Accessing Software using Distributed Environment Modules
Introduction
This page covers use of the module command in the OSG computing environment.
Environment modules have historically been used in HPC environments to provide users with an easy way to access different versions of software and to access various libraries, compilers, and software (c.f. the wikipedia reference). OSG has implemented a version based on Lmod to provide the typical module commands on any site in the OSG. You can test workflows on the OSG Connect login node and then submit the same workflow without any changes.
Using modules on OSG Connect
Use module avail to see available software applications and libraries:
$ module avail
ANTS/1.9.4 gcc/4.6.4 pbsuite/14.9.9
ANTS/2.1.0 (D) gcc/4.8.1 pcre/8.35
Julia/0.6.0 gcc/4.9.2 (D) pegasus/4.4.2-image_tools
MUMmer3.23/3.23 gcc/4.9.3 pegasus/4.5.3
OpenBUGS/3.2.3 gcc/6.2.0 pegasus/4.6.0dev
OpenBUGS-3.2.3/3.2.3 gd/2.1.1 pegasus/4.6.0cvs
R/3.1.1 (D) gdal/2.0.0 pegasus/4.6.0
R/3.2.0 geant4/9.4p02 pegasus/4.6.1dev
R/3.2.1 geant4/10.02 pegasus/4.6.1
R/3.2.2 geant4/10.3p01 (D) pegasus/4.7.0
R/3.3.1 geos/3.4.2 pegasus/4.7.1
R/3.3.2 gfal/7.20 pegasus/4.7.3
RAxML/8.2.9 git/1.9.0 pegasus/4.7.4 (D)
SeqGen/1.3.3 glpk/4.54 phenix/1.10
Shelx/2015 gmp/6.0.0 poppler/0.24.1 (D)
SitePackage gnome_libs/1.0 poppler/0.32
SparseSuite/4.2.1 gnuplot/4.6.5 povray/3.7
ViennaRNA/2.2 graphviz/2.38.0 proj/4.9.1
abyss/2.0.2 grass/6.4.4 proot/2014
ant/1.9.4 gromacs/4.6.5 protobuf/2.5
apr/1.5.1 gromacs/5.0.0 (D) psi4/0.3.74
aprutil/1.5.3 gromacs/5.0.5.cuda python/2.7 (D)
arc-lite/2015 gromacs/5.0.5 python/3.4
atlas/3.10.1 gromacs/5.1.2-cuda python/3.5.2
atlas/3.10.2 (D) gsl/1.16 qhull/2012.1
autodock/4.2.6 gsl/2.3 (D) root/5.34-32-py34
bedtools/2.21 hdf5/1.8.9 root/5.34-32
binutils/2.26 hdf5/1.8.12-cxx11 root/6.06-02-py34 (D)
blasr/1.3.1 hdf5/1.8.12 rosetta/2015
blast hdf5/1.8.13-cxx11 rosetta/2016-02
blender hdf5/1.8.13 (D) rosetta/2016-32 (D)
boost/1.50.0 healpix/3.30 ruby/2.1
boost/1.56 hisat2/2.0.3-beta rucio/1.6.6
boost/1.57.0 hmmer/3.1 sac/10.1.6a
boost/1.62.0-cxx11 igraph/0.7.1 saga/2.2.0
boost/1.62.0 (D) imagemagick/7.0.2 samtools/0.1.17
bowtie/2.2.3 intelMKL/11.3.0.109 samtools/1.3.1 (D)
bowtie/2.2.9 (D) ipopt/3.12.6 sca/10.1.6a
bwa/0.7.12 jasper/1.900.1 scons/2.3.4
bwa/2014 (D) java/7u71 sdpa/7.3.8
bzip2/1.0.6 java/8u25 (D) serf/1.37
canopy/1.4.1 jpeg/6b settarg/5.6.2
casino/2.13.211 jpeg/9a (D) shelx/2015
cblosc/1.7.1 julia/0.6.0 shrimp/2.2.3
ccp4/2015 lammps/2.0 siesta/3.2
cctools/4.4.2 lammps/15May15 (D) simbody/3.5.3
cctools/5.2.3 lapack/3.5.0 snappy/1.1.3
cctools/5.4.7 lapack/3.6.1 (D) sqlite/3.8.11.1
cctools/6.0.7 (D) libXpm/3.5.10 sra/2.5.4
cdo/1.6.4 libgfortran/4.4.7 sra/2.8.0 (D)
cfitsio/3.37 libtiff/4.0.4 stashcp/2.2
circos/0.68 llvm/3.6 stashcp/2.5
clhep/2.1.0.1 llvm/3.7 stashcp/2.6
clhep/2.2.0.8 llvm/3.8.0 (D) stashcp/3.0
clhep/2.3.1.0 lmod/5.6.2 stashcp/3.1
clhep/2.3.1.1 madgraph/2.1.2 stashcp/3.2
clhep/2.3.4.4 (D) madgraph/2.2.2 (D) stashcp/3.3
cmake/3.0.1 matlab/2013b stashcp/3.4
cmake/3.4.1 matlab/2014a stashcp/4.0
cmake/3.8.0 (D) matlab/2014b stashcp/4.0.1
connect-client/0.2.1 matlab/2015a stashcp/4.1.0
connect-client/0.3.0 matlab/2015b stashcp/4.1.1
connect-client/0.4.0 matlab/2016b (D) stashcp/4.2.0
connect-client/0.5.3 (D) mercurial/1.9.1 stashcp/4.2.1
cp2k/2.5.1 mixmodlib/3.1 stashcp/4.3.0
cpan/perl-5.10 mono/4.2.1 stashcp/4.3.1 (D)
cufflinks/2.2.1 mothur/1.39.0 stringtie/1.1.2
curl/7.37.1 mpc/1.0.3 stringtie/1.2.2 (D)
dakota/6.4.0 mpfr/3.1.3 subversion/1.8.10
dmtcp/2.5.0 mplayer/1.1 sundials/2.5
ectools mrbayes/3.2.2 swift/0.94.1
eemt/0.1 muscle/3.8.31 swift/0.96.2 (D)
elastix/2015 mysql/5.1.73 tassel/5.0
entropy/2017.03.16 namd/2.9 tcl/8.6.2
espresso/5.1 namd/2.10.cuda tcsh/6.20.00
espresso/5.2 (D) namd/2.10 (D) tophat/2.0.13
ete2/2.3.8 nco/4.3.0 tophat/2.1.1 (D)
expat/2.1.0 netcdf/4.2.0 transabyss/1.5.5
