MPI on B4F cluster

A simple 'Hello World' example

Consider the following simple MPI version, in C, of the 'Hello World' example:

<source lang='cpp'>

1. include <stdio.h>
2. include <mpi.h>

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

 int size,rank,namelen;
 char processor_name[MPI_MAX_PROCESSOR_NAME];
 MPI_Init(&argc, &argv);
 MPI_Comm_rank(MPI_COMM_WORLD,&rank);
 MPI_Comm_size(MPI_COMM_WORLD,&size);
 MPI_Get_processor_name(processor_name, &namelen);
 printf("Hello MPI! Process %d of %d on %s\n", rank, size, processor_name);
 MPI_Finalize();

} </source>

Before compiling, make sure that the compilers that are required available.

module list

To avoid conflicts between libraries, the safest way is purging all modules: <source lang='bash'> module purge </source>

The load both gcc and openmpi libraries. If modules were purged, then slurm needs to be reloaded too. <source lang='bash'> module load gcc/4.8.1 openmpi/gcc/64/1.6.5 slurm/2.5.7 </source>

Compile the hello_mpi.c code. <source lang='bash'> mpicc hello_mpi.c -o test_hello_world </source>

If desired, a list of libraries compiled into the executable can be viewed: <source lang='bash'> ldd test_hello_world </source>

 linux-vdso.so.1 =>  (0x00002aaaaaacb000)
 libmpi.so.1 => /shared/apps/openmpi/gcc/64/1.6.5/lib64/libmpi.so.1 (0x00002aaaaaccd000)
 libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaab080000)
 libm.so.6 => /lib64/libm.so.6 (0x00002aaaab284000)
 libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x0000003e29400000)
 librt.so.1 => /lib64/librt.so.1 (0x00002aaaab509000)
 libnsl.so.1 => /lib64/libnsl.so.1 (0x00002aaaab711000)
 libutil.so.1 => /lib64/libutil.so.1 (0x00002aaaab92a000)
 libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aaaabb2e000)
 libc.so.6 => /lib64/libc.so.6 (0x00002aaaabd4b000)
 /lib64/ld-linux-x86-64.so.2 (0x00002aaaaaaab000)

Running the executable on two nodes, with four tasks per node, can be done like this: <source lang='bash'> srun --nodes=2 --ntasks-per-node=4 --mpi=openmpi ./test_hello_world </source>

This will result in the following output:

 Hello MPI! Process 4 of 8 on node011
 Hello MPI! Process 1 of 8 on node010
 Hello MPI! Process 7 of 8 on node011
 Hello MPI! Process 6 of 8 on node011
 Hello MPI! Process 5 of 8 on node011
 Hello MPI! Process 2 of 8 on node010
 Hello MPI! Process 0 of 8 on node010
 Hello MPI! Process 3 of 8 on node010

A mvapich2 sbatch example

A mpi job using mvapich2 on 32 cores, using the normal compute nodes and the fast infiniband interconnect for RDMA traffic. <source lang='bash'> $ module load mvapich2/gcc $ vim batch.sh

#!/bin/sh
#SBATCH --comment=projectx
#SBATCH --time=30-0
#SBATCH  -n 32
#SBATCH --constraint=4gpercpu
#SBATCH --output=output_%j.txt
#SBATCH --error=error_output_%j.txt
#SBATCH --job-name=MPItest
#SBATCH --mail-type=ALL
#SBATCH --mail-user=user@wur.nl

echo "Starting at `date`"
echo "Running on hosts: $SLURM_NODELIST"
echo "Running on $SLURM_NNODES nodes."
echo "Running on $SLURM_NPROCS processors."
echo "Current working directory is `pwd`"
# echo "Env var MPIR_CVAR_NEMESIS_TCP_NETWORK_IFACE is $MPIR_CVAR_NEMESIS_TCP_NETWORK_IFACE"
# export MPIR_CVAR_NEMESIS_TCP_NETWORK_IFACE=ib0

mpirun -iface ib0 -np 32 ./tmf_par.out -NX 480 -NY 240 -alpha  11 -chi 1.3 -psi_b 5e-2  -beta  0.0 -zeta 3.5 -kT 0.10 

echo "Program finished with exit code $? at: `date`"

$ sbatch batch.sh

</source>