Difference between revisions of "Weekend Projekt - Test Cluster"

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m (→‎PXE netinstaller)
m (→‎PXE netinstaller)
 
Line 110: Line 110:
 
   hardware ethernet 0:0:c0:5d:bd:95;
 
   hardware ethernet 0:0:c0:5d:bd:95;
 
   server-name "node1.cluster.tekkom.dk";
 
   server-name "node1.cluster.tekkom.dk";
 +
  fixed-address 10.0.0.30;
 +
 
}
 
}
 
</source>
 
</source>

Latest revision as of 13:40, 6 November 2012

Udstyr

  • 5 stk. Lenovo ThinkCenter (C01, C04, C05, C06, C17)
  • Cisco 2950

Setup

C01 bliver master server, med apt-cacher til installation og PXE netinstallation server. Den skal også have MRTG og nagios.

  • C01 sidder i Gi0/2
  • C04 sidder i Fa0/1
  • C05 sidder i Fa0/2
  • C06 sidder i Fa0/3
  • C17 sidder i Fa0/4

2950

enable password cisco
!
interface range fa 0/1 - 24
 switchport mode access
 switchport access vlan 2
 spanning-tree portfast
!
interface range gi 0/1 - 2
 switchport mode access
 switchport access vlan 2
 spanning-tree portfast
!
interface Vlan2
 ip address 10.1.2.50 255.255.255.0
!
snmp-server community public RO
!
line con 0
line vty 0 4
 no login
line vty 5 15
 no login

C01

Denne node skal være installtions og mangement node for clusteret.

Std applicationer

Installtion af det nødvendig samt noget random. 

aptitude -y install apt-cacher tftpd-hpa tftp-hpa xinetd nagios3 mrtg nmap screen bmon iperf bonnie++ lmbench lm-sensors snmpd snmp build-essential gcc openssh-client nfs-kernel-server

Apt-cacher

Ændre i /etc/apt-cacher/apt-cacher.conf 

path_map = ubuntu de.archive.ubuntu.com/ubuntu; ubuntu-updates de.archive.ubuntu.com/ubuntu ; ubuntu-security security.ubuntu.com/ubuntu
allowed_hosts=*

Ændre i /etc/default/apt-cacher også: 

AUTOSTART=1

Og genstart apt-cacher: 

/etc/init.d/apt-cacher restart

Vær opmærksom på at installations serveren hedder 10.1.2.100:3142/ubuntu/ nu

PXE netinstaller

Hent og installer pxelinux til tftp roden: 

cd /var/lib/tftpboot/
wget http://archive.ubuntu.com/ubuntu/dists/lucid/main/installer-amd64/current/images/netboot/netboot.tar.gz
tar -xvzf netboot.tar.gz

Sæt IOS DHCP serveren op til at dele statiske IP adresser ud og pege på PXE serveren og filen: 

ip dhcp pool Pool-VLAN2
   network 10.1.2.0 255.255.255.0
   bootfile pxelinux.0
   next-server 10.1.2.100
   default-router 10.1.2.1
   dns-server 89.150.129.4 89.150.129.10
   lease 0 0 30
!
ip dhcp pool C04-Pool
   host 10.1.2.101 255.255.255.0
   hardware-address 0021.86f3.caa5
   client-name C04
!
ip dhcp pool C05-Pool
   host 10.1.2.102 255.255.255.0
   hardware-address 0021.86f4.00e9
   client-name C05
!
ip dhcp pool C06-Pool
   host 10.1.2.103 255.255.255.0
   hardware-address 0021.86f4.030d
   client-name C06
!
ip dhcp pool C17-Pool
   host 10.1.2.104 255.255.255.0
   hardware-address 0021.86f4.1d79
   client-name C17

Skal det isteder være på linux skal man installere dhcp3 og oprette et scope i /etc/dhcp3/dhcpd.conf" 

subnet 10.0.0.0 netmask 255.255.255.0 {
  range 10.0.0.50 10.0.0.100;
  option domain-name-servers 172.16.4.66;
  option domain-name "cluster.tekkom.dk";
  option routers 10.0.0.1;
  default-lease-time 360;
  max-lease-time 360;
  next-server 10.0.0.1;
  filename "pxelinux.0";
}
host node1 {
  hardware ethernet 0:0:c0:5d:bd:95;
  server-name "node1.cluster.tekkom.dk";
  fixed-address 10.0.0.30;

}

Lav en F12 og det spiller bare.

