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milot-mirditamilot-mirdita
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Try to build GPU binary within old glibc docker for compatibility
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Diff for: ‎.github/workflows/Dockerfile.GPU-manylinux2014

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FROM quay.io/pypa/manylinux2014_x86_64
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ARG VER="12-6"
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ARG ARCH="x86_64"
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# CUDA
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RUN yum install -y yum-utils
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RUN yum-config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
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# libcublas-devel-${VER}.${ARCH}
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RUN yum -y install cuda-nvcc-${VER}.${ARCH} cuda-cudart-devel-${VER}.${ARCH}
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RUN echo "/usr/local/cuda/lib64" >> /etc/ld.so.conf.d/999_nvidia_cuda.conf
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ENV PATH="/usr/local/cuda/bin:${PATH}"
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ENV LD_LIBRARY_PATH="/usr/local/cuda/lib64:${LD_LIBRARY_PATH}"
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ENV CUDA_HOME=/usr/local/cuda
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ENV CUDA_ROOT=/usr/local/cuda
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ENV CUDA_PATH=/usr/local/cuda
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ENV CUDADIR=/usr/local/cuda
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# Build system
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RUN yum install -y git wget vim zlib-devel bzip2-devel ninja-build centos-release-scl
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RUN mv /etc/yum.repos.d/CentOS-SCLo-scl.repo /etc/yum.repos.d/CentOS-SCLo-scl.repo.disabled
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RUN yum install -y devtoolset-11-gcc devtoolset-11-gcc-c++ devtoolset-11-libatomic-devel
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ENV CC=/opt/rh/devtoolset-11/root/bin/gcc
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ENV CXX=/opt/rh/devtoolset-11/root/bin/g++
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ENV CUDAHOSTCXX=/opt/rh/devtoolset-11/root/bin/g++
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ENV CUDACXX=/usr/local/cuda/bin/nvcc
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ENV LIBGCC=/opt/rh/devtoolset-11/root/usr/lib/gcc/x86_64-redhat-linux/11
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# cmake
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RUN wget https://github.com/Kitware/CMake/releases/download/v3.31.0/cmake-3.31.0-linux-x86_64.sh; \
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chmod +x cmake-3.31.0-linux-x86_64.sh; \
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./cmake-3.31.0-linux-x86_64.sh --skip-license --prefix=/usr/local;
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RUN mkdir /deps; \
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cd /deps; \
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wget https://sourceware.org/pub/bzip2/bzip2-1.0.8.tar.gz; \
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tar xzvf bzip2-1.0.8.tar.gz; \
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cd bzip2-1.0.8; \
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make install PREFIX=/deps;
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RUN cd /deps; \
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wget https://www.zlib.net/zlib-1.3.1.tar.gz; \
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tar xzvf zlib-1.3.1.tar.gz; \
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cd zlib-1.3.1; \
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./configure --prefix=/deps --static; \
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make install;
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# compile
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WORKDIR /work
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ADD . .
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RUN mkdir -p /work/build && cd /work/build; \
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if [ -e "${LIBGCC}/libgomp.so" ]; then \
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mv -f -- "${LIBGCC}/libgomp.so" "${LIBGCC}/libgomp.so.disabled"; \
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fi; \
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/usr/local/bin/cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=1 -DHAVE_AVX2=1 \
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-DOpenMP_C_FLAGS="-fopenmp -I${LIBGCC} -L${LIBGCC}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGCC} -L${LIBGCC}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY="${LIBGCC}/libgomp.a" \
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-DATOMIC_LIB_OVERRIDE="${LIBGCC}/libatomic.a" \
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-DCMAKE_POLICY_DEFAULT_CMP0074=NEW -DCMAKE_POLICY_DEFAULT_CMP0144=NEW \
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-DZLIB_ROOT=/deps -DBZIP2_ROOT=/deps \
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-DFORCE_STATIC_DEPS=1 -DENABLE_CUDA=1 -DCMAKE_CUDA_ARCHITECTURES="75-real;80-real;86-real;89-real;90" ..; \
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cmake --build . -j$(nproc --all) -v;
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RUN if ldd /work/build/src/mmseqs | grep -P -v "linux-vdso.so|/lib64/(ld-linux-x86-64|libc|libm|libdl|librt|libpthread).so" | grep -q .; then \
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echo "Error: unwanted libraries found"; \
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ldd /work/build/src/mmseqs; \
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exit 1; \
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fi; \
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if readelf -Ws /work/build/src/mmseqs | grep -q GLIBC_PRIVATE; then \
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echo "Error: binary contains private glibc symbols"; \
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readelf -Ws /work/build/src/mmseqs; \
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exit 1; \
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fi; \
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LIBC_V=$(readelf -V /work/build/src/mmseqs | awk '$3 ~ /^GLIBC_/ { print $3 }' | sort -V | tail -n1); \
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if [[ "$LIBC_V" > "GLIBC_2.17" ]]; then \
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echo "Error: glibc too new"; \
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readelf -V /work/build/src/mmseqs; \
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exit 1; \
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fi;

