Actual source code: bddcgraph.c
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: {
7: if (graph->dirdofsB) {
8: PetscObjectReference((PetscObject)graph->dirdofsB);
9: } else if (graph->has_dirichlet) {
10: PetscInt i,size;
11: PetscInt *dirdofs_idxs;
13: size = 0;
14: for (i=0;i<graph->nvtxs;i++) {
15: if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++;
16: }
18: PetscMalloc1(size,&dirdofs_idxs);
19: size = 0;
20: for (i=0;i<graph->nvtxs;i++) {
21: if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i;
22: }
23: ISCreateGeneral(PETSC_COMM_SELF,size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofsB);
24: PetscObjectReference((PetscObject)graph->dirdofsB);
25: }
26: *dirdofs = graph->dirdofsB;
27: return 0;
28: }
30: PetscErrorCode PCBDDCGraphGetDirichletDofs(PCBDDCGraph graph, IS* dirdofs)
31: {
32: if (graph->dirdofs) {
33: PetscObjectReference((PetscObject)graph->dirdofs);
34: } else if (graph->has_dirichlet) {
35: PetscInt i,size;
36: PetscInt *dirdofs_idxs;
38: size = 0;
39: for (i=0;i<graph->nvtxs;i++) {
40: if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++;
41: }
43: PetscMalloc1(size,&dirdofs_idxs);
44: size = 0;
45: for (i=0;i<graph->nvtxs;i++) {
46: if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i;
47: }
48: ISCreateGeneral(PetscObjectComm((PetscObject)graph->l2gmap),size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofs);
49: PetscObjectReference((PetscObject)graph->dirdofs);
50: }
51: *dirdofs = graph->dirdofs;
52: return 0;
53: }
55: PetscErrorCode PCBDDCGraphASCIIView(PCBDDCGraph graph, PetscInt verbosity_level, PetscViewer viewer)
56: {
57: PetscInt i,j,tabs;
58: PetscInt* queue_in_global_numbering;
60: PetscViewerASCIIPushSynchronized(viewer);
61: PetscViewerASCIIGetTab(viewer,&tabs);
62: PetscViewerASCIIPrintf(viewer,"--------------------------------------------------\n");
63: PetscViewerFlush(viewer);
64: PetscViewerASCIISynchronizedPrintf(viewer,"Local BDDC graph for subdomain %04d\n",PetscGlobalRank);
65: PetscViewerASCIISynchronizedPrintf(viewer,"Number of vertices %d\n",graph->nvtxs);
66: PetscViewerASCIISynchronizedPrintf(viewer,"Number of local subdomains %d\n",graph->n_local_subs ? graph->n_local_subs : 1);
67: PetscViewerASCIISynchronizedPrintf(viewer,"Custom minimal size %d\n",graph->custom_minimal_size);
68: if (graph->maxcount != PETSC_MAX_INT) {
69: PetscViewerASCIISynchronizedPrintf(viewer,"Max count %d\n",graph->maxcount);
70: }
71: PetscViewerASCIISynchronizedPrintf(viewer,"Topological two dim? %d (set %d)\n",graph->twodim,graph->twodimset);
72: if (verbosity_level > 2) {
73: for (i=0;i<graph->nvtxs;i++) {
74: PetscViewerASCIISynchronizedPrintf(viewer,"%d:\n",i);
75: PetscViewerASCIISynchronizedPrintf(viewer," which_dof: %d\n",graph->which_dof[i]);
76: PetscViewerASCIISynchronizedPrintf(viewer," special_dof: %d\n",graph->special_dof[i]);
77: PetscViewerASCIISynchronizedPrintf(viewer," neighbours: %d\n",graph->count[i]);
78: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
79: if (graph->count[i]) {
80: PetscViewerASCIISynchronizedPrintf(viewer," set of neighbours:");
81: for (j=0;j<graph->count[i];j++) {
82: PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[i][j]);
83: }
84: PetscViewerASCIISynchronizedPrintf(viewer,"\n");
85: }
86: PetscViewerASCIISetTab(viewer,tabs);
87: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
88: if (graph->mirrors) {
89: PetscViewerASCIISynchronizedPrintf(viewer," mirrors: %d\n",graph->mirrors[i]);
90: if (graph->mirrors[i]) {
91: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
92: PetscViewerASCIISynchronizedPrintf(viewer," set of mirrors:");
93: for (j=0;j<graph->mirrors[i];j++) {
94: PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->mirrors_set[i][j]);
95: }
96: PetscViewerASCIISynchronizedPrintf(viewer,"\n");
97: PetscViewerASCIISetTab(viewer,tabs);
98: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
99: }
100: }
101: if (verbosity_level > 3) {
102: if (graph->xadj) {
103: PetscViewerASCIISynchronizedPrintf(viewer," local adj list:");
104: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
105: for (j=graph->xadj[i];j<graph->xadj[i+1];j++) {
106: PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->adjncy[j]);
107: }
108: PetscViewerASCIISynchronizedPrintf(viewer,"\n");
109: PetscViewerASCIISetTab(viewer,tabs);
110: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
111: } else {
112: PetscViewerASCIISynchronizedPrintf(viewer," no adj info\n");
113: }
114: }
115: if (graph->n_local_subs) {
116: PetscViewerASCIISynchronizedPrintf(viewer," local sub id: %d\n",graph->local_subs[i]);
117: }
118: PetscViewerASCIISynchronizedPrintf(viewer," interface subset id: %d\n",graph->subset[i]);
119: if (graph->subset[i] && graph->subset_ncc) {
120: PetscViewerASCIISynchronizedPrintf(viewer," ncc for subset: %d\n",graph->subset_ncc[graph->subset[i]-1]);
121: }
122: }
123: }
124: PetscViewerASCIISynchronizedPrintf(viewer,"Total number of connected components %d\n",graph->ncc);
125: PetscMalloc1(graph->cptr[graph->ncc],&queue_in_global_numbering);
126: ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_in_global_numbering);
127: for (i=0;i<graph->ncc;i++) {
128: PetscInt node_num=graph->queue[graph->cptr[i]];
129: PetscBool printcc = PETSC_FALSE;
130: PetscViewerASCIISynchronizedPrintf(viewer," cc %d (size %d, fid %d, neighs:",i,graph->cptr[i+1]-graph->cptr[i],graph->which_dof[node_num]);
131: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
132: for (j=0;j<graph->count[node_num];j++) {
