MeshDistributor.h 19.8 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


Thomas Witkowski's avatar
Thomas Witkowski committed
27
#include <mpi.h>
28
#include "parallel/DofComm.h"
29
#include "parallel/ElementObjectDatabase.h"
30
#include "parallel/ParallelTypes.h"
31
#include "parallel/MeshLevelData.h"
32
#include "parallel/MeshPartitioner.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
33
#include "parallel/InteriorBoundary.h"
34
#include "parallel/ParallelDofMapping.h"
35
#include "parallel/PeriodicMap.h"
36
#include "parallel/StdMpi.h"
37
#include "AMDiS_fwd.h"
38
#include "Containers.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
39
#include "Global.h"
40 41
#include "ProblemTimeInterface.h"
#include "ProblemIterationInterface.h"
42
#include "FiniteElemSpace.h"
43
#include "Serializer.h"
Thomas Witkowski's avatar
Thomas Witkowski committed
44
#include "BoundaryManager.h"
45
#include "SystemVector.h"
46

47
namespace AMDiS {
48 49

  using namespace std;
Thomas Witkowski's avatar
Thomas Witkowski committed
50 51 52 53


  struct BoundaryDofInfo
  {
54
    map<GeoIndex, DofContainerSet> geoDofs;
Thomas Witkowski's avatar
Thomas Witkowski committed
55 56
  };

57

58
  class MeshDistributor
59
  {
60
  private:
61
    MeshDistributor();
62 63
	          
  public:
Thomas Witkowski's avatar
Thomas Witkowski committed
64 65
    ~MeshDistributor();

66
    void initParallelization();
67

68
    void exitParallelization();
69

70 71 72
    /// Adds a DOFVector to the set of \ref interchangeVecs. Thus, this vector 
    /// will be automatically interchanged between ranks when mesh is 
    /// repartitioned.
73 74 75 76 77
    void addInterchangeVector(DOFVector<double> *vec)
    {
      interchangeVectors.push_back(vec);
    }

78 79 80 81 82 83 84
    /// 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));
    }
    
85
    /** \brief
86 87 88 89 90
     * 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.
91
     *
92 93 94 95 96
     * \param[in]  tryRepartition   If this parameter is true, repartitioning 
     *                              may be done. This depends on several other 
     *                              parameters. If the parameter is false, the 
     *                              mesh is only checked and adapted but never 
     *                              repartitioned.
97
     */
98
    void checkMeshChange(bool tryRepartition = true);
99

Thomas Witkowski's avatar
Thomas Witkowski committed
100 101 102
    /// 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.
103 104
    void repartitionMesh();
    
Thomas Witkowski's avatar
Thomas Witkowski committed
105 106 107 108 109 110 111
    void getImbalanceFactor(double &imbalance, 
			    int &minDofs, 
			    int &maxDofs,
			    int &sumDofs);

    double getImbalanceFactor();

112 113 114
    /// Calculates the imbalancing factor and prints it to screen.
    void printImbalanceFactor();

Thomas Witkowski's avatar
Thomas Witkowski committed
115 116 117 118
    /// 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.
119
    void testForMacroMesh();
120

121 122
    /// Set for each element on the partitioning level the number of 
    /// leaf elements.
123
    void setInitialElementWeights();
124

Thomas Witkowski's avatar
Thomas Witkowski committed
125
    inline 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
    /// Returns an FE space from \ref feSpaces.
    inline const FiniteElemSpace* getFeSpace(unsigned int i = 0)
137
    {
138 139 140 141 142
      FUNCNAME("MeshDistributor::getFeSpace()");

      TEST_EXIT_DBG(i < feSpaces.size())("Should not happen!\n");

      return feSpaces[i];
143
    }
144 145 146 147 148 149 150

    /// Returns all FE spaces, thus \ref feSpaces.
    inline vector<const FiniteElemSpace*>& getFeSpaces()
    {
      return feSpaces;
    }

151 152
    /// Returns the DOF mapping object, \ref dofMap.
    inline ParallelDofMapping& getDofMap()
Thomas Witkowski's avatar
Thomas Witkowski committed
153
    {
154
      return dofMap;
Thomas Witkowski's avatar
Thomas Witkowski committed
155 156
    }

157 158 159 160 161
    inline ParallelDofMapping& getDofMapSd()
    {
      return dofMapSd;
    }

