MeshDistributor.h 20.2 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

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

42
namespace AMDiS {
43
44

  using namespace std;
45
  
46
47
  class ParMetisPartitioner;

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
98
99
    /** \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();

100
101
102
103
104
105
106
    /** \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();
107
108

    /// Set for each element on the partitioning level the number of leaf elements.
109
    void setInitialElementWeights();
110

111
    inline virtual string getName() 
112
113
114
    { 
      return name; 
    }
115

Thomas Witkowski's avatar
Thomas Witkowski committed
116
117
118
119
120
    inline Mesh* getMesh()
    {
      return mesh;
    }

121
122
123
124
125
    /// Returns \ref feSpace.
    inline const FiniteElemSpace* getFeSpace()
    {
      return feSpace;
    }
126
127
128
    
    /// Returns \ref nRankDOFs, the number of DOFs in the rank mesh.
    inline int getNumberRankDofs() 
129
    {
130
      return nRankDofs;
131
    }
132

133
    /// Returns \ref nOverallDofs, the global number of DOFs.
134
    inline int getNumberOverallDofs()
135
    {
136
      return nOverallDofs;
137
    }
138

Thomas Witkowski's avatar
Thomas Witkowski committed
139
140
141
142
143
    inline DofMapping& getMapLocalGlobalDofs()
    {
      return mapLocalGlobalDofs;
    }

144
    /// Maps a local dof to its global index.
145
    inline DegreeOfFreedom mapLocalToGlobal(DegreeOfFreedom dof)
146
    {
147
      return mapLocalGlobalDofs[dof];
148
    }
149

150
    /// Maps a local dof to its local index.
151
152
153
154
155
    inline DegreeOfFreedom mapLocalToDofIndex(DegreeOfFreedom dof)
    {
      return mapLocalDofIndex[dof];
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
156
157
158
159
160
161
    /// Returns the periodic mapping for all boundary DOFs in rank.
    inline PeriodicDofMap& getPeriodicMapping()
    {
      return periodicDof;
    }

162
163
    /// Returns for a global dof index its periodic mapping for a given boundary type.
    inline int getPeriodicMapping(BoundaryType type, int globalDofIndex)
164
    {
Thomas Witkowski's avatar
Thomas Witkowski committed
165
166
      FUNCNAME("MeshDistributor::getPeriodicMapping()");

167
      TEST_EXIT_DBG(periodicDof[type].count(globalDofIndex) == 1)
Thomas Witkowski's avatar
Thomas Witkowski committed
168
169
	("There is no periodic association for global DOF %d for boundary type %d!\n",
	 globalDofIndex, type);
170
171
172
173

      return periodicDof[type][globalDofIndex];
    }

174
175
176
    /// 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)
177
    {      
178
      return periodicDofAssociations[globalDofIndex];
179
    }
180

181
    /// Returns true, if the DOF (global index) is a periodic DOF.
182
    inline bool isPeriodicDof(int globalDofIndex)
183
    {
184
      return (periodicDofAssociations.count(globalDofIndex) > 0);
185
186
    }

187
188
189
    /// Returns true, if the DOF (global index) is a periodic DOF for the given
    /// boundary type.
    inline bool isPeriodicDof(int globalDofIndex, BoundaryType type)
190
191
    {
      return (periodicDof[type].count(globalDofIndex) > 0);
192
193
    }

194
195
    /// 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.
196
197
198
199
    inline bool getIsRankDof(DegreeOfFreedom dof)
    {
      return isRankDof[dof];
    }
200

201
    inline long getLastMeshChangeIndex()
202
    {
203
      return lastMeshChangeIndex;
204
    }
205

206
207
208
209
    inline int getRstart()
    {
      return rstart;
    }
210

211
    inline int getMpiRank()
212
    {
213
      return mpiRank;
214
    }
215

Thomas Witkowski's avatar
Thomas Witkowski committed
216
217
218
219
220
    inline int getMpiSize()
    {
      return mpiSize;
    }

221
222
223
    inline MPI::Intracomm& getMpiComm()
    {
      return mpiComm;
224
225
    }

226
    inline RankToDofContainer& getSendDofs()
227
    {
228
      return sendDofs;
229
230
    }

231
    inline RankToDofContainer& getRecvDofs()
232
    {
233
      return recvDofs;
234
    }
235

236
    // Writes all data of this object to an output stream.
237
    void serialize(ostream &out);
238

239
    // Reads the object data from an input stream.
240
    void deserialize(istream &in);
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260

    /** \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);

261
  protected:
262
    /** \brief
Thomas Witkowski's avatar
Thomas Witkowski committed
263
     * Determines the interior boundaries, i.e. boundaries between ranks, and stores
264
265
     * all information about them in \ref interiorBoundary.
     */
266
    void createInteriorBoundaryInfo();
267

Thomas Witkowski's avatar
Thomas Witkowski committed
268
269
270
271
272
    void updateInteriorBoundaryInfo();

    void createMeshElementData();

    void createBoundaryData();
Thomas Witkowski's avatar
Thomas Witkowski committed
273

