changes to HDF5 support (mostly for Windows compatibility)

- use version HDF5 1.8.12 on Windows if Matlab is being built (see #208). At the moment the version is hard-wired. However, this likely introduced a conflict with Python as it usually uses a more recent version of HDF5 (certainly the Anaconda version does) - add a patch for HDF5 1.8.12 such that it compiles post VS 2013. - introduce a HDF5_DOWNLOAD_VERSION variable - introduce a HDF5_CMAKE_ARGS variable for use in the cmake files that depend on HDF5 This now works fine on Windows as far as I see. On Windows, we will need to have 2 separate builds for MATLAB or Python support unfortunately.
SyneRBI · Jun 21, 2019 · b6993a0 · b6993a0
1 parent 2ed82ce
commit b6993a0
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Showing 3 changed files with 87 additions and 16 deletions.
diff --git a/SuperBuild/External_HDF5.cmake b/SuperBuild/External_HDF5.cmake
@@ -42,6 +42,7 @@ set(${proj}_TMP_DIR "${SUPERBUILD_WORK_DIR}/builds/${proj}/tmp" )
 
 if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalProjName}}" ) )
   message(STATUS "${__indent}Adding project ${proj}")
+  message(STATUS "HDF5_DOWNLOAD_VERSION=${HDF5_DOWNLOAD_VERSION}")
 
   ### --- Project specific additions here
   set(HDF5_Install_Dir ${SUPERBUILD_INSTALL_DIR})
@@ -58,34 +59,76 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
      set(HDF5_BUILD_HL_LIB "ON")
   endif()
 
-  ExternalProject_Add(${proj}
+  if (WIN32 AND (${HDF5_DOWNLOAD_VERSION} STREQUAL 1.8.12))
+    find_program(GIT "git")
+    set(PATCHFILE "${CMAKE_SOURCE_DIR}/patches/hdf5-${HDF5_DOWNLOAD_VERSION}.patch")
+    set(PATCH_COMMAND "git apply -v --ignore-space-change --ignore-whitespace ${PATCHFILE}")
+  endif()
+
+  if (PATCH_COMMAND)
+    message(STATUS "HDF5 PATCH_COMMAND=${PATCH_COMMAND}")
+  endif()
+
+  # sadly, cannot use    "PATCH_COMMAND ${PATCH_COMMAND}" below. with weird error
+  if (PATCHFILE)
+   ExternalProject_Add(${proj}
     ${${proj}_EP_ARGS}
     URL ${${proj}_URL}
     URL_HASH MD5=${${proj}_MD5}
+    PATCH_COMMAND ${GIT} apply -v --ignore-space-change --ignore-whitespace ${PATCHFILE}
+    #PATCH_COMMAND ${PATCH_COMMAND}
+    SOURCE_DIR ${${proj}_SOURCE_DIR}
+    BINARY_DIR ${${proj}_BINARY_DIR}
+    DOWNLOAD_DIR ${${proj}_DOWNLOAD_DIR}
+    STAMP_DIR ${${proj}_STAMP_DIR}
+    TMP_DIR ${${proj}_TMP_DIR}
 
+    CMAKE_ARGS
+        ${CLANG_ARG}
+        -DHDF5_BUILD_EXAMPLES:BOOL=OFF
+        -DHDF5_BUILD_TOOLS:BOOL=OFF
+        -DHDF5_BUILD_HL_LIB:BOOL=${HDF5_BUILD_HL_LIB}
+        -DBUILD_TESTING:BOOL=OFF
+    INSTALL_DIR ${HDF5_Install_Dir}
+   )
+  else()
+   ExternalProject_Add(${proj}
+    ${${proj}_EP_ARGS}
+    URL ${${proj}_URL}
+    URL_HASH MD5=${${proj}_MD5}
     SOURCE_DIR ${${proj}_SOURCE_DIR}
     BINARY_DIR ${${proj}_BINARY_DIR}
     DOWNLOAD_DIR ${${proj}_DOWNLOAD_DIR}
     STAMP_DIR ${${proj}_STAMP_DIR}
     TMP_DIR ${${proj}_TMP_DIR}
 
-
     CMAKE_ARGS
         ${CLANG_ARG}
-        -DHDF5_BUILD_EXAMPLES=OFF 
-        -DHDF5_BUILD_TOOLS=OFF 
-	-DHDF5_BUILD_HL_LIB=${HDF5_BUILD_HL_LIB} 
-        -DBUILD_TESTING=OFF
+        -DHDF5_BUILD_EXAMPLES:BOOL=OFF
+        -DHDF5_BUILD_TOOLS:BOOL=OFF
+        -DHDF5_BUILD_HL_LIB:BOOL=${HDF5_BUILD_HL_LIB}
+        -DBUILD_TESTING:BOOL=OFF
     INSTALL_DIR ${HDF5_Install_Dir}
-  )
+   )
+  endif()
 
   set( HDF5_ROOT ${HDF5_Install_Dir} )
   set( HDF5_INCLUDE_DIRS ${HDF5_ROOT}/include )
+  set(HDF5_CMAKE_ARGS
+    "-DHDF5_ROOT:PATH=${HDF5_ROOT}
+     -DHDF5_INCLUDE_DIRS:PATH=${HDF5_INCLUDE_DIRS}
+     -DHDF5_FIND_DEBUG:BOOL=ON"
+  )
 
