Merge branch 'master' of ssh://hsai-dev.arl.army.mil/data/Repository/Xdmf2

CMakeLists.txt

 project(Xdmf)
 cmake_minimum_required(VERSION 2.6)
 
+#Needed to build DSM because relative paths are used to add its libraries
+if (POLICY CMP0015)
+	cmake_policy(SET CMP0015 NEW)
+endif (POLICY CMP0015)
+
 if(MSVC10)
 	SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY_RELEASE ${CMAKE_BINARY_DIR})
 	SET(CMAKE_LIBRARY_OUTPUT_DIRECTORY_RELEASE ${CMAKE_BINARY_DIR})
@@ -41,6 +46,13 @@ endif(BUILD_TESTING)
 option(XDMF_WRAP_PYTHON OFF)
 option(XDMF_WRAP_JAVA OFF)
 
+# Test for DSM
+option(XDMF_BUILD_DSM OFF)
+
+if(XDMF_BUILD_DSM)
+  option(XDMF_BUILD_DSM_THREADS ON)
+endif(XDMF_BUILD_DSM)
+
 # If we are wrapping either, we need swig
 if(XDMF_WRAP_PYTHON OR XDMF_WRAP_JAVA)
   find_package(SWIG REQUIRED)
@@ -54,7 +66,11 @@ endif(XDMF_WRAP_PYTHON OR XDMF_WRAP_JAVA)
 if(XDMF_WRAP_PYTHON)
   find_package(PythonInterp REQUIRED)
   find_package(PythonLibs REQUIRED)
-  include_directories(${PYTHON_INCLUDE_DIRS})
+  if (XDMF_BUILD_DSM)
+    include_directories(${PYTHON_INCLUDE_DIRS} ${MPI_CXX_INCLUDE_PATH})
+  else (XDMF_BUILD_DSM)
+    include_directories(${PYTHON_INCLUDE_DIRS})
+  endif (XDMF_BUILD_DSM)
 
   # A macro to swig and create the python files
   # Since we essentually do the same thing inside and outside core, it
@@ -69,6 +85,10 @@ if(XDMF_WRAP_PYTHON)
     # optimize swig generation --- these are all flags corresponding to -O
     # except -fvirtual which breaks visitor operation
     set(CMAKE_SWIG_FLAGS ${XDMF_SWIG_FLAGS} -modern -fastdispatch -nosafecstrings -noproxydel -fastproxy -fastinit -fastunpack -fastquery -modernargs -nobuildnone)
+    #Enables DSM
+    if (XDMF_BUILD_DSM)
+      set(CMAKE_SWIG_FLAGS ${CMAKE_SWIG_FLAGS} -DXDMF_BUILD_DSM)
+    endif (XDMF_BUILD_DSM)
     set_source_files_properties(${python_name}.i PROPERTIES CPLUSPLUS ON)
     set(swig_extra_generated_files "")
     swig_add_module(${python_name} python ${python_name}.i)
@@ -198,7 +218,7 @@ if(XDMF_WRAP_JAVA)
 endif(XDMF_WRAP_JAVA)
 
 add_subdirectory(core)
-include_directories(${XdmfCore_INCLUDE_DIRS})
+include_directories(${XdmfCore_INCLUDE_DIRS} ${XdmfDSM_INCLUDE_DIRS})
 link_directories(${XDMF_LIBRARY_DIRS})
 
 option(XDMF_BUILD_CORE_ONLY OFF)
@@ -228,7 +248,11 @@ if(NOT XDMF_BUILD_CORE_ONLY)
     XdmfUnstructuredGrid)
 
   add_library(Xdmf ${XdmfSources})
-  target_link_libraries(Xdmf XdmfCore)
+  if(XDMF_BUILD_DSM)
+    target_link_libraries(Xdmf XdmfCore XdmfDSM)
+  else(XDMF_BUILD_DSM)
+    target_link_libraries(Xdmf XdmfCore)
+  endif(XDMF_BUILD_DSM)
 
   if(WIN32)
 	set_target_properties(Xdmf PROPERTIES
@@ -248,7 +272,7 @@ if(NOT XDMF_BUILD_CORE_ONLY)
   endif(XDMF_WRAP_JAVA)
 
   if(XDMF_WRAP_PYTHON)
-    XDMF_SWIG_PYTHON(Xdmf XdmfCore)
+    XDMF_SWIG_PYTHON(Xdmf XdmfCore XdmfDSM)
   endif(XDMF_WRAP_PYTHON)
 
   if(BUILD_TESTING)

