Content
Code Compilation
For code compilation you can choose one of the two compilers - Intel oneAPI or GnuGNU. Both compilers are able to include the Intel MPI library.
Intel one API compiler
| Codeblock |
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| title | plain MPI, icc |
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| collapse | true |
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module load intel/19.0.5
module load impi/2019.5
mpiiccmpiicx -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c
mpiifortmpiifx -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.f90
mpiicpcmpiicpx -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.cpp |
| Codeblock |
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| title | hybrid MPI, /OpenMP, icc |
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| collapse | true |
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module load intel/19.0.5
module load impi/2019.5
mpiiccmpiicx -qopenmpfopenmp -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c
mpiifortmpiifx -qopenmpfopenmp -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.f90
mpiicpcmpiicpx -qopenmpfopenmp -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.cpp |
...
GNU compiler
| Codeblock |
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| title | plain MPI, gcc |
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| collapse | true |
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module load gcc/9.3.0
module load impi/2019.5
mpigcc -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c
mpif90 -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.f90
mpigxx -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.cpp |
| Codeblock |
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| title | hybrid MPI, /OpenMP gcc |
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| collapse | true |
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module load gcc/9.3.0
module load impi/2019.5
mpigcc -fopenmp -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c
mpif90 -fopenmp -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.f90
mpigxx -fopenmp -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.cpp |
Slurm job script
You need to start the MPI parallelized code on the system. You can choose between two approaches, namely
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Using mpirun
Using mpirun the pinning is controlled by the MPI library. Pinning by slurm SLURM you need to switch off 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=standard96:test
module load impi/2019.5
export SLURM_CPU_BIND=none
mpirun -ppn 96 ./hello.bin |
...
| Codeblock |
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| title | MPI, hyperthreading |
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| collapse | true |
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#!/bin/bash
#SBATCH --nodes=2
#SBATCH --partition=standard96:test
module load impi/2019.5
export SLURM_CPU_BIND=none
mpirun -ppn 192 ./hello.bin |
MPI, OpenMP
You can run one code compiled with MPI and OpenMP. The examples cover the setup
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| Codeblock |
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| title | MPI, OpenMP hyperthreading |
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| collapse | true |
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#!/bin/bash
#SBATCH --nodes=2
#SBATCH --partition=standard96:test
module load impi/2019.5
export SLURM_CPU_BIND=none
export OMP_PROC_BIND=spread
export OMP_NUM_THREADS=48
mpirun -ppn 4 ./hello.bin |
Using srun
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=standard96:test
srun --ntasks-per-node=96 ./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=standard96:test
srun --ntasks-per-node=48 ./hello.bin |
MPI, OpenMP
You can run one code compiled with MPI and OpenMP. The example covers the setup
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