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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -68,22 +68,22 @@ jobs: | |
| SIMD: 'AVX2' | ||
| STATIC: 1 | ||
| MPI: 0 | ||
| BUILD_TYPE: RelWithDebInfo | ||
| BUILD_TYPE: Release | ||
| sse41: | ||
| SIMD: 'SSE4_1' | ||
| STATIC: 1 | ||
| MPI: 0 | ||
| BUILD_TYPE: RelWithDebInfo | ||
| BUILD_TYPE: Release | ||
| sse2: | ||
| SIMD: 'SSE2' | ||
| STATIC: 1 | ||
| MPI: 0 | ||
| BUILD_TYPE: RelWithDebInfo | ||
| BUILD_TYPE: Release | ||
| avx2_mpi: | ||
| SIMD: 'AVX2' | ||
| STATIC: 0 | ||
| MPI: 1 | ||
| BUILD_TYPE: RelWithDebInfo | ||
| BUILD_TYPE: Release | ||
| asan: | ||
| SIMD: 'AVX2' | ||
| STATIC: 0 | ||
|
|
@@ -94,10 +94,9 @@ jobs: | |
| - checkout: self | ||
| submodules: true | ||
| - script: | | ||
| #sudo add-apt-repository ppa:ubuntu-toolchain-r/test | ||
| #sudo apt-get update | ||
| sudo apt-get install -y g++-10 | ||
| condition: eq(variables['BUILD_TYPE'], 'ASanOpt') | ||
| 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 build-essential | ||
| displayName: Install newer G++ | ||
| - script: | | ||
| sudo apt-get update | ||
|
|
@@ -106,28 +105,21 @@ jobs: | |
| condition: eq(variables['MPI'], 1) | ||
| - script: | | ||
| mkdir build && cd build | ||
| if [ "${BUILD_TYPE}" = "ASanOpt" ]; then | ||
| export CC=gcc-10 ; export CXX=g++-10 | ||
| fi | ||
| export CC=gcc-11 ; export CXX=g++-11 | ||
| if [ "${STATIC}" -eq "1" ]; then | ||
| cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DHAVE_TESTS=1 \ | ||
| -DBUILD_SHARED_LIBS=OFF \ | ||
| -DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc \ | ||
| -static-libstdc++" -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \ | ||
| -DENABLE_WERROR=1 -DHAVE_${SIMD}=1 -DHAVE_MPI=${MPI} .. | ||
| LIBGOMP=/usr/lib/gcc/x86_64-linux-gnu/11 | ||
| cmake -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DFORCE_STATIC_DEPS=1 -DHAVE_TESTS=1 \ | ||
| -DOpenMP_C_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY=${LIBGOMP}/libgomp.a \ | ||
| -DENABLE_WERROR=1 -DHAVE_${SIMD}=1 -DHAVE_MPI=${MPI} .. | ||
| else | ||
| cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DHAVE_TESTS=1 \ | ||
| -DENABLE_WERROR=1 -DHAVE_${SIMD}=1 -DHAVE_MPI=${MPI} .. | ||
| cmake -DHAVE_SANITIZER=1 -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DHAVE_TESTS=1 \ | ||
| -DENABLE_WERROR=1 -DHAVE_${SIMD}=1 -DHAVE_MPI=${MPI} .. | ||
| fi | ||
| make -j $(nproc --all) | ||
| make -j $(nproc --all) VERBOSE=1 | ||
| displayName: Build MMseqs2 | ||
| - script: | | ||
| export TTY=0 | ||
| if [ "${BUILD_TYPE}" = "ASan" ]; then | ||
| echo "leak:libgomp1" > ${BUILD_SOURCESDIRECTORY}/ASan.supp | ||
| export ASAN_OPTIONS=suppressions=${BUILD_SOURCESDIRECTORY}/ASan.supp | ||
| fi | ||
| ${BUILD_SOURCESDIRECTORY}/util/regression/run_regression.sh ${BUILD_SOURCESDIRECTORY}/build/src/mmseqs ${BUILD_SOURCESDIRECTORY}/regression | ||
| displayName: Run Regression Suite | ||
