Heterogeneous Multi-Computer System A New Platform for Multi-Paradigm Scientific Simulation
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1 Heterogeneous Multi-Computer System A New Platform for Multi-Paradigm Scientific Simulation Taisuke Boku, Hajime Susa, Masayuki Umemura, Akira Ukawa Center for Computational Physics, University of Tsukuba Junichiro Makino, Toshiyuki Fukushige Department of Astronomy, University of Tokyo
2 Outline Background Concept and Design of HMCS prototype Implementation of prototype Performance evaluation Computational physics result Variation of HMCS Conclusions 06/24/2002 ICS02, New York 2
3 Background Requirements to Platforms for Next Generation Large Scale Scientific Simulation More powerful computation power Large capacity of Memory, Wide bandwidth of Network High speed & Wide bandwidth of I/O High speed Networking Interface (outside) Is it enough? How about the quality? Multi-Scale or Multi-Paradigm Simulation 06/24/2002 ICS02, New York 3
4 Multi-Scale Physics Simulation Various level of interaction Newton Dynamics, Electro-Magnetic interaction, Quantum Dynamics, Microscopic and Macroscopic Interactions Difference in Computation Order O(N 2 ): ex. N-body O(N log N): ex. FFT O(N): ex. straight-cfd Combining these simulation, Multi-Scale or Multi- Paradigm Computational Physics is realized 06/24/2002 ICS02, New York 4
5 HMCS Heterogeneous Multi-Computer System Combining Particle Simulation (ex: Gravity interaction) and Continuum Simulation (ex: SPH) in a Platform Combining General Purpose Processor (flexibility) and Special Purpose Processor (high-speed) Connecting General Purpose MPP and Special Purpose MPP via high-throughput network Exchanging particle data at every time-step Prototype System: CP-PACS + GRAPE-6 (JSPS Research for the Future Project Computational Science and Engineering ) 06/24/2002 ICS02, New York 5
6 Block Diagram of HMCS MPP for Continuum Simulation (CP-PACS) Parallel I/O System PAVEMENT/PIO Paralel File Server (SGI Origin2000) 100base-TX Switches 32bit PCI N MPP for Particle Simulation (GRAPE-6) Hybrid System Communication Cluster (Compaq Alpha) Parallel Visualization Server (SGI Onyx2) Parallel Visualization System PAVEMENT/VIZ
7 CP-PACS Pseudo Vector Processor with 300 Mflops of Peak Performance Gflops I/O node with the same performance 128 Interconnection Network: 3-D Hyper Crossbar (300MB/s / link) Platform for General Purpose Scientific Calculation 100base-TX NIC on 16 IOUs for outside comm. Partitioning is available (Any partition can access any IOU) Manufactured by Hitachi Co. Operation from with 1024 PUs, from with 2048 PUs 06/24/2002 ICS02, New York 7
8 CP-PACS (Center for Computational Physics) 06/24/2002 ICS02, New York 8
9 GRAPE-6 The 6th generation of GRAPE (Gravity Pipe) Project Gravity calculation for many particles with 31 Gflops/chip 32 chips / board 0.99 Tflops/board 64 boards of full system is under implementation 63 Tflops On each board, all particles (j-particles) data are set onto SRAM memory, and each target particle (i-particle) data is injected into the pipeline and acceleration data is calculated Gordon Bell Prize at SC01 Denver 06/24/2002 ICS02, New York 9
10 GRAPE-6 (University of Tokyo) GRAPE-6 board (32 chips) 8 board 4 system 06/24/2002 ICS02, New York 10
11 GRAPE-6 (cont d) (Top View) (Bottom View) Daughter Card Module (4 chip / module) 06/24/2002 ICS02, New York 11
12 Host Computer for GRAPE-6 GRAPE-6 is not a stand-alone system Host computer is required Alpha CPU base PC (Intel x86, AMD Ahtlon are also available) Connected via 32bit PCI Interface Card to GRAPE-6 board A host computer can handle several GRAPE-6 boards It is impossible to handle an enormous number of particles with a single host computer for complicated calculation 06/24/2002 ICS02, New York 12
13 Hyades (Alpha CPU base Cluster) Cluster with Alpha 21264A (600MHz) 16 node Samsung UP1100 (single CPU) board 768 MB memory / node Dual 100base-TX NIC 8 nodes are equipped with GRAPE-6 PCI card Cooperative work with 8 GRAPE-6 boards under MPI programming One of 100base-TX NICs is connected with CP-PACS via PIO (Parallel I/O System) Linux RedHat 6.2 (kernel ) Operated as a data exchanging and controlling system to connect CP-PACS and GRAPE-6 06/24/2002 ICS02, New York 13
