Merge pull request #3 from alan-wu/master

Improve cmake script, hdf5; read from memory buffer

Author: rchristie

CMakeLists.txt

@@ -41,6 +41,7 @@ CMAKE_MINIMUM_REQUIRED( VERSION 2.6 )
 
 # Set this nampspace to keep these options seperate from other project options
 SET( FIELDML_NAMESPACE_NAME FIELDML )
+PROJECT(fieldml)
 
 MACRO( OPTION_WITH_DEFAULT OPTION_NAME OPTION_STRING OPTION_DEFAULT )
 	IF( NOT DEFINED ${OPTION_NAME} )
@@ -102,9 +103,17 @@ ADD_SUBDIRECTORY( core )
 SET( LIBRARY_TARGET_NAME fieldml_io_api )
 SET( FIELDML_IO_API_LIBRARY_TARGET_NAME ${LIBRARY_TARGET_NAME} )
 ADD_SUBDIRECTORY( io )
-
+GET_DIRECTORY_PROPERTY(HDF5_INCLUDE_DIRS DIRECTORY io DEFINITION HDF5_INCLUDE_DIRS)
+GET_DIRECTORY_PROPERTY(HDF5_MINE_LIBRARIES DIRECTORY io DEFINITION HDF5_MINE_LIBRARIES)
+GET_DIRECTORY_PROPERTY(MPI_LIBRARIES DIRECTORY io DEFINITION MPI_MINE_LIBRARIES)
+GET_DIRECTORY_PROPERTY(MPI_INCLUDE_DIRS DIRECTORY io DEFINITION MPI_INCLUDE_DIRS)
+GET_DIRECTORY_PROPERTY(HDF5_USE_MPI DIRECTORY io DEFINITION HDF5_USE_MPI)
 ADD_SUBDIRECTORY( test )
 
+foreach(arg ${MPI_LIBRARIES})
+	set(MPI_MINE_LIBRARIES "${MPI_MINE_LIBRARIES} ${arg}")
+endforeach(arg ${MPI_LIBRARIES})
+
 IF( ${FIELDML_NAMESPACE_NAME}_INSTALL_CONFIG )
 	SET( LIBRARY_CONFIG_FILE ${CMAKE_CURRENT_BINARY_DIR}/fieldml-config.cmake )
 	SET( CONFIG_FILE_CONTENTS 
@@ -113,8 +122,8 @@ IF( ${FIELDML_NAMESPACE_NAME}_INSTALL_CONFIG )
 		"\nGET_FILENAME_COMPONENT( SELF_DIR \"\${CMAKE_CURRENT_LIST_FILE}\" PATH )"
 		"\nINCLUDE( \${SELF_DIR}/fieldml-targets.cmake )"
 		"\nGET_FILENAME_COMPONENT( ${FIELDML_NAMESPACE_NAME}_INCLUDE_DIRS \"\${SELF_DIR}/../../include\" ABSOLUTE )"
-		"\nSET( ${FIELDML_NAMESPACE_NAME}_INCLUDE_DIRS \"\${${FIELDML_NAMESPACE_NAME}_INCLUDE_DIRS}\" \"${LIBXML2_INCLUDE_DIR}\" \"${HDF5_INCLUDE_DIR}\" )"
-		"\nSET( ${FIELDML_NAMESPACE_NAME}_LIBRARIES ${FIELDML_API_LIBRARY_TARGET_NAME} ${FIELDML_IO_API_LIBRARY_TARGET_NAME} )"
+		"\nSET( ${FIELDML_NAMESPACE_NAME}_INCLUDE_DIRS \"\${${FIELDML_NAMESPACE_NAME}_INCLUDE_DIRS}\" \"${LIBXML2_INCLUDE_DIR}\" \"${HDF5_INCLUDE_DIRS}\" \"${MPI_INCLUDE_DIRS}\" )"
+		"\nSET( ${FIELDML_NAMESPACE_NAME}_LIBRARIES ${FIELDML_API_LIBRARY_TARGET_NAME} ${FIELDML_IO_API_LIBRARY_TARGET_NAME} ${HDF5_MINE_LIBRARIES} ${MPI_MINE_LIBRARIES})"
 		"\nSET( ${FIELDML_NAMESPACE_NAME}_DEFINITIONS )"
 		"\nSET( ${FIELDML_NAMESPACE_NAME}_FOUND TRUE )" 
 		"\nENDIF( NOT DEFINED _${FIELDML_NAMESPACE_NAME}_CONFIG_CMAKE )" 

