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Jenkinsfile
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#!/usr/bin/groovy
def printVariation(def it) {
println ("Variation: " +
"VECTORIZE_CODE is " + it[0] + " \n" +
"TARGET is " + it[1] + " \n" +
"OPENMP is " + it[2] + " \n" +
"PARTYPE is " + it[3] + " \n" +
"PRECISION is " + it[4] + " \n" +
"REDUCED_MEMORY_MODE is " + it[5] + " \n")
}
def ciMatrix = [
["SSE",
"NOVEC",
"AVX",
"AVX2",
// "KNL_MASK",
// "KNL_G_S",
], // VECTORIZE_CODE
["DEBUG","RELEASE"], // TARGET
["0","1"], // OPENMP
["PAR","SEQ"], // PARTYPE
["DOUBLE","SINGLE","MIXED"], // PRECISION
["0","1"] // REDUCED_MEMORY_MODE
]
def combinationFilter(def it) {
def VECTORIZE_CODE = it[0]
def TARGET = it[1]
def OPENMP = it[2]
def PARTYPE = it[3]
def PRECISION = it[4]
def REDUCED_MEMORY_MODE = it[5]
return (
( // 42
TARGET=="RELEASE" && OPENMP=="1" && PARTYPE=="PAR"
) ||
( // 16
VECTORIZE_CODE=="AVX2" && PRECISION=="DOUBLE"
)
)
}
// Holds the build results
def results = [:]
// Needed due to scope issues with global variables in groovy
def getKnlJobid() {
def ret = sh(
returnStdout: true,
script: 'export SLURM_CONF=$HOME/slurm.conf && squeue -O jobid | sed -n 2p'
).replace("\n", "")
println ret
return ret
}
// Needed due to scope issues with global variables in groovy
def getKnlJobstate(def knl_jobid) {
def ret = sh(
returnStdout: true,
script: 'export SLURM_CONF=$HOME/slurm.conf && squeue -j $knl_jobid -O state | sed -n 2p'
).replace("\n", "")
println ret
return ret
}
pipeline {
agent none
options {
buildDiscarder logRotator(artifactDaysToKeepStr: '7', artifactNumToKeepStr: '1', daysToKeepStr: '7', numToKeepStr: '2')
skipDefaultCheckout true
skipStagesAfterUnstable()
timeout(activity: true, time: 3, unit: 'HOURS')
}
stages{
stage('fetch git repo') {
agent { label 'atsccs11_prio' }
steps {
checkout scm
stash 'repo'
}
}
stage('check ADIOS2 integration') {
agent { label 'atsccs11' }
stages {
stage('build with ADIOS2 sequential') {
steps {
unstash 'repo'
dir ("build_adios"){
sh """
cmake -DENABLE_ADIOS2=ON -DENABLE_UNIT_TESTS=1 ..
make -j4
"""
}
stash includes: "build_adios/src/MarDyn", name: "adios2_exec"
}
}
stage('build with ADIOS2 MPI') {
steps {
unstash 'repo'
dir ("build_adios_mpi"){
sh """
CC=mpicc CXX=mpicxx cmake -DENABLE_MPI=ON -DENABLE_ADIOS2=ON -DENABLE_UNIT_TESTS=1 ..
make -j4
"""
}
stash includes: "build_adios_mpi/src/MarDyn", name: "adios2_mpi_exec"
}
}
stage('unit test with adios2') {
parallel {
stage('test sequential') {
steps {
dir("seq"){
unstash 'repo'
unstash 'adios2_exec'
dir ("build_adios"){
sh """
./src/MarDyn -t -d ../test_input/
"""
}
}
}
}
stage('test mpi') {
steps {
dir("mpi"){
unstash 'repo'
unstash 'adios2_mpi_exec'
dir ("build_adios_mpi"){
sh """
mpirun -n 1 ./src/MarDyn -t -d ../test_input/
mpirun -n 4 ./src/MarDyn -t -d ../test_input/
"""
}
}
}
}
}
}
stage('validation tests with adios2') {
parallel {
stage('run seq') {
steps {
dir('adios2test'){
unstash 'repo'
unstash 'adios2_exec'
dir ("build_adios"){
sh """
pwd
cd ../examples/adios/CO2_Merker
rm -rf co2_merkers.bp
../../../build_adios/src/MarDyn config.xml --steps=20
[ -d "co2_merkers.bp" ] && echo "File written."
