Changeset 624 for XIOS/trunk/src/transformation

Timestamp:

06/22/15 13:36:37 (9 years ago)

Author:

mhnguyen

Message:

Final tests of zoom and inverse on axis

+) Modify test_client and test_complete to work with new grid definition
+) Correct some bugs causing memory leak
+) Clean abundant code
+) Add more comments to new files

Test
+) On Curie
+) test_client and test_complete pass with correct results

Location:

XIOS/trunk/src/transformation

Files:

• . (added)
• axis_algorithm_inverse.cpp (moved) (moved from XIOS/trunk/src/filter/axis_algorithm_inverse.cpp) (1 diff)
• axis_algorithm_inverse.hpp (moved) (moved from XIOS/trunk/src/filter/axis_algorithm_inverse.hpp) (2 diffs)
• axis_algorithm_transformation.cpp (moved) (moved from XIOS/trunk/src/filter/axis_algorithm_transformation.cpp) (3 diffs)
• axis_algorithm_transformation.hpp (moved) (moved from XIOS/trunk/src/filter/axis_algorithm_transformation.hpp) (3 diffs)
• axis_algorithm_zoom.cpp (moved) (moved from XIOS/trunk/src/filter/axis_algorithm_zoom.cpp) (4 diffs)
• axis_algorithm_zoom.hpp (moved) (moved from XIOS/trunk/src/filter/axis_algorithm_zoom.hpp) (3 diffs)
• generic_algorithm_transformation.cpp (moved) (moved from XIOS/trunk/src/filter/generic_algorithm_transformation.cpp) (2 diffs)
• generic_algorithm_transformation.hpp (moved) (moved from XIOS/trunk/src/filter/generic_algorithm_transformation.hpp) (2 diffs)
• grid_transformation.cpp (moved) (moved from XIOS/trunk/src/filter/grid_transformation.cpp) (19 diffs)
• grid_transformation.hpp (moved) (moved from XIOS/trunk/src/filter/grid_transformation.hpp) (2 diffs)
• transformation_mapping.cpp (moved) (moved from XIOS/trunk/src/filter/transformation_mapping.cpp) (2 diffs)
• transformation_mapping.hpp (moved) (moved from XIOS/trunk/src/filter/transformation_mapping.hpp) (1 diff)

XIOS/trunk/src/transformation/axis_algorithm_inverse.cpp

@@ +1 @@
+/*!
+   \file axis_algorithm_inverse.hpp
+   \author Ha NGUYEN
+   \since 14 May 2015
+   \date 09 June 2015
+
+   \brief Algorithm for inversing an axis..
+ */
 #include "axis_algorithm_inverse.hpp"
 

XIOS/trunk/src/transformation/axis_algorithm_inverse.hpp

@@ +1 @@
+/*!
+   \file axis_algorithm_inverse.hpp
+   \author Ha NGUYEN
+   \since 14 May 2015
+   \date 09 June 2015
+
+   \brief Algorithm for inversing an axis..
+ */
 #ifndef __XIOS_AXIS_ALGORITHM_INVERSE_HPP__
 #define __XIOS_AXIS_ALGORITHM_INVERSE_HPP__
@@ -6 +14 @@
 
 namespace xios {
-
+/*!
+  \class CAxisAlgorithmInverse
+  Inversing an axis
+*/
 class CAxisAlgorithmInverse : public CAxisAlgorithmTransformation
 {

XIOS/trunk/src/transformation/axis_algorithm_transformation.cpp

@@ +1 @@
+/*!
+   \file axis_algorithm_transformation.hpp
+   \author Ha NGUYEN
+   \since 14 May 2015
+   \date 09 June 2015
+
+   \brief Interface for all axis transformation algorithms.
+ */
+
 #include "axis_algorithm_transformation.hpp"
-#include "axis_inverse.hpp"
-#include "axis_zoom.hpp"
+#include "axis_algorithm_inverse.hpp"
+#include "axis_algorithm_zoom.hpp"
 
 namespace xios {
@@ -8 +17 @@
  : CGenericAlgorithmTransformation()
 {
-//  if (axisDestination->size.getValue() != axisSource->size.getValue())
-//  {
-//    ERROR("CAxisZoom::CAxisZoom(CAxis* axisDestination, CAxis* axisSource)",
-//           << "Two axis have different size"
-//           << "Size of axis source " <<axisSource->getId() << " is " << axisSource->size.getValue()  << std::endl
-//           << "Size of axis destionation " <<axisDestination->getId() << " is " << axisDestination->size.getValue());
-//  }
-//
-//
-//  axisDestGlobalSize_ = axisDestination->size.getValue();
-//  int niDest = axisDestination->ni.getValue();
-//  int ibeginDest = axisDestination->ibegin.getValue();
-//
-//  for (int idx = 0; idx < niDest; ++idx) axisDestGlobalIndex_.push_back(ibeginDest+idx);
 }
 
