5.22. SALMON

Following version is available.

version	module	execution queue
2.2.2	/work/app/SALMON/SALMON_v2.2.2/bin/salmon	P_030 TP_002 MP_001 CP_001 DP_002 S_001 CS_001

Attention

Execute following command in advance.

module load oneapi/2025.3.1

• Job Submission Script

#!/bin/sh
#PBS -l select=nodes
#PBS -q queue
#PBS -N jobname

module -s load oneapi/2025.3.1

cd ${PBS_O_WORKDIR}

mpirun [ -np total tasks ][ -ppn MPI tasks per node ] -hostfile $PBS_NODEFILE /work/app/SALMON/SALMON_v2.2.2/bin/salmon < input file > output file 2> error file

• Example

Hybrid parallelization

#!/bin/sh
#PBS -l select=1
#PBS -q P_030
#PBS -N salmon

module -s load oneapi/2025.3.1
export OMP_NUM_THREADS=2

cd ${PBS_O_WORKDIR}

mpirun -np 56 -ppn 56 -hostfile $PBS_NODEFILE /work/app/SALMON/SALMON_v2.2.2/bin/salmon < input.inp > salmon.out 2> salmon.err

MPI parallelization

#!/bin/sh
#PBS -l select=1
#PBS -q P_030
#PBS -N salmon

module -s load oneapi/2025.3.1

cd ${PBS_O_WORKDIR}

mpirun -np 112 -ppn 112 -hostfile $PBS_NODEFILE /work/app/SALMON/SALMON_v2.2.2/bin/salmon < input.inp > salmon.out 2> salmon.err