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MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations

We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs)...

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Detalles Bibliográficos
Autores principales: Ohmura, Itta, Morimoto, Gentaro, Ohno, Yousuke, Hasegawa, Aki, Taiji, Makoto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society Publishing 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084528/
https://www.ncbi.nlm.nih.gov/pubmed/24982255
http://dx.doi.org/10.1098/rsta.2013.0387
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author Ohmura, Itta
Morimoto, Gentaro
Ohno, Yousuke
Hasegawa, Aki
Taiji, Makoto
author_facet Ohmura, Itta
Morimoto, Gentaro
Ohno, Yousuke
Hasegawa, Aki
Taiji, Makoto
author_sort Ohmura, Itta
collection PubMed
description We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s(−1) for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks.
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spelling pubmed-40845282014-08-06 MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations Ohmura, Itta Morimoto, Gentaro Ohno, Yousuke Hasegawa, Aki Taiji, Makoto Philos Trans A Math Phys Eng Sci Articles We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s(−1) for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks. The Royal Society Publishing 2014-08-06 /pmc/articles/PMC4084528/ /pubmed/24982255 http://dx.doi.org/10.1098/rsta.2013.0387 Text en http://creativecommons.org/licenses/by/3.0/ © 2014 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited.
spellingShingle Articles
Ohmura, Itta
Morimoto, Gentaro
Ohno, Yousuke
Hasegawa, Aki
Taiji, Makoto
MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations
title MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations
title_full MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations
title_fullStr MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations
title_full_unstemmed MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations
title_short MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations
title_sort mdgrape-4: a special-purpose computer system for molecular dynamics simulations
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084528/
https://www.ncbi.nlm.nih.gov/pubmed/24982255
http://dx.doi.org/10.1098/rsta.2013.0387
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