Blog

Optimising sparse matrix-vector products at EPCC

Author: Guest blogger
Posted: 15 Aug 2019 | 11:35

Edoardo Coronado visited EPCC from 18th May–15th August 2019 under the HPC-Europa3 programme. 

Hi! My name is Edoardo Coronado. I am a Mexican PhD student in Technologies of Information at the "Centro Singular de Investigación en Tecnoloxías Intelixentes" (CiTIUS) at the "Universidad de Santiago de Compostela" in Spain. I work on the optimisation of iterative solvers on accelerator devices. I have spent three months at EPCC at the University of Edinburgh under the HPC-Europa3 transnational access programme with Mr Adrian Jackson acting as my host.

PRACE SoHPC: Wee Archie project overview

Author: Guest blogger
Posted: 12 Aug 2019 | 11:02

Caelen Feller, a PRACE Summer of HPC (SoHPC) student working with Wee Archie, gives us an overview and status report of his project.

As I have said previously, I’m working with Wee ARCHIE, EPCC's mini supercomputer, this summer. Wee Archie is made of 16 Raspberry Pi chips – each very small, lightweight computers connected together to work as a single machine. With each chip is an attached LED panel, allowing me to display what is occurring on the chip and how it is communicating to other chips. I have created a series of tutorials and simple demonstrations to be run on Wee Archie which explain the basics of message passing using MPI to a complete novice in parallel computing and non-expert in computers in general. 

Understanding protein synthesis via analysis of ribosome profiling data

Author: Mike Jackson
Posted: 8 Aug 2019 | 10:51

The molecular structure of a yeast ribosome, composed of 79 proteins

A multi-disciplinary team of biologists, bioinformaticians and research software engineers based at EPCC and The Wallace Lab at University of Edinburgh, The Shah Lab at Rutgers University, and The Lareau Lab at University of California, Berkeley, will enhance and extend a software suite called RiboViz to extract biological insight from "ribosome profiling" data and drive forward understanding of protein synthesis.

ARCHER Training report Summer 2019

Author: Clair Barrass
Posted: 7 Aug 2019 | 15:59

ARCHER Training report Summer 2019

So, it's been another busy end to the academic year and summer training season for the ARCHER Training team.

Since June we have managed to cram in no less than twelve training courses, in locations from London to Leeds, and Oxford to EPCC here in Edinburgh.

My HPC-Europa visit to Cambridge

Author: Guest blogger
Posted: 29 Jul 2019 | 16:27

Hi! My name is Concetta Cozza. I am a PhD student in Life Science at University ‘Magna Graecia’ of Catanzaro. This summer I visited the research group of Professor Michele Vendruscolo based at the University of Cambridge for three months with the HPC-Europa3 transnational access programme.

PRACE Summer of HPC 2019

Author: Mario Antonioletti
Posted: 29 Jul 2019 | 14:55

PRACE Summer of HPC (SoHPC) offers summer placements at HPC centres across Europe to late-stage undergraduates and/or Masters students. Up to twenty top applicants from across Europe spend two months working on projects related to PRACE technical or industrial work. Here are the three SoHPC visitors who are collaborating on projects with EPCC staff. 

Computational optimisation of materials at St Andrews

Author: Guest blogger
Posted: 22 Jul 2019 | 11:53

EPCC staff supported Dr Rincon Bonilla in his HPC-Europa3 research visit to the University of St Andrews earlier this year. 

My name is Mauricio Rincon Bonilla. I work as a postdoctoral fellow at the Basque Centre for Applied Mathematics in Bilbao, Spain, where I combine advanced sampling methods with physico-chemical insights to investigate ion dynamics in advanced battery materials. With the sponsorship of an HPC-Europa3 grant, I was able to spend seven weeks at the University of St Andrews with my hosts Prof. Tanja van Mourik and Herbert Fruchtl, who have lots of expertise in density functional theory for biological and inorganic materials. 

Software Carpentry at York

Author: Juan Rodriguez Herrera
Posted: 22 Jul 2019 | 11:14

Last month a Software Carpentry workshop organised by EPCC in collaboration with ARCHER and the Software Sustainability Institute was held in York. We had around twenty attendees from various backgrounds such as genetics, physical sciences, and engineering among others. My EPCC colleague Mario joined me as my fellow instructor and we also had the valuable support of three knowledgeable helpers from the Department of Physics at the University of York: Phil Hasnip, Peter Hill, and Killian Murphy.

Evaluation of a phase diagram with a novel technique in an HPC-Europa3 funded collaboration

Author: Guest blogger
Posted: 19 Jul 2019 | 09:22

György Hantal was an HPC-Europa3 visitor from 18th March to 17th May 2019.

I am György Hantal (pictured here with Durham castle in the background), a postdoctoral researcher from the University of Vienna. I was an HPC-Europa3 visitor for two months, hosted by Dr. Lívia Bartók-Pártay at the University of Reading's Department of Chemistry and supported by EPCC in Edinburgh.

Multi-network MPI on Intel Omni-Path

Author: Adrian Jackson
Posted: 17 Jul 2019 | 14:11

Networks

As part of the NEXTGenIO project we have a prototype HPC system that has two Intel Omni-Path networks attached to each node. The aim of having a dual-rail network setup for that system is to investigate the performance and functionality benefits of having separate networks for MPI communications and for I/O storage communications, either directing Lustre traffic and MPI traffic over separate networks, or using a separate network to access NVDIMMs over RDMA. We were also interested in the performance benefits for general applications exploiting multiple networks for MPI traffic, if and where possible.

Pages

Contact

Tracy Peet
+44 (0) 131 650 5362
t.peet@epcc.ed.ac.uk