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4PC junichi@mikilab.doshisha.ac.jpPC 1 PC DQS benchmark PC PC PC
PC 2000 93 1) 2 CPU • • I/O I/O • • • • • /PC 100 4.1
PC 94 LINPACK LMBENCH STREAM NPB PARKBENCH SPEC Splash 4.1: 1)(1) (2) (A)CPU CPU (B) CPU FSB(Front Side Bus) LINPACK / ScaLAPACK 4)LINPACK Jack Dongarra LU LINPACK LU LINPACK LINPACK TOP500 SupercomputerTOP5 4.2 R max N max R max N 1/2 R max R peak LINPACK CPU ScaLA-PACK ScaLAPACK 1 MPI PVM PC Himeno Benchmark 5)
PC 2000 95 4.2: 2000 7 TOP 5 Rank Computer Proc R max R peak N max N 1/2(Gflop/s) (Gflop/s) (order) (order)1 ASCI Red 9632 2379.6 3207 362880 754002 ASCI Blue-Pacific SST 5808 2144 3868 431344 .3 ASCI Blue Mountain 6144 1608 3072 374400 1380004 SP Power3 375 MHz 1336 1417 2004 374000 .5 SR8000-F1/112 112 1035 1344 120000 15160Windows Machintosh eb NPB Nas Parallel Benchmark Suite ?)NAS Parallel BenchmarksNPBNASA Ames Research Center Numerical AerodynamicSimulation (NAS) NPB CFD Application NASA Ames Research Center WWW NAS Parallel Benchmark Results 1 elapsed timeY-MP/1 C90/1 PC NPB NPB 5 Parallel Kernel BenchmarkEP, MG, CG, FT, IS(LU, SP, BT) IS 5 2 The Embarrassingly Parallel (EP) Benchmark EP Multigrid (MG) Benchmark MG 1 2 S(ample), W(orkstation), A, B, C 5 C
PC 96 Class B Class A Class A Conjugate Gradient (CG) Benchmark CG 3-D FFT PDE (FT) Benchmark FT FFT Integer Sort (IS) Benchmark IS particle-in-cell Simulated CFD Application Benchmarks LU(Block lower triangular, block upper triangular)SP(ScalarPenta-diagonal) Navier-Stokes 12 2 • • RTTEthernet RRTRound Trip Time:telnet • • • 1 •
PC 2000 97TCP/UDP netperf 7)netperf TCP UDP NFS NFSNetwork File System NFS NFS NFS NFS GA Benchmark(GAPPA bench) 6)Genetic Algorithms: GA Simulated Aneering: SA GAPPA GAPPAGA with Pawerful PArallel library !! 4.1: GAPPAhttp://is.doshisha.ac.jp/gappa/GA GA GA GA
PC 98 PC GAPPA NPB MPI MPI 3 • • NAS Parallel Benchmark• Netperf 1. Web ( http://w3cic.riken.go.jp/HPC/HimenoBMT/ ) Fortran + MPI C + MPI C+MPI 2. C + MPI Makefile himenoBMT m.c Makefile make bmt ✓# make ✒✏✑3. ”bmt” MPI CPU 2 n n=0,1,2,,,,k✓# mpirun -np 8 bmt 8CPU ✒✏✑3 MPI MPI
PC 2000 99NAS Parallel Benchmark (NPB) NPB /Doc/README.install 1. NPB 4 NPB2.3 ✓# tar xvzf NPB-2.3.tar.gz ✒2. make NPB2.3/config/ make.def.template make.def MPICC MPIF77 MPI make.def 4.2 mpicc #---------------------------------------------------------------------------# This is the fortran compiler used for MPI programs#---------------------------------------------------------------------------MPIF77 = mpif77# This links MPI fortran programs; usually the same as ${MPIF77}FLINK = ${MPIF77}#---------------------------------------------------------------------------# These macros are passed to the linker to help link with MPI correctly#---------------------------------------------------------------------------FMPI_LIB = -L/usr/local/mpich/lib -lmpich#---------------------------------------------------------------------------# These macros are passed to the compiler to help find ’mpif.h’#---------------------------------------------------------------------------FMPI_INC = -I/usr/local/mpich/include#---------------------------------------------------------------------------# Global *compile time* flags for Fortran programs#---------------------------------------------------------------------------FFLAGS = -O3# FFLAGS = -g#---------------------------------------------------------------------------# Global *link time* flags. Flags for increasing maximum executable# size usually go here.#---------------------------------------------------------------------------FLINKFLAGS = 4.2: make.def ✏✑3. make make.def NPB2.3 make NPBmake make S LU 2 make ✓# make LU NPROCS=2 CLASS=S ✒4 ✏✑