133: PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[node_num][j]);
134: }
135: if (verbosity_level > 1) {
136: PetscViewerASCIISynchronizedPrintf(viewer,"):");
137: if (verbosity_level > 2 || graph->twodim || graph->count[node_num] > 1 || (graph->count[node_num] == 1 && graph->special_dof[node_num] == PCBDDCGRAPH_NEUMANN_MARK)) {
138: printcc = PETSC_TRUE;
139: }
140: if (printcc) {
141: for (j=graph->cptr[i];j<graph->cptr[i+1];j++) {
142: PetscViewerASCIISynchronizedPrintf(viewer," %d (%d)",graph->queue[j],queue_in_global_numbering[j]);
143: }
144: }
145: } else {
146: PetscViewerASCIISynchronizedPrintf(viewer,")");
147: }
148: PetscViewerASCIISynchronizedPrintf(viewer,"\n");
149: PetscViewerASCIISetTab(viewer,tabs);
150: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
151: }
152: PetscFree(queue_in_global_numbering);
153: PetscViewerFlush(viewer);
154: return 0;
155: }
157: PetscErrorCode PCBDDCGraphRestoreCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS)
158: {
159: PetscInt i;
161: if (n_faces) {
162: if (FacesIS) {
163: for (i=0;i<*n_faces;i++) {
164: ISDestroy(&((*FacesIS)[i]));
165: }
166: PetscFree(*FacesIS);
167: }
168: *n_faces = 0;
169: }
170: if (n_edges) {
171: if (EdgesIS) {
172: for (i=0;i<*n_edges;i++) {
173: ISDestroy(&((*EdgesIS)[i]));
174: }
175: PetscFree(*EdgesIS);
176: }
177: *n_edges = 0;
178: }
179: if (VerticesIS) {
180: ISDestroy(VerticesIS);
181: }
182: return 0;
183: }
185: PetscErrorCode PCBDDCGraphGetCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS)
186: {
187: IS *ISForFaces,*ISForEdges,ISForVertices;
188: PetscInt i,nfc,nec,nvc,*idx,*mark;
190: PetscCalloc1(graph->ncc,&mark);
191: /* loop on ccs to evalute number of faces, edges and vertices */
192: nfc = 0;
193: nec = 0;
194: nvc = 0;
195: for (i=0;i<graph->ncc;i++) {
196: PetscInt repdof = graph->queue[graph->cptr[i]];
197: if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size && graph->count[repdof] < graph->maxcount) {
198: if (!graph->twodim && graph->count[repdof] == 1 && graph->special_dof[repdof] != PCBDDCGRAPH_NEUMANN_MARK) {
199: nfc++;
200: mark[i] = 2;
201: } else {
202: nec++;
203: mark[i] = 1;
204: }
205: } else {
206: nvc += graph->cptr[i+1]-graph->cptr[i];
207: }
208: }
210: /* allocate IS arrays for faces, edges. Vertices need a single index set. */
211: if (FacesIS) {
212: PetscMalloc1(nfc,&ISForFaces);
213: }
214: if (EdgesIS) {
215: PetscMalloc1(nec,&ISForEdges);
216: }
217: if (VerticesIS) {
218: PetscMalloc1(nvc,&idx);
219: }
221: /* loop on ccs to compute index sets for faces and edges */
222: if (!graph->queue_sorted) {
223: PetscInt *queue_global;
225: PetscMalloc1(graph->cptr[graph->ncc],&queue_global);
226: ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);
227: for (i=0;i<graph->ncc;i++) {
228: PetscSortIntWithArray(graph->cptr[i+1]-graph->cptr[i],&queue_global[graph->cptr[i]],&graph->queue[graph->cptr[i]]);
229: }
230: PetscFree(queue_global);
231: graph->queue_sorted = PETSC_TRUE;
232: }
233: nfc = 0;
234: nec = 0;
235: for (i=0;i<graph->ncc;i++) {
236: if (mark[i] == 2) {
237: if (FacesIS) {
238: ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_USE_POINTER,&ISForFaces[nfc]);
239: }
240: nfc++;
241: } else if (mark[i] == 1) {
242: if (EdgesIS) {
243: ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_USE_POINTER,&ISForEdges[nec]);
244: }
245: nec++;
246: }
247: }
249: /* index set for vertices */
250: if (VerticesIS) {
251: nvc = 0;
252: for (i=0;i<graph->ncc;i++) {
253: if (!mark[i]) {
254: PetscInt j;
256: for (j=graph->cptr[i];j<graph->cptr[i+1];j++) {
257: idx[nvc]=graph->queue[j];
258: nvc++;
259: }
260: }
261: }
262: /* sort vertex set (by local ordering) */
263: PetscSortInt(nvc,idx);
264: ISCreateGeneral(PETSC_COMM_SELF,nvc,idx,PETSC_OWN_POINTER,&ISForVertices);
265: }
266: PetscFree(mark);
268: /* get back info */
269: if (n_faces) *n_faces = nfc;
270: if (FacesIS) *FacesIS = ISForFaces;
271: if (n_edges) *n_edges = nec;
272: if (EdgesIS) *EdgesIS = ISForEdges;
273: if (VerticesIS) *VerticesIS = ISForVertices;
274: return 0;
275: }
277: PetscErrorCode PCBDDCGraphComputeConnectedComponents(PCBDDCGraph graph)
278: {
279: PetscBool adapt_interface_reduced;
280: MPI_Comm interface_comm;
281: PetscMPIInt size;
282: PetscInt i;
283: PetscBT cornerp;
285: /* compute connected components locally */
286: PetscObjectGetComm((PetscObject)(graph->l2gmap),&interface_comm);
287: PCBDDCGraphComputeConnectedComponentsLocal(graph);
289: cornerp = NULL;
290: if (graph->active_coords) { /* face based corner selection */
291: PetscBT excluded;
292: PetscReal *wdist;
293: PetscInt n_neigh,*neigh,*n_shared,**shared;
294: PetscInt maxc, ns;
296: PetscBTCreate(graph->nvtxs,&cornerp);
297: ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
298: for (ns = 1, maxc = 0; ns < n_neigh; ns++) maxc = PetscMax(maxc,n_shared[ns]);
299: PetscMalloc1(maxc*graph->cdim,&wdist);
300: PetscBTCreate(maxc,&excluded);
302: for (ns = 1; ns < n_neigh; ns++) { /* first proc is self */
303: PetscReal *anchor,mdist;
304: PetscInt fst,j,k,d,cdim = graph->cdim,n = n_shared[ns];
305: PetscInt point1,point2,point3,point4;
307: /* import coordinates on shared interface */
308: PetscBTMemzero(n,excluded);
309: for (j=0,fst=-1,k=0;j<n;j++) {
310: PetscBool skip = PETSC_FALSE;
311: for (d=0;d<cdim;d++) {
312: PetscReal c = graph->coords[shared[ns][j]*cdim+d];
313: skip = (PetscBool)(skip || c == PETSC_MAX_REAL);
314: wdist[k++] = c;
315: }
316: if (skip) {
317: PetscBTSet(excluded,j);
318: } else if (fst == -1) fst = j;
319: }
320: if (fst == -1) continue;
