Actual source code: bddcgraph.c
petsc-3.11.4 2019-09-28
1: #include <petsc/private/petscimpl.h>
2: #include <../src/ksp/pc/impls/bddc/bddcprivate.h>
3: #include <../src/ksp/pc/impls/bddc/bddcstructs.h>
5: PetscErrorCode PCBDDCGraphGetDirichletDofsB(PCBDDCGraph graph, IS* dirdofs)
6: {
10: if (graph->dirdofsB) {
11: PetscObjectReference((PetscObject)graph->dirdofsB);
12: } else if (graph->has_dirichlet) {
13: PetscInt i,size;
14: PetscInt *dirdofs_idxs;
16: size = 0;
17: for (i=0;i<graph->nvtxs;i++) {
18: if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++;
19: }
21: PetscMalloc1(size,&dirdofs_idxs);
22: size = 0;
23: for (i=0;i<graph->nvtxs;i++) {
24: if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i;
25: }
26: ISCreateGeneral(PETSC_COMM_SELF,size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofsB);
27: PetscObjectReference((PetscObject)graph->dirdofsB);
28: }
29: *dirdofs = graph->dirdofsB;
30: return(0);
31: }
33: PetscErrorCode PCBDDCGraphGetDirichletDofs(PCBDDCGraph graph, IS* dirdofs)
34: {
38: if (graph->dirdofs) {
39: PetscObjectReference((PetscObject)graph->dirdofs);
40: } else if (graph->has_dirichlet) {
41: PetscInt i,size;
42: PetscInt *dirdofs_idxs;
44: size = 0;
45: for (i=0;i<graph->nvtxs;i++) {
46: if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++;
47: }
49: PetscMalloc1(size,&dirdofs_idxs);
50: size = 0;
51: for (i=0;i<graph->nvtxs;i++) {
52: if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i;
53: }
54: ISCreateGeneral(PetscObjectComm((PetscObject)graph->l2gmap),size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofs);
55: PetscObjectReference((PetscObject)graph->dirdofs);
56: }
57: *dirdofs = graph->dirdofs;
58: return(0);
59: }
61: PetscErrorCode PCBDDCGraphASCIIView(PCBDDCGraph graph, PetscInt verbosity_level, PetscViewer viewer)
62: {
63: PetscInt i,j,tabs;
64: PetscInt* queue_in_global_numbering;
68: PetscViewerASCIIPushSynchronized(viewer);
69: PetscViewerASCIIGetTab(viewer,&tabs);
70: PetscViewerASCIIPrintf(viewer,"--------------------------------------------------\n");
71: PetscViewerFlush(viewer);
72: PetscViewerASCIISynchronizedPrintf(viewer,"Local BDDC graph for subdomain %04d\n",PetscGlobalRank);
73: PetscViewerASCIISynchronizedPrintf(viewer,"Number of vertices %d\n",graph->nvtxs);
74: PetscViewerASCIISynchronizedPrintf(viewer,"Custom minimal size %d\n",graph->custom_minimal_size);
75: if (graph->maxcount != PETSC_MAX_INT) {
76: PetscViewerASCIISynchronizedPrintf(viewer,"Max count %d\n",graph->maxcount);
77: }
78: PetscViewerASCIISynchronizedPrintf(viewer,"Topological two dim? %d (set %d)\n",graph->twodim,graph->twodimset);
79: if (verbosity_level > 2) {
80: for (i=0;i<graph->nvtxs;i++) {
81: PetscViewerASCIISynchronizedPrintf(viewer,"%d:\n",i);
82: PetscViewerASCIISynchronizedPrintf(viewer," which_dof: %d\n",graph->which_dof[i]);
83: PetscViewerASCIISynchronizedPrintf(viewer," special_dof: %d\n",graph->special_dof[i]);
84: PetscViewerASCIISynchronizedPrintf(viewer," neighbours: %d\n",graph->count[i]);
85: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
86: if (graph->count[i]) {
87: PetscViewerASCIISynchronizedPrintf(viewer," set of neighbours:");
88: for (j=0;j<graph->count[i];j++) {
89: PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[i][j]);
90: }
91: PetscViewerASCIISynchronizedPrintf(viewer,"\n");
92: }
93: PetscViewerASCIISetTab(viewer,tabs);
94: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
95: if (graph->mirrors) {
96: PetscViewerASCIISynchronizedPrintf(viewer," mirrors: %d\n",graph->mirrors[i]);
97: if (graph->mirrors[i]) {
98: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
99: PetscViewerASCIISynchronizedPrintf(viewer," set of mirrors:");
100: for (j=0;j<graph->mirrors[i];j++) {
101: PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->mirrors_set[i][j]);
102: }
103: PetscViewerASCIISynchronizedPrintf(viewer,"\n");
104: PetscViewerASCIISetTab(viewer,tabs);
105: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
106: }
107: }
108: if (verbosity_level > 3) {
109: if (graph->xadj) {
110: PetscViewerASCIISynchronizedPrintf(viewer," local adj list:");
111: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
112: for (j=graph->xadj[i];j<graph->xadj[i+1];j++) {
113: PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->adjncy[j]);
114: }
115: PetscViewerASCIISynchronizedPrintf(viewer,"\n");
116: PetscViewerASCIISetTab(viewer,tabs);
117: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
118: } else {
119: PetscViewerASCIISynchronizedPrintf(viewer," no adj info\n");
120: }
121: }
122: if (graph->n_local_subs) {
123: PetscViewerASCIISynchronizedPrintf(viewer," local sub id: %d\n",graph->local_subs[i]);
124: }
125: PetscViewerASCIISynchronizedPrintf(viewer," interface subset id: %d\n",graph->subset[i]);
126: if (graph->subset[i] && graph->subset_ncc) {
127: PetscViewerASCIISynchronizedPrintf(viewer," ncc for subset: %d\n",graph->subset_ncc[graph->subset[i]-1]);
128: }
129: }
130: }
131: PetscViewerASCIISynchronizedPrintf(viewer,"Total number of connected components %d\n",graph->ncc);
132: PetscMalloc1(graph->cptr[graph->ncc],&queue_in_global_numbering);
133: ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_in_global_numbering);
134: for (i=0;i<graph->ncc;i++) {
135: PetscInt node_num=graph->queue[graph->cptr[i]];
136: PetscBool printcc = PETSC_FALSE;
137: PetscViewerASCIISynchronizedPrintf(viewer," cc %d (size %d, fid %d, neighs:",i,graph->cptr[i+1]-graph->cptr[i],graph->which_dof[node_num]);
138: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
139: for (j=0;j<graph->count[node_num];j++) {
140: PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[node_num][j]);
141: }
142: if (verbosity_level > 1) {
143: PetscViewerASCIISynchronizedPrintf(viewer,"):");
