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Jenkinsfile
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Jenkinsfile
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@Library('StanUtils')
import org.stan.Utils
def utils = new org.stan.Utils()
def skipRemainingStages = false
def skipOpenCL = false
def setupCXX(failOnError = true, CXX = CXX, String stanc3_bin_url = "nightly") {
errorStr = failOnError ? "-Werror " : ""
stanc3_bin_url_str = stanc3_bin_url != "nightly" ? "\nSTANC3_TEST_BIN_URL=${stanc3_bin_url}\n" : ""
writeFile(file: "make/local", text: "CXX=${CXX} -Wno-inconsistent-missing-override ${errorStr}${stanc3_bin_url_str}")
}
def runTests(String testPath, Boolean separateMakeStep=true) {
if (separateMakeStep) {
sh "python3 runTests.py -j${PARALLEL} ${testPath} --make-only"
}
try { sh "python3 runTests.py -j${PARALLEL} ${testPath}" }
finally { junit 'test/**/*.xml' }
}
def runTestsWin(String testPath, Boolean separateMakeStep=true) {
withEnv(['PATH+TBB=./lib/stan_math/lib/tbb']) {
if (separateMakeStep) {
bat """
SET \"PATH=C:\\Users\\jenkins\\Anaconda3;%PATH%\"
SET \"PATH=${env.RTOOLS40_HOME};%PATH%\"
SET \"PATH=${env.RTOOLS40_HOME}\\usr\\bin;${LLVM7}\\bin;%PATH%\" //
SET \"PATH=${env.RTOOLS40_HOME}\\mingw64\\bin;%PATH%\"
SET \"PATH=C:\\PROGRA~1\\R\\R-4.1.2\\bin;%PATH%\"
SET \"PATH=C:\\PROGRA~1\\Microsoft^ MPI\\Bin;%PATH%\"
SET \"MPI_HOME=C:\\PROGRA~1\\Microsoft^ MPI\\Bin\"
python runTests.py -j${PARALLEL} ${testPath} --make-only
"""
}
try {
bat """
SET \"PATH=C:\\Users\\jenkins\\Anaconda3;%PATH%\"
SET \"PATH=${env.RTOOLS40_HOME};%PATH%\"
SET \"PATH=${env.RTOOLS40_HOME}\\usr\\bin;${LLVM7}\\bin;%PATH%\" //
SET \"PATH=${env.RTOOLS40_HOME}\\mingw64\\bin;%PATH%\"
SET \"PATH=C:\\PROGRA~1\\R\\R-4.1.2\\bin;%PATH%\"
SET \"PATH=C:\\PROGRA~1\\Microsoft^ MPI\\Bin;%PATH%\"
SET \"MPI_HOME=C:\\PROGRA~1\\Microsoft^ MPI\\Bin\"
python runTests.py -j${PARALLEL} ${testPath}
"""
}
finally { junit 'test/**/*.xml' }
}
}
def deleteDirWin() {
bat "attrib -r -s /s /d"
deleteDir()
}
String stanc3_bin_url() { params.stanc3_bin_url ?: "nightly" }
String cmdstan_pr() { params.cmdstan_pr ?: "downstream_tests" }
String stan_pr() {
if (env.BRANCH_NAME == 'downstream_tests') {
''
} else if (env.BRANCH_NAME == 'downstream_hotfix') {
'master'
} else {
env.BRANCH_NAME
}
}
String integration_tests_flags() {
if (params.compile_all_model) {
'--no-ignore-models '
} else {
''
}
}
def isBranch(String b) { env.BRANCH_NAME == b }
Boolean isPR() { env.CHANGE_URL != null }
String fork() { env.CHANGE_FORK ?: "stan-dev" }
String branchName() { isPR() ? env.CHANGE_BRANCH :env.BRANCH_NAME }
pipeline {
agent none
parameters {
string(defaultValue: '', name: 'math_pr', description: "Leave blank "
+ "unless testing against a specific math repo pull request, "
+ "e.g. PR-640.")
string(defaultValue: 'downstream_tests', name: 'cmdstan_pr',
description: 'PR to test CmdStan upstream against e.g. PR-630')
string(defaultValue: 'nightly', name: 'stanc3_bin_url',
description: 'Custom stanc3 binary url')
booleanParam(defaultValue: false, name: 'run_tests_all_os', description: 'Run unit and integration tests on all OS.')
booleanParam(defaultValue: false, name: 'compile_all_models', description: 'Run integration tests on the full test model suite.')
