High Performance Computing Service

Centrally installed software

All Darwin nodes are installed with a customised version of Scientific Linux 6 (SL6), which is itself a rebuild of the freely available Red Hat Enterprise Linux 6 sources. Software packaged in SL6 and not already present may be installed, in principle, on both the login and the compute nodes by email request to support'at'hpc.cam.ac.uk.

In addition, a number of software packages (in some cases, in several versions) have been installed centrally under /usr/local (which is an NFS mount). These are available via environment modules, and in some cases have licenses which impose special conditions. Please see below for a table attempting to list these packages; this does not represent a complete list of the modules available, some of which are deprecated or for experimental purposes, and support'at'hpc.cam.ac.uk should be consulted before attempting to use a module not described below.

In particular the only supported flavours of MPI are supplied by centrally installed modules; if you believe you require a different MPI implementation please don't try to compile your own implementation as there are dependencies on the hardware; instead please contact support.

The use of modules means that a module load command is normally needed in order for the installation directories to be added to the relevant search paths, and for the software to become visible. This load can be performed on the command line to affect just the current interactive session, or added to ~/.bashrc to affect all future sessions. Editing ~/.bashrc will also affect all jobs submitted to the queueing system, which may or may not be what is desired; for clarity it is best to specify explicitly the module state in the submission script (the template scripts under /usr/local/Cluster-Docs/SLURM contain a section dealing with this).

Note that the modules loaded by default into the user environment are necessary for the proper operation of the user account and should not be removed except on advice. The default environments are loaded via modules such as default-impi (for Sandy Bridge/ConnectX3, Westmere/ConnectX2 or Nehalem/ConnectX2 nodes using Intel MPI) and default-mva2 (for Sandy Bridge/ConnectX3, Westmere/ConnectX2 or Nehalem/ConnectX2 nodes using MVAPICH2).

In some cases, alternative modules may exist with sandybridge in their name. Among modules for the same version of the same software, the sandybridge modules are the best choices for use on the Sandy Bridge nodes of Darwin, but they may not work on the Westmere or Tesla nodes (as they may contain instructions not supported by Westmere/Nehalem CPUs). In general if for the latest version of a piece of software a module with the sandybridge prefix does not exist, then the generic module should be safe to use on Sandy Bridge nodes (more recent builds have tried to optimise for all current cpu types).

For historical reasons there may also be modules with nehalem in their name. These were originally created to provide Westmere/Nehalem-optimised versions of software using Intel MPI distinguished from versions intended to run on the old Woodcrest nodes (which had an older CPU type and a different recommended MPI). Since the Woodcrests have been decommissioned the need for a separate category of nehalem modules has disappeared (nehalem has become the default for new builds); please check that there is not a more recent version of the same module without the `nehalem' label before using one of these modules. In some cases the same build of the software may be referenced in both locations as the Woodcrest-specific variants are being cleared away.

List of centrally installed software

Some of the packages listed below may require rebuilding following the June 2012 upgrade. If you encounter one of these, please advise support'at'hpc.cam.ac.uk.

