Software

The main software services provided are
  • scientific software, installed and maintained by the ARC team on the ARC systems to support research in the University;
  • performance compilers, available for building scientific applications on the ARC systems as well as on departmental or personal computers.

 


Scientific software

A large number of applications, libraries and tools are available on the ARC systems.  The table below lists some of the most popular software available.  Please use the module utility (in particular the command module avail) for a complete list of software (including version information) available on a particular ARC system.

Ideally, applications run on the ARC systems should be parallel in order to benefit from the availability of multiple cores and/or distributed computing over a fast network.  However, while some applications do indeed scale extremely well on large computer resources, most do not.  Moreover, many applications that are relevant to research are serial (e.g. many computational genomics applications) or only partially parallel through multi-threading (e.g. Matlab or R).

Having your research interest as a priority, we attempt to make the best use of the parallel resources.  Usually, this means applications are built using MPI for distributed parallel processing (e.g. NAMD and ABySS), multi-threaded execution (e.g. Velvet) or even both (e.g. Gromacs).  When the application itself is not parallel, we work with the users to parallelise the workflow, e.g. allowing several instances of the same program to process different parts of the data.

Below are tabulated some of the applications available on the ARC systems.

Domain of Application Software
Structural Mechanics

abaqus

Computational Chemistry

abinit, adf, castep, dalton,

gaussian03, gaussian09,

gamess, gromacs, namd

Computational Genomics

abyss, beast, impute,

mrbayes, orca, velvet

General Computing

mathematica, matlab, python

Performance Compilers

Intel, PGI

Performance Libraries

MKL, ACML,

GSL, PETSc

Medical imaging

FSL

Statistics

R, stata

Software Development Tools

DDT, Intel Debugger, valgrind

 


Performance Compilers

What does the service cover?

This service provides researchers across the University with free access to commercial performance compilers (and associated performance libraries).  The service covers

  • Intel C/C++/Fortran compilers and MKL library;
  • Portland C/C++/Fortran/CUDA compilers and ACML library.

(please contact us regarding available versions for both compilers). This service is for Linux platforms only, there are no licenses for Windows.

These products are installed on all the ARC systems and can be used by all users.  Additionally, they can be installed and used on departmental machines and run locally.

Can I use the Intel or Portland compilers on my departmental desktop?

Yes, as long as you are running Linux.  Installation kits are available here.

Instructions on the license details are as follows:

  • For the Intel compiler, set the environment variable INTEL_LICENSE_FILE to 28518@flexlm.nsms.ox.ac.uk.
  • For the Portland compiler, set the environment variable LM_LICENSE_FILE to 22226@flexlm.nsms.ox.ac.uk.

The ARC hosted the license server for the Intel and Portland compilers until October 2011, when the service was taken over by the IT Services.  Please address queries concerning the licenses to the IT Services license server help desk at nsms@rt.oucs.ox.ac.uk.