Merge branch 'master' of https://github.com/hpcraink/fsprj2

libiotrace/scripts/testscripts/config/config.sample

@@ -6,7 +6,9 @@ base_path="/home/es/es_es/<username>/<path>"
 # test_mpi_file_io_2
 # test_posix_file_io_random
 # test_openFOAM_VirgilioRe22Pr7_Perfomance_2_worker
+# test_openFOAM_VirgilioRe22Pr7_Perfomance_2_worker_measurement
 # test_openFOAM_VirgilioRe22Pr7_Perfomance_4_worker
+# test_python_simple_write
 test_config="test_mpi_file_io"
 
 export test_base_script_dir="$(dirname "$0")"

libiotrace/scripts/testscripts/config/test_mpi_file_io

@@ -25,6 +25,7 @@ test_libiotrace_cmake_options=(
 # slurm
 test_nodes=3
 test_processes_per_worker=40
+export test_processes_per_influxdb=40
 test_mem="90000mb"
 test_time="00:10:00"
 test_queue_name="dev_multiple"

libiotrace/scripts/testscripts/config/test_mpi_file_io_2

@@ -25,6 +25,7 @@ test_libiotrace_cmake_options=(
 # slurm
 test_nodes=3
 test_processes_per_worker=40
+export test_processes_per_influxdb=40
 test_mem="90000mb"
 test_time="00:10:00"
 test_queue_name="dev_multiple"

libiotrace/scripts/testscripts/config/test_openFOAM_VirgilioRe22Pr7_Perfomance_2_worker

@@ -27,6 +27,7 @@ test_libiotrace_cmake_options=(
 # slurm
 test_nodes=3
 test_processes_per_worker=40
+export test_processes_per_influxdb=40
 test_mem="249600mb"
 test_time="00:30:00"
 test_queue_name="dev_multiple_il"

libiotrace/scripts/testscripts/config/test_openFOAM_VirgilioRe22Pr7_Perfomance_2_worker_measurement

@@ -0,0 +1,79 @@
+# dependencies
+test_source_configs=("influxdb" "gcc_mpi" "openfoam_com_2106")
+test_source=("${test_openfoam_dir}/etc/bashrc")
+test_modules=("compiler/gnu/${test_gcc_version}" "mpi/openmpi/${test_mpi_version}")
+test_file_url=("https://bwsyncandshare.kit.edu/s/MQfkypzfHfmZZtM/download VirgilioRe22Pr7_Perfomance.zip")
+test_unzip_files=("VirgilioRe22Pr7_Perfomance.zip")
+
+# libiotrace
+test_libiotrace_cmake_options=(
+-DALL_WRAPPERS_ACTIVE=OFF
+-DENABLE_FILESYSTEM_METADATA=OFF
+-DENABLE_OUTPUT=INFLUXDB
+-DENABLE_REMOTE_CONTROL=OFF
+-DFILENAME_RESOLUTION_ENABLED=OFF
+-DLOGGING=OFF
+-DLOG_WRAPPER_TIME=OFF
+-DREALTIME=ON
+-DSENDING=ON
+-DWITH_ALLOC=OFF
+-DWITH_DL_IO=OFF
+-DWITH_MPI_IO=OFF
+-DWITH_POSIX_AIO=OFF
+-DWITH_POSIX_IO=ON
+-DWITH_STD_IO=OFF
+)
+
+# slurm
+test_nodes=3
+test_processes_per_worker=40
+export test_processes_per_influxdb=80
+test_mem="249600mb"
+test_time="05:00:00"
+test_queue_name="multiple_il"
+
+# test script
+test_script="./openFOAM_VirgilioRe22Pr7_Perfomance_measurement.sh"
+export test_source_dir="${PWD}/VirgilioRe22Pr7_Perfomance"
+export test_source_1="${test_source_dir}/1"
+export test_source_constant="${test_source_dir}/constant"
+export test_source_system="${test_source_dir}/system"
+export test_end_time=1.001
+export test_iterations=20
+# newline separated list of functions to trace
+#export IOTRACE_WHITELIST_FUNCTIONS=""
+export IOTRACE_WHITELIST_FUNCTIONS="
+read
+pread
+pread64
+write
+pwrite
+pwrite64
+readv
+writev
+preadv
+preadv64
+pwritev
+pwritev64
+preadv2
+preadv64v2
+pwritev2
+pwritev64v2
+copy_file_range
+getline
+getdelim
+fread
+fwrite
+fprintf
+fwprintf
+vfprintf
+vfwprintf
+fscanf
+fwscanf
+vfscanf
+vfwscanf"
+
+# output
+test_name="3_nodes_VirgilioRe22Pr7_Perfomance"
+export IOTRACE_LOG_NAME=openFOAM_VirgilioRe22Pr7_Perfomance_test1
+export performance_data_file=${PWD}/performance_test

