MeshDistributor.h 18.7 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"
Thomas Witkowski's avatar
Thomas Witkowski committed
34
#include "Global.h"
35 36
#include "ProblemTimeInterface.h"
#include "ProblemIterationInterface.h"
37
#include "FiniteElemSpace.h"
38
#include "Serializer.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
39
#include "BoundaryManager.h"
40
#include "ElementObjectData.h"
41 42
#include "AMDiS_fwd.h"

43
namespace AMDiS {
44 45

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

    /// Defines a mapping type from DOFs to a set of rank numbers.
54
    typedef map<const DegreeOfFreedom*, std::set<int> > DofToPartitions;
Thomas Witkowski's avatar
Thomas Witkowski committed
55 56

    /// Defines a mapping type from rank numbers to sets of DOFs.
57
    typedef map<int, DofContainer> RankToDofContainer;
Thomas Witkowski's avatar
Thomas Witkowski committed
58 59

    /// Defines a mapping type from DOF indices to DOF indices.
60
    typedef map<DegreeOfFreedom, DegreeOfFreedom> DofMapping;
Thomas Witkowski's avatar
Thomas Witkowski committed
61

62
    /// Defines a mapping type from DOFs to boolean values.
63
    typedef map<const DegreeOfFreedom*, bool> DofToBool;
64

Thomas Witkowski's avatar
Thomas Witkowski committed
65
    /// Defines a mapping type from DOF indices to boolean values.
66
    typedef map<DegreeOfFreedom, bool> DofIndexToBool;
Thomas Witkowski's avatar
Thomas Witkowski committed
67

Thomas Witkowski's avatar
Thomas Witkowski committed
68 69 70
    /// Forward type (it maps rank numbers to the interior boundary objects).
    typedef InteriorBoundary::RankToBoundMap RankToBoundMap;

71
    typedef map<const DegreeOfFreedom*, DegreeOfFreedom> DofIndexMap;
Thomas Witkowski's avatar
Thomas Witkowski committed
72

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

    typedef vector<MeshStructure> MeshCodeVec;
78

79
  public:
80
    MeshDistributor(string str);
81 82
		          
    virtual ~MeshDistributor() {}
83

84
    void initParallelization();
85

86
    void exitParallelization();
87 88

    void addProblemStat(ProblemVec *probVec);
89

90 91 92 93 94 95 96
    /// 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);
    }

97 98 99 100 101 102 103 104 105
    /** \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();

106 107 108 109 110 111 112
    /** \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();
113 114

    /// Set for each element on the partitioning level the number of leaf elements.
115
    void setInitialElementWeights();
116

117
    inline virtual string getName() 
118 119 120
    { 
      return name; 
    }
121

Thomas Witkowski's avatar
Thomas Witkowski committed
122 123 124 125 126
    inline Mesh* getMesh()
    {
      return mesh;
    }

127 128 129 130 131
    /// Returns \ref feSpace.
    inline const FiniteElemSpace* getFeSpace()
    {
      return feSpace;
    }
132 133 134
    
    /// Returns \ref nRankDOFs, the number of DOFs in the rank mesh.
    inline int getNumberRankDofs() 
135
    {
136
      return nRankDofs;
137
    }
138

139
    /// Returns \ref nOverallDofs, the global number of DOFs.
140
    inline int getNumberOverallDofs()
141
    {
142
      return nOverallDofs;
143
    }
144

Thomas Witkowski's avatar
Thomas Witkowski committed
145 146 147 148 149
    inline DofMapping& getMapLocalGlobalDofs()
    {
      return mapLocalGlobalDofs;
    }

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

156 157
    DegreeOfFreedom mapGlobalToLocal(DegreeOfFreedom dof);

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

Thomas Witkowski's avatar
Thomas Witkowski committed
164 165 166 167 168 169
    /// Returns the periodic mapping for all boundary DOFs in rank.
    inline PeriodicDofMap& getPeriodicMapping()
    {
      return periodicDof;
    }

