MeshDistributor.h 18.8 KB
Newer Older
1 2 3 4
// ============================================================================
// ==                                                                        ==
// == AMDiS - Adaptive multidimensional simulations                          ==
// ==                                                                        ==
5
// ==  http://www.amdis-fem.org                                              ==
6 7
// ==                                                                        ==
// ============================================================================
8 9 10 11 12 13 14 15 16 17 18 19
//
// Software License for AMDiS
//
// Copyright (c) 2010 Dresden University of Technology 
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
// This file is part of AMDiS
//
// See also license.opensource.txt in the distribution.


20

21
/** \file MeshDistributor.h */
22

23 24
#ifndef AMDIS_MESHDISTRIBUTOR_H
#define AMDIS_MESHDISTRIBUTOR_H
25 26 27


#include <map>
28
#include <set>
29
#include <vector>
Thomas Witkowski's avatar
Thomas Witkowski committed
30
#include <mpi.h>
31

32
#include "parallel/MeshPartitioner.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
33
#include "parallel/InteriorBoundary.h"
34
#include "AMDiS_fwd.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
35
#include "Global.h"
36 37
#include "ProblemTimeInterface.h"
#include "ProblemIterationInterface.h"
38
#include "FiniteElemSpace.h"
39
#include "Serializer.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
40
#include "BoundaryManager.h"
41
#include "ElementObjectData.h"
42
#include "SystemVector.h"
43

44
namespace AMDiS {
45 46

  using namespace std;
47
  
48
  class MeshDistributor
49
  {
50
  protected:
Thomas Witkowski's avatar
Thomas Witkowski committed
51
    /// Defines a mapping type from DOFs to rank numbers.
52
    typedef map<const DegreeOfFreedom*, int> DofToRank;
Thomas Witkowski's avatar
Thomas Witkowski committed
53 54

    /// Defines a mapping type from DOFs to a set of rank numbers.
55
    typedef map<const DegreeOfFreedom*, std::set<int> > DofToPartitions;
Thomas Witkowski's avatar
Thomas Witkowski committed
56 57

    /// Defines a mapping type from rank numbers to sets of DOFs.
58
    typedef map<int, DofContainer> RankToDofContainer;
Thomas Witkowski's avatar
Thomas Witkowski committed
59 60

    /// Defines a mapping type from DOF indices to DOF indices.
61
    typedef map<DegreeOfFreedom, DegreeOfFreedom> DofMapping;
Thomas Witkowski's avatar
Thomas Witkowski committed
62

63
    /// Defines a mapping type from DOFs to boolean values.
64
    typedef map<const DegreeOfFreedom*, bool> DofToBool;
65

Thomas Witkowski's avatar
Thomas Witkowski committed
66
    /// Defines a mapping type from DOF indices to boolean values.
67
    typedef map<DegreeOfFreedom, bool> DofIndexToBool;
Thomas Witkowski's avatar
Thomas Witkowski committed
68

Thomas Witkowski's avatar
Thomas Witkowski committed
69 70 71
    /// Forward type (it maps rank numbers to the interior boundary objects).
    typedef InteriorBoundary::RankToBoundMap RankToBoundMap;

72
    typedef map<const DegreeOfFreedom*, DegreeOfFreedom> DofIndexMap;
Thomas Witkowski's avatar
Thomas Witkowski committed
73

74 75
    /// Mapps a boundar type, i.e., a boundary identifier index, to a periodic 
    /// dof mapping.
76 77 78
    typedef map<BoundaryType, DofMapping> PeriodicDofMap;

    typedef vector<MeshStructure> MeshCodeVec;
79

80
  public:
81
    MeshDistributor(string str);
82 83
		          
    virtual ~MeshDistributor() {}
84

85
    void initParallelization();
86

87
    void exitParallelization();
88 89

    void addProblemStat(ProblemVec *probVec);
90

91 92 93 94 95 96 97
    /// Adds a DOFVector to the set of \ref interchangeVecs. Thus, this vector will
    /// be automatically interchanged between ranks when mesh is repartitioned.
    void addInterchangeVector(DOFVector<double> *vec)
    {
      interchangeVectors.push_back(vec);
    }

