ParMetisPartitioner.cc 12.7 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
//
// 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.


13
#include <queue>
14
15
16
17
18
19
20
21
22
23
24
#include "ParMetisPartitioner.h"
#include "Mesh.h"
#include "Traverse.h"
#include "ElInfo.h"
#include "Element.h"
#include "FixVec.h"
#include "DOFVector.h"
#include "mpi.h"

namespace AMDiS {

25
  ParMetisMesh::ParMetisMesh(Mesh *mesh, MPI::Intracomm *comm, 
26
			     std::map<int, bool>& elementInRank,
27
			     std::map<DegreeOfFreedom, DegreeOfFreedom> *mapLocalGlobal)
Thomas Witkowski's avatar
Thomas Witkowski committed
28
29
    : dim(mesh->getDim()),
      nElements(0),
30
      mpiComm(comm)
31
32
  {
    FUNCNAME("ParMetisMesh::ParMetisMesh()");
33
34

    int mpiSize = mpiComm->Get_size();
35
36
37
38
39
    int nodeCounter = 0;
    int elementCounter = 0;
    int dow = Global::getGeo(WORLD);

    TraverseStack stack;
40
    ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
41
    while (elInfo) {
42
      if (elementInRank[elInfo->getElement()->getIndex()])
43
	elementCounter++;      
44
45
46
47

      elInfo = stack.traverseNext(elInfo);
    }

48
    nElements = elementCounter;
49

50
    TEST_EXIT(nElements > 0)("No elements in ParMETIS mesh!\n");
51
52

    // allocate memory
Thomas Witkowski's avatar
Thomas Witkowski committed
53
    eptr = new int[nElements + 1];
Thomas Witkowski's avatar
huh  
Thomas Witkowski committed
54
    eind = new int[nElements * (dim + 1)];
Thomas Witkowski's avatar
Thomas Witkowski committed
55
56
    elmdist = new int[mpiSize + 1];
    elem_p2a = new int[nElements];
57

58
    if (dim == dow)
Thomas Witkowski's avatar
Thomas Witkowski committed
59
      xyz = new float[nElements * dim];
60
61
    else
      xyz = NULL;    
62

Thomas Witkowski's avatar
Thomas Witkowski committed
63
    eptr[0] = 0;
64

Thomas Witkowski's avatar
Thomas Witkowski committed
65
66
67
    int *ptr_eptr = eptr + 1;
    int *ptr_eind = eind;
    float *ptr_xyz = xyz;
68
69
    
    // gather element numbers and create elmdist
70
    mpiComm->Allgather(&nElements, 1, MPI_INT, elmdist + 1, 1, MPI_INT);
71

72
    elmdist[0] = 0;
73
    for (int i = 2; i < mpiSize + 1; i++)
74
      elmdist[i] += elmdist[i - 1];
75
76

    // traverse mesh and fill distributed ParMETIS data
Thomas Witkowski's avatar
Thomas Witkowski committed
77
    DimVec<double> bary(dim, DEFAULT_VALUE, 1.0 / (dim + 1));
78
79
80
81
    WorldVector<double> world;

    elementCounter = 0;

82
    elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL | Mesh::FILL_COORDS);
83
    while (elInfo) {
84
85
86
87
      Element *element = elInfo->getElement();
      int index = element->getIndex();

      // if element in partition
88
      if (elementInRank[index]) {
89
90
91
92
93
	// remember index
	setParMetisIndex(index, elementCounter);
	setAMDiSIndex(elementCounter, index);

	// write eptr entry
Thomas Witkowski's avatar
Thomas Witkowski committed
94
	nodeCounter += dim + 1;
95
96
97
98
	*ptr_eptr = nodeCounter;
	ptr_eptr++;

	// write eind entries (element nodes)
Thomas Witkowski's avatar
Thomas Witkowski committed
99
	for (int i = 0; i < dim + 1; i++) {
100
	  if (mapLocalGlobal)
101
	    *ptr_eind = (*mapLocalGlobal)[element->getDof(i, 0)];
102
	  else
103
	    *ptr_eind = element->getDof(i, 0);
104

