Refactored code scripts to use auxiliary scripts when performing similar...

Refactored code scripts to use auxiliary scripts when performing similar steps. Those tasks are getting the number of cores, initial hostlist and initial number of processes. Trace and Valgrind scripts are not fully tested.

Codes/runBase.sh

@@ -5,7 +5,11 @@
 #SBATCH --exclude=c01,c00,c02
 
 dir="/home/martini/malleability_benchmark"
+partition='P1'
+
 codeDir="/Codes"
+execDir="/Exec"
+cores=$(bash $dir$execDir/BashScripts/getCores.sh $partition)
 
 nodelist=$SLURM_JOB_NODELIST
 nodes=$SLURM_JOB_NUM_NODES
@@ -18,21 +22,14 @@ then
 fi
 
 echo "MPICH"
-#module load mpich-3.4.1-noucx
 #export HYDRA_DEBUG=1
 
-aux=$(grep "\[resize0\]" -n $configFile | cut -d ":" -f1)
-read -r ini fin <<<$(echo $aux)
-diff=$(( fin - ini ))
-numP=$(head -$fin $configFile | tail -$diff | cut -d ';' -f1 | grep Procs | cut -d '=' -f2)
-
-ls /home/martini/malleability_benchmark/Codes/build/a.out
-
-echo "Test PreRUN $numP $nodes"
-mpirun -np $numP $dir$codeDir/build/a.out $configFile $outIndex $nodelist $nodes
+numP=$(bash $dir$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
+initial_nodelist=$(bash $dir$execDir/BashScripts/createInitialNodelist.sh $numP $cores $nodelist)
+echo $initial_nodelist
+echo "Test PreRUN $numP $nodelist"
+mpirun -hosts $initial_nodelist -np $numP $dir$codeDir/build/a.out $configFile $outIndex $nodelist $nodes
 
 echo "END RUN"
 sed -i 's/application called MPI_Abort(MPI_COMM_WORLD, -100) - process/shrink cleaning/g' slurm-$SLURM_JOB_ID.out
 sed -i 's/Abort(-100)/shrink cleaning/g' slurm-$SLURM_JOB_ID.out
-
-

Codes/runTrace.sh

@@ -15,10 +15,7 @@ outIndex=$2
 
 echo "MPICH"
 
-aux=$(grep "\[resize0\]" -n $configFile | cut -d ":" -f1)
-read -r ini fin <<<$(echo $aux)
-diff=$(( fin - ini ))
-numP=$(head -$fin $configFile | tail -$diff | cut -d ';' -f1 | grep Procs | cut -d '=' -f2)
+numP=$(bash $dir$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
 
 name_res="Extrae_"$nodes"_Test_"$numP
 dir_name_res=$dir$resultsDir"/"$name_res
@@ -28,6 +25,7 @@ srun -n$numP --mpi=pmi2 ./trace.sh $dir$codeDir/a.out $configFile $outIndex $nod
 
 echo "END RUN"
 sed -i 's/application called MPI_Abort(MPI_COMM_WORLD, -100) - process/shrink cleaning/g' slurm-$SLURM_JOB_ID.out
+sed -i 's/Abort(-100)/shrink cleaning/g' slurm-$SLURM_JOB_ID.out
 rm hostfile.o$SLURM_JOB_ID
 
 echo "MOVING DATA"

Codes/runValgrind.sh

@@ -16,12 +16,9 @@ echo "MPICH"
 #module load mpich-3.4.1-noucx
 #export HYDRA_DEBUG=1
 
-aux=$(grep "\[resize0\]" -n $1 | cut -d ":" -f1)
-read -r ini fin <<<$(echo $aux)
-diff=$(( fin - ini ))
-numP=$(head -$fin $1 | tail -$diff | cut -d ';' -f1 | grep Procs | cut -d '=' -f2)
-
+numP=$(bash $dir$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
 mpirun -np $numP valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --trace-children=yes --log-file=nc.vg.%p $dir$codeDir/build/a.out $configFile $outIndex $nodelist $nodes
 
 echo "END RUN"
 sed -i 's/application called MPI_Abort(MPI_COMM_WORLD, -100) - process/shrink cleaning/g' slurm-$SLURM_JOB_ID.out
+sed -i 's/Abort(-100)/shrink cleaning/g' slurm-$SLURM_JOB_ID.out