Program:module

module is a utility used to manage multiple compilers on a single system, as well as set environment variables for other programs and utilities.

Available Modules

The following command will list all available modules.

[tulaneID@cypress1 ~]$ module avail

----------------------------------------------------------------------------------- /cm/local/modulefiles ------------------------------------------------------------------------------------
cluster-tools/7.0                 freeipmi/1.3.4                    module-git                        null                              shared
cmd                               intel/mic/sdk/3.3                 module-info                       openldap                          use.own
dot                               ipmitool/1.8.13                   mvapich2/gcc/64/2.0rc1-mlnx-ofed2 openmpi/gcc/64/1.8.2-mlnx-ofed2   version

----------------------------------------------------------------------------------- /cm/shared/modulefiles -----------------------------------------------------------------------------------
acml/gcc/64/5.3.1                     blas/gcc/64/1                         hadoop/oak/Apache/2.5.0               mvapich/open64/64/1.2rc1
acml/gcc/fma4/5.3.1                   blas/open64/64/1                      hdf5/1.6.10                           mvapich2/gcc/64/2.0b
acml/gcc/mp/64/5.3.1                  bonnie++/1.97.1                       hdf5_18/1.8.12                        mvapich2/open64/64/2.0b
acml/gcc/mp/fma4/5.3.1                cmgui/7.0                             hpl/2.1                               netcdf/gcc/64/4.3.1.1
acml/gcc-int64/64/5.3.1               cuda60/blas/6.0.37                    hwloc/1.8.1                           netcdf/open64/64/4.3.1.1
acml/gcc-int64/fma4/5.3.1             cuda60/fft/6.0.37                     intel/compiler/64/14.0/2013_sp1.3.174 netperf/2.6.0
acml/gcc-int64/mp/64/5.3.1            cuda60/nsight/6.0.37                  intel-cluster-checker/2.1.2           open64/4.5.2.1
acml/gcc-int64/mp/fma4/5.3.1          cuda60/profiler/6.0.37                intel-cluster-runtime/ia32/3.6        openblas/dynamic/0.2.8
acml/open64/64/5.3.1                  cuda60/toolkit/6.0.37                 intel-cluster-runtime/intel64/3.6     openmpi/gcc/64/1.8.1
acml/open64/fma4/5.3.1                default-environment                   intel-cluster-runtime/mic/3.6         openmpi/open64/64/1.8.1
acml/open64/mp/64/5.3.1               fftw2/openmpi/gcc/64/double/2.1.5     intel-tbb-oss/ia32/42_20140601oss     pbspro/12.2.1.140292
acml/open64/mp/fma4/5.3.1             fftw2/openmpi/gcc/64/float/2.1.5      intel-tbb-oss/intel64/42_20140601oss  pig/oak/Apache/0.15.0
acml/open64-int64/64/5.3.1            fftw2/openmpi/open64/64/double/2.1.5  iozone/3_420                          scalapack/gcc/64/1.8.0
acml/open64-int64/fma4/5.3.1          fftw2/openmpi/open64/64/float/2.1.5   lapack/gcc/64/3.5.0                   scalapack/open64/64/1.8.0
acml/open64-int64/mp/64/5.3.1         fftw3/openmpi/gcc/64/3.3.3            lapack/open64/64/3.5.0                sge/2011.11p1
acml/open64-int64/mp/fma4/5.3.1       fftw3/openmpi/open64/64/3.3.3         mpich/ge/gcc/64/3.1                   slurm/14.03.0
blacs/mpichge/gcc/64/1.1patch03       gcc/4.8.2                             mpich/ge/open64/64/3.1                torque/4.2.6.1
blacs/openmpi/gcc/64/1.1patch03       globalarrays/openmpi/gcc/64/5.3       mpiexec/0.84_432                      tulane/intel-psxe/2015
blacs/openmpi/open64/64/1.1patch03    globalarrays/openmpi/open64/64/5.3    mvapich/gcc/64/1.2rc1