105
106
107
108
	  ptr_eind++;
	}

	// write xyz element coordinates
109
	if (ptr_xyz) {
110
	  elInfo->coordToWorld(bary, world);
Thomas Witkowski's avatar
Thomas Witkowski committed
111
	  for (int i = 0; i < dim; i++) {
112
113
114
115
116
117
118
	    *ptr_xyz = static_cast<float>(world[i]); 
	    ptr_xyz++;
	  }
	}

	elementCounter++;
      }
119

120
121
122
123
      elInfo = stack.traverseNext(elInfo);
    }
  }

124

125
126
  ParMetisMesh::~ParMetisMesh()
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
127
    if (eptr)
Thomas Witkowski's avatar
Thomas Witkowski committed
128
      delete [] eptr;
129
    
Thomas Witkowski's avatar
Thomas Witkowski committed
130
    if (eind)     
Thomas Witkowski's avatar
Thomas Witkowski committed
131
      delete [] eind;
132
    
133
    if (elmdist)
Thomas Witkowski's avatar
Thomas Witkowski committed
134
      delete [] elmdist;
135
    
Thomas Witkowski's avatar
Thomas Witkowski committed
136
    if (xyz)
Thomas Witkowski's avatar
Thomas Witkowski committed
137
      delete [] xyz;
138
    
Thomas Witkowski's avatar
Thomas Witkowski committed
139
    if (elem_p2a) 
Thomas Witkowski's avatar
Thomas Witkowski committed
140
      delete [] elem_p2a;
141
142
  }

143

144
  ParMetisGraph::ParMetisGraph(ParMetisMesh *parMesh,
145
			       MPI::Intracomm *comm,
146
			       int ncommonnodes)
147
    : parMetisMesh(parMesh)
148
  {
149
150
151
152
153
    FUNCNAME("ParMetisGraph::ParMetisGraph()");

    TEST_EXIT(parMesh)("No ParMetisMesh defined!\n");
    TEST_EXIT(comm)("No MPI communicator defined!\n");

154
155
    int numflag = 0;

156
157
    if (ncommonnodes == -1) 
      ncommonnodes = parMetisMesh->getDim();
158

159
    MPI_Comm tmpComm = MPI_Comm(*comm);
160

161
162
163
    ParMETIS_V3_Mesh2Dual(parMetisMesh->getElementDist(),
			  parMetisMesh->getElementPtr(),
			  parMetisMesh->getElementInd(),
164
165
			  &numflag,
			  &ncommonnodes,
Thomas Witkowski's avatar
Thomas Witkowski committed
166
167
			  &xadj,
			  &adjncy,
168
			  &tmpComm);
169
170
  }

171

172
173
  ParMetisGraph::~ParMetisGraph()
  {
Thomas Witkowski's avatar
Thomas Witkowski committed
174
175
    free(xadj);
    free(adjncy);
176
177
  }

178

179
180
  void ParMetisPartitioner::createPartitionData() 
  {
181
182
    FUNCNAME("ParMetrisPartitioner::createPartitionData()");

183
184
    int mpiRank = mpiComm->Get_rank();
    int mpiSize = mpiComm->Get_size();
185
186
    int nLeaves = mesh->getNumberOfLeaves();
    int elPerRank = nLeaves / mpiSize;
187

188
    // === Create initial partitioning of the AMDiS mesh. ===
189

190
191
    elementInRank.clear();

192
    TraverseStack stack;
193
    ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
194
    while (elInfo) {
195
196
      Element *element = elInfo->getElement();

197
198
199
200
      if ((element->getIndex() >= mpiRank * elPerRank &&
	   element->getIndex() < (mpiRank + 1) * elPerRank) ||
	  (element->getIndex() >= mpiSize * elPerRank &&
	   mpiRank == mpiSize - 1))
201
	elementInRank[element->getIndex()] = true;
202
      else
203
	elementInRank[element->getIndex()] = false;
204
      
