Running an Anaconda script as a Slurm job

An example for running a Python script as a job using Anaconda on a GPU node.

Code

Python script

We'll use a simple Python Hello World script as an example.

anaconda.py

#!/usr/bin/env python3
import sys
import os

print("hello, world")

Job script

Now we'll add a Slurm job script named anaconda.sh in the same directory as anaconda.py that directs Slurm to use 1 GPU node with a wall time of 30 minutes.

anaconda.sh

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=gpu
#SBATCH --gres=gpu:2
#SBATCH --mem=4G
#SBATCH --time=00:30:00

module load python/anaconda3

. ~/.bashrc
python3 ./anaconda.py

Run

Job submission

Make the Python script executable:

[juser@picotte001]$ chmod +x anaconda.py

Submit the job script using sbatch:

[juser@picotte001 ~]$ sbatch anaconda.sh