ARCHER News

Tuesday 5th June 2018

ARCHER Embedded CSE Call - Open Now

We are very pleased to announce that the 13th ARCHER embedded CSE (eCSE) call is now open and proposals are invited up to the deadline of 4pm (UK time) on Tuesday 17th July 2018. Embedded CSE (eCSE) support provides funding for the ARCHER user community to develop software in a sustainable manner for running on ARCHER and future UK Tier-1 services.

More details of how to apply are available by following the link to the eCSE calls page from here: www.archer.ac.uk/community/eCSE/. This also includes details of the application and review process, assessment criteria eligibility, etc.

The 13th eCSE call opened on: 5th June 2018

Deadline for proposals: 1600 BST on Tuesday 17th July 2018.

Proposals received after the deadline cannot be accepted. More information is available from the ARCHER helpdesk (support@archer.ac.uk).

CompBioMed Webinar: Introduction to Biomedical Applications on High Performance Computers

This webinar introduces the fundamental concepts and basic tools of HPC environments, and includes an application example of flowing red blood cells in a vessel section. It is divided into 2 major sections. The first part, presented by Dr Gavin J. Pringle (EPCC), presents a high-level overview of HPC along with practical examples. The second part, presented by Dr Gábor Závodszky (UvA), showcases the usage of an open-source HPC code (www.hemocell.eu), which is built to simulate blood flows on the level of single cells. The whole talk forms a coherent unit providing a brief guide that takes you from the conceptual basics of HPC computing to an actual application.

Presentation given by:

Dr Gavin J Pringle (Application Consultant in High Performance Computing, EPCC)

Dr Gábor Závodszky(PostDoc at the Computational Science Lab of the University of Amsterdam)

Full details available at /www.compbiomed.eu/compbiomed-webinar-4/.

Corrected module: OpenFOAM 4.1

OpenFOAM 4.1 for the pre-/post-processing nodes was missing the decomposePar and reconstructPar utilities. OpenFOAM 4.1 for the pre-/post-processing nodes will be updated during the At Risk maintenance session on 13 June 2018, between 1500 and 1600 BST. During this time, OpenFOAM 4.1 for the pre-/post-processing nodes may not work correctly.

Corrected module: GROMACS 5.1.4

GROMACS 5.1.4 was partially overwritten with GROMACS 5.0.2 on 27 March 2018. This affects the gmx program (and its aliases) and some topology files:

  • share/gromacs/top/amber03.ff/aminoacids.rtp
  • share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
  • share/gromacs/top/charmm27.ff/aminoacids.hdb
  • share/gromacs/top/charmm27.ff/ffnabonded.itp
  • share/gromacs/top/charmm27.ff/ffnonbonded.itp
  • share/gromacs/top/oplsaa.ff/aminoacids.hdb
  • share/gromacs/top/oplsaa.ff/aminoacids.rtp
  • share/gromacs/top/oplsaa.ff/atomtypes.atp
  • share/gromacs/top/oplsaa.ff/ffbonded.itp
  • share/gromacs/top/oplsaa.ff/ffnonbonded.itp
  • share/gromacs/top/oplsaa.ff/ions.itp
  • share/gromacs/top/oplsaa.ff/watermodels.dat
  • share/gromacs/top/residuetypes.dat

The correct Gromacs 5.1.4 will be re-installed between 1500 and 1600 BST 13 June 2018. In the meantime, you can access the correct Gromacs 5.1.4 with:

module load gromacs/5.1.4_original

Webinar: Modern C++ for Computational Scientists

Wednesday 13th June 2018 14:00 BST & 27th June 2018 14:00 BST - Note earlier-than-usual start time

Rupert Nash, EPCC, will present a four-part tutorial, over two afternoons, on the use of Modern C++ for Computational Scientists.

Since the 2011 revision to the C++ language and standard library, the ways it is now being used are quite different. Used well, these features enable the programmer to write elegant, reusable and portable code that runs efficiently on a variety of architectures.

However, it is still a very large and complex tool. This set of online lectures, delivered over two Wednesday afternoons and including practical exercises, will cover a minimal set of features to allow an experienced non-C++ programmer to get to grips with language. These include: overloading, templates, containers, iterators, lambdas and standard algorithms. It concludes with a brief discussion of modern frameworks for portable parallel performance which are commonly implemented in C++.

The course would appeal to existing C++ programmers wanting to learn techniques that are applicable to numerical computing, or C programmers who want to know what parts of the C++ standard they should prioritise when learning new features.

Details and join link : www.archer.ac.uk/training/virtual

Performance Analysis Workshop

19-21 June 2018, UCL

This workshop is organised by VI-HPS for the UK PRACE Advanced Training Centre to:

  • give an overview of the VI-HPS programming tools suite
  • explain the functionality of individual tools, and how to use them effectively
  • offer hands-on experience and expert assistance using the tools

All attendees will be given access to ARCHER, however, all tools covered are designed for portability so will be applicable to any HPC system. On completion participants should be familiar with common performance analysis and diagnosis techniques and how they can be employed in practice (on a range of HPC systems). Those who prepared their own application test cases will have been coached in the tuning of their measurement and analysis, and provided optimization suggestions.

Programme Overview

Presentations and hands-on sessions are on the following topics:

  • BSC tools for trace analysis and performance prediction
  • Score-P instrumentation and measurement
  • Scalasca automated trace analysis
  • MAQAO performance analysis and optimization
  • Full details and registration at www.vi-hps.org/training/tws/tw28.html.

    Upcoming Training Opportunities

    Registration open now

    • Software Carpentry London School of Economics 18-19 June 2018
    • Performance Analysis Workshop UCL 19-21 June 2018
    • Data Analytics with HPC Belfast 20-21 June 2018
    • Advanced OpenMP Cambridge 17 - 19 July 2018
    • Advanced MPI Milton Keynes 30 - 31 July 2018

    ARCHER Summer School

    • Hands-on Introduction to HPC Edinburgh 2-3 July 2018
    • Message-passing Programming with MPI Edinburgh 4-6 July 2018

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

    EPCC Training Privacy Statement is now available at http://www.archer.ac.uk/training/privacy.php