Code refactoring to make the implementation of mesh repartitioning easier.

AMDiS/libtool

@@ -51,32 +51,32 @@ build_old_libs=yes
 pic_mode=default
 
 # Whether or not to optimize for fast installation.
-fast_install=yes
+fast_install=needless
 
 # The host system.
 host_alias=
-host=i686-redhat-linux-gnu
+host=x86_64-unknown-linux-gnu
 host_os=linux-gnu
 
 # The build system.
 build_alias=
-build=i686-redhat-linux-gnu
+build=x86_64-unknown-linux-gnu
 build_os=linux-gnu
 
 # A sed program that does not truncate output.
-SED="/bin/sed"
+SED="/usr/bin/sed"
 
 # Sed that helps us avoid accidentally triggering echo(1) options like -n.
 Xsed="$SED -e 1s/^X//"
 
 # A grep program that handles long lines.
-GREP="/bin/grep"
+GREP="/usr/bin/grep"
 
 # An ERE matcher.
-EGREP="/bin/grep -E"
+EGREP="/usr/bin/grep -E"
 
 # A literal string matcher.
-FGREP="/bin/grep -F"
+FGREP="/usr/bin/grep -F"
 
 # A BSD- or MS-compatible name lister.
 NM="/usr/bin/nm -B"
@@ -85,7 +85,7 @@ NM="/usr/bin/nm -B"
 LN_S="ln -s"
 
 # What is the maximum length of a command?
-max_cmd_len=98304
+max_cmd_len=1572864
 
 # Object file suffix (normally "o").
 objext=o
@@ -128,7 +128,7 @@ old_postinstall_cmds="chmod 644 \$oldlib~\$RANLIB \$oldlib"
 old_postuninstall_cmds=""
 
 # A C compiler.
-LTCC="gcc"
+LTCC="/usr/lib64/mpi/gcc/openmpi//bin/mpicc"
 
 # LTCC compiler flags.
 LTCFLAGS="-g -O2"
@@ -204,7 +204,7 @@ runpath_var=LD_RUN_PATH
 shlibpath_var=LD_LIBRARY_PATH
 
 # Is shlibpath searched before the hard-coded library search path?
-shlibpath_overrides_runpath=no
+shlibpath_overrides_runpath=yes
 
 # Format of library name prefix.
 libname_spec="lib\$name"
@@ -233,10 +233,10 @@ finish_eval=""
 hardcode_into_libs=yes
 
 # Compile-time system search path for libraries.
-sys_lib_search_path_spec="/u/backofen/adds/local/lib /usr/lib/gcc/i386-redhat-linux/4.1.2 /usr/lib /lib"
+sys_lib_search_path_spec="/usr/lib64/gcc/x86_64-suse-linux/4.5 /usr/lib64 /lib64 /usr/x86_64-suse-linux/lib"
 
 # Run-time system search path for libraries.
-sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib/mysql /usr/lib/octave-3.0.1 /usr/lib/qt-3.3/lib /usr/lib/qt4/lib /usr/lib/xulrunner-1.9.2 "
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/X11R6/lib64/Xaw3d /usr/X11R6/lib64 /usr/lib64/Xaw3d /usr/X11R6/lib/Xaw3d /usr/X11R6/lib /usr/lib/Xaw3d /usr/x86_64-suse-linux/lib /usr/local/lib /opt/kde3/lib /lib64 /lib /usr/lib64 /usr/lib /usr/local/lib64 /opt/kde3/lib64 /usr/lib64/graphviz /usr/lib64/graphviz/sharp /usr/lib64/graphviz/java /usr/lib64/graphviz/perl /usr/lib64/graphviz/php /usr/lib64/graphviz/ocaml /usr/lib64/graphviz/python /usr/lib64/graphviz/lua /usr/lib64/graphviz/tcl /usr/lib64/graphviz/guile /usr/lib64/graphviz/ruby /usr/lib64/octave-3.2.4 "
 
 # Whether dlopen is supported.
 dlopen_support=unknown
@@ -253,13 +253,13 @@ striplib="strip --strip-unneeded"
 
 
 # The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
 
 # Commands used to build an old-style archive.
 old_archive_cmds="\$AR \$AR_FLAGS \$oldlib\$oldobjs~\$RANLIB \$oldlib"
 
 # A language specific compiler.
-CC="gcc"
+CC="/usr/lib64/mpi/gcc/openmpi//bin/mpicc"
 
 # Is the compiler the GNU compiler?
 with_gcc=yes
@@ -274,7 +274,7 @@ wl="-Wl,"
 pic_flag=" -fPIC -DPIC"
 
 # Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
 
 # Does compiler simultaneously support -c and -o options?
 compiler_c_o="yes"
@@ -8908,13 +8908,13 @@ build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac`
 # ### BEGIN LIBTOOL TAG CONFIG: CXX
 