322: /* the dofs are sorted by global numbering, so each rank starts from the same id
323: and it will detect the same corners from the given set */
325: /* find the farthest point from the starting one */
326: anchor = wdist + fst*cdim;
327: mdist = -1.0;
328: point1 = fst;
329: for (j=fst;j<n;j++) {
330: PetscReal dist = 0.0;
332: if (PetscUnlikely(PetscBTLookup(excluded,j))) continue;
333: for (d=0;d<cdim;d++) dist += (wdist[j*cdim+d]-anchor[d])*(wdist[j*cdim+d]-anchor[d]);
334: if (dist > mdist) { mdist = dist; point1 = j; }
335: }
337: /* find the farthest point from point1 */
338: anchor = wdist + point1*cdim;
339: mdist = -1.0;
340: point2 = point1;
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; point2 = j; }
347: }
349: /* find the third point maximizing the triangle area */
350: point3 = point2;
351: if (cdim > 2) {
352: PetscReal a = 0.0;
354: for (d=0;d<cdim;d++) a += (wdist[point1*cdim+d]-wdist[point2*cdim+d])*(wdist[point1*cdim+d]-wdist[point2*cdim+d]);
355: a = PetscSqrtReal(a);
356: mdist = -1.0;
357: for (j=fst;j<n;j++) {
358: PetscReal area,b = 0.0, c = 0.0,s;
360: if (PetscUnlikely(PetscBTLookup(excluded,j))) continue;
361: for (d=0;d<cdim;d++) {
362: b += (wdist[point1*cdim+d]-wdist[j*cdim+d])*(wdist[point1*cdim+d]-wdist[j*cdim+d]);
363: c += (wdist[point2*cdim+d]-wdist[j*cdim+d])*(wdist[point2*cdim+d]-wdist[j*cdim+d]);
364: }
365: b = PetscSqrtReal(b);
366: c = PetscSqrtReal(c);
367: s = 0.5*(a+b+c);
369: /* Heron's formula, area squared */
370: area = s*(s-a)*(s-b)*(s-c);
371: if (area > mdist) { mdist = area; point3 = j; }
372: }
373: }
375: /* find the farthest point from point3 different from point1 and point2 */
376: anchor = wdist + point3*cdim;
377: mdist = -1.0;
378: point4 = point3;
379: for (j=fst;j<n;j++) {
380: PetscReal dist = 0.0;
382: if (PetscUnlikely(PetscBTLookup(excluded,j)) || j == point1 || j == point2 || j == point3) continue;
383: for (d=0;d<cdim;d++) dist += (wdist[j*cdim+d]-anchor[d])*(wdist[j*cdim+d]-anchor[d]);
384: if (dist > mdist) { mdist = dist; point4 = j; }
385: }
387: PetscBTSet(cornerp,shared[ns][point1]);
388: PetscBTSet(cornerp,shared[ns][point2]);
389: PetscBTSet(cornerp,shared[ns][point3]);
390: PetscBTSet(cornerp,shared[ns][point4]);
392: /* all dofs having the same coordinates will be primal */
393: for (j=fst;j<n;j++) {
394: PetscBool same[] = {PETSC_TRUE,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: same[3] = (PetscBool)(same[3] && (PetscAbsReal(wdist[j*cdim + d]-wdist[point4*cdim+d]) < PETSC_SMALL));
402: }
403: if (same[0] || same[1] || same[2] || same[3]) {
404: PetscBTSet(cornerp,shared[ns][j]);
405: }
406: }
407: }
408: PetscBTDestroy(&excluded);
409: PetscFree(wdist);
410: ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
411: }
413: /* check consistency of connected components among neighbouring subdomains -> it adapt them in case it is needed */
414: MPI_Comm_size(interface_comm,&size);
415: adapt_interface_reduced = PETSC_FALSE;
416: if (size > 1) {
417: PetscInt i;
418: PetscBool adapt_interface = cornerp ? PETSC_TRUE : PETSC_FALSE;
419: for (i=0;i<graph->n_subsets && !adapt_interface;i++) {
420: /* We are not sure that on a given subset of the local interface,
421: with two connected components, the latters be the same among sharing subdomains */
422: if (graph->subset_ncc[i] > 1) adapt_interface = PETSC_TRUE;
423: }
424: MPIU_Allreduce(&adapt_interface,&adapt_interface_reduced,1,MPIU_BOOL,MPI_LOR,interface_comm);
425: }
427: if (graph->n_subsets && adapt_interface_reduced) {
428: PetscBT subset_cc_adapt;
429: MPI_Request *send_requests,*recv_requests;
430: PetscInt *send_buffer,*recv_buffer;
431: PetscInt sum_requests,start_of_recv,start_of_send;
432: PetscInt *cum_recv_counts;
433: PetscInt *labels;
434: PetscInt ncc,cum_queue,mss,mns,j,k,s;
435: PetscInt **refine_buffer=NULL,*private_labels = NULL;
436: PetscBool *subset_has_corn,*recv_buffer_bool,*send_buffer_bool;
438: PetscCalloc1(graph->n_subsets,&subset_has_corn);
439: if (cornerp) {
440: for (i=0;i<graph->n_subsets;i++) {
441: for (j=0;j<graph->subset_size[i];j++) {
442: if (PetscBTLookup(cornerp,graph->subset_idxs[i][j])) {
443: subset_has_corn[i] = PETSC_TRUE;
444: break;
445: }
446: }
447: }
448: }
449: PetscMalloc1(graph->nvtxs,&labels);
450: PetscArrayzero(labels,graph->nvtxs);
451: for (i=0,k=0;i<graph->ncc;i++) {
452: PetscInt s = 1;
453: for (j=graph->cptr[i];j<graph->cptr[i+1];j++) {
454: if (cornerp && PetscBTLookup(cornerp,graph->queue[j])) {
455: labels[graph->queue[j]] = k+s;
456: s += 1;
457: } else {
458: labels[graph->queue[j]] = k;
459: }
460: }
461: k += s;
462: }
464: /* allocate some space */
465: PetscMalloc1(graph->n_subsets+1,&cum_recv_counts);
466: PetscArrayzero(cum_recv_counts,graph->n_subsets+1);
468: /* first count how many neighbours per connected component I will receive from */
469: cum_recv_counts[0] = 0;
470: for (i=0;i<graph->n_subsets;i++) cum_recv_counts[i+1] = cum_recv_counts[i]+graph->count[graph->subset_idxs[i][0]];
471: PetscMalloc1(graph->n_subsets,&send_buffer_bool);
472: PetscMalloc1(cum_recv_counts[graph->n_subsets],&recv_buffer_bool);
473: PetscMalloc2(cum_recv_counts[graph->n_subsets],&send_requests,cum_recv_counts[graph->n_subsets],&recv_requests);
474: for (i=0;i<cum_recv_counts[graph->n_subsets];i++) {
475: send_requests[i] = MPI_REQUEST_NULL;
476: recv_requests[i] = MPI_REQUEST_NULL;
477: }
479: /* exchange with my neighbours the number of my connected components on the subset of interface */
480: sum_requests = 0;
481: for (i=0;i<graph->n_subsets;i++) {
