First work in repartitioning in parallel computations. A lot of clean up in code structure.

AMDiS/CMakeLists.txt

@@ -75,6 +75,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/DOFIndexed.cc
 	      ${SOURCE_DIR}/CreatorMap.cc 
 	      ${SOURCE_DIR}/ProblemInterpolScal.cc 
 	      ${SOURCE_DIR}/ProblemInterpolVec.cc 
+              ${SOURCE_DIR}/MacroInfo.cc
 	      ${SOURCE_DIR}/MacroReader.cc 
 	      ${SOURCE_DIR}/ValueReader.cc 
 	      ${SOURCE_DIR}/Projection.cc 
@@ -165,10 +166,6 @@ if(ENABLE_PARMETIS)
 	CMAKE_FORCE_CXX_COMPILER(mpiCC "MPI C++ compiler")
 
 	include_directories( ${LIB_DIR}/ParMetis-3.1)
-	SET(PARALLEL_AMDIS_SRC  ${SOURCE_DIR}/ConditionalEstimator.cc ${SOURCE_DIR}/ConditionalMarker.cc 
-				${SOURCE_DIR}/ParallelProblem.cc ${SOURCE_DIR}/ParMetisPartitioner.cc 
-				${SOURCE_DIR}/PollutionError.cc)
-	SET(COMPILEFLAGS "${COMPILEFLAGS} -DHAVE_PARALLEL_AMDIS=1")
         INSTALL(FILES ${LIB_DIR}/ParMetis-3.1/parmetis.h
 		${LIB_DIR}/ParMetis-3.1/libparmetis.a
 		${LIB_DIR}/ParMetis-3.1/libmetis.a
@@ -179,6 +176,7 @@ endif(ENABLE_PARMETIS)
 if(ENABLE_PARALLEL_DOMAIN)
 	include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
 	SET(PARALLEL_DOMAIN_AMDIS_SRC
+                ${SOURCE_DIR}/parallel/ParMetisPartitioner.cc
 		${SOURCE_DIR}/parallel/MeshDistributor.cc 
 		${SOURCE_DIR}/parallel/StdMpi.cc
 		${SOURCE_DIR}/parallel/ParallelDebug.cc
@@ -247,7 +245,7 @@ SET(COMPOSITE_FEM_SRC ${COMPOSITE_SOURCE_DIR}/CFE_Integration.cc ${COMPOSITE_SOU
 include_directories(${MTL_DIR})
 include_directories(${SOURCE_DIR})
 
-add_library(amdis SHARED ${AMDIS_SRC} ${PARALLEL_AMDIS_SRC} ${PARALLEL_DOMAIN_AMDIS_SRC})
+add_library(amdis SHARED ${AMDIS_SRC} ${PARALLEL_DOMAIN_AMDIS_SRC})
 add_library(compositeFEM SHARED ${COMPOSITE_FEM_SRC})
 target_link_libraries(compositeFEM amdis)
 

AMDiS/bin/Makefile.am

@@ -10,25 +10,13 @@ AMDIS_INCLUDES = -I$(SOURCE_DIR)
 
 libamdis_la_CXXFLAGS = 
 
-if USE_PARALLEL_AMDIS
-  PARALLEL_AMDIS_SOURCES = \
-  $(PARALLEL_DIR)/ConditionalEstimator.h $(PARALLEL_DIR)/ConditionalEstimator.cc \
-  $(PARALLEL_DIR)/ConditionalMarker.h \ $(PARALLEL_DIR)/ConditionalMarker.cc \
-  $(PARALLEL_DIR)/ParallelError.h $(PARALLEL_DIR)/ParallelError.hh \
-  $(PARALLEL_DIR)/ParallelProblem.h $(PARALLEL_DIR)/ParallelProblem.cc \
-  $(PARALLEL_DIR)/ParMetisPartitioner.h $(PARALLEL_DIR)/ParMetisPartitioner.cc \
-  $(PARALLEL_DIR)/PartitionElementData.h \
-  $(PARALLEL_DIR)/PollutionError.h $(PARALLEL_DIR)/PollutionError.cc
-  PARALLEL_INCLUDES = -I$(MPI_DIR)/include -I$(PARMETIS_DIR)
-  libamdis_la_CXXFLAGS += -DHAVE_PARALLEL_AMDIS=1
-else
-  PARALLEL_AMDIS_SOURCES = 
-  PARALLEL_INCLUDES =
-endif
+PARALLEL_AMDIS_SOURCES = 
+PARALLEL_INCLUDES =
 
