Compucell3d<\/a> is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials.<\/p>\n Version 4.2.4 is installed on the CSF, via a singularity image.<\/p>\n There are no restrictionson access Compucell3d on the CSF.<\/p>\n We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n Load one of the following modulefiles:<\/p>\n Please do not run compucell3d on the login node. The GUI should be used via an interactive session<\/em> (see below). Non-GUI jobs should be submitted to the compute nodes via batch.<\/p>\n Please DO NOT run the compucell3d GUI on the login node. The login node is a light-weight node for job-submission and file management. <\/p>\n Instead please start an interactive session<\/em>. This will log you in to one of the back-end compute-nodes (where batch jobs usually run) and allow you to use it as though you were at the login node. The compute nodes are more powerful – they have more memory and more CPU cores.<\/p>\n So please run:<\/p>\n Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n Submit the jobscript using: <\/p>\n where scriptname<\/em> is the name of your jobscript.<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview Compucell3d is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. Version 4.2.4 is installed on the CSF, via a singularity image. Restrictions on use There are no restrictionson access Compucell3d on the CSF. Set up procedure We now.. Read more »<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-5292","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5292","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=5292"}],"version-history":[{"count":2,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5292\/revisions"}],"predecessor-version":[{"id":10395,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/5292\/revisions\/10395"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=5292"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/singularity\/compucell3d\/4.2.4\r\n<\/pre>\n
Running the application<\/h2>\n
Interactive Gui session<\/h3>\n
\r\n# To use a single CPU core run the following on the login node\r\nqrsh -l inter\r\n #\r\n # Wait until you logged in to a backend node.\r\n\r\n# Now on the backend node\r\nmodule load apps\/singularity\/compucell3d\/4.2.4\r\n\r\n# Start the app\r\ncompucell3d\r\n #\r\n # Occasionally you might be asked if you like to install a new version.\r\n # Please click No (you don't have write-permission to the install area).\r\n # Instead contact us<\/a> to tell use a new version\r\n # is available.\r\n\r\n# You can also run these apps\r\nparamScan.sh\r\nrunScript.sh\r\ntwedit++.sh\r\n\r\n# When you have finished with your interactive session, to go back to the login node:\r\nexit\r\n<\/pre>\n
Serial batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\n # NO -V line - we load modulefiles in the jobscript\r\n\r\nmodule load apps\/singularity\/compucell3d\/4.2.4\r\n\r\nrunScript.sh -i INPUT<\/em> args...<\/em>\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Parallel batch job submission<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd # Job will run from the current directory\r\n#$ -pe smp.pe 8 # Number of cores (can be 2--32)\r\n # NO -V line - we load modulefiles in the jobscript\r\n\r\nmodule load apps\/singularity\/compucell3d\/4.2.4\r\n\r\n# Inform python how many cores it can use\r\nexport OMP_NUM_THREADS=$NSLOTS\r\n\r\nrunScript.sh -i INPUT<\/em> args...<\/em>\r\n<\/pre>\n
qsub scriptname<\/em><\/pre>\n
Further info<\/h2>\n
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Updates<\/h2>\n