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Code execution

To execute your code you need to

  1. have a binary, which is the result of code compilation,
  2. create a slurm job script,
  3. submit the slurm jobs script.
Job submission 
blogin> sbatch myjobscipt.slurm
Submitted batch job 8028673
blogin> ls slurm-8028673.out
slurm-8028673.out

Slurm jobs using mpirun

Using mpirun the pinning is controlled by the MPI library. Pinning by slurm you need to switch off by adding export SLURM_CPU_BIND=none.

MPI only

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

MPI, OpenMP

You can run one code compiled with MPI and OpenMP. The examples cover 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
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