DSM working with mpich2-1.5

CMakeLists.txt

@@ -46,6 +46,9 @@ endif(BUILD_TESTING)
 option(XDMF_WRAP_PYTHON OFF)
 option(XDMF_WRAP_JAVA OFF)
 
+# Test for DSM
+option(XDMF_BUILD_DSM OFF)
+
 # If we are wrapping either, we need swig
 if(XDMF_WRAP_PYTHON OR XDMF_WRAP_JAVA)
   find_package(SWIG REQUIRED)
@@ -59,7 +62,11 @@ 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
@@ -74,6 +81,10 @@ 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)

Xdmf.i

@@ -3,9 +3,15 @@ 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>
@@ -15,10 +21,8 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
     #include <XdmfError.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>
@@ -53,6 +57,55 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
     #include <XdmfUnstructuredGrid.hpp>
 %}
 
+#else
+%module Xdmf
+%{
+
+    // XdmfCore Includes
+    #include <Xdmf.hpp>
+    #include <XdmfArray.hpp>
+    #include <XdmfArrayType.hpp>
+    #include <XdmfCoreItemFactory.hpp>
+    #include <XdmfCoreReader.hpp>
+    #include <XdmfError.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 <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 <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>
+%}
+
+#endif
+
 %import XdmfCore.i
 
 #ifdef SWIGJAVA
@@ -169,6 +222,9 @@ swig -v -c++ -python -o XdmfPython.cpp Xdmf.i
 %include std_set.i
 %include std_map.i
 %include std_vector.i
+%include mpi4py/mpi4py.i
+
+%mpi4py_typemap(Comm, MPI_Comm);
 
 %template(XdmfMapNodeIdSet) std::set<int>;
 %template(XdmfMapNodeIdMap) std::map<int, std::set<int> >;

XdmfAttribute.hpp

@@ -77,13 +77,13 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfAttribute.cpp
-   * Assuming that exampleAttribute is a shared pointer to an XdmfAttribute object with its center set
+   * @skipline Assuming
    * @skipline getCenter
    *
    * Python
    *
    * @dontinclude XdmfExampleAttribute.py
-   * Assuming that exampleAttribute is a shared pointer to an XdmfAttribute object with its center set
+   * @skipline Assuming
    * @skipline getCenter
    *
    * @return XdmfAttributeCenter of the attribute.
@@ -102,13 +102,13 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfAttribute.cpp
-   * Assuming that exampleAttribute is a shared pointer to an XdmfAttribute object
+   * @skipline Assuming
    * @skipline getName
    *
    * Python
    *
    * @dontinclude XdmfExampleAttribute.py
-   * Assuming that exampleAttribute is a shared pointer to an XdmfAttribute object
+   * @skipline Assuming
    * @skipline getName
    *
    * @return a string containing the name of the attribute.
@@ -123,13 +123,13 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfAttribute.cpp
-   * Assuming that exampleAttribute is a shared pointer to an XdmfAttribute object with its type set
+   * @skipline Assuming
    * @skipline getType
    *
    * Python
    *
    * @dontinclude XdmfExampleAttribute.py
-   * Assuming that exampleAttribute is a shared pointer to an XdmfAttribute object with its type set
+   * @skipline Assuming
    * @skipline getType
    *
    * @return XdmfAttributeType of the attribute.

