Difference between revisions of "Installed Application Software and Libraries"

Revision as of 12:46, 17 January 2019

Introduction

This page was created to give you an overview of the installed software on the cluster (name/version). The list will be updated at least once per week.

If you find a program in this list, but cant find it on the cluster (for example when looking at the output of the command module avail) it has most likely been hidden. Its also possible that a module isnt listed here because it is hidden. You can find every hidden module here: /cm/shared/uniol/modules/.hidden. If you want to access a hidden module, you have to add a "." in front of the version number, e.g.:

[abcd1234@hpcl001 ~]$ module load PCRE/8.39-intel-2016b
Lmod has detected the following error:  The following module(s) are unknown: "PCRE/8.39-intel-2016b"

Please check the spelling or version number. Also try "module spider ..."

[abcd1234@hpcl001 ~]$ module load PCRE/.8.39-intel-2016b
[abcd1234@hpcl001 ~]$ ml 

Currently Loaded Modules:
 1) hpc-uniol-env   3) icc/2016.3.210   5) binutils/.2.26-GCCcore-5.4.0   7) impi/5.1.3.210   9) imkl/11.3.3.210  11) PCRE/.8.39-intel-2016b
 2) slurm/current   4) GCCcore/.5.4.0   6) ifort/2016.3.210               8) iimpi/2016b     10) intel/2016b

Latest installed programs and version updates

To keep you up to date, all newly installed programs and version updates within the last two months (ca.) are listed in this section. Every new program will be installed in the new environment hpc-env/6.4 from now on.

Software	Version	Toolchain	Date of Installation
gffread	0.9.12	foss-2017b	17/01/2019
STAR	2.6.1 d	foss-2017b	15/01/2019
StringTie	1.3.5	GCCcore/6.4.0	15/01/2019
FSL	6.0.0	foss-2017b	14/01/2019
MATLAB	2018b	none	21/12/2018
Singularity	2.4.2	GCCcore/6.4.0	20/12/2018
ANTs	2.2.0	foss-2017b	19/12/2018
FSL	6.0.0	foss-2017b	18/12/2018
HISAT2	2.1.0	intel-2018a	03/12/2018
TopHat	2.1.1	intel-2018a	03/12/2018
bam_to_mate_hist	2018.11	intel-2018a	27/11/2018
FreeSurfer	6.0.1	None	28/11/2018
KNIME	3.6.2	None	14/11/2018
Spark	2.4.0 + Hadoop-2.7	intel-2018a	12/11/2018
Gaussian	g16.a03	None	09/11/2018
ORCA	4.0.1.2	GCCcore/6.4.0	08/11/2018
PVMOS	0.84	intel-2018a	08/11/2018
SuiteSparse	5.2.0	intel-2018a	08/11/2018
Parallel	20180422	intel-2018a	07/11/2018
EGSnrc	2018	GCC/6.4.0-2.28	06/11/2018
ESMF	7.1.0r	intel-2018a	05/11/2018

Installed Software

/cm/local/modulefiles

cluster-tools/7.3
cmd
dot
freeipmi/1.5.2
gcc/6.1.0
ipmitool/1.8.17
module-git
module-info
openldap
shared

/cm/shared/uniol/modules/core

hpc-uniol-env (L)
slurm/current (L)

