build fails on pip install #1
Comments
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Hi Alistair, what version of GCC are you using to build this? |
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gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44) Do you have a recommended version for building? |
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Hi Alister Ah, ok so this looks like a too old version of gcc I think. I have built this using gcc version 7.5.0 but apparently c++14 features were available from gcc version 5.2 onwards. (https://stackoverflow.com/questions/31965413/compile-c14-code-with-g). I've logged into scarf and gcc version 7.2.0 is available and this seems to work but scarf only seems to have old cuda versions. I've been using cuda 11 and when I compile using the version of cuda on scarf it gives me errors. Is it possible to get a newer version of cuda installed there? For reference, if I try to compile on a Diamond machine, the following set of commands seem to work: $ module load cuda/11.2 |
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That’s great, thanks James! I've sent an email off to scarf to ask them to install an updated version of CUDA.
… On 27 Jul 2021, at 15:23, James Parkhurst ***@***.***> wrote:
Hi Alistair
Ah, ok so this looks like a too old version of gcc I think. I have built this using gcc version 7.5.0 but apparently c++14 features were available from gcc version 5.2 onwards. (https://stackoverflow.com/questions/31965413/compile-c14-code-with-g <https://stackoverflow.com/questions/31965413/compile-c14-code-with-g>).
I've logged into scarf and gcc version 7.2.0 is available and this seems to work but scarf only seems to have old cuda versions. I've been using cuda 11 and when I compile using the version of cuda on scarf it gives me errors. Is it possible to get a newer version of cuda installed there?
For reference, if I try to compile on a Diamond machine, the following set of commands seem to work:
$ module load cuda/11.2
$ module load gcc/7.2.0
$ module load python/3
$ python3 -m venv test
$ . test/bin/activate
$ python -m pip install ***@***.*** ***@***.***>
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Hey James, The guys at SCARF put cuda 11.1 on there for me but I'm still running into errors, tried with gcc==7.2.0 and gcc==10.2.0. Sorry about this, do you have any ideas? Building wheel for guanaco (PEP 517) ... error
ERROR: Command errored out with exit status 1:
command: /home/vol01/scarf1041/programs/miniconda3/envs/parakeet/bin/python /home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpi0o9m9jm
cwd: /tmp/pip-install-pmj4mmuq/guanaco_50c7d31c5c5a49f2916de80051e0eb66
Complete output (114 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.9
creating build/lib.linux-x86_64-3.9/guanaco
copying src/guanaco/__init__.py -> build/lib.linux-x86_64-3.9/guanaco
copying src/guanaco/command_line.py -> build/lib.linux-x86_64-3.9/guanaco
copying src/guanaco/plot.py -> build/lib.linux-x86_64-3.9/guanaco
creating build/lib.linux-x86_64-3.9/guanaco/detail
copying src/guanaco/detail/__init__.py -> build/lib.linux-x86_64-3.9/guanaco/detail
copying src/guanaco/detail/correct.py -> build/lib.linux-x86_64-3.9/guanaco/detail
copying src/guanaco/detail/mp.py -> build/lib.linux-x86_64-3.9/guanaco/detail
copying src/guanaco/detail/reconstruct.py -> build/lib.linux-x86_64-3.9/guanaco/detail
running build_ext
-- The CXX compiler identification is GNU 10.2.0
-- The CUDA compiler identification is unknown
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /apps/eb/software/GCCcore/10.2.0/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting CUDA compiler ABI info
-- Detecting CUDA compiler ABI info - failed
-- Check for working CUDA compiler: /apps/cuda/10.0.130/bin/nvcc
-- Check for working CUDA compiler: /apps/cuda/10.0.130/bin/nvcc - broken
CMake Error at /tmp/pip-build-env-r4zhhjrx/overlay/lib/python3.9/site-packages/cmake/data/share/cmake-3.21/Modules/CMakeTestCUDACompiler.cmake:56 (message):
The CUDA compiler
"/apps/cuda/10.0.130/bin/nvcc"
is not able to compile a simple test program.
