Solving Software Challenges for Exascale: International Conference on Exascale Applications and Software, EASC 2014, Stockholm, Sweden, April 2-3, 2014, Revised Selected Papers

154 Pages·2015·16 MB·English

by  Stefano Markidis

Stefano Markidis
Erwin Laure (Eds.)
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Solving Software Challenges
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for Exascale
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International Conference
on Exascale Applications and Software, EASC 2014
Stockholm, Sweden, April 2–3, 2014
Revised Selected Papers
123
Lecture Notes in Computer Science 8759
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Weizmann Institute of Science, Rehovot, Israel
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Indian Institute of Technology, Madras, India
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TU Dortmund University, Dortmund, Germany
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University of California, Los Angeles, CA, USA
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Stefano Markidis Erwin Laure (Eds.)
(cid:129)
Solving Software Challenges
for Exascale
International Conference
on Exascale Applications and Software,
EASC 2014
–
Stockholm, Sweden, April 2 3, 2014
Revised Selected Papers
123
Editors
Stefano Markidis Erwin Laure
KTHRoyal InstituteofTechnology KTHRoyal InstituteofTechnology
Stockholm Stockholm
Sweden Sweden
ISSN 0302-9743 ISSN 1611-3349 (electronic)
Lecture Notesin ComputerScience
ISBN 978-3-319-15975-1 ISBN 978-3-319-15976-8 (eBook)
DOI 10.1007/978-3-319-15976-8
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Preface
Exascale supercomputers will deliver an unprecedented computing power of 1018
floating point operations per second through extreme parallelism likely achieved from
hybridcomputerarchitectures.Softwareandscientificapplicationsrunningonexascale
supercomputer face the challenge of effectively exploiting this computing power.
To address this challenge, many potentially disruptive changes are needed in software
and applications. The Exascale Applications and Software Conference (EASC) brings
together all developers and researchers involved in solving the software challenges
oftheexascaleera.ThisvolumecollectedselectedcontributionsfromthesecondEASC
inStockholmduringApril2–3,2014.Thevolumeisintendedforusebyresearchersand
students of computer science and computational physics. In particular, the volume is
verywellsuitedforusebydevelopersofparallelcodes,newprogrammingmodels,run-
time systems, andtoolsfor petascale and exascalesupercomputers.
Thisvolumeisorganizedintotwoparts.Thefirstseriesofarticlespresentsthenew
developments and algorithms in large scientific applications from different scientific
domains, such as biochemistry, computational fluid dynamics, and neutronics. In
particular, these articles show how to exploit different levels of parallelism (vector
instructions, intra-node and inter-node levels) on hybrid supercomputers in the
molecular dynamics GROMACS and computational fluid dynamics Nek5000 codes.
Innovative algorithms for reducing memory storage in Monte Carlo methods for
neutronics and for improving the quality of sparse domain decomposition in lattice-
Boltzmann methods are presented. The second part of the volume presents advance-
mentsinsoftwaredevelopmentenvironmentsforexascale.Theperformancemodeling
oftheHPX-5run-timesystemfortheLULESHproxyapplicationispresentedandthe
co-design work is explained. One article analyzes the effect of system noise on dis-
tributed applications at large scale. The new developments in the MUST MPI cor-
rectnesscheckerandtheVAMPIRperformancemonitoringtoolarepresented.Finally,
an article on the Vistle visualization tool for distributed environments concludes the
volume.
January 2015 Stefano Markidis
Organization
EASC 2014 was organized by the European Commission funded projects CRESTA
(Grant Agreement No. 287703, cresta-project.eu), EPiGRAM (Grant Agreement No.
610598, epigram-project.eu), and by the Swedish e-Science Research Center SeRC
(e-science.se)
Steering Group
Erwin Laure KTH Royal Institute of Technology, Sweden
Stefano Markidis KTH Royal Institute of Technology, Sweden
William D. Gropp University of Illinois at Urbana–Champaign, USA
Mark Parsons EPCC, University of Edinburgh, Scotland, UK
Lorna Smith EPCC, University of Edinburgh, Scotland, UK
Bastian Koller HLRS, Germany
Program Committee
Erwin Laure KTH Royal Institute of Technology, Sweden
Stefano Markidis KTH Royal Institute of Technology, Sweden
William D. Gropp University of Illinois, USA
Satoshi Matsuoka Tokyo Institute of Technology, Japan
Mark Parsons EPCC, University of Edinburgh, Scotland, UK
Lorna Smith EPCC, University of Edinburgh, Scotland, UK
Daniel Holmes EPCC, University of Edinburgh, Scotland, UK
Bastian Koller HLRS, Germany
Pavan Balaji Argonne National Laboratory, USA
Jed Brown Argonne National Laboratory, USA
Robert Clay Sandia National Laboratories, USA
Roberto Gioiosa Pacific Northwest National Laboratory, USA
Katie Antypas NERSC, USA
Leroy Drummond-Lewis Lawrence Berkeley National Laboratory, USA
Alec Johnson Katholieke Universiteit Leuven, Belgium
Sponsoring Institutions
Cray Inc., Seattle, WA, USA
Mellanox Technologies, Sunnyvale, CA, USA
Contents
Towards Exascale Scientific Applications
Tackling Exascale Software Challenges in Molecular Dynamics Simulations
with GROMACS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess,
and Erik Lindahl
Weighted Decomposition in High-Performance Lattice-Boltzmann
Simulations: Are Some Lattice Sites More Equal than Others? . . . . . . . . . . . 28
Derek Groen, David Abou Chacra, Rupert W. Nash, Jiri Jaros,
Miguel O. Bernabeu, and Peter V. Coveney
Performance Analysis of a Reduced Data Movement Algorithm for Neutron
Cross Section Data in Monte Carlo Simulations . . . . . . . . . . . . . . . . . . . . . 39
John R. Tramm, Andrew R. Siegel, Benoit Forget, and Colin Josey
Nek5000 with OpenACC. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Jing Gong, Stefano Markidis, Michael Schliephake, Erwin Laure,
Dan Henningson, Philipp Schlatter, Adam Peplinski, Alistair Hart,
Jens Doleschal, David Henty, and Paul Fischer
Auto-tuning an OpenACC Accelerated Version of Nek5000. . . . . . . . . . . . . 69
Luis Cebamanos, David Henty, Harvey Richardson, and Alistair Hart
Development Environment for Exascale Applications
Towards Exascale Co-Design in a Runtime System. . . . . . . . . . . . . . . . . . . 85
Thomas Sterling, Matthew Anderson, P. Kevin Bohan, Maciej Brodowicz,
Abhishek Kulkarni, and Bo Zhang
Overcoming Asynchrony: An Analysis of the Effects of Asynchronous Noise
on Nearest Neighbor Synchronizations. . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Adam Hammouda, Andrew Siegel, and Stephen Siegel
Memory Usage Optimizations for Online Event Analysis. . . . . . . . . . . . . . . 110
Tobias Hilbrich, Joachim Protze, Michael Wagner, Matthias S. Müller,
Martin Schulz, Bronis R. de Supinski, and Wolfgang E. Nagel
Towards Detailed Exascale Application Analysis — Selective Monitoring
and Visualisation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Jens Doleschal, Thomas William, Bert Wesarg, Johannes Ziegenbalg,
Holger Brunst, Andreas Knüpfer, and Wolfgang E. Nagel
VIII Contents
Performance Analysis of Irregular Collective Communication
with the Crystal Router Algorithm. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Michael Schliephake and Erwin Laure
The Architecture of Vistle, a Scalable Distributed Visualization System. . . . . 141
Martin Aumüller
Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Towards Exascale
Scientific Applications