 CAxisAlgorithmTransformation::~CAxisAlgorithmTransformation()
 {
-//  for (int idx = 0; idx < algosOfAnAxis_.size(); ++idx) delete algosOfAnAxis_[idx];
 }
 
 void CAxisAlgorithmTransformation::computeIndexSourceMapping()
 {
-//  if (!algosOfAnAxis_.empty())
-//  {
-//    algosOfAnAxis_[0]->computeIndexSourceMapping(this->transformationMapping_);
-//    for (int idx = 1; idx < algosOfAnAxis_.size(); ++idx)
-//    {
-//      algosOfAnAxis_[idx]->computeIndexSourceMapping(algosOfAnAxis_[idx-1]->getTransformationMapping());
-//    }
-//    this->transformationMapping_ = algosOfAnAxis_[algosOfAnAxis_.size()-1]->getTransformationMapping();
-//  }
 }
 
@@ -162 +147 @@
   }
 }
-
-
 }

XIOS/trunk/src/transformation/axis_algorithm_transformation.hpp

@@ +1 @@
+/*!
+   \file axis_algorithm_transformation.hpp
+   \author Ha NGUYEN
+   \since 14 May 2015
+   \date 09 June 2015
+
+   \brief Interface for all axis transformation algorithms.
+ */
 #ifndef __XIOS_AXIS_ALGORITHM_TRANSFORMATION_HPP__
 #define __XIOS_AXIS_ALGORITHM_TRANSFORMATION_HPP__
@@ -4 +12 @@
 #include "generic_algorithm_transformation.hpp"
 #include "axis.hpp"
-#include "concrete_algo.hpp"
 
 namespace xios {
 
+/*!
+  \class CAxisAlgorithmTransformation
+  Algorithms for axis.
+*/
 class CAxisAlgorithmTransformation : public virtual CGenericAlgorithmTransformation
 {
@@ -24 +35 @@
                                                         std::vector<CArray<size_t,1> >& globalIndexSrcGrid);
   void computeIndexSourceMapping();
+
 protected:
+  //! Global index of an axis on grid destination
   std::vector<int> axisDestGlobalIndex_;
+
+  //! Size of
   int axisDestGlobalSize_;
 

XIOS/trunk/src/transformation/axis_algorithm_zoom.cpp

@@ +1 @@
+/*!
+   \file axis_algorithm_zoom.cpp
+   \author Ha NGUYEN
+   \since 03 June 2015
+   \date 12 June 2015
+
+   \brief Algorithm for zooming on an axis.
+ */
 #include "axis_algorithm_zoom.hpp"
 
@@ -22 +30 @@
 }
 
+/*!
+  Compute the index mapping between axis on grid source and one on grid destination
+*/
 void CAxisAlgorithmZoom::computeIndexSourceMapping()
 {
@@ -43 +54 @@
 }
 
+/*!
+  After a zoom on axis, it should be certain that (global) zoom begin and (global) zoom size are updated
+*/
 void CAxisAlgorithmZoom::updateZoom()
 {
@@ -49 +63 @@
 }
 
+/*!
+  Update mask on axis
+  Because only zoomed region on axis is not masked, the remaining must be masked to make sure
+correct index be extracted
+*/
 void CAxisAlgorithmZoom::updateAxisDestinationMask()
 {

XIOS/trunk/src/transformation/axis_algorithm_zoom.hpp

@@ +1 @@
+/*!
+   \file axis_algorithm_zoom.hpp
+   \author Ha NGUYEN
+   \since 03 June 2015
+   \date 12 June 2015
+
+   \brief Algorithm for zooming on an axis.
+ */
 #ifndef __XIOS_AXIS_ALGORITHM_ZOOM_HPP__
 #define __XIOS_AXIS_ALGORITHM_ZOOM_HPP__
@@ -7 +15 @@
 
 namespace xios {
-
+/*!
+  \class CAxisAlgorithmZoom
+  Implementing zoom on axis
+  A zoomed region can be considered as region that isnt masked.
+  Only this zoomed region is extracted to write on Netcdf.
+*/
 class CAxisAlgorithmZoom : public CAxisAlgorithmTransformation
 {
@@ -20 +33 @@
   void updateAxisDestinationMask();
   void updateZoom();
+
 private:
+  //! Global zoom begin on axis
   StdSize zoomBegin_;
+
+  //! Global zoom end on axis
   StdSize zoomEnd_;
+
+  //! Global zoom size on axis
   StdSize zoomSize_;
 
 private:
+  //! Axis on grid destination
   CAxis* axisDest_;
+
+  //! Axis on grid source
   CAxis* axisSrc_;
 };

