MeshDistributor.h 21.5 KB
Newer Older
1
2
3
4
5
6
// ============================================================================
// ==                                                                        ==
// == AMDiS - Adaptive multidimensional simulations                          ==
// ==                                                                        ==
// ============================================================================
// ==                                                                        ==
7
// ==  TU Dresden                                                            ==
8
// ==                                                                        ==
9
10
11
// ==  Institut fr Wissenschaftliches Rechnen                               ==
// ==  Zellescher Weg 12-14                                                  ==
// ==  01069 Dresden                                                         ==
12
13
14
15
// ==  germany                                                               ==
// ==                                                                        ==
// ============================================================================
// ==                                                                        ==
16
// ==  https://gforge.zih.tu-dresden.de/projects/amdis/                      ==
17
18
19
// ==                                                                        ==
// ============================================================================

20
/** \file MeshDistributor.h */
21

22
23
#ifndef AMDIS_MESHDISTRIBUTOR_H
#define AMDIS_MESHDISTRIBUTOR_H
24
25
26


#include <map>
27
#include <set>
28
#include <vector>
Thomas Witkowski's avatar
Thomas Witkowski committed
29
#include <mpi.h>
30

Thomas Witkowski's avatar
Thomas Witkowski committed
31
#include "Global.h"
32
33
#include "ProblemTimeInterface.h"
#include "ProblemIterationInterface.h"
34
#include "FiniteElemSpace.h"
35
#include "AdaptInfo.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
36
#include "parallel/InteriorBoundary.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
45
  class ParMetisPartitioner;

46
  class MeshDistributor
47
  {
48
  protected:
Thomas Witkowski's avatar
Thomas Witkowski committed
49
50
51
52
53
54
55
56
57
58
59
60
    /// Defines a mapping type from DOFs to rank numbers.
    typedef std::map<const DegreeOfFreedom*, int> DofToRank;

    /// Defines a mapping type from DOFs to a set of rank numbers.
    typedef std::map<const DegreeOfFreedom*, std::set<int> > DofToPartitions;

    /// Defines a mapping type from rank numbers to sets of DOFs.
    typedef std::map<int, DofContainer> RankToDofContainer;

    /// Defines a mapping type from DOF indices to DOF indices.
    typedef std::map<DegreeOfFreedom, DegreeOfFreedom> DofMapping;

61
62
63
    /// Defines a mapping type from DOFs to boolean values.
    typedef std::map<const DegreeOfFreedom*, bool> DofToBool;

Thomas Witkowski's avatar
Thomas Witkowski committed
64
    /// Defines a mapping type from DOF indices to boolean values.
65
    typedef std::map<DegreeOfFreedom, bool> DofIndexToBool;
Thomas Witkowski's avatar
Thomas Witkowski committed
66

Thomas Witkowski's avatar
Thomas Witkowski committed
67
68
69
    /// Forward type (it maps rank numbers to the interior boundary objects).
    typedef InteriorBoundary::RankToBoundMap RankToBoundMap;

Thomas Witkowski's avatar
Thomas Witkowski committed
70
71
    typedef std::map<const DegreeOfFreedom*, DegreeOfFreedom> DofIndexMap;

72
73
74
    /// Mapps a boundar type, i.e., a boundary identifier index, to a periodic 
    /// dof mapping.
    typedef std::map<BoundaryType, DofMapping> PeriodicDofMap;
75
76
    
    typedef std::vector<MeshStructure> MeshCodeVec;
77

78
  public:
79
80
81
    MeshDistributor(std::string str);
		          
    virtual ~MeshDistributor() {}
82

83
    void initParallelization(AdaptInfo *adaptInfo);
84

85
86
87
    void exitParallelization(AdaptInfo *adaptInfo);

    void addProblemStat(ProblemVec *probVec);
88

89
90
91
92
93
94
95
96
97
    /** \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();

98
    void updateDofAdmins();    
99

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
109
110
111
112

    /// Set for each element on the partitioning level the number of leaf elements.
    double setElemWeights(AdaptInfo *adaptInfo);

    void partitionMesh(AdaptInfo *adaptInfo);

113
114
115
116
    inline virtual std::string getName() 
    { 
      return name; 
    }
117
118
119
120
121
122

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

130
    /// Returns \ref nOverallDofs, the global number of DOFs.
131
    inline int getNumberOverallDofs()
132
    {
133
      return nOverallDofs;
134
    }
135

136
    /// Maps a local dof to its global index.
137
    inline DegreeOfFreedom mapLocalToGlobal(DegreeOfFreedom dof)
138
    {
139
      return mapLocalGlobalDofs[dof];
140
    }
141