144: if (verbosity_level > 2 || graph->twodim || graph->count[node_num] > 1 || (graph->count[node_num] == 1 && graph->special_dof[node_num] == PCBDDCGRAPH_NEUMANN_MARK)) {
145: printcc = PETSC_TRUE;
146: }
147: if (printcc) {
148: for (j=graph->cptr[i];j<graph->cptr[i+1];j++) {
149: PetscViewerASCIISynchronizedPrintf(viewer," %d (%d)",graph->queue[j],queue_in_global_numbering[j]);
150: }
151: }
152: } else {
153: PetscViewerASCIISynchronizedPrintf(viewer,")");
154: }
155: PetscViewerASCIISynchronizedPrintf(viewer,"\n");
156: PetscViewerASCIISetTab(viewer,tabs);
157: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
158: }
159: PetscFree(queue_in_global_numbering);
160: PetscViewerFlush(viewer);
161: return(0);
162: }
164: PetscErrorCode PCBDDCGraphRestoreCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS)
165: {
166: PetscInt i;
170: if (n_faces) {
171: if (FacesIS) {
172: for (i=0;i<*n_faces;i++) {
173: ISDestroy(&((*FacesIS)[i]));
174: }
175: PetscFree(*FacesIS);
176: }
177: *n_faces = 0;
178: }
179: if (n_edges) {
180: if (EdgesIS) {
181: for (i=0;i<*n_edges;i++) {
182: ISDestroy(&((*EdgesIS)[i]));
183: }
184: PetscFree(*EdgesIS);
185: }
186: *n_edges = 0;
187: }
188: if (VerticesIS) {
189: ISDestroy(VerticesIS);
190: }
191: return(0);
192: }
194: PetscErrorCode PCBDDCGraphGetCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS)
195: {
196: IS *ISForFaces,*ISForEdges,ISForVertices;
197: PetscInt i,nfc,nec,nvc,*idx,*mark;
201: PetscCalloc1(graph->ncc,&mark);
202: /* loop on ccs to evalute number of faces, edges and vertices */
203: nfc = 0;
204: nec = 0;
205: nvc = 0;
206: for (i=0;i<graph->ncc;i++) {
207: PetscInt repdof = graph->queue[graph->cptr[i]];
208: if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size && graph->count[repdof] < graph->maxcount) {
209: if (!graph->twodim && graph->count[repdof] == 1 && graph->special_dof[repdof] != PCBDDCGRAPH_NEUMANN_MARK) {
210: nfc++;
211: mark[i] = 2;
212: } else {
213: nec++;
214: mark[i] = 1;
215: }
216: } else {
217: nvc += graph->cptr[i+1]-graph->cptr[i];
218: }
219: }
221: /* allocate IS arrays for faces, edges. Vertices need a single index set. */
222: if (FacesIS) {
223: PetscMalloc1(nfc,&ISForFaces);
224: }
225: if (EdgesIS) {
226: PetscMalloc1(nec,&ISForEdges);
227: }
228: if (VerticesIS) {
229: PetscMalloc1(nvc,&idx);
230: }
232: /* loop on ccs to compute index sets for faces and edges */
233: if (!graph->queue_sorted) {
234: PetscInt *queue_global;
236: PetscMalloc1(graph->cptr[graph->ncc],&queue_global);
237: ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);
238: for (i=0;i<graph->ncc;i++) {
239: PetscSortIntWithArray(graph->cptr[i+1]-graph->cptr[i],&queue_global[graph->cptr[i]],&graph->queue[graph->cptr[i]]);
240: }
241: PetscFree(queue_global);
242: graph->queue_sorted = PETSC_TRUE;
243: }
244: nfc = 0;
245: nec = 0;
246: for (i=0;i<graph->ncc;i++) {
247: if (mark[i] == 2) {
248: if (FacesIS) {
249: ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_USE_POINTER,&ISForFaces[nfc]);
250: }
251: nfc++;
252: } else if (mark[i] == 1) {
253: if (EdgesIS) {
254: ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_USE_POINTER,&ISForEdges[nec]);
255: }
256: nec++;
257: }
258: }
260: /* index set for vertices */
261: if (VerticesIS) {
262: nvc = 0;
263: for (i=0;i<graph->ncc;i++) {
264: if (!mark[i]) {
265: PetscInt j;
267: for (j=graph->cptr[i];j<graph->cptr[i+1];j++) {
268: idx[nvc]=graph->queue[j];
269: nvc++;
270: }
271: }
272: }
273: /* sort vertex set (by local ordering) */
274: PetscSortInt(nvc,idx);
275: ISCreateGeneral(PETSC_COMM_SELF,nvc,idx,PETSC_OWN_POINTER,&ISForVertices);
276: }
277: PetscFree(mark);
279: /* get back info */
280: if (n_faces) *n_faces = nfc;
281: if (FacesIS) *FacesIS = ISForFaces;
282: if (n_edges) *n_edges = nec;
283: if (EdgesIS) *EdgesIS = ISForEdges;
284: if (VerticesIS) *VerticesIS = ISForVertices;
285: return(0);
286: }
288: PetscErrorCode PCBDDCGraphComputeConnectedComponents(PCBDDCGraph graph)
289: {
290: PetscBool adapt_interface_reduced;
291: MPI_Comm interface_comm;
292: PetscMPIInt size;
293: PetscInt i;
294: PetscBT cornerp;
298: /* compute connected components locally */
299: PetscObjectGetComm((PetscObject)(graph->l2gmap),&interface_comm);
300: PCBDDCGraphComputeConnectedComponentsLocal(graph);
302: cornerp = NULL;
303: if (graph->active_coords) { /* face based corner selection */
304: PetscBT excluded;
305: PetscReal *wdist;
306: PetscInt n_neigh,*neigh,*n_shared,**shared;
307: PetscInt maxc, ns;
309: PetscBTCreate(graph->nvtxs,&cornerp);
310: ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
311: for (ns = 1, maxc = 0; ns < n_neigh; ns++) maxc = PetscMax(maxc,n_shared[ns]);
312: PetscMalloc1(maxc*graph->cdim,&wdist);
313: PetscBTCreate(maxc,&excluded);
315: for (ns = 1; ns < n_neigh; ns++) { /* first proc is self */
316: PetscReal *anchor,mdist;
317: PetscInt fst,j,k,d,cdim = graph->cdim,n = n_shared[ns];
318: PetscInt point1,point2,point3;
320: /* import coordinates on shared interface */
321: PetscBTMemzero(n,excluded);
322: for (j=0,fst=-1,k=0;j<n;j++) {
323: PetscBool skip = PETSC_FALSE;
324: for (d=0;d<cdim;d++) {
325: PetscReal c = graph->coords[shared[ns][j]*cdim+d];
326: skip = (PetscBool)(skip || c == PETSC_MAX_REAL);
327: wdist[k++] = c;
328: }
329: if (skip) {
330: PetscBTSet(excluded,j);
331: } else if (fst == -1) fst = j;
332: }
333: if (fst == -1) continue;
335: /* the dofs are sorted by global numbering, so each rank start from the same id and will detect the same corners from the given set */
336: anchor = wdist + fst*cdim;
338: /* find the farthest point from the starting one */
339: mdist = -1.0;
340: point1 = fst;
341: for (j=fst;j<n;j++) {
342: PetscReal dist = 0.0;