MRTG opsætning

Gør som beskrevet her Netband_Project_-_Ubuntu_server
Quick Guide

cfgmaker --no-down --output /etc/mrtg-10.1.2.50.cfg public@10.1.2.50
cfgmaker --no-down --output /etc/mrtg-10.1.2.1.cfg public@10.1.2.1

Ændre lidt i /etc/mrtg.cfg 

Options[_]: bits, unknaszero
Include: /etc/mrtg-10.1.2.50.cfg
Include: /etc/mrtg-10.1.2.1.cfg

Husk at lave WorkDir: 

mkdir /var/www/mrtg

Tilføj MRTG til cron sammen med indexmaker, så den selv opdaterer index siden når du tilføjer enheder til /etc/mrtg.cfg 

crontab -e
        m      h       dom     mon     dow     command
*/2      *       *       *       *       env LANG=C /usr/bin/mrtg /etc/mrtg.cfg  --logging /var/log/mrtg/mrtg.log
*/5      *       *       *       *       /usr/bin/indexmaker /etc/mrtg.cfg > /var/www/mrtg/index.html

Og så kan man se alle interfaces på http://10.1.2.100/mrtg

Virker det ikke tjek loggen i /var/log/mrtg/mrtg.log

Nagios3

Ændre i /etc/nagios3/conf.d/hostgroups_nagios2.cfg, så under hostgroup_name ping-servers skal members laves om til *

Ændre også i /etc/nagios3/conf.d/host-gateway_nagios3.cfg 

define host {
        host_name       Switch
        alias           Switch
        address         10.1.2.50
        use             generic-host
        }
define host {
        host_name       C04
        alias           C04
        address         10.1.2.101
        use             generic-host
        }
define host {
        host_name       C05
        alias           C05
        address         10.1.2.102
        use             generic-host
        }
define host {
        host_name       C06
        alias           C06
        address         10.1.2.103
        use             generic-host
        }
define host {
        host_name       C17
        alias           C17
        address         10.1.2.104
        use             generic-host
        }

Vi ændrer også lige disse linier i config filen så der ikke går flere minutter før den opdager en fejl. De skriver det bruger mere CPU og netværk, men jeg er da ligeglad...
/etc/nagios3/nagios.cfg 

service_freshness_check_interval=15
interval_length=15
host_inter_check_delay_method=d
service_interleave_factor=1
service_inter_check_delay_method=d
status_update_interval=10

Genstart Nagios 

/etc/init.d/nagios3 restart

Nagios kan nu tilgåes på http://10.1.2.100/nagios3 std brugernavn er nagiosadmin og bruger navn er det du satte under installtionen.

Links

http://www.ubuntugeek.com/nagios-configuration-tools-web-frontends-or-gui.html

Auto SSH login

På C01 generere man nogle nøgler som kan bruges til at logge ind på alle maskinerne med. 

ssh-keygen -t dsa

Kopier vores public key ind i authorized_keys, så vi kan SSH til os selv 

cat .ssh/id_dsa.pub >> .ssh/authorized_keys

Så opretter man en .ssh folder i /root eller /home dir for den bruger man lyster. 

ssh 10.1.2.101 mkdir .ssh
ssh 10.1.2.102 mkdir .ssh
ssh 10.1.2.103 mkdir .ssh
ssh 10.1.2.104 mkdir .ssh

Kopierer Certifikaterne over på dem: 

scp .ssh/* 10.1.2.101:.ssh/
scp .ssh/* 10.1.2.102:.ssh/
scp .ssh/* 10.1.2.103:.ssh/
scp .ssh/* 10.1.2.104:.ssh/

Og man kan nu SSH rundt til alle maskiner uden password 

ssh 10.1.2.101


Auto SSH Bruger Login

Vil man gerne undgå at bruge brugernavn/pass kan man generere en Priv/Pub keypair med puttygen og smide den public key den laver ind i .ssh/autorized_keys

NFS server

Lav en folder til at exportere med NFS 

mkdir /var/mirror

Tilføj den til /etc/exports 

/var/mirror     *(rw,sync,no_subtree_check)

Og genstart NFS serveren 

/etc/init.d/nfs-kernel-server restart

Node installation

Manuel installation

Maskiner køres op i hånden gennem PXE boot og hånd installeres.
Installation af nodes kan gøre med 

ssh <ip> aptitude -y install nmap screen bmon iperf bonnie++ lmbench lm-sensors snmpd snmp build-essential gcc openssh-client nfs-common mpich2

Og så tilføj /var/mirror til /etc/fstab 

c01:/var/mirror/ /var/mirror nfs rw 0 0

Automount /home

Hvis man gerne vil have brugerrettigheder med over NFS når man mounter skal man ændre lidt i nogle filer.

On ubuntu, I edited /etc/idmapd.conf and changed Domain to be the same value as what I set for NFSMAPID_DOMAIN, edit /etc/default/nfs-common and set NEED_STATD=no and NEED_IDMAPD=yes, then service rpc_pipefs restart and service idmapd restart, remount your nfs shares (in my case, service autofs restart); and all the uid/gid mapping should now be correct. 

NewClusterH:/home/ /home nfs rw 0 0

Automastisk installation

Maskinerne kan også installeres efter en kickstart seed fil.

