March 2021 Newsletter

12 March 2021 10:00

University of Sheffield Research Software Engineering Team Newsletter March 2021

This is the 9th monthly newsletter from the Research Software Engineering Team at The University of Sheffield. We aim to share our experiences and information of other communities for those using software for research. This newsletter collects interesting events and opportunities over the coming month. It also signposts to other resources that we find beneficial or interesting. You may find the content interesting if you are someone in research using software, are a person paid to develop software (like a Research Software Engineer (RSE)). or are somewhere in-between (a research developer).

To receive this newsletter as an email each month, please sign up to our Google Group.

All times are GMT (UTC+00)

News

The University of Sheffield has released a statement on open research. It officially recognises that making research transparent and freely accessible plays a vital part in promoting research excellence.


The UKRN Academy forum was created for doctoral students working on reproducibility and metascience projects. It is a part of the UK Reproducibility Network. The UKRN contact for the Academy is Tom Stafford (@tomstafford), institutional lead for the University of Sheffield.


The Society of Research Software Engineering have published their strategy for 2020/2021. Informed by the community feedback event, they’ve proposed a strategy around the following three pillars:

  • Environment: Creating a research environment which recognises software and its contributors
  • Skills: Enhancing the provision of skills for researchers and the RSE community
  • People: Increasing awareness and opportunities for the role of RSEs

The Reprohack NL team have won this year’s Open Initiative Trophy. We’d like to congratulate the team including Anna Krystalli who is also a member of our Sheffield RSE group.


The RSE Society is developing a mentoring scheme to facilitate additional community support for RSEs. You can register your interest with this form.

Future events

Introduction to Deep Learning Course with Tensorflow Keras (in Python), 15th April

A one-day introduction to deep learning with practical labs using Tensorflow Keras in Python. The session is led by Twin Karmakharm.

Register with eventbrite


Introduction to Deep Learning Course with Keras (in R), 22nd April

A one-day introduction to deep learning with practical labs using Keras (Tensorflow) in R. The session is led by Anna Krystalli.

Register with eventbrite


Upcoming ARCHER 2 training events:

  • Introduction to ARCHER2 for software developers, 29-30th of March
  • Containers in HPC, 30th March
  • Quantum Computing Without A Quantum Computer, 31st March
  • Shared Memory programming with OpenMP, online self-service course.

Details and registration for the courses can be found on their upcoming training page.


Upcoming N8 CIR training events:

  • Fundamentals of Accelerated Computing with CUDA C/C++, 17th March
  • IBM Training for Bede - AI, 19th March
  • Research Data Management Network Event, 24th March
  • RSE Leaders and Aspiring Leaders Event, 26th March
  • Coputer Vision for the Humanities, 13th April

Details and registration for the courses and events can be found on their events page.


POP is offering training on performance analysis, methodology and tools for women and underrepresented groups in the HPC community on the 19th of April.


LunchBytes is a monthly series of short talks for those in the research community at TUOS who work with/write code, use/manage research data and use/manage research infrastructure. Through these talks we come together as a community to discuss best practices and useful methods/tools. If you’re interested in curating a session or giving a talk, get in touch at: lunchbytes-organisers-group@sheffield.ac.uk

The next LunchBytes event will be in early April, with a provisional theme of Making GPU programming more accessible with two confirmed speakers:

  • Freddie Witherden, developer of PyFR, a CUDA accelerated python CFD library

  • James Knight, developer of PyNN/GeNN, a GPU enhanced Neuronal Network simulation environment

The exact date and details of talks will be advertised soon via the RSE team’s mailing list.

Previous events

The Sheffield Metascience Network, a network for University of Sheffield researchers & staff engaged in metascience & research on research, kicked off with their launch event on the 3rd of March.

Opportunities

The Society of Research Software Engineering (SocRSE) are providing an Events and Initiatives Grant. It funds up to £1,000 per event or initiative that supports their mission statement or charitable objectives.


The 4th Cycle of the CZI Essential Open Source Software for Science is now open for applications. Funding is available for software maintenance, growth, development, and community engagement.


The EPSRC have released a call (with a deadline of 30 April 2021 for applications) for access to high performance computing.

The services available are:

  • Tier 1 ARCHER2, for simulations and calculations that need parallelised processing cores
  • Tier 2 services with a range of architectures for different computational needs.

The Met Office SPF EXCALIBUR Programme launched the Cross-cutting research for exascale software and algorithms call with the 15th April deadline and addresses the themes of future computing paradigms, coupling, verification, validation and uncertainty quantification, and domain-specific languages.

Further information on the Cross-cutting themes can be found here.


Nvidia are offering an Applied Research Accelerator Program for research projects which “has been demonstrated to be feasible with an identified path to a GPU-accelerated application, which could be deployed within three years”. It offers varying levels of hardware grant (e.g. up to 4-8 workstations) and technical expertise depending on project requirements.


For RSE vacancies across the UK and elsewhere see the Society of RSE’s jobs board.

Web and Blogs

RSE Stories: Working with you rather than for you podcast is an interview of our group lead Paul Richmond and his journey as an RSE.


Code for Thought podcast’s 9th February edition on the topic of It’s All About Reproducibility features our very own Anna Krystalli talking about the award-winning ReproHack events.


N8 Bede supercomputer accelerates research in the north of England. Scientists and researchers across the North of England will benefit from the arrival of a new £3.8m supercomputer to support projects in areas such as Artificial Intelligence (AI), energy storage and therapeutic drug design.

Software and Updates

Google released the Model Search framework that implements AutoML algorithms for deep learning model architecture search at scale. The post Introducing Model Search: An Open Source Platform for Finding Optimal ML Models offers more detail on the framework.


The Python language continues to evolve after ~30 years: it’s gaining ‘pattern matching’ functionality similar to what can be found in Rust and functional programming languages such as Haskell and Scala. This superficially looks like the case/switch statements one gets in languages such as C/C++/Java but offers much richer functionality.

Resources

Need access to managed desktop software? The University provides a Find a pc website allowing students to remotely access PCs running University Desktop.


Introduction to Data Science online book covers a wide range of data science topics including machine learning. Practical examples are provided in R.


Using MATLAB with Python livestream: Heather Gorr and Yann Debray walk through the ways you can use MATLAB and Python together. They answer questions about how to call Python libraries from MATLAB (and vice versa), package and deploy your MATLAB programs, and more.


Global.health provides open access to real-time epidemiological anonymized line-list COVID-19 data that contains over five million anonymized cases from over 100 countries.


If you think there are other great training resources we should advertise, please get in contact (rse@sheffield.ac.uk).

RSE Sheffield’s Services

The RSE Sheffield team aims to collaborate with you to help improve your research software. We can provide dedicated staff to ensure that you can deliver excellent research software engineering on your research projects.

The RSE Sheffield team provides free Code Clinics (in collaboration with IT Services), plus paid services that allow us to collaborate longer term.

Contact Us

For queries relating to collaborating with the RSE team on projects: rse@sheffield.ac.uk

To contact the RSE team about seminars, training or JADE: rse-team-group@sheffield.ac.uk

Join our mailing list so as to be notified when we advertise talks and workshops by subscribing to this Google Group.

Queries regarding free research computing support/guidance should be raised via our Code clinic or directed to University central IT support.