In February 2014, we installed the 'module' command to manage different software environments.
Using modules
If you are in an interactive shell, module is available automatically. When submitting qsub scripts, however, you need to ensure that you include the line
source /etc/profile.d/modules.sh
befor invoking the module command.
Available modules
Typing
module avail
will list available modules and software packages. For instance,
----------------------- /usr/share/Modules/modulefiles ------------------------ R/3.0.1(default) python/2.6(default) R/ACML/3.0.2 python/anaconda/2.7 R/ACML/MP/3.0.2 python/anaconda/3.3 R/MKL/3.0.2 python/anaconda/econometrics R/MKL/MP/3.0.2 rocks-openmpi dot rocks-openmpi_ib matlab/R2012b sas/9.2 matlab/R2013b(default) sas/9.3(default) module-cvs stata/13(default) module-info stata/mp/13 modules stata/se/13
Loading a module
One can choose different versions of the software by simply modifying a line in the qsub program, or calling a module in an interactive qsub shell:
>module load R >module list Currently Loaded Modulefiles: 1) rocks-openmpi 2) R/3.0.1 >R --version R version 3.0.1 (2013-05-16) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit)
Unloading modules
One can swap modules, which resets (most) of the parameters that the original load modified:
>module unload R
Specifying a specific version
Specific versions can now be specified, swapping entire environments:
>module load R/MKL/3.0.2 >R --version R version 3.0.2 Patched (2014-01-22 r64855) -- "Frisbee Sailing" Copyright (C) 2014 The R Foundation for Statistical Computing
A sample qsub program
Note that it is important that you specify a login shell for qsub! Otherwise, the 'module' command will not work.
#!/bin/bash -l #PBS ncpus=4 module load R/MKL/MP/3.0.2 export OMP_NUM_THREADS=4 R --vanilla < myprog.R > myprog.$(date +%F).Rout
This will load the MKL-multi-threaded version of R, set the number of threads to be used to 4 (the same number of CPUs requested from PBS), and run the program 'myprog.R', storing results in a date-stamped log file.