205
206
207
208
      elInfo = stack.traverseNext(elInfo);
    }
  }

209

210
  void ParMetisPartitioner::partition(std::map<int, double> &elemWeights,
211
212
213
				      PartitionMode mode,
				      float itr) 
  {
214
    FUNCNAME("ParMetisPartitioner::partition()");
215

216
    int mpiSize = mpiComm->Get_size();
217
218

    // === create parmetis mesh ===
219
    if (parMetisMesh) 
Thomas Witkowski's avatar
Thomas Witkowski committed
220
      delete parMetisMesh;
221

222
223
    TEST_EXIT_DBG(elementInRank.size() != 0)("Should not happen!\n");

224
    parMetisMesh = new ParMetisMesh(mesh, mpiComm, elementInRank, mapLocalGlobal);
225

226
    int nElements = parMetisMesh->getNumElements();
227
228

    // === create weight array ===
229
230
231
    std::vector<int> wgts(nElements);
    std::vector<float> floatWgts(nElements);
    unsigned int floatWgtsPos = 0;
232
233
    float maxWgt = 0.0;

234
    TraverseStack stack;
235
    ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
236
    while (elInfo) {
237
      int index = elInfo->getElement()->getIndex();
238

239
      if (elementInRank[index]) {
240
	// get weight 
241
	float wgt = static_cast<float>(elemWeights[index]);
242
243
244
	maxWgt = max(wgt, maxWgt);

	// write float weight
245
246
	TEST_EXIT_DBG(floatWgtsPos < floatWgts.size())("Should not happen!\n");
	floatWgts[floatWgtsPos++] = wgt;
247
248
249
250
      }
      elInfo = stack.traverseNext(elInfo);
    }

251
252
    TEST_EXIT_DBG(floatWgtsPos == floatWgts.size())("Should not happen!\n");

253
    float tmp;
254
    mpiComm->Allreduce(&maxWgt, &tmp, 1, MPI_FLOAT, MPI_MAX);
255
256
257
    maxWgt = tmp;

    // === create dual graph ===
258
    ParMetisGraph parMetisGraph(parMetisMesh, mpiComm);
259
260

    // === partitioning of dual graph ===
261
    int wgtflag = 2; // weights at vertices only!
262
    int numflag = 0; // c numbering style!
263
    int ncon = 1; // one weight at each vertex!
264
    int nparts = mpiSize; // number of partitions
265

266
    std::vector<float> tpwgts(mpiSize);
267
    float ubvec = 1.05;
268
    int options[4] = {0, 0, 15, 1}; // default options
269
    int edgecut = -1;
270
    std::vector<int> part(nElements);
271

272
273
274
275
276
277
278
279
    // set tpwgts
    for (int i = 0; i < mpiSize; i++)
      tpwgts[i] = 1.0 / nparts;
    
    float scale = 10000.0 / maxWgt;
    // scale wgts
    for (int i = 0; i < nElements; i++)
      wgts[i] = static_cast<int>(floatWgts[i] * scale);
280

281
282
    MPI_Comm tmpComm = MPI_Comm(*mpiComm);

283
    switch (mode) {
284
    case INITIAL:
285
      ParMETIS_V3_PartKway(parMetisMesh->getElementDist(),
286
287
			   parMetisGraph.getXAdj(),
			   parMetisGraph.getAdjncy(),
288
			   &(wgts[0]),
289
			   NULL,
290
			   &wgtflag,
291
292
293
			   &numflag,
			   &ncon,
			   &nparts,
294
			   &(tpwgts[0]),
295
296
297
			   &ubvec,
			   options,
			   &edgecut,
298
			   &(part[0]),
299
			   &tmpComm);
300
301
302
      break;
    case ADAPTIVE_REPART:
      {
303
	std::vector<int> vsize(nElements);
Thomas Witkowski's avatar
Thomas Witkowski committed
304
	for (int i = 0; i < nElements; i++)
305
306
	  vsize[i] = static_cast<int>(floatWgts[i]);

