READEX scripts for autofilter, dyndetect and PTF

OpenFOAM-v1612+/tutorials/incompressible/simpleFoam/motorBike/do_ptf.sh

+#!/bin/sh
+
+#SBATCH --time=00:30:00   # walltime
+#SBATCH --nodes=2  # number of processor cores (i.e. tasks)
+#SBATCH --ntasks=24
+#SBATCH --tasks-per-node=24
+#SBATCH --cpus-per-task=1
+#SBATCH --exclusive
+#SBATCH --partition=haswell
+#SBATCH --comment="cpufreqchown"
+#SBATCH --cpu-freq=Low
+#SBATCH --mem-per-cpu=2500M   # memory per CPU core
+#SBATCH -J "PTFfoam"   # job name
+#SBATCH --mail-user=ondrej.vysocky@vsb.cz   # email address
+#SBATCH --mail-type=ALL
+#SBATCH -A p_readex
+
+handle_error() {
+        if [ $1 != 0 ]; then
+                echo "Error from job_build.sh on $2."
+                exit 1
+        fi
+}
+
+#module purge
+#module use /projects/p_readex/modules
+#module load readex/ci_readex_bullxmpi1.2.8.4_gcc5.3.0
+
+#source env/set_env_es_rrl
+#source env/paths.default
+#source env/threading.openmp 1
+#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
+
+cd $HOME/OpenFOAM
+source $HOME/OpenFOAM/FOAMMODULES-ScorepGCC-Taurus.sh
+cd $HOME/OpenFOAM/OpenFOAM-v1612+/tutorials/incompressible/simpleFoam/motorBike
+
+export SCOREP_SUBSTRATE_PLUGINS=rrl
+export SCOREP_RRL_PLUGINS=cpu_freq_plugin,uncore_freq_plugin
+export SCOREP_RRL_VERBOSE="WARN"
+
+#module load scorep-hdeem/sync-2017-01-31-git-hdeem2.2.20ms-xmpi-gcc5.3
+#module load scorep-uncore
+module load scorep-hdeem/sync-2017-04-13-git-hdeem2.2.20ms-xmpi-gcc6.3
+export SCOREP_METRIC_PLUGINS=hdeem_sync_plugin
+export SCOREP_METRIC_HDEEM_SYNC_PLUGIN_CONNECTION="INBAND"
+export SCOREP_METRIC_HDEEM_SYNC_PLUGIN_VERBOSE="WARN"
+export SCOREP_METRIC_HDEEM_SYNC_PLUGIN_STATS_TIMEOUT_MS=1000
+
+#module load valgrind
+
+export SCOREP_MPI_ENABLE_GROUPS=ENV
+
+export SCOREP_FILTERING_FILE=scorep.filt
+
+#export OMP_NUM_THREADS=1
+#psc_frontend --apprun="./miniMD_openmpi -i in2.data" --mpinumprocs=8 --ompnumthreads=1 --phase=INTEGRATE_RUN_LOOP --tune=readex_tuning --config-file=readex_config.xml --info=20 --force-localhost --selective-info=AutotuneAll,AutotunePlugins
+#psc_frontend --apprun="./miniMD_openmpi -i in2.data" --mpinumprocs=8 --ompnumthreads=1 --phase=INTEGRATE_RUN_LOOP --tune=readex_tuning --config-file=readex_config.xml --force-localhost #--info=20 --selective-info=AutotuneAll,AutotunePlugins
+psc_frontend --apprun="simpleFoam -parallel" --mpinumprocs=24 --ompnumthreads=1 --phase=iteration --tune=readex_tuning --config-file=readex_config_extended.xml --force-localhost --info=7 --selective-info=AutotuneAll,AutotunePlugins
+handle_error $? "\"sh -l job_psc.sh\""
+
+# $1 = mpi procs
+# $2 = omp threads
+# $3 = input file name
+# $4 = -t for scorep_autofilter
+# $5 = phase region for readex-dyn-detect and psc_frontend
+# $6 = -t for readex-dyn-detect
+# $7 = -c for readex-dyn-detect
+# $8 = -v for readex-dyn-detect
+# $9 = -w for readex-dyn-detect

OpenFOAM-v1612+/tutorials/incompressible/simpleFoam/motorBike/do_readex_dyn_detect.sh

