Actual source code: geo.c
1: /*
2: GAMG geometric-algebraic multigrid PC - Mark Adams 2011
3: */
5: #include <../src/ksp/pc/impls/gamg/gamg.h>
7: #if PetscDefined(HAVE_TRIANGLE)
8: #if !defined(ANSI_DECLARATORS)
9: #define ANSI_DECLARATORS
10: #endif
11: #include <triangle.h>
12: #endif
14: #include <petscblaslapack.h>
16: /* Private context for the GAMG preconditioner */
17: typedef struct {
18: PetscInt lid; /* local vertex index */
19: PetscInt degree; /* vertex degree */
20: } GAMGNode;
22: static inline int petsc_geo_mg_compare(const void *a, const void *b)
23: {
24: return (int)(((GAMGNode *)a)->degree - ((GAMGNode *)b)->degree);
25: }
27: // PetscClangLinter pragma disable: -fdoc-sowing-chars
28: /*
29: PCSetCoordinates_GEO
31: Input Parameter:
32: . pc - the preconditioner context
33: */
34: static PetscErrorCode PCSetCoordinates_GEO(PC pc, PetscInt ndm, PetscInt a_nloc, PetscReal *coords)
35: {
36: PC_MG *mg = (PC_MG *)pc->data;
37: PC_GAMG *pc_gamg = (PC_GAMG *)mg->innerctx;
38: PetscInt arrsz, bs, my0, kk, ii, nloc, Iend, aloc;
39: Mat Amat = pc->pmat;
41: PetscFunctionBegin;
43: PetscCall(MatGetBlockSize(Amat, &bs));
44: PetscCall(MatGetOwnershipRange(Amat, &my0, &Iend));
45: aloc = (Iend - my0);
46: nloc = (Iend - my0) / bs;
48: PetscCheck(nloc == a_nloc || aloc == a_nloc, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Number of local blocks %" PetscInt_FMT " must be %" PetscInt_FMT " or %" PetscInt_FMT ".", a_nloc, nloc, aloc);
50: pc_gamg->data_cell_rows = 1;
51: PetscCheck(coords || (nloc <= 0), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Need coordinates for pc_gamg_type 'geo'.");
52: pc_gamg->data_cell_cols = ndm; /* coordinates */
54: arrsz = nloc * pc_gamg->data_cell_rows * pc_gamg->data_cell_cols;
56: /* create data - syntactic sugar that should be refactored at some point */
57: if (!pc_gamg->data || (pc_gamg->data_sz != arrsz)) {
58: PetscCall(PetscFree(pc_gamg->data));
59: PetscCall(PetscMalloc1(arrsz + 1, &pc_gamg->data));
60: }
61: for (kk = 0; kk < arrsz; kk++) pc_gamg->data[kk] = -999.;
62: pc_gamg->data[arrsz] = -99.;
63: /* copy data in - column-oriented */
64: if (nloc == a_nloc) {
65: for (kk = 0; kk < nloc; kk++) {
66: for (ii = 0; ii < ndm; ii++) pc_gamg->data[ii * nloc + kk] = coords[kk * ndm + ii];
67: }
68: } else { /* assumes the coordinates are blocked */
69: for (kk = 0; kk < nloc; kk++) {
70: for (ii = 0; ii < ndm; ii++) pc_gamg->data[ii * nloc + kk] = coords[bs * kk * ndm + ii];
71: }
72: }
73: PetscCheck(pc_gamg->data[arrsz] == -99., PETSC_COMM_SELF, PETSC_ERR_PLIB, "pc_gamg->data[arrsz %" PetscInt_FMT "] %g != -99.", arrsz, (double)pc_gamg->data[arrsz]);
74: pc_gamg->data_sz = arrsz;
75: PetscFunctionReturn(PETSC_SUCCESS);
76: }
78: // PetscClangLinter pragma disable: -fdoc-sowing-chars
79: /*
80: PCSetData_GEO
82: Input Parameter:
83: . pc -
84: */
85: static PetscErrorCode PCSetData_GEO(PC pc, Mat m)
86: {
87: PetscFunctionBegin;
88: SETERRQ(PetscObjectComm((PetscObject)pc), PETSC_ERR_PLIB, "GEO MG needs coordinates");
89: }
91: static PetscErrorCode PCSetFromOptions_GEO(PC pc, PetscOptionItems PetscOptionsObject)
92: {
93: PetscFunctionBegin;
94: PetscOptionsHeadBegin(PetscOptionsObject, "GAMG-GEO options");
95: {
96: /* -pc_gamg_sa_nsmooths */
97: /* pc_gamg_sa->smooths = 0; */
98: /* ierr = PetscOptionsInt("-pc_gamg_agg_nsmooths", */
99: /* "smoothing steps for smoothed aggregation, usually 1 (0)", */
100: /* "PCGAMGSetNSmooths_AGG", */
101: /* pc_gamg_sa->smooths, */
102: /* &pc_gamg_sa->smooths, */
103: /* &flag); */
104: }
105: PetscOptionsHeadEnd();
106: PetscFunctionReturn(PETSC_SUCCESS);
107: }
109: // PetscClangLinter pragma disable: -fdoc-sowing-chars
110: /*
111: triangulateAndFormProl
113: Input Parameter:
114: . selected_2 - list of selected local ID, includes selected ghosts
115: . data_stride -
116: . coords[2*data_stride] - column vector of local coordinates w/ ghosts
117: . nselected_1 - selected IDs that go with base (1) graph includes selected ghosts
118: . clid_lid_1[nselected_1] - lids of selected (c) nodes ???????????
