Documentation/Module System
Module Systems:
HPC cluster comes with a module system that allows easy loading of specific versions of supported applications. Keep in mind you need to be on a computational node to use the module system (So either as part of qsub script or using an interactive session with qrsh or qsh commands. The module systems is not available on the login nodes.)
To use a software package, you need to load its module. You may either select a specific version or use the default version for a software package.
Here are some important commands:
List all availalable modules:
module avail
List all loaded modules:
module list
Load specific module (you can use tab for autocomplete.):
module load <module name>
Unload a module:
module unload <module name>
For more information, consult the documentation:
https://www.tacc.utexas.edu/research-development/tacc-projects/lmod/user-guide
https://www.tacc.utexas.edu/research-development/tacc-projects/lmod/user-guide
Example: Using R
$ qrsh $ which R /usr/bin/which: no R in (/nfs/apps/experimental/lmod/lmod/libexec:/opt/gridengine/bin/lx-amd64:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:.) $ module avail -------------------------------------------------------------------- /nfs/apps/experimental/lmod/lmod/modulefiles/Core --------------------------------------------------------------------- CUDA/5.0.35 R/3.4.3 gcc/4.9.2 (D) matlab/2016b python3/3.3.3 CUDA/5.5.22 R/3.5.0 gcc/4.9.3 matlab/2017a python3/3.5.2 (D) CUDA/6.0.37 R/3.5.1 (D) gcc/5.3.0 matlab/2018a python3/3.6.4 CUDA/7.5.18 (D) R-java/3.4.2 gcc/6.1.0 mrtrix3/3.0_RC3 qiime/1.9.1 JAGS/4.2.0 R-java/3.4.3 (D) git/2.13.4 namd-ib/2.11b1-gcc-4.9.3-openmpi-ib samtools/0.1.19 MACS/1.4.2 StdEnv (L) glibc/2.14 openmpi/1.6.5 samtools/1.3.0 MRtrix3/MRtrix3 autoconf/2.69 gurobi/6.0.0 openmpi/1.8.1 samtools/1.3.1 R/2.12.2 bcftools/1.6 gurobi/7.0.1 (D) openmpi/1.10.1-GCC-4.9.3 samtools/1.6.0 (D) R/2.15.2 bedtools/2.25.0 java/1.7.0_25 openmpi/1.10.1 (D) schrodinger/2016-1 (D) R/3.0.1 binutils/2.4 java/1.8.0_91 (D) perl/5.10.0 schrodinger/2016-2 R/3.1.1 bowtie/2.2.9 lmod/6.1 (L) perl/5.14.2 schrodinger/2016-3 R/3.1.2 cmake/2.8.11.2 matlab/2013b perl/5.18.1 (D) settarg/6.1 R/3.2.5 cmake/3.2.2 (D) matlab/2014a picard/1.81 tcl/8.6.5 R/3.3.0 cufflinks/2.2.1 matlab/2014b picard/2.4.1 (D) tophat/2.0.12 R/3.3.1 desmond-maestro/2016-1 (D) matlab/2015a python/2.7.5 tophat/2.1.0 (D) R/3.4.0 desmond-maestro/2016-2 matlab/2015aSP1 python/2.7.11 R/3.4.1 desmond-maestro/2016-3 matlab/2015b python/2.7.14 (D) R/3.4.2 fftw/2.1.5-GCC-4.9.3-openmpi matlab/2016a (D) python3/3.3.2 Where: L: Module is loaded D: Default Module $ module load R $ module list Currently Loaded Modules: 1) lmod/6.1 2) StdEnv 3) R/3.3.1 $ which R /nfs/apps/R/3.3.1/bin/R $ R R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" Copyright (C) 2016 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) … > q() Save workspace image? [y/n/c]: n $ module unload R $ module load R/[tab] R/2.12.2 R/2.15.2 R/3.0.1 R/3.1.1 R/3.1.2 R/3.2.5 R/3.3.0 R/3.3.1 $ module load R/2.15.2 $ module list Currently Loaded Modules: 1) lmod/6.1 2) StdEnv 3) R/2.15.2 $ which R /nfs/apps/R/2.15.2/bin/R $ module load R/3.1.2 The following have been reloaded with a version change: 1) R/2.15.2 => R/3.1.2 $ module list Currently Loaded Modules: 1) lmod/6.1 2) StdEnv 3) R/3.1.2 $ which R /nfs/apps/R/3.1.2/bin/R $ module unload R $ module list Currently Loaded Modules: 1) lmod/6.1 2) StdEnv $ which R /usr/bin/which: no R in (/nfs/apps/experimental/lmod/lmod/libexec:/opt/gridengine/bin/lx-amd64:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:.)
function or expression too complex near '{' error
This usually means your cache is corrupted. Delete ~/.lmod.d/.cache folder and try again.