482: send_buffer_bool[i] = (PetscBool)(graph->subset_ncc[i] > 1 || subset_has_corn[i]);
483: }
484: for (i=0;i<graph->n_subsets;i++) {
485: PetscMPIInt neigh,tag;
486: PetscInt count,*neighs;
488: count = graph->count[graph->subset_idxs[i][0]];
489: neighs = graph->neighbours_set[graph->subset_idxs[i][0]];
490: PetscMPIIntCast(2*graph->subset_ref_node[i],&tag);
491: for (k=0;k<count;k++) {
493: PetscMPIIntCast(neighs[k],&neigh);
494: MPI_Isend(send_buffer_bool + i, 1,MPIU_BOOL,neigh,tag,interface_comm,&send_requests[sum_requests]);
495: MPI_Irecv(recv_buffer_bool + sum_requests,1,MPIU_BOOL,neigh,tag,interface_comm,&recv_requests[sum_requests]);
496: sum_requests++;
497: }
498: }
499: MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);
500: MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);
502: /* determine the subsets I have to adapt (those having more than 1 cc) */
503: PetscBTCreate(graph->n_subsets,&subset_cc_adapt);
504: PetscBTMemzero(graph->n_subsets,subset_cc_adapt);
505: for (i=0;i<graph->n_subsets;i++) {
506: if (graph->subset_ncc[i] > 1 || subset_has_corn[i]) {
507: PetscBTSet(subset_cc_adapt,i);
508: continue;
509: }
510: for (j=cum_recv_counts[i];j<cum_recv_counts[i+1];j++) {
511: if (recv_buffer_bool[j]) {
512: PetscBTSet(subset_cc_adapt,i);
513: break;
514: }
515: }
516: }
517: PetscFree(send_buffer_bool);
518: PetscFree(recv_buffer_bool);
519: PetscFree(subset_has_corn);
521: /* determine send/recv buffers sizes */
522: j = 0;
523: mss = 0;
524: for (i=0;i<graph->n_subsets;i++) {
525: if (PetscBTLookup(subset_cc_adapt,i)) {
526: j += graph->subset_size[i];
527: mss = PetscMax(graph->subset_size[i],mss);
528: }
529: }
530: k = 0;
531: mns = 0;
532: for (i=0;i<graph->n_subsets;i++) {
533: if (PetscBTLookup(subset_cc_adapt,i)) {
534: k += (cum_recv_counts[i+1]-cum_recv_counts[i])*graph->subset_size[i];
535: mns = PetscMax(cum_recv_counts[i+1]-cum_recv_counts[i],mns);
536: }
537: }
538: PetscMalloc2(j,&send_buffer,k,&recv_buffer);
540: /* fill send buffer (order matters: subset_idxs ordered by global ordering) */
541: j = 0;
542: for (i=0;i<graph->n_subsets;i++)
543: if (PetscBTLookup(subset_cc_adapt,i))
544: for (k=0;k<graph->subset_size[i];k++)
545: send_buffer[j++] = labels[graph->subset_idxs[i][k]];
547: /* now exchange the data */
548: start_of_recv = 0;
549: start_of_send = 0;
550: sum_requests = 0;
551: for (i=0;i<graph->n_subsets;i++) {
552: if (PetscBTLookup(subset_cc_adapt,i)) {
553: PetscMPIInt neigh,tag;
554: PetscInt size_of_send = graph->subset_size[i];
556: j = graph->subset_idxs[i][0];
557: PetscMPIIntCast(2*graph->subset_ref_node[i]+1,&tag);
558: for (k=0;k<graph->count[j];k++) {
559: PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);
560: MPI_Isend(&send_buffer[start_of_send],size_of_send,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);
561: MPI_Irecv(&recv_buffer[start_of_recv],size_of_send,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);
562: start_of_recv += size_of_send;
563: sum_requests++;
564: }
565: start_of_send += size_of_send;
566: }
567: }
568: MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);
570: /* refine connected components */
571: start_of_recv = 0;
572: /* allocate some temporary space */
573: if (mss) {
574: PetscMalloc1(mss,&refine_buffer);
575: PetscMalloc2(mss*(mns+1),&refine_buffer[0],mss,&private_labels);
576: }
577: ncc = 0;
578: cum_queue = 0;
579: graph->cptr[0] = 0;
580: for (i=0;i<graph->n_subsets;i++) {
581: if (PetscBTLookup(subset_cc_adapt,i)) {
582: PetscInt subset_counter = 0;
583: PetscInt sharingprocs = cum_recv_counts[i+1]-cum_recv_counts[i]+1; /* count myself */
584: PetscInt buffer_size = graph->subset_size[i];
586: /* compute pointers */
587: for (j=1;j<buffer_size;j++) refine_buffer[j] = refine_buffer[j-1] + sharingprocs;
588: /* analyze contributions from subdomains that share the i-th subset
589: The structure of refine_buffer is suitable to find intersections of ccs among sharingprocs.
590: 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)
591: sharing procs connected components:
592: neigh 0: [0 1 4], [2 3], labels [4,7] (2 connected components)
593: neigh 1: [0 1], [2 3 4], labels [3 2] (2 connected components)
594: neigh 2: [0 4], [1], [2 3], labels [1 5 6] (3 connected components)
595: refine_buffer will be filled as:
596: [ 4, 3, 1;
597: 4, 2, 1;
598: 7, 2, 6;
599: 4, 3, 5;
600: 7, 2, 6; ];
601: The connected components in local ordering are [0], [1], [2 3], [4] */
602: /* fill temp_buffer */
603: for (k=0;k<buffer_size;k++) refine_buffer[k][0] = labels[graph->subset_idxs[i][k]];
604: for (j=0;j<sharingprocs-1;j++) {
605: for (k=0;k<buffer_size;k++) refine_buffer[k][j+1] = recv_buffer[start_of_recv+k];
606: start_of_recv += buffer_size;
607: }
608: PetscArrayzero(private_labels,buffer_size);
609: for (j=0;j<buffer_size;j++) {
610: if (!private_labels[j]) { /* found a new cc */
611: PetscBool same_set;
613: graph->cptr[ncc] = cum_queue;
614: ncc++;
615: subset_counter++;
616: private_labels[j] = subset_counter;
617: graph->queue[cum_queue++] = graph->subset_idxs[i][j];
618: for (k=j+1;k<buffer_size;k++) { /* check for other nodes in new cc */
619: same_set = PETSC_TRUE;
620: for (s=0;s<sharingprocs;s++) {
621: if (refine_buffer[j][s] != refine_buffer[k][s]) {
622: same_set = PETSC_FALSE;
623: break;
624: }
625: }
626: if (same_set) {
627: private_labels[k] = subset_counter;
628: graph->queue[cum_queue++] = graph->subset_idxs[i][k];
629: }
630: }
631: }
632: }
633: graph->cptr[ncc] = cum_queue;
634: graph->subset_ncc[i] = subset_counter;
