{"id":1005,"date":"2011-12-22T15:01:34","date_gmt":"2011-12-22T13:01:34","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2011\/12\/22\/submitting-jobs-with-a-environment-tool-called-modules"},"modified":"2015-08-14T13:17:33","modified_gmt":"2015-08-14T11:17:33","slug":"submitting-jobs-with-a-environment-tool-called-modules","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/12\/22\/submitting-jobs-with-a-environment-tool-called-modules\/","title":{"rendered":"Submitting jobs with a environment tool called ‘modules’"},"content":{"rendered":" \r\n

We've been busy looking for new ways to\r\nreduce complexity in our HPC environment. One tool which has been\r\naround for many years assists with setting up your environment where\r\nmultiple versions of the same application exists. The name of the\r\ntool is called \u201cmodules\u201d -\r\nhttp:\/\/sourceforge.net\/projects\/modules\/files\/Modules\/modules-3.2.8\/<\/a><\/p>\r\n

<\/p>\r\n

Modules allows the user to select a\r\nparticular version of application where multiples exist. For example,\r\nif the system had gcc 4.1.2 installed but you wanted gcc 4.6.1 loaded\r\nthen you would use modules to setup the 4.6.1 environment.<\/p>\r\n

Let us list the modules which are\r\navailable on the head node. Executing \u201c module avail<\/strong>\u00a0\u201c at\r\nthe shell should list the following.<\/p>\r\n

----------------------------------\r\n\/opt\/exp_soft\/Modules\/3.2.8\/modulefiles\r\n-----------------------------------\r\n<\/span><\/p>\r\n

module-gcc46\r\n<\/span><\/p>\r\n \r\n

To activate gcc 4.6.1 ,execute \u201c\r\nmodule load\u00a0<\/strong>module-gcc46<\/strong>\r\n\u201c. This will not return any data to\r\nthe prompt but when you execute \u201c gcc \u2013version \u201c you should\r\nsee a different version of gcc configured. The include paths and\r\nlibrary paths should reflect the new location for gcc as well.<\/p>\r\n

An example of a job submission script\r\nwould look something like the following below.<\/p>\r\n

#PBS -N TestJob<\/span><\/p>\r\n

#PBS -m e\r\n<\/span><\/p>\r\n

#PBS -M e-mail_address<\/span><\/p>\r\n

#PBS -l nodes=1:series400:ppn=2<\/span><\/p>\r\n

#PBS -V\r\n<\/span><\/p>\r\n

whoami\r\n<\/span><\/p>\r\n

gcc --version\r\n<\/span><\/p>\r\n

module load module-gcc46\r\n<\/span><\/p>\r\n

gcc \u2013version\r\n<\/span><\/p>\r\n

<\/p>\r\n

Notice the #PBS directive. If you load\r\na module for an application and submit a job without -V set, the\r\nmodule is not present on the compute nodes and your job will most\r\nlikely fail.<\/p>\r\n

Execute \u201c module list\u201d will list\r\nthe current modules which are loaded under your environment. \u201c\r\nmodule \u2013help \u201c will list the usage commands.<\/p>","protected":false},"excerpt":{"rendered":"<\/p>\n

We’ve been busy looking for new ways to
\nreduce complexity in our HPC environment. One tool which has been
\naround for many years assists with setting up your environment where
\nmultiple versions of the same application exists. The name of the
\ntool is called “modules” –
\nhttp:\/\/sourceforge.net\/projects\/modules\/files\/Modules\/modules-3.2.8\/<\/a><\/p>\n

<\/p>\n

Modules allows the user to select a
\nparticular version of application where multiples exist. For example,
\nif the system had gcc 4.1.2 installed but you wanted gcc 4.6.1 loaded
\nthen you would use modules to setup the 4.6.1 environment.\n<\/p>\n

Let us list the modules which are
\navailable on the head node. Executing “ module avail<\/strong> “ at
\nthe shell should list the following.<\/p>\n

———————————-
\n\/opt\/exp_soft\/Modules\/3.2.8\/modulefiles
\n———————————–
\n<\/span><\/p>\n

module-gcc46
\n<\/span><\/p>\n

 <\/p>\n

To activate gcc 4.6.1 ,execute “
\nmodule load <\/strong>module-gcc46<\/strong>
\n “. This will not return any data to
\nthe prompt but when you execute “ gcc –version “ you should
\nsee a different version of gcc configured. The include paths and
\nlibrary paths should reflect the new location for gcc as well.<\/p>\n

An example of a job submission script
\nwould look something like the following below.\n<\/p>\n