XdmfCurvilinearGrid.hpp

@@ -142,13 +142,13 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * Assuming that exampleGrid is a shared pointer to an XdmfCurvilinearGrid object
+   * @skipline Assuming
    * @skipline getDimensions
    *
    * Python
    *
    * @dontinclude XdmfExampleCurvilinearGrid.py
-   * Assuming that exampleGrid is a shared pointer to an XdmfCurvilinearGrid object
+   * @skipline Assuming
    * @skipline getDimensions
    *
    * @return XdmfArray containing dimensions of this grid.
@@ -164,7 +164,7 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * Assuming that exampleGrid is a shared pointer to an XdmfCurvilinearGrid object
+   * @skipline Assuming
    * @skipline const
    *
    * Python: Python doesn't have a constant version
@@ -181,13 +181,13 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * Assuming that exampleGrid is a sharedPointer to an XdmfCurvilinearGrid object
+   * @skipline Assuming
    * @skipline getGeometry
    *
    * Python
    *
    * @dontinclude XdmfExampleCurvilinearGrid.py
-   * Assuming that exampleGrid is a sharedPointer to an XdmfCurvilinearGrid object
+   * @skipline Assuming
    * @skipline getGeometry
    *
    * @return the geometry associated with this grid.
@@ -203,13 +203,14 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
+   * @skipline Assuming
    * @skipline XdmfArray::New
    * @until setDimensions
-   * Assumng that exampleGrid is a shared pointer to an XdmfCurvilinearGrid object
    *
    * Python
    *
    * @dontinclude XdmfExampleCurvilinearGrid.py
+   * @skipline Assuming
    * @skip setDimensions
    * @skipline newPoints
    * @until setDimensions

XdmfGeometry.hpp

@@ -79,13 +79,13 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGeometry.cpp
-   * assuming that exampleGeometry is a shared pointer to a XdmfGeometry object that has been filled with data
+   * @skipline Assuming
    * @skipline getNumberPoints
    *
    * Python
    *
    * @dontinclude XdmfExampleGeometry.py
-   * assuming that exampleGeometry is a shared pointer to a XdmfGeometry object that has been filled with data
+   * @skipline Assuming
    * @skipline getNumberPoints
    */
   virtual unsigned int getNumberPoints() const;
@@ -98,13 +98,13 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGeometry.cpp
-   * assuming that exampleGeometry is a shared pointer to a XdmfGeometry object
+   * @skipline Assuming
    * @skipline getType
    *
    * Python
    *
    * @dontinclude XdmfExampleGeometry.py
-   * assuming that exampleGeometry is a shared pointer to a XdmfGeometry object
+   * @skipline Assuming
    * @skipline getType
    *
    * @return XdmfGeometryType of this geometry.

XdmfGeometryType.hpp

@@ -72,13 +72,11 @@ public:
    *
    * @dontinclude ExampleXdmfGeometryType.cpp
    * @skipline getDimensions
-   * The variable exampleDimensions now holds the number of dimensions that XYZ has
    *
    * Python
    *
    * @dontinclude XdmfExampleGeometryType.py
    * @skipline getDimensions
-   * The variable exampleDimensions now holds the number of dimensions that XYZ has
    *
    * @return an int containing number of dimensions.
    */
@@ -93,13 +91,11 @@ public:
    *
    * @dontinclude ExampleXdmfGeometryType.cpp
    * @skipline getName
-   * The variable exampleName now holds the name of XYZ
    *
    * Python
    *
    * @dontinclude XdmfExampleGeometryType.py
    * @skipline getName
-   * The variable exampleName now holds the name of XYZ
    *
    * @return the name of this geometry type.
    */

XdmfGrid.hpp

@@ -71,15 +71,15 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGrid.cpp
-   * using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline getGeometry
    *
    * Python
    *
    * @dontinclude XdmfExampleGrid.py
-   * using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline getGeometry
    *
    * @return the geometry associated with this grid.
@@ -98,15 +98,15 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGrid.cpp
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline getName
    *
    * Python
    *
    * @dontinclude XdmfExampleGrid.py
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline getName
    *
    * @return the name of the grid.
@@ -121,15 +121,15 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGrid.cpp
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline getTime
    *
    * Python
    *
    * @dontinclude XdmfExampleGrid.py
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline getTime
    *
    * @return pointer to the XdmfTime attached to this grid. If no
@@ -145,8 +145,8 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGrid.cpp
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline exampleTimeConst
    *
    * Python: Python doesn't have a constant version
@@ -164,15 +164,15 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGrid.cpp
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline getTopology
    *
    * Python
    *
    * @dontinclude XdmfExampleGrid.py
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline getTopology
    *
    * @return the topology associated with this grid.
@@ -189,16 +189,16 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGrid.cpp
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline newName
    * @skipline setName
    *
    * Python
    *
    * @dontinclude XdmfExampleGrid.py
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline newName
    * @skipline setName
    *
@@ -214,16 +214,16 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGrid.cpp
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline newTime
    * @skipline setTime
    *
    * Python
    *
    * @dontinclude XdmfExampleGrid.py
-   * Using an unstructured grid since XdmfGrid is an abstract class
-   * Assumming that exampleGrid is a shared pointer to an XdmfUnstructuredGrid object
+   * @skipline Using
+   * @until Assumming
    * @skipline newTime
    * @skipline setTime
    *

