Actual source code: bddcgraph.c
1: #include <petsc/private/petscimpl.h>
2: #include <petsc/private/pcbddcprivateimpl.h>
3: #include <petsc/private/pcbddcstructsimpl.h>
5: PetscErrorCode PCBDDCDestroyGraphCandidatesIS(void *ctx)
6: {
7: PCBDDCGraphCandidates cand = (PCBDDCGraphCandidates)ctx;
9: PetscFunctionBegin;
10: for (PetscInt i = 0; i < cand->nfc; i++) PetscCall(ISDestroy(&cand->Faces[i]));
11: for (PetscInt i = 0; i < cand->nec; i++) PetscCall(ISDestroy(&cand->Edges[i]));
12: PetscCall(PetscFree(cand->Faces));
13: PetscCall(PetscFree(cand->Edges));
14: PetscCall(ISDestroy(&cand->Vertices));
15: PetscCall(PetscFree(cand));
16: PetscFunctionReturn(PETSC_SUCCESS);
17: }
19: PetscErrorCode PCBDDCGraphGetDirichletDofsB(PCBDDCGraph graph, IS *dirdofs)
20: {
21: PetscFunctionBegin;
22: if (graph->dirdofsB) {
23: PetscCall(PetscObjectReference((PetscObject)graph->dirdofsB));
24: } else if (graph->has_dirichlet) {
25: PetscInt i, size;
26: PetscInt *dirdofs_idxs;
28: size = 0;
29: for (i = 0; i < graph->nvtxs; i++) {
30: if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++;
31: }
33: PetscCall(PetscMalloc1(size, &dirdofs_idxs));
34: size = 0;
35: for (i = 0; i < graph->nvtxs; i++) {
36: if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i;
37: }
38: PetscCall(ISCreateGeneral(PETSC_COMM_SELF, size, dirdofs_idxs, PETSC_OWN_POINTER, &graph->dirdofsB));
39: PetscCall(PetscObjectReference((PetscObject)graph->dirdofsB));
40: }
41: *dirdofs = graph->dirdofsB;
42: PetscFunctionReturn(PETSC_SUCCESS);
43: }
45: PetscErrorCode PCBDDCGraphGetDirichletDofs(PCBDDCGraph graph, IS *dirdofs)
46: {
47: PetscFunctionBegin;
48: if (graph->dirdofs) {
49: PetscCall(PetscObjectReference((PetscObject)graph->dirdofs));
50: } else if (graph->has_dirichlet) {
51: PetscInt i, size;
52: PetscInt *dirdofs_idxs;
54: size = 0;
55: for (i = 0; i < graph->nvtxs; i++) {
56: if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++;
57: }
59: PetscCall(PetscMalloc1(size, &dirdofs_idxs));
60: size = 0;
61: for (i = 0; i < graph->nvtxs; i++) {
62: if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i;
63: }
64: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)graph->l2gmap), size, dirdofs_idxs, PETSC_OWN_POINTER, &graph->dirdofs));
65: PetscCall(PetscObjectReference((PetscObject)graph->dirdofs));
66: }
67: *dirdofs = graph->dirdofs;
68: PetscFunctionReturn(PETSC_SUCCESS);
69: }
71: PetscErrorCode PCBDDCGraphASCIIView(PCBDDCGraph graph, PetscInt verbosity_level, PetscViewer viewer)
72: {
73: PetscInt i, j, tabs;
74: PetscInt *queue_in_global_numbering;
76: PetscFunctionBegin;
77: PetscCall(PetscViewerASCIIPushSynchronized(viewer));
78: PetscCall(PetscViewerASCIIGetTab(viewer, &tabs));
79: PetscCall(PetscViewerASCIIPrintf(viewer, "--------------------------------------------------\n"));
80: PetscCall(PetscViewerFlush(viewer));
81: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Local BDDC graph for subdomain %04d\n", PetscGlobalRank));
82: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Number of vertices %" PetscInt_FMT "\n", graph->nvtxs));
83: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Number of local subdomains %" PetscInt_FMT "\n", graph->n_local_subs ? graph->n_local_subs : 1));
84: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Custom minimal size %" PetscInt_FMT "\n", graph->custom_minimal_size));
85: if (graph->maxcount != PETSC_MAX_INT) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Max count %" PetscInt_FMT "\n", graph->maxcount));
86: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Topological two dim? %s (set %s)\n", PetscBools[graph->twodim], PetscBools[graph->twodimset]));
87: if (verbosity_level > 2) {
88: for (i = 0; i < graph->nvtxs; i++) {
89: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%" PetscInt_FMT ":\n", i));
90: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " which_dof: %" PetscInt_FMT "\n", graph->which_dof[i]));
91: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " special_dof: %" PetscInt_FMT "\n", graph->special_dof[i]));
92: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " neighbours: %" PetscInt_FMT "\n", graph->count[i]));
93: PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_FALSE));
94: if (graph->count[i]) {
95: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " set of neighbours:"));
96: for (j = 0; j < graph->count[i]; j++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %" PetscInt_FMT, graph->neighbours_set[i][j]));
97: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n"));
98: }
99: PetscCall(PetscViewerASCIISetTab(viewer, tabs));
100: PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_TRUE));
101: if (graph->mirrors) {
102: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " mirrors: %" PetscInt_FMT "\n", graph->mirrors[i]));
103: if (graph->mirrors[i]) {
104: PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_FALSE));
105: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " set of mirrors:"));
106: for (j = 0; j < graph->mirrors[i]; j++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %" PetscInt_FMT, graph->mirrors_set[i][j]));
107: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n"));
108: PetscCall(PetscViewerASCIISetTab(viewer, tabs));
109: PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_TRUE));
110: }
111: }
112: if (verbosity_level > 3) {
113: if (graph->xadj) {
114: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " local adj list:"));
115: PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_FALSE));
116: for (j = graph->xadj[i]; j < graph->xadj[i + 1]; j++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %" PetscInt_FMT, graph->adjncy[j]));
117: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n"));
118: PetscCall(PetscViewerASCIISetTab(viewer, tabs));
119: PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_TRUE));
120: } else {
121: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " no adj info\n"));
122: }
123: }
124: if (graph->n_local_subs) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " local sub id: %" PetscInt_FMT "\n", graph->local_subs[i]));
125: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " interface subset id: %" PetscInt_FMT "\n", graph->subset[i]));
126: if (graph->subset[i] && graph->subset_ncc) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " ncc for subset: %" PetscInt_FMT "\n", graph->subset_ncc[graph->subset[i] - 1]));
127: }
128: }