/cm/shared/uniol/modules/bio

AUGUSTUS/3.2.3-intel-2016b-Python-2.7.12
AUGUSTUS/3.2.3-intel-2018a-Python-2.7.14
bam_to_mate_hist/no versioning
BCFtools/1.3.1
bcl2fastq2/2.18.0.12
bcl2fastq2/2.19.0
BEDTools/2.26.0
BLAST/2.2.26
BLAST/2.6.0 (D)
BLAT/3.5
BamTools/2.4.0
BamTools/2.4.1-intel-2018a
BamTools/2.5.1-intel-2018a
BCFtools/1.6
Beast/2.4.5
BioPerl/1.7.0
Biopython/1.68
Bowtie/1.1.2
Bowtie/1.2.2-intel-2018a
Bowtie2/2.2.9
Bowtie2/2.3.2-intel-2017a
Bowtie2/2.3.4.1-intel-2018a
Bowtie2/2.3.4.3-foss-2017b
BRAKER2/2.1.2
bwa.kit/0.7.12
bwa.kit/0.7.17
CD-HIT/4.6.4
cutadapt/1.9.1
Exonerate/2.4.0-foss-2017b
Exonerate/2.4.0-intel-2018a
FASTX-Toolkit/0.0.14
FastQC/0.11.5
FreeSurfer/6.0.1
FSL/6.0.0-foss-2017b
GATK/3.7-Java-8.112
GeneMark-EX/4.33
GROMACS/5.1.4-intel-2016b-mt
HTSlib/1.8
HISAT2//2.1.0-intel-2018a
IGV/2.3.80
IGVTools/2.3.75
KNIME
Lighter/1.0
lpsolve/5.5.2.5-intel-2016b
lpsolve/5.5.2.5-intel-2018a
Lumpy/0.1
MrBayes/3.2.6-foss-2017b
NextGenMap/0.5.2
Picard/2.9.0
RSEM/1.3.1-intel-2018a
Salmon/0.11.2-intel-2018a-Python-2.7.14
Salmon/0.11.3-foss-2017b-Python-2.7.14
SAMtools/1.3.1
SAMtools/1.7
SAMtools/1.8
SOAPdenovo2/r240
Stacks/1.42
STAR/2.6.1 d-foss-2017b
StringTie/1.3.5-GCCcore-6.4.0
tabix/0.2.6
TopHat/2.1.1
Trimmomatic/0.36
Trinity/2.2.0
Trinity/2.4.0
Trinity/2.6.6
Trinity/2.8.4
VCFTools/0.1.14
ViennaRNA/2.3.1

/cm/shared/uniol/modules/cfd

ESMF/7.0.0
ESMF/7.1.0r
GMT/5.3.1
OpenFOAM/1.7.1
OpenFOAM/2.1.1
OpenFOAM/2.3.1
OpenFOAM/2.4.0
OpenFOAM/3.0.1
OpenFOAM/4.0
OpenFOAM/4.1-gcc
OpenFOAM/4.1-se
OpenFOAM/4.1 (D)
OpenFOAM-Extend/3.2
PALMDependencies/all
ThetaDependencies/all
WPS/3.6.1
WPS/3.7.1
WPS/3.8.0
WPS/3.8.1
WPS/3.9 (D)
WPSGeodata/3.8 (D)
WRF/3.6.1
WRF/3.7.1
WRF/3.8.0
WRF/3.8.1
WRF/3.9 (D)
WRFGeodata/all

/cm/shared/uniol/modules/chem

CP2K/3.0
CP2K/5.1
gaussian/g09.b01
gaussian/g09.d01
gaussian/g16.a03
NAMD/2.12
NBO 2016/6.0
ORCA/3.0.3
ORCA/4.0.0
ORCA/4.0.1.2
pDynamo/1.9.0
PLUMED/2.2.3

/cm/shared/uniol/modules/compiler

CUDA-Toolkit/8.0.44
CUDA-Toolkit/recent
GCC/4.9.4-2.25
GCC/5.4.0-2.26
GCC/6.2.0-2.27 (D)
LLVM/3.8.1-goolf-5.2.01
LLVM/3.8.1-intel-2016b
LLVM/3.8.1-gimpi-6.2016
LLVM/3.9.0-intel-2016b (D)
NAG_Fortran/5.2
PGI/12.10
PGI/15.10
PGI/16.10 (D)
icc/2016.3.210
ifort/2016.3.210

