Content

Code execution

To execute your code you need to

compile a binary (executable, model code), see Workflow OpenMPI,
create a slurm job script, see Slurm script,
submit the slurm job script.

Job submission

> sbatch myjobscipt.slurm
Submitted batch job 8028673
> ls slurm-8028673.out
slurm-8028673.out

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 script

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

the request for compute nodes 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