Actual source code: geo.c
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: #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: PETSC_STATIC_INLINE int petsc_geo_mg_compare(const void *a, const void *b)
23: {
24: return (((GAMGNode*)a)->degree - ((GAMGNode*)b)->degree);
25: }
27: /* -------------------------------------------------------------------------- */
28: /*
29: PCSetCoordinates_GEO
31: Input Parameter:
32: . pc - the preconditioner context
33: */
34: 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;
39: PetscInt arrsz,bs,my0,kk,ii,nloc,Iend,aloc;
40: Mat Amat = pc->pmat;
44: MatGetBlockSize(Amat, &bs);
45: MatGetOwnershipRange(Amat, &my0, &Iend);
46: aloc = (Iend-my0);
47: nloc = (Iend-my0)/bs;
49: 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);
51: pc_gamg->data_cell_rows = 1;
52: if (!coords && nloc > 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG, "Need coordinates for pc_gamg_type 'geo'.");
53: pc_gamg->data_cell_cols = ndm; /* coordinates */
55: arrsz = nloc*pc_gamg->data_cell_rows*pc_gamg->data_cell_cols;
57: /* create data - syntactic sugar that should be refactored at some point */
58: if (!pc_gamg->data || (pc_gamg->data_sz != arrsz)) {
59: PetscFree(pc_gamg->data);
60: PetscMalloc1(arrsz+1, &pc_gamg->data);
61: }
62: for (kk=0; kk<arrsz; kk++) pc_gamg->data[kk] = -999.;
63: pc_gamg->data[arrsz] = -99.;
64: /* copy data in - column oriented */
65: if (nloc == a_nloc) {
66: for (kk = 0; kk < nloc; kk++) {
67: for (ii = 0; ii < ndm; ii++) {
68: pc_gamg->data[ii*nloc + kk] = coords[kk*ndm + ii];
69: }
70: }
71: } else { /* assumes the coordinates are blocked */
72: for (kk = 0; kk < nloc; kk++) {
73: for (ii = 0; ii < ndm; ii++) {
74: pc_gamg->data[ii*nloc + kk] = coords[bs*kk*ndm + ii];
75: }
76: }
77: }
78: 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]);
79: pc_gamg->data_sz = arrsz;
80: return(0);
81: }
83: /* -------------------------------------------------------------------------- */
84: /*
85: PCSetData_GEO
87: Input Parameter:
88: . pc -
89: */
90: PetscErrorCode PCSetData_GEO(PC pc, Mat m)
91: {
93: SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_PLIB,"GEO MG needs coordinates");
94: }
96: /* -------------------------------------------------------------------------- */
97: /*
98: PCSetFromOptions_GEO
100: Input Parameter:
101: . pc -
102: */
103: PetscErrorCode PCSetFromOptions_GEO(PetscOptionItems *PetscOptionsObject,PC pc)
104: {
108: PetscOptionsHead(PetscOptionsObject,"GAMG-GEO options");
109: {
110: /* -pc_gamg_sa_nsmooths */
111: /* pc_gamg_sa->smooths = 0; */
112: /* PetscOptionsInt("-pc_gamg_agg_nsmooths", */
113: /* "smoothing steps for smoothed aggregation, usually 1 (0)", */
114: /* "PCGAMGSetNSmooths_AGG", */
115: /* pc_gamg_sa->smooths, */
116: /* &pc_gamg_sa->smooths, */
117: /* &flag); */
118: /* */
119: }
120: PetscOptionsTail();
121: return(0);
122: }
124: /* -------------------------------------------------------------------------- */
125: /*
126: triangulateAndFormProl
128: Input Parameter:
129: . selected_2 - list of selected local ID, includes selected ghosts
130: . data_stride -
131: . coords[2*data_stride] - column vector of local coordinates w/ ghosts
132: . nselected_1 - selected IDs that go with base (1) graph includes selected ghosts
133: . clid_lid_1[nselected_1] - lids of selected (c) nodes ???????????
