jobscript.pbs

#!/bin/bash --login

# PBS job options (name, compute nodes, job time)
#PBS -N q3d_no_beam
# The following should be 16, 32, 64, 128, 256 or 512
#PBS -l select=128
#PBS -l walltime=01:00:00
#PBS -m abe
#PBS -M email
#PBS -l place=scatter

# Replace [budget code] below with your project code (e.g. t01)
#PBS -A dp152            

# Change to the directory that the job was submitted from
cd $PBS_O_WORKDIR
  
# Load any required modules
module purge
module load packages-tesseract
module load intel-tools-18
module load hdf5-parallel/1.10.1-intel18

# Set the number of threads to 1
#   This prevents any threaded system libraries from automatically 
#   using threading.
export OMP_NUM_THREADS=1

echo "--------------------------------------------------"
echo "total nodes: $PBS_NODENUM                         "
echo "tasks per node: $PBS_TASKNUM                      "
echo "nodes: $PBS_NODEFILE                              "
echo "--------------------------------------------------"

# Launch the parallel job
# Using 6144 MPI processes and 24 MPI processes per node
# Adapt for your simulation
date
start_time="$(date -u +%s.%N)"

mpirun -n 3072 -ppn 24 --bind-to core /home/dp152/dp152/dc-clos1/osiris-dev/bin/osiris--2D.e /work/dp152/dp152/dc-clos1/q3d_no_beam.inp > my_stdout.txt 2> my_stderr.txt

touch completionTest

end_time="$(date -u +%s.%N)"
elapsed="$(bc <<<"$end_time-$start_time")"
echo "Total of $elapsed seconds elapsed for process"
date