344: if (PetscUnlikely(PetscBTLookup(excluded,j))) continue;
345: for (d=0;d<cdim;d++) dist += (wdist[j*cdim+d]-anchor[d])*(wdist[j*cdim+d]-anchor[d]);
346: if (dist > mdist) { mdist = dist; point1 = j; }
347: }
349: /* find the farthest point from point1 */
350: anchor = wdist + point1*cdim;
351: mdist = -1.0;
352: point2 = point1;
353: for (j=fst;j<n;j++) {
354: PetscReal dist = 0.0;
356: if (PetscUnlikely(PetscBTLookup(excluded,j))) continue;
357: for (d=0;d<cdim;d++) dist += (wdist[j*cdim+d]-anchor[d])*(wdist[j*cdim+d]-anchor[d]);
358: if (dist > mdist) { mdist = dist; point2 = j; }
359: }
362: /* find the third point maximizing the triangle area */
363: point3 = point2;
364: if (cdim > 2) {
365: PetscReal a = 0.0;
367: for (d=0;d<cdim;d++) a += (wdist[point1*cdim+d]-wdist[point2*cdim+d])*(wdist[point1*cdim+d]-wdist[point2*cdim+d]);
368: a = PetscSqrtReal(a);
369: mdist = -1.0;
370: for (j=fst;j<n;j++) {
371: PetscReal area,b = 0.0, c = 0.0,s;
373: if (PetscUnlikely(PetscBTLookup(excluded,j))) continue;
374: for (d=0;d<cdim;d++) {
375: b += (wdist[point1*cdim+d]-wdist[j*cdim+d])*(wdist[point1*cdim+d]-wdist[j*cdim+d]);
376: c += (wdist[point2*cdim+d]-wdist[j*cdim+d])*(wdist[point2*cdim+d]-wdist[j*cdim+d]);
377: }
378: b = PetscSqrtReal(b);
379: c = PetscSqrtReal(c);
380: s = 0.5*(a+b+c);
382: /* Heron's formula, area squared */
383: area = s*(s-a)*(s-b)*(s-c);
384: if (area > mdist) { mdist = area; point3 = j; }
385: }
386: }
388: PetscBTSet(cornerp,shared[ns][point1]);
389: PetscBTSet(cornerp,shared[ns][point2]);
390: PetscBTSet(cornerp,shared[ns][point3]);
392: /* all dofs having the same coordinates will be primal */
393: for (j=fst;j<n;j++) {
394: PetscBool same[3] = {PETSC_TRUE,PETSC_TRUE,PETSC_TRUE};
396: if (PetscUnlikely(PetscBTLookup(excluded,j))) continue;
397: for (d=0;d<cdim;d++) {
398: same[0] = (PetscBool)(same[0] && (PetscAbsReal(wdist[j*cdim + d]-wdist[point1*cdim+d]) < PETSC_SMALL));
399: same[1] = (PetscBool)(same[1] && (PetscAbsReal(wdist[j*cdim + d]-wdist[point2*cdim+d]) < PETSC_SMALL));
400: same[2] = (PetscBool)(same[2] && (PetscAbsReal(wdist[j*cdim + d]-wdist[point3*cdim+d]) < PETSC_SMALL));
401: }
402: if (same[0] || same[1] || same[2]) {
403: PetscBTSet(cornerp,shared[ns][j]);
404: }
405: }
406: }
407: PetscBTDestroy(&excluded);
408: PetscFree(wdist);
409: ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
410: }
412: /* check consistency of connected components among neighbouring subdomains -> it adapt them in case it is needed */
413: MPI_Comm_size(interface_comm,&size);
414: adapt_interface_reduced = PETSC_FALSE;
415: if (size > 1) {
416: PetscInt i;
417: PetscBool adapt_interface = cornerp ? PETSC_TRUE : PETSC_FALSE;
418: for (i=0;i<graph->n_subsets && !adapt_interface;i++) {
419: /* We are not sure that on a given subset of the local interface,
420: with two connected components, the latters be the same among sharing subdomains */
421: if (graph->subset_ncc[i] > 1) adapt_interface = PETSC_TRUE;
422: }
423: MPIU_Allreduce(&adapt_interface,&adapt_interface_reduced,1,MPIU_BOOL,MPI_LOR,interface_comm);
424: }
426: if (graph->n_subsets && adapt_interface_reduced) {
427: PetscBT subset_cc_adapt;
428: MPI_Request *send_requests,*recv_requests;
429: PetscInt *send_buffer,*recv_buffer;
430: PetscInt sum_requests,start_of_recv,start_of_send;
431: PetscInt *cum_recv_counts;
432: PetscInt *labels;
433: PetscInt ncc,cum_queue,mss,mns,j,k,s;
434: PetscInt **refine_buffer=NULL,*private_labels = NULL;
435: PetscBool *subset_has_corn,*recv_buffer_bool,*send_buffer_bool;
437: PetscCalloc1(graph->n_subsets,&subset_has_corn);
438: if (cornerp) {
439: for (i=0;i<graph->n_subsets;i++) {
440: for (j=0;j<graph->subset_size[i];j++) {
441: if (PetscBTLookup(cornerp,graph->subset_idxs[i][j])) {
442: subset_has_corn[i] = PETSC_TRUE;
443: break;
444: }
445: }
446: }
447: }
448: PetscMalloc1(graph->nvtxs,&labels);
449: PetscMemzero(labels,graph->nvtxs*sizeof(*labels));
450: for (i=0,k=0;i<graph->ncc;i++) {
451: PetscInt s = 1;
452: for (j=graph->cptr[i];j<graph->cptr[i+1];j++) {
453: if (cornerp && PetscBTLookup(cornerp,graph->queue[j])) {
454: labels[graph->queue[j]] = k+s;
455: s += 1;
456: } else {
457: labels[graph->queue[j]] = k;
458: }
459: }
460: k += s;
461: }
463: /* allocate some space */
464: PetscMalloc1(graph->n_subsets+1,&cum_recv_counts);
465: PetscMemzero(cum_recv_counts,(graph->n_subsets+1)*sizeof(*cum_recv_counts));
467: /* first count how many neighbours per connected component I will receive from */
468: cum_recv_counts[0] = 0;
469: for (i=0;i<graph->n_subsets;i++) cum_recv_counts[i+1] = cum_recv_counts[i]+graph->count[graph->subset_idxs[i][0]];
470: PetscMalloc1(graph->n_subsets,&send_buffer_bool);
471: PetscMalloc1(cum_recv_counts[graph->n_subsets],&recv_buffer_bool);
472: PetscMalloc2(cum_recv_counts[graph->n_subsets],&send_requests,cum_recv_counts[graph->n_subsets],&recv_requests);
473: for (i=0;i<cum_recv_counts[graph->n_subsets];i++) {
474: send_requests[i] = MPI_REQUEST_NULL;
475: recv_requests[i] = MPI_REQUEST_NULL;
476: }
478: /* exchange with my neighbours the number of my connected components on the subset of interface */
479: sum_requests = 0;
480: for (i=0;i<graph->n_subsets;i++) {
481: send_buffer_bool[i] = (PetscBool)(graph->subset_ncc[i] > 1 || subset_has_corn[i]);
482: }
483: for (i=0;i<graph->n_subsets;i++) {
484: PetscMPIInt neigh,tag;
485: PetscInt count,*neighs;
487: count = graph->count[graph->subset_idxs[i][0]];
488: neighs = graph->neighbours_set[graph->subset_idxs[i][0]];
489: PetscMPIIntCast(2*graph->subset_ref_node[i],&tag);
490: for (k=0;k<count;k++) {
492: PetscMPIIntCast(neighs[k],&neigh);
493: MPI_Isend(send_buffer_bool + i, 1,MPIU_BOOL,neigh,tag,interface_comm,&send_requests[sum_requests]);
