{"id":822,"date":"2022-04-22T16:27:12","date_gmt":"2022-04-22T15:27:12","guid":{"rendered":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/?page_id=822"},"modified":"2022-04-22T16:33:58","modified_gmt":"2022-04-22T15:33:58","slug":"singularity","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf4\/software\/applications\/singularity\/","title":{"rendered":"Singularity"},"content":{"rendered":"

Overview<\/h2>\n

Singularity<\/a> provides a mechanism to run containers where containers can be used to package entire scientific workflows, software and libraries, and even data.<\/p>\n

Version 3.5.3-1.1 is installed on CSF4.<\/p>\n

Restrictions on use<\/h2>\n

The software is licensed under the BSD 3-clause “New” or “Revised” License<\/a>. <\/p>\n

Set up procedure<\/h2>\n

Please note:<\/strong> 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.<\/p>\n

For example:<\/p>\n

\r\n[username<\/em>@login02 [CSF4] ~]$ singularity --version\r\nsingularity version 3.5.3-1.1.el7\r\n<\/pre>\n
Running the application<\/h2>\n
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:<\/p>\n
\r\nsingularity\r\nUSAGE: singularity [global options...]  [command options...] ...\r\n\r\nONTAINER USAGE COMMANDS:\r\n    exec       Execute a command within container                               \r\n    run        Launch a runscript within container                              \r\n    shell      Run a Bourne shell within container                              \r\n    test       Launch a testscript within container                             \r\n\r\nCONTAINER MANAGEMENT COMMANDS:\r\n    apps       List available apps within a container                           \r\n    bootstrap  *Deprecated* use build instead                                   \r\n    build      Build a new Singularity container                                \r\n    check      Perform container lint checks                                    \r\n    inspect    Display container's metadata                                     \r\n    mount      Mount a Singularity container image                              \r\n    pull       Pull a Singularity\/Docker container to $PWD\r\n<\/pre>\n
Please note that users will not be permitted to run singularity containers in --writeable<\/code> mode. You should build containers on your own platform where you have root access.<\/p>\n
Serial batch job<\/h3>\n
Create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash --login \r\n#SBATCH -p serial            # Optional, default partition is serial\r\n#SBATCH -n 1                 # Optional, jobs in serial partition always use 1 core\r\n\r\nsingularity run mystack<\/em>.simg\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
sbatch scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Single-node Parallel batch job<\/h3>\n
You should check the Singularity Documentation<\/a> 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<\/code> in the jobscript.<\/p>\n
Create a jobscript similar to the following:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#SBATCH -p multicore        # Single-node parallel job\r\n#SBATCH -n 8                # Number of cores, can be 2--40\r\n\r\n# mpirun knows how many cores to use\r\nmpirun singularity exec name_of_container<\/em> name_of_app_inside_container<\/em>\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
sbatch scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Multi-node Parallel batch job<\/h3>\n
You should check the Singularity Documentation<\/a> 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<\/code> in the jobscript.<\/p>\n
Create a jobscript similar to the following:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#SBATCH -p multinode        # Multi-node parallel job\r\n#SBATCH -n 120              # Number of cores, can be 80 or more in multiples of 40\r\n\r\n# mpirun knows how many cores to use\r\nmpirun singularity exec name_of_container<\/em> name_of_app_inside_container<\/em>\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
sbatch scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n