119: . agg_lists_1 - list of aggregates selected_1 vertices of aggregate unselected vertices
120: . crsGID[selected.size()] - global index for prolongation operator
121: . bs - block size
122: Output Parameter:
123: . a_Prol - prolongation operator
124: . a_worst_best - measure of worst missed fine vertex, 0 is no misses
125: */
126: static PetscErrorCode triangulateAndFormProl(IS selected_2, PetscInt data_stride, PetscReal coords[], PetscInt nselected_1, const PetscInt clid_lid_1[], const PetscCoarsenData *agg_lists_1, const PetscInt crsGID[], PetscInt bs, Mat a_Prol, PetscReal *a_worst_best)
127: {
128: #if PetscDefined(HAVE_TRIANGLE)
129: PetscInt jj, tid, tt, idx, nselected_2;
130: struct triangulateio in, mid;
131: const PetscInt *selected_idx_2;
132: PetscMPIInt rank;
133: PetscInt Istart, Iend, nFineLoc, myFine0;
134: int kk, nPlotPts, sid;
135: MPI_Comm comm;
137: PetscFunctionBegin;
138: PetscCall(PetscObjectGetComm((PetscObject)a_Prol, &comm));
139: PetscCallMPI(MPI_Comm_rank(comm, &rank));
140: PetscCall(ISGetSize(selected_2, &nselected_2));
141: if (nselected_2 == 1 || nselected_2 == 2) { /* 0 happens on idle processors */
142: *a_worst_best = 100.0; /* this will cause a stop, but not globalized (should not happen) */
143: } else *a_worst_best = 0.0;
144: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, a_worst_best, 1, MPIU_REAL, MPIU_MAX, comm));
145: if (*a_worst_best > 0.0) {
146: *a_worst_best = 100.0;
147: PetscFunctionReturn(PETSC_SUCCESS);
148: }
149: PetscCall(MatGetOwnershipRange(a_Prol, &Istart, &Iend));
150: nFineLoc = (Iend - Istart) / bs;
151: myFine0 = Istart / bs;
152: PetscCall(PetscCIntCast(nFineLoc, &nPlotPts)); /* locals */
153: /* triangle */
154: /* Define input points - in */
155: PetscCall(PetscCIntCast(nselected_2, &in.numberofpoints));
156: in.numberofpointattributes = 0;
157: /* get nselected points */
158: PetscCall(PetscMalloc1(2 * nselected_2, &in.pointlist));
159: PetscCall(ISGetIndices(selected_2, &selected_idx_2));
161: for (kk = 0, sid = 0; kk < nselected_2; kk++, sid += 2) {
162: PetscInt lid = selected_idx_2[kk];
163: in.pointlist[sid] = coords[lid];
164: in.pointlist[sid + 1] = coords[data_stride + lid];
165: if (lid >= nFineLoc) nPlotPts++;
166: }
167: PetscCheck(sid == 2 * nselected_2, PETSC_COMM_SELF, PETSC_ERR_PLIB, "sid %d != 2*nselected_2 %" PetscInt_FMT, sid, nselected_2);
169: in.numberofsegments = 0;
170: in.numberofedges = 0;
171: in.numberofholes = 0;
172: in.numberofregions = 0;
173: in.trianglelist = NULL;
174: in.segmentmarkerlist = NULL;
175: in.pointattributelist = NULL;
176: in.pointmarkerlist = NULL;
177: in.triangleattributelist = NULL;
178: in.trianglearealist = NULL;
179: in.segmentlist = NULL;
180: in.holelist = NULL;
181: in.regionlist = NULL;
182: in.edgelist = NULL;
183: in.edgemarkerlist = NULL;
184: in.normlist = NULL;
186: /* triangulate */
187: mid.pointlist = NULL; /* Not needed if -N switch used. */
188: /* Not needed if -N switch used or number of point attributes is zero: */
189: mid.pointattributelist = NULL;
190: mid.pointmarkerlist = NULL; /* Not needed if -N or -B switch used. */
191: mid.trianglelist = NULL; /* Not needed if -E switch used. */
192: /* Not needed if -E switch used or number of triangle attributes is zero: */
193: mid.triangleattributelist = NULL;
194: mid.neighborlist = NULL; /* Needed only if -n switch used. */
195: /* Needed only if segments are output (-p or -c) and -P not used: */
196: mid.segmentlist = NULL;
197: /* Needed only if segments are output (-p or -c) and -P and -B not used: */
198: mid.segmentmarkerlist = NULL;
199: mid.edgelist = NULL; /* Needed only if -e switch used. */