Fortran/InterfaceGen.py

@@ -203,7 +203,7 @@ def processLine( line, state ):
   return state
 
 
-def processFile():
+def processFiles():
   headerFile = open( "../core/src/fieldml_api.h" )
 
   state = ParseState.InHeader
@@ -235,6 +235,37 @@ def processFile():
 
   headerFile.close()
 
+  headerFile = open( "../io/src/FieldmlIoApi.h" )
+
+  state = ParseState.InHeader
+  inComment = False
+
+  for line in headerFile:
+    startSegment = 0
+
+    if( inComment ):
+      pos = line.find( "*/" )
+      if( pos == -1 ):
+        continue
+      inComment = False
+      startSegment = pos + 2
+
+    #Does not cope with mixing line and block comments.
+    endSegment = line.find( "/*", startSegment )
+    while( endSegment != -1 ):
+      state = processLine( line[ startSegment : endSegment ], state )
+      startSegment = line.find( "*/", endSegment + 2 )
+      if( startSegment == -1 ):
+        break
+      endSegment = line.find( "/*", startSegment )
+
+    if( startSegment == -1 ):
+      inComment = True
+    else:
+      state = processLine( line[ startSegment : ], state )
+
+  headerFile.close()
+
 
   writeHeader()
 
@@ -261,4 +292,4 @@ def processFile():
 
   writeFooter()
 
-processFile()
+processFiles()

core/src/FieldmlSession.cpp

@@ -200,6 +200,46 @@ FieldmlRegion *FieldmlSession::addResourceRegion( string href, string name )
     return resourceRegion;
 }
 
+FieldmlRegion *FieldmlSession::addResourceRegionFromBuffer( const void *buffer, unsigned int buffer_length, string name )
+{
+    if((buffer == 0) || (1 > buffer_length))
+    {
+        return 0;
+    }
+
+    //NOTE: This will be insufficient when the region name starts being used.
+    if( FmlUtil::contains( importHrefStack, name ) )
+    {
+        addError( "Recursive import involving " + name );
+        return NULL;
+    }
+
+    importHrefStack.push_back( name );
+
+    FieldmlRegion *resourceRegion = new FieldmlRegion( name, name, "", objects );
+    FieldmlRegion *currentRegion = region;
+    region = resourceRegion;
+
+    int result = 0;
+
+    result = FieldmlDOM::parseFieldmlString( (const char *)buffer, "memory buffer", "memory", this, getSessionHandle() );
+
+    importHrefStack.pop_back();
+
+    region = currentRegion;
+
+    if( ( result != 0 ) || ( getErrorCount() != 0 ) )
+    {
+        delete resourceRegion;
+        resourceRegion = NULL;
+    }
+    else
+    {
+        regions.push_back( resourceRegion );
+    }
+
+    return resourceRegion;
+}
 
 void FieldmlSession::pushErrorContext( const char *file, const int line, const char *function )
 {

core/src/FieldmlSession.h

@@ -117,6 +117,8 @@ class FieldmlSession :
 
     FieldmlRegion *addResourceRegion( std::string location, std::string name );
 
+    FieldmlRegion *addResourceRegionFromBuffer( const void *buffer, unsigned int buffer_length, std::string name );
+
     FieldmlRegion *addNewRegion( std::string location, std::string name );
 
     FieldmlRegion *getRegion( std::string location, std::string name );

core/src/fieldml_api.cpp

@@ -514,6 +514,31 @@ FmlSessionHandle Fieldml_CreateFromFile( const char * filename )
     return session->getSessionHandle();
 }
 