494: MPI_Irecv(recv_buffer_bool + sum_requests,1,MPIU_BOOL,neigh,tag,interface_comm,&recv_requests[sum_requests]);
495: sum_requests++;
496: }
497: }
498: MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);
499: MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);
501: /* determine the subsets I have to adapt (those having more than 1 cc) */
502: PetscBTCreate(graph->n_subsets,&subset_cc_adapt);
503: PetscBTMemzero(graph->n_subsets,subset_cc_adapt);
504: for (i=0;i<graph->n_subsets;i++) {
505: if (graph->subset_ncc[i] > 1 || subset_has_corn[i]) {
506: PetscBTSet(subset_cc_adapt,i);
507: continue;
508: }
509: for (j=cum_recv_counts[i];j<cum_recv_counts[i+1];j++){
510: if (recv_buffer_bool[j]) {
511: PetscBTSet(subset_cc_adapt,i);
512: break;
513: }
514: }
515: }
516: PetscFree(send_buffer_bool);
517: PetscFree(recv_buffer_bool);
518: PetscFree(subset_has_corn);
520: /* determine send/recv buffers sizes */
521: j = 0;
522: mss = 0;
523: for (i=0;i<graph->n_subsets;i++) {
524: if (PetscBTLookup(subset_cc_adapt,i)) {
525: j += graph->subset_size[i];
526: mss = PetscMax(graph->subset_size[i],mss);
527: }
528: }
529: k = 0;
530: mns = 0;
531: for (i=0;i<graph->n_subsets;i++) {
532: if (PetscBTLookup(subset_cc_adapt,i)) {
533: k += (cum_recv_counts[i+1]-cum_recv_counts[i])*graph->subset_size[i];
534: mns = PetscMax(cum_recv_counts[i+1]-cum_recv_counts[i],mns);
535: }
536: }
537: PetscMalloc2(j,&send_buffer,k,&recv_buffer);
539: /* fill send buffer (order matters: subset_idxs ordered by global ordering) */
540: j = 0;
541: for (i=0;i<graph->n_subsets;i++)
542: if (PetscBTLookup(subset_cc_adapt,i))
543: for (k=0;k<graph->subset_size[i];k++)
544: send_buffer[j++] = labels[graph->subset_idxs[i][k]];
546: /* now exchange the data */
547: start_of_recv = 0;
548: start_of_send = 0;
549: sum_requests = 0;
550: for (i=0;i<graph->n_subsets;i++) {
551: if (PetscBTLookup(subset_cc_adapt,i)) {
552: PetscMPIInt neigh,tag;
553: PetscInt size_of_send = graph->subset_size[i];
555: j = graph->subset_idxs[i][0];
556: PetscMPIIntCast(2*graph->subset_ref_node[i]+1,&tag);
557: for (k=0;k<graph->count[j];k++) {
558: PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);
559: MPI_Isend(&send_buffer[start_of_send],size_of_send,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);
560: MPI_Irecv(&recv_buffer[start_of_recv],size_of_send,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);
561: start_of_recv += size_of_send;
562: sum_requests++;
563: }
564: start_of_send += size_of_send;
565: }
566: }
567: MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);
569: /* refine connected components */
570: start_of_recv = 0;
571: /* allocate some temporary space */
572: if (mss) {
573: PetscMalloc1(mss,&refine_buffer);
574: PetscMalloc2(mss*(mns+1),&refine_buffer[0],mss,&private_labels);
575: }
576: ncc = 0;
577: cum_queue = 0;
578: graph->cptr[0] = 0;
579: for (i=0;i<graph->n_subsets;i++) {
580: if (PetscBTLookup(subset_cc_adapt,i)) {
581: PetscInt subset_counter = 0;
582: PetscInt sharingprocs = cum_recv_counts[i+1]-cum_recv_counts[i]+1; /* count myself */
583: PetscInt buffer_size = graph->subset_size[i];
585: /* compute pointers */
586: for (j=1;j<buffer_size;j++) refine_buffer[j] = refine_buffer[j-1] + sharingprocs;
587: /* analyze contributions from subdomains that share the i-th subset
588: The structure of refine_buffer is suitable to find intersections of ccs among sharingprocs.
589: supposing the current subset is shared by 3 processes and has dimension 5 with global dofs 0,1,2,3,4 (local 0,4,3,1,2)
590: sharing procs connected components:
591: neigh 0: [0 1 4], [2 3], labels [4,7] (2 connected components)
592: neigh 1: [0 1], [2 3 4], labels [3 2] (2 connected components)
593: neigh 2: [0 4], [1], [2 3], labels [1 5 6] (3 connected components)
594: refine_buffer will be filled as:
595: [ 4, 3, 1;
596: 4, 2, 1;
597: 7, 2, 6;
598: 4, 3, 5;
599: 7, 2, 6; ];
600: The connected components in local ordering are [0], [1], [2 3], [4] */
601: /* fill temp_buffer */
602: for (k=0;k<buffer_size;k++) refine_buffer[k][0] = labels[graph->subset_idxs[i][k]];
603: for (j=0;j<sharingprocs-1;j++) {
604: for (k=0;k<buffer_size;k++) refine_buffer[k][j+1] = recv_buffer[start_of_recv+k];
605: start_of_recv += buffer_size;
606: }
607: PetscMemzero(private_labels,buffer_size*sizeof(PetscInt));
608: for (j=0;j<buffer_size;j++) {
609: if (!private_labels[j]) { /* found a new cc */
610: PetscBool same_set;
612: graph->cptr[ncc] = cum_queue;
613: ncc++;
614: subset_counter++;
615: private_labels[j] = subset_counter;
616: graph->queue[cum_queue++] = graph->subset_idxs[i][j];
617: for (k=j+1;k<buffer_size;k++) { /* check for other nodes in new cc */
618: same_set = PETSC_TRUE;
619: for (s=0;s<sharingprocs;s++) {
620: if (refine_buffer[j][s] != refine_buffer[k][s]) {
621: same_set = PETSC_FALSE;
622: break;
623: }
624: }
625: if (same_set) {
626: private_labels[k] = subset_counter;
627: graph->queue[cum_queue++] = graph->subset_idxs[i][k];
628: }
629: }
630: }
631: }
632: graph->cptr[ncc] = cum_queue;
633: graph->subset_ncc[i] = subset_counter;
634: graph->queue_sorted = PETSC_FALSE;
635: } else { /* this subset does not need to be adapted */
636: PetscMemcpy(graph->queue+cum_queue,graph->subset_idxs[i],graph->subset_size[i]*sizeof(PetscInt));
637: ncc++;
638: cum_queue += graph->subset_size[i];
639: graph->cptr[ncc] = cum_queue;
640: }
641: }
642: graph->cptr[ncc] = cum_queue;
643: graph->ncc = ncc;
644: if (mss) {
645: PetscFree2(refine_buffer[0],private_labels);
646: PetscFree(refine_buffer);
647: }
648: PetscFree(labels);
649: MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);
650: PetscFree2(send_requests,recv_requests);
651: PetscFree2(send_buffer,recv_buffer);
