{"id":99,"date":"2016-04-08T15:08:03","date_gmt":"2016-04-08T13:08:03","guid":{"rendered":"http:\/\/benediktehinger.de\/blog\/science\/?p=99"},"modified":"2020-06-01T13:00:23","modified_gmt":"2020-06-01T11:00:23","slug":"sun-grid-engine-command-dump","status":"publish","type":"post","link":"https:\/\/benediktehinger.de\/blog\/science\/sun-grid-engine-command-dump\/","title":{"rendered":"Sun Grid Engine Command-Dump"},"content":{"rendered":"<p>Here in the institute we have a Sun Grid Engine available. It is a tool to post computing-jobs on other workspaces (we have I think up to 60 available). There are certain commands and things that I do regularly which I tend to forget after half a year, or which might be useful for orthes.<\/p>\n<ul>\n<li><strong>Show all jobs that are running on the grid<\/strong><br \/>\n<code>qstat -u \\*<\/code> or alternativly for a single user <code>qstat -u behinger<\/code><\/li>\n<li><strong>exclude a single computer\/host from running a job<\/strong><br \/>\n<code>qsub -l mem=5G,h=!computername.domain script.sh<\/code><br \/>\nto exclude multiple hosts: <code> h=!h4&amp;!h5 or h=!(h4|h5) <\/code>  <a href=\"http:\/\/stackoverflow.com\/questions\/9263327\/exclude-certain-nodes-when-submitting-jobs-with-qsub-torque\"> Source <\/a><br \/>\nof course <code>mem=5G<\/code> is an arbitrary other requirement.<\/li>\n<li><strong>Run a gridjob on a single R-File<\/strong><br \/>\nadd <code>#!\/usr\/bin\/Rscript<\/code>  in the beginning of the file, then you can simply run  <code>qsub Rscript_name.R<\/code>. I had problems using <code>qsub Rscript -e \"Rscript_name.R\"<\/code> due to the many quotes that would need escaping (I use to call the grid using <code>system()<\/code> command in matlab\/R).<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Here in the institute we have a Sun Grid Engine available. It is a tool to post computing-jobs on other workspaces (we have I think up to 60 available). There are certain commands and things that I do regularly which I tend to forget after half a year, or which might be useful for orthes. Show all jobs that are running on the grid qstat -u \\* or alternativly for a single user qstat -u behinger exclude a single computer\/host from running a job qsub -l mem=5G,h=!computername.domain script.sh to exclude multiple hosts: h=!h4&amp;!h5 or h=!(h4|h5) Source of course mem=5G is&#8230;<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[5],"tags":[],"class_list":["post-99","post","type-post","status-publish","format-standard","hentry","category-blog"],"_links":{"self":[{"href":"https:\/\/benediktehinger.de\/blog\/science\/wp-json\/wp\/v2\/posts\/99","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/benediktehinger.de\/blog\/science\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/benediktehinger.de\/blog\/science\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/benediktehinger.de\/blog\/science\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/benediktehinger.de\/blog\/science\/wp-json\/wp\/v2\/comments?post=99"}],"version-history":[{"count":0,"href":"https:\/\/benediktehinger.de\/blog\/science\/wp-json\/wp\/v2\/posts\/99\/revisions"}],"wp:attachment":[{"href":"https:\/\/benediktehinger.de\/blog\/science\/wp-json\/wp\/v2\/media?parent=99"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/benediktehinger.de\/blog\/science\/wp-json\/wp\/v2\/categories?post=99"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/benediktehinger.de\/blog\/science\/wp-json\/wp\/v2\/tags?post=99"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}