+#!/bin/sh
+
+cp ../scorep.filt .
+
+#source ../environment.sh
+#module use /projects/p_readex/modules
+#module load ptf/ci_readex_bullxmpi1.2.8.4_gcc5.3.0_slurm_starter_with_scorep
+
+export SCOREP_ENABLE_TRACING=false
+export SCOREP_ENABLE_PROFILING=true
+export SCOREP_TOTAL_MEMORY=3G
+export SCOREP_FILTERING_FILE="$(pwd)/scorep.filt"
+
+export SCOREP_PROFILING_FORMAT=cube_tuple
+export SCOREP_METRIC_PAPI=PAPI_TOT_INS,PAPI_L3_TCM
+export SCOREP_FILTERING_FILE=scorep.filt
+
+echo "running simpleFoam for readex-dyn-detect"
+# run the application.. update this line for different applications
+#srun -n 24 ./kripke $KRIPKE_COMMAND
+srun -n 24 simpleFoam -parallel
+echo "running simpleFoam done"
+
+echo "running readex-dyn-detect"
+#echo "phase region = $2"
+#readex-dyn-detect -t $1 -p $2 -c $3 -v $4 -w $5 scorep-*/profile.cubex
+#readex-dyn-detect -t $1 -p $2 scorep-*/profile.cubex
+readex-dyn-detect -p "iteration" -t 0.001 scorep-*/profile.cubex
+echo
+echo "running readex-dyn-detect done" 
+
+echo "extending readex_config.xml"
+#module switch python/2.7 python
+#python3 add_tuning_settings.py -i readex_config.xml -o readex_config_extended.xml
+#module switch python python/2.7
+echo "extension done"
+
+cp -R scorep-* ../
+cp readex_config.xml ../
+cp readex_config_extended.xml ../

OpenFOAM-v1612+/tutorials/incompressible/simpleFoam/motorBike/do_scorep_autofilter_loop.sh

+#!/bin/sh
+
+#source ../environment.sh
+
+export SCOREP_ENABLE_TRACING=false
+export SCOREP_ENABLE_PROFILING=true
+export SCOREP_TOTAL_MEMORY=3G
+export SCOREP_PROFILING_FORMAT=cube_tuple
+export SCOREP_METRIC_PAPI=PAPI_TOT_INS,PAPI_L3_TCM
+
+export SCOREP_FILTERING_FILE=scorep.filt
+#export LD_LIBRARY_PATH=/sw/global/compilers/intel/2016/compilers_and_libraries_2016/linux/lib/intel64
+
+rm -rf scorep-*
+rm -f old_scorep.filt
+echo "" > scorep.filt
+
+result=1
+while [ $result != 0 ]; do
+  echo "result = "$result
+  # run the application.. update this for different applications
+  #mpirun -np $3 ./miniMD_openmpi -i $2 1>/dev/null
+#  srun -n 24 ./kripke --procs 2,2,6 --niter 20 --nest GZD --zones 4,4,4 --groups 200
+#  srun -n 24 ./kripke --procs 2,2,6 --niter 10 --nest GZD --zones 32,32,32 --legendre 8 --dset 32
+  #srun -n 24 ./kripke $KRIPKE_COMMAND #--procs 2,2,6 --niter 10 --nest GZD --zones 64,64,64 --legendre 8 --dset 32
+  srun -n 24 simpleFoam -parallel
+  echo "ITERATION done."
+  sh -l do_scorep_autofilter_single.sh 1.0 #$1
+  result=$?
+  echo "scorep_autofilter_singe done ($result)."
+
+  result=0
+
+done
+echo "end." 
+
+cp scorep.filt ../

OpenFOAM-v1612+/tutorials/incompressible/simpleFoam/motorBike/do_scorep_autofilter_single.sh

+#!/bin/sh
+
+cp scorep.filt old_scorep.filt
+
+scorep-autofilter -t $1 -f scorep scorep-*/profile.cubex # 1>/dev/null
+echo "#############"
+cat scorep.filt
+echo "#############"
+
+#rm -rf scorep-*
+commString=$(comm -1 -2 scorep.filt old_scorep.filt)
+if [ "$commString" == "" ]; then
+  cp scorep.filt old_scorep.filt
+  exit 1
+else
+  filtFileBeginString="SCOREP_REGION_NAMES_BEGIN"
+  filtFileEndString="SCOREP_REGION_NAMES_END"
+  filtFileExcludeString="EXCLUDE"        
+  sort scorep.filt > sorted_scorep.filt
+  sort old_scorep.filt > sorted_old_scorep.filt
+  commString=$(comm -2 -3 sorted_scorep.filt sorted_old_scorep.filt)
+  if [ "$commString" != "" ]; then
+    echo $filtFileBeginString > new_scorep.filt
+    echo $filtFileExcludeString >> new_scorep.filt
+    comm -2 -3 sorted_scorep.filt sorted_old_scorep.filt > comm1.txt
+    exec < "old_scorep.filt"
+    while read line; do
+      if [ "$line" != "$filtFileEndString" ] && [ "$line" != "$filtFileBeginString" ] && [ "$line" != "$filtFileExcludeString" ]; then
+        echo $line >> new_scorep.filt
+      fi
+    done
+    cat comm1.txt >> new_scorep.filt
+    echo $filtFileEndString >> new_scorep.filt
+    mv new_scorep.filt scorep.filt
+    rm -f sorted_scorep.filt sorted_old_scorep.filt comm1.txt
+    echo "++++++++++++"
+    echo $commString
+    echo "++++++++++++"
+    exit 1
+  else
+    mv old_scorep.filt scorep.filt
+    rm -f sorted_scorep.filt sorted_old_scorep.filt comm1.txt
+    echo "++++++++++++"
+    echo $commString
+    echo "++++++++++++"
+    exit 0
+  fi
+fi
+