Xdmf.hpp

@@ -65,8 +65,68 @@
 * constructors in the XDMF API are protected, ensuring that only
 * shared pointers can be created. These pointers are freed
 * automatically by the shared pointer reference counting mechanism.
+*
+*
+* Structure:
+*
+* Xdmf2 is structured in a tree format with an XdmfDomain serving
+* as the base. The Domain contains multiple grid collections or
+* grids; each with their own geometries, topologies, attributes,
+* and/or sets. With the inclusion of shared pointers in Xdmf2
+* a topology could be shared across multiple grids or a grid 
+* could be included in multiple grid collections and/or the domain.
+*
+*
+* C++ Examples:
+*
+* \subpage cppwrite "C++ Example of Xdmf Creation"
+*
+* \subpage cppread "C++ Example of Reading Xdmf"
+*
+* \subpage cppedit "C++ Example of Reading and Modifying Xdmf"
+*
+* Python Examples:
+*
+* \subpage pywrite "Python Example of Xdmf Creation"
+*
+* \subpage pyread "Python Example of Reading Xdmf"
+*
+* \subpage pyedit "Python Example of Reading and Modifying Xdmf"
+*
+*/
+
+/*!
+* \page cppwrite Example of Xdmf Creation
+* \include ExampleXdmfWrite.cpp
+*/
+
+/*!
+* \page cppread Example of Reading Xdmf
+* \include ExampleXdmfRead.cpp
+*/
+
+/*!
+* \page cppedit Example of Reading and Modifying
+* \include ExampleXdmfEdit.cpp
+*/
+
+/*!
+* \page pywrite Example of Xdmf Creation
+* \include XdmfExampleWrite.py
 */
 
+/*!
+* \page pyread Example of Reading Xdmf
+* \include XdmfExampleRead.py
+*/
+
+/*!
+* \page pyedit Example of Reading and Modifying
+* \include XdmfExampleEdit.py
+*/
+
+
+
 /* Keep all our Win32 Conversions here */
 #ifdef _WIN32
 /* Used to export/import from the dlls */
@@ -75,6 +135,11 @@
 #undef XDMFCORE_TEMPLATE
 #define XDMFCORE_TEMPLATE extern
 
+#undef XDMFDSM_EXPORT
+#define XDMFDSM_EXPORT __declspec(dllimport)
+#undef XDMFDSM_TEMPLATE
+#define XDMFDSM_TEMPLATE extern
+
 #ifdef Xdmf_EXPORTS
 #define XDMF_EXPORT __declspec(dllexport)
 #define XDMF_TEMPLATE
@@ -98,8 +163,10 @@
 #else /* _WIN32 */
 /* We don't need to export/import since there are no dlls */
 #define XDMFCORE_EXPORT
+#define XDMFDSM_EXPORT
 #define XDMF_EXPORT
 #define XDMFCORE_TEMPLATE
+#define XDMFDSM_TEMPLATE
 #define XDMF_TEMPLATE
 #endif /* _WIN32 */
 #endif /* _XDMF_HPP */

Xdmf.i

@@ -3,22 +3,31 @@ XdmfPython.cpp:
 swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
 */
 