98 99 100 101 102 103 104
    /// Adds all DOFVectors of a SystemVector to \ref interchangeVecs.
    void addInterchangeVector(SystemVector *vec)
    {
      for (int i = 0; i < vec->getSize(); i++)
	interchangeVectors.push_back(vec->getDOFVector(i));
    }
    
105 106 107 108 109 110 111 112 113
    /** \brief
     * This function checks if the mesh has changed on at least on rank. In this case,
     * the interior boundaries are adapted on all ranks such that they fit together on
     * all ranks. Furthermore the function \ref updateLocalGlobalNumbering() is called
     * to update the dof numberings and mappings on all rank due to the new mesh
     * structure.
     */
    void checkMeshChange();

114 115 116 117 118 119 120
    /** \brief
     * Test, if the mesh consists of macro elements only. The mesh partitioning of
     * the parallelization works for macro meshes only and would fail, if the mesh
     * is already refined in some way. Therefore, this function will exit the program
     * if it finds a non macro element in the mesh.
     */
    void testForMacroMesh();
121 122

    /// Set for each element on the partitioning level the number of leaf elements.
123
    void setInitialElementWeights();
124

125
    inline virtual string getName() 
126 127 128
    { 
      return name; 
    }
129

Thomas Witkowski's avatar
Thomas Witkowski committed
130 131 132 133 134
    inline Mesh* getMesh()
    {
      return mesh;
    }

135 136 137 138 139
    /// Returns \ref feSpace.
    inline const FiniteElemSpace* getFeSpace()
    {
      return feSpace;
    }
140 141 142
    
    /// Returns \ref nRankDOFs, the number of DOFs in the rank mesh.
    inline int getNumberRankDofs() 
143
    {
144
      return nRankDofs;
145
    }
146

147
    /// Returns \ref nOverallDofs, the global number of DOFs.
148
    inline int getNumberOverallDofs()
149
    {
150
      return nOverallDofs;
151
    }
152

Thomas Witkowski's avatar
Thomas Witkowski committed
153 154 155 156 157
    inline DofMapping& getMapLocalGlobalDofs()
    {
      return mapLocalGlobalDofs;
    }

158
    /// Maps a local dof to its global index.
159
    inline DegreeOfFreedom mapLocalToGlobal(DegreeOfFreedom dof)
160
    {
161
      return mapLocalGlobalDofs[dof];
162
    }
163

164 165
    DegreeOfFreedom mapGlobalToLocal(DegreeOfFreedom dof);

166
    /// Maps a local dof to its local index.
167 168 169 170 171
    inline DegreeOfFreedom mapLocalToDofIndex(DegreeOfFreedom dof)
    {
      return mapLocalDofIndex[dof];
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
172 173 174 175 176 177
    /// Returns the periodic mapping for all boundary DOFs in rank.
    inline PeriodicDofMap& getPeriodicMapping()
    {
      return periodicDof;
    }

178
    /// Returns for a global dof index its periodic mapping for a given boundary type.
179
    inline int getPeriodicMapping(int globalDofIndex, BoundaryType type)
180
    {
Thomas Witkowski's avatar
Thomas Witkowski committed
181 182
      FUNCNAME("MeshDistributor::getPeriodicMapping()");

183
      TEST_EXIT_DBG(periodicDof[type].count(globalDofIndex) == 1)
Thomas Witkowski's avatar
Thomas Witkowski committed
184 185
	("There is no periodic association for global DOF %d for boundary type %d!\n",
	 globalDofIndex, type);
186 187 188 189

      return periodicDof[type][globalDofIndex];
    }

190 191 192
    /// For a given global DOF index, this function returns the set of periodic
    /// associations, i.e., the boundary types the DOF is associated to, for this DOF.
    inline std::set<BoundaryType>& getPerDofAssociations(int globalDofIndex)
193
    {      
194 195 196
      TEST_EXIT_DBG(periodicDofAssociations.count(globalDofIndex)) 
 	("Should not happen!\n"); 