129: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "Total number of connected components %" PetscInt_FMT "\n", graph->ncc));
130: PetscCall(PetscMalloc1(graph->cptr[graph->ncc], &queue_in_global_numbering));
131: PetscCall(ISLocalToGlobalMappingApply(graph->l2gmap, graph->cptr[graph->ncc], graph->queue, queue_in_global_numbering));
132: for (i = 0; i < graph->ncc; i++) {
133: PetscInt node_num = graph->queue[graph->cptr[i]];
134: PetscBool printcc = PETSC_FALSE;
135: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " cc %" PetscInt_FMT " (size %" PetscInt_FMT ", fid %" PetscInt_FMT ", neighs:", i, graph->cptr[i + 1] - graph->cptr[i], graph->which_dof[node_num]));
136: PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_FALSE));
137: for (j = 0; j < graph->count[node_num]; j++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %" PetscInt_FMT, graph->neighbours_set[node_num][j]));
138: if (verbosity_level > 1) {
139: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "):"));
140: if (verbosity_level > 2 || graph->twodim || graph->count[node_num] > 1 || (graph->count[node_num] == 1 && graph->special_dof[node_num] == PCBDDCGRAPH_NEUMANN_MARK)) printcc = PETSC_TRUE;
141: if (printcc) {
142: for (j = graph->cptr[i]; j < graph->cptr[i + 1]; j++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " %" PetscInt_FMT " (%" PetscInt_FMT ")", graph->queue[j], queue_in_global_numbering[j]));
143: }
144: } else {
145: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, ")"));
146: }
147: PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n"));
148: PetscCall(PetscViewerASCIISetTab(viewer, tabs));
149: PetscCall(PetscViewerASCIIUseTabs(viewer, PETSC_TRUE));
150: }
151: PetscCall(PetscFree(queue_in_global_numbering));
152: PetscCall(PetscViewerFlush(viewer));
153: PetscFunctionReturn(PETSC_SUCCESS);
154: }
156: PetscErrorCode PCBDDCGraphRestoreCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS)
157: {
158: PetscInt i;
159: PetscContainer gcand;
161: PetscFunctionBegin;
162: PetscCall(PetscObjectQuery((PetscObject)graph->l2gmap, "_PCBDDCGraphCandidatesIS", (PetscObject *)&gcand));
163: if (gcand) {
164: if (n_faces) *n_faces = 0;
165: if (n_edges) *n_edges = 0;
166: if (FacesIS) *FacesIS = NULL;
167: if (EdgesIS) *EdgesIS = NULL;
168: if (VerticesIS) *VerticesIS = NULL;
169: }
170: if (n_faces) {
171: if (FacesIS) {
172: for (i = 0; i < *n_faces; i++) PetscCall(ISDestroy(&((*FacesIS)[i])));
173: PetscCall(PetscFree(*FacesIS));
174: }
175: *n_faces = 0;
176: }
177: if (n_edges) {
178: if (EdgesIS) {
179: for (i = 0; i < *n_edges; i++) PetscCall(ISDestroy(&((*EdgesIS)[i])));
180: PetscCall(PetscFree(*EdgesIS));
181: }
182: *n_edges = 0;
183: }
184: if (VerticesIS) PetscCall(ISDestroy(VerticesIS));
185: PetscFunctionReturn(PETSC_SUCCESS);
186: }
188: PetscErrorCode PCBDDCGraphGetCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS)
189: {
190: IS *ISForFaces, *ISForEdges, ISForVertices;
191: PetscInt i, nfc, nec, nvc, *idx, *mark;
192: PetscContainer gcand;
194: PetscFunctionBegin;
195: PetscCall(PetscObjectQuery((PetscObject)graph->l2gmap, "_PCBDDCGraphCandidatesIS", (PetscObject *)&gcand));
196: if (gcand) {
197: PCBDDCGraphCandidates cand;
199: PetscCall(PetscContainerGetPointer(gcand, (void **)&cand));
200: if (n_faces) *n_faces = cand->nfc;
201: if (FacesIS) *FacesIS = cand->Faces;
202: if (n_edges) *n_edges = cand->nec;
203: if (EdgesIS) *EdgesIS = cand->Edges;
204: if (VerticesIS) *VerticesIS = cand->Vertices;
205: PetscFunctionReturn(PETSC_SUCCESS);
206: }
207: PetscCall(PetscCalloc1(graph->ncc, &mark));
208: /* loop on ccs to evaluate number of faces, edges and vertices */
209: nfc = 0;
210: nec = 0;
211: nvc = 0;
212: for (i = 0; i < graph->ncc; i++) {
213: PetscInt repdof = graph->queue[graph->cptr[i]];
214: if (graph->cptr[i + 1] - graph->cptr[i] > graph->custom_minimal_size && graph->count[repdof] < graph->maxcount) {
215: if (!graph->twodim && graph->count[repdof] == 1 && graph->special_dof[repdof] != PCBDDCGRAPH_NEUMANN_MARK) {
216: nfc++;
217: mark[i] = 2;
218: } else {
219: nec++;
220: mark[i] = 1;
221: }
222: } else {
223: nvc += graph->cptr[i + 1] - graph->cptr[i];
224: }
225: }
227: /* allocate IS arrays for faces, edges. Vertices need a single index set. */
228: if (FacesIS) PetscCall(PetscMalloc1(nfc, &ISForFaces));
229: if (EdgesIS) PetscCall(PetscMalloc1(nec, &ISForEdges));
230: if (VerticesIS) PetscCall(PetscMalloc1(nvc, &idx));
232: /* loop on ccs to compute index sets for faces and edges */
233: if (!graph->queue_sorted) {
234: PetscInt *queue_global;
236: PetscCall(PetscMalloc1(graph->cptr[graph->ncc], &queue_global));
237: PetscCall(ISLocalToGlobalMappingApply(graph->l2gmap, graph->cptr[graph->ncc], graph->queue, queue_global));
238: for (i = 0; i < graph->ncc; i++) PetscCall(PetscSortIntWithArray(graph->cptr[i + 1] - graph->cptr[i], &queue_global[graph->cptr[i]], &graph->queue[graph->cptr[i]]));
239: PetscCall(PetscFree(queue_global));
240: graph->queue_sorted = PETSC_TRUE;
241: }
242: nfc = 0;
243: nec = 0;
244: for (i = 0; i < graph->ncc; i++) {
245: if (mark[i] == 2) {
246: if (FacesIS) PetscCall(ISCreateGeneral(PETSC_COMM_SELF, graph->cptr[i + 1] - graph->cptr[i], &graph->queue[graph->cptr[i]], PETSC_USE_POINTER, &ISForFaces[nfc]));
247: nfc++;
248: } else if (mark[i] == 1) {
249: if (EdgesIS) PetscCall(ISCreateGeneral(PETSC_COMM_SELF, graph->cptr[i + 1] - graph->cptr[i], &graph->queue[graph->cptr[i]], PETSC_USE_POINTER, &ISForEdges[nec]));
250: nec++;
251: }
252: }
254: /* index set for vertices */
255: if (VerticesIS) {
256: nvc = 0;
257: for (i = 0; i < graph->ncc; i++) {
258: if (!mark[i]) {
259: PetscInt j;
261: for (j = graph->cptr[i]; j < graph->cptr[i + 1]; j++) {
262: idx[nvc] = graph->queue[j];
263: nvc++;
264: }
265: }
266: }
267: /* sort vertex set (by local ordering) */
268: PetscCall(PetscSortInt(nvc, idx));
269: PetscCall(ISCreateGeneral(PETSC_COMM_SELF, nvc, idx, PETSC_OWN_POINTER, &ISForVertices));
270: }
271: PetscCall(PetscFree(mark));
273: /* get back info */
274: if (n_faces) *n_faces = nfc;
275: if (FacesIS) *FacesIS = ISForFaces;
276: if (n_edges) *n_edges = nec;
277: if (EdgesIS) *EdgesIS = ISForEdges;
278: if (VerticesIS) *VerticesIS = ISForVertices;
279: PetscFunctionReturn(PETSC_SUCCESS);
280: }
282: PetscErrorCode PCBDDCGraphComputeConnectedComponents(PCBDDCGraph graph)
283: {
284: PetscBool adapt_interface_reduced;
285: MPI_Comm interface_comm;
