a few comments for serial batch jobs

Author: jdherman

pbs-serial-batch/multi-jobs-per-proc.sh

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+#!/bin/bash
+#PBS -j oe
+#PBS -l nodes=4:ppn=2
+#PBS -l walltime=1:00:00
+
+cd $PBS_O_WORKDIR
+
+# Run 20 serial jobs, 8 at a time (using 8 processors)
+
+# define the total number of jobs here 
+num_serial_jobs=20
+num_procs=$(cat $PBS_NODEFILE | wc -l)
+count=0
+
+while [ $count -lt $num_serial_jobs ]
+do
+  rank_base=$count
+  count=`expr $count + $num_procs`
+  remain=`expr $num_serial_jobs - $count`
+  if [ $remain -lt 0 ]; then
+    run_count=`expr $num_serial_jobs % $num_procs`
+  else
+    run_count=$num_procs
+  fi
+  mpirun -np $run_count ./wrapper.sh $rank_base
+done

pbs-serial-batch/one-job-per-proc.sh

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+#!/bin/bash
+#PBS -j oe
+#PBS -l nodes=2:ppn=4
+#PBS -l walltime=1:00:00
+
+cd $PBS_O_WORKDIR
+num_procs=$(cat $PBS_NODEFILE | wc -l)
+
+# run the mpi process with total number of 8 processes ( 2 x 8 ) 
+# 'wrapper.sh' is the wrapper script for instructing mpi how to 
+# execute the program in batch 
+# '0' is the command line input that can be arbitrarily defined 
+mpirun -np $num_procs wrapper.sh 0 

pbs-serial-batch/wrapper.sh

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+#!/bin/bash
+# this the shell script for wrapping your program
+
+# 'rank' is taken from the MPI environment variable
+# for the 'multi-jobs' case, it also needs the command line argument $1
+rank=`expr ${OMPI_COMM_WORLD_RANK} + $1`
+
+# define your commands here
+echo "hello, this is processor ${rank}!" > output_${rank}.out