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Running Multiple Sub-Jobs with One Job Script on the Eagle System

If your workload consists of serial or modestly parallel programs, you can run multiple instances of your program at the same time using different processor cores on a single node. This will allow you to make better use of your allocation because it will use the resources on the node that would otherwise be idle.

Example

For illustration, we use a simple C code to calculate pi. The source code and instructions for building that program are provided below:

cat << eof > pi.c
#include <stdio.h>

// pi.c: A sample C code calculating pi

main() {
 double x,h,sum = 0;
 int i,N;
printf("Input number of iterations: ");
 scanf("%d",&N);
 h=1.0/(double) N;

 for (i=0; i<N; i++) {
  x=h*((double) i + 0.5);
  sum += 4.0*h/(1.0+x*x);
 }

 printf("\nN=%d, PI=%.15f\n", N,sum);
}

eof

#Compile the code using the Intel C compiler
module purge
module load intel-mpi
icc -O2 pi.c -o pi_test
./pi_test

A sample batch job script file to run 8 copies of the pi_test program on a node with 24 processor cores is given below. This script creates 8 directories and starts 8 jobs, each in the background. It waits for all 8 jobs to complete before finishing.

#!/bin/bash
## Required Parameters ##############################################
#SBATCH --time 10:00   # WALLTIME limit of 10 minutes

## Double ## will cause SLURM to ignore the directive:
#SBATCH -A <handle> # Account (replace with appropriate)

#SBATCH -n 8 # ask for 8 tasks        
## Optional Parameters ##############################################
#SBATCH --job-name wait_test # name to display in queue
#SBATCH --output std.out
#SBATCH --error std.err

JOBNAME=$SLURM_JOB_NAME # re-use the job-name specified above

# Run 1 job per task
N_JOB=$SLURM_NTASKS # create as many jobs as tasks

for((i=1;i<=$N_JOB;i++))
do
mkdir $JOBNAME.run$i             # Make subdirectories for each job
cd $JOBNAME.run$i                # Go to job directory
echo 10*10^$i | bc > input       # Make input files
time ../pi_test < input > log &  # Run your executable, note the "&"
cd ..
done

#Wait for all
wait

echo
echo "All done. Checking results:"
grep "PI" $JOBNAME.*/log

To submit the batch script on Eagle, the Slurm sbatch command should be used:

$ sbatch -A <project-handle> <batch_file>