Contents Post Genome Platform PKG

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1 March 5,, 2002 ) m.okuda okuda@jp.fujitsu.com

2 Contents Post Genome Platform PKG

3 PKG PKG ( MDL MDL MACCS MACCS) ( ANCHOR ANCHOR) (ADAPT ADAPT) (BIORESEARCH Series BIORESEARCH Series) (MOPAC MOPAC) HTS HTS ( OMG OMG RS RS 3 HTS HTS) DB DB (Biofrontier Biofrontier) & ( ) (SINCA) SINCA) JBiC JBiC EC EC ( ) & Grp Grp Bioinformatics Bioinformatics

4 PKG Main Frame computer WS software Client/Server Soft Web computing HEMICAL NFORMATION ANAGEMENT YSTEMS OLECULAR ODELING MACCS/MACCS-II REACCS MOLECULAR ORBITAL ISIS ANCHOR ANCHOR-II for Mainframe for SGI WS MOPAC93 ChemLib RS 3 discovery ChemDraw / ChemOffice WinMOPAC MOPAC2000 BioFrontier MOPAC2002 CAChe MOLECULAR DYNAMICS MASPHYC for VP MASPHYC WinMASPHYC for Sun WS LEAD EVOLUTION CHEMICAL SPREADSHEET ADAPT ADAPT for Mainframe f or SGI WS Emil for WS KAMELO for WS Tsar TOPKAT

5 Bioinformatics 110 Cheminformatics 40 Modeling 200 (Modeling Cheminformatics ) 15,000 global 30,000

6 Bioinformatics 30 DNA DB () LAMP () MEIBIS (MEiji Integrated BioInformatics System)

7 () ()

8 H.12 H.12 JBiC JBiC SNPs SNPs H.12 H.12 NEDO NEDO H.12 H.12 P450 P450 DB DB NEDO NEDO H.11 H.11

9 & : VPP5000/30 (NIG) :VPP5000/12, PRIMEPOWER2000/128 2 (JST) JST): VPP300/16, PRIMEPOWER600/4 : PRIMERGY N400 (GSC) GSC): GP7000F-M2000/52 M2000/52 (BERI) : VX/4, PC

10 DDBJ Homology Search Server(2set) GP7000Sm1000 2set CPU:UltraSPARC-II (400MHz)64 Main memory:64gb Disk: 500GB Backup instrument TIMBERWOLF(350GB) Graphics server Bio simulation database server Super Computer VPP5000 / 12PE vector processor: 9.6GFLOPS12 Main memory :176GB Disk :576GB Large scale analysis server(2set) PRIMEPOWER2000 2set CPU:SPARC64-GP(450MHz)128 Main memory: 128GB Disk: 5TB Large volume backup management Server Genome information server ftp Server(2set) GP7000Sm550 2set CPU:UltraSPARC II(400MHz)12 Main memory: 12GB Disk: 2.3TB GP7000Sm650 CPU:UltraSPARC II(400MHz)12 Main memory: 12GB Disk: 3TB Database server B GP7000Sm350 CPU:UltraSPARC II(400MHz)4 Main Memory : 4GB Disk : 500GB SGI Onyx3000 CPU:R12000(300MHz) 8 Main memory:4gb Disk: 500GB Backup equipment: TIMBERWOLF(350GB) SGI Onyx3000 CPU:R12000(300MHz)8 Main memory: 500GB Backup equipment TIMBERWOLF (350GB) GP7000Sm350 CPU: UltraSPARC II (400MHz)6 Main memory :6GB Disk:300GB Backup equipment TIMBERWOLF (350GB) GP7000Sm350 CPU:UltraSPARCII(400MHz)1 Main memory:1gb Disk:500GB Backup instrument :POWDERHORN (100TB) Genome analysis sever DeCypher D40 - B15 Network server(4set) GP7000Sm350 4set CPU:UltraSPARC II(400MHz)2 Main memory:1gb Disk: 150GB/500GB SuperSINET Internet 1

11 理研ゲノム科学総合研究センター殿システム 多目的サーバ FUJITSU GP7000F M200 ファイルサーバ IBM p680 S85 5TB 計算サーバ Compaq GS320 2 インターネットへ GigabitEthernet ユーザネットワーク ユーザ端末 SN200 DB 提供サーバ FUJITSU GP7000F M2000 (52CPU/52GBMem) バックアップサーバ FUJITSU GP7000F M400 FUJITSU GR720 (8TB SOMY PetaSite All Rights Reserved, Copyright FUJITSU LTD

12 Contents PKG Post Genome Platform

13 PKG ASP contents System Integration /

14

15 Bioinformatics XML Agent PKG

16 Bioinformatics Bioinformatics QSAR QSAR HTS HTS PRIMEPOWER PRIMEPOWER VPP5000 VPP5000 /

17 NetLaboratory Outsourcing Web Solution LabBook ChemOffice WebServer Application PKG Genomic XML Browser GeneDiscovery BioFrontier RS3 HTS CAChe WinMOPAC ChemDraw TOPKAT Infrastructure Post Genome Platform

18 Contents Post Genome Platform PKG

19 fastdn A fastdn A BLAST BLAST EM BL PD B wiss rot PIR GenB ank FASTA FASTA & & &

20 Post Genome Platform Post Genome Platform *: *: & EIDOS EIDOS* (Web Web DB& DB& I/F I/F ) HPC HPC PRIMEPOWER PRIMEPOWER PC PC XML XML BSML BSML MOPAC MOPAC BLAST BLAST GRID GRID I/F I/F