It fails with the following output:
Change Dir: /tmp/pip-install-pmj4mmuq/guanaco_50c7d31c5c5a49f2916de80051e0eb66/build/temp.linux-x86_64-3.9/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/gmake -f Makefile cmTC_28fce/fast && /usr/bin/gmake -f CMakeFiles/cmTC_28fce.dir/build.make CMakeFiles/cmTC_28fce.dir/build
gmake[1]: Entering directory `/tmp/pip-install-pmj4mmuq/guanaco_50c7d31c5c5a49f2916de80051e0eb66/build/temp.linux-x86_64-3.9/CMakeFiles/CMakeTmp'
Building CUDA object CMakeFiles/cmTC_28fce.dir/main.cu.o
/apps/cuda/10.0.130/bin/nvcc -c /tmp/pip-install-pmj4mmuq/guanaco_50c7d31c5c5a49f2916de80051e0eb66/build/temp.linux-x86_64-3.9/CMakeFiles/CMakeTmp/main.cu -o CMakeFiles/cmTC_28fce.dir/main.cu.o
In file included from /tmp/tmpxft_00005b37_00000000-5_main.cudafe1.stub.c:9,
from tmpxft_00005b37_00000000-5_main.cudafe1.stub.c:1:
/tmp/tmpxft_00005b37_00000000-2_main.fatbin.c:47:14: error: ‘__fatBinC_Wrapper_t’ does not name a type
47 | static const __fatBinC_Wrapper_t __fatDeviceText __attribute__ ((aligned (8))) __attribute__ ((section (__CUDAFATBINSECTION)))=
| ^~~~~~~~~~~~~~~~~~~
In file included from /tmp/tmpxft_00005b37_00000000-5_main.cudafe1.stub.c:8,
from tmpxft_00005b37_00000000-5_main.cudafe1.stub.c:1:
/tmp/tmpxft_00005b37_00000000-5_main.cudafe1.stub.c: In function ‘void __sti____cudaRegisterAll()’:
/tmp/tmpxft_00005b37_00000000-5_main.cudafe1.stub.c:13:44: error: ‘__fatDeviceText’ was not declared in this scope
13 | static void __sti____cudaRegisterAll(void){__cudaRegisterBinary(__nv_cudaEntityRegisterCallback);}
| ^~~~~~~~~~~~~~~~~~~~
gmake[1]: *** [CMakeFiles/cmTC_28fce.dir/main.cu.o] Error 1
gmake[1]: Leaving directory `/tmp/pip-install-pmj4mmuq/guanaco_50c7d31c5c5a49f2916de80051e0eb66/build/temp.linux-x86_64-3.9/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_28fce/fast] Error 2
CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:8 (project)
-- Configuring incomplete, errors occurred!
See also "/tmp/pip-install-pmj4mmuq/guanaco_50c7d31c5c5a49f2916de80051e0eb66/build/temp.linux-x86_64-3.9/CMakeFiles/CMakeOutput.log".
See also "/tmp/pip-install-pmj4mmuq/guanaco_50c7d31c5c5a49f2916de80051e0eb66/build/temp.linux-x86_64-3.9/CMakeFiles/CMakeError.log".
Traceback (most recent call last):
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 280, in <module>
main()
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 263, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 204, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "/tmp/pip-build-env-r4zhhjrx/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 221, in build_wheel
return self._build_with_temp_dir(['bdist_wheel'], '.whl',
File "/tmp/pip-build-env-r4zhhjrx/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 207, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-r4zhhjrx/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 150, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 82, in <module>
main()
File "setup.py", line 57, in main
setup(
File "/tmp/pip-build-env-r4zhhjrx/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 153, in setup
return distutils.core.setup(**attrs)
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/distutils/core.py", line 148, in setup
dist.run_commands()
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-r4zhhjrx/overlay/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 299, in run
self.run_command('build')
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-r4zhhjrx/overlay/lib/python3.9/site-packages/setuptools/command/build_ext.py", line 79, in run
_build_ext.run(self)
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "setup.py", line 42, in build_extensions
subprocess.check_call(
File "/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-pmj4mmuq/guanaco_50c7d31c5c5a49f2916de80051e0eb66', '-DCMAKE_BUILD_TYPE=Release', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-pmj4mmuq/guanaco_50c7d31c5c5a49f2916de80051e0eb66/build/lib.linux-x86_64-3.9', '-DPYTHON_EXECUTABLE=/home/vol01/scarf1041/programs/miniconda3/envs/parakeet/bin/python']' returned non-zero exit status 1.
----------------------------------------
ERROR: Failed building wheel for guanaco
Successfully built python-parakeet
Failed to build guanaco
ERROR: Could not build wheels for guanaco which use PEP 517 and cannot be installed directly |
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Hi Alister, sorry this hasn't been as easy to install as advertised! The line in the output saying " -- Check for working CUDA compiler: /apps/cuda/10.0.130/bin/nvcc" suggests that it's still picking up the old version of cuda. I have managed to install this on scarf with the following commands. I found that it kept trying to choose an old Intel compiler in my case so I think it is best to make sure it uses the correct compilers by being explicit (the export CXX and CUDACXX statements). Let me know if you have any more issues! |
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Not your fault! These things can be a pain - looks like you’ve got a recipe together :) I’ll give it a whirl tomorrow, thanks for your help!
… On 28 Jul 2021, at 17:00, James Parkhurst ***@***.***> wrote:
Hi Alister, sorry this hasn't been as easy to install as advertised!
The line in the output saying " -- Check for working CUDA compiler: /apps/cuda/10.0.130/bin/nvcc" suggests that it's still picking up the old version of cuda.
I have managed to install this on scarf with the following commands. I found that it kept trying to choose an old Intel compiler in my case so I think it is best to make sure it uses the correct compilers by being explicit (the export CXX and CUDACXX statements). Let me know if you have any more issues!
# Load necessary modules
module load python/3
module load GPUmodules
module load CUDA/11.1.1-GCC-10.2.0
module load gcc/7.2.0
# Setup python3 environment
python3 -m venv test
. test/bin/activate
# Lets export the compilers to use
NVCC=$(which nvcc)
GCC=$(which gcc)
export CXX=${GCC}
export CUDACXX=${NVCC}
# Install
python -m pip install git+https://github.com/rosalindfranklininstitute/amplus-di
***@***.***
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🎉 all appears to be working - time to do some simulations, thanks so much for your patience James! |
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Running into some issues with installing
guanaco(during the install of parakeet)I've checked that cmake is installed/available, unfortunately the error isn't very informative as to what went wrong - have you run into this?
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