caa a22 4500 445852364 CHVBK 20180317145417.0 cr unu---uuuuu 170323e20110701xx s 000 0 eng 10.1007/s11227-011-0560-1 doi (NATIONALLICENCE)springer-10.1007/s11227-011-0560-1 Exploiting hierarchical parallelisms for molecular dynamics simulation on multicore clusters [Elektronische Daten] [Liu Peng, Manaschai Kunaseth, Hikmet Dursun, Ken-ichi Nomura, Weiqiang Wang, Rajiv Kalia, Aiichiro Nakano, Priya Vashishta] We have developed a scalable hierarchical parallelization scheme for molecular dynamics (MD) simulation on multicore clusters. The scheme explores multilevel parallelism combining: (1)Internode parallelism using spatial decomposition via message passing; (2)intercore parallelism using cellular decomposition via multithreading employing a master/worker model; (3)data-level optimization via single-instruction multiple-data (SIMD) parallelism with various code transformation techniques. By using a hierarchy of parallelisms, the scheme exposes very high concurrency and data locality, thereby achieving: (1)internode weak-scaling parallel efficiency 0.985 on 106,496 BlueGene/L nodes (0.975 on 32,768 BlueGene/P nodes), internode strong-scaling parallel efficiency 0.90 on 8,192 BlueGene/L nodes; (2)intercore multithread parallel efficiency 0.65 for eight threads on a dual quadcore Xeon platform; and (3)SIMD speedup around2 for problem sizes ranging from3,072 to98,304atoms. Furthermore, the effect of memory-access penalty on SIMD performance is analyzed, and an application-based SIMD analysis scheme is proposed to help programmers determine whether their applications are amenable to SIMDization. Springer Science+Business Media, LLC, 2011 Molecular dynamics simulation nationallicence Multicore cluster nationallicence Single instruction multiple data nationallicence Scalable hierarchical parallelization scheme nationallicence Peng Liu Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut Kunaseth Manaschai Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut Dursun Hikmet Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut Nomura Ken-ichi Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut Wang Weiqiang Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut Kalia Rajiv Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut Nakano Aiichiro Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut Vashishta Priya Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut The Journal of Supercomputing Springer US; http://www.springer-ny.com 57/1(2011-07-01), 20-33 0920-8542 57:1<20 2011 57 11227 https://doi.org/10.1007/s11227-011-0560-1 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s11227-011-0560-1 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Peng Liu Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut NATIONALLICENCE 700 1- Kunaseth Manaschai Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut NATIONALLICENCE 700 1- Dursun Hikmet Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut NATIONALLICENCE 700 1- Nomura Ken-ichi Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut NATIONALLICENCE 700 1- Wang Weiqiang Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut NATIONALLICENCE 700 1- Kalia Rajiv Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut NATIONALLICENCE 700 1- Nakano Aiichiro Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut NATIONALLICENCE 700 1- Vashishta Priya Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, 90089-0242, Los Angeles, CA, USA aut NATIONALLICENCE 773 0- The Journal of Supercomputing Springer US; http://www.springer-ny.com 57/1(2011-07-01), 20-33 0920-8542 57:1<20 2011 57 11227 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer