Software

ICHEC provides access to a large range of compilers, libraries and high-performance computing packages on it's supercomputer systems (Fionn). If you are interested in using software which is not on the list, it is best to email us at support@ichec.ie or log a query at helpdesk.ichec.ie. ICHEC can also assist you with installing packages for your own use.

We do our best to offer latest versions of all required software. If you require a newer version please ask us for it. Also please note that installations per user/project packages with special licensing, (like Comsol, IDL, CRYSTAL, GAMESS-UK and other) are also available.

This list is not exhaustive and does not include many packages one might take for granted, e.g. perl. Certain packages are installed on a request basis and so may not yet have been requested on a given system.

 

Package Name

Software Version(s)

ABAQUS 6.11-1 / 6.13-2 / 6.14-2 / 6.14-4
ABINIT 7.6.1
Afterburner 4.7.0
ALLINEA 4.1 / 4.1.1 / 4.2 / 4.2.1 / 5.0
ALLPATH-LG 50095/ 52488
AMBER 11 / 12
AMOS 3.1.0
ANSYS CFX & Fluent 15.0 / 16.0 / 17.1 / 17.2
AUGUSTUS 3.1
Bali-phy 2.3.4
Bamtools 0.6.0
Bamtools and Pybedtools 2.3.0
basemap 1.0.7, compiled with intel compilers, available in both python 2 and python 3
BEAM 4_2.4.0
bedtools and pybedtools 2.21.0 / 0.6.9
Bioconductor 2.14
BioPerl 1.6.923
Biopython 1.63 / 1.67
BLASR 20150416
blat 35
BOWTIE/BOWTIE2 1.0.0 / 1.1.1 / 2.1.0 / 2.2.4
BWA 0.7.5a
Bx-python 0.7.1
Caffe May_2014
CDO (Climate Data Operators) 1.6.2
Celera Assembler 8.3rc1
CFITSIO 3.25
CheckM 0.9.7
CMAKE: Cross-platform make 2.6-patch 2 / 2.8.12
CP2K 2.5 r13225/ 2.6 r 14813 / 2.6 r 16223
CPMD 4.1
Cufflinks 2.2.1
cutadapt 1.3
Cython 0.22 compiled in both Python-2 and Pyton-3
DALIGNER 20150526
Dazzler DB 20150526
deFuse 0.6.2
DendroPy 3.12.0
DL_POLY 4.05.1/4.06.1
Doxygen 1.8.9.1
DSSP 2.2.1
ECACCESS - Access tools for ECMWF 3.3.0
Eigensoft 6.1.2
EMBOSS 6.6.0
EMOSLIB: ECMWF Interpolation library 000392
ExaML 2.0.4
Exonerate 2.2.0
fasta-splitter 0.2.0 / 0.2.4
FastQC 0.10.1
FFTW3 3.3.3/3.3.4
FusionCatcher 0.99.3d
GAMESS-US 13 ( and an extended version)
Gaussian 09b01 / 09c01 / 09d01 / 09e01 / 16a03
GCC4 Compilers 4.3.4 / 4.7.3 / 4.8.3 / 4.9.0 / 4.9.1
GDAL 1.10.1 / 2.1.2
Geant4 10.0.2
GEMINI 0.6.2
Genome MuSiC 0.4.1
Git 1.6.0.2 / 1.8.4.3
Gmap 2014-08-04
Gnuplot 4.6.4
GPAW 1.1.0
Grace 5.1.23
grib-api: GRIB decoder library 1.11.0
GROMACS 4.5.7 / 4.6.3 / 4.6.5 (Interfaced with PLUMED 2.0.2) / 5.0 / 5.0.4 / 5.1.1 / 5.1.4
GSL 1.16
GULP 4.3.3
HDF-EOS5 Libraries 1.14
HDF4 4.2.9
HDF5 1.8.11 / 1.8.12 / 1.8.13/ 1.8.14 / 1.8.15p1 /1.8.16
HMMER 3.1b1
HTLib 1.2.1
