{"id":4878,"date":"2020-11-27T11:03:44","date_gmt":"2020-11-27T11:03:44","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4878"},"modified":"2020-11-27T11:03:44","modified_gmt":"2020-11-27T11:03:44","slug":"monai","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/monai\/","title":{"rendered":"Monai"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/docs.monai.io\/en\/latest\/index.html\">Monai<\/a> is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing the software on the CSF. It is released under the <a href=\"https:\/\/github.com\/Project-MONAI\/MONAI\/blob\/master\/LICENSE\">Apache 2.0 License<\/a> and all use must adhere to that license.<\/p>\n<h2>Set up procedure<\/h2>\n<p>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 <abbr title=\"add '#$ -V' to your jobscript\">inherit these settings<\/abbr>.<\/p>\n<p>Load one of the following modulefiles:<\/p>\n<pre>\r\nmodule load apps\/python\/monai\/0.3.0        # Loads Anaconda3 2020.07 (python 3.8)\r\n<\/pre>\n<p>The Anaconda Python modulefile will be loaded automatically.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run Monai on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\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\n# We recommend loading modulefiles in jobscripts. Use your requried version.\r\nmodule load apps\/python\/monai\/0.3.0\r\n\r\npython mymonai.py\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Given an example parallel jobscript, including suitable PE<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/docs.monai.io\/en\/latest\/index.html\">Monai docs website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Monai is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem Restrictions on use There are no restrictions on accessing the software on the CSF. It is released under the Apache 2.0 License and all use must adhere to that license. Set up procedure 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.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/monai\/\">Read more &raquo;<\/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-4878","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4878","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=4878"}],"version-history":[{"count":1,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4878\/revisions"}],"predecessor-version":[{"id":4879,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4878\/revisions\/4879"}],"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=4878"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}