Snippets

This page contains useful snippets for performing common tasks.

Modulefiles

Create a modulefile from a script

Lmod provides a handy utility sh_to_modulefile for creating modulefiles from scripts. sh_to_modulefile records the initial environment, runs the script, and compares the final environment to determine the changes. It then converts these changes to Lua commands and prints them to the terminal. Given a shell script, my_script.sh, one can run the following command to generate an Lmod-compatible modulefile written in Lua.

$LMOD_DIR/sh_to_modulefile my_script.sh > my_script.lua

The command $LMOD_DIR/sh_to_modulefile calls the utility by using the Lmod-defined environment variable LMOD_DIR, which points to the directory in which Lmod is installed. my_script.sh is the name of the script to be converted into a modulefile. The output of the command is redirected (>) to the file my_script.lua.

SLURM

Attaching to Existing Jobs

Say, you have a job running on Cedar (this could be an interactive job launched with salloc or a job submitted with sbatch) and you would like to run some commands on the compute node with the job's resources (cores, memory, GPU, etc.). If the job ID for the job is JOBID, you can "attach" to the job with the command:

srun --pty --overlap --jobid JOBID bash

This snippet calls the srun command of SLURM. The --pty option launches a task in "pseudo terminal mode", allowing for you to specify commands from the command line as if you were running a terminal session on the compute node. The --overlap option allows your terminal session to share resources with the running job. The --jobid option specifies the SLURM job ID to attach to.

Warning

Since the commands that you run in this terminal will share the resources of the running job, if you exceed the memory request for the job, you can cause your original job to fail due to an out-of-memory (OOM) error.