OPENMP and MPICH2 Quick Install and Examples

Environment: (@VM)

        host : CentOS-6.0
        kernel: 2.6.32-71.el6.x86_64 #1 SMP
        MemTotal: 7891424 kB(/proc/meminfo)
        CPU(Quad core) : Intel(R) Core(TM) i3-2130 CPU @ 3.40GHz
        HDD： 1TB＊2 （LVM ＝＝＞ 2T）

        guest: CentOS-6.0
        kernel: 2.6.32-71.el6.x86_64 #1 SMP
        MemTotal: 1G
        CPU *1
        HDD： 200GB 


172.16.173.143     172.16.173.144
+------------+     +------------+
|mpich2      |     |mpich2      |
|            |     |            |
|------------|     |------------|     
|cent143     |     |cent144     |
+-----+------+     +------+-----+            +----NAT(@VM)
      |                  |                  |
------+------------------+------------------+
      |            
+-----+------+     
|mpich2      |     
|openmp      |     
|------------|     
|cent142     |     
+------------+     

172.16.173.142     

Purpose:

1. install a openmp environment in a server and test it
2. install a mpi(with mpich2) environment in all servers and test it

OPENMP:

[Setup]

[root@cent142 ~]# yum install libgomp.x86_64 gcc-gfortran-4.4.6-4.el6.x86_64 -y

[C/C++ Code Example]

[root@cent142 ~]# mkdir -p ~/src/openmp; cd ~/src/openmp

[root@cent142 openmp]# vi ttt.c

#include

#include

int main()

{

        int x;

        x=2;

        #pragma omp parallel num_threads(2) shared(x)

        {

                if(omp_get_thread_num() == 1)

                        x = 5;

                else

                {

                        printf("1: Thread %d: x = %d\n", omp_get_thread_num(),x);

                }

                #pragma omp barrier

                if( omp_get_thread_num() == 0)

                {

                        printf("2: Thread# %d, x = %d\n", omp_get_thread_num(),x);

                }

                else

                {

                        printf("3: Thread# %d, x = %d\n", omp_get_thread_num(),x);

                }

        }

        return 0;

}

[root@cent142 openmp]# gcc -fopenmp -o ttt ttt.c

[root@cent142 openmp]# ./ttt

1: Thread 0: x = 2

2: Thread# 0, x = 5

3: Thread# 1, x = 5

[Fortran Code Example]

[root@cent142 openmp]# vi ttt.f

        PROGRAM A2

        INCLUDE "omp_lib.h"

        INTEGER X

        X = 2

!$OMP PARALLEL NUM_THREADS(2) SHARED(X)

        IF( OMP_GET_THREAD_NUM() .EQ. 0) THEN

                X=5

        ELSE

                ! PRINT 1: The following read of x has a race

                  PRINT *,"1: THREAD# ", OMP_GET_THREAD_NUM(), "X = ", X

        ENDIF

!$OMP BARRIER

        IF (OMP_GET_THREAD_NUM() .EQ. 0) THEN

                ! PRINT 2

                  PRINT *,"2: THREAD# ", OMP_GET_THREAD_NUM(), "X =", X

        ELSE

                ! PRINT 3

                  PRINT *,"3: THREAD# ", OMP_GET_THREAD_NUM(), "X =", X

        ENDIF

!$OMP END PARALLEL

        END

[root@cent142 openmp]# gfortran -fopenmp -o ttt.for ttt.f

[root@cent142 openmp]# ./ttt.for

 1: THREAD#            1 X =            5

 2: THREAD#            0 X =           5

 3: THREAD#            1 X =           5

MPICH2:

[Setup]

(1) Install Packages

[root@cent142 ~]# yum install mpich2.x86_64 mpich2-devel.x86_64

 -y

[root@cent143 ~]# yum install mpich2.x86_64 mpich2-devel.x86_64

 -y

[root@cent144 ~]# yum install mpich2.x86_64 mpich2-devel.x86_64

 -y

[root@cent142 mpich2]# mpich2version
MPICH2 Version:         1.2.1
MPICH2 Release date:    Unknown, built on Fri Nov 12 05:07:30 GMT 2010
MPICH2 Device:          ch3:nemesis
MPICH2 configure:       --build=x86_64-unknown-linux-gnu....
MPICH2 CC:      gcc ....
MPICH2 CXX:     c++ ....
MPICH2 F77:     gfortran ....
MPICH2 F90:     gfortran ....