134: . agg_lists_1 - list of aggregates selected_1 vertices of aggregate unselected vertices
135: . crsGID[selected.size()] - global index for prolongation operator
136: . bs - block size
137: Output Parameter:
138: . a_Prol - prolongation operator
139: . a_worst_best - measure of worst missed fine vertex, 0 is no misses
140: */
141: static PetscErrorCode triangulateAndFormProl(IS selected_2,PetscInt data_stride,PetscReal coords[],PetscInt nselected_1,const PetscInt clid_lid_1[],const PetscCoarsenData *agg_lists_1,
142: const PetscInt crsGID[],PetscInt bs,Mat a_Prol,PetscReal *a_worst_best)
143: {
144: #if defined(PETSC_HAVE_TRIANGLE)
145: PetscErrorCode ierr;
146: PetscInt jj,tid,tt,idx,nselected_2;
147: struct triangulateio in,mid;
148: const PetscInt *selected_idx_2;
149: PetscMPIInt rank;
150: PetscInt Istart,Iend,nFineLoc,myFine0;
151: int kk,nPlotPts,sid;
152: MPI_Comm comm;
153: PetscReal tm;
156: PetscObjectGetComm((PetscObject)a_Prol,&comm);
157: MPI_Comm_rank(comm,&rank);
158: ISGetSize(selected_2, &nselected_2);
159: if (nselected_2 == 1 || nselected_2 == 2) { /* 0 happens on idle processors */
160: *a_worst_best = 100.0; /* this will cause a stop, but not globalized (should not happen) */
161: } else *a_worst_best = 0.0;
162: MPIU_Allreduce(a_worst_best, &tm, 1, MPIU_REAL, MPIU_MAX, comm);
163: if (tm > 0.0) {
164: *a_worst_best = 100.0;
165: return(0);
166: }
167: MatGetOwnershipRange(a_Prol, &Istart, &Iend);
168: nFineLoc = (Iend-Istart)/bs; myFine0 = Istart/bs;
169: nPlotPts = nFineLoc; /* locals */
170: /* triangle */
171: /* Define input points - in*/
172: in.numberofpoints = nselected_2;
173: in.numberofpointattributes = 0;
174: /* get nselected points */
175: PetscMalloc1(2*nselected_2, &in.pointlist);
176: ISGetIndices(selected_2, &selected_idx_2);
178: for (kk=0,sid=0; kk<nselected_2; kk++,sid += 2) {
179: PetscInt lid = selected_idx_2[kk];
180: in.pointlist[sid] = coords[lid];
181: in.pointlist[sid+1] = coords[data_stride + lid];
182: if (lid>=nFineLoc) nPlotPts++;
183: }
184: if (sid != 2*nselected_2) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != 2*nselected_2 %D",sid,nselected_2);
186: in.numberofsegments = 0;
187: in.numberofedges = 0;
188: in.numberofholes = 0;
189: in.numberofregions = 0;
190: in.trianglelist = NULL;
191: in.segmentmarkerlist = NULL;
192: in.pointattributelist = NULL;
193: in.pointmarkerlist = NULL;
194: in.triangleattributelist = NULL;
195: in.trianglearealist = NULL;
196: in.segmentlist = NULL;
197: in.holelist = NULL;
198: in.regionlist = NULL;
199: in.edgelist = NULL;
200: in.edgemarkerlist = NULL;
201: in.normlist = NULL;
203: /* triangulate */
204: mid.pointlist = NULL; /* Not needed if -N switch used. */
205: /* Not needed if -N switch used or number of point attributes is zero: */
206: mid.pointattributelist = NULL;
207: mid.pointmarkerlist = NULL; /* Not needed if -N or -B switch used. */
208: mid.trianglelist = NULL; /* Not needed if -E switch used. */
209: /* Not needed if -E switch used or number of triangle attributes is zero: */
210: mid.triangleattributelist = NULL;
211: mid.neighborlist = NULL; /* Needed only if -n switch used. */
212: /* Needed only if segments are output (-p or -c) and -P not used: */
213: mid.segmentlist = NULL;
214: /* Needed only if segments are output (-p or -c) and -P and -B not used: */
215: mid.segmentmarkerlist = NULL;
216: mid.edgelist = NULL; /* Needed only if -e switch used. */
217: mid.edgemarkerlist = NULL; /* Needed if -e used and -B not used. */
218: mid.numberoftriangles = 0;
220: /* Triangulate the points. Switches are chosen to read and write a */
221: /* PSLG (p), preserve the convex hull (c), number everything from */
