Actual source code: hem.c

petsc-3.4.4 2014-03-13
  2: #include <petsc-private/matimpl.h>    /*I "petscmat.h" I*/
  3: #include <../src/mat/impls/aij/seq/aij.h>
  4: #include <../src/mat/impls/aij/mpi/mpiaij.h>

  6: /* linked list methods
  7:  *
  8:  *  PetscCDCreate
  9:  */
 12: PetscErrorCode PetscCDCreate(PetscInt a_size, PetscCoarsenData **a_out)
 13: {
 14:   PetscErrorCode   ierr;
 15:   PetscCoarsenData *ail;
 16:   PetscInt         ii;

 19:   /* alocate pool, partially */
 20:   PetscMalloc(sizeof(PetscCoarsenData), &ail);
 21:   *a_out               = ail;
 22:   ail->pool_list.next  = NULL;
 23:   ail->pool_list.array = NULL;
 24:   ail->chk_sz          = 0;
 25:   /* allocate array */
 26:   ail->size = a_size;
 27:   PetscMalloc(a_size*sizeof(PetscCDIntNd*), &ail->array);
 28:   for (ii=0; ii<a_size; ii++) ail->array[ii] = NULL;
 29:   ail->extra_nodes = NULL;
 30:   ail->mat         = NULL;
 31:   /* ail->removedIS = NULL; */
 32:   return(0);
 33: }

 35: /* NPDestroy
 36:  */
 39: PetscErrorCode PetscCDDestroy(PetscCoarsenData *ail)
 40: {
 42:   PetscCDArrNd   *n = &ail->pool_list;

 45:   n = n->next;
 46:   while (n) {
 47:     PetscCDArrNd *lstn = n;
 48:     n    = n->next;
 49:     PetscFree(lstn);
 50:   }
 51:   if (ail->pool_list.array) {
 52:     PetscFree(ail->pool_list.array);
 53:   }
 54:   /* if (ail->removedIS) { */
 55:   /*   ISDestroy(&ail->removedIS); */
 56:   /* } */
 57:   /* delete this (+array) */
 58:   PetscFree(ail->array);
 59:   /* delete this (+agg+pool array) */
 60:   PetscFree(ail);
 61:   return(0);
 62: }
 63: /* PetscCDSetChuckSize
 64:  */
 67: PetscErrorCode PetscCDSetChuckSize(PetscCoarsenData *ail, PetscInt a_sz)
 68: {
 70:   ail->chk_sz = a_sz;
 71:   return(0);
 72: }
 73: /*  PetscCDGetNewNode
 74:  */
 77: PetscErrorCode PetscCDGetNewNode(PetscCoarsenData *ail, PetscCDIntNd **a_out, PetscInt a_id)
 78: {

 82:   if (ail->extra_nodes) {
 83:     PetscCDIntNd *node = ail->extra_nodes;
 84:     ail->extra_nodes = node->next;
 85:     node->gid        = a_id;
 86:     node->next       = NULL;
 87:     *a_out           = node;
 88:   } else {
 89:     if (!ail->pool_list.array) {
 90:       if (!ail->chk_sz) ail->chk_sz = 10; /* use a chuck size of ail->size? */
 91:       PetscMalloc(ail->chk_sz*sizeof(PetscCDIntNd), &ail->pool_list.array);
 92:       ail->new_node       = ail->pool_list.array;
 93:       ail->new_left       = ail->chk_sz;
 94:       ail->new_node->next = NULL;
 95:     } else if (!ail->new_left) {
 96:       PetscCDArrNd *node;
 97:       PetscMalloc(ail->chk_sz*sizeof(PetscCDIntNd) + sizeof(PetscCDArrNd), &node);
 98:       node->array         = (PetscCDIntNd*)(node + 1);
 99:       node->next          = ail->pool_list.next;
100:       ail->pool_list.next = node;
101:       ail->new_left       = ail->chk_sz;
102:       ail->new_node       = node->array;
103:     }
104:     ail->new_node->gid  = a_id;
105:     ail->new_node->next = NULL;
106:     *a_out              = ail->new_node++; ail->new_left--;
107:   }
108:   return(0);
109: }

111: /* PetscLLNSetID
112:  */
115: PetscErrorCode PetscLLNSetID(PetscCDIntNd *a_this, PetscInt a_id)
116: {
118:   a_this->gid = a_id;
119:   return(0);
120: }
121: /* PetscLLNGetID
122:  */
125: PetscErrorCode PetscLLNGetID(const PetscCDIntNd *a_this, PetscInt *a_gid)
126: {
128:   *a_gid = a_this->gid;
129:   return(0);
130: }
131: /* PetscCDGetHeadPos
132:  */
135: PetscErrorCode PetscCDGetHeadPos(const PetscCoarsenData *ail, PetscInt a_idx, PetscCDPos *pos)
136: {
138:   if (a_idx>=ail->size) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"a_idx >= ail->size: a_idx=%d.",a_idx);
139:   *pos = ail->array[a_idx];
140:   return(0);
141: }
142: /* PetscCDGetNextPos
143:  */
146: PetscErrorCode PetscCDGetNextPos(const PetscCoarsenData *ail, PetscInt l_idx, PetscCDPos *pos)
147: {
149:   if (!(*pos)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"NULL input position.");
150:   *pos = (*pos)->next;
151:   return(0);
152: }

154: /* PetscCDAppendID
155:  */
158: PetscErrorCode PetscCDAppendID(PetscCoarsenData *ail, PetscInt a_idx, PetscInt a_id)
159: {
161:   PetscCDIntNd   *n,*n2;

164:   PetscCDGetNewNode(ail, &n, a_id);
165:   if (a_idx>=ail->size) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Index %d out of range.",a_idx);
166:   if (!(n2=ail->array[a_idx])) ail->array[a_idx] = n;
167:   else {
168:     do {
169:       if (!n2->next) {
170:         n2->next = n;
171:         if (n->next) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"n should not have a next");
172:         break;
173:       }
174:       n2 = n2->next;
175:     } while (n2);
176:     if (!n2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"n2 should be non-null");
177:   }
178:   return(0);
179: }
180: /* PetscCDAppendNode
181:  */
184: PetscErrorCode PetscCDAppendNode(PetscCoarsenData *ail, PetscInt a_idx,  PetscCDIntNd *a_n)
185: {
186:   PetscCDIntNd *n2;

189:   if (a_idx>=ail->size) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Index %d out of range.",a_idx);
190:   if (!(n2=ail->array[a_idx])) ail->array[a_idx] = a_n;
191:   else {
192:     do {
193:       if (!n2->next) {
194:         n2->next  = a_n;
195:         a_n->next = NULL;
196:         break;
197:       }
198:       n2 = n2->next;
199:     } while (n2);
200:     if (!n2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"n2 should be non-null");
201:   }
202:   return(0);
203: }

