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 availand 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".