ffmpeg/0.10.15 ngsTools/2017.03.16 tutorial/1.0
ffmpeg/2.5.2 (D) octave/3.8.1 uclust/2.22
fftw/3.3.4-gromacs openbabel/2.3.2 udunits/2.2.17
fftw/3.3.4 (D) opencv/2.4.10 unixodbc/2.3.2
fiji/2.0 opensees/6482 valgrind/3.10
fpc/2.6.4 opensim/3.3 vmd/1.9.1
freesurfer/5.1.0 orca/3.0.3 wget/1.15
freesurfer/5.3.0 papi/5.3.2 wxgtk/3.0.2
freesurfer/6.0.0 (D) pari/2.7.5 xrootd/4.1.1
freetype/2.5.5 pax/evan-testing xrootd/4.2.1 (D)
fsl/5.0.8 pax/4.5.0 xz/5.2.2
gamess/2013 pax/4.6.1 zlib/1.2.8
gate/7.2 pax/4.9.1
gcc/4.6.2 pax/4.11.0 (D)
Where:
(D): Default Module
Note that currently, most of our login and compute nodes are based on RHEL 6. RHEL 7 hosts can be loaded with Singularity and the software catalog availalbe for that operating system is not as extensive, but growing:
bowtie/2.2.9 gsl/2.3 (D) mpfr/3.1.3 sra/2.5.4
cmake/3.8.0 java/8u25 pegasus/4.7.3 sra/2.8.0 (D)
cufflinks/2.2.1 lapack/3.6.1 pegasus/4.7.4 (D) stashcp/3.1
gcc/4.9.2 libgfortran/4.4.7 python/2.6.9 stringtie/1.2.2
gmp/6.0.0 mixmodlib/3.1 samtools/1.3.1 tophat/2.1.1
gsl/1.16 mpc/1.0.3 sqlite/3.8.11.1
In order to load a module, you should run module load [modulename].
For example:
$ 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:
$ 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
In addition, some modules such as the all-pkgs for python won't be available until the relevant packages are loaded.
For example:
$ module avail
---- /cvmfs/oasis.opensciencegrid.org/osg/modules/modulefiles/Core -----
atlas fftw/fftw-3.3.4-gromacs lapack lmod/5.6.2 (D)
blast gromacs/4.6.5 lmod/SiteHook namd/2.9
blender jpeg lmod/SitePackage python/2.7 (D)
python/3.4 settarg/5.6.2
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".
$ module load python/2.7
$ module avail
--- /cvmfs/oasis.opensciencegrid.org/osg/modules/modulefiles/python/2.7.7 ---
all-pkgs
---- /cvmfs/oasis.opensciencegrid.org/osg/modules/modulefiles/Core -----
atlas fftw/fftw-3.3.4-gromacs lapack lmod/5.6.2 (D)
blast gromacs/4.6.5 lmod/SiteHook namd/2.9
blender jpeg lmod/SitePackage python/2.7 (D)
python/3.4 settarg/5.6.2
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".
To unload a package and remove it from the environment, use `module unload [modulename]`.
For example:
$ module unload python/2.7
To see currently loaded modules, use module list.
For example:
$ module list
Currently Loaded Modules:
1) python/2.7
Finally, module help will give you more detailed information.
Using environment modules in jobs
Not all resources available through OSG Connect support distributed environment modules. In order to make sure that the jobs you submit run on resources that do support distributed environment modules, you will need to add the following condition to the requirements in your HTCondor job submission file. E.g. :
Requirements = (HAS_MODULES =?= true) && (OSGVO_OS_STRING == "RHEL 6") && (OpSys == "LINUX")
or
Requirements = [Other requirements ] && (HAS_MODULES =?= true) && (OSGVO_OS_STRING == "RHEL 6") && (OpSys == "LINUX")
if you already have other requirements specified and need to append the OASIS requirement.
Jobs submitted with the HTCondor requirement given above will automatically have the module system set up for them when run. So the only change needed to job scripts would be to add module load commands to load the appropriate modules.
Available Software
A list of currently installed software is available here. If your software is not already listed, you can request it.
Using modules outside of OSG Connect
In order to use distributed environment modules outside of OSG Connect, you'll need to load the modules code manually from OASIS. You can do this by running
$ source /cvmfs/oasis.opensciencegrid.org/osg/modules/lmod/current/init/SHELL
where SHELL is the shell that you are using (this is usually bash).
This page was updated on Dec 19, 2018 at 07:01 from setting-up-and-using-environment-modules.md.