222: /* zero (z), assign a regional attribute to each element (A), and */
223: /* produce an edge list (e), a Voronoi diagram (v), and a triangle */
224: /* neighbor list (n). */
225: if (nselected_2 != 0) { /* inactive processor */
226: char args[] = "npczQ"; /* c is needed ? */
227: triangulate(args, &in, &mid, (struct triangulateio*) NULL);
228: /* output .poly files for 'showme' */
229: if (!PETSC_TRUE) {
230: static int level = 1;
231: FILE *file; char fname[32];
233: sprintf(fname,"C%d_%d.poly",level,rank); file = fopen(fname, "w");
234: /*First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)>*/
235: fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0);
236: /*Following lines: <vertex #> <x> <y> */
237: for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid += 2) {
238: fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]);
239: }
240: /*One line: <# of segments> <# of boundary markers (0 or 1)> */
241: fprintf(file, "%d %d\n",0,0);
242: /*Following lines: <segment #> <endpoint> <endpoint> [boundary marker] */
243: /* One line: <# of holes> */
244: fprintf(file, "%d\n",0);
245: /* Following lines: <hole #> <x> <y> */
246: /* Optional line: <# of regional attributes and/or area constraints> */
247: /* Optional following lines: <region #> <x> <y> <attribute> <maximum area> */
248: fclose(file);
250: /* elems */
251: sprintf(fname,"C%d_%d.ele",level,rank); file = fopen(fname, "w");
252: /* First line: <# of triangles> <nodes per triangle> <# of attributes> */
253: fprintf(file, "%d %d %d\n",mid.numberoftriangles,3,0);
254: /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */
255: for (kk=0,sid=0; kk<mid.numberoftriangles; kk++,sid += 3) {
256: fprintf(file, "%d %d %d %d\n",kk,mid.trianglelist[sid],mid.trianglelist[sid+1],mid.trianglelist[sid+2]);
257: }
258: fclose(file);
260: sprintf(fname,"C%d_%d.node",level,rank); file = fopen(fname, "w");
261: /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */
262: /* fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); */
263: fprintf(file, "%d %d %d %d\n",nPlotPts,2,0,0);
264: /*Following lines: <vertex #> <x> <y> */
265: for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid+=2) {
266: fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]);
267: }
269: sid /= 2;
270: for (jj=0; jj<nFineLoc; jj++) {
271: PetscBool sel = PETSC_TRUE;
272: for (kk=0; kk<nselected_2 && sel; kk++) {
273: PetscInt lid = selected_idx_2[kk];
274: if (lid == jj) sel = PETSC_FALSE;
275: }
276: if (sel) fprintf(file, "%d %e %e\n",sid++,coords[jj],coords[data_stride + jj]);
277: }
278: fclose(file);
279: if (sid != nPlotPts) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != nPlotPts %D",sid,nPlotPts);
280: level++;
281: }
282: }
283: PetscLogEventBegin(petsc_gamg_setup_events[FIND_V],0,0,0,0);
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: PetscLogEventEnd(petsc_gamg_setup_events[FIND_V],0,0,0,0);
414: free(mid.trianglelist);
415: free(mid.neighborlist);
416: free(mid.segmentlist);
417: free(mid.segmentmarkerlist);
418: free(mid.pointlist);
419: free(mid.pointmarkerlist);
420: PetscFree(in.pointlist);
421: return(0);
422: #else
423: SETERRQ(PetscObjectComm((PetscObject)a_Prol),PETSC_ERR_PLIB,"configure with TRIANGLE to use geometric MG");
424: #endif
425: }
426: /* -------------------------------------------------------------------------- */
427: /*
428: getGIDsOnSquareGraph - square graph, get
430: Input Parameter:
431: . nselected_1 - selected local indices (includes ghosts in input Gmat1)
432: . clid_lid_1 - [nselected_1] lids of selected nodes
433: . Gmat1 - graph that goes with 'selected_1'
434: Output Parameter:
435: . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2)
436: . a_Gmat_2 - graph that is squared of 'Gmat_1'
437: . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes
438: */
439: 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)
440: {
442: PetscMPIInt size;
443: PetscInt *crsGID, kk,my0,Iend,nloc;
444: MPI_Comm comm;
447: PetscObjectGetComm((PetscObject)Gmat1,&comm);
448: MPI_Comm_size(comm,&size);
449: MatGetOwnershipRange(Gmat1,&my0,&Iend); /* AIJ */
450: nloc = Iend - my0; /* this does not change */
452: if (size == 1) { /* not much to do in serial */
453: PetscMalloc1(nselected_1, &crsGID);
454: for (kk=0; kk<nselected_1; kk++) crsGID[kk] = kk;
455: *a_Gmat_2 = NULL;
456: ISCreateGeneral(PETSC_COMM_SELF,nselected_1,clid_lid_1,PETSC_COPY_VALUES,a_selected_2);
457: } else {
458: PetscInt idx,num_fine_ghosts,num_crs_ghost,myCrs0;
459: Mat_MPIAIJ *mpimat2;
460: Mat Gmat2;
461: Vec locState;
462: PetscScalar *cpcol_state;
464: /* scan my coarse zero gid, set 'lid_state' with coarse GID */
465: kk = nselected_1;
466: MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPI_SUM, comm);
467: myCrs0 -= nselected_1;
469: if (a_Gmat_2) { /* output */
470: /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */
471: PCGAMGSquareGraph_GAMG(pc,Gmat1,&Gmat2);
472: *a_Gmat_2 = Gmat2; /* output */
473: } else Gmat2 = Gmat1; /* use local to get crsGIDs at least */
474: /* get coarse grid GIDS for selected (locals and ghosts) */
475: mpimat2 = (Mat_MPIAIJ*)Gmat2->data;
476: MatCreateVecs(Gmat2, &locState, NULL);
477: VecSet(locState, (PetscScalar)(PetscReal)(-1)); /* set with UNKNOWN state */
478: for (kk=0; kk<nselected_1; kk++) {
479: PetscInt fgid = clid_lid_1[kk] + my0;
480: PetscScalar v = (PetscScalar)(kk+myCrs0);
481: VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES); /* set with PID */
482: }
483: VecAssemblyBegin(locState);
484: VecAssemblyEnd(locState);
485: VecScatterBegin(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);
486: VecScatterEnd(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);
487: VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts);
488: VecGetArray(mpimat2->lvec, &cpcol_state);
489: for (kk=0,num_crs_ghost=0; kk<num_fine_ghosts; kk++) {
490: if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++;
491: }
492: PetscMalloc1(nselected_1+num_crs_ghost, &crsGID); /* output */
493: {
494: PetscInt *selected_set;
495: PetscMalloc1(nselected_1+num_crs_ghost, &selected_set);
496: /* do ghost of 'crsGID' */
497: for (kk=0,idx=nselected_1; kk<num_fine_ghosts; kk++) {
498: if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) {
499: PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]);
500: selected_set[idx] = nloc + kk;
501: crsGID[idx++] = cgid;
502: }
503: }
504: 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);
505: VecRestoreArray(mpimat2->lvec, &cpcol_state);
506: /* do locals in 'crsGID' */
507: VecGetArray(locState, &cpcol_state);
508: for (kk=0,idx=0; kk<nloc; kk++) {
509: if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) {
510: PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]);
511: selected_set[idx] = kk;
512: crsGID[idx++] = cgid;
513: }
514: }
515: if (idx != nselected_1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"idx %D != nselected_1 %D",idx,nselected_1);
516: VecRestoreArray(locState, &cpcol_state);
518: if (a_selected_2 != NULL) { /* output */
519: ISCreateGeneral(PETSC_COMM_SELF,(nselected_1+num_crs_ghost),selected_set,PETSC_OWN_POINTER,a_selected_2);
520: } else {
521: PetscFree(selected_set);
522: }
523: }
524: VecDestroy(&locState);
525: }
526: *a_crsGID = crsGID; /* output */
527: return(0);
528: }
