{"id":819,"date":"2013-08-01T10:56:45","date_gmt":"2013-08-01T08:56:45","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2013\/08\/01\/raxml"},"modified":"2022-09-26T20:30:15","modified_gmt":"2022-09-26T18:30:15","slug":"raxml","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/","title":{"rendered":"RAxML"},"content":{"rendered":"<div>We recently deployed\u00a0<a href=\"http:\/\/sco.h-its.org\/exelixis\/software.html\">RAxML<\/a>\u00a0to our cluster. \u00a0RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel maximum likelihood based inference of large phylogenetic trees. It has 3 different modes of operation: \u00a0Sequential on one CPU only, MPI where jobs distribute work across multiple bootstraps (instantiations), Pthreads which gives most consistency and is well load balanced (the more threads the faster the job) and Hybrid which gives better options than MPI but is still dependent on the number of bootstraps.<\/div>\r\n<div>As expected the hybrid methods converge as the number of threads increase. \u00a0The Hybrid TxJ slows down as the number of bootstraps for this job was set at 2 and hence increasing the number of jobs does not improve performance.<\/div>\r\n<div><img src=\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/RAxML.jpg\" alt=\"RAxML\" border=\"0\" \/><\/div>\r\n<div>Our best times were produced on the GPU series as RAxML is highly memory intensive. \u00a0As the memory chips in the GPU servers are faster than the 600 series (1.6GHz vs 1.3GHz) the jobs ran faster. \u00a0Please note that the RAxML jobs were not running on the GPU cards but on the CPUs in the GPU servers. \u00a0From the graph below this software ranks in our top 10 for both hours per job and memory consumed per job:<\/div>\r\n<div><img src=\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/RAxML2.jpg\" alt=\"RAxML\" border=\"0\" \/><\/div>\r\n<div>NB, CUDA and MATLAB above indicate software written in that application and not the application itself.<\/div>","protected":false},"excerpt":{"rendered":"<p>    We recently deployed&nbsp;RAxML&nbsp;to our cluster. &nbsp;RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel maximum likelihood based inference of large phylogenetic trees. It has 3 different modes of operat&#8230;<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[4],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v21.4 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>RAxML - UCT HPC<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"RAxML - UCT HPC\" \/>\n<meta property=\"og:description\" content=\"We recently deployed&nbsp;RAxML&nbsp;to our cluster. &nbsp;RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel maximum likelihood based inference of large phylogenetic trees. It has 3 different modes of operat...\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/\" \/>\n<meta property=\"og:site_name\" content=\"UCT HPC\" \/>\n<meta property=\"article:published_time\" content=\"2013-08-01T08:56:45+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-09-26T18:30:15+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/RAxML.jpg\" \/>\n<meta name=\"author\" content=\"Andrew Lewis\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Andrew Lewis\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/\"},\"author\":{\"name\":\"Andrew Lewis\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/c183ad1c0a1063124a72d63963ae9c7e\"},\"headline\":\"RAxML\",\"datePublished\":\"2013-08-01T08:56:45+00:00\",\"dateModified\":\"2022-09-26T18:30:15+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/\"},\"wordCount\":213,\"publisher\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\"},\"articleSection\":[\"hpc\"],\"inLanguage\":\"en-ZA\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/\",\"name\":\"RAxML - UCT HPC\",\"isPartOf\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#website\"},\"datePublished\":\"2013-08-01T08:56:45+00:00\",\"dateModified\":\"2022-09-26T18:30:15+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/#breadcrumb\"},\"inLanguage\":\"en-ZA\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/ucthpc.uct.ac.za\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"RAxML\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#website\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/\",\"name\":\"UCT HPC\",\"description\":\"University of Cape Town High Performance Computing\",\"publisher\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/ucthpc.uct.ac.za\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-ZA\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\",\"name\":\"University of Cape Town High Performance Computing\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-ZA\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/09\/logocircless.png\",\"contentUrl\":\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/09\/logocircless.png\",\"width\":450,\"height\":423,\"caption\":\"University of Cape Town High Performance Computing\"},\"image\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/logo\/image\/\"}},{\"@type\":\"Person\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/c183ad1c0a1063124a72d63963ae9c7e\",\"name\":\"Andrew Lewis\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-ZA\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/image\/\",\"url\":\"https:\/\/secure.gravatar.com\/avatar\/9652c9c73beeab594b8dc2383a880048?s=96&d=mm&r=g\",\"contentUrl\":\"https:\/\/secure.gravatar.com\/avatar\/9652c9c73beeab594b8dc2383a880048?s=96&d=mm&r=g\",\"caption\":\"Andrew Lewis\"},\"sameAs\":[\"http:\/\/blogs.uct.ac.za\/blog\/big-bytes\"]}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"RAxML - UCT HPC","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/ucthpc.uct.ac.za\/index.php\/2013\/08\/01\/raxml\/","og_locale":"en_US","og_type":"article","og_title":"RAxML - UCT HPC","og_description":"We recently deployed&nbsp;RAxML&nbsp;to our cluster. &nbsp;RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel maximum likelihood based inference of large phylogenetic trees. 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