"""
}
}
}
}
stage('run mpi') {
steps {
dir('adios2test'){
unstash 'repo'
unstash 'adios2_mpi_exec'
dir ("build_adios_mpi"){
sh """
pwd
cd ../examples/adios/CO2_Merker
rm -rf co2_merkers.bp
mpirun -n 4 ../../../build_adios_mpi/src/MarDyn config.xml --steps=20
[ -d "co2_merkers.bp" ] && echo "File written."
"""
}
}
}
}
stage('parallel read') {
steps {
dir('adios2test'){
unstash 'repo'
unstash 'adios2_mpi_exec'
dir ("build_adios_mpi"){
sh """
pwd
cd ../examples/adios/read
mpirun -n 4 ../../../build_adios_mpi/src/MarDyn config_parallel.xml --steps=20
"""
}
}
}
}
}
}
}
}
stage('check AutoPas integration') {
agent { label 'atsccs11' }
stages {
// parallel build currently disabled, because of OOM errors on atsccs11, when compiling two builds in parallel.
//stage('build with autopas') {
// parallel {
stage('build with autopas sequential') {
steps {
unstash 'repo'
dir ("build"){
sh """
cmake -DENABLE_AUTOPAS=ON -DOPENMP=ON -DENABLE_UNIT_TESTS=1 -DENABLE_ADIOS2=OFF ..
make -j4
"""
}
stash includes: "build/src/MarDyn", name: "autopas_exec"
}
}
stage('build with autopas MPI') {
steps {
unstash 'repo'
dir ("build-mpi"){
sh """
CC=mpicc CXX=mpicxx cmake -DENABLE_ALLLBL=ON -DENABLE_MPI=ON -DENABLE_AUTOPAS=ON -DOPENMP=ON -DENABLE_UNIT_TESTS=1 -DENABLE_ADIOS2= ..
make -j4
"""
}
stash includes: "build-mpi/src/MarDyn", name: "autopas_mpi_exec"
}
}
// }
//}
stage('unit test with autopas') {
parallel {
stage('test sequential') {
steps {
dir("seq"){
unstash 'repo'
unstash 'autopas_exec'
dir ("build"){
sh """
./src/MarDyn -t -d ../test_input/
"""
}
}
}
}
stage('test mpi') {
steps {
dir("mpi"){
unstash 'repo'
unstash 'autopas_mpi_exec'
dir ("build-mpi"){
sh """
mpirun -n 1 ./src/MarDyn -t -d ../test_input/
mpirun -n 4 ./src/MarDyn -t -d ../test_input/
"""
}
}
}
}
}
}
stage('validation tests with autopas') {
parallel {
stage('run with autopas aos') {
steps {
dir('aostest'){
unstash 'repo'
unstash 'autopas_exec'
dir ("build"){
sh """
./src/MarDyn ../examples/Argon/200K_18mol_l/config_autopas_aos.xml --steps=20 | tee autopas_run_log.txt
grep "Simstep = 20" autopas_run_log.txt > simstep20.txt
grep "T = 0.000633975" simstep20.txt
grep "U_pot = -2.14161" simstep20.txt
grep "p = 5.34057e-07" simstep20.txt
"""
}
}
}
}
stage('run with autopas soa') {
steps {
dir('soatest'){
unstash 'repo'
unstash 'autopas_exec'
dir ("build"){
sh """
./src/MarDyn ../examples/Argon/200K_18mol_l/config_autopas_soa.xml --steps=20 | tee autopas_run_log.txt
grep "Simstep = 20" autopas_run_log.txt > simstep20.txt
grep "T = 0.000633975" simstep20.txt
grep "U_pot = -2.14161" simstep20.txt
grep "p = 5.34057e-07" simstep20.txt
"""
}
}
}
}
stage('run with autopas DD') {
steps {
dir('ddtest'){
unstash 'repo'
unstash 'autopas_mpi_exec'
dir ("build-mpi"){
sh """
mpirun -n 4 ./src/MarDyn ../examples/Argon/200K_18mol_l/config_autopas_aos.xml --steps=20 | tee autopas_run_log.txt
grep "Simstep = 20" autopas_run_log.txt > simstep20.txt
grep "T = 0.000633975" simstep20.txt
grep "U_pot = -2.14161" simstep20.txt
grep "p = 5.34057e-07" simstep20.txt
"""
}
}
}
}
stage('run with autopas ALLLB') {
steps {
dir('alltest'){
unstash 'repo'
unstash 'autopas_mpi_exec'
dir ("build-mpi"){
sh """
mpirun -n 2 ./src/MarDyn ../examples/Argon/200K_18mol_l/config_autopas_lc_ALL.xml --steps=20 | tee autopas_run_log.txt
grep "Simstep = 20" autopas_run_log.txt > simstep20.txt
grep "T = 0.000633975" simstep20.txt
grep "U_pot = -2.14161" simstep20.txt
grep "p = 5.34057e-07" simstep20.txt
"""
}
}
}
}
}
}
}
}
stage('run ci-matrix') {
steps {
println "setting up and running ci-matrix..."