635: graph->queue_sorted = PETSC_FALSE;
636: } else { /* this subset does not need to be adapted */
637: PetscArraycpy(graph->queue+cum_queue,graph->subset_idxs[i],graph->subset_size[i]);
638: ncc++;
639: cum_queue += graph->subset_size[i];
640: graph->cptr[ncc] = cum_queue;
641: }
642: }
643: graph->cptr[ncc] = cum_queue;
644: graph->ncc = ncc;
645: if (mss) {
646: PetscFree2(refine_buffer[0],private_labels);
647: PetscFree(refine_buffer);
648: }
649: PetscFree(labels);
650: MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);
651: PetscFree2(send_requests,recv_requests);
652: PetscFree2(send_buffer,recv_buffer);
653: PetscFree(cum_recv_counts);
654: PetscBTDestroy(&subset_cc_adapt);
655: }
656: PetscBTDestroy(&cornerp);
658: /* Determine if we are in 2D or 3D */
659: if (!graph->twodimset) {
660: PetscBool twodim = PETSC_TRUE;
661: for (i=0;i<graph->ncc;i++) {
662: PetscInt repdof = graph->queue[graph->cptr[i]];
663: PetscInt ccsize = graph->cptr[i+1]-graph->cptr[i];
664: if (graph->count[repdof] > 1 && ccsize > graph->custom_minimal_size) {
665: twodim = PETSC_FALSE;
666: break;
667: }
668: }
669: MPIU_Allreduce(&twodim,&graph->twodim,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)graph->l2gmap));
670: graph->twodimset = PETSC_TRUE;
671: }
672: return 0;
673: }
675: 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);
683: n = 0;
684: if (havecsr && !havesubs) {
685: for (i=-n_prev;i<0;i++) {
686: PetscInt start_dof = queue_tip[i];
687: /* we assume that if a dof has a size 1 adjacency list and the corresponding entry is negative, it is connected to all dofs */
688: if (xadj[start_dof+1]-xadj[start_dof] == 1 && adjncy[xadj[start_dof]] < 0) {
689: for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
690: PetscInt dof = graph->subset_idxs[pid-1][j];
691: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) {
692: PetscBTSet(touched,dof);
693: queue_tip[n] = dof;
694: n++;
695: }
696: }
697: } else {
698: for (j=xadj[start_dof];j<xadj[start_dof+1];j++) {
699: PetscInt dof = adjncy[j];
700: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) {
701: PetscBTSet(touched,dof);
702: queue_tip[n] = dof;
703: n++;
704: }
705: }
706: }
707: }
708: } else if (havecsr && havesubs) {
709: PetscInt sid = graph->local_subs[queue_tip[-n_prev]];
710: for (i=-n_prev;i<0;i++) {
711: PetscInt start_dof = queue_tip[i];
712: /* 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 */
713: if (xadj[start_dof+1]-xadj[start_dof] == 1 && adjncy[xadj[start_dof]] < 0) {
714: for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
715: PetscInt dof = graph->subset_idxs[pid-1][j];
716: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
717: PetscBTSet(touched,dof);
718: queue_tip[n] = dof;
719: n++;
720: }
721: }
722: } else {
723: for (j=xadj[start_dof];j<xadj[start_dof+1];j++) {
724: PetscInt dof = adjncy[j];
725: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
726: PetscBTSet(touched,dof);
727: queue_tip[n] = dof;
728: n++;
729: }
730: }
731: }
732: }
733: } else if (havesubs) { /* sub info only */
734: PetscInt sid = graph->local_subs[queue_tip[-n_prev]];
735: for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
736: PetscInt dof = graph->subset_idxs[pid-1][j];
737: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
738: PetscBTSet(touched,dof);
739: queue_tip[n] = dof;
740: n++;
741: }
742: }
743: } else {
744: for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
745: PetscInt dof = graph->subset_idxs[pid-1][j];
746: if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) {
747: PetscBTSet(touched,dof);
748: queue_tip[n] = dof;
749: n++;
750: }
751: }
752: }
753: *n_added = n;
754: return 0;
755: }
757: PetscErrorCode PCBDDCGraphComputeConnectedComponentsLocal(PCBDDCGraph graph)
758: {
759: PetscInt ncc,cum_queue,n;
760: PetscMPIInt commsize;
763: /* quiet return if there isn't any local info */
764: if (!graph->xadj && !graph->n_local_subs) {
765: return 0;
766: }
768: /* reset any previous search of connected components */
769: PetscBTMemzero(graph->nvtxs,graph->touched);
770: MPI_Comm_size(PetscObjectComm((PetscObject)graph->l2gmap),&commsize);
771: if (commsize > graph->commsizelimit) {
772: PetscInt i;
773: for (i=0;i<graph->nvtxs;i++) {
774: if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK || !graph->count[i]) {
775: PetscBTSet(graph->touched,i);
776: }
777: }
778: }
780: /* begin search for connected components */
781: cum_queue = 0;
782: ncc = 0;
783: for (n=0;n<graph->n_subsets;n++) {
784: PetscInt pid = n+1; /* partition labeled by 0 is discarded */
785: PetscInt found = 0,prev = 0,first = 0,ncc_pid = 0;
786: while (found != graph->subset_size[n]) {
787: PetscInt added = 0;
788: if (!prev) { /* search for new starting dof */
789: while (PetscBTLookup(graph->touched,graph->subset_idxs[n][first])) first++;
790: PetscBTSet(graph->touched,graph->subset_idxs[n][first]);
791: graph->queue[cum_queue] = graph->subset_idxs[n][first];
792: graph->cptr[ncc] = cum_queue;
793: prev = 1;
794: cum_queue++;
795: found++;
796: ncc_pid++;
797: ncc++;
798: }
799: PCBDDCGraphComputeCC_Private(graph,pid,graph->queue + cum_queue,prev,&added);
800: if (!added) {
801: graph->subset_ncc[n] = ncc_pid;
802: graph->cptr[ncc] = cum_queue;
803: }
804: prev = added;
805: found += added;
806: cum_queue += added;
807: if (added && found == graph->subset_size[n]) {
808: graph->subset_ncc[n] = ncc_pid;
809: graph->cptr[ncc] = cum_queue;
810: }
811: }
812: }
813: graph->ncc = ncc;
814: graph->queue_sorted = PETSC_FALSE;
815: return 0;
816: }