 # The linker used to build libraries.
-LD="/usr/bin/ld"
+LD="/usr/x86_64-suse-linux/bin/ld -m elf_x86_64"
 
 # Commands used to build an old-style archive.
 old_archive_cmds="\$AR \$AR_FLAGS \$oldlib\$oldobjs~\$RANLIB \$oldlib"
 
 # A language specific compiler.
-CC="g++"
+CC="/usr/lib64/mpi/gcc/openmpi//bin/mpicxx"
 
 # Is the compiler the GNU compiler?
 with_gcc=yes
@@ -8929,7 +8929,7 @@ wl="-Wl,"
 pic_flag=" -fPIC -DPIC"
 
 # Compiler flag to prevent dynamic linking.
-link_static_flag="-static"
+link_static_flag=""
 
 # Does compiler simultaneously support -c and -o options?
 compiler_c_o="yes"
@@ -9039,17 +9039,17 @@ file_list_spec=""
 hardcode_action=immediate
 
 # The directories searched by this compiler when creating a shared library.
-compiler_lib_search_dirs="/u/backofen/adds/local/lib /usr/lib/gcc/i386-redhat-linux/4.1.2 /usr/lib/gcc/i386-redhat-linux/4.1.2 /usr/lib/gcc/i386-redhat-linux/4.1.2/../../.."
+compiler_lib_search_dirs="/usr/lib64/mpi/gcc/openmpi/lib64 /usr/lib64/gcc/x86_64-suse-linux/4.5 /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64 /lib/../lib64 /usr/lib/../lib64 /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib /usr/lib64/gcc/x86_64-suse-linux/4.5/../../.."
 
 # Dependencies to place before and after the objects being linked to
 # create a shared library.
-predep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbeginS.o"
-postdep_objects="/usr/lib/gcc/i386-redhat-linux/4.1.2/crtendS.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o"
+predep_objects="/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-suse-linux/4.5/crtbeginS.o"
+postdep_objects="/usr/lib64/gcc/x86_64-suse-linux/4.5/crtendS.o /usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64/crtn.o"
 predeps=""
-postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
+postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
 
 # The library search path used internally by the compiler when linking
 # a shared library.
-compiler_lib_search_path="-L/u/backofen/adds/local/lib -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../.."
+compiler_lib_search_path="-L/usr/lib64/mpi/gcc/openmpi/lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.5 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.5/../../.."
 
 # ### END LIBTOOL TAG CONFIG: CXX

AMDiS/src/AMDiS.h

@@ -65,7 +65,6 @@
 #include "OperatorTerm.h"
 #include "Parameters.h"
 #include "Parametric.h"
-#include "PartitionElementData.h"
 #include "PeriodicMap.h"
 #include "PeriodicBC.h"
 #include "PngWriter.h"

AMDiS/src/ArhReader.cc

@@ -51,7 +51,7 @@ namespace AMDiS {
 
       MeshStructure elementStructure;
       elementStructure.init(structureCode, codeSize);
-      elementStructure.fitMeshToStructure(mesh, refManager, false, 
+      elementStructure.fitMeshToStructure(mesh, refManager, 
 					  false, elIndex, ignoreFinerMesh);
 
       uint32_t nValuesPerVector = 0;

AMDiS/src/CreatorMap.cc

@@ -11,7 +11,6 @@
 #include "LeafData.h"
 #include "SurfaceRegion_ED.h"
 #include "ElementRegion_ED.h"
-#include "PartitionElementData.h"
 #include "DOFMatrix.h"
 #include "UmfPackSolver.h"
 #include "time/RosenbrockMethod.h"
@@ -120,9 +119,6 @@ namespace AMDiS {
 
     creator = new ElementRegion_ED::Creator;
     addCreator("ElementRegion_ED", creator);
-
-    creator = new PartitionElementData::Creator;
-    addCreator("PartitionElementData", creator);
   }
 
 

AMDiS/src/ElementData.cc

 #include "ElementData.h"
-#include "PartitionElementData.h"
+
 namespace AMDiS {
 
   void ElementData::coarsenElementData(Element* parent, 
@@ -8,13 +8,6 @@ namespace AMDiS {
 				       int elTypeParent) 
   {
     if (decorated) {
-      PartitionElementData* ped = NULL;
-      ped = dynamic_cast<PartitionElementData*>(thisChild->getElementData(PARTITION_ED));
-      ped = NULL;
-      ped = dynamic_cast<PartitionElementData*>(otherChild->getElementData(PARTITION_ED));     
-      ped = NULL;
-      ped = dynamic_cast<PartitionElementData*> (parent->getElementData(PARTITION_ED));
-      
       decorated->coarsenElementData(parent, thisChild, otherChild, elTypeParent);
       delete decorated;
       decorated = NULL;