SoftwareVersionsModule Name
(i.e. module load modulename)
(see module help modulename)
Availability on HPCS Systems Website
ABAQUS6.10-1abaqus/6.10-1Proprietary (not generally available)http://www.simulia.com/products/abaqus_fea.html
AMBER 10 (AmberTools 1.0)
10 (AmberTools 1.2)
amber/10
amber/10_AT-1.2
Restricted (1)http://ambermd.org/
AMBER 11 (AmberTools 1.4)amber/11
amber/11_AT-1.4
Restricted (1)http://ambermd.org/
Beagle-Libr1010 (uses Intel compilers 12.0.2.137)beagle-lib/r1010Freely available (GNU LGPL)http://beagle-lib.googlecode.com/
BEAST 1.6.1beast/1.6.1Freely available (GNU LGPL)http://beast.bio.ed.ac.uk/
BioScope (SOLiD analysis software)1.0.1bioscope/1.0.1Proprietary (not generally available)
CASTEP 7.0.3castep/7.0.3Restricted (2)http://www.castep.org/
CFITSIO 3.300cfitsio/intel/3.300Freely availablehttp://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html
cmake 2.8.8cmake/2.8.8Freely availablehttp://www.cmake.org/
CP2K 2.4.0cp2k/2.4.0Freely availablehttp://www.cp2k.org/
Desmond 2010desmond/2010Restricted (7)https://www.schrodinger.com/products/14/3/
FFTW 3.3.3
2.1.5
fftw/intel/3.3.3
fftw2/intel/double/2.1.5
fftw2/intel/float/2.1.5
Freely available (GNU GPL)http://www.fftw.org/
Fluent14.0fluent/14.0Proprietary (not generally available)http://www.ansys.com
GAMESS11 AUG 2011 (R1)gamessRegistered University users onlyhttp://www.msg.ameslab.gov/gamess/
GCC4.7.2
4.8.1
gcc/4.7.2
gcc/4.8.1
Freely available (GNU GPL)http://gcc.gnu.org/
GotoBLAS1.19gotoblas/intel/64/1.19Restricted (3)http://www.tacc.utexas.edu/resources/software/
grace5.1.22grace/5.1.22Freely available (GNU GPL)http://plasma-gate.weizmann.ac.il/Grace/
GROMACS4.5.5gromacs/impi/4.5.5Freely available (GNU GPL)http://www.gromacs.org/
GULP 4.0gulp/4.0Restricted (8)https://projects.ivec.org/gulp/
h5utils1.11.1h5utils/1.11.1Freely availablehttp://ab-initio.mit.edu/wiki/index.php/H5utils
HDF44.2r3 (uses Intel compilers 11.0.074)hdf4/4.2r3Freely availablehttp://hdf.ncsa.uiuc.edu/products/hdf4/index.html
HDF51.6.8 (uses Intel compilers)
1.8.10 (uses Intel compilers)
hdf5/1.6.8
hdf5/impi/1.8.10
Freely availablehttp://hdf.ncsa.uiuc.edu/HDF5/
HEALPIX2.01healpix/2.01Freely available (GNU GPL)http://healpix.jpl.nasa.gov/
IDL6.4
7.0
8.0.1
idl/6.4
idl/7.0
idl/8.0.1
Restricted (4)http://www.ittvis.com/idl/
Java1.6.0_18java/jdk1.6.0_18Restrictedhttp://www.sun.com/download/index.jsp
LAPACK++2.5.3lapackpp/2.5.3Freely available (GNU GPL)http://sourceforge.net/projects/lapackpp/
MatlabR2014amatlab/r2014aProprietary (University only)http://www.mathworks.co.uk/products/matlab/
Mayavi4.2.0python/2.7.3Freely availablehttp://code.enthought.com/projects/mayavi/
Meep &
MPB
1.2 (uses Intel compilers)
1.4.2 (uses Intel compilers)
meep/1.2Freely available (GNU GPL)http://ab-initio.mit.edu/wiki/index.php/Meep
MrBayesv3.2.2 (uses Intel compilers)mrbayes/3.2.2Freely available (GNU GPL)http://mrbayes.csit.fsu.edu/
NAg C LibraryMark 9nag/cl/9Licensedhttp://www.nag.co.uk/
NAg C LibraryMark 23nag/cl/23Licensedhttp://www.nag.co.uk/
NAg Fortran LibraryMark 22nag/fl/22Licensedhttp://www.nag.co.uk/
NAg Fortran LibraryMark 23nag/fl/23Licensedhttp://www.nag.co.uk/
NAg Fortran90 LibraryRelease 4nag/fn/4Licensedhttp://www.nag.co.uk/
NAg SMP LibraryMark 22nag/fs/22Licensedhttp://www.nag.co.uk/
NAg SMP LibraryMark 23nag/fs/23Licensedhttp://www.nag.co.uk/
