Added flags for compiling with Intel C++ compiler. Fixed some real compiler warnings.

AMDiS/CMakeLists.txt

@@ -31,7 +31,11 @@ if(CMAKE_BUILD_TYPE STREQUAL "")
 	set(CMAKE_BUILD_TYPE "Release")
 endif()
 
-#option(ENABLE_INTEL "use intel compiler" false)
+if(CMAKE_CXX_COMPILER MATCHES ".*icpc")
+	Message("Compiler: Intel")
+	set(CMAKE_CXX_FLAGS "-diag-disable 654 -diag-disable 858") 
+endif()
+
 SET(ENABLE_PARALLEL_DOMAIN "OFF" CACHE STRING "use parallel domain decomposition. please set to one of: PMTL, PETSC, OFF" )
 option(USE_PETSC_DEV false)
 option(ENABLE_ZOLTAN false)
@@ -39,15 +43,6 @@ option(ENABLE_UMFPACK "Use of UMFPACK solver" false)
 option(ENABLE_PNG "use png reader/writer" false)
 option(ENABLE_BDDCML "Use of BDDCML library" false)
 
-if(ENABLE_INTEL)
-	Message("please set the icc manually")
-	INCLUDE (CMakeForceCompiler)
-	CMAKE_FORCE_C_COMPILER(icc "intel C compiler")
-	CMAKE_FORCE_CXX_COMPILER(icpc "intel C++ compiler")
-	#SET(CMAKE_C_COMPILER "icc")
-endif(ENABLE_INTEL)
-
-
 find_package(Boost 1.42 REQUIRED)
 if(Boost_FOUND)
   list(APPEND AMDIS_INCLUDE_DIRS ${Boost_INCLUDE_DIR})

AMDiS/src/DOFMatrix.h

@@ -262,12 +262,14 @@ namespace AMDiS {
       inserter= 0;
     }
 
+#if 0
     /// Returns whether restriction should be performed after coarsening
     /// (false by default)
     virtual bool coarseRestrict() 
     {
       return false;
     }
+#endif
 
     /// Returns const \ref rowFeSpace
     const FiniteElemSpace* getRowFeSpace() const 

AMDiS/src/ProblemInstat.h

@@ -93,7 +93,8 @@ namespace AMDiS {
     }
 
     /// Implementation of ProblemTimeInterface::closeTimestep().
-    virtual void closeTimestep() {}
+    virtual void closeTimestep(AdaptInfo *adaptInfo) 
+    {}
 
     /// Returns \ref name.
     inline std::string getName() 

AMDiS/src/ProblemInterpol.cc

@@ -35,7 +35,7 @@ namespace AMDiS {
   }
 
 
-  void ProblemInterpol::solve(AdaptInfo *adaptInfo) 
+  void ProblemInterpol::solve(AdaptInfo *adaptInfo, bool, bool) 
   {
     int size = static_cast<int>(meshes.size());
     for (int i = 0; i < size; i++)
@@ -45,7 +45,7 @@ namespace AMDiS {
   }
 
 
-  void ProblemInterpol::estimate(AdaptInfo *adaptInfo, double) 
+  void ProblemInterpol::estimate(AdaptInfo *adaptInfo) 
   {
     FUNCNAME("ProblemIterpolVec::estimate()");
 

AMDiS/src/ProblemInterpol.h

@@ -50,13 +50,18 @@ namespace AMDiS {
     virtual void buildbeforeCoarsen(AdaptInfo *adaptInfo, Flag) {}
 
     /// No system assemblage.
-    virtual void buildAfterCoarsen(AdaptInfo *adaptInfo, Flag) {}
+    virtual void buildAfterCoarsen(AdaptInfo *adaptInfo, Flag,
+				   bool assembleMatrix = true,
+				   bool assembleVector = true)
+    {}
 
     /// No equation system ins solved. Instead fct is interpolated to uh.
-    virtual void solve(AdaptInfo *adaptInfo);
+    virtual void solve(AdaptInfo *adaptInfo,
+		       bool createMatrixData = true,
+		       bool storeMatrixData = false);
 
     /// True H1 or L2 error is calculated.
-    virtual void estimate(AdaptInfo *adaptInfo, double);
+    virtual void estimate(AdaptInfo *adaptInfo);
 
   protected:
     /// Function to interpolate.