200: mid.edgemarkerlist = NULL; /* Needed if -e used and -B not used. */
201: mid.numberoftriangles = 0;
203: /* Triangulate the points. Switches are chosen to read and write a */
204: /* PSLG (p), preserve the convex hull (c), number everything from */
205: /* zero (z), assign a regional attribute to each element (A), and */
206: /* produce an edge list (e), a Voronoi diagram (v), and a triangle */
207: /* neighbor list (n). */
208: if (nselected_2 != 0) { /* inactive processor */
209: char args[] = "npczQ"; /* c is needed ? */
210: triangulate(args, &in, &mid, (struct triangulateio *)NULL);
211: /* output .poly files for 'showme' */
212: if (!PETSC_TRUE) {
213: static int level = 1;
214: FILE *file;
215: char fname[32];
217: PetscCall(PetscSNPrintf(fname, PETSC_STATIC_ARRAY_LENGTH(fname), "C%d_%d.poly", level, rank));
218: file = fopen(fname, "w");
219: /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */
220: fprintf(file, "%d %d %d %d\n", in.numberofpoints, 2, 0, 0);
221: /* Following lines: <vertex #> <x> <y> */
222: for (kk = 0, sid = 0; kk < in.numberofpoints; kk++, sid += 2) fprintf(file, "%d %e %e\n", kk, in.pointlist[sid], in.pointlist[sid + 1]);
223: /* One line: <# of segments> <# of boundary markers (0 or 1)> */
224: fprintf(file, "%d %d\n", 0, 0);
225: /* Following lines: <segment #> <endpoint> <endpoint> [boundary marker] */
226: /* One line: <# of holes> */
227: fprintf(file, "%d\n", 0);
228: /* Following lines: <hole #> <x> <y> */
229: /* Optional line: <# of regional attributes and/or area constraints> */
230: /* Optional following lines: <region #> <x> <y> <attribute> <maximum area> */
231: fclose(file);
233: /* elems */
234: PetscCall(PetscSNPrintf(fname, PETSC_STATIC_ARRAY_LENGTH(fname), "C%d_%d.ele", level, rank));
235: file = fopen(fname, "w");
236: /* First line: <# of triangles> <nodes per triangle> <# of attributes> */
237: fprintf(file, "%d %d %d\n", mid.numberoftriangles, 3, 0);
238: /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */
239: for (kk = 0, sid = 0; kk < mid.numberoftriangles; kk++, sid += 3) fprintf(file, "%d %d %d %d\n", kk, mid.trianglelist[sid], mid.trianglelist[sid + 1], mid.trianglelist[sid + 2]);
240: fclose(file);
242: PetscCall(PetscSNPrintf(fname, PETSC_STATIC_ARRAY_LENGTH(fname), "C%d_%d.node", level, rank));
243: file = fopen(fname, "w");
244: /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */
245: /* fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); */
246: fprintf(file, "%d %d %d %d\n", nPlotPts, 2, 0, 0);
247: /* Following lines: <vertex #> <x> <y> */
248: for (kk = 0, sid = 0; kk < in.numberofpoints; kk++, sid += 2) fprintf(file, "%d %e %e\n", kk, in.pointlist[sid], in.pointlist[sid + 1]);
250: sid /= 2;
251: for (jj = 0; jj < nFineLoc; jj++) {
252: PetscBool sel = PETSC_TRUE;
253: for (kk = 0; kk < nselected_2 && sel; kk++) {
254: PetscInt lid = selected_idx_2[kk];
255: if (lid == jj) sel = PETSC_FALSE;
256: }
257: if (sel) fprintf(file, "%d %e %e\n", sid++, (double)coords[jj], (double)coords[data_stride + jj]);
258: }
259: fclose(file);
260: PetscCheck(sid == nPlotPts, PETSC_COMM_SELF, PETSC_ERR_PLIB, "sid %d != nPlotPts %d", sid, nPlotPts);
261: level++;
262: }
263: }
264: { /* form P - setup some maps */
265: PetscInt clid, mm, *nTri, *node_tri;
267: PetscCall(PetscMalloc2(nselected_2, &node_tri, nselected_2, &nTri));
269: /* need list of triangles on node */
270: for (kk = 0; kk < nselected_2; kk++) nTri[kk] = 0;
271: for (tid = 0, kk = 0; tid < mid.numberoftriangles; tid++) {
272: for (jj = 0; jj < 3; jj++) {
273: PetscInt cid = mid.trianglelist[kk++];
274: if (nTri[cid] == 0) node_tri[cid] = tid;