| condition: eq(variables['regression'], 1) | ||
|
|
@@ -149,7 +141,7 @@ jobs: | |
| wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.1-1_all.deb | ||
| sudo dpkg -i cuda-keyring_1.1-1_all.deb | ||
| sudo apt-get update | ||
| sudo apt-get install -y gcc-10 g++-10 cuda-nvcc-12-6 build-essential libgcc-10-dev ninja-build | ||
| sudo apt-get install -y gcc-10 g++-10 cuda-nvcc-12-6 cuda-cudart-dev-12-6 build-essential libgcc-10-dev ninja-build | ||
| sudo apt-get purge -y cmake | ||
| wget https://github.com/Kitware/CMake/releases/download/v3.31.0/cmake-3.31.0-linux-x86_64.sh | ||
| chmod +x cmake-3.31.0-linux-x86_64.sh | ||
|
|
@@ -158,18 +150,25 @@ jobs: | |
| - script: | | ||
| mkdir build && cd build | ||
| export CC=gcc-10 ; export CXX=g++-10; export CUDAHOSTCXX=$CXX; export CUDACXX=/usr/local/cuda/bin/nvcc; | ||
| LIBGCC=/usr/lib/gcc/x86_64-linux-gnu/10; | ||
| /usr/local/bin/cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=1 -DHAVE_AVX2=1 \ | ||
| -DPREFER_STATIC=1 -DCMAKE_LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10 -DBUILD_SHARED_LIBS=OFF \ | ||
| -DCMAKE_EXE_LINKER_FLAGS="-static-libgcc -static-libstdc++" \ | ||
| -DENABLE_CUDA=1 -DCMAKE_CUDA_ARCHITECTURES="75-real;80-real;86-real;89-real;90" .. | ||
| cmake --build . -j$(nproc --all) | ||
| -DOpenMP_C_FLAGS="-fopenmp -I${LIBGCC}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGCC}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY=${LIBGCC}/libgomp.a \ | ||
| -DATOMIC_LIB_OVERRIDE=${LIBGCC}/libatomic.a \ | ||
| -DFORCE_STATIC_DEPS=1 -DENABLE_CUDA=1 -DCMAKE_CUDA_ARCHITECTURES="75-real;80-real;86-real;89-real;90" .. | ||
| cmake --build . -j$(nproc --all) -v | ||
| # fail if GLIBC_PRIVATE or too new GLIBC is present | ||
| if readelf -Ws mmseqs | grep -q GLIBC_PRIVATE; then | ||
| if readelf -Ws src/mmseqs | grep -q GLIBC_PRIVATE; then | ||
| echo "Error: binary contains private glibc symbols" | ||
| exit 1 | ||
| fi | ||
| LIBC_V=$(readelf -V mmseqs | awk '$3 ~ /^GLIBC_/ { print $3 }' | sort -V | tail -n1) | ||
| LIBC_V=$(readelf -V src/mmseqs | awk '$3 ~ /^GLIBC_/ { print $3 }' | sort -V | tail -n1) | ||
| if [[ "$LIBC_V" > "GLIBC_2.29" ]]; then | ||
| exit 1 | ||
| echo "Error: glibc too new" | ||
| exit 1 | ||
| fi | ||
| if readelf -d src/mmseqs | grep -q "libatomic.so"; then | ||
| echo "Error: libatomic.so is present as a dependency" | ||
| exit 1 | ||
| fi | ||
| displayName: Build MMseqs2 | ||
| - task: PublishPipelineArtifact@0 | ||
|
|
@@ -184,10 +183,10 @@ jobs: | |
| timeoutInMinutes: 120 | ||
| strategy: | ||
| matrix: | ||
| power8: | ||
| SIMD: POWER8 | ||
| ARCH: ppc64el | ||
| CPREF: powerpc64le | ||
| # power8: | ||
| # SIMD: POWER8 | ||
| # ARCH: ppc64el | ||
| # CPREF: powerpc64le | ||
| power9: | ||
| SIMD: POWER9 | ||
| ARCH: ppc64el | ||
|
|
@@ -215,11 +214,10 @@ jobs: | |
| displayName: Install Toolchain | ||
| - script: | | ||
| mkdir build && cd build | ||
