GitLab

Environment Modules

• All environmens on the new Shark are controlled with environment modules.
• The default modules that are loaded are OpenGridScheduler and History.
• Modules can be loaded, unloaded and switched.
• Multiple modules can be loaded, Your $PATH will be adjusted and the latest module will have it's path as first path in your PATH environment!

To view the loaded modules use;

    #!sh
    $ module list 
    Currently Loaded Modulefiles:
      1) OpenGridScheduler   2) History

To view the modules available:

    #!sh
    $ module avail 

   ------------------------------------------------------------------------------------ /usr/local/Modules/versions    -------------------------------------------------------------------------------------
3.2.10

------------------------------------------------------------------------------- /usr/local/Modules/3.2.10/modulefiles --------------------------------------------------------------------------------
dot                             java/Oracle-JRE-1.7             module-info                     OpenGridScheduler               python/3.4.1                    R/3.0.2
History                         java/Oracle-JRE-1.8             modules                         PacificBiosciences/rDnaTools    qiime                           R/3.1.1
java/openjdk-7                  module-git                      null                            PacificBiosciences/smrtanalysis R/2.15.3                        use.own

To load a module:

#!sh
$ module load R/3.1.1

To switch a module from R3.1.1 to R3.0.2 use:

#!sh
$ module switch R/3.1.1 R/3.0.2

To unload a module:

#!sh
$ 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.
An example script that would submit a R v3.2.3 job 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