Sync back mmseqs build system changes

steineggerlab · Jan 7, 2025 · 84ccdb4 · 84ccdb4
1 parent 8d6fca9
commit 84ccdb4
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Showing 2 changed files with 18 additions and 12 deletions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -18,12 +18,12 @@ 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
@@ -33,7 +33,7 @@ jobs:
           SIMD: 'AVX2'
           STATIC: 0
           MPI: 1
-          BUILD_TYPE: RelWithDebInfo
+          BUILD_TYPE: Release
         asan:
           SIMD: 'AVX2'
           STATIC: 0
@@ -102,19 +102,25 @@ jobs:
       - script: |
           mkdir build && cd build
           export CC=gcc-10 ; export CXX=g++-10; export CUDAHOSTCXX=$CXX; export CUDACXX=/usr/local/cuda/bin/nvcc;
-          LIBGOMP=/usr/lib/gcc/x86_64-linux-gnu/10;
-          /usr/local/bin/cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=1 -DHAVE_AVX2=1 \
-            -DFORCE_STATIC_DEPS=1 -DCMAKE_LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10 -DBUILD_SHARED_LIBS=OFF \
-            -DOpenMP_C_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY=${LIBGOMP}/libgomp.a \
+          LIBGCC=/usr/lib/gcc/x86_64-linux-gnu/10;
+          /usr/local/bin/cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=0 -DENABLE_WERROR=1 -DHAVE_AVX2=1 \
+            -DFORCE_STATIC_DEPS=1 -DATOMIC_LIB_OVERRIDE=${LIBGCC}/libatomic.a \
+            -DOpenMP_C_FLAGS="-fopenmp -I${LIBGCC}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGCC}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY=${LIBGCC}/libgomp.a \
             -DENABLE_CUDA=1 -DCMAKE_CUDA_ARCHITECTURES="75-real;80-real;86-real;89-real;90" ..
-          cmake --build . -j$(nproc --all)
+          cmake --build . -j$(nproc --all) -v
           # fail if GLIBC_PRIVATE or too new GLIBC is present
           if readelf -Ws src/foldseek | grep -q GLIBC_PRIVATE; then
+            echo "Error: binary contains private glibc symbols"
             exit 1
           fi
           LIBC_V=$(readelf -V src/foldseek | 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/foldseek | grep -q "libatomic.so"; then
+            echo "Error: libatomic.so is present as a dependency"
+            exit 1
           fi
         displayName: Build GPU
       - task: PublishPipelineArtifact@0
@@ -151,7 +157,7 @@ jobs:
         displayName: Install Toolchain
       - script: |
           mkdir build && cd build
-          LIBGOMP=/usr/lib/gcc-cross/aarch64-linux-gnu/9
+          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 -DFORCE_STATIC_DEPS=1 \
             -DRust_CARGO_TARGET=${CPREF}-unknown-linux-gnu \

diff --git a/util/build_osx.sh b/util/build_osx.sh
@@ -50,7 +50,7 @@ cmake \
     -DCMAKE_BUILD_TYPE=Release \
     -DHAVE_TESTS=0 -DHAVE_MPI=0 -DHAVE_AVX2=1 \
     -DCMAKE_OSX_ARCHITECTURES=x86_64 \
-    -DCMAKE_C_FLAGS="-arch x86_64" -DCMAKE_CXX_FLAGS="-arch x86_64" \
+    -DCMAKE_C_FLAGS="-arch x86_64" -DCMAKE_CXX_FLAGS="-arch x86_64" -DCMAKE_ASM_FLAGS="-arch arm64" \
     -DBUILD_SHARED_LIBS=OFF -DCMAKE_FIND_LIBRARY_SUFFIXES=".a" \
     -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I${LIBOMP_AMD64}" -DOpenMP_C_LIB_NAMES=omp -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I${LIBOMP_AMD64}" -DOpenMP_CXX_LIB_NAMES=omp -DOpenMP_omp_LIBRARY=${LIBOMP_AMD64}/libomp.a \
     -DRust_CARGO_TARGET=x86_64-apple-darwin -DGGML_METAL=OFF \
@@ -98,7 +98,7 @@ fi
 
 lipo \
     -create \
-    -arch x86_64  "$BUILD/build_avx2/src/${BINARY_NAME}" \
+    -arch x86_64 "$BUILD/build_avx2/src/${BINARY_NAME}" \
     -arch arm64 "$BUILD/build_arm64/src/${BINARY_NAME}" \
     -output "$BUILD/${BINARY_NAME}"