{"id":1768,"date":"2015-08-06T21:09:40","date_gmt":"2015-08-06T19:09:40","guid":{"rendered":"http:\/\/srvcnthpc001.uct.ac.za\/?page_id=1768"},"modified":"2022-11-04T10:22:03","modified_gmt":"2022-11-04T08:22:03","slug":"supported-software","status":"publish","type":"page","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/supported-software\/","title":{"rendered":"Supported Software"},"content":{"rendered":"<section class=\"l-section wpb_row height_medium\"><div class=\"l-section-h i-cf\"><div class=\"g-cols vc_row type_default valign_top\"><div class=\"vc_col-sm-12 wpb_column vc_column_container\"><div class=\"vc_column-inner\"><div class=\"wpb_wrapper\">\r\n\t<div class=\"wpb_text_column \">\r\n\t\t<div class=\"wpb_wrapper\">\r\n\t\t\t<h2 style=\"text-align: center;\">Cluster Software<\/h2>\n<p>Apart from the base OS software (gcc, python and perl) by default all software is installed into a shared folder called \/opt\/exp_soft. This is visible to all worker nodes. Some software can be called directly by referencing the path, for example \/opt\/exp_soft\/MySoft\/bin\/MySoft. Other software requires multiple path and environmental variables to be set correctly. To assist in this we run the module package on all servers. To see a list of all modules type:<\/p>\n<pre>module avail<\/pre>\n<p>This is a long list and you will need to press enter or space to &#8216;tab&#8217; through it completely to return to the prompt.<\/p>\n<p>To activate a module type:<\/p>\n<pre>module load modulename<\/pre>\n<p>Python and R users should be extra cautious as there are default versions of these programs available on all worker nodes. It is recommended that the miniconda version of python be used instead, for example:<\/p>\n<pre>module load python\/miniconda3-py39<\/pre>\n<p>The module statement should be placed in your shell script, or executed once an interactive job has started. You may also place module commands in your .bashrc file, just exercise caution as this may come back to bite you if you forget about it and try to load a similar module in a shell script.<\/p>\n<p>Additional commands:<\/p>\n<pre>module list \u00a0- shows which modules you have loaded\r\n\r\nmodule unload modulename\u00a0 \u00a0- unload a specific module\r\n\r\nmodule purge\u00a0  - unload all modules<\/pre>\n<hr \/>\n<p>&nbsp;<\/p>\n\r\n\t\t<\/div>\r\n\t<\/div>\r\n<div class=\"w-tabs layout_timeline icon_chevron iconpos_right \"><div class=\"w-tabs-list items_1\"><div class=\"w-tabs-list-h\"><div class=\"w-tabs-item active\"><a href=\"#1532523762245-7c979b82-e507\" class=\"w-tabs-item-h\"><span class=\"w-tabs-item-title\">HPC<\/span><\/a><\/div>\n<\/div><\/div><div class=\"w-tabs-sections\"><div class=\"w-tabs-sections-h\"><div class=\"w-tabs-section active\" id=\"1532523762245-7c979b82-e507\"><a href=\"#1532523762245-7c979b82-e507\" class=\"w-tabs-section-header\"><div class=\"w-tabs-section-header-h\"><div class=\"w-tabs-section-title\">HPC<\/div><div class=\"w-tabs-section-control\"><\/div><\/div><\/a><div class=\"w-tabs-section-content\"><div class=\"w-tabs-section-content-h i-cf\">\r\n\t<div class=\"wpb_text_column \">\r\n\t\t<div class=\"wpb_wrapper\">\r\n\t\t\t<p><center><strong>HPC Cluster Supported Software:<\/strong><\/center><style type=\"text\/css\">\r\n       .errordiv { padding:10px; margin:10px; border: 1px solid #555555;color: #000000;background-color: #f8f8f8; width:500px; }#advanced_iframe {visibility:visible;opacity:1;vertical-align:top;}.ai-info-bottom-iframe { position: fixed; z-index: 10000; bottom:0; left: 0; margin: 0px; text-align: center; width: 100%; background-color: #ff9999; padding-left: 5px;padding-bottom: 5px; border-top: 1px solid #aaa } a.ai-bold {font-weight: bold;}#ai-layer-div-advanced_iframe p {height:100%;margin:0;padding:0}<\/style><script type=\"text\/javascript\">var ai_iframe_width_advanced_iframe = 0;var ai_iframe_height_advanced_iframe = 0;var aiIsIe8=false;var aiOnloadScrollTop=\"true\";var aiShowDebug=false;\r\n\t\tif (typeof aiReadyCallbacks === 'undefined') {\r\n\t\t\tvar aiReadyCallbacks = [];  \r\n\t\t} else if (!(aiReadyCallbacks instanceof Array)) {\r\n\t\t\tvar aiReadyCallbacks = [];\r\n\t\t}    function aiShowIframeId(id_iframe) { jQuery(\"#\"+id_iframe).css(\"visibility\", \"visible\");    }    function aiResizeIframeHeight(height) { aiResizeIframeHeight(height,advanced_iframe); }    function aiResizeIframeHeightId(height,width,id) {aiResizeIframeHeightById(id,height);}<\/script><iframe id=\"advanced_iframe\"  name=\"advanced_iframe\"  src=\"https:\/\/ucthpc.uct.ac.za\/crm-dashboard.html\"  width=\"1500\"  height=\"4300\"  scrolling=\"auto\"  frameborder=\"0\"  allowtransparency=\"true\"  loading=\"lazy\"  style=\";width:1500px;height:4300px;\" ><\/iframe><script type=\"text\/javascript\">var ifrm_advanced_iframe = document.getElementById(\"advanced_iframe\");var hiddenTabsDoneadvanced_iframe = false;\r\nfunction resizeCallbackadvanced_iframe() {}<\/script><script type=\"text\/javascript\"><\/script><\/p>\n\r\n\t\t<\/div>\r\n\t<\/div>\r\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/section>\n","protected":false},"excerpt":{"rendered":"Cluster Software Apart from the base OS software (gcc, python and perl) by default all software is installed into a shared folder called \/opt\/exp_soft. This is visible to all worker nodes. Some software can be called directly by referencing the path, for example \/opt\/exp_soft\/MySoft\/bin\/MySoft. Other software requires multiple path and environmental variables to be set...","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v21.4 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Supported Software - 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\/supported-software\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Supported Software - UCT HPC\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ucthpc.uct.ac.za\/index.php\/supported-software\/\" \/>\n<meta property=\"og:site_name\" content=\"UCT HPC\" \/>\n<meta property=\"article:modified_time\" content=\"2022-11-04T08:22:03+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/supported-software\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/supported-software\/\",\"name\":\"Supported Software - 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