Actual source code: geo.c
petsc-3.11.4 2019-09-28
1: /*
2: GAMG geometric-algebric multiogrid PC - Mark Adams 2011
3: */
5: #include <../src/ksp/pc/impls/gamg/gamg.h>
7: #if defined(PETSC_HAVE_TRIANGLE)
8: #define REAL PetscReal
9: #include <triangle.h>
10: #endif
12: #include <petscblaslapack.h>
14: /* Private context for the GAMG preconditioner */
15: typedef struct {
16: PetscInt lid; /* local vertex index */
17: PetscInt degree; /* vertex degree */
18: } GAMGNode;
20: PETSC_STATIC_INLINE int petsc_geo_mg_compare(const void *a, const void *b)
21: {
22: return (((GAMGNode*)a)->degree - ((GAMGNode*)b)->degree);
23: }
25: /* -------------------------------------------------------------------------- */
26: /*
27: PCSetCoordinates_GEO
29: Input Parameter:
30: . pc - the preconditioner context
31: */
32: PetscErrorCode PCSetCoordinates_GEO(PC pc, PetscInt ndm, PetscInt a_nloc, PetscReal *coords)
33: {
34: PC_MG *mg = (PC_MG*)pc->data;
35: PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx;
37: PetscInt arrsz,bs,my0,kk,ii,nloc,Iend,aloc;
38: Mat Amat = pc->pmat;
42: MatGetBlockSize(Amat, &bs);
43: MatGetOwnershipRange(Amat, &my0, &Iend);
44: aloc = (Iend-my0);
45: nloc = (Iend-my0)/bs;
47: if (nloc!=a_nloc && aloc!=a_nloc) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Number of local blocks %D must be %D or %D.",a_nloc,nloc,aloc);
49: pc_gamg->data_cell_rows = 1;
50: if (!coords && nloc > 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG, "Need coordinates for pc_gamg_type 'geo'.");
51: pc_gamg->data_cell_cols = ndm; /* coordinates */
53: arrsz = nloc*pc_gamg->data_cell_rows*pc_gamg->data_cell_cols;
55: /* create data - syntactic sugar that should be refactored at some point */
56: if (!pc_gamg->data || (pc_gamg->data_sz != arrsz)) {
57: PetscFree(pc_gamg->data);
58: PetscMalloc1(arrsz+1, &pc_gamg->data);
59: }
60: for (kk=0; kk<arrsz; kk++) pc_gamg->data[kk] = -999.;
61: pc_gamg->data[arrsz] = -99.;
62: /* copy data in - column oriented */
63: if (nloc == a_nloc) {
64: for (kk = 0; kk < nloc; kk++) {
65: for (ii = 0; ii < ndm; ii++) {
66: pc_gamg->data[ii*nloc + kk] = coords[kk*ndm + ii];
67: }
68: }
69: } else { /* assumes the coordinates are blocked */
70: for (kk = 0; kk < nloc; kk++) {
71: for (ii = 0; ii < ndm; ii++) {
72: pc_gamg->data[ii*nloc + kk] = coords[bs*kk*ndm + ii];
73: }
74: }
75: }
76: if (pc_gamg->data[arrsz] != -99.) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"pc_gamg->data[arrsz %D] %g != -99.",arrsz,pc_gamg->data[arrsz]);
77: pc_gamg->data_sz = arrsz;
78: return(0);
79: }
81: /* -------------------------------------------------------------------------- */
82: /*
83: PCSetData_GEO
85: Input Parameter:
86: . pc -
87: */
88: PetscErrorCode PCSetData_GEO(PC pc, Mat m)
89: {
91: SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_PLIB,"GEO MG needs coordinates");
92: }
94: /* -------------------------------------------------------------------------- */
95: /*
96: PCSetFromOptions_GEO
98: Input Parameter:
99: . pc -
100: */
101: PetscErrorCode PCSetFromOptions_GEO(PetscOptionItems *PetscOptionsObject,PC pc)
102: {
106: PetscOptionsHead(PetscOptionsObject,"GAMG-GEO options");
107: {
108: /* -pc_gamg_sa_nsmooths */
109: /* pc_gamg_sa->smooths = 0; */
110: /* PetscOptionsInt("-pc_gamg_agg_nsmooths", */
111: /* "smoothing steps for smoothed aggregation, usually 1 (0)", */
112: /* "PCGAMGSetNSmooths_AGG", */
113: /* pc_gamg_sa->smooths, */
114: /* &pc_gamg_sa->smooths, */
115: /* &flag); */
116: /* */
117: }
118: PetscOptionsTail();
119: return(0);
120: }
122: /* -------------------------------------------------------------------------- */
123: /*
124: triangulateAndFormProl
126: Input Parameter:
127: . selected_2 - list of selected local ID, includes selected ghosts
128: . data_stride -
129: . coords[2*data_stride] - column vector of local coordinates w/ ghosts
130: . nselected_1 - selected IDs that go with base (1) graph includes selected ghosts
131: . clid_lid_1[nselected_1] - lids of selected (c) nodes ???????????
