Skip to content
GitLab
Projects Groups Topics Snippets
  • /
  • Help
    • Help
    • Support
    • Community forum
    • Submit feedback
    • Contribute to GitLab
  • Sign in
  • SHARK SHARK
  • Project information
    • Project information
    • Activity
    • Labels
    • Members
  • Repository
    • Repository
    • Files
    • Commits
    • Branches
    • Tags
    • Contributor statistics
    • Graph
    • Compare revisions
  • Issues 0
    • Issues 0
    • List
    • Boards
    • Service Desk
    • Milestones
  • Merge requests 0
    • Merge requests 0
  • Deployments
    • Deployments
    • Releases
  • Packages and registries
    • Packages and registries
    • Model experiments
  • Monitor
    • Monitor
    • Incidents
  • Analytics
    • Analytics
    • Value stream
    • Repository
  • Wiki
    • Wiki
  • Activity
  • Graph
  • Create a new issue
  • Commits
  • Issue Boards
Collapse sidebar
  • SharkShark
  • SHARKSHARK
  • Wiki
  • EnvironmentModules

EnvironmentModules · Changes

Page history
added how to use module load inside you qsub script authored Apr 05, 2016 by Villerius's avatar Villerius
Hide whitespace changes
Inline Side-by-side
EnvironmentModules.md
View page @ 05eb67e6
...@@ -45,4 +45,27 @@ To unload a module: ...@@ -45,4 +45,27 @@ To unload a module:
#!sh #!sh
$ module unload R/3.0.2 $ module unload R/3.0.2
## Use environment modules with qsub script
If you want to use the modules command within a script that you want to submit with qsub
you need to source /usr/local/Modules/current/init/bash.
A example script that you would submit would look like this:
```
#!/bin/bash
#$ -S /bin/bash
#$ -q all.q
#$ -N my_first_job
#$ -l h_vmem=1G
#$ -cwd
#$ -j Y
#$ -V
#$ -m be
#$ -M email@address.lumc
. /usr/local/Modules/current/init/bash
module load R/3.2.3
R CMD BATCH test.R
```
Clone repository
  • AccessingGridStorage
  • ChangePasswd
  • CheckpointingQueue
  • Configuration
  • Contact_info_shark
  • DescriptionExenode
  • EnvironmentModules
  • Errorqueue
  • Examples
  • Examples_slurm
  • FAQ
  • FineTune__SLASH__Solutions
  • GetConnected
  • Graphical
  • Graphicalview
View All Pages