---------------------------------------------------------------------------------- /share/apps/modulefiles -----------------------------------------------------------------------------------
anaconda/2.1.0                   fftw/2.1.5/single                intel-psxe/2016                  openfoam/2.3.1                   rstudio/0.98.1103
anaconda/2.5.0                   fftw/3.3.4                       jags/4.2.0                       openmpi/1.8.4                    ruby/2.2.3
anaconda3/4.0.0                  fseq/1.85                        lammps/stable-17Nov2016          parmetis/4.0.3                   samtools/0.1.19
atlas/3.10.2                     gcc/4.7.4                        macaulay2/1.6-1                  pcre/8.39                        samtools/1.1
bbcp/amd64_rhel60                gcta/1.24.7                      matlab/r2013b                    petsc/3.4.5                      smrt/2.3.0
bcl2fastq2/2.17.1                gdc-client/1.0.1                 matlab/r2015a                    petsc/3.5.3                      stacks/1.41
berkeleygw/1.1-beta2             genetorrent/3.8.7                matlab/r2015b                    petsc/3.5.4                      star/2.4.0i
boost/1.57.0                     git/2.4.1                        matlab/r2016a                    plink/1.07                       star/2.4.2a
bowtie/1.1.1                     gnuplot/5.0.1                    mercurial/3.7.3                  pyrad/3.0.66                     star/2.5.2a
bowtie2/2.2.4                    gromacs/5.1.1                    metis/5.1.0                      python/2.7.11                    structure/2.3.4
bwa/0.7.15                       gromacs/5.1.2                    micsmc-gui                       qiime/1.9.1                      sundials/2.5.0
bzip2/1.0.6                      hdf5/1.8.14                      migraten/3.6.11                  qt/4.8.6                         tinker/7.1.2
cellranger/1.1.0                 hdf5-parallel/1.8.14             mosaik/2.2.3                     R/3.1.2(default)                 tophat/2.0.13
cmake/3.0.2                      hypre/2.10.1                     mpich/3.1.4                      R/3.2.4                          vcftools/0.1.14
cpat/1.2.2                       ibamr/0.1-rc1                    ncbi-blast/2.5.0+                R/3.2.5-intel                    viennacl/1.7.0
diamond/0.6.12                   idev                             netcdf/4.3.2                     R/3.3.1-intel                    visit/2.9.2
eigen/3.2.4                      igrepertoireconstructor/2.2.0    netcdf-cxx4/4.2.1                R/3.4.1-intel                    vtk/6.1.0
emacs/24.4                       intel-opencl/1.2-4.5.0.8         netcdf-fortran/4.4.1             rsem/1.2.19                      xz/5.2.2
espresso/5.1.2                   intel-opencl-devel/1.2-4.6.0.178 netmhciipan/3.1                  rsem/1.2.22                      zlib/1.2.8
fftw/2.1.5/double(default)       intel-psxe/2015-update1(default) netmhcpan/3.0                    rsem/1.2.31

Loading & Unloading Modules

This will load the Intel Parallel Studio XE which contains the Intel compiler suite:

[tulaneID@cypress1 ~]$ module load intel-psxe

To unload the same package:

[tulaneID@cypress1 ~]$ module unload intel-psxe

Listing Loaded Modules

[tulaneID@cypress1 ~]$ module load intel-psxe
[tulaneID@cypress1 ~]$ module list
Currently Loaded Modulefiles:
  1) slurm/14.03.0             2) idev                      3) intel-psxe/2015-update1

​Details

Using $HOME/.modulerc

This file can be used to load or to define your own environment during each login. An example looks like this:

#%Module
module load intel-psxe/2016

A .modulerc begins with the magic cookie, '#%Module'.

Define your own module

Compiling software in a user directory then defining personal environment modules is useful when software one needs are not installed on Cypress, or the installed ones are not of the desired version.

For example, ​SuperLU is not available on the main module.

Download the source codes, and compile and install it, for example, on /lustre/project/dpg/local/SuperLU_5.2.1

Create a ​module-definition file, for example, as /lustre/project/dpg/local/modulefiles/SuperLU/5.2.1 where the directory name SuperLU is the software name without version number, and the file name, 5.2.1 is the version number. The file looks like this:

#%Module1.0 -*- tcl -*-
##
## modulefile
##

module-whatis "a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations."

set curMod [module-info name]
if { [ module-info mode load ] } {
    system "/bin/logger -p local0.info 'module_load: $curMod.'"
}

conflict SuperLU/4.3

module load intel-psxe/2016
set    INSTALL_ROOT    /lustre/project/dpg/local/SuperLU_5.2.1

prepend-path    PATH               $INSTALL_ROOT/bin
prepend-path	LD_LIBRARY_PATH    $INSTALL_ROOT/lib
prepend-path	LIBRARY_PATH       $INSTALL_ROOT/lib
setenv		SLU_DIR            $INSTALL_ROOT

Edit your .modulerc that looks like this:

#%Module
module use /lustre/project/dpg/local/modulefiles

Now your new module will be listed and you can load it with the usual commands.

[tulaneID@cypress1 ~]$ module avail

------------------------------------------------ /lustre/project/dpg/local/modulefiles ------------------------------------------------
SuperLU/5.2.1
-------------------------------------------------------- /cm/local/modulefiles --------------------------------------------------------
cluster-tools/7.0                 ipmitool/1.8.13                   openldap
:
:

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