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 3.8.6-1 is installed on the iCSF.<\/p>\n The software is licensed under the BSD 3-clause “New” or “Revised” License<\/a>.<\/p>\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 You may run the command on its own to obtain a list of flags:<\/p>\n Please note that users will not be permitted to run singularity containers in You may want to use your own containers on the iCSF – that’s fine. You will need to have the ‘\/scratch’ directory within the container to bind to the ‘\/scratch’ directory on the iCSF.<\/p>\n If building from a .def file, please include the line<\/p>\n in the “%post” section.<\/p>\n If using a prebuilt sif (or simg), then follow the steps below to rebuild with a ‘\/scratch’ directory within:<\/p>\n Please note this will not<\/strong> work on the iCSF – as you cannot have sudo (admin) rights. The steps are necessary before<\/em> the image is used on the iCSF. If you cannot, we can do this for you: its-ri-team@manchester.ac.uk<\/a>.<\/p>\n Many Docker images exist that can be converted to singularity images, then uploaded to the iCSF and run. As before, these steps must be completed on your own machine with a singularity \/ apptainer install. The Please remember to bind scratch (and also \/mnt which will make your home directory available) and run your jobs from there:<\/p>\n Alternatively, you can set the following environment variable:<\/p>\n You can build your own sifs for use on the iCSF via the online resource: https:\/\/cloud.sylabs.io\/builder<\/a><\/p>\n Please remember to include <\/p>\n in the definition instructions. Be aware also that this resource is not affiliated with The University of Manchester.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview Singularity provides a mechanism to run containers where containers can be used to package entire scientific workflows, software and libraries, and even data. Version 3.8.6-1 is installed on the iCSF. Restrictions on use The software is licensed under the BSD 3-clause “New” or “Revised” License. Set up procedure Please note: 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.. Read more »<\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"parent":43,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1252","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/1252","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=1252"}],"version-history":[{"count":1,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/1252\/revisions"}],"predecessor-version":[{"id":1253,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/1252\/revisions\/1253"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=1252"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
# Ensure you have NO singularity modulefiles loaded ('module purge' will unload all modulefiles)\r\n\r\n[username<\/em>@incline34 ~]$ singularity --version\r\nsingularity version 3.8.6-1.el7\r\n<\/pre>\nRunning the application<\/h2>\n
singularity\r\nUSAGE: singularity [global options...]
--writeable<\/code> mode. You should build containers on your own platform where you have root access.<\/p>\nRunning a container image<\/h3>\n
\r\nsingularity run mystack.simg\r\n<\/pre>\n
Further info<\/h2>\n
\n
Using your own containers<\/h2>\n
\r\n%post\r\n...\r\nmkdir \/scratch\r\n<\/pre>\n
\r\n# You must run these commands on your own Linux system (you don't have sudo rights on the iCSF)\r\nsudo singularity build --sandbox mysandbox myimage.sif\r\nsudo mkdir mysandbox\/scratch\r\nsudo singularity build myimage-icsf.sif mysandbox\r\n<\/pre>\n
Converting from a Docker container<\/h3>\n
\nThe example below uses https:\/\/hub.docker.com\/r\/cp2k\/cp2k\/<\/a>.<\/p>\n\r\n# You must run these commands on your own Linux system (you don't have sudo rights on the iCSF)\r\nsudo singularity build cp2k.sif docker:\/\/cp2k\/cp2k\r\nsingularity run cp2k.sif cp2k --version | head -1\r\n# returns 'CP2K version 2023.1', which we use to label\r\nsudo singularity build --sandbox cp2k-2023.1-sandbox cp2k.sif \r\nsudo mkdir cp2k-2023.1-sandbox\/scratch\r\nsudo singularity build cp2k-2023.1-csf.sif cp2k-2023.1-sandbox\r\n<\/pre>\n
cp2k-2023.1-csf.sif<\/code> can then be uploaded and run on the iCSF.<\/p>\n\r\nsingularity run --bind \/scratch:\/scratch,\/mnt:\/mnt my_container.sif arg1 arg2 ...<\/em>\r\n<\/pre>\n
\r\nexport SINGULARITY_BINDPATH=\"\/scratch,\/mnt\"\r\nsingularity run my_container.sif arg1 arg2 ...<\/em>\r\n<\/pre>\n
Building your own Singularity image<\/h3>\n
mkdir \/scratch<\/pre>\n
Updates<\/h2>\n