Content
Code execution
To execute your code you need to
- have a binary, which is the result of code compilation,
- create a slurm job script,
- submit the slurm jobs script.
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For examples for code execution, please visit Slurm partition CPU CLX.
Code compilation
For code compilation please use gnu compiler.
| Codeblock |
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| title | MPI, gnu |
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| collapse | true |
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module load gcc/13.3.0
module load openmpi/gcc/5.0.3
mpicc -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c |
| Codeblock |
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| title | MPI, OpenMP, gnu |
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| collapse | true |
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load gcc/13.3.0
module load openmpi/gcc/5.0.3
mpicc -fopenmp -Wl,-rpath,$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 mpirun (from the pinning is controlled by the MPI library. Pinning by slurm ) to start the binary you need to switch off slurm binding by adding export SLURM_CPU_BIND=none.
MPI only| Codeblock |
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| title | MPI, full node |
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| collapse | true |
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#!/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 |
| Codeblock |
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| title | MPI, half node |
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| collapse | true |
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#!/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.
| Codeblock |
|---|
| title | MPI, OpenMPI, full node |
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| collapse | true |
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#!/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
| Codeblock |
|---|
| title | MPI, full node |
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| collapse | true |
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#!/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.
| Codeblock |
|---|
| title | MPI, OpenMP, full node |
|---|
| collapse | true |
|---|
|
#!/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 |