Posted: 1 Mar 2021 | 14:03
Choosing the right software for use in a research software project can be challenging. How do we know which software is both fit for purpose and provides a sound basis for our project for the foreseeable future? And, how do we make such a choice given that the time and effort to explore what could be myriad alternatives may be limited?
This was a challenge we faced in the RiboViz project, 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. RiboViz is an open source package to help us develop our understanding of protein synthesis via analysis of ribosome profiling data. At the heart of RiboViz is an analysis workflow, implemented in a Python script. To conform to best practices for scientific computing, which recommend the use of build tools to automate workflows and to reuse code instead of rewriting it, we sought to reimplement this workflow within a bioinformatics workflow management system.
Posted: 11 Nov 2020 | 10:51
I am delighted to announce that EPCC has passed our annual external ISO 27001 Information Security and ISO 9001 Quality audits with flying colours.
EPCC recognises the importance of a process-led approach to the delivery of National Tier-1 and Tier-2 services such as ARCHER, ARCHER2 and Cirrus. The implementation of an ISO 9001-based Quality Management Systems has provided a framework to ensure that the services delivered meet user and customer requirements. It requires that service improvements are identified and the impacts of their implementation tracked, ensuring that the improvement is effective.
Posted: 31 Aug 2020 | 15:33
SC, the world's largest high-performance computing conference, will be held virtually during the week of November 9-13. It is a disappointment not to be going to SC in person, but the flip side is that the conference will be open to a wider audience than would have been possible had it been held in Atlanta as originally planned.
This year I am organising the second run of the Urgent HPC workshop, which is an event aimed at bringing together those who are researching the role of HPC and data science in making urgent decisions to tackle disasters. The event first ran last year at SC19 and comprised a keynote talk by the founder of Technosylva – the world’s leading wildfire simulation code development company – six technical papers, and a panel. Based upon that success we decided to run the workshop again this year, and given all that has happened since then, exploring this topic is more timely than ever before!
Posted: 24 Aug 2020 | 18:11
Edoardo Coronado visited EPCC from 18th May–15th August 2019 under the HPC-Europa3 programme. Here he gives us an update on his research since his previous blog article.
During my visit to EPCC in 2019 under the auspices of the HPC-Europa3 programme, I worked on optimising routines to perform the Sparse Matrix-Vector (SpMV) product, a common operation in lots of scientific applications, on Intel Xeon Gold processors and Graphics Processing Units (GPUs).
Posted: 29 Jun 2020 | 14:38
We currently have applications open for PhD students, starting late 2020/early 2021 depending upon their situation. Four of these have been advertised on findaphd, with the closing date at the end of the month.
In addition to our MSc programmes, EPCC also hosts a number of PhD students who are researching a diverse set of areas: from traditional performance optimisation for HPC, to new data science technologies and novel computing architectures. Supervised by EPCC members of staff and housed in the Bayes, not only do these students benefit from being part of the UK’s leading HPC centre, but they also have access to the wider University’s large range of resources.
Posted: 23 Jun 2020 | 15:10
This week ISC, one of the largest conferences in the supercomputing calendar, should have been running in Frankfurt. It’s a funny feeling because, as I type, I realise that if it wasn’t for COVID-19 then, instead of being stuck at home, I would have been busy navigating the Messe Frankfurt, going from one session to another.
Posted: 15 Jun 2020 | 11:18
We have become an accredited processor under the UK Digital Economy Act, following an audit process conducted by the Office for National Statistics. EPCC is one of only seven UK organisations to gain this accreditation.
The Digital Economy Act (DEA) came into force in 2017 and covers issues related to electronic communications infrastructure and services. Under the Act, an organisation may become accredited for the purposes of processing data, principally with the linkage or de-identification of data, or the storage and provision of secure access to the de-identified data. EPCC is accredited for storage and provision for the National Safe Haven that it operates on behalf of Public Health Scotland.
Posted: 12 Feb 2020 | 11:34
Javier Fernández Muñoz was an HPC-Europa3 visitor from 1st June 2019–30th August 2019 hosted at EPCC by Rosa Filgueira. Here he tells us about his experiences.
Hi! My name Javier Fernández Muñoz, I am working as a Visiting Professor in the Computer Architecture and Technology Area of the Computer Science Department at the University Carlos III de Madrid (Spain).
My research field includes the development of parallel programming frameworks that enhance usability and portability. In this regard, I have been working several years in the development of GrPPI (Generic Reusable Parallel Pattern Interface), an open source generic and reusable parallel pattern programming interface. Basically, GRPPI accommodates a layer between developers and existing parallel programming frameworks targeted at multi-core processor capabilities, such as ISO C++ Threads, OpenMP, Intel TBB, and FastFlow. To achieve this goal, the interface leverages modern C++ features, meta-programming concepts, and generic programming to act as a switch between those frameworks.
Posted: 27 Jan 2020 | 08:47
Marcos Maroñas was a visitor from BSC who, under the HPC-Europa3 Programme, was hosted here at EPCC from 1st Sep to 1st Dec 2019 by Dr Mark Bull. In this blog article he tell us about his visit.
Hi! My name is Marcos Maroñas. I am currently a PhD student at Barcelona Supercomputing Center (BSC) in the Programming Models group of the Computer Science department. I spent most of my time there doing research on runtime systems for parallel programming models such as OmpSs-2.
Posted: 27 Nov 2019 | 12:21
EPSRC has recently announced the new Tier-1 ARCHER2 HPC service and is also in the process of extending the UK's Tier-2 HPC systems. This will give users access to substantial amounts of new CPU and GPU hardware, so it's a perfect time to learn about how to use parallel HPC systems and how to program GPUs.