Pre-Installed Software

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.

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.

Toolchains

If you need to compile any application, we suggest to load a toolchain. There are various toolchains available, to list some:

Toolchain packacges
GCC GCC compiler
gompi GCC, OpenMPI
gompic GCC, OpenMPI, CUDA
foss GCC, OpenMPI, OpenBLAS, FFTW, ScaLAPACK
fosscuda GCC, OpenMPI, OpenBLAS, FFTW, ScaLAPACK, CUDA
intel Intel compiler, (GCC required), MKL, Intel MPI
iompi Intel compiler, OpenMPI
iomkl Intel compiler, OpenMPI, MKL

Note: this list is not meant to be complete but to give an idea of high level toolchains. you can list all available toolchains using module avail and see the containing packages using, e.g. module show gompic

List all Available Modulefiles

$ module avail

--------------------------------------------------------------------------------------- /software.el7/modulefiles/all ----------------------------------------------------------------------------------------
   Advisor/2018_update3                     foss/2017a                                iccifort/2017.4.196-GCC-6.4.0-2.28                        numactl/2.0.11-GCC-5.4.0-2.26
   Autotools/20150215-GCC-5.4.0-2.26        foss/2017b                                iccifort/2018.1.163-GCC-6.4.0-2.28                        numactl/2.0.11-GCC-6.3.0-2.27
   Autotools/20150215-GCCcore-6.3.0         foss/2018a                                iccifort/2018.3.222-GCC-7.3.0-2.30                 (D)    numactl/2.0.11-GCCcore-6.4.0
   Autotools/20170619-GCCcore-6.4.0         foss/2018b                                ICU/61.1-GCCcore-6.4.0                                    numactl/2.0.11-GCCcore-7.3.0
   Autotools/20180311-GCCcore-7.3.0         foss/2019a                         (D)    IDL/8.6                                                   numactl/2.0.12-GCCcore-8.2.0                             (D)
   Autotools/20180311-GCCcore-8.2.0  (D)    fosscuda/2019a                            iimpi/2017b                                               OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1
   Boost/1.66.0-foss-2018a                  Gaussian/g09.D01                          iimpi/2018a                                               OpenBLAS/0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0
   CMake/3.9.1-GCCcore-6.4.0                Gaussian/g16.A03                   (D)    iimpi/2018b                                        (D)    OpenBLAS/0.2.20-GCC-6.4.0-2.28
   CMake/3.9.5-GCCcore-6.4.0                GCC/5.4.0-2.26                            imkl/2017.3.196-iimpi-2017b                               OpenBLAS/0.3.1-GCC-7.3.0-2.30
   CMake/3.10.2-GCCcore-6.4.0               GCC/6.3.0-2.27                            imkl/2017.3.196-iompi-2017b                               OpenBLAS/0.3.5-GCC-8.2.0-2.31.1                          (D)
   CMake/3.11.1-GCCcore-6.4.0               GCC/6.4.0-2.28                            imkl/2018.1.163-iimpi-2018a                               OpenMPI/1.10.3-GCC-5.4.0-2.26
   CMake/3.11.4-GCCcore-7.3.0        (D)    GCC/7.3.0-2.30                            imkl/2018.1.163-iompi-2018a                               OpenMPI/2.0.2-GCC-6.3.0-2.27
   CUDA/8.0.61                              GCC/8.2.0-2.31.1                   (D)    imkl/2018.3.222-iimpi-2018b                               OpenMPI/2.1.1-GCC-6.4.0-2.28
   CUDA/9.0.176                             GCCcore/5.4.0                             imkl/2018.3.222-iompi-2018b                        (D)    OpenMPI/2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28
   CUDA/9.1.85                              GCCcore/6.3.0                             impi/2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28        OpenMPI/2.1.2-GCC-6.4.0-2.28
   CUDA/9.2.88                              GCCcore/6.4.0                             impi/2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28        OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28
   CUDA/10.1.105-GCC-8.2.0-2.31.1    (D)    GCCcore/7.3.0                             impi/2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30 (D)    OpenMPI/3.1.1-GCC-7.3.0-2.30
   cuDNN/6.0-CUDA-8.0.61                    GCCcore/8.2.0                      (D)    Inspector/2018_update3                                    OpenMPI/3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30
   cuDNN/7.0.5-CUDA-9.0.176                 gcccuda/2019a                             intel/2017b                                               OpenMPI/3.1.3-GCC-8.2.0-2.31.1
   cuDNN/7.0.5-CUDA-9.1.85                  GEOS/3.6.2-foss-2018a-Python-3.6.4        intel/2018a                                               OpenMPI/3.1.3-gcccuda-2019a                              (D)