NAMD &
VMD
2.9
1.8.7
namd/2.9Restricted (5)http://www.ks.uiuc.edu/Research/namd/
NetCDF3.6.2netcdf/3.6.2Freely availablehttp://www.unidata.ucar.edu/software/netcdf/
NWChem6.1.1sandybridge/nwchem/6.1.1Freely available (Educational Community License, Version 2.0)http://www.nwchem-sw.org/
Octave3.6.4 (uses GCC)octave/3.6.4Freely available (GNU GPL)http://www.gnu.org/software/octave/
ONETEP2.2.0onetep/2.2.0Restricted (6)http://www2.tcm.phy.cam.ac.uk/onetep/Main/HomePage
OpenMPI1.6openmpi/1.6Freely available (New BSD)http://www.open-mpi.org/
ParaView 3.14.1paraview/3.14.1Open Sourcehttp://www.paraview.org/
PartiviewCVS 2009Globally availableFreely available (Illinois Open Source License)http://virdir.ncsa.illinois.edu/partiview/
PETSc3.1-p8nehalem/petsc/3.1-p8Freely availablehttp://www.mcs.anl.gov/petsc/petsc-as/index.html
PGPLOT5.2pgplot/5.2Restricted (7)http://www.astro.caltech.edu/~tjp/pgplot/
PLPLOT5.8.0-RC1plplot/5.8.0-RC1Freely available (GNU LGPL)http://plplot.sourceforge.net/
pNetCDF1.1.1pnetcdf/openmpi/1.1.1Freely availablehttp://www.mcs.anl.gov/parallel-netcdf
python2.7.5python/2.7.5Freely availablehttp://www.python.org/
python
ipython
matplotlib
numexpr
numpy
scipy
2.7.3
0.12.1
1.1.0
1.4.2
1.6.2
0.10.1
python/2.7.3Freely available (various open source)http://www.python.org/
http://ipython.scipy.org/
http://matplotlib.sourceforge.net/
http://code.google.com/p/numexpr/
http://www.scipy.org/
http://www.scipy.org/
PyMOL1.3r2pymol/1.3r2Open Source (Python)http://pymol.org/
R2.13.0R/2.13.0Freely available (GNU GPL)http://www.r-project.org/
Roche Genome Sequencer Software2.3roche/2.3Proprietary
SAMtools0.1.7asamtools/0.1.7aFreely available (MIT)http://samtools.sourceforge.net/
SLALIB2.5.4slalib/2.5.4Restricted (7)http://dev.starlink.ac.uk/
Star-CCM+7.06starccm+/7.06Proprietary (not generally available)http://www.cd-adapco.com/
Star-CD4.12.038starcd/4.12.038Proprietary (not generally available)http://www.cd-adapco.com/
valgrind3.8.1valgrind/3.8.1GNU GPLhttp://valgrind.org/
VisIt2.3.0visit/2.3.0Open Source (BSD)https://wci.llnl.gov/codes/visit/
Yorick2.1.06yorick/2.1.06Open Source (BSD)http://yorick.sourceforge.net

(1) AMBER is available to users from non-profit organizations only. Please see the license.

(2) CASTEP is only available to users who have obtained a license in the normal way from CCPForge (see this page). The binary is only accessible to license holders.

Alternatively, please see these contributed instructions for compiling CASTEP yourself.

(3) GotoBLAS is available to academic users only.

(4) IDL is only available if you have local licenses and your institution is prepared to serve these to Darwin. The software is only accessible to license holders.

(5) NAMD and VMD are only available to academic users who have registered at the website and agreed to the license by downloading both packages. The software is only accessible to users who can show they have done this.

(6) ONETEP is currently only available to participants of the July 2008 ONETEP Summer School. The binary is accessible to these users only.

(7) Available for non-commercial use only.

(8) GULP is only available to academic users - please contact support to arrange access. The author has requested that anyone using the software kindly register at https://projects.ivec.org/gulp/register.cgi.