Squashing Your Python Environment

This guide walks you through creating a Python virtual environment using uv, compressing it into a SquashFS image using makesquash, and mounting it for use.

1. Create a Virtual Environment with uv

Create a virtual environment (e.g., named venv):

# Create a relocatable virtual environment named 'venv'
uv venv venv --relocatable --link-mode=copy
# Activate it
source venv/bin/activate

Install your dependencies (example with requirements.txt):

uv pip install -r requirements.txt

2. Package the Environment with makesquash

Compress the virtual environment into a SquashFS file:

# Create a compressed SquashFS image of the virtual environment
mksquashfs venv venv.squashfs -no-recovery -noappend -Xcompression-level 3

This creates a compressed, read-only venv.squashfs file that contains the entire environment.

3. Mount the SquashFS File

To use the environment without unpacking it, mount it with squashfuse:

# Create a mount point (adjust path as needed)
mkdir -p /jetfs/home/$USER/venv
# Mount the SquashFS image (venv.squashfs) to that mount point
squashfuse venv.squashfs /jetfs/home/$USER/venv

You can now access and use the environment at /jetfs/home/$USER/venv.

Remember to use a path that you have access to.

Using the SHM for Performance (Optional)

The SHM (shared memory) filesystem can provide faster access times. When using slurm, the /dev/shm directory is available for temporary storage with the environment variable SHM_DIR pointing to it.

On Aurora or JET01, JET02 you can use /dev/shm/$USER for mounting:

# make sure to create a user directory in /dev/shm
mkdir -p /dev/shm/$USER/venv
# using slurm
mkdir -p $SHM_DIR/venv
# mount the SquashFS image to the SHM location
squashfuse venv.squashfs /dev/shm/$USER/venv
# or slurm
squashfuse venv.squashfs $SHM_DIR/venv

To activate the mounted environment:

# Activate the virtual environment from the mounted location
source /jetfs/home/$USER/venv/bin/activate
# or SHM
source /dev/shm/$USER/venv/bin/activate
# SLURM
source $SHM_DIR/venv/bin/activate

4. Unmount When Done

When you're finished:

fusermount -u /jetfs/home/$USER/venv

As a Slurm Job

On Jet one would want to use the SHM for better performance. Here is an example slurm script:

#!/bin/bash
#SBATCH --job-name=test_squash
#SBATCH --output=output.log
#SBATCH --error=error.log
#SBATCH --time=00:10:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=2G
#SBATCH --partition=general

# Load necessary modules
# Create a user directory
mkdir -p $SHM_DIR/venv
# Mount the SquashFS image to the SHM location
squashfuse $HOME/venv.squashfs $SHM_DIR/venv
# Activate the virtual environment from the mounted location
source $SHM_DIR/venv/bin/activate
# run your python script
python your_script.py
# Unmount when done
fusermount -u $SHM_DIR/venv

Slurm will clean up the SHM directory after the job ends, so no need to remove it manually.