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Software Management

The INCD software is managed using a softwaretool called modules. This doftwaretool allows the user to load the correct environment (PATH, LD_LIBRARY_PATH, etc) for thateach specific software.software package. The main commands are explained in the next sections.

List of available Software

  • All software available to INCD users is usable using modules
[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 ti will show the following parameters: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] thisthese isare just examples and the full list of available software can be accessed by logginglogging-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 INCD software can be compile using several types of compilers (gcc, cland (AMD), Intel etc)

Load Software

  • Please select a name using previous comand
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 areis available to ALL users at INCD. For non-free software please contact the INCD support helpdesk

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