PC (PC Cluster Building and Parallel Computing)

Transcription

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2 PC (PC Cluster Building and Parallel Computing)

3 כ., כ כ. כ. PC. כ. כ. 1 כ, 2. 1 PC. PC. 2. MPI(Message Passing Interface),. 3

4 1 PC 7 1 PC (Master computer) Linux Clustering (Util) Message Passing Interface(MPI) (Parallel Computing) Sequential MPI GNUPLOT

5 1 PC 1 PC (Cluster). Cluster כ (Master) MPI(Message Passing Interface). 3. (Slave) MPI PC כ. 1.1 ( DB-Z70)., 1 Master Slave. 7

6 1 PC 9 (Switching Hub) ( 1.3) (LAN). 1.3: Route KVM,,. כ.,,. KVM(Keyboard, Video, Mouse). 1.4: Switch

7 1 PC : :,, ( 1.8 ) PC. 1.9,,. PC. PC. 1.8: 1.10 KVM PC.. LED PC.

8 1 PC 13 כ LAN כ 2 LAN. כ 1.11: LAN 1.12:

9 1 PC 15 rsh-server rlogin, rsh rsh, rsh-server. rsh rsh-server. rlogin, rsh MPI כ. lam-mpi LAM/MPI The Laboratory for Scientific Computing(LSC) at the University of Notre Dame MPI. MPI-2 MPICH2. LAM/MPI MPICH, MPICH2 LAM/MPI PVM. Fedora Download 1. KAIST FTP Server Download : ftp://ftp.kaist.ac.kr/fedora/linux/releases/11/fedora/i386/iso/ Fedora-11-i386-DVD.iso. 1.14: KAIST FTP Server

10 1 PC Directroy 1.17: 11 Directroy - Fedora Directroy 1.18: Fedora Directroy

11 2 (MASTER COMPUTER) LINUX 19 - Fedora-11-i386-DVD.iso. 1.21: Fedora iso Download 2 (Master computer) Linux * Fedora 11.. BIOS Fedora11 DVD CDROM. CDROM BIOS CDROM. BIOS F2. CDROM F10 BIOS.

12 2 (MASTER COMPUTER) LINUX 21 Media Test CD Tab [Skip] Enter. Next. 1.23: Media Test Language. English(English) Next 1.24: Language

13 2 (MASTER COMPUTER) LINUX : 1.27:

14 2 (MASTER COMPUTER) LINUX 25 Partition Hard Partition Hard Create custom layout. Next. 1.30: Partition Hard

15 2 (MASTER COMPUTER) LINUX 27 New Partition. Mount Point / File System Type ext3 Additional Size Options Fill to maximum allowable size. OK. Next. Yes. 1.32: Partition Add 1.33: Partition Warning

16 2 (MASTER COMPUTER) LINUX 29 Include Application Office and Productivity Software Development. LAM-MPI כ Software Development. Next. ( ) 1.36: Include Application (a) (b) 1.37: (a) Install (b) Reboot Reboot Fedora 11DVD CDROM.

17 2 (MASTER COMPUTER) LINUX : Create User 1.40: Date And Time

18 2 (MASTER COMPUTER) LINUX : Login 1.43: Main

19 2 (MASTER COMPUTER) LINUX 35 ( eth1. Network configuration Hardware Description..) Terminal system-config-network. (eth1) Controlled by NetworkManager Activate device when computer starts Statically set IP address Address, Subnet mask, Default gateway address, Primary DNS, secondary DNS. IP. OK File > Save. Quit. Address : Subnet mask : Default gateway address : Primary DNS : Secondary DNS :

20 2 (MASTER COMPUTER) LINUX 37 ( eth0.) Terminal system-config-network. (et0) Controlled by NetworkManager Activate device when computer starts Statically set IP address Address, Subnet mask. IP. IP. OK File > Save. Quit. ( 1.46) Address : Subnet mask : ( 1.47) Address : Subnet mask : Network network Terminal service network restart.

21 2 (MASTER COMPUTER) LINUX : Network

22 2 (MASTER COMPUTER) LINUX 41 xinetd fc10.i386.rpm rpm -ivh xinetd fc10.i386.rpm. 1.49: Rpm Xinetd rsh-server fc10.i386.rpm rpm -ivh rsh-server fc10.i386.rpm. 1.50: Rpm Rsh-Server LAM-MPI tar -C /home/korea/download -zxvf lam-7.1.5b2.tar.gz. -C. korea. lam-7.1.5b2. cd /home/korea/download/lam-7.1.5b2/.

