Setting up autocmake to compile gimic

[mariavd]

@bast I'm not sure if the gimic repo is the right place to ask about autocmake, but I ran into trouble recompiling gimic on the CSC computers. We no longer have a full Anaconda but containerized Miniconda. Apparently, autocmake is missing. I downloaded the tar with the latest release of autocmake, but I couldn't figure out how to get it running to compile gimic.

I tried making a custom environment from a yml file but it fails to install autocmake. One of my attempts was:

channels:
  - conda-forge
dependencies:
  - python=3.10
  - pip=22.2.2
  - cython
  - numpy
  - pyparsing=2.4.7
  - pyyaml
  - sphinx
  - sphinx_rtd_theme
  - pip:
      - runtest=2.3.2
      - autocmake

[bast]

The autocmake part is not distributed via PyPI and it should not be needed to list it in environment.yml. Does it not work when you remove it? What error do you get then?

[mariavd]

I first tried cloning the gimic repo and loading the python and the cmake modules but there was an error that autocmake is missing. This happened for the first time to me. The CSC computers got an update to RHEL 8.

$ module load python-data
$ module load cmake
$ ../setup --omp --blas
Traceback (most recent call last):
  File "/projappl/pyykko2/mariavd/gimic/2023/build/../setup", line 11, in <module>
    from autocmake import configure
ModuleNotFoundError: No module named 'autocmake'

I then tried setting up a python environment with autocmake but it was not working with variations of the yaml script above.

[bast]

I will look and test ...

[bast]

I think I understand. You need to invoke the setup script from the top-level folder. You seem to call it from the build directory.

In other words:

$ ./setup ...

but not:

$ cd build
$ ../setup ...

[mariavd]

Thank you very much, indeed, that was the problem. I should have replied earlier but I came across another issue that I only now started looking into. What is the correct way of specifying the path to the python libraries? Below is the output of the setup script.

-- Found Cython: /CSC_CONTAINER/miniconda/envs/env1/bin/cython
-- Configuring incomplete, errors occurred!
See also "/projappl/pyykko2/mariavd/gimic/2023/build/CMakeFiles/CMakeOutput.log".
See also "/projappl/pyykko2/mariavd/gimic/2023/build/CMakeFiles/CMakeError.log".

CMake Deprecation Warning at CMakeLists.txt:5 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


CMake Error at /appl/spack/v018/install-tree/gcc-8.5.0/cmake-3.23.1-vrdlmy/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
  Could NOT find Python (missing: PYTHON_LIBRARY)
Call Stack (most recent call first):
  /appl/spack/v018/install-tree/gcc-8.5.0/cmake-3.23.1-vrdlmy/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
  cmake/custom/FindPython.cmake:141 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  cmake/custom/cython.cmake:75 (find_package)
  cmake/custom/own.cmake:11 (include)
  CMakeLists.txt:104 (include)

I tried specifying the path to the site-packages directory, but it seems not to work.

export PYTHON_LIBRARY=/CSC_CONTAINER/miniconda/envs/env1/lib/python3.10/site-packages

Do you have any hints about that?

[bast]

I am looking at it ...

[mariavd]

Actually, a person at CSC noted this morning that the paths related to the containerized python are not visible outside of the container, so that is causing the problem. I will have to try an alternative python.

[bast]

OK. But please know that I am now working on removing dust from the autocmake code so there will be some improvements soon.

[heikef]

Assigning @bast hope this is OK for you. While reading through the conversation I realized that you might want to close this issue when the "dust" from autocmake has been removed.

[bast]

Thanks! Yes. Also thanks for the issue cleanup across the repository. That is helpful to increase focus.