The Cambridge University Centre for Computational Chemistry groups theoretically-minded members of the Cambridge Department of Chemistry in premises on the recently refurbished third floor of the Department. Around 50 members, comprising staff, research fellows, postdoctoral associates, postgraduate students, and visiting scientists from all over the world, work on many aspects of theoretical and computational chemistry.
The theoretical research and modelling carried out at CUC³ covers an exceptionally broad range of topics in theoretical and quantum chemistry, condensed matter physics, surface science, and statistical mechanics of complex and disordered systems including macromolecular aggregates. The theoretical tools include quantum theory and density functional theory (DFT) of electronic structure, classical DFT of inhomogeneous fluids, statistical mechanics, and a variety of simulation methods, including Monte Carlo, Molecular Dynamics (MD), and ab initio MD, as well as global optimization algorithms for the exploration of multi-dimensional energy surfaces.
CUC3 Computing: Standard Linux Workstations
These pages are out of date and only cover old versions of the workstation image. For the current image please see http://www-co.ch.cam.ac.uk/facilities/linux-workstations/current/.
The Theory sector computer officers provide a Linux workstation service for the sector. The workstations are installed and managed centrally, automatically backed up, and contain a wide variety of software.
Latest news
070) 21/05/09 Mathematica 7.0.1 installed
069) 19/05/09 Workstations patched today
068) 18/05/09 SuSE 11.1 image is now the default for new machines
067) 30/03/09 Workstations patched today
066) 27/03/09 g95 wrapped to support library modules better
065) 26/03/09 Cambridge Structural Database 2009 installed
Click here for complete news file
Getting started
Available software
Hardware
The sector has a pool of hardware that the computer officers assign as necessary. New hardware is purchased by research groups when they want to update their machines or we run out; please check with the computer officers before buying anything so that you get something that is compatible with the current version of the Linux workstation image. New hardware stays in the purchasing group for two years and then goes into the general pool.
The workstations are all covered by our contract with University Hardware Support, but they have to go off site to be repaired which can take a few days. The computer officers can provide a replacement machine while this is happening, although it will not be of the same spec as the failed machine. Failed hard disks, mice, and keyboards are replaced on site out of a stock kept by the computer officers.
The computer office stocks several different types of mice and keyboards so feel free to come and swap yours if you would prefer another sort. We can also provide monitor stands, wrist rests, and footrests if needed.
CUC³ Software.
Local workstations and servers generally run Linux: usually either Debian or SuSE. These machines have a variety of free and proprietary packages installed. A list of software installed on the standard SuSE workstations is available. For software installed on the servers, please see the local documentation for that server. The /info and /usr/share/doc directories on the machine are a good place to start looking.
The University Public Workstation Facility (PWF) provides Windows and Mac machines in the cybercafe, library, and G29 within the department. These machines have licences for Microsoft Office and many other useful packages. Almost everyone working in the Theory sector will be entitled to a PWF account, so this is often the best method to access Windows/Mac software if you only need it infrequently. Those needing access to Windows apps from their Linux desktop can use the department-wide Terminal Services Service. Please note that you must purchase your own software licences for applications such as Office for this service.
Attention is drawn to the department's Software Policy. All proprietary software used in the sector must be recorded on the list kept by the group's computer representative, including any on personal laptops. The computer representative for groups in the Theory sector is currently Catherine Pitt.
The University Computing Service has a Software Sales section which sells some software at academic prices to members of the University. There are often restrictions on the use of such software.
If the package you want doesn't seem to be installed anywhere in the sector, please ask for it as it may be possible to obtain it. Suggestions for useful new packages to install are always welcome.
Here's a catchall list of local documentation for software. Everything here can be found somewhere in the sector, but may not be on all machines or under active maintenance; see individual pages for details.
Chemistry
Amber 8 (Molecular Dynamics)
AmberTools (Molecular Dynamics)
Cambridge Structural Database (Database of small molecule crystal structures)
Dalton 2.0 (quantum chemistry)
GAMESS-UK (Quantum chemistry package)
GAMESS-US (Quantum chemistry package)
Gaussian 03 (Quantum chemistry package)
Alpine
Maths
Mathematica (Symbolic maths package)
R (statistical computing environment)
MPI
Intel Cluster Toolkit (MPI library and tools)
LAM MPI (MPI library)
MPI-CH (MPI library)
OSC mpiexec (Torque-speaking MPI job launcher)
OpenMPI (MPI library)
Programming tools
ACML (Maths library for AMD)
ATLAS (BLAS and LAPACK library)
CUDA (GPU programming with Nvidia GPUs)
Intel C/C++ compiler (icc) (C compiler)
Intel Fortran (ifort) (Fortran compiler)
Intel Math Kernel Library (High performance maths library)
gfortran (Free Fortran 90 compiler)
g95 (Fortran compiler)
NAG f95 Fortran compiler (Fortran compiler)
NAG nagfor Fortran compiler (Fortran compiler)
NAG Numerical library (Maths library)
Pathscale EKO compiler suite (high performance Fortran 95, C, and C++ compilers plus developer tools)
Portland compiler suite (Fortran, C, C++ and HPF compiler)
GNU Scientific Library (Maths library)
Plotting
g3data (Tool for getting data from graphs)
gnuplot (graph plotting)
xmgrace (Graph plotting program)
Python
Python (An object oriented scripting language)
Biopython (Python tools for molecular biology)
egenix-mx-base (extensions for python)
Gary Strangman's python modules (Python modules)
Matplotlib (A python module for drawing graphs)
numarray (array module for Python)
Numeric Python (another array module for Python)
Numpy (Numeric Python module)
Scientific Python (python modules)
SciPy (python modules)
Visualisation
Aten (visualisation)
gOpenMol (Molecular visualization)
JavaView (visualisation addon for Mathematica)
Molden (Molecular visualization)
MolMol (Molecular visualization)
pymol
VMD (Molecular visualization)
XCrySDen (Molecular visualization)
xmakemol (Molecular visualization)
Utilities
git (version control system)
ical (an old but reliable calendar app)
Meld (diff and merge tool)
Modules environment (Support software)
mpeg_encode (MPEG-1 encoder)
nfswatch (NFS monitoring program)
pico (User-friendly editor)
PDFlib Lite (Library for creating PDFs, for non-profit use only)
ppmtompeg (utility to make mpeg files)
qgit (GUI for git)
rdesktop (Remote access to Windows Terminal Servers)
Subversion (Version control system)
Texmaker (GUI Latex editor)
xwrits (Typing interruption software for RSI sufferers)
xxdiff (Graphical diff program)
xf4vnc (VNC server)
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