275: nTri[cid]++;
276: }
277: }
278: #define EPS 1.e-12
279: /* find points and set prolongation */
280: for (mm = clid = 0; mm < nFineLoc; mm++) {
281: PetscBool ise;
282: PetscCall(PetscCDIsEmptyAt(agg_lists_1, mm, &ise));
283: if (!ise) {
284: const PetscInt lid = mm;
285: PetscScalar AA[3][3];
286: PetscBLASInt N = 3, NRHS = 1, LDA = 3, IPIV[3], LDB = 3;
287: PetscCDIntNd *pos;
289: PetscCall(PetscCDGetHeadPos(agg_lists_1, lid, &pos));
290: while (pos) {
291: PetscInt flid;
292: PetscCall(PetscCDIntNdGetID(pos, &flid));
293: PetscCall(PetscCDGetNextPos(agg_lists_1, lid, &pos));
295: if (flid < nFineLoc) { /* could be a ghost */
296: PetscInt bestTID = -1;
297: PetscReal best_alpha = 1.e10;
298: const PetscInt fgid = flid + myFine0;
299: /* compute shape function for gid */
300: const PetscReal fcoord[3] = {coords[flid], coords[data_stride + flid], 1.0};
301: PetscBool haveit = PETSC_FALSE;
302: PetscScalar alpha[3];
303: PetscInt clids[3];
305: /* look for it */
306: for (tid = node_tri[clid], jj = 0; jj < 5 && !haveit && tid != -1; jj++) {
307: for (tt = 0; tt < 3; tt++) {
308: PetscInt cid2 = mid.trianglelist[3 * tid + tt];
309: PetscInt lid2 = selected_idx_2[cid2];
310: AA[tt][0] = coords[lid2];
311: AA[tt][1] = coords[data_stride + lid2];
312: AA[tt][2] = 1.0;
313: clids[tt] = cid2; /* store for interp */
314: }
316: for (tt = 0; tt < 3; tt++) alpha[tt] = (PetscScalar)fcoord[tt];
318: PetscCallLAPACKInfo("LAPACKgesv", LAPACKgesv_(&N, &NRHS, (PetscScalar *)AA, &LDA, IPIV, alpha, &LDB, &info));
319: {
320: PetscBool have = PETSC_TRUE;
321: PetscReal lowest = 1.e10;
322: for (tt = 0, idx = 0; tt < 3; tt++) {
323: if (PetscRealPart(alpha[tt]) > (1.0 + EPS) || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE;
324: if (PetscRealPart(alpha[tt]) < lowest) {
325: lowest = PetscRealPart(alpha[tt]);
326: idx = tt;
327: }
328: }
329: haveit = have;
330: }
331: tid = mid.neighborlist[3 * tid + idx];
332: }
334: if (!haveit) {
335: /* brute force */
336: for (tid = 0; tid < mid.numberoftriangles && !haveit; tid++) {
337: for (tt = 0; tt < 3; tt++) {
338: PetscInt cid2 = mid.trianglelist[3 * tid + tt];
339: PetscInt lid2 = selected_idx_2[cid2];
340: AA[tt][0] = coords[lid2];
341: AA[tt][1] = coords[data_stride + lid2];
342: AA[tt][2] = 1.0;
343: clids[tt] = cid2; /* store for interp */
344: }
345: for (tt = 0; tt < 3; tt++) alpha[tt] = fcoord[tt];
346: PetscCallLAPACKInfo("LAPACKgesv", LAPACKgesv_(&N, &NRHS, (PetscScalar *)AA, &LDA, IPIV, alpha, &LDB, &info));
347: {
348: PetscBool have = PETSC_TRUE;
349: PetscReal worst = 0.0, v;
350: for (tt = 0; tt < 3 && have; tt++) {
351: if (PetscRealPart(alpha[tt]) > 1.0 + EPS || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE;
352: if ((v = PetscAbs(PetscRealPart(alpha[tt]) - 0.5)) > worst) worst = v;
353: }
354: if (worst < best_alpha) {
355: best_alpha = worst;
356: bestTID = tid;
357: }
358: haveit = have;
359: }
360: }
361: }
362: if (!haveit) {
363: if (best_alpha > *a_worst_best) *a_worst_best = best_alpha;
364: /* use best one */
365: for (tt = 0; tt < 3; tt++) {
366: PetscInt cid2 = mid.trianglelist[3 * bestTID + tt];
367: PetscInt lid2 = selected_idx_2[cid2];
368: AA[tt][0] = coords[lid2];
369: AA[tt][1] = coords[data_stride + lid2];
370: AA[tt][2] = 1.0;
371: clids[tt] = cid2; /* store for interp */
372: }
373: for (tt = 0; tt < 3; tt++) alpha[tt] = fcoord[tt];
374: PetscCallLAPACKInfo("LAPACKgesv", LAPACKgesv_(&N, &NRHS, (PetscScalar *)AA, &LDA, IPIV, alpha, &LDB, &info));
375: }
377: /* put in row of P */
378: for (idx = 0; idx < 3; idx++) {
379: PetscScalar shp = alpha[idx];
380: if (PetscAbs(PetscRealPart(shp)) > 1.e-6) {