652: PetscFree(cum_recv_counts);
653: PetscBTDestroy(&subset_cc_adapt);
654: }
655: PetscBTDestroy(&cornerp);
657: /* Determine if we are in 2D or 3D */
658: if (!graph->twodimset) {
659: PetscBool twodim = PETSC_TRUE;
660: for (i=0;i<graph->ncc;i++) {
661: PetscInt repdof = graph->queue[graph->cptr[i]];
662: PetscInt ccsize = graph->cptr[i+1]-graph->cptr[i];
663: if (graph->count[repdof] > 1 && ccsize > graph->custom_minimal_size) {
664: twodim = PETSC_FALSE;
665: break;
666: }
667: }
668: MPIU_Allreduce(&twodim,&graph->twodim,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)graph->l2gmap));
669: graph->twodimset = PETSC_TRUE;
670: }
671: return(0);
672: }
675: PETSC_STATIC_INLINE PetscErrorCode PCBDDCGraphComputeCC_Private(PCBDDCGraph graph,PetscInt pid,PetscInt* queue_tip,PetscInt n_prev,PetscInt* n_added)
676: {
677: PetscInt i,j,n;
678: PetscInt *xadj = graph->xadj,*adjncy = graph->adjncy;
679: PetscBT touched = graph->touched;
680: PetscBool havecsr = (PetscBool)(!!xadj);
681: PetscBool havesubs = (PetscBool)(!!graph->n_local_subs);
685: n = 0;
686: if (havecsr && !havesubs) {
687: for (i=-n_prev;i<0;i++) {
688: PetscInt start_dof = queue_tip[i];
689: /* we assume that if a dof has a size 1 adjacency list and the corresponding entry is negative, it is connected to all dofs */
690: if (xadj[start_dof+1]-xadj[start_dof] == 1 && adjncy[xadj[start_dof]] < 0) {
691: for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
692: PetscInt dof = graph->subset_idxs[pid-1][j];
693: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) {
694: PetscBTSet(touched,dof);
695: queue_tip[n] = dof;
696: n++;
697: }
698: }
699: } else {
700: for (j=xadj[start_dof];j<xadj[start_dof+1];j++) {
701: PetscInt dof = adjncy[j];
702: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) {
703: PetscBTSet(touched,dof);
704: queue_tip[n] = dof;
705: n++;
706: }
707: }
708: }
709: }
710: } else if (havecsr && havesubs) {
711: PetscInt sid = graph->local_subs[queue_tip[-n_prev]];
712: for (i=-n_prev;i<0;i++) {
713: PetscInt start_dof = queue_tip[i];
714: /* we assume that if a dof has a size 1 adjacency list and the corresponding entry is negative, it is connected to all dofs belonging to the local sub */
715: if (xadj[start_dof+1]-xadj[start_dof] == 1 && adjncy[xadj[start_dof]] < 0) {
716: for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
717: PetscInt dof = graph->subset_idxs[pid-1][j];
718: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
719: PetscBTSet(touched,dof);
720: queue_tip[n] = dof;
721: n++;
722: }
723: }
724: } else {
725: for (j=xadj[start_dof];j<xadj[start_dof+1];j++) {
726: PetscInt dof = adjncy[j];
727: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
728: PetscBTSet(touched,dof);
729: queue_tip[n] = dof;
730: n++;
731: }
732: }
733: }
734: }
735: } else if (havesubs) { /* sub info only */
736: PetscInt sid = graph->local_subs[queue_tip[-n_prev]];
737: for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
738: PetscInt dof = graph->subset_idxs[pid-1][j];
739: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
740: PetscBTSet(touched,dof);
741: queue_tip[n] = dof;
742: n++;
743: }
744: }
745: } else {
746: for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
747: PetscInt dof = graph->subset_idxs[pid-1][j];
748: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) {
749: PetscBTSet(touched,dof);
750: queue_tip[n] = dof;
751: n++;
752: }
753: }
754: }
755: *n_added = n;
756: return(0);
757: }
759: PetscErrorCode PCBDDCGraphComputeConnectedComponentsLocal(PCBDDCGraph graph)
760: {
761: PetscInt ncc,cum_queue,n;
762: PetscMPIInt commsize;
766: if (!graph->setupcalled) SETERRQ(PetscObjectComm((PetscObject)graph->l2gmap),PETSC_ERR_ORDER,"PCBDDCGraphSetUp should be called first");
767: /* quiet return if there isn't any local info */
768: if (!graph->xadj && !graph->n_local_subs) {
769: return(0);
770: }
772: /* reset any previous search of connected components */
773: PetscBTMemzero(graph->nvtxs,graph->touched);
774: MPI_Comm_size(PetscObjectComm((PetscObject)graph->l2gmap),&commsize);
775: if (commsize > graph->commsizelimit) {
776: PetscInt i;
777: for (i=0;i<graph->nvtxs;i++) {
778: if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK || !graph->count[i]) {
779: PetscBTSet(graph->touched,i);
780: }
781: }
782: }
784: /* begin search for connected components */
785: cum_queue = 0;
786: ncc = 0;
787: for (n=0;n<graph->n_subsets;n++) {
788: PetscInt pid = n+1; /* partition labeled by 0 is discarded */
789: PetscInt found = 0,prev = 0,first = 0,ncc_pid = 0;
790: while (found != graph->subset_size[n]) {
791: PetscInt added = 0;
792: if (!prev) { /* search for new starting dof */
793: while (PetscBTLookup(graph->touched,graph->subset_idxs[n][first])) first++;
794: PetscBTSet(graph->touched,graph->subset_idxs[n][first]);
795: graph->queue[cum_queue] = graph->subset_idxs[n][first];
796: graph->cptr[ncc] = cum_queue;
797: prev = 1;
798: cum_queue++;
799: found++;
800: ncc_pid++;
801: ncc++;
802: }
803: PCBDDCGraphComputeCC_Private(graph,pid,graph->queue + cum_queue,prev,&added);
804: if (!added) {
805: graph->subset_ncc[n] = ncc_pid;
806: graph->cptr[ncc] = cum_queue;
807: }
808: prev = added;
809: found += added;
810: cum_queue += added;
811: if (added && found == graph->subset_size[n]) {
812: graph->subset_ncc[n] = ncc_pid;
813: graph->cptr[ncc] = cum_queue;
814: }
815: }
816: }
817: graph->ncc = ncc;
818: graph->queue_sorted = PETSC_FALSE;
819: return(0);
820: }
822: PetscErrorCode PCBDDCGraphSetUp(PCBDDCGraph graph, PetscInt custom_minimal_size, IS neumann_is, IS dirichlet_is, PetscInt n_ISForDofs, IS ISForDofs[], IS custom_primal_vertices)
823: {
824: IS subset,subset_n;
825: MPI_Comm comm;
826: const PetscInt *is_indices;