205: /* PetscCDRemoveNextNode: a_last->next, this exposes single linked list structure to API
206:  */
209: PetscErrorCode PetscCDRemoveNextNode(PetscCoarsenData *ail, PetscInt a_idx,  PetscCDIntNd *a_last)
210: {
211:   PetscCDIntNd *del;

214:   if (a_idx>=ail->size) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Index %d out of range.",a_idx);
215:   if (!a_last->next) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"a_last should have a next");
216:   del          = a_last->next;
217:   a_last->next = del->next;
218:   /* del->next = NULL; -- this still used in a iterator so keep it intact -- need to fix this with a double linked list */
219:   /* could reuse n2 but PetscCDAppendNode sometimes uses it */
220:   return(0);
221: }

223: /* PetscCDPrint
224:  */
227: PetscErrorCode PetscCDPrint(const PetscCoarsenData *ail, MPI_Comm comm)
228: {
230:   PetscCDIntNd   *n;
231:   PetscInt       ii,kk;
232:   PetscMPIInt    rank;

235:   MPI_Comm_rank(comm, &rank);
236:   for (ii=0; ii<ail->size; ii++) {
237:     kk = 0;
238:     n  = ail->array[ii];
239:     if (n) PetscPrintf(comm,"[%d]%s list %d:\n",rank,__FUNCT__,ii);
240:     while (n) {
241:       PetscPrintf(comm,"\t[%d] %d) id %d\n",rank,++kk,n->gid);
242:       n = n->next;
243:     }
244:   }
245:   return(0);
246: }
247: /* PetscCDAppendRemove
248:  */
251: PetscErrorCode PetscCDAppendRemove(PetscCoarsenData *ail, PetscInt a_destidx, PetscInt a_srcidx)
252: {
253:   PetscCDIntNd *n;

256:   if (a_srcidx>=ail->size) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Index %d out of range.",a_srcidx);
257:   if (a_destidx>=ail->size) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Index %d out of range.",a_destidx);
258:   if (a_destidx==a_srcidx) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"a_destidx==a_srcidx %d.",a_destidx);
259:   n = ail->array[a_destidx];
260:   if (!n) ail->array[a_destidx] = ail->array[a_srcidx];
261:   else {
262:     do {
263:       if (!n->next) {
264:         n->next = ail->array[a_srcidx];
265:         break;
266:       }
267:       n = n->next;
268:     } while (1);
269:   }
270:   ail->array[a_srcidx] = NULL;
271:   return(0);
272: }

274: /* PetscCDRemoveAll
275:  */
278: PetscErrorCode PetscCDRemoveAll(PetscCoarsenData *ail, PetscInt a_idx)
279: {
280:   PetscCDIntNd *rem,*n1;

283:   if (a_idx>=ail->size) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Index %d out of range.",a_idx);
284:   rem               = ail->array[a_idx];
285:   ail->array[a_idx] = NULL;
286:   if (!(n1=ail->extra_nodes)) ail->extra_nodes = rem;
287:   else {
288:     while (n1->next) n1 = n1->next;
289:     n1->next = rem;
290:   }
291:   return(0);
292: }

294: /* PetscCDSizeAt
295:  */
298: PetscErrorCode PetscCDSizeAt(const PetscCoarsenData *ail, PetscInt a_idx, PetscInt *a_sz)
299: {
300:   PetscCDIntNd *n1;
301:   PetscInt     sz = 0;

304:   if (a_idx>=ail->size) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Index %d out of range.",a_idx);
305:   n1 = ail->array[a_idx];
306:   while (n1) {
307:     n1 = n1->next;
308:     sz++;
309:   }
310:   *a_sz = sz;
311:   return(0);
312: }

314: /* PetscCDEmptyAt
315:  */
318: PetscErrorCode PetscCDEmptyAt(const PetscCoarsenData *ail, PetscInt a_idx, PetscBool *a_e)
319: {
321:   if (a_idx>=ail->size) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Index %d out of range.",a_idx);
322:   *a_e = (PetscBool)(ail->array[a_idx]==NULL);
323:   return(0);
324: }

326: /* PetscCDGetMIS
327:  */
330: PetscErrorCode PetscCDGetMIS(PetscCoarsenData *ail, IS *a_mis)
331: {
333:   PetscCDIntNd   *n;
334:   PetscInt       ii,kk;
335:   PetscInt       *permute;

338:   for (ii=kk=0; ii<ail->size; ii++) {
339:     n = ail->array[ii];
340:     if (n) kk++;
341:   }
342:   PetscMalloc(kk*sizeof(PetscInt), &permute);
343:   for (ii=kk=0; ii<ail->size; ii++) {
344:     n = ail->array[ii];
345:     if (n) permute[kk++] = ii;
346:   }
347:   ISCreateGeneral(PETSC_COMM_SELF, kk, permute, PETSC_OWN_POINTER, a_mis);
348:   return(0);
349: }
350: /* PetscCDGetMat
351:  */
354: PetscErrorCode PetscCDGetMat(const PetscCoarsenData *ail, Mat *a_mat)
355: {
357:   *a_mat = ail->mat;
358:   return(0);
359: }

361: /* PetscCDSetMat
362:  */
365: PetscErrorCode PetscCDSetMat(PetscCoarsenData *ail, Mat a_mat)
366: {
368:   ail->mat = a_mat;
369:   return(0);
370: }


373: /* PetscCDGetASMBlocks
374:  */
377: PetscErrorCode PetscCDGetASMBlocks(const PetscCoarsenData *ail, const PetscInt a_bs, PetscInt *a_sz, IS **a_local_is)
378: {
380:   PetscCDIntNd   *n;
381:   PetscInt       lsz,ii,kk,*idxs,jj;
382:   IS             *is_loc;

385:   for (ii=kk=0; ii<ail->size; ii++) {
386:     if (ail->array[ii]) kk++;
387:   }
388:   *a_sz = kk; /* out */

390:   PetscMalloc(kk*sizeof(IS*), &is_loc);
391:   *a_local_is = is_loc; /* out */

393:   for (ii=kk=0; ii<ail->size; ii++) {
394:     for (lsz=0, n=ail->array[ii]; n; lsz++, n=n->next) /* void */;
395:     if (lsz) {
396:       PetscMalloc(a_bs*lsz*sizeof(PetscInt), &idxs);
397:       for (lsz = 0, n=ail->array[ii]; n; n = n->next) {
398:         PetscInt gid;
399:         PetscLLNGetID(n, &gid);
400:         for (jj=0; jj<a_bs; lsz++,jj++) idxs[lsz] = a_bs*gid + jj;
401:       }
402:       ISCreateGeneral(PETSC_COMM_SELF, lsz, idxs, PETSC_OWN_POINTER, &is_loc[kk++]);
403:     }
404:   }
405:   if (*a_sz != kk) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"*a_sz %D != kk %D",*a_sz,kk);
406:   return(0);
407: }


