User Tools

Site Tools


singularity

This is an old revision of the document!


Singularity

Singularity http://singularity.lbl.gov/ is a software container system. It allows users to build and run entire scientific workflows, software and libraries using a specific distribution and version of Linux all packaged into a single image file. It is based on the Linux “chroot” command which allows users to switch the environment from the operating system installed on the host node to the one inside the singularity image file.

Many pre-built container images are available for download in the singularity hub https://singularity-hub.org/ and the docker hub https://singularity-hub.org/ repositories.

Local Image Files

Start an interactive job and load the singularity module

razor-l2:pwolinsk:$ qsub -I -q tiny12core -l walltime=1:00:00 -l nodes=1:ppn=12
qsub: waiting for job 3608596.sched to start
qsub: job 3608596.sched ready
compute1144:pwolinsk:$ module load singularity

Open a shell inside a prebuilt container stored locally on Razor in /share/apps/singularity/images/hello-world.simg

compute1144:pwolinsk:$ cat /etc/issue
CentOS release 6.8 (Final)
Kernel \r on an \m

compute1144:pwolinsk:$ singularity shell /share/apps/singularity/images/hello-world.simg 
Singularity: Invoking an interactive shell within container...

Singularity hello-world.simg:~> cat /etc/issue
Ubuntu 14.04.5 LTS \n \l

Singularity hello-world.simg:~> exit
exit
compute1144:pwolinsk:$ 

Remote Repository Image Files

Open a shell inside a container stored on singularity hub shub:/ /vsoch/hello-world

compute1144:pwolinsk:$ singularity shell shub://vsoch/hello-world
Progress |===================================| 100.0% 
Singularity: Invoking an interactive shell within container...

Singularity vsoch-hello-world-master.simg:~> cat /etc/issue
Ubuntu 14.04.5 LTS \n \l

Singularity vsoch-hello-world-master.simg:~> 

Open a shell inside a container pulled for the docker repository

compute1144:pwolinsk:$ singularity shell docker://ubuntu
Docker image path: index.docker.io/library/ubuntu:latest
Cache folder set to /gpfs_home/pwolinsk/.singularity/docker
[5/5] |===================================| 100.0% 
Creating container runtime...
Singularity: Invoking an interactive shell within container...

Singularity ubuntu:~> cat /etc/issue
Ubuntu 16.04.3 LTS \n \l

Singularity ubuntu:~> 
singularity.1512161497.txt.gz · Last modified: 2017/12/01 20:51 by pwolinsk