23 2 (MASTER COMPUTER) LINUX : configure make make LAMMPI Build. Terminal make. 1.54: make

24 2 (MASTER COMPUTER) LINUX : LAMMPI bashrc Terminal source ~/.bahsrc. 1.57: bashrc ntsysv Terminal ntsysv.. nfs, rexec, rlogin, rpcbind, rsh,. Tab. Tab Enter.,. NFS(Network File System) NFS Sun Microsystems כ TCP/IP

25 2 (MASTER COMPUTER) LINUX 47. rpc RPC., ntsysv. Terminal service xinetd restart Starting xinetd OK כ. 1.59: Xinetd Restart

26 2 (MASTER COMPUTER) LINUX 49 Exports ( ) Terminal vi /etc/exports. /etc/exports. /home /home node1(rw,async,no_root_squash) node2(rw,async,no_root_squash) 1.61: Exports Terminal service nfs restart. Starting NFS OK כ. 1.62: NFS Restart portmapper RPC portmapper RPC TCP/IP( UDP/IP). כ RPC

27 2 (MASTER COMPUTER) LINUX 51 Host /etc/hosts.equiv. host /etc/hosts. Terminal vi /etc/hosts.equiv. node 2, host node1 node2, 1.65 node1, node : Hosts

28 3 53 mount Terminal vi /etc/rc.local.. sleep 7 mount -a 1.67: Mount mount mount, mount. Terminal mount -t nfs node1:/home /home. 1.68: Mount

29 3 55 lamboot LAM/MPI MPI Job Node lamd(lam demon), lamboot. Cluster Node. Terminal root vi lamhosts.. node1 node : Cluster Node lamboot lamd. Terminal lamboot -v lamhosts( ). 1.72: Node

30 2,. GNUPLOT. 1 Message Passing Interface(MPI) C, C++, FORTRAN. Message Passing Interface(MPI). MPI-I MPI-II OpenMP MPI (Parallel Computing), (mpicc) (mpirun) 57

31 3 SEQUENTIAL 59 } C compiler gcc compile. gcc -o hello.exe hello.c ( 2.1). 2.1: hello.c Compile compile../hello.exe ( 2.2).. 2.2: hello.exe 1 C כ. (4.3). #include <stdio.h> #include <math.h> #include <stdlib.h>

32 4 61 for (i=0; i<=n; i++) { printf("%f\n", h[i]);} free_dvector(h,0,n+1); free_dvector(h_new,0,n+1); return 0; } double *dvector (long nl, long nh) { double *v; v=(double *) malloc((nh-nl+1+1)*sizeof(double)); return v-nl+1; } void free_dvector(double *v, long nl, long nh) { free (v+nl-1); return; } 4 (CPU) 0 כ. p, rank 0, 1,,p 1 כ. 0. כ

33 4 63. CPU p כ 2. my rank p כ.., (my rank) (p) MPI_Send MPI_Recv. MPI MPI_Finalize(void); MPI.. MPI. serial.. MPI mpicc. -o. Terminal mpicc -o (.exe) ( _.c)... mpirun. כ.. Terminal mpirun -np ( ) (.exe). -np. כ p כ.

34 4 65 from process 1!) lamboot -v lamhosts lamboot. /******************** hellompi.c **********************/ #include <stdio.h> #include <string.h> #include "mpi.h" void main(int argc, char* argv[]) { int my_rank, p, source, dest, tag=0; char message[100]; MPI_Status status; MPI_Init(&argc, &argv); MPI_Comm_rank(MPI_COMM_WORLD, &my_rank); MPI_Comm_size(MPI_COMM_WORLD, &p); if (my_rank!= 0) { sprintf(message, "Greetings from process %d!", my_rank); dest = 0; MPI_Send(message, strlen(message)+1, MPI_CHAR, dest, tag, MPI_COMM_WORLD); } else { for (source = 1; source < p; source++) { MPI_Recv(message, 100, MPI_CHAR, source, tag, MPI_COMM_WORLD, &status); printf("%s\n", message);

35 (2.2). d 2 u dx 2 = 0, 0 x 1 (2.1) u(0) = 0 and u(1) = 0 (2.2) Ω=[0, 1] [0,T =0.001] sine כ u(x, 0) = sin(πx) 1 (2.11). w(x, t) =e πt sin πx Taylor u(x + h, t) (x, t) u כ. u(x + h, t) =u(x, t)+u x (x, t)h + u xx(x, t) h 2 + (2.3) 2! u(x h, t) כ. u(x h, t) =u(x, t) u x (x, t)h + u xx(x, t) h 2 + (2.4) 2! (2.3) (2.4) (2.5). u(x + h, t) 2u(x, t)+u(x h, t) u xx (x, t) = h 2 + O(h 2 ) (2.5) כ (2.3). u t (x, t) = u(x, t +1) u(x, t) h 2 + O(h) (2.6)

36 4 69 כ כ. (2.5) M 0 כ. /***************** heat_mpi.c *********************/ # include <stdlib.h> # include <stdio.h> # include <math.h> # include "mpi.h" double *dvector (long nl, long nh); void free_dvector(double *v, long nl, long nh); int main ( int argc, char *argv[] ) { int id, p, i, it, it_max = 10, m = 4, tag; double pi, dt, h, *u_old, *u_new, start,etime; MPI_Init ( &argc, &argv ); start = MPI_Wtime(); MPI_Comm_rank ( MPI_COMM_WORLD, &id ); MPI_Comm_size ( MPI_COMM_WORLD, &p ); pi=4.0*atan(1.0); dt = 0.001; h=1.0/(2.0*m-1.0); u_old=dvector(0,m); u_new=dvector(0,m); for (i=0; i<=m; i++) {

