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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, andsupport'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 notexist, 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.

Software Versions Module Name
(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/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-Lib r1010 (uses Intel compilers 12.0.2.137) 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 7.0.3 castep/7.0.3 Restricted (2) http://www.castep.org/
CFITSIO 3.300 cfitsio/intel/3.300 Freely available http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html
cmake 2.8.8 cmake/2.8.8 Freely available http://www.cmake.org/
CP2K 2.4.0 cp2k/2.4.0 Freely available http://www.cp2k.org/
Desmond 2010 desmond/2010 Restricted (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/
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/
GCC 4.7.2
4.8.1
gcc/4.7.2
gcc/4.8.1
Freely available (GNU GPL) http://gcc.gnu.org/
GotoBLAS 1.19 gotoblas/intel/64/1.19 Restricted (3) http://www.tacc.utexas.edu/resources/software/
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/
h5utils 1.11.1 h5utils/1.11.1 Freely available http://ab-initio.mit.edu/wiki/index.php/H5utils
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)
hdf5/1.6.8
hdf5/impi/1.8.10
Freely available http://hdf.ncsa.uiuc.edu/HDF5/
HEALPIX 2.01 healpix/2.01 Freely available (GNU GPL) http://healpix.jpl.nasa.gov/
IDL 6.4
7.0
8.0.1
idl/6.4
idl/7.0
idl/8.0.1
Restricted (4) http://www.ittvis.com/idl/
Java 1.8.0_45 java/jdk1.8.0_45 Restricted http://www.sun.com/download/index.jsp
LAPACK++ 2.5.3 lapackpp/2.5.3 Freely available (GNU GPL) http://sourceforge.net/projects/lapackpp/
Matlab R2015b matlab/r2015b Proprietary (University only) http://www.mathworks.co.uk/products/matlab/
Mayavi 4.2.0 python/2.7.3 Freely available http://code.enthought.com/projects/mayavi/
Meep &
MPB
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 v3.2.2 (uses Intel compilers) mrbayes/3.2.2 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/
NAMD &
VMD
2.9
1.8.7
namd/2.9 Restricted (5) http://www.ks.uiuc.edu/Research/namd/
NetCDF 3.6.2 netcdf/3.6.2 Freely available http://www.unidata.ucar.edu/software/netcdf/
NWChem 6.1.1 sandybridge/nwchem/6.1.1 Freely available (Educational Community License, Version 2.0) http://www.nwchem-sw.org/
Octave 3.6.4 (uses GCC) octave/3.6.4 Freely available (GNU GPL) http://www.gnu.org/software/octave/
ONETEP 2.2.0 onetep/2.2.0 Restricted (6) http://www2.tcm.phy.cam.ac.uk/onetep/Main/HomePage
OpenMPI 1.6 openmpi/1.6 Freely available (New BSD) http://www.open-mpi.org/
ParaView  3.14.1 paraview/3.14.1 Open Source http://www.paraview.org/
Partiview CVS 2009 Globally available Freely available (Illinois Open Source License) http://virdir.ncsa.illinois.edu/partiview/
PETSc 3.1-p8 nehalem/petsc/3.1-p8 Freely available http://www.mcs.anl.gov/petsc/petsc-as/index.html
PGPLOT 5.2 pgplot/5.2 Restricted (7) http://www.astro.caltech.edu/~tjp/pgplot/
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 2.7.5 python/2.7.5 Freely available http://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/2.7.3 Freely 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/
PyMOL 1.3r2 pymol/1.3r2 Open Source (Python) http://pymol.org/
R 3.2.1 R/3.2.1 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/
SLALIB 2.5.4 slalib/2.5.4 Restricted (7) http://dev.starlink.ac.uk/
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/
valgrind 3.8.1 valgrind/3.8.1 GNU GPL http://valgrind.org/
VisIt 2.3.0 visit/2.3.0 Open Source (BSD) https://wci.llnl.gov/codes/visit/
Yorick 2.1.06 yorick/2.1.06 Open 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 athttps://projects.ivec.org/gulp/register.cgi.