197
      return periodicDofAssociations[globalDofIndex];
198
    }
199

200
    /// Returns true, if the DOF (global index) is a periodic DOF.
201
    inline bool isPeriodicDof(int globalDofIndex)
202
    {
203 204
      return (periodicDofAssociations.count(globalDofIndex) > 0 &&
	       periodicDofAssociations[globalDofIndex].size() > 0);
205 206
    }

207 208 209
    /// Returns true, if the DOF (global index) is a periodic DOF for the given
    /// boundary type.
    inline bool isPeriodicDof(int globalDofIndex, BoundaryType type)
210 211
    {
      return (periodicDof[type].count(globalDofIndex) > 0);
212 213
    }

214 215
    /// Return true, if the given DOF is owned by the rank. If false, the DOF is in
    /// rank's partition, but is owned by some other rank.
216 217
    inline bool getIsRankDof(DegreeOfFreedom dof)
    {
218 219 220 221
      if (isRankDof.count(dof))
	return isRankDof[dof];

      return false;
222
    }
223

224
    inline long getLastMeshChangeIndex()
225
    {
226
      return lastMeshChangeIndex;
227
    }
228

229 230 231 232
    inline int getRstart()
    {
      return rstart;
    }
233

234
    inline int getMpiRank()
235
    {
236
      return mpiRank;
237
    }
238

Thomas Witkowski's avatar
Thomas Witkowski committed
239 240 241 242 243
    inline int getMpiSize()
    {
      return mpiSize;
    }

244 245 246
    inline MPI::Intracomm& getMpiComm()
    {
      return mpiComm;
247 248
    }

249
    inline RankToDofContainer& getSendDofs()
250
    {
251
      return sendDofs;
252 253
    }

254
    inline RankToDofContainer& getRecvDofs()
255
    {
256
      return recvDofs;
257
    }
258

259
    // Writes all data of this object to an output stream.
260
    void serialize(ostream &out);
261

262
    // Reads the object data from an input stream.
263
    void deserialize(istream &in);
264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283

    /** \brief
     * This function must be used if the values of a DOFVector must be synchronised
     * over all ranks. That means, that each rank sends the values of the DOFs, which
     * are owned by the rank and lie on an interior bounday, to all other ranks also
     * having these DOFs.
     *
     * This function must be used, for example, after the lineary system is solved, or
     * after the DOFVector is set by some user defined functions, e.g., initial
     * solution functions.
     */    
    void synchVector(DOFVector<double> &vec);

    /** \brief
     * Works in the same way as the function above defined for DOFVectors. Due to
     * performance, this function does not call \ref synchVector for each DOFVector,
     * but instead sends all values of all DOFVectors all at once.
     */
    void synchVector(SystemVector &vec);

284 285
    void check3dValidMesh();

286
  protected:
287
    /** \brief
Thomas Witkowski's avatar
Thomas Witkowski committed
288
     * Determines the interior boundaries, i.e. boundaries between ranks, and stores
289 290
     * all information about them in \ref interiorBoundary.
     */
291
    void createInteriorBoundaryInfo();
292

Thomas Witkowski's avatar
Thomas Witkowski committed
293 294 295 296 297
    void updateInteriorBoundaryInfo();

    void createMeshElementData();

    void createBoundaryData();
Thomas Witkowski's avatar
Thomas Witkowski committed
298

299 300 301
    /// Removes all macro elements from the mesh that are not part of ranks partition.
    void removeMacroElements();

302
    /// Updates the local and global DOF numbering after the mesh has been changed.
303
    void updateLocalGlobalNumbering();
304

305 306 307 308 309
    /** \brief
     * Creates to all dofs in rank's partition that are on a periodic boundary the
     * mapping from dof index to the other periodic dof indices. This information
     * is stored in \ref periodicDof.
     */
310 311
    void createPeriodicMap();