132: . agg_lists_1 - list of aggregates selected_1 vertices of aggregate unselected vertices
133: . crsGID[selected.size()] - global index for prolongation operator
134: . bs - block size
135: Output Parameter:
136: . a_Prol - prolongation operator
137: . a_worst_best - measure of worst missed fine vertex, 0 is no misses
138: */
139: static PetscErrorCode triangulateAndFormProl(IS selected_2,PetscInt data_stride,PetscReal coords[],PetscInt nselected_1,const PetscInt clid_lid_1[],const PetscCoarsenData *agg_lists_1,
140: const PetscInt crsGID[],PetscInt bs,Mat a_Prol,PetscReal *a_worst_best)
141: {
142: #if defined(PETSC_HAVE_TRIANGLE)
143: PetscErrorCode ierr;
144: PetscInt jj,tid,tt,idx,nselected_2;
145: struct triangulateio in,mid;
146: const PetscInt *selected_idx_2;
147: PetscMPIInt rank;
148: PetscInt Istart,Iend,nFineLoc,myFine0;
149: int kk,nPlotPts,sid;
150: MPI_Comm comm;
151: PetscReal tm;
154: PetscObjectGetComm((PetscObject)a_Prol,&comm);
155: MPI_Comm_rank(comm,&rank);
156: ISGetSize(selected_2, &nselected_2);
157: if (nselected_2 == 1 || nselected_2 == 2) { /* 0 happens on idle processors */
158: *a_worst_best = 100.0; /* this will cause a stop, but not globalized (should not happen) */
159: } else *a_worst_best = 0.0;
160: MPIU_Allreduce(a_worst_best, &tm, 1, MPIU_REAL, MPIU_MAX, comm);
161: if (tm > 0.0) {
162: *a_worst_best = 100.0;
163: return(0);
164: }
165: MatGetOwnershipRange(a_Prol, &Istart, &Iend);
166: nFineLoc = (Iend-Istart)/bs; myFine0 = Istart/bs;
167: nPlotPts = nFineLoc; /* locals */
168: /* traingle */
169: /* Define input points - in*/
170: in.numberofpoints = nselected_2;
171: in.numberofpointattributes = 0;
172: /* get nselected points */
173: PetscMalloc1(2*nselected_2, &in.pointlist);
174: ISGetIndices(selected_2, &selected_idx_2);
176: for (kk=0,sid=0; kk<nselected_2; kk++,sid += 2) {
177: PetscInt lid = selected_idx_2[kk];
178: in.pointlist[sid] = coords[lid];
179: in.pointlist[sid+1] = coords[data_stride + lid];
180: if (lid>=nFineLoc) nPlotPts++;
181: }
182: if (sid != 2*nselected_2) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != 2*nselected_2 %D",sid,nselected_2);
184: in.numberofsegments = 0;
185: in.numberofedges = 0;
186: in.numberofholes = 0;
187: in.numberofregions = 0;
188: in.trianglelist = 0;
189: in.segmentmarkerlist = 0;
190: in.pointattributelist = 0;
191: in.pointmarkerlist = 0;
192: in.triangleattributelist = 0;
193: in.trianglearealist = 0;
194: in.segmentlist = 0;
195: in.holelist = 0;
196: in.regionlist = 0;
197: in.edgelist = 0;
198: in.edgemarkerlist = 0;
199: in.normlist = 0;
201: /* triangulate */
202: mid.pointlist = 0; /* Not needed if -N switch used. */
203: /* Not needed if -N switch used or number of point attributes is zero: */
204: mid.pointattributelist = 0;
205: mid.pointmarkerlist = 0; /* Not needed if -N or -B switch used. */
206: mid.trianglelist = 0; /* Not needed if -E switch used. */
207: /* Not needed if -E switch used or number of triangle attributes is zero: */
208: mid.triangleattributelist = 0;
209: mid.neighborlist = 0; /* Needed only if -n switch used. */
210: /* Needed only if segments are output (-p or -c) and -P not used: */
211: mid.segmentlist = 0;
212: /* Needed only if segments are output (-p or -c) and -P and -B not used: */
213: mid.segmentmarkerlist = 0;
214: mid.edgelist = 0; /* Needed only if -e switch used. */
215: mid.edgemarkerlist = 0; /* Needed if -e used and -B not used. */
216: mid.numberoftriangles = 0;
218: /* Triangulate the points. Switches are chosen to read and write a */
219: /* PSLG (p), preserve the convex hull (c), number everything from */
