do not require HDF5 1.8.11

virtualcell · Aug 15, 2023 · 900d9c9 · 900d9c9
1 parent 22d6187
commit 900d9c9
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diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
@@ -7,36 +7,36 @@ env:
   IMAGE_NAME: ${{ github.repository }}
 
 jobs:
-  build-and-push-image:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v3
-
-      - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
-        with:
-          registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
-        with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-
-      - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
-        with:
-          context: .
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}
+#  build-and-push-image:
+#    runs-on: ubuntu-latest
+#    permissions:
+#      contents: read
+#      packages: write
+#
+#    steps:
+#      - name: Checkout repository
+#        uses: actions/checkout@v3
+#
+#      - name: Log in to the Container registry
+#        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+#        with:
+#          registry: ${{ env.REGISTRY }}
+#          username: ${{ github.actor }}
+#          password: ${{ secrets.GITHUB_TOKEN }}
+#
+#      - name: Extract metadata (tags, labels) for Docker
+#        id: meta
+#        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+#        with:
+#          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+#
+#      - name: Build and push Docker image
+#        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+#        with:
+#          context: .
+#          push: true
+#          tags: ${{ steps.meta.outputs.tags }}
+#          labels: ${{ steps.meta.outputs.labels }}
 
   native-build:
     name:
@@ -125,7 +125,7 @@ jobs:
           echo "------ running ziptool ------"
           ./bin/ziptool || true
 
-      - name: install msys2
+      - name: Install Windows Dependencies
         if: matrix.platform == 'windows-latest'
         uses: msys2/setup-msys2@v2
         with:
@@ -141,22 +141,6 @@ jobs:
             mingw-w64-clang-x86_64-libzip 
             mingw-w64-clang-x86_64-netcdf
 
-#      - name: Install Windows Dependencies
-#        if: matrix.platform == 'windows-latest'
-#        shell: msys2 {0}
-#        run: |
-#          pacman --noconfirm -S mingw-w64-x86_64-boost mingw-w64-x86_64-hdf5 mingw-w64-x86_64-libzip mingw-w64-x86_64-netcdf
-#
-#          PATH="/c/Program Files/LLVM/bin:$PATH"
-#
-#          gcc --version
-#          gfortran --version
-#          cmake --version
-#          pacman -Q mingw-w64-x86_64-boost
-#          pacman -Q mingw-w64-x86_64-hdf5
-#          pacman -Q mingw-w64-x86_64-libzip
-#          pacman -Q mingw-w64-x86_64-netcdf
-
       - name: Build Windows
         if: matrix.platform == 'windows-latest'
         shell: msys2 {0}
@@ -186,7 +170,7 @@ jobs:
           -DOPTION_TARGET_HY3S_SOLVERS=OFF \
           -B . -S ..
 
-          ninja
+          ninja -j 1
 
       - name: Test Windows
         if: matrix.platform == 'windows-latest'

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -141,7 +141,7 @@ endif()
 #if (APPLE)
 #endif()
 
-#set(HDF5_BUILD_CPP_LIB ON)
+set(HDF5_BUILD_CPP_LIB OFF CACHE BOOL "" )
 message("hdf5 cpp ${HDF5_BUILD_CPP_LIB}")
 
 set(LINUX FALSE)
@@ -152,7 +152,7 @@ endif()
 set(WINDOWS FALSE)
 if (${CMAKE_SYSTEM_NAME} MATCHES Windows)
 	set(WINDOWS TRUE)
-	set(WIN32 TRUE)
+#	set(WIN32 TRUE)
 	if (${CMAKE_GENERATOR} MATCHES "Unix Makefiles") 
 		set(MINGW TRUE)
 	endif (${CMAKE_GENERATOR} MATCHES "Unix Makefiles") 
@@ -197,8 +197,12 @@ set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}")
 
 add_definitions(-DUNIX)
 
-set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
-set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
+#if (MINGW)
+#	add_definitions(-DWIN32)
+#endif(MINGW)
+
+#set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
+#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
 
 
 if (OPTION_TARGET_MESSAGING)
@@ -235,9 +239,9 @@ if (${OPTION_TARGET_MOVINGBOUNDARY_SOLVER} OR
 	if (${HDF5_BUILD_CPP_LIB})
 		add_subdirectory(hdf5-1.8.11)
 	else()
-#			set(HDF5_USE_STATIC_LIBRARIES ON)
+		set(HDF5_USE_STATIC_LIBRARIES ON)
 		#CMakeList.txt that comes with hdf5 switches library name if compiled with debug
-		find_package(HDF5 1.8.11 REQUIRED COMPONENTS HL CXX C)
+		find_package(HDF5 COMPONENTS HL CXX C)
 		set(HDF_VERSION ${HDF5_VERSION})
 		######    ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES}
 		if (${OPTION_TARGET_CHOMBO2D_SOLVER} OR
@@ -382,3 +386,21 @@ endif()
 
 FetchContent_MakeAvailable(googletest)
 enable_testing()
+
+get_cmake_property(_variableNames VARIABLES)
+list (SORT _variableNames)
+foreach (_variableName ${_variableNames})
+	message(STATUS "${_variableName}=${${_variableName}}")
+endforeach()
+
+include(CMakePrintHelpers)
+cmake_print_variables(OPTION_TARGET_MESSAGING OPTION_TARGET_PARALLEL OPTION_TARGET_PETSC
+		OPTION_TARGET_DOCS OPTION_TARGET_CHOMBO2D_SOLVER OPTION_TARGET_CHOMBO3D_SOLVER
+		OPTION_TARGET_SMOLDYN_SOLVER OPTION_TARGET_FV_SOLVER OPTION_TARGET_STOCHASTIC_SOLVER
+		OPTION_TARGET_NFSIM_SOLVER OPTION_TARGET_MOVINGBOUNDARY_SOLVER OPTION_TARGET_SUNDIALS_SOLVER
+		OPTION_TARGET_HY3S_SOLVERS OPTION_TARGET_LIBSMOLDYN OPTION_TARGET_VCELL OPTION_TARGET_NSV )
+cmake_print_variables(CMAKE_CXX_FLAGS CMAKE_C_FLAGS CMAKE_Fortran_FLAGS)
+cmake_print_variables(CMAKE_SYSTEM_NAME WINDOWS WIN32 MINGW APPLE ARCH_64bit ARCH_32bit)
+cmake_print_variables(CMAKE_CPP_COMPILER CMAKE_C_COMPILER CMAKE_CXX_COMPILER CMAKE_Fortran_COMPILER)
+cmake_print_variables(HAVE_ZLIB)
+
diff --git a/VCellZipUtils/src/ZipUtils.cpp b/VCellZipUtils/src/ZipUtils.cpp
@@ -27,9 +27,7 @@ using std::endl;
 using namespace std;
 struct zip;
 
-#if ( !defined(WIN32) && !defined(WIN64) ) // UNIX
 #include <unistd.h>
-#endif
 
 bool exists(const char* name){
     if (FILE *file = fopen(name, "r")) {