312 313
    void createMacroElementInfo();

314 315
    void updateMacroElementInfo();

316 317 318 319 320 321 322 323 324
    /** \brief
     * Checks for all given interior boundaries if the elements fit together on both
     * sides of the boundaries. If this is not the case, the mesh is adapted. Because
     * refinement of a certain element may forces the refinement of other elements,
     * it is not guaranteed that all rank's meshes fit together after this function
     * terminates. Hence, it must be called until a stable mesh refinement is reached.
     *
     * \param[in] allBound   Defines a map from rank to interior boundaries which 
     *                       should be checked.
325 326 327 328
     *
     * \return    If the mesh has  been changed by this function, it returns true. 
     *            Otherwise, it returns false, i.e., the given interior boundaries 
     *            fit together on both sides.
329 330
     */
    bool checkAndAdaptBoundary(RankToBoundMap &allBound);
331 332 333 334 335 336 337 338
  
    /** \brief
     * Checks if is required to repartition the mesh. If this is the case, a new
     * partition will be created and the mesh will be redistributed between the
     * ranks.
     */
    void repartitionMesh();

339 340 341
    /// Sets \ref isRankDof to all matrices and rhs vectors in all stationary problems.
    void setRankDofs();

342 343 344 345
    /// Removes all periodic boundary condition information from all matrices and
    /// vectors of all stationary problems and from the mesh itself.
    void removePeriodicBoundaryConditions();

Thomas Witkowski's avatar
Thomas Witkowski committed
346
    // Removes all periodic boundaries from a given boundary map.
347
    void removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap);
Thomas Witkowski's avatar
Thomas Witkowski committed
348

349
    /// Writes a vector of dof pointers to an output stream.
350
    void serialize(ostream &out, DofContainer &data);
351 352

    /// Reads a vector of dof pointers from an input stream.
353 354
    void deserialize(istream &in, DofContainer &data,
		     map<int, const DegreeOfFreedom*> &dofMap);
355 356

    /// Writes a \ref RankToDofContainer to an output stream.
357
    void serialize(ostream &out, RankToDofContainer &data);
358 359

    /// Reads a \ref RankToDofContainer from an input stream.
360 361
    void deserialize(istream &in, RankToDofContainer &data,
		     map<int, const DegreeOfFreedom*> &dofMap);
362

363
    /// Writes a periodic dof mapping to an output stream.
364
    void serialize(ostream &out, PeriodicDofMap &data);
365

366
    void serialize(ostream &out, map<int, std::set<int> >& data);
367

368
    /// Reads a periodic dof mapping from an input stream.
369
    void deserialize(istream &in, PeriodicDofMap &data);
370

371
    void deserialize(istream &in, map<int, std::set<int> >& data);
372

373 374
    /// Writes a mapping from dof pointers to some values to an output stream.
    template<typename T>
375
    void serialize(ostream &out, map<const DegreeOfFreedom*, T> &data)
376
    {
377 378
      FUNCNAME("ParallelDomainBase::serialize()");

379
      int mapSize = data.size();
380
      SerUtil::serialize(out, mapSize);
381
      for (typename map<const DegreeOfFreedom*, T>::iterator it = data.begin();
382 383 384
	   it != data.end(); ++it) {
	int v1 = (*(it->first));
	T v2 = it->second;
385 386
	SerUtil::serialize(out, v1);
	SerUtil::serialize(out, v2);
387 388 389 390 391
      }
    }

    /// Reads a mapping from dof pointer to some values from an input stream.
    template<typename T>
392 393
    void deserialize(istream &in, map<const DegreeOfFreedom*, T> &data,
		     map<int, const DegreeOfFreedom*> &dofMap)
394
    {
395 396
      FUNCNAME("ParallelDomainBase::deserialize()");