  else()
     if(${USE_SYSTEM_${externalProjName}})
       find_package(${proj} ${${externalProjName}_REQUIRED_VERSION} REQUIRED)
       message(STATUS "USING the system ${externalProjName}, found HDF5_INCLUDE_DIRS=${HDF5_INCLUDE_DIRS}, HDF5_C_LIBRARY_hdf5=${HDF5_C_LIBRARY_hdf5},HDF5_LIBRARIES=${HDF5_LIBRARIES}")
+      set(HDF5_CMAKE_ARGS
+        "-DHDF5_INCLUDE_DIRS:PATH=${HDF5_INCLUDE_DIRS}
+         -DHDF5_LIBRARIES:STRING=${HDF5_LIBRARIES}
+         -DHDF5_FIND_DEBUG:BOOL=ON"
+      )
   endif()
   ExternalProject_Add_Empty(${proj} DEPENDS "${${proj}_DEPENDENCIES}"
     SOURCE_DIR ${${proj}_SOURCE_DIR}
@@ -96,9 +139,4 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   )
 endif()
 
-mark_as_superbuild(
-  VARS
-    ${externalProjName}_DIR:PATH
-  LABELS
-    "FIND_PACKAGE"
-)
+message(STATUS "HDF5_CMAKE_ARGS=${HDF5_CMAKE_ARGS}")
diff --git a/patches/hdf5-1.8.12.patch b/patches/hdf5-1.8.12.patch
@@ -0,0 +1,11 @@
+--- xx  2019-06-20 20:38:35.399865600 +0000
++++ ./config/cmake/ConfigureChecks.cmake        2019-06-20 20:20:00.586270800 +0000
+@@ -185,7 +185,7 @@
+   ENDIF (NOT UNIX AND NOT CYGWIN AND NOT MINGW)
+   SET (H5_HAVE_FUNCTION 1)
+   SET (H5_GETTIMEOFDAY_GIVES_TZ 1)
+-  SET (H5_HAVE_TIMEZONE 1)
++  SET (H5_HAVE_TIMEZONE 0)
+   SET (H5_HAVE_GETTIMEOFDAY 1)
+   SET (H5_LONE_COLON 0)
+   IF (MINGW)
diff --git a/version_config.cmake b/version_config.cmake
@@ -65,12 +65,34 @@ set(FFTW3double_MD5 ${FFTW3_MD5})
 if (WIN32)
   # 1.8.15 hdf5-targets.cmake refers to non-existent zlib files
   # (or at least this was the case for older Anaconda installations)
-  set(HDF5_REQUIRED_VERSION 1.8.17)
+  if (USE_SYSTEM_HDF5)
+    set(HDF5_REQUIRED_VERSION 1.8.17)
+    #set(HDF5_REQUIRED_VERSION 1.8)
+  endif()
+  if (BUILD_MATLAB)
+    set(HDF5_DOWNLOAD_MAJOR_MINOR_VERSION "1.8")
+    set(HDF5_DOWNLOAD_PATCH_VERSION "12")
+  else()
+    set(HDF5_DOWNLOAD_MAJOR_MINOR_VERSION "1.10")
+    set(HDF5_DOWNLOAD_PATCH_VERSION "1")
+  endif()
+  set(HDF5_DOWNLOAD_VERSION "${HDF5_DOWNLOAD_MAJOR_MINOR_VERSION}.${HDF5_DOWNLOAD_PATCH_VERSION}")
+  set(HDF5_URL https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_DOWNLOAD_MAJOR_MINOR_VERSION}/hdf5-${HDF5_DOWNLOAD_VERSION}/src/hdf5-${HDF5_DOWNLOAD_VERSION}.tar.gz)
 else()
   set(HDF5_REQUIRED_VERSION 1.8)
+  set(HDF5_DOWNLOAD_MAJOR_MINOR_VERSION "1.10")
+  set(HDF5_DOWNLOAD_PATCH_VERSION "1")
+  set(HDF5_DOWNLOAD_VERSION "${HDF5_DOWNLOAD_MAJOR_MINOR_VERSION}.${HDF5_DOWNLOAD_PATCH_VERSION}")
+  set(HDF5_URL https://www.ccppetmr.ac.uk/sites/www.ccppetmr.ac.uk/files/downloads/hdf5-${HDF5_DOWNLOAD_VERSION}.tar.gz)
+endif()
+
+if (${HDF5_DOWNLOAD_VERSION} STREQUAL 1.8.12)
+  set(HDF5_MD5 4711e0d6b87d442f194c5d29ba7fbe62 )
+elseif (${HDF5_DOWNLOAD_VERSION} STREQUAL 1.10.1)
+  set(HDF5_MD5 43a2f9466702fb1db31df98ae6677f15 )
+else()
+  message(FATAL_ERROR "Developer error: need to set HDF5_MD5 for version ${HDF5_DOWNLOAD_VERSION}")
 endif()
-set(HDF5_URL https://www.ccppetmr.ac.uk/sites/www.ccppetmr.ac.uk/files/downloads/hdf5-1.10.1.tar.gz)
-set(HDF5_MD5 43a2f9466702fb1db31df98ae6677f15 )
 
 ## SWIG
 set (SWIG_REQUIRED_VERSION 2)