Software development

Precision persistent programming

Author: Adrian Jackson
Posted: 30 Oct 2019 | 12:48

Targeted Performance

Optane DIMM

Blog post updated 8th November 2019 to add Figure 6 highlighting PMDK vs fsdax performance for a range of node counts.

Following on from the recent blog post on our initial performance experiences when using byte-addressable persistent memory (B-APM) in the form of Intel's Optane DCPMM memory modules for data storage and access within compute nodes, we have been exploring performance and programming such memory beyond simple filesystem functionality.

For our previous performance results we used what is known as a fsdax (Filesystem Direct Access) filesystem, which enables bypassing the operating system (O/S) page cache and associated extra memory copies for I/O operations. We were using an ext4 filesystem on fsdax, although ext2 and xfs filesystems are also supported.

Optimizing CPU oversubscribed reductions

Author: Guest blogger
Posted: 6 Sep 2019 | 11:17

Gladys Utrera was an HPC Europa3 visitor to EPCC from 1st of July to the 3rd of August 2019. She has been an HPC Europa visitor before - in this brief blog article she tells us what she did this time.

Hi! My name is Gladys Utrera and I currently work at the Computer Architecture Department of the Universitat Politècnica de Catalunya in Barcelona, Spain. There I combine teaching of parallel computing and operating systems subjects with research on HPC topics and parallel programming models. Thanks to the HPC-Europa3 programme I could spend four weeks at the EPCC in the University of Edinburgh with my host Mark Bull who is a very well-known expert in my research areas. This is my third research visit to EPCC, and the second as an HPC-Europa visitor. 

My research involves executions on large multi-core node clusters. In addition, performance evaluations on machines with different architectures characteristics like ARCHER and Cirrus, enrich my results greatly. 

Benchmarking MPI implementations on ARM

Author: Nick Brown
Posted: 30 Aug 2019 | 11:32

The recent installation of Fulhame, the ARM HPC machine based here in EPCC as part of the Catalyst UK programme, raises plenty of interesting opportunities for exploring the HPC software ecosystem for ARM. One such aspect is the relative performance of different MPI implementations on these machines and this is what I was talking about last week at the MVAPICH User Group (MUG) workshop.

Analysing historical newspapers and books using Apache Spark and Cray Urika-GX

Author: Mike Jackson
Posted: 16 Aug 2019 | 16:25

Library booksIn our October 2018 blog post on Analysing humanities data using Cray Urika-GX, we described how we had been collaborating with Melissa Terras of the College of Arts, Humanities and Social Sciences (CAHSS) at The University of Edinburgh to explore historical newspapers and books using the Alan Turing Institute's deployment of a Cray Urika-GX system ("Urika"). In this blog post we describe additional work we have done, to look at the origins of the term "stranger danger", find reports on the Krakatoa volcanic eruption of 1883, and explore the concept of "female emigration".

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.

Taking the sting out of gout

Author: Amy Krause
Posted: 1 Jul 2019 | 10:48

 

 

 

 

Gout is estimated to affect 2.5% of the UK population, and is increasing globally in association with cardiovascular disease and obesity. EPCC has been working with Dr Philip Riches of the MRC Institute of Genetics and Molecular Medicine to develop a new app that could lead to improved treatment and better quality of life for patients.

Gout is a type of arthritis caused by excess uric acid in the blood. It is characterised by sudden attacks of intense pain that result in reduced quality of life, work absence and disability. The standard treatment for the condition involves close monitoring of blood urate levels and medication, but the high level of health professional support required to ensure a long term cure of gout is rarely delivered: fewer than half of eligible patients receive preventive treatment and fewer than half of those on treatment receive an adequate dose of medication.

Too much choice?

Author: Nick Brown
Posted: 17 Jun 2019 | 14:24

When is enough, enough? With so many parallel programming technologies, should we focus on consolidating them?

At the ISC conference in June I will moderate a panel discussion on whether it is time to focus on the consolidation and interoperability of existing parallel programming technologies, rather than the development of new ones.

Building research collaborations across Europe

Author: Catherine Inglis
Posted: 12 May 2019 | 14:31

The HPC-Europa3 project funds short collaborative “Transnational Access” research visits using HPC.

In just 17 months EPCC has supported 50 HPC-Europa visits from research groups in a total of 15 countries. We are already seeing great results from our visitors, including at least seven publications.

Applications for repeat or reciprocal visits – either between the same researchers, or different members of the same groups – are testimony to the strength of the ongoing collaborative links fostered by the programme. Two of our first HPC-Europa3 visitors have even returned to their former host research groups for longer visits.

Software Sustainability Institute's Collaborations Workshop 2019 (CW19)

Author: Mario Antonioletti
Posted: 19 Mar 2019 | 10:16

The Software Sustainability Institute's (SSI) Collaborations Workshop 2019 (CW19) will be held at the West Park Teaching Hub, Loughborough University, Loughborough from 1-3 April 2019. This year the workshop will be themed around topics based on interoperability, documentation, training, and sustainability. Keynote speakers will include Catherine Stihler, CEO of Open Knowledge International, and Franziska Heine (link points to a German article), Head of Software & Development at Wikimedia Deutschland. They will open the event on 1st April.

Proof-driven queries to preserve patient privacy

Author: Mike Jackson
Posted: 4 Mar 2019 | 09:42

StethoscopeIn our role as members of the Research Engineering Group of the Alan Turing Institute, Anna Roubickova and I worked with Efi Tsamoura and Benjamin Spencer (Department of Computer Science at the University of Oxford) on PDQ, a proof-driven query planner that has great potential within the realm of data science for medical research. 

Pages