Performance Optimization/Multiple nodes (MPI): Difference between revisions

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MPI (the Message Passing Interface) lets a single program run across many cores, and even many nodes, at once by passing messages between its processes. Use it for software written to scale beyond one node. To use several cores within a single node, see [[Performance Optimization/Multiple CPUs]]; for many independent tasks, see [[Performance Optimization/Multiple nodes (arrayjobs)]].


== A simple 'Hello World' example ==
== Compiling an MPI program ==
Consider the following simple MPI version, in C, of the 'Hello World' example:


<source lang='cpp'>
Load a software bucket, then a compiler and an MPI library, through the module system. A bucket has to be loaded before its modules are visible (see [[Environment Modules]]). To avoid library conflicts it is safest to start from a clean environment — note that purging also removes the <code>slurm</code> module, so reload it:
#include <stdio.h>
#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.
<source lang='bash'>
module list
</source>


To avoid conflicts between libraries, the safest way is purging all modules:
<syntaxhighlight lang="bash">
<source lang='bash'>
module purge
module purge
</source>
module load 2025
module load OpenMPI/5.0.7
</syntaxhighlight>


The load both gcc and openmpi libraries. If modules were purged, then slurm needs to be reloaded too.
As a simple example, here is the classic MPI "Hello World" in C:
<source lang='bash'>
module load gcc/4.8.1 openmpi/gcc/64/1.6.5 slurm/2.5.7
</source>


Compile the <code>hello_mpi.c</code> code.
<syntaxhighlight lang="c">
<source lang='bash'>
#include <stdio.h>
mpicc hello_mpi.c -o test_hello_world
#include <mpi.h>
</source>
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();
}
</syntaxhighlight>


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


  linux-vdso.so.1 => (0x00002aaaaaacb000)
<syntaxhighlight lang="bash">
  libmpi.so.1 => /cm/shared/apps/openmpi/gcc/64/1.6.5/lib64/libmpi.so.1 (0x00002aaaaaccd000)
mpicc hello_mpi.c -o hello_mpi
  libdl.so.2 => /lib64/libdl.so.2 (0x00002aaaab080000)
</syntaxhighlight>
  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:
== Running an MPI program ==
<source lang='bash'>
srun --nodes=2 --ntasks-per-node=4 --partition=ABGC --mpi=openmpi ./test_hello_world
</source>


This will result in the following output:
Launch the MPI processes with <code>srun</code>, which spreads them across the nodes your job was allocated. For example, two nodes with four tasks each:
  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 ==
<syntaxhighlight lang="bash">
A mpi job using mvapich2 on 32 cores, using the normal compute nodes and the fast infiniband interconnect for RDMA traffic.
srun --nodes=2 --ntasks-per-node=4 ./hello_mpi
<source lang='bash'>
</syntaxhighlight>
$ module load mvapich2/gcc
$ vim batch.sh
#!/bin/sh
#SBATCH --account=projectx
#SBATCH --time=0
#SBATCH  -n 32
#SBATCH --constraint=normalmem
#SBATCH --output=output_%j.txt
#SBATCH --error=error_output_%j.txt
#SBATCH --job-name=MPItest
#SBATCH --partition=ABGC_Production
#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
In a batch job, request the nodes and tasks with <code>#SBATCH</code> and launch with <code>srun</code>:


mpirun -iface ib0 -np 32 ./tmf_par.out -NX 480 -NY 240 -alpha  11 -chi 1.3 -psi_b 5e--beta  0.0 -zeta 3.5 -kT 0.10
<syntaxhighlight lang="bash">
#!/bin/bash
#SBATCH --job-name=mpi-test
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --time=00:30:00
#SBATCH --output=mpi-%j.out


echo "Program finished with exit code $? at: `date`"
module purge
module load 2025
module load OpenMPI/5.0.7
srun ./hello_mpi
</syntaxhighlight>


$ sbatch batch.sh
<!-- TODO: confirm the recommended MPI library and module names for the current cluster, any required `srun --mpi=...` plugin flag, and whether specific interconnect/fabric tuning is needed. The previous page documented an mvapich2 + InfiniBand (ib0) setup from the Breed4Food cluster, which may no longer match Anunna's hardware. -->


</source>
== See also ==
* [[Performance Optimization/Multiple CPUs]]
* [[Performance Optimization/Multiple nodes (arrayjobs)]]
* [[Environment Modules]]
* [[Batch Jobs]]
* [[Scheduler Overview (Slurm)]]
* [[Cluster Architecture Overview]]

Latest revision as of 11:34, 21 July 2026

MPI (the Message Passing Interface) lets a single program run across many cores, and even many nodes, at once by passing messages between its processes. Use it for software written to scale beyond one node. To use several cores within a single node, see Performance Optimization/Multiple CPUs; for many independent tasks, see Performance Optimization/Multiple nodes (arrayjobs).

Compiling an MPI program

Load a software bucket, then a compiler and an MPI library, through the module system. A bucket has to be loaded before its modules are visible (see Environment Modules). To avoid library conflicts it is safest to start from a clean environment — note that purging also removes the slurm module, so reload it:

module purge
module load 2025
module load OpenMPI/5.0.7

As a simple example, here is the classic MPI "Hello World" in C:

#include <stdio.h>
#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();
}

Compile it with the MPI compiler wrapper:

mpicc hello_mpi.c -o hello_mpi

Running an MPI program

Launch the MPI processes with srun, which spreads them across the nodes your job was allocated. For example, two nodes with four tasks each:

srun --nodes=2 --ntasks-per-node=4 ./hello_mpi

In a batch job, request the nodes and tasks with #SBATCH and launch with srun:

#!/bin/bash
#SBATCH --job-name=mpi-test
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --time=00:30:00
#SBATCH --output=mpi-%j.out

module purge
module load 2025
module load OpenMPI/5.0.7
srun ./hello_mpi


See also