220: /* zero (z), assign a regional attribute to each element (A), and */
221: /* produce an edge list (e), a Voronoi diagram (v), and a triangle */
222: /* neighbor list (n). */
223: if (nselected_2 != 0) { /* inactive processor */
224: char args[] = "npczQ"; /* c is needed ? */
225: triangulate(args, &in, &mid, (struct triangulateio*) NULL);
226: /* output .poly files for 'showme' */
227: if (!PETSC_TRUE) {
228: static int level = 1;
229: FILE *file; char fname[32];
231: sprintf(fname,"C%d_%d.poly",level,rank); file = fopen(fname, "w");
232: /*First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)>*/
233: fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0);
234: /*Following lines: <vertex #> <x> <y> */
235: for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid += 2) {
236: fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]);
237: }
238: /*One line: <# of segments> <# of boundary markers (0 or 1)> */
239: fprintf(file, "%d %d\n",0,0);
240: /*Following lines: <segment #> <endpoint> <endpoint> [boundary marker] */
241: /* One line: <# of holes> */
242: fprintf(file, "%d\n",0);
243: /* Following lines: <hole #> <x> <y> */
244: /* Optional line: <# of regional attributes and/or area constraints> */
245: /* Optional following lines: <region #> <x> <y> <attribute> <maximum area> */
246: fclose(file);
248: /* elems */
249: sprintf(fname,"C%d_%d.ele",level,rank); file = fopen(fname, "w");
250: /* First line: <# of triangles> <nodes per triangle> <# of attributes> */
251: fprintf(file, "%d %d %d\n",mid.numberoftriangles,3,0);
252: /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */
253: for (kk=0,sid=0; kk<mid.numberoftriangles; kk++,sid += 3) {
254: fprintf(file, "%d %d %d %d\n",kk,mid.trianglelist[sid],mid.trianglelist[sid+1],mid.trianglelist[sid+2]);
255: }
256: fclose(file);
258: sprintf(fname,"C%d_%d.node",level,rank); file = fopen(fname, "w");
259: /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */
260: /* fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); */
261: fprintf(file, "%d %d %d %d\n",nPlotPts,2,0,0);
262: /*Following lines: <vertex #> <x> <y> */
263: for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid+=2) {
264: fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]);
265: }
267: sid /= 2;
268: for (jj=0; jj<nFineLoc; jj++) {
269: PetscBool sel = PETSC_TRUE;
270: for (kk=0; kk<nselected_2 && sel; kk++) {
271: PetscInt lid = selected_idx_2[kk];
272: if (lid == jj) sel = PETSC_FALSE;
273: }
274: if (sel) fprintf(file, "%d %e %e\n",sid++,coords[jj],coords[data_stride + jj]);
275: }
276: fclose(file);
277: if (sid != nPlotPts) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != nPlotPts %D",sid,nPlotPts);
278: level++;
279: }
280: }
281: #if defined PETSC_GAMG_USE_LOG
282: PetscLogEventBegin(petsc_gamg_setup_events[FIND_V],0,0,0,0);
283: #endif
284: { /* form P - setup some maps */
285: PetscInt clid,mm,*nTri,*node_tri;
287: PetscMalloc2(nselected_2, &node_tri,nselected_2, &nTri);
289: /* need list of triangles on node */
290: for (kk=0; kk<nselected_2; kk++) nTri[kk] = 0;
291: for (tid=0,kk=0; tid<mid.numberoftriangles; tid++) {
292: for (jj=0; jj<3; jj++) {
293: PetscInt cid = mid.trianglelist[kk++];
294: if (nTri[cid] == 0) node_tri[cid] = tid;
295: nTri[cid]++;
296: }
297: }
298: #define EPS 1.e-12
299: /* find points and set prolongation */
300: for (mm = clid = 0; mm < nFineLoc; mm++) {
301: PetscBool ise;
302: PetscCDEmptyAt(agg_lists_1,mm,&ise);
303: if (!ise) {
304: const PetscInt lid = mm;
305: PetscScalar AA[3][3];
306: PetscBLASInt N=3,NRHS=1,LDA=3,IPIV[3],LDB=3,INFO;