381: PetscInt cgid = crsGID[clids[idx]];
382: PetscInt jj = cgid * bs, ii = fgid * bs; /* need to gloalize */
383: for (tt = 0; tt < bs; tt++, ii++, jj++) PetscCall(MatSetValues(a_Prol, 1, &ii, 1, &jj, &shp, INSERT_VALUES));
384: }
385: }
386: }
387: } /* aggregates iterations */
388: clid++;
389: } /* a coarse agg */
390: } /* for all fine nodes */
392: PetscCall(ISRestoreIndices(selected_2, &selected_idx_2));
393: PetscCall(MatAssemblyBegin(a_Prol, MAT_FINAL_ASSEMBLY));
394: PetscCall(MatAssemblyEnd(a_Prol, MAT_FINAL_ASSEMBLY));
396: PetscCall(PetscFree2(node_tri, nTri));
397: }
398: free(mid.trianglelist);
399: free(mid.neighborlist);
400: free(mid.segmentlist);
401: free(mid.segmentmarkerlist);
402: free(mid.pointlist);
403: free(mid.pointmarkerlist);
404: PetscCall(PetscFree(in.pointlist));
405: PetscFunctionReturn(PETSC_SUCCESS);
406: #else
407: SETERRQ(PetscObjectComm((PetscObject)a_Prol), PETSC_ERR_PLIB, "configure with TRIANGLE to use geometric MG");
408: #endif
409: }
411: // PetscClangLinter pragma disable: -fdoc-sowing-chars
412: /*
413: getGIDsOnSquareGraph - square graph, get
415: Input Parameter:
416: . nselected_1 - selected local indices (includes ghosts in input Gmat1)
417: . clid_lid_1 - [nselected_1] lids of selected nodes
418: . Gmat1 - graph that goes with 'selected_1'
419: Output Parameter:
420: . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2)
421: . a_Gmat_2 - graph that is squared of 'Gmat_1'
422: . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes
423: */
424: static PetscErrorCode getGIDsOnSquareGraph(PC pc, PetscInt nselected_1, const PetscInt clid_lid_1[], const Mat Gmat1, IS *a_selected_2, Mat *a_Gmat_2, PetscInt **a_crsGID)
425: {
426: PetscMPIInt size;
427: PetscInt *crsGID, kk, my0, Iend, nloc;
428: MPI_Comm comm;
430: PetscFunctionBegin;
431: PetscCall(PetscObjectGetComm((PetscObject)Gmat1, &comm));
432: PetscCallMPI(MPI_Comm_size(comm, &size));
433: PetscCall(MatGetOwnershipRange(Gmat1, &my0, &Iend)); /* AIJ */
434: nloc = Iend - my0; /* this does not change */
436: if (size == 1) { /* not much to do in serial */
437: PetscCall(PetscMalloc1(nselected_1, &crsGID));
438: for (kk = 0; kk < nselected_1; kk++) crsGID[kk] = kk;
439: *a_Gmat_2 = NULL;
440: PetscCall(ISCreateGeneral(PETSC_COMM_SELF, nselected_1, clid_lid_1, PETSC_COPY_VALUES, a_selected_2));
441: } else {
442: PetscInt idx, num_fine_ghosts, num_crs_ghost, myCrs0;
443: Mat_MPIAIJ *mpimat2;
444: Mat Gmat2;
445: Vec locState;
446: PetscScalar *cpcol_state;
448: /* scan my coarse zero gid, set 'lid_state' with coarse GID */
449: kk = nselected_1;
450: PetscCallMPI(MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPI_SUM, comm));
451: myCrs0 -= nselected_1;
453: if (a_Gmat_2) { /* output */
454: /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */
455: PetscCall(PCGAMGSquareGraph_GAMG(pc, Gmat1, &Gmat2));
456: *a_Gmat_2 = Gmat2; /* output */
457: } else Gmat2 = Gmat1; /* use local to get crsGIDs at least */
458: /* get coarse grid GIDS for selected (locals and ghosts) */
459: mpimat2 = (Mat_MPIAIJ *)Gmat2->data;
460: PetscCall(MatCreateVecs(Gmat2, &locState, NULL));
461: PetscCall(VecSet(locState, -1)); /* set with UNKNOWN state */
462: for (kk = 0; kk < nselected_1; kk++) {
463: PetscInt fgid = clid_lid_1[kk] + my0;
464: PetscScalar v = (PetscScalar)(kk + myCrs0);
465: PetscCall(VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES)); /* set with PID */
466: }
467: PetscCall(VecAssemblyBegin(locState));
468: PetscCall(VecAssemblyEnd(locState));
469: PetscCall(VecScatterBegin(mpimat2->Mvctx, locState, mpimat2->lvec, INSERT_VALUES, SCATTER_FORWARD));