For at køre maskinerne op med seed filen kan den ligge på en webserver og henvises til igennem bootscreen installations menuen.
nano /var/lib/tftpboot/ubuntu-installer/amd64/boot-screens/text.cfg 

label kickstart
        menu label ^Kickstart
        kernel ubuntu-installer/amd64/linux
        append ks=http://10.1.2.100/ks.cfg vga=normal initrd=ubuntu-installer/amd64/initrd.gz -- quiet

Og kickstart filen vil se sådan ud: 

#Generated by Kickstart Configurator
#platform=AMD64 or Intel EM64T

#Vælger hvilket sprog der skal installeres på
#System language
lang en_US
#Language modules to install
langsupport en_US

#Definerer hvilket tastatur vi bruger
#System keyboard
keyboard dk
#System mouse
mouse

#Tidszonen vi er i
#System timezone
timezone Europe/Copenhagen

#Root password = cisco
#Root password
rootpw --iscrypted $1$T5Fz4QeH$sY307XHHaNCfxL4ODXNyG.

#Vi har defineret at der ikke skal oprettes en alm. bruger.
#Initial user
user --disabled
#Reboot after installation
reboot
#Use text mode install
text
#Install OS instead of upgrade
install

#Hvilken source skal vi installere fra, her er det vores apt-cacher server
#Use Web installation
url --url http://10.1.2.100:3142/ubuntu/

#indstallerer en bootloader.
#System bootloader configuration
bootloader --location=mbr
#Clear the Master Boot Record
zerombr yes

#Rykker disken rundt!!!
#Partition clearing information
clearpart --all --initlabel

#Opretter en swap disk på anbefaler størrelse og bruger resten til en ext4 partition /
#Disk partition information
part swap --recommended
part / --fstype ext4 --size 1 --grow

#Selvfølgelig skal vi have shadow password og md5
#System authorization infomation
auth  --useshadow  --enablemd5
#Firewall configuration
firewall --disabled

#Jeg vil da ikke have desktop på en server.
#Do not configure the X Window System
skipx

#Her definerer vi de pakker der skal installeres, er det til desktop så kunne ubuntu-desktop være et bud
%packages
openssh-server
nmap
screen
bmon
iperf
bonnie++
lmbench
lm-sensors
snmpd
snmp
build-essential
gcc
openssh-client
nfs-common
mpich2

Cluster installation

Host filer

opret alle nodes i /etc/hosts: 

127.0.0.1     localhost
10.1.2.100 C01
10.1.2.101 C04
10.1.2.102 C05
10.1.2.103 C06
10.1.2.104 C17

Lav et script der hedder CopyToClients.sh 

#!/bin/bash
scp $1 10.1.2.101:$2
scp $1 10.1.2.102:$2
scp $1 10.1.2.103:$2
scp $1 10.1.2.104:$2

Smid den rundt til alle de andre nodes med: 

./CopyToClients.sh /etc/hosts /etc/hosts

Installer MPICH2

Installer MPICH2 på alle maskiner 

aptitude install mpich2

Lav en fil i home dir der hedder mpd.hosts der indeholder: 

C01
C04
C05
C06
C17

Og lav et password i filen /etc/mpd.conf 

echo MPD_SECRETWORD=cisco >> /etc/mpd.conf
chmod 600 /etc/mpd.conf

Den skal ligge i home dir, hvis man er andre brugere end root!!

Flyt den til de andre maskiner 

./CopyToClients.sh /etc/mpd.conf /etc/mpd.conf

Start MPD på alle nodes 

mpdboot ­-n 4

Og test at det virker, skulle gerne returnere hostnavn på alle nodes 

mpdtrace



Test fil i /var/mirror/test.sh 

#!/bin/bash
cat /etc/hostname

Kald den 

mpiexec -n 40 /var/mirror/test.sh

Have Fun 

 mpiexec -n 1000 /var/mirror/test.sh | sort | uniq -c

Sluk for MPD igen 

mpdallexit

Installer OpenMPI

Skal selvfølgelig installeres på alle maskiner 

install libopenmpi-dev openmpi-bin openmpi-doc

Eksekver et program 

mpicc /var/mirror/MPI_Hello.c -o /var/mirror/MPI_Hello
mpiexec -n 6 -hostfile mpd.hosts /var/mirror/MPI_Hello
Hello World from process 3, of 6 on Cl1N0
Hello World from process 0, of 6 on Cl1N0
Hello World from process 2, of 6 on Cl1N2
Hello World from process 5, of 6 on Cl1N2
Hello World from process 1, of 6 on Cl1N1
Hello World from process 4, of 6 on Cl1N1

http://auriza.site40.net/notes/mpi/openmpi-on-ubuntu-904/

Installer Torque

Torque er den scheduler de fleste HPC bruger. Man smider sine jobs til den og så klarer den at dele dem ud til nødvendige maskiner og når et job er færdig sender den det næste afsted.

Links

Andre Scheduler

  • Loadleveler
  • LSF
  • Sun Grid Engine

Notater

Tilføj torque server til /etc/hosts 

127.0.0.1 torqueserver

installer pakker 

aptitude install torque-client torque-common torque-mom torque-scheduler torque-server

Stop torque 

qterm

Programmering med MPI

http://www.lam-mpi.org/tutorials/one-step/ezstart.php

Geany IDE

Der findes et IDE man kan tilrette til cluster kompilering og eksekvering kaldet geany. Installation: 

aptitude install geany

For at kompilere det med mpicc og eksekvere med mpiexec skal man lige rette lidt til under "Build > Set Includes and Arguments".