}
options {
skipDefaultCheckout()
preserveStashes(buildCount: 7)
parallelsAlwaysFailFast()
buildDiscarder(logRotator(numToKeepStr: '20', daysToKeepStr: '30'))
disableConcurrentBuilds(abortPrevious: env.BRANCH_NAME != "downstream_tests" && env.BRANCH_NAME != "downstream_hotfix")
}
environment {
GCC = 'g++'
PARALLEL = 4
MAC_CXX = 'clang++'
LINUX_CXX = 'clang++-6.0'
WIN_CXX = 'g++'
GIT_AUTHOR_NAME = 'Stan Jenkins'
GIT_AUTHOR_EMAIL = '[email protected]'
GIT_COMMITTER_NAME = 'Stan Jenkins'
GIT_COMMITTER_EMAIL = '[email protected]'
OPENCL_DEVICE_ID_CPU = 0
OPENCL_DEVICE_ID_GPU = 0
OPENCL_PLATFORM_ID = 1
OPENCL_PLATFORM_ID_CPU = 0
OPENCL_PLATFORM_ID_GPU = 0
}
stages {
stage("Clang-format") {
agent {
docker {
image 'stanorg/ci:gpu'
label 'linux'
}
}
steps {
retry(3) { checkout scm }
withCredentials([usernamePassword(credentialsId: 'a630aebc-6861-4e69-b497-fd7f496ec46b',
usernameVariable: 'GIT_USERNAME', passwordVariable: 'GIT_PASSWORD')]) {
sh """#!/bin/bash
set -x
git checkout -b ${branchName()}
clang-format --version
find src -name '*.hpp' -o -name '*.cpp' | xargs -n20 -P${PARALLEL} clang-format -i
if [[ `git diff` != "" ]]; then
git config user.email "[email protected]"
git config user.name "Stan Jenkins"
git add src
git commit -m "[Jenkins] auto-formatting by `clang-format --version`"
git push https://${GIT_USERNAME}:${GIT_PASSWORD}@github.com/${fork()}/stan.git ${branchName()}
echo "Exiting build because clang-format found changes."
echo "Those changes are now found on stan-dev/stan under branch ${branchName()}"
echo "Please 'git pull' before continuing to develop."
exit 1
fi
"""
}
}
post {
always { deleteDir() }
failure {
script {
emailext (
subject: "[StanJenkins] Autoformattted: Job '${env.JOB_NAME} [${env.BUILD_NUMBER}]'",
body: "Job '${env.JOB_NAME} [${env.BUILD_NUMBER}]' " +
"has been autoformatted and the changes committed " +
"to your branch, if permissions allowed." +
"Please pull these changes before continuing." +
"\n\n" +
"See https://github.com/stan-dev/stan/wiki/Coding-Style-and-Idioms" +
" for setting up the autoformatter locally.\n"+
"(Check console output at ${env.BUILD_URL})",
recipientProviders: [[$class: 'RequesterRecipientProvider']],
to: "${env.CHANGE_AUTHOR_EMAIL}"
)
}
}
}
}
stage('Linting & Doc checks') {
agent {
docker {
image 'stanorg/ci:gpu'
label 'linux'
}
}
steps {
script {
retry(3) { checkout scm }
sh """
make math-revert
make clean-all
git clean -xffd
"""
utils.checkout_pr("math", "lib/stan_math", params.math_pr)
stash 'StanSetup'
setupCXX(true, LINUX_CXX)