/cm/shared/uniol/modules/data

ANTs/2.2.0-foss-2017b-Python-2.7.14
CDO/1.7.2-intel-2016b
HDF/4.2.11-intel-2016b
HDF/4.2.12-gimkl-7.2017.3
HDF/4.2.12-goolf-7.2.11
HDF5/1.8.17-intel-2016b
merra2wrf/2.0
NCL/6.3.0-intel-2016b
g2clib/1.4.0-intel-2016b
g2lib/1.4.0-intel-2016b
grib_api/1.16.0-intel-2016b
netCDF/4.4.1-intel-2016b
netCDF/4.4.1-intel-2016b-with-HDF4
netCDF-Fortran/4.4.4-intel-2016b
netCDF-Fortran/4.4.4-intel-2016b-with-HDF4
ROOT/v5.34.36
ROOT/v6.08.02

/cm/shared/uniol/modules/devel

Autoconf/2.69-gimpi-6.2016
Autoconf/2.69-gimpi-6.2016
Automake/1.16.1-GCCcore-6.4.0
Autotools/20150215
Autotools/20150215-gimpi-6.2016
Autotools/20170619-GCCcore-6.4.0
Autotools/20180311-GCCcore-6.4.0
ant/1.10.1-Java-1.8.0_172
Boost/1.61.0-gimpi-6.2016
Boost/1.61.0-goolf-5.2.01
Boost/1.61.0-intel-2016b
Boost/1.64.0-intel-2017a
Boost/1.65.1-foss-2017b-Python-3.6.3
Boost/1.66.0-intel-2018a
Boost/1.67.0-foss-2017b-Python-2.7.14
catkin/0.7.14-foss-2017b-Python-2.7.14
catkin-dep/1.0-foss-2017b-Python-2.7.14
CMake/2.8.12
CMake/3.6.2 (D)
CMake/3.5.2-gimpi-6.2016
CMake/3.6.1-gimpi-6.2016
CMake/3.9.1-GCCcore-6.4.0
CMake/3.9.5-GCCcore-6.4.0
CUDA-Profiler/8.0.44
CUDA-Visual-Profiler/8.0.44
Cube/4.3.4
GObject-Introspection/1.52.0-intel-2016b
gtest/1.8.0-GCCcore-6.4.0
libXmu/1.1.2-goolf-5.2.01
M4/1.4.17
M4/1.4.17-gimpi-6.2016
Mako/1.0.4-gimpi-6.2016-Python-2.7.12
ncurses/6.0
ncurses/6.0-gimpi-6.2016
Nvidia-Tesla-GDK/352.79
OTF2/2.0
PCRE/8.40
pkg-config/0.29.1-gimpi-6.2016
Qt/4.8.7-goolf-5.2.01
Qt/4.8.7-intel-2016b
ROS/1.14.4-foss-2017b-Python-2.7.14
SQLite/3.9.2-intel-2016b
SQLite/3.13.0-goolf-5.2.01
SQLite/3.13.0-intel-2016b
SQLite/3.19.3
SQLite/3.20.1-GCCcore-6.4.0
SQLite/3.23.0-intel-2018a
Spark/2.4.0-intel-2018a-Hadoop-2.7
SWIG/3.0.8-intel-2016b-Python-2.7.12
SWIG/3.0.12-Python-3.6.1
Scalasca/2.3
Valgrind/3.12.0
xbitmaps/1.1.1
xcb-proto/1.7-goolf-5.2.01-Python-2.7.3
xextproto/7.2.1-goolf-5.2.01
xproto/7.0.23-goolf-5.2.01
xtrans/1.2-goolf-5.2.01
xorg-macros/1.19.0

/cm/shared/uniol/modules/lang

Anaconda3/4.3.0
Bison/3.0.4
Bison/3.0.4-gimpi-6.2016
Gurobi/7.0.2
flex/2.6.0-gimpi-6.2016
flex/2.6.4-GCCcore-6.4.0
Java/8.112
Julia/1.0.1-intel-2018a-Perl-5.28.0
nodejs/4.4.7-intel-2016b
Perl/5.20.3
Perl/5.26.0-foss-2017b
Perl/5.26.0-GCCcore-6.4.0
Perl/5.28.0-GCCcore-6.4.0
Python/2.7.3-goolf-5.2.01
Python/2.7.11-intel-2016b
Python/2.7.12
Python/3.5.2 (D)
Python/3.6.1-goolf-5.2.01
R/3.3.1
ScientificPython/2.9.4-Python-2.7.12 (D)
TCL/8.6.4-intel-2016b
TCL/8.6.5
TCL/Tcl/8.6.7-GCCcore-6.4.0
TCL/Tcl/8.6.8-GCCcore-6.4.0
Yasm/1.3.0