14 GRAPE-6 & Hyades GRAPE-6 & Hyades Connection between GRAPE-6 and Hyades 06/24/2002 ICS02, New York 14
15 PAVEMENT/PIO Parallel I/O and Visualization Environment Connecting multiple parallel processing platforms with commodity-based parallel network Automatic and dynamic load balancing feature to utilize spatial parallelism for applications Utilizing multiple I/O processors of MPP not to make bottleneck in communication Providing easy-to-program API with various operation modes (user-oriented, static or dynamic load balancing) 06/24/2002 ICS02, New York 15
16 MPP DSM system example CP-PACS SMP or Cluster Switch I/O processor (PIO server) Calculation processor (user process) PIO server User process (thread) 06/24/2002 ICS02, New York 16
17 HMCS Prototype Massively Parallel Processor CP-PACS (2048 PUs, 128 IOUs) 8 links Parallel Visualization Server SGI Onyx2 (4 Processors) Switching HUB 2 Parallel 100Base-TX Ethernet 8 links Parallel File Server SGI Origin-2000 (8 Processors) GRAPE-6 & Hyades (16 node, 8 board)
18 SPH (Smoothed Particle Hydrodynamics) Representing the material as a collection of particles ρ ρ( r) = ρ W ( r r ) i j 0 i j j W : kernel function
19 RT (Radiative Transfer) for SPH Accurate calculation of optical depth along light paths required. Use the method by Kessel-Deynet & Burkert (2000). ( n n )( s s ) τ TS = E + i Ei 1 E + i+ 1 Ei 2 i σ Target P2 P3 P5 Source T θ E1 E2 E3 E4 E5 S P1 P4
20 SPH Algorithm with Self-Gravity Interaction GRAPE-6 calculation O(N 2 ) Gravity SPH (Dencity) Radiation Trans. Comm. O(N) Iteration Chemistry Temperature CP-PACS O(N) Pressure Calculation Newton Dynamics
21 g6cpplib CP-PACS API g6cpp_start(myid, nio, mode, error) g6cpp_unit(n, t_unit, x_unit, eps2, error) g6cpp_calc(mass, r, f_old, phi_old, error) g6cpp_wait(acc, pot, error) g6cpp_end(error) 06/24/2002 ICS02, New York 21
22 Performance (raw G6 cluster) GRAPE-6 cluster performance with dummy data (without real RT-SPH) GRAPE-6 board 4 with 128K particles (sec) process particle data trans. all-to-all data circulation set-up data in SRAM N-body comp. result return time Processing time for 1 iteration = 3.24 sec (total) 06/24/2002 ICS02, New York 22
23 Scalability with problem size (sec.) process n=15 n=16 n=17 data trans all-to-all circulation set data to SRAM RT-SPH calculation is included calculation TOTAL # of particles N = 2 n (#P=512) 06/24/2002 ICS02, New York 23
24 Scalability with # of PUs process #P=512 #P=1024 data trans all-to-all circulation set data to SRAM RT-SPH calculation is included calculation TOTAL # of particles (N) = /24/2002 ICS02, New York 24
25 Example of Physics Results (64K SPH particles + 64K dark matters) 06/24/2002 ICS02, New York 25
26 Various implementation methods of HMCS HMCS-L (Local) Same as current prototype Simple, but the system is closed HMCS-R (Remote) Remote access to GRAPE-6 server through Network (LAN or WAN = Grid) Utilizing GRAPE-6 cluster in time-sharing manner as Gravity Server HMCS-E (Embedded) Enhanced HMCS-L : Each node of MPP (or large scale cluster) is equipped with GRAPE chip Combining wide network bandwidth of MPP (or cluster) and powerful node processing power 06/24/2002 ICS02, New York 26
27 HMCS-R on Grid Client Computer (general) Client Computer (general) Client Computer (general) High Speed Network GRAPE + HOST Remote acess to GRAPE-6 server via g6cpp API no persistency on particle data suitable for Grid O(N 2 ) of calculation with O(N) of data amount 06/24/2002 ICS02, New York 27
28 HMCS-E (Embedded) G-P NIC M S-P Local comm. between general purpose and special purpose processors Utilizing wide bandwidth of large scale network Ideal fusion of flexibility and high performance High Speed Network Switch
29 Conclusions HMCS Platform for Multi-Scale Scientific Simulation Combining General Purpose MPP (CP-PACS) and Special Purpose MPP (GRAPE-6) with parallel network under PAVEMENT/PIO middleware SPH + Radiation Transfer with Gravity Interaction Detailed simulation for Galaxy formation 128K particle real simulation with 1024PU CP-PACS makes new epoch of simulation Next Step: HMCS-R and HMCS-E 06/24/2002 ICS02, New York 29
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