Content
Code Compilation
For code compilation you can choose one of the two compilers Intel or Gnu. Both compilers are able to include the Intel MPI library.
Intel compiler
| Codeblock |
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| title | MPI, intel |
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| collapse | true |
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module load intel/2024.2
module load impi/2021.13
export I_MPI_CC=icx
mpiicc -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c |
| Codeblock |
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| title | MPI, OpenMP, intel |
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| collapse | true |
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module load intel/2024.2
module load impi/2021.13
export I_MPI_CC=icx
mpiicc -qopenmp -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c |
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,$LD_RUN_PATH -o hello.bin hello.c |
| Codeblock |
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| title | MPI, OpenMP, gnu |
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| collapse | true |
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module load gcc/13.3.0
module load openmpi/gcc/5.0.3
mpicc -fopenmp -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c |
Code execution
To execute your code you need to
- have a binary (executable, model code), which is the result of code compilation,
- create a slurm job script,
- submit the slurm jobs script.
| Codeblock |
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| title | Job submission |
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| collapse | true |
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blogin> sbatch myjobscipt.slurm
Submitted batch job 8028673
blogin> ls slurm-8028673.out
slurm-8028673.out |
A slurm script is submitted to the job scheduler slurm. It contains
- the control about requested compute nodes and
- commands to start your binary. 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 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 |
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.
| Codeblock |
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| 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 |