| Package Name | Description |
|---|---|
| ansys100 | Ansys 10.0 |
| aria | Aria 2.2 (built against CNS 1.21, GNU compilers) |
| bio-bwa | Burrows-Wheeler Aligner 0.6.2 |
| blast-old | BLAST 2.2.18 |
| blast | BLAST 2.2.25 |
| blcr | BLCR 0.8.1 |
| boost | Boost C++ libraries, v 1.47.0 |
| bowtie | Bowtie ultrafast short read DNA aligner |
| cap3 | CAP3 compiled with Intel compilers |
| clustalw | ClustalW 1.83 compiled with Intel compilers |
| cns | CNS 1.2 compiled with Intel compilers |
| cns121 | CNS 1.21 compiled with GNU compilers |
| cufflinks | cufflinks RNA-Seq: transcript assembly and differential expression and regulation |
| esma | ESMA- Earth System Modeling Framework Application Env, based on ESMF 4.0.0rp2, intel compilers, intel mpi |
| espresso | ESPResSO 2.2.0b Molecular Dynamics simulations package |
| espresso215 | ESPResSO 2.1.5c Molecular Dynamics simulations package |
| fds | FDS 5.5.0 (built with GNU compilers, openmpi) |
| fftw | DEPRECATED, use fftw--gnu-lam. FFTW 2.1.5 (w MPI exts, built with lam-gnu, static only) |
| fftw-gnu-lam fftw-gnu-openmpi fftw-intel-openmpi |
FFTW 2.1.5 (with MPI extensions) Built with gnu4.6 and LAM MPI, gnu4.6 and OpenmPI 1.4.3, and intel compilers and OpenmPI 1.4.3, respectively |
| fftw32 | FFTW 3.2 (with MPI extensions, built with lam-gnu) |
| flame | Flame (built against openmpi 1.4.3, gnu 4.6 ) |
| garli | GARLI 0.951 compiled with Intel compilers (single process version) |
| garli-mpi | GARLI 0.942 compiled with Intel compilers and OpenMPI (MPI version) |
| gromacs | GROMACS version 3.3.3 compiled with Intel compilers, serial version only |
| gromacs-new | GROMACS version 4.5.4 compiled with openmpi143-gnu support |
| gsl | GNU Scientific Library version 1.8 |
| gulp | General Utility Lattice Program, 4.0 w openmpi 1.6, GNU compilers |
| haddock | Haddock 2.0 (built against CNS 1.21, GNU compilers) |
| hdf | HDF 4.2r1 |
| hdf425 | HDF 4.2.5, shared build, w/out netcdf, fortran support |
| hdf425.static | HDF 4.2.5, static build, w/out netcdf support, with fortran support |
| hdf5 | HDF 1.6.5 |
| hdf5-new | HDF5 v1.8.6, using openmpi143-gnu, with Fortran bindings |
| intel | Intel Compilers 10.1.008, MKL 10.0.011. |
| intel-mpi | Intel MPI 3.1 - note that this does NOT work with InfiniBand. It is for use with 'intel' package only; later versions of intel compilers do not need to tap this to use Intel MPI |
| intel322 | Intel Compilers 11.1, Intel MPI 3.2.2, MKL 10.2.2 |
| intel400 | Intel Compilers 11.1, Intel MPI 4.0.0, MKL 10.2.5 |
| intel2011 | Intel Compilers 12.0, Intel MPI 4.0.3, MKL 10.3 |
| java | Java 1.5.0_11 |
| java6 | Java 1.6.0_04 |
| lam-gnu lam-intel |
LAM 7.1.2 compiled with Gnu and Intel compilers, resp. |
| lammps | Large-scale Atomic/Molecular Massively Parallel Simulator (Sandia),
Version 9Jan2009/19May2009 compiled with Gnu compilers, OpenMPI Deprecated: use lammps-new instead |
| lammps-new | Large-scale Atomic/Molecular Massively Parallel Simulator (Sandia), Version 2013.01.12 (Gnu compilers, OpenMPI 1.6, most packages) |
| lapack | LAPACK 3.1.0 (This is the reference implementation -
non-optimised) It includes the BLAS library as well. |
| lapack32 | LAPACK 3.2.1 (This is the reference implementation -
non-optimised) It includes the BLAS library as well. |
| lucy | lucy 1.19 compiled with Intel compilers |
| mangled-mesa | Mesa v7.4.4, with symbols mangled |
| mathematica60 | Mathematica 6.0 |
| matlab | Matlab 7.0.4 |
| matlab2007b | Matlab 7.5.0 |
| matlab2008b | Matlab 2008b (7.7.0) |
| mesa | Mesa v7.4.4, standard version |
| modeltest | modeltest 3.7 compiled with Intel compilers also includes MrModeltest 2.2 |
| mpich-gnu | MPICH 1.0.4p1 compiled with Gnu compilers |
| mpich-intel | MPICH 1.0.4p1 compiled with Intel compilers |
| mrbayes | MrBayes 3.1.2 compiled with Intel compilers (single process version) |
| mrbayes-mpi | MrBayes 3.1.2 compiled with Intel compilers and OpenMPI (MPI version) |
| muscle | MUSCLE 3.6 compiled with Intel compilers |
| namd | NAMD 2.6 |
| namd27b1 | NAMD 2.7b1 |
| namd28 | NAMD 2.8 (from NAMD_2.8_Linux-amd64-TCP tarball) |
| nwchem | nwchem 5.1.1 compiled with Intel compilers, openmpi
For use by abinitio group only |
| openm-4 | OpenMM version 4 Molecular Modeling libraries |
| openmpi143-gnu openmpi-gnu46 openmpi-intel |
OpenMPI 1.4.3 libraries Compiled with Gnu (<4.6)compilers, Gnu v4.6, and intel compilers, resp. |
| netcdf411-gnu netcdf411-intel400 netcdf411-pgi | NetCDF 4.1.1 compiled with Gnu,intel400, or PGI compilers, resp.
