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PRACE Spring School 2016 and E-CAM Tutorial on Molecular & Atomic Modelling

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Location : O’Brien Centre for Science, University College Dublin, Belfield, Dublin 4, Ireland
May 16-20, 2016

Organizers

  • Simon Wong
    Irish Centre for High-End Computing, Ireland
  • Michael Lysaght
    Irish Centre for High-End Computing, Ireland

PRACE SCHOOL & ECAM-CECAM Tutorial

Description

The PRACE Spring School 2016 and E-CAM Tutorial on Molecular and Atomic Modelling will take place on 16-20 May 2016 at University College Dublin, Dublin, Ireland. The school is aimed at researchers who wish to gain a better understanding of methodologies and best practices in exploiting molecular and atomic modelling applications on HPC systems.

The programme will contain a mixture of scientific talks (HPC challenges in the field), sessions on HPC skills (parallel programming, numerical libraries) as well as application-oriented sessions with a large emphasis on hands-on practical exercises (e.g. classic molecular dynamics packages such as DL_POLY and Gromacs, electronic structure calculation packages such as CP2K and Quantum Espresso, covering example calculations, scalability and performance considerations, suggestions for development such as implementing custom functions and the Python-based Atomic Simulation Environment).

This school is jointly organised and funded by PRACE and the Horizon 2020 E-CAM project, an e-infrastructure for software, training and consultancy in simulation and modelling. The local organisers are the Irish Centre for High-End Computing (ICHEC) and CECAM-IRL (the Irish node of CECAM and partner in E-CAM).

Participation at the school is free of charge (not including travel and accommodation). Tea/coffee/lunch and a social dinner will be provided at the event. All lectures and training sessions will be conducted in English. For the hands-on sessions, participants are expected to bring their own laptops. We also ask that each participant prepare a 2-3 slide presentation of their research for the electronic poster session on Day 2.

The registration deadline has been extended to Tuesday 3rd May 2016.


Prerequisites

Participants are expected to have some experience with Linux systems and programming in C/C++/Fortran. The overview of parallel programming (OpenMP, MPI) on Day 1 and 2 only serve as a fast-paced introduction or re-cap of the main concepts (key to understanding parallel performance of simulation packages); it is not a full course on OpenMP and MPI for beginners. Participants are also expected to be familiar with either classical molecular dynamics and/or Density Functional Theory to fully benefit from the course.


Programme

Monday 16th May
09:30 – 09:50 Welcome and opening TBC
09:50 – 10:30 Introduction to parallel programming concepts Michael Lysaght
10:30 – 11:00 BREAK
11:00 – 12:30 OpenMP overview I (main concepts, parallel loops) Alin Elena
12:30 – 13:30 LUNCH
13:30 – 15:00 OpenMP overview II (synchronisation, tasks) Alin Elena
15:00 – 15:30 BREAK
15:30 – 17:00 MPI overview I (main concepts, point-to-point communication) Michael Lysaght
Tuesday 17th May
09:30 – 11:00 MPI overview II (collective communication, decomposition) Michael Lysaght
11:00 – 11:30 BREAK
11:30 – 12:30 Numerical libraries (overview of libraries, linking) Alin Elena
12:30 – 13:30 LUNCH
13:30 – 15:00 Numerical libraries (parallel libraries, performance considerations) Alin Elena
15:00 – 15:30 BREAK
15:30 – 17:30 Electronic poster session
Wednesday 18th May
09:30 – 10:30 Scientific & HPC challenges talk Erik Lindahl
10:30 – 11:00 BREAK
11:00 – 12:30 Overview of classical molecular dynamics packages (DL_POLY, Gromacs) and introduction to practical exercises Alin Elena (DL_POLY)
Erik Lindahl (Gromacs)
12:30 – 13:30 LUNCH
13:30 – 15:00 Practical session on DL_POLY & Gromacs
Free-form tutorial with example calculations, scalability tests, performance considerations, suggestions for development, etc.
Alin Elena (DL_POLY)
Erik Lindahl (Gromacs)
15:00 – 15:30 BREAK
15:30 – 17:00 Practical session on DL_POLY & Gromacs
Free-form tutorial with example calculations, scalability tests, performance considerations, suggestions for development, etc.
Alin Elena (DL_POLY)
Erik Lindahl (Gromacs)
19:00 – 21:30 Social dinner (venue to be confirmed)
Thursday 19th May
09:30 – 10:30 Scientific & HPC challenges talk Emilio Artacho
10:30 – 11:00 BREAK
11:00 – 12:30 Overview of electronic structure calculation packages (CP2K, QuantumEspresso) and introduction to practical exercises Iain Bethune (CP2K)
Stefano de Gironcoli (QuantumEspresso)
12:30 – 13:30 LUNCH
13:30 – 15:00 Practical session on CP2K and QuantumEspresso
Free-form tutorial with example calculations, scalability tests, performance considerations, suggestions for development, etc.
Iain Bethune (CP2K)
Stefano de Gironcoli (QuantumEspresso)
15:00 – 15:30 BREAK
15:30 – 17:00 Practical session on CP2K and QuantumEspresso
Free-form tutorial with example calculations, scalability tests, performance considerations, suggestions for development, etc.
Iain Bethune (CP2K)
Stefano de Gironcoli (QuantumEspresso)
Friday 20th May
09:30 – 10:30 Atomic Simulation Environment I Jussi Enkovaara
10:30 – 11:00 BREAK
11:00 – 12:30 Atomic Simulation Environment II Jussi Enkovaara
12:30 – 13:30 LUNCH
13:30 – 14:30 [to be confirmed] Atomic Simulation Environment III

Speakers and instructors

  • Prof. Emlio Artacho, CIC nanoGUNE, Spain
  • Mr. Iain Bethune, EPCC at the University of Edinburgh, UK
  • Dr. Alin M Elena, STFC Daresbury, UK
  • Dr. Jussi Enkovaara, CSC, Finland
  • Prof. Stefano de Gironcoli, SISSA, Italy
  • Prof. Erik Lindahl, Stockholm University, Sweden
  • Dr. Michael Lysaght, ICHEC, Ireland
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