307
	ParMETIS_V3_AdaptiveRepart(parMetisMesh->getElementDist(),
308
309
				   parMetisGraph.getXAdj(),
				   parMetisGraph.getAdjncy(),
310
				   &(wgts[0]),
311
				   NULL,
312
				   &(vsize[0]),
313
314
315
316
				   &wgtflag,
				   &numflag,
				   &ncon,
				   &nparts,
317
				   &(tpwgts[0]),
318
319
320
321
				   &ubvec,
				   &itr,
				   options,
				   &edgecut,
322
				   &(part[0]),
323
				   &tmpComm);
324
325
326
      }
      break;
    case REFINE_PART:
327
      ParMETIS_V3_RefineKway(parMetisMesh->getElementDist(),
328
329
			     parMetisGraph.getXAdj(),
			     parMetisGraph.getAdjncy(),
330
			     &(wgts[0]),
331
332
333
334
335
			     NULL,
			     &wgtflag,
			     &numflag,
			     &ncon,
			     &nparts,
336
			     &(tpwgts[0]),
337
338
339
			     &ubvec,
			     options,
			     &edgecut,
340
			     &(part[0]),
341
			     &tmpComm);
342

343
344
345
346
347
348
      break;
    default: 
      ERROR_EXIT("unknown partitioning mode\n");
    }

    // === distribute new partition data ===
349
    distributePartitioning(&(part[0]));
350
351
  }

352

353
354
  void ParMetisPartitioner::fillCoarsePartitionVec(std::map<int, int> *partitionVec)
  {
355
356
357
    FUNCNAME("ParMetisPartitioner::fillCoarsePartitionVec()");

    TEST_EXIT_DBG(partitionVec)("no partition vector\n");
358
359
360
361

    partitionVec->clear();

    // update ParMETIS mesh to new partitioning
362
    if (!parMetisMesh)
363
      parMetisMesh = new ParMetisMesh(mesh, mpiComm, elementInRank, mapLocalGlobal);
364

365
366
    int mpiRank = mpiComm->Get_rank();
    int mpiSize = mpiComm->Get_size();
367
    std::vector<int> nPartitionElements(mpiSize);
368
    int *elmdist = parMetisMesh->getElementDist();
Thomas Witkowski's avatar
Thomas Witkowski committed
369

370
    for (int i = 0; i < mpiSize; i++)
371
      nPartitionElements[i] = elmdist[i + 1] - elmdist[i];
372
373

    // === count number of elements ===
374
375
376
    int nElements = 0;
    int localElements = parMetisMesh->getNumElements();
    mpiComm->Allreduce(&localElements, &nElements, 1, MPI_INT, MPI_SUM);
377

378
    std::vector<int> partitionElements(nElements);
379
380

    // distribute partition elements
381
382
    mpiComm->Allgatherv(parMetisMesh->getAMDiSIndices(),
			nPartitionElements[mpiRank], 
383
			MPI_INT, 
384
385
			&(partitionElements[0]), 
			&(nPartitionElements[0]), 
386
387
			elmdist, 
			MPI_INT);
388
389

    // fill partitionVec
Thomas Witkowski's avatar
Thomas Witkowski committed
390
391
    for (int i = 0; i < mpiSize; i++)
      for (int j = 0; j < nPartitionElements[i]; j++)
392
393
394
	(*partitionVec)[partitionElements[elmdist[i] + j]] = i;
  }

395

396
397
  void ParMetisPartitioner::distributePartitioning(int *part) 
  {
398
399
    FUNCNAME("ParMetisPartitioner::distributePartitioning()");

400
401
    int mpiSize = mpiComm->Get_size();
    int mpiRank = mpiComm->Get_rank();
402
    int nElements = parMetisMesh->getNumElements();
403

404
    // nPartitionElements[i] is the number of elements for the i-th partition
Thomas Witkowski's avatar
Thomas Witkowski committed
405
    int *nPartitionElements = new int[mpiSize];
406
    for (int i = 0; i < mpiSize; i++) 
407
      nPartitionElements[i] = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
408
    for (int i = 0; i < nElements; i++)
409
      nPartitionElements[part[i]]++;    
410
411