286: PetscMPIInt size;
287: PetscInt i;
288: PetscBT cornerp;
290: PetscFunctionBegin;
291: /* compute connected components locally */
292: PetscCall(PetscObjectGetComm((PetscObject)(graph->l2gmap), &interface_comm));
293: PetscCall(PCBDDCGraphComputeConnectedComponentsLocal(graph));
295: cornerp = NULL;
296: if (graph->active_coords) { /* face based corner selection */
297: PetscBT excluded;
298: PetscReal *wdist;
299: PetscInt n_neigh, *neigh, *n_shared, **shared;
300: PetscInt maxc, ns;
302: PetscCall(PetscBTCreate(graph->nvtxs, &cornerp));
303: PetscCall(ISLocalToGlobalMappingGetInfo(graph->l2gmap, &n_neigh, &neigh, &n_shared, &shared));
304: for (ns = 1, maxc = 0; ns < n_neigh; ns++) maxc = PetscMax(maxc, n_shared[ns]);
305: PetscCall(PetscMalloc1(maxc * graph->cdim, &wdist));
306: PetscCall(PetscBTCreate(maxc, &excluded));
308: for (ns = 1; ns < n_neigh; ns++) { /* first proc is self */
309: PetscReal *anchor, mdist;
310: PetscInt fst, j, k, d, cdim = graph->cdim, n = n_shared[ns];
311: PetscInt point1, point2, point3, point4;
313: /* import coordinates on shared interface */
314: PetscCall(PetscBTMemzero(n, excluded));
315: for (j = 0, fst = -1, k = 0; j < n; j++) {
316: PetscBool skip = PETSC_FALSE;
317: for (d = 0; d < cdim; d++) {
318: PetscReal c = graph->coords[shared[ns][j] * cdim + d];
319: skip = (PetscBool)(skip || c == PETSC_MAX_REAL);
320: wdist[k++] = c;
321: }
322: if (skip) {
323: PetscCall(PetscBTSet(excluded, j));
324: } else if (fst == -1) fst = j;
325: }
326: if (fst == -1) continue;
328: /* the dofs are sorted by global numbering, so each rank starts from the same id
329: and it will detect the same corners from the given set */
331: /* find the farthest point from the starting one */
332: anchor = wdist + fst * cdim;
333: mdist = -1.0;
334: point1 = fst;
335: for (j = fst; j < n; j++) {
336: PetscReal dist = 0.0;
338: if (PetscUnlikely(PetscBTLookup(excluded, j))) continue;
339: for (d = 0; d < cdim; d++) dist += (wdist[j * cdim + d] - anchor[d]) * (wdist[j * cdim + d] - anchor[d]);
340: if (dist > mdist) {
341: mdist = dist;
342: point1 = j;
343: }
344: }
346: /* find the farthest point from point1 */
347: anchor = wdist + point1 * cdim;
348: mdist = -1.0;
349: point2 = point1;
350: for (j = fst; j < n; j++) {
351: PetscReal dist = 0.0;
353: if (PetscUnlikely(PetscBTLookup(excluded, j))) continue;
354: for (d = 0; d < cdim; d++) dist += (wdist[j * cdim + d] - anchor[d]) * (wdist[j * cdim + d] - anchor[d]);
355: if (dist > mdist) {
356: mdist = dist;
357: point2 = j;
358: }
359: }
361: /* find the third point maximizing the triangle area */
362: point3 = point2;
363: if (cdim > 2) {
364: PetscReal a = 0.0;
366: for (d = 0; d < cdim; d++) a += (wdist[point1 * cdim + d] - wdist[point2 * cdim + d]) * (wdist[point1 * cdim + d] - wdist[point2 * cdim + d]);
367: a = PetscSqrtReal(a);
368: mdist = -1.0;
369: for (j = fst; j < n; j++) {
370: PetscReal area, b = 0.0, c = 0.0, s;
372: if (PetscUnlikely(PetscBTLookup(excluded, j))) continue;
373: for (d = 0; d < cdim; d++) {
374: b += (wdist[point1 * cdim + d] - wdist[j * cdim + d]) * (wdist[point1 * cdim + d] - wdist[j * cdim + d]);
375: c += (wdist[point2 * cdim + d] - wdist[j * cdim + d]) * (wdist[point2 * cdim + d] - wdist[j * cdim + d]);
376: }
377: b = PetscSqrtReal(b);
378: c = PetscSqrtReal(c);
379: s = 0.5 * (a + b + c);
381: /* Heron's formula, area squared */
382: area = s * (s - a) * (s - b) * (s - c);
383: if (area > mdist) {
384: mdist = area;
385: point3 = j;
386: }
387: }
388: }
390: /* find the farthest point from point3 different from point1 and point2 */
391: anchor = wdist + point3 * cdim;
392: mdist = -1.0;
393: point4 = point3;
394: for (j = fst; j < n; j++) {
395: PetscReal dist = 0.0;
397: if (PetscUnlikely(PetscBTLookup(excluded, j)) || j == point1 || j == point2 || j == point3) continue;
398: for (d = 0; d < cdim; d++) dist += (wdist[j * cdim + d] - anchor[d]) * (wdist[j * cdim + d] - anchor[d]);
399: if (dist > mdist) {
400: mdist = dist;
401: point4 = j;
402: }
403: }
405: PetscCall(PetscBTSet(cornerp, shared[ns][point1]));
406: PetscCall(PetscBTSet(cornerp, shared[ns][point2]));
407: PetscCall(PetscBTSet(cornerp, shared[ns][point3]));
408: PetscCall(PetscBTSet(cornerp, shared[ns][point4]));
410: /* all dofs having the same coordinates will be primal */
411: for (j = fst; j < n; j++) {
412: PetscBool same[] = {PETSC_TRUE, PETSC_TRUE, PETSC_TRUE, PETSC_TRUE};
414: if (PetscUnlikely(PetscBTLookup(excluded, j))) continue;
415: for (d = 0; d < cdim; d++) {
416: same[0] = (PetscBool)(same[0] && (PetscAbsReal(wdist[j * cdim + d] - wdist[point1 * cdim + d]) < PETSC_SMALL));
417: same[1] = (PetscBool)(same[1] && (PetscAbsReal(wdist[j * cdim + d] - wdist[point2 * cdim + d]) < PETSC_SMALL));
418: same[2] = (PetscBool)(same[2] && (PetscAbsReal(wdist[j * cdim + d] - wdist[point3 * cdim + d]) < PETSC_SMALL));
419: same[3] = (PetscBool)(same[3] && (PetscAbsReal(wdist[j * cdim + d] - wdist[point4 * cdim + d]) < PETSC_SMALL));
420: }
421: if (same[0] || same[1] || same[2] || same[3]) PetscCall(PetscBTSet(cornerp, shared[ns][j]));
422: }
423: }
424: PetscCall(PetscBTDestroy(&excluded));
425: PetscCall(PetscFree(wdist));
426: PetscCall(ISLocalToGlobalMappingRestoreInfo(graph->l2gmap, &n_neigh, &neigh, &n_shared, &shared));
427: }
429: /* check consistency of connected components among neighbouring subdomains -> it adapt them in case it is needed */
430: PetscCallMPI(MPI_Comm_size(interface_comm, &size));
431: adapt_interface_reduced = PETSC_FALSE;
432: if (size > 1) {
433: PetscInt i;
434: PetscBool adapt_interface = cornerp ? PETSC_TRUE : PETSC_FALSE;
435: for (i = 0; i < graph->n_subsets && !adapt_interface; i++) {
436: /* We are not sure that on a given subset of the local interface,
437: with two connected components, the latters be the same among sharing subdomains */
438: if (graph->subset_ncc[i] > 1) adapt_interface = PETSC_TRUE;
439: }
440: PetscCall(MPIU_Allreduce(&adapt_interface, &adapt_interface_reduced, 1, MPIU_BOOL, MPI_LOR, interface_comm));
441: }
443: if (graph->n_subsets && adapt_interface_reduced) {
444: PetscBT subset_cc_adapt;
445: MPI_Request *send_requests, *recv_requests;
446: PetscInt *send_buffer, *recv_buffer;
447: PetscInt sum_requests, start_of_recv, start_of_send;
448: PetscInt *cum_recv_counts;
449: PetscInt *labels;
450: PetscInt ncc, cum_queue, mss, mns, j, k, s;