818: PetscErrorCode PCBDDCGraphSetUp(PCBDDCGraph graph, PetscInt custom_minimal_size, IS neumann_is, IS dirichlet_is, PetscInt n_ISForDofs, IS ISForDofs[], IS custom_primal_vertices)
819: {
820: IS subset,subset_n;
821: MPI_Comm comm;
822: const PetscInt *is_indices;
823: PetscInt n_neigh,*neigh,*n_shared,**shared,*queue_global;
824: PetscInt i,j,k,s,total_counts,nodes_touched,is_size;
825: PetscMPIInt commsize;
826: PetscBool same_set,mirrors_found;
829: if (neumann_is) {
832: }
833: graph->has_dirichlet = PETSC_FALSE;
834: if (dirichlet_is) {
837: graph->has_dirichlet = PETSC_TRUE;
838: }
840: for (i=0;i<n_ISForDofs;i++) {
843: }
844: if (custom_primal_vertices) {
847: }
848: PetscObjectGetComm((PetscObject)(graph->l2gmap),&comm);
849: MPI_Comm_size(comm,&commsize);
851: /* custom_minimal_size */
852: graph->custom_minimal_size = custom_minimal_size;
853: /* get info l2gmap and allocate work vectors */
854: ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
855: /* check if we have any local periodic nodes (periodic BCs) */
856: mirrors_found = PETSC_FALSE;
857: if (graph->nvtxs && n_neigh) {
858: for (i=0; i<n_shared[0]; i++) graph->count[shared[0][i]] += 1;
859: for (i=0; i<n_shared[0]; i++) {
860: if (graph->count[shared[0][i]] > 1) {
861: mirrors_found = PETSC_TRUE;
862: break;
863: }
864: }
865: }
866: /* compute local mirrors (if any) */
867: if (mirrors_found) {
868: IS to,from;
869: PetscInt *local_indices,*global_indices;
871: ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);
872: ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);
873: /* get arrays of local and global indices */
874: PetscMalloc1(graph->nvtxs,&local_indices);
875: ISGetIndices(to,(const PetscInt**)&is_indices);
876: PetscArraycpy(local_indices,is_indices,graph->nvtxs);
877: ISRestoreIndices(to,(const PetscInt**)&is_indices);
878: PetscMalloc1(graph->nvtxs,&global_indices);
879: ISGetIndices(from,(const PetscInt**)&is_indices);
880: PetscArraycpy(global_indices,is_indices,graph->nvtxs);
881: ISRestoreIndices(from,(const PetscInt**)&is_indices);
882: /* allocate space for mirrors */
883: PetscMalloc2(graph->nvtxs,&graph->mirrors,graph->nvtxs,&graph->mirrors_set);
884: PetscArrayzero(graph->mirrors,graph->nvtxs);
885: graph->mirrors_set[0] = NULL;
887: k=0;
888: for (i=0;i<n_shared[0];i++) {
889: j=shared[0][i];
890: if (graph->count[j] > 1) {
891: graph->mirrors[j]++;
892: k++;
893: }
894: }
895: /* allocate space for set of mirrors */
896: PetscMalloc1(k,&graph->mirrors_set[0]);
897: for (i=1;i<graph->nvtxs;i++)
898: graph->mirrors_set[i]=graph->mirrors_set[i-1]+graph->mirrors[i-1];
900: /* fill arrays */
901: PetscArrayzero(graph->mirrors,graph->nvtxs);
902: for (j=0;j<n_shared[0];j++) {
903: i=shared[0][j];
904: if (graph->count[i] > 1)
905: graph->mirrors_set[i][graph->mirrors[i]++]=global_indices[i];
906: }
907: PetscSortIntWithArray(graph->nvtxs,global_indices,local_indices);
908: for (i=0;i<graph->nvtxs;i++) {
909: if (graph->mirrors[i] > 0) {
910: PetscFindInt(graph->mirrors_set[i][0],graph->nvtxs,global_indices,&k);
911: j = global_indices[k];
912: while (k > 0 && global_indices[k-1] == j) k--;
913: for (j=0;j<graph->mirrors[i];j++) {
914: graph->mirrors_set[i][j]=local_indices[k+j];
915: }
916: PetscSortInt(graph->mirrors[i],graph->mirrors_set[i]);
917: }
918: }
919: PetscFree(local_indices);
920: PetscFree(global_indices);
921: ISDestroy(&to);
922: ISDestroy(&from);
923: }
924: PetscArrayzero(graph->count,graph->nvtxs);
926: /* Count total number of neigh per node */
927: k = 0;
928: for (i=1;i<n_neigh;i++) {
929: k += n_shared[i];
930: for (j=0;j<n_shared[i];j++) {
931: graph->count[shared[i][j]] += 1;
932: }
933: }
934: /* Allocate space for storing the set of neighbours for each node */
935: if (graph->nvtxs) {
936: PetscMalloc1(k,&graph->neighbours_set[0]);
937: }
938: for (i=1;i<graph->nvtxs;i++) { /* dont count myself */
939: graph->neighbours_set[i]=graph->neighbours_set[i-1]+graph->count[i-1];
940: }
941: /* Get information for sharing subdomains */
942: PetscArrayzero(graph->count,graph->nvtxs);
943: for (i=1;i<n_neigh;i++) { /* dont count myself */
944: s = n_shared[i];
945: for (j=0;j<s;j++) {
946: k = shared[i][j];
947: graph->neighbours_set[k][graph->count[k]] = neigh[i];
948: graph->count[k] += 1;
949: }
950: }
951: /* sort set of sharing subdomains */
952: for (i=0;i<graph->nvtxs;i++) {
953: PetscSortRemoveDupsInt(&graph->count[i],graph->neighbours_set[i]);
954: }
955: /* free memory allocated by ISLocalToGlobalMappingGetInfo */
956: ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
958: /*
959: Get info for dofs splitting
960: User can specify just a subset; an additional field is considered as a complementary field
961: */
962: for (i=0,k=0;i<n_ISForDofs;i++) {
963: PetscInt bs;
965: ISGetBlockSize(ISForDofs[i],&bs);
966: k += bs;
967: }
968: for (i=0;i<graph->nvtxs;i++) graph->which_dof[i] = k; /* by default a dof belongs to the complement set */
969: for (i=0,k=0;i<n_ISForDofs;i++) {
970: PetscInt bs;
972: ISGetLocalSize(ISForDofs[i],&is_size);
973: ISGetBlockSize(ISForDofs[i],&bs);
974: ISGetIndices(ISForDofs[i],(const PetscInt**)&is_indices);
975: for (j=0;j<is_size/bs;j++) {
976: PetscInt b;
978: for (b=0;b<bs;b++) {
979: PetscInt jj = bs*j + b;
981: if (is_indices[jj] > -1 && is_indices[jj] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
982: graph->which_dof[is_indices[jj]] = k+b;
983: }
984: }
985: }
986: ISRestoreIndices(ISForDofs[i],(const PetscInt**)&is_indices);
987: k += bs;
988: }
990: /* Take into account Neumann nodes */
991: if (neumann_is) {