XIOS/trunk/src/transformation/generic_algorithm_transformation.cpp

@@ +1 @@
+/*!
+   \file generic_algorithm_transformation.hpp
+   \author Ha NGUYEN
+   \since 14 May 2015
+   \date 09 June 2015
+
+   \brief Interface for all transformation algorithms.
+ */
 #include "generic_algorithm_transformation.hpp"
 
@@ -26 +34 @@
                                                    iteTransMap = transformationMapping_.end();
   std::vector<int>::const_iterator itbVec, itVec, iteVec;
-  std::vector<CArray<size_t,1> > globalIndexSrcGrid((itTransMap->second).size());
+  std::vector<CArray<size_t,1> > globalIndexSrcGrid; //((itTransMap->second).size());
   CArray<size_t,1> globalIndexDestGrid;
-
   for (itTransMap = itbTransMap; itTransMap != iteTransMap; ++itTransMap)
   {
+
     this->computeGlobalIndexFromGlobalIndexElement(itTransMap->first,
                                                    itTransMap->second,

XIOS/trunk/src/transformation/generic_algorithm_transformation.hpp

@@ +1 @@
+/*!
+   \file generic_algorithm_transformation.hpp
+   \author Ha NGUYEN
+   \since 14 May 2015
+   \date 09 June 2015
+
+   \brief Interface for all transformation algorithms.
+ */
 #ifndef __XIOS_GENERIC_ALGORITHM_TRANSFORMATION_HPP__
 #define __XIOS_GENERIC_ALGORITHM_TRANSFORMATION_HPP__
@@ -7 +15 @@
 
 namespace xios {
-
+  /*!
+  \class CGenericAlgorithmTransformation
+  This class defines the interface for all other inherted algorithms class
+  */
 class CGenericAlgorithmTransformation
 {

XIOS/trunk/src/transformation/grid_transformation.cpp

@@ -3 +3 @@
    \author Ha NGUYEN
    \since 14 May 2015
-   \date 09 June 2015
+   \date 18 June 2015
 
    \brief Interface for all transformations.
@@ -62 +62 @@
 }
 
+/*!
+  Initialize the mapping between the first grid source and the original one
+  In a series of transformation, for each step, there is a need to "create" a new grid that plays a role of "temporary" source.
+Because at the end of the series, we need to know about the index mapping between the final grid destination and original grid source,
+for each transformation, we need to make sure that the current "temporary source" maps its global index correctly to the original one.
+*/
 void CGridTransformation::initializeMappingOfOriginalGridSource()
 {
@@ -100 +106 @@
 }
 
+/*!
+  Initialize the algorithms (transformations)
+*/
 void CGridTransformation::initializeAlgorithms()
 {
@@ -154 +163 @@
 }
 
+/*!
+  Select algorithm correspoding to its transformation type and its position in each element
+  \param [in] elementPositionInGrid position of element in grid. e.g: a grid has 1 domain and 1 axis, then position of domain is 1 (because it contains 2 basic elements)
+                                             and position of axis is 2
+  \param [in] transType transformation type, for now we have Zoom_axis, inverse_axis
+  \param [in] transformationOrder position of the transformation in an element (an element can have several transformation)
+*/
 void CGridTransformation::selectAlgo(int elementPositionInGrid, ETranformationType transType, int transformationOrder)
 {
@@ -159 +175 @@
 }
 
+/*!
+  Select algorithm of an axis correspoding to its transformation type and its position in each element
+  \param [in] elementPositionInGrid position of element in grid. e.g: a grid has 1 domain and 1 axis, then position of domain is 1 (because it contains 2 basic elements)
+                                             and position of axis is 2
+  \param [in] transType transformation type, for now we have Zoom_axis, inverse_axis
+  \param [in] transformationOrder position of the transformation in an element (an element can have several transformation)
+*/
 void CGridTransformation::selectAxisAlgo(int elementPositionInGrid, ETranformationType transType, int transformationOrder)
 {
@@ -188 +211 @@
 }
 
