Introduction This Rough Guide is a Crib Sheet for improving the efficiency of parallel software for future supercomputers, and was last updated 17th February, 2023 by g.pringle@epcc.ed.ac.uk. This guide first appeared as an appendix of a CompBioMed deliverable [1]. This guide was then updated and appeared as an appendix for the CoE EXCELERAT deliverable [2].…
CompBioMed’s 29th e-seminar took place at on 18 January 2023, titled “OpenMP in the Exascale Era”. Modern supercomputer nodes now contain more than 100 cores, and often several GPUs. This means that the “MPI only” approach to parallel programming is coming under increasing strain and can no longer deliver the maximum performance from the hardware.…
CompBioMed’s 28th e-seminar took place on 23 November 2022 and focused on Predicting and preventing bone fractures with HPC. Femur fracture is a catastrophic event for elderly women, resulting in severe impairment of life quality or even death in many cases. One of the major risk factor is osteoporosis, an asymptomatic metabolic disorder that causes…
CompBioMed will be at the Le Studium Conference on “Cardiovascular Modelling: Basic Science to Clinical Translation” to be held in Tours (France) on 13th and 14th December 2022. The symposium is being organised, managed and sponsored by the Le Studium Institute for Advanced Studies – Loire Valley and the INSERM Unit iBrain Imagerie et Cerveau.…
CompBioMed’s 27th e-seminar took place on 19 October 2022 focused on DNA Point Mutations in the Absence and Presence of Electric Fields. DNA mutations can occur spontaneously or can be induced by external factors such as electric fields, intercalators, radiations, etc. One of the point mutation mechanisms, known as the Löwdin’s mechanism, is the double…
The CompBiomed centre of excellence organised, in collaboration with the VPH Institute, a special session on the The role of exascale computing in computational biomedicine at the VPH2022 conference in Porto (PL) on Friday 9 September 2022. The session included four speakers from our consortium. Mariano Vasquez (BSC) showed concrete examples of how Alya can…
More than 350 people attended the virtual presentation at Supercomputing 2020 featuring the work done in remote training in the QIIME2 application by consortia members, UCL and the University of Sheffield. This project, which took place over a 4-month period with a 6-week live course, introduced medical students into HPC. Led by Andrea Townsend-Nicholson of…
A major effort is now underway to perform the first full scale 3-D high fidelity simulations of blood flow in the human vasculature. Led by Peter Coveney within his Centre for Computational Science (CCS) at University College London (UCL), this major, large scale team endeavour, involves colleagues and collaborators from across Europe and the USA.…
The CompBioMed code HemeLB, developed at UCL was assessed by the POP Centre of Excellence to determine scaling ability of the code on SuperMUC-NG at LRZ. Peter Coveney and Jon McCullough at UCL worked with Brian Wylie at Jülich Supercomputing Centre to enable this assessment. This audit examined strong scaling of HemeLB on the SuperMUC-NG…
A joint UCL / Janssen team has performed a statistically robust head-to-head comparison between the Centre for Computational Science’s high performance computational method, TIES, and that offered by a commercial provider, Schrödinger Inc, FEP+, for calculating relative free energies of binding of candidate drugs to target proteins. TIES and FEP+ use different so-called “alchemical” free…