397
      int mapSize = 0;
398
      SerUtil::deserialize(in, mapSize);
399 400 401
      for (int i = 0; i < mapSize; i++) {
	int v1 = 0;
	T v2;
402 403
	SerUtil::deserialize(in, v1);
	SerUtil::deserialize(in, v2);
404 405 406

	TEST_EXIT_DBG(dofMap.count(v1) != 0)("Cannot find DOF %d in map!\n", v1);

407 408 409
	data[dofMap[v1]] = v2;
      }
    }
410

411
  protected:
Thomas Witkowski's avatar
Thomas Witkowski committed
412
    ///
413
    vector<ProblemVec*> probStat;
Thomas Witkowski's avatar
Thomas Witkowski committed
414

415 416 417 418 419 420 421 422 423 424 425 426 427 428
    /// The rank of the current process.
    int mpiRank;

    /// Overall number of processes.
    int mpiSize;

    /** \brief
     * MPI communicator collected all processes, which should
     * be used for calculation. The Debug procces is not included
     * in this communicator.
     */
    MPI::Intracomm mpiComm;

    /// Name of the problem (as used in the init files)
429
    string name;
430

431 432 433
    /// Finite element space of the problem.
    FiniteElemSpace *feSpace;

434 435 436
    /// Mesh of the problem.
    Mesh *mesh;

437 438 439 440 441 442 443
    /** \brief
     * A refinement manager that should be used on the mesh. It is used to refine
     * elements at interior boundaries in order to fit together with elements on the
     * other side of the interior boundary.
     */    
    RefinementManager *refineManager;

444 445 446
    /// Info level.
    int info;

447 448
    /// Pointer to a mesh partitioner that is used to partition the mesh to the ranks.
    MeshPartitioner *partitioner;
449 450

    /// Weights for the elements, i.e., the number of leaf elements within this element.
451
    map<int, double> elemWeights;
452 453

    /** \brief
454 455
     * Stores to every macro element index the number of the rank that owns this
     * macro element.
456
     */
457
    map<int, int> partitionMap;
458

459
    /// Number of DOFs in the rank mesh.
460
    int nRankDofs;
Thomas Witkowski's avatar
Thomas Witkowski committed
461

462
    /// Number of DOFs in the whole domain.
463 464
    int nOverallDofs;

Thomas Witkowski's avatar
Thomas Witkowski committed
465 466 467 468
    // Data structure to store all sub-objects of all elements of the macro mesh.
    ElementObjects elObjects;

    // Maps to each macro element index a pointer to the corresponding element.
469
    map<int, Element*> macroElIndexMap;
Thomas Witkowski's avatar
Thomas Witkowski committed
470 471
    
    // Maps to each macro element index the type of this element.
472
    map<int, int> macroElIndexTypeMap;
Thomas Witkowski's avatar
Thomas Witkowski committed
473

Thomas Witkowski's avatar
Thomas Witkowski committed
474
    /** \brief 
Thomas Witkowski's avatar
Thomas Witkowski committed
475 476 477 478 479 480 481 482 483 484 485 486
     * Defines the interior boundaries of the domain that result from partitioning
     * the whole mesh. Contains only the boundaries, which are owned by the rank, i.e.,
     * the object gives for every neighbour rank i the boundaries this rank owns and 
     * shares with rank i.
     */
    InteriorBoundary myIntBoundary;
    
    /** \brief
     * Defines the interior boundaries of the domain that result from partitioning
     * the whole mesh. Contains only the boundaries, which are not owned by the rank,
     * i.e., the object gives for every neighbour rank i the boundaries that are
     * owned by rank i and are shared with this rank.
Thomas Witkowski's avatar
Thomas Witkowski committed
487
     */
Thomas Witkowski's avatar
Thomas Witkowski committed
488
    InteriorBoundary otherIntBoundary;
Thomas Witkowski's avatar
Thomas Witkowski committed
489

490
    /** \brief
491 492
     * Defines the periodic boundaries with other ranks. Periodic boundaries have
     * no owner, as it is the case of interior boundaries.
493 494 495
     */
    InteriorBoundary periodicBoundary;