/cm/shared/uniol/modules/lib

CFITSIO/3.410
CUDA-Blas/8.0.44
CUDA-FFT/8.0.44
GlobalArrays/5.4b-intel-2016b
libdrm/2.4.70-gimpi-6.2016
libffi/3.2.1-gimpi-6.2016
libglade/2.6.4-intel-2016b
libharu/2.3.0-intel-2016b
libtool/2.4.6
libtool/2.4.6-gimpi-6.2016
libpng/1.6.24
libpng/1.6.24-gimpi-6.2016
libreadline/6.3-gimpi-6.2016
libreadline/6.2-goolf-5.2.01
libxcb/1.8-goolf-5.2.01-Python-2.7.3
libXft/2.3.2-intel-2016b
libxml2/2.9.4
libxml2/2.9.4-gimpi-6.2016
libXpm/3.5.11-goolf-5.2.01
libXpm/3.5.11-intel-2016b
nettle/3.2-gimpi-6.2016
path.py/8.2.1-intel-2016b-Python-3.5.2
SIONlib/1.6.1
testpath/0.3-intel-2016b-Python-3.5.2
Xerces-C++/3.1.3
xforms/1.2.4
zlib/1.2.7-goolf-5.2.01
zlib/1.2.8
zlib/1.2.8-gimpi-6.2016
zlib/1.2.11
zlib/1.2.11-GCCcore-6.4.0
zoltan/3.83

/cm/shared/uniol/modules/math

Eigen/3.2.9-gimpi-6.2016
bgc/1.03-intel-2018a
GMP/6.1.0-intel-2016b
GMP/6.1.1
METIS/5.1.0-gimpi-6.2016 (D)
NEURON/7.5-intel-2016b
NEURON/7.6.2-intel-2018a
MPFR/3.1.4
SCOTCH/6.0.4-gimpi-6.2016 (D)
Theano/1.0.1-foss-2017b-Python-3.6.3

/cm/shared/uniol/modules/mpi

OpenMPI/1.10.4-GCC-4.9.4
OpenMPI/2.0.1-GCC-5.4.0
OpenMPI/2.0.1-GCC-6.2.0
OpenMPI/2.0.2-GCC-5.4.0-2.26 (D)
impi/5.1.3.210

/cm/shared/uniol/modules/numlib

ATLAS/3.10.2
Armadillo/7.500.1
CGAL/4.8.1-gimpi-6.2016
CLHEP/2.1.3.1
CLHEP/2.2.0.4
CLHEP/2.3.1.1
CLHEP/2.3.4.3
cuDNN/5.1-CUDA-8.0.44
cvx/2.1
Eigen/3.2.9
Eigen/3.2.9-gimpi-6.2016
FFTW/3.3.5-gompi-5.2.01
FIAT/1.6.0-intel-2016b-Python-2.7.12
GMP/6.1.1 (D)
GSL/2.1-intel-2016b
GSL/2.3-goolf-6.2.01
GSL/2.3-intel-2016b
GSL/2.4-GCCcore-6.4.0
GSL/2.4-goolf-7.2.11
Hypre/2.11.1
imkl/11.3.3.210
leda/6.3
LinBox/1.4.0
maple/18
maple/2016 (D)
MATLAB/2016b
MATLAB/2017b
MATLAB/2018b
MPFR/3.1.4
NTL/9.8.1
Octave/4.0.3
OpenBLAS/0.2.19
Qhull/2015.2
ScaLAPACK/2.0.2
SuiteSparse/4.5.3
SuiteSparse/4.5.3-intel-2018a-METIS-5.1.0
SuiteSparse/5.2.0-intel-2016b-METIS-5.1.0
SuiteSparse/5.2.0-intel-2018a-METIS-5.1.0
stata/13