AMDiS/src/io/GNUPlotWriter.cc

@@ -31,7 +31,9 @@ namespace AMDiS {
     filename = fn;
   }
 
-  void GNUPlotWriter::writeFiles(AdaptInfo *adaptInfo, bool force)
+
+  void GNUPlotWriter::writeFiles(AdaptInfo *adaptInfo, bool force, 
+				 int, Flag, bool (*)(ElInfo*))
   {
     DOFVector<WorldVector<double> > coords(feSpace_, "coords");
     Mesh *mesh = feSpace_->getMesh();

AMDiS/src/io/GNUPlotWriter.h

@@ -43,7 +43,10 @@ namespace AMDiS {
     virtual ~GNUPlotWriter() {}
 
     ///
-    virtual void writeFiles(AdaptInfo *adaptInfo, bool force);
+    virtual void writeFiles(AdaptInfo *adaptInfo, bool force,
+			    int level = -1,
+			    Flag traverseFlag = Mesh::CALL_LEAF_EL,
+			    bool (*writeElem)(ElInfo*) = NULL);
 
   protected:
     /// Contains the mesh

AMDiS/src/nonlin/ProblemNonLin.cc

@@ -19,7 +19,7 @@
 namespace AMDiS {
 
   void ProblemNonLin::initialize(Flag initFlag,
-				 ProblemStat *adoptProblem /*= NULL*/,
+				 ProblemStatSeq *adoptProblem /*= NULL*/,
 				 Flag adoptFlag /*= INIT_NOTHING*/) 
   {
     FUNCNAME("ProblemNonLin::initialize()");

AMDiS/src/nonlin/ProblemNonLin.h

@@ -77,7 +77,7 @@ namespace AMDiS {
 
     /// Initialization of the problem.
     virtual void initialize(Flag initFlag,
-			    ProblemStat *adoptProblem = NULL,
+			    ProblemStatSeq *adoptProblem = NULL,
 			    Flag adoptFlag = INIT_NOTHING);
 
     /// Used in \ref initialize().

AMDiS/src/parallel/MeshDistributor.cc

@@ -969,7 +969,7 @@ namespace AMDiS {
 // 	(static_cast<double>(maxDofs - avrgDofs) /  avrgDofs) * 100.0;
       double imbalance1 = (static_cast<double>(maxDofs) / minDofs - 1.0) * 100.0;
 
-      MSG("Imbalancing factor: %.1f\%\n", imbalance1);
+      MSG("Imbalancing factor: %.1f\n", imbalance1);
     }
   }
 
@@ -2264,7 +2264,7 @@ namespace AMDiS {
   {
     FUNCNAME("MeshDistributor::mapGlobalToLocal()");
 
-    for (map<DegreeOfFreedom, MultiIndex>::iterator it = dofMap[feSpace].getMap().begin();
+    for (DofMap::iterator it = dofMap[feSpace].getMap().begin();
 	 it != dofMap[feSpace].getMap().end(); ++it) 
       if (it->second.global == dof)
 	return it->first;

AMDiS/src/parallel/MeshDistributor.h

@@ -225,6 +225,12 @@ namespace AMDiS {
       return dofMap[feSpace][dof].local;
     }
 
+    /// Returns the DOF mapping object, \ref dofMap.
+    inline ParallelDofMapping& getDofMap()
+    {
+      return dofMap;
+    }
+
     /// Returns the periodic mapping handler, \ref periodicMap.
     inline PeriodicMap& getPeriodicMap()
     {
@@ -555,6 +561,7 @@ namespace AMDiS {
     /// macro element.
     map<int, int> partitionMap;
 
+    /// Mapping object to map from local DOF indices to global ones.
     ParallelDofMapping dofMap;
 
     /// Database to store and query all sub-objects of all elements of the 

AMDiS/src/parallel/MeshPartitioner.h

@@ -107,11 +107,7 @@ namespace AMDiS {
       boxPartitioning = b;
     }
 
-#if 0
-    void setLocalGlobalDofMap(map<DegreeOfFreedom, DegreeOfFreedom> *m)
-#else
-      void setLocalGlobalDofMap(map<DegreeOfFreedom, MultiIndex> *m)
-#endif
+    void setLocalGlobalDofMap(DofMap *m)
     {
       mapLocalGlobal = m;
     }
@@ -173,7 +169,7 @@ namespace AMDiS {
     /// macro element index the box number it belongs to.
     map<int, int> elInBox;
 