+
+#ifdef XDMF_BUILD_DSM
+
 %module Xdmf
 %{
 
+    // MPI Includes
+    #include <mpi.h>
+
     // XdmfCore Includes
     #include <Xdmf.hpp>
     #include <XdmfArray.hpp>
+    #include <XdmfArrayReference.hpp>
     #include <XdmfArrayType.hpp>
     #include <XdmfCoreItemFactory.hpp>
     #include <XdmfCoreReader.hpp>
+    #include <XdmfDSMManager.hpp>
+    #include <XdmfDSMBuffer.hpp>
+    #include <XdmfDSMCommMPI.hpp>
     #include <XdmfError.hpp>
+    #include <XdmfFunction.hpp>
     #include <XdmfHDF5Controller.hpp>
     #include <XdmfHDF5Writer.hpp>
-#ifdef XDMF_BUILD_DSM
     #include <XdmfHDF5ControllerDSM.hpp>
     #include <XdmfHDF5WriterDSM.hpp>
-#endif
     #include <XdmfHeavyDataController.hpp>
     #include <XdmfHeavyDataWriter.hpp>
     #include <XdmfInformation.hpp>
@@ -26,6 +35,62 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
     #include <XdmfItemProperty.hpp>
     #include <XdmfSharedPtr.hpp>
     #include <XdmfSparseMatrix.hpp>
+    #include <XdmfSubset.hpp>
+    #include <XdmfSystemUtils.hpp>
+    #include <XdmfVisitor.hpp>
+    #include <XdmfWriter.hpp>
+
+    // Xdmf Includes
+    #include <XdmfAttribute.hpp>
+    #include <XdmfAttributeCenter.hpp>
+    #include <XdmfAttributeType.hpp>
+    #include <XdmfCurvilinearGrid.hpp>
+    #include <XdmfDomain.hpp>
+    #include <XdmfGeometry.hpp>
+    #include <XdmfGeometryType.hpp>
+    #include <XdmfGraph.hpp>
+    #include <XdmfGrid.hpp>
+    #include <XdmfGridCollection.hpp>
+    #include <XdmfGridCollectionType.hpp>
+    #include <XdmfItemFactory.hpp>
+    #include <XdmfMap.hpp>
+    #include <XdmfReader.hpp>
+    #include <XdmfRectilinearGrid.hpp>
+    #include <XdmfRegularGrid.hpp>
+    #include <XdmfSet.hpp>
+    #include <XdmfSetType.hpp>
+    #include <XdmfTime.hpp>
+    #include <XdmfTopology.hpp>
+    #include <XdmfTopologyType.hpp>
+    #include <XdmfUnstructuredGrid.hpp>
+
+%}
+
+%import XdmfDSM.i
+
+#else
+%module Xdmf
+%{
+
+    // XdmfCore Includes
+    #include <Xdmf.hpp>
+    #include <XdmfArray.hpp>
+    #include <XdmfArrayReference.hpp>
+    #include <XdmfArrayType.hpp>
+    #include <XdmfCoreItemFactory.hpp>
+    #include <XdmfCoreReader.hpp>
+    #include <XdmfError.hpp>
+    #include <XdmfFunction.hpp>
+    #include <XdmfHDF5Controller.hpp>
+    #include <XdmfHDF5Writer.hpp>
+    #include <XdmfHeavyDataController.hpp>
+    #include <XdmfHeavyDataWriter.hpp>
+    #include <XdmfInformation.hpp>
+    #include <XdmfItem.hpp>
+    #include <XdmfItemProperty.hpp>
+    #include <XdmfSharedPtr.hpp>
+    #include <XdmfSparseMatrix.hpp>
+    #include <XdmfSubset.hpp>
     #include <XdmfSystemUtils.hpp>
     #include <XdmfVisitor.hpp>
     #include <XdmfWriter.hpp>
@@ -55,6 +120,8 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
     #include <XdmfUnstructuredGrid.hpp>
 %}
 
+#endif
+
 %import XdmfCore.i
 
 #ifdef SWIGJAVA
@@ -171,15 +238,39 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
 
 %include std_set.i
 %include std_map.i
+%include std_vector.i
+
+#ifdef XDMF_BUILD_DSM
+
+%include mpi4py/mpi4py.i
+
+%mpi4py_typemap(Comm, MPI_Comm);
+
+#endif /* XDMF_BUILD_DSM */
 
 %template(XdmfMapNodeIdSet) std::set<int>;
 %template(XdmfMapNodeIdMap) std::map<int, std::set<int> >;
 %template(XdmfMapMap) std::map<int, std::map<int, std::set<int> > >;
+%template(AttributeVector) std::vector<shared_ptr<XdmfAttribute> >;
+%template(MapVector) std::vector<shared_ptr<XdmfMap> >;
+%template(ArrayVector) std::vector<shared_ptr<XdmfArray> >;
+
+#ifdef XDMF_BUILD_DSM
 
 %pythoncode {
     from XdmfCore import *
+    from XdmfDSM import *
 }
 
+#else
+
+%pythoncode {
+    from XdmfCore import *
+}
+
+#endif /* XDMF_BUILD_DSM */
+
+
 %fragment("XdmfItemCast", "header") {
     #include <XdmfSharedPtr.hpp>
     PyObject * XdmfItemCast(shared_ptr<XdmfItem> obj) {

