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azure-pipelines.yml
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azure-pipelines.yml
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# https://aka.ms/yaml
trigger:
- master
variables:
regression: 1
jobs:
- job: build_ubuntu_1804
displayName: Ubuntu 1804
pool:
vmImage: 'Ubuntu-18.04'
timeoutInMinutes: 120
strategy:
matrix:
avx2:
SIMD: 'AVX2'
ARCHIVE_NAME: 'avx2'
STATIC: 1
MPI: 0
BUILD_TYPE: Release
sse2:
SIMD: 'SSE2'
ARCHIVE_NAME: 'sse2'
STATIC: 1
MPI: 0
BUILD_TYPE: Release
avx2_mpi:
SIMD: 'AVX2'
ARCHIVE_NAME: 'avx2-mpi'
STATIC: 0
MPI: 1
BUILD_TYPE: RelWithDebInfo
asan:
SIMD: 'AVX2'
ARCHIVE_NAME: 'avx2-asan'
STATIC: 0
MPI: 1
BUILD_TYPE: ASanOpt
steps:
- script: |
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install -y g++-10
displayName: Install newer GCC
condition: eq(variables['BUILD_TYPE'], 'ASanOpt')
- script: |
sudo apt-get update
sudo apt-get -y install mpi-default-dev mpi-default-bin
displayName: Install MPI dependencies
condition: eq(variables['MPI'], 1)
- script: |
mkdir build && cd build
if [ "${BUILD_TYPE}" = "ASanOpt" ]; then
export CC=gcc-10 ; export CXX=g++-10
fi
if [ "${STATIC}" -eq "1" ]; then
cmake -DCMAKE_INSTALL_PREFIX=${BUILD_SOURCESDIRECTORY}/hhsuite \
-DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
-DBUILD_SHARED_LIBS=OFF \
-DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc -static-libstdc++" \
-DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \
-DHAVE_${SIMD}=1 \
-DCHECK_MPI=${MPI} \
..
else
cmake -DCMAKE_INSTALL_PREFIX=${BUILD_SOURCESDIRECTORY}/hhsuite \
-DHAVE_SANITIZER=1 \
-DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
-DHAVE_${SIMD}=1 \
-DCHECK_MPI=${MPI} \
..
fi
make -j $(nproc --all)
make install
cd ${BUILD_SOURCESDIRECTORY}
cp LICENSE README.md hhsuite
tar -czvf hhsuite-linux-${ARCHIVE_NAME}.tar.gz hhsuite
displayName: Build HHsuite
- script: |
if [ "${BUILD_TYPE}" = "ASanOpt" ]; then
echo "leak:libgomp1" > ${BUILD_SOURCESDIRECTORY}/ASan.supp
export ASAN_OPTIONS=suppressions=${BUILD_SOURCESDIRECTORY}/ASan.supp
fi
cd ${BUILD_SOURCESDIRECTORY}/data
PATH="${BUILD_SOURCESDIRECTORY}/hhsuite/bin:$PATH"
./test.sh
displayName: Run regression
condition: eq(variables['regression'], 1)
- task: PublishPipelineArtifact@0
inputs:
targetPath: $(Build.SourcesDirectory)/hhsuite-linux-$(ARCHIVE_NAME).tar.gz
artifactName: hhsuite-linux-$(ARCHIVE_NAME)
condition: eq(variables['STATIC'], 1)
- job: build_ubuntu_cross_2004
displayName: Ubuntu 2004 cross-compile
pool:
vmImage: 'Ubuntu-20.04'
strategy:
matrix:
power8:
SIMD: POWER8
ARCH: ppc64el
ARCHIVE_NAME: ppc64el-power8
CPREF: powerpc64le
power9:
SIMD: POWER9
ARCH: ppc64el
ARCHIVE_NAME: ppc64el-power9
CPREF: powerpc64le
arm64:
SIMD: ARM8
ARCH: arm64
ARCHIVE_NAME: arm64
CPREF: aarch64
steps:
- script: |
sudo dpkg --add-architecture $ARCH
cat << HEREDOC | sudo tee /etc/apt/sources.list
deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ focal main universe multiverse
deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ focal-updates main universe multiverse
deb [arch=amd64,i386] http://archive.ubuntu.com/ubuntu/ focal-backports main universe multiverse
deb [arch=amd64,i386] http://security.ubuntu.com/ubuntu/ focal-security main universe multiverse
deb [arch=$ARCH] http://ports.ubuntu.com/ubuntu-ports/ focal main universe multiverse
deb [arch=$ARCH] http://ports.ubuntu.com/ubuntu-ports/ focal-updates main universe multiverse
deb [arch=$ARCH] http://ports.ubuntu.com/ubuntu-ports/ focal-backports main universe multiverse
deb [arch=$ARCH] http://ports.ubuntu.com/ubuntu-ports/ focal-security main universe multiverse
HEREDOC
sudo apt-get update
sudo apt-get -y install -o APT::Immediate-Configure=false crossbuild-essential-$ARCH qemu-user-static
displayName: Install crossbuild toolchain
- script: |
mkdir build && cd build
CC=${CPREF}-linux-gnu-gcc CXX=${CPREF}-linux-gnu-g++ \
cmake -DCMAKE_INSTALL_PREFIX=${BUILD_SOURCESDIRECTORY}/hhsuite \
-DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
-DBUILD_SHARED_LIBS=OFF \
-DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc -static-libstdc++" \
-DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \
-DHAVE_${SIMD}=1 \
-DCHECK_MPI=0 \
..