script {
def variations = [:]
def matrixEntry = []
def matrixBuilder // needs to be defined beforehand to overload
// construct and return jobs
def variation = {
def VECTORIZE_CODE = it[0]
def TARGET = it[1]
def OPENMP = it[2]
def PARTYPE = it[3]
def PRECISION = it[4]
def REDUCED_MEMORY_MODE = it[5]
// return the job
if (combinationFilter(it)) {
return {
node(VECTORIZE_CODE) {
def ARCH = (NODE_NAME == "KNL-Cluster-login") ? "KNL" : "HSW"
def build_result = "not run"
def unit_test_result = "not run"
def validation_test_result = "not run"
stage("${it.join('-')}") {
sh "rm -rf ${it.join('-')} || echo ''"
ws("${WORKSPACE}/${it.join('-')}") {
try {
unstash 'repo'
stage("build/${it.join('-')}") {
try {
printVariation(it)
dir("src") {
if(ARCH == "HSW") {
sh "export VTK_INCDIR=/usr/include/vtk-6.3"
sh "export VTK_LIBDIR=/usr/lib"
} else {
sh "source /etc/profile.d/modules.sh"
}
sh """
make TARGET=$TARGET \
PARTYPE=$PARTYPE \
PRECISION=$PRECISION \
OPENMP=$OPENMP \
REDUCED_MEMORY_MODE=$REDUCED_MEMORY_MODE \
UNIT_TESTS=1 \
VECTORIZE_CODE=$VECTORIZE_CODE \
""" +
((ARCH=="KNL") ?
"VTK=0 CFG=" + (PARTYPE == "PAR" ? "icc-impi" : "icc") :
"VTK=1"
) + " -j4"
sh "mv `readlink MarDyn` ${it.join('-')}"
build_result = "success"
}
} catch (err) {
build_result = "failure"
error err
}
}
// FIXME: Mixed precision unit-tests fail with rmm
if ((PRECISION=="MIXED").implies(REDUCED_MEMORY_MODE=="0")) {
stage("unit-test/${it.join('-')}") {
try {
printVariation(it)
def knl_jobid
def knl_jobstate
if (ARCH=="KNL") {
knl_jobid = getKnlJobid()
knl_jobstate = getKnlJobstate(knl_jobid)
while (knl_jobstate.contains("PENDING")) {
echo "Pending..."
sleep 300
knl_jobstate = getKnlJobstate(knl_jobid)
}
if (knl_jobstate.contains("RUNNING")) {
echo "Job running!"
} else {
error "Unrecognized job state " + knl_jobstate
}
}
def legacyCellProcessorOptions = ((VECTORIZE_CODE == "NOVEC") && (REDUCED_MEMORY_MODE == "0") ? [false, true] : [false])
for (legacyCellProcessor in legacyCellProcessorOptions) {
def legacyCellProcessorOption = (legacyCellProcessor ? "--legacy-cell-processor" : "")
println "Cell processor is " + (legacyCellProcessor ? "legacy" : "vectorized")
if (ARCH=="HSW" && PARTYPE=="PAR") {
sh "mpirun -n 4 ./src/${it.join('-')} $legacyCellProcessorOption -t -d ./test_input/"
} else if (ARCH=="HSW" && PARTYPE=="SEQ") {
sh "./src/${it.join('-')} $legacyCellProcessorOption -t -d ./test_input/"
} else if (ARCH=="KNL" && PARTYPE=="PAR") {
sh """
source /etc/profile.d/modules.sh
export SLURM_CONF=$HOME/slurm.conf
export OMP_NUM_THREADS=10
export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so
while : ; do
set +e
output=`srun --jobid=$knl_jobid -n 4 --time=00:10:00 ./src/${it.join('-')} $legacyCellProcessorOption -t -d ./test_input/ 2>&1`
rc=\$?