410: /* PetscCDSetRemovedIS
411:  */
412: /* PetscErrorCode PetscCDSetRemovedIS(PetscCoarsenData *ail, MPI_Comm comm, const PetscInt a_sz, PetscInt a_ids[]) */
413: /* { */

416: /*   if (ail->removedIS) { */
417: /*     ISDestroy(&ail->removedIS); */
418: /*   } */
419: /*   ISCreateGeneral(comm, a_sz, a_ids, PETSC_COPY_VALUES, &ail->removedIS); */
420: /*   return(0); */
421: /* } */

423: /* PetscCDGetRemovedIS
424:  */
425: /* PetscErrorCode PetscCDGetRemovedIS(PetscCoarsenData *ail, IS *a_is) */
426: /* { */
427: /*   *a_is = ail->removedIS; */
428: /*   ail->removedIS = NULL; /\* hack to relinquish ownership *\/ */
429: /*   return(0); */
430: /* } */

432: /* ********************************************************************** */
433: /* edge for priority queue */
434: typedef struct edge_tag {
435:   PetscReal weight;
436:   PetscInt  lid0,gid1,cpid1;
437: } Edge;

439: int gamg_hem_compare(const void *a, const void *b)
440: {
441:   PetscReal va = ((Edge*)a)->weight, vb = ((Edge*)b)->weight;
442:   return (va < vb) ? 1 : (va == vb) ? 0 : -1; /* 0 for equal */
443: }

445: /* -------------------------------------------------------------------------- */
446: /*
447:    heavyEdgeMatchAgg - parallel heavy edge matching (HEM). MatAIJ specific!!!

449:    Input Parameter:
450:    . perm - permutation
451:    . a_Gmat - glabal matrix of graph (data not defined)
452:    . verbose -
453:    Output Parameter:
454:    . a_locals_llist - array of list of local nodes rooted at local node
455: */
458: PetscErrorCode heavyEdgeMatchAgg(IS perm,Mat a_Gmat,PetscInt verbose,PetscCoarsenData **a_locals_llist)
459: {
460:   PetscErrorCode   ierr;
461:   PetscBool        isMPI;
462:   MPI_Comm         comm;
463:   PetscInt         sub_it,kk,n,ix,*idx,*ii,iter,Iend,my0;
464:   PetscMPIInt      rank,size;
465:   const PetscInt   nloc = a_Gmat->rmap->n,n_iter=6; /* need to figure out how to stop this */
466:   PetscInt         *lid_cprowID,*lid_gid;
467:   PetscBool        *lid_matched;
468:   Mat_SeqAIJ       *matA, *matB=0;
469:   Mat_MPIAIJ       *mpimat     =0;
470:   PetscScalar      one         =1.;
471:   PetscCoarsenData *agg_llists = NULL,*deleted_list = NULL;
472:   Mat              cMat,tMat,P;
473:   MatScalar        *ap;
474:   PetscMPIInt      tag1,tag2;

477:   PetscObjectGetComm((PetscObject)a_Gmat,&comm);
478:   MPI_Comm_rank(comm, &rank);
479:   MPI_Comm_size(comm, &size);
480:   MatGetOwnershipRange(a_Gmat, &my0, &Iend);
481:   PetscCommGetNewTag(comm, &tag1);
482:   PetscCommGetNewTag(comm, &tag2);

484:   PetscMalloc(nloc*sizeof(PetscInt), &lid_gid); /* explicit array needed */
485:   PetscMalloc(nloc*sizeof(PetscInt), &lid_cprowID);
486:   PetscMalloc(nloc*sizeof(PetscBool), &lid_matched);

488:   PetscCDCreate(nloc, &agg_llists);
489:   /* PetscCDSetChuckSize(agg_llists, nloc+1); */
490:   *a_locals_llist = agg_llists;
491:   PetscCDCreate(size, &deleted_list);
492:   PetscCDSetChuckSize(deleted_list, 100);
493:   /* setup 'lid_gid' for scatters and add self to all lists */
494:   for (kk=0; kk<nloc; kk++) {
495:     lid_gid[kk] = kk + my0;
496:     PetscCDAppendID(agg_llists, kk, my0+kk);
497:   }

499:   /* make a copy of the graph, this gets destroyed in iterates */
500:   MatDuplicate(a_Gmat,MAT_COPY_VALUES,&cMat);
501:   PetscObjectTypeCompare((PetscObject)a_Gmat, MATMPIAIJ, &isMPI);
502:   iter = 0;
503:   while (iter++ < n_iter) {
504:     PetscScalar    *cpcol_gid,*cpcol_max_ew,*cpcol_max_pe,*lid_max_ew;
505:     PetscBool      *cpcol_matched;
506:     PetscMPIInt    *cpcol_pe,proc;
507:     Vec            locMaxEdge,locMaxPE,ghostMaxEdge,ghostMaxPE;
508:     PetscInt       nEdges,n_nz_row,jj;
509:     Edge           *Edges;
510:     PetscInt       gid;
511:     const PetscInt *perm_ix, n_sub_its = 120;

513:     /* get submatrices of cMat */
514:     if (isMPI) {
515:       mpimat = (Mat_MPIAIJ*)cMat->data;
516:       matA   = (Mat_SeqAIJ*)mpimat->A->data;
517:       matB   = (Mat_SeqAIJ*)mpimat->B->data;
518:       /* force compressed storage of B */
519:       matB->compressedrow.check = PETSC_TRUE;

521:       MatCheckCompressedRow(mpimat->B,&matB->compressedrow,matB->i,cMat->rmap->n,-1.0);
522:       if (!matB->compressedrow.use) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"matB must have compressed row usage");
523:     } else {
524:       matA = (Mat_SeqAIJ*)cMat->data;
525:     }

527:     /* set max edge on nodes */
528:     MatGetVecs(cMat, &locMaxEdge, 0);
529:     MatGetVecs(cMat, &locMaxPE, 0);

531:     /* get 'cpcol_pe' & 'cpcol_gid' & init. 'cpcol_matched' using 'mpimat->lvec' */
532:     if (mpimat) {
533:       Vec         vec;
534:       PetscScalar vval;

536:       MatGetVecs(cMat, &vec, 0);
537:       /* cpcol_pe */
538:       vval = (PetscScalar)(rank);
539:       for (kk=0,gid=my0; kk<nloc; kk++,gid++) {
540:         VecSetValues(vec, 1, &gid, &vval, INSERT_VALUES); /* set with GID */
541:       }
542:       VecAssemblyBegin(vec);
543:       VecAssemblyEnd(vec);
544:       VecScatterBegin(mpimat->Mvctx,vec,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);
545:       VecScatterEnd(mpimat->Mvctx,vec,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);
546:       VecGetArray(mpimat->lvec, &cpcol_gid); /* get proc ID in 'cpcol_gid' */
547:       VecGetLocalSize(mpimat->lvec, &n);
548:       PetscMalloc(n*sizeof(PetscInt), &cpcol_pe);
549:       for (kk=0; kk<n; kk++) cpcol_pe[kk] = (PetscMPIInt)PetscRealPart(cpcol_gid[kk]);
550:       VecRestoreArray(mpimat->lvec, &cpcol_gid);