170
    /// Returns for a global dof index its periodic mapping for a given boundary type.
171
    inline int getPeriodicMapping(int globalDofIndex, BoundaryType type)
172
    {
Thomas Witkowski's avatar
Thomas Witkowski committed
173 174
      FUNCNAME("MeshDistributor::getPeriodicMapping()");

175
      TEST_EXIT_DBG(periodicDof[type].count(globalDofIndex) == 1)
Thomas Witkowski's avatar
Thomas Witkowski committed
176 177
	("There is no periodic association for global DOF %d for boundary type %d!\n",
	 globalDofIndex, type);
178 179 180 181

      return periodicDof[type][globalDofIndex];
    }

182 183 184
    /// 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)
185
    {      
186 187 188
      TEST_EXIT_DBG(periodicDofAssociations.count(globalDofIndex)) 
 	("Should not happen!\n"); 

189
      return periodicDofAssociations[globalDofIndex];
190
    }
191

192
    /// Returns true, if the DOF (global index) is a periodic DOF.
193
    inline bool isPeriodicDof(int globalDofIndex)
194
    {
195 196
      return (periodicDofAssociations.count(globalDofIndex) > 0 &&
	       periodicDofAssociations[globalDofIndex].size() > 0);
197 198
    }

199 200 201
    /// Returns true, if the DOF (global index) is a periodic DOF for the given
    /// boundary type.
    inline bool isPeriodicDof(int globalDofIndex, BoundaryType type)
202 203
    {
      return (periodicDof[type].count(globalDofIndex) > 0);
204 205
    }

206 207
    /// 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.
208 209
    inline bool getIsRankDof(DegreeOfFreedom dof)
    {
210 211 212 213
      if (isRankDof.count(dof))
	return isRankDof[dof];

      return false;
214
    }
215

216
    inline long getLastMeshChangeIndex()
217
    {
218
      return lastMeshChangeIndex;
219
    }
220

221 222 223 224
    inline int getRstart()
    {
      return rstart;
    }
225

226
    inline int getMpiRank()
227
    {
228
      return mpiRank;
229
    }
230

Thomas Witkowski's avatar
Thomas Witkowski committed
231 232 233 234 235
    inline int getMpiSize()
    {
      return mpiSize;
    }

236 237 238
    inline MPI::Intracomm& getMpiComm()
    {
      return mpiComm;
239 240
    }

241
    inline RankToDofContainer& getSendDofs()
242
    {
243
      return sendDofs;
244 245
    }

246
    inline RankToDofContainer& getRecvDofs()
247
    {
248
      return recvDofs;
249
    }
250

251
    // Writes all data of this object to an output stream.
252
    void serialize(ostream &out);
253

254
    // Reads the object data from an input stream.
255
    void deserialize(istream &in);
256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275

    /** \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);

276 277
    void check3dValidMesh();

278
  protected:
279
    /** \brief
Thomas Witkowski's avatar
Thomas Witkowski committed
280
     * Determines the interior boundaries, i.e. boundaries between ranks, and stores
281 282
     * all information about them in \ref interiorBoundary.
     */
283
    void createInteriorBoundaryInfo();
284

Thomas Witkowski's avatar
Thomas Witkowski committed
285 286 287 288 289
    void updateInteriorBoundaryInfo();

    void createMeshElementData();

    void createBoundaryData();
Thomas Witkowski's avatar
Thomas Witkowski committed
290

291 292 293
    /// Removes all macro elements from the mesh that are not part of ranks partition.
    void removeMacroElements();

294
    /// Updates the local and global DOF numbering after the mesh has been changed.
295
    void updateLocalGlobalNumbering();
296

297 298 299 300 301
    /** \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.
     */
302 303
    void createPeriodicMap();

304 305
    void createMacroElementInfo();

306 307
    void updateMacroElementInfo();

308 309 310 311 312 313 314 315 316
    /** \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.
317 318 319 320
     *
     * \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.
321 322
     */
    bool checkAndAdaptBoundary(RankToBoundMap &allBound);
323 324 325 326 327 328 329 330
  
