{"id":2021,"date":"2010-09-21T12:58:06","date_gmt":"2010-09-21T10:58:06","guid":{"rendered":"http:\/\/www.ehu.es\/sgi\/Arina\/?p=2021"},"modified":"2016-02-12T12:59:47","modified_gmt":"2016-02-12T10:59:47","slug":"namd-2","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/kalkulu-softwarea\/namd-2","title":{"rendered":"NAMD"},"content":{"rendered":"<p>Illinois-eko Uniberstitateak Dinamika Molekularreko kulkuluak egiten dituen kodea da NAMD. 2.6 Bertsioa dago instalatuta.<br \/>\n<!--more--><\/p>\n<h2>Nola Erabili<\/h2>\n<p>Softwarea <code>\/software\/NAMD_2.8_Linux-x86_64-ibverbs<\/code>\u00a0katalogoan dago instalatuta, eta<br \/>\n<tt>send_namd<\/tt> scripta sortu dugu NAMD lanak bidaltzeko.<\/p>\n<p>Hurrengo modura bidali daiteke NAMD arina zein Pendulon:<\/p>\n<ul>\n<li>send_namd erabiliz.<\/li>\n<li>Torque script bat sortu eta hau kolara bidaliz.<\/li>\n<\/ul>\n<ol>\n<li><strong>send_namd<\/strong>\n<ul>\n<li>Agindu hau aldagairik gabe egikaritzean, erabilera erakusten du.<\/li>\n<li>Erabiltzeko modua :\u00a0send_namd JOBNAME NODES PROCS_PER_NODE[property] TIME MEM [\u00abOther queue options\u00bb ]<\/li>\n<\/ul>\n<table cellpadding=\"3\">\n<tbody>\n<tr>\n<td align=\"LEFT\"><tt>JOBNAME:<\/tt><\/td>\n<td align=\"LEFT\">NAMD fitxetegiaren inputa extensioa barne.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\">NODES:<\/td>\n<td align=\"LEFT\">Nodo kopurua.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt>PROCS:<\/tt><\/td>\n<td align=\"LEFT\">Prozesagailu kopurua.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt>TIME:<\/tt><\/td>\n<td align=\"LEFT\">Kalkulua egiteko eskatzen den denbora <tt>hh:mm:ss<\/tt> formatuan.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt>MEM:<\/tt><\/td>\n<td align=\"LEFT\">memoria Gb-etan.<\/td>\n<\/tr>\n<tr>\n<td align=\"LEFT\"><tt>[`` Torque beste aukerak'' ]<\/tt><\/td>\n<td align=\"LEFT\">Kola sistemari pasa nahi zaizkion beste aginduen zerrenda.<br \/>\nIkus adibideak. [intlink id=\u00bb632&#8243; type=\u00bbpost\u00bb]. informazio gehiago[\/intlink]<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>Adibideak:<\/h3>\n<p><tt>send_namd job.namd 1 8 04:00:00 1<\/tt><\/p>\n<p><tt>send_namd job2.conf 8 192:00:00 8 ``-W depend=afterany:1234'<\/tt>&#8216;<\/li>\n<\/ol>\n<h2>Kalkuluen Monitorizazioa:<\/h2>\n<p>remote_vi erabili daiteke lanen egoera ikusteko, *.out fitxategia irekiko du gvin editorearekin (bakarrik<tt>send_namd<\/tt> erabili bada lana bidaltzeko).<\/p>\n<p>Adibidea:<\/p>\n<p><tt>remote_vi <\/tt>38143.arina<\/p>\n<h2>Benchmarkak<\/h2>\n<p>Hainbat benchmark egin ditugu NAMD-akin eta hau da ikusitakoa:<\/p>\n<p>&nbsp;<\/p>\n<table border=\"1\" cellpadding=\"3\">\n<tbody>\n<tr>\n<td align=\"CENTER\">nodesxCores<\/td>\n<td align=\"CENTER\">xeon8 (days\/ns)<\/td>\n<td align=\"CENTER\">xeon12\u00a0(days\/ns)<\/td>\n<td align=\"CENTER\">zeon20 (days\/ns)<\/td>\n<\/tr>\n<tr>\n<td align=\"CENTER\">1&#215;4<\/td>\n<td align=\"CENTER\">4.99249<\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\">3.84913<\/td>\n<\/tr>\n<tr>\n<td align=\"CENTER\">1&#215;8<\/td>\n<td align=\"CENTER\">2.50337<\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\">2.10316<\/td>\n<\/tr>\n<tr>\n<td align=\"CENTER\">2&#215;8<\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\">0.836564<\/td>\n<\/tr>\n<tr>\n<td align=\"CENTER\">3&#215;8<\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\">0.773642<\/td>\n<\/tr>\n<tr>\n<td align=\"CENTER\">4&#215;8<\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\">0.683973<\/td>\n<\/tr>\n<tr>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\"><\/td>\n<\/tr>\n<tr>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\"><\/td>\n<td align=\"CENTER\"><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>8 Core arte, itanium arkitektura da eraginkorrena, baina nodo bat baino gehiago erabiltzean, eraginkortasuna erabat galzen da. Pendulon berriz, NAMD-ek askoz hobeto eskalatzen duenez,arkitektura horretarako oso programa egokia dela deritzogu, kalkuluak 16\/32 Coretan egin daitezkelarik.<\/p>\n<h2>Informazio Gehiago:<\/h2>\n<p><a href=\"http:\/\/www.ks.uiuc.edu\/Research\/namd\" target=\"_top\">NAMD home page<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Illinois-eko Uniberstitateak Dinamika Molekularreko kulkuluak egiten dituen kodea da NAMD. 2.6 Bertsioa dago instalatuta.<\/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":[66],"tags":[],"_links":{"self":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/2021"}],"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=2021"}],"version-history":[{"count":8,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/2021\/revisions"}],"predecessor-version":[{"id":8388,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/2021\/revisions\/8388"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=2021"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=2021"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=2021"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}