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This page is for advanced users who have experience with building applications on a Linux machine. Below xyz is your group name and abc is your userid.


Creating a Singularity Container

Some applications may have dependencies which require root access for installing. If these dependencies are not installed on mox.hyak, then you can use Singularity to run such applications.

Singularity (https://sylabs.io/singularity/) allows you to package your application with all its dependencies into a single singularity image file ( .sif file).

If you know how to install your application on a Linux machine where you have root permissions than you can prepare a Singularity .def file and request the Hyak team to prepare a Singularity container for your application.

See below for an example of a Singularity definition file (.def file)

/sw/singularity-images/testing/ngsolve.def

See below link for more information on a Singularity .def file:

https://sylabs.io/guides/3.0/user-guide/definition_files.html

If you have root access to a Linux machine then you can install Singularity CE and use it to prepare a .sif image file.

https://sylabs.io/singularity/

If you have admin access to a Mac machine then you can install Singularity Desktop macOS and use it to prepare a .sif image file.

https://sylabs.io/singularity-desktop-macos/


Example of using a Singularity container on mox.hyak

srun -p xyz -A xyz -t 1:00:00 --pty /bin/bash
[abc@n2212 ~]$ module load singularity gcc_8.2.1-ompi_3.1.4
[abc@n2212 ~]$ singularity run --app ngsolve /sw/singularity-images/testing/ngsolve.sif


Further information:

See the below link for creating a Singularity image from a dockerfile:

Mox_docker



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