tk-rusch / lem Goto Github PK

Hi there!
I faced with the problem where forward for the 'LEMcuda' layer not working (as a comparison I left the same code for the LSTM layer to make sure all works well).
I tried to set the 'CUDA_LAUNCH_BLOCKING' variable to 1 but it didn't help me.

Hi,

I am very new to CUDA and I am running into some issues when compiling CUDA extension for LEM.

I am working on a windows machine. First, I used conda install -c nvidia cuda to install cuda version 12.2 and this is the detailed information:
(base) C:\Users\yihan>nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Tue_Aug_15_22:09:35_Pacific_Daylight_Time_2023
Cuda compilation tools, release 12.2, V12.2.140
Build cuda_12.2.r12.2/compiler.33191640_0

Then, when I was running python setup.py install in conda, I got the error message as below:

No CUDA runtime is found, using CUDA_HOME='C:\Users\yihan\anaconda3'
running install
C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!!
self.initialize_options()
C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

    ********************************************************************************
    Please avoid running ``setup.py`` and ``easy_install``.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://github.com/pypa/setuptools/issues/917 for details.
    ********************************************************************************

!!
self.initialize_options()
running bdist_egg
running egg_info
creating lem_cuda.egg-info
writing lem_cuda.egg-info\PKG-INFO
writing dependency_links to lem_cuda.egg-info\dependency_links.txt
writing top-level names to lem_cuda.egg-info\top_level.txt
writing manifest file 'lem_cuda.egg-info\SOURCES.txt'
reading manifest file 'lem_cuda.egg-info\SOURCES.txt'
writing manifest file 'lem_cuda.egg-info\SOURCES.txt'
installing library code to build\bdist.win-amd64\egg
running install_lib
running build_ext
C:\Users\yihan\anaconda3\lib\site-packages\torch\utils\cpp_extension.py:359: UserWarning: Error checking compiler version for cl: [WinError 2] The system cannot find the file specified
warnings.warn(f'Error checking compiler version for {compiler}: {error}')
Traceback (most recent call last):
File "C:\Users\yihan\OneDrive\OU\LEM\LEM-main\LEM_cuda\LEM_cuda_extension\setup.py", line 4, in
setup(
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_init_.py", line 107, in setup
return distutils.core.setup(**attrs)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\core.py", line 185, in setup
return run_commands(dist)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\core.py", line 201, in run_commands
dist.run_commands()
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\dist.py", line 969, in run_commands
self.run_command(cmd)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools\dist.py", line 1234, in run_command
super().run_command(command)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools\command\install.py", line 80, in run
self.do_egg_install()
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools\command\install.py", line 129, in do_egg_install
self.run_command('bdist_egg')
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools\dist.py", line 1234, in run_command
super().run_command(command)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools\command\bdist_egg.py", line 164, in run
cmd = self.call_command('install_lib', warn_dir=0)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools\command\bdist_egg.py", line 150, in call_command
self.run_command(cmdname)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools\dist.py", line 1234, in run_command
super().run_command(command)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools\command\install_lib.py", line 11, in run
self.build()
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\command\install_lib.py", line 111, in build
self.run_command('build_ext')
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools\dist.py", line 1234, in run_command
super().run_command(command)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command
cmd_obj.run()
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools\command\build_ext.py", line 84, in run
_build_ext.run(self)
File "C:\Users\yihan\anaconda3\lib\site-packages\setuptools_distutils\command\build_ext.py", line 345, in run
self.build_extensions()
File "C:\Users\yihan\anaconda3\lib\site-packages\torch\utils\cpp_extension.py", line 499, in build_extensions
_check_cuda_version(compiler_name, compiler_version)
File "C:\Users\yihan\anaconda3\lib\site-packages\torch\utils\cpp_extension.py", line 383, in _check_cuda_version
torch_cuda_version = packaging.version.parse(torch.version.cuda)
File "C:\Users\yihan\anaconda3\lib\site-packages\pkg_resources_vendor\packaging\version.py", line 52, in parse
return Version(version)
File "C:\Users\yihan\anaconda3\lib\site-packages\pkg_resources_vendor\packaging\version.py", line 196, in init
match = self._regex.search(version)
TypeError: expected string or bytes-like object

Any inputs are appreciated!

For the experiment with EigenWorms dataset, is the best result reproducible with the default arguments here https://github.com/tk-rusch/LEM/blob/main/src/eigenWorms/eigenWorms_task.py?

HI! Great job! Thank you! Do you have any ideas about bidirectional LEM (like lstm)? Can it work and do you wanna code it?