| LIBGOMP=/usr/lib/gcc-cross/${CPREF}-linux-gnu/9; | ||
| CC=${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" \ | ||
| cmake -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DHAVE_TESTS=1 -DFORCE_STATIC_DEPS=1 \ | ||
| -DOpenMP_C_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY=${LIBGOMP}/libgomp.a \ | ||
| -DENABLE_WERROR=1 -DHAVE_${SIMD}=1 .. | ||
| make -j $(nproc --all) | ||
| displayName: Build MMseqs2 | ||
|
|
@@ -382,18 +380,18 @@ jobs: | |
| archiveFile: $(Build.SourcesDirectory)/mmseqs-linux-ppc64le-power9.tar.gz | ||
| includeRootFolder: true | ||
| archiveType: tar | ||
| - task: DownloadPipelineArtifact@1 | ||
| inputs: | ||
| artifactName: mmseqs-linux-POWER8 | ||
| targetPath: $(Build.SourcesDirectory)/mmseqs/bin | ||
| - script: | ||
| chmod +x "${BUILD_SOURCESDIRECTORY}/mmseqs/bin/mmseqs" | ||
| - task: ArchiveFiles@2 | ||
| inputs: | ||
| rootFolderOrFile: $(Build.SourcesDirectory)/mmseqs | ||
| archiveFile: $(Build.SourcesDirectory)/mmseqs-linux-ppc64le-power8.tar.gz | ||
| includeRootFolder: true | ||
| archiveType: tar | ||
| # - task: DownloadPipelineArtifact@1 | ||
| # inputs: | ||
| # artifactName: mmseqs-linux-POWER8 | ||
| # targetPath: $(Build.SourcesDirectory)/mmseqs/bin | ||
| # - script: | ||
| # chmod +x "${BUILD_SOURCESDIRECTORY}/mmseqs/bin/mmseqs" | ||
| # - task: ArchiveFiles@2 | ||
| # inputs: | ||
| # rootFolderOrFile: $(Build.SourcesDirectory)/mmseqs | ||
| # archiveFile: $(Build.SourcesDirectory)/mmseqs-linux-ppc64le-power8.tar.gz | ||
| # includeRootFolder: true | ||
| # archiveType: tar | ||
| - task: DownloadPipelineArtifact@1 | ||
| inputs: | ||
| artifactName: mmseqs-linux-ARM8 | ||
|
|
@@ -431,6 +429,8 @@ jobs: | |
| ssh-keygen -f ~/.ssh/id_rsa -y > ~/.ssh/id_rsa.pub | ||
| cd "${BUILD_SOURCESDIRECTORY}" | ||
| cp mmseqs/userguide.pdf userguide.pdf | ||
| # disabled: mmseqs-linux-ppc64le-power8.tar.gz | ||
| # -F file[][email protected] -F signature[][email protected] | ||
| ssh-keygen -Y sign -f ~/.ssh/id_rsa -n file \ | ||
| userguide.pdf \ | ||
| mmseqs-osx-universal.tar.gz \ | ||
|
|
@@ -439,7 +439,6 @@ jobs: | |
| mmseqs-linux-avx2.tar.gz \ | ||
| mmseqs-linux-gpu.tar.gz \ | ||
| mmseqs-linux-arm64.tar.gz \ | ||
| mmseqs-linux-ppc64le-power8.tar.gz \ | ||
| mmseqs-linux-ppc64le-power9.tar.gz \ | ||
| mmseqs-win64.zip | ||
| curl --retry 5 --retry-all-errors -X POST \ | ||
|
|
@@ -450,7 +449,6 @@ jobs: | |
| -F file[][email protected] -F signature[][email protected] \ | ||
| -F file[][email protected] -F signature[][email protected] \ | ||
| -F file[][email protected] -F signature[][email protected] \ | ||
| -F file[][email protected] -F signature[][email protected] \ | ||
| -F file[][email protected] -F signature[][email protected] \ | ||
| -F file[][email protected] -F signature[][email protected] \ | ||
| -F identifier="mmseqs" -F directory="${BUILD_SOURCEVERSION}" \ | ||
|
|
||
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