-    map<DegreeOfFreedom, MultiIndex> *mapLocalGlobal;
+    DofMap *mapLocalGlobal;
 
     map<int, vector<int> > elNeighbours;
 

AMDiS/src/parallel/ParMetisPartitioner.cc

@@ -29,7 +29,7 @@ namespace AMDiS {
 
   ParMetisMesh::ParMetisMesh(Mesh *mesh, MPI::Intracomm *comm, 
 			     std::map<int, bool>& elementInRank,
-			     map<DegreeOfFreedom, MultiIndex> *mapLocalGlobal)
+			     DofMap *mapLocalGlobal)
     : dim(mesh->getDim()),
       nElements(0),
       mpiComm(comm)

AMDiS/src/parallel/ParMetisPartitioner.h

@@ -44,7 +44,7 @@ namespace AMDiS {
   public:
     ParMetisMesh(Mesh *mesh, MPI::Intracomm *comm, 
 		 map<int, bool>& elementInRank,
-		 map<DegreeOfFreedom, MultiIndex> *mapLocalGlobal);
+		 DofMap *mapLocalGlobal);
 
     ~ParMetisMesh();
 

AMDiS/src/parallel/ParallelDebug.cc

@@ -640,20 +640,21 @@ namespace AMDiS {
 
       cout << "====== DOF MAP LOCAL -> GLOBAL ====== " << endl;
             
-      map<DegreeOfFreedom, MultiIndex> &dofMap = pdb.dofMap[feSpace].getMap();
-      for (map<DegreeOfFreedom, MultiIndex>::iterator it = dofMap.begin();
-	   it != dofMap.end(); ++it) {
+      DofMap &dofMap = pdb.dofMap[feSpace].getMap();
+      for (DofMap::iterator it = dofMap.begin(); it != dofMap.end(); ++it) {
 	cout << "DOF " << it->first << " " << it->second.global << "\n";
 	WorldVector<double> coords;
 	pdb.mesh->getDofIndexCoords(it->first, feSpace, coords);
 	coords.print();
 
-	for (DofComm::Iterator rit(pdb.sendDofs, feSpace); !rit.end(); rit.nextRank())
+	for (DofComm::Iterator rit(pdb.sendDofs, feSpace); 
+	     !rit.end(); rit.nextRank())
 	  for (; !rit.endDofIter(); rit.nextDof())
 	    if (it->first == rit.getDofIndex())
 	      cout << "SEND DOF TO " << rit.getRank() << endl;
 	
-	for (DofComm::Iterator rit(pdb.recvDofs, feSpace); !rit.end(); rit.nextRank())
+	for (DofComm::Iterator rit(pdb.recvDofs, feSpace); 
+	     !rit.end(); rit.nextRank())
 	  for (; !rit.endDofIter(); rit.nextDof())
 	    if (it->first == rit.getDofIndex())
 	      cout << "RECV DOF FROM " << rit.getRank() << endl;

AMDiS/src/parallel/ParallelDofMapping.cc

@@ -32,7 +32,7 @@ namespace AMDiS {
   {
     // === Compute local indices for all rank owned DOFs. ===
 
-    for (map<DegreeOfFreedom, MultiIndex>::iterator it = dofMap.begin(); it != dofMap.end(); ++it)
+    for (DofMap::iterator it = dofMap.begin(); it != dofMap.end(); ++it)
       if (it->second.local == -1 && nonRankDofs.count(it->first) == 0)
 	it->second.local = nRankDofs++;
         
@@ -55,7 +55,7 @@ namespace AMDiS {
 
   void FeSpaceDofMap::computeGlobalMapping()
   {
-    for (map<DegreeOfFreedom, MultiIndex>::iterator it = dofMap.begin(); it != dofMap.end(); ++it)
+    for (DofMap::iterator it = dofMap.begin(); it != dofMap.end(); ++it)
       it->second.global = it->second.local + rStartDofs;
   }
 
