Sync build system changes with foldseek

changes relicensed as MIT for MMseqs2
soedinglab · Jan 7, 2025 · 9927445 · 9927445
1 parent b0e91c1
commit 9927445
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Showing 5 changed files with 124 additions and 108 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,4 +1,6 @@
-cmake_minimum_required(VERSION 2.8.12 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.15 FATAL_ERROR)
+cmake_policy(SET CMP0060 OLD)
+cmake_policy(SET CMP0074 NEW)
 project(MMseqs CXX C)
 message("-- Source Directory: ${CMAKE_CURRENT_SOURCE_DIR}")
 message("-- Project Directory: ${PROJECT_SOURCE_DIR}")
@@ -18,12 +20,24 @@ set(HAVE_ARM8 0 CACHE BOOL "Have ARMv8 CPU")
 set(HAVE_S390X 0 CACHE BOOL "Have s390x architecture")
 set(NATIVE_ARCH 1 CACHE BOOL "Assume native architecture for SIMD. Use one of the HAVE_* options or set CMAKE_CXX_FLAGS to the appropriate flags if you disable this.")
 set(USE_SYSTEM_ZSTD 0 CACHE BOOL "Use zstd provided by system instead of bundled version")
-
 set(ENABLE_CUDA 0 CACHE BOOL "Enable CUDA")
+set(FORCE_STATIC_DEPS 0 CACHE BOOL "Force static linking of deps")
+
+if(FORCE_STATIC_DEPS)
+    if(ENABLE_CUDA)
+        set(CMAKE_FIND_LIBRARY_SUFFIXES .a .so CACHE INTERNAL "" FORCE)
+        set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static-libgcc -static-libstdc++")
+    else()
+        set(CMAKE_FIND_LIBRARY_SUFFIXES .a CACHE INTERNAL "" FORCE)
+        set(CMAKE_LINK_SEARCH_START_STATIC ON CACHE INTERNAL "" FORCE)
+        set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static -static-libgcc -static-libstdc++")
+    endif()
+    set(BUILD_SHARED_LIBS OFF CACHE INTERNAL "" FORCE)
+endif()
 
-set(PREFER_STATIC 0 CACHE BOOL "Prefer finding .a libs")
-if (PREFER_STATIC)
-    set(CMAKE_FIND_LIBRARY_SUFFIXES ".a" ".so")
+if(NOT XCODE AND NOT MSVC AND NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
+    set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
 endif()
 
 if (HAVE_SANITIZER)
@@ -33,10 +47,6 @@ if (HAVE_SANITIZER)
     include(FindTSan)
 endif ()
 
-if (NOT CMAKE_BUILD_TYPE)
-    set(CMAKE_BUILD_TYPE Release)
-endif ()
-
 # find compiler
 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
     message("-- Compiler is clang(++)")

diff --git a/Dockerfile b/Dockerfile
@@ -13,7 +13,7 @@ RUN dpkg --add-architecture $TARGETARCH \
     if [ "$GPU" = "1" ]; then \
       wget https://developer.download.nvidia.com/compute/cuda/repos/debian12/x86_64/cuda-keyring_1.1-1_all.deb; \
       dpkg -i cuda-keyring_1.1-1_all.deb; \
-      apt-get update && apt-get install -y cuda-nvcc-12-6 ninja-build; \
+      apt-get update && apt-get install -y cuda-nvcc-12-6 cuda-cudart-dev-12-6 ninja-build; \
     fi; \
     rm -rf /var/lib/apt/lists/*;
 
@@ -32,10 +32,10 @@ RUN if [ "$TARGETARCH" = "arm64" ]; then \
         export CUDACXX=/usr/local/cuda/bin/nvcc; \
         mkdir -p build_avx2/src; \
         cd /opt/build/build_avx2; \
-        cmake -GNinja -DHAVE_AVX2=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 \
-        -DPREFER_STATIC=1 -DBUILD_SHARED_LIBS=OFF \
-        -DCMAKE_EXE_LINKER_FLAGS="-static-libgcc -static-libstdc++" \
+        LIBGOMP=/usr/lib/gcc/x86_64-linux-gnu/12/; \
+        cmake -GNinja -DHAVE_AVX2=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DFORCE_STATIC_DEPS=1 \
         -DENABLE_CUDA=1 -DCMAKE_CUDA_ARCHITECTURES="75-real;80-real;86-real;89-real;90" \
+        -DOpenMP_C_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY=${LIBGOMP}/libgomp.a \
         -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
         cmake --build . -j$(nproc --all); \
         mv src/${APP} /opt/build/${APP}_avx2; \