Geany IDE
mpicc -Wall "%f" -o "%e"

mpiexec -n 20 -hostfile ~/mpd.hosts "%e"

Og til C++ bruger man mpic++ -Wall "%f" -o "%e"

Programmet man skriver skal selvfølgelig ligge i /var/mirror for de andre noder også har adgang til det.

Og den kan man selvfølgelig X'e over med 

env DISPLAY=172.16.4.105:1 geany

Hello World eksempel

HelloWorld program 

#include "mpi.h"
#include <stdio.h>

int main (int argc, char *argv[] )
{
        int rank, size, namelen;
        char processor_name[MPI_MAX_PROCESSOR_NAME];


        MPI_Init( &argc, &argv );

        MPI_Get_processor_name( processor_name, &namelen );
        MPI_Comm_rank( MPI_COMM_WORLD, &rank );
        MPI_Comm_size( MPI_COMM_WORLD, &size );
        printf( "Hello World from process %d, of %d on %s\n", rank, size, processor_name );
        MPI_Finalize();
        return 0;
}

Compile det med 

 mpicxx -o helloWorld helloWorld.c

og kør det med 

mpiexec -n 10 /var/mirror/helloWorld

Resultatet skulle gerne blive 

Hello World from process 2, of 10 on C05
Hello World from process 6, of 10 on C05
Hello World from process 3, of 10 on C06
Hello World from process 1, of 10 on C04
Hello World from process 5, of 10 on C04
Hello World from process 7, of 10 on C06
Hello World from process 9, of 10 on C04
Hello World from process 0, of 10 on C01
Hello World from process 4, of 10 on C01
Hello World from process 8, of 10 on C01

Hello World med MPI

Det forrige eksempel brugte ikke rigtig MPI til noget, ud over at få rank og size.
Hvis vi skal lave det om til at rank 0 er den der printer til skærmen og alle de andre sender via MPI til den, ville det se sådan ud: 

#include "mpi.h"
#include <stdio.h>
#include <string.h>

int main (int argc, char *argv[] )
{
        int rank, size, namelen, i;
        char processor_name[MPI_MAX_PROCESSOR_NAME];
        char greeting[MPI_MAX_PROCESSOR_NAME + 100];
        MPI_Status status;

        MPI_Init( &argc, &argv );

        MPI_Get_processor_name( processor_name, &namelen );
        MPI_Comm_rank( MPI_COMM_WORLD, &rank );
        MPI_Comm_size( MPI_COMM_WORLD, &size );
        sprintf( greeting,  "Hello World from process %d, of %d on %s\n", rank, size, processor_name );

        if ( rank == 0 ) {
                printf( "%s", greeting );
                for (i = 1; i < size; i++ ) {
                        MPI_Recv( greeting, sizeof( greeting ), MPI_CHAR, i, 1, MPI_COMM_WORLD, &status );
                        printf( "%s", greeting );
                }
        }
        else {
                MPI_Send( greeting, strlen( greeting ) + 1, MPI_CHAR, 0, 1, MPI_COMM_WORLD );
        }
        MPI_Finalize();
        return 0;
}

Hvilket returnenrer: 

0: Hello World from process 0, of 10 on C01
0: Hello World from process 1, of 10 on C04
0: Hello World from process 2, of 10 on C05
0: Hello World from process 3, of 10 on C06
0: Hello World from process 4, of 10 on C01
0: Hello World from process 5, of 10 on C04
0: Hello World from process 6, of 10 on C05
0: Hello World from process 7, of 10 on C06
0: Hello World from process 8, of 10 on C01
0: Hello World from process 9, of 10 on C04

MPI PingPong program

PingPong programmet er lavet for at benchmarke MPI på forskellige typer netværk.

Kode

/*                  pong.c Generic Benchmark code
 *               Dave Turner - Ames Lab - July of 1994+++
 *
 *  Most Unix timers can't be trusted for very short times, so take this
 *  into account when looking at the results.  This code also only times
 *  a single message passing event for each size, so the results may vary
 *  between runs.  For more accurate measurements, grab NetPIPE from
 *  http://www.scl.ameslab.gov/ .
 */

#include "mpi.h"

#include <stdio.h>
#include <stdlib.h>

int main (int argc, char **argv)
{
   int myproc, size, other_proc, nprocs, i, last;
   double t0, t1, time;
   double *a, *b;
   double max_rate = 0.0, min_latency = 10e6;
   MPI_Request request, request_a, request_b;
   MPI_Status status;

#if defined (_CRAYT3E)
   a = (double *) shmalloc (132000 * sizeof (double));
   b = (double *) shmalloc (132000 * sizeof (double));
#else
   a = (double *) malloc (132000 * sizeof (double));
   b = (double *) malloc (132000 * sizeof (double));
#endif

   for (i = 0; i < 132000; i++) {
      a[i] = (double) i;
      b[i] = 0.0;
   }

   MPI_Init(&argc, &argv);
   MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
   MPI_Comm_rank(MPI_COMM_WORLD, &myproc);

   if (nprocs != 2) exit (1);
   other_proc = (myproc + 1) % 2;

   printf("Hello from %d of %d\n", myproc, nprocs);
   MPI_Barrier(MPI_COMM_WORLD);