+FmlSessionHandle Fieldml_CreateFromBuffer( const void *buffer, unsigned int buffer_length, const char * name )
+{
+    FieldmlSession *session = new FieldmlSession();
+    ErrorContextAutostack bob( session, __FILE__, __LINE__, __ECA_FUNC__ );
+
+    if( buffer == NULL || 1 > buffer_length )
+    {
+        session->setError( FML_ERR_INVALID_PARAMETER_1, "Cannot create FieldML session. Invalid buffer." );
+    }
+    else
+    {
+        session->region = session->addResourceRegionFromBuffer( buffer, buffer_length, name );
+        if( session->region == NULL )
+        {
+            session->setError( FML_ERR_READ_ERR, "Cannot create FieldML session. Invalid document or read error." );
+        }
+        else
+        {
+            session->region->finalize();
+        }
+    }
+
+    return session->getSessionHandle();
+}
+
 
 FmlSessionHandle Fieldml_Create( const char * location, const char * name )
 {

core/src/fieldml_api.h

@@ -273,6 +273,8 @@ extern "C" {
  */
 FmlSessionHandle Fieldml_CreateFromFile( const char * filename );
 
+FmlSessionHandle Fieldml_CreateFromBuffer( const void *buffer, unsigned int buffer_length, const char * name );
+
 
 /**
  * Creates an empty FieldML handle.

io/CMakeLists.txt

@@ -38,23 +38,21 @@
 PROJECT( io )
 
 OPTION_WITH_DEFAULT( FIELDML_USE_HDF5 "Do you want to use netgen?" FALSE )
-
+SET( HDF5_USE_MPI FALSE )
+SET( HDF5_INCLUDE_DIRS "" )
+SET( HDF5_MINE_LIBRARIES "" )
+SET( MPI_INCLUDE_DIRS "" )
+SET( MPI_MINE_LIBRARIES "" )
+				     
 IF( FIELDML_USE_HDF5 )
-	FIND_PATH(HDF5_INCLUDE_DIR hdf5.h
-		NO_DEFAULT_PATH
-	)
-	FIND_LIBRARY(HDF5_LIBRARY NAMES hdf5
-		NO_DEFAULT_PATH
-	)
-	MARK_AS_ADVANCED(HDF5_INCLUDE_DIR)
-	MARK_AS_ADVANCED(HDF5_LIBRARY)
+	FIND_PACKAGE( HDF5 REQUIRED C )
+	SET( HDF5_USE_MPI ${HDF5_ENABLE_PARALLEL} )
+	IF ( HDF5_USE_MPI )
+		FIND_PACKAGE( MPI REQUIRED )
+	ENDIF (HDF5_USE_MPI)
 	ADD_DEFINITIONS( -DFIELDML_HDF5_ARRAY )
-	SET( HDF5_INCLUDE_DIRS ${HDF5_INCLUDE_DIR} )
-	SET( HDF5_LIBRARIES ${HDF5_LIBRARY} )
-	SET( CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} ${IELDML_HDF5_ARRAY_DEFINE} )
-	SET( CMAKE ${CMAKE_C_FLAGS} ${IELDML_HDF5_ARRAY_DEFINE} )
-	SET( DEPENDENT_LIBS ${DEPENDENT_LIBS} ${HDF5_LIBRARIES} )
-	SET( INCLUDE_DIRS ${INCLUDE_DIRS} ${HDF5_INCLUDE_DIRS} )
+	SET( CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} ${FIELDML_HDF5_ARRAY_DEFINE} )
+	SET( CMAKE ${CMAKE_C_FLAGS} ${FIELDML_HDF5_ARRAY_DEFINE} )
 ENDIF( FIELDML_USE_HDF5 )
 
 IF( ${FIELDML_NAMESPACE_NAME}_BUILD_STATIC_LIB )
@@ -68,6 +66,30 @@ ELSE( ${FIELDML_NAMESPACE_NAME}_BUILD_STATIC_LIB )
 	ENDIF( WIN32 )
 ENDIF( ${FIELDML_NAMESPACE_NAME}_BUILD_STATIC_LIB )
 