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -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 ${BUILD_SOURCESDIRECTORY}/regression
         displayName: Run Regression Suite
         condition: eq(variables['regression'], 1)
@@ -149,7 +141,7 @@ jobs:
           wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.1-1_all.deb
           sudo dpkg -i cuda-keyring_1.1-1_all.deb
           sudo apt-get update
-          sudo apt-get install -y gcc-10 g++-10 cuda-nvcc-12-6 build-essential libgcc-10-dev ninja-build
+          sudo apt-get install -y gcc-10 g++-10 cuda-nvcc-12-6 cuda-cudart-dev-12-6 build-essential libgcc-10-dev ninja-build
           sudo apt-get purge -y cmake
           wget https://github.com/Kitware/CMake/releases/download/v3.31.0/cmake-3.31.0-linux-x86_64.sh
           chmod +x cmake-3.31.0-linux-x86_64.sh
@@ -158,16 +150,15 @@ jobs:
       - script: |
           mkdir build && cd build
           export CC=gcc-10 ; export CXX=g++-10; export CUDAHOSTCXX=$CXX; export CUDACXX=/usr/local/cuda/bin/nvcc;
+          LIBGOMP=/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" ..
+            -DFORCE_STATIC_DEPS=1 -DENABLE_CUDA=1 -DCMAKE_CUDA_ARCHITECTURES="75-real;80-real;86-real;89-real;90" ..
           cmake --build . -j$(nproc --all)
           # fail if GLIBC_PRIVATE or too new GLIBC is present
-          if readelf -Ws mmseqs | grep -q GLIBC_PRIVATE; then
+          if readelf -Ws src/mmseqs | grep -q GLIBC_PRIVATE; then
             exit 1
           fi
-          LIBC_V=$(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
           fi
@@ -184,10 +175,10 @@ 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 +206,14 @@ jobs:
         displayName: Install Toolchain
       - script: |
           mkdir build && cd build
+          if [ "${ARCH}" = "ppc64el" ]; then
+            LIBGOMP=/usr/lib/gcc-cross/powerpc64-linux-gnu/9;
+          else
+            LIBGOMP=/usr/lib/gcc-cross/${CPREF}-linux-gnu/9;
+          fi
           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 +376,18 @@ 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: $(Build.SourcesDirectory)/mmseqs-linux-ppc64le-power8.tar.gz
+      #     includeRootFolder: true
+      #     archiveType: tar
       - task: DownloadPipelineArtifact@1
         inputs:
           artifactName: mmseqs-linux-ARM8
@@ -431,6 +425,8 @@ jobs:
           ssh-keygen -f ~/.ssh/id_rsa -y > ~/.ssh/id_rsa.pub
           cd "${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 +435,6 @@ 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 +445,6 @@ 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}" \

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -215,20 +215,7 @@ find_package(OpenMP QUIET)
 if (OPENMP_FOUND)
     message("-- Found OpenMP")
     target_compile_definitions(mmseqs-framework PUBLIC -DOPENMP=1)
-    # Try to get "nearly" static builds working with everything except libc static
-    if (PREFER_STATIC)
-        set(FILTERED_LIBRARIES "")
-        foreach(LIB ${OpenMP_CXX_LIBRARIES})
-            if (NOT LIB MATCHES "pthread" AND NOT LIB MATCHES "gcc_s")
-                list(APPEND FILTERED_LIBRARIES ${LIB})
-            endif ()
-        endforeach()
-        set(OpenMP_CXX_LIBRARIES ${FILTERED_LIBRARIES})
-    endif ()
     target_link_libraries(mmseqs-framework ${OpenMP_CXX_LIBRARIES})
-    if (PREFER_STATIC)
-        target_link_libraries(mmseqs-framework dl)
-    endif ()
     target_include_directories(mmseqs-framework PUBLIC ${OpenMP_CXX_INCLUDE_DIRS})
     append_target_property(mmseqs-framework COMPILE_FLAGS ${OpenMP_CXX_FLAGS})
     append_target_property(mmseqs-framework LINK_FLAGS ${OpenMP_CXX_FLAGS})
@@ -250,12 +237,7 @@ endif ()
 if (ENABLE_CUDA)
     find_package(CUDAToolkit REQUIRED)
     target_compile_definitions(mmseqs-framework PUBLIC -DHAVE_CUDA=1)
-    target_link_libraries(mmseqs-framework marv)
-    if (PREFER_STATIC)
-        # link to rt explicitly so it doesn't get statically compiled and adds GLIBC_PRIVATE symbols
-        target_link_libraries(mmseqs-framework rt)
-    endif ()
-    target_link_libraries(mmseqs-framework CUDA::cudart_static)
+    target_link_libraries(mmseqs-framework marv CUDA::cudart_static)
 endif ()
 
 if (NOT FRAMEWORK_ONLY)