{"id":462,"date":"2021-01-18T13:57:33","date_gmt":"2021-01-18T18:57:33","guid":{"rendered":"https:\/\/psycomp.utsc.utoronto.ca\/support\/?p=462"},"modified":"2021-01-18T14:33:49","modified_gmt":"2021-01-18T19:33:49","slug":"run-afni-on-cluster","status":"publish","type":"post","link":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/2021\/01\/18\/run-afni-on-cluster\/","title":{"rendered":"Run AFNI on Cluster"},"content":{"rendered":"<p><strong>Please be noted that SUMA (suma) won&#8217;t run when connecting to the cluster using X2Go, so we have to use <a href=\"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/2021\/01\/18\/connect-to-cluster-with-gui-using-ssh-command\/\">ssh (Linux \/ MacOS users)<\/a> or <a href=\"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/2021\/01\/18\/connect-to-cluster-with-gui-using-git-bash-and-vcxsrv\/\">git bash (Windows users)<\/a> to connect to the cluster if we need to run suma.<\/strong><\/p>\r\n<strong>After you connect to the head node, you can start a Slurm session using the following command, for example:<\/strong>\r\n<pre>\r\nsrun -c 12 --x11 --pty bash -i\r\n<\/pre>\r\n<strong>Then load the &#8220;afni&#8221; module:<\/strong>\r\n<pre>\r\nmodule load afni\r\n<\/pre>\r\nThe first time you run the above command, it will configure AFNI for you and copy the default data to your home folder. Configuration and data copying won&#8217;t happen again unless your &#8220;~\/.afnirc&#8221; file is deleted or modified, or a newer version of AFNI is available on the cluster.<br\/><br\/>\r\n<strong>We can then run &#8220;afni&#8221; or &#8220;suma&#8221; commands, for example, to check vesions and the current AFNI installation:<\/strong>\r\n<pre>\r\nafni -version\r\n<\/pre>\r\n<pre>\r\nsuma -version\r\n<\/pre>\r\n<pre>\r\nafni_system_check.py -check_all\r\n<\/pre>\r\n<p><strong>The current AFNI version is AFNI_21.0.03 (Jan 14, 2021).<\/strong><\/p>\r\n","protected":false},"excerpt":{"rendered":"<p>Please be noted that SUMA (suma) won&#8217;t run when connecting to the cluster using X2Go, so we have to use ssh (Linux \/ MacOS users) or git bash (Windows users) to connect to the cluster if we need to run &hellip;<\/p>\n<p class=\"read-more\"> <a class=\"\" href=\"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/2021\/01\/18\/run-afni-on-cluster\/\"> <span class=\"screen-reader-text\">Run AFNI on Cluster<\/span> Read More &raquo;<\/a><\/p>\n","protected":false},"author":5,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[3,7,2,10,4],"tags":[],"class_list":["post-462","post","type-post","status-publish","format-standard","hentry","category-clusterinfo","category-linuxshell","category-quickstart","category-slurm","category-software"],"_links":{"self":[{"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/posts\/462","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/comments?post=462"}],"version-history":[{"count":14,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/posts\/462\/revisions"}],"predecessor-version":[{"id":464,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/posts\/462\/revisions\/464"}],"wp:attachment":[{"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/media?parent=462"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/categories?post=462"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/psycomp.utsc.utoronto.ca\/support\/index.php\/wp-json\/wp\/v2\/tags?post=462"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}