グリッドにおけるプログラミング
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1 National Institute of Advanced Industrial Science and Technology Is Grid ready for e-science?
2 1995 Parallel GC (Garbage Collection) 1996~1999: SMP 2000: 2001~:
3 Environment Material Bio/Life science Standards (JIS/OSI) Geographical survey Semiconductor device Computer Science etc. 3, , AIST Tsukuba Main Campus 50km 40km 50km
4 Since Jan. 1, years term 24 th Research Center of AIST Tsukuba Central Umezono 1-1, Tsukuba Tokyo Office 30 people for software development Researchers 2002/ /1 Full time Fellowship 1 9 Collaborators 7 32 Staff Sub total 22 Administration 2 Support /
5 National Institute of Advanced Industrial Science and Technology
6 e-science Is Grid ready for e-science? e
7
8 user resource investigation disaster prevention Environment Cluster Computer Satellite Web Service: Meta Database Storage Cluster Computer Thailand Japan Mirror DB Data Grid: Grid File Systems
9 UK-eScience, Enabling Grid for E-Science in Europe (EGEE), International Virtual Data Grid Laboratory (ivdgl), Open Science Grid, NEESit, CJK e-science Testbed NAREGI(National Research Grid Initiative)
10 National Institute of Advanced Industrial Science and Technology
11
12
13 The Grid Problem (definition) Flexible, secure, coordinated resource sharing among dynamic collections of individuals, institutions, and resources From The Anatomy of the Grid: Enabling Scalable Virtual Organizations
14 (Virtual Organization) (Virtual computing environment) (QoS QoS) (Web ) A B
15 90 90 Grid 979 NASA IPG, TeraGrid, UK-eScience, EUDG, EGEE, ApGrid, Globus Toolkit TM mature Global Grid Forum: ~1000 people, 30+ countries
16 (427 27) GGF
17 GridWorld GridWorld GridWorld GridWorld2006 6GGF
18 review National Institute of Advanced Industrial Science and Technology
19 秭 Flops (floating ops. per second) - -1 bps (bits per second) - -1
20 (PC) Gflops, 100 Workstations Gflops, 1000 Supercomputers Tflops, As of Nov No. 1: BlueGene/L (IBM/DOE) 0.7GHz PowerPC 440 / 32768cpu / TFlops No. 2: Columbia (NASA/Ames Research Center) SGI Altix 1.5GHz / 10160cpu / TFlops No. 3: Earth Simulator (The Earth Simulator Center) 5120cpu / TFlops No. 4: MareNostrum (Barcelona Supercomputer Center) PowerPC GHz / 3564cpu / TFlops No. 5: Thunder (Lawrence Livermore National Laboratory) Intel Itanium2 Tiger 4 1.4GHz Quadrics / 4096cpu / TFlops
21 Myrinet 1Tflops == Tflops CPU CPU
22 AIST Super Cluster 10,200mm P32: IBM eserver325 Opteron 2.0GHz, 6GB 2way x 1074 node Myrinet TFlops/peak 10,800mm M64: Intel Tiger 4 Madison 1.3GHz, 16GB 4way x 131 node Myrinet TFlops/peak total 14.44TFlops/peak, 3192 CPUs F32: Linux Networx Xeon 3.06GHz, 2GB 2way x 260+ node GbE 3.13TFlops/peak
23
24 Grid National Institute of Advanced Industrial Science and Technology
25 TCP/IP Internet Browser PDA PDA $5K NY = $500 Africa (by CeC) / Bandwidth, routing, scheduling, Accounting, Security Servers/Clients location, OS, CPU, etc Power Grid (GRID)
26 Supercomputer (100G x 2010T x 100) PC (1GFlops x 100,000) e.g. SETI@HOME Grand Challenge (( ) HPC ASPVirtual Laboratory
27 What Grid makes it possible? Online Access to Remote Instruments Petabyte-scale Data Analysis Detector for LHCb experiment Detector for ALICE experiment
