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 /usr/local/Cluster-Docs/Torque/mpi_submit* 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. These 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).
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.
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.
(i.e. module load modulename)
(see module help modulename)
|Availability on HPCS Systems||Website|
|ABAQUS||6.10-1||abaqus/6.10-1||Proprietary (not generally available)||http://www.simulia.com/products/abaqus_fea.html|
|AMBER|| 10 (AmberTools 1.0)|
10 (AmberTools 1.2)
|AMBER||11 (AmberTools 1.4)||amber/11|
|Beagle-Lib||r1010 (uses Intel compilers 220.127.116.11)||beagle-lib/r1010||Freely available (GNU LGPL)||http://beagle-lib.googlecode.com/|
|BEAST||1.6.1||beast/1.6.1||Freely available (GNU LGPL)||http://beast.bio.ed.ac.uk/||BioScope (SOLiD analysis software)||1.0.1||bioscope/1.0.1||Proprietary (not generally available)||CASTEP||6.1.1||castep/6.1.1||Restricted (2)||http://www.castep.org/|
|cmake||2.8.8||cmake/2.8.8||Freely available||http://www.cmake.org/||Desmond||2010||desmond/2010||Restricted (7)||https://www.schrodinger.com/products/14/3/|
|Freely available (GNU GPL)||http://www.fftw.org/|
|Fluent||14.0||fluent/14.0||Proprietary (not generally available)||http://www.ansys.com|
|GAMESS||11 AUG 2011 (R1)||gamess||Registered University users only||http://www.msg.ameslab.gov/gamess/|
|Freely available (GNU GPL)||http://gcc.gnu.org/|
|grace||5.1.22||grace/5.1.22||Freely available (GNU GPL)||http://plasma-gate.weizmann.ac.il/Grace/|
|GROMACS||4.5.5||gromacs/impi/4.5.5||Freely available (GNU GPL)||http://www.gromacs.org/||GULP||4.0||gulp/4.0||Restricted (8)||https://projects.ivec.org/gulp/|
|HDF4||4.2r3 (uses Intel compilers 11.0.074)||hdf4/4.2r3||Freely available||http://hdf.ncsa.uiuc.edu/products/hdf4/index.html|
|HDF5||1.6.8 (uses Intel compilers)|
1.8.10 (uses Intel compilers)
|HEALPIX||2.01||healpix/2.01||Freely available (GNU GPL)||http://healpix.jpl.nasa.gov/|
|LAPACK++||2.5.3||lapackpp/2.5.3||Freely available (GNU GPL)||http://sourceforge.net/projects/lapackpp/|
|Matlab||R2012b||matlab/r2012b||Proprietary (University only)||http://www.mathworks.co.uk/products/matlab/|
|1.2 (uses Intel compilers)|
1.4.2 (uses Intel compilers)
|meep/1.2||Freely available (GNU GPL)||http://ab-initio.mit.edu/wiki/index.php/Meep|
|MrBayes||v3.2-svn(r388) (uses Intel compilers)||mrbayes/3.2.r388||Freely available (GNU GPL)||http://mrbayes.csit.fsu.edu/|
|NAg C Library||Mark 9||nag/cl/9||Licensed||http://www.nag.co.uk/|
|NAg C Library||Mark 23||nag/cl/23||Licensed||http://www.nag.co.uk/|
|NAg Fortran Library||Mark 22||nag/fl/22||Licensed||http://www.nag.co.uk/|
|NAg Fortran Library||Mark 23||nag/fl/23||Licensed||http://www.nag.co.uk/|
|NAg Fortran90 Library||Release 4||nag/fn/4||Licensed||http://www.nag.co.uk/|
|NAg SMP Library||Mark 22||nag/fs/22||Licensed||http://www.nag.co.uk/|
|NAg SMP Library||Mark 23||nag/fs/23||Licensed||http://www.nag.co.uk/|
|NWChem||6.1.1||sandybridge/nwchem/6.1.1||Freely available (Educational Community License, Version 2.0)||http://www.nwchem-sw.org/|
|Octave||3.2.3 (uses Intel compilers 11.0.081)||octave/3.2.3||Freely available (GNU GPL)||http://www.gnu.org/software/octave/|
|OpenMPI||1.6||openmpi/1.6||Freely available (New BSD)||http://www.open-mpi.org/|
|Partiview||CVS 2009||Globally available||Freely available (Illinois Open Source License)||http://virdir.ncsa.illinois.edu/partiview/|
|PLPLOT||5.8.0-RC1||plplot/5.8.0-RC1||Freely available (GNU LGPL)||http://plplot.sourceforge.net/||pNetCDF||1.1.1||pnetcdf/openmpi/1.1.1||Freely available||http://www.mcs.anl.gov/parallel-netcdf|
|python/2.7.3||Freely available (various open source)||http://www.python.org/
|PyMOL||1.3r2||pymol/1.3r2||Open Source (Python)||http://pymol.org/|
|R||2.13.0||R/2.13.0||Freely available (GNU GPL)||http://www.r-project.org/|
|Roche Genome Sequencer Software||2.3||roche/2.3||Proprietary||SAMtools||0.1.7a||samtools/0.1.7a||Freely available (MIT)||http://samtools.sourceforge.net/|
|Star-CCM+||7.06||starccm+/7.06||Proprietary (not generally available)||http://www.cd-adapco.com/|
|Star-CD||4.12.038||starcd/4.12.038||Proprietary (not generally available)||http://www.cd-adapco.com/|
|VisIt||2.3.0||visit/2.3.0||Open Source (BSD)||https://wci.llnl.gov/codes/visit/|
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.