37 4 71 for (i=0; i<m; i++) { printf("node %d %f\n",id,u_old[i+id]);} free_dvector(u_old,0,m); free_dvector(u_new,0,m); etime = (MPI_Wtime() - start); } if (id==1){ printf("tasks took %6.6f seconds\n",etime); } MPI_Finalize ( ); return 0; double *dvector (long nl, long nh) { double *v; v=(double *) malloc((nh-nl+1+1)*sizeof(double)); return v-nl+1; } void free_dvector(double *v, long nl, long nh) { free (v+nl-1); } dvector free dvector.

38 rank כ Communication Blocking Nonblocking. Blocking Communication rank., rank MPI Send rank MPI Recv.( (2.9)) Blocking MPI Send MPI Recv process כ. MPI Send MPI Recv 2.8: blocking כ

39 4 75 /******************* PART A ***********************/ MPI_Request requests[2*p]; MPI_Status status[2*p]; for (i=0; i<(2*p); i++) requests[i] = MPI_REQUEST_NULL; for (it=1; it<=it_max; it++) { if (id==1) { tag = 1; MPI_Isend(&u_old[1],1,MPI_DOUBLE,0,tag,MPI_COMM_WORLD, &requests[0] );} if (id==0) { tag = 1; MPI_Irecv(&u_old[m],1,MPI_DOUBLE,1,tag,MPI_COMM_WORLD, &requests[1]);} if (id==0) { tag = 2; MPI_Isend(&u_old[m-1],1,MPI_DOUBLE,1,tag,MPI_COMM_WORLD, &requests[2]);} if (id==1) { tag = 2; MPI_Irecv(&u_old[0],1,MPI_DOUBLE,0,tag,MPI_COMM_WORLD, &requests[3]);} /***************************************************/

40 4 77. plot "data.dat" using 1:2 title a with lines,\ "data.dat" using 1:3 title b with lines, data.dat 1 x 2 y a כ data.dat 1 x 3 y b כ. 2.10: GNUPLOT 1.. Gather heat1d.dat.

41 4 79 void free_dvector(double *v, long nl, long nh); int main ( int argc, char *argv[] ) { int id, p, i,it, it_max, m = 10, s_tag,r_tag; double pi, T, dt,l=1.0, h, *gather,*buffer,*exact_u, *x,*xp, *u_old, *u_new, start,etime; MPI_Init ( &argc, &argv ); start = MPI_Wtime(); MPI_Comm_rank ( MPI_COMM_WORLD, &id ); MPI_Comm_size ( MPI_COMM_WORLD, &p ); pi=4.0*atan(1.0); dt = 0.001; T=0.5; it_max=(int)(t/dt); h=(double)l/(p*m-1.0); x =dvector(1,m); xp =dvector(1,p*m); u_old =dvector(0,m+1); u_new =dvector(0,m+1); buffer =dvector(0,m-1); gather =dvector(1,p*m); exact_u=dvector(1,p*m); for (i=1; i<=m; i++){ x[i]=(double) 0+((i+m*id)-1)*h; } for (i=1; i<=p*m; i++){

42 4 81 } else { for (i=2; i<=m; i++ ) { u_new[i] = u_old[i]+dt*(u_old[i-1]-2.0*u_old[i] +u_old[i+1])/(h*h);} } } for (i=1; i<=m; i++) { u_old[i] = u_new[i];} for (i=1;i<=m;i++){ buffer[i-1]=u_old[i]; } MPI_Gather(buffer,m,MPI_DOUBLE, gather,m,mpi_double,0,mpi_comm_world); etime = (MPI_Wtime() - start); if (id==0) { FILE *fpp; for (i=1;i<=p*m;i++){ exact_u[i]=sin(pi*h*(i-1))*exp(-1*pow(pi,2)*t); } fpp=fopen("heat1d.dat", "w"); /* heat1d.dat.*/ for (i=1; i<=2*m; i++) { /*for.*/

43 [1],,,, MPI, Oxford ( ), 2010 [2], CPU, 2010, [3] Petersen W.P., Arbenz P, An Introduction to Parallel Computing, Oxford University Press, 2004 [4] Mattson Timonthy G., Sanders Veverly A., Massingill Berna L., Patterns for Parallel Programming, Addsison Wesley, 2005 [5] Gropp W., Lusk E., Skellum A. Using MPI Portable Parallel Programming with the Message-Passing Interface, 2/E, The MIT Press, 1999 [6] Pacheco P.S.,Parallel Programming with MPI,Morgan Kaufmann Publishers, 1997 [7] Quinn Micheal J., Parallel Programming in C with MPI and OPENMP, McGraw Hill,