552:       /* cpcol_gid */
553:       for (kk=0,gid=my0; kk<nloc; kk++,gid++) {
554:         vval = (PetscScalar)(gid);
555:         VecSetValues(vec, 1, &gid, &vval, INSERT_VALUES); /* set with GID */
556:       }
557:       VecAssemblyBegin(vec);
558:       VecAssemblyEnd(vec);
559:       VecScatterBegin(mpimat->Mvctx,vec,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);
560:       VecScatterEnd(mpimat->Mvctx,vec,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);
561:       VecDestroy(&vec);
562:       VecGetArray(mpimat->lvec, &cpcol_gid); /* get proc ID in 'cpcol_gid' */

564:       /* cpcol_matched */
565:       VecGetLocalSize(mpimat->lvec, &n);
566:       PetscMalloc(n*sizeof(PetscBool), &cpcol_matched);
567:       for (kk=0; kk<n; kk++) cpcol_matched[kk] = PETSC_FALSE;
568:     }

570:     /* need an inverse map - locals */
571:     for (kk=0; kk<nloc; kk++) lid_cprowID[kk] = -1;
572:     /* set index into compressed row 'lid_cprowID' */
573:     if (matB) {
574:       ii = matB->compressedrow.i;
575:       for (ix=0; ix<matB->compressedrow.nrows; ix++) {
576:         lid_cprowID[matB->compressedrow.rindex[ix]] = ix;
577:       }
578:     }

580:     /* get removed IS, use '' */
581:     /* if (iter==1) { */
582:     /*   PetscInt *lid_rem,idx; */
583:     /*   PetscMalloc(nloc*sizeof(PetscInt), &lid_rem); */
584:     /*   for (kk=idx=0;kk<nloc;kk++) { */
585:     /*     PetscInt nn,lid=kk; */
586:     /*     ii = matA->i; nn = ii[lid+1] - ii[lid]; */
587:     /*     if ((ix=lid_cprowID[lid]) != -1) { /\* if I have any ghost neighbors *\/ */
588:     /*       ii = matB->compressedrow.i; */
589:     /*       nn += ii[ix+1] - ii[ix]; */
590:     /*     } */
591:     /*     if (nn < 2) { */
592:     /*       lid_rem[idx++] = kk + my0; */
593:     /*     } */
594:     /*   } */
595:     /*   PetscCDSetRemovedIS(agg_llists, comm, idx, lid_rem); */
596:     /*   PetscFree(lid_rem); */
597:     /* } */

599:     /* compute 'locMaxEdge' & 'locMaxPE', and create list of edges, count edges' */
600:     for (nEdges=0,kk=0,gid=my0; kk<nloc; kk++,gid++) {
601:       PetscReal   max_e = 0., tt;
602:       PetscScalar vval;
603:       PetscInt    lid   = kk;
604:       PetscMPIInt max_pe=rank,pe;
605:       ii = matA->i; n = ii[lid+1] - ii[lid]; idx = matA->j + ii[lid];
606:       ap = matA->a + ii[lid];
607:       for (jj=0; jj<n; jj++) {
608:         PetscInt lidj = idx[jj];
609:         if (lidj != lid && PetscRealPart(ap[jj]) > max_e) max_e = PetscRealPart(ap[jj]);
610:         if (lidj > lid) nEdges++;
611:       }
612:       if ((ix=lid_cprowID[lid]) != -1) { /* if I have any ghost neighbors */
613:         ii  = matB->compressedrow.i; n = ii[ix+1] - ii[ix];
614:         ap  = matB->a + ii[ix];
615:         idx = matB->j + ii[ix];
616:         for (jj=0; jj<n; jj++) {
617:           if ((tt=PetscRealPart(ap[jj])) > max_e) max_e = tt;
618:           nEdges++;
619:           if ((pe=cpcol_pe[idx[jj]]) > max_pe) max_pe = pe;
620:         }
621:       }
622:       vval = max_e;
623:       VecSetValues(locMaxEdge, 1, &gid, &vval, INSERT_VALUES);

625:       vval = (PetscScalar)max_pe;
626:       VecSetValues(locMaxPE, 1, &gid, &vval, INSERT_VALUES);
627:     }
628:     VecAssemblyBegin(locMaxEdge);
629:     VecAssemblyEnd(locMaxEdge);
630:     VecAssemblyBegin(locMaxPE);
631:     VecAssemblyEnd(locMaxPE);

633:     /* get 'cpcol_max_ew' & 'cpcol_max_pe' */
634:     if (mpimat) {
635:       VecDuplicate(mpimat->lvec, &ghostMaxEdge);
636:       VecScatterBegin(mpimat->Mvctx,locMaxEdge,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);
637:       VecScatterEnd(mpimat->Mvctx,locMaxEdge,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);
638:       VecGetArray(ghostMaxEdge, &cpcol_max_ew);

640:       VecDuplicate(mpimat->lvec, &ghostMaxPE);
641:       VecScatterBegin(mpimat->Mvctx,locMaxPE,ghostMaxPE,INSERT_VALUES,SCATTER_FORWARD);
642:         VecScatterEnd(mpimat->Mvctx,locMaxPE,ghostMaxPE,INSERT_VALUES,SCATTER_FORWARD);
643:       VecGetArray(ghostMaxPE, &cpcol_max_pe);
644:     }

646:     /* setup sorted list of edges */
647:     PetscMalloc(nEdges*sizeof(Edge), &Edges);
648:     ISGetIndices(perm, &perm_ix);
649:     for (nEdges=n_nz_row=kk=0; kk<nloc; kk++) {
650:       PetscInt nn, lid = perm_ix[kk];
651:       ii = matA->i; nn = n = ii[lid+1] - ii[lid]; idx = matA->j + ii[lid];
652:       ap = matA->a + ii[lid];
653:       for (jj=0; jj<n; jj++) {
654:         PetscInt lidj = idx[jj];
655:         if (lidj > lid) {
656:           Edges[nEdges].lid0   = lid;
657:           Edges[nEdges].gid1   = lidj + my0;
658:           Edges[nEdges].cpid1  = -1;
659:           Edges[nEdges].weight = PetscRealPart(ap[jj]);
660:           nEdges++;
661:         }
662:       }
663:       if ((ix=lid_cprowID[lid]) != -1) { /* if I have any ghost neighbors */
664:         ii  = matB->compressedrow.i; n = ii[ix+1] - ii[ix];
665:         ap  = matB->a + ii[ix];
666:         idx = matB->j + ii[ix];
667:         nn += n;
668:         for (jj=0; jj<n; jj++) {
669:           Edges[nEdges].lid0   = lid;
670:           Edges[nEdges].gid1   = (PetscInt)PetscRealPart(cpcol_gid[idx[jj]]);
671:           Edges[nEdges].cpid1  = idx[jj];
672:           Edges[nEdges].weight = PetscRealPart(ap[jj]);
673:           nEdges++;
674:         }
675:       }
676:       if (nn > 1) n_nz_row++;
677:       else if (iter == 1) {
678:         /* should select this because it is technically in the MIS but lets not */
679:         PetscCDRemoveAll(agg_llists, lid);
680:       }
681:     }
682:     ISRestoreIndices(perm,&perm_ix);