451: PetscInt **refine_buffer = NULL, *private_labels = NULL;
452: PetscBool *subset_has_corn, *recv_buffer_bool, *send_buffer_bool;
454: PetscCall(PetscCalloc1(graph->n_subsets, &subset_has_corn));
455: if (cornerp) {
456: for (i = 0; i < graph->n_subsets; i++) {
457: for (j = 0; j < graph->subset_size[i]; j++) {
458: if (PetscBTLookup(cornerp, graph->subset_idxs[i][j])) {
459: subset_has_corn[i] = PETSC_TRUE;
460: break;
461: }
462: }
463: }
464: }
465: PetscCall(PetscMalloc1(graph->nvtxs, &labels));
466: PetscCall(PetscArrayzero(labels, graph->nvtxs));
467: for (i = 0, k = 0; i < graph->ncc; i++) {
468: PetscInt s = 1;
469: for (j = graph->cptr[i]; j < graph->cptr[i + 1]; j++) {
470: if (cornerp && PetscBTLookup(cornerp, graph->queue[j])) {
471: labels[graph->queue[j]] = k + s;
472: s += 1;
473: } else {
474: labels[graph->queue[j]] = k;
475: }
476: }
477: k += s;
478: }
480: /* allocate some space */
481: PetscCall(PetscMalloc1(graph->n_subsets + 1, &cum_recv_counts));
482: PetscCall(PetscArrayzero(cum_recv_counts, graph->n_subsets + 1));
484: /* first count how many neighbours per connected component I will receive from */
485: cum_recv_counts[0] = 0;
486: for (i = 0; i < graph->n_subsets; i++) cum_recv_counts[i + 1] = cum_recv_counts[i] + graph->count[graph->subset_idxs[i][0]];
487: PetscCall(PetscMalloc1(graph->n_subsets, &send_buffer_bool));
488: PetscCall(PetscMalloc1(cum_recv_counts[graph->n_subsets], &recv_buffer_bool));
489: PetscCall(PetscMalloc2(cum_recv_counts[graph->n_subsets], &send_requests, cum_recv_counts[graph->n_subsets], &recv_requests));
490: for (i = 0; i < cum_recv_counts[graph->n_subsets]; i++) {
491: send_requests[i] = MPI_REQUEST_NULL;
492: recv_requests[i] = MPI_REQUEST_NULL;
493: }
495: /* exchange with my neighbours the number of my connected components on the subset of interface */
496: sum_requests = 0;
497: for (i = 0; i < graph->n_subsets; i++) send_buffer_bool[i] = (PetscBool)(graph->subset_ncc[i] > 1 || subset_has_corn[i]);
498: for (i = 0; i < graph->n_subsets; i++) {
499: PetscMPIInt neigh, tag;
500: PetscInt count, *neighs;
502: count = graph->count[graph->subset_idxs[i][0]];
503: neighs = graph->neighbours_set[graph->subset_idxs[i][0]];
504: PetscCall(PetscMPIIntCast(2 * graph->subset_ref_node[i], &tag));
505: for (k = 0; k < count; k++) {
506: PetscCall(PetscMPIIntCast(neighs[k], &neigh));
507: PetscCallMPI(MPI_Isend(send_buffer_bool + i, 1, MPIU_BOOL, neigh, tag, interface_comm, &send_requests[sum_requests]));
508: PetscCallMPI(MPI_Irecv(recv_buffer_bool + sum_requests, 1, MPIU_BOOL, neigh, tag, interface_comm, &recv_requests[sum_requests]));
509: sum_requests++;
510: }
511: }
512: PetscCallMPI(MPI_Waitall(sum_requests, recv_requests, MPI_STATUSES_IGNORE));
513: PetscCallMPI(MPI_Waitall(sum_requests, send_requests, MPI_STATUSES_IGNORE));
515: /* determine the subsets I have to adapt (those having more than 1 cc) */
516: PetscCall(PetscBTCreate(graph->n_subsets, &subset_cc_adapt));
517: PetscCall(PetscBTMemzero(graph->n_subsets, subset_cc_adapt));
518: for (i = 0; i < graph->n_subsets; i++) {
519: if (graph->subset_ncc[i] > 1 || subset_has_corn[i]) {
520: PetscCall(PetscBTSet(subset_cc_adapt, i));
521: continue;
522: }
523: for (j = cum_recv_counts[i]; j < cum_recv_counts[i + 1]; j++) {
524: if (recv_buffer_bool[j]) {
525: PetscCall(PetscBTSet(subset_cc_adapt, i));
526: break;
527: }
528: }
529: }
530: PetscCall(PetscFree(send_buffer_bool));
531: PetscCall(PetscFree(recv_buffer_bool));
532: PetscCall(PetscFree(subset_has_corn));
534: /* determine send/recv buffers sizes */
535: j = 0;
536: mss = 0;
537: for (i = 0; i < graph->n_subsets; i++) {
538: if (PetscBTLookup(subset_cc_adapt, i)) {
539: j += graph->subset_size[i];
540: mss = PetscMax(graph->subset_size[i], mss);
541: }
542: }
543: k = 0;
544: mns = 0;
545: for (i = 0; i < graph->n_subsets; i++) {
546: if (PetscBTLookup(subset_cc_adapt, i)) {
547: k += (cum_recv_counts[i + 1] - cum_recv_counts[i]) * graph->subset_size[i];
548: mns = PetscMax(cum_recv_counts[i + 1] - cum_recv_counts[i], mns);
549: }
550: }
551: PetscCall(PetscMalloc2(j, &send_buffer, k, &recv_buffer));
553: /* fill send buffer (order matters: subset_idxs ordered by global ordering) */
554: j = 0;
555: for (i = 0; i < graph->n_subsets; i++)
556: if (PetscBTLookup(subset_cc_adapt, i))
557: for (k = 0; k < graph->subset_size[i]; k++) send_buffer[j++] = labels[graph->subset_idxs[i][k]];
559: /* now exchange the data */
560: start_of_recv = 0;
561: start_of_send = 0;
562: sum_requests = 0;
563: for (i = 0; i < graph->n_subsets; i++) {
564: if (PetscBTLookup(subset_cc_adapt, i)) {
565: PetscMPIInt neigh, tag;
566: PetscInt size_of_send = graph->subset_size[i];
568: j = graph->subset_idxs[i][0];
569: PetscCall(PetscMPIIntCast(2 * graph->subset_ref_node[i] + 1, &tag));
570: for (k = 0; k < graph->count[j]; k++) {
571: PetscCall(PetscMPIIntCast(graph->neighbours_set[j][k], &neigh));
572: PetscCallMPI(MPI_Isend(&send_buffer[start_of_send], size_of_send, MPIU_INT, neigh, tag, interface_comm, &send_requests[sum_requests]));
573: PetscCallMPI(MPI_Irecv(&recv_buffer[start_of_recv], size_of_send, MPIU_INT, neigh, tag, interface_comm, &recv_requests[sum_requests]));
574: start_of_recv += size_of_send;
575: sum_requests++;
576: }
577: start_of_send += size_of_send;
578: }
579: }
580: PetscCallMPI(MPI_Waitall(sum_requests, recv_requests, MPI_STATUSES_IGNORE));
582: /* refine connected components */
583: start_of_recv = 0;
584: /* allocate some temporary space */
585: if (mss) {
586: PetscCall(PetscMalloc1(mss, &refine_buffer));
587: PetscCall(PetscMalloc2(mss * (mns + 1), &refine_buffer[0], mss, &private_labels));
588: }
589: ncc = 0;
590: cum_queue = 0;
591: graph->cptr[0] = 0;
592: for (i = 0; i < graph->n_subsets; i++) {
593: if (PetscBTLookup(subset_cc_adapt, i)) {
594: PetscInt subset_counter = 0;
595: PetscInt sharingprocs = cum_recv_counts[i + 1] - cum_recv_counts[i] + 1; /* count myself */
596: PetscInt buffer_size = graph->subset_size[i];
598: PetscCheck(buffer_size >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Expected buffer_size %" PetscInt_FMT " >= 0", buffer_size);
599: /* compute pointers */
600: for (j = 1; j < buffer_size; j++) refine_buffer[j] = refine_buffer[j - 1] + sharingprocs;
601: /* analyze contributions from subdomains that share the i-th subset
602: The structure of refine_buffer is suitable to find intersections of ccs among sharingprocs.
