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.:
[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.
[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:
[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".
[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.:
[user@login ~]$ module unload python/2.7
To see currently loaded modules, you can should use module list
, e.g.:
[user@login ~]$ module list Currently Loaded Modules: 1) python/2.7
Typing module help
will give you more detailed information.