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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_2004
displayName: Ubuntu 2004
pool:
vmImage: 'Ubuntu-20.04'
timeoutInMinutes: 120
strategy:
matrix:
avx2:
SIMD: 'AVX2'
STATIC: 1
MPI: 0
BUILD_TYPE: RelWithDebInfo
# sse41:
# SIMD: 'SSE4_1'
# STATIC: 1
# MPI: 0
# BUILD_TYPE: RelWithDebInfo
sse2:
SIMD: 'SSE2'
STATIC: 1
MPI: 0
BUILD_TYPE: RelWithDebInfo
avx2_mpi:
SIMD: 'AVX2'
STATIC: 0
MPI: 1
BUILD_TYPE: RelWithDebInfo
asan:
SIMD: 'AVX2'
STATIC: 0
MPI: 0
BUILD_TYPE: ASanOpt
steps:
- checkout: self
submodules: true
- script: |
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install -y gcc-11 g++-11 libgcc-11-dev rustc cargo build-essential
displayName: Install newer GCC
- script: |
sudo apt-get update
sudo apt-get -y install mpi-default-dev mpi-default-bin
displayName: Install Dependencies
condition: eq(variables['MPI'], 1)
- script: |
mkdir build && cd build
export CC=gcc-11 ; export CXX=g++-11
if [ "${STATIC}" -eq "1" ]; then
cmake -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILD_SHARED_LIBS=OFF \
-DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc \
-static-libstdc++" -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \
-DENABLE_WERROR=1 -DHAVE_${SIMD}=1 -DHAVE_MPI=${MPI} ..
else
cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=${BUILD_TYPE} \
-DENABLE_WERROR=1 -DHAVE_${SIMD}=1 -DHAVE_MPI=${MPI} ..
fi
make -j $(nproc --all)
displayName: Build foldseek
- script: |
cd ${BUILD_SOURCESDIRECTORY}
./regression/run_regression.sh ./build/src/foldseek examples
displayName: Run Regression Suite
condition: eq(variables['regression'], 1)
- task: PublishPipelineArtifact@0
condition: eq(variables['STATIC'], 1)
inputs:
targetPath: $(Build.SourcesDirectory)/build/src/foldseek
artifactName: foldseek-linux-$(SIMD)
- job: build_ubuntu_cross_2004
displayName: Ubuntu 2004 Cross-Compile
pool:
vmImage: 'Ubuntu-20.04'
strategy:
matrix:
arm64:
SIMD: ARM8
ARCH: 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 zlib1g-dev:$ARCH libbz2-dev:$ARCH
rustup target add ${CPREF}-unknown-linux-gnu
displayName: Install Toolchain
- script: |
mkdir build && cd build
CC=${CPREF}-linux-gnu-gcc CXX=${CPREF}-linux-gnu-g++ \
cmake -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DHAVE_TESTS=1 \
-DBUILD_SHARED_LIBS=OFF \
-DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc \
-static-libstdc++" -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \
-DRust_CARGO_TARGET=${CPREF}-unknown-linux-gnu \
-DENABLE_WERROR=1 -DHAVE_${SIMD}=1 ..
make -j $(nproc --all)
displayName: Build foldseek
- task: PublishPipelineArtifact@0
inputs:
targetPath: $(Build.SourcesDirectory)/build/src/foldseek
artifactName: foldseek-linux-$(SIMD)
- job: build_macos
displayName: macOS
pool:
vmImage: 'macos-12'
steps:
- checkout: self
submodules: true
- script: |
rustup update
rustup target install x86_64-apple-darwin
rustup target install aarch64-apple-darwin
displayName: Install Rust Toolchain
- script: |
cd ${BUILD_SOURCESDIRECTORY}
./util/build_osx.sh . build foldseek
displayName: Build foldseek
- script: |
cd ${BUILD_SOURCESDIRECTORY}
./regression/run_regression.sh ./build/foldseek examples
displayName: Run Regression Suite
condition: eq(variables['regression'], 1)
- task: PublishPipelineArtifact@0
inputs:
targetPath: $(Build.SourcesDirectory)/build/foldseek
artifactName: foldseek-darwin-universal
- job: upload_artifacts
displayName: Upload Artifacts
condition: and(succeeded(), ne(variables['Build.Reason'], 'PullRequest'))
pool:
vmImage: 'ubuntu-latest'
dependsOn:
- build_macos
- build_ubuntu_2004
- build_ubuntu_cross_2004
steps:
- script: |
cd "${BUILD_SOURCESDIRECTORY}"
mkdir foldseek
cp -f README.md LICENCE.md foldseek
mkdir foldseek/bin
- task: DownloadPipelineArtifact@1
inputs:
artifactName: foldseek-darwin-universal
