LLNL / LEAP

comprehensive library of 3D transmission Computed Tomography (CT) algorithms with Python API and fully integrated with PyTorch
https://leapct.readthedocs.io
MIT License
74 stars 9 forks source link

errors when running demo #13

Closed lonelyatu closed 5 months ago

lonelyatu commented 6 months ago

I have installed the leapct, but the errors encounter when I run the demo as below: image

Can you help me with this issue?

kylechampley commented 6 months ago

The install probably did not complete successfully because it cannot find libleap.so which is the LEAP compiled dynamic library. Please run the following command: pip install -v .

This print a message of why it did not compile. Send me this text if you need further help.

lonelyatu commented 6 months ago

Maybe the visual studio Version is not right. I use the VS 2022 to compile the leapct and I will use vs 2019 to re-compile this project.

kylechampley commented 6 months ago

Ya, that could be it. The newest versions of VS do not always support CUDA, so that is why we suggest 2019.

kylechampley commented 6 months ago

Could you pull the latest code and try again? I made changes to the pip install script, setup.py. I think the setup routine was not copying the dynamic library for Windows.

Sorry I did not catch this earlier. I don't use the pip install because I need to make constant changes and thus I did not see that it was not working.

JoosenLi commented 6 months ago

The install probably did not complete successfully because it cannot find libleap.so which is the LEAP compiled dynamic library. Please run the following command: pip install -v .

This print a message of why it did not compile. Send me this text if you need further help.

I‘m encountering the same error as @lonelyatu , and it persists even after installing the latest version (the setup.py version was updated 15 hours ago). When I run ‘pip install -v’, the version returned is ‘Using pip 23.3.2 from /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages/pip (python 3.9)’. Can you help me solve these problems?

kylechampley commented 6 months ago

I think you forgot to add the "dot". The command should be: pip install -v .

Do this and then send me the output.

JoosenLi commented 6 months ago

I think you forgot to add the "dot". The command should be: pip install -v .

Do this and then send me the output.

the outputs are as follow:

pip install -v . Using pip 23.3.2 from /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages/pip (python 3.9) Looking in indexes: http://mirrors.aliyun.com/pypi/simple/ Processing /data4/liqiaoxin/code/LEAP-main Running command python setup.py egg_info ./etc/build.sh: 13: cmake: not found /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages/setuptools/dist.py:472: SetuptoolsDeprecationWarning: Invalid dash-separated options !!

      ********************************************************************************
      Usage of dash-separated 'description-file' will not be supported in future
      versions. Please use the underscore name 'description_file' instead.

      By 2024-Sep-26, you need to update your project and remove deprecated calls
      or your builds will no longer be supported.

      See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
      ********************************************************************************

!! opt = self.warn_dash_deprecation(opt, section) running egg_info creating /tmp/pip-pip-egg-info-qfon70i9/leapct.egg-info writing /tmp/pip-pip-egg-info-qfon70i9/leapct.egg-info/PKG-INFO writing dependency_links to /tmp/pip-pip-egg-info-qfon70i9/leapct.egg-info/dependency_links.txt writing requirements to /tmp/pip-pip-egg-info-qfon70i9/leapct.egg-info/requires.txt writing top-level names to /tmp/pip-pip-egg-info-qfon70i9/leapct.egg-info/top_level.txt writing manifest file '/tmp/pip-pip-egg-info-qfon70i9/leapct.egg-info/SOURCES.txt' reading manifest file '/tmp/pip-pip-egg-info-qfon70i9/leapct.egg-info/SOURCES.txt' writing manifest file '/tmp/pip-pip-egg-info-qfon70i9/leapct.egg-info/SOURCES.txt' Preparing metadata (setup.py) ... done Requirement already satisfied: numpy in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from leapct==0.99) (1.26.2) Requirement already satisfied: torch in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from leapct==0.99) (2.1.2) Requirement already satisfied: filelock in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (3.13.1) Requirement already satisfied: typing-extensions in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (4.9.0) Requirement already satisfied: sympy in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (1.12) Requirement already satisfied: networkx in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (3.2.1) Requirement already satisfied: jinja2 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (3.1.2) Requirement already satisfied: fsspec in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (2023.12.2) Requirement already satisfied: nvidia-cuda-nvrtc-cu12==12.1.105 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (12.1.105) Requirement already satisfied: nvidia-cuda-runtime-cu12==12.1.105 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (12.1.105) Requirement already satisfied: nvidia-cuda-cupti-cu12==12.1.105 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (12.1.105) Requirement already satisfied: nvidia-cudnn-cu12==8.9.2.26 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (8.9.2.26) Requirement already satisfied: nvidia-cublas-cu12==12.1.3.1 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (12.1.3.1) Requirement already satisfied: nvidia-cufft-cu12==11.0.2.54 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (11.0.2.54) Requirement already satisfied: nvidia-curand-cu12==10.3.2.106 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (10.3.2.106) Requirement already satisfied: nvidia-cusolver-cu12==11.4.5.107 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (11.4.5.107) Requirement already satisfied: nvidia-cusparse-cu12==12.1.0.106 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (12.1.0.106) Requirement already satisfied: nvidia-nccl-cu12==2.18.1 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (2.18.1) Requirement already satisfied: nvidia-nvtx-cu12==12.1.105 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (12.1.105) Requirement already satisfied: triton==2.1.0 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from torch->leapct==0.99) (2.1.0) Requirement already satisfied: nvidia-nvjitlink-cu12 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from nvidia-cusolver-cu12==11.4.5.107->torch->leapct==0.99) (12.3.101) Requirement already satisfied: MarkupSafe>=2.0 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from jinja2->torch->leapct==0.99) (2.1.3) Requirement already satisfied: mpmath>=0.19 in /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages (from sympy->torch->leapct==0.99) (1.3.0) Building wheels for collected packages: leapct Running command python setup.py bdist_wheel ./etc/build.sh: 13: cmake: not found /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/site-packages/setuptools/dist.py:472: SetuptoolsDeprecationWarning: Invalid dash-separated options !!