XdmfGridCollection.hpp

@@ -84,13 +84,13 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGridCollection.cpp
-   * Assuming that exampleCollection is a shared pointer to an XdmfGridCollection object with its type set
+   * @skipline Assuming
    * @skipline getType
    *
    * Python
    *
    * @dontinclude XdmfExampleGridCollection.py
-   * Assuming that exampleCollection is a shared pointer to an XdmfGridCollection object with its type set
+   * @skipline Assuming
    * @skipline getType
    *
    * @return XdmfGridCollectionType of this collection.
@@ -108,17 +108,17 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGridCollection.cpp
+   * @skipline Assuming
    * @skipline exampleInformation
    * @until setValue
-   * Assuming that exampleCollection is a shared pointer to an XdmfGridCollection object
-   * skipline insert
+   * @skipline insert
    *
    * Python
    *
    * @dontinclude XdmfExampleGridCollection.py
+   * @skipline Assuming
    * @skipline exampleInformation
    * @until setValue
-   * Assuming that exampleCollection is a shared pointer to an XdmfGridCollection object
    * @skipline insert
    *
    * @param information an XdmfInformation to attach to this item.
@@ -134,13 +134,13 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfGridCollection.cpp
-   * Assuming that exampleCollection is a shared pointer to an XdmfGridCollection object
+   * @skipline Assuming
    * @skipline setType
    *
    * Python
    *
    * @dontinclude XdmfExampleGridCollection.py
-   * Assuming that exampleCollection is a shared pointer to an XdmfGridCollection object
+   * @skipline Assuming
    * @skipline setType
    *
    * @param type the XdmfGridCollectionType to set.