142
    /// Maps a local dof to its local index.
143
144
145
146
147
    inline DegreeOfFreedom mapLocalToDofIndex(DegreeOfFreedom dof)
    {
      return mapLocalDofIndex[dof];
    }

148
149
    /// Returns for a global dof index its periodic mapping for a given boundary type.
    inline int getPeriodicMapping(BoundaryType type, int globalDofIndex)
150
    {
151
152
153
154
155
156
      TEST_EXIT_DBG(periodicDof[type].count(globalDofIndex) == 1)
	("Should not happen!\n");

      return periodicDof[type][globalDofIndex];
    }

157
158
159
    /// 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)
160
    {      
161
      return periodicDofAssociations[globalDofIndex];
162
    }
163

164
    /// Returns true, if the DOF (global index) is a periodic DOF.
165
    inline bool isPeriodicDof(int globalDofIndex)
166
    {
167
      return (periodicDofAssociations.count(globalDofIndex) > 0);
168
169
    }

170
171
172
    /// Returns true, if the DOF (global index) is a periodic DOF for the given
    /// boundary type.
    inline bool isPeriodicDof(int globalDofIndex, BoundaryType type)
173
174
    {
      return (periodicDof[type].count(globalDofIndex) > 0);
175
176
    }

177
178
    /// 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.
179
180
181
182
    inline bool getIsRankDof(DegreeOfFreedom dof)
    {
      return isRankDof[dof];
    }
183

184
    inline long getLastMeshChangeIndex()
185
    {
186
      return lastMeshChangeIndex;
187
    }
188

189
190
191
192
    inline int getRstart()
    {
      return rstart;
    }
193

194
    inline int getMpiRank()
195
    {
196
      return mpiRank;
197
    }
198

199
200
201
    inline MPI::Intracomm& getMpiComm()
    {
      return mpiComm;
202
203
    }

204
    inline RankToDofContainer& getSendDofs()
205
    {
206
      return sendDofs;
207
208
    }

209
    inline RankToDofContainer& getRecvDofs()
210
    {
211
      return recvDofs;
212
    }
213

214
    // Writes all data of this object to an output stream.
215
    void serialize(std::ostream &out);
216

217
    // Reads the object data from an input stream.
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
    void deserialize(std::istream &in);

    /** \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);

239
  protected:
240
    /** \brief
Thomas Witkowski's avatar
Thomas Witkowski committed
241
     * Determines the interior boundaries, i.e. boundaries between ranks, and stores
242
243
     * all information about them in \ref interiorBoundary.
     */
244
    void createInteriorBoundaryInfo();
245

246
    void createBoundaryDataStructure();
Thomas Witkowski's avatar
Thomas Witkowski committed
247

248
249
250
    /// Removes all macro elements from the mesh that are not part of ranks partition.
    void removeMacroElements();

251
252
    /// Creates from a macro mesh a correct local and global DOF index numbering.
    void createLocalGlobalNumbering();
253

254
255
    /// Updates the local and global DOF numbering after the mesh has been changed.
    void updateLocalGlobalNumbering();
256

257
258
259
260
261
    /** \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.
     */
262
263
    void createPeriodicMap();

264
265
    /** \brief
     * This function create new mappings from local to global indices, 
266
     * \ref mapLocalGlobalDofs, and from local to dof indices, \ref mapLocalDofIndex.
267
268
269
270
271
272
273
274
275
276
277
278
279
280
     * Furthermore, using the first argument the dof indices in ranks partition are
     * changed.
     * 
     * \param[in] rankDofsNewLocalIndex       Map from dof pointers of all dofs in rank
     *                                        to new dof indices.
     * \param[in] rankOwnedDofsNewLocalIndex  Map from dof pointers of dofs owned by
     *                                        the rank to the new local index.
     * \param[in] rankDofsNewGlobalIndex      Map from dof pointers of all dofs in rank
     *                                        to the new global index.
     */
    void createLocalMappings(DofIndexMap &rankDofsNewLocalIndex,
			     DofIndexMap &rankOwnedDofsNewLocalIndex,
			     DofIndexMap &rankDofsNewGlobalIndex);

281
282
    /** \brief
     * This function traverses the whole mesh, i.e. before it is really partitioned,
Thomas Witkowski's avatar
Thomas Witkowski committed
283
284
285
     * and collects information about which DOF corresponds to which rank. Can only
     * be used, if \ref partitionVec is set correctly. This is only the case, when
     * the macro mesh is partitioned.
286
     *
287
288
289
290
291
     * \param[out] partitionDOFs   Stores to each DOF pointer the set of ranks the DOF
     *                             is part of.
     * \param[out] rankDOFs        Stores all rank DOFs.
     * \param[out] boundaryDOFs    Stores all DOFs in ranks partition that are on an 
     *                             interior boundary but correspond to another rank.
292
     */
293
    void createDofMemberInfo(DofToPartitions& partitionDofs,
Thomas Witkowski's avatar
n    
Thomas Witkowski committed
294
295
			     DofContainer& rankOwnedDofs,
			     DofContainer& rankAllDofs,
296
			     DofToRank& boundaryDofs);
Thomas Witkowski's avatar
Thomas Witkowski committed
297