      ********************************************************************************
      Usage of dash-separated 'description-file' will not be supported in future
      versions. Please use the underscore name 'description_file' instead.

      By 2024-Sep-26, you need to update your project and remove deprecated calls
      or your builds will no longer be supported.

      See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
      ********************************************************************************

!! opt = self.warn_dash_deprecation(opt, section) running bdist_wheel running build running build_py creating build/lib copying src/leaptorch.py -> build/lib copying src/leapctype.py -> build/lib /home/liqiaoxin/anaconda3/envs/pytorch/lib/python3.9/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() installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel copying build/lib/leaptorch.py -> build/bdist.linux-x86_64/wheel copying build/lib/leapctype.py -> build/bdist.linux-x86_64/wheel running install_egg_info running egg_info writing src/leapct.egg-info/PKG-INFO writing dependency_links to src/leapct.egg-info/dependency_links.txt writing requirements to src/leapct.egg-info/requires.txt writing top-level names to src/leapct.egg-info/top_level.txt reading manifest file 'src/leapct.egg-info/SOURCES.txt' writing manifest file 'src/leapct.egg-info/SOURCES.txt' Copying src/leapct.egg-info to build/bdist.linux-x86_64/wheel/leapct-0.99-py3.9.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/leapct-0.99.dist-info/WHEEL creating '/tmp/pip-wheel-tbcjr9xr/leapct-0.99-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'leapctype.py' adding 'leaptorch.py' adding 'leapct-0.99.dist-info/METADATA' adding 'leapct-0.99.dist-info/WHEEL' adding 'leapct-0.99.dist-info/top_level.txt' adding 'leapct-0.99.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Building wheel for leapct (setup.py) ... done Created wheel for leapct: filename=leapct-0.99-py3-none-any.whl size=27111 sha256=7f7128bdef8c07cfd40dd288bc13cb39a8f74b93d3df9885383fc4d5e3d75d3d Stored in directory: /data4/liqiaoxin/.cache/pip/wheels/7d/1d/94/4df1ba5b11c10424179467f3cfcc967f1ccd00c93433c90412 Successfully built leapct Installing collected packages: leapct Successfully installed leapct-0.99

kylechampley commented 6 months ago

Yep, I see the issue. You either don't have CMake installed or your system cannot find it. Look at around line 5 where it says: ./etc/build.sh: 13: cmake: not found

Note that the list of dependencies are here: https://github.com/LLNL/LEAP/wiki/Installing-and-Using-LEAP

lonelyatu commented 6 months ago

I am so sorry that I have used the updated files and VS2019 to compile the project. But I don't know why the cmake (version 3.28.1) can't find the VS compilers as reported below: image Can you provide another way to compile this package?

kylechampley commented 6 months ago

Try using the build script. Like this: cd LEAP .\etc\win_build.bat

lonelyatu commented 6 months ago

The same problem occurs.

kylechampley commented 6 months ago

What version of cmake do you have? Make sure it is at least version 3.0.

lonelyatu commented 6 months ago

cmake version is 3.28.1

kylechampley commented 6 months ago

When you install VS, did you check the box that says "Desktop development with C++"?

lonelyatu commented 6 months ago

Yes.

kylechampley commented 6 months ago

Try running the VS installer again and look for a check box that says something like "Visual C++ tools for CMake".

lonelyatu commented 6 months ago

OK. I will try again.

kylechampley commented 6 months ago

Good luck. I hope you figure it out. In case you cannot, I just released the first version of LEAP and included pre-compiled libraries in the release which you can download. You can find this here: https://github.com/LLNL/LEAP/releases

lonelyatu commented 6 months ago

Bad news is I still cannot compile the project. Good news is your released .dll file works perfectly. I'm really very grateful to you!!!