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biac:cluster:modules [2021/05/12 12:22]
cmp12 		biac:cluster:modules [2021/05/12 12:40]
cmp12
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 The cluster uses [[https://modules.readthedocs.io/en/latest/module.html|environment modules v3.2]] to control what software is loaded in your environment.  Certain software will be loaded by default, but there are other versions available to keep analyses consistent across a study or additional software that you may wish to load. The cluster uses [[https://modules.readthedocs.io/en/latest/module.html|environment modules v3.2]] to control what software is loaded in your environment.  Certain software will be loaded by default, but there are other versions available to keep analyses consistent across a study or additional software that you may wish to load.
  
 +==== What's Loaded? ====
 - "**module list**" will show you what is currently loaded  - "**module list**" will show you what is currently loaded 
 <code> <code>
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 </code> </code>
  
 +==== What's Available? ====
 - "**module avail**" will show you what additional software or alternative are available  - "**module avail**" will show you what additional software or alternative are available 
 <code> <code>
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 </code> </code>
  
- +==== How to modify the environment ==== 
- - to load additional software use "**module load modulename(s)**"+ - to load additional software use "**module load modulename(s)**"\\ 
 + - just calling the modulename will load the highest version number of an available software, unless there is a "default" designation in the listing
  
 <code> <code>
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 </code> </code>
  
-- to switch to an alternative version of a loaded software use "**module switch modulename/version**"+If there is a package already loaded you should use the **switch** command to change versions\\ 
 +- "**module switch modulename/version**"
  
 <code> <code>
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 </code> </code>
 +
 +
 +==== Make it consistent ====
  
 You can add module calls to your submission scripts to keep the environment consistent for your jobs or you can add module calls to your ~/.bashrc initialization file to have a specific set of modules across all of your cluster jobs or interactive sessions. You can add module calls to your submission scripts to keep the environment consistent for your jobs or you can add module calls to your ~/.bashrc initialization file to have a specific set of modules across all of your cluster jobs or interactive sessions.
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   1) fsl/6.0.0          2) freesurfer/6.0.1   3) matlab/R2018a   1) fsl/6.0.0          2) freesurfer/6.0.1   3) matlab/R2018a
  
 +</code>
 +
 +
 +If there are certain packages that are not available you can always email biac-help@duke.edu to request them.  Additionally, standard linux software will not show up in the module list ( ie: cmake3, gcc ).  Usually the which or locate command is an easy way to see of they are available.
 +
 +<code>
 +[cmp12@blade01 ~]$ which python3
 +/usr/bin/python3
 +
 +[cmp12@blade01 ~]$ which cmake3
 +~/bin/cmake3
 </code> </code>
  
  
  
biac/cluster/modules.txt · Last modified: 2023/04/06 18:35 by cmp12

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