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biac:cluster:modules [2021/05/12 12:34]
cmp12 		biac:cluster:modules [2021/05/12 18:00]
cmp12
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 ====== Accessing Available Software ====== ====== Accessing Available Software ======
  
-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.  Modules work by adding specific environmental variables needed for each package and/or adding them to your default search path. 
  
 ==== What's Loaded? ==== ==== What's Loaded? ====
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 dramms/1.5.1                fscan                       hcp_workbench/1.5.0         medinria/2.2.3(default)     rar/5.70 dramms/1.5.1                fscan                       hcp_workbench/1.5.0         medinria/2.2.3(default)     rar/5.70
 dtiprep/1.2.4               fsl/5.0.1                   laynii/1.5.6                medinria/4.0.0              simnibs/2.0.1 dtiprep/1.2.4               fsl/5.0.1                   laynii/1.5.6                medinria/4.0.0              simnibs/2.0.1
 +
 +</code>
 +
 +==== Get more info about a module ====
 +To get more info about a specific module use the "module display" or "module whatis" command.
 +
 +<code>
 +[cmp12@blade01 ~]$ module display fsl
 +-------------------------------------------------------------------
 +/etc/modulefiles/fsl/6.0.3:
 +
 +module-whatis loads the fsl v6.0.3 environment 
 +setenv FSLDIR /usr/local/packages/fsl-6.0.3 
 +setenv FSLSUBMIT 0 
 +setenv FSL_DIR /usr/local/packages/fsl-6.0.3 
 +setenv FSL_BIN /usr/local/packages/fsl-6.0.3/bin 
 +setenv FSLTCLSH /usr/local/packages/fsl-6.0.3/bin/fsltclsh 
 +setenv FSLWISH /usr/local/packages/fsl-6.0.3/bin/fslwish 
 +setenv FSLOUTPUTTYPE NIFTI_GZ 
 +prepend-path PATH /usr/local/packages/fsl-6.0.3/bin 
 +-------------------------------------------------------------------
 +
 +
 +[cmp12@blade01 ~]$ module whatis fsl
 +fsl                  : loads the fsl v6.0.3 environment
  
 </code> </code>
  
 ==== How to modify the environment ==== ==== 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  - just calling the modulename will load the highest version number of an available software, unless there is a "default" designation in the listing
  
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 </code> </code>
  
-If there is a package already loaded you should use the **switch** command to change versions+If there is a package already loaded you should use the **switch** command to change versions\\
 - "**module switch modulename/version**" - "**module switch modulename/version**"
  
biac/cluster/modules.txt · Last modified: 2023/04/06 18:35 by cmp12

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