 if USE_PARALLEL_DOMAIN_AMDIS
   PARALLEL_AMDIS_SOURCES += \
   $(SOURCE_DIR)/parallel/StdMpi.h $(SOURCE_DIR)/parallel/StdMpi.cc \
+  $(SOURCE_DIR)/parallel/ParMetisPartitioner.h $(SOURCE_DIR)/parallel/ParMetisPartitioner.cc \
   $(SOURCE_DIR)/parallel/MeshDistributor.h $(SOURCE_DIR)/parallel/MeshDistributor.cc \
   $(SOURCE_DIR)/parallel/ParallelDebug.h $(SOURCE_DIR)/parallel/ParallelDebug.cc \
   $(SOURCE_DIR)/parallel/ParallelProblemStatBase.h \
@@ -98,6 +86,7 @@ $(SOURCE_DIR)/ProblemInterpolVec.h $(SOURCE_DIR)/ProblemInterpolVec.cc \
 $(SOURCE_DIR)/Serializable.h \
 $(SOURCE_DIR)/BallProject.h \
 $(SOURCE_DIR)/CylinderProject.h \
+$(SOURCE_DIR)/MacroInfo.h $(SOURCE_DIR)/MacroInfo.cc \
 $(SOURCE_DIR)/MacroReader.h $(SOURCE_DIR)/MacroReader.cc \
 $(SOURCE_DIR)/ValueReader.h $(SOURCE_DIR)/ValueReader.cc \
 $(SOURCE_DIR)/Projection.h $(SOURCE_DIR)/Projection.cc \

AMDiS/src/CoarseningManager1d.cc

@@ -75,7 +75,7 @@ namespace AMDiS {
       }
 
       if (mesh->getNumberOfDOFs(CENTER) && !mesh->queryCoarseDOFs()) {
-	parent->setDOF(mesh->getNode(CENTER), mesh->getDOF(CENTER));
+	parent->setDOF(mesh->getNode(CENTER), mesh->getDof(CENTER));
       }
 
       /*--------------------------------------------------------------------------*/

AMDiS/src/CoarseningManager2d.cc

@@ -84,7 +84,7 @@ namespace AMDiS {
       // get new dof on el at the midpoint of the coarsening edge
 
       if (!el->getDOF(node + 2)) {
-	el->setDOF(node + 2, mesh->getDOF(EDGE));
+	el->setDOF(node + 2, mesh->getDof(EDGE));
 	if (neigh)
 	  neigh->setDOF(node + 2, const_cast<int*>(el->getDOF(node + 2)));
       }

AMDiS/src/CoarseningManager3d.cc

@@ -324,7 +324,7 @@ namespace AMDiS {
       /****************************************************************************/
       node = mesh->getNode(EDGE);
       if (!(dof = const_cast<int*>( el->getDOF(node))))
-	dof = mesh->getDOF(EDGE);
+	dof = mesh->getDof(EDGE);
     } else {
       dof = NULL;
     }