HTSeq 0.5.4p5 / 0.6.1
HyPhy 2.2
Infernal 1.1.1
Intel Compilers 14.0.0/14.0.3 / 15.0.0
Intel MKL 11.1.0 / 11.1.3 / 11.2.0
Intel MPI 4.1.1.036/4.1.3.048/5.0.1
Intel Trace Analyzer 8.1.3.037/8.1.4.045/9.0.1
InterProScan 5.7-48.0
IPython 1.2.1 / 2.0.0 / 5.1.0
JasPer Libraries 1.900.1
jModelTest 2.1.4
LAMMPS 11-Nov-2013, 1-Feb-2014, 30-Jul-2016, 31Mar17
LLVM and Clang 4.0
LS-BSR 2015-1
MAFFT 7.127
Magma 2.19-4 / 2.20-5 (Contact ICHEC for access)
Magma Libs 1.4.1 (gpu), 1.1 (mic)
MAKER 2.31.8
MaSuRCA 2.2.2
Matlab R2015b / R2016a / R2016b
Matplotlib 1.3.1 and 1.4.3, compiled with intel compilers, available in both python 2 and python 3
Mauve 2015-08-11
MCL 12-135
MinCED 0.1.6
MPJ 0_38
MrBayes 3.2.3-rev855 / 3.2.2
MuTect 1.1.7
NAMD 2.9 / 2.10 / 2.11
NCBI-BLAST 2.2.28+
NCIPlot 3.0
NCL: NCAR Command Language 6.1.2
NCO: Network Climate Operators 4.3.7
Ncview: a netCDF visual browser 2.1.2
NetCDF 1.0.7 / 1.1.6 / 4.3.0 / 4.3.2 / 4.4.0
NGS QC Toolkit 2.3.3
NumPy 1.8.0 and 1.10.1, compiled with intel compilers, available in both python 2 and python 3
nVidia CUDA compiler and SDK 5.0 / 5.5 / 6.5
NWChem 6.3/6.5
Octave 3.6.4 / 3.8.2 / 4.0.0
Octopus 4.1.1 / 4.1.2 / 6.0
OMA 1.0.1 / 1.0.2 / 1.0.3 / 1.0.4 / 1.0.5 / 1.0.6 / 1.1.2
OneDMin 0.0.0
OpenCV 2.4.9 / 2.4.10 / 2.4.13
OpenFOAM 2.2.2 / 2.4.0 / 3.0.1 / 4.0 / 4.1
OpenFOAM® Extend 1.6/ 3.0/ 3.1/ 3.2
OpenJPEG Libraries 1.5.0
OpenMX 3.7.8 / 3.7.10 / 3.8
p4 0.90 / 0.91
P4VASP 0.3.29
PAML 4.4e / 4.7a
Pandas 0.12.0 / 0.13.1
Paraview 5.0.1
PhyloBayes 3.3f / 1.5a (MPI)
Picard Tools 1.118
Pindel 0.2.4
PLINK 1.9
PLUMED 2.0.2 / 2.2.0
Pplacer 1.1.a16
PRANK 130802
Prodigal 2.6.1
PROJ.4 - Cartographic Projections Library 4.8.0 / 4.9.3
Prokka 1.10
ProtTest 3.4
pysam 0.8.1
Python 2.7.6 / 3.3.2 / 3.4.0
Qbox 1.62.3
Quantum Espresso 5.0.3-rev10599/5.1-rev11071/5.1-rev11200/5.3-all/ 6.1-all
R 3.0.2 / 3.1.1 / 3.2.1
RAxML 8.0.19
RAxML-Light 1.0.9
Root 5.34.21
SAMTOOLS 0.1.19
Scientific Python 2.8.1
Scikit-learn 0.15.2 / 0.16.1 / 0.17
SciPy 0.13.0 intel both python2 and python3
SGI Message Passing Toolkit (MPT) 2.08
Siesta 3.2-pl3 / 3.2-rev462 / 4.0b
SNAP 2.2
SRA Toolkit 2.4.2-1
SymPy 0.7.6
SZIP Compression Libraries 2.1
Tensorflow 0.5 / 0.6 / 0.7.1 / 0.8.0 / 0.12.1, compiled for GPU and CPU
The Boost Library 1.55.0
The libsequence Library 1.8.2
Theano 0.7 available in both Python2 and Python 3
TopMod 09
TREE-PUZZLE 5.2
Trinity 2.1.1 / r2013_08_14 / 20140717
Turbomole 5.10
udunits 2.1.24
VASP 5.3.3 / 5.3.5 / 5.4.1
velvet/VelvetOptimiser 1.2.10/2.2.5
virtualenv 1.11.5 / 15.0.3
VMD Visualisation Molecular Dynamics 1.9.2a34
Voro++ 0.4.6
XCrySDen 1.5.53
XOOPIC 2.70.2
Yambo 3.4.1