307: PetscCDIntNd *pos;
309: PetscCDGetHeadPos(agg_lists_1,lid,&pos);
310: while (pos) {
311: PetscInt flid;
312: PetscCDIntNdGetID(pos, &flid);
313: PetscCDGetNextPos(agg_lists_1,lid,&pos);
315: if (flid < nFineLoc) { /* could be a ghost */
316: PetscInt bestTID = -1; PetscReal best_alpha = 1.e10;
317: const PetscInt fgid = flid + myFine0;
318: /* compute shape function for gid */
319: const PetscReal fcoord[3] = {coords[flid],coords[data_stride+flid],1.0};
320: PetscBool haveit =PETSC_FALSE; PetscScalar alpha[3]; PetscInt clids[3];
322: /* look for it */
323: for (tid = node_tri[clid], jj=0;
324: jj < 5 && !haveit && tid != -1;
325: jj++) {
326: for (tt=0; tt<3; tt++) {
327: PetscInt cid2 = mid.trianglelist[3*tid + tt];
328: PetscInt lid2 = selected_idx_2[cid2];
329: AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0;
330: clids[tt] = cid2; /* store for interp */
331: }
333: for (tt=0; tt<3; tt++) alpha[tt] = (PetscScalar)fcoord[tt];
335: /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */
336: PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO));
337: {
338: PetscBool have=PETSC_TRUE; PetscReal lowest=1.e10;
339: for (tt = 0, idx = 0; tt < 3; tt++) {
340: if (PetscRealPart(alpha[tt]) > (1.0+EPS) || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE;
341: if (PetscRealPart(alpha[tt]) < lowest) {
342: lowest = PetscRealPart(alpha[tt]);
343: idx = tt;
344: }
345: }
346: haveit = have;
347: }
348: tid = mid.neighborlist[3*tid + idx];
349: }
351: if (!haveit) {
352: /* brute force */
353: for (tid=0; tid<mid.numberoftriangles && !haveit; tid++) {
354: for (tt=0; tt<3; tt++) {
355: PetscInt cid2 = mid.trianglelist[3*tid + tt];
356: PetscInt lid2 = selected_idx_2[cid2];
357: AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0;
358: clids[tt] = cid2; /* store for interp */
359: }
360: for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt];
361: /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */
362: PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO));
363: {
364: PetscBool have=PETSC_TRUE; PetscReal worst=0.0, v;
365: for (tt=0; tt<3 && have; tt++) {
366: if (PetscRealPart(alpha[tt]) > 1.0+EPS || PetscRealPart(alpha[tt]) < -EPS) have=PETSC_FALSE;
367: if ((v=PetscAbs(PetscRealPart(alpha[tt])-0.5)) > worst) worst = v;
368: }
369: if (worst < best_alpha) {
370: best_alpha = worst; bestTID = tid;
371: }
372: haveit = have;
373: }
374: }
375: }
376: if (!haveit) {
377: if (best_alpha > *a_worst_best) *a_worst_best = best_alpha;
378: /* use best one */
379: for (tt=0; tt<3; tt++) {
380: PetscInt cid2 = mid.trianglelist[3*bestTID + tt];
381: PetscInt lid2 = selected_idx_2[cid2];
382: AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0;
383: clids[tt] = cid2; /* store for interp */
384: }
385: for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt];
386: /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */
387: PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO));
388: }
390: /* put in row of P */
391: for (idx=0; idx<3; idx++) {
392: PetscScalar shp = alpha[idx];
393: if (PetscAbs(PetscRealPart(shp)) > 1.e-6) {
394: PetscInt cgid = crsGID[clids[idx]];
395: PetscInt jj = cgid*bs, ii = fgid*bs; /* need to gloalize */
396: for (tt=0; tt < bs; tt++, ii++, jj++) {
397: MatSetValues(a_Prol,1,&ii,1,&jj,&shp,INSERT_VALUES);
398: }
399: }
400: }
401: }
402: } /* aggregates iterations */
403: clid++;
404: } /* a coarse agg */
405: } /* for all fine nodes */
407: ISRestoreIndices(selected_2, &selected_idx_2);
408: MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);