827: PetscInt n_neigh,*neigh,*n_shared,**shared,*queue_global;
828: PetscInt i,j,k,s,total_counts,nodes_touched,is_size;
829: PetscMPIInt commsize;
830: PetscBool same_set,mirrors_found;
835: if (neumann_is) {
838: }
839: graph->has_dirichlet = PETSC_FALSE;
840: if (dirichlet_is) {
843: graph->has_dirichlet = PETSC_TRUE;
844: }
846: for (i=0;i<n_ISForDofs;i++) {
849: }
850: if (custom_primal_vertices) {
853: }
854: PetscObjectGetComm((PetscObject)(graph->l2gmap),&comm);
855: MPI_Comm_size(comm,&commsize);
857: /* custom_minimal_size */
858: graph->custom_minimal_size = custom_minimal_size;
859: /* get info l2gmap and allocate work vectors */
860: ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
861: /* check if we have any local periodic nodes (periodic BCs) */
862: mirrors_found = PETSC_FALSE;
863: if (graph->nvtxs && n_neigh) {
864: for (i=0; i<n_shared[0]; i++) graph->count[shared[0][i]] += 1;
865: for (i=0; i<n_shared[0]; i++) {
866: if (graph->count[shared[0][i]] > 1) {
867: mirrors_found = PETSC_TRUE;
868: break;
869: }
870: }
871: }
872: /* compute local mirrors (if any) */
873: if (mirrors_found) {
874: IS to,from;
875: PetscInt *local_indices,*global_indices;
877: ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);
878: ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);
879: /* get arrays of local and global indices */
880: PetscMalloc1(graph->nvtxs,&local_indices);
881: ISGetIndices(to,(const PetscInt**)&is_indices);
882: PetscMemcpy(local_indices,is_indices,graph->nvtxs*sizeof(PetscInt));
883: ISRestoreIndices(to,(const PetscInt**)&is_indices);
884: PetscMalloc1(graph->nvtxs,&global_indices);
885: ISGetIndices(from,(const PetscInt**)&is_indices);
886: PetscMemcpy(global_indices,is_indices,graph->nvtxs*sizeof(PetscInt));
887: ISRestoreIndices(from,(const PetscInt**)&is_indices);
888: /* allocate space for mirrors */
889: PetscMalloc2(graph->nvtxs,&graph->mirrors,graph->nvtxs,&graph->mirrors_set);
890: PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));
891: graph->mirrors_set[0] = 0;
893: k=0;
894: for (i=0;i<n_shared[0];i++) {
895: j=shared[0][i];
896: if (graph->count[j] > 1) {
897: graph->mirrors[j]++;
898: k++;
899: }
900: }
901: /* allocate space for set of mirrors */
902: PetscMalloc1(k,&graph->mirrors_set[0]);
903: for (i=1;i<graph->nvtxs;i++)
904: graph->mirrors_set[i]=graph->mirrors_set[i-1]+graph->mirrors[i-1];
906: /* fill arrays */
907: PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));
908: for (j=0;j<n_shared[0];j++) {
909: i=shared[0][j];
910: if (graph->count[i] > 1)
911: graph->mirrors_set[i][graph->mirrors[i]++]=global_indices[i];
912: }
913: PetscSortIntWithArray(graph->nvtxs,global_indices,local_indices);
914: for (i=0;i<graph->nvtxs;i++) {
915: if (graph->mirrors[i] > 0) {
916: PetscFindInt(graph->mirrors_set[i][0],graph->nvtxs,global_indices,&k);
917: j = global_indices[k];
918: while ( k > 0 && global_indices[k-1] == j) k--;
919: for (j=0;j<graph->mirrors[i];j++) {
920: graph->mirrors_set[i][j]=local_indices[k+j];
921: }
922: PetscSortInt(graph->mirrors[i],graph->mirrors_set[i]);
923: }
924: }
925: PetscFree(local_indices);
926: PetscFree(global_indices);
927: ISDestroy(&to);
928: ISDestroy(&from);
929: }
930: PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));
932: /* Count total number of neigh per node */
933: k = 0;
934: for (i=1;i<n_neigh;i++) {
935: k += n_shared[i];
936: for (j=0;j<n_shared[i];j++) {
937: graph->count[shared[i][j]] += 1;
938: }
939: }
940: /* Allocate space for storing the set of neighbours for each node */
941: if (graph->nvtxs) {
942: PetscMalloc1(k,&graph->neighbours_set[0]);
943: }
944: for (i=1;i<graph->nvtxs;i++) { /* dont count myself */
945: graph->neighbours_set[i]=graph->neighbours_set[i-1]+graph->count[i-1];
946: }
947: /* Get information for sharing subdomains */
948: PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));
949: for (i=1;i<n_neigh;i++) { /* dont count myself */
950: s = n_shared[i];
951: for (j=0;j<s;j++) {
952: k = shared[i][j];
953: graph->neighbours_set[k][graph->count[k]] = neigh[i];
954: graph->count[k] += 1;
955: }
956: }
957: /* sort set of sharing subdomains */
958: for (i=0;i<graph->nvtxs;i++) {
959: PetscSortRemoveDupsInt(&graph->count[i],graph->neighbours_set[i]);
960: }
961: /* free memory allocated by ISLocalToGlobalMappingGetInfo */
962: ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
964: /*
965: Get info for dofs splitting
966: User can specify just a subset; an additional field is considered as a complementary field
967: */
968: for (i=0,k=0;i<n_ISForDofs;i++) {
969: PetscInt bs;
971: ISGetBlockSize(ISForDofs[i],&bs);
972: k += bs;
973: }
974: for (i=0;i<graph->nvtxs;i++) graph->which_dof[i] = k; /* by default a dof belongs to the complement set */
975: for (i=0,k=0;i<n_ISForDofs;i++) {
976: PetscInt bs;
978: ISGetLocalSize(ISForDofs[i],&is_size);
979: ISGetBlockSize(ISForDofs[i],&bs);
980: ISGetIndices(ISForDofs[i],(const PetscInt**)&is_indices);
981: for (j=0;j<is_size/bs;j++) {
982: PetscInt b;
984: for (b=0;b<bs;b++) {
985: PetscInt jj = bs*j + b;
987: if (is_indices[jj] > -1 && is_indices[jj] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
988: graph->which_dof[is_indices[jj]] = k+b;
989: }
990: }
991: }
992: ISRestoreIndices(ISForDofs[i],(const PetscInt**)&is_indices);
993: k += bs;
994: }
996: /* Take into account Neumann nodes */
997: if (neumann_is) {
998: ISGetLocalSize(neumann_is,&is_size);
999: ISGetIndices(neumann_is,(const PetscInt**)&is_indices);
1000: for (i=0;i<is_size;i++) {
1001: if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
1002: graph->special_dof[is_indices[i]] = PCBDDCGRAPH_NEUMANN_MARK;
1003: }
1004: }
1005: ISRestoreIndices(neumann_is,(const PetscInt**)&is_indices);