496 497 498 499
    /** \brief
     * This map contains for each rank the list of dofs the current rank must send
     * to exchange solution dofs at the interior boundaries.
     */
Thomas Witkowski's avatar
Thomas Witkowski committed
500
    RankToDofContainer sendDofs;
501 502

    /** \brief
503 504 505
     * This map contains for each rank the list of DOFs from which the current rank 
     * will receive DOF values (i.e., this are all DOFs at an interior boundary). The
     * DOF indices are given in rank's local numbering.
506
     */
Thomas Witkowski's avatar
Thomas Witkowski committed
507
    RankToDofContainer recvDofs;
508 509

    /// Maps local to global dof indices.
510
    DofMapping mapLocalGlobalDofs;
511

Thomas Witkowski's avatar
Thomas Witkowski committed
512
    /// Maps local dof indices to real dof indices.
513
    DofMapping mapLocalDofIndex;  
514 515 516 517 518 519

    /** \brief
     * Maps all DOFs in ranks partition to a bool value. If it is true, the DOF is
     * owned by the rank. Otherwise, its an interior boundary DOF that is owned by
     * another rank.
     */
520 521
    DofIndexToBool isRankDof;

522
    /** \brief
523 524 525 526
     * If periodic boundaries are used, this map stores, for each periodic boundary
     * type, for all DOFs in rank's partition (that are on periodic boundaries), the 
     * corresponding mapped periodic DOFs. The mapping is defined by using global 
     * dof indices.
527
     */
528
    PeriodicDofMap periodicDof;
529 530 531 532 533
    
    /** \brief
     * If periodic boundaries are used, this map stores to each periodic DOF in rank's
     * partition the set of periodic boundaries the DOF is associated to. In 2D, most
     * DOFs are only on one periodic boundary. Only, e.g., in a box with all boundaries
534
     * being periodic, the four corners are associated by two different boundaries.
535
     */
536
    map<int, std::set<BoundaryType> > periodicDofAssociations;
537

538 539 540 541 542
    
    /// This set of values must be interchanged between ranks when the mesh is 
    /// repartitioned.
    vector<DOFVector<double>*> interchangeVectors;
		        
543
    /// Is the index of the first row of the linear system, which is owned by the rank.
Thomas Witkowski's avatar
n  
Thomas Witkowski committed
544
    int rstart;
545

546 547 548 549 550 551 552
    /** \brief
     * If the problem definition has been read from a serialization file, this 
     * variable is true, otherwise it is false. This variable is used to stop the
     * initialization function, if the problem definition has already been read from
     * a serialization file.
     */
    bool deserialized;
553

554 555 556
    /// Denotes whether there exists a filewriter for this object.
    bool writeSerializationFile;

557 558 559
    /// If true, it is possible to repartition the mesh during computations.
    bool repartitioningAllowed;

560
    /// Stores the number of mesh changes that must lie in between to repartitionings.
561 562
    int repartitionIthChange;

563 564
    /// Counts the number of mesh changes after the last mesh repartitioning was done.
    int nMeshChangesAfterLastRepartitioning;
565

566 567 568
    /// Countes the number of mesh repartitions that were done. Till now, this 
    /// variable is used only for debug outputs.
    int repartitioningCounter;
569

570
    /// Directory name where all debug output files should be written to.
571
    string debugOutputDir;
572

573 574 575 576 577
    /** \brief
     * Stores the mesh change index. This is used to recognize changes in the mesh 
     * structure (e.g. through refinement or coarsening managers).
     */
    long lastMeshChangeIndex;
578

579
    map<int, vector<int> > macroElementNeighbours;
580

581 582
    /// Store all macro elements of the overall mesh, i.e., before the macro mesh is
    /// redistributed for the first time.
583
    vector<MacroElement*> allMacroElements;
584

585
    friend class ParallelDebug;
586 587 588
  };
}

589
#endif // AMDIS_MESHDISTRIBUTOR_H