409: MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);
411: PetscFree2(node_tri,nTri);
412: }
413: #if defined PETSC_GAMG_USE_LOG
414: PetscLogEventEnd(petsc_gamg_setup_events[FIND_V],0,0,0,0);
415: #endif
416: free(mid.trianglelist);
417: free(mid.neighborlist);
418: PetscFree(in.pointlist);
419: return(0);
420: #else
421: SETERRQ(PetscObjectComm((PetscObject)a_Prol),PETSC_ERR_PLIB,"configure with TRIANGLE to use geometric MG");
422: #endif
423: }
424: /* -------------------------------------------------------------------------- */
425: /*
426: getGIDsOnSquareGraph - square graph, get
428: Input Parameter:
429: . nselected_1 - selected local indices (includes ghosts in input Gmat1)
430: . clid_lid_1 - [nselected_1] lids of selected nodes
431: . Gmat1 - graph that goes with 'selected_1'
432: Output Parameter:
433: . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2)
434: . a_Gmat_2 - graph that is squared of 'Gmat_1'
435: . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes
436: */
437: static PetscErrorCode getGIDsOnSquareGraph(PetscInt nselected_1,const PetscInt clid_lid_1[],const Mat Gmat1,IS *a_selected_2,Mat *a_Gmat_2,PetscInt **a_crsGID)
438: {
440: PetscMPIInt size;
441: PetscInt *crsGID, kk,my0,Iend,nloc;
442: MPI_Comm comm;
445: PetscObjectGetComm((PetscObject)Gmat1,&comm);
446: MPI_Comm_size(comm,&size);
447: MatGetOwnershipRange(Gmat1,&my0,&Iend); /* AIJ */
448: nloc = Iend - my0; /* this does not change */
450: if (size == 1) { /* not much to do in serial */
451: PetscMalloc1(nselected_1, &crsGID);
452: for (kk=0; kk<nselected_1; kk++) crsGID[kk] = kk;
453: *a_Gmat_2 = 0;
454: ISCreateGeneral(PETSC_COMM_SELF,nselected_1,clid_lid_1,PETSC_COPY_VALUES,a_selected_2);
455: } else {
456: PetscInt idx,num_fine_ghosts,num_crs_ghost,myCrs0;
457: Mat_MPIAIJ *mpimat2;
458: Mat Gmat2;
459: Vec locState;
460: PetscScalar *cpcol_state;
462: /* scan my coarse zero gid, set 'lid_state' with coarse GID */
463: kk = nselected_1;
464: MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPI_SUM, comm);
465: myCrs0 -= nselected_1;
467: if (a_Gmat_2) { /* output */
468: /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */
469: MatTransposeMatMult(Gmat1, Gmat1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Gmat2);
470: *a_Gmat_2 = Gmat2; /* output */
471: } else Gmat2 = Gmat1; /* use local to get crsGIDs at least */
472: /* get coarse grid GIDS for selected (locals and ghosts) */
473: mpimat2 = (Mat_MPIAIJ*)Gmat2->data;
474: MatCreateVecs(Gmat2, &locState, 0);
475: VecSet(locState, (PetscScalar)(PetscReal)(-1)); /* set with UNKNOWN state */
476: for (kk=0; kk<nselected_1; kk++) {
477: PetscInt fgid = clid_lid_1[kk] + my0;
478: PetscScalar v = (PetscScalar)(kk+myCrs0);
479: VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES); /* set with PID */
480: }
481: VecAssemblyBegin(locState);
482: VecAssemblyEnd(locState);
483: VecScatterBegin(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);
484: VecScatterEnd(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);
485: VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts);
486: VecGetArray(mpimat2->lvec, &cpcol_state);
487: for (kk=0,num_crs_ghost=0; kk<num_fine_ghosts; kk++) {
488: if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++;
489: }
490: PetscMalloc1(nselected_1+num_crs_ghost, &crsGID); /* output */
491: {
492: PetscInt *selected_set;
493: PetscMalloc1(nselected_1+num_crs_ghost, &selected_set);
494: /* do ghost of 'crsGID' */
495: for (kk=0,idx=nselected_1; kk<num_fine_ghosts; kk++) {
496: if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) {