1006: }
1007: /* Take into account Dirichlet nodes (they overwrite any neumann boundary mark previously set) */
1008: if (dirichlet_is) {
1009: ISGetLocalSize(dirichlet_is,&is_size);
1010: ISGetIndices(dirichlet_is,(const PetscInt**)&is_indices);
1011: for (i=0;i<is_size;i++){
1012: if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
1013: if (commsize > graph->commsizelimit) { /* dirichlet nodes treated as internal */
1014: PetscBTSet(graph->touched,is_indices[i]);
1015: graph->subset[is_indices[i]] = 0;
1016: }
1017: graph->special_dof[is_indices[i]] = PCBDDCGRAPH_DIRICHLET_MARK;
1018: }
1019: }
1020: ISRestoreIndices(dirichlet_is,(const PetscInt**)&is_indices);
1021: }
1022: /* mark local periodic nodes (if any) and adapt CSR graph (if any) */
1023: if (graph->mirrors) {
1024: for (i=0;i<graph->nvtxs;i++)
1025: if (graph->mirrors[i])
1026: graph->special_dof[i] = PCBDDCGRAPH_LOCAL_PERIODIC_MARK;
1028: if (graph->xadj) {
1029: PetscInt *new_xadj,*new_adjncy;
1030: /* sort CSR graph */
1031: for (i=0;i<graph->nvtxs;i++)
1032: PetscSortInt(graph->xadj[i+1]-graph->xadj[i],&graph->adjncy[graph->xadj[i]]);
1034: /* adapt local CSR graph in case of local periodicity */
1035: k = 0;
1036: for (i=0;i<graph->nvtxs;i++)
1037: for (j=graph->xadj[i];j<graph->xadj[i+1];j++)
1038: k += graph->mirrors[graph->adjncy[j]];
1040: PetscMalloc1(graph->nvtxs+1,&new_xadj);
1041: PetscMalloc1(k+graph->xadj[graph->nvtxs],&new_adjncy);
1042: new_xadj[0] = 0;
1043: for (i=0;i<graph->nvtxs;i++) {
1044: k = graph->xadj[i+1]-graph->xadj[i];
1045: PetscMemcpy(&new_adjncy[new_xadj[i]],&graph->adjncy[graph->xadj[i]],k*sizeof(PetscInt));
1046: new_xadj[i+1] = new_xadj[i]+k;
1047: for (j=graph->xadj[i];j<graph->xadj[i+1];j++) {
1048: k = graph->mirrors[graph->adjncy[j]];
1049: PetscMemcpy(&new_adjncy[new_xadj[i+1]],graph->mirrors_set[graph->adjncy[j]],k*sizeof(PetscInt));
1050: new_xadj[i+1] += k;
1051: }
1052: k = new_xadj[i+1]-new_xadj[i];
1053: PetscSortRemoveDupsInt(&k,&new_adjncy[new_xadj[i]]);
1054: new_xadj[i+1] = new_xadj[i]+k;
1055: }
1056: /* set new CSR into graph */
1057: PetscFree(graph->xadj);
1058: PetscFree(graph->adjncy);
1059: graph->xadj = new_xadj;
1060: graph->adjncy = new_adjncy;
1061: }
1062: }
1064: /* mark special nodes (if any) -> each will become a single node equivalence class */
1065: if (custom_primal_vertices) {
1066: ISGetLocalSize(custom_primal_vertices,&is_size);
1067: ISGetIndices(custom_primal_vertices,(const PetscInt**)&is_indices);
1068: for (i=0,j=0;i<is_size;i++){
1069: if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs && graph->special_dof[is_indices[i]] != PCBDDCGRAPH_DIRICHLET_MARK) { /* out of bounds indices (if any) are skipped */
1070: graph->special_dof[is_indices[i]] = PCBDDCGRAPH_SPECIAL_MARK-j;
1071: j++;
1072: }
1073: }
1074: ISRestoreIndices(custom_primal_vertices,(const PetscInt**)&is_indices);
1075: }
1077: /* mark interior nodes (if commsize > graph->commsizelimit) as touched and belonging to partition number 0 */
1078: if (commsize > graph->commsizelimit) {
1079: for (i=0;i<graph->nvtxs;i++) {
1080: if (!graph->count[i]) {
1081: PetscBTSet(graph->touched,i);
1082: graph->subset[i] = 0;
1083: }
1084: }
1085: }
1087: /* init graph structure and compute default subsets */
1088: nodes_touched = 0;
1089: for (i=0;i<graph->nvtxs;i++) {
1090: if (PetscBTLookup(graph->touched,i)) {
1091: nodes_touched++;
1092: }
1093: }
1094: i = 0;
1095: graph->ncc = 0;
1096: total_counts = 0;
1098: /* allocated space for queues */
1099: if (commsize == graph->commsizelimit) {
1100: PetscMalloc2(graph->nvtxs+1,&graph->cptr,graph->nvtxs,&graph->queue);
1101: } else {
1102: PetscInt nused = graph->nvtxs - nodes_touched;
1103: PetscMalloc2(nused+1,&graph->cptr,nused,&graph->queue);
1104: }
1106: while (nodes_touched<graph->nvtxs) {
1107: /* find first untouched node in local ordering */
1108: while (PetscBTLookup(graph->touched,i)) i++;
1109: PetscBTSet(graph->touched,i);
1110: graph->subset[i] = graph->ncc+1;
1111: graph->cptr[graph->ncc] = total_counts;
1112: graph->queue[total_counts] = i;
1113: total_counts++;
1114: nodes_touched++;
1115: /* now find all other nodes having the same set of sharing subdomains */
1116: for (j=i+1;j<graph->nvtxs;j++) {
1117: /* check for same number of sharing subdomains, dof number and same special mark */
1118: if (!PetscBTLookup(graph->touched,j) && graph->count[i] == graph->count[j] && graph->which_dof[i] == graph->which_dof[j] && graph->special_dof[i] == graph->special_dof[j]) {
1119: /* check for same set of sharing subdomains */
1120: same_set = PETSC_TRUE;
1121: for (k=0;k<graph->count[j];k++){
1122: if (graph->neighbours_set[i][k] != graph->neighbours_set[j][k]) {
1123: same_set = PETSC_FALSE;
1124: }
1125: }
1126: /* I have found a friend of mine */
1127: if (same_set) {
1128: PetscBTSet(graph->touched,j);
1129: graph->subset[j] = graph->ncc+1;
1130: nodes_touched++;
1131: graph->queue[total_counts] = j;
1132: total_counts++;
1133: }
1134: }
1135: }
1136: graph->ncc++;
1137: }
1138: /* set default number of subsets (at this point no info on csr and/or local_subs has been taken into account, so n_subsets = ncc */
1139: graph->n_subsets = graph->ncc;
1140: PetscMalloc1(graph->n_subsets,&graph->subset_ncc);
1141: for (i=0;i<graph->n_subsets;i++) {
1142: graph->subset_ncc[i] = 1;
1143: }
1144: /* final pointer */
1145: graph->cptr[graph->ncc] = total_counts;
1147: /* For consistency reasons (among neighbours), I need to sort (by global ordering) each connected component */
1148: /* Get a reference node (min index in global ordering) for each subset for tagging messages */
1149: PetscMalloc1(graph->ncc,&graph->subset_ref_node);
1150: PetscMalloc1(graph->cptr[graph->ncc],&queue_global);