162 163
    /// Returns the periodic mapping handler, \ref periodicMap.
    inline PeriodicMap& getPeriodicMap()
164
    {
165
      return periodicMap;
166
    }
167

168
    DofComm& getDofComm()
169
    {
170
      return dofComm;
171 172
    }

173 174 175 176 177
    DofComm& getDofCommSd()
    {
      return dofCommSd;
    }

178 179 180 181 182
    InteriorBoundary& getIntBoundary()
    {
      return intBoundary;
    }

183 184 185 186 187
    InteriorBoundary& getIntBoundarySd()
    {
      return intBoundarySd;
    }

188
    inline long getLastMeshChangeIndex()
189
    {
190
      return lastMeshChangeIndex;
191
    }
192

193
    inline int getMpiRank()
194
    {
195
      return mpiRank;
196
    }
197

Thomas Witkowski's avatar
Thomas Witkowski committed
198 199 200 201 202
    inline int getMpiSize()
    {
      return mpiSize;
    }

203 204 205
    inline MPI::Intracomm& getMpiComm()
    {
      return mpiComm;
206 207
    }

208 209 210 211 212
    inline bool isInitialized()
    {
      return initialized;
    }

213
    // Writes all data of this object to an output stream.
214
    void serialize(ostream &out);
215

216
    // Reads the object data from an input stream.
217
    void deserialize(istream &in);
218 219

    /** \brief
220 221 222 223
     * 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.
224
     *
225 226 227
     * 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.
228
     */    
229 230 231 232 233
    template<typename T>
    void synchVector(DOFVector<T> &vec) 
    {
      StdMpi<vector<T> > stdMpi(mpiComm);

234 235
      const FiniteElemSpace *fe = vec.getFeSpace();

236 237
      for (DofComm::Iterator it(dofComm.getSendDofs(), fe); 
	   !it.end(); it.nextRank()) {
238
	vector<T> dofs;
239
	dofs.reserve(it.getDofs().size());
240
	
241 242
	for (; !it.endDofIter(); it.nextDof())
	  dofs.push_back(vec[it.getDofIndex()]);
243
	
244
	stdMpi.send(it.getRank(), dofs);
245
      }
246
	     
247 248
      for (DofComm::Iterator it(dofComm.getRecvDofs()); 
	   !it.end(); it.nextRank())
249 250
        stdMpi.recv(it.getRank());
	     
251
      stdMpi.startCommunication();
252

253 254
      for (DofComm::Iterator it(dofComm.getRecvDofs(), fe); 
	   !it.end(); it.nextRank())
255 256 257
	for (; !it.endDofIter(); it.nextDof())
	  vec[it.getDofIndex()] = 
	     stdMpi.getRecvData(it.getRank())[it.getDofCounter()];
258
    }
Thomas Witkowski's avatar
Thomas Witkowski committed
259
   
Thomas Witkowski's avatar
Blub  
Thomas Witkowski committed
260 261 262 263
    /// 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, int level = 0);
264

Thomas Witkowski's avatar
Thomas Witkowski committed
265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299
    /// Works quite similar to the function \ref synchVector, but instead the 
    /// values of subdomain vectors are add along the boundaries.
    template<typename T>
    void synchAddVector(DOFVector<T> &vec)
    {
      StdMpi<vector<T> > stdMpi(mpiComm);

      const FiniteElemSpace *fe = vec.getFeSpace();

      for (DofComm::Iterator it(dofComm.getRecvDofs(), fe);
	   !it.end(); it.nextRank()) {
	vector<T> dofs;
	dofs.reserve(it.getDofs().size());
	
	for (; !it.endDofIter(); it.nextDof())
	  dofs.push_back(vec[it.getDofIndex()]);
	
	stdMpi.send(it.getRank(), dofs);
      }

      for (DofComm::Iterator it(dofComm.getSendDofs()); 
	   !it.end(); it.nextRank())
        stdMpi.recv(it.getRank());
	     
      stdMpi.startCommunication();

      for (DofComm::Iterator it(dofComm.getSendDofs(), fe); 
	   !it.end(); it.nextRank())
	for (; !it.endDofIter(); it.nextDof())
	  vec[it.getDofIndex()] += 
	     stdMpi.getRecvData(it.getRank())[it.getDofCounter()];

      synchVector(vec);
    }

300 301 302 303 304 305
    /// In 3D, a subdomain may not be a valid AMDiS mesh if it contains two
    /// parts which are only connected by an edge. In this case, the standard
    /// refinement algorithm does not work correctly, as two elements connected
    /// only on one edge are not neighours by definition. This functions checks
    /// for this situation and fix the problem. For this, the mesh is search for
    /// all edges connecting two elements that are otherwise not connected.
306 307
    void check3dValidMesh();

