Cbb/Baobab

The Baobab Cluster

CBB's internal cluster.

The new cluster is made up of 6 nodes with 24 cores and 64 GB RAM on each node.

Before submitting your jobs you need a PBS submission script

Test MPI program:

/******************************************************************************
 * * FILE: mpi_hello.c
 * * DESCRIPTION:
 * *   MPI tutorial example code: Simple hello world program
 * * AUTHOR: Blaise Barney
 * * LAST REVISED: 03/05/10
 * ******************************************************************************/
#include "mpi.h"
#include <stdio.h>
#include <stdlib.h>
#define  MASTER         0

int main (int argc, char *argv[])
{
int   numtasks, taskid, len;
char hostname[MPI_MAX_PROCESSOR_NAME];

MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &numtasks);
MPI_Comm_rank(MPI_COMM_WORLD,&taskid);
MPI_Get_processor_name(hostname, &len);
printf ("Hello from task %d on %s!\n", taskid, hostname);
if (taskid == MASTER)
   printf("MASTER: Number of MPI tasks is: %d\n",numtasks);
MPI_Finalize();
}

Example PBS script:

#PBS -l nodes=6:ppn=24,walltime=00:01:00
module add openmpi-x86_64
########################################
cd $PBS_O_WORKDIR
## How many cores total do we have?
NO_OF_CORES=`cat $PBS_NODEFILE | egrep -v '^#'\|'^$' | wc -l | awk '{print $1}'`
##
## Main execution
echo "Job Started at: `date`"
mpiexec -np $NO_OF_CORES -machinefile $PBS_NODEFILE hello2
echo "Job Ended at: `date`"

To submit the jobs to the cluster from the headnode:

qsub <yoursPBSscript>

To check the status of your jobs:

qstat -a

To delete your jobs from the queue:

qdel <Job_Number/Identifier>