Static libs only, with curl support |
| netcdf412-gnu netcdf412-intel netcdf412-pgi |
NetCDF 4.1.2, for Gnu, intel, and PGI compilers, res. Includes HDF5 support,no HDF4 or curl support. |
| openfoam | openFOAM CDR toolkit |
| paml | PAML 4b compiled with Intel compilers |
| povray | POV-Ray 3.6 |
| qespresso | Quantum Espresso 4.0.5 (with intel/mkl, openmpi) |
| R | R 2.4.1 |
| R280 | R version 2.8.0 |
| R2.13.1 | R version 2.13.1 |
| RAxML | RAxML phylogenetic software.
"serial" version, intel compiler, openMP parallel version, intel compiler, openMPI |
| rosetta | Rosetta v3.3 software suite for predicting and designing protein structures |
| samtools | SAM (Sequence/Alignment Mapping) Tools, version 0.1.18 |
| sctk | NIST Speech Recognition Scoring Toolkit v2.3 |
| siesta | siesta: Ab initio electronic dynamics program, v 2.0.2
abinitio group only |
| silo | Silo Scientific Data File Format Library v 4.7 |
| snack | Snack Sound Toolkit v2.2.10 |
| speech_tools | Edinburgh Speech Tools Library v1.2.96-beta |
| tophat | TopHat splided read mapper for RNA-Seq |
| unio08 | UNIO'08 NMR Data Analysis Tool |
| vasp46 | VASP 4.6, restricted to licensed groups only. Intel + MPICH |
| vasp46vtst | VASP 4.6 with VTST 2.03d extenstions, restricted to licensed groups only. Intel + MPICH |
| vasp5211 | VASP 5.2.11, restricted to licensed groups only. Intel + openMPI(1.2.5) |
| vasp522 | VASP 5.2.2, restricted to licensed groups only. Intel + openMPI |
| vasp522vtst | VASP 5.2.2 with VTST 2.03d extenstions, restricted to licensed groups only. Intel + OpenMPI |
| visit | VisIt scientific visualization and graphical analysis package |
| vmd | Visual Molecular Dynamics program |
| vtk500c | Visualization Toolkit v5.0.0c (mainly for ViSit) |
| xplor-nih | xplor-nih 2.19 |
In addition, there are modules for parallel computing/HPCC stuff on some scripting and other languages, as listed below. These generally do not require issuing tap commands for the parallel computing/HPCC modules, any exceptions will be noted. (This table is still being completed; if your favorite language is missing or a module is not listed, try loading it anyway and see if it works; if it does please email us so we can add it to the list).
| Language | Module | tap cmds | Notes |
|---|---|---|---|
| Python v2.6 | (python2.6) | ||
| mpi4py | openmpi1.4.3, gnu compilers | ||
| PyOpenMM | tap openmm-4 | ||
| R v2.8.0 | tap R280 | Deepthought/Evergreen clusters | |
| Rmpi | gnu, MPICH | R v2.8.0 | tap R280 | SEIL cluster |
| Rmpi | gnu, LAM | R v2.13.1 | tap R2.13.1 | Deepthought/Evergreen clusters |
| Rmpi | openmpi143-gnu46 | R v2.15.0 | tap R2.15 | Deepthought/Evergreen clusters |
| Rmpi | openmpi143-gnu46 | ||