497: PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]);
498: selected_set[idx] = nloc + kk;
499: crsGID[idx++] = cgid;
500: }
501: }
502: if (idx != (nselected_1+num_crs_ghost)) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"idx %D != (nselected_1 %D + num_crs_ghost %D)",idx,nselected_1,num_crs_ghost);
503: VecRestoreArray(mpimat2->lvec, &cpcol_state);
504: /* do locals in 'crsGID' */
505: VecGetArray(locState, &cpcol_state);
506: for (kk=0,idx=0; kk<nloc; kk++) {
507: if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) {
508: PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]);
509: selected_set[idx] = kk;
510: crsGID[idx++] = cgid;
511: }
512: }
513: if (idx != nselected_1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"idx %D != nselected_1 %D",idx,nselected_1);
514: VecRestoreArray(locState, &cpcol_state);
516: if (a_selected_2 != 0) { /* output */
517: ISCreateGeneral(PETSC_COMM_SELF,(nselected_1+num_crs_ghost),selected_set,PETSC_OWN_POINTER,a_selected_2);
518: } else {
519: PetscFree(selected_set);
520: }
521: }
522: VecDestroy(&locState);
523: }
524: *a_crsGID = crsGID; /* output */
525: return(0);
526: }
528: /* -------------------------------------------------------------------------- */
529: /*
530: PCGAMGGraph_GEO
532: Input Parameter:
533: . pc - this
534: . Amat - matrix on this fine level
535: Output Parameter:
536: . a_Gmat
537: */
538: PetscErrorCode PCGAMGGraph_GEO(PC pc,Mat Amat,Mat *a_Gmat)
539: {
540: PetscErrorCode ierr;
541: PC_MG *mg = (PC_MG*)pc->data;
542: PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx;
543: const PetscReal vfilter = pc_gamg->threshold[0];
544: MPI_Comm comm;
545: Mat Gmat;
546: PetscBool set,flg,symm;
549: PetscObjectGetComm((PetscObject)Amat,&comm);
550: PetscLogEventBegin(PC_GAMGGraph_GEO,0,0,0,0);
552: MatIsSymmetricKnown(Amat, &set, &flg);
553: symm = (PetscBool)!(set && flg);
555: PCGAMGCreateGraph(Amat, &Gmat);
556: PCGAMGFilterGraph(&Gmat, vfilter, symm);
558: *a_Gmat = Gmat;
559: PetscLogEventEnd(PC_GAMGGraph_GEO,0,0,0,0);
560: return(0);
561: }
563: /* -------------------------------------------------------------------------- */
564: /*
565: PCGAMGCoarsen_GEO
567: Input Parameter:
568: . a_pc - this
569: . a_Gmat - graph
570: Output Parameter:
571: . a_llist_parent - linked list from selected indices for data locality only
572: */
573: PetscErrorCode PCGAMGCoarsen_GEO(PC a_pc,Mat *a_Gmat,PetscCoarsenData **a_llist_parent)
574: {
576: PetscInt Istart,Iend,nloc,kk,Ii,ncols;
577: IS perm;
578: GAMGNode *gnodes;
579: PetscInt *permute;
580: Mat Gmat = *a_Gmat;
581: MPI_Comm comm;
582: MatCoarsen crs;
585: PetscObjectGetComm((PetscObject)a_pc,&comm);
586: PetscLogEventBegin(PC_GAMGCoarsen_GEO,0,0,0,0);
587: MatGetOwnershipRange(Gmat, &Istart, &Iend);
588: nloc = (Iend-Istart);
590: /* create random permutation with sort for geo-mg */
591: PetscMalloc1(nloc, &gnodes);
592: PetscMalloc1(nloc, &permute);
594: for (Ii=Istart; Ii<Iend; Ii++) { /* locals only? */
595: MatGetRow(Gmat,Ii,&ncols,0,0);
596: {
597: PetscInt lid = Ii - Istart;
598: gnodes[lid].lid = lid;
599: gnodes[lid].degree = ncols;
600: }
601: MatRestoreRow(Gmat,Ii,&ncols,0,0);
602: }
603: if (PETSC_TRUE) {
604: PetscRandom rand;
605: PetscBool *bIndexSet;
606: PetscReal rr;
607: PetscInt iSwapIndex;
609: PetscRandomCreate(comm,&rand);
610: PetscCalloc1(nloc, &bIndexSet);
611: for (Ii = 0; Ii < nloc; Ii++) {
612: PetscRandomGetValueReal(rand,&rr);
613: iSwapIndex = (PetscInt) (rr*nloc);
614: if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) {
615: GAMGNode iTemp = gnodes[iSwapIndex];
616: gnodes[iSwapIndex] = gnodes[Ii];