if [[ \$rc == 1 && (\$output == *"Job violates accounting/QOS policy"* || \$output == *"Socket timed out on send/recv"* || \$output == *"Communication connection failure"*)]] ; then
echo "srun submit limit reached or socket timed out error, trying again in 60s"
sleep 60
continue
fi
set -e
echo \$output
exit \$rc
done
"""
} else if (ARCH=="KNL" && PARTYPE=="SEQ") {
sh """
source /etc/profile.d/modules.sh
export SLURM_CONF=$HOME/slurm.conf
export OMP_NUM_THREADS=10
export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so
while : ; do
set +e
output=`srun --jobid=$knl_jobid -n 1 --time=00:10:00 ./src/${it.join('-')} $legacyCellProcessorOption -t -d ./test_input/ 2>&1`
rc=\$?
if [[ \$rc == 1 && (\$output == *"Job violates accounting/QOS policy"* || \$output == *"Socket timed out on send/recv"* || \$output == *"Communication connection failure"*)]] ; then
echo "srun submit limit reached or socket timed out error, trying again in 60s"
sleep 60
continue
fi
set -e
echo \$output
exit \$rc
done
"""
}
}
unit_test_result = "success"
} catch (err) {
unit_test_result = "failure"
error err
}
xunit([CppUnit(deleteOutputFiles: true, failIfNotNew: false, pattern: 'results.xml', skipNoTestFiles: false, stopProcessingIfError: true)])
}
}
if (PRECISION=="DOUBLE" && REDUCED_MEMORY_MODE=="0") {
stage("validation-test/${it.join('-')}") {
try {
copyArtifacts filter: '**/*', fingerprintArtifacts: true, projectName: 'MardynUpdateValidationBase', selector: lastSuccessful()
sh "pwd && ls"
def configDirs = [
"simple-lj",
"simple-lj-mp",
"surface-tension_LRC_CO2_Merker_280",
"simple-lj_kdd",
"simple-lj-direct-mp",
"simple-lj-direct",
"LRC_planar_2020"
]
def legacyCellProcessorOptions = ((VECTORIZE_CODE == "NOVEC") && (REDUCED_MEMORY_MODE == "0") ? [false, true] : [false])
for (legacyCellProcessor in legacyCellProcessorOptions) {
println "Cell processor is " + (legacyCellProcessor ? "legacy" : "vectorized")
for (configDirVar in configDirs) {
println configDirVar
dir("validation/validationBase") {
def sameParTypeOption = (fileExists ('../validationInput/' + configDirVar + '/compareSameParType')) ? "" : "-b"
def mpicmd = (PARTYPE=="PAR" ? "-m 4" : "-m 1")
def mpiextra = (ARCH=="KNL" ? "-M \"srun --jobid=" + getKnlJobid() + "\"" : "")
def allmpi = (ARCH=="KNL" ? "--allMPI" : "")
def legacyCellProcessorOption = (legacyCellProcessor ? "--legacy-cell-processor" : "")
def srunfix = (ARCH=="KNL" ? "--srunFix" : "")
def icount = (ARCH=="KNL" ? "-I 5" : "")
def oldexec = "MarDyn_ValidationBase" + (ARCH=="KNL" ? "_KNL" : "")
def plugins = (legacyCellProcessor ? "" : "--disablePlugin RDF") +
((fileExists ('../validationInput/' + configDirVar + '/noGamma') ) ?
" --disablePlugin GammaWriter" : "")
for (partypeToCompare in ["PAR", "SEQ"]) {
if ((sameParTypeOption=="").implies(partypeToCompare == PARTYPE)) {
dir(partypeToCompare) {
printVariation(it)
if (!fileExists ("./${oldexec}")) {
sh "ls -Ra"
error 'Validation base not found!'
