Software Management

The Cirrus software is managed using a tool called modules. This tool allows the user to load the correct environment (PATH, LD_LIBRARY_PATH, etc) for each specific software package. The main commands are explained in the next sections. 
 List of available Software 
 
 All software available to Cirrus users is usable using modules, the presented list is context depended, some groups have customized environment bundles showed only to them: 
 
 [jpina@hpc7 ~]$ module avail

------------------------------------------------------------------------------------------ /cvmfs/sw.el7/modules/LIP ------------------------------------------------------------------------------------------
clhep/2.3.4.3 delphes/3.4.2pre15 geant/4.10.03 lhapdf/6.1.6 pythia/6.4.26 pythia/8.2.35 root/6.08.00 root/6.16.00
delphes/3.4.1 fastjet/3.3.0 hepmc/2.6.9 madgraph/2.6.0 pythia/6.4.28 root/5.34.36 root/6.10.02 root/6.16.00-RUBEN
delphes/3.4.2pre10 geant/4.10.02.p01 heptoptagger/2.0 madgraph/2.6.1 pythia/8.2.15 root/6.04.02 root/6.14.06 xroot/4.3.0

----------------------------------------------------------------------------------------- /cvmfs/sw.el7/modules/soft ------------------------------------------------------------------------------------------
aster-13.1.0 cmake-3.5.2 gcc63/netcdf-fortran/4.4.4 hdf5-1.8.16 ngspice/30 r-3.2.5 udocker/1.0.4
blat-36.2 cuda-8.0 gcc63/ngspice/30 homer-4.8 openmpi/2.1.0 r-3.5.2 udocker/1.1.0
boost-1.55 cuda-9.0 gcc63/openmpi/2.1.0 kallisto-0.43.0 openmpi-1.10.2 rt udocker/1.1.0-devel
bowtie2-2.3.0 DATK gcc63/openmpi-1.10.2 macs-1.4.2 openmpi-2.1.0 sbcl-1.3.4 udocker/1.1.1
clang/7.0.0 fastqc-0.11.5 gcc63/openmpi-2.1.0 matlab/R2018a parallel/20180622 schism/5.4.0 weblogo-2.8.2
clang/ngspice/30 fftw-3.3.4 gcc63/r-3.4.2 mpich-3.2 plumed-2.2.1 sicer-1.1 wine/4.2
clhep-2.2.0.8 fftw-3.3.5 gcc63/schism/5.4.0 mvapich2-1.8 python/3.7.2 star-2.5.2b
clhep-2.3.1.1 gcc-4.8 gcc-6.3 netcdf/4.6.1 python-2.7.11 teste
clhep-2.3.2.2 gcc63/mpich-3.2 gcc-7.3 netcdf2/4.6.1 python-3.5.1 trimmomatic-0.33
cmake/3.11.2 gcc63/netcdf/4.6.1 gromacs-4.6.7 netcdf-fortran/4.4.4 python-3.5.4 udocker/1.0.2
...
### Show / list module information
* Using this option will show the following information: 

 
 [jpina@hpc7 ~]$ module show gcc63/ngspice/30
-------------------------------------------------------------------
/cvmfs/sw.el7/modules/soft/gcc63/ngspice/30:

module-whatis	 Sets up NGSpice 
system		 test -d /cvmfs/sw.el7/ar/ix_5400/gcc63/ngspice/30 
-------------------------------------------------------------------
 
 Summary 
 
 
 
 software[1] 
 Location[2] 
 software 
 availability 
 complex software[3] 
 type of compiler[4] 
 
 
 
 
 gromacs-4.6.7 
 /cvmfs/sw.el7/modules/LIP 
 Gromacs 4.6.7 
 usable by everyone 
 no 
 OS default (gcc -V) 
 
 
 clang/7.0.0 
 /cvmfs/sw.el7/modules/soft 
 AMD compiler 
 usable by everyone 
 no 
 clang 7.0.0 
 
 
 gcc63/r-3.4.2 
 /cvmfs/sw.el7/modules/soft 
 R software compiled with gcc 6.3 
 usable by everyone 
 yes 
 gcc 6.3 
 
 
 
 [1] these are just examples and the full list of available software can be accessed by logging-in into the login machine and run command 'module avail' 
[2] Path of the installed software. No action needed from the user 
[3] This means if a software is composed by more than one module (compiler + software + modules) 
[4] At Cirrus the software can be compiled using several types of compilers (gcc, cland (AMD), Intel etc) 
 Load Software 
 
 Please select a name using previous command 
 
 module load gcc63/ngspice/30 
 
 Loaded software 
 
 How to list your loaded modules 
 
 [jpina@hpc7 ~]$ module list
Currently Loaded Modulefiles:
 1) gcc-6.3 2) gcc63/ngspice/30

 
 
 On this example two different software gcc 6.3 plus ngsipe 3.9. 
 
 Unload software 
 [jpina@hpc7 ~]$ module list
Currently Loaded Modulefiles:
 1) gcc-6.3 2) gcc63/ngspice/30
[jpina@hpc7 ~]$ module unload gcc63/ngspice/30
[jpina@hpc7 ~]$ module list
Currently Loaded Modulefiles:
 1) gcc-6.3
[jpina@hpc7 ~]$ module unload gcc-6.3
[jpina@hpc7 ~]$ module list
No Modulefiles Currently Loaded.

 
 
 Do no unload gcc-6.3 or ngspice will stop working because this software was compiled against gcc 6.3. 
 
 Help 
 
 List usefull comands for modules software 
 
 [jpina@hpc7 ~]$ module help

 Modules Release 3.2.10 2012-12-21 (Copyright GNU GPL v2 1991):

 Usage: module [ switches ] [ subcommand ] [subcommand-args ]

 
 
 NOTE only free software is available to ALL users at INCD. For non-free software please contact the INCD support helpdesk