(2)/etc/hosts for all servers(scp /etc/hosts cent14X:/etc/.)

172.16.173.142  cent142

172.16.173.143  cent143

172.16.173.144  cent144

(3)a hosts file for mpi(~/src/mpich2/mpd.hosts)

cent142

cent143

cent144

(4)mpd.conf for all servers( password when inserting a task)

## all servers must have the same password

cat > /etc/mpd.conf << "EOF"

secretword=********

EOF

chmod 600 /etc/mpd.conf

scp /etc/mpd.conf cent142:/etc/.

scp /etc/mpd.conf cent143:/etc/.

scp /etc/mpd.conf cent144:/etc/.

(5)password when client try to insert a task to server

##it must the same with server

cat > ~/.mpd.conf << "EOF"

secretword=********

EOF

(6)password-less ssh

(7)start up mpich2

cd ~/src/mpich2

mpdboot -n 3 -f ./mpd.hosts

mpdboot_cent142 (handle_mpd_output 420): from mpd on cent142, invalid port info:

no_port

(1) check the ~/.mpd.conf exist , and only named as ~/.mpd.conf

(2) permission 600 for ~/.mpd.conf and /etc/mpd.conf

(3) x86 - x64 hybrid architechure is not allow for mpich2

    openmpi or mpich2 instead

mpdtrace

cent142

cent144

cent143

[root@cent142 mpich2]# mpiexec  -n 6  /bin/hostname

cent143

cent142

cent142

cent143

cent144

cent144

[root@cent142 mpich2]# mpiexec  -n 3 date : -n 4 hostname

cent144

銝?10?? 3 18:53:19 CST 2012

cent143

銝?10?? 3 18:53:19 CST 2012

cent142

cent142

銝?10?? 3 18:53:19 CST 2012

[root@cent142 mpich2]# mpiexec -n 3 /bin/date : -n 2 -host cent143 /bin/hostname

瞻T 10瞻禱  3 15:02:00 CST 2012

cent143

cent143

瞻T 10瞻禱  3 15:02:00 CST 2012

瞻T 10瞻禱  3 15:02:00 CST 2012

[root@cent142 mpich2]# mpiexec -machinefile mpd2.hosts -n 3 /bin/date

銝?10?? 3 18:54:47 CST 2012

銝?10?? 3 18:54:47 CST 2012

銝?10?? 3 18:54:47 CST 2012

(8)close mpd service for all servers

mpdallexit

[C/C++ Code Example]

[root@cent142 ~]# mkdir -p ~/src/mpich2; cd ~/src/mpich2

[root@cent142 mpich2]# cat pi_cc.cc

#include

#include "mpi.h"

#include

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

{

    int n, rank, size, i;

    double PI25DT = 3.141592653589793238462643;

    double mypi, pi, h, sum, x;

    MPI::Init(argc, argv);

    size = MPI::COMM_WORLD.Get_size();

    rank = MPI::COMM_WORLD.Get_rank();

    while (1) {

        if (rank == 0) {

            std::cout << "Enter the number of intervals: (0 quits)"

                 << std::endl;

            std::cin >> n;

        }

        MPI::COMM_WORLD.Bcast(&n, 1, MPI::INT, 0);

        if (n==0)

            break;

        else {

            h = 1.0 / (double) n;

            sum = 0.0;

            for (i = rank + 1; i <= n; i += size) {

                x = h * ((double)i - 0.5);

                sum += (4.0 / (1.0 + x*x));

            }

            mypi = h * sum;