684:     qsort(Edges, nEdges, sizeof(Edge), gamg_hem_compare);

686:     /* projection matrix */
687:     MatCreateAIJ(comm, nloc, nloc, PETSC_DETERMINE, PETSC_DETERMINE, 1, 0, 1, 0, &P);

689:     /* clear matched flags */
690:     for (kk=0; kk<nloc; kk++) lid_matched[kk] = PETSC_FALSE;
691:     /* process - communicate - process */
692:     for (sub_it=0; sub_it<n_sub_its; sub_it++) {
693:       PetscInt nactive_edges;

695:       VecGetArray(locMaxEdge, &lid_max_ew);
696:       for (kk=nactive_edges=0; kk<nEdges; kk++) {
697:         /* HEM */
698:         const Edge     *e   = &Edges[kk];
699:         const PetscInt lid0 =e->lid0,gid1=e->gid1,cpid1=e->cpid1,gid0=lid0+my0,lid1=gid1-my0;
700:         PetscBool      isOK = PETSC_TRUE;

702:         /* skip if either (local) vertex is done already */
703:         if (lid_matched[lid0] || (gid1>=my0 && gid1<Iend && lid_matched[gid1-my0])) continue;

705:         /* skip if ghost vertex is done */
706:         if (cpid1 != -1 && cpcol_matched[cpid1]) continue;

708:         nactive_edges++;
709:         /* skip if I have a bigger edge someplace (lid_max_ew gets updated) */
710:         if (PetscRealPart(lid_max_ew[lid0]) > e->weight + 1.e-12) continue;

712:         if (cpid1 == -1) {
713:           if (PetscRealPart(lid_max_ew[lid1]) > e->weight + 1.e-12) continue;
714:         } else {
715:           /* see if edge might get matched on other proc */
716:           PetscReal g_max_e = PetscRealPart(cpcol_max_ew[cpid1]);
717:           if (g_max_e > e->weight + 1.e-12) continue;
718:           else if (e->weight > g_max_e - 1.e-12 && (PetscMPIInt)PetscRealPart(cpcol_max_pe[cpid1]) > rank) {
719:             /* check for max_e == to this edge and larger processor that will deal with this */
720:             continue;
721:           }
722:         }

724:         /* check ghost for v0 */
725:         if (isOK) {
726:           PetscReal max_e,ew;
727:           if ((ix=lid_cprowID[lid0]) != -1) { /* if I have any ghost neighbors */
728:             ii  = matB->compressedrow.i; n = ii[ix+1] - ii[ix];
729:             ap  = matB->a + ii[ix];
730:             idx = matB->j + ii[ix];
731:             for (jj=0; jj<n && isOK; jj++) {
732:               PetscInt lidj = idx[jj];
733:               if (cpcol_matched[lidj]) continue;
734:               ew = PetscRealPart(ap[jj]); max_e = PetscRealPart(cpcol_max_ew[lidj]);
735:               /* check for max_e == to this edge and larger processor that will deal with this */
736:               if (ew > max_e - 1.e-12 && ew > PetscRealPart(lid_max_ew[lid0]) - 1.e-12 && (PetscMPIInt)PetscRealPart(cpcol_max_pe[lidj]) > rank) {
737:                 isOK = PETSC_FALSE;
738:               }
739:             }
740:           }

742:           /* for v1 */
743:           if (cpid1 == -1 && isOK) {
744:             if ((ix=lid_cprowID[lid1]) != -1) { /* if I have any ghost neighbors */
745:               ii  = matB->compressedrow.i; n = ii[ix+1] - ii[ix];
746:               ap  = matB->a + ii[ix];
747:               idx = matB->j + ii[ix];
748:               for (jj=0; jj<n && isOK; jj++) {
749:                 PetscInt lidj = idx[jj];
750:                 if (cpcol_matched[lidj]) continue;
751:                 ew = PetscRealPart(ap[jj]); max_e = PetscRealPart(cpcol_max_ew[lidj]);
752:                 /* check for max_e == to this edge and larger processor that will deal with this */
753:                 if (ew > max_e - 1.e-12 && ew > PetscRealPart(lid_max_ew[lid1]) - 1.e-12 && (PetscMPIInt)PetscRealPart(cpcol_max_pe[lidj]) > rank) {
754:                   isOK = PETSC_FALSE;
755:                 }
756:               }
757:             }
758:           }
759:         }

761:         /* do it */
762:         if (isOK) {
763:           if (cpid1 == -1) {
764:             lid_matched[lid1] = PETSC_TRUE;  /* keep track of what we've done this round */
765:             PetscCDAppendRemove(agg_llists, lid0, lid1);
766:           } else if (sub_it != n_sub_its-1) {
767:             /* add gid1 to list of ghost deleted by me -- I need their children */
768:             proc = cpcol_pe[cpid1];

770:             cpcol_matched[cpid1] = PETSC_TRUE; /* messing with VecGetArray array -- needed??? */

772:             PetscCDAppendID(deleted_list, proc, cpid1); /* cache to send messages */
773:             PetscCDAppendID(deleted_list, proc, lid0);
774:           } else continue;

776:           lid_matched[lid0] = PETSC_TRUE; /* keep track of what we've done this round */
777:           /* set projection */
778:           MatSetValues(P,1,&gid0,1,&gid0,&one,INSERT_VALUES);
779:           MatSetValues(P,1,&gid1,1,&gid0,&one,INSERT_VALUES);
780:         } /* matched */
781:       } /* edge loop */

783:       /* deal with deleted ghost on first pass */
784:       if (size>1 && sub_it != n_sub_its-1) {
785:         PetscCDPos pos;  PetscBool ise = PETSC_FALSE;
786:         PetscInt   nSend1, **sbuffs1,nSend2;
787: #define REQ_BF_SIZE 100
788:         MPI_Request *sreqs2[REQ_BF_SIZE],*rreqs2[REQ_BF_SIZE];
789:         MPI_Status status;