AMDiS/src/MeshStructure.cc

 #include "MeshStructure.h"
 #include "MeshStructure_ED.h"
-#include "PartitionElementData.h"
 #include "Mesh.h"
 #include "Element.h"
 #include "Traverse.h"
@@ -226,7 +225,6 @@ namespace AMDiS {
 
   void MeshStructure::fitMeshToStructure(Mesh *mesh,
 					 RefinementManager *manager,
-					 bool checkPartition,
 					 bool debugMode,
 					 int macroElIndex,
 					 bool ignoreFinerMesh) 
@@ -267,23 +265,9 @@ namespace AMDiS {
 	cont = skipBranch(structure);
 	structure->commit();
 
-	bool decorate = true;
-	if (checkPartition) {
-	  PartitionElementData *partitionData = dynamic_cast<PartitionElementData*>
-	    (element->getElementData(PARTITION_ED));
-	  TEST_EXIT_DBG(partitionData)("no partition element data\n");
-	  PartitionStatus status = partitionData->getPartitionStatus();
-	  if (debugMode == false && (status == OUT || status == UNDEFINED))
-	    decorate = false;
-	}
-
-	if (decorate) {
-	  MeshStructure_ED *elData = new MeshStructure_ED(element->getElementData());
-	  elData->setStructure(structure);
-	  element->setElementData(elData);
-	} else {
-	  delete structure;
-	}
+	MeshStructure_ED *elData = new MeshStructure_ED(element->getElementData());
+	elData->setStructure(structure);
+	element->setElementData(elData);
       } else {
 	cont = nextElement();
       }

AMDiS/src/MeshStructure.h

@@ -109,7 +109,6 @@ namespace AMDiS {
      */
     void fitMeshToStructure(Mesh *mesh,
 			    RefinementManager *manager,
-			    bool checkPartition = false,
 			    bool debugMode = false,
 			    int macroElIndex = -1,
 			    bool ignoreFinerMesh = false);

AMDiS/src/PartitionElementData.h

-// ============================================================================
-// ==                                                                        ==
-// == AMDiS - Adaptive multidimensional simulations                          ==
-// ==                                                                        ==
-// ============================================================================
-// ==                                                                        ==
-// ==  TU Dresden                                                            ==
-// ==                                                                        ==
-// ==  Institut fr Wissenschaftliches Rechnen                               ==
-// ==  Zellescher Weg 12-14                                                  ==
-// ==  01069 Dresden                                                         ==
-// ==  germany                                                               ==
-// ==                                                                        ==
-// ============================================================================
-// ==                                                                        ==
-// ==  https://gforge.zih.tu-dresden.de/projects/amdis/                      ==
-// ==                                                                        ==
-// ============================================================================
-
-/** \file PartitionElementData.h */
-
-#ifndef AMDIS_PARTITIONELEMENTDATA_H
-#define AMDIS_PARTITIONELEMENTDATA_H
-
-#include "Element.h"
-#include "ElementData.h"
-#include "FixVec.h"
-#include "Serializer.h"
-
-namespace AMDiS {
-
-  const int PARTITION_ED = 7;
-
-  enum PartitionStatus {
-    UNDEFINED = -1,
-    IN = 0,
-    OVERLAP = 1,
-    OUT = 2
-  };
-
-  class PartitionElementData : public ElementData
-  {
-  public:
-    inline bool isOfType(int typeID) const 
-    {
-      if (typeID == PARTITION_ED) 
-	return true;
-      return false;
-    }
-
-    class Creator : public CreatorInterface<ElementData>
-    {
-    public:
-      ElementData* create() 
-      {
-	return new PartitionElementData;
-      }
-    };
-
-    PartitionElementData(ElementData *decorated = NULL)
-      : ElementData(decorated),
-	status(UNDEFINED),
-	level(0)
-    {}
-
-    ~PartitionElementData()
-    {}
-
-    bool refineElementData(Element* parent, 
-			   Element* child1,
-			   Element* child2,
-			   int elType)
-    {
-      ElementData::refineElementData(parent, child1, child2, elType);
-	
-      PartitionElementData *child1Data = 
-	new PartitionElementData(child1->getElementData());
-      PartitionElementData *child2Data = 
-	new PartitionElementData(child2->getElementData());
-      child1Data->setPartitionStatus(status);
-      child2Data->setPartitionStatus(status);
-      child1Data->setLevel(level + 1);
-      child2Data->setLevel(level + 1);
-      child1->setElementData(child1Data);
-      child2->setElementData(child2Data);
-      return false;
-    }
-
-    ElementData *clone() const 
-    { 
-      PartitionElementData *newObj = new PartitionElementData;
-      newObj->decorated = ElementData::clone();
-      return newObj; 
-    }
-
-    inline std::string getTypeName() const 
-    { 
-      return "PartitionElementData"; 
-    }
-
-    inline const int getTypeID() const 
-    { 
-      return PARTITION_ED; 
-    }
-
-    void serialize(std::ostream& out) 
-    {
-      ElementData::serialize(out);
-      SerUtil::serialize(out, status);
-      SerUtil::serialize(out, level);
-    }
-
-    void deserialize(std::istream& in) 
-    {
-      ElementData::deserialize(in);
-      SerUtil::deserialize(in, status);
-      SerUtil::deserialize(in, level);
-    }
-
-    inline void setPartitionStatus(PartitionStatus s) 
-    { 
-      status = s; 
-    }
-
-    inline PartitionStatus getPartitionStatus() 
-    { 
-      return status; 
-    }
-
-    inline void setLevel(int l) 
-    {
-      level = l;
-    }
-
-    inline int getLevel() 
-    { 
-      return level; 
-    }
-
-    void descend(Element *element) 
-    {
-      if (!element->isLeaf()) {
-	Element *child0 = element->getChild(0);
-	Element *child1 = element->getChild(1);
-
-	// get partition data
-	PartitionElementData *child0Data = dynamic_cast<PartitionElementData*>
-	  (child0->getElementData(PARTITION_ED));
-	PartitionElementData *child1Data = dynamic_cast<PartitionElementData*>
-	  (child1->getElementData(PARTITION_ED));
-      
-	TEST_EXIT(child0Data && child1Data)("no partition data\n");
-
-	child0Data->setPartitionStatus(this->getPartitionStatus());
-	child1Data->setPartitionStatus(this->getPartitionStatus());
-
-	child0Data->descend(child0);
-	child1Data->descend(child1);
-      }    
-    }
-
-  protected:
-    PartitionStatus status;
-
-    int level;
-  };
-
-}
-
-#endif

