Cargando…
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)...
Autores principales: | , , , , |
---|---|
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 |
_version_ | 1782324549180719104 |
---|---|
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. |
format | Online Article Text |
id | pubmed-4084528 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | The Royal Society Publishing |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT ohmuraitta mdgrape4aspecialpurposecomputersystemformoleculardynamicssimulations AT morimotogentaro mdgrape4aspecialpurposecomputersystemformoleculardynamicssimulations AT ohnoyousuke mdgrape4aspecialpurposecomputersystemformoleculardynamicssimulations AT hasegawaaki mdgrape4aspecialpurposecomputersystemformoleculardynamicssimulations AT taijimakoto mdgrape4aspecialpurposecomputersystemformoleculardynamicssimulations |