Singularity Module

install_singularity_module.md

Singualarity Module

A convenience python script that helps create shortcuts in host machine to programs inside of singularity containers.

• Place this inside ~/.local/bin and make sure you have export PATH="$HOME/.local/bin:$PATH" in .bashrc or .zshrc
• Make module executable by running chmod +x ~/.local/bin/module
• To load a shortcut to node from dev singularity instance into ~/.local/bin:

module load node dev

Then simply doing node --version should use the node inside the container.

• To remove node,

module remove node

This obviously requires the instance to be loaded when the executable is used.

module

#!/usr/bin/python3
import argparse
import subprocess
import sys
import os


sys.tracebacklimit = 0

parser = argparse.ArgumentParser()
parser.add_argument('action', choices=['load', 'remove'])
parser.add_argument('module')
parser.add_argument('instance', nargs='?', default='', 
                    help='instance[:module_path], if module path is not given, '
                         'an executable with the module name should be present inside the container')
args = parser.parse_args()

action = args.action
module = args.module
instance = args.instance
module_path = module
filepath = os.path.expanduser(f'~/.local/bin/{module}')

if action == 'load' and len(instance) == 0:
    parser.error('instance is required when using load')

colon_idx = instance.find(':')
if colon_idx >= 0:
    instance = instance[:colon_idx]
    module_path = instance[colon_idx+1:]

if action == 'load':
    # validate
    cmd = f'singularity exec instance://{instance} which {module_path} | wc -l'
    result = subprocess.run(cmd, shell=True, capture_output=True, text=True)
    if result.returncode == 0 and not result.stderr:
        num_lines_which = int(result.stdout)
        if not num_lines_which > 0:
            raise IOError(f'Could not find {module_path} in instance {instance}')
    else:
        print(result.stderr, end='')
        exit()

    # create file
    content = [
      f'#!/bin/sh',
      f'singularity exec instance://{instance} {module_path} "$@"'
    ]
    with open(filepath, 'w') as f:
        for line in content:
            print(line, file=f)

    # verify if file exists
    if not os.path.exists(filepath):
        raise IOError(f'could not create {filepath}')

    # make file executable
    cmd = f'chmod +x {filepath}'
    result = subprocess.run(cmd, shell=True)
    if result.returncode == 0:
        print(f'module {module} loaded successfully')
    else:
        print(f'Process exited with return code {result.returncode}')

if action == 'remove':
    if not os.path.exists(filepath):
        raise IOError(f'module {module} does not exist')

    os.remove(filepath)
    print(f'module {module} unloaded successfully')