Deploy a new conda environment for xmipp

[albertmena]

Add a new option to install Xmipp in its own Conda environment, xmipp3, enabled by default. The installer will automatically detect the CUDA version supported by the NVIDIA driver and use the corresponding environment definition (CPU, CUDA 11, 12, or 13).

Users can disable this behaviour with a new parameter to skip the creation and use of the xmipp3 environment.

1. New parameter to omit the environment creation and omit the use of that environment in the installation xmipp3_environment_ommited

2. New 4 yaml files with the requirements of the environment (one for no GPU, and CUDA 11, 12, 13)
   xmipp_CPU.yml
   xmipp_CUDA11.yml
   xmipp_CUDA12.yml
   xmipp_CUDA13.yml

3. Before the installation of xmipp if the parameter collect the nvidia drivers and decide the yaml file based on that
   nvidia-smi | grep -oP 'CUDA Version: \K[0-9.]+' or something more robust

4. Set some environment variables as this:

# Conda environment activation
PATH_CONDA="/home/agarcia/miniconda/bin/conda"
eval "$($PATH_CONDA shell.bash hook)"
conda activate xmipp3

# Exports to let conda side libraries be used for compilation
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib #:$LD_LIBRARY_PATH
export CPATH=$CONDA_PREFIX/include:$CONDA_PREFIX/targets/x86_64-linux/include #:$CPATH
export XMIPP3_CMAKE_CUDA_COMPILER=$CONDA_PREFIX/bin/nvcc

# Fix link.stub issues
mkdir -p $CONDA_PREFIX/targets/x86_64-linux/bin
if [[ ! -d "$CONDA_PREFIX/targets/x86_64-linux/bin/crt" ]]; then
  ln -s $CONDA_PREFIX/bin/crt $CONDA_PREFIX/targets/x86_64-linux/bin/crt
fi
if [[ ! -d "$CONDA_PREFIX/targets/x86_64-linux/lib" ]]; then
  ln -s $CONDA_PREFIX/lib $CONDA_PREFIX/targets/x86_64-linux/lib
fi

5. launch the compillation with that flag: CMAKE_PREFIX_PATH_LIB=CONDA_PREFIX @oierlauzi please review that, not sure about ir

[martin-s-a]

This does not explain the current target process of this new mode, and more context is needed. As of now, the installer does not know about the existance of any xmipp3 conda env, neither does anything about it.

So, the new para is supposed to skip the env creation. What env creation? There is no conda environment creation right now. If there were to be one, should it be created and installed dependencies in it right at the start?

Also, the yaml files should not be stored inside this git repository. xmipp3's dependencies and it's versions are tightly tied to xmipp3's source code, so, changes in the code of xmipp3 can impy changes within the dependency yaml files, which would mean a needless PR in this repo if they were to be stored here. Imo, they should be stored in xmipp3's repo, and kept always in the same path with the same file names, as a contract between the installer and the repo, just like version-info.json.

Finally, the CMake flag is CMAKE_PREFIX_PATH, and we cannot send "CONDA_PREFIX" as a string, or it won't be evaluated. The cleanest way will probably be to evaluate the Conda env path within the Python code and send the evaluated path directly.

[albertmena]

Workflow definition -> I2PC/xmipp3#1064 (comment)