/cm/shared/uniol/modules/phys

EGSnrc/2017
EGSnrc/2018
FDTD Solutions/8.20.1634
FDTD Solutions/8.20.1731 (D)
Geant4/9.6.p04
Geant4/10.01.p01
Geant4/10.01.p03
Geant4/10.02.p01 (D)
Geant4/10.03.p01
fluka/2011.2c
PVMOS/0.48

/cm/shared/uniol/modules/toolchain

foss/2016b
gimpi/6.2016
gompi/4.1.10
gompi/5.2.01
gompi/6.2.01 (D)
goolf/4.1.10
goolf/5.2.01
goolf/6.2.01
iimpi/2013b
iimpi/2016b (D)
intel/2013b
intel/2016b (D)

/cm/shared/uniol/modules/tools

ansys/18.0
bzip2/1.0.6-gimpi-6.2016
configurable-http-proxy/1.3.0-intel-2016b-nodejs-4.4.7
EasyBuild/3.0.0
expat/2.2.0-gimpi-6.2016
Ghostscript/9.19-intel-2016b
NCO/4.6.0-intel-2016b
parallel/20160622-GCC-5.4.0-2.26
parallel/20180422-intel-2018a
tree/1.7.0
util-linux/2.29-intel-2016b
XZ/5.2.2-gimpi-6.2016
XZ/5.2.2-intel-2016b

/cm/shared/uniol/modules/vis

ATK/2.24.0-intel-2016b
FFmpeg/3.1.3-intel-2016b
fontconfig/2.12.1-gimpi-6.2016
freetype/2.7.1
freetype/2.6.5-gimpi-6.2016
gettext/0.18.2-goolf-5.2.01
gettext/0.19.8-gimpi-6.2016
Glade/3.8.5-intel-2016b-Python-2.7.12
GLib/2.49.5
GLib/2.52.0-intel-2016b
GraphicsMagick/1.3.25-intel-2016b
GTK+/2.24.3-intel-2016b
gv/3.7.4
inputproto/2.3-goolf-5.2.01
kbproto/1.0.6-goolf-5.2.01
Mesa/17.2.5-foss-2017b
Mesa/17.2.5-GCCcore-6.4.0
Mesa/17.3.6-intel-2018a
OpenCV/3.1.0-intel-2016b
p4vasp/0.3.29-intel-2016b-Python-2.7.12
ParaView/5.1.2-goolf-5.2.01-mpi
ParaView/5.1.2-intel-2016b-mpi (D)
Tk/8.6.4-intel-2016b-no-X11
Tk/8.6.5-gimpi-6.2016
UDUNITS/2.2.20-intel-2016b
gettext/0.19.8
gnuplot/5.0.5-intel-2016b
grace/5.1.25
libICE/1.0.8-goolf-5.2.01
libSM/1.2.1-goolf-5.2.01
libX11/1.6.1-goolf-5.2.01
libX11/1.6.3-intel-2016b
libXaw/1.0.12-goolf-5.2.01
libXpm/3.5.11-goolf-5.2.01
libXt/1.1.4-goolf-5.2.01
motif/2.3.6
ncview/2.1.7-intel-2016b
PyCairo/1.10.0-intel-2016b-Python-2.7.12
PyGObject/2.28.6-intel-2016b-Python-2.7.12
PyGTK/2.24.0-intel-2016b-Python-2.7.12
PyOpenGL/3.1.1a1-intel-2016b
X11/20160819-goolf-5.2.01
X11/20171023-GCCcore-6.4.0
X11/20180604-GCCcore-6.4.0
X11/all

The list above is based on the information gathered by the command

module avail

If you want to create a list of every available software on the cluster, on your own, you can do this by simply using the command:

module spider

The available software will be listed in the format: name, version

@@ Line 219: / Line 219: @@
 ===/cm/shared/uniol/modules/data===
+*[[ANTs 2016 | ANTs]]/2.2.0-foss-2017b-Python-2.7.14
 *CDO/1.7.2-intel-2016b
 *[[HDF5 2016|HDF]]/4.2.11-intel-2016b