TY - GEN
T1 - Openatom
T2 - 31st International Conference on High Performance Computing, ISC High Performance 2016
AU - Jain, Nikhil
AU - Bohm, Eric
AU - Mikida, Eric
AU - Mandal, Subhasish
AU - Kim, Minjung
AU - Jindal, Prateek
AU - Li, Qi
AU - Ismail-Beigi, Sohrab
AU - Martyna, Glenn J.
AU - Kale, Laxmikant V.
N1 - Funding Information:
This research is partly funded by the NSF SI2-SSI grant titled Collaborative Research: Scalable, Extensible, and Open Framework for Ground and Excited State Properties of Complex Systems with ID ACI 13-39715. This research is also part of the Blue Waters sustained-petascale computing project, which is supported by the National Science Foundation (award number OCI 07-25070) and the state of Illinois. Blue Waters is a joint effort of the University of Illinois at Urbana-Champaign and its National Center for Supercomputing Applications.
Funding Information:
This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-06CH11357. This research also used computer time on Livermore Computing’s high performance computing resources, provided under the M&IC Program.
Publisher Copyright:
© Springer International Publishing Switzerland 2016.
PY - 2016
Y1 - 2016
N2 - The complex interplay of tightly coupled, but disparate, computation and communication operations poses several challenges for simulating atomic scale dynamics on multi-petaflops architectures. OpenAtom addresses these challenges by exploiting overdecomposition and asynchrony in Charm++, and scales to thousands of cores for realistic scientific systems with only a few hundred atoms. At the same time, it supports several interesting ab-initio molecular dynamics simulation methods including the Car-Parrinello method, Born-Oppenheimer method, k-points, parallel tempering, and path integrals. This paper showcases the diverse functionalities as well as scalability of OpenAtom via performance case studies, with focus on the recent additions and improvements to OpenAtom. In particular, we study a metal organic framework (MOF) that consists of 424 atoms and is being explored as a candidate for a hydrogen storage material. Simulations of this system are scaled to large core counts on Cray XE6 and IBM Blue Gene/Q systems, and time per step as low as 1.7 s is demonstrated for simulating path integrals with 32-beads of MOF on 262,144 cores of Blue Gene/Q.
AB - The complex interplay of tightly coupled, but disparate, computation and communication operations poses several challenges for simulating atomic scale dynamics on multi-petaflops architectures. OpenAtom addresses these challenges by exploiting overdecomposition and asynchrony in Charm++, and scales to thousands of cores for realistic scientific systems with only a few hundred atoms. At the same time, it supports several interesting ab-initio molecular dynamics simulation methods including the Car-Parrinello method, Born-Oppenheimer method, k-points, parallel tempering, and path integrals. This paper showcases the diverse functionalities as well as scalability of OpenAtom via performance case studies, with focus on the recent additions and improvements to OpenAtom. In particular, we study a metal organic framework (MOF) that consists of 424 atoms and is being explored as a candidate for a hydrogen storage material. Simulations of this system are scaled to large core counts on Cray XE6 and IBM Blue Gene/Q systems, and time per step as low as 1.7 s is demonstrated for simulating path integrals with 32-beads of MOF on 262,144 cores of Blue Gene/Q.
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U2 - 10.1007/978-3-319-41321-1_8
DO - 10.1007/978-3-319-41321-1_8
M3 - Conference contribution
AN - SCOPUS:84977564577
SN - 9783319413204
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 139
EP - 158
BT - High Performance Computing - 31st International Conference, ISC High Performance 2016, Proceedings
A2 - Dongarra, Jack
A2 - Kunkel, Julian M.
A2 - Balaji, Pavan
PB - Springer
Y2 - 19 June 2016 through 23 June 2016
ER -