603: 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)
604: sharing procs connected components:
605: neigh 0: [0 1 4], [2 3], labels [4,7] (2 connected components)
606: neigh 1: [0 1], [2 3 4], labels [3 2] (2 connected components)
607: neigh 2: [0 4], [1], [2 3], labels [1 5 6] (3 connected components)
608: refine_buffer will be filled as:
609: [ 4, 3, 1;
610: 4, 2, 1;
611: 7, 2, 6;
612: 4, 3, 5;
613: 7, 2, 6; ];
614: The connected components in local ordering are [0], [1], [2 3], [4] */
615: /* fill temp_buffer */
616: for (k = 0; k < buffer_size; k++) refine_buffer[k][0] = labels[graph->subset_idxs[i][k]];
617: for (j = 0; j < sharingprocs - 1; j++) {
618: for (k = 0; k < buffer_size; k++) refine_buffer[k][j + 1] = recv_buffer[start_of_recv + k];
619: start_of_recv += buffer_size;
620: }
621: PetscCall(PetscArrayzero(private_labels, buffer_size));
622: for (j = 0; j < buffer_size; j++) {
623: if (!private_labels[j]) { /* found a new cc */
624: PetscBool same_set;
626: graph->cptr[ncc] = cum_queue;
627: ncc++;
628: subset_counter++;
629: private_labels[j] = subset_counter;
630: graph->queue[cum_queue++] = graph->subset_idxs[i][j];
631: for (k = j + 1; k < buffer_size; k++) { /* check for other nodes in new cc */
632: same_set = PETSC_TRUE;
633: for (s = 0; s < sharingprocs; s++) {
634: if (refine_buffer[j][s] != refine_buffer[k][s]) {
635: same_set = PETSC_FALSE;
636: break;
637: }
638: }
639: if (same_set) {
640: private_labels[k] = subset_counter;
641: graph->queue[cum_queue++] = graph->subset_idxs[i][k];
642: }
643: }
644: }
645: }
646: graph->cptr[ncc] = cum_queue;
647: graph->subset_ncc[i] = subset_counter;
648: graph->queue_sorted = PETSC_FALSE;
649: } else { /* this subset does not need to be adapted */
650: PetscCall(PetscArraycpy(graph->queue + cum_queue, graph->subset_idxs[i], graph->subset_size[i]));
651: ncc++;
652: cum_queue += graph->subset_size[i];
653: graph->cptr[ncc] = cum_queue;
654: }
655: }
656: graph->cptr[ncc] = cum_queue;
657: graph->ncc = ncc;
658: if (mss) {
659: PetscCall(PetscFree2(refine_buffer[0], private_labels));
660: PetscCall(PetscFree(refine_buffer));
661: }
662: PetscCall(PetscFree(labels));
663: PetscCallMPI(MPI_Waitall(sum_requests, send_requests, MPI_STATUSES_IGNORE));
664: PetscCall(PetscFree2(send_requests, recv_requests));
665: PetscCall(PetscFree2(send_buffer, recv_buffer));
666: PetscCall(PetscFree(cum_recv_counts));
667: PetscCall(PetscBTDestroy(&subset_cc_adapt));
668: }
669: PetscCall(PetscBTDestroy(&cornerp));
671: /* Determine if we are in 2D or 3D */
672: if (!graph->twodimset) {
673: PetscBool twodim = PETSC_TRUE;
674: for (i = 0; i < graph->ncc; i++) {
675: PetscInt repdof = graph->queue[graph->cptr[i]];
676: PetscInt ccsize = graph->cptr[i + 1] - graph->cptr[i];
677: if (graph->count[repdof] > 1 && ccsize > graph->custom_minimal_size) {
678: twodim = PETSC_FALSE;
679: break;
680: }
681: }
682: PetscCall(MPIU_Allreduce(&twodim, &graph->twodim, 1, MPIU_BOOL, MPI_LAND, PetscObjectComm((PetscObject)graph->l2gmap)));
683: graph->twodimset = PETSC_TRUE;
684: }
685: PetscFunctionReturn(PETSC_SUCCESS);
686: }
688: static inline PetscErrorCode PCBDDCGraphComputeCC_Private(PCBDDCGraph graph, PetscInt pid, PetscInt *queue_tip, PetscInt n_prev, PetscInt *n_added)
689: {
690: PetscInt i, j, n;
691: PetscInt *xadj = graph->xadj, *adjncy = graph->adjncy;
692: PetscBT touched = graph->touched;
693: PetscBool havecsr = (PetscBool)(!!xadj);
694: PetscBool havesubs = (PetscBool)(!!graph->n_local_subs);
696: PetscFunctionBegin;
697: n = 0;
698: if (havecsr && !havesubs) {
699: for (i = -n_prev; i < 0; i++) {
700: PetscInt start_dof = queue_tip[i];
701: /* we assume that if a dof has a size 1 adjacency list and the corresponding entry is negative, it is connected to all dofs */
702: if (xadj[start_dof + 1] - xadj[start_dof] == 1 && adjncy[xadj[start_dof]] < 0) {
703: for (j = 0; j < graph->subset_size[pid - 1]; j++) { /* pid \in [1,graph->n_subsets] */
704: PetscInt dof = graph->subset_idxs[pid - 1][j];
705: if (!PetscBTLookup(touched, dof) && graph->subset[dof] == pid) {
706: PetscCall(PetscBTSet(touched, dof));
707: queue_tip[n] = dof;
708: n++;
709: }
710: }
711: } else {
712: for (j = xadj[start_dof]; j < xadj[start_dof + 1]; j++) {
713: PetscInt dof = adjncy[j];
714: if (!PetscBTLookup(touched, dof) && graph->subset[dof] == pid) {
715: PetscCall(PetscBTSet(touched, dof));
716: queue_tip[n] = dof;
717: n++;
718: }
719: }
720: }
721: }
722: } else if (havecsr && havesubs) {
723: PetscInt sid = graph->local_subs[queue_tip[-n_prev]];
724: for (i = -n_prev; i < 0; i++) {
725: PetscInt start_dof = queue_tip[i];
726: /* 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 */
727: if (xadj[start_dof + 1] - xadj[start_dof] == 1 && adjncy[xadj[start_dof]] < 0) {
728: for (j = 0; j < graph->subset_size[pid - 1]; j++) { /* pid \in [1,graph->n_subsets] */
729: PetscInt dof = graph->subset_idxs[pid - 1][j];
730: if (!PetscBTLookup(touched, dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
731: PetscCall(PetscBTSet(touched, dof));
732: queue_tip[n] = dof;
733: n++;
734: }
735: }
736: } else {
737: for (j = xadj[start_dof]; j < xadj[start_dof + 1]; j++) {
738: PetscInt dof = adjncy[j];
739: if (!PetscBTLookup(touched, dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
740: PetscCall(PetscBTSet(touched, dof));
741: queue_tip[n] = dof;
742: n++;
743: }
744: }
745: }
746: }
747: } else if (havesubs) { /* sub info only */
748: PetscInt sid = graph->local_subs[queue_tip[-n_prev]];
749: for (j = 0; j < graph->subset_size[pid - 1]; j++) { /* pid \in [1,graph->n_subsets] */
750: PetscInt dof = graph->subset_idxs[pid - 1][j];
751: if (!PetscBTLookup(touched, dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
752: PetscCall(PetscBTSet(touched, dof));
753: queue_tip[n] = dof;
754: n++;
755: }
756: }
757: } else {
758: for (j = 0; j < graph->subset_size[pid - 1]; j++) { /* pid \in [1,graph->n_subsets] */
759: PetscInt dof = graph->subset_idxs[pid - 1][j];
760: if (!PetscBTLookup(touched, dof) && graph->subset[dof] == pid) {
761: PetscCall(PetscBTSet(touched, dof));
762: queue_tip[n] = dof;
763: n++;
764: }
765: }
766: }
767: *n_added = n;
768: PetscFunctionReturn(PETSC_SUCCESS);
769: }
771: PetscErrorCode PCBDDCGraphComputeConnectedComponentsLocal(PCBDDCGraph graph)
772: {
773: PetscInt ncc, cum_queue, n;
774: PetscMPIInt commsize;
776: PetscFunctionBegin;
777: PetscCheck(graph->setupcalled, PetscObjectComm((PetscObject)graph->l2gmap), PETSC_ERR_ORDER, "PCBDDCGraphSetUp should be called first");
778: /* quiet return if there isn't any local info */
779: if (!graph->xadj && !graph->n_local_subs) PetscFunctionReturn(PETSC_SUCCESS);
781: /* reset any previous search of connected components */
782: PetscCall(PetscBTMemzero(graph->nvtxs, graph->touched));
783: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)graph->l2gmap), &commsize));
