Difference between revisions of "Biocluster Singularity"
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__TOC__ | __TOC__ | ||
| + | == About == | ||
| + | * Containers contain applications in a way that keep them isolated from the host system that they run on. Containers allow a developer to package up an application with all of the parts it needs, such as libraries and other dependencies, and ship it all out as one package. | ||
| + | * Singularity is a program that can launch containers securely in a HPC environment. Other similar programs are Docker, LXD, and Kubernetes. | ||
| + | |||
== Module == | == Module == | ||
*Load Singularity Module to run any singularity commands | *Load Singularity Module to run any singularity commands | ||
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singularity exec r-base_latest.sif R | singularity exec r-base_latest.sif R | ||
</pre> | </pre> | ||
| + | |||
| + | == Storage == | ||
| + | * Your home folder is automatically mounted | ||
* You should have access to any group folders in /home/groups, /home/labs, and /private_stores | * You should have access to any group folders in /home/groups, /home/labs, and /private_stores | ||
* The local /scratch space is accessible. | * The local /scratch space is accessible. | ||
| − | == | + | == References == |
| − | * | + | * [https://singularity.lbl.gov/ https://singularity.lbl.gov/] |
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Revision as of 11:22, 3 February 2020
Contents
About[edit]
- Containers contain applications in a way that keep them isolated from the host system that they run on. Containers allow a developer to package up an application with all of the parts it needs, such as libraries and other dependencies, and ship it all out as one package.
- Singularity is a program that can launch containers securely in a HPC environment. Other similar programs are Docker, LXD, and Kubernetes.
Module[edit]
- Load Singularity Module to run any singularity commands
module load singularity/3.4.1
Creating Containers[edit]
- This can not be done on the Biocluster. It has to be done on your local machine. This is a security risk to allow users to create or edit containers on a HPC resource
Download Containers[edit]
- You need to use the biologin nodes (biologin-0 and biologin-1) to download containers
- This will not work from the compute nodes as they do not have access to the internet
- Download a pre-existing container from Singularity Hub - https://singularity-hub.org/. singularity-r is an example R container
singularity pull --name singularity-r.simg shub://nickjer/singularity-r
- Download a pre-existing container from Docker - https://hub.docker.com/. r-base is an example R container
singularity pull docker://r-base
Running Containers[edit]
- Do not use the biologin nodes (biologin-0 and biologin-1) to run containers. The login nodes are only allowed to be used to download containers
- From a compute node or a SLURM job script, run the following. r-base_latest.sif is name of the container. R is the program to run in the container. This can be bash to get a command line.
singularity exec r-base_latest.sif R
Storage[edit]
- Your home folder is automatically mounted
- You should have access to any group folders in /home/groups, /home/labs, and /private_stores
- The local /scratch space is accessible.