992: ISGetLocalSize(neumann_is,&is_size);
993: ISGetIndices(neumann_is,(const PetscInt**)&is_indices);
994: for (i=0;i<is_size;i++) {
995: if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
996: graph->special_dof[is_indices[i]] = PCBDDCGRAPH_NEUMANN_MARK;
997: }
998: }
999: ISRestoreIndices(neumann_is,(const PetscInt**)&is_indices);
1000: }
1001: /* Take into account Dirichlet nodes (they overwrite any neumann boundary mark previously set) */
1002: if (dirichlet_is) {
1003: ISGetLocalSize(dirichlet_is,&is_size);
1004: ISGetIndices(dirichlet_is,(const PetscInt**)&is_indices);
1005: for (i=0;i<is_size;i++) {
1006: if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
1007: if (commsize > graph->commsizelimit) { /* dirichlet nodes treated as internal */
1008: PetscBTSet(graph->touched,is_indices[i]);
1009: graph->subset[is_indices[i]] = 0;
1010: }
1011: graph->special_dof[is_indices[i]] = PCBDDCGRAPH_DIRICHLET_MARK;
1012: }
1013: }
1014: ISRestoreIndices(dirichlet_is,(const PetscInt**)&is_indices);
1015: }
1016: /* mark local periodic nodes (if any) and adapt CSR graph (if any) */
1017: if (graph->mirrors) {
1018: for (i=0;i<graph->nvtxs;i++)
1019: if (graph->mirrors[i])
1020: graph->special_dof[i] = PCBDDCGRAPH_LOCAL_PERIODIC_MARK;
1022: if (graph->xadj) {
1023: PetscInt *new_xadj,*new_adjncy;
1024: /* sort CSR graph */
1025: for (i=0;i<graph->nvtxs;i++) {
1026: PetscSortInt(graph->xadj[i+1]-graph->xadj[i],&graph->adjncy[graph->xadj[i]]);
1027: }
1028: /* adapt local CSR graph in case of local periodicity */
1029: k = 0;
1030: for (i=0;i<graph->nvtxs;i++)
1031: for (j=graph->xadj[i];j<graph->xadj[i+1];j++)
1032: k += graph->mirrors[graph->adjncy[j]];
1034: PetscMalloc1(graph->nvtxs+1,&new_xadj);
1035: PetscMalloc1(k+graph->xadj[graph->nvtxs],&new_adjncy);
1036: new_xadj[0] = 0;
1037: for (i=0;i<graph->nvtxs;i++) {
1038: k = graph->xadj[i+1]-graph->xadj[i];
1039: PetscArraycpy(&new_adjncy[new_xadj[i]],&graph->adjncy[graph->xadj[i]],k);
1040: new_xadj[i+1] = new_xadj[i]+k;
1041: for (j=graph->xadj[i];j<graph->xadj[i+1];j++) {
1042: k = graph->mirrors[graph->adjncy[j]];
1043: PetscArraycpy(&new_adjncy[new_xadj[i+1]],graph->mirrors_set[graph->adjncy[j]],k);
1044: new_xadj[i+1] += k;
1045: }
1046: k = new_xadj[i+1]-new_xadj[i];
1047: PetscSortRemoveDupsInt(&k,&new_adjncy[new_xadj[i]]);
1048: new_xadj[i+1] = new_xadj[i]+k;
1049: }
1050: /* set new CSR into graph */
1051: PetscFree(graph->xadj);
1052: PetscFree(graph->adjncy);
1053: graph->xadj = new_xadj;
1054: graph->adjncy = new_adjncy;
1055: }
1056: }
1058: /* mark special nodes (if any) -> each will become a single node equivalence class */
1059: if (custom_primal_vertices) {
1060: ISGetLocalSize(custom_primal_vertices,&is_size);
1061: ISGetIndices(custom_primal_vertices,(const PetscInt**)&is_indices);
1062: for (i=0,j=0;i<is_size;i++) {
1063: 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 */
1064: graph->special_dof[is_indices[i]] = PCBDDCGRAPH_SPECIAL_MARK-j;
1065: j++;
1066: }
1067: }
1068: ISRestoreIndices(custom_primal_vertices,(const PetscInt**)&is_indices);
1069: }
1071: /* mark interior nodes (if commsize > graph->commsizelimit) as touched and belonging to partition number 0 */
1072: if (commsize > graph->commsizelimit) {
1073: for (i=0;i<graph->nvtxs;i++) {
1074: if (!graph->count[i]) {
1075: PetscBTSet(graph->touched,i);
1076: graph->subset[i] = 0;
1077: }
1078: }
1079: }
1081: /* init graph structure and compute default subsets */
1082: nodes_touched = 0;
1083: for (i=0;i<graph->nvtxs;i++) {
1084: if (PetscBTLookup(graph->touched,i)) {
1085: nodes_touched++;
1086: }
1087: }
1088: i = 0;
1089: graph->ncc = 0;
1090: total_counts = 0;
1092: /* allocated space for queues */
1093: if (commsize == graph->commsizelimit) {
1094: PetscMalloc2(graph->nvtxs+1,&graph->cptr,graph->nvtxs,&graph->queue);
1095: } else {
1096: PetscInt nused = graph->nvtxs - nodes_touched;
1097: PetscMalloc2(nused+1,&graph->cptr,nused,&graph->queue);
1098: }
1100: while (nodes_touched<graph->nvtxs) {
1101: /* find first untouched node in local ordering */
1102: while (PetscBTLookup(graph->touched,i)) i++;
1103: PetscBTSet(graph->touched,i);
1104: graph->subset[i] = graph->ncc+1;
1105: graph->cptr[graph->ncc] = total_counts;
1106: graph->queue[total_counts] = i;
1107: total_counts++;
1108: nodes_touched++;
1109: /* now find all other nodes having the same set of sharing subdomains */
1110: for (j=i+1;j<graph->nvtxs;j++) {
1111: /* check for same number of sharing subdomains, dof number and same special mark */
1112: 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]) {
1113: /* check for same set of sharing subdomains */
1114: same_set = PETSC_TRUE;
1115: for (k=0;k<graph->count[j];k++) {
1116: if (graph->neighbours_set[i][k] != graph->neighbours_set[j][k]) {
1117: same_set = PETSC_FALSE;
1118: }
1119: }
1120: /* I have found a friend of mine */
1121: if (same_set) {
1122: PetscBTSet(graph->touched,j);
1123: graph->subset[j] = graph->ncc+1;
1124: nodes_touched++;
1125: graph->queue[total_counts] = j;
1126: total_counts++;
1127: }
1128: }
1129: }
1130: graph->ncc++;
1131: }
1132: /* 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 */
1133: graph->n_subsets = graph->ncc;
1134: PetscMalloc1(graph->n_subsets,&graph->subset_ncc);
1135: for (i=0;i<graph->n_subsets;i++) {
1136: graph->subset_ncc[i] = 1;
1137: }
1138: /* final pointer */
1139: graph->cptr[graph->ncc] = total_counts;
1141: /* For consistency reasons (among neighbours), I need to sort (by global ordering) each connected component */