@@ -255,6 +255,21 @@ namespace AMDiS {
     computeMatIndex();
   }
   
+
+  void ParallelDofMapping::update(vector<const FiniteElemSpace*>& fe)
+  {
+    FUNCNAME("ParallelDofMapping::update()");
+
+    for (vector<const FiniteElemSpace*>::iterator it = fe.begin();
+	 it != fe.end(); ++it)
+      if (find(feSpacesUnique.begin(), feSpacesUnique.end(), *it) == 
+	  feSpacesUnique.end())
+	ERROR_EXIT("Wrong FE space!\n");
+
+    feSpaces = fe;
+    update();
+  }
+
   
   void ParallelDofMapping::computeMatIndex()
   {
@@ -274,9 +289,8 @@ namespace AMDiS {
 
       // Traverse all DOFs of the FE space and create for all rank owned DOFs
       // a matrix index.
-      map<DegreeOfFreedom, MultiIndex>& dofMap = data[feSpaces[i]].getMap();
-      typedef map<DegreeOfFreedom, MultiIndex>::iterator ItType;
-      for (ItType it = dofMap.begin(); it != dofMap.end(); ++it) {
+      DofMap& dofMap = data[feSpaces[i]].getMap();
+      for (DofMap::iterator it = dofMap.begin(); it != dofMap.end(); ++it) {
 	if (data[feSpaces[i]].isRankDof(it->first)) {
 	  int globalMatIndex = it->second.local + offset;
 	  dofToMatIndex.add(i, it->first, globalMatIndex);

AMDiS/src/parallel/ParallelDofMapping.h

@@ -35,14 +35,6 @@ namespace AMDiS {
 
   using namespace std;
 
-  /// Is used if a DOF index is mapped to multiple indices, i.e., to both, a local
-  /// and a global one.
-  struct MultiIndex
-  {
-    int local, global;
-  };
-
-
   /** \brief
    * Is used to store matrix indices to all DOFs in rank's subdomain. Thus, the
    * class defines a mapping from component number and DOF index to a global
@@ -183,7 +175,7 @@ namespace AMDiS {
     }
     
     /// Returns the raw data of the mapping.
-    map<DegreeOfFreedom, MultiIndex>& getMap()
+    DofMap& getMap()
     {
       return dofMap;
     }
@@ -237,7 +229,7 @@ namespace AMDiS {
     const FiniteElemSpace *feSpace;
 
     /// Mapping data from DOF indices to local and global indices.
-    map<DegreeOfFreedom, MultiIndex> dofMap;
+    DofMap dofMap;
 
     /// Set of all DOFs that are in mapping but are not owned by the rank.
     std::set<DegreeOfFreedom> nonRankDofs;
@@ -348,6 +340,9 @@ namespace AMDiS {
     /// Update the mapping.
     void update();
 
+    /// Update the mapping.
+    void update(vector<const FiniteElemSpace*>& feSpaces);
+
     /// Returns the global matrix index of a given DOF for a given 
     /// component number.
     inline int getMatIndex(int ithComponent, DegreeOfFreedom d)

AMDiS/src/parallel/ParallelTypes.h

@@ -70,7 +70,15 @@ namespace AMDiS {
   /// need to have a periodic DOF mapping for each FE space.
   typedef std::map<const FiniteElemSpace*, PeriodicDofMap> PeriodicDofMapFeSpace;
   
-  
+  /// Is used if a DOF index is mapped to multiple indices, i.e., to both, a local
+  /// and a global one.
+  struct MultiIndex
+  {
+    int local, global;
+  };
+
+  typedef std::map<DegreeOfFreedom, MultiIndex> DofMap;
+ 
   typedef vector<MeshStructure> MeshCodeVec;
 }
 

AMDiS/src/parallel/PetscSolver.cc

@@ -20,6 +20,7 @@ namespace AMDiS {
 
   PetscSolver::PetscSolver()
     : meshDistributor(NULL),
+      dofMap(NULL),
       mpiRank(-1),
       kspPrefix(""),
       removeRhsNullSpace(false)

AMDiS/src/parallel/PetscSolver.h

@@ -53,6 +53,7 @@ namespace AMDiS {
     void setMeshDistributor(MeshDistributor *m)
     {
       meshDistributor = m;
+      dofMap = &(meshDistributor->getDofMap());
       mpiRank = meshDistributor->getMpiRank();
       mpiComm = meshDistributor->getMpiComm();
       mpiSelfComm = PETSC_COMM_SELF;
@@ -138,7 +139,9 @@ namespace AMDiS {
 
   protected:
     MeshDistributor *meshDistributor;
-    
+
+    ParallelDofMapping *dofMap;
+
     int mpiRank;
 
     MPI::Intracomm mpiComm;