Software Packages
ICHEC provides access to a large range of compilers, libraries and high-performance computing packages on it's supercomputer systems. If you are interested in using software which is not on the list it is best to contact us with your query. ICHEC can also assist you with installing packages for your own use.
Please note this list is not exhaustive and does not include many packages one might take for granted, e.g. python. Certain packages are installed on an on request basis and so may not yet have been requested on a given system.
Software List
| Misc. Application packages | |||
|---|---|---|---|
| Package name | Stokes | Stoney | |
| ABAQUS | 6.8-1 / 6.9-1 | 6.8-1 / 6.9-1 | |
| ABINIT | 5.4.4 / 5.7.3 / 5.8.3 / 6.0 | ||
| Amber | 10 | ||
| CFX | 11.0-1 / 12.1 | 12.1 | |
| CPMD | 3.13.2 | ||
| CRYSTAL | 06 v1_0_2 | 06 v1_0_2 | |
| DL_POLY | 2.19 / 2.20 / 3.09.4 | ||
| FLUENT | 12.1 | 12.1 | |
| Quantum Espresso | 4.0.5 / 4.1 / 4.2 | 4.1 | |
| GAMESS-UK | 7.0 | ||
| Gaussian | 03d01 / 03e01 / 09a02 | 09a01 / 09a02 | |
| GROMACS | 4.0.2 / 4.0.4 / 4.0.5 / 4.0.7 | ||
| NAMD | 2.6 / 2.7b1 | ||
| NWChem | 5.1 / 5.1.1 | ||
| Octave | 3.0.3 / 3.2.4 | 3.2.3 | |
| OpenMX | 3.4 / 3.4.4 / 3.5 | 3.4.4 / 3.5 | |
| Turbomole | 5.9.1 / 5.10 | ||
| VASP | 4.6 / 5.2 | 4.6 / 5.2 | |
| Bioinformatics packages | |||
| Package name | Stokes | Stoney | |
| BEAST | 1.6.0pre | ||
| Bioconductor | 2.4 | ||
| BioPerl | 1.6.0 | ||
| Biopython | 1.50 | ||
| ClustalW | 2.0.10 | 2.0.12 | |
| Crann | 1.04 | ||
| Crux | 1.1.0 | ||
| EMBOSS | 6.0.1 | 6.2.0 | |
| FASTA | 35.4.4 | ||
| HMMER | 3.0b2 | 3.0 | |
| MCL | 08-312 | 09-308 | |
| MEME | 4.3.0 | ||
| mpiBLAST | 1.5.0-pio | 1.6.0-beta1 | |
| MrBayes | 3.1.2 / 3.1.2h / 3.2-cvs / 3.2-svn-rev51 | 3.1.2 | |
| MUSCLE | 3.7 | 3.8.31 | |
| NCBI-BLAST | 2.2.17 / 2.2.18 / 2.2.19 / 2.2.19+ | 2.2.22 | |
| p4 | 0.87.r132 | ||
| PAML | 3.15 / 4.1 / 4.2a / 4.3 / 4.4a | 4.4a | |
| PHYLIP | 3.68 | ||
| PhyloBayes | 2.3c / 3.2e | 3.2e | |
| PhyML | 3.0 | 3.0 | |
| PLINK | 1.06 | 1.07 | |
| PRANK | 081202 | ||
| R | 2.8.0 / 2.9.0 / 2.10.0 | 2.11.0 | |
| RAxML | 7.0.4 / 7.2.6 | ||
| SWAPSC | 1.0b | ||
| TREE-PUZZLE | 5.2 | ||
| Climate & Forecasting packages | |||
| Package name | Stokes | Stoney | |
| CDAT | 5.2 | ||
| CDO | 1.3.1 / 1.4.4 | 1.4.4 | |
| EMOSLIB | 000360 / 000380 | 000380 | |
| FERRET | 6.6.2 | 6.6.2 | |
| GMT | 4.5.1 | ||
| GrADS | 2.0.8a | 2.0.8a | |
| grib-api | 1.6.4 / 1.9.0 | 1.6.4 / 1.9.0 | |
| NCL | 5.1.0 | 5.1.0 | |
| NCO | 4.0.0 / 4.0.1 | 4.0.1 | |
| OASIS3 | 3.3 | ||
| SMS | 4.4.13 | ||
| udunits | 2.1.4 | 2.1.4 | |
| WRF | 3.1.1 | ||
| Analysis and visualisation tools | |||
| Package name | Stokes | ||
| Grace | 5.1.22 / 5.99 | ||
| IDL | 7.0 | ||
| VISIT | 1.12.0 / 2.0 | ||
| Communication libraries | |||
| Package name | Stokes | Stoney | |
| Intel MPI | 3.1 / 3.2 / 3.2.1 / 3.2.2 / 4.0 | 3.2 / 3.2.1 / 3.2.2 / 4.0 | |
| MVAPICH2 | 1.2 / 1.2p1 / 1.4.1 | 1.2p1 / 1.4.1 | |
| sgi-mpt | 1.20-sgi600r1 | ||
| I/O libraries | |||
| Package name | Stokes | Stoney | |
| GridFTP | 4.2.1 | ||
| HDF4 | 4.2r3 | 4.2.5 | |
| HDF5 | 1.6.9 / 1.8.2 / 1.8.4 | 1.8.4 | |
| NetCDF | 4.0 / 4.1 | 4.1 | |
| CFITSIO | 3.10 | ||
| Numerical libraries | |||
| Package name | Stokes | Stoney | |
| FFTW3 | 3.2 | ||
| GSL | 1.11 / 1.12 / 1.14 | 1.14 | |
| Intel MKL | 10.0 / 10.1 / 10.2 | 10.1 / 10.2 | |
| PETSc | 2.3.3-p15 | ||
| Programming tools | |||
| Package name | Stokes | Stoney | |
| Charm++ | 6.0 / 6.1 | ||
| cmake | 2.6.4 | ||
| DDT | 2.3.1 / 2.4.1 / 2.5.1 | 2.4.1 / 2.5.1 / 2.6 | |
| GCC4 Compilers | 4.1.2 / 4.4.0 | 4.1.2 | |
| Git | 1.6.0.4 | 1.6.0.4 | |
| Intel Compilers | 9.1 / 10.1 / 11.0 / 11.1 | 9.1 / 10.1 / 11.0 / 11.1 | |
| Intel Trace Analyzer | 7.1 / 7.2 / 8.0 | 7.2 / 8.0 | |
| OPT | 1.4.3 | ||
| Splint | 3.1.2 | ||
| subversion | 1.5.4 | 1.4.2 | |
| Tcl/Tk | 8.4.19 | ||
| valgrind | 3.3.1 / 3.4.0 | ||
ICHEC advises users to benchmark their particular application in order to facilitate running their jobs in an efficient regime.