    // collect number of partition elements from all ranks for this rank
Thomas Witkowski's avatar
Thomas Witkowski committed
412
    int *nRankElements = new int[mpiSize];
413
    mpiComm->Alltoall(nPartitionElements, 1, MPI_INT, nRankElements, 1, MPI_INT);
414

415

416
    // sum up partition elements over all ranks
Thomas Witkowski's avatar
Thomas Witkowski committed
417
    int *sumPartitionElements = new int[mpiSize];
418
    mpiComm->Allreduce(nPartitionElements, sumPartitionElements, mpiSize,
419
		       MPI_INT, MPI_SUM);
420
421
    
    // prepare distribution (fill partitionElements with AMDiS indices)
Thomas Witkowski's avatar
Thomas Witkowski committed
422
    int *bufferOffset = new int[mpiSize];
423
    bufferOffset[0] = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
424
    for (int i = 1; i < mpiSize; i++)
425
      bufferOffset[i] = bufferOffset[i - 1] + nPartitionElements[i - 1];
426

Thomas Witkowski's avatar
Thomas Witkowski committed
427
428
    int *partitionElements = new int[nElements];
    int **partitionPtr = new int*[mpiSize];
429

430
    for (int i = 0; i < mpiSize; i++)
431
432
      partitionPtr[i] = partitionElements + bufferOffset[i];

433
    sendElements.clear();
434
    for (int i = 0; i < nElements; i++) {
435
      int partition = part[i];
436
      int amdisIndex = parMetisMesh->getAMDiSIndex(i);
437

438
439
440
      if (partition != mpiRank)
	sendElements[partition].push_back(amdisIndex);

441
442
443
444
445
      *(partitionPtr[partition]) = amdisIndex;
      ++(partitionPtr[partition]);
    }

    // all to all: partition elements to rank elements
Thomas Witkowski's avatar
Thomas Witkowski committed
446
447
    int *rankElements = new int[sumPartitionElements[mpiRank]];
    int *recvBufferOffset = new int[mpiSize];
448
    recvBufferOffset[0] = 0;
Thomas Witkowski's avatar
Thomas Witkowski committed
449
    for (int i = 1; i < mpiSize; i++)
450
      recvBufferOffset[i] = recvBufferOffset[i - 1] + nRankElements[i - 1];
451

452
    mpiComm->Alltoallv(partitionElements, 
453
		       nPartitionElements,
454
455
456
		       bufferOffset,
		       MPI_INT,
		       rankElements,
457
		       nRankElements,
458
459
		       recvBufferOffset,
		       MPI_INT);
460
    
461
462
463
464
    TEST_EXIT(elementInRank.size() != 0)("Should not happen!\n");
    for (std::map<int, bool>::iterator it = elementInRank.begin();
	 it != elementInRank.end(); ++it)
      elementInRank[it->first] = false;
465

466
467
    // Create map which stores for each element index on ther partitioning level
    // if the element is in the partition of this rank.
468
    recvElements.clear();
469
    for (int i = 0; i < mpiSize; i++) {
470
      int *rankStart = rankElements + recvBufferOffset[i];
471
      int *rankEnd = rankStart + nRankElements[i];
472
473
      for (int *rankPtr = rankStart; rankPtr < rankEnd; ++rankPtr) {
	elementInRank[*rankPtr] = true;
474
475
	if (i != mpiRank)
	  recvElements[i].push_back(*rankPtr);
476
477
478
      }
    }

Thomas Witkowski's avatar
Thomas Witkowski committed
479
    delete parMetisMesh;
480
    parMetisMesh = NULL;
481

Thomas Witkowski's avatar
Thomas Witkowski committed
482
483
484
485
486
487
488
    delete [] rankElements;
    delete [] nPartitionElements;
    delete [] nRankElements;
    delete [] sumPartitionElements;
    delete [] partitionElements;
    delete [] partitionPtr;
    delete [] bufferOffset;
Thomas Witkowski's avatar
huh  
Thomas Witkowski committed
489
    delete [] recvBufferOffset;
490
491
492
  }

}