470: PetscCall(VecScatterEnd(mpimat2->Mvctx, locState, mpimat2->lvec, INSERT_VALUES, SCATTER_FORWARD));
471: PetscCall(VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts));
472: PetscCall(VecGetArray(mpimat2->lvec, &cpcol_state));
473: for (kk = 0, num_crs_ghost = 0; kk < num_fine_ghosts; kk++) {
474: if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++;
475: }
476: PetscCall(PetscMalloc1(nselected_1 + num_crs_ghost, &crsGID)); /* output */
477: {
478: PetscInt *selected_set;
479: PetscCall(PetscMalloc1(nselected_1 + num_crs_ghost, &selected_set));
480: /* do ghost of 'crsGID' */
481: for (kk = 0, idx = nselected_1; kk < num_fine_ghosts; kk++) {
482: if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) {
483: PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]);
484: selected_set[idx] = nloc + kk;
485: crsGID[idx++] = cgid;
486: }
487: }
488: PetscCheck(idx == (nselected_1 + num_crs_ghost), PETSC_COMM_SELF, PETSC_ERR_PLIB, "idx %" PetscInt_FMT " != (nselected_1 %" PetscInt_FMT " + num_crs_ghost %" PetscInt_FMT ")", idx, nselected_1, num_crs_ghost);
489: PetscCall(VecRestoreArray(mpimat2->lvec, &cpcol_state));
490: /* do locals in 'crsGID' */
491: PetscCall(VecGetArray(locState, &cpcol_state));
492: for (kk = 0, idx = 0; kk < nloc; kk++) {
493: if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) {
494: PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]);
495: selected_set[idx] = kk;
496: crsGID[idx++] = cgid;
497: }
498: }
499: PetscCheck(idx == nselected_1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "idx %" PetscInt_FMT " != nselected_1 %" PetscInt_FMT, idx, nselected_1);
500: PetscCall(VecRestoreArray(locState, &cpcol_state));
502: if (a_selected_2 != NULL) { /* output */
503: PetscCall(ISCreateGeneral(PETSC_COMM_SELF, nselected_1 + num_crs_ghost, selected_set, PETSC_OWN_POINTER, a_selected_2));
504: } else {
505: PetscCall(PetscFree(selected_set));
506: }
507: }
508: PetscCall(VecDestroy(&locState));
509: }
510: *a_crsGID = crsGID; /* output */
511: PetscFunctionReturn(PETSC_SUCCESS);
512: }
514: static PetscErrorCode PCGAMGCreateGraph_GEO(PC pc, Mat Amat, Mat *a_Gmat)
515: {
516: PC_MG *mg = (PC_MG *)pc->data;
517: PC_GAMG *pc_gamg = (PC_GAMG *)mg->innerctx;
518: const PetscReal vfilter = pc_gamg->threshold[0];
520: PetscFunctionBegin;
521: PetscCall(MatCreateGraph(Amat, PETSC_TRUE, PETSC_TRUE, vfilter, 0, NULL, a_Gmat));
522: PetscFunctionReturn(PETSC_SUCCESS);
523: }
525: static PetscErrorCode PCGAMGCoarsen_GEO(PC a_pc, Mat *a_Gmat, PetscCoarsenData **a_llist_parent)
526: {
527: PetscInt Istart, Iend, nloc, kk, Ii, ncols;
528: IS perm;
529: GAMGNode *gnodes;
530: PetscInt *permute;
531: Mat Gmat = *a_Gmat;
532: MPI_Comm comm;
533: MatCoarsen crs;
535: PetscFunctionBegin;
536: PetscCall(PetscObjectGetComm((PetscObject)a_pc, &comm));
538: PetscCall(MatGetOwnershipRange(Gmat, &Istart, &Iend));
539: nloc = (Iend - Istart);
541: /* create random permutation with sort for geo-mg */
542: PetscCall(PetscMalloc1(nloc, &gnodes));
543: PetscCall(PetscMalloc1(nloc, &permute));
545: for (Ii = Istart; Ii < Iend; Ii++) { /* locals only? */
546: PetscCall(MatGetRow(Gmat, Ii, &ncols, NULL, NULL));
547: {
548: PetscInt lid = Ii - Istart;
549: gnodes[lid].lid = lid;
550: gnodes[lid].degree = ncols;
551: }
552: PetscCall(MatRestoreRow(Gmat, Ii, &ncols, NULL, NULL));
553: }
554: if (PETSC_TRUE) {
555: PetscRandom rand;
556: PetscBool *bIndexSet;
557: PetscReal rr;
558: PetscInt iSwapIndex;
560: PetscCall(PetscRandomCreate(comm, &rand));
561: PetscCall(PetscCalloc1(nloc, &bIndexSet));
562: for (Ii = 0; Ii < nloc; Ii++) {
563: PetscCall(PetscRandomGetValueReal(rand, &rr));