} else if (!fileExists ("${WORKSPACE}/src/${it.join('-')}")) {
sh "ls -Ra ../../.."
error 'New build not found!'
}
sh """
export OMP_NUM_THREADS=64
export SLURM_CONF=$HOME/slurm.conf
echo "Running validation tests"
rm ${it.join('-')} || echo ""
cp ${WORKSPACE}/src/${it.join('-')} .
pwd && ls
../../validationRun/validationRun.py \
$srunfix \
-o ./$oldexec \
-n ./${it.join('-')} \
$legacyCellProcessorOption \
$allmpi \
-c \"\$(realpath ../../validationInput/$configDirVar/config.xml)\" \
$plugins $icount $sameParTypeOption $mpicmd $mpiextra
"""
}
}
}
}
}
}
validation_test_result = "success"
} catch (err) {
validation_test_result = "failure"
error err
}
}
}
results.put(it.join('-'), [:])
results[it.join('-')].put("runOn", ARCH)
results[it.join('-')].put("build", build_result)
results[it.join('-')].put("unit-test", unit_test_result)
results[it.join('-')].put("validation-test", validation_test_result)
cleanWs(deleteDirs:true, disableDeferredWipeout: true)
} catch (err) {
results.put(it.join('-'), [:])
results[it.join('-')].put("runOn", ARCH)
results[it.join('-')].put("build", build_result)
results[it.join('-')].put("unit-test", unit_test_result)
results[it.join('-')].put("validation-test", validation_test_result)
cleanWs(deleteDirs:true, disableDeferredWipeout: true)
error err
}
}
}
}
}
}
}
// return all combinations
// FIXME can't be defined globally due to a bug in Jenkins:
// https://issues.jenkins-ci.org/browse/JENKINS-49826
matrixBuilder = { def matrix, int level ->
// Fail the entire pipeline if one step fails
variations.failFast = false
// HACK Jobs to manage resource allocation on the knl cluster
/* // START temporary disabled knl-cluster
variations["slurm"] = {
try {
node("KNL_PRIO") { // Executor on the CoolMUC3 login node reserved for slurm allocation and management
parallel "allocation": {
try {
timeout(time: 10, unit: 'HOURS') {
// Allocate a new interactive job with up to three nodes
// and one hour maximum run time. The ci-matrix will
// attach subjobs to this via srun and the slurm.slurmcontrol
// stage will revoke the allocation as soon as we are done.
// Until that, the shell needs to stay open for the job
// to survive. Hence the second sleep.
sh """
export SLURM_CONF=$HOME/slurm.conf
salloc --job-name=mardyn-test --nodes=1-4 --partition=mpp3_batch\
--tasks-per-node=3 --time=04:00:00 --begin=now+150\
sleep 4h || echo 0
sleep 6h
"""
}
}
// Stop the slurm.allocation on any error, but do not
// propatate. Needed to allow slurm.slurmcontrol (below)
// to kill slurm.* by throwing an error.
catch (err) {
println err
}
}, "slurmcontrol": {
// Wait for slurm.allocation to work its magic
sleep 10
// Store jobid
knl_jobid = getKnlJobid()
println "Scheduled job " + knl_jobid
// Wait for all jobs to finish by comparing the list of
// scheduled jobs with the list of results
while (results.size() < (variations.size()-2)) {
sleep 150
println "variations: " + variations.size()
println "results: " + results.size()
}
// Revoke slurm job allocation
sh "scancel $knl_jobid -f --user=ga38cor3"
// Throw an error (that will not be propagated) to kill the
// slurm.* stages. Without this, slurm.allocation would keep
// running even after the allocation is revoked.
error "all finished"
},
failFast: true // If one of the slurm.* stages throws an error, slurm.* is cancelled
}
}
// Only print all error signals. See above.
catch (err) {
println err
}
}*/ // END temporary disabled knl-cluster
// Assemble CI-Matrix in a map
for ( entry in matrix[0] ) {
matrixEntry[level] = entry
if (matrix.size() > 1 ) {
matrixBuilder(matrix.drop(1), level + 1)
}
else {
def _variation = variation(matrixEntry.collect())
if (_variation != null)
variations[matrixEntry.join("-")] = _variation
}
}
}
node { matrixBuilder(ciMatrix, 0) }
// Lock the KNL cluster while running the ci-matrix. This is needed
// because we are not allowed to submit more than one interactive job
// at a time. As soon as we're in post-build, the lock is released
// and another running job can access KNL.