            MPI::COMM_WORLD.Reduce(&mypi, &pi, 1, MPI::DOUBLE,

                                   MPI::SUM, 0);

            if (rank == 0)

                std::cout << "pi is approximately " << pi

                     << ", Error is " << fabs(pi - PI25DT)

                     << std::endl;

        }

    }

    MPI::Finalize();

    return 0;

}

[root@cent142 mpich2]# mpic++  -o pi_cc pi_cc.cc

[root@cent142 mpich2]# mpdboot -n 3 -f ./mpd.hosts

[root@cent142 mpich2]# mpiexec -n 12 ./pi_cc

[root@cent142 mpich2]# ps -ef | grep pi_cc

root      4039  2350  0 16:27 pts/0    00:00:00 python2.6 /usr/bin/mpiexec -n 12 ./pi_cc

root      4045  4043 49 16:27 ?        00:01:01 ./pi_cc

root      4046  4044 49 16:27 ?        00:01:00 ./pi_cc

root      4047  4041  0 16:27 ?        00:00:00 ./pi_cc

root      4052  1357  0 16:29 pts/1    00:00:00 grep pi_cc

[root@cent143 ~]# ps -ef | grep pi_cc

root      4171  4166 20 16:27 ?        00:00:29 ./pi_cc

root      4172  4168 19 16:27 ?        00:00:27 ./pi_cc

root      4173  4169 18 16:27 ?        00:00:26 ./pi_cc

root      4174  4165 20 16:27 ?        00:00:29 ./pi_cc

root      4175  4170 20 16:27 ?        00:00:28 ./pi_cc

root      4180  2277  0 16:30 pts/0    00:00:00 grep pi_cc

[root@cent144 ~]# ps -ef | grep pi_cc

root      3696  3692 25 16:27 ?        00:00:16 ./pi_cc

root      3697  3691 22 16:27 ?        00:00:14 ./pi_cc

root      3698  3694 25 16:27 ?        00:00:16 ./pi_cc

root      3699  3695 23 16:27 ?        00:00:15 ./pi_cc

root      3703  2428  0 16:28 pts/0    00:00:00 grep pi_cc

Enter the number of intervals: (0 quits)

50

pi is approximately 3.14163, Error is 3.33333e-05

Enter the number of intervals: (0 quits)

0

[root@cent142 mpich2]# mpdallexit

[Fortran Code Example]

[root@cent142 mpich2]# cat pi_ff.f

      program main

      include "mpif.h"

      double precision  PI25DT

      parameter        (PI25DT = 3.141592653589793238462643d0)

      double precision  mypi, pi, h, sum, x, f, a

      integer n, myid, numprocs, i, ierr

c                                 function to integrate

      f(a) = 4.d0 / (1.d0 + a*a)

      call MPI_INIT(ierr)

      call MPI_COMM_RANK(MPI_COMM_WORLD, myid, ierr)

      call MPI_COMM_SIZE(MPI_COMM_WORLD, numprocs, ierr)

 10   if ( myid .eq. 0 ) then

         print *, 'Enter the number of intervals: (0 quits) '

         read(*,*) n

      endif

c                                 broadcast n

      call MPI_BCAST(n,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)

c                                 check for quit signal

      if ( n .le. 0 ) goto 30

c                                 calculate the interval size

      h = 1.0d0/n

      sum  = 0.0d0

      do 20 i = myid+1, n, numprocs

         x = h * (dble(i) - 0.5d0)

         sum = sum + f(x)

 20   continue

      mypi = h * sum

c                                 collect all the partial sums

      call MPI_REDUCE(mypi,pi,1,MPI_DOUBLE_PRECISION,MPI_SUM,0,

     &                  MPI_COMM_WORLD,ierr)

c                                 node 0 prints the answer.