XdmfAttribute.cpp

@@ -94,9 +94,14 @@ XdmfAttribute::populateItem(const std::map<std::string, std::string> & itemPrope
     mName = name->second;
   }
   else {
-    XdmfError::message(XdmfError::FATAL,
-                       "'Name' not found in itemProperties in "
-                       "XdmfAttribute::populateItem");
+    try {
+      XdmfError::message(XdmfError::FATAL,
+                         "'Name' not found in itemProperties in "
+                         "XdmfAttribute::populateItem");
+    }
+    catch (XdmfError e) {
+      throw e;
+    }
   }
 
   mCenter = XdmfAttributeCenter::New(itemProperties);

XdmfAttribute.hpp

@@ -48,7 +48,21 @@ public:
   /**
    * Create a new XdmfAttribute.
    *
-   * @return constructed XdmfAttribute.
+   * Example of use:
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfAttribute.cpp
+   * @skipline //#initialization
+   * @until //#initialization
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleAttribute.py
+   * @skipline #//initialization
+   * @until #//initialization
+   *
+   * @return    Constructed XdmfAttribute.
    */
   static shared_ptr<XdmfAttribute> New();
 
@@ -60,7 +74,29 @@ public:
   /**
    * Get the XdmfAttributeCenter associated with this attribute.
    *
-   * @return XdmfAttributeCenter of the attribute.
+   * Example of use:
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfAttribute.cpp
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setCenter
+   * @until //#setCenter
+   * @skipline //#getCenter
+   * @until //#getCenter
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleAttribute.py
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setCenter
+   * @until #//setCenter
+   * @skipline #//getCenter
+   * @until #//getCenter
+   *
+   * @return    XdmfAttributeCenter of the attribute.
    */
   shared_ptr<const XdmfAttributeCenter> getCenter() const;
 
@@ -71,35 +107,133 @@ public:
   /**
    * Get the name of the attribute.
    *
-   * @return a string containing the name of the attribute.
+   * Example of use:
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfAttribute.cpp
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setName
+   * @until //#setName
+   * @skipline //#getName
+   * @until //#getName
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleAttribute.py
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setName
+   * @until #//setName
+   * @skipline #//getName
+   * @until #//getName
+   *
+   * @return    A string containing the name of the attribute.
    */
   std::string getName() const;
 
   /**
    * Get the XdmfAttributeType associated with this attribute.
    *
-   * @return XdmfAttributeType of the attribute.
+   * Example of use:
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfAttribute.cpp
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setType
+   * @until //#setType
+   * @skipline //#getType
+   * @until //#getType
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleAttribute.py
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setType
+   * @until #//setType
+   * @skipline #//getType
+   * @until #//getType
+   *
+   * @return    XdmfAttributeType of the attribute.
    */
   shared_ptr<const XdmfAttributeType> getType() const;
 
   /**
    * Set the XdmfAttributeCenter associated with this attribute.
    *
-   * @param center the XdmfAttributeCenter to set.
+   * Example of use:
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfAttribute.cpp
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setCenter
+   * @until //#setCenter
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleAttribute.py
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setCenter
+   * @until #//setCenter
+   *
+   * @param     center  The XdmfAttributeCenter to set.
    */
   void setCenter(const shared_ptr<const XdmfAttributeCenter> center);
 
   /**
    * Set the name of the attribute.
    *
-   * @param name a string containing the name to set.
+   * Example of use:
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfAttribute.cpp
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setName
+   * @until //#setName
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleAttribute.py
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setName
+   * @until #//setName
+   *
+   * @param     name    A string containing the name to set.
    */
   void setName(const std::string & name);
 
   /**
    * Set the XdmfAttributeType associated with this attribute.
    *
-   * @param type XdmfAttributeType to set.
+   * Example of use:
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfAttribute.cpp
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setType
+   * @until //#setType
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleAttribute.py
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setType
+   * @until #//setType
+   *
+   * @param     type    XdmfAttributeType to set.
    */
   void setType(const shared_ptr<const XdmfAttributeType> type);
 

XdmfAttributeCenter.cpp

@@ -81,9 +81,14 @@ XdmfAttributeCenter::New(const std::map<std::string, std::string> & itemProperti
   std::map<std::string, std::string>::const_iterator center =
     itemProperties.find("Center");
   if(center == itemProperties.end()) {
-    XdmfError::message(XdmfError::FATAL, 
-                       "'Center' not found in itemProperties in "
-                       "XdmfAttributeCenter::New");
+    try {
+      XdmfError::message(XdmfError::FATAL, 
+                         "'Center' not found in itemProperties in "
+                         "XdmfAttributeCenter::New");
+    }
+    catch (XdmfError e) {
+      throw e;
+    }
   }
   const std::string & centerVal = center->second;