{"id":889,"date":"2017-10-17T12:58:13","date_gmt":"2017-10-17T11:58:13","guid":{"rendered":"https:\/\/research.reading.ac.uk\/act\/?post_type=kbe_knowledgebase&p=889"},"modified":"2022-11-04T11:39:17","modified_gmt":"2022-11-04T11:39:17","slug":"accessing-software-on-the-cluster","status":"publish","type":"kbe_knowledgebase","link":"https:\/\/research.reading.ac.uk\/act\/knowledgebase\/accessing-software-on-the-cluster\/","title":{"rendered":"Accessing Software on the Cluster"},"content":{"rendered":"
\n
On the Reading Academic Computing cluster the locally built software packages are not available right away. They can be loaded into your environment using environmental modules (http:\/\/modules.sourceforge.net\/<\/a>). The ‘module’ command modify your environmental variables and in particular change the version of software that you use by changing the PATH and other environment variables. The strength of this approach is that it works with all shells and that you can unload modules as opposed to having to start a new shell to get a clean environment. The old command ‘setup’ is no longer supported on the met-cluster and is not available for new user accounts.<\/div>\n<\/div>\n
<\/div>\n
<\/div>\n
<\/div>\n
\n
\n 
\nListing available modules<\/u><\/b><\/p>\n

You can list the available software modules on the cluster with the command<\/p>\n

module avail<\/pre>\n
Note that you’ll have to be on one of the compute nodes on the cluster to see the full range of available software as the head node only has a limited amount of applications available.<\/p>\n
If you want to find out what versions of a module are available, for example gcc, then you can specify this in the above command, e.g.:<\/p>\n
module avail gcc<\/pre>\n
This will show a list of all available versions of gcc in an output like this:<\/p>\n
[dk913223@racc-login-4 ~]$ module avail gcc\r\n\r\n------------------------ \/share\/apps\/modules\/compilers -------------------------\r\ngcc\/6.4.0 gcc\/7.3.0 gcc\/8.4.0 \r\n<\/pre>\n<\/div>\n
 <\/p>\n
\n
Loading a module<\/u><\/b> You can load a module, e.g. gcc, using the command<\/p>\n
module load gcc<\/pre>\n
or
\n<\/b><\/p>\n
module add gcc<\/pre>\n
The will load a default value of the module, which in the case of gcc is the newest version, here 8.4.0. For some software, the default version is indicated by ‘(default)’ in the output from ‘module avail ‘. If you want a specific version, for example gcc 6.4.0 then append the version to the above command:<\/p>\n
module load gcc\/6.4.0<\/pre>\n
 <\/p>\n
Listing loaded modules
\n<\/u><\/b><\/p>\n
You can list the modules that you have loaded with the command<\/p>\n
module list<\/pre>\n
 <\/p>\n
Switching between module versions
\n<\/u><\/b><\/p>\n
If you want to change the version of a module you have loaded, for example from gcc version 8.4.0 to 6.4.0, then you can use the command<\/p>\n
module switch gcc\/6.4.0<\/pre>\n
 <\/p>\n
Adding your own module files<\/u><\/b><\/p>\n
If you have a directory of your own modules in your home directory, in \/home\/username\/privatemodules, then you can make them available to load with the command<\/p>\n
module use ~\/privatemodules<\/pre>\n
This can also be done by adding the module ‘use.own’ and it has the advantage that you can call it many times without it being added more than once.<\/p>\n
module load use.own<\/pre>\n
 <\/p>\n
Setting preferred module versions<\/u><\/b><\/p>\n
You can use your own modules as a way of loading your preferred versions of a module. If you then change your module preferences you only need to update one file.<\/p>\n
The following example shows the contents of a sample file called e.g. ‘mypython’, which could be used to set up your preferred version of the python module (shown here for anaconda\/2020.11).<\/p>\n
#%Module1.0#####################################################################\r\n##\r\n## use.own modulefile\r\n##\r\n## modulefiles\/use.own.  Generated from use.own.in by configure.\r\n##\r\nproc ModulesHelp { } {\r\nglobal version\r\n\r\nputs stderr \"\\tThis module adds my prefered version of python\"\r\nputs stderr \"\\n\\tVersion $version\\n\"\r\n}\r\n\r\nmodule-whatis    \"adds my prefered version of anaconda\"\r\n\r\nset    version    2020.11\r\nmodule    load    anaconda\/$version<\/pre>\n
When this is set up and you want to load python you would need to load the two modules<\/p>\n
module load use.own\r\nmodule load mypython<\/pre>\n
Your personal module file could also be used to load multiple modules.<\/p>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"
On the Reading Academic Computing cluster the locally built software packages are not available right away. They can be loaded into your environment using environmental modules (http:\/\/modules.sourceforge.net\/). The ‘module’ command modify your environmental variables and in particular change the version of software that you use by changing the PATH and other environment variables. The strength<\/p>\n","protected":false},"author":316,"featured_media":1717,"template":"","meta":{"_acf_changed":false,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"__cvm_playback_settings":[],"__cvm_video_id":"","_links_to":"","_links_to_target":""},"kbe_taxonomy":[61,91],"kbe_tags":[70,73,72,71],"class_list":["post-889","kbe_knowledgebase","type-kbe_knowledgebase","status-publish","has-post-thumbnail","hentry","kbe_taxonomy-academic-cluster-articles","kbe_taxonomy-software","kbe_tags-environmental-modules","kbe_tags-modules","kbe_tags-racc","kbe_tags-software"],"acf":[],"yoast_head":"\nAccessing Software on the Cluster - Academic Computing Team<\/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:\/\/research.reading.ac.uk\/act\/knowledgebase\/accessing-software-on-the-cluster\/\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Accessing Software on the Cluster - Academic Computing Team\" \/>\n<meta property=\"og:description\" content=\"On the Reading Academic Computing cluster the locally built software packages are not available right away. 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