Using Python Virtual Environments with Slurm

Overview

• virtualenv - command used to create our virtual environments.
• $HOME/.virtualenvs/ - the chosen directory to contain our virtual environments.
• $HOME/.virtualenvs/AdS/ - the directory where this specific virtual environment will be placed in.
• sympy - in this example we will be installing the sympy Python package.
• source bin/activate - to enter the virtual environment we have to source its bin/activate file.
• deactivate - to exit the virtual environment we have to issue the deactivate command.
• AdS_sympy.sbatch - Slurm jobs use a batch file with specific headers.

Requirements

To be able to replicate this guide will need:

• python
• pip
• virtualenv

Virtual Environment

First let's create our virtual environment

t0rrant@bastion01 $ mkdir $HOME/.virtualenvs
t0rrant@bastion01 $ virtualenv $HOME/.virtualenvs/AdS

Now let's get into the virtual environment

t0rrant@bastion01 $ source $HOME/.virtualenvs/AdS/bin/activate
(AdS) t0rrant@bastion01 $

We can now install the sympy package

(AdS) t0rrant@bastion01 $ pip install sympy

Now let's take a look at our test file:

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# AdS_sympy_test.py
#!/usr/bin/env python
from sympy import test

test("_basic")

We only need to be within the virtual environment to actually use the sympy package (i.e: execute our test file) or to install new packages. The virtual environment will be used by the Slurm job as we will see.

So, let us exit the virtual environment:

(AdS) t0rrant@bastion01 $ deactivate
t0rrant@bastion01 $

Slurm Batch File

A quick look into the batch file, we must activate the virtual environment before running our code (deactivating it here is not mandatory as the process will end):

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# AdS_sympy_test/AdS_sympy.sbatch
#!/bin/bash
#SBATCH --job-name=AdS_sympy_test
#SBATCH --output=/home/t0rrant/AdS_sympy_test/AdS_sympy_test-%j.out
#SBATCH --error=/home/t0rrant/AdS_sympy_test/AdS_sympy_test-%j.err
#SBATCH --mail-user=<your e-mail should go here>
#SBATCH --mail-type=ALL
#SBATCH --time=1:00:00
#SBATCH --mem=1G

RUNPATH=/home/t0rrant/AdS_sympy_test/
cd $RUNPATH
source $HOME/.virtualenvs/AdS/bin/activate
python AdS_sympy_test.py

Slurm options:

Looks good, let's submit it to the queue:

t0rrant@bastion01 $ sbatch AdS_sympy.sbatch
Submitted batch job 27047

Now check for errors and output:

t0rrant@bastion01 $ cat /home/t0rrant/AdS_sympy_test/AdS_sympy_test-27047.err

No errors! =)

t0rrant@bastion01 $ cat /home/t0rrant/AdS_sympy_test/AdS_sympy_test-27047.out
============================= test process starts ==============================
executable:         /home/t0rrant/.virtualenvs/AdS/bin/python  (2.7.13-final-0) [CPython]
architecture:       64-bit
cache:              yes
ground types:       python
numpy:              None
random seed:        7576360
hash randomization: on (PYTHONHASHSEED=1519633959)

sympy/core/tests/test_basic.py[16] ................                         [OK]

================== tests finished: 16 passed, in 0.09 seconds ==================
t0rrant@bastion01 $

As we can see it used the python executable from our virtual environment, used the sympy package also from that virtual environment and successfully ran the basic tests from the sympy package.