{"id":2310,"date":"2019-02-18T13:18:56","date_gmt":"2019-02-18T13:18:56","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=2310"},"modified":"2019-02-18T13:33:28","modified_gmt":"2019-02-18T13:33:28","slug":"mdanalysis","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/mdanalysis\/","title":{"rendered":"MDAnalysis"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/www.mdanalysis.org\/\">MDAnalysis<\/a> is a program to<\/p>\n<p>Version 0.19.2 is installed on the CSF and is part of the anaconda3 installation.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing MDanalysis on the CSF. The source is released under the GNU GPL v2 license.<\/p>\n<p>All users should cite their use of the software as per the <a href=\"https:\/\/www.mdanalysis.org\/pages\/citations\/\">MDAnalysis website<\/a>.<\/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 the anaconda python:<\/p>\n<pre>\r\nmodule load apps\/anaconda3\/5.2.0\/bin\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Include the following in your python code<\/p>\n<pre>\r\nimport MDAnalysis\r\n<\/pre>\n<p>Please do not run MDAnalysis jobs on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<p>Please refer to the <a href=\"\/csf3\/software\/applications\/anaconda-python\/\">CSF Anaconda Python documentation for further guidance.<\/p>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview MDAnalysis is a program to Version 0.19.2 is installed on the CSF and is part of the anaconda3 installation. Restrictions on use There are no restrictions on accessing MDanalysis on the CSF. The source is released under the GNU GPL v2 license. All users should cite their use of the software as per the MDAnalysis website. Set up procedure We now recommend loading modulefiles within your jobscript so that you have a full record.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/mdanalysis\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-2310","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2310","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\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=2310"}],"version-history":[{"count":6,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2310\/revisions"}],"predecessor-version":[{"id":2317,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/2310\/revisions\/2317"}],"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=2310"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}