AMDiS/src/ConditionalEstimator.cc

-#include "ConditionalEstimator.h"
-#include "ElInfo.h"
-#include "PartitionElementData.h"
-#include "Element.h"
-#include "Traverse.h"
-#include "mpi.h"
-
-namespace AMDiS {
-
-  ConditionalEstimator::ConditionalEstimator(Estimator* decorated)
-    : decoratedEstimator_(decorated),
-      elementCount_(0), 
-      row_(decorated ? decorated->getRow() : 0)	
-  {
-    FUNCNAME("ConditionalEstimator::ConditionalEstimator(Estimator* decorated)");
-    
-    if (decorated!=NULL) {
-      name = decorated->getName();
-      int swap;
-      int retVal = 
-	Parameters::getGlobalParameter(0, name + "->estimate outer", "%d", &swap);
-
-      if (retVal > 0)
-	estimateOut = (bool)swap;
-      else
-	estimateOut = false;
-    }
-  }
-
-  double ConditionalEstimator::estimate(double ts) 
-  {
-    if (decoratedEstimator_) {
-
-      double partition_sum = 0.0;
-      elementCount_ = 0;
-      decoratedEstimator_->init(ts);
-
-      mesh = decoratedEstimator_->getMesh();
-      traverseFlag = decoratedEstimator_->getTraverseFlag();
-
-      TraverseStack stack;
-      ElInfo *elInfo = stack.traverseFirst(mesh, -1, traverseFlag);
-      while (elInfo) {
-	PartitionElementData *elData = dynamic_cast<PartitionElementData*>
-	  (elInfo->getElement()->getElementData(PARTITION_ED));
-
-	TEST_EXIT_DBG(elInfo->getElement()->isLeaf())("element not leaf\n");
-	TEST_EXIT_DBG(elData)("no partition data on leaf element %d (rank %d)\n", 
-			      elInfo->getElement()->getIndex(),
-			      MPI::COMM_WORLD.Get_rank());
-
-	PartitionStatus status = elData->getPartitionStatus();
-      
-	if (status == IN || status == OVERLAP || (estimateOut && status==OUT)) 
-	  decoratedEstimator_->estimateElement(elInfo);
-	else   
-	  elInfo->getElement()->setMark(0);
-
-	elInfo = stack.traverseNext(elInfo);
-      }
-
-      elInfo = stack.traverseFirst(mesh, -1, traverseFlag);
-      while (elInfo) {
-	PartitionElementData *elData = dynamic_cast<PartitionElementData*>
-	  (elInfo->getElement()->getElementData(PARTITION_ED));
-	PartitionStatus status = elData->getPartitionStatus();
-	if (status == IN || status==OVERLAP || (estimateOut && status==OUT)) {
-	  elementCount_++;
-	  partition_sum += elInfo->getElement()->getEstimation(row_);
-	}
-
-	elInfo = stack.traverseNext(elInfo);
-      }
-
-      // !!! test !!!
-      double total_sum = 0.0;
-      MPI::COMM_WORLD.Allreduce(&partition_sum,
-				&total_sum,
-				1,
-				MPI_DOUBLE,
-				MPI_SUM);
-
-      decoratedEstimator_->setErrorSum(total_sum);
-
-      double total_max = 0.0;
-      est_max = decoratedEstimator_->getErrorMax();
-      MPI::COMM_WORLD.Allreduce(&est_max,
-				&total_max,
-				1,
-				MPI_DOUBLE,
-				MPI_MAX);
-
-      decoratedEstimator_->setErrorMax(total_max);
-    
-      decoratedEstimator_->exit();
-
-      est_sum = decoratedEstimator_->getErrorSum();
-      est_max = decoratedEstimator_->getErrorMax();
-
-      // !!! test !!!
-#if 0
-      decoratedEstimator_->exit();
-
-      est_sum = sqrt(partition_sum); //decoratedEstimator_->getErrorSum();
-      est_t_sum = decoratedEstimator_->getTimeEst();
-      est_max = decoratedEstimator_->getErrorMax();
-#endif
-
-      //   MSG("rank %d , estimate %e (total %e) elements %d (total %d)\n", 
-      //       MPI::COMM_WORLD.Get_rank(), est_sum, total_sum,
-      //       elementCount_,
-      //       mesh->getNumberOfLeaves());
-
-      return est_sum;
-    } else {
-      return 0.0;
-    }
-  }
-
-}

