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Specification and software

Hardware specification

Compute nodes

The cluster consists of 110 compute nodes, each containing 32 cores (two 2.1GHz 16-core Intel Broadwell (Xeon E5-2683 or Gold 6130) processors), between 128GB and 1.5TB of memory and some local scratch disk. Two nodes are equipped with two NVidia Tesla V100 GPU processors each.

Storage

400TB of shared disk are available as scratch space via the parallel GPFS file system.

Network

All components are linked via FDR Infiniband and Gigabit Ethernet. 18 blades inside one chassis are share full FDR connectivity; the maximum contention between different chassis is 2:1.

Available software

A variety of application software is installed on kennedy. The following is an incomplete list. If you require a package that is currently not installed, you can either request it to be installed, or install or compile your own software.

It is your responsibility to ensure that your use of kennedy and any software installed on it is legal and covered by the license of this software, in addition to being ethical and for the purposes of your research.

General Computing

MATLAB

MATLAB scripts can be run without graphical output (with the -nodisplay -nodesktop -nosplash) flags through the SLURM batch queue.

License: St Andrews site license
Installed version: R2020a
Example batch job: /usr/local/examples/job-matlab

Materials Science

Quantum Espresso

Quantum Espresso is a suite of programs based on the plane-wave DFT code pwscf.

License: free and open source
Installed version: 6.5
Example batch job: /usr/local/examples/job-pwscf

CP2K

CP2K implements molecular dynamics and geometry optimization using DFT (via the Gaussian/plane wave method), semiempirical and force field methods, as well as mixed applications (QM/MM).

License: free and open source
Installed version: 4.1
Example batch job: /usr/local/examples/job-cp2k

CASTEP

CASTEP is a plane-wave DFT code to calculate material properties, including NMR parameters.

License: Free for academic use, but requires license at research group level. Please "buy" a license from STFC.
Installed version: 19.11
Example batch job: /usr/local/examples/job-castep

Molecular Quantum Chemistry

Gaussian

Gaussian is a quantum chemistry code for molecular systems. It also includes molecular mechanics methods and some functionality for periodic systems.

License: St Andrews site license for academic use
Installed version: Gaussian 16, Revision C.01
Example batch job: /usr/local/examples/job-g16

ORCA

ORCA is another quantum chemistry code for molecular systems. It offers a wide variety of methods using particularly efficient RI (resolution of the identity) approximations.

License: Free for academic use, but requires registration at the ORCA Forum.
Installed version: 5.0.0
Example batch job: /usr/local/examples/job-orca