/* Timer accuracy test */

   t0 = MPI_Wtime();
   t1 = MPI_Wtime();

   while (t1 == t0) t1 = MPI_Wtime();

   if (myproc == 0)
      printf("Timer accuracy of ~%f usecs\n\n", (t1 - t0) * 1000000);

/* Communications between nodes
 *   - Blocking sends and recvs
 *   - No guarantee of prepost, so might pass through comm buffer
 */

   for (size = 8; size <= 1048576; size *= 2) {
      for (i = 0; i < size / 8; i++) {
         a[i] = (double) i;
         b[i] = 0.0;
      }
      last = size / 8 - 1;

      MPI_Barrier(MPI_COMM_WORLD);
      t0 = MPI_Wtime();

      if (myproc == 0) {

         MPI_Send(a, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD);
         MPI_Recv(b, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD, &status);

      } else {

         MPI_Recv(b, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD, &status);

         b[0] += 1.0;
         if (last != 0)
         b[last] += 1.0;

         MPI_Send(b, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD);

      }

      t1 = MPI_Wtime();
      time = 1.e6 * (t1 - t0);
      MPI_Barrier(MPI_COMM_WORLD);

      if ((b[0] != 1.0 || b[last] != last + 1)) {
         printf("ERROR - b[0] = %f b[%d] = %f\n", b[0], last, b[last]);
         exit (1);
      }
      for (i = 1; i < last - 1; i++)
         if (b[i] != (double) i)
            printf("ERROR - b[%d] = %f\n", i, b[i]);
      if (myproc == 0 && time > 0.000001) {
         printf(" %7d bytes took %9.0f usec (%8.3f MB/sec)\n",
                     size, time, 2.0 * size / time);
         if (2 * size / time > max_rate) max_rate = 2 * size / time;
         if (time / 2 < min_latency) min_latency = time / 2;
      } else if (myproc == 0) {
         printf(" %7d bytes took less than the timer accuracy\n", size);
      }
   }

/* Async communications
 *   - Prepost receives to guarantee bypassing the comm buffer
 */

   MPI_Barrier(MPI_COMM_WORLD);
   if (myproc == 0) printf("\n  Asynchronous ping-pong\n\n");

   for (size = 8; size <= 1048576; size *= 2) {
      for (i = 0; i < size / 8; i++) {
         a[i] = (double) i;
         b[i] = 0.0;
      }
      last = size / 8 - 1;

      MPI_Irecv(b, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD, &request);
      MPI_Barrier(MPI_COMM_WORLD);
      t0 = MPI_Wtime();

      if (myproc == 0) {

         MPI_Send(a, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD);
         MPI_Wait(&request, &status);

      } else {

         MPI_Wait(&request, &status);

         b[0] += 1.0;
         if (last != 0)
         b[last] += 1.0;

         MPI_Send(b, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD);

      }

      t1 = MPI_Wtime();
      time = 1.e6 * (t1 - t0);
      MPI_Barrier(MPI_COMM_WORLD);

      if ((b[0] != 1.0 || b[last] != last + 1))
         printf("ERROR - b[0] = %f b[%d] = %f\n", b[0], last, b[last]);

      for (i = 1; i < last - 1; i++)
         if (b[i] != (double) i)
            printf("ERROR - b[%d] = %f\n", i, b[i]);
      if (myproc == 0 && time > 0.000001) {
         printf(" %7d bytes took %9.0f usec (%8.3f MB/sec)\n",
                  size, time, 2.0 * size / time);
         if (2 * size / time > max_rate) max_rate = 2 * size / time;
         if (time / 2 < min_latency) min_latency = time / 2;
      } else if (myproc == 0) {
         printf(" %7d bytes took less than the timer accuracy\n", size);
      }
   }

/* Bidirectional communications
 *   - Prepost receives to guarantee bypassing the comm buffer
 */

   MPI_Barrier(MPI_COMM_WORLD);
   if (myproc == 0) printf("\n  Bi-directional asynchronous ping-pong\n\n");

   for (size = 8; size <= 1048576; size *= 2) {
      for (i = 0; i < size / 8; i++) {
         a[i] = (double) i;
         b[i] = 0.0;
      }
      last = size / 8 - 1;

      MPI_Irecv(b, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD, &request_b);
      MPI_Irecv(a, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD, &request_a);
      MPI_Barrier(MPI_COMM_WORLD);

      t0 = MPI_Wtime();

      MPI_Send(a, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD);
      MPI_Wait(&request_b, &status);

      b[0] += 1.0;
      if (last != 0)
      b[last] += 1.0;

