ARCHER News

Wednesday 29th April 2020

• Porting and performance of DiRAC HPC benchmarks on Oracle bare metal cloud - Webinar
• "covid-sim" COVID-19 pandemic modelling tool available on ARCHER
• Frequently asked questions (and answers) to support transition to ARCHER2
• LAMMPS course
• Message-passing programming with MPI course
• Reproducible computational environments using containers course
• Other upcoming ARCHER training
• HPC-Europa3 Transnational Access programme

Porting and performance of DiRAC HPC benchmarks on Oracle bare metal cloud

Wednesday 29th April 2020 11:00-12:00 BST

Andy Turner, EPCC/ARCHER2

The DiRAC facility provides access to HPC resources for researchers in the particle physics, cosmology and astrophysics and nuclear physics community. At the moment all of these resources are provided through a variety of on-premises systems that are designed to meet different technical requirements of different research communities. As part of our forward technology watch, the DiRAC RSE team are currently working with Oracle to evaluate the performance of their bare-metal HPC instances with RDMA-enabled interconnects on the recently developed DiRAC application benchmarking suite. In this presentation we will give details of progress with this project, including:

• assessing usability of the cloud resources for typical DiRAC users;
• reporting on application porting experience; and
• analysis of performance of the application benchmarks.

We will finish with a summary of readiness of the Oracle bare metal cloud service for use for researchers currently using DiRAC facilities; provide an overview of how the user experience could be improved for researchers; and note the next steps for our work in evaluating use of cloud to provide HPC resources to support academic researchers.

This online session is open to all.

Join link and full details : https://www.archer2.ac.uk/training/courses/200429-oracle-cloud-benchmarking/

"covid-sim" COVID-19 pandemic modelling tool available on ARCHER

Following the recent work to make available the source code for the influential "covid-sim" COVID-19 pandemic modelling tool from the group of Neil Ferguson at Imperial College, we are happy to announce that the tool is now installed for use on ARCHER (and Cirrus: http://www.cirrus.ac.uk) for use by all users. You can access the tool by using the 'module load covid-sim' command. Once loaded, the UK model is available with the command 'CovidSim_UK' and the US model with the command 'CovidSim_US'. You can find more information on the modelling tool, including source code and documentation, on the GitHub repository at:

https://github.com/mrc-ide/covid-sim

and reports on COVID-19, including modelling using this tool, from the MRC Centre for Global Infectious Disease Analysis at Imperial College at:

https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/covid-19-reports/

Frequently asked questions (and answers) to support transition to ARCHER2

We have recently published an FAQ to assist users with the migration from ARCHER to ARCHER2 including information about data migration, allocations for projects which migrate and advice on preparation.

This FAQ will be regularly updated as new information becomes available.

You can find the FAQ at http://www.archer.ac.uk/support/faq/end_of_service.php

LAMMPS course

4 - 18 May 2020

Julien Sindt, EPCC

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a widely-used classical molecular dynamics (MD) code. This C++ code is easy to use, incredibly versatile, and parallelised to run efficiently on both small-scale personal computers and CPU/GPU/CPU&GPU HPC clusters. As of 2018, LAMMPS has been used, to some degree, in over 14,000 publications in fields as varied as chemistry, physics, material science, granular and lubricated-granular flow, etc.

The course will be run over three 2.5 hour-long sessions.

The first session will be an introduction to setting up and running an MD simulation using LAMMPS. We will begin by running a simulation of a Lennard-Jones fluid before delving deeper into how simulations can be set up and run in LAMMPS.

In the second session, we will discuss how to download and install LAMMPS, with a more in-depth discussion of the various packages LAMMPS offers and how to use them efficiently.

The third session will be a follow-up session for exercises, discussion and questions.

Details and registration: https://www.archer2.ac.uk/training/courses/200504-lammps/

Message-passing programming with MPI

14 - 22 May 2020

David Henty, EPCC

The world’s largest supercomputers are used almost exclusively to run applications which are parallelised using Message Passing. The course covers all the basic knowledge required to write parallel programs using this programming model, and is directly applicable to almost every parallel computer architecture.

Parallel programming by definition involves co-operation between processes to solve a common task. The programmer has to define the tasks that will be executed by the processors, and also how these tasks are to synchronise and exchange data with one another. In the message-passing model the tasks are separate processes that communicate and synchronise by explicitly sending each other messages. All these parallel operations are performed via calls to some message-passing interface that is entirely responsible for interfacing with the physical communication network linking the actual processors together. This course uses the de facto standard for message passing, the Message Passing Interface (MPI). It covers point-to-point communication, non-blocking operations, derived datatypes, virtual topologies, collective communication and general design issues.

The course is normally delivered in an intensive three-day format using EPCC’s dedicated training facilities. It is taught using a variety of methods including formal lectures, practical exercises, programming examples and informal tutorial discussions. This enables lecture material to be supported by the tutored practical sessions in order to reinforce the key concepts.

Details and registration: https://www.archer2.ac.uk/training/courses/200514-mpi/

Other upcoming ARCHER2 Training

• Oracle Cloud HPC benchmarking results, Online, Wednesday 29th April 2020 11:00-12:00 BST
• ARCHER2 Training, Online, Wednesday 6th May 2020, 15:00-16:00 BST
• ARCHER2 Spectrum of Support, Online, Wednesday 13th May 2020 15:00-16:00 BST
• The determination of clusters structures combining infrared spectroscopy and density functional theory calculations, Online, Wednesday 20th May 2020 15:00-16:00 BST
• Reproducible computational environments using containers, Online, 13-14 July 2020

Further details https://www.archer2.ac.uk/training/#upcoming-training

HPC-Europa3 Transnational Access programme

Collaborative research visits using High Performance Computing

Call for applications: next closing date 14th May 2020, for visits during the second half of 2020.

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 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.

Coronavirus travel restrictions: Applicants will be notified of the selection panel’s decisions around the end of June. We hope that the travel situation should be returning to normal by this time. Visits should be planned for July to December, but there can be some flexibility if there are continuing restrictions on travel at that stage.

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/AssociatedStates for full list of Associated States).
• Researchers may not visit a group in the country where they currently work.
• A small number of places may be 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 2020. 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