libiotrace/scripts/testscripts/config/test_openFOAM_VirgilioRe22Pr7_Perfomance_4_worker

@@ -27,6 +27,7 @@ test_libiotrace_cmake_options=(
 # slurm
 test_nodes=5
 test_processes_per_worker=40
+export test_processes_per_influxdb=40
 test_mem="249600mb"
 test_time="00:30:00"
 test_queue_name="multiple_il"

libiotrace/scripts/testscripts/config/test_openFOAM_VirgilioRe22Pr7_Perfomance_4_worker_measurement

@@ -0,0 +1,79 @@
+# dependencies
+test_source_configs=("influxdb" "gcc_mpi" "openfoam_com_2106")
+test_source=("${test_openfoam_dir}/etc/bashrc")
+test_modules=("compiler/gnu/${test_gcc_version}" "mpi/openmpi/${test_mpi_version}")
+test_file_url=("https://bwsyncandshare.kit.edu/s/MQfkypzfHfmZZtM/download VirgilioRe22Pr7_Perfomance.zip")
+test_unzip_files=("VirgilioRe22Pr7_Perfomance.zip")
+
+# libiotrace
+test_libiotrace_cmake_options=(
+-DALL_WRAPPERS_ACTIVE=OFF
+-DENABLE_FILESYSTEM_METADATA=OFF
+-DENABLE_OUTPUT=INFLUXDB
+-DENABLE_REMOTE_CONTROL=OFF
+-DFILENAME_RESOLUTION_ENABLED=OFF
+-DLOGGING=OFF
+-DLOG_WRAPPER_TIME=OFF
+-DREALTIME=ON
+-DSENDING=ON
+-DWITH_ALLOC=OFF
+-DWITH_DL_IO=OFF
+-DWITH_MPI_IO=OFF
+-DWITH_POSIX_AIO=OFF
+-DWITH_POSIX_IO=ON
+-DWITH_STD_IO=OFF
+)
+
+# slurm
+test_nodes=5
+test_processes_per_worker=40
+export test_processes_per_influxdb=80
+test_mem="249600mb"
+test_time="03:00:00"
+test_queue_name="multiple_il"
+
+# test script
+test_script="./openFOAM_VirgilioRe22Pr7_Perfomance_measurement.sh"
+export test_source_dir="${PWD}/VirgilioRe22Pr7_Perfomance"
+export test_source_1="${test_source_dir}/1"
+export test_source_constant="${test_source_dir}/constant"
+export test_source_system="${test_source_dir}/system"
+export test_end_time=1.001
+export test_iterations=20
+# newline separated list of functions to trace
+#export IOTRACE_WHITELIST_FUNCTIONS=""
+export IOTRACE_WHITELIST_FUNCTIONS="
+read
+pread
+pread64
+write
+pwrite
+pwrite64
+readv
+writev
+preadv
+preadv64
+pwritev
+pwritev64
+preadv2
+preadv64v2
+pwritev2
+pwritev64v2
+copy_file_range
+getline
+getdelim
+fread
+fwrite
+fprintf
+fwprintf
+vfprintf
+vfwprintf
+fscanf
+fwscanf
+vfscanf
+vfwscanf"
+
+# output
+test_name="3_nodes_VirgilioRe22Pr7_Perfomance"
+export IOTRACE_LOG_NAME=openFOAM_VirgilioRe22Pr7_Perfomance_test1
+export performance_data_file=${PWD}/performance_test

