EnvironmentModules

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