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Special-purpose computers for scientific simulationsMakoto Taiji

Processor Research TeamRIKEN Advanced Institute for Computational Science

Computational Biology Research CoreRIKEN Quantitative Biology Center

taiji@riken.jp

1Accelerators for Scientific Simulations(1):Ising MachinesIsing MachinesDelft/ Santa Barbara/Bell Lab.Classical spin = a few bits: simple hardwarem-TIS (Taiji, Ito, Suzuki):the first accelerator that coupled tightly with the host computer.

m-TIS I (1987)2Accelerators for Scientific Simulations(2):FPGA-based SystemsSplashm-TIS IIEdinburghHeidelberg

3Accelerators for Scientific Simulations(3):GRAPE SystemsGRAvity PipE: Accelerators for particle simulationsOriginally proposed by Prof. Chikada, NAOJ.

Recently D. E. Shaw group developed Anton,highly-optimized system for particle simulations

GRAPE-4 (1995)

MDGRAPE-3 (2006)4Classical Molecular Dynamics SimulationsForce calculation based onForce field

Integrate NewtonsEquation of motion

Evaluate physical quantitiesBonding+-Coulombvan der Waals

Challenges in Molecular Dynamics simulations of biomoleculesS. O. Nielsen, et al, J. Phys. (Condens. Matter.), 15 (2004) R481

Femtosecond tomilliseconddifference=1012StrongScalingWeak ScalingScaling challenges in MD50,000 FLOP/particle/stepTypical system size : N=1055 GFLOP/step5TFLOPS effective performance1msec/step = 170nsec/dayRather Easy5PFLOPS effective performance1sec/step = 200sec/day???Difficult, but importantWhat is GRAPE?GRAvity PipESpecial-purpose accelerator for classical particle simulationsAstrophysical N-body simulationsMolecular Dynamics Simulations

J. Makino & M. Taiji, Scientific Simulations with Special-Purpose Computers,John Wiley & Sons, 1997.8History of GRAPE computers

Eight Gordon Bell Prizes`95, `96, `99, `00 (double), `01, `03, `069This shows the history of GRAPE systems. Red line shows the machines for molecular dynamics. MDM developed in RIKEN at 2000 has 78 Tflops performance and it still stands as the fastest nominal peak-performance machine. Blue and magenta line denotes the machines for astrophysics, while magenta line is machines with low-precision arithmetics. Simulations with GRAPE systems won seven Gordon Bell prizes in total.GRAPE as AcceleratorAccelerator to calculate forcesby dedicated pipelines

HostComputerGRAPEMost of Calculation GRAPEOthers Host computerParticle DataResultsCommunication = O (N) 1/10 of the MDGRAPE-4 system can be embedded with 11nm processFor typical simulation system it will be the most convenientStill network is necessary inside SoCFor further strong scaling# of operations / step / 20Katom ~ 109 # of arithmetic units in system ~ 106 /PflopsExascale means Flash (one-path) calculationMore specialization is requiredAcknowledgementsRIKENMr. Itta OhmuraDr. Gentaro MorimotoDr. Yousuke OhnoHitachi Co. Ltd.Mr. Iwao YamazakiMr. Tetsuya FukuokaMr. Makio UchidaMr. Toru Kobayashiand many other staffs

Hitachi JTE Co. Ltd.Mr. Satoru InazawaMr. Takeshi OhminatoJapan IBM ServiceMr. Ken NamuraMr. Mitsuru SugimotoMr. Masaya MoriMr. Tsubasa Saitoh