{"id":61,"date":"2009-11-22T22:01:00","date_gmt":"2009-11-22T22:01:00","guid":{"rendered":"http:\/\/zensonic.dk\/?p=61"},"modified":"2017-04-09T10:03:56","modified_gmt":"2017-04-09T10:03:56","slug":"problems-continuing-calculations-on-using-schrodinger-checkpoint-files","status":"publish","type":"post","link":"https:\/\/zensonic.dk\/?p=61","title":{"rendered":"Problems continuing calculations on using Schr\u00c3\u00b6dinger checkpoint files."},"content":{"rendered":"<p>I recently helped identifying a problem with continuing calculations from a checkpoint file performed by desmond of the Schr\u00c3\u00b6dinger software portfolio. The error we got was<\/p>\n<pre style=\"text-align: center;\">fail to extract simulation parameters from checkpoint file &lt;filename&gt;<\/pre>\n<p>It worked for a lot of people, but not for others. I searched high and low for differences:<\/p>\n<ul>\n<li>Different unix environment settings.<\/li>\n<li>Differnet MPI settings (intel mpi vs. gcc mpi vs. software mpi)<\/li>\n<li>Different permission settings on home dirs<\/li>\n<li>Differences in groupmembership between those who could continue calculations and those who couldn&#8217;t.<\/li>\n<li>Performing the calculations on different nodes in the calculation clusters.<\/li>\n<\/ul>\n<p>As it turned out it was neither of these points that was responsible for problems. Instead it was the use of non-english chars in the comment field in the \/etc\/password file for the users who could not continue the calculations from a checkpoint file. The fix for this is simple:<\/p>\n<pre style=\"text-align: center;\">usermod -c \"new name, only english chars\" &lt;userid&gt;<\/pre>\n<p>Everything was fine after that.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>I recently helped identifying a problem with continuing calculations from a checkpoint file performed by desmond of the Schr\u00c3\u00b6dinger software portfolio. The error we got was fail to extract simulation parameters from checkpoint file &lt;filename&gt; It worked for a lot of people, but not for others. I searched high and low for differences: Different unix [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[6,3],"tags":[],"class_list":["post-61","post","type-post","status-publish","format-standard","hentry","category-unix","category-work"],"_links":{"self":[{"href":"https:\/\/zensonic.dk\/index.php?rest_route=\/wp\/v2\/posts\/61"}],"collection":[{"href":"https:\/\/zensonic.dk\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/zensonic.dk\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/zensonic.dk\/index.php?rest_route=\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/zensonic.dk\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=61"}],"version-history":[{"count":0,"href":"https:\/\/zensonic.dk\/index.php?rest_route=\/wp\/v2\/posts\/61\/revisions"}],"wp:attachment":[{"href":"https:\/\/zensonic.dk\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/zensonic.dk\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/zensonic.dk\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}