+IF( FIELDML_USE_HDF5 )
+	IF( HDF5_FOUND )
+		SET( HDF5_INCLUDE_DIRS ${HDF5_INCLUDE_DIR} )
+		SET( HDF5_MINE_LIBRARIES ${HDF5_LIBRARIES} )
+		SET( DEPENDENT_LIBS ${DEPENDENT_LIBS} ${HDF5_MINE_LIBRARIES} )
+		SET( INCLUDE_DIRS ${INCLUDE_DIRS} ${HDF5_INCLUDE_DIRS} )
+		IF( HDF5_USE_MPI )
+			IF( MPI_FOUND )
+				SET( MPI_INCLUDE_DIRS ${MPI_INCLUDE_PATH} )
+				SET( MPI_MINE_LIBRARIES ${MPI_LIBRARIES} )
+				SET( DEPENDENT_LIBS ${DEPENDENT_LIBS} ${MPI_MINE_LIBRARIES} )
+				SET( INCLUDE_DIRS ${INCLUDE_DIRS} ${MPI_INCLUDE_DIRS} )
+			ELSE( MPI_FOUND )
+				MESSAGE( FATAL_ERROR "MPI was requested but not found." )
+			ENDIF( MPI_FOUND )
+			ADD_DEFINITIONS( -DFIELDML_PHDF5_ARRAY )
+			SET( CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} ${FIELDML_PHDF5_ARRAY_DEFINE} )
+			SET( CMAKE ${CMAKE_C_FLAGS} ${FIELDML_PHDF5_ARRAY_DEFINE} )
+		ENDIF( HDF5_USE_MPI )
+	ELSE( HDF5_FOUND )
+		MESSAGE( FATAL_ERROR "HDF5 was requested but not found." )
+	ENDIF( HDF5_FOUND )
+ENDIF( FIELDML_USE_HDF5 )
+
 SET( CMAKE_PREFIX_PATH ${CMAKE_INSTALL_PREFIX} )
 FIND_PACKAGE( LibXml2 REQUIRED )
 
@@ -112,11 +134,11 @@ ENDIF( "${CMAKE_BUILD_TYPE}" STREQUAL "Debug" )
 IF( WIN32 )
 	ADD_DEFINITIONS( -D_CRT_SECURE_NO_WARNINGS )
 ENDIF( WIN32 )
-INCLUDE_DIRECTORIES( ${FIELDML_API_PUBLIC_HDRS} ${HDF5_INCLUDE_DIR} )
+INCLUDE_DIRECTORIES( ${FIELDML_API_PUBLIC_HDRS} ${HDF5_INCLUDE_DIRS} ${MPI_INCLUDE_DIRS} )
 
 # Create library
 ADD_LIBRARY( ${LIBRARY_TARGET_NAME} ${LIBRARY_BUILD_TYPE} ${FIELDML_IO_API_SRCS} ${FIELDML_IO_API_PUBLIC_HDRS} ${FIELDML_IO_API_PRIVATE_HDRS} ${LIBRARY_WIN32_XTRAS} )
-TARGET_LINK_LIBRARIES( ${LIBRARY_TARGET_NAME} ${HDF5_LIBRARY} )
+TARGET_LINK_LIBRARIES( ${LIBRARY_TARGET_NAME} ${HDF5_MINE_LIBRARIES} ${MPI_MINE_LIBRARIES} )
 
 # Install targets
 IF( WIN32 AND NOT ${UPPERCASE_LIBRARY_TARGET_NAME}_BUILD_STATIC_LIB )

io/src/ArrayDataReader.cpp

@@ -48,7 +48,8 @@
 
 using namespace std;
 
-ArrayDataReader * ArrayDataReader::create( FieldmlIoContext *context, const string root, FmlObjectHandle source )
+ArrayDataReader * ArrayDataReader::createInternal( FieldmlIoContext *context, const string root,
+	FmlObjectHandle source, void *buffer )
 {
     ArrayDataReader *reader = NULL;
 
@@ -73,7 +74,7 @@ ArrayDataReader * ArrayDataReader::create( FieldmlIoContext *context, const stri
     }
     else if( format == StringUtil::PLAIN_TEXT_NAME )
     {
-        reader = TextArrayDataReader::create( context, root, source );
+    		reader = TextArrayDataReader::create( context, root, source, buffer );
     }
     else
     {
@@ -83,6 +84,17 @@ ArrayDataReader * ArrayDataReader::create( FieldmlIoContext *context, const stri
     return reader;
 }
 