617: gnodes[Ii] = iTemp;
618: bIndexSet[Ii] = PETSC_TRUE;
619: bIndexSet[iSwapIndex] = PETSC_TRUE;
620: }
621: }
622: PetscRandomDestroy(&rand);
623: PetscFree(bIndexSet);
624: }
625: /* only sort locals */
626: qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare);
627: /* create IS of permutation */
628: for (kk=0; kk<nloc; kk++) permute[kk] = gnodes[kk].lid; /* locals only */
629: PetscFree(gnodes);
630: ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm);
632: /* get MIS aggs */
634: MatCoarsenCreate(comm, &crs);
635: MatCoarsenSetType(crs, MATCOARSENMIS);
636: MatCoarsenSetGreedyOrdering(crs, perm);
637: MatCoarsenSetAdjacency(crs, Gmat);
638: MatCoarsenSetStrictAggs(crs, PETSC_FALSE);
639: MatCoarsenApply(crs);
640: MatCoarsenGetData(crs, a_llist_parent);
641: MatCoarsenDestroy(&crs);
643: ISDestroy(&perm);
644: PetscLogEventEnd(PC_GAMGCoarsen_GEO,0,0,0,0);
645: return(0);
646: }
648: /* -------------------------------------------------------------------------- */
649: /*
650: PCGAMGProlongator_GEO
652: Input Parameter:
653: . pc - this
654: . Amat - matrix on this fine level
655: . Graph - used to get ghost data for nodes in
656: . selected_1 - [nselected]
657: . agg_lists - [nselected]
658: Output Parameter:
659: . a_P_out - prolongation operator to the next level
660: */
661: PetscErrorCode PCGAMGProlongator_GEO(PC pc,Mat Amat,Mat Gmat,PetscCoarsenData *agg_lists,Mat *a_P_out)
662: {
663: PC_MG *mg = (PC_MG*)pc->data;
664: PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx;
665: const PetscInt dim = pc_gamg->data_cell_cols, data_cols = pc_gamg->data_cell_cols;
667: PetscInt Istart,Iend,nloc,my0,jj,kk,ncols,nLocalSelected,bs,*clid_flid;
668: Mat Prol;
669: PetscMPIInt rank, size;
670: MPI_Comm comm;
671: IS selected_2,selected_1;
672: const PetscInt *selected_idx;
673: MatType mtype;
676: PetscObjectGetComm((PetscObject)Amat,&comm);
677: PetscLogEventBegin(PC_GAMGProlongator_GEO,0,0,0,0);
678: MPI_Comm_rank(comm,&rank);
679: MPI_Comm_size(comm,&size);
680: MatGetOwnershipRange(Amat, &Istart, &Iend);
681: MatGetBlockSize(Amat, &bs);
682: nloc = (Iend-Istart)/bs; my0 = Istart/bs;
683: if ((Iend-Istart) % bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(Iend %D - Istart %D) % bs %D",Iend,Istart,bs);
685: /* get 'nLocalSelected' */
686: PetscCDGetMIS(agg_lists, &selected_1);
687: ISGetSize(selected_1, &jj);
688: PetscMalloc1(jj, &clid_flid);
689: ISGetIndices(selected_1, &selected_idx);
690: for (kk=0,nLocalSelected=0; kk<jj; kk++) {
691: PetscInt lid = selected_idx[kk];
692: if (lid<nloc) {
693: MatGetRow(Gmat,lid+my0,&ncols,0,0);
694: if (ncols>1) clid_flid[nLocalSelected++] = lid; /* fiter out singletons */
695: MatRestoreRow(Gmat,lid+my0,&ncols,0,0);
696: }
697: }
698: ISRestoreIndices(selected_1, &selected_idx);
699: ISDestroy(&selected_1); /* this is selected_1 in serial */
701: /* create prolongator matrix */
702: MatGetType(Amat,&mtype);
703: MatCreate(comm, &Prol);
704: MatSetSizes(Prol,nloc*bs,nLocalSelected*bs,PETSC_DETERMINE,PETSC_DETERMINE);
705: MatSetBlockSizes(Prol, bs, bs);
706: MatSetType(Prol, mtype);
707: MatSeqAIJSetPreallocation(Prol,3*data_cols,NULL);
708: MatMPIAIJSetPreallocation(Prol,3*data_cols,NULL,3*data_cols,NULL);
710: /* can get all points "removed" - but not on geomg */
711: MatGetSize(Prol, &kk, &jj);
712: if (!jj) {
713: PetscInfo(pc,"ERROE: no selected points on coarse grid\n");
714: PetscFree(clid_flid);
715: MatDestroy(&Prol);
716: *a_P_out = NULL; /* out */
717: return(0);
718: }
720: {
721: PetscReal *coords;
722: PetscInt data_stride;
723: PetscInt *crsGID = NULL;
