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OpenMPI on CPU CLX

OpenMPI on CPU CLX

Owned by Matthias Läuter (Unlicensed)

Content

Code execution

For examples for code execution, please visit Slurm partition CPU CLX.


Code compilation

For code compilation please use gnu compiler.

MPI, gnu 
module load gcc/13.3.0
module load openmpi/gcc/5.0.3
mpicc -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c
MPI, OpenMP, gnu 
module load gcc/13.3.0
module load openmpi/gcc/5.0.3
mpicc -fopenmp -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c

Slurm job script

A slurm script is submitted to the job scheduler slurm. It contains

  • the request for compute nodes of a Slurm partition CPU CLX and
  • commands to start your binary. You have two options to start an MPI binary.
    • using mpirun
    • using srun

Using mpirun

Using mpirun (from the MPI library) to start the binary you need to switch off slurm binding by adding export SLURM_CPU_BIND=none.

MPI, full node 
#!/bin/bash
#SBATCH --nodes=2
#SBATCH --partition=cpu-clx:test
module load openmpi/gcc/5.0.3
export SLURM_CPU_BIND=none
mpirun -np 192 --map-by ppr:96:node ./hello.bin
MPI, half node 
#!/bin/bash
#SBATCH --nodes=2
#SBATCH --partition=cpu-clx:test
module load openmpi/gcc/5.0.3
export SLURM_CPU_BIND=none
mpirun -np 96 --map-by ppr:48:node ./hello.bin

You can run one code compiled with MPI and OpenMP. The example covers the setup

  • 2 nodes,
  • 4 processes per node, 24 threads per process.
MPI, OpenMPI, full node 
#!/bin/bash
#SBATCH --nodes=2
#SBATCH --partition=cpu-clx:test
module load openmpi/gcc/5.0.3
export SLURM_CPU_BIND=none
export OMP_NUM_THREADS=24
mpirun -np 8 --map-by ppr:4:node:pe=24 ./hello.bin

Using srun

MPI, full node 
#!/bin/bash
#SBATCH --nodes=2
#SBATCH --partition=cpu-clx:test
srun --ntasks-per-node=96 ./hello.bin

You can run one code compiled with MPI and OpenMP. The example covers the setup

  • 2 nodes,
  • 4 processes per node, 24 threads per process.
MPI, OpenMP, full node 
#!/bin/bash
#SBATCH --nodes=2
#SBATCH --partition=cpu-clx:test
export OMP_PROC_BIND=spread
export OMP_NUM_THREADS=24
srun --ntasks-per-node=4 --cpus-per-task=48 ./hello.bin

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