AMDiS/src/parallel/MeshDistributor.cc

@@ -14,7 +14,6 @@
 #include "ElInfo.h"
 #include "Element.h"
 #include "MacroElement.h"
-#include "PartitionElementData.h"
 #include "DOFMatrix.h"
 #include "DOFVector.h"
 #include "SystemVector.h"
@@ -112,7 +111,6 @@ namespace AMDiS {
 	MSG("Skip write part mesh!\n");
       }
     }
-    ParallelDebug::testAllElements(*this);
 #endif
 
 
@@ -145,6 +143,7 @@ namespace AMDiS {
 
 #if (DEBUG != 0)
     MSG("AMDiS runs in debug mode, so make some test ...\n");
+    ParallelDebug::testAllElements(*this);
     debug::testSortedDofs(mesh, elMap);
     ParallelDebug::testInteriorBoundary(*this);
     ParallelDebug::testCommonDofs(*this, true);
@@ -944,7 +943,7 @@ namespace AMDiS {
       partitioner->partition(&elemWeights, INITIAL);
     } else {
       oldPartitionVec = partitionVec;
-      partitioner->partition(&elemWeights, ADAPTIVE_REPART, 100.0 /*0.000001*/);
+      partitioner->partition(&elemWeights, ADAPTIVE_REPART, 1000.0);
     }    
 
     partitioner->fillCoarsePartitionVec(&partitionVec);
@@ -1003,6 +1002,10 @@ namespace AMDiS {
     partitioner->useLocalGlobalDofMap(&mapLocalGlobalDofs);
     partitionMesh();
 
+#if (DEBUG != 0)
+    ParallelDebug::testAllElements(*this);
+#endif
+
     MSG("DONE\n");
   }
 
@@ -1412,13 +1415,9 @@ namespace AMDiS {
     std::set<MacroElement*> macrosToRemove;
     for (std::deque<MacroElement*>::iterator it = mesh->firstMacroElement();
 	 it != mesh->endOfMacroElements();
-	 ++it) {
-      PartitionElementData *partitionData = 
-	dynamic_cast<PartitionElementData*>
-	((*it)->getElement()->getElementData(PARTITION_ED));
-      if (partitionData->getPartitionStatus() != IN)
-	macrosToRemove.insert(*it);
-    }
+	 ++it)
+      if (partitioner->getElementInRank()[(*it)->getIndex()] == false)
+	macrosToRemove.insert(*it);