AMDiS/src/ConditionalMarker.cc

-#include "ConditionalMarker.h"
-
-namespace AMDiS
-{
-  ConditionalMarker::ConditionalMarker(const std::string name_,
-				       int row,
-				       Marker *decoratedMarker,
-				       int globalCoarseGridLevel,
-				       int localCoarseGridLevel)
-    : Marker(name_, row), 
-      decoratedMarker_(decoratedMarker),
-      globalCoarseGridLevel_(globalCoarseGridLevel),    
-      localCoarseGridLevel_(localCoarseGridLevel)
-  {
-    if (decoratedMarker != NULL)
-      name = decoratedMarker->getName();
-    else
-      std::cout << "no decorated Marker, mark outer path is" << name << "->mark outer" << std::endl;
-    
-    int swap;      
-    int retVal = Parameters::getGlobalParameter(0, name + "->mark outer", "%d", &swap);
-
-    if (retVal>0)
-      markOuter = (bool)swap;
-    else
-      markOuter = false;
-
-    MSG("markOuter:" + markOuter);
-  }
-
-  void ConditionalMarker::initMarking(AdaptInfo *adaptInfo, Mesh *mesh) 
-  {
-    if (decoratedMarker_) 
-      decoratedMarker_->initMarking(adaptInfo, mesh);
-  }
-
-  void ConditionalMarker::finishMarking(AdaptInfo *adaptInfo)
-  {
-    if (decoratedMarker_) {
-      int tmp = decoratedMarker_->getElMarkRefine();
-      MPI::COMM_WORLD.Allreduce(&tmp,
-				&elMarkRefine,
-				1,
-				MPI_INT,
-				MPI_SUM);
-      tmp = decoratedMarker_->getElMarkCoarsen();
-      MPI::COMM_WORLD.Allreduce(&tmp,
-				&elMarkCoarsen,
-				1,
-				MPI_INT,
-				MPI_SUM);
-      decoratedMarker_->finishMarking(adaptInfo);
-    }
-  }
-
-
-  void ConditionalMarker::markElement(AdaptInfo *adaptInfo, ElInfo *elInfo) 
-  {
-    FUNCNAME("ConditionalMarker::markElement()");
-
-    if (decoratedMarker_) {
-      PartitionElementData *elData = 
-	dynamic_cast<PartitionElementData*>(elInfo->getElement()->
-					    getElementData(PARTITION_ED));
-
-      TEST_EXIT_DBG(elData)("no partition data\n");
-
-      decoratedMarker_->markElement(adaptInfo, elInfo);
-
-      if (!markOuter && elData->getPartitionStatus() == OUT) {
-	Element *element = elInfo->getElement();
-	if (element->getMark() > 0)
-	  element->setMark(0);	  
-      }
-
-      int minLevel = 
-	elData->getPartitionStatus() != OUT ? 
-	localCoarseGridLevel_ :
-	globalCoarseGridLevel_;
-
-      if (elData->getLevel() + elInfo->getElement()->getMark() < minLevel)
-	elInfo->getElement()->setMark(-(elData->getLevel() - minLevel));
-    }
-  }
-}

