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.
...
| title | Job submission |
|---|
| collapse | true |
|---|
...
For examples for code execution, please visit Slurm partition CPU CLX.
Code compilation
For code compilation please use Gnu gnu compiler.
| Codeblock |
|---|
| title | MPI, gnu |
|---|
| collapse | true |
|---|
|
module load gcc/13.3.0
module load openmpi/gcc/5.0.3
mpicc -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c |
...
| Codeblock |
|---|
| title | MPI, OpenMP, gnu |
|---|
| collapse | true |
|---|
|
module load gcc/13.3.0
module load openmpi/gcc/5.0.3
mpicc -fopenmp -Wl,-rpath,$LD_RUN_PATH -o hello.bin hello.c |
Slurm job script
A slurm script is submitted to the job scheduler slurm. It contains
- the control about requested request for compute nodes andof 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 MPI library) to start the binary you need to switch off slurm binding by adding export SLURM_CPU_BIND=none.
| Codeblock |
|---|
| title | MPI, full node |
|---|
| collapse | true |
|---|
|
#!/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 |
|---|
| title | MPI, half node |
|---|
| collapse | true |
|---|
|
#!/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, OpenMPYou 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 |
|---|
| collapse | true |
|---|
|
#!/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 |
|---|
| collapse | true |
|---|
|
#!/bin/bash
#SBATCH --nodes=2
#SBATCH --partition=cpu-clx:test
srun --ntasks-per-node=96 ./hello.bin |
...