libiotrace/scripts/testscripts/config/test_openFOAM_motorBike

@@ -25,6 +25,7 @@ test_libiotrace_cmake_options=(
 # slurm
 test_nodes=3
 test_processes_per_worker=16
+export test_processes_per_influxdb=40
 test_mem="90000mb"
 test_time="00:10:00"
 test_queue_name="dev_multiple"

libiotrace/scripts/testscripts/config/test_posix_file_io_random

@@ -25,6 +25,7 @@ test_libiotrace_cmake_options=(
 # slurm
 test_nodes=3
 test_processes_per_worker=2
+export test_processes_per_influxdb=40
 test_mem="90000mb"
 test_time="00:20:00"
 test_queue_name="dev_multiple"

libiotrace/scripts/testscripts/config/test_python_simple_write

@@ -0,0 +1,36 @@
+# dependencies
+test_source_configs=("influxdb")
+
+# libiotrace
+test_libiotrace_cmake_options=(
+-DALL_WRAPPERS_ACTIVE=ON
+-DENABLE_FILESYSTEM_METADATA=OFF
+-DENABLE_OUTPUT=INFLUXDB
+-DENABLE_REMOTE_CONTROL=OFF
+-DFILENAME_RESOLUTION_ENABLED=OFF
+-DLOGGING=OFF
+-DLOG_WRAPPER_TIME=OFF
+-DREALTIME=ON
+-DSENDING=ON
+-DWITH_ALLOC=OFF
+-DWITH_DL_IO=OFF
+-DWITH_MPI_IO=OFF
+-DWITH_POSIX_AIO=OFF
+-DWITH_POSIX_IO=ON
+-DWITH_STD_IO=OFF
+)
+
+# slurm
+test_nodes=2
+test_processes_per_worker=1
+export test_processes_per_influxdb=40
+test_mem="90000mb"
+test_time="00:30:00"
+test_queue_name="dev_multiple"
+
+# test script
+test_script="./python_simple_write.sh"
+
+# output
+test_name="2_nodes_python_simple_write"
+export IOTRACE_LOG_NAME=python_simple_write_test1

libiotrace/scripts/testscripts/manage_db_and_worker_nodes.sh

@@ -64,7 +64,7 @@ export PATH="$PWD:$PATH"
 rm -f ${GLOBAL_TMP_DIR}/ib0_${TEST_NAME}
 
 # start influxDB
-bash -c "srun -N 1 -n 1 -w $DBNODE bash -c \"export PATH="${PATH}" && ${test_base_script_dir}/runs_on_db_node.sh ${TEST_NAME} ${INFLUXDB_DIR} ${GLOBAL_TMP_DIR}\"" &
+bash -c "srun -N 1 -n 1 -c ${test_processes_per_influxdb} -w $DBNODE bash -c \"export PATH="${PATH}" && ${test_base_script_dir}/runs_on_db_node.sh ${TEST_NAME} ${INFLUXDB_DIR} ${GLOBAL_TMP_DIR}\"" &
 echo "influxDB starting on node ${DBNODE}"
 
 # wait until influxDB is started

libiotrace/scripts/testscripts/tests/openFOAM_VirgilioRe22Pr7_Perfomance_measurement.sh