AMDiS/src/ConditionalMarker.h

-// ============================================================================
-// ==                                                                        ==
-// == AMDiS - Adaptive multidimensional simulations                          ==
-// ==                                                                        ==
-// ============================================================================
-// ==                                                                        ==
-// ==  crystal growth group                                                  ==
-// ==                                                                        ==
-// ==  Stiftung caesar                                                       ==
-// ==  Ludwig-Erhard-Allee 2                                                 ==
-// ==  53175 Bonn                                                            ==
-// ==  germany                                                               ==
-// ==                                                                        ==
-// ============================================================================
-// ==                                                                        ==
-// ==  http://www.caesar.de/cg/AMDiS                                         ==
-// ==                                                                        ==
-// ============================================================================
-
-/** \file ConditionalMarker.h */
-
-#ifndef AMDIS_CONDITIONALMARKER_H
-#define AMDIS_CONDITIONALMARKER_H
-
-#include "mpi.h"
-#include "Marker.h"
-#include "Marker.h"
-#include "PartitionElementData.h"
-#include "Traverse.h"
-#include "ElInfo.h"
-
-namespace AMDiS {
-
-  /**
-   * \ingroup Adaption
-   * 
-   * \brief
-   * 
-   */
-  class ConditionalMarker : public Marker
-  {
-  public:
-    /// Constructor.
-    ConditionalMarker(const std::string name,
-		      int row,
-		      Marker *decoratedMarker,
-		      int globalCoarseGridLevel,
-		      int localCoarseGridLevel);
-      
-
-    /// Implementation of MarkScal::initMarking().
-    virtual void initMarking(AdaptInfo *adaptInfo, Mesh *mesh);   
-
-    virtual void finishMarking(AdaptInfo *adaptInfo);
-
-    void markElement(AdaptInfo *adaptInfo, ElInfo *elInfo);
-
-  protected:
-    Marker *decoratedMarker_;
-    int globalCoarseGridLevel_;
-    int localCoarseGridLevel_;
-    bool markOuter;
-  };
-
-}
-
-#endif

AMDiS/src/FixVecConvert.h

@@ -32,7 +32,7 @@ namespace AMDiS {
   public:
     static FixVec<T,d1>& convertVec(FixVec<T,d2>& rhs, Mesh* mesh) 
     {
-      TEST_EXIT(mesh->getGeo(d1)==mesh->getGeo(d2))("Incompatible dimensions.\n");
+      TEST_EXIT(mesh->getGeo(d1) == mesh->getGeo(d2))("Incompatible dimensions!\n");
       return reinterpret_cast<FixVec<T,d1>&>(rhs);
     }
   };