1151: ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);
1152: for (j=0;j<graph->ncc;j++) {
1153: PetscSortIntWithArray(graph->cptr[j+1]-graph->cptr[j],&queue_global[graph->cptr[j]],&graph->queue[graph->cptr[j]]);
1154: graph->subset_ref_node[j] = graph->queue[graph->cptr[j]];
1155: }
1156: PetscFree(queue_global);
1157: graph->queue_sorted = PETSC_TRUE;
1159: /* save information on subsets (needed when analyzing the connected components) */
1160: if (graph->ncc) {
1161: PetscMalloc2(graph->ncc,&graph->subset_size,graph->ncc,&graph->subset_idxs);
1162: PetscMalloc1(graph->cptr[graph->ncc],&graph->subset_idxs[0]);
1163: PetscMemzero(graph->subset_idxs[0],graph->cptr[graph->ncc]*sizeof(PetscInt));
1164: for (j=1;j<graph->ncc;j++) {
1165: graph->subset_size[j-1] = graph->cptr[j] - graph->cptr[j-1];
1166: graph->subset_idxs[j] = graph->subset_idxs[j-1] + graph->subset_size[j-1];
1167: }
1168: graph->subset_size[graph->ncc-1] = graph->cptr[graph->ncc] - graph->cptr[graph->ncc-1];
1169: PetscMemcpy(graph->subset_idxs[0],graph->queue,graph->cptr[graph->ncc]*sizeof(PetscInt));
1170: }
1172: /* renumber reference nodes */
1173: ISCreateGeneral(PetscObjectComm((PetscObject)(graph->l2gmap)),graph->ncc,graph->subset_ref_node,PETSC_COPY_VALUES,&subset_n);
1174: ISLocalToGlobalMappingApplyIS(graph->l2gmap,subset_n,&subset);
1175: ISDestroy(&subset_n);
1176: ISRenumber(subset,NULL,NULL,&subset_n);
1177: ISDestroy(&subset);
1178: ISGetLocalSize(subset_n,&k);
1179: if (k != graph->ncc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Invalid size of new subset! %D != %D",k,graph->ncc);
1180: ISGetIndices(subset_n,&is_indices);
1181: PetscMemcpy(graph->subset_ref_node,is_indices,graph->ncc*sizeof(PetscInt));
1182: ISRestoreIndices(subset_n,&is_indices);
1183: ISDestroy(&subset_n);
1185: /* free workspace */
1186: graph->setupcalled = PETSC_TRUE;
1187: return(0);
1188: }
1190: PetscErrorCode PCBDDCGraphResetCoords(PCBDDCGraph graph)
1191: {
1195: if (!graph) return(0);
1196: PetscFree(graph->coords);
1197: graph->cdim = 0;
1198: graph->cnloc = 0;
1199: graph->cloc = PETSC_FALSE;
1200: return(0);
1201: }
1203: PetscErrorCode PCBDDCGraphResetCSR(PCBDDCGraph graph)
1204: {
1208: if (!graph) return(0);
1209: if (graph->freecsr) {
1210: PetscFree(graph->xadj);
1211: PetscFree(graph->adjncy);
1212: } else {
1213: graph->xadj = NULL;
1214: graph->adjncy = NULL;
1215: }
1216: graph->freecsr = PETSC_FALSE;
1217: graph->nvtxs_csr = 0;
1218: return(0);
1219: }
1221: PetscErrorCode PCBDDCGraphReset(PCBDDCGraph graph)
1222: {
1226: if (!graph) return(0);
1227: ISLocalToGlobalMappingDestroy(&graph->l2gmap);
1228: PetscFree(graph->subset_ncc);
1229: PetscFree(graph->subset_ref_node);
1230: if (graph->nvtxs) {
1231: PetscFree(graph->neighbours_set[0]);
1232: }
1233: PetscBTDestroy(&graph->touched);
1234: PetscFree5(graph->count,
1235: graph->neighbours_set,
1236: graph->subset,
1237: graph->which_dof,
1238: graph->special_dof);
1239: PetscFree2(graph->cptr,graph->queue);
1240: if (graph->mirrors) {
1241: PetscFree(graph->mirrors_set[0]);
1242: }
1243: PetscFree2(graph->mirrors,graph->mirrors_set);
1244: if (graph->subset_idxs) {
1245: PetscFree(graph->subset_idxs[0]);
1246: }
1247: PetscFree2(graph->subset_size,graph->subset_idxs);
1248: ISDestroy(&graph->dirdofs);
1249: ISDestroy(&graph->dirdofsB);
1250: if (graph->n_local_subs) {
1251: PetscFree(graph->local_subs);
1252: }
1253: graph->has_dirichlet = PETSC_FALSE;
1254: graph->twodimset = PETSC_FALSE;
1255: graph->twodim = PETSC_FALSE;
1256: graph->nvtxs = 0;
1257: graph->nvtxs_global = 0;
1258: graph->n_subsets = 0;
1259: graph->custom_minimal_size = 1;
1260: graph->n_local_subs = 0;
1261: graph->maxcount = PETSC_MAX_INT;
1262: graph->setupcalled = PETSC_FALSE;
1263: return(0);
1264: }
1266: PetscErrorCode PCBDDCGraphInit(PCBDDCGraph graph, ISLocalToGlobalMapping l2gmap, PetscInt N, PetscInt maxcount)
1267: {
1268: PetscInt n;
1276: /* raise an error if already allocated */
1277: if (graph->nvtxs_global) SETERRQ(PetscObjectComm((PetscObject)l2gmap),PETSC_ERR_PLIB,"BDDCGraph already initialized");
1278: /* set number of vertices */
1279: PetscObjectReference((PetscObject)l2gmap);
1280: graph->l2gmap = l2gmap;
1281: ISLocalToGlobalMappingGetSize(l2gmap,&n);
1282: graph->nvtxs = n;
1283: graph->nvtxs_global = N;
1284: /* allocate used space */
1285: PetscBTCreate(graph->nvtxs,&graph->touched);
1286: PetscMalloc5(graph->nvtxs,&graph->count,
1287: graph->nvtxs,&graph->neighbours_set,
1288: graph->nvtxs,&graph->subset,
1289: graph->nvtxs,&graph->which_dof,
1290: graph->nvtxs,&graph->special_dof);
1291: /* zeroes memory */
1292: PetscMemzero(graph->count,graph->nvtxs*sizeof(PetscInt));
1293: PetscMemzero(graph->subset,graph->nvtxs*sizeof(PetscInt));
1294: /* use -1 as a default value for which_dof array */
1295: for (n=0;n<graph->nvtxs;n++) graph->which_dof[n] = -1;
1296: PetscMemzero(graph->special_dof,graph->nvtxs*sizeof(PetscInt));
1297: /* zeroes first pointer to neighbour set */
1298: if (graph->nvtxs) {
1299: graph->neighbours_set[0] = 0;
1300: }
1301: /* zeroes workspace for values of ncc */
1302: graph->subset_ncc = 0;
1303: graph->subset_ref_node = 0;
1304: /* maxcount for cc */
1305: graph->maxcount = maxcount;
1306: return(0);
1307: }
1309: PetscErrorCode PCBDDCGraphDestroy(PCBDDCGraph* graph)
1310: {
1314: PCBDDCGraphResetCSR(*graph);
1315: PCBDDCGraphResetCoords(*graph);
1316: PCBDDCGraphReset(*graph);
1317: PetscFree(*graph);
1318: return(0);
1319: }
1321: PetscErrorCode PCBDDCGraphCreate(PCBDDCGraph *graph)
1322: {
1323: PCBDDCGraph new_graph;
1327: PetscNew(&new_graph);
1328: new_graph->custom_minimal_size = 1;
1329: new_graph->commsizelimit = 1;
1330: *graph = new_graph;
1331: return(0);
1332: }