Software access using OASIS

Overview

The softwares in CMS Connect are centrally managed. The users have convenient access to the softwares and their dependent libraries with module command. We will see how to use the centrally managed softwares via module command.

Using the Modules on CMS Connect

Load Modules

You can use the module avail command to see available modules, e.g.:

Listing available modules

[user@login ~]$ module avail
Rebuilding cache, please wait ... (written to file) done.

--------------------------------------------------------------------- /cvmfs/oasis.opensciencegrid.org/osg/modules/modulefiles/Core ---------------------------------------------------------------------
   MUMmer3.23/3.23      blender                espresso/5.1              gnuplot/4.6.5          libgfortran/4.4.7        octave/3.8.1           samtools/0.1.17      uclust/2.22
   R/3.1.1              boost/1.50.0           expat/2.1.0               graphviz/2.38.0        lmod/5.6.2               openbabel/2.3.2        scons/2.3.4          udunits/2.2.17
   SitePackage          boost/1.56      (D)    ffmpeg/0.10.15            gromacs/4.6.5          madgraph/2.1.2           opencv/2.4.10          sdpa/7.3.8           valgrind/3.10
   SparseSuite/4.2.1    bowtie/2.2.3           ffmpeg/2.5.2       (D)    gromacs/5.0.0   (D)    madgraph/2.2.2    (D)    papi/5.3.2             serf/1.37            vmd/1.9.1
   ant/1.9.4            bwa/2014               fftw/3.3.4-gromacs        hdf5/1.8.9             matlab/2013b             pbsuite/14.9.9         settarg/5.6.2        wget/1.15
   apr/1.5.1            canopy/1.4.1           fftw/3.3.4         (D)    hdf5/1.8.12            matlab/2014a      (D)    pcre/8.35              shrimp/2.2.3         xrootd/4.1.1
   apr-util/1.5.3       casino/2.13.211        fpc/2.6.4                 hdf5/1.8.13     (D)    mercurial/1.9.1          proot/2014             siesta/3.2
   aprutil/1.5.3        cdo/1.6.4              gamess/2013               hmmer/3.1              mplayer/1.1              protobuf/2.5           stashcp/1.0.0
   atlas                cmake/3.0.1            gcc/4.6.2                 java/7u71              mrbayes/3.2.2            python/2.7      (D)    subversion/1.8.10
   autodock/4.2.6       cp2k/2.5.1             geos/3.4.2                java/8u25       (D)    muscle/3.8.31            python/3.4             sundials/2.5
   bedtools/2.21        cufflinks/2.2.1        git/1.9.0                 jpeg                   namd/2.9                 qhull/2012.1           swift/0.94.1
   blasr/1.3.1          curl/7.37.1            glpk/4.54                 lammps/2.0             nco/4.3.0                root/5.34-21           tcl/8.6.2
   blast                ectools                gnome_libs/1.0            lapack                 netcdf/4.2.0             ruby/2.1               tophat/2.0.13

  Where:
   (D):  Default Module

Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

In order to load a module, you should run module load [modulename], e.g.

Loading modules

[user@login ~]$ module load python/2.7

Some modules require other modules to be loaded, if that occurs then you'll get an error message indicating this:

Package Dependences

[user@login ~]$ module load all-pkgs

Lmod has detected the following error: Cannot load module "all-pkgs" without these modules loaded:
  atlas, lapack


While processing the following module(s):

Module fullname  Module Filename
---------------  ---------------
all-pkgs         /cvmfs/oasis.opensciencegrid.org/osg/modules/modulefiles/python/2.7.7/all-pkgs.lua

To resolve the above conflict, load the "atlas" and "lapack" module before loading "all-pkgs".

Dependent availability of packages

[user@login ~]$ module load atlas
[user@login ~]$ module load lapack
[user@login ~]$ module load all-pkgs

To unload a package and remove it from the environment, you should use module unload [modulename], e.g.:

Unloading packages

[user@login ~]$ module unload python/2.7

To see currently loaded modules, you can should use module list , e.g.:

Listing currently loaded modules

[user@login ~]$ module list
Currently Loaded Modules:
  1) python/2.7

Typing module help will give you more detailed information.