cowsay - icaoberg

Does anyone use @SingularityApp and modules to load pre-existing images into their workspace? Just curious if we are reinventing the wheel by doing so and there exists another solution https://t.co/KL0GilswXA
— icaoberg (@icaoberg) February 26, 2020

Working with environment modules makes my life so much easier.

For example, for cowsay,I created a modulefile that will load the Singularity container to the workspace along with a script that calls it. Making the process transparent to the user (very little changes to their scripts, may be their SLURM submission scripts).

To make this work you need three things

an executable script that calls singularity (avoid using alias)
the Singularity container file
a modulefile

The modulefile file I created for cowsay is the following

#%Module
##
## cowsay modulefile
##
## modulefiles/
##

set ver 3.03

set msg "This module adds cowsay $ver to various paths\n"

proc ModulesHelp { } {
        puts stderr $msg
}

module-whatis "Use cowsay tools $ver"

prepend-path PATH /path/to/containers/cowsay/v3.03/

The modulefile itself is very straightforward, all it does is prepend a folder. Now the folder its prepending has two files

the Singularity image
an executable script that calls the image

In my system, there exists a folder with the following files

[icaoberg] $ ls -lt
total 68899
-rwxr-xr-x 1 root root 70799360 Feb 26 17:48 singularity-debian-buster-cowsay-v3.03.simg
-rwxr-xr-x 1 root root      366 Feb 26 17:48 cowsay

The contents of cowsay (the script I built, not the actual binary) are

#!/bin/bash

IMAGE=singularity-debian-buster-cowsay-v3.03.simg

function is_compute_node(){
if [ -x "$(command -v singularity)" ]; then
	return 0
else
	return 1
fi
}

if is_compute_node; then
	singularity run --app cowsay $(pwd)/$IMAGE "$1"
else
	echo "Singularity apps cannot run in the head node. Please request an allocation or call Singularity within a job."
fi

Now, the function

function is_compute_node(){
if [ -x "$(command -v singularity)" ]; then
        return 0
else
        return 1
fi
}

is neccesary because the singularity binary is not accesible from the head node of our HPC cluster. Users must request an allocation to a compute node in order to run apps in Singularity containers.

Screenshot

Example

Say I have the script example.sh

#!/bin/bash
#
#$ -j y
#$ -S /bin/bash
#$ -cwd

echo "TOTAL SUCCESS" | cowsay

With the changes above, it will now become

#!/bin/bash
#
#$ -j y
#$ -S /bin/bash
#$ -cwd

module load singularity/cowsay-3.03
echo "TOTAL SUCCESS" | cowsay

Submitting the script above using SLURM

sbatch -p public --mem=1Gb example.sh

should lead to

 _______________
< TOTAL SUCCESS >
 ---------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Source code

I hope you found this post useful.

icaoberg/cowsay

Example

Source code