784: if (commsize > graph->commsizelimit) {
785: PetscInt i;
786: for (i = 0; i < graph->nvtxs; i++) {
787: if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK || !graph->count[i]) PetscCall(PetscBTSet(graph->touched, i));
788: }
789: }
791: /* begin search for connected components */
792: cum_queue = 0;
793: ncc = 0;
794: for (n = 0; n < graph->n_subsets; n++) {
795: PetscInt pid = n + 1; /* partition labeled by 0 is discarded */
796: PetscInt found = 0, prev = 0, first = 0, ncc_pid = 0;
797: while (found != graph->subset_size[n]) {
798: PetscInt added = 0;
799: if (!prev) { /* search for new starting dof */
800: while (PetscBTLookup(graph->touched, graph->subset_idxs[n][first])) first++;
801: PetscCall(PetscBTSet(graph->touched, graph->subset_idxs[n][first]));
802: graph->queue[cum_queue] = graph->subset_idxs[n][first];
803: graph->cptr[ncc] = cum_queue;
804: prev = 1;
805: cum_queue++;
806: found++;
807: ncc_pid++;
808: ncc++;
809: }
810: PetscCall(PCBDDCGraphComputeCC_Private(graph, pid, graph->queue + cum_queue, prev, &added));
811: if (!added) {
812: graph->subset_ncc[n] = ncc_pid;
813: graph->cptr[ncc] = cum_queue;
814: }
815: prev = added;
816: found += added;
817: cum_queue += added;
818: if (added && found == graph->subset_size[n]) {
819: graph->subset_ncc[n] = ncc_pid;
820: graph->cptr[ncc] = cum_queue;
821: }
822: }
823: }
824: graph->ncc = ncc;
825: graph->queue_sorted = PETSC_FALSE;
826: PetscFunctionReturn(PETSC_SUCCESS);
827: }
829: PetscErrorCode PCBDDCGraphSetUp(PCBDDCGraph graph, PetscInt custom_minimal_size, IS neumann_is, IS dirichlet_is, PetscInt n_ISForDofs, IS ISForDofs[], IS custom_primal_vertices)
830: {
831: IS subset, subset_n;
832: MPI_Comm comm;
833: const PetscInt *is_indices;
834: PetscInt n_neigh, *neigh, *n_shared, **shared, *queue_global;
835: PetscInt i, j, k, s, total_counts, nodes_touched, is_size;
836: PetscMPIInt commsize;
837: PetscBool same_set, mirrors_found;
839: PetscFunctionBegin;
841: if (neumann_is) {
843: PetscCheckSameComm(graph->l2gmap, 1, neumann_is, 3);
844: }
845: graph->has_dirichlet = PETSC_FALSE;
846: if (dirichlet_is) {
848: PetscCheckSameComm(graph->l2gmap, 1, dirichlet_is, 4);
849: graph->has_dirichlet = PETSC_TRUE;
850: }
852: for (i = 0; i < n_ISForDofs; i++) {
854: PetscCheckSameComm(graph->l2gmap, 1, ISForDofs[i], 6);
855: }
856: if (custom_primal_vertices) {
858: PetscCheckSameComm(graph->l2gmap, 1, custom_primal_vertices, 7);
859: }
860: PetscCall(PetscObjectGetComm((PetscObject)(graph->l2gmap), &comm));
861: PetscCallMPI(MPI_Comm_size(comm, &commsize));
863: /* custom_minimal_size */
864: graph->custom_minimal_size = custom_minimal_size;
865: /* get info l2gmap and allocate work vectors */
866: PetscCall(ISLocalToGlobalMappingGetInfo(graph->l2gmap, &n_neigh, &neigh, &n_shared, &shared));
867: /* check if we have any local periodic nodes (periodic BCs) */
868: mirrors_found = PETSC_FALSE;
869: if (graph->nvtxs && n_neigh) {
870: for (i = 0; i < n_shared[0]; i++) graph->count[shared[0][i]] += 1;
871: for (i = 0; i < n_shared[0]; i++) {
872: if (graph->count[shared[0][i]] > 1) {
873: mirrors_found = PETSC_TRUE;
874: break;
875: }
876: }
877: }
878: /* compute local mirrors (if any) */
879: if (mirrors_found) {
880: IS to, from;
881: PetscInt *local_indices, *global_indices;
883: PetscCall(ISCreateStride(PETSC_COMM_SELF, graph->nvtxs, 0, 1, &to));
884: PetscCall(ISLocalToGlobalMappingApplyIS(graph->l2gmap, to, &from));
885: /* get arrays of local and global indices */
886: PetscCall(PetscMalloc1(graph->nvtxs, &local_indices));
887: PetscCall(ISGetIndices(to, (const PetscInt **)&is_indices));
888: PetscCall(PetscArraycpy(local_indices, is_indices, graph->nvtxs));
889: PetscCall(ISRestoreIndices(to, (const PetscInt **)&is_indices));
890: PetscCall(PetscMalloc1(graph->nvtxs, &global_indices));
891: PetscCall(ISGetIndices(from, (const PetscInt **)&is_indices));
892: PetscCall(PetscArraycpy(global_indices, is_indices, graph->nvtxs));
893: PetscCall(ISRestoreIndices(from, (const PetscInt **)&is_indices));
894: /* allocate space for mirrors */
895: PetscCall(PetscMalloc2(graph->nvtxs, &graph->mirrors, graph->nvtxs, &graph->mirrors_set));
896: PetscCall(PetscArrayzero(graph->mirrors, graph->nvtxs));
897: graph->mirrors_set[0] = NULL;
899: k = 0;
900: for (i = 0; i < n_shared[0]; i++) {
901: j = shared[0][i];
902: if (graph->count[j] > 1) {
903: graph->mirrors[j]++;
904: k++;
905: }
906: }
907: /* allocate space for set of mirrors */
908: PetscCall(PetscMalloc1(k, &graph->mirrors_set[0]));
909: for (i = 1; i < graph->nvtxs; i++) graph->mirrors_set[i] = graph->mirrors_set[i - 1] + graph->mirrors[i - 1];
911: /* fill arrays */
912: PetscCall(PetscArrayzero(graph->mirrors, graph->nvtxs));
913: for (j = 0; j < n_shared[0]; j++) {
914: i = shared[0][j];
915: if (graph->count[i] > 1) graph->mirrors_set[i][graph->mirrors[i]++] = global_indices[i];
916: }
917: PetscCall(PetscSortIntWithArray(graph->nvtxs, global_indices, local_indices));
918: for (i = 0; i < graph->nvtxs; i++) {
919: if (graph->mirrors[i] > 0) {
920: PetscCall(PetscFindInt(graph->mirrors_set[i][0], graph->nvtxs, global_indices, &k));
921: j = global_indices[k];
922: while (k > 0 && global_indices[k - 1] == j) k--;
923: for (j = 0; j < graph->mirrors[i]; j++) graph->mirrors_set[i][j] = local_indices[k + j];
924: PetscCall(PetscSortInt(graph->mirrors[i], graph->mirrors_set[i]));
925: }
926: }
927: PetscCall(PetscFree(local_indices));
928: PetscCall(PetscFree(global_indices));
929: PetscCall(ISDestroy(&to));
930: PetscCall(ISDestroy(&from));
931: }
932: PetscCall(PetscArrayzero(graph->count, graph->nvtxs));
934: /* Count total number of neigh per node */
935: k = 0;
936: for (i = 1; i < n_neigh; i++) {
937: k += n_shared[i];
938: for (j = 0; j < n_shared[i]; j++) graph->count[shared[i][j]] += 1;
939: }
940: /* Allocate space for storing the set of neighbours for each node */
941: if (graph->nvtxs) PetscCall(PetscMalloc1(k, &graph->neighbours_set[0]));
942: for (i = 1; i < graph->nvtxs; i++) { /* dont count myself */
943: graph->neighbours_set[i] = graph->neighbours_set[i - 1] + graph->count[i - 1];
944: }
945: /* Get information for sharing subdomains */
946: PetscCall(PetscArrayzero(graph->count, graph->nvtxs));
947: for (i = 1; i < n_neigh; i++) { /* dont count myself */
948: s = n_shared[i];
949: for (j = 0; j < s; j++) {
950: k = shared[i][j];
951: graph->neighbours_set[k][graph->count[k]] = neigh[i];
952: graph->count[k] += 1;
953: }
954: }
955: /* sort set of sharing subdomains */
956: for (i = 0; i < graph->nvtxs; i++) PetscCall(PetscSortRemoveDupsInt(&graph->count[i], graph->neighbours_set[i]));
957: /* free memory allocated by ISLocalToGlobalMappingGetInfo */
958: PetscCall(ISLocalToGlobalMappingRestoreInfo(graph->l2gmap, &n_neigh, &neigh, &n_shared, &shared));
960: /*
961: Get info for dofs splitting
