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