21 Contents Post Genome Platform PKG

22 & UNIX PRIMEPOWR & DB Solaris HPC TB HPC PC PRIMERGY PC CPU : Pen3,Pen4 1way 4Way : Myrinet GigabitEthernet : Score, Beowolf HPC DB PC

23 HPC HPC HPC VPP5000 PRIMEPOWER HPC

24 HPC over 1GHz 1 : 500 Gflops : 60 Tflops & 1 : 0.5TB : 64TB 1 : 128CPU CPU : 16,000 cpu

25 Contents Post Genome Platform PKG

26 DB DB DB DB DB PC & 3 HPC Homology search, Alignment, Clustering, EIDOS EIDOS EIDOS* EIDOS* 6 1! *: *: GenBank GenBank,EMBL,PDB,PIR,,EMBL,PDB,PIR,SwissProt SwissProt / DB

27 EIDOS Web http D: X3626 ID: X3626 UDS (User Defined Service Script) service requests request request request responses response http DB I/F html Servlet SOAP I/F XML XX

28 EIDOS ( ) UI Web (UDS) ( ) ( ) & DB I/F

29 EIDOS DB GenBank,, DDBJ, EMBL DB PDB, PIR, SWISS-PROT : BLAST, FASTA : ClustalW DB Oracle BizSearch : RDBMS : XML : SOAP, Bean, XSLT, JavaMail EIDOS EIDOS

30 EIDOS SODHO SODHO PAT. DB 2 1 WEB server with EIDOS 4 PC 3 PC Protein HPC browser on notebook PC on site browser on desktop PC Motif

31 Post Genome Platform HPC HPC MOPAC MOPAC2002 MASPHYC MASPHYC PC PC BLAST BLAST & XML BizSearch () BizSearch ( +XML )

32

33 BizSearch BizSearch XML XML XML XML XML XML BizSearch BizSearch XML XML XML XML-DB DB XML XML XML XML aaa BizSearch id text text

34 Post Genome Platform HPC DB EDLINE PDB DDBJ Post Genome Platform DB DB DB DB DB DB PRIMEPOWER EIDOS SAN MOPAC MASPHYC : HPC BLAST : PRIMERGY DB ( ) (PC ) ( )

35 Contents Post Genome Platform PKG MOPAC2002

36 PKG Main Frame computer WS software Client/Server Soft Web computing HEMICAL NFORMATION ANAGEMENT YSTEMS OLECULAR ODELING MACCS/MACCS-II REACCS MOLECULAR ORBITAL ISIS ANCHOR ANCHOR-II for Mainframe for SGI WS MOPAC93 RS 3 discovery ChemDraw / ChemOffice WinMOPAC MOPAC2000 ChemLib BioFrontier MOPAC2002 CAChe MOLECULAR DYNAMICS MASPHYC for VP MASPHYC WinMASPHYC for Sun WS LEAD EVOLUTION CHEMICAL SPREADSHEET ADAPT ADAPT for Mainframe f or SGI WS Emil for WS KAMELO for WS Tsar TOPKAT

37

38 L-Tyrosine L-DOPA Dopamine L-Adrenaline

39 FORTRAN Chemlib DB

40 D D D 10 Z-matrix Z-matrix :

41 Contents Post Genome Platform PKG MOPAC2002

42 MOPAC2002 MOPAC2002

43 MOPAC CPU time / min CPU time N Number of atoms

44 bacteriorhodopsin Chemical Physics Letters 294(1998)

45 MOPAC Linear-scaling COSMO- COSMO Memory needed / MB Memory needed / MB Number of atoms

46

47 MOPAC2002 MOPAC2002 MPI MPI OpenMP OpenMP MPI MPI % UP UP % UP UP % UP UP OpenMP OpenMP SPARC SPARC M&A M&A TLB TLB

48 MPI MPI OpenMP OpenMP [ p ]!$OMP PARALLEL DEFAULT(PRIVATE) &!$OMP SHARED(pbuf pbuf,loc,f,p) do i =... [ p,pbuf pbuf ] if (Mod(i,nnodes nnodes)== )==myid)) then!$omp DO DO do j =... do i =... do k =... do j =... l = loc(i,j,k) do k =... p(l) = p(l) + f(i,j) l = loc(i,j,k) end do pbuf(l, (l,iam)=pbuf(l,iam)+f(i,j) end do ppbuf end do end do end if end do end do!$omp END DO call mpi_allreduce (p, pbuf, do ip=1, =1,np & mpack1, mpi_double_precision,!$omp DO do i=1,mpack1 & mpi_sum, mpi_comm_world, ierr) p(i) = p(i) + pbuf(i, (i,ip) enddo do i = 1, mpack1!$omp END DO p(i) = pbuf(i) enddo end do!$omp END PARALLEL

49 * : MOPAC2002 ( 3686 ) *

50 500 MOPAC2002 (1) ( 3,686 ) * [] C 833MHz 4CPU H 550MHz 6CPU S 400MH 6CPU PRIMEPOWER (675MHz/8CPU) * :

51 * : MOPAC2002 (2) HIV (Efavirenz) * 200 :15, [] S UNIX (400MHz) 6CPU 10CPU PRIMEPOWER (675MHz) 6CPU 10CPU

52 & / ( ) 5 (8CPU) 25 25(14CPU) Sun

53 Contents Post Genome Platform PKG MOPAC2002

54 Outsourcing : Web Solution : Application : PKG Infrastructure : Post Genome Platform ( PKG )

55

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