      MPI_Send(b, size/8, MPI_DOUBLE, other_proc, 0, MPI_COMM_WORLD);
      MPI_Wait(&request_a, &status);

      t1 = MPI_Wtime();
      time = 1.e6 * (t1 - t0);
      MPI_Barrier(MPI_COMM_WORLD);


      if ((a[0] != 1.0 || a[last] != last + 1))
         printf("ERROR - a[0] = %f a[%d] = %f\n", a[0], last, a[last]);
      for (i = 1; i < last - 1; i++)
      if (a[i] != (double) i)
         printf("ERROR - a[%d] = %f\n", i, a[i]);
      if (myproc == 0 && time > 0.000001) {
         printf(" %7d bytes took %9.0f usec (%8.3f MB/sec)\n",
                    size, time, 2.0 * size / time);
         if (2 * size / time > max_rate) max_rate = 2 * size / time;
         if (time / 2 < min_latency) min_latency = time / 2;
      } else if (myproc == 0) {
         printf(" %7d bytes took less than the timer accuracy\n", size);
      }
   }

   if (myproc == 0)
      printf("\n Max rate = %f MB/sec  Min latency = %f usec\n",
               max_rate, min_latency);

   MPI_Finalize();
   return 0;
}

100mbit/s netværk

Hello from 0 of 2
Hello from 1 of 2
Timer accuracy of ~0.953674 usecs

       8 bytes took       353 usec (   0.045 MB/sec)
      16 bytes took       268 usec (   0.119 MB/sec)
      32 bytes took       245 usec (   0.261 MB/sec)
      64 bytes took       274 usec (   0.467 MB/sec)
     128 bytes took       281 usec (   0.911 MB/sec)
     256 bytes took       245 usec (   2.091 MB/sec)
     512 bytes took       300 usec (   3.414 MB/sec)
    1024 bytes took       403 usec (   5.083 MB/sec)
    2048 bytes took       628 usec (   6.522 MB/sec)
    4096 bytes took       873 usec (   9.383 MB/sec)
    8192 bytes took      1597 usec (  10.258 MB/sec)
   16384 bytes took      3188 usec (  10.278 MB/sec)
   32768 bytes took      5866 usec (  11.172 MB/sec)
   65536 bytes took     11476 usec (  11.421 MB/sec)
  131072 bytes took     23561 usec (  11.126 MB/sec)
  262144 bytes took     45460 usec (  11.533 MB/sec)
  524288 bytes took     93597 usec (  11.203 MB/sec)
 1048576 bytes took    179155 usec (  11.706 MB/sec)

  Asynchronous ping-pong

       8 bytes took       256 usec (   0.063 MB/sec)
      16 bytes took       277 usec (   0.116 MB/sec)
      32 bytes took       259 usec (   0.247 MB/sec)
      64 bytes took       271 usec (   0.472 MB/sec)
     128 bytes took       290 usec (   0.882 MB/sec)
     256 bytes took       284 usec (   1.802 MB/sec)
     512 bytes took       300 usec (   3.414 MB/sec)
    1024 bytes took       345 usec (   5.936 MB/sec)
    2048 bytes took       679 usec (   6.032 MB/sec)
    4096 bytes took       856 usec (   9.571 MB/sec)
    8192 bytes took      1609 usec (  10.182 MB/sec)
   16384 bytes took      3177 usec (  10.314 MB/sec)
   32768 bytes took      5837 usec (  11.228 MB/sec)
   65536 bytes took     11531 usec (  11.367 MB/sec)
  131072 bytes took     23597 usec (  11.109 MB/sec)
  262144 bytes took     45400 usec (  11.548 MB/sec)
  524288 bytes took     89853 usec (  11.670 MB/sec)
 1048576 bytes took    179022 usec (  11.715 MB/sec)

  Bi-directional asynchronous ping-pong

       8 bytes took       246 usec (   0.065 MB/sec)
      16 bytes took       249 usec (   0.129 MB/sec)
      32 bytes took       247 usec (   0.259 MB/sec)
      64 bytes took       250 usec (   0.512 MB/sec)
     128 bytes took       251 usec (   1.021 MB/sec)
     256 bytes took       249 usec (   2.057 MB/sec)
     512 bytes took       300 usec (   3.411 MB/sec)
    1024 bytes took       345 usec (   5.936 MB/sec)
    2048 bytes took       660 usec (   6.207 MB/sec)
    4096 bytes took       854 usec (   9.592 MB/sec)
    8192 bytes took      1692 usec (   9.683 MB/sec)
   16384 bytes took      3148 usec (  10.409 MB/sec)
   32768 bytes took      5913 usec (  11.083 MB/sec)
   65536 bytes took     13798 usec (   9.499 MB/sec)
  131072 bytes took     27642 usec (   9.484 MB/sec)
  262144 bytes took     72140 usec (   7.268 MB/sec)
  524288 bytes took    146771 usec (   7.144 MB/sec)
 1048576 bytes took    298708 usec (   7.021 MB/sec)