791:         /* send request */
792:         for (proc=0,nSend1=0; proc<size; proc++) {
793:           PetscCDEmptyAt(deleted_list,proc,&ise);
794:           if (!ise) nSend1++;
795:         }
796:         PetscMalloc(nSend1*sizeof(PetscInt*), &sbuffs1);
797:         /* PetscMalloc4(nSend1, PetscInt*, sbuffs1, nSend1, PetscInt*, rbuffs1, nSend1, MPI_Request*, sreqs1, nSend1, MPI_Request*, rreqs1); */
798:         /* PetscFree4(sbuffs1,rbuffs1,sreqs1,rreqs1); */
799:         for (proc=0,nSend1=0; proc<size; proc++) {
800:           /* count ghosts */
801:           PetscCDSizeAt(deleted_list,proc,&n);
802:           if (n>0) {
803: #define CHUNCK_SIZE 100
804:             PetscInt    *sbuff,*pt;
805:             MPI_Request *request;
806:             n   /= 2;
807:             PetscMalloc((2 + 2*n + n*CHUNCK_SIZE)*sizeof(PetscInt) + 2*sizeof(MPI_Request), &sbuff);
808:             /* PetscMalloc4(2+2*n,PetscInt,sbuffs1[nSend1],n*CHUNCK_SIZE,PetscInt,rbuffs1[nSend1],1,MPI_Request,rreqs2[nSend1],1,MPI_Request,sreqs2[nSend1]); */
809:             /* save requests */
810:             sbuffs1[nSend1] = sbuff;
811:             request         = (MPI_Request*)sbuff;
812:             sbuff           = pt = (PetscInt*)(request+1);
813:             *pt++           = n; *pt++ = rank;

815:             PetscCDGetHeadPos(deleted_list,proc,&pos);
816:             while (pos) {
817:               PetscInt lid0, cpid, gid;
818:               PetscLLNGetID(pos, &cpid);
819:               gid   = (PetscInt)PetscRealPart(cpcol_gid[cpid]);
820:               PetscCDGetNextPos(deleted_list,proc,&pos);
821:               PetscLLNGetID(pos, &lid0);
822:               PetscCDGetNextPos(deleted_list,proc,&pos);
823:               *pt++ = gid; *pt++ = lid0;
824:             }
825:             /* send request tag1 [n, proc, n*[gid1,lid0] ] */
826:             MPI_Isend(sbuff, 2*n+2, MPIU_INT, proc, tag1, comm, request);
827:             /* post recieve */
828:             request        = (MPI_Request*)pt;
829:             rreqs2[nSend1] = request; /* cache recv request */
830:             pt             = (PetscInt*)(request+1);
831:             MPI_Irecv(pt, n*CHUNCK_SIZE, MPIU_INT, proc, tag2, comm, request);
832:             /* clear list */
833:             PetscCDRemoveAll(deleted_list, proc);
834:             nSend1++;
835:           }
836:         }
837:         /* recieve requests, send response, clear lists */
838:         kk     = nactive_edges;
839:         MPI_Allreduce(&kk,&nactive_edges,1,MPIU_INT,MPI_SUM,comm); /* not correct syncronization and global */
840:         nSend2 = 0;
841:         while (1) {
842: #define BF_SZ 10000
843:           PetscMPIInt flag,count;
844:           PetscInt rbuff[BF_SZ],*pt,*pt2,*pt3,count2,*sbuff,count3;
845:           MPI_Request *request;
846:           MPI_Iprobe(MPI_ANY_SOURCE, tag1, comm, &flag, &status);
847:           if (!flag) break;
848:           MPI_Get_count(&status, MPIU_INT, &count);
849:           if (count > BF_SZ) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"buffer too small for recieve: %d",count);
850:           proc = status.MPI_SOURCE;
851:           /* recieve request tag1 [n, proc, n*[gid1,lid0] ] */
852:           MPI_Recv(rbuff, count, MPIU_INT, proc, tag1, comm, &status);
853:           /* count sends */
854:           pt = rbuff; count3 = count2 = 0;
855:           n  = *pt++; kk = *pt++;
856:           while (n--) {
857:             PetscInt gid1=*pt++, lid1=gid1-my0; kk=*pt++;
858:             if (lid_matched[lid1]) {
859:               PetscPrintf(PETSC_COMM_SELF,"\t *** [%d]%s %d) ERROR recieved deleted gid %d, deleted by (lid) %d from proc %d\n",rank,__FUNCT__,sub_it,gid1,kk);
860:               PetscSleep(1);
861:             }
862:             lid_matched[lid1] = PETSC_TRUE; /* keep track of what we've done this round */
863:             PetscCDSizeAt(agg_llists, lid1, &kk);
864:             count2           += kk + 2;
865:             count3++; /* number of verts requested (n) */
866:           }
867:           if (count2 > count3*CHUNCK_SIZE) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Irecv will be too small: %d",count2);
868:           /* send tag2 *[lid0, n, n*[gid] ] */
869:           PetscMalloc(count2*sizeof(PetscInt) + sizeof(MPI_Request), &sbuff);
870:           request          = (MPI_Request*)sbuff;
871:           sreqs2[nSend2++] = request; /* cache request */
872:           if (nSend2==REQ_BF_SIZE) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"buffer too small for requests: %d",nSend2);
873:           pt2 = sbuff = (PetscInt*)(request+1);
874:           pt  = rbuff;
875:           n   = *pt++; kk = *pt++;
876:           while (n--) {
877:             /* read [n, proc, n*[gid1,lid0] */
878:             PetscInt gid1=*pt++, lid1=gid1-my0, lid0=*pt++;
879:             /* write [lid0, n, n*[gid] ] */
880:             *pt2++ = lid0;
881:             pt3    = pt2++; /* save pointer for later */
882:             /* for (pos=PetscCDGetHeadPos(agg_llists,lid1) ; pos ; pos=PetscCDGetNextPos(agg_llists,lid1,pos)) { */
883:             PetscCDGetHeadPos(agg_llists,lid1,&pos);
884:             while (pos) {
885:               PetscInt gid;
886:               PetscLLNGetID(pos, &gid);
887:               PetscCDGetNextPos(agg_llists,lid1,&pos);
888:               *pt2++ = gid;
889:             }
890:             *pt3 = (pt2-pt3)-1;
891:             /* clear list */
892:             PetscCDRemoveAll(agg_llists, lid1);
893:           }
894:           /* send requested data tag2 *[lid0, n, n*[gid1] ] */
895:           MPI_Isend(sbuff, count2, MPIU_INT, proc, tag2, comm, request);
896:         }

898:         /* recieve tag2 *[lid0, n, n*[gid] ] */
899:         for (kk=0; kk<nSend1; kk++) {
900:           PetscMPIInt count;
901:           MPI_Request *request;
902:           PetscInt    *pt, *pt2;
903:           request = rreqs2[kk]; /* no need to free -- buffer is in 'sbuffs1' */
904:           MPI_Wait(request, &status);
905:           MPI_Get_count(&status, MPIU_INT, &count);
906:           pt      = pt2 = (PetscInt*)(request+1);
907:           while (pt-pt2 < count) {
908:             PetscInt lid0 = *pt++, n = *pt++;
909:             while (n--) {
910:               PetscInt gid1 = *pt++;
911:               PetscCDAppendID(agg_llists, lid0, gid1);
912:             }
913:           }
914:         }