parallel(
CppLint: { sh "make cpplint" },
API_docs: { sh 'make doxygen' },
)
}
}
post {
always {
recordIssues(
id: "lint_doc_checks",
name: "Linting & Doc checks",
enabledForFailure: true,
aggregatingResults : true,
tools: [
cppLint(id: "cpplint", name: "Linting & Doc checks@CPPLINT")
],
qualityGates: [[threshold: 1, type: 'TOTAL', unstable: true]],
healthy: 10, unhealthy: 100, minimumSeverity: 'HIGH'
)
deleteDir()
}
}
}
stage('Verify changes') {
agent {
docker {
image 'stanorg/ci:gpu'
label 'linux'
}
}
steps {
script {
retry(3) { checkout scm }
sh 'git clean -xffd'
// These paths will be passed to git diff
// If there are changes to them, CI/CD will continue else skip
def paths = ['make', 'src/stan', 'src/test', 'Jenkinsfile', 'makefile', 'runTests.py',
'lib/stan_math/stan', 'lib/stan_math/make', 'lib/stan_math/lib', 'lib/stan_math/test',
'lib/stan_math/runTests.py', 'lib/stan_math/runChecks.py', 'lib/stan_math/makefile',
'lib/stan_math/Jenkinsfile', 'lib/stan_math/.clang-format'
].join(" ")
skipRemainingStages = utils.verifyChanges(paths)
def openCLPaths = ['src/stan/model/indexing'].join(" ")
skipOpenCL = utils.verifyChanges(openCLPaths)
}
}
post {
always {
deleteDir()
}
}
}
stage('Unit tests') {
when {
expression {
!skipRemainingStages
}
}
parallel {
stage('Windows Headers & Unit') {
agent { label 'windows' }
when {
expression {
!skipRemainingStages
}
}
steps {
deleteDirWin()
unstash 'StanSetup'
bat """
SET \"PATH=${env.RTOOLS40_HOME};%PATH%\"
SET \"PATH=${env.RTOOLS40_HOME}\\usr\\bin;${LLVM7}\\bin;%PATH%\" //
SET \"PATH=${env.RTOOLS40_HOME}\\mingw64\\bin;%PATH%\"
SET \"PATH=C:\\PROGRA~1\\R\\R-4.1.2\\bin;%PATH%\"
SET \"PATH=C:\\PROGRA~1\\Microsoft^ MPI\\Bin;%PATH%\"
SET \"MPI_HOME=C:\\PROGRA~1\\Microsoft^ MPI\\Bin\"
make.exe -f lib/stan_math/make/standalone math-libs
make.exe -j${PARALLEL} test-headers
"""
setupCXX(false, WIN_CXX, stanc3_bin_url())
runTestsWin("src/test/unit")
}
post { always { deleteDirWin() } }
}
stage('Linux Unit') {
agent {
docker {
image 'stanorg/ci:gpu'
label 'linux'
args '--pull always --gpus 1'
}
}
steps {
unstash 'StanSetup'
setupCXX(true, LINUX_CXX, stanc3_bin_url())
sh """
echo STAN_OPENCL=true > make/local
echo OPENCL_PLATFORM_ID=${OPENCL_PLATFORM_ID_GPU} >> make/local
echo OPENCL_DEVICE_ID=${OPENCL_DEVICE_ID_GPU} >> make/local
"""
sh """
make -j${PARALLEL} test-headers
"""
runTests("src/test/unit")
}
post { always { deleteDir() } }
}
stage('Mac Unit') {
agent { label 'osx' }
when {
expression {
( env.BRANCH_NAME == "develop" ||