 Max rate = 11.714504 MB/sec  Min latency = 122.427940 usec

1Gbit/s netværk

Hello from 0 of 2
Hello from 1 of 2
Timer accuracy of ~1.192093 usecs

       8 bytes took       169 usec (   0.095 MB/sec)
      16 bytes took       158 usec (   0.202 MB/sec)
      32 bytes took       162 usec (   0.395 MB/sec)
      64 bytes took       151 usec (   0.848 MB/sec)
     128 bytes took       158 usec (   1.620 MB/sec)
     256 bytes took       158 usec (   3.239 MB/sec)
     512 bytes took       165 usec (   6.207 MB/sec)
    1024 bytes took       193 usec (  10.605 MB/sec)
    2048 bytes took       226 usec (  18.122 MB/sec)
    4096 bytes took       233 usec (  35.133 MB/sec)
    8192 bytes took       321 usec (  51.055 MB/sec)
   16384 bytes took       565 usec (  57.991 MB/sec)
   32768 bytes took      1410 usec (  46.479 MB/sec)
   65536 bytes took      2577 usec (  50.861 MB/sec)
  131072 bytes took      3138 usec (  83.537 MB/sec)
  262144 bytes took      5585 usec (  93.875 MB/sec)
  524288 bytes took     10363 usec ( 101.186 MB/sec)
 1048576 bytes took     19895 usec ( 105.411 MB/sec)

  Asynchronous ping-pong

       8 bytes took       254 usec (   0.063 MB/sec)
      16 bytes took       131 usec (   0.244 MB/sec)
      32 bytes took       129 usec (   0.496 MB/sec)
      64 bytes took       131 usec (   0.976 MB/sec)
     128 bytes took       129 usec (   1.985 MB/sec)
     256 bytes took       136 usec (   3.768 MB/sec)
     512 bytes took       141 usec (   7.267 MB/sec)
    1024 bytes took       157 usec (  13.035 MB/sec)
    2048 bytes took       151 usec (  27.140 MB/sec)
    4096 bytes took       206 usec (  39.768 MB/sec)
    8192 bytes took       293 usec (  55.915 MB/sec)
   16384 bytes took       438 usec (  74.817 MB/sec)
   32768 bytes took       921 usec (  71.157 MB/sec)
   65536 bytes took      1538 usec (  85.220 MB/sec)
  131072 bytes took      3050 usec (  85.946 MB/sec)
  262144 bytes took      5217 usec ( 100.495 MB/sec)
  524288 bytes took      9749 usec ( 107.558 MB/sec)
 1048576 bytes took     18777 usec ( 111.688 MB/sec)

  Bi-directional asynchronous ping-pong

       8 bytes took       191 usec (   0.084 MB/sec)
      16 bytes took       137 usec (   0.233 MB/sec)
      32 bytes took       123 usec (   0.520 MB/sec)
      64 bytes took       123 usec (   1.040 MB/sec)
     128 bytes took       129 usec (   1.985 MB/sec)
     256 bytes took       123 usec (   4.162 MB/sec)
     512 bytes took       122 usec (   8.389 MB/sec)
    1024 bytes took       125 usec (  16.393 MB/sec)
    2048 bytes took       172 usec (  23.828 MB/sec)
    4096 bytes took       205 usec (  39.953 MB/sec)
    8192 bytes took       306 usec (  53.520 MB/sec)
   16384 bytes took       488 usec (  67.142 MB/sec)
   32768 bytes took       988 usec (  66.332 MB/sec)
   65536 bytes took      1694 usec (  77.376 MB/sec)
  131072 bytes took      4879 usec (  53.729 MB/sec)
  262144 bytes took      8126 usec (  64.520 MB/sec)
  524288 bytes took     15152 usec (  69.204 MB/sec)
 1048576 bytes took     29886 usec (  70.172 MB/sec)

 Max rate = 111.687910 MB/sec  Min latency = 61.035156 usec

Konklusion

Hurtige netværk = hurtigere overførsel, og så skal man ikke sende for mange små pakker på ethernet

Matrix program med C++

For at kunne kompilere den skal man have installeret g++ og så skal den kompileres med mpiCC 

// matrixstats.cpp
// Written by Drew Weitz
// Last Modified: June 9, 2003

// This program is intended to be a very basic introduction to MPI programming.
// For informationa bout each specific function call, consult the man pages
// available on the cluster, or check out information available online at
// www.iitk.ac.in/cc/param/mpi_calls.html

// to include the MPI function library

#include "mpi.h"
#include <stdio.h>
#include <string>

int main (int argc, char *argv[]) {

	// these variables will hold MPI specific information.
	// numprocs will store the total number of processors allocated
	// for the program run; myrank will store each individual procssors
	// number assigned by the master.

	int numprocs, myrank;

	// In general, all nodes have a copy of all the variables defined.

	// MPI_Init prepares the program run to communicate between all the
	// nodes.  It is necessary to have this function call in all MPI
	// code.

	MPI_Init(&argc, &argv);

	// MPI_Comm_size initializes the numprocs variable to be the number
	// of processors alloocated to the program run.  MPI_COMM_WORLD is
	// a macro that MPI uses to address the correct MPI netowrk.  Since
	// multiple MPI jobs could be running at once, we want to have a way
	// of addressing only the processors in our program run (or our 
	// "world").