916:         /* wait for tag1 isends */
917:         while (nSend1--) {
918:           MPI_Request *request;
919:           request = (MPI_Request*)sbuffs1[nSend1];
920:           MPI_Wait(request, &status);
921:           PetscFree(request);
922:         }
923:         PetscFree(sbuffs1);

925:         /* wait for tag2 isends */
926:         while (nSend2--) {
927:           MPI_Request *request = sreqs2[nSend2];
928:           MPI_Wait(request, &status);
929:           PetscFree(request);
930:         }

932:         VecRestoreArray(ghostMaxEdge, &cpcol_max_ew);
933:         VecRestoreArray(ghostMaxPE, &cpcol_max_pe);

935:         /* get 'cpcol_matched' - use locMaxPE, ghostMaxEdge, cpcol_max_ew */
936:         for (kk=0,gid=my0; kk<nloc; kk++,gid++) {
937:           PetscScalar vval = lid_matched[kk] ? 1.0 : 0.0;
938:           VecSetValues(locMaxPE, 1, &gid, &vval, INSERT_VALUES); /* set with GID */
939:         }
940:         VecAssemblyBegin(locMaxPE);
941:         VecAssemblyEnd(locMaxPE);
942:         VecScatterBegin(mpimat->Mvctx,locMaxPE,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);
943:           VecScatterEnd(mpimat->Mvctx,locMaxPE,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);
944:         VecGetArray(ghostMaxEdge, &cpcol_max_ew);
945:         VecGetLocalSize(mpimat->lvec, &n);
946:         for (kk=0; kk<n; kk++) {
947:           cpcol_matched[kk] = (PetscBool)(PetscRealPart(cpcol_max_ew[kk]) != 0.0);
948:         }

950:         VecRestoreArray(ghostMaxEdge, &cpcol_max_ew);
951:       } /* size > 1 */

953:       /* compute 'locMaxEdge' */
954:       VecRestoreArray(locMaxEdge, &lid_max_ew);
955:       for (kk=0,gid=my0; kk<nloc; kk++,gid++) {
956:         PetscReal max_e = 0.,tt;
957:         PetscScalar vval;
958:         PetscInt lid = kk;
959:         if (lid_matched[lid]) vval = 0.;
960:         else {
961:           ii = matA->i; n = ii[lid+1] - ii[lid]; idx = matA->j + ii[lid];
962:           ap = matA->a + ii[lid];
963:           for (jj=0; jj<n; jj++) {
964:             PetscInt lidj = idx[jj];
965:             if (lid_matched[lidj]) continue; /* this is new - can change local max */
966:             if (lidj != lid && PetscRealPart(ap[jj]) > max_e) max_e = PetscRealPart(ap[jj]);
967:           }
968:           if (lid_cprowID && (ix=lid_cprowID[lid]) != -1) { /* if I have any ghost neighbors */
969:             ii  = matB->compressedrow.i; n = ii[ix+1] - ii[ix];
970:             ap  = matB->a + ii[ix];
971:             idx = matB->j + ii[ix];
972:             for (jj=0; jj<n; jj++) {
973:               PetscInt lidj = idx[jj];
974:               if (cpcol_matched[lidj]) continue;
975:               if ((tt=PetscRealPart(ap[jj])) > max_e) max_e = tt;
976:             }
977:           }
978:         }
979:         vval = (PetscScalar)max_e;
980:         VecSetValues(locMaxEdge, 1, &gid, &vval, INSERT_VALUES); /* set with GID */
981:       }
982:       VecAssemblyBegin(locMaxEdge);
983:       VecAssemblyEnd(locMaxEdge);

985:       if (size>1 && sub_it != n_sub_its-1) {
986:         /* compute 'cpcol_max_ew' */
987:         VecScatterBegin(mpimat->Mvctx,locMaxEdge,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);
988:           VecScatterEnd(mpimat->Mvctx,locMaxEdge,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);
989:         VecGetArray(ghostMaxEdge, &cpcol_max_ew);
990:         VecGetArray(locMaxEdge, &lid_max_ew);

992:         /* compute 'cpcol_max_pe' */
993:         for (kk=0,gid=my0; kk<nloc; kk++,gid++) {
994:           PetscInt lid = kk;
995:           PetscReal ew,v1_max_e,v0_max_e=PetscRealPart(lid_max_ew[lid]);
996:           PetscScalar vval;
997:           PetscMPIInt max_pe=rank,pe;
998:           if (lid_matched[lid]) vval = (PetscScalar)rank;
999:           else if ((ix=lid_cprowID[lid]) != -1) { /* if I have any ghost neighbors */
1000:             ii  = matB->compressedrow.i; n = ii[ix+1] - ii[ix];
1001:             ap  = matB->a + ii[ix];
1002:             idx = matB->j + ii[ix];
1003:             for (jj=0; jj<n; jj++) {
1004:               PetscInt lidj = idx[jj];
1005:               if (cpcol_matched[lidj]) continue;
1006:               ew = PetscRealPart(ap[jj]); v1_max_e = PetscRealPart(cpcol_max_ew[lidj]);
1007:               /* get max pe that has a max_e == to this edge w */
1008:               if ((pe=cpcol_pe[idx[jj]]) > max_pe && ew > v1_max_e - 1.e-12 && ew > v0_max_e - 1.e-12) max_pe = pe;
1009:             }
1010:             vval = (PetscScalar)max_pe;
1011:           }
1012:           VecSetValues(locMaxPE, 1, &gid, &vval, INSERT_VALUES);
1013:         }
1014:         VecAssemblyBegin(locMaxPE);
1015:         VecAssemblyEnd(locMaxPE);

1017:         VecScatterBegin(mpimat->Mvctx,locMaxPE,ghostMaxPE,INSERT_VALUES,SCATTER_FORWARD);
1018:           VecScatterEnd(mpimat->Mvctx,locMaxPE,ghostMaxPE,INSERT_VALUES,SCATTER_FORWARD);
1019:         VecGetArray(ghostMaxPE, &cpcol_max_pe);
1020:         VecRestoreArray(locMaxEdge, &lid_max_ew);
1021:       } /* deal with deleted ghost */
1022:       if (verbose>2) PetscPrintf(comm,"\t[%d]%s %d.%d: %d active edges.\n",rank,__FUNCT__,iter,sub_it,nactive_edges);
1023:       if (!nactive_edges) break;
1024:     } /* sub_it loop */

1026:     /* clean up iteration */
1027:     PetscFree(Edges);
1028:     if (mpimat) {
1029:       VecRestoreArray(ghostMaxEdge, &cpcol_max_ew);
1030:       VecDestroy(&ghostMaxEdge);
1031:       VecRestoreArray(ghostMaxPE, &cpcol_max_pe);
1032:       VecDestroy(&ghostMaxPE);
1033:       PetscFree(cpcol_pe);
1034:       PetscFree(cpcol_matched);
1035:     }

1037:     VecDestroy(&locMaxEdge);
1038:     VecDestroy(&locMaxPE);