Thomas Witkowski's avatar
Thomas Witkowski committed
308 309 310 311 312
    void setBoundaryDofRequirement(Flag flag)
    {
      createBoundaryDofFlag = flag;
    }

313 314
    BoundaryDofInfo& getBoundaryDofInfo(const FiniteElemSpace *feSpace,
					int level)
315
    {
316 317 318 319 320 321 322
      FUNCNAME("MeshDistributor::getBoundaryDofInfo()");

      TEST_EXIT_DBG(level < static_cast<int>(boundaryDofInfo.size()))
	("Wrong level number: %d, whereas array size is %d!\n", 
	 level, boundaryDofInfo.size());

      return boundaryDofInfo[level][feSpace];
323 324
    }

325 326
    void getAllBoundaryDofs(const FiniteElemSpace *feSpace, 
			    int level,
327
			    DofContainer& dofs);
328

329 330 331 332
    const ElementObjectDatabase& getElementObjectDb() 
    {
      return elObjDb;
    }
333 334 335

    /// Adds a stationary problem to the global mesh distributor objects.
    static void addProblemStatGlobal(ProblemStatSeq *probStat);
Thomas Witkowski's avatar
Thomas Witkowski committed
336 337 338 339 340 341

    MeshLevelData& getMeshLevelData() 
    {
      return levelData;
    }

342 343 344 345 346 347 348 349
    void updateLocalGlobalNumbering();

    /// Updates the local and global DOF numbering after the mesh has been 
    /// changed.
    void updateLocalGlobalNumbering(ParallelDofMapping &dmap,
				    DofComm &dcom,
				    const FiniteElemSpace *feSpace);

350
  protected:
351 352
    void addProblemStat(ProblemStatSeq *probStat);

353 354
    /// Determines the interior boundaries, i.e. boundaries between ranks, and
    /// stores all information about them in \ref interiorBoundary.
355
    void createInteriorBoundary(bool firstCall);
Thomas Witkowski's avatar
Thomas Witkowski committed
356

Thomas Witkowski's avatar
Thomas Witkowski committed
357 358
    void createBoundaryDofs();

359 360
    /// Removes all macro elements from the mesh that are not part of ranks 
    /// partition.
361 362
    void removeMacroElements();

363 364 365 366
    /// Calls \ref createPeriodicMap(feSpace) for all FE spaces that are
    /// handled by the mesh distributor.
    void createPeriodicMap();

367 368 369
    /// Creates, for a specific FE space, 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 periodicDofMap.  
370
    void createPeriodicMap(const FiniteElemSpace *feSpace);
371

372 373 374 375 376 377
    /// This function is called only once during the initialization when the
    /// whole macro mesh is available on all cores. It copies the pointers of all
    /// macro elements to \ref allMacroElements and stores all neighbour 
    /// information based on macro element indices (and not pointer based) in 
    /// \ref macroElementNeighbours. These information are then used to 
    /// reconstruct macro elements during mesh redistribution.
378 379
    void createMacroElementInfo();

380 381
    void updateMacroElementInfo();

382
    /** \brief
383 384 385 386 387 388
     * 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.
389
     *
390 391
     * \param[in] allBound   Defines a map from rank to interior boundaries 
     *                       which should be checked.
392
     *
393 394 395
     * \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.
396 397
     */
    bool checkAndAdaptBoundary(RankToBoundMap &allBound);
398
  
399 400 401 402
    /// Removes all periodic boundary condition information from all matrices and
    /// vectors of all stationary problems and from the mesh itself.
    void removePeriodicBoundaryConditions();

403 404 405 406
    /// Removes all periodic boundary condition information from all matrices and
    /// vector of a given stationary problem.
    void removePeriodicBoundaryConditions(ProblemStatSeq *probStat);

