Using prototyping to select software for a research software project

Author: Mike Jackson
Posted: 1 Mar 2021 | 14:03

A selection of macaronsChoosing 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.

Novel ammonia-hydrogen sulphide mixtures under extreme conditions: Implications for Ice-giant planets

Author: Guest blogger
Posted: 12 Feb 2021 | 13:14

Sudip Kumar Mondal from Jadavpur University in Kolkata visited the University of Edinburgh through the HPC-Europa3 Transnational Access programme. Falling from 11 October to 29 January, Sudip's visit was unlike most others because the Covid pandemic was ongoing. In this blog post Sudip describes his experiences in coming to and working in Edinburgh.

My doctoral research focuses on the physical behaviour of naturally occurring mineral phases at high temperature and pressure conditions by employing quantum chemical simulations which are hard to realize through experiments at the laboratory. Dr Andreas Hermann, my supervisor at the University of Edinburgh, was undoubtedly perfect for supervising this project, being an expert on materials at extreme conditions.

EPCC's Advanced Computing Facility: planning for future growth

Author: Paul Clark
Posted: 1 Feb 2021 | 12:10

Since 2005, the Advanced Computing Facility (ACF) has housed all the major systems managed by EPCC. It has expanded and evolved since its creation, becoming one of the most innovative and efficient facilities of its kind in the world.

The building and its internals have changed greatly since I started in February 2018, as part of a drive to ensure that our wider master planning for the site is reflected in what visitors see. This includes a video wall using Raspberry Pis and PiWall software to allow us demonstrate HPC visualisations to visitors.

We are developing a site-wide Data Centre Infrastructure Management (DCIM) approach which allows us to view real-time data or room and system performance on screens outside of different rooms and on our video wall.

In addition, the ACF has had significant investment over the years, most recently with the creation of Computer Room 4, the home of the new Edinburgh International Data Facility (EIDF). We also host and support a number of other HPC systems at the ACF, such as the National Tier-2 system, Cirrus. The first phase of the next UK national supercomputing service, ARCHER2, has also been installed.

EPCC’s Advanced Computing Facility: how it all began

Author: Guest blogger
Posted: 29 Jan 2021 | 11:03

EPCC's Advanced Computing Facility (ACF) was born through necessity – but the opportunity was taken to create an expandable and highly-efficient facility that attracted future business including national computing services. Mike Brown, EPCC’s Director of HPC Operations until 2017, gives an overview of the development of this unique building.

Update: The Edinburgh International Data Facility

Author: Rob Baxter
Posted: 13 Jan 2021 | 10:35

Work on the Edinburgh International Data Facility has passed three key milestones, bringing the infrastructure that will underpin the £600m Data-Driven Innovation Programme significantly closer to reality.

Firstly, and perhaps most importantly, EIDF’s home, Computer Room 4 (cr4) at the University’s Advanced Computing Facility, completed its main construction phase at the end of the third quarter of 2020 and cr4 has entered its commissioning and fit-out phase.  If everything goes to plan, we will start to build infrastructure in the room from January 2021.

A researcher's perspective on working with the Software Sustainability Institute

Author: Guest blogger
Posted: 11 Dec 2020 | 08:50

By Edward Wallace, School of Biological Sciences, University of Edinburgh.

Why I need sustainable software for my research

I run a lab, or research group, in the School of Biological Sciences at Edinburgh. My group  is funded by the Wellcome Trust, the Royal Society and BBSRC. We're interested in questions about how cells decide which proteins to make and when. Also, how cells change which proteins they make when they learn something from the environment and need to change what they're doing. In the 21st century we collect some very large datasets to measure this. There are datasets based on sequencing the RNA, which encodes protein, and datasets that measure all the proteins in cells at the same time. These datasets are measuring thousands of different things in many samples, often dozens of samples. Each dataset is gigabytes in size, and so it's quite hard work to dig into them and get the simplest and most relevant answers about what cells are doing.

Software Sustainability Institute’s Collaborations Workshop 2021

Author: Mario Antonioletti
Posted: 8 Dec 2020 | 14:47

The Software Sustainability Institute’s Collaborations Workshop 2021 (CW21) will take place online from March 30–April 1 2021. Registration is now open!

Modelling triple stellar interactions during a pandemic

Author: Guest blogger
Posted: 8 Dec 2020 | 10:46

Alexey Bobrick (Lund UniversitySpirit of 2020. My host and me, on one of the top floors in Birmingham University.(link is external), Sweden) was an HPC-Europa3 visitor hosted by Dr Silvia Toonen (link is external)at the Institute of Gravitational Wave Astronomy(link is external), University of Birmingham, UK. Because of COVID-19 restrictions, Alexey's visit has been split between his time in Birmingham (from 1–23 November), and working remotely from Sweden until 23 December. In this post Alexey tells us about his trip to Birmingham.

I study binary stellar astrophysics at Lund University, Sweden. In Birmingham my host, Dr Silvia Toonen, is one of the leading experts in triple and binary stellar evolution. I arrived at my accommodation in the middle of the autumnal Edgbaston Park area next to Birmingham University, and next morning I met my host. She kindly showed me around the campus and introduced me to her colleagues. The image shows me and my host, on one of the top floors in Birmingham University.  We then launched into many science discussions, which continued in the following weeks, together with meetings, work, calculations and more discussions.

Exploring Fujitsu’s A64FX CPU

Author: Nick Brown
Posted: 2 Dec 2020 | 14:20

The release of Fujitsu’s A64FX CPU has been a high point in an otherwise disappointing year. This next-generation CPU is the brain in Fugaku, the supercomputer at RIKEN in Japan, which was number one in the June 2020 TOP500 list.

Since February, Fujitsu has given EPCC access to a development A64FX machine as part of an early-access programme. We have been exploring the performance of this technology applied to numerous HPC workloads.

Extreme-scale precision imaging in radio astronomy

Author: Adrian Jackson
Posted: 2 Dec 2020 | 10:00

EPCC has embarked on a new collaboration with Prof. Yves Wiaux (Heriot-Watt University) to advance algorithms for high-precision and high-sensitivity computational imaging. 

The EIRA (Extreme-Scale Precision Imaging in Radio Astronomy) collaboration will focus on radio astronomy, which uses radio telescopes to collect data. This allows observation of the sky with antennae arrays at otherwise inaccessible angular resolutions and sensitivities. Algorithms being developed at Heriot-Watt University will address the challenges of building images from these incomplete linear data sets.


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