Readd tweaked hack to remove GLIBC_PRIVATE symbols

soedinglab · Jan 7, 2025 · 7e2732c · 7e2732c
1 parent 8bf7c5e
commit 7e2732c
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Showing 2 changed files with 21 additions and 8 deletions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -152,19 +152,18 @@ jobs:
           export CC=gcc-10 ; export CXX=g++-10; export CUDAHOSTCXX=$CXX; export CUDACXX=/usr/local/cuda/bin/nvcc;
           LIBGOMP=/usr/lib/gcc/x86_64-linux-gnu/10;
           /usr/local/bin/cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=1 -DHAVE_AVX2=1 \
+            -DOpenMP_C_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_C_LIB_NAMES=gomp -DOpenMP_CXX_FLAGS="-fopenmp -I${LIBGOMP}" -DOpenMP_CXX_LIB_NAMES=gomp -DOpenMP_gomp_LIBRARY=${LIBGOMP}/libgomp.a \
             -DFORCE_STATIC_DEPS=1 -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
+          readelf -Ws src/mmseqs
+          readelf -V src/mmseqs
           if readelf -Ws src/mmseqs | grep -q GLIBC_PRIVATE; then
-            readelf -Ws src/mmseqs
-            readelf -V src/mmseqs
-            # exit 1
+            exit 1
           fi
           LIBC_V=$(readelf -V src/mmseqs | awk '$3 ~ /^GLIBC_/ { print $3 }' | sort -V | tail -n1)
           if [[ "$LIBC_V" > "GLIBC_2.29" ]]; then
-            readelf -Ws src/mmseqs
-            readelf -V src/mmseqs
-            # exit 1
+            exit 1
           fi
         displayName: Build MMseqs2
       - task: PublishPipelineArtifact@0

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -247,7 +247,21 @@ endif ()
 if (ENABLE_CUDA)
     find_package(CUDAToolkit REQUIRED)
     target_compile_definitions(mmseqs-framework PUBLIC -DHAVE_CUDA=1)
-    target_link_libraries(mmseqs-framework marv CUDA::cudart_static)
+    target_link_libraries(mmseqs-framework marv)
+    if (FORCE_STATIC_DEPS)
+        # link to rt explicitly so it doesn't get statically compiled and adds GLIBC_PRIVATE symbols
+        target_link_libraries(mmseqs-framework rt)
+        # remove librt.a which introduces GLIBC_PRIVATE symbols
+        get_property(linked_libraries TARGET CUDA::cudart_static_deps PROPERTY INTERFACE_LINK_LIBRARIES)
+        set(FILTERED_LIBRARIES "")
+        foreach (LIB ${linked_libraries})
+            if (NOT LIB MATCHES ".*librt\\.a$")
+                list(APPEND FILTERED_LIBRARIES ${LIB})
+            endif ()
+        endforeach ()
+        set_target_properties(CUDA::cudart_static_deps PROPERTIES INTERFACE_LINK_LIBRARIES "${FILTERED_LIBRARIES}")
+    endif ()
+    target_link_libraries(mmseqs-framework CUDA::cudart_static)
 endif ()
 
 if (NOT FRAMEWORK_ONLY)