Thomas Witkowski's avatar
Thomas Witkowski committed
407
    // Removes all periodic boundaries from a given boundary map.
408
    void removePeriodicBoundaryConditions(BoundaryIndexMap& boundaryMap);
Thomas Witkowski's avatar
Thomas Witkowski committed
409

410 411
    void createMeshLevelStructure();

412
    /// Writes a vector of dof pointers to an output stream.
413
    void serialize(ostream &out, DofContainer &data);
414

415 416 417 418
    /// Writes a \ref RankToDofContainer to an output stream.
    void serialize(ostream &out, 
		   map<int, map<const FiniteElemSpace*, DofContainer> > &data);

419
    /// Reads a vector of dof pointers from an input stream.
420
    void deserialize(istream &in, DofContainer &data,
421
		     map<int, const DegreeOfFreedom*> &dofIndexMap);
422 423

    /// Reads a \ref RankToDofContainer from an input stream.
424 425
    void deserialize(istream &in, 
		     map<int, map<const FiniteElemSpace*, DofContainer> > &data,
426
		     map<const FiniteElemSpace*, map<int, const DegreeOfFreedom*> > &dofIndexMap);
427 428 429

    /// Writes a mapping from dof pointers to some values to an output stream.
    template<typename T>
430
    void serialize(ostream &out, map<const DegreeOfFreedom*, T> &data)
431
    {
432 433
      FUNCNAME("ParallelDomainBase::serialize()");

434
      int mapSize = data.size();
435
      SerUtil::serialize(out, mapSize);
436
      for (typename map<const DegreeOfFreedom*, T>::iterator it = data.begin();
437 438 439
	   it != data.end(); ++it) {
	int v1 = (*(it->first));
	T v2 = it->second;
440 441
	SerUtil::serialize(out, v1);
	SerUtil::serialize(out, v2);
442 443 444 445 446
      }
    }

    /// Reads a mapping from dof pointer to some values from an input stream.
    template<typename T>
447
    void deserialize(istream &in, map<const DegreeOfFreedom*, T> &data,
448
		     map<int, const DegreeOfFreedom*> &dofIndexMap)
449
    {
450 451
      FUNCNAME("ParallelDomainBase::deserialize()");

452
      int mapSize = 0;
453
      SerUtil::deserialize(in, mapSize);
454 455 456
      for (int i = 0; i < mapSize; i++) {
	int v1 = 0;
	T v2;
457 458
	SerUtil::deserialize(in, v1);
	SerUtil::deserialize(in, v2);
459

460 461
	TEST_EXIT_DBG(dofIndexMap.count(v1) != 0)
	  ("Cannot find DOF %d in map!\n", v1);
462

463
	data[dofIndexMap[v1]] = v2;
464 465
      }
    }
466

467
  protected:
468 469
    /// List of all stationary problems that are managed by this mesh 
    /// distributor.
470
    vector<ProblemStatSeq*> problemStat;
Thomas Witkowski's avatar
Thomas Witkowski committed
471

472 473 474
    /// If true, the mesh distributor is already initialized;
    bool initialized;

475 476 477 478 479 480
    /// The rank of the current process.
    int mpiRank;

    /// Overall number of processes.
    int mpiSize;

481 482
    /// MPI communicator collected all processes, which should be used for
    /// calculation. The Debug procces is not included in this communicator.
483 484 485
    MPI::Intracomm mpiComm;

    /// Name of the problem (as used in the init files)
486
    string name;
487

488 489
    /// Finite element spaces of the problem.
    vector<const FiniteElemSpace*> feSpaces;
490

491 492 493
    /// Mesh of the problem.
    Mesh *mesh;

494 495 496
    /// 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.    
497 498
    RefinementManager *refineManager;

499 500 501
    /// Info level.
    int info;

502 503
    /// Pointer to a mesh partitioner that is used to partition the mesh to 
    /// the ranks.
504
    MeshPartitioner *partitioner;
505

506 507
    /// Weights for the elements, i.e., the number of leaf elements within 
    /// this element.
508
    map<int, double> elemWeights;
509

510 511
    /// Stores to every macro element index the number of the rank that owns this
    /// macro element.
512
    map<int, int> partitionMap;
513

514
    /// Mapping object to map from local DOF indices to global ones.
515 516
    ParallelDofMapping dofMap;