    /** \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();

331 332 333
    /// Sets \ref isRankDof to all matrices and rhs vectors in all stationary problems.
    void setRankDofs();

334 335 336 337
    /// 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
338
    // Removes all periodic boundaries from a given boundary map.
339
    void removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap);
Thomas Witkowski's avatar
Thomas Witkowski committed
340

341
    /// Writes a vector of dof pointers to an output stream.
342
    void serialize(ostream &out, DofContainer &data);
343 344

    /// Reads a vector of dof pointers from an input stream.
345 346
    void deserialize(istream &in, DofContainer &data,
		     map<int, const DegreeOfFreedom*> &dofMap);
347 348

    /// Writes a \ref RankToDofContainer to an output stream.
349
    void serialize(ostream &out, RankToDofContainer &data);
350 351

    /// Reads a \ref RankToDofContainer from an input stream.
352 353
    void deserialize(istream &in, RankToDofContainer &data,
		     map<int, const DegreeOfFreedom*> &dofMap);
354

355
    /// Writes a periodic dof mapping to an output stream.
356
    void serialize(ostream &out, PeriodicDofMap &data);
357

358
    void serialize(ostream &out, map<int, std::set<int> >& data);
359

360
    /// Reads a periodic dof mapping from an input stream.
361
    void deserialize(istream &in, PeriodicDofMap &data);
362

363
    void deserialize(istream &in, map<int, std::set<int> >& data);
364

365 366
    /// Writes a mapping from dof pointers to some values to an output stream.
    template<typename T>
367
    void serialize(ostream &out, map<const DegreeOfFreedom*, T> &data)
368
    {
369 370
      FUNCNAME("ParallelDomainBase::serialize()");

371
      int mapSize = data.size();
372
      SerUtil::serialize(out, mapSize);
373
      for (typename map<const DegreeOfFreedom*, T>::iterator it = data.begin();
374 375 376
	   it != data.end(); ++it) {
	int v1 = (*(it->first));
	T v2 = it->second;
377 378
	SerUtil::serialize(out, v1);
	SerUtil::serialize(out, v2);
379 380 381 382 383
      }
    }

    /// Reads a mapping from dof pointer to some values from an input stream.
    template<typename T>
384 385
    void deserialize(istream &in, map<const DegreeOfFreedom*, T> &data,
		     map<int, const DegreeOfFreedom*> &dofMap)
386
    {
387 388
      FUNCNAME("ParallelDomainBase::deserialize()");

389
      int mapSize = 0;
390
      SerUtil::deserialize(in, mapSize);
391 392 393
      for (int i = 0; i < mapSize; i++) {
	int v1 = 0;
	T v2;
394 395
	SerUtil::deserialize(in, v1);
	SerUtil::deserialize(in, v2);
396 397 398

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

399 400 401
	data[dofMap[v1]] = v2;
      }
    }
402

403
  protected:
Thomas Witkowski's avatar
Thomas Witkowski committed
404
    ///
405
    vector<ProblemVec*> probStat;
Thomas Witkowski's avatar
Thomas Witkowski committed
406

407 408 409 410 411 412 413 414 415 416 417 418 419 420
    /// 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)
421
    string name;
422

423 424 425
    /// Finite element space of the problem.
    FiniteElemSpace *feSpace;

426 427 428
    /// Mesh of the problem.
    Mesh *mesh;

429 430 431 432 433 434 435
    /** \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;

436 437 438
    /// Info level.
    int info;

439 440
    /// Pointer to a mesh partitioner that is used to partition the mesh to the ranks.
    MeshPartitioner *partitioner;
441 442

    /// Weights for the elements, i.e., the number of leaf elements within this element.
443
    map<int, double> elemWeights;
444 445

    /** \brief
446 447
     * Stores to every macro element index the number of the rank that owns this
     * macro element.
448
     */
449
    map<int, int> partitionMap;
450 451

