Try building precompiled binaries for GPU

soedinglab · Nov 15, 2024 · 73a8127 · 73a8127
1 parent b63668c
commit 73a8127
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Showing 4 changed files with 79 additions and 7 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -21,6 +21,11 @@ set(USE_SYSTEM_ZSTD 0 CACHE BOOL "Use zstd provided by system instead of bundled
 
 set(ENABLE_CUDA 0 CACHE BOOL "Enable CUDA")
 
+set(PREFER_STATIC 0 CACHE BOOL "Prefer finding .a libs")
+if (PREFER_STATIC)
+    set(CMAKE_FIND_LIBRARY_SUFFIXES ".a" ".so")
+endif()
+
 if (HAVE_SANITIZER)
     include(FindUBSan)
     include(FindASan)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -137,6 +137,38 @@ jobs:
           targetPath: $(Build.SourcesDirectory)/build/src/mmseqs
           artifactName: mmseqs-linux-$(SIMD)
 
+  - job: build_ubuntu_gpu
+    displayName: Ubuntu MMseqs2
+    pool:
+      vmImage: 'Ubuntu-20.04'
+    timeoutInMinutes: 120
+    steps:
+      - checkout: self
+        submodules: false
+      - script: |
+          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 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
+          sudo ./cmake-3.31.0-linux-x86_64.sh --skip-license --prefix=/usr/local
+        displayName: Install newer G++
+      - script: |
+          mkdir build && cd build
+          export CC=gcc-10 ; export CXX=g++-10; export CUDAHOSTCXX=$CXX; export CUDACXX=/usr/local/cuda/bin/nvcc;
+          /usr/local/bin/cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=1 -DHAVE_AVX2=1 \
+            -PREFER_STATIC=1 -DCMAKE_LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/10 -DBUILD_SHARED_LIBS=OFF \
+            -DCMAKE_EXE_LINKER_FLAGS="-static-libgcc -static-libstdc++" \
+            -DENABLE_CUDA=1 -DCMAKE_CUDA_ARCHITECTURES="75-real;80-real;86-real;89-real;90" ..
+          cmake --build . -j$(nproc --all)
+        displayName: Build MMseqs2
+      - task: PublishPipelineArtifact@0
+        inputs:
+          targetPath: $(Build.SourcesDirectory)/build/src/mmseqs
+          artifactName: mmseqs-linux-gpu
+
   - job: build_ubuntu_cross
     displayName: Ubuntu Cross-Compile
     pool:
@@ -252,6 +284,7 @@ jobs:
       - build_ubuntu_userguide
       - build_macos
       - build_ubuntu
+      - build_ubuntu_gpu
       - build_ubuntu_cross
       - build_windows
     steps:
@@ -317,6 +350,18 @@ jobs:
           archiveFile: $(Build.SourcesDirectory)/mmseqs-linux-sse2.tar.gz
           includeRootFolder: true
           archiveType: tar
+      - task: DownloadPipelineArtifact@1
+        inputs:
+          artifactName: mmseqs-linux-gpu
+          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-cuda12-libc.tar.gz
+          includeRootFolder: true
+          archiveType: tar
       - task: DownloadPipelineArtifact@1
         inputs:
           artifactName: mmseqs-linux-POWER9

diff --git a/cmake/FindAtomic.cmake b/cmake/FindAtomic.cmake
@@ -18,7 +18,17 @@ if (ATOMIC_NATIVE)
   set(ATOMIC_LIBRARY)
 else ()
   set(_OLD_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
-  set(CMAKE_REQUIRED_LIBRARIES "-latomic")
+  find_library(ATOMIC_LIBRARY_PATH
+    NAMES atomic
+  )
+
+  if (ATOMIC_LIBRARY_PATH)
+    set(ATOMIC_LIBRARY ${ATOMIC_LIBRARY_PATH})
+  else ()
+    set(ATOMIC_LIBRARY "-latomic")
+  endif ()
+
+  set(CMAKE_REQUIRED_LIBRARIES "${ATOMIC_LIBRARY}")
     check_cxx_source_compiles("
       int main() {
           volatile unsigned __int128 i = 4;
@@ -32,7 +42,9 @@ else ()
     unset(_OLD_CMAKE_REQUIRED_LIBRARIES)
     if (ATOMIC_WITH_LIB)
       set(ATOMIC_FOUND 1)
-      set(ATOMIC_LIBRARY -latomic)
+    else ()
+      set(ATOMIC_FOUND 0)
+      unset(ATOMIC_LIBRARY)
     endif ()
     include(FindPackageHandleStandardArgs)
     find_package_handle_standard_args(Atomic DEFAULT_MSG ATOMIC_LIBRARY)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -215,12 +215,22 @@ find_package(OpenMP QUIET)
 if (OPENMP_FOUND)
     message("-- Found OpenMP")
     target_compile_definitions(mmseqs-framework PUBLIC -DOPENMP=1)
-    # For GCC we dont want to do this since it breaks macOS static builds
-    # It will link libgomp.a internally (through -fopenmp I guess)
-    # and also link libgomp.dylib thus breaking static builds
-    if (NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    # 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")
+                list(APPEND FILTERED_LIBRARIES ${LIB})
+            endif ()
+        endforeach()
+        set(OpenMP_CXX_LIBRARIES ${FILTERED_LIBRARIES})
+    endif ()
+    if (NOT APPLE)
         target_link_libraries(mmseqs-framework ${OpenMP_CXX_LIBRARIES})
-    endif()
+    endif ()
+    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})