564: iSwapIndex = (PetscInt)(rr * nloc);
565: if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) {
566: GAMGNode iTemp = gnodes[iSwapIndex];
567: gnodes[iSwapIndex] = gnodes[Ii];
568: gnodes[Ii] = iTemp;
569: bIndexSet[Ii] = PETSC_TRUE;
570: bIndexSet[iSwapIndex] = PETSC_TRUE;
571: }
572: }
573: PetscCall(PetscRandomDestroy(&rand));
574: PetscCall(PetscFree(bIndexSet));
575: }
576: /* only sort locals */
577: if (gnodes) qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare);
578: /* create IS of permutation */
579: for (kk = 0; kk < nloc; kk++) permute[kk] = gnodes[kk].lid; /* locals only */
580: PetscCall(PetscFree(gnodes));
581: PetscCall(ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm));
583: /* get MIS aggs */
585: PetscCall(MatCoarsenCreate(comm, &crs));
586: PetscCall(MatCoarsenSetType(crs, MATCOARSENMIS));
587: PetscCall(MatCoarsenSetGreedyOrdering(crs, perm));
588: PetscCall(MatCoarsenSetAdjacency(crs, Gmat));
589: PetscCall(MatCoarsenSetStrictAggs(crs, PETSC_FALSE));
590: PetscCall(MatCoarsenApply(crs));
591: PetscCall(MatCoarsenGetData(crs, a_llist_parent));
592: PetscCall(MatCoarsenDestroy(&crs));
594: PetscCall(ISDestroy(&perm));
595: PetscFunctionReturn(PETSC_SUCCESS);
596: }
598: static PetscErrorCode PCGAMGProlongator_GEO(PC pc, Mat Amat, PetscCoarsenData *agg_lists, Mat *a_P_out)
599: {
600: PC_MG *mg = (PC_MG *)pc->data;
601: PC_GAMG *pc_gamg = (PC_GAMG *)mg->innerctx;
602: const PetscInt dim = pc_gamg->data_cell_cols, data_cols = pc_gamg->data_cell_cols;
603: PetscInt Istart, Iend, nloc, my0, jj, kk, ncols, nLocalSelected, bs, *clid_flid;
604: Mat Prol, Gmat;
605: PetscMPIInt rank, size;
606: MPI_Comm comm;
607: IS selected_2, selected_1;
608: const PetscInt *selected_idx;
609: MatType mtype;
611: PetscFunctionBegin;
612: PetscCall(PetscObjectGetComm((PetscObject)Amat, &comm));
614: PetscCallMPI(MPI_Comm_rank(comm, &rank));
615: PetscCallMPI(MPI_Comm_size(comm, &size));
616: PetscCall(MatGetOwnershipRange(Amat, &Istart, &Iend));
617: PetscCall(MatGetBlockSize(Amat, &bs));
618: nloc = (Iend - Istart) / bs;
619: my0 = Istart / bs;
620: PetscCheck((Iend - Istart) % bs == 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "(Iend %" PetscInt_FMT " - Istart %" PetscInt_FMT ") %% bs %" PetscInt_FMT, Iend, Istart, bs);
622: /* get 'nLocalSelected' */
623: PetscCall(PetscCDGetMat(agg_lists, &Gmat)); // get auxiliary matrix for ghost edges
624: PetscCall(PetscCDGetNonemptyIS(agg_lists, &selected_1));
625: PetscCall(ISGetSize(selected_1, &jj));
626: PetscCall(PetscMalloc1(jj, &clid_flid));
627: PetscCall(ISGetIndices(selected_1, &selected_idx));
628: for (kk = 0, nLocalSelected = 0; kk < jj; kk++) {
629: PetscInt lid = selected_idx[kk];
630: if (lid < nloc) {
631: PetscCall(MatGetRow(Gmat, lid + my0, &ncols, NULL, NULL));
632: if (ncols > 1) clid_flid[nLocalSelected++] = lid; /* filter out singletons */
633: PetscCall(MatRestoreRow(Gmat, lid + my0, &ncols, NULL, NULL));
634: }
635: }
636: PetscCall(ISRestoreIndices(selected_1, &selected_idx));
637: PetscCall(ISDestroy(&selected_1)); /* this is selected_1 in serial */
639: /* create prolongator matrix */
640: PetscCall(MatGetType(Amat, &mtype));
641: PetscCall(MatCreate(comm, &Prol));
642: PetscCall(MatSetSizes(Prol, nloc * bs, nLocalSelected * bs, PETSC_DETERMINE, PETSC_DETERMINE));
643: PetscCall(MatSetBlockSizes(Prol, bs, bs));
644: PetscCall(MatSetType(Prol, mtype));
645: PetscCall(MatSeqAIJSetPreallocation(Prol, 3 * data_cols, NULL));
646: PetscCall(MatMPIAIJSetPreallocation(Prol, 3 * data_cols, NULL, 3 * data_cols, NULL));
648: /* can get all points "removed" - but not on geomg */
649: PetscCall(MatGetSize(Prol, &kk, &jj));