env.BRANCH_NAME == "master" ||
params.run_tests_all_os ) &&
!skipRemainingStages
}
}
steps {
unstash 'StanSetup'
setupCXX(false, MAC_CXX, stanc3_bin_url())
runTests("src/test/unit")
}
post { always { deleteDir() } }
}
}
}
stage('Integration') {
when {
expression {
!skipRemainingStages
}
}
parallel {
stage('Integration Linux') {
agent {
docker {
image 'stanorg/ci:gpu'
label 'linux'
}
}
steps {
sh """
git clone --recursive https://github.com/stan-dev/performance-tests-cmdstan
git clone https://github.com/stan-dev/stanc3/ performance-tests-cmdstan/stanc3
"""
script {
if (params.cmdstan_pr != 'downstream_tests') {
if(params.cmdstan_pr.contains("PR-")){
pr_number = params.cmdstan_pr.split("-")[1]
sh """
cd performance-tests-cmdstan/cmdstan
git fetch origin pull/${pr_number}/head:pr/${pr_number}
git checkout pr/${pr_number}
"""
}else{
sh """
cd performance-tests-cmdstan/cmdstan
git checkout develop && git pull && git checkout ${params.cmdstan_pr}
"""
}
}
if (params.stanc3_bin_url != 'nightly') {
sh """
cd performance-tests-cmdstan/cmdstan
echo 'STANC3_TEST_BIN_URL=${params.stanc3_bin_url}' >> make/local
"""
}
}
dir('performance-tests-cmdstan/cmdstan/stan'){
unstash 'StanSetup'
script {
if (params.stanc3_bin_url != 'nightly') {
sh """
echo 'STANC3_TEST_BIN_URL=${params.stanc3_bin_url}' >> make/local
"""
}
}
}
sh """
cd performance-tests-cmdstan/cmdstan
echo 'O=0' >> make/local
echo 'CXX=${LINUX_CXX}' >> make/local
make clean-all
make -j${PARALLEL} build
cd ..
python3 ./runPerformanceTests.py -j${PARALLEL} ${integration_tests_flags()}--runs=0 stanc3/test/integration/good
python3 ./runPerformanceTests.py -j${PARALLEL} ${integration_tests_flags()}--runs=0 example-models
"""
sh """
cd performance-tests-cmdstan/cmdstan/stan
python3 ./runTests.py src/test/integration/compile_standalone_functions_test.cpp
python3 ./runTests.py src/test/integration/standalone_functions_test.cpp
python3 ./runTests.py src/test/integration/multiple_translation_units_test.cpp
"""
}
post { always { deleteDir() } }
}
stage('Integration Mac') {
agent { label 'osx' }
when {
expression {
( env.BRANCH_NAME == "develop" ||
env.BRANCH_NAME == "master" ||
params.run_tests_all_os ) &&
!skipRemainingStages
}
}
steps {
sh """
git clone --recursive https://github.com/stan-dev/performance-tests-cmdstan
"""
dir('performance-tests-cmdstan/cmdstan/stan'){
unstash 'StanSetup'
}
sh """
cd performance-tests-cmdstan/cmdstan
echo 'O=0' >> make/local
echo 'CXX=${MAC_CXX}' >> make/local
make clean-all
make -j${PARALLEL} build
cd ..