AMDiS/src/MacroInfo.cc

+#include "MacroInfo.h"
+#include "Mesh.h"
+#include "MacroReader.h"
+#include "FixVecConvert.h"
+#include "SurfaceRegion_ED.h"
+#include "ElementRegion_ED.h"
+
+namespace AMDiS {
+
+  void MacroInfo::fill(Mesh *pmesh, int nElements, int nVertices)
+  {
+    FUNCNAME("MacroInfo::fill()");
+
+    TEST_EXIT(pmesh)("no mesh\n");
+
+    int dim = pmesh->getDim(); 
+    mesh = pmesh;
+
+    mesh->setNumberOfElements(nElements);
+    mesh->setNumberOfLeaves(nElements);
+    mesh->setNumberOfVertices(nVertices);
+
+    for (int i = 0; i < nElements; i++) {
+      MacroElement *newMacro = new MacroElement(mesh->getDim());
+      mel.push_back(newMacro);
+      mesh->addMacroElement(mel[i]);
+    }
+
+    dof = new DegreeOfFreedom*[nVertices];
+    coords = new WorldVector<double>[nVertices];
+    mel_vertex = new int*[nElements];
+
+    for (int i = 0; i < nElements; i++)
+      mel_vertex[i] = new int[mesh->getGeo(VERTEX)];
+
+    for (int i = 0; i < nVertices; i++)
+      dof[i] = mesh->getDof(VERTEX);
+
+    for (int i = 0; i < nElements; i++) {
+      mel[i]->element = mesh->createNewElement();
+      mel[i]->index = i;
+
+      if (dim == 3)
+	mel[i]->elType = 0;
+    }
+    neigh_set = false;
+    bound_set = false;
+  }
+
+
+  void MacroInfo::clear()
+  {
+    for (int i = 0; i < mesh->getNumberOfMacros(); i++)
+      delete [] mel_vertex[i];
+
+    delete [] mel_vertex;
+    delete [] coords;
+    coords = NULL;  
+    delete [] dof;
+    dof = NULL;
+
+    mesh = NULL;
+    neigh_set = false;
+  }
+
+
+  /****************************************************************************/
+  /*  read_indices()  reads dim+1 indices from  file  into  id[0-dim],        */
+  /*    returns true if dim+1 inputs arguments could be read successfully by  */
+  /*    fscanf(), else false                                                  */
+  /****************************************************************************/
+
+  int MacroInfo::read_indices(FILE *file, DimVec<int> &id)
+  {
+    int dim = mesh->getDim();
+
+    for (int i = 0; i <= dim; i++)
+      if (fscanf(file, "%d", &id[i]) != 1)
+	return(false);
+
+    return(true);
+  }
+
+#define N_KEYS      14
+#define N_MIN_KEYS  7
+  static const char *keys[N_KEYS] = {
+    "DIM",                   //  0 
+    "DIM_OF_WORLD",          //  1
+    "number of vertices",    //  2
+    "number of elements",    //  3
+    "vertex coordinates",    //  4
+    "element vertices",      //  5
+    "element boundaries",    //  6
+    "element neighbours",    //  7
+    "element type",          //  8
+    "projections",           //  9
+    "element region",        // 10
+    "surface region",        // 11
+    "mesh name",             // 12
+    "time"                   // 13
+  };
+
+
+  static int get_key_no(const char *key)
+  {
+    for (int i = 0; i < N_KEYS; i++)
+      if (!strcmp(keys[i], key))  
+	return i;
+
+    return -1;
+  }
+
+#include <ctype.h>
+
+  static const char *read_key(const char *line)
+  {
+    static char key[100];
+    char *k = key;
+
+    while (isspace(*line)) 
+      line++;
+    while ((*k++ = *line++) != ':');
+    *--k = '\0';
+  
+    return const_cast<const char *>(key);
+  }
+
+
+  void MacroInfo::readAMDiSMacro(std::string filename, Mesh* mesh)
+  {
+    FUNCNAME("MacroInfo::readAMDiSMacro()");
+
+    int dim, dow;
+    int nElements, nVertices;
+    int j, k;
+    double dbl;
+    char line[256];
+    int line_no, n_keys, sort_key[N_KEYS], nv_key, ne_key;
+    int key_def[N_KEYS] = {0,0,0,0,0,0,0,0,0,0,0,0};
+    const char *key;
+    DimVec<int> *ind = NULL;
+
+    TEST_EXIT(filename != "")("No filename specified!\n");
+    TEST_EXIT(filename.length() < static_cast<unsigned int>(127))
+      ("can only handle filenames up to 127 characters\n");
+
+    FILE *file = fopen(filename.c_str(), "r");
+    TEST_EXIT(file)("cannot open file %s\n", filename.c_str());
+
+
+    // === Looking for all keys in the macro file. ===
+
+    line_no = n_keys = 0;
+    while (fgets(line, 255, file)) {
+      line_no++;
+      if (!strchr(line, ':'))  
+	continue;
+      key = read_key(line);
+      int i_key = get_key_no(key);
+      TEST_EXIT(i_key >= 0)
+	("macro file %s must not contain key %s on line %d\n",
+	 filename.c_str(), key, line_no);
+      TEST_EXIT(!key_def[i_key])("key %s defined second time on line %d in file %s\n");
+
+      sort_key[n_keys++] = i_key;
+      key_def[i_key] = true;
+    }
+    fclose(file);
+
+
+    // === Test, if there is data for every key and if all is defined in === 
+    // === right order.                                                  ===
+
+    for (int i_key = 0; i_key < N_MIN_KEYS; i_key++) {
+      for (j = 0; j < n_keys; j++)
+	if (sort_key[j] == i_key)  
+	  break;