We are constantly contributing to efforts to develop infrastructural software with a focus on HPC and benchmarking. Our developer organisation is on github and we will curate a selection of our works below.
Longbow
Longbow is an automated simulation submission and monitoring tool. Longbow is designed to reproduce the look and feel of using software on the users local computer with the difference that the heavy lifting is done by a supercomputer.
Longbow will automatically generate the necessary submit files and handle all initial file transfer, monitor jobs, transfer files at configurable intervals and perform final file transfer and cleanup.
Longbow can be used to launch one-off jobs, generate ensembles of similar jobs or even run many different jobs over many different supercomputers.
Out of the box, Longbow is currently supporting the PBS/Torque, LSF, SGE, Slurm, SoGE schedulers and ships with application plugins for commonly used bio-molecular simulation softwares AMBER, CHARMM, GROMACS, LAMMPS, NAMD. Longbow is however highly configurable and will function normally with generic software without plugins, however plugins can easily be made to extend Longbow to fully support applications and schedulers that do not ship out of the box.
Getting Started - Documentation
Source Code - Repository
hpcbench
hpcbench is a HECBioSim adopted tool that was developed as part of the EPSRC funded ExCALIBUR programme in which the biomolecular simulation community were successful in obtaining funding for ExaBioSim, an initiative to explore and benchmark a wider range of hardware than is currently available in existing generations of supercomputers. hpcbench is an automated benchmarking utility specialised to standardising, running and interpreting the HECBioSim benchmarking suite of tools.
Source Code - Repository
HPC Calculator
The HECBioSim HPC calculator is a javascript based web app that extended the functionality of the HECBioSim website with an interactive calculator to explore the HPC requirements for simulations on different HPC platforms. The calculator has the following main features, CPUs and GPUs, wall time and resource prediction, energy consumption and efficiency recommendations. This calculator was built on the data obtained by our benchmarking suite.
Source Code - Repository