XdmfMap.hpp

@@ -92,40 +92,15 @@ public:
    *
    * @dontinclude ExampleXdmfMap.cpp
    * @skipline holdGlobalNodes
-   * @until New
-   * The globalNodeIDs are placed into the attribute
-   * The index they are at in the attribute corresponds to their localNodeID
-   * @skipline nodeAttribute
-   * @until push_back
-   * The Attribute is then added to the vector
-   * The index that the Attribute has in the vector corresponds to a task id
-   * Using this method add all the required nodes
-   * @skipline nodeAttribute
-   * until vector
-   * returns a vector of maps that holds the equivalencies for the nodes provided
-   * for example if Attribute 1 had globalNodeID 3 at localNodeID 2
-   * and Attribute 3 had globalNodeID 3 at localNodeID 5
-   * then map 1 would have an entry of (3, 5, 2)
-   * and map 3 would have an entry of (1, 2, 5)
-   * The entries are formatted (remoteTaskID, remoteLocalNodeID, localNodeID)
+   * @until localNodeID)
    *
    * Python
    *
    * @dontinclude XdmfExampleMap.py
-   * create attributes for each task id
-   * the index of the node id in the attribute is the local node id
-   * @skipline map1Attribute
-   * @until map2Attribute.insertAsInt32
-   * insert the attributes into a vector
-   * the id of the attribute in the vector is equal to the task id
-   * @skipline testVector
-   * @until New
-   * returns a vector of maps that holds the equivalencies for the nodes provided
-   * for example if Attribute 1 had globalNodeID 3 at localNodeID 2
-   * and Attribute 3 had globalNodeID 3 at localNodeID 5
-   * then map 1 would have an entry of (3, 5, 2)
-   * and map 3 would have an entry of (1, 2, 5)
-   * The entries are formatted (remoteTaskID, remoteLocalNodeID, localNodeID)
+   * @skipline #create
+   * @until push_back(map2Attribute)
+   * @skipline New
+   * @until localNodeID)
    *
    * @param globalNodeIds a vector of attributes containing globalNodeId
    * values for each partition to be mapped.
@@ -151,57 +126,16 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfMap.cpp
-   * Assuming that exampleMap is a shared pointer to an XdmfMap object filled with the following tuples
-   * (1, 1, 9)
-   * (1, 2, 8)
-   * (2, 3, 7)
-   * (2, 4, 6)
-   * (3, 5, 5)
-   * (3, 6, 4)
-   * @skipline getMap
-   * taskIDMap now contains the same tuples as exampleMap
-   * @skipline begin
-   * @until first
-   * taskIDValue is now equal to 1, because that is the first taskID listed
-   * @skipline nodeIDMap
-   * nodeIDMap now contains the following tuples because it retrieved the tuples associated with taskID 1
-   * (1, 9)
-   * (2, 8)
-   * @skipline begin
-   * @until first
-   * localNodeValue is now equal to 1, because it is the first entry in the first tuple in the set
-   * @skipline remoteNodeSet
-   * remoteNodeSet now contains all remoteLocalNodeIDs for taskID 1 and LocalNode 1
-   * in this case remoteNodeSet contains (9)
-   * @skipline begin
-   * @until remoteNodeValue
-   * remoteNodeValue now equals 9
+   * @skip getMap
+   * @skipline Assuming
+   * @until //remoteNodeValue
    *
    * Python
    *
    * @dontinclude XdmfExampleMap.py
-   * Assuming that exampleMap is a shared pointer to an XdmfMap object filled with the following tuples
-   * (1, 1, 9)
-   * (1, 2, 8)
-   * (2, 3, 7)
-   * (2, 4, 6)
-   * (3, 5, 5)
-   * (3, 6, 4)
-   * @skipline getMap
-   * @until break
-   * This prints out all the task IDs
-   * unless the break is called on the last iteration the program will fail because of an issue with SWIG
-   * @skipline nodeIDMap
-   * nodeIDMap now contains the following tuples because it retrieved the tuples associated with taskID 1
-   * (1, 9)
-   * (2, 8)
-   * @skipline 0
-   * @until break
-   * This prints out all the local node IDs
-   * unless the break is called on the last iteration the program will fail because of an issue with SWIG
-   * @skipline val
-   * @until print
-   * prints out all the remote node values associated with taskID 1 and localNode 1
+   * @skip getMap
+   * @skipline Assuming
+   * @until #prints
    *
    * @return stored boundary communicator map.
    */
@@ -215,13 +149,13 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfMap.cpp
-   * Assumming that exampleMap is a shared pointer to a XdmfMap object
+   * @skipline Assumming
    * @skipline getName
    *
    * Python
    *
    * @dontinclude XdmfExampleMap.py
-   * Assumming that exampleMap is a shared pointer to a XdmfMap object
+   * @skipline Assumming
    * @skipline getName
    *
    * @return name of boundary communicator map.
@@ -237,48 +171,20 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfMap.cpp
-   * Assuming that exampleMap is a shared pointer to an XdmfMap object filled with the following tuples
-   * (1, 1, 9)
-   * (1, 2, 8)
-   * (2, 3, 7)
-   * (2, 4, 6)
-   * (3, 5, 5)
-   * (3, 6, 4)
+   * @skip getMap
+   * @skipline Assuming
+   * @until 4)
    * @skipline getRemoteNodeIds
-   * nodeIDMap now contains the following tuples because it retrieved the tuples associated with taskID 1
-   * (1, 9)
-   * (2, 8)
-   * @skipline begin
-   * @until first
-   * localNodeValue is now equal to 1, because it is the first entry in the first tuple in the set
-   * @skipline remoteNodeSet
-   * remoteNodeSet now contains all remoteLocalNodeIDs for taskID 1 and LocalNode 1
-   * in this case remoteNodeSet contains (9)
-   * @skipline begin
-   * @until remoteNodeValue
-   * remoteNodeValue now equals 9
+   * @until //remoteNodeValue
    *
    * Python
    *
    * @dontinclude XdmfExampleMap.py
-   * Assuming that exampleMap is a shared pointer to an XdmfMap object filled with the following tuples
-   * (1, 1, 9)
-   * (1, 2, 8)
-   * (2, 3, 7)
-   * (2, 4, 6)
-   * (3, 5, 5)