Singularity

Overview

Singularity provides a mechanism to run containers where containers can be used to package entire scientific workflows, software and libraries, and even data.

Version 3.5.3-1.1 is installed on CSF4.

Restrictions on use

The software is licensed under the BSD 3-clause “New” or “Revised” License.

Set up procedure

Please note: you no longer need to use a modulefile. We have installed singularity as a system-wide command. So you can simply run the singularity commands you wish to run without loading any modulefiles.

For example:

[username@login02 [CSF4] ~]$ singularity --version
singularity version 3.5.3-1.1.el7

Running the application

Please do not run Singularity containers on the login node. Jobs should be submitted to the compute nodes via batch. You may run the command on its own to obtain a list of flags:

singularity
USAGE: singularity [global options...]  [command options...] ...

ONTAINER USAGE COMMANDS:
    exec       Execute a command within container                               
    run        Launch a runscript within container                              
    shell      Run a Bourne shell within container                              
    test       Launch a testscript within container                             

CONTAINER MANAGEMENT COMMANDS:
    apps       List available apps within a container                           
    bootstrap  *Deprecated* use build instead                                   
    build      Build a new Singularity container                                
    check      Perform container lint checks                                    
    inspect    Display container's metadata                                     
    mount      Mount a Singularity container image                              
    pull       Pull a Singularity/Docker container to $PWD

Please note that users will not be permitted to run singularity containers in --writeable mode. You should build containers on your own platform where you have root access.

Serial batch job

Create a batch submission script, for example:

#!/bin/bash --login 
#SBATCH -p serial            # Optional, default partition is serial
#SBATCH -n 1                 # Optional, jobs in serial partition always use 1 core

singularity run mystack.simg

Submit the jobscript using:

sbatch scriptname

where scriptname is the name of your jobscript.

Single-node Parallel batch job

You should check the Singularity Documentation for how to ensure your Singularity container can access the cores available to your job. For example, MPI applications inside a container usually require the singularity command itself to be run via mpirun in the jobscript.

Create a jobscript similar to the following:

#!/bin/bash --login
#SBATCH -p multicore        # Single-node parallel job
#SBATCH -n 8                # Number of cores, can be 2--40

# mpirun knows how many cores to use
mpirun singularity exec name_of_container name_of_app_inside_container

Submit the jobscript using:

sbatch scriptname

where scriptname is the name of your jobscript.

Multi-node Parallel batch job

You should check the Singularity Documentation for how to ensure your Singularity container can access the cores available to your job. For example, MPI applications inside a container usually require the singularity command itself to be run via mpirun in the jobscript.

Create a jobscript similar to the following:

#!/bin/bash --login
#SBATCH -p multinode        # Multi-node parallel job
#SBATCH -n 120              # Number of cores, can be 80 or more in multiples of 40

# mpirun knows how many cores to use
mpirun singularity exec name_of_container name_of_app_inside_container

Submit the jobscript using:

sbatch scriptname

where scriptname is the name of your jobscript.

Further info

• Singularity Documentation

Updates

None.