   cuDNN/7.1.4-CUDA-9.2.88                  git-lfs/2.4.2                             intel/2018b                                        (D)    Perl/5.26.1-GCCcore-6.4.0
   cuDNN/7.6.0.64-gcccuda-2019a      (D)    GMP/6.1.2-GCCcore-6.4.0                   iomkl/2017b                                               PGI/17.10-GCC-6.4.0-2.28
   cURL/7.58.0-GCCcore-6.4.0                gompi/2016b                               iomkl/2018a                                               PGI/18.4-GCC-6.4.0-2.28
   cURL/7.60.0-GCCcore-7.3.0         (D)    gompi/2017a                               iomkl/2018b                                        (D)    PGI/19.4-GCC-8.2.0-2.31.1                                (D)
   Doxygen/1.8.13-GCCcore-6.4.0             gompi/2017b                               iompi/2017b                                               Python/2.7.14-foss-2018a
   Doxygen/1.8.14-GCCcore-7.3.0      (D)    gompi/2018a                               iompi/2018a                                               Python/2.7.14-GCCcore-6.4.0-bare
   EasyBuild/3.6.1                          gompi/2018b                               iompi/2018b                                        (D)    Python/3.6.4-foss-2018a                                  (D)
   EasyBuild/3.6.2                          gompi/2019a                        (D)    itac/2018.3.022                                           R/3.4.4-foss-2018a-X11-20180131
   EasyBuild/3.7.1                          gompic/2019a                              Java/1.7.0_60                                             ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1
   EasyBuild/3.9.1                   (D)    GSL/2.4-GCCcore-6.4.0                     Java/1.7.0_80                                             ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0
   FFTW/3.3.4-gompi-2016b                   HDF5/1.10.1-foss-2018a                    Java/1.8.0_121                                            ScaLAPACK/2.0.2-gompi-2017b-OpenBLAS-0.2.20
   FFTW/3.3.6-gompi-2017a                   HDF5/1.10.2-foss-2018b             (D)    Java/1.8.0_152                                            ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20
   FFTW/3.3.6-gompi-2017b                   help2man/1.47.4-GCCcore-6.3.0             Java/1.8.0_162                                     (D)    ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1
   FFTW/3.3.7-gompi-2018a                   help2man/1.47.4-GCCcore-6.4.0             libsndfile/1.0.28-GCCcore-6.4.0                           ScaLAPACK/2.0.2-gompi-2019a-OpenBLAS-0.3.5
   FFTW/3.3.7-intel-2017b                   help2man/1.47.4-GCCcore-7.3.0             LLVM/5.0.1-GCCcore-6.4.0                                  ScaLAPACK/2.0.2-gompic-2019a-OpenBLAS-0.3.5              (D)
   FFTW/3.3.7-intel-2018a                   help2man/1.47.4                           Mako/1.0.7-foss-2018a-Python-2.7.14                       SQLite/3.20.1-GCCcore-6.4.0
   FFTW/3.3.7-iomkl-2018a                   help2man/1.47.7-GCCcore-8.2.0      (D)    MATLAB/2016b                                              SQLite/3.21.0-GCCcore-6.4.0                              (D)
   FFTW/3.3.8-gompi-2018b                   hwloc/1.11.3-GCC-5.4.0-2.26               MATLAB/2017b                                              tmux/2.7
   FFTW/3.3.8-gompi-2019a                   hwloc/1.11.5-GCC-6.3.0-2.27               MATLAB/2018b                                       (D)    UDUNITS/2.2.26-foss-2018a
   FFTW/3.3.8-gompic-2019a                  hwloc/1.11.7-GCCcore-6.4.0                netCDF/4.6.0-foss-2018a                                   vital-it/7
   FFTW/3.3.8-intel-2018b                   hwloc/1.11.8-GCCcore-6.4.0                netCDF/4.6.1-foss-2018b                            (D)    VTune/2018_update3
   FFTW/3.3.8-iomkl-2018b            (D)    hwloc/1.11.10-GCCcore-7.3.0               nettle/3.4-foss-2018a                                     X11/20180131-GCCcore-6.4.0
   foss/2016b                               hwloc/1.11.11-GCCcore-8.2.0        (D)    NLopt/2.4.2-foss-2018a

  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".

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/latest                                                       SequenceAnalysis/primer3/2.3.7                                        UHTS/Analysis/mummer/4.0.0beta1           (D)
   Blast/blast/2.2.26                                                (D)    SequenceAnalysis/PrimerDesign/iPCR/1.0                                UHTS/Analysis/NanoOK/1.2.6
   Blast/ncbi-blast/latest                                                  SequenceAnalysis/ProtoGene/4.2.2                                      UHTS/Analysis/nanoraw/0.5
   Blast/ncbi-blast/2.2.31+                                                 SequenceAnalysis/readseq/2.1.30                                       UHTS/Analysis/oncodrivefm/1.0.3

   (...)