962: User can specify just a subset; an additional field is considered as a complementary field
963: */
964: for (i = 0, k = 0; i < n_ISForDofs; i++) {
965: PetscInt bs;
967: PetscCall(ISGetBlockSize(ISForDofs[i], &bs));
968: k += bs;
969: }
970: for (i = 0; i < graph->nvtxs; i++) graph->which_dof[i] = k; /* by default a dof belongs to the complement set */
971: for (i = 0, k = 0; i < n_ISForDofs; i++) {
972: PetscInt bs;
974: PetscCall(ISGetLocalSize(ISForDofs[i], &is_size));
975: PetscCall(ISGetBlockSize(ISForDofs[i], &bs));
976: PetscCall(ISGetIndices(ISForDofs[i], (const PetscInt **)&is_indices));
977: for (j = 0; j < is_size / bs; j++) {
978: PetscInt b;
980: for (b = 0; b < bs; b++) {
981: PetscInt jj = bs * j + b;
983: if (is_indices[jj] > -1 && is_indices[jj] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
984: graph->which_dof[is_indices[jj]] = k + b;
985: }
986: }
987: }
988: PetscCall(ISRestoreIndices(ISForDofs[i], (const PetscInt **)&is_indices));
989: k += bs;
990: }
992: /* Take into account Neumann nodes */
993: if (neumann_is) {
994: PetscCall(ISGetLocalSize(neumann_is, &is_size));
995: PetscCall(ISGetIndices(neumann_is, (const PetscInt **)&is_indices));
996: for (i = 0; i < is_size; i++) {
997: if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
998: graph->special_dof[is_indices[i]] = PCBDDCGRAPH_NEUMANN_MARK;
999: }
1000: }
1001: PetscCall(ISRestoreIndices(neumann_is, (const PetscInt **)&is_indices));
1002: }
1003: /* Take into account Dirichlet nodes (they overwrite any neumann boundary mark previously set) */
1004: if (dirichlet_is) {
1005: PetscCall(ISGetLocalSize(dirichlet_is, &is_size));
1006: PetscCall(ISGetIndices(dirichlet_is, (const PetscInt **)&is_indices));
1007: for (i = 0; i < is_size; i++) {
1008: if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
1009: if (commsize > graph->commsizelimit) { /* dirichlet nodes treated as internal */
1010: PetscCall(PetscBTSet(graph->touched, is_indices[i]));
1011: graph->subset[is_indices[i]] = 0;
1012: }
1013: graph->special_dof[is_indices[i]] = PCBDDCGRAPH_DIRICHLET_MARK;
1014: }
1015: }
1016: PetscCall(ISRestoreIndices(dirichlet_is, (const PetscInt **)&is_indices));
1017: }
1018: /* mark local periodic nodes (if any) and adapt CSR graph (if any) */
1019: if (graph->mirrors) {
1020: for (i = 0; i < graph->nvtxs; i++)
1021: if (graph->mirrors[i]) graph->special_dof[i] = PCBDDCGRAPH_LOCAL_PERIODIC_MARK;
1023: if (graph->xadj) {
1024: PetscInt *new_xadj, *new_adjncy;
1025: /* sort CSR graph */
1026: for (i = 0; i < graph->nvtxs; i++) PetscCall(PetscSortInt(graph->xadj[i + 1] - graph->xadj[i], &graph->adjncy[graph->xadj[i]]));
1027: /* adapt local CSR graph in case of local periodicity */
1028: k = 0;
1029: for (i = 0; i < graph->nvtxs; i++)
1030: for (j = graph->xadj[i]; j < graph->xadj[i + 1]; j++) k += graph->mirrors[graph->adjncy[j]];
1032: PetscCall(PetscMalloc1(graph->nvtxs + 1, &new_xadj));
1033: PetscCall(PetscMalloc1(k + graph->xadj[graph->nvtxs], &new_adjncy));
1034: new_xadj[0] = 0;
1035: for (i = 0; i < graph->nvtxs; i++) {
1036: k = graph->xadj[i + 1] - graph->xadj[i];
1037: PetscCall(PetscArraycpy(&new_adjncy[new_xadj[i]], &graph->adjncy[graph->xadj[i]], k));
1038: new_xadj[i + 1] = new_xadj[i] + k;
1039: for (j = graph->xadj[i]; j < graph->xadj[i + 1]; j++) {
1040: k = graph->mirrors[graph->adjncy[j]];
1041: PetscCall(PetscArraycpy(&new_adjncy[new_xadj[i + 1]], graph->mirrors_set[graph->adjncy[j]], k));
1042: new_xadj[i + 1] += k;
1043: }
1044: k = new_xadj[i + 1] - new_xadj[i];
1045: PetscCall(PetscSortRemoveDupsInt(&k, &new_adjncy[new_xadj[i]]));
1046: new_xadj[i + 1] = new_xadj[i] + k;
1047: }
1048: /* set new CSR into graph */
1049: PetscCall(PetscFree(graph->xadj));
1050: PetscCall(PetscFree(graph->adjncy));
1051: graph->xadj = new_xadj;
1052: graph->adjncy = new_adjncy;
1053: }
1054: }
1056: /* mark special nodes (if any) -> each will become a single node equivalence class */
1057: if (custom_primal_vertices) {
1058: PetscCall(ISGetLocalSize(custom_primal_vertices, &is_size));
1059: PetscCall(ISGetIndices(custom_primal_vertices, (const PetscInt **)&is_indices));
1060: for (i = 0, j = 0; i < is_size; i++) {
1061: 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 */
1062: graph->special_dof[is_indices[i]] = PCBDDCGRAPH_SPECIAL_MARK - j;
1063: j++;
1064: }
1065: }
1066: PetscCall(ISRestoreIndices(custom_primal_vertices, (const PetscInt **)&is_indices));
1067: }
1069: /* mark interior nodes (if commsize > graph->commsizelimit) as touched and belonging to partition number 0 */
1070: if (commsize > graph->commsizelimit) {
1071: for (i = 0; i < graph->nvtxs; i++) {
1072: if (!graph->count[i]) {
1073: PetscCall(PetscBTSet(graph->touched, i));
1074: graph->subset[i] = 0;
1075: }
1076: }
1077: }
1079: /* init graph structure and compute default subsets */
1080: nodes_touched = 0;
1081: for (i = 0; i < graph->nvtxs; i++) {
1082: if (PetscBTLookup(graph->touched, i)) nodes_touched++;
1083: }
1084: i = 0;
1085: graph->ncc = 0;
1086: total_counts = 0;
1088: /* allocated space for queues */
1089: if (commsize == graph->commsizelimit) {
1090: PetscCall(PetscMalloc2(graph->nvtxs + 1, &graph->cptr, graph->nvtxs, &graph->queue));
1091: } else {
1092: PetscInt nused = graph->nvtxs - nodes_touched;
1093: PetscCall(PetscMalloc2(nused + 1, &graph->cptr, nused, &graph->queue));
1094: }
1096: while (nodes_touched < graph->nvtxs) {
1097: /* find first untouched node in local ordering */
1098: while (PetscBTLookup(graph->touched, i)) i++;
1099: PetscCall(PetscBTSet(graph->touched, i));
1100: graph->subset[i] = graph->ncc + 1;
1101: graph->cptr[graph->ncc] = total_counts;
1102: graph->queue[total_counts] = i;
1103: total_counts++;
1104: nodes_touched++;
1105: /* now find all other nodes having the same set of sharing subdomains */
1106: for (j = i + 1; j < graph->nvtxs; j++) {
1107: /* check for same number of sharing subdomains, dof number and same special mark */
1108: 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]) {
1109: /* check for same set of sharing subdomains */
1110: same_set = PETSC_TRUE;
1111: for (k = 0; k < graph->count[j]; k++) {
1112: if (graph->neighbours_set[i][k] != graph->neighbours_set[j][k]) same_set = PETSC_FALSE;
1113: }
1114: /* I have found a friend of mine */
1115: if (same_set) {
1116: PetscCall(PetscBTSet(graph->touched, j));
1117: graph->subset[j] = graph->ncc + 1;
1118: nodes_touched++;
1119: graph->queue[total_counts] = j;
1120: total_counts++;
1121: }
1122: }
1123: }
1124: graph->ncc++;
1125: }
1126: /* 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 */
1127: graph->n_subsets = graph->ncc;
1128: PetscCall(PetscMalloc1(graph->n_subsets, &graph->subset_ncc));
1129: for (i = 0; i < graph->n_subsets; i++) graph->subset_ncc[i] = 1;
1130: /* final pointer */
1131: graph->cptr[graph->ncc] = total_counts;
1133: /* For consistency reasons (among neighbours), I need to sort (by global ordering) each connected component */
