Reference

Last updated on 2026-08-24 | Edit this page

Quick Reference: Lmod Commands

Listing and Finding Modules

Command	Purpose
`module avail`	List all available modules
`module avail r`	List modules matching “r”
`module avail name`	Filter the listing (substring match)
`module list`	Show currently loaded modules
`module --list-collections`	Show your saved collections

Loading and Unloading

Command	Purpose
`module load name`	Load a module (default version)
`module load name/version`	Load specific version
`module load a b c`	Load multiple modules
`module unload name`	Unload a module
`module purge`	Unload all modules
`module swap old new`	Replace one module with another

Learning About Modules

Command	Purpose
`module help name`	Show module documentation
`module show name`	Display what module modifies

Managing Collections

Command	Purpose
`module save mycollection`	Save current modules as “mycollection”
`module restore mycollection`	Load a saved collection
`module restore default`	Load default collection (auto-loaded on login)
`module save default`	Save current modules as auto-load default

Quick Reference: Conda Commands

Environment Management

Command	Purpose
`conda create -n name python=3.10`	Create new environment
`conda activate name`	Activate an environment
`conda deactivate`	Exit current environment
`conda env list`	List all environments
`conda env remove -n name`	Delete an environment
`conda env export > env.yml`	Save environment to file
`conda env create -f env.yml`	Create environment from file

Package Management

Command	Purpose
`conda install package`	Install a package
`conda install -c conda-forge package`	Install from conda-forge channel
`conda list`	List installed packages
`conda update package`	Update a package
`conda remove package`	Uninstall a package
`conda search package`	Search for a package

Maintenance

Command	Purpose
`conda clean --all`	Remove unused packages and cache

Quick Reference: Python Virtual Environments

Creating and Using

Command	Purpose
`python -m venv envname`	Create virtual environment
`source envname/bin/activate`	Activate (Linux/macOS)
`envname\Scripts\activate`	Activate (Windows)
`deactivate`	Exit virtual environment

Pip Package Management

Command	Purpose
`pip install package`	Install a package
`pip list`	List installed packages
`pip freeze > requirements.txt`	Save dependencies
`pip install -r requirements.txt`	Install from file

Example: Complete Workflow

1. Load Modules

BASH

$ module load openblas/0.3.25
$ module load r/4.5.1
$ module load miniconda3

2. Create Conda Environment

BASH

$ conda create -n myproject python=3.10
$ conda activate myproject
(myproject) $ conda install numpy scipy pandas

3. Export Environment

BASH

(myproject) $ conda env export > environment.yml
(myproject) $ cat environment.yml

4. Write Job Script

BASH

#!/bin/bash
#SBATCH --job-name=analysis
#SBATCH --time=01:00:00
#SBATCH --cpus-per-task=4
#SBATCH --mem=16G

module load openblas/0.3.25
module load r/4.5.1
module load miniconda3

conda activate myproject
python analysis.py

5. Submit and Check

BASH

$ sbatch job_script.sh
Submitted batch job 12345

$ squeue -u $USER

Common Patterns

Load Specific Compiler Version for Compatibility

BASH

module load cuda/11.8.0   # For older code
module load cuda/12.2.1   # For newer code
module swap cuda cuda/12.2.1  # Change between versions

Create Project-Specific Environment

BASH

conda create -n project_name python=3.10
conda activate project_name
conda install package1 package2 package3
conda env export > environment.yml

Use Both Conda and Pip

BASH

conda create -n myenv python=3.10 numpy scipy
conda activate myenv
pip install package_not_on_conda
conda env export > environment.yml

Reproducible Job Script Template

BASH

#!/bin/bash
#SBATCH --job-name=descriptive_name
#SBATCH --time=HH:MM:SS
#SBATCH --cpus-per-task=N
#SBATCH --mem=NGb

# Clean environment
module purge

# Load required modules
# gcc is available system-wide on Sagehen -- no module load needed
module load miniconda3

# Activate environment
conda activate myproject

# Run analysis
python main_script.py

Troubleshooting

Module Not Found

BASH

# Check spelling
$ module avail name          # built-in filter
$ module spider name         # deep search, all versions
$ module -t avail 2>&1 | grep -i name   # grep form (options BEFORE avail)

# Check dependencies
$ module show module_name

Conda: “No such file or directory”

Make sure you loaded miniconda3:

BASH

$ module load miniconda3

Permission Denied in Job

Check file permissions:

BASH

$ chmod +x script.sh
$ ls -la script.sh
# Should show x in permissions

Out of Disk Quota

Check usage and remove unused environments. Note: Bare quota is unreliable on BeeGFS; use Pomona’s quota_check.sh wrapper which handles BeeGFS quota correctly.

BASH

$ quota_check.sh
$ conda env list
$ conda env remove -n unused_env
$ conda clean --all

Wrong Python Version in Job

Verify in job script:

BASH

# Add diagnostic commands
python --version
which python
conda list

Contact Information

Email: its-hpc@pomona.edu

When to contact: - Module not available - Software installation request - Quota issues - Job failures - Account issues

Include in email: - Your username - Job ID (if applicable) - Error message (copy and paste) - What you’ve tried