   SequenceAnalysis/OrthologyAnalysis/OMA/2.1.1                             UHTS/Analysis/msprime/0.7.0                                           Utility/rpy2/2.9.1                        (D)
   SequenceAnalysis/orthomclSoftware/2.0.9                                  UHTS/Analysis/MultiQC/1.3                                             Utility/Solver/SoPlex/4.0.0
   SequenceAnalysis/patsearch/1                                             UHTS/Analysis/MultiQC/1.7                                      (D)    Utility/Tarql/1.1
   SequenceAnalysis/pftools/2.3.4                                           UHTS/Analysis/mummer/3.9.4alpha                                       Utility/UCSC-utils/359
   SequenceAnalysis/pftools/2.3.5.d                                  (D)    UHTS/Analysis/mummer/4.0.0beta

--------------------------------------------------------------------------------------- /software.el7/modulefiles/all ----------------------------------------------------------------------------------------
   Advisor/2018_update3                     foss/2017a                                iccifort/2017.4.196-GCC-6.4.0-2.28                        numactl/2.0.11-GCC-5.4.0-2.26
   Autotools/20150215-GCC-5.4.0-2.26        foss/2017b                                iccifort/2018.1.163-GCC-6.4.0-2.28                        numactl/2.0.11-GCC-6.3.0-2.27
   Autotools/20150215-GCCcore-6.3.0         foss/2018a                                iccifort/2018.3.222-GCC-7.3.0-2.30                 (D)    numactl/2.0.11-GCCcore-6.4.0
   Autotools/20170619-GCCcore-6.4.0         foss/2018b                                ICU/61.1-GCCcore-6.4.0                                    numactl/2.0.11-GCCcore-7.3.0
   Autotools/20180311-GCCcore-7.3.0         foss/2019a                         (D)    IDL/8.6                                                   numactl/2.0.12-GCCcore-8.2.0                             (D)
   Autotools/20180311-GCCcore-8.2.0  (D)    fosscuda/2019a                            iimpi/2017b                                               OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1
   Boost/1.66.0-foss-2018a                  Gaussian/g09.D01                          iimpi/2018a                                               OpenBLAS/0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0
   CMake/3.9.1-GCCcore-6.4.0                Gaussian/g16.A03                   (D)    iimpi/2018b                                        (D)    OpenBLAS/0.2.20-GCC-6.4.0-2.28
   CMake/3.9.5-GCCcore-6.4.0                GCC/5.4.0-2.26                            imkl/2017.3.196-iimpi-2017b                               OpenBLAS/0.3.1-GCC-7.3.0-2.30
   CMake/3.10.2-GCCcore-6.4.0               GCC/6.3.0-2.27                            imkl/2017.3.196-iompi-2017b                               OpenBLAS/0.3.5-GCC-8.2.0-2.31.1                          (D)
   CMake/3.11.1-GCCcore-6.4.0               GCC/6.4.0-2.28                            imkl/2018.1.163-iimpi-2018a                               OpenMPI/1.10.3-GCC-5.4.0-2.26
   CMake/3.11.4-GCCcore-7.3.0        (D)    GCC/7.3.0-2.30                            imkl/2018.1.163-iompi-2018a                               OpenMPI/2.0.2-GCC-6.3.0-2.27
   CUDA/8.0.61                              GCC/8.2.0-2.31.1                   (D)    imkl/2018.3.222-iimpi-2018b                               OpenMPI/2.1.1-GCC-6.4.0-2.28
   CUDA/9.0.176                             GCCcore/5.4.0                             imkl/2018.3.222-iompi-2018b                        (D)    OpenMPI/2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28
   CUDA/9.1.85                              GCCcore/6.3.0                             impi/2017.3.196-iccifort-2017.4.196-GCC-6.4.0-2.28        OpenMPI/2.1.2-GCC-6.4.0-2.28
   CUDA/9.2.88                              GCCcore/6.4.0                             impi/2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28        OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28
   CUDA/10.1.105-GCC-8.2.0-2.31.1    (D)    GCCcore/7.3.0                             impi/2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30 (D)    OpenMPI/3.1.1-GCC-7.3.0-2.30
   cuDNN/6.0-CUDA-8.0.61                    GCCcore/8.2.0                      (D)    Inspector/2018_update3                                    OpenMPI/3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30
   cuDNN/7.0.5-CUDA-9.0.176                 gcccuda/2019a                             intel/2017b                                               OpenMPI/3.1.3-GCC-8.2.0-2.31.1
