MPI job

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Latest revision as of 13:33, 12 October 2009

Submiting MPI job how-to

This is simple MPI job submiting example. For demonstration use attached file.

1.Extract file with:

 [ngrkic@ui ~]$ unzip mpi.zip

2.Enter directory mpi with:

 [ngrkic@ui ~]$ cd mpi

3.List directory:

[ngrkic@ui mpi]$ ll
-rw-r--r--  1 ngrkic ngrkic  561 Aug 22  2007 test-mpi.c
-rw-r--r--  1 ngrkic ngrkic  295 Oct  2 10:21 test-mpi.jdl
-rw-r--r--  1 ngrkic ngrkic 1751 Aug 22  2007 test-mpi.sh

Content of file test-mpi.c

[ngrkic@ui mpi]$ cat test-mpi.c 
/*  hello.c
*
*  Simple "Hello World" program in MPI.
*
*/
   
#include "mpi.h"
#include <stdio.h>
int main(int argc, char *argv[])
{
  int numprocs;  /* Number of processors */
  int procnum;   /* Processor number */
  /* Initialize MPI */
  MPI_Init(&argc, &argv);
  /* Find this processor number */
  MPI_Comm_rank(MPI_COMM_WORLD, &procnum);
  /* Find the number of processors */
  MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
  printf ("Hello world! from processor %d out of %d\n", procnum, numprocs);
  /* Shut down MPI */
  MPI_Finalize();
  return 0;
}

This is content of file test-mpi.jdl

[ngrkic@ui mpi]$ cat test-mpi.jdl 
Type = "Job";
JobType = "MPICH";
CpuNumber = 2;
Executable = "test-mpi.sh";
Arguments = "test-mpi";
StdOutput = "test-mpi.out";
StdError = "test-mpi.err";
InputSandbox = {"test-mpi.sh","test-mpi.c"};
OutputSandbox = {"test-mpi.err","test-mpi.out","mpiexec.out"};
Requirements = Member("MPICH");

This is content of file test-mpi.sh

[ngrkic@ui mpi]$ cat test-mpi.sh
#!/bin/sh -x

# the binary to execute
EXE=$1 

echo "***********************************************************************" 
echo "Running on: $HOSTNAME" 
echo "As:       " `whoami` 
echo "***********************************************************************" 

echo "***********************************************************************" 
echo "Compiling binary: $EXE" 
echo mpicc -o ${EXE} ${EXE}.c
mpicc -o ${EXE} ${EXE}.c
echo "*************************************" 

if [ "x$PBS_NODEFILE" != "x" ] ; then 
  echo "PBS Nodefile: $PBS_NODEFILE" 
  HOST_NODEFILE=$PBS_NODEFILE 
fi 

if [ "x$LSB_HOSTS" != "x" ] ; then 
  echo "LSF Hosts: $LSB_HOSTS" 
  HOST_NODEFILE=`pwd`/lsf_nodefile.$$ 
  for host in ${LSB_HOSTS} 
  do 
    echo $host >> ${HOST_NODEFILE} 
  done 
fi

if [ "x$HOST_NODEFILE" = "x" ]; then
  echo "No hosts file defined.  Exiting..."
  exit
fi  

echo "***********************************************************************" 
CPU_NEEDED=`cat $HOST_NODEFILE | wc -l` 
echo "Node count: $CPU_NEEDED"
echo "Nodes in $HOST_NODEFILE: "
cat $HOST_NODEFILE
echo "***********************************************************************"  

echo "***********************************************************************" 
CPU_NEEDED=`cat $HOST_NODEFILE | wc -l` 
echo "Checking ssh for each node:"
NODES=`cat $HOST_NODEFILE`
for host in ${NODES}
do
  echo "Checking $host..." 
  ssh $host hostname
done
echo "***********************************************************************"  

echo "***********************************************************************" 
echo "Executing $EXE with mpiexec"  
chmod 755 $EXE 
mpiexec `pwd`/$EXE > mpiexec.out 2>&1 
echo "***********************************************************************"

4.Creating VOMS proxy:

[ngrkic@ui single]$ voms-proxy-init -voms aegis

Cannot find file or dir: /home/ngrkic/.glite/vomses
Enter GRID pass phrase:
Your identity: /C=RS/O=AEGIS/OU=Institute of Physics Belgrade/CN=Nikola Grkic
Creating temporary proxy ......................... Done
Contacting  voms.ipb.ac.rs:15001 [/C=RS/O=AEGIS/OU=Institute of Physics Belgrade/CN=host/voms.ipb.ac.rs] "aegis" Done
Creating proxy ..................................................... Done
Your proxy is valid until Fri Oct  2 01:11:00 2009 </code>

Now we are ready to submit job.

5.Submiting single job: