Using MPI on Clipper

HPC Clipper MPI

What is MPI?

The Message Passing Interface (MPI) is a portable message-passing standard designed to function on parallel computing architectures. The MPI standard defines the syntax and semantics of library routines that are useful to a wide range of users writing portable message-passing programs in C, C++, and Fortran. There are several open-source MPI implementations, which fostered the development of a parallel software industry, and encouraged development of portable and scalable large-scale parallel applications.

MPI can be used to communicate between processes located on a single system or on a collection of distributed systems.

Clipper provides four different implementations of MPI: OpenMPI, MVAPICH2, MPICH and Intel MPI. Each has been compiled with GCC and with support the cluster’s high speed, low latency Infiniband network.

MPI Hello World

The following examples utilize the following MPI Hello World C application written by Wes Kendall:

// Author: Wes Kendall
// Copyright 2011 www.mpitutorial.com
// This code is provided freely with the tutorials on mpitutorial.com. Feel
// free to modify it for your own use. Any distribution of the code must
// either provide a link to www.mpitutorial.com or keep this header intact.
//
// An intro MPI hello world program that uses MPI_Init, MPI_Comm_size,
// MPI_Comm_rank, MPI_Finalize, and MPI_Get_processor_name.
//
#include <mpi.h>
#include <stdio.h>

int main(int argc, char** argv) {
  // Initialize the MPI environment. The two arguments to MPI Init are not
  // currently used by MPI implementations, but are there in case future
  // implementations might need the arguments.
  MPI_Init(NULL, NULL);

  // Get the number of processes
  int world_size;
  MPI_Comm_size(MPI_COMM_WORLD, &world_size);

  // Get the rank of the process
  int world_rank;
  MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);

  // Get the name of the processor
  char processor_name[MPI_MAX_PROCESSOR_NAME];
  int name_len;
  MPI_Get_processor_name(processor_name, &name_len);

  // Print off a hello world message
  printf("Hello world from processor %s, rank %d out of %d processors\n",
         processor_name, world_rank, world_size);

  // Finalize the MPI environment. No more MPI calls can be made after this
  MPI_Finalize();
}

OpenMPI Show

OpenMPI

After saving the example program, load the openmpi module and compile the program with the mpicc compiler wrapper:

module load openmpi

mpicc mpi_hello_world.c -o mpi_hello_world

Create a Slurm script mpi_hello_world.sbatch requesting multiple tasks (cores) across multiple nodes:

#!/bin/bash
#SBATCH --job-name=mpi-hello-world
#SBATCH --output=mpi-hello-world.out
#SBATCH --time=00:30:00
#SBATCH --partition=cpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=10
#SBATCH --mem-per-cpu=4G
#SBATCH --mail-user username@gvsu.edu
#SBATCH --mail-type BEGIN
#SBATCH --mail-type END
#SBATCH --mail-type FAIL

module purge
module load openmpi

srun ~/mpi-hello-world-openmpi/mpi_hello_world

Submit the job to the cluster:

sbatch mpi_hello_world.sbatch

The output shows multiple processes running across multiple cores and systems:

Hello world from processor c001.clipper.gvsu.edu, rank 1 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 14 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 15 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 6 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 18 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 16 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 12 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 13 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 19 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 17 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 11 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 10 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 4 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 8 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 2 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 3 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 7 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 0 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 9 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 5 out of 20 processors

MPICH Show

MPICH

After saving the example program, load the mpich module and compile the program with the mpicc compiler wrapper:

module load mpich

mpicc mpi_hello_world.c -o mpi_hello_world

Create a Slurm script mpi_hello_world.sbatch requesting multiple tasks (cores) across multiple nodes:

#!/bin/bash
#SBATCH --job-name=mpi-hello-world
#SBATCH --output=mpi-hello-world.out
#SBATCH --time=00:30:00
#SBATCH --partition=cpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=10
#SBATCH --mem-per-cpu=4G
#SBATCH --mail-user username@gvsu.edu
#SBATCH --mail-type BEGIN
#SBATCH --mail-type END
#SBATCH --mail-type FAIL

module purge
module load mpich

srun ~/mpi-hello-world-mpich/mpi_hello_world

Submit the job to the cluster:

sbatch mpi_hello_world.sbatch

The output shows multiple processes running across multiple cores and systems:

Hello world from processor c001.clipper.gvsu.edu, rank 1 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 14 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 15 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 6 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 18 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 16 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 12 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 13 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 19 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 17 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 11 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 10 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 4 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 8 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 2 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 3 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 7 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 0 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 9 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 5 out of 20 processors

Intel MPI Show

Intel MPI

After saving the example program, load the intel-oneapi-mpi module and compile the program with the mpicc compiler wrapper:

module load intel-oneapi-mpi

mpicc mpi_hello_world.c -o mpi_hello_world

Create a Slurm script mpi_hello_world.sbatch requesting multiple tasks (cores) across multiple nodes:

#!/bin/bash
#SBATCH --job-name=mpi-hello-world
#SBATCH --output=mpi-hello-world.out
#SBATCH --time=00:30:00
#SBATCH --partition=cpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=10
#SBATCH --mem-per-cpu=4G
#SBATCH --mail-user username@gvsu.edu
#SBATCH --mail-type BEGIN
#SBATCH --mail-type END
#SBATCH --mail-type FAIL

module purge
module load intel-oneapi-mpi

srun ~/mpi-hello-world-intel/mpi_hello_world

Submit the job to the cluster:

sbatch mpi_hello_world.sbatch

The output shows multiple processes running across multiple cores and systems:

Hello world from processor c001.clipper.gvsu.edu, rank 1 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 5 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 6 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 8 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 9 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 3 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 4 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 7 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 2 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 0 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 14 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 15 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 17 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 10 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 11 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 12 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 16 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 18 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 19 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 13 out of 20 processors

MVAPICH2 Show

MVAPICH2

After saving the example program, load the mvapich2 module and compile the program with the mpicc compiler wrapper:

module load mvapich2

mpicc mpi_hello_world.c -o mpi_hello_world

Create a Slurm script mpi_hello_world.sbatch requesting multiple tasks (cores) across multiple nodes:

#!/bin/bash
#SBATCH --job-name=mpi-hello-world
#SBATCH --output=mpi-hello-world.out
#SBATCH --time=00:30:00
#SBATCH --partition=cpu
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=10
#SBATCH --mem-per-cpu=4G
#SBATCH --mail-user username@gvsu.edu
#SBATCH --mail-type BEGIN
#SBATCH --mail-type END
#SBATCH --mail-type FAIL

module purge
module load mvapich

export MV2_USE_CUDA=0
export MV2_SUPPRESS_CUDA_USAGE_WARNING=1

srun ~/mpi-hello-world-mvapich2/mpi_hello_world

Submit the job to the cluster:

sbatch mpi_hello_world.sbatch

The output shows multiple processes running across multiple cores and systems. For MVAPICH2, it is also normal to receive some informational message that can be ignored.

CUDA: Failed to get number of devices with cudaGetDeviceCount(): no CUDA-capable device is detected
CUDA: Failed to get number of devices with cudaGetDeviceCount(): no CUDA-capable device is detected
CUDA: Failed to get number of devices with cudaGetDeviceCount(): no CUDA-capable device is detected
CUDA: Failed to get number of devices with cudaGetDeviceCount(): no CUDA-capable device is detected
[c001.clipper.gvsu.edu:mpi_rank_0][rdma_param_handle_heterogeneity] All nodes involved in the job were detected to be homogeneous in terms of processors and interconnects. Setting MV2_HOMOGENEOUS_CLUSTER=1 can improve job startup performance on such systems. The following link has more details on enhancing job startup performance. http://mvapich.cse.ohio-state.edu/performance/job-startup/.
[c001.clipper.gvsu.edu:mpi_rank_0][rdma_param_handle_heterogeneity] To suppress this warning, please set MV2_SUPPRESS_JOB_STARTUP_PERFORMANCE_WARNING to 1
Hello world from processor c001.clipper.gvsu.edu, rank 0 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 10 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 11 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 4 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 12 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 6 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 13 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 1 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 14 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 3 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 15 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 5 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 16 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 7 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 17 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 8 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 18 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 9 out of 20 processors
Hello world from processor c002.clipper.gvsu.edu, rank 19 out of 20 processors
Hello world from processor c001.clipper.gvsu.edu, rank 2 out of 20 processors

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Using MPI on Clipper

What is MPI?

MPI Hello World

OpenMPI

MPICH

Intel MPI

MVAPICH2

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