1142: /* Get a reference node (min index in global ordering) for each subset for tagging messages */
1143: PetscMalloc1(graph->ncc,&graph->subset_ref_node);
1144: PetscMalloc1(graph->cptr[graph->ncc],&queue_global);
1145: ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);
1146: for (j=0;j<graph->ncc;j++) {
1147: PetscSortIntWithArray(graph->cptr[j+1]-graph->cptr[j],&queue_global[graph->cptr[j]],&graph->queue[graph->cptr[j]]);
1148: graph->subset_ref_node[j] = graph->queue[graph->cptr[j]];
1149: }
1150: PetscFree(queue_global);
1151: graph->queue_sorted = PETSC_TRUE;
1153: /* save information on subsets (needed when analyzing the connected components) */
1154: if (graph->ncc) {
1155: PetscMalloc2(graph->ncc,&graph->subset_size,graph->ncc,&graph->subset_idxs);
1156: PetscMalloc1(graph->cptr[graph->ncc],&graph->subset_idxs[0]);
1157: PetscArrayzero(graph->subset_idxs[0],graph->cptr[graph->ncc]);
1158: for (j=1;j<graph->ncc;j++) {
1159: graph->subset_size[j-1] = graph->cptr[j] - graph->cptr[j-1];
1160: graph->subset_idxs[j] = graph->subset_idxs[j-1] + graph->subset_size[j-1];
1161: }
1162: graph->subset_size[graph->ncc-1] = graph->cptr[graph->ncc] - graph->cptr[graph->ncc-1];
1163: PetscArraycpy(graph->subset_idxs[0],graph->queue,graph->cptr[graph->ncc]);
1164: }
1166: /* renumber reference nodes */
1167: ISCreateGeneral(PetscObjectComm((PetscObject)(graph->l2gmap)),graph->ncc,graph->subset_ref_node,PETSC_COPY_VALUES,&subset_n);
1168: ISLocalToGlobalMappingApplyIS(graph->l2gmap,subset_n,&subset);
1169: ISDestroy(&subset_n);
1170: ISRenumber(subset,NULL,NULL,&subset_n);
1171: ISDestroy(&subset);
1172: ISGetLocalSize(subset_n,&k);
1174: ISGetIndices(subset_n,&is_indices);
1175: PetscArraycpy(graph->subset_ref_node,is_indices,graph->ncc);
1176: ISRestoreIndices(subset_n,&is_indices);
1177: ISDestroy(&subset_n);
1179: /* free workspace */
1180: graph->setupcalled = PETSC_TRUE;
1181: return 0;
1182: }
1184: PetscErrorCode PCBDDCGraphResetCoords(PCBDDCGraph graph)
1185: {
1186: if (!graph) return 0;
1187: PetscFree(graph->coords);
1188: graph->cdim = 0;
1189: graph->cnloc = 0;
1190: graph->cloc = PETSC_FALSE;
1191: return 0;
1192: }
1194: PetscErrorCode PCBDDCGraphResetCSR(PCBDDCGraph graph)
1195: {
1196: if (!graph) return 0;
1197: if (graph->freecsr) {
1198: PetscFree(graph->xadj);
1199: PetscFree(graph->adjncy);
1200: } else {
1201: graph->xadj = NULL;
1202: graph->adjncy = NULL;
1203: }
1204: graph->freecsr = PETSC_FALSE;
1205: graph->nvtxs_csr = 0;
1206: return 0;
1207: }
1209: PetscErrorCode PCBDDCGraphReset(PCBDDCGraph graph)
1210: {
1213: if (!graph) return 0;
1214: ISLocalToGlobalMappingDestroy(&graph->l2gmap);
1215: PetscFree(graph->subset_ncc);
1216: PetscFree(graph->subset_ref_node);
1217: if (graph->nvtxs) {
1218: PetscFree(graph->neighbours_set[0]);
1219: }
1220: PetscBTDestroy(&graph->touched);
1221: PetscFree5(graph->count,
1222: graph->neighbours_set,
1223: graph->subset,
1224: graph->which_dof,
1225: graph->special_dof);
1226: PetscFree2(graph->cptr,graph->queue);
1227: if (graph->mirrors) {
1228: PetscFree(graph->mirrors_set[0]);
1229: }
1230: PetscFree2(graph->mirrors,graph->mirrors_set);
1231: if (graph->subset_idxs) {
1232: PetscFree(graph->subset_idxs[0]);
1233: }
1234: PetscFree2(graph->subset_size,graph->subset_idxs);
1235: ISDestroy(&graph->dirdofs);
1236: ISDestroy(&graph->dirdofsB);
1237: if (graph->n_local_subs) {
1238: PetscFree(graph->local_subs);
1239: }
1240: graph->has_dirichlet = PETSC_FALSE;
1241: graph->twodimset = PETSC_FALSE;
1242: graph->twodim = PETSC_FALSE;
1243: graph->nvtxs = 0;
1244: graph->nvtxs_global = 0;
1245: graph->n_subsets = 0;
1246: graph->custom_minimal_size = 1;
1247: graph->n_local_subs = 0;
1248: graph->maxcount = PETSC_MAX_INT;
1249: graph->setupcalled = PETSC_FALSE;
1250: return 0;
1251: }
1253: PetscErrorCode PCBDDCGraphInit(PCBDDCGraph graph, ISLocalToGlobalMapping l2gmap, PetscInt N, PetscInt maxcount)
1254: {
1255: PetscInt n;
1261: /* raise an error if already allocated */
1263: /* set number of vertices */
1264: PetscObjectReference((PetscObject)l2gmap);
1265: graph->l2gmap = l2gmap;
1266: ISLocalToGlobalMappingGetSize(l2gmap,&n);
1267: graph->nvtxs = n;
1268: graph->nvtxs_global = N;
1269: /* allocate used space */
1270: PetscBTCreate(graph->nvtxs,&graph->touched);
1271: PetscMalloc5(graph->nvtxs,&graph->count,graph->nvtxs,&graph->neighbours_set,graph->nvtxs,&graph->subset,graph->nvtxs,&graph->which_dof,graph->nvtxs,&graph->special_dof);
1272: /* zeroes memory */
1273: PetscArrayzero(graph->count,graph->nvtxs);
1274: PetscArrayzero(graph->subset,graph->nvtxs);
1275: /* use -1 as a default value for which_dof array */
1276: for (n=0;n<graph->nvtxs;n++) graph->which_dof[n] = -1;
1277: PetscArrayzero(graph->special_dof,graph->nvtxs);
1278: /* zeroes first pointer to neighbour set */
1279: if (graph->nvtxs) {
1280: graph->neighbours_set[0] = NULL;
1281: }
1282: /* zeroes workspace for values of ncc */
1283: graph->subset_ncc = NULL;
1284: graph->subset_ref_node = NULL;
1285: /* maxcount for cc */
1286: graph->maxcount = maxcount;
1287: return 0;
1288: }
1290: PetscErrorCode PCBDDCGraphDestroy(PCBDDCGraph* graph)
1291: {
1292: PCBDDCGraphResetCSR(*graph);
1293: PCBDDCGraphResetCoords(*graph);
1294: PCBDDCGraphReset(*graph);
1295: PetscFree(*graph);
1296: return 0;
1297: }
1299: PetscErrorCode PCBDDCGraphCreate(PCBDDCGraph *graph)
1300: {
1301: PCBDDCGraph new_graph;
1303: PetscNew(&new_graph);
1304: new_graph->custom_minimal_size = 1;
1305: new_graph->commsizelimit = 1;
1306: *graph = new_graph;
1307: return 0;
1308: }