724: Mat Gmat2;
726: if (dim != data_cols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"dim %D != data_cols %D",dim,data_cols);
727: /* grow ghost data for better coarse grid cover of fine grid */
728: #if defined PETSC_GAMG_USE_LOG
729: PetscLogEventBegin(petsc_gamg_setup_events[SET5],0,0,0,0);
730: #endif
731: /* messy method, squares graph and gets some data */
732: getGIDsOnSquareGraph(nLocalSelected, clid_flid, Gmat, &selected_2, &Gmat2, &crsGID);
733: /* llist is now not valid wrt squared graph, but will work as iterator in 'triangulateAndFormProl' */
734: #if defined PETSC_GAMG_USE_LOG
735: PetscLogEventEnd(petsc_gamg_setup_events[SET5],0,0,0,0);
736: #endif
737: /* create global vector of coorindates in 'coords' */
738: if (size > 1) {
739: PCGAMGGetDataWithGhosts(Gmat2, dim, pc_gamg->data, &data_stride, &coords);
740: } else {
741: coords = (PetscReal*)pc_gamg->data;
742: data_stride = pc_gamg->data_sz/pc_gamg->data_cell_cols;
743: }
744: MatDestroy(&Gmat2);
746: /* triangulate */
747: if (dim == 2) {
748: PetscReal metric,tm;
749: #if defined PETSC_GAMG_USE_LOG
750: PetscLogEventBegin(petsc_gamg_setup_events[SET6],0,0,0,0);
751: #endif
752: triangulateAndFormProl(selected_2, data_stride, coords,nLocalSelected, clid_flid, agg_lists, crsGID, bs, Prol, &metric);
753: #if defined PETSC_GAMG_USE_LOG
754: PetscLogEventEnd(petsc_gamg_setup_events[SET6],0,0,0,0);
755: #endif
756: PetscFree(crsGID);
758: /* clean up and create coordinates for coarse grid (output) */
759: if (size > 1) PetscFree(coords);
761: MPIU_Allreduce(&metric, &tm, 1, MPIU_REAL, MPIU_MAX, comm);
762: if (tm > 1.) { /* needs to be globalized - should not happen */
763: PetscInfo1(pc," failed metric for coarse grid %e\n",(double)tm);
764: MatDestroy(&Prol);
765: } else if (metric > .0) {
766: PetscInfo1(pc,"worst metric for coarse grid = %e\n",(double)metric);
767: }
768: } else SETERRQ(comm,PETSC_ERR_PLIB,"3D not implemented for 'geo' AMG");
769: { /* create next coords - output */
770: PetscReal *crs_crds;
771: PetscMalloc1(dim*nLocalSelected, &crs_crds);
772: for (kk=0; kk<nLocalSelected; kk++) { /* grab local select nodes to promote - output */
773: PetscInt lid = clid_flid[kk];
774: for (jj=0; jj<dim; jj++) crs_crds[jj*nLocalSelected + kk] = pc_gamg->data[jj*nloc + lid];
775: }
777: PetscFree(pc_gamg->data);
778: pc_gamg->data = crs_crds; /* out */
779: pc_gamg->data_sz = dim*nLocalSelected;
780: }
781: ISDestroy(&selected_2);
782: }
784: *a_P_out = Prol; /* out */
785: PetscFree(clid_flid);
786: PetscLogEventEnd(PC_GAMGProlongator_GEO,0,0,0,0);
787: return(0);
788: }
790: static PetscErrorCode PCDestroy_GAMG_GEO(PC pc)
791: {
795: PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",NULL);
796: return(0);
797: }
799: /* -------------------------------------------------------------------------- */
800: /*
801: PCCreateGAMG_GEO
803: Input Parameter:
804: . pc -
805: */
806: PetscErrorCode PCCreateGAMG_GEO(PC pc)
807: {
809: PC_MG *mg = (PC_MG*)pc->data;
810: PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx;
813: pc_gamg->ops->setfromoptions = PCSetFromOptions_GEO;
814: pc_gamg->ops->destroy = PCDestroy_GAMG_GEO;
815: /* reset does not do anything; setup not virtual */
817: /* set internal function pointers */
818: pc_gamg->ops->graph = PCGAMGGraph_GEO;
819: pc_gamg->ops->coarsen = PCGAMGCoarsen_GEO;
820: pc_gamg->ops->prolongator = PCGAMGProlongator_GEO;
821: pc_gamg->ops->optprolongator = NULL;
822: pc_gamg->ops->createdefaultdata = PCSetData_GEO;
824: PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",PCSetCoordinates_GEO);
825: return(0);
826: }