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D8.1.4: Plan for Community Code Refactoring 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 Project Grant Agreement Number: RI-283493 D8.1.4 Plan for Community Code Refactoring Final Version: 1.0 Author(s): Claudio Gheller, Will Sawyer (CSCS) Date: 24.02.2012 D8.1.4 Plan for Community Code Refactoring Project and Deliverable Information Sheet PRACE Project Project Ref. №: RI-283493 Project Title: PRACE Second Implementation Project Project Web Site: http://www.prace-project.eu Deliverable ID: D8.1.4 Deliverable Nature: Report Deliverable Level: Contractual Date of Delivery: PU * 29 / 02 / 2012 Actual Date of Delivery: 29 / 02 / 2012 EC Project Officer: Thomas Reibe * - 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: Plan for Community Code Refactoring Document ID: D8.1.4 Version: 1.0 Status: Final Available at: http://www.prace-project.eu Software Tool: Microsoft Word 2007 File(s): D8.1.4.docx Written by: Claudio Gheller, Will Sawyer (CSCS) Authorship Contributors: Thomas Schulthess, CSCS; Fabio Affinito, CINECA; Ivan Girotto, Alastair McKinstry, Filippo Spiga, ICHEC; Laurent Crouzet, CEA; Andy Sunderland, STFC; Giannis Koutsou, Abdou Abdel-Rehim, CASTORC; Fernando Nogueira, Miguel Avillez , UC-LCA; Georg Huhs, José María Cela, and Mohammad Jowkar, BSC, Nikos Anastopoulos (ICCS-GRNET), Paulo Silva (UC) Reviewed by: Michael Schliephake, KTH Thomas Eickermann, JUELICH Approved by: MB/EB PRACE-2IP - RI-283493 i 24.02.20122 D8.1.4 Plan for Community Code Refactoring Document Status Sheet Version Date Status Comments 0.1 02/01/2012 First skeleton 0.2 10/01/2012 Overall structure defined 0.3 21/01/2012 First performance model added 0.4 23/01/2012 More performance models 0.5 26/01/2012 More performance models 0.6 01/02/2012 Appendix B added 0.7 03/02/2012 More performance models 0.8 07/02/2012 More performance models and conclusions added 0.9 08/02/2012 Proofreading 1.0 09/02/2012 Final version PRACE-2IP - RI-283493 ii 24.02.20122 D8.1.4 Plan for Community Code Refactoring Document Keywords Keywords: PRACE, HPC, Research Infrastructure, scientific applications, libraries, performance modelling. Disclaimer This deliverable has been prepared by Work Package 8 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 2011 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 24.02.20122 D8.1.4 Plan for Community Code Refactoring 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 ...................................................................................................................... vi References and Applicable Documents ............................................................................. viii List of Acronyms and Abbreviations ..................................................................................... x Executive Summary ............................................................................................................ 1 1 Introduction ..................................................................................................................... 1 2 Astrophysics ..................................................................................................................... 4 2.1 RAMSES ................................................................................................................................. 4 2.2 PKDGRAV ............................................................................................................................ 10 2.3 PFARM ................................................................................................................................ 12 Implementation ........................................................................................................................ 16 Testing and Optimization .......................................................................................................... 16 3 Climate .......................................................................................................................... 18 3.1 Couplers: OASIS ................................................................................................................... 18 3.2 Input/Output: CDI, XIOS, PIO ............................................................................................... 19 3.3 Dynamical Cores: ICON ........................................................................................................ 20 3.4 Ocean Models: NEMO and Fluidity‐ICOM ............................................................................ 24 4 Material Science ............................................................................................................ 39 4.1 ABINIT ................................................................................................................................. 39 4.2 Quantum ESPRESSO ............................................................................................................ 55 4.3 Yambo ................................................................................................................................. 59 4.4 Siesta .................................................................................................................................. 59 4.5 Octopus ............................................................................................................................... 62 4.6 Exciting/ELK ......................................................................................................................... 63 5 Particle Physics .............................................................................................................. 67 5.1 Target codes, algorithms, and architectures ........................................................................ 67 5.2 Workplan ............................................................................................................................ 71 6 Conclusions and next steps ............................................................................................ 74 Appendix A. Engineering Community ................................................................................ 75 A.1 Scientific Challenges ............................................................................................................ 75 A.2 Method to approach the Community .................................................................................. 77 A.3 Numerical Approaches and Community Codes .................................................................... 80 A.4 Community involvement, expected outcomes and their impact .......................................... 89 A.5 Relevant Bibliography ......................................................................................................... 90 Appendix B. Description of the linear‐response methodology of ABINIT, and performance analysis. ............................................................................................................................ 93 B.1 Motivation .......................................................................................................................... 93 B.2 Performances of the linear‐response part of ABINIT ............................................................ 93 PRACE-2IP - RI-283493 iv 24.02.20122 D8.1.4 Plan for Community Code Refactoring B.3 Performance improvement of the linear‐response part of ABINIT. ...................................... 97 PRACE-2IP - RI-283493 v 24.02.20122 D8.1.4 Plan for Community Code Refactoring List of Figures Figure 1: GANTT for RAMSES refactoring ........................................................................................
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