298
299
300
301
302
303
304
305
306
307
308
309
310
    /** \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);
Thomas Witkowski's avatar
Thomas Witkowski committed
311
    
312
313
314
315
316
317
318
    /** \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.
     */
    void writePartitioningMesh(std::string filename);

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
374
375
376
377
378
379
380
381
382
383
384
385
    /// Writes a vector of dof pointers to an output stream.
    void serialize(std::ostream &out, DofContainer &data);

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

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

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

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

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

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

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

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

403
      int mapSize = data.size();
404
      SerUtil::serialize(out, mapSize);
405
406
407
408
      for (typename std::map<const DegreeOfFreedom*, T>::iterator it = data.begin();
	   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
416
417
418
      }
    }

    /// Reads a mapping from dof pointer to some values from an input stream.
    template<typename T>
    void deserialize(std::istream &in, std::map<const DegreeOfFreedom*, T> &data,
		     std::map<int, const DegreeOfFreedom*> &dofMap)
    {
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
434
	data[dofMap[v1]] = v2;
      }
    }
		        
435
  protected:
Thomas Witkowski's avatar
Thomas Witkowski committed
436
    ///
437
    std::vector<ProblemVec*> probStat;
Thomas Witkowski's avatar
Thomas Witkowski committed
438

439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
    /// 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)
    std::string name;

455
456
457
    /// Finite element space of the problem.
    FiniteElemSpace *feSpace;

458
459
460
    /// Mesh of the problem.
    Mesh *mesh;

461
462
463
464
465
466
467
    /** \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;

468
469
470
    /// Info level.
    int info;

471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
    /// 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.
    std::map<int, double> elemWeights;

    /// Is true, if the mesh was not partitioned before, otherwise it's false.
    bool initialPartitionMesh;

    /** \brief
     * Stores to every coarse element index the number of the partition it 
     * corresponds to.
     */
    std::map<int, int> partitionVec;

    /** \brief
     * Stores an old partitioning of elements. To every element index the number
     * of the parition it corresponds to is stored.
     */
    std::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
    /** \brief 
Thomas Witkowski's avatar
Thomas Witkowski committed
499
500
501
502
503
504
505
506
507
508
509
510
     * 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
511
     */
Thomas Witkowski's avatar
Thomas Witkowski committed
512
    InteriorBoundary otherIntBoundary;
Thomas Witkowski's avatar
Thomas Witkowski committed
513

514
    /** \brief
515
516
     * Defines the periodic boundaries with other ranks. Periodic boundaries have
     * no owner, as it is the case of interior boundaries.
517
518
519
     */
    InteriorBoundary periodicBoundary;

520
521
522
523
    /** \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
524
    RankToDofContainer sendDofs;
525
526

    /** \brief
527
528
529
     * 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.
530
     */
Thomas Witkowski's avatar
Thomas Witkowski committed
531
    RankToDofContainer recvDofs;
532
533

    /// Maps local to global dof indices.
534
    DofMapping mapLocalGlobalDofs;
535

Thomas Witkowski's avatar
Thomas Witkowski committed
536
    /// Maps local dof indices to real dof indices.
537
    DofMapping mapLocalDofIndex;  
538
539
540
541
542
543

    /** \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.
     */
544
545
    DofIndexToBool isRankDof;

546
    /** \brief
547
548
549
550
     * 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.
551
     */
552
    PeriodicDofMap periodicDof;
553
554
555
556
557
558
559
560
    
    /** \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.     
     */
    std::map<int, std::set<BoundaryType> > periodicDofAssociations;
561

562
    /// 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
563
    int rstart;
564

565
566
567
568
569
570
571
    /** \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;
572

573
574
575
    /// Denotes whether there exists a filewriter for this object.
    bool writeSerializationFile;

576
577
578
579
580
    /** \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;
581

582
583
584
585
586
    /// This variable is true, if the macro elements are consistent with all other
    /// data structures. Within the initialization and during mesh redistribution this
    /// may not be the case.
    bool macroElementStructureConsisten;

587
    friend class ParallelDebug;
588
589
590
  };
}

591
#endif // AMDIS_MESHDISTRIBUTOR_H