+ArrayDataReader * ArrayDataReader::create( FieldmlIoContext *context, const string root, FmlObjectHandle source )
+{
+    return ArrayDataReader::createInternal( context, root, source, 0 );
+}
+
+
+ArrayDataReader * ArrayDataReader::createWithBuffer( FieldmlIoContext *context, const string root, FmlObjectHandle source, void *buffer )
+{
+    return ArrayDataReader::createInternal( context, root, source, buffer );
+}
+
 
 ArrayDataReader::ArrayDataReader( FieldmlIoContext *_context ) :
     context( _context )

io/src/ArrayDataReader.h

@@ -44,13 +44,23 @@
 
 #include "FieldmlIoContext.h"
 
+enum ArrayDataSourceType
+{
+    ARRAY_DATA_SOURCE_UNKNOWN,
+    ARRAY_DATA_SOURCE_DEFAULT,
+    ARRAY_DATA_SOURCE_BUFFER,
+};
+
 class ArrayDataReader
 {
 protected:
     FieldmlIoContext * const context;
 
     ArrayDataReader( FieldmlIoContext *_context );
 
+    static ArrayDataReader *createInternal( FieldmlIoContext *context, const std::string root,
+    	FmlObjectHandle source, void *buffer );
+
 public:
     virtual FmlIoErrorNumber readIntSlab( const int *offsets, const int *sizes, int *valueBuffer ) = 0;
 
@@ -63,7 +73,10 @@ class ArrayDataReader
 
     virtual ~ArrayDataReader();
 
-    static ArrayDataReader *create( FieldmlIoContext *context, const std::string root, FmlObjectHandle source );
+    static ArrayDataReader *create( FieldmlIoContext *context, const std::string root, FmlObjectHandle source);
+
+    static ArrayDataReader *createWithBuffer( FieldmlIoContext *context, const std::string root,
+    	FmlObjectHandle source, void *buffer );
 };
 
 

io/src/FieldmlIoApi.cpp

@@ -72,8 +72,8 @@ FmlIoErrorNumber FieldmlIo_GetLastError()
     return FieldmlIoSession::getSession().getLastError();
 }
 
-
-FmlReaderHandle Fieldml_OpenReader( FmlSessionHandle handle, FmlObjectHandle objectHandle )
+FmlReaderHandle Fieldml_OpenReaderInternal( FmlSessionHandle handle, FmlObjectHandle objectHandle,
+	ArrayDataSourceType sourceType, void *buffer)
 {
     if( Fieldml_IsObjectLocal( handle, objectHandle, 0 ) != 1 )
     {
@@ -92,7 +92,11 @@ FmlReaderHandle Fieldml_OpenReader( FmlSessionHandle handle, FmlObjectHandle obj
         }
         else
         {
-            reader = ArrayDataReader::create( FieldmlIoSession::getSession().createContext( handle ), root, objectHandle );
+        	if (sourceType == ARRAY_DATA_SOURCE_DEFAULT)
+        		reader = ArrayDataReader::create( FieldmlIoSession::getSession().createContext( handle ), root, objectHandle);
+        	else
+        		reader = ArrayDataReader::createWithBuffer( FieldmlIoSession::getSession().createContext( handle ),
+        			root, objectHandle, buffer);
         }
         Fieldml_FreeString(region_string);
     }
@@ -111,6 +115,16 @@ FmlReaderHandle Fieldml_OpenReader( FmlSessionHandle handle, FmlObjectHandle obj
 }
 
 
+FmlReaderHandle Fieldml_OpenReader( FmlSessionHandle handle, FmlObjectHandle objectHandle)
+{
+    return Fieldml_OpenReaderInternal(handle, objectHandle, ARRAY_DATA_SOURCE_DEFAULT, 0);
+}
+
+FmlReaderHandle Fieldml_OpenReaderWithBuffer( FmlSessionHandle handle, FmlObjectHandle objectHandle, void *buffer)
+{
+	return Fieldml_OpenReaderInternal(handle, objectHandle, ARRAY_DATA_SOURCE_BUFFER, buffer);
+}
+
 FmlIoErrorNumber Fieldml_ReadIntSlab( FmlReaderHandle readerHandle, const int *offsets, const int *sizes, int *valueBuffer )
 {
     ArrayDataReader *reader = FieldmlIoSession::getSession().handleToReader( readerHandle );