517 518
    ParallelDofMapping dofMapSd;

519
    /// Database to store and query all sub-objects of all elements of the 
520
    /// macro mesh.
521
    ElementObjectDatabase elObjDb;
Thomas Witkowski's avatar
Thomas Witkowski committed
522

523
    /// Defines the interior boundaries of the domain that result from 
524 525
    /// partitioning the whole mesh. 
    InteriorBoundary intBoundary;
526

527 528
    InteriorBoundary intBoundarySd;

529
    DofComm dofComm;
530

531 532
    DofComm dofCommSd;

533
    PeriodicMap periodicMap;
534

535 536 537 538
    /// This set of values must be interchanged between ranks when the mesh is 
    /// repartitioned.
    vector<DOFVector<double>*> interchangeVectors;
		        
539 540 541 542
    /// 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.
543
    bool deserialized;
544

545 546 547
    /// Denotes whether there exists a filewriter for this object.
    bool writeSerializationFile;

548 549 550
    /// If true, it is possible to repartition the mesh during computations.
    bool repartitioningAllowed;

551 552
    /// Stores the number of mesh changes that must lie in between to 
    /// repartitionings.
553 554
    int repartitionIthChange;

555 556
    /// Counts the number of mesh changes after the last mesh repartitioning 
    /// was done.
557
    int nMeshChangesAfterLastRepartitioning;
558

559 560 561
    /// Countes the number of mesh repartitions that were done. Till now, this 
    /// variable is used only for debug outputs.
    int repartitioningCounter;
562

563 564 565 566 567
    /// If repartitioning of the mesh fail, this variable has a positive value
    /// that gives the number of mesh changes the mesh distributer will wait
    /// before trying new mesh repartitioning.
    int repartitioningFailed;

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

571 572
    /// Stores the mesh change index. This is used to recognize changes in the
    /// mesh structure (e.g. through refinement or coarsening managers).
573
    long lastMeshChangeIndex;
574

575 576 577 578
    /// Stores for all macro elements of the original macro mesh the
    /// neighbourhood information based on element indices. Thus, each macro
    /// element index is mapped to a vector containing all indices of 
    /// neighbouring macro elements.
579
    map<int, vector<int> > macroElementNeighbours;
580

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

Thomas Witkowski's avatar
Thomas Witkowski committed
585 586
    Flag createBoundaryDofFlag;

587 588 589
    /// Stores on each mesh level for all FE spaces the information about
    /// all boundary DOFs.
    vector<map<const FiniteElemSpace*, BoundaryDofInfo> > boundaryDofInfo;
590

591 592
    MeshLevelData levelData;

Thomas Witkowski's avatar
bla  
Thomas Witkowski committed
593 594 595 596 597 598
    /// If there is no mesh adaptivity, the mesh distributor can remove some
    /// data structures which are only used if mesh changes or it must be
    /// redistributed due to some local adaptivity. By default, this variable
    /// is set to true, and thus no special assumption are made.
    bool meshAdaptivity;

Thomas Witkowski's avatar
Thomas Witkowski committed
599
  public:
600 601
    static bool sebastianMode;

602 603 604
    /// The boundary DOFs are sorted by subobject entities, i.e., first all
    /// face DOFs, edge DOFs and to the last vertex DOFs will be set to
    /// communication structure vectors, \ref sendDofs and \ref recvDofs.
Thomas Witkowski's avatar
Thomas Witkowski committed
605 606
    static const Flag BOUNDARY_SUBOBJ_SORTED;

607 608 609 610 611 612 613 614 615
    /// When boundary DOFs are created, \ref boundaryDofInfo is filled for
    /// all DOFs that this rank will send to other ranks (thus, rank 
    /// owned DOFs.
    static const Flag BOUNDARY_FILL_INFO_SEND_DOFS;

    /// When boundary DOFs are created, \ref boundaryDofInfo is filled for
    /// all DOFs that this rank will receive from other ranks (thus, DOFs
    /// that are owned by another rank).
    static const Flag BOUNDARY_FILL_INFO_RECV_DOFS;
Thomas Witkowski's avatar
Thomas Witkowski committed
616

617 618
    static MeshDistributor *globalMeshDistributor;

619
    friend class ParallelDebug;
620 621 622
  };
}

623
#endif // AMDIS_MESHDISTRIBUTOR_H