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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.
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:$
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:~>