530: /* -------------------------------------------------------------------------- */
531: /*
532: PCGAMGGraph_GEO
534: Input Parameter:
535: . pc - this
536: . Amat - matrix on this fine level
537: Output Parameter:
538: . a_Gmat
539: */
540: PetscErrorCode PCGAMGGraph_GEO(PC pc,Mat Amat,Mat *a_Gmat)
541: {
542: PetscErrorCode ierr;
543: PC_MG *mg = (PC_MG*)pc->data;
544: PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx;
545: const PetscReal vfilter = pc_gamg->threshold[0];
546: MPI_Comm comm;
547: Mat Gmat;
548: PetscBool set,flg,symm;
551: PetscObjectGetComm((PetscObject)Amat,&comm);
552: PetscLogEventBegin(PC_GAMGGraph_GEO,0,0,0,0);
554: MatIsSymmetricKnown(Amat, &set, &flg);
555: symm = (PetscBool)!(set && flg);
557: PCGAMGCreateGraph(Amat, &Gmat);
558: PCGAMGFilterGraph(&Gmat, vfilter, symm);
560: *a_Gmat = Gmat;
561: PetscLogEventEnd(PC_GAMGGraph_GEO,0,0,0,0);
562: return(0);
563: }
565: /* -------------------------------------------------------------------------- */
566: /*
567: PCGAMGCoarsen_GEO
569: Input Parameter:
570: . a_pc - this
571: . a_Gmat - graph
572: Output Parameter:
573: . a_llist_parent - linked list from selected indices for data locality only
574: */
575: PetscErrorCode PCGAMGCoarsen_GEO(PC a_pc,Mat *a_Gmat,PetscCoarsenData **a_llist_parent)
576: {
578: PetscInt Istart,Iend,nloc,kk,Ii,ncols;
579: IS perm;
580: GAMGNode *gnodes;
581: PetscInt *permute;
582: Mat Gmat = *a_Gmat;
583: MPI_Comm comm;
584: MatCoarsen crs;
587: PetscObjectGetComm((PetscObject)a_pc,&comm);
588: PetscLogEventBegin(PC_GAMGCoarsen_GEO,0,0,0,0);
589: MatGetOwnershipRange(Gmat, &Istart, &Iend);
590: nloc = (Iend-Istart);
592: /* create random permutation with sort for geo-mg */
593: PetscMalloc1(nloc, &gnodes);
594: PetscMalloc1(nloc, &permute);
596: for (Ii=Istart; Ii<Iend; Ii++) { /* locals only? */
597: MatGetRow(Gmat,Ii,&ncols,NULL,NULL);
598: {
599: PetscInt lid = Ii - Istart;
600: gnodes[lid].lid = lid;
601: gnodes[lid].degree = ncols;
602: }
603: MatRestoreRow(Gmat,Ii,&ncols,NULL,NULL);
604: }
605: if (PETSC_TRUE) {
606: PetscRandom rand;
607: PetscBool *bIndexSet;
608: PetscReal rr;
609: PetscInt iSwapIndex;
611: PetscRandomCreate(comm,&rand);
612: PetscCalloc1(nloc, &bIndexSet);
613: for (Ii = 0; Ii < nloc; Ii++) {
614: PetscRandomGetValueReal(rand,&rr);
615: iSwapIndex = (PetscInt) (rr*nloc);
616: if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) {
617: GAMGNode iTemp = gnodes[iSwapIndex];
618: gnodes[iSwapIndex] = gnodes[Ii];
619: gnodes[Ii] = iTemp;
620: bIndexSet[Ii] = PETSC_TRUE;
621: bIndexSet[iSwapIndex] = PETSC_TRUE;
622: }
623: }
624: PetscRandomDestroy(&rand);
625: PetscFree(bIndexSet);
626: }
627: /* only sort locals */
628: qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare);
629: /* create IS of permutation */
630: for (kk=0; kk<nloc; kk++) permute[kk] = gnodes[kk].lid; /* locals only */
631: PetscFree(gnodes);
632: ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm);
634: /* get MIS aggs */
636: MatCoarsenCreate(comm, &crs);
637: MatCoarsenSetType(crs, MATCOARSENMIS);
638: MatCoarsenSetGreedyOrdering(crs, perm);
639: MatCoarsenSetAdjacency(crs, Gmat);
640: MatCoarsenSetStrictAggs(crs, PETSC_FALSE);
641: MatCoarsenApply(crs);
642: MatCoarsenGetData(crs, a_llist_parent);
643: MatCoarsenDestroy(&crs);
645: ISDestroy(&perm);
646: PetscLogEventEnd(PC_GAMGCoarsen_GEO,0,0,0,0);
647: return(0);
648: }
650: /* -------------------------------------------------------------------------- */
651: /*
652: PCGAMGProlongator_GEO
654: Input Parameter:
655: . pc - this
656: . Amat - matrix on this fine level
657: . Graph - used to get ghost data for nodes in
658: . selected_1 - [nselected]
