title: MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations.
abstract: 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.
authors: Laboratory for Computational Molecular Design, RIKEN QBiC (Quantitative Biology Center), 6F, 1-6-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors: Itta
authors: I
authors: Ohmura
authors: Laboratory for Computational Molecular Design, RIKEN QBiC (Quantitative Biology Center), 6F, 1-6-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors: Gentaro
authors: G
authors: Morimoto
authors: Laboratory for Computational Molecular Design, RIKEN QBiC (Quantitative Biology Center), 6F, 1-6-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors: Yousuke
authors: Y
authors: Ohno
authors: Laboratory for Computational Molecular Design, RIKEN QBiC (Quantitative Biology Center), 6F, 1-6-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors: Aki
authors: A
authors: Hasegawa
authors: Laboratory for Computational Molecular Design, RIKEN QBiC (Quantitative Biology Center), 6F, 1-6-5, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan taiji@riken.jp.
authors: Makoto
authors: M
authors: Taiji
mesh_terms: D003198:Computer Simulation; D016248:Computer Storage Devices; D003201:Computers; D004867:Equipment Design; D019544:Equipment Failure Analysis; D056004:Molecular Dynamics Simulation; D012815:Signal Processing, Computer-Assisted / Q000295:instrumentation*; D012984:Software; D018511:Systems Integration
keywords: hardware accelerator; high performance computing; molecular dynamics simulation; multiscale simulation; scalable parallel system