      if (myid .eq. 0) then

         print *, 'pi is ', pi, ' Error is', abs(pi - PI25DT)

      endif

      goto 10

 30   call MPI_FINALIZE(ierr)

      stop

      end

[root@cent142 mpich2]# cat make_pi_ff.sh

#!/bin/bash

## mpif77 -f77=gfortran -o pi_ff pi_ff.f

## mpif77 -f77=f77 -o pi_ff pi_ff.f      <-- so different with gfortran>

mpif77 -o pi_ff pi_ff.f

[root@cent142 mpich2]# ./make_pi_ff.sh

[root@cent142 mpich2]# mpdboot -n 3 -f ./mpd.hosts

[root@cent142 mpich2]# mpiexec -n 12 ./pi_ff

10

0

 Enter the number of intervals: (0 quits)

 pi is    3.1424259850010983       Error is  8.33331411305149317E-004

 Enter the number of intervals: (0 quits)

[A]comparasion between -n when computating of pi with Monte Carlo

[root@cent142 mpich2]# time mpiexec -n 3 ./monte_cc 0.00001

pi =  3.14159455782312946326

points: 735000

in: 577268, out: 157732, to exit

real    0m8.805s

user    0m0.052s

sys     0m0.015s

[root@cent142 mpich2]# time mpiexec -n 6 ./monte_cc 0.00001

pi =  3.14159455782312946326

points: 735000

in: 577268, out: 157732, to exit

real    0m5.406s

user    0m0.047s

sys     0m0.015s

[root@cent142 mpich2]# time mpiexec -n 42 ./monte_cc 0.00001

pi =  3.14158287705326033645

points: 1004500

in: 788930, out: 215570, to exit

real    0m6.829s

user    0m0.053s

sys     0m0.012s

[source code]

[root@cent142 mpich2]# cat monte_cc.c
#include
#include
#include "mpi.h"
#include "mpe.h"
#define CHUNKSIZE      1000
/* We'd like a value that gives the maximum value returned by the function
   random, but no such value is *portable*.  RAND_MAX is available on many
   systems but is not always the correct value for random (it isn't for
   Solaris).  The value ((unsigned(1)<<31 but="but" common="common" guaranteed="guaranteed" is="is" not="not" p="p">#define INT_MAX 1000000000

/* message tags */
#define REQUEST  1
#define REPLY    2
int main( int argc, char *argv[] )
{
    int iter;
    int in, out, i, iters, max, ix, iy, ranks[1], done, temp;
    double x, y, Pi, error, epsilon;
    int numprocs, myid, server, totalin, totalout, workerid;
    int rands[CHUNKSIZE], request;
    MPI_Comm world, workers;
    MPI_Group world_group, worker_group;
    MPI_Status status;

    if(argc < 2)
    {
        printf("you must give a number of tolerance of pi when approaching it!!, ex:\n mpiexec -n ./monte_cc 0.01\n");
        return -1;
    }
    MPI_Init(&argc,&argv);
    world  = MPI_COMM_WORLD;
    MPI_Comm_size(world,&numprocs);
    MPI_Comm_rank(world,&myid);
    server = numprocs-1;        /* last proc is server */
    if (myid == 0)
        sscanf( argv[1], "%lf", &epsilon );
    MPI_Bcast( &epsilon, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
    MPI_Comm_group( world, &world_group );
    ranks[0] = server;
    MPI_Group_excl( world_group, 1, ranks, &worker_group );
    MPI_Comm_create( world, worker_group, &workers );
    MPI_Group_free(&worker_group);
    if (myid == server) {       /* I am the rand server */
        do {
            MPI_Recv(&request, 1, MPI_INT, MPI_ANY_SOURCE, REQUEST,
                     world, &status);
            if (request) {
                for (i = 0; i < CHUNKSIZE; ) {
                        rands[i] = random();
                        if (rands[i] <= INT_MAX) i++;
                }
                MPI_Send(rands, CHUNKSIZE, MPI_INT,
                         status.MPI_SOURCE, REPLY, world);
            }
        }
        while( request>0 );
    }
    else {                      /* I am a worker process */
        request = 1;
        done = in = out = 0;
        max  = INT_MAX;         /* max int, for normalization */
        MPI_Send( &request, 1, MPI_INT, server, REQUEST, world );
        MPI_Comm_rank( workers, &workerid );
        iter = 0;
        while (!done) {
            iter++;
            request = 1;
            MPI_Recv( rands, CHUNKSIZE, MPI_INT, server, REPLY,
                     world, &status );
            for (i=0; i                x = (((double) rands[i++])/max) * 2 - 1;
                y = (((double) rands[i++])/max) * 2 - 1;
                if (x*x + y*y < 1.0)
                    in++;
                else
                    out++;
            }
            MPI_Allreduce(&in, &totalin, 1, MPI_INT, MPI_SUM,
                          workers);
            MPI_Allreduce(&out, &totalout, 1, MPI_INT, MPI_SUM,
                          workers);
            Pi = (4.0*totalin)/(totalin + totalout);
            error = fabs( Pi-3.141592653589793238462643);
            done = (error < epsilon || (totalin+totalout) > 1000000);
            request = (done) ? 0 : 1;
            if (myid == 0) {
                printf( "\rpi = %23.20f", Pi );
                MPI_Send( &request, 1, MPI_INT, server, REQUEST,
                         world );
            }
            else {
                if (request)
                    MPI_Send(&request, 1, MPI_INT, server, REQUEST,
                             world);
            }
        }
        MPI_Comm_free(&workers);
    }

