Dear RSE community, it is great to write to you after an interesting July. At least in London, we have had some lovely weather as well as an unexpectedly high amount of rainfall. Research shows that these new extremes are a consequence of global warming. Importantly, research software has been crucial for climate and environmental science. The software that implements climate models has improved our understanding of the causal relationship between global warming and climate change. Additionally, greenhouse gas visualisation software provides strong arguments in support of a faster energy transition.
Now let’s turn our attention to the core of the newsletter that covers a broader spectrum of research software. Have a great weekend, and looking forward to speaking with you in our weekly RSE coffee and through our Slack channels!
In this month’s newsletter:
The Software Sustainability Institute’s autumn Research Software Camp “Beyond the Spreadsheet” will take place over two weeks in November: a call for ideas is currently open and closes at the end of July.
The “Research Software Engineers in HPC (RSE-HPC-2021)” workshop will take place on November 15th, 2021, as part of SuperComputing (SC21). We had a submission from our community accepted at last year’s RSE-HPC workshop. If you’re working with or building research software that runs on or has links with HPC infrastructure, do consider submitting something to this workshop. The call for papers is currently open and the submission deadline is 6th August 2021.
BSC (Barcelona Supercomputing Center) is running a GPU Hackathon across 4 dates in late October and early November 2021. An application process is required to participate in the event and the deadline for applications is 14th August 2021.
sktime is a unified framework for machine learning with time series. The sktime community of the Alan Turing Institute is organising the 2021 summer programme, held virtually. It consists of events and activities which can be joined separately, from May to August, with the remaining two events in the series taking place between the 16th and 20th August.
Firedrake is a finite element code to solve partial differential equations. Members of the Firedrake team are running a short course on using Firedrake on ARCHER2 - Introduction to using Firedrake on ARCHER2. The session takes place on 23rd August 2021, 13:00 - 17:00 and you can register via the course page.
PackagingCon 2021 is a two-day virtual conference that will bring together software packagers and developers of package management software from many different communities. The conference takes place 9th-10th November 2021. The call for presentations is open and the submission deadline is 31st August 2021.
The 11th international Women in HPC workshop will take place as part of Supercomputing 21 on Sunday 14th November 2021. The Call for Lightning Talks is currently open and the deadline for submissions is 8th September 2021.
After a two-year gap, the annual RSE conference is back this year but in a rather different format. SeptembRSE, the 5th Conference of Research Software Engineers will take place online throughout the month of September. Registration for the conference is now open at £35 for non-members of the Society of RSE and £15 for Society members. See the registration page for more details.
GitHub now supports software citation based on the Citation File Format! More info and links here.
EPSRC have released a new funding call - Software for research communities. The call is aimed at supporting a community-driven approach to the development and maintenance of software. The deadline for the intention to submit - a required step - is the 14th September and the deadline for submission of full proposals is the 14th October. Get in touch with Imperial’s RSE Team to find out how we can support your application - or be part of it!
Deployment of ARCHER2, the UK’s new national supercomputing resource and the successor to ARCHER, is continuing. A recent article on the ARCHER2 blog shows the arrival of the final system cabinets.
The DeepLearners group from the Imperial Research Software Community held its first event on Monday 5th July. The session included an introduction to the group followed by a series of lightning talks from 6 members of the community and some interesting discussion. Look out for details of future group sessions and join the #deeplearners Slack channel to get answers to technical AI/ML-related questions or help answer questions raised by others.
The latest episode of the RSE Stories podcast is out. “A Life Of Its Own” is an interview with Kalina Borkiewicz, an RSE at the Advanced Visualization Lab at the National Center for Supercomputing Applications (NCSA), University of Illinois.
Make your software reproducible and highlight this to others! Did you know that you can complete this checklist and get a badge for your repository to highlight the degree of reproducibility of your software?
A recent post on the StackOverflow blog looks at “Best practices for writing code comments”.
The Software Sustainability Institute has published another blog post from CW21 speed blog series. This two part post looks at Coding Clubs For Research Software Communities: Questions to Consider - Part 1, Part 2.
numfmt GNU utility.Software for the birds: A blog post from SSI Fellow Philipp Boersch-Supan looking at the use of R within ornithology.
Videos from the SSIs Collaborations Workshop 2021 (CW21) are now online.
Code for Thought: From Research To Startup
Getting started with… Python - a post from the StackOverflow blog highlighting some pros and cons of learning Python along with a number of useful links.
“Leap australia” published an interesting artcile about the application of CFD in tunnel ventilation scenarios.
“FLUBIO” is a relatively new, open-source Fortran CFD code design for teaching and research purposes.
“OpenFOAM-v2106” has been released! Improvements in stability and solvers have been implemented, but also some of the code structure has changed. If you use dynamic boundary conditions or customised solvers, your code may need rewriting slightly to run in the new version of OpenFOAM.
Our research software of the month for July is KungFu. KungFu is a novel distributed machine learning library that helps users achieve scalable and adaptive training of large deep learning models. It exposes rich high-level Python APIs. These APIs allow users to monitor statistical metrics of gradients, optimise training parameters according to monitored metrics, and scale operation to many machines without incurring communication bottlenecks. KungFu can support multiple machine learning frameworks, including TensorFlow, Keras, PyTorch and MindSpore. It has become a popular project on Github and has attracted users and developers from both industry and academy.
See this paper and presentation for more details of the library. The project is available on GitHub at https://github.com/lsds/KungFu.
…continues weekly via Teams - normally on Friday afternoons at 3pm but check our Slack workspace for exact times and connection details.
The Imperial Research Software Community Slack workspace is a place for general community discussion as well as featuring channels for individuals interested in particular tools or topics. If you’re an OpenFOAM user, why not join the #OpenFOAM channel where regular code review sessions are announced (amongst other CFD-related discussions…). Users of the Nextflow workflow tool can find other Imperial Nextflow users in #nextflow. You can find other R developers in #r-users and there is the #DeepLearners channel for our new AI/ML group. Take a look at the other available channels by clicking the “+” next to “Channels” in the Slack app and selecting “Browse channels”. If you want to start your own group around a tool, programming language or topic not currently represented, feel free to create a new channel and advertise it in #general.
See the Research Computing Service’s Research Computing Tips series for a variety of helpful tips for using RCS resources and related tools and services.
Imperial’s Research Software Directory provides details of a range of research software and tools developed by groups and individuals at the College. If you’d like to see your software included in the directory, you can open a pull request in the GitHub Repository or get in touch with the Research Software Community Committee.
Drop us a line with anything you’d like included in the newsletter, ideas about how it could be improved… or even offer to guest-edit a future edition! rse-committee@imperial.ac.uk.
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This issue of the Research Software Community Newsletter was edited by Felipe Huerta. All previous newsletters are available in our online archive.