650: if (!jj) {
651: PetscCall(PetscInfo(pc, "ERROE: no selected points on coarse grid\n"));
652: PetscCall(PetscFree(clid_flid));
653: PetscCall(MatDestroy(&Prol));
654: *a_P_out = NULL; /* out */
655: PetscFunctionReturn(PETSC_SUCCESS);
656: }
658: {
659: PetscReal *coords;
660: PetscInt data_stride;
661: PetscInt *crsGID = NULL;
662: Mat Gmat2;
664: PetscCheck(dim == data_cols, PETSC_COMM_SELF, PETSC_ERR_PLIB, "dim %" PetscInt_FMT " != data_cols %" PetscInt_FMT, dim, data_cols);
665: /* grow ghost data for better coarse grid cover of fine grid */
666: /* messy method, squares graph and gets some data */
667: PetscCall(getGIDsOnSquareGraph(pc, nLocalSelected, clid_flid, Gmat, &selected_2, &Gmat2, &crsGID));
668: /* llist is now not valid wrt squared graph, but will work as iterator in 'triangulateAndFormProl' */
669: /* create global vector of coorindates in 'coords' */
670: if (size > 1) {
671: PetscCall(PCGAMGGetDataWithGhosts(Gmat2, dim, pc_gamg->data, &data_stride, &coords));
672: } else {
673: coords = pc_gamg->data;
674: data_stride = pc_gamg->data_sz / pc_gamg->data_cell_cols;
675: }
676: PetscCall(MatDestroy(&Gmat2));
677: /* triangulate */
678: {
679: PetscReal metric, tm;
681: PetscCheck(dim == 2, comm, PETSC_ERR_PLIB, "3D not implemented for 'geo' AMG");
682: PetscCall(triangulateAndFormProl(selected_2, data_stride, coords, nLocalSelected, clid_flid, agg_lists, crsGID, bs, Prol, &metric));
683: PetscCall(PetscFree(crsGID));
685: /* clean up and create coordinates for coarse grid (output) */
686: if (size > 1) PetscCall(PetscFree(coords));
688: PetscCallMPI(MPIU_Allreduce(&metric, &tm, 1, MPIU_REAL, MPIU_MAX, comm));
689: if (tm > 1.) { /* needs to be globalized - should not happen */
690: PetscCall(PetscInfo(pc, " failed metric for coarse grid %e\n", (double)tm));
691: PetscCall(MatDestroy(&Prol));
692: } else if (metric > .0) {
693: PetscCall(PetscInfo(pc, "worst metric for coarse grid = %e\n", (double)metric));
694: }
695: }
696: { /* create next coords - output */
697: PetscReal *crs_crds;
698: PetscCall(PetscMalloc1(dim * nLocalSelected, &crs_crds));
699: for (kk = 0; kk < nLocalSelected; kk++) { /* grab local select nodes to promote - output */
700: PetscInt lid = clid_flid[kk];
701: for (jj = 0; jj < dim; jj++) crs_crds[jj * nLocalSelected + kk] = pc_gamg->data[jj * nloc + lid];
702: }
704: PetscCall(PetscFree(pc_gamg->data));
705: pc_gamg->data = crs_crds; /* out */
706: pc_gamg->data_sz = dim * nLocalSelected;
707: }
708: PetscCall(ISDestroy(&selected_2));
709: }
711: *a_P_out = Prol; /* out */
712: PetscCall(PetscFree(clid_flid));
713: PetscFunctionReturn(PETSC_SUCCESS);
714: }
716: static PetscErrorCode PCDestroy_GAMG_GEO(PC pc)
717: {
718: PetscFunctionBegin;
719: PetscCall(PetscObjectComposeFunction((PetscObject)pc, "PCSetCoordinates_C", NULL));
720: PetscFunctionReturn(PETSC_SUCCESS);
721: }
723: PetscErrorCode PCCreateGAMG_GEO(PC pc)
724: {
725: PC_MG *mg = (PC_MG *)pc->data;
726: PC_GAMG *pc_gamg = (PC_GAMG *)mg->innerctx;
728: PetscFunctionBegin;
729: pc_gamg->ops->setfromoptions = PCSetFromOptions_GEO;
730: pc_gamg->ops->destroy = PCDestroy_GAMG_GEO;
731: /* reset does not do anything; setup not virtual */
733: /* set internal function pointers */
734: pc_gamg->ops->creategraph = PCGAMGCreateGraph_GEO;
735: pc_gamg->ops->coarsen = PCGAMGCoarsen_GEO;
736: pc_gamg->ops->prolongator = PCGAMGProlongator_GEO;
737: pc_gamg->ops->optprolongator = NULL;
738: pc_gamg->ops->createdefaultdata = PCSetData_GEO;
740: PetscCall(PetscObjectComposeFunction((PetscObject)pc, "PCSetCoordinates_C", PCSetCoordinates_GEO));
741: PetscFunctionReturn(PETSC_SUCCESS);
742: }