Parallel Computing

We recommend using Intel MPI unless you have a specific reason for using other implementations of MPI such as OpenMPI. We recommend Intel MPI over other implementations because it results in better scaling and performance.

Note

Only one MPI module should be loaded at a time.

Sample parallel programs:

C++ source code and compilation

mpi_example1.cpp

---

//=================================================================
// C++ example: MPI Example 1
//=================================================================
#include <iostream>
#include <mpi.h>
using namespace std;
int main(int argc, char** argv){
  int iproc;
  MPI_Comm icomm;
  int nproc;
  int i;
  MPI_Init(&argc,&argv);
  icomm = MPI_COMM_WORLD;
  MPI_Comm_rank(icomm,&iproc);
  MPI_Comm_size(icomm,&nproc);
  for ( i = 0; i <= nproc - 1; i++ ){
    MPI_Barrier(icomm);
    if ( i == iproc ){
      cout << "Rank " << iproc << " out of " << nproc << endl;
    }
  }
  MPI_Finalize();
  return 0;
}

[username@pegasus ~]$ mpicxx -o mpi_example1.x mpi_example1.cpp

C source code and compilation:

mpi_example1.c

---

//=================================================================
// C example: MPI Example 1
//=================================================================
#include <stdio.h>
#include "mpi.h"
int main(int argc, char** argv){
int iproc;
int icomm;
int nproc;
int i;
MPI_Init(&argc,&argv);
icomm = MPI_COMM_WORLD;
MPI_Comm_rank(icomm,&iproc);
MPI_Comm_size(icomm,&nproc);
for ( i = 0; i <= nproc - 1; i++ ){
  MPI_Barrier(icomm);
  if ( i == iproc ){
    printf("%s %d %s %d \n","Rank",iproc,"out of",nproc);
  }
}
MPI_Finalize();
return 0;
}

[username@pegasus ~]$ mpicc -o mpi_example1.x mpi_example1.c

Fortran 90 source code and compilation:

mpi_example1.f90

---

!=====================================================
! Fortran 90 example: MPI test
!=====================================================
program mpiexample1
implicit none
include 'mpif.h'
integer(4) :: ierr
integer(4) :: iproc
integer(4) :: nproc
integer(4) :: icomm
integer(4) :: i
call MPI_INIT(ierr)
icomm = MPI_COMM_WORLD
call MPI_COMM_SIZE(icomm,nproc,ierr)
call MPI_COMM_RANK(icomm,iproc,ierr)
do i = 0, nproc-1
  call MPI_BARRIER(icomm,ierr)
  if ( iproc == i ) then
    write (6,*) "Rank",iproc,"out of",nproc
  end if
end do
call MPI_FINALIZE(ierr)
if ( iproc == 0 ) write(6,*)'End of program.'
  stop
end program mpiexample1

[username@pegasus ~]$ mpif90 -o mpi_example1.x mpi_example1.f90

Fortran 77 source code and compilation:

mpi_example1.f

---

c=====================================================
c Fortran 77 example: MPI Example 1
c=====================================================
program mpitest
implicit none
include 'mpif.h'
integer(4) :: ierr
integer(4) :: iproc
integer(4) :: nproc
integer(4) :: icomm
integer(4) :: i
call MPI_INIT(ierr)
icomm = MPI_COMM_WORLD
call MPI_COMM_SIZE(icomm,nproc,ierr)
call MPI_COMM_RANK(icomm,iproc,ierr)
do i = 0, nproc-1
  call MPI_BARRIER(icomm,ierr)
  if ( iproc == i ) then
    write (6,*) "Rank",iproc,"out of",nproc
  end if
end do
call MPI_FINALIZE(ierr)
if ( iproc == 0 ) write(6,*)'End of program.'
  stop
end

[username@pegasus ~]$ mpif77 -o mpi_example1.x mpi_example1.f

The LSF script to run parallel jobs

This batch script mpi_example1.job instructs LSF to reserve computational resources for your job. Change the -P flag argument to your project before running.

mpi_example1.job

---

#!/bin/sh
#BSUB -n 32
#BSUB -J test
#BSUB -o test.out
#BSUB -e test.err
#BSUB -a openmpi
#BSUB -R "span[ptile=16]"
#BSUB -q parallel
#BSUB -P hpc
mpirun.lsf ./mpi_example1.x

Submit this scriptfile using bsub. For job script information, see Scheduling Jobs on Pegasus.

[username@pegasus ~]$ bsub -q parallel < mpi_example1.job
Job <6021006> is submitted to queue <parallel>.
...