+/*!
+  Select algorithm of a domain correspoding to its transformation type and its position in each element
+  \param [in] elementPositionInGrid position of element in grid. e.g: a grid has 1 domain and 1 axis, then position of domain is 1 (because it contains 2 basic elements)
+                                             and position of axis is 2
+  \param [in] transType transformation type, for now we have Zoom_axis, inverse_axis
+  \param [in] transformationOrder position of the transformation in an element (an element can have several transformation)
+*/
 void CGridTransformation::selectDomainAlgo(int elementPositionInGrid, ETranformationType transType, int transformationOrder)
 {
-
-}
-
+}
+
+/*!
+  Assign the current grid destination to the grid source in the new transformation.
+The current grid destination plays the role of grid source in next transformation (if any).
+Only element on which the transformation is performed is modified
+  \param [in] elementPositionInGrid position of element in grid
+  \param [in] transType transformation type
+*/
 void CGridTransformation::setUpGrid(int elementPositionInGrid, ETranformationType transType)
 {
@@ -211 +247 @@
 }
 
+/*!
+  Perform all transformations
+  For each transformation, there are some things to do:
+  -) Chose the correct algorithm by transformation type and position of element
+  -) Calculate the mapping of global index between the current grid source and grid destination
+  -) Calculate the mapping of global index between current grid DESTINATION and ORIGINAL grid SOURCE
+  -) Make current grid destination become grid source in the next transformation
+*/
 void CGridTransformation::computeAll()
 {
@@ -234 +278 @@
     const CArray<size_t,1>& globalIndexGridDestSendToServer = distributionClientDest.getGlobalDataIndexSendToServer();
 
-   std::cout << "global index grid  dest send to server " << globalIndexGridDestSendToServer << std::endl;
     // ComputeTransformation of global index of each element
     std::vector<int> gridDestinationDimensionSize = gridDestination_->getGlobalDimension();
@@ -250 +293 @@
   }
 
- std::cout << "global index destination 0 final " << *globalIndexOfCurrentGridSource_ << std::endl;
- std::cout << "global index destination 1 final " << *globalIndexOfOriginalGridSource_ << std::endl;
   updateFinalGridDestination();
   computeFinalTransformationMapping();
@@ -269 +310 @@
   CDistributionClient distributionClientDest(client->clientRank, gridDestination_);
   const CArray<int, 1>& localMaskIndexOnClientDest = distributionClientDest.getLocalMaskIndexOnClient();
-  std::cout << "local mask " << localMaskIndexOnClientDest << std::endl;
-
   const CArray<size_t,1>& globalIndexOnClientDest = distributionClientDest.getGlobalDataIndexSendToServer();
-  std::cout << "global index " << globalIndexOnClientDest <<  std::endl;
+
   CArray<size_t, 1>::const_iterator itbArr, itArr, iteArr;
   itbArr = globalIndexOnClientDest.begin();
@@ -308 +347 @@
   }
 
-  std::cout << "index to modify " << *maskIndexToModify << std::endl;
   gridDestination_->modifyMask(*maskIndexToModify);
 
@@ -339 +377 @@
  int sendBuffSize = 0;
  for (itSend = itbSend; itSend != iteSend; ++itSend) sendBuffSize += (itSend->second).size();
-
- std::cout << "global index destination 0 before" << *globalIndexOfCurrentGridSource_ << std::endl;
- std::cout << "global index destination 1 before" << *globalIndexOfOriginalGridSource_ << std::endl;
 
  typedef unsigned long Scalar;
@@ -401 +436 @@
  if (globalIndexOfCurrentGridSource_->numElements()  != nbCurrentGridSource)
  {
-   if ((0 != nbCurrentGridSource) && (0 != globalIndexOfCurrentGridSource_))
-   {
-     delete globalIndexOfCurrentGridSource_;
-     globalIndexOfCurrentGridSource_ = new CArray<size_t,1>(nbCurrentGridSource);
-   }
+   delete globalIndexOfCurrentGridSource_;
+   globalIndexOfCurrentGridSource_ = new CArray<size_t,1>(nbCurrentGridSource);
  }
 
  if (globalIndexOfOriginalGridSource_->numElements() != nbCurrentGridSource)
  {
-   if ((0 != nbCurrentGridSource) && (0 != globalIndexOfOriginalGridSource_))
-   {
-     delete globalIndexOfOriginalGridSource_;
-     globalIndexOfOriginalGridSource_ = new CArray<size_t,1>(nbCurrentGridSource);
-   }
+   delete globalIndexOfOriginalGridSource_;
+   globalIndexOfOriginalGridSource_ = new CArray<size_t,1>(nbCurrentGridSource);
  }
 
