biac:cluster:modules
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biac:cluster:modules [2021/05/12 12:11] – [This topic does not exist yet] cmp12 | biac:cluster:modules [2023/03/15 14:45] – cmp12 | ||
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====== Accessing Available Software ====== | ====== Accessing Available Software ====== | ||
- | The cluster uses environment modules to control what software is loaded in your environment. | + | The cluster uses [[https:// |
+ | ==== What's Loaded? ==== | ||
- " | - " | ||
< | < | ||
Line 12: | Line 12: | ||
</ | </ | ||
+ | ==== What's Available? ==== | ||
- " | - " | ||
< | < | ||
Line 31: | Line 31: | ||
</ | </ | ||
+ | ==== Get more info about a module ==== | ||
+ | To get more info about a specific module use the " | ||
- | - to load additional software use " | + | < |
+ | [cmp12@blade01 ~]$ module display fsl | ||
+ | ------------------------------------------------------------------- | ||
+ | / | ||
+ | |||
+ | module-whatis loads the fsl v6.0.3 environment | ||
+ | setenv FSLDIR / | ||
+ | setenv FSLSUBMIT 0 | ||
+ | setenv FSL_DIR / | ||
+ | setenv FSL_BIN / | ||
+ | setenv FSLTCLSH / | ||
+ | setenv FSLWISH / | ||
+ | setenv FSLOUTPUTTYPE NIFTI_GZ | ||
+ | prepend-path PATH / | ||
+ | ------------------------------------------------------------------- | ||
+ | |||
+ | |||
+ | [cmp12@blade01 ~]$ module whatis fsl | ||
+ | fsl : loads the fsl v6.0.3 environment | ||
+ | |||
+ | </ | ||
+ | |||
+ | ==== How to modify the environment ==== | ||
+ | - to load additional software use " | ||
+ | - just calling the modulename will load the highest version number of an available software, unless there is a " | ||
< | < | ||
Line 43: | Line 69: | ||
</ | </ | ||
- | - to switch to an alternative version of a loaded | + | If there is a package already |
+ | - " | ||
< | < | ||
+ | [cmp12@blade08 ~]$ which feat | ||
+ | / | ||
+ | |||
[cmp12@blade08 ~]$ module switch fsl/5.0.10 | [cmp12@blade08 ~]$ module switch fsl/5.0.10 | ||
[cmp12@blade08 ~]$ module list | [cmp12@blade08 ~]$ module list | ||
Currently Loaded Modulefiles: | Currently Loaded Modulefiles: | ||
- | 1) **fsl/ | + | 1) **fsl/ |
2) freesurfer/ | 2) freesurfer/ | ||
+ | |||
+ | [cmp12@blade08 ~]$ which feat | ||
+ | / | ||
+ | |||
</ | </ | ||
+ | |||
+ | - to remove a loaded package " | ||
+ | - to unload everything " | ||
+ | |||
+ | < | ||
+ | [cmp12@blade08 ~]$ module rm fsl | ||
+ | |||
+ | [cmp12@blade08 ~]$ module list | ||
+ | Currently Loaded Modulefiles: | ||
+ | 1) freesurfer/ | ||
+ | 2) afni/ | ||
+ | |||
+ | [cmp12@blade08 ~]$ module purge | ||
+ | |||
+ | [cmp12@blade08 ~]$ module list | ||
+ | No Modulefiles Currently Loaded. | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | ==== 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. | ||
+ | |||
+ | < | ||
+ | [cmp12@blade01 ~]$ tail -n 10 ~/ | ||
+ | |||
+ | module purge | ||
+ | module load fsl/6.0.0 freesurfer/ | ||
+ | |||
+ | |||
+ | [cmp12@blade01 ~]$ module list | ||
+ | Currently Loaded Modulefiles: | ||
+ | 1) fsl/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | If there are certain packages that are not available you can always email biac-help@duke.edu to request them. Additionally, | ||
+ | |||
+ | < | ||
+ | [cmp12@blade01 ~]$ which python3 | ||
+ | / | ||
+ | |||
+ | [cmp12@blade01 ~]$ which cmake3 | ||
+ | ~/ | ||
+ | </ | ||
+ | |||
+ | |||
+ | ====== Setting Up and Maintaining Experiment Specific Conda Environments ====== | ||
biac/cluster/modules.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1