1040:     if (mpimat) {
1041:       VecRestoreArray(mpimat->lvec, &cpcol_gid);
1042:     }

1044:     /* create next G if needed */
1045:     if (iter == n_iter) { /* hard wired test - need to look at full surrounded nodes or something */
1046:       MatDestroy(&P);
1047:       MatDestroy(&cMat);
1048:       break;
1049:     } else {
1050:       Vec diag;
1051:       /* add identity for unmatched vertices so they stay alive */
1052:       for (kk=0,gid=my0; kk<nloc; kk++,gid++) {
1053:         if (!lid_matched[kk]) {
1054:           gid  = kk+my0;
1055:           MatGetRow(cMat,gid,&n,0,0);
1056:           if (n>1) {
1057:             MatSetValues(P,1,&gid,1,&gid,&one,INSERT_VALUES);
1058:           }
1059:           MatRestoreRow(cMat,gid,&n,0,0);
1060:         }
1061:       }
1062:       MatAssemblyBegin(P,MAT_FINAL_ASSEMBLY);
1063:       MatAssemblyEnd(P,MAT_FINAL_ASSEMBLY);

1065:       /* project to make new graph with colapsed edges */
1066:       MatPtAP(cMat,P,MAT_INITIAL_MATRIX,1.0,&tMat);
1067:       MatDestroy(&P);
1068:       MatDestroy(&cMat);
1069:       cMat = tMat;
1070:       MatGetVecs(cMat, &diag, 0);
1071:       MatGetDiagonal(cMat, diag); /* effectively PCJACOBI */
1072:       VecReciprocal(diag);
1073:       VecSqrtAbs(diag);
1074:       MatDiagonalScale(cMat, diag, diag);
1075:       VecDestroy(&diag);
1076:     }
1077:   } /* coarsen iterator */

1079:   /* make fake matrix */
1080:   if (size>1) {
1081:     Mat mat;
1082:     PetscCDPos pos;
1083:     PetscInt gid, NN, MM, jj = 0, mxsz = 0;

1085:     for (kk=0; kk<nloc; kk++) {
1086:       PetscCDSizeAt(agg_llists, kk, &jj);
1087:       if (jj > mxsz) mxsz = jj;
1088:     }
1089:     MatGetSize(a_Gmat, &MM, &NN);
1090:     if (mxsz > MM-nloc) mxsz = MM-nloc;

1092:     MatCreateAIJ(comm, nloc, nloc,PETSC_DETERMINE, PETSC_DETERMINE,0, 0, mxsz, 0, &mat);

1094:     /* */
1095:     for (kk=0,gid=my0; kk<nloc; kk++,gid++) {
1096:       /* for (pos=PetscCDGetHeadPos(agg_llists,kk) ; pos ; pos=PetscCDGetNextPos(agg_llists,kk,pos)) { */
1097:       PetscCDGetHeadPos(agg_llists,kk,&pos);
1098:       while (pos) {
1099:         PetscInt gid1;
1100:         PetscLLNGetID(pos, &gid1);
1101:         PetscCDGetNextPos(agg_llists,kk,&pos);

1103:         if (gid1 < my0 || gid1 >= my0+nloc) {
1104:           MatSetValues(mat,1,&gid,1,&gid1,&one,ADD_VALUES);
1105:         }
1106:       }
1107:     }
1108:     MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);
1109:     MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);

1111:     PetscCDSetMat(agg_llists, mat);
1112:   }

1114:   PetscFree(lid_cprowID);
1115:   PetscFree(lid_gid);
1116:   PetscFree(lid_matched);
1117:   PetscCDDestroy(deleted_list);
1118:   return(0);
1119: }

1121: typedef struct {
1122:   int dummy;
1123: } MatCoarsen_HEM;
1124: /*
1125:    HEM coarsen, simple greedy.
1126: */
1129: static PetscErrorCode MatCoarsenApply_HEM(MatCoarsen coarse)
1130: {
1131:   /* MatCoarsen_HEM *HEM = (MatCoarsen_HEM*)coarse->subctx; */
1133:   Mat            mat = coarse->graph;

1137:   if (!coarse->perm) {
1138:     IS       perm;
1139:     PetscInt n,m;
1140: 
1141:     MatGetLocalSize(mat, &m, &n);
1142:     ISCreateStride(PetscObjectComm((PetscObject)mat), m, 0, 1, &perm);
1143:     heavyEdgeMatchAgg(perm, mat, coarse->verbose, &coarse->agg_lists);
1144:     ISDestroy(&perm);
1145:   } else {
1146:     heavyEdgeMatchAgg(coarse->perm, mat, coarse->verbose, &coarse->agg_lists);
1147:   }
1148:   return(0);
1149: }

1153: PetscErrorCode MatCoarsenView_HEM(MatCoarsen coarse,PetscViewer viewer)
1154: {
1155:   /* MatCoarsen_HEM *HEM = (MatCoarsen_HEM*)coarse->subctx; */
1157:   PetscMPIInt    rank;
1158:   PetscBool      iascii;

1162:   MPI_Comm_rank(PetscObjectComm((PetscObject)coarse),&rank);
1163:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
1164:   if (iascii) {
1165:     PetscViewerASCIISynchronizedPrintf(viewer,"  [%d] HEM aggregator\n",rank);
1166:     PetscViewerFlush(viewer);
1167:     PetscViewerASCIISynchronizedAllow(viewer,PETSC_FALSE);
1168:   }
1169:   return(0);
1170: }

1174: PetscErrorCode MatCoarsenDestroy_HEM(MatCoarsen coarse)
1175: {
1176:   MatCoarsen_HEM *HEM = (MatCoarsen_HEM*)coarse->subctx;

1181:   PetscFree(HEM);
1182:   return(0);
1183: }

1185: /*MC
1186:    MATCOARSENHEM - Creates a coarsen context via the external package HEM.

1188:    Collective on MPI_Comm

1190:    Input Parameter:
1191: .  coarse - the coarsen context

1193:    Options Database Keys:
1194: +  -mat_coarsen_HEM_xxx -

1196:    Level: beginner

1198: .keywords: Coarsen, create, context

1200: .seealso: MatCoarsenSetType(), MatCoarsenType

1202: M*/

1206: PETSC_EXTERN PetscErrorCode MatCoarsenCreate_HEM(MatCoarsen coarse)
1207: {
1209:   MatCoarsen_HEM *HEM;

1212:   PetscNewLog(coarse, MatCoarsen_HEM, &HEM);
1213:   coarse->subctx       = (void*)HEM;
1214:   coarse->ops->apply   = MatCoarsenApply_HEM;
1215:   coarse->ops->view    = MatCoarsenView_HEM;
1216:   coarse->ops->destroy = MatCoarsenDestroy_HEM;
1217:   /* coarse->ops->setfromoptions = MatCoarsenSetFromOptions_HEM; */
1218:   return(0);
1219: }