@@ -434 +463 @@
  }
 
- std::cout << "global index destination 0 after " << *globalIndexOfCurrentGridSource_ << std::endl;
- std::cout << "global index destination 1 after " << *globalIndexOfOriginalGridSource_ << std::endl;
  if (0 != sendBuffSize) delete [] sendBuff;
  if (0 != recvBuffSize) delete [] recvBuff;
@@ -475 +502 @@
   const CArray<size_t,1>& globalIndexOnClientDest = distributionClientDest.getGlobalDataIndexSendToServer(); //gridDestination_->getDistributionClient()->getGlobalDataIndexSendToServer();
 
- std::cout << "dest: local index " << localIndexOnClientDest << std::endl;
- std::cout << "dest: global index " << globalIndexOnClientDest << std::endl;
   const CArray<int, 1>& localIndexOnClientSrc = distributionClientSrc.getLocalDataIndexOnClient(); //gridSource_->getDistributionClient()->getLocalDataIndexOnClient();
   const CArray<size_t,1>& globalIndexOnClientSrc = distributionClientSrc.getGlobalDataIndexSendToServer(); //gridSource_->getDistributionClient()->getGlobalDataIndexSendToServer();
- std::cout << "src: local index " << localIndexOnClientSrc << std::endl;
- std::cout << "src: global index " << globalIndexOnClientSrc << std::endl;
+
   std::vector<size_t>::const_iterator itbVec, itVec, iteVec;
   CArray<size_t, 1>::const_iterator itbArr, itArr, iteArr;
@@ -506 +530 @@
         {
           int localIdx = std::distance(itbArr, itArr);
-          (*localIndexToReceiveOnGridDest_[sourceRank][i])(idx) = localIndexOnClientDest(localIdx); // Local index of un-extracted data (only domain)
-//          (*localIndexToReceiveOnGridDest_[sourceRank][i])(idx) = (localIdx); // Local index of extracted data
+//          (*localIndexToReceiveOnGridDest_[sourceRank][i])(idx) = localIndexOnClientDest(localIdx); // Local index of un-extracted data (only domain)
+          (*localIndexToReceiveOnGridDest_[sourceRank][i])(idx) = (localIdx); // Local index of extracted data
         }
       }
     }
-//    std::cout << "local index to receive from source Rank = " << sourceRank << (*localIndexToReceiveOnGridDest_[sourceRank][i]) << std::endl;
   }
 
@@ -536 +559 @@
       }
     }
-    std::cout << "local index to send to dest Rank = " << destRank << (*localIndexToSendFromGridSource_[destRank]) << std::endl;
   }
 }
@@ -544 +566 @@
   \return local index of data
 */
-std::map<int, CArray<int,1>* > CGridTransformation::getLocalIndexToSendFromGridSource()
+const std::map<int, CArray<int,1>* >& CGridTransformation::getLocalIndexToSendFromGridSource() const
 {
   return localIndexToSendFromGridSource_;
@@ -553 +575 @@
   \return local index of data
 */
-std::map<int, std::vector<CArray<int,1>* > > CGridTransformation::getLocalIndexToReceiveOnGridDest()
+const std::map<int, std::vector<CArray<int,1>* > >& CGridTransformation::getLocalIndexToReceiveOnGridDest() const
 {
   return localIndexToReceiveOnGridDest_;

XIOS/trunk/src/transformation/grid_transformation.hpp

@@ -3 +3 @@
    \author Ha NGUYEN
    \since 14 May 2015
-   \date 09 June 2015
+   \date 18 June 2015
 
    \brief Interface for all transformations.
@@ -40 +40 @@
   void computeAll();
 
-
-  std::map<int, CArray<int,1>* > getLocalIndexToSendFromGridSource();
-  std::map<int, std::vector<CArray<int,1>* > > getLocalIndexToReceiveOnGridDest();
+  const std::map<int, CArray<int,1>* >& getLocalIndexToSendFromGridSource() const;
+  const std::map<int, std::vector<CArray<int,1>* > >& getLocalIndexToReceiveOnGridDest() const;
 
 private:

XIOS/trunk/src/transformation/transformation_mapping.cpp

@@ -3 +3 @@
    \author Ha NGUYEN
    \since 14 May 2015
-   \date 09 June 2015
+   \date 18 June 2015
 
    \brief Take charge of communication among clients to exchange transformed data.
@@ -33 +33 @@
   }
 
-  std::cout << "global index grid src " << globalIndexGridSrc << std::endl;
   gridIndexClientClientMapping_ = new CClientServerMappingDistributed(globalIndexOfServer,
                                                                       client->intraComm,

XIOS/trunk/src/transformation/transformation_mapping.hpp

@@ -47 +47 @@
   //! Mapping of client rank of grid destination and global index to send from grid source
   std::map<int,std::vector<size_t> > globalIndexSendToGridDestMapping_;
-
 };