e.g. anim, that exists until you have outputted the Animation using plt.show() or anim.save().
'Animation was deleted without rendering anything. This is '
Traceback (most recent call last):
File "/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/scipy/io/matlab/mio.py", line 39, in _open_file
return open(file_like, mode), True
FileNotFoundError: [Errno 2] No such file or directory: '/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/tigre/utilities/./../../data/head.mat'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "d02_SampleData.py", line 64, in
head = sample_loader.load_head_phantom(geo.nVoxel)
File "/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/tigre/utilities/sample_loader.py", line 16, in load_head_phantom
test_data = scipy.io.loadmat(dirname)
File "/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/scipy/io/matlab/mio.py", line 224, in loadmat
with _open_file_context(file_name, appendmat) as f:
File "/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/contextlib.py", line 112, in enter
return next(self.gen)
File "/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/scipy/io/matlab/mio.py", line 17, in _open_file_context
f, opened = _open_file(file_like, appendmat, mode)
File "/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/scipy/io/matlab/mio.py", line 45, in _open_file
return open(file_like, mode), True
FileNotFoundError: [Errno 2] No such file or directory: '/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/tigre/utilities/./../../data/head.mat'
I don't know how can I find the'/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/tigre/utilities/./../../data/head.mat'?
@Window-Duo This error is on us (#493), still trying to solve it, but it has an easy solution:
take the file https://github.com/CERN/TIGRE/tree/master/Common/data/head.mat and then copy it in /users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/tigre/utilities/./../../data/head.mat
you can do it with the mv command in command line.
@Window-Duo I just updated the master branch to fix this, if you can pull again and try installing again, that would be great.
Hi AnderBiguri, thanks so much! It's fine now. But when I run d04_SimpleReconstruction.py, it shows:
(NeRP) [wxie@fasso demos]$ python d04_SimpleReconstruction.py
OSSART algorithm in progress.
Estimated time until completion : 00:00:48
/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/matplotlib/animation.py:888: UserWarning: Animation was deleted without rendering anything. This is most likely not intended. To prevent deletion, assign the Animation to a variable, e.g. anim, that exists until you have outputted the Animation using plt.show() or anim.save().
'Animation was deleted without rendering anything. This is '
And When I run d03_generateData.py ,it shows:
(NeRP) [wxie@fasso demos]$ python d03_generateData.py
/users/psi/wxie/anaconda3/envs/NeRP/lib/python3.7/site-packages/matplotlib/animation.py:888: UserWarning: Animation was deleted without rendering anything. This is most likely not intended. To prevent deletion, assign the Animation to a variable, e.g. anim, that exists until you have outputted the Animation using plt.show() or anim.save().
'Animation was deleted without rendering anything. This is
I know it's just a Warning I can ignore. But I still want to double check if it's okay and if this warning will cause some bad things when I use it in the future?
@Window-Duo It seems that you are using an older version of python + matplotlib, so some displaying stuff may not work for you, but it should not stop the code from working.
I got it. Thanks so much! AnderBiguri.