274
275
276
    /// Removes all macro elements from the mesh that are not part of ranks partition.
    void removeMacroElements();

277
    /// Updates the local and global DOF numbering after the mesh has been changed.
278
    void updateLocalGlobalNumbering();
279

280
281
282
283
284
    /** \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.
     */
285
286
    void createPeriodicMap();

287
288
    void createMacroElementInfo();

289
290
    void updateMacroElementInfo();

291
292
293
294
295
296
297
298
299
300
301
302
303
    /** \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.
     * 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.
     *
     * \param[in] allBound   Defines a map from rank to interior boundaries which 
     *                       should be checked.
     */
    bool checkAndAdaptBoundary(RankToBoundMap &allBound);
304
305
306
307
308
309
310
311
  
    /** \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();

312
313
314
315
316
    /** \brief
     * This functions create a Paraview file with the macro mesh where the elements
     * are colored by the partition they are part of. This function can be used for
     * debugging.
     */
317
    void writePartitioningMesh(string filename);
318

319
320
321
    /// Sets \ref isRankDof to all matrices and rhs vectors in all stationary problems.
    void setRankDofs();

322
323
324
325
    /// 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
326
    // Removes all periodic boundaries from a given boundary map.
327
    void removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap);
Thomas Witkowski's avatar
Thomas Witkowski committed
328

329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
    /** \brief
     * Starts the procedure to fit a given edge/face of an element with a mesh
     * structure code. This functions prepares some data structures and call
     * then \ref fitElementToMeshCode, that mainly refines the element such that
     * it fits to the mesh structure code.
     *
     * \param[in] code         The mesh structure code to which the edge/face of
     *                         an element must be fitted.
     * \param[in] el           Pointer to the element.
     * \param[in] subObj       Defines whether an edge or a face must be fitted.
     * \param[in] ithObj       Defines which edge/face must be fitted.
     * \param[in] elType       Element type of the element (only important in 3D).
     * \param[in] reverseMode  Defines, whether the mesh structure code is given
     *                         in reverse mode, i.e., left and right children where
     *                         changed when the code was created.
     */
    bool startFitElementToMeshCode(MeshStructure &code, 
				   Element *el, 
				   GeoIndex subObj,
				   int ithObj, 
				   int elType,
				   bool reverseMode);
    
    /** \brief
     * Recursively fits a given mesh structure code to an edge/face of an element.
     * This function is always initialy called from \ref startFitElementToMeshCode.
     *
     * \param[in] code         The mesh structure code which is used to fit an
     *                         edge/face of an element.
     * \param[in] stack        A traverse stack object. The upper most element in this
     *                         stack must be used for fitting the mesh structure code
     *                         at the current position.
     * \param[in] subObj       Defines whether an edge or a face must be fitted.
     * \param[in] ithObj       Defines which edge/face must be fitted.
     * \param[in] reverseMode  Defines, whether the mesh structure code is given
     *                         in reverse mode, i.e., left and right children where
     *                         changed when the code was created.
     */
367
    bool fitElementToMeshCode(MeshStructure &code, 
368
			      TraverseStack &stack,
369
			      GeoIndex subObj,
370
			      int ithObj,
371
			      bool reverseMode);
372

373
    /// Writes a vector of dof pointers to an output stream.
374
    void serialize(ostream &out, DofContainer &data);
375
376

    /// Reads a vector of dof pointers from an input stream.
377
378
    void deserialize(istream &in, DofContainer &data,
		     map<int, const DegreeOfFreedom*> &dofMap);
379
380

    /// Writes a \ref RankToDofContainer to an output stream.
381
    void serialize(ostream &out, RankToDofContainer &data);
382
383

    /// Reads a \ref RankToDofContainer from an input stream.
384
385
    void deserialize(istream &in, RankToDofContainer &data,
		     map<int, const DegreeOfFreedom*> &dofMap);
386

387
    /// Writes a periodic dof mapping to an output stream.
388
    void serialize(ostream &out, PeriodicDofMap &data);
389

390
    void serialize(ostream &out, map<int, std::set<int> >& data);
391

392
    /// Reads a periodic dof mapping from an input stream.
393
    void deserialize(istream &in, PeriodicDofMap &data);
394

395
    void deserialize(istream &in, map<int, std::set<int> >& data);
396

397
398
    /// Writes a mapping from dof pointers to some values to an output stream.
    template<typename T>
399
    void serialize(ostream &out, map<const DegreeOfFreedom*, T> &data)
400
    {
401
402
      FUNCNAME("ParallelDomainBase::serialize()");

403
      int mapSize = data.size();
404
      SerUtil::serialize(out, mapSize);
405
      for (typename map<const DegreeOfFreedom*, T>::iterator it = data.begin();
406
407
408
	   it != data.end(); ++it) {
	int v1 = (*(it->first));
	T v2 = it->second;
409
410
	SerUtil::serialize(out, v1);
	SerUtil::serialize(out, v2);
411
412
413
414
415
      }
    }