    /** \brief
452 453
     * Stores an old partitioning of elements. To every macro element index the
     * number of the rank it corresponds to is stored.
454
     */
455
    map<int, int> oldPartitionMap; 
456
   
457
    /// Number of DOFs in the rank mesh.
458
    int nRankDofs;
Thomas Witkowski's avatar
Thomas Witkowski committed
459

460
    /// Number of DOFs in the whole domain.
461 462
    int nOverallDofs;

Thomas Witkowski's avatar
Thomas Witkowski committed
463 464 465 466
    // 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.
467
    map<int, Element*> macroElIndexMap;
Thomas Witkowski's avatar
Thomas Witkowski committed
468 469
    
    // Maps to each macro element index the type of this element.
470
    map<int, int> macroElIndexTypeMap;
Thomas Witkowski's avatar
Thomas Witkowski committed
471

Thomas Witkowski's avatar
Thomas Witkowski committed
472
    /** \brief 
Thomas Witkowski's avatar
Thomas Witkowski committed
473 474 475 476 477 478 479 480 481 482 483 484
     * 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
485
     */
Thomas Witkowski's avatar
Thomas Witkowski committed
486
    InteriorBoundary otherIntBoundary;
Thomas Witkowski's avatar
Thomas Witkowski committed
487

488
    /** \brief
489 490
     * Defines the periodic boundaries with other ranks. Periodic boundaries have
     * no owner, as it is the case of interior boundaries.
491 492 493
     */
    InteriorBoundary periodicBoundary;

494 495 496 497
    /** \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
498
    RankToDofContainer sendDofs;
499 500

    /** \brief
501 502 503
     * 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.
504
     */
Thomas Witkowski's avatar
Thomas Witkowski committed
505
    RankToDofContainer recvDofs;
506 507

    /// Maps local to global dof indices.
508
    DofMapping mapLocalGlobalDofs;
509

Thomas Witkowski's avatar
Thomas Witkowski committed
510
    /// Maps local dof indices to real dof indices.
511
    DofMapping mapLocalDofIndex;  
512 513 514 515 516 517

    /** \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.
     */
518 519
    DofIndexToBool isRankDof;

520
    /** \brief
521 522 523 524
     * 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.
525
     */
526
    PeriodicDofMap periodicDof;
527 528 529 530 531
    
    /** \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
532
     * being periodic, the four corners are associated by two different boundaries.
533
     */
534
    map<int, std::set<BoundaryType> > periodicDofAssociations;
535

536 537 538 539 540
    
    /// This set of values must be interchanged between ranks when the mesh is 
    /// repartitioned.
    vector<DOFVector<double>*> interchangeVectors;
		        
541
    /// 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
542
    int rstart;
543

544 545 546 547 548 549 550
    /** \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;
551

552 553 554
    /// Denotes whether there exists a filewriter for this object.
    bool writeSerializationFile;

555 556 557
    /// If true, it is possible to repartition the mesh during computations.
    bool repartitioningAllowed;

558
    /// Stores the number of mesh changes that must lie in between to repartitionings.
559 560
    int repartitionIthChange;

561 562
    /// Counts the number of mesh changes after the last mesh repartitioning was done.
    int nMeshChangesAfterLastRepartitioning;
563

564 565 566
    /// Countes the number of mesh repartitions that were done. Till now, this 
    /// variable is used only for debug outputs.
    int repartitioningCounter;
567

568
    /// Directory name where all debug output files should be written to.
569
    string debugOutputDir;
570

571 572 573 574 575
    /** \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;
576

577
    map<int, vector<int> > macroElementNeighbours;
578

579 580
    /// Store all macro elements of the overall mesh, i.e., before the macro mesh is
    /// redistributed for the first time.
581
    vector<MacroElement*> allMacroElements;
582

583
    friend class ParallelDebug;
584 585 586
  };
}

587
#endif // AMDIS_MESHDISTRIBUTOR_H