Diff for: ‎azure-pipelines.yml

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@@ -137,43 +137,26 @@ jobs:
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steps:
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- checkout: self
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submodules: false
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- script: |
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wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.1-1_all.deb
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sudo dpkg -i cuda-keyring_1.1-1_all.deb
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sudo apt-get update
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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
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sudo apt-get purge -y cmake
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wget https://github.com/Kitware/CMake/releases/download/v3.31.0/cmake-3.31.0-linux-x86_64.sh
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chmod +x cmake-3.31.0-linux-x86_64.sh
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sudo ./cmake-3.31.0-linux-x86_64.sh --skip-license --prefix=/usr/local
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displayName: Install newer G++
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- script: |
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mkdir build && cd build
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export CC=gcc-10 ; export CXX=g++-10; export CUDAHOSTCXX=$CXX; export CUDACXX=/usr/local/cuda/bin/nvcc;
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LIBGCC=/usr/lib/gcc/x86_64-linux-gnu/10;
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/usr/local/bin/cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=1 -DHAVE_AVX2=1 \
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-DOpenMP_C_FLAGS="-fopenmp -I${LIBGCC}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGCC}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY=${LIBGCC}/libgomp.a \
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-DATOMIC_LIB_OVERRIDE=${LIBGCC}/libatomic.a \
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-DFORCE_STATIC_DEPS=1 -DENABLE_CUDA=1 -DCMAKE_CUDA_ARCHITECTURES="75-real;80-real;86-real;89-real;90" ..
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cmake --build . -j$(nproc --all) -v
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# fail if GLIBC_PRIVATE or too new GLIBC is present
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if readelf -Ws src/mmseqs | grep -q GLIBC_PRIVATE; then
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echo "Error: binary contains private glibc symbols"
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exit 1
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fi
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LIBC_V=$(readelf -V src/mmseqs | awk '$3 ~ /^GLIBC_/ { print $3 }' | sort -V | tail -n1)
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if [[ "$LIBC_V" > "GLIBC_2.29" ]]; then
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echo "Error: glibc too new"
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exit 1
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fi
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if readelf -d src/mmseqs | grep -q "libatomic.so"; then
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echo "Error: libatomic.so is present as a dependency"
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exit 1
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fi
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displayName: Build MMseqs2
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- task: PublishPipelineArtifact@0
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- task: Docker@2
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displayName: Build Docker Image
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inputs:
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targetPath: $(Build.SourcesDirectory)/build/src/mmseqs
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command: build
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dockerfile: '.github/workflows/Dockerfile.GPU-manylinux2014'
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tags: |
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manylinux-latest:latest
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buildContext: '$(Build.SourcesDirectory)'
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- script: mkdir -p ${BUILD_SOURCESDIRECTORY}/output
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- task: Docker@2
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displayName: Run Build in Docker
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inputs:
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command: run
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imageName: 'manylinux-latest:latest'
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options: >
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-v $(Build.SourcesDirectory)/output:/output
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arguments: /bin/bash -c "cp /work/build/src/mmseqs /output/"
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- task: PublishPipelineArtifact@1
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inputs:
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targetPath: $(Build.SourcesDirectory)/output/mmseqs
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artifactName: mmseqs-linux-gpu
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- job: build_ubuntu_cross

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