   cuDNN/7.0.5-CUDA-9.1.85                  GEOS/3.6.2-foss-2018a-Python-3.6.4        intel/2018a                                               OpenMPI/3.1.3-gcccuda-2019a                              (D)
   cuDNN/7.1.4-CUDA-9.2.88                  git-lfs/2.4.2                             intel/2018b                                        (D)    Perl/5.26.1-GCCcore-6.4.0
   cuDNN/7.6.0.64-gcccuda-2019a      (D)    GMP/6.1.2-GCCcore-6.4.0                   iomkl/2017b                                               PGI/17.10-GCC-6.4.0-2.28
   cURL/7.58.0-GCCcore-6.4.0                gompi/2016b                               iomkl/2018a                                               PGI/18.4-GCC-6.4.0-2.28
   cURL/7.60.0-GCCcore-7.3.0         (D)    gompi/2017a                               iomkl/2018b                                        (D)    PGI/19.4-GCC-8.2.0-2.31.1                                (D)
   Doxygen/1.8.13-GCCcore-6.4.0             gompi/2017b                               iompi/2017b                                               Python/2.7.14-foss-2018a
   Doxygen/1.8.14-GCCcore-7.3.0      (D)    gompi/2018a                               iompi/2018a                                               Python/2.7.14-GCCcore-6.4.0-bare
   EasyBuild/3.6.1                          gompi/2018b                               iompi/2018b                                        (D)    Python/3.6.4-foss-2018a                                  (D)
   EasyBuild/3.6.2                          gompi/2019a                        (D)    itac/2018.3.022                                           R/3.4.4-foss-2018a-X11-20180131
   EasyBuild/3.7.1                          gompic/2019a                              Java/1.7.0_60                                             ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1
   EasyBuild/3.9.1                   (D)    GSL/2.4-GCCcore-6.4.0                     Java/1.7.0_80                                             ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0
   FFTW/3.3.4-gompi-2016b                   HDF5/1.10.1-foss-2018a                    Java/1.8.0_121                                            ScaLAPACK/2.0.2-gompi-2017b-OpenBLAS-0.2.20
   FFTW/3.3.6-gompi-2017a                   HDF5/1.10.2-foss-2018b             (D)    Java/1.8.0_152                                            ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20
   FFTW/3.3.6-gompi-2017b                   help2man/1.47.4-GCCcore-6.3.0             Java/1.8.0_162                                     (D)    ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1
   FFTW/3.3.7-gompi-2018a                   help2man/1.47.4-GCCcore-6.4.0             libsndfile/1.0.28-GCCcore-6.4.0                           ScaLAPACK/2.0.2-gompi-2019a-OpenBLAS-0.3.5
   FFTW/3.3.7-intel-2017b                   help2man/1.47.4-GCCcore-7.3.0             LLVM/5.0.1-GCCcore-6.4.0                                  ScaLAPACK/2.0.2-gompic-2019a-OpenBLAS-0.3.5              (D)
   FFTW/3.3.7-intel-2018a                   help2man/1.47.4                           Mako/1.0.7-foss-2018a-Python-2.7.14                       SQLite/3.20.1-GCCcore-6.4.0
   FFTW/3.3.7-iomkl-2018a                   help2man/1.47.7-GCCcore-8.2.0      (D)    MATLAB/2016b                                              SQLite/3.21.0-GCCcore-6.4.0                              (D)
   FFTW/3.3.8-gompi-2018b                   hwloc/1.11.3-GCC-5.4.0-2.26               MATLAB/2017b                                              tmux/2.7
   FFTW/3.3.8-gompi-2019a                   hwloc/1.11.5-GCC-6.3.0-2.27               MATLAB/2018b                                       (D)    UDUNITS/2.2.26-foss-2018a
   FFTW/3.3.8-gompic-2019a                  hwloc/1.11.7-GCCcore-6.4.0                netCDF/4.6.0-foss-2018a                                   vital-it/7                                               (L)
   FFTW/3.3.8-intel-2018b                   hwloc/1.11.8-GCCcore-6.4.0                netCDF/4.6.1-foss-2018b                            (D)    VTune/2018_update3
   FFTW/3.3.8-iomkl-2018b            (D)    hwloc/1.11.10-GCCcore-7.3.0               nettle/3.4-foss-2018a                                     X11/20180131-GCCcore-6.4.0
   foss/2016b                               hwloc/1.11.11-GCCcore-8.2.0        (D)    NLopt/2.4.2-foss-2018a

  Where:
   L:  Module is loaded
   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".