python3 ./runPerformanceTests.py -j${PARALLEL} ${integration_tests_flags()}--runs=0 stanc3/test/integration/good
python3 ./runPerformanceTests.py -j${PARALLEL} ${integration_tests_flags()}--runs=0 example-models
"""
sh """
cd performance-tests-cmdstan/cmdstan/stan
python3 ./runTests.py src/test/integration/compile_standalone_functions_test.cpp
python3 ./runTests.py src/test/integration/standalone_functions_test.cpp
python3 ./runTests.py src/test/integration/multiple_translation_units_test.cpp
"""
}
post { always { deleteDir() } }
}
stage('Integration Windows') {
agent { label 'windows' }
when {
expression {
!skipRemainingStages
}
}
steps {
deleteDirWin()
bat """
git clone --recursive https://github.com/stan-dev/performance-tests-cmdstan
"""
dir('performance-tests-cmdstan/cmdstan/stan'){
unstash 'StanSetup'
}
writeFile(file: "performance-tests-cmdstan/cmdstan/make/local", text: "CXX=${WIN_CXX}\nPRECOMPILED_HEADERS=true")
withEnv(["PATH+TBB=${WORKSPACE}\\performance-tests-cmdstan\\cmdstan\\stan\\lib\\stan_math\\lib\\tbb"]) {
bat """
SET \"PATH=C:\\Users\\jenkins\\Anaconda3;%PATH%\"
SET \"PATH=${env.RTOOLS40_HOME};%PATH%\"
SET \"PATH=${env.RTOOLS40_HOME}\\usr\\bin;${LLVM7}\\bin;%PATH%\" //
SET \"PATH=${env.RTOOLS40_HOME}\\mingw64\\bin;%PATH%\"
SET \"PATH=C:\\PROGRA~1\\R\\R-4.1.2\\bin;%PATH%\"
SET \"PATH=C:\\PROGRA~1\\Microsoft^ MPI\\Bin;%PATH%\"
SET \"MPI_HOME=C:\\PROGRA~1\\Microsoft^ MPI\\Bin\"
cd performance-tests-cmdstan/cmdstan
make.exe -j${PARALLEL} build
cd ..
python ./runPerformanceTests.py -j${PARALLEL} ${integration_tests_flags()}--runs=0 stanc3/test/integration/good
python ./runPerformanceTests.py -j${PARALLEL} ${integration_tests_flags()}--runs=0 example-models
"""
}
bat """
SET \"PATH=C:\\Users\\jenkins\\Anaconda3;%PATH%\"
SET \"PATH=${env.RTOOLS40_HOME};%PATH%\"
SET \"PATH=${env.RTOOLS40_HOME}\\usr\\bin;${LLVM7}\\bin;%PATH%\" //
SET \"PATH=${env.RTOOLS40_HOME}\\mingw64\\bin;%PATH%\"
SET \"PATH=C:\\PROGRA~1\\R\\R-4.1.2\\bin;%PATH%\"
SET \"PATH=C:\\PROGRA~1\\Microsoft^ MPI\\Bin;%PATH%\"
SET \"MPI_HOME=C:\\PROGRA~1\\Microsoft^ MPI\\Bin\"
cd performance-tests-cmdstan/cmdstan/stan
python ./runTests.py src/test/integration/compile_standalone_functions_test.cpp
python ./runTests.py src/test/integration/standalone_functions_test.cpp
python ./runTests.py src/test/integration/multiple_translation_units_test.cpp
"""
}
post { always { deleteDirWin() } }
}
}
}
stage('Upstream CmdStan tests') {
when {
expression {
( env.BRANCH_NAME ==~ /PR-\d+/ ||
env.BRANCH_NAME == "downstream_tests" ||
env.BRANCH_NAME == "downstream_hotfix" ) &&
!skipRemainingStages
}
}
steps {
build(job: "Stan/CmdStan/${cmdstan_pr()}",
parameters: [
string(name: 'stan_pr', value: stan_pr()),
string(name: 'math_pr', value: params.math_pr),
string(name: 'stanc3_bin_url', value: stanc3_bin_url())
])
}
}
}
// Below lines are commented to avoid spamming emails during migration/debug
post {
always {
node("linux") {
recordIssues(
id: "pipeline",
name: "Entire pipeline results",
enabledForFailure: true,
aggregatingResults : false,
filters: [
excludeFile('lib/.*')
],
tools: [
gcc4(id: "pipeline_gcc4", name: "GNU C Compiler"),
clang(id: "pipeline_clang", name: "LLVM/Clang")
],
qualityGates: [[threshold: 30, type: 'TOTAL', unstable: true]],
healthy: 10, unhealthy: 100, minimumSeverity: 'HIGH'
)
}
}
success {
script {
utils.updateUpstream(env,'cmdstan')
utils.mailBuildResults("SUCCESSFUL")
}
}
unstable { script { utils.mailBuildResults("UNSTABLE", "[email protected]") } }
failure { script { utils.mailBuildResults("FAILURE", "[email protected]") } }
}
}