@@ -0,0 +1,106 @@
+#!/bin/bash
+IOTRACE_DATABASE_IP=$1
+MPI_PATH=$(which mpirun)
+MPI_PATH="${MPI_PATH%/*}/../lib64/libmpi.so"
+IOTRACE_LD_PRELOAD=${MPI_PATH}:${test_libiotrace_so}
+IOTRACE_WHITELIST=${3}/${2}/whitelist
+
+format="\t%E\t%U\t%S\t%D\t%K\t%M"
+
+PROCESS_COUNT=$(( ${5} * ${6} ))
+echo "    process count: ${PROCESS_COUNT}"
+
+# source tutorial run functions
+echo "    source tutorial run functions"
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+# copy testcase to test directory
+echo "    copy test case"
+rm -rf ${3}/${2}
+mkdir -p ${3}/${2}
+ln -s ${test_source_1} ${3}/${2}/
+ln -s ${test_source_constant} ${3}/${2}/
+cp -r ${test_source_system} ${3}/${2}/
+
+# patch test case
+echo "    patch test case (use ${PROCESS_COUNT} subdomains with ${PROCESS_COUNT} processes)"
+sed -i -r "s:^numberOfSubdomains 280;:numberOfSubdomains  ${PROCESS_COUNT};:" "${3}/${2}/system/decomposeParDict"
+case ${PROCESS_COUNT} in
+    4)
+        SUBDOMAINS="2 2 1"
+        ;;
+    20)
+        SUBDOMAINS="20 1 1"
+        ;;
+    40)
+        SUBDOMAINS="40 1 1"
+        ;;
+    80)
+        SUBDOMAINS="80 1 1"
+        ;;
+    160)
+        SUBDOMAINS="160 1 1"
+        ;;
+    168)
+        SUBDOMAINS="168 1 1"
+        ;;
+    320)
+        SUBDOMAINS="320 1 1"
+        ;;
+    *)
+        echo "unknown subdomain count: ${PROCESS_COUNT}"
+        exit 1
+        ;;
+esac
+sed -i -r "s:^    n               \(168 1 1\);:    n               (${SUBDOMAINS});:" "${3}/${2}/system/decomposeParDict"
+sed -i -r "s:^SimuEnd\t\t100;:SimuEnd         ${test_end_time};:" "${3}/${2}/system/controlDict"
+
+# prepare whitelist
+rm -f $IOTRACE_WHITELIST
+# prepare output file
+rm -f ${performance_data_file}
+echo -e "name\ttest\treal h:m:s\tuser CPU-seconds\tsys CPU-seconds\tavg unshared data kb\tavg data+stack+text kb\tmax kb">>${performance_data_file}
+
+# define libiotrace and necessary environment variables for use with and without mpirun
+LIBIOTRACE_WITH_ENV="IOTRACE_LOG_NAME=$IOTRACE_LOG_NAME IOTRACE_DATABASE_IP=$IOTRACE_DATABASE_IP IOTRACE_DATABASE_PORT=$IOTRACE_INFLUX_PORT IOTRACE_INFLUX_ORGANIZATION=$IOTRACE_INFLUX_ORGANIZATION IOTRACE_INFLUX_BUCKET=$IOTRACE_INFLUX_BUCKET IOTRACE_INFLUX_TOKEN=$IOTRACE_INFLUX_TOKEN IOTRACE_WHITELIST=$IOTRACE_WHITELIST LD_PRELOAD=$IOTRACE_LD_PRELOAD"
+MPI_LIBIOTRACE_WITH_ENV="-x "${LIBIOTRACE_WITH_ENV// / -x }
+
+# start test
+echo "    start test"
+echo "        running redistributePar"
+#cd ${3}/${2}/ && mpirun -N ${6} -H ${4} -np ${PROCESS_COUNT} ${MPI_LIBIOTRACE_WITH_ENV} redistributePar -decompose -parallel < /dev/null > log.redistributePar 2>&1
+cd ${3}/${2}/ && mpirun -N ${6} -H ${4} -np ${PROCESS_COUNT} redistributePar -decompose -parallel < /dev/null > log.redistributePar 2>&1
+
+# test with libiotrace and POSIX functions in whitelist
+echo -e "${IOTRACE_WHITELIST_FUNCTIONS}">$IOTRACE_WHITELIST
+for ((i = 0; i < test_iterations; i += 1)); do
+    echo "        running buoyantPimpleFoam"
+    cd ${3}/${2}/ && /usr/bin/time -o ${performance_data_file} -a -f "posix_active\t$i$format" mpirun -N ${6} -H ${4} -np ${PROCESS_COUNT} ${MPI_LIBIOTRACE_WITH_ENV} buoyantPimpleFoam -parallel < /dev/null > log.buoyantPimpleFoam 2>&1
+    rm -rf ${3}/${2}/processor[0-9]*/1.*
+    rm -f log.*
+    rm -rf postProcessing
+done
+echo "    with libiotrace and active wrapper: done"
+
+# test with libiotrace and empty whitelist
+echo -e "">$IOTRACE_WHITELIST
+for ((i = 0; i < test_iterations; i += 1)); do
+    echo "        running buoyantPimpleFoam"
+    cd ${3}/${2}/ && /usr/bin/time -o ${performance_data_file} -a -f "all_inactive\t$i$format" mpirun -N ${6} -H ${4} -np ${PROCESS_COUNT} ${MPI_LIBIOTRACE_WITH_ENV} buoyantPimpleFoam -parallel < /dev/null > log.buoyantPimpleFoam 2>&1
+    rm -rf ${3}/${2}/processor[0-9]*/1.*
+    rm -f log.*
+    rm -rf postProcessing
+done
+echo "    with libiotrace and inactive wrapper: done"
+
+# test without libiotrace
+for ((i = 0; i < test_iterations; i += 1)); do
+    echo "        running buoyantPimpleFoam"
+    cd ${3}/${2}/ && /usr/bin/time -o ${performance_data_file} -a -f "without_libiotrace\t$i$format" mpirun -N ${6} -H ${4} -np ${PROCESS_COUNT} buoyantPimpleFoam -parallel < /dev/null > log.buoyantPimpleFoam 2>&1
+    rm -rf ${3}/${2}/processor[0-9]*/1.*
+    rm -f log.*
+    rm -rf postProcessing
+done
+echo "    without libiotrace: done"
+
+rm -f $IOTRACE_WHITELIST