#PBS -N TestJob<\/span><\/p>\n

#PBS -m e
\n<\/span><\/p>\n

#PBS -M e-mail_address<\/span><\/p>\n

#PBS -l nodes=1:series400:ppn=2<\/span><\/p>\n

#PBS -V
\n<\/span><\/p>\n

whoami
\n<\/span><\/p>\n

gcc –version
\n<\/span><\/p>\n

module load module-gcc46
\n<\/span><\/p>\n

gcc –version
\n<\/span><\/p>\n

<\/p>\n

Notice the #PBS directive. If you load
\na module for an application and submit a job without -V set, the
\nmodule is not present on the compute nodes and your job will most
\nlikely fail. <\/p>\n

Execute “ module list” will list
\nthe current modules which are loaded under your environment. “
\nmodule –help “ will list the usage commands.<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[8],"tags":[],"yoast_head":"\nSubmitting jobs with a environment tool called 'modules' - 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\/2011\/12\/22\/submitting-jobs-with-a-environment-tool-called-modules\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Submitting jobs with a environment tool called 'modules' - UCT HPC\" \/>\n<meta property=\"og:description\" content=\"We've been busy looking for new ways to reduce complexity in our HPC environment. One tool which has been around for many years assists with setting up your environment where multiple versions of the same application exists. The name of the tool is called “modules” - http:\/\/sourceforge.net\/projects\/modules\/files\/Modules\/modules-3.2.8\/ Modules allows the user to select a particular version of application where multiples exist. For example, if the system had gcc 4.1.2 installed but you wanted gcc 4.6.1 loaded then you would use modules to setup the 4.6.1 environment. Let us list the modules which are available on the head node. Executing “ module avail “ at the shell should list the following. ---------------------------------- \/opt\/exp_soft\/Modules\/3.2.8\/modulefiles ----------------------------------- module-gcc46  To activate gcc 4.6.1 ,execute “ module load module-gcc46 “. This will not return any data to the prompt but when you execute “ gcc –version “ you should see a different version of gcc configured. The include paths and library paths should reflect the new location for gcc as well. An example of a job submission script would look something like the following below. #PBS -N TestJob #PBS -m e #PBS -M e-mail_address #PBS -l nodes=1:series400:ppn=2 #PBS -V whoami gcc --version module load module-gcc46 gcc –version Notice the #PBS directive. If you load a module for an application and submit a job without -V set, the module is not present on the compute nodes and your job will most likely fail. Execute “ module list” will list the current modules which are loaded under your environment. “ module –help “ will list the usage commands.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/12\/22\/submitting-jobs-with-a-environment-tool-called-modules\/\" \/>\n<meta property=\"og:site_name\" content=\"UCT HPC\" \/>\n<meta property=\"article:published_time\" content=\"2011-12-22T13:01:34+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2015-08-14T11:17:33+00:00\" \/>\n<meta name=\"author\" content=\"Timothy Carr\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Timothy Carr\" \/>\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\/2011\/12\/22\/submitting-jobs-with-a-environment-tool-called-modules\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/12\/22\/submitting-jobs-with-a-environment-tool-called-modules\/\"},\"author\":{\"name\":\"Timothy Carr\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/41f6cd039836d7741f2b82a7b7cfe8d0\"},\"headline\":\"Submitting jobs with a environment tool called ‘modules’\",\"datePublished\":\"2011-12-22T13:01:34+00:00\",\"dateModified\":\"2015-08-14T11:17:33+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/12\/22\/submitting-jobs-with-a-environment-tool-called-modules\/\"},\"wordCount\":271,\"publisher\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\"},\"articleSection\":[\"programming\"],\"inLanguage\":\"en-ZA\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/12\/22\/submitting-jobs-with-a-environment-tool-called-modules\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2011\/12\/22\/submitting-jobs-with-a-environment-tool-called-modules\/\",\"name\":\"Submitting jobs with a environment tool called 'modules' - 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One tool which has been around for many years assists with setting up your environment where multiple versions of the same application exists. The name of the tool is called “modules” - http:\/\/sourceforge.net\/projects\/modules\/files\/Modules\/modules-3.2.8\/ Modules allows the user to select a particular version of application where multiples exist. For example, if the system had gcc 4.1.2 installed but you wanted gcc 4.6.1 loaded then you would use modules to setup the 4.6.1 environment. Let us list the modules which are available on the head node. Executing “ module avail “ at the shell should list the following. ---------------------------------- \/opt\/exp_soft\/Modules\/3.2.8\/modulefiles ----------------------------------- module-gcc46  To activate gcc 4.6.1 ,execute “ module load module-gcc46 “. This will not return any data to the prompt but when you execute “ gcc –version “ you should see a different version of gcc configured. The include paths and library paths should reflect the new location for gcc as well. An example of a job submission script would look something like the following below. #PBS -N TestJob #PBS -m e #PBS -M e-mail_address #PBS -l nodes=1:series400:ppn=2 #PBS -V whoami gcc --version module load module-gcc46 gcc –version Notice the #PBS directive. If you load a module for an application and submit a job without -V set, the module is not present on the compute nodes and your job will most likely fail. 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