{"id":5809,"date":"2012-01-26T12:27:37","date_gmt":"2012-01-26T10:27:37","guid":{"rendered":"http:\/\/www.ehu.es\/sgi\/?p=5809"},"modified":"2012-01-30T13:28:41","modified_gmt":"2012-01-30T11:28:41","slug":"towhee","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/scientific-software\/towhee","title":{"rendered":"MCCCS Towhee 7.0.2"},"content":{"rendered":"<p>Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases.<\/p>\n<h2>General Information<\/h2>\n<p>Towhee serves as a useful tool for the molecular simulation community and allows science to move forward more quickly by eliminating the need for individual research groups to rewrite routines that already exist and instead allows them to focus on algorithm advancement, force field development, and application to interesting systems.<\/p>\n<p>Towhee may use different type of ensembles and Monte Carlo moves implemented into Towhee and can alos used different \u00a0force fields included with the distribution. (<a href=\"http:\/\/towhee.sourceforge.net\/towhee_capabilities.html\">See here for more information <\/a>)<\/p>\n<h2>How to Use<\/h2>\n<p><strong>send_towhee<\/strong><\/p>\n<ul>\n<li>\ufeffTo send Towhee to the queue\u00a0system \u00a0use the send_gulp utility.\u00a0When\u00a0executed,<br \/>\nshows\u00a0the\u00a0command\u00a0syntax,\u00a0which is\u00a0summarized\u00a0below:<\/li>\n<li><tt>send_towhee JOBNAME NODES PROCS_PER_NODE TIME [ MEM ] [``Other queue options'' ]<\/tt><\/li>\n<\/ul>\n<table cellpadding=\"3\">\n<tbody>\n<tr>\n<td align=\"LEFT\"><tt><strong>JOBNAME<\/strong>:<\/tt><\/td>\n<td align=\"LEFT\">Is the \u00a0name of the Output.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt><strong>NODES<\/strong>:<\/tt><\/td>\n<td align=\"LEFT\">Number of nodes.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt><strong>PROCS<\/strong>:<\/tt><\/td>\n<td align=\"LEFT\">Number of \u00a0processors.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt><strong>TIME<\/strong>:<\/tt><\/td>\n<td align=\"LEFT\">Time requested to the queue system, format\u00a0<tt>hh:mm:ss.<\/tt><\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt><strong>MEM<\/strong>:<\/tt><\/td>\n<td align=\"LEFT\"><strong>Optional<\/strong>. Memory in Gb ( It will used 1GB\/core if not set).<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><strong><tt>[``Other Torque Options'' ]<\/tt><\/strong><\/td>\n<td align=\"LEFT\"><strong>Optional<\/strong>. There is\u00a0the possibility to pass\u00a0more variables\u00a0to the\u00a0queuing system.<br \/>\nSee examples\u00a0below.\u00a0\ufeff\u00a0<a href=\"http:\/\/www.ehu.es\/sgi\/mandar-trabajos\/comandos-de-interes-del-sistema-de-colas\"> More information about this options<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>Examples<\/h3>\n<p>We send\u00a0a Towhee job1\u00a0to\u00a01 node,\u00a04\u00a0processors\u00a0on that node,\u00a0with\u00a0a\u00a0requested time\u00a0of 4\u00a0hours . The results will be in the OUT file.<\/p>\n<pre><tt>send_towhee OUT 1 4 04:00:00<\/tt><\/pre>\n<p>We send job2 \u00a0to 2\u00a0compuation nodes,\u00a08\u00a0processors\u00a0on each\u00a0node,\u00a0with\u00a0a requested time\u00a0of 192\u00a0hours,\u00a08\u00a0GB\u00a0of\u00a0RAM\u00a0and to start running\u00a0after\u00a0work\u00a01234.arinab is finished:<\/p>\n<pre><tt>send_towhee OUT 2 8 192:00:00 8 ``-W depend=afterany:1234'<\/tt><\/pre>\n<p>We \u00a0send\u00a0the\u00a0input\u00a0job3\u00a0to\u00a04\u00a0nodes\u00a0and\u00a04\u00a0processors\u00a0on\u00a0each\u00a0node,\u00a0with\u00a0arequested time\u00a0of\u00a0200:00:00\u00a0hours,\u00a02\u00a0GB\u00a0of\u00a0RAM\u00a0and\u00a0we request to be\u00a0send an\u00a0email\u00a0at the beginning\u00a0and\u00a0end of the\u00a0calculation\u00a0to the direction\u00a0specified.<\/p>\n<pre><tt>send_towhee OUT 4 4 200:00:00 2 ``-m be -M mi.email@ehu.es''<\/tt><\/pre>\n<p>\ufeffsend_towhee command\u00a0copies\u00a0the\u00a0contents\u00a0of the\u00a0directory\u00a0from\u00a0which the job is sent to\u00a0\/scratch\u00a0or\u00a0\/\u00a0gscratch,\u00a0if\u00a0we use 2\u00a0or more\u00a0nodes.\u00a0And\u00a0there is where\u00a0the calculation is done.<\/p>\n<h2>Jobs Monitoring<\/h2>\n<p>\ufeffTo\u00a0facilitate monitoring and\/or\u00a0control\u00a0of the Towhee calculations, you can use\u00a0<strong>remote_vi<\/strong><\/p>\n<pre>remote_vi JOBID<\/pre>\n<p>It show us\u00a0the *.out file \u00a0(only\u00a0if it was\u00a0sent\u00a0using\u00a0send_towhee).<\/p>\n<div>\n<h2>More information<\/h2>\n<\/div>\n<p>\ufeff<a href=\"http:\/\/towhee.sourceforge.net\/\">http:\/\/towhee.sourceforge.net\/<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases. &hellip; <a href=\"https:\/\/www.ehu.eus\/sgi\/scientific-software\/towhee\" class=\"more-link\">Seguir leyendo <span class=\"screen-reader-text\">MCCCS Towhee 7.0.2<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_links_to":"","_links_to_target":""},"categories":[212,196,216],"tags":[],"_links":{"self":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/5809"}],"collection":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/comments?post=5809"}],"version-history":[{"count":4,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/5809\/revisions"}],"predecessor-version":[{"id":5973,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/5809\/revisions\/5973"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=5809"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=5809"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=5809"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}