PC 100make NPB2.3/bin/ lu.S.2 make make.def 4. lu.s.2 NPB2.3/bin/ ✓# mpirun -mp2 lu.S.2 ✒✏✑make NPB make 1. NPB ct, ft, mg, lu, is 2 2 ∗ :1,2,4,8 sp, bt n 2 n 2 :1,4,9, 2. make NPB make make config/suite.def.templete config/suite.def make 4.3 # This is a sample suite file to build several executablessp A 16sp A 25sp A 36ft B 1ft B 2ft B 4 4.3: suite.def suite.def NPB2.3 ✓# make suite ✒✏✑suite.def make Netperf 8)Netperf root
PC 2000 1011. Netperf Web http://www.netperf.org 2. makefile makefile makefile netperf /opt/netperf ,makefile /usr/local/netperf NETPERF HOME = /usr/local/netperfcc CC = /usr/bin/ccmakefile 3. make makefile netperf ✓# make install ✒✏✑netperf makefile /usr/local/netperf4. /etc/services /etc/inted.conf /etc/services /etc/inted.conf root • /etc/services netperf 12865/tcp• /etc/inted.conf netperf stream tcp nowait root /usr/local/netperf/netserver netservernetperf netserver✓✏# /usr/local/netperf/netserver✒✑netperf ✓✏# /usr/local/netperf/netperf✒✑ netperf
PC 102TCP STREAM TEST to localhostRecv Send SendSocket Socket Message ElapsedSize Size Size Time Throughputbytes bytes bytes secs. 10^6bits/sec65535 65535 65535 10.00 530.89 netperf netserver ✓✏# /usr/local/netperf/netperf -H node01✒✑ netperf netperf PC 3 4.3 3 ruins 1CPU 100BASE-T Ethernet furalein 1 8 9 2CPU SMP(Symmetric Multiple Processor) . ruins 100BASE-T Ethernet jupiter 100BASE-T Myricom Myrinet GbitEthernet 100BASE-T 4.3: PC fraulein jupiter ruinsCPU Pentium III 500MHz Pentium III 600MHz Pentium II 400MHzSMP 2 procs Node 8 1 8 1 16 PROC 18 9 16Memory/node 128MB 128MB 128MBOS Linux 2.2.15 Linux 2.2.14 Linux 2.2.12Distribution Debian/GNU Linux Debian/GNU Linux Debian/GNU LinuxCompiler gcc 2.95.2 gcc 2.95.2 gcc 2.95.2Network 100BASE-T Myrinet 100BASE-T Switching HUB Switching HUB
PC 2000 1033 3 4.4 Mfolps/secjupiter TCP/IP GM 2 GM Myrinet Himeno Benchmark (C+MPI)600500400Mflops/s300200100frauleinjupiter(tcp)jupiter(GM)ruins00 2 4 6 8 10 12 14 16Number of Prosessors 4.4: C+MPI8CPU GM+Myrinet jupiter 16CPU fraulein SMP NPB LU CLASS=A NPB NPB 4.5 CPU 16CPU Intel Paragon SUN UltraEnterprize CPU
PC 104Mops/s15001000IBM SP(66/WN)Cray T3E-900Cray T3E-1200UCB NOWIntel Paragon (GP)SGI Origin 2000-195Hitachi SR2201HP/Convex Exemplar SPP2000SUN Ultra Enterprise 4000ruinsfrauleinjupiterNPB 2.3 LU Class A50001 2 4 8 16 32 64 128Number of processors 4.5: NPB2.3 LU CLASS=A 4.5 PC Web 4.4 PC VPP5000(Fujitusu) 4.5 PC VPP500 3 PC PC PC PC CPU CPU 5 5 CPU AMD Athlon 1.1GHz Intel PentiumIII 1GHz Athlon 1.1GHz 8
PC 106•
PC 2000 107 JobManagementSystem: JMS JMS DQS(Distributed Queueing System) JMS CPU PS ✓✏# rsh ps ax node01 ✒✑ rsh PS Beowulf WatchBeowulf WatchbWatch Tcl/tk rsh 4.6: Beowulf Watch (http://www.sci.usq.edu.au/staff/jacek/bWatch/) BWatch Tcl/tk 6 1. BWatch Web ( http://www.sci.usq.edu.au/staff/jacek/bWatch/ ) 6 tcl/tk John Ousterhout Tcl Tk Tcl Tk GUI
PC 1082. makemake ✓# make bwatch ✒✏✑3. bWatch ✓# ./bWatch.tcl ✒✏✑4. /usr/local/bin ✓# make install ✒✏✑/usr/local/bin bWatch Makefile bWatch Saphir NASA TheNumerical Aerodynamic Simulation (NAS) parallel system • userserver• job scheduler• resource managerJMS JMS JMS JMS 4.7
PC 2000 109JMSJOBmasteruserQUEUEnode node node node 4.7: JMS JMS JMS 4.7 JMS PVM MPI JMS 4.6 4.6:
PC 110 • intaractive job• batch job CPU JMS JMS foreign job calender scheduling event scheduling• static priority• dynamic prioritytiling
