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D7.1: Scaling Support for Preparatory Access Users SEVENTH FRAMEWORK PROGRAMME Research Infrastructures INFRA-2011-2.3.5 – Second Implementation Phase of the European High Performance Computing (HPC) service PRACE PRACE-2IP PRACE Second Implementation Phase Project Grant Agreement Number: RI-283493 D7.1 Scaling Support for Preparatory Access Users Final Version: 1.0 Authors: Stefanie Janetzko, GCS-FZJ, Alexander Schnurpfeil, GCS-FZJ Date: 21.08.2013 D7.1 Scaling Support for Preparatory Access Users Project and Deliverable Information Sheet PRACE Project Project Ref. №: RI-283493 Project Title: PRACE Second Implementation Phase Project Project Web Site:http://www.prace-project.eu Deliverable ID: D7.1 Deliverable Nature: Report Deliverable Level: Contractual Date of Delivery: PU * 31 / August / 2013 Actual Date of Delivery: 31 / August / 2013 EC Project Officer: Leonardo Flores Añover * - The dissemination level are indicated as follows: PU – Public, PP – Restricted to other participants (including the Commission Services), RE – Restricted to a group specified by the consortium (including the Commission Services). CO – Confidential, only for members of the consortium (including the Commission Services). Document Control Sheet Title: Scaling Support for Preparatory Access Users Document ID: D7.1 Version: 1.0 Status: Final Available at: http://www.prace-project.eu Software Tool: Microsoft Word 2010 File(s): D7.1.docx.docx Written by: Stefanie Janetzko, GCS-FZJ, Alexander Authorship Schnurpfeil, GCS-FZJ Contributors: Pierre Kestener, CEA, Franck Houssen, CEA, Carlo Cavazzoni, CINECA, Francesco Salvadore, CINECA, Nicole Audiffren, CINES, Sami Saarinen, CSC, Martti Louhivuori, CSC, Jussi Enkovaara, CSC, Iain Bethune, EPCC, Joerg Hertzer, GCS-HLRS, Volker Weinberg, GCS-LRZ, Anupam Karmakar, GCS-LRZ, Paschalis Korosoglou, GRNET, Alexandra Charalampidou, GRNET, Pavlos Daoglou, GRNET, Maciej Szpindler, ICM, Maciej Cytowski, ICM, Isabelle Dupays, IDRIS, Margareta Boiarciuc, IDRIS, Vladimir Slavnic, IPB, Petar Jovanovic, IPB, Dusan Stankovic, IPB, Valentin Pavlov, NCSA, Vegard Eide, NTNU, Luis Fazendeiro, SNIC-Chalmers, Michael Schliephake, SNIC-KTH, Jonathan Vincent, SNIC-KTH, Soon-Heum Ko, SNIC-LiU, Joachim Hein, SNIC-LU, Mikael Rännar, SNIC-UmU, Petros Souvatzis, SNIC-UU, Jeroen Engelberts, SURFsara PRACE-2IP - RI-283493 i 21.08.2013 D7.1 Scaling Support for Preparatory Access Users Reviewed by: Stelios Erotokritou, CaSToRC Dietmar Erwin, GCS-FZJ Approved by: MB/TB Document Status Sheet Version Date Status Comments 0.1 11/July/2013 Draft Structure and chapters 1 and 2 0.2 29/July/2013 Draft Project reports included, Summary 0.3 05/August/2013 Draft After task-internal review 0.4 20/August/2013 Draft After project-internal review 1.0 21/August/2013 Final version PRACE-2IP - RI-283493 ii 21.08.2013 D7.1 Scaling Support for Preparatory Access Users Document Keywords Keywords: PRACE, HPC, Research Infrastructure, Preparatory Access Disclaimer This deliverable has been prepared by the responsible Work Package of the Project in accordance with the Consortium Agreement and the Grant Agreement n°RI-283493. It solely reflects the opinion of the parties to such agreements on a collective basis in the context of the Project and to the extent foreseen in such agreements. Please note that even though all participants to the Project are members of PRACE AISBL, this deliverable has not been approved by the Council of PRACE AISBL and therefore does not emanate from it nor should it be considered to reflect PRACE AISBL’s individual opinion. Copyright notices 2013 PRACE Consortium Partners. All rights reserved. This document is a project document of the PRACE project. All contents are reserved by default and may not be disclosed to third parties without the written consent of the PRACE partners, except as mandated by the European Commission contract RI-283493 for reviewing and dissemination purposes. All trademarks and other rights on third party products mentioned in this document are acknowledged as own by the respective holders. PRACE-2IP - RI-283493 iii 21.08.2013 D7.1 Scaling Support for Preparatory Access Users Table of Contents Project and Deliverable Information Sheet ......................................................................................... i Document Control Sheet ........................................................................................................................ i Document Status Sheet ......................................................................................................................... ii Document Keywords ............................................................................................................................ iii Table of Contents ................................................................................................................................. iv List of Figures ........................................................................................................................................ v List of Tables .......................................................................................................................................... v References and Applicable Documents .............................................................................................. vi List of Acronyms and Abbreviations .................................................................................................. vi Executive Summary .............................................................................................................................. 1 1 Introduction ................................................................................................................................... 2 2 Preparatory Access Calls .............................................................................................................. 2 2.1 Cut-off Statistics .................................................................................................................................. 3 2.2 The Review Process ............................................................................................................................. 5 2.3 Assigning of PRACE Collaborators ................................................................................................... 5 2.4 Monitoring of Projects ........................................................................................................................ 6 2.5 Hand-over between PRACE IP Projects ........................................................................................... 6 2.6 Dissemination ....................................................................................................................................... 7 3 Optimization Work ....................................................................................................................... 8 3.1 Cut-off December 2011 ....................................................................................................................... 8 3.1.1 Increasing the QUANTUM ESPRESSO capabilities: towards the DFT simulation of realistic nanoparticles ......................................................................................................................................... 8 3.1.2 High Performance MP2 for condensed phase simulations ......................................................... 11 3.1.3 I/O-optimization to improve parallel scalability of the meso-scale NWP-model HARMONIE .. 14 3.2 Cut-off March 2012 ........................................................................................................................... 16 3.2.1 Implementation of an Efficient Semi-implicit PDE Solver in the Cardiac Simulation Environment Beatbox .......................................................................................................................... 16 3.2.2 Optimizing GPAW on GPUs....................................................................................................... 18 3.3 Cut-off June 2012 .............................................................................................................................. 20 3.3.1 Massive Parallel Navier-Stokes Solver for Breaking Waves ...................................................... 21 3.3.2 Linear Scaling Methods for Quantum Hall Transport Simulations ............................................ 21 3.3.3 GPU Implementation of TD-DFT algorithm and parallel IO improvements for the DP code ... 21 3.3.4 FLY on Cray: Porting of a Cosmological Parallel Treecode ..................................................... 22 3.3.5 Optimization of multiple sequence alignment software clustalw ................................................ 22 3.4 Cut-off September 2012 .................................................................................................................... 23 3.4.1 Strong Scaling of LibGeoDecomp on Blue Gene/Q .................................................................... 23 3.4.2 CASINO for large solid catalyst systems: configuration numbers and population control ........ 23 3.4.3 Combinatorial Models for Topology Aware Mapping................................................................ 24 3.5 Cut-off December 2012 ..................................................................................................................... 24 3.5.1 MAGICS - Modelling the ArrhythmoGenic Influence of the Cardiac conduction System .......... 24 3.5.2 Numerical model for the thermal energy storage tank with integrated steam generator (TES-SG)
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