    /// Reads a mapping from dof pointer to some values from an input stream.
    template<typename T>
416
417
    void deserialize(istream &in, map<const DegreeOfFreedom*, T> &data,
		     map<int, const DegreeOfFreedom*> &dofMap)
418
    {
419
420
      FUNCNAME("ParallelDomainBase::deserialize()");

421
      int mapSize = 0;
422
      SerUtil::deserialize(in, mapSize);
423
424
425
      for (int i = 0; i < mapSize; i++) {
	int v1 = 0;
	T v2;
426
427
	SerUtil::deserialize(in, v1);
	SerUtil::deserialize(in, v2);
428
429
430

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

431
432
433
	data[dofMap[v1]] = v2;
      }
    }
434
435

  public:
436
    vector<DOFVector<double>* > testVec;
437
		        
438
  protected:
Thomas Witkowski's avatar
Thomas Witkowski committed
439
    ///
440
    vector<ProblemVec*> probStat;
Thomas Witkowski's avatar
Thomas Witkowski committed
441

442
443
444
445
446
447
448
449
450
451
452
453
454
455
    /// 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)
456
    string name;
457

458
459
460
    /// Finite element space of the problem.
    FiniteElemSpace *feSpace;

461
462
463
    /// Mesh of the problem.
    Mesh *mesh;

464
465
466
467
468
469
470
    /** \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;

471
472
473
    /// Info level.
    int info;

474
475
476
477
    /// Pointer to the paritioner which is used to devide a mesh into partitions.
    ParMetisPartitioner *partitioner;

    /// Weights for the elements, i.e., the number of leaf elements within this element.
478
    map<int, double> elemWeights;
479
480

    /** \brief
481
482
     * Stores to every macro element index the number of the rank that owns this
     * macro element.
483
     */
484
    map<int, int> partitionVec;
485
486

    /** \brief
487
488
     * Stores an old partitioning of elements. To every macro element index the
     * number of the rank it corresponds to is stored.
489
     */
490
    map<int, int> oldPartitionVec;    
491
   
492
    /// Number of DOFs in the rank mesh.
493
    int nRankDofs;
Thomas Witkowski's avatar
Thomas Witkowski committed
494

495
    /// Number of DOFs in the whole domain.
496
497
    int nOverallDofs;

Thomas Witkowski's avatar
Thomas Witkowski committed
498
499
500
501
    // 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.
502
    map<int, Element*> macroElIndexMap;
Thomas Witkowski's avatar
Thomas Witkowski committed
503
504
    
    // Maps to each macro element index the type of this element.
505
    map<int, int> macroElIndexTypeMap;
Thomas Witkowski's avatar
Thomas Witkowski committed
506

Thomas Witkowski's avatar
Thomas Witkowski committed
507
    /** \brief 
Thomas Witkowski's avatar
Thomas Witkowski committed
508
509
510
511
512
513
514
515
516
517
518
519
     * 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
520
     */
Thomas Witkowski's avatar
Thomas Witkowski committed
521
    InteriorBoundary otherIntBoundary;
Thomas Witkowski's avatar
Thomas Witkowski committed
522

523
    /** \brief
524
525
     * Defines the periodic boundaries with other ranks. Periodic boundaries have
     * no owner, as it is the case of interior boundaries.
526
527
528
     */
    InteriorBoundary periodicBoundary;

529
530
531
532
    /** \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
533
    RankToDofContainer sendDofs;
534
535

    /** \brief
536
537
538
     * 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.
539
     */
Thomas Witkowski's avatar
Thomas Witkowski committed
540
    RankToDofContainer recvDofs;
541
542

    /// Maps local to global dof indices.
543
    DofMapping mapLocalGlobalDofs;
544

Thomas Witkowski's avatar
Thomas Witkowski committed
545
    /// Maps local dof indices to real dof indices.
546
    DofMapping mapLocalDofIndex;  
547
548
549
550
551
552

    /** \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.
     */
553
554
    DofIndexToBool isRankDof;

555
    /** \brief
556
557
558
559
     * 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.
560
     */
561
    PeriodicDofMap periodicDof;
562
563
564
565
566
567
568
    
    /** \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
     * being periodic, the for corners are associated by two different boundaries.     
     */
569
    map<int, std::set<BoundaryType> > periodicDofAssociations;
570

571
    /// 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
572
    int rstart;
573

574
575
576
577
578
579
580
    /** \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;
581

582
583
584
    /// Denotes whether there exists a filewriter for this object.
    bool writeSerializationFile;

585
586
587
    /// If true, it is possible to repartition the mesh during computations.
    bool repartitioningAllowed;

588
589
    int repartitionIthChange;

590
591
    int nTimestepsAfterLastRepartitioning;

592
593
    int repartCounter;

594
    /// Directory name where all debug output files should be written to.
595
    string debugOutputDir;
596

597
598
599
600
601
    /** \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;
602

603
    map<int, vector<int> > macroElementNeighbours;
604

605
606
    /// Store all macro elements of the overall mesh, i.e., before the macro mesh is
    /// redistributed for the first time.
607
    vector<MacroElement*> allMacroElements;
608

609
    friend class ParallelDebug;
610
611
612
  };
}

613
#endif // AMDIS_MESHDISTRIBUTOR_H