make -j $(nproc --all)
make install
cd ${BUILD_SOURCESDIRECTORY}
cp LICENSE README.md hhsuite
tar -czvf hhsuite-linux-${ARCHIVE_NAME}.tar.gz hhsuite
displayName: Build HHsuite
- script: |
cd ${BUILD_SOURCESDIRECTORY}/data
PATH="${BUILD_SOURCESDIRECTORY}/hhsuite/bin:$PATH"
./test.sh
displayName: Run regression in QEMU
# POWER9 test needs at least qemu 5.2 as GCC emits lxvwsx instructions
# https://bugs.launchpad.net/qemu/+bug/1793608
condition: and(eq(variables['regression'], 1), ne(variables['SIMD'], 'POWER9'))
- task: PublishPipelineArtifact@0
inputs:
targetPath: $(Build.SourcesDirectory)/hhsuite-linux-$(ARCHIVE_NAME).tar.gz
artifactName: hhsuite-linux-$(ARCHIVE_NAME)
- job: build_macos_1015
displayName: macOS 1015
pool:
vmImage: 'macos-10.15'
steps:
- script: |
cd ${BUILD_SOURCESDIRECTORY}
./scripts/build_darwin_universal.sh . build_osx
cp ${BUILD_SOURCESDIRECTORY}/LICENSE ${BUILD_SOURCESDIRECTORY}/README.md ${BUILD_SOURCESDIRECTORY}/build_osx/hhsuite/
tar -czvf ${BUILD_SOURCESDIRECTORY}/hhsuite-osx-universal.tar.gz -C ${BUILD_SOURCESDIRECTORY}/build_osx hhsuite
displayName: Build HHsuite
- script: |
cd ${BUILD_SOURCESDIRECTORY}/data
PATH="${BUILD_SOURCESDIRECTORY}/build_osx/hhsuite/bin:$PATH"
./test.sh
displayName: Run regression
condition: eq(variables['regression'], 1)
- task: PublishPipelineArtifact@0
inputs:
targetPath: $(Build.SourcesDirectory)/hhsuite-osx-universal.tar.gz
artifactName: hhsuite-osx-universal
- job: upload_artifacts
displayName: Upload Artifacts
condition: and(succeeded(), ne(variables['Build.Reason'], 'PullRequest'))
pool:
vmImage: 'Ubuntu-18.04'
dependsOn:
- build_macos_1015
- build_ubuntu_1804
- build_ubuntu_cross_2004
steps:
- checkout: none
- task: DownloadPipelineArtifact@1
inputs:
targetPath: $(Build.SourcesDirectory)
- task: DownloadSecureFile@1
inputs:
secureFile: secretKeyPleaseDontSteal
displayName: Get Deployment Key
- script: |
mkdir ~/.ssh && mv $DOWNLOADSECUREFILE_SECUREFILEPATH ~/.ssh/id_rsa
chmod 700 ~/.ssh && chmod 600 ~/.ssh/id_rsa
ssh-keyscan -t rsa uniclust.mmseqs.com >> ~/.ssh/known_hosts
cd "${BUILD_SOURCESDIRECTORY}"
ssh codeship@uniclust.mmseqs.com "mkdir -p \"/home/mirdita/repositories/mmseqs-webserver/archive/${BUILD_SOURCEVERSION}\""
scp hhsuite-*/*.tar.gz codeship@uniclust.mmseqs.com:"/home/mirdita/repositories/mmseqs-webserver/archive/${BUILD_SOURCEVERSION}"
ssh codeship@uniclust.mmseqs.com "update-latest-hhsuite.sh \"${BUILD_SOURCEVERSION}\""