	MPI_Comm_size(MPI_COMM_WORLD, &numprocs);

	// MPI_Comm_rank initializes each nodes myrank variable to be it's
	// processor number.

	MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
	
	MPI_Status status;
	char greeting[MPI_MAX_PROCESSOR_NAME + 80];

	int thematrix[numprocs-1][numprocs-1];
	int thecube[numprocs-1][numprocs-1][numprocs-1];
	int resultmatrix[numprocs-1][numprocs-1];
 	int temp  = 0;	
	if (myrank == 0) {

		printf("Preparing the matrix...\n");

		for (int i=0; i < numprocs-1; i++) {
			for (int j=0; j < numprocs-1; j++) {
				thematrix[i][j] = 0;
			}
		}

		printf("The matrix is:\n");
		for (int i=0; i < numprocs-1; i++) {
			for (int j=0; j < numprocs-1; j++) {
				printf("%i\t", thematrix[i][j]);
			}
			printf("\n");
		}

		printf("Sending the matrix to the other nodes...\n");

		for (int k=1; k < numprocs; k++) {

	// MPI_Send is the function call that sends the values of one nodes'
	// variable out to another node.  In effect, it is the way in which
	// data can be passed to another node.  A node can either receive this
	// "message" (via MPI_RECV), or it can be ignored.

			MPI_Send(thematrix, (numprocs-1)*(numprocs-1), 
					MPI_INT, k, 1, 
					MPI_COMM_WORLD);
		}

		printf("Waiting for responses...\n");
		for (int k=1; k < numprocs; k++) {

	// MPI_Recv is the compliament to MPI_Send.  This is one way
	// in which the processor will receive data.  In the case of
	// MPI_Recv, the processor will stop executing it's code and
	// wait for the expected message.  If you do not want the processor
	// to stop executing code while waiting for a "message", you must
	// use a "non-blocking" receive function.  See the website listed
	// at the tope of the program for more information.

			MPI_Recv(thematrix, (numprocs-1)*(numprocs-1), 
					MPI_INT, k, 1,
					MPI_COMM_WORLD, &status);
			for (int i=0; i < numprocs-1; i++) {
				for (int j=0; j < numprocs-1; j++) {
					thecube[k-1][i][j] = thematrix[i][j];
				}
			}
		}

		printf("The result is...\n");
		for (int k=0; k < numprocs-1; k++) {
			printf("Level %i:\n", k);
			for (int i=0; i < numprocs-1; i++) {
				for (int j=0; j < numprocs-1; j++) {
					printf("%i\t", thecube[k][i][j]);
				}
				printf("\n");
			}
		}
	
		printf("Collapsing results...\n");
		for (int i=0; i < numprocs-1; i++) {
			for (int j=0; j < numprocs-1; j++) {
				for (int k=0; k < numprocs -1; k++) {
					temp = temp + thecube [k][i][j];
				}
				resultmatrix[i][j] = temp;
				temp = 0;
			}
		}

		for (int i=0; i < numprocs-1; i++) {
			for (int j=0; j < numprocs-1; j++) {
				printf("%i\t", resultmatrix[i][j]);
			}
			printf("\n");
		}

	}
	
	else {

		MPI_Recv(thematrix, (numprocs-1)*(numprocs-1), MPI_INT, 0, 1, 
			MPI_COMM_WORLD, &status);
		sprintf(greeting, "matrix received...");
		for (int j=0; j < numprocs-1; j++) {
			thematrix[myrank-1][j] = myrank*j;
		}
		MPI_Send(thematrix, (numprocs-1)*(numprocs-1), MPI_INT, 0, 1, 
				MPI_COMM_WORLD);		
	}

	// MPI_FINALIZE closes all the connections opened during the MPI
	// program run.  It is necessary for MPI Programs.

	MPI_Finalize();
	return 0;
}

Cluster Management

Små scripts til at udføre handlinger på clienterne

Shutdown af nodes

ShutdownClients.sh 

#!/bin/bash
ssh 10.1.2.101 shutdown -h now &
ssh 10.1.2.102 shutdown -h now &
ssh 10.1.2.103 shutdown -h now &
ssh 10.1.2.104 shutdown -h now &

Wake On Lan af nodes

WakeClients.sh 

wakeonlan 00:21:86:f3:ca:a5
wakeonlan 00:21:86:f4:00:e9
wakeonlan 00:21:86:f4:03:0d
wakeonlan 00:21:86:f4:1d:79

Mount NFS mirror på nodes

MountMirrorOnClients.sh 

#!/bin/bash
ssh 10.1.2.101 mount c01:/var/mirror /var/mirror
ssh 10.1.2.102 mount c01:/var/mirror /var/mirror
ssh 10.1.2.103 mount c01:/var/mirror /var/mirror
ssh 10.1.2.104 mount c01:/var/mirror /var/mirror

Opdater alle maskiner

updateAllMachines.sh 

#!/bin/bash
dsh -M -q -c -f mpd.hosts aptitude update
dsh -M -q -c -f mpd.hosts aptitude -y upgrade
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