Advanced Computing Research Centre

Software - BlueCrystal Phase 1

The following software is available on the Phase 1. For software installed on BlueCrystal Phase 2, please see BlueCrystal Phase 2 software.

• Users from the School of Social and Community Medicine can find additional applications listed here.

• Users of commercial software with built in MPICH2 e.g. Amber can find a script here to use when running such codes.

Applications

Abaqus - http://www.simulia.com/. There are only a limited number of Abaqus licenses, sothere are now two special queues, abaqus (for standard nodes), and abaqus-himem (for the large memory nodes). Users should submit Abaqus jobs to one or the other of these queues. They will only let a certain number of jobs run at one time, and hold any other jobs ready to run when a license becomes free, instead of letting the job try to run and then fail.

BEAST - http://beast.bio.ed.ac.uk/

Bioconductor - http://www.bioconductor.org/whatisit

ChaNGA - http://www-hpcc.astro.washington.edu/tools/changa.html

GAUSS - http://www.aptech.com/. The licences are held by the School of Economics, Finance and Management.

Gaussian - http://www.gaussian.com/

HSL - http://www.cse.scitech.ac.uk/nag/hsl/

MPB - http://ab-initio.mit.edu/wiki/index.php/MPB

Maple - http://www.maplesoft.com/

Matlab - http://www.mathworks.com/

Meep - http://ab-initio.mit.edu/wiki/index.php/Meep

Moses - Statistical Machine Translation http://www.statmt.org/moses/

MrBayes - http://mrbayes.csit.fsu.edu/index.php

NAMD - http://www.ks.uiuc.edu/Research/namd/

R - http://www.r-project.org/

SeDuMi - http://sedumi.mcmaster.ca/

Stata - http://www.stata.com/. The licences are held by the School of Economics, Finance and Management.

Statistical Parametric Mapping (SPM) - http://www.fil.ion.ucl.ac.uk/spm/

svm-light - http://www-ai.cs.uni-dortmund.de/SOFTWARE/SVM_LIGHT/index.html

Tetex - http://www.tug.org/tetex/

Tipsy - http://www-hpcc.astro.washington.edu/tools/tipsy/tipsy.html

TNT - http://www.zmuc.dk/public/Phylogeny/TNT/

Weka - http://www.cs.waikato.ac.nz/ml/weka/

Compilers/Debuggers

Gnu compilers and utilities - http://gcc.gnu.org/gcc-4.1/

Intel compilers - http://software.intel.com/en-us/intel-compilers/

Pathscale compilers - http://www.pathscale.com/

Portland Group Inc. compilers - http://www.pgroup.com/

Debuggers

DDT and OPT- http://www.allinea.com/

Development IDE

Eclipse IDE for C and Java Developers - http://www.eclipse.org/

Languages

Java - http://docs.oracle.com/javase/6/docs/

Python, Numerical Python and Scientific Python

• Python
• Matplotlib
• NumPy
• SciPy
• SciPy - Getting Started
• Tcl Developer Exchange
• MPI for Python

Libraries

ATLAS 3.6.0 - http://math-atlas.sourceforge.net/

BLAS, CBLAS, PBLAS, LAPACK ScaLAPACK and MPI BLACS

• BLAS
• LAPACK
• ScaLAPACK
• PBLAS
• CBLAS
• MPI BLACS

FFTW (2.1.5) - Inc. MPI support - http://www.fftw.org/

FFTW (3.1.2) - No MPI support

Global Arrays - http://www.emsl.pnl.gov/docs/global/

gsl (1.8) - http://www.gnu.org/software/gsl/

HDF 5-1.6.5 - http://hdf.ncsa.uiuc.edu/HDF5/

PVM - http://www.netlib.org/pvm3/

NAG C - http://www.nag.co.uk/numeric/CL/CLdescription.asp

NAG Fortran (PGI and Intel) - http://www.nag.co.uk/numeric/fl/manual/html/FLlibrarymanual.asp

NetCDF - http://www.unidata.ucar.edu/software/netcdf/

PETSc - http://www-unix.mcs.anl.gov/petsc/petsc-as/index.html

Visualisation

gnuplot 4.0 - http://www.gnuplot.info/

Grace - http://plasma-gate.weizmann.ac.il/Grace/