1134: /* Get a reference node (min index in global ordering) for each subset for tagging messages */
1135: PetscCall(PetscMalloc1(graph->ncc, &graph->subset_ref_node));
1136: PetscCall(PetscMalloc1(graph->cptr[graph->ncc], &queue_global));
1137: PetscCall(ISLocalToGlobalMappingApply(graph->l2gmap, graph->cptr[graph->ncc], graph->queue, queue_global));
1138: for (j = 0; j < graph->ncc; j++) {
1139: PetscCall(PetscSortIntWithArray(graph->cptr[j + 1] - graph->cptr[j], &queue_global[graph->cptr[j]], &graph->queue[graph->cptr[j]]));
1140: graph->subset_ref_node[j] = graph->queue[graph->cptr[j]];
1141: }
1142: PetscCall(PetscFree(queue_global));
1143: graph->queue_sorted = PETSC_TRUE;
1145: /* save information on subsets (needed when analyzing the connected components) */
1146: if (graph->ncc) {
1147: PetscCall(PetscMalloc2(graph->ncc, &graph->subset_size, graph->ncc, &graph->subset_idxs));
1148: PetscCall(PetscMalloc1(graph->cptr[graph->ncc], &graph->subset_idxs[0]));
1149: PetscCall(PetscArrayzero(graph->subset_idxs[0], graph->cptr[graph->ncc]));
1150: for (j = 1; j < graph->ncc; j++) {
1151: graph->subset_size[j - 1] = graph->cptr[j] - graph->cptr[j - 1];
1152: graph->subset_idxs[j] = graph->subset_idxs[j - 1] + graph->subset_size[j - 1];
1153: }
1154: graph->subset_size[graph->ncc - 1] = graph->cptr[graph->ncc] - graph->cptr[graph->ncc - 1];
1155: PetscCall(PetscArraycpy(graph->subset_idxs[0], graph->queue, graph->cptr[graph->ncc]));
1156: }
1158: /* renumber reference nodes */
1159: PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)(graph->l2gmap)), graph->ncc, graph->subset_ref_node, PETSC_COPY_VALUES, &subset_n));
1160: PetscCall(ISLocalToGlobalMappingApplyIS(graph->l2gmap, subset_n, &subset));
1161: PetscCall(ISDestroy(&subset_n));
1162: PetscCall(ISRenumber(subset, NULL, NULL, &subset_n));
1163: PetscCall(ISDestroy(&subset));
1164: PetscCall(ISGetLocalSize(subset_n, &k));
1165: PetscCheck(k == graph->ncc, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid size of new subset! %" PetscInt_FMT " != %" PetscInt_FMT, k, graph->ncc);
1166: PetscCall(ISGetIndices(subset_n, &is_indices));
1167: PetscCall(PetscArraycpy(graph->subset_ref_node, is_indices, graph->ncc));
1168: PetscCall(ISRestoreIndices(subset_n, &is_indices));
1169: PetscCall(ISDestroy(&subset_n));
1171: /* free workspace */
1172: graph->setupcalled = PETSC_TRUE;
1173: PetscFunctionReturn(PETSC_SUCCESS);
1174: }
1176: PetscErrorCode PCBDDCGraphResetCoords(PCBDDCGraph graph)
1177: {
1178: PetscFunctionBegin;
1179: if (!graph) PetscFunctionReturn(PETSC_SUCCESS);
1180: PetscCall(PetscFree(graph->coords));
1181: graph->cdim = 0;
1182: graph->cnloc = 0;
1183: graph->cloc = PETSC_FALSE;
1184: PetscFunctionReturn(PETSC_SUCCESS);
1185: }
1187: PetscErrorCode PCBDDCGraphResetCSR(PCBDDCGraph graph)
1188: {
1189: PetscFunctionBegin;
1190: if (!graph) PetscFunctionReturn(PETSC_SUCCESS);
1191: if (graph->freecsr) {
1192: PetscCall(PetscFree(graph->xadj));
1193: PetscCall(PetscFree(graph->adjncy));
1194: } else {
1195: graph->xadj = NULL;
1196: graph->adjncy = NULL;
1197: }
1198: graph->freecsr = PETSC_FALSE;
1199: graph->nvtxs_csr = 0;
1200: PetscFunctionReturn(PETSC_SUCCESS);
1201: }
1203: PetscErrorCode PCBDDCGraphReset(PCBDDCGraph graph)
1204: {
1205: PetscFunctionBegin;
1206: if (!graph) PetscFunctionReturn(PETSC_SUCCESS);
1207: PetscCall(ISLocalToGlobalMappingDestroy(&graph->l2gmap));
1208: PetscCall(PetscFree(graph->subset_ncc));
1209: PetscCall(PetscFree(graph->subset_ref_node));
1210: if (graph->nvtxs) PetscCall(PetscFree(graph->neighbours_set[0]));
1211: PetscCall(PetscBTDestroy(&graph->touched));
1212: PetscCall(PetscFree5(graph->count, graph->neighbours_set, graph->subset, graph->which_dof, graph->special_dof));
1213: PetscCall(PetscFree2(graph->cptr, graph->queue));
1214: if (graph->mirrors) PetscCall(PetscFree(graph->mirrors_set[0]));
1215: PetscCall(PetscFree2(graph->mirrors, graph->mirrors_set));
1216: if (graph->subset_idxs) PetscCall(PetscFree(graph->subset_idxs[0]));
1217: PetscCall(PetscFree2(graph->subset_size, graph->subset_idxs));
1218: PetscCall(ISDestroy(&graph->dirdofs));
1219: PetscCall(ISDestroy(&graph->dirdofsB));
1220: if (graph->n_local_subs) PetscCall(PetscFree(graph->local_subs));
1221: graph->has_dirichlet = PETSC_FALSE;
1222: graph->twodimset = PETSC_FALSE;
1223: graph->twodim = PETSC_FALSE;
1224: graph->nvtxs = 0;
1225: graph->nvtxs_global = 0;
1226: graph->n_subsets = 0;
1227: graph->custom_minimal_size = 1;
1228: graph->n_local_subs = 0;
1229: graph->maxcount = PETSC_MAX_INT;
1230: graph->setupcalled = PETSC_FALSE;
1231: PetscFunctionReturn(PETSC_SUCCESS);
1232: }
1234: PetscErrorCode PCBDDCGraphInit(PCBDDCGraph graph, ISLocalToGlobalMapping l2gmap, PetscInt N, PetscInt maxcount)
1235: {
1236: PetscInt n;
1238: PetscFunctionBegin;
1239: PetscAssertPointer(graph, 1);
1243: /* raise an error if already allocated */
1244: PetscCheck(!graph->nvtxs_global, PetscObjectComm((PetscObject)l2gmap), PETSC_ERR_PLIB, "BDDCGraph already initialized");
1245: /* set number of vertices */
1246: PetscCall(PetscObjectReference((PetscObject)l2gmap));
1247: graph->l2gmap = l2gmap;
1248: PetscCall(ISLocalToGlobalMappingGetSize(l2gmap, &n));
1249: graph->nvtxs = n;
1250: graph->nvtxs_global = N;
1251: /* allocate used space */
1252: PetscCall(PetscBTCreate(graph->nvtxs, &graph->touched));
1253: PetscCall(PetscMalloc5(graph->nvtxs, &graph->count, graph->nvtxs, &graph->neighbours_set, graph->nvtxs, &graph->subset, graph->nvtxs, &graph->which_dof, graph->nvtxs, &graph->special_dof));
1254: /* zeroes memory */
1255: PetscCall(PetscArrayzero(graph->count, graph->nvtxs));
1256: PetscCall(PetscArrayzero(graph->subset, graph->nvtxs));
1257: /* use -1 as a default value for which_dof array */
1258: for (n = 0; n < graph->nvtxs; n++) graph->which_dof[n] = -1;
1259: PetscCall(PetscArrayzero(graph->special_dof, graph->nvtxs));
1260: /* zeroes first pointer to neighbour set */
1261: if (graph->nvtxs) graph->neighbours_set[0] = NULL;
1262: /* zeroes workspace for values of ncc */
1263: graph->subset_ncc = NULL;
1264: graph->subset_ref_node = NULL;
1265: /* maxcount for cc */
1266: graph->maxcount = maxcount;
1267: PetscFunctionReturn(PETSC_SUCCESS);
1268: }
1270: PetscErrorCode PCBDDCGraphDestroy(PCBDDCGraph *graph)
1271: {
1272: PetscFunctionBegin;
1273: PetscCall(PCBDDCGraphResetCSR(*graph));
1274: PetscCall(PCBDDCGraphResetCoords(*graph));
1275: PetscCall(PCBDDCGraphReset(*graph));
1276: PetscCall(PetscFree(*graph));
1277: PetscFunctionReturn(PETSC_SUCCESS);
1278: }
1280: PetscErrorCode PCBDDCGraphCreate(PCBDDCGraph *graph)
1281: {
1282: PCBDDCGraph new_graph;
1284: PetscFunctionBegin;
1285: PetscCall(PetscNew(&new_graph));
1286: new_graph->custom_minimal_size = 1;
1287: new_graph->commsizelimit = 1;
1288: *graph = new_graph;
1289: PetscFunctionReturn(PETSC_SUCCESS);
1290: }