Configure VS-Code to use the remote environment on the HPC cluster with LMOD modules. This speicific integration is for Python based LMOD packages. Use Python venv to create a remote activation script that can be used by VS-Code.

There are many different software tools based on Python Modules. A unique project directory should be created for each software project.

Steps to Implement

  • Save the lmod_venv.sh script bellow to your Linux home directory
  • From Linux command line, loading your required modules
  • Create a project folder and cd to folder 
    mkdir -p ~/projects/scGPT
cd projects/scGPT
  • Create a python virtual envirmen python3 -m venv venv-name
  • Active the lmod_venv functions. This can be done at anytime before accessing the create_lmod_venv function and only should be done once per login session. 
    source ~/lmod_venv.sh

    Modify the project based virtual environment to support use of loaded modules.

    create_lmod_venv venv-name

This virtual environment can now be used from VS-Code.

  • Start VS-code
  • Open Remote SSH connect
  • From command Pallet use: Python: Create Environment
  • Select the venv/bin/activate script

lmod_venv.sh Script

#!/bin/bash

function create_lmod_venv() {
    local venv_name=$1
    
    # Store current LMOD environment
    module list 2>&1 | awk '{if ( NF == 2){print $2}}' > "${venv_name}/module_list"
 
    # Store LD_LIBRARY_PATH
    echo $LD_LIBRARY_PATH > "${venv_name}/ld_library_path"
 
    # Save current PYTHONPATH
    echo "export _OLD_PYTHONPATH=\"\${PYTHONPATH:-}\"" >> "${venv_name}/bin/activate"
    
    # Create function to load LMOD modules
    cat >> "${venv_name}/bin/activate" << 'EOL'

# Load LMOD modules specific to this environment
if [ -f "$VIRTUAL_ENV/module_list" ]; then
    while IFS= read -r module; do
        module load "$module"
    done < "$VIRTUAL_ENV/module_list"
fi

# Set LD_LIBRARY_PATH
export LD_LIBRARY_PATH=`cat ${VIRTUAL_ENV}/ld_library_path`

# Modify deactivate to handle LMOD environment
deactivate_lmod() {
    # Reset PYTHONPATH
    if [ -n "${_OLD_PYTHONPATH:-}" ] ; then
        PYTHONPATH="${_OLD_PYTHONPATH:-}"
        export PYTHONPATH
        unset _OLD_PYTHONPATH
    fi
    
    # Unload all modules
    module purge
    
    # Remove LD_LIBRARY_PATH
    unset LD_LIBRARY_PATH

    # Call original deactivate
    deactivate
}

# Override deactivate command
alias deactivate=deactivate_lmod
EOL
}

# Usage
# After loading your required modules, run:
# python3 -m venv venv-name
# source ~/lmod_venv.sh
# create_lmod_venv venv-name

Updated: