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Pre-Installed Software

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Description

This page contains a list of pre-installed software that is available for all UBELIX users. If you want to install custom software yourself, take a look here. If you think that some missing software could be of general interest for the UBELIX community, you can ask us to install the software system wide. Since maintaining software is a lot of work, we will select carefully which software we will install globally.

On this page

Environment Modules

To make certain versions of a software available, the user must first "load/add" the corresponding modulefile. Environment modules allow to maintain different versions of the same software by altering the shell environment variables (e.g. $PATH) accordingly. Each modulefile contains all information needed to configure the shell for a specific software.

List all Available Modulefiles

		
    $ module avail
------------------------ /usr/share/Modules/modulefiles ------------------------
dot         module-git  module-info modules     null        use.own
------------------------------- /etc/modulefiles -------------------------------
acml/5.1.0-gcc       gnuplot/4.6.6        mvapich2/1.7-intel
acml/5.1.0-intel     idl/6.3              mvapich2/1.7-pgi
acml/5.1.0-pgi       idl/7.0              NAMD/2.9-ibverbs
acml/5.3.1-gcc       idl/8.3              NAMD/2.9-ibverbs-smp
acml/5.3.1-intel     intel/13.1           openmpi/1.6.5-gcc
acml/5.3.1-pgi       intel/14.0           openmpi/1.6.5-intel
atlas/3.8.4          intel/15.0           openmpi/1.6.5-pgi
codeml/4.7           intel/2013           pdftk/1.45
gaussian/g03         intel/2013-ia32      pgi/13.9
gaussian/g09         intel/2015           pgi/14.10
gaussian/g09.A02     intel/2015-ia32      pgi/15.10
gaussian/g09.D01     intel/2016           pgi/2013
gcc/4.8              matlab/R2014b        pgi/2014
gcc/4.9              matlab/R2015b        pgi/2015
gcc/4.9.3            molden/5.0           python/2.7
gcc/5.3.0            mvapich2/1.7-gcc     vital-it

Bioinformatics Software

In co-operation with the Vital-IT Group of the SIB Swiss Institute of Bioinformatics, a large set of bioinformatics software tools and databases is available to the life science community.

To also list all modulefiles provided by Vital-IT, you have to first load the vital-it modulefile:

Loading the vital-it modulefile automatically configures the environment to use specific versions of selected software, e.g. python v2.7.5, and gcc v4.9.1

		
    $ module load vital-it
$ module avail
------------------------------ /software/module/ -------------------------------
Blast/blast/2.2.22
Blast/blast/2.2.26
Blast/blast/latest
Blast/csblast/2.2.3
Blast/csblast/latest
Blast/ncbi-blast/2.2.28+
(...)
Utility/rpy2/2.5.6
Utility/rpy2/2.7.7
Utility/snakemake/3.5.4
Utility/Weka/3.6.12
------------------------ /usr/share/Modules/modulefiles ------------------------
dot         module-git  module-info modules     null        use.own
------------------------------- /etc/modulefiles -------------------------------
acml/5.1.0-gcc       gnuplot/4.6.6        mvapich2/1.7-intel
acml/5.1.0-intel     idl/6.3              mvapich2/1.7-pgi
acml/5.1.0-pgi       idl/7.0              NAMD/2.9-ibverbs
acml/5.3.1-gcc       idl/8.3              NAMD/2.9-ibverbs-smp
acml/5.3.1-intel     intel/13.1           openmpi/1.6.5-gcc
acml/5.3.1-pgi       intel/14.0           openmpi/1.6.5-intel
atlas/3.8.4          intel/15.0           openmpi/1.6.5-pgi
codeml/4.7           intel/2013           pdftk/1.45
gaussian/g03         intel/2013-ia32      pgi/13.9
gaussian/g09         intel/2015           pgi/14.10
gaussian/g09.A02     intel/2015-ia32      pgi/15.10
gaussian/g09.D01     intel/2016           pgi/2013
gcc/4.8              matlab/R2014b        pgi/2014
gcc/4.9              matlab/R2015b        pgi/2015
gcc/4.9.3            molden/5.0           python/2.7
gcc/5.3.0            mvapich2/1.7-gcc     vital-it
 

Load/Add a Modulefile

To load the gcc compiler in version 5.3.0:

		
    $ module load gcc/5.3.0

or equivalently:

		
    $ module add gcc/5.3.0

List all Loaded Modulefiles

		
    $ module list
Currently Loaded Modulefiles:
  1) gcc/5.3.0

Unload/remove a Modulefile

To unload the gcc compiler in version 5.3.0:

		
    $ module unload gcc/5.3.0

or equivalently:

		
    $ module rm gcc/5.3.0

Related pages: