Examples¶

Simple Python program using virtualenv and pip¶

First we need to create a working directory and move there

mkdir python_test
cd python_test

Next we load the python 3 module and use python 3 to create a python virtualenv. This way we can install pip packages which are not installed on the cluster

module load python/3.6.6
python3 -m venv mytest

Activate the mytest virtualenv and use pip to install the webcolors package

source mytest/bin/activate
pip install webcolors

Create the file test.py with the following contents using nano

import webcolors
from random import randint
from socket import gethostname

colour_list = list(webcolors.css3_hex_to_names.items())
requested_colour = randint(0,len(colour_list))
colour_name = colour_list[requested_colour][1]

print("Random colour name:", colour_name, " on host: ", gethostname())

Alternatively download it with wget:

wget https://raw.githubusercontent.com/vuw-research-computing/raapoi-tools/master/examples/python_venv/test.py

Using nano create the submissions script called python_submit.sh with the following content - change me@email.com to your email address.

#!/bin/bash
#
#SBATCH --job-name=python_test
#SBATCH -o python_test.out
#SBATCH -e python_test.err
#
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=1G
#SBATCH --time=10:00
#
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=me@email.com

module load python/3.6.6

source mytest/bin/activate
python test.py

Alternatively download it with wget

wget https://raw.githubusercontent.com/vuw-research-computing/raapoi-tools/master/examples/python_venv/python_submit.sh

To submit your job to the Slurm scheduler

sbatch python_submit.sh

Check for your job on the queue with squeue though it might finish very fast. The output files will appear in your working directory.