    if (myid == 0) {
        printf( "\npoints: %d\nin: %d, out: %d, to exit\n",
               totalin+totalout, totalin, totalout );
        getchar();
    }
    MPI_Finalize();
}

[B]mpiexec for fortran

[root@cent142 mpich2]# mpiexec -n 3 ./pitm_ff

20

0

 Enter the number of intervals: (0 quits)

 pi is    3.1418009868930934       Error is  2.08333303300278772E-004

 time is   7.91406631469726563E-003  seconds

 Enter the number of intervals: (0 quits)

[source code]

[root@cent142 mpich2]# cat pitm_ff.f
      program main
      include "mpif.h"
      double precision  PI25DT
      parameter        (PI25DT = 3.141592653589793238462643d0)
      double precision  mypi, pi, h, sum, x, f, a
      double precision starttime, endtime
      integer n, myid, numprocs, i, ierr
c                                 function to integrate
      f(a) = 4.d0 / (1.d0 + a*a)

      call MPI_INIT(ierr)
      call MPI_COMM_RANK(MPI_COMM_WORLD, myid, ierr)
      call MPI_COMM_SIZE(MPI_COMM_WORLD, numprocs, ierr)


 10   if ( myid .eq. 0 ) then
         print *, 'Enter the number of intervals: (0 quits) '
         read(*,*) n
      endif
c                                 broadcast n
      starttime = MPI_WTIME()
      call MPI_BCAST(n,1,MPI_INTEGER,0,MPI_COMM_WORLD,ierr)
c                                 check for quit signal
      if ( n .le. 0 ) goto 30
c                                 calculate the interval size
      h = 1.0d0/n
      sum  = 0.0d0
      do 20 i = myid+1, n, numprocs
         x = h * (dble(i) - 0.5d0)
         sum = sum + f(x)
 20   continue
      mypi = h * sum
c                                 collect all the partial sums
      call MPI_REDUCE(mypi,pi,1,MPI_DOUBLE_PRECISION,MPI_SUM,0,
     &                  MPI_COMM_WORLD,ierr)
c                                 node 0 prints the answer.
      endtime = MPI_WTIME()
      if (myid .eq. 0) then
         print *, 'pi is ', pi, ' Error is', abs(pi - PI25DT)
         print *, 'time is ', endtime-starttime, ' seconds'
      endif
      goto 10
 30   call MPI_FINALIZE(ierr)
      stop
      end

[Reference]

http://trac.nchc.org.tw/grid/wiki/mpich
http://www.mcs.anl.gov/research/projects/mpich2/
http://openmp.org/wp/
http://www.mcs.anl.gov/research/projects/mpi/usingmpi/examples/simplempi/main.htm