targetPath: $(Build.SourcesDirectory)/foldseek/bin
- script:
chmod +x "${BUILD_SOURCESDIRECTORY}/foldseek/bin/foldseek"
- task: ArchiveFiles@2
inputs:
rootFolderOrFile: $(Build.SourcesDirectory)/foldseek
archiveFile: $(Build.SourcesDirectory)/foldseek-osx-universal.tar.gz
includeRootFolder: true
archiveType: tar
- task: DownloadPipelineArtifact@1
inputs:
artifactName: foldseek-linux-SSE2
targetPath: $(Build.SourcesDirectory)/foldseek/bin
- script:
chmod +x "${BUILD_SOURCESDIRECTORY}/foldseek/bin/foldseek"
- task: ArchiveFiles@2
inputs:
rootFolderOrFile: $(Build.SourcesDirectory)/foldseek
archiveFile: $(Build.SourcesDirectory)/foldseek-linux-sse2.tar.gz
includeRootFolder: true
archiveType: tar
# - task: DownloadPipelineArtifact@1
# inputs:
# artifactName: foldseek-linux-SSE4_1
# targetPath: $(Build.SourcesDirectory)/foldseek/bin
# - script:
# chmod +x "${BUILD_SOURCESDIRECTORY}/foldseek/bin/foldseek"
# - task: ArchiveFiles@2
# inputs:
# rootFolderOrFile: $(Build.SourcesDirectory)/foldseek
# archiveFile: $(Build.SourcesDirectory)/foldseek-linux-sse41.tar.gz
# includeRootFolder: true
# archiveType: tar
- task: DownloadPipelineArtifact@1
inputs:
artifactName: foldseek-linux-AVX2
targetPath: $(Build.SourcesDirectory)/foldseek/bin
- script:
chmod +x "${BUILD_SOURCESDIRECTORY}/foldseek/bin/foldseek"
- task: ArchiveFiles@2
inputs:
rootFolderOrFile: $(Build.SourcesDirectory)/foldseek
archiveFile: $(Build.SourcesDirectory)/foldseek-linux-avx2.tar.gz
includeRootFolder: true
archiveType: tar
- task: DownloadPipelineArtifact@1
inputs:
artifactName: foldseek-linux-ARM8
targetPath: $(Build.SourcesDirectory)/foldseek/bin
- script:
chmod +x "${BUILD_SOURCESDIRECTORY}/foldseek/bin/foldseek"
- task: ArchiveFiles@2
inputs:
rootFolderOrFile: $(Build.SourcesDirectory)/foldseek
archiveFile: $(Build.SourcesDirectory)/foldseek-linux-arm64.tar.gz
includeRootFolder: true
archiveType: tar
# - task: DownloadPipelineArtifact@1
# inputs:
# artifactName: foldseek-linux-POWER8
# targetPath: $(Build.SourcesDirectory)/foldseek/bin
# - script:
# chmod +x "${BUILD_SOURCESDIRECTORY}/foldseek/bin/foldseek"
# - task: ArchiveFiles@2
# inputs:
# rootFolderOrFile: $(Build.SourcesDirectory)/foldseek
# archiveFile: $(Build.SourcesDirectory)/foldseek-linux-ppc64le-POWER8.tar.gz
# includeRootFolder: true
# archiveType: tar
# - task: DownloadPipelineArtifact@1
# inputs:
# artifactName: foldseek-linux-POWER9
# targetPath: $(Build.SourcesDirectory)/foldseek/bin
# - script:
# chmod +x "${BUILD_SOURCESDIRECTORY}/foldseek/bin/foldseek"
# - task: ArchiveFiles@2
# inputs:
# rootFolderOrFile: $(Build.SourcesDirectory)/foldseek
# archiveFile: $(Build.SourcesDirectory)/foldseek-linux-ppc64le-POWER9.tar.gz
# includeRootFolder: true
# archiveType: tar
- task: DownloadSecureFile@1
inputs:
secureFile: azure_upload_foldseek
displayName: Get Deployment Key
- script: |
mkdir ~/.ssh && mv $DOWNLOADSECUREFILE_SECUREFILEPATH ~/.ssh/id_rsa
chmod 700 ~/.ssh && chmod 600 ~/.ssh/id_rsa
ssh-keygen -f ~/.ssh/id_rsa -y > ~/.ssh/id_rsa.pub
cd "${BUILD_SOURCESDIRECTORY}"
# disabled:foldseek-linux-sse41.tar.gz foldseek-linux-ppc64le-POWER8.tar.gz foldseek-linux-ppc64le-POWER9.tar.gz
ssh-keygen -Y sign -f ~/.ssh/id_rsa -n file \
foldseek-osx-universal.tar.gz \
foldseek-linux-sse2.tar.gz \
foldseek-linux-avx2.tar.gz \
foldseek-linux-arm64.tar.gz
curl --retry 5 --retry-all-errors -X POST \
-F file[]=@foldseek-osx-universal.tar.gz -F signature[]=@foldseek-osx-universal.tar.gz.sig \
-F file[]=@foldseek-linux-sse2.tar.gz -F signature[]=@foldseek-linux-sse2.tar.gz.sig \
-F file[]=@foldseek-linux-avx2.tar.gz -F signature[]=@foldseek-linux-avx2.tar.gz.sig \
-F file[]=@foldseek-linux-arm64.tar.gz -F signature[]=@foldseek-linux-arm64.tar.gz.sig \
-F identifier="foldseek" -F directory="${BUILD_SOURCEVERSION}" \
https://mmseqs.com/upload