Next try with build system cleanup

Author: milot-mirdita

.cirrus.yml

@@ -24,10 +24,7 @@ task:
         echo "deb [trusted=yes] http://archive.debian.org/debian jessie main" > /etc/apt/sources.list
         echo "deb [trusted=yes] http://archive.debian.org/debian-security jessie/updates main" >> /etc/apt/sources.list
         apt-get update --yes --force-yes || true
-        apt-get install wget clang-4.0 libc++-dev make git ca-certificates --yes --force-yes --no-install-suggests --no-install-recommends
-        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
-        ./cmake-3.31.0-linux-x86_64.sh --skip-license --prefix=/usr/local
+        apt-get install cmake clang-4.0 libc++-dev make git ca-certificates --yes --force-yes --no-install-suggests --no-install-recommends
       env:
         CC: clang-4.0
         CXX: clang++-4.0
@@ -36,16 +33,13 @@ task:
         echo "deb [trusted=yes] http://archive.debian.org/debian jessie main" > /etc/apt/sources.list
         echo "deb [trusted=yes] http://archive.debian.org/debian-security jessie/updates main" >> /etc/apt/sources.list
         apt-get update --yes --force-yes || true
-        apt-get install wget gcc-4.9 g++-4.9 make git ca-certificates --yes --force-yes --no-install-suggests --no-install-recommends
-        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
-        ./cmake-3.31.0-linux-x86_64.sh --skip-license --prefix=/usr/local
+        apt-get install cmake gcc-4.9 g++-4.9 make git ca-certificates --yes --force-yes --no-install-suggests --no-install-recommends
       env:
         CC: gcc-4.9
         CXX: g++-4.9
   compile_script: |
     mkdir build && cd build
-    /usr/local/bin/cmake -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=0 -DHAVE_SSE4_1=1 -DREQUIRE_OPENMP=0 ..
+    cmake -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=1 -DENABLE_WERROR=0 -DHAVE_SSE4_1=1 -DREQUIRE_OPENMP=0 ..
     make -j $(nproc --all)
   test_script: MMSEQS_NUM_THREADS=4 ./util/regression/run_regression.sh ./build/src/mmseqs SCRATCH SEARCH
 

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.15 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.0 FATAL_ERROR)
 cmake_policy(SET CMP0060 OLD)
 cmake_policy(SET CMP0074 NEW)
 project(MMseqs CXX C)

src/CMakeLists.txt

@@ -215,6 +215,16 @@ find_package(OpenMP QUIET)
 if (OPENMP_FOUND)
     message("-- Found OpenMP")
     target_compile_definitions(mmseqs-framework PUBLIC -DOPENMP=1)
+    # hack: remove pthread from openmp deps, it gets linked correctly by cuda later
+    if (FORCE_STATIC_DEPS AND ENABLE_CUDA)
+        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 ()
     target_link_libraries(mmseqs-framework ${OpenMP_CXX_LIBRARIES})
     target_include_directories(mmseqs-framework PUBLIC ${OpenMP_CXX_INCLUDE_DIRS})
     append_target_property(mmseqs-framework COMPILE_FLAGS ${OpenMP_CXX_FLAGS})