libiotrace/scripts/testscripts/tests/python_simple_write.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+IOTRACE_DATABASE_IP=$1
+IOTRACE_LD_PRELOAD=${test_libiotrace_so}
+
+# define libiotrace and necessary environment variables 
+LIBIOTRACE_WITH_ENV="IOTRACE_LOG_NAME=$IOTRACE_LOG_NAME IOTRACE_DATABASE_IP=$IOTRACE_DATABASE_IP IOTRACE_DATABASE_PORT=$IOTRACE_INFLUX_PORT IOTRACE_INFLUX_ORGANIZATION=$IOTRACE_INFLUX_ORGANIZATION IOTRACE_INFLUX_BUCKET=$IOTRACE_INFLUX_BUCKET IOTRACE_INFLUX_TOKEN=$IOTRACE_INFLUX_TOKEN IOTRACE_WHITELIST=$IOTRACE_WHITELIST LD_PRELOAD=$IOTRACE_LD_PRELOAD"
+
+# start test
+echo "    start test"
+python_script='import os
+import time
+
+data_size = 1 << 30
+data_buffer = bytearray(data_size)
+start_time = time.time()
+
+with open("output.txt", "wb") as file:
+    file.write(data_buffer)
+
+end_time = time.time()
+
+os.remove("output.txt")
+
+elapsed_time = end_time - start_time
+print(f"Wrote {data_size} bytes to file in {elapsed_time:.4f} seconds.")
+'
+python3 -c "${python_script}"
+env ${LIBIOTRACE_WITH_ENV} python3 -c "${python_script}"