Feature/parallelhdf5

.gitignore

@@ -1,3 +1,4 @@
 cmake-build-*/
 .idea/
 build/
+*.h.gch

CMakeLists.txt

@@ -1,17 +1,76 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.13)
 project(hdf_convert)
 
 set(default_build_type "Release")
-
+set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
 set(CMAKE_CXX_STANDARD 11)
-FIND_PACKAGE(HDF5 REQUIRED COMPONENTS CXX)
-INCLUDE_DIRECTORIES(${HDF5_INCLUDE_DIR})
+
+#
+# Options users can give on the command line via -D
+#
+macro(hdfconvert_option optname optdesc status)
+	option(HDFCONVERT_${optname} "${optdesc}" "${status}")
+endmacro()
+
+# set default options
+hdfconvert_option(USEMPI "Use MPI" OFF)
+hdfconvert_option(USEOPENMP "Use OpenMP" ON)
+hdfconvert_option(ALLOWCOMPRESSIONHDF5 "Attempt to include HDF5 compression support " ON)
+hdfconvert_option(ALLOWPARALLELHDF5 "Attempt to include parallel HDF5 support " ON)
+hdfconvert_option(ALLOWCOMPRESSIONPARALLELHDF5 "Attempt to include parallel HDF5 compression support " OFF)
+
+# find hdf5 macro where flags set if parallel, if particular version, if compression
+macro(find_hdf5)
+	find_package(HDF5 REQUIRED COMPONENTS C)
+	if (HDF5_FOUND)
+		include_directories(${HDF5_INCLUDE_DIRS})
+		if (HDF5_IS_PARALLEL AND HDFCONVERT_ALLOWPARALLELHDF5)
+			set (ENV{HDF5_PREFER_PARALLEL} true)
+			set(HDFCONVERT_HAS_PARALLEL_HDF5 Yes)
+			list(APPEND HDFCONVERT_DEFINES USEPARALLELHDF)
+			if (HDF5_VERSION VERSION_GREATER "1.10.0" AND HDFCONVERT_ALLOWCOMPRESSIONPARALLELHDF5)
+				set(HDFCONVERT_HAS_COMPRESSED_HDF5 Yes)
+				list(APPEND HDFCONVERT_DEFINES USEHDFCOMPRESSION)
+				list(APPEND HDFCONVERT_DEFINES PARALLELCOMPRESSIONACTIVE)
+			endif()
+		else()
+			if (HDFCONVERT_ALLOWCOMPRESSIONHDF5)
+				set(HDFCONVERT_HAS_COMPRESSED_HDF5 Yes)
+				list(APPEND HDFCONVERT_DEFINES USEHDFCOMPRESSION)
+			endif()
+		endif()
+    endif()
+endmacro()
+
+#
+# How we find MPI and set it up
+#
+macro(find_mpi)
+	find_package(MPI)
+	if (MPI_FOUND)
+        include_directories(${MPI_CXX_INCLUDE_PATH})
+		list(APPEND HDF5_CONVERT_DEFINES USEMPI)
+		set(HDFCONVERT_HAS_MPI Yes)
+	endif()
+endmacro()
+
+find_package(CFITSIO 3.000 REQUIRED)
+set(HDFCONVERT_HAS_OPENMP No)
 find_package(OpenMP)
+set(HDFCONVERT_HAS_COMPRESSED_HDF5 No)
+set(HDFCONVERT_HAS_PARALLEL_HDF5 No)
+find_hdf5()
+set(HDFCONVERT_HAS_MPI No)
+if (HDFCONVERT_MPI)
+	find_mpi()
+endif()
+
 
 if (OPENMP_FOUND)
     set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
     set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
     set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+    set (HDFCONVERT_USEOPENMP)
 endif()
 
 if (Verbose)
@@ -22,17 +81,63 @@ if (Timer)
     ADD_DEFINITIONS(-D_TIMER_)
 endif()
 
+#
+# Tell the world what what we are doing
+#
+macro(hdf_convert_report feature)
+
+	# Output feature name and underscore it in the next line
+	message("\n${feature}")
+	string(REGEX REPLACE "." "-" _underscores ${feature})
+	message("${_underscores}\n")
+
+	set(_args "${ARGN}")
+	list(LENGTH _args _nargs)
+	math(EXPR _nargs "${_nargs} - 1")
+	foreach(_idx RANGE 0 ${_nargs} 2)
+
+		# Items in the list come with a message first, then the variable name
+		list(GET _args ${_idx} _msg)
+		math(EXPR _idx2 "${_idx} + 1")
+		list(GET _args ${_idx2} _varname)
+
+		# We try to keep things up to 80 cols
+		string(LENGTH ${_msg} _len)
+		math(EXPR _nspaces "75 - ${_len}")
+		string(RANDOM LENGTH ${_nspaces} _spaces)
+		string(REGEX REPLACE "." " " _spaces "${_spaces}")
+		string(CONCAT _msg "${_msg}" ${_spaces})
+		message(" ${_msg} ${HDFCONVERT_HAS_${_varname}}")
+	endforeach()
+endmacro()
+
+message("\nHDF Converter successfully configured with the following settings:")
+hdf_convert_report("HDF5 Settings"
+    "Compressed HDF5" COMPRESSED_HDF5
+    "Parallel HDF5" PARALLEL_HDF5
+)
+if (HDFCONVERT_HAS_COMPRESSED_HDF5 AND HDFCONVERT_HAS_PARALLEL_HDF5)
+	message("\n WARNING: Parallel Compression HDF5 active, use with caution as it is unstable!\n")
+endif()
+hdf_convert_report("Parallel settings"
+    "OpenMP" OPENMP
+    "MPI" MPI
+)
+
+
 set(LINK_LIBS ${LINK_LIBS} cfitsio ${HDF5_LIBRARIES})
 
 set(SOURCE_FILES
     ${SOURCE_FILES}
-    main.cc
-    Stats.cc
-    MipMap.cc
+    HDF5Wrapper.cc
     Converter.cc
     FastConverter.cc
     SlowConverter.cc
-    Util.cc)
+    Stats.cc
+    MipMap.cc
+    Util.cc
+    main.cc
+    )
 
 add_executable(hdf_convert ${SOURCE_FILES})
 target_link_libraries(hdf_convert ${LINK_LIBS})