ARCHER News

Tuesday 7th May 2019

GROMACS 2019 overview of the new features and capabilities

Friday 17th May 2019 14:00 BST

Presented by BioExcel, but likely to be of interest to ARCHER users

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Each new major release of GROMACS brings with it the latest in feature development, hardware support, performance enhancements, and usability improvements. In this webinar we will review and describe the major new changes, and guide you to make best use of the new opportunities.

https://bioexcel.eu/gromacs-2019-overview-of-the-new-features-and-capabilities-2019-05-17/

Open Source HPC Benchmarking Virtual Tutorial

Wednesday 22nd May 2019, 15:00

Andy Turner, EPCC

There is a large and continuing investment in HPC services around the UK, Europe and beyond and this, along with new processor technologies appearing on the HPC market, has led to a wider range of advanced computing architectures available to researchers.

We have undertaken a comparative benchmarking exercise across a range of architectures to help improve our understanding of the performance characteristics of these platforms and help researchers choose the best services for different stages of their research workflows.

We will present results comparing the performance of different architectures for traditional HPC applications (e.g. CFD, periodic electronic structure) and synthetic benchmarks (for assessing I/O and interconnect performance limits). We will also describe how we have used an open research model where all the results and analysis methodologies are publicly available at all times. We will comment on differences between architectures and demonstrate the benefits of working in an open way.

Full details and join link : http://www.archer.ac.uk/training/virtual

Sheffield GPU Hackathon 2019

We are pleased to announce the Sheffield GPU Hackathon 2019, a hackathon devoted to porting scientific applications to GPUs as well optimizing existing GPU-enabled codes.

Sheffield GPU Hackathon 2019 will take place August 19-23, 2019 at Halifax Hall at Sheffield, United Kingdom. Prior GPU experience is not required, as those selected will be paired with experienced mentors who will teach them how to leverage accelerated computing in their own applications or further optimize their codes. We are looking for teams of 3-5 developers, ideally postdocs, research software engineers (RSEs) or graduate students with a scalable application to port to (or optimize on) GPU accelerators. Successful teams will be joined by two mentors with extensive GPU programming experience. Full details including the link for submissions can be found in the official announcement:

http://gpuhack.shef.ac.uk/

The submission deadline is July 1st, 2019.

While teams will have to pay for their own travel and accommodation, the hackathon itself (including lunches) is sponsored by NVIDIA and is thus free of charge.

Please feel free to pass this announcement on to interested colleagues. Any questions should be directed to gpuhack-organisers@sheffield.ac.uk

HPC-Europa3 Transnational Access programme

Collaborative research visits using High Performance Computing

Call for applications: next closing date 14th May 2019

HPC-Europa3 funds research visits for computational scientists in any discipline which can use High Performance Computing (HPC).

Visits can be made to research institutes in Finland, Germany, Greece, Ireland, Italy, the Netherlands, Spain, Sweden or the UK.

UK-based researchers can benefit in two ways: either by visiting a research group elsewhere in Europe, or by hosting a research visitor from another country.

What does HPC-Europa3 provide?

  • Funding for travel, living and accommodation expenses for visits of up to 13 weeks.
  • Access to world-class High Performance Computing (HPC) facilities.
  • Technical support to help you make best use of the HPC systems.
  • Collaborative environment with an expert in your field of research.

Who can apply?

  • Researchers of all levels, from postgraduate to full professors.
  • Researchers from academia or industry.
  • Researchers currently working in a European Union country or Associated State (see http://bit.ly/2PkVsSV for full list of Associated States).
  • Researchers may not visit a group in the country where they currently work.
  • A small number of places are available for researchers working outside these countries - please contact staff@hpc-europa.org for more information.

How do I apply?

Apply online at http://www.hpc-europa.org

The next closing date is 14th May 2019. Closing dates are held 4 times per year. Applications can be submitted at any time. You should receive a decision approximately 6 weeks after the closing date.

For more information and to apply online, visit: http://www.hpc-europa.org/

Follow us on Twitter for project news: https://twitter.com/HPCEuropa3

CompBioMed Conference

CompBioMed is a European Commission H2020 funded Centre of Excellence focussed on the use and development of computational methods for biomedical applications, and CompBioMed is hold its first Conference in London on 25-27 September, 2019.

The conference will address all aspects of the rapidly burgeoning domain of computational biomedicine, from genome through organ to whole human and population levels, embracing data driven, mechanistic modelling and simulation, machine learning and combinations thereof. We welcome contributions from academic, clinical and industrial participants alike.

Early Bird Registration and Abstract Submission deadline 15th May 2019.

For more details, please visit https://www.compbiomed-conference.org/.

Upcoming Training Opportunities

Registration open now

  • Open Source HPC Benchmarking, Online, 22 May 2019 15:00
  • Software Carpentry, York, 10-11 June 2019
  • Introduction to Code_Saturne, Manchester, 19-20 June 2019
  • Advanced OpenMP, Manchester, 25-27 June 2019
  • Practical Software Development, Leeds, 10-11 July 2019
  • ARCHER Summer School 2019
    • Hands-on Introduction to HPC, EPCC, Edinburgh, 15-16 July 2019
    • Message-passing Programming with MPI, EPCC, Edinburgh, 17-19 July 2019
  • Advanced MPI, Oxford, 22-23 July 2019

Full details and registration at http://www.archer.ac.uk/training/index.php