28 What Grid makes it possible? (cont d) Large-scale Distributed Computing Large-scale Metacomputing
29 What Grid makes it possible? (cont d) High Throughput Computing Integration of Human Resources
30
31
32 Web NPACI HotPage, GridPort, Ninf-G Portal, QC Portal Operating System (Ninf-G) APIGGF Globus Toolkit
33 MPI
34 MPI (cont d) SPMD (Single Program Multiple Data) MPI_Send(), MPI_Recv() MPI_Barrier() MPI_Reduce()
35 multi thread thread thread thread thread
36 RPC (Remote Procedure Call) rpc rpc rpc Structural Optimization Vehicle Routing Problem
37 GridRPC
38 GridRPC Internet 1
39 RPCRPC RPC grpc_call(...); Client ServerA RPC grpc_call_async(...); grpc_wait_*( ); _*( ); Client ServerA ServerB
40 PC, PC, server ASP client arguments results Numerical Libraries Applications Ninf_call(FUNC, arg1,...)
41 Client eg. TDDFT, Servers Servers
42 GridRPC+MPI Client MPI) MPI) eg. QM/MD by GridRPC) (by MPI) Servers Servers
43 GridRPC v.s. MPI API co-allocation private IP GridRPC GridRPC API MPI SPMD MPI well known MPI2spawn
44 GridRPC NinfNetSolve NetSolve1994 (11) (1) NetSolve (MCell) OmniRPC HMCS-G (GRAPE-6 + CP-PACS) Ninf BMI, SDPA) (HPC SC2002) Ninf-G ApGrid Testbed QM/MD simulation, TDDFT ApGrid/TeraGrid
45 Ninf-G? GridRPC Ninf-G G includes C/C++, Java APIs IDL
46
47 Ninf-G SC2002Metacomputing Testbed 700CPU Time Dependent DFT ApGrid 1 Supply Chain Management S-model SC2003TeraGrid/ApGrid/PRAGMA testbed
48 @SC2003 CPU TeraGrid Severs NCSA Cluster (225 CPU) Client (AIST) perturbation Sample simulation Time evolution Sample simulation Time evolution statistics mean 100 ~ 1000 Sample simulation Time evolution
49 A 1 B C ~1000 CPUs application 1 ~ 1 Resource A application TD-DFT Resource B Current target application REX-MC Climate simulation Next Target Resource C ~10000 CPUs 1 ~ 1 CPU
50 Grid Grid Grid GridRPC co-allocation Grid-enabled MPI co-allocation 1 Fault tolerant MPI
51 GridRPCMPIGrid Grid Grid Grid RPC MPI MPI (loose) MPI (tight) (loosely coupled) (multi-disciplinary) Hybrid QM/MD simulation GridRPC GridRPC Ninf-G client GridRPC MPI Programs
![] [ Deformation](/docs-images/98/136745120/images/52-2.jpg "process ]")
52 Atomistic Simulation Atomistic Simulation Quantum description of bond breaking [ Stress distribution ] [ Deformation process ]
53 Atomistic Simulation 2 MD Simulation: (~10-6 m, 10-9 sec, 10 8 atoms) QM Simulation: (< 10-8 m, sec, 10 3 atoms) (~10 3 sec) Benchmark tests on 1024-node Cray T3E
54 Hybrid QM/MD Simulation Atomistic simulation MD SimulationQM simulation MD simulation MD QM simulation MD Density Functional Theory (DFT)QM MD Simulation QM simulation based on DFT
55 Hybrid QM/MD Simulation Algorithm Dr. Nakano (USC), Dr. Ogata (Nitech), et.al initial set-up Calculate MD forces of QM+MD regions Initial parameters Data of QM atoms initial set-up Initialization Initialization Initialization MD prog. Calculate MD forces of QM region Update atomic positions and velocities QM forces Calculate QM force Calculate QM QM force force of of the QM of the the QM QM region region QM prog. MPI MPI MPICH-G2Grid aware MPIGrid Co-allocation problem Ninf-G Static configuration Weak fault tolerance
56 SC2004 StressNanostructured Si system 2 Si slabs 0.11million atoms 4QM #0: 69 atoms including 2H 2 O+2OH #1: 68 atoms including H 2 O #2: 44 atoms including H 2 O #3: 56 atoms including H 2 O Close-up view
57 P32 (512 CPU) QM #0: 69 atoms including 2H 2 O+2OH Totally 1792 CPUs on 3 clusters P32 (512 CPU) QM #1: 68 atoms including H 2 O F32 (1 CPU) MD: 110,000 atoms TCS (512 PSC QM #3: 56 atoms including H 2 O F32 (256 CPU) QM #2: 44 atoms including H 2 O TCS@ PSC (512 CPU) ES45 alpha (1.0 GHz) 4-way cluster ASC@AIST (1281 CPU) P32 (1024 CPU) Opteron (2.0 GHz) 2-way cluster F32 (257 CPU) Xeon (3.06 GHz) 2-way cluster
58 QM/MD simulation over the Pacific P32 (512 CPU) Total number of CPUs: 1792 TCS (512 PSC P32 (512 CPU) Ninf-G MD Client QM Server F32 (256 CPU) initial set-up QM Server Calculate MD forces of QM+MD regions Calculate MD forces of QM region Calculate Calculate QM QM force force of the Calculate of the QM QM region QM force region of the QM region Update atomic positions and velocities
59 2: : production run SCF negligible Simulation time of each time step QM/MD: 5 ~ 8 KB/call ASC: 0.08 sec/call ASC ~ TCS@PSC: 0.8 sec/call (0.001% (hour) : 10 (~ 7 fs ) P32 (~1000CPU)1 ~90 fs (SCF) (time step)
60 1800cpu 1800cpu x 4 32 x 8
61 Is Grid ready for e-science? YES 0-1
62 co-allocation allocation
63 For more Info Ninf / Ninf-G ApGrid Global Grid Forum Global Grid Forum
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1 NAREGI 2 (NSF) CyberInfrastructure Teragrid (EU) E-Infrastructure EGEE Enabling Grids for E-science E ) DEISA (Distributed European Infrastructure for Supercomputing applications) EPSRC) UK e-science
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