// https://doku.lrz.de/display/PUBLIC/Resource+limits+for+parallel+jobs+on+Linux+Cluster
lock('KNL_slurm_allocation') {
parallel variations
}
}
}
}
stage('post-build'){
parallel {
stage('documentation') {
agent { label 'atsccs11' }
stages {
stage('build documentation') {
steps {
unstash 'repo'
sh "mkdir doxygen_doc || echo 'doxygen_doc Folder exists already'"
sh "doxygen"
}
}
stage('release documentation') {
when { branch 'master' }
steps {
sh "rm -rf /home/wwwsccs/html/mardyn/doc /home/wwwsccs/html/mardyn/doxygen_doc"
sh "cp -r doc /home/wwwsccs/html/mardyn"
sh "cp -r doxygen_doc /home/wwwsccs/html/mardyn"
sh "chmod -R 775 /home/wwwsccs/html/mardyn/doc"
sh "chmod -R 775 /home/wwwsccs/html/mardyn/doxygen_doc"
}
}
}
}
stage('libs and generators') {
agent { label 'atsccs11' }
steps {
unstash 'repo'
dir('src') {
sh label: "Build libs", script: """
pwd
make -f ../makefile/Makefile.lib UNIT_TESTS=0 VTK=0 PARTYPE=SEQ TARGET=RELEASE -j3 clean
make -f ../makefile/Makefile.lib UNIT_TESTS=0 VTK=0 PARTYPE=SEQ TARGET=RELEASE -j3 lib
"""
}
dir ('tools/gui') {
sh label: "Build generators", script: """
export VTKINCLUDEPATH=/usr/include/vtk-6.3
tar xfz ScenarioGenerator.tar.gz
qmake DEFINES+="MARDYN_DPDP" DropletGenerator.pro -o Makefile.droplet
qmake DEFINES+="MARDYN_DPDP" CubicGridGenerator.pro -o Makefile.cubic
qmake DEFINES+="MARDYN_DPDP" AqueousNaClGenerator.pro -o Makefile.aqueous
qmake DEFINES+="MARDYN_DPDP" CrystalLatticeGenerator.pro -o Makefile.crystal
qmake DEFINES+="MARDYN_DPDP" MS2RSTGenerator.pro -o Makefile.ms2
qmake DEFINES+="MARDYN_DPDP" RayleighTaylorGenerator.pro -o Makefile.rayleigh
rm -r libMardyn* || :
make -f Makefile.droplet -j2
make -f Makefile.cubic -j2
make -f Makefile.aqueous -j2
make -f Makefile.crystal -j2
make -f Makefile.ms2 -j2
make -f Makefile.rayleigh -j2
"""
}
dir ('src') {
sh label: "Build again normally", script: """
export VTK_INCDIR=/usr/include/vtk-6.3
export VTK_LIBDIR=/usr/lib7
make cleanall
make TARGET=DEBUG PARTYPE=PAR PRECISION=DOUBLE OPENMP=0 \
REDUCED_MEMORY_MODE=0 UNIT_TESTS=1 VECTORIZE_CODE=AVX2 VTK=1 -j4
"""
}
dir ('executablerun') {
sh label: "Mktcts generator", script: """
mv ../src/MarDyn*.PAR_DEBUG_AVX2 ./MarDyn
chmod 770 ./MarDyn
mpirun -n 2 ./MarDyn ../examples/Generators/mkTcTS/config.xml \
--steps 100 --final-checkpoint=0
"""
}
dir ('tools/standalone-generators/build') {
sh label: "Build package", script: """
cmake ..
make package
make
"""
}
}
}
stage('export-src') {
agent { label 'atsccs11' }
steps {
unstash 'repo'
sh './export-src.sh'
dir('unarchive') {
sh 'tar -xf ../Mardyn-src.tar.gz'
dir('src') {
sh 'make -j4'
}
dir('build') {
sh 'cmake .. && make -j4'
}
}
}
}
}
}
}
}