PC 2000 111Node1 Node2 Node3 Node41243TimeNode1 Node2 Node3 Node41 32 4(a) First-come-first-served(b) After tiling 4.8: JMS JMS JMS JMS PVM MPI Dedicated modeDedicated mode Space sharing modeSpace sharing mode 4.8 large-job time sharinig Time sharingtmesharing mode Time
PC 112sharing • Independent scheduling Time sharing OS • Gang SchedulingGang Scheduling Gang Scheduling • stay scheme• migrate scheme
PC 2000 113 JMS 20 Baker JMS JMS MPI Alermbusy JMS • DQSDistributed Queuing SystemFlorida State University JMSMPI HPF Codine GENIAS GmbH Debian GNU/Linux http://www.scri.fsu.edu/ pasko/dqs.html (DQS)http://www.scri.fsu.edu/ pasko/dqs.html (Codine)• LSFLoad Sharing Facility Platform Computing Corporation 20000 Scarable Parallel Computing 1) JMS http://www.platform.com/• CondorUniversity of Wisconsin I/O http://www.cs.wisc.edu/condor/• NQS / Generic NQS / The Connect:QueueNQS JMS JMS NQSNQS Stirling Software 1980 NQS The Connect:Queue Generic NQS University of Sheffield • PBSPortable Batch SystemNASA BSD licence http://pbs.mrj.com
PC 114Distributed Queuing System (DQS) JMS Florida State University JMS DQS DQS 1. 2. DQS JMS JMS 3. Debian JMS Debian/GNU Linux deb Debian Debian DQS JMS qconf -ah qconf queue -ah Add Hosts qconf -sh -Show Hosts /etc/dqs/ conf file resolve file DQS NFS qconf -aq qmod -e ✓✏# qstat -f ✒ qstat -f -ext ✑
PC 2000 115✓✏# qstat -f Queue Name Queue Type Quan Load State---------- ---------- ---- ---- -----node01 batch 0/1 0.00 er UPnode02 batch 0/1 0.00 er UPnode03 batch 0/1 0.00 er UPnode04 batch 0/1 0.00 er UP✒✑ 4.9: qstat -f qstat -f 4.9 Queue Name Load State UP Alarm DISABLE DQS DQS DQS DQS #! /bin/sh#$ -l qty.eq.1 #$ -N DQSTEST #$ -cwdhostname sleep10 4.10: DQS ( dqs.sh )DQS qsub dqs.sh #$ l N cwd Current Working DirectoryMPI
PC 116✓✏# qstat -f Queue Name Queue Type Quan Load State---------- ---------- ---- ---- -----node01 batch 0/1 0.00 er UPnode02 batch 0/1 0.00 er UPnode03 batch 0/1 0.00 er UPnode04 batch 1/1 0.01 er UPusername DQSTEST 99 0:5 r RUNNING 05/07/00 21:08:12✒✑ 4.12: #!/bin/sh#$ -l qty.eq.8#$ -N luA8#$ -A dummy_account#$ -cwdmpirun.ch_gm -np 8 lu.A.8 4.11: DQS (MPI ) ✓✏# qsub dqs.sh your job 99 has been submitted✒✑DQS qsub dqs.sh 99 DQS ID DQS qstat -f 4.12 QUEUED DQS ✓# qdel ** ** IDusername has deleted the job "**"✒✏✑
PC 2000 117 qdel ID qstat -f qdel Qmonitor(qmon)DQS X-Windows GUI qmon qmon 4.13 qmonitor qmon ✓✏# qmon ✒✑ 4.13: Qmon GUI
PC 118PC JMS JMS Tips Web Web URL ✓✏PC http://mikilab.doshisha.ac.jp/dia/SMPP/✒2000 8 30 ✑1) Kai Hwang and Zhiwei Xu, Scalable Parallel Computing, WCB/McGraw-Hill (1998)2) TOP500 Super Computing Sites, http://www.top500.org/3) NAS Parallel Benchmarks Home Page, http://www.nas.nasa.gov/Software/NPB/4) ScaLAPACK Project, http://www.netlib.org/scalapack/5) , http://w3cic.riken.go.jp/HPC/HimenoBMT/6) GAPPA: parallel distributed genetic algorithm library,http://is.doshisha.ac.jp/gappa/index.html7) The Publuic Netperf Homepage, http://www.netperf.org8) Information Networks Division, Hewlet-Packard Company, Netperf: A Network PerformanceBenchmark, http://www.netperf.org ,(1995)9) Florida State Univ. Supercomputer computation research institute, DQS3.2.X USERGUIDE,(1998)10) Florida State Univ. Supercomputer computation research institute,DQS3.2.X Insstration andmaintenance manual,(1998)11) Florida State Univ. Supercomputer computation research institute, DQS3.2.X REFERENCEMANUAL,(1998)
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