659: . agg_lists - [nselected]
660: Output Parameter:
661: . a_P_out - prolongation operator to the next level
662: */
663: PetscErrorCode PCGAMGProlongator_GEO(PC pc,Mat Amat,Mat Gmat,PetscCoarsenData *agg_lists,Mat *a_P_out)
664: {
665: PC_MG *mg = (PC_MG*)pc->data;
666: PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx;
667: const PetscInt dim = pc_gamg->data_cell_cols, data_cols = pc_gamg->data_cell_cols;
669: PetscInt Istart,Iend,nloc,my0,jj,kk,ncols,nLocalSelected,bs,*clid_flid;
670: Mat Prol;
671: PetscMPIInt rank, size;
672: MPI_Comm comm;
673: IS selected_2,selected_1;
674: const PetscInt *selected_idx;
675: MatType mtype;
678: PetscObjectGetComm((PetscObject)Amat,&comm);
679: PetscLogEventBegin(PC_GAMGProlongator_GEO,0,0,0,0);
680: MPI_Comm_rank(comm,&rank);
681: MPI_Comm_size(comm,&size);
682: MatGetOwnershipRange(Amat, &Istart, &Iend);
683: MatGetBlockSize(Amat, &bs);
684: nloc = (Iend-Istart)/bs; my0 = Istart/bs;
685: if ((Iend-Istart) % bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(Iend %D - Istart %D) % bs %D",Iend,Istart,bs);
687: /* get 'nLocalSelected' */
688: PetscCDGetMIS(agg_lists, &selected_1);
689: ISGetSize(selected_1, &jj);
690: PetscMalloc1(jj, &clid_flid);
691: ISGetIndices(selected_1, &selected_idx);
692: for (kk=0,nLocalSelected=0; kk<jj; kk++) {
693: PetscInt lid = selected_idx[kk];
694: if (lid<nloc) {
695: MatGetRow(Gmat,lid+my0,&ncols,NULL,NULL);
696: if (ncols>1) clid_flid[nLocalSelected++] = lid; /* fiter out singletons */
697: MatRestoreRow(Gmat,lid+my0,&ncols,NULL,NULL);
698: }
699: }
700: ISRestoreIndices(selected_1, &selected_idx);
701: ISDestroy(&selected_1); /* this is selected_1 in serial */
703: /* create prolongator matrix */
704: MatGetType(Amat,&mtype);
705: MatCreate(comm, &Prol);
706: MatSetSizes(Prol,nloc*bs,nLocalSelected*bs,PETSC_DETERMINE,PETSC_DETERMINE);
707: MatSetBlockSizes(Prol, bs, bs);
708: MatSetType(Prol, mtype);
709: MatSeqAIJSetPreallocation(Prol,3*data_cols,NULL);
710: MatMPIAIJSetPreallocation(Prol,3*data_cols,NULL,3*data_cols,NULL);
712: /* can get all points "removed" - but not on geomg */
713: MatGetSize(Prol, &kk, &jj);
714: if (!jj) {
715: PetscInfo(pc,"ERROE: no selected points on coarse grid\n");
716: PetscFree(clid_flid);
717: MatDestroy(&Prol);
718: *a_P_out = NULL; /* out */
719: return(0);
720: }
722: {
723: PetscReal *coords;
724: PetscInt data_stride;
725: PetscInt *crsGID = NULL;
726: Mat Gmat2;
728: if (dim != data_cols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"dim %D != data_cols %D",dim,data_cols);
729: /* grow ghost data for better coarse grid cover of fine grid */
730: PetscLogEventBegin(petsc_gamg_setup_events[SET5],0,0,0,0);
731: /* messy method, squares graph and gets some data */
732: getGIDsOnSquareGraph(pc, 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: PetscLogEventEnd(petsc_gamg_setup_events[SET5],0,0,0,0);
735: /* create global vector of coorindates in 'coords' */
736: if (size > 1) {
737: PCGAMGGetDataWithGhosts(Gmat2, dim, pc_gamg->data, &data_stride, &coords);
738: } else {
739: coords = (PetscReal*)pc_gamg->data;
740: data_stride = pc_gamg->data_sz/pc_gamg->data_cell_cols;
741: }
742: MatDestroy(&Gmat2);
744: /* triangulate */
745: if (dim == 2) {
746: PetscReal metric,tm;
747: PetscLogEventBegin(petsc_gamg_setup_events[SET6],0,0,0,0);
748: triangulateAndFormProl(selected_2, data_stride, coords,nLocalSelected, clid_flid, agg_lists, crsGID, bs, Prol, &metric);
749: PetscLogEventEnd(petsc_gamg_setup_events[SET6],0,0,0,0);
750: PetscFree(crsGID);
752: /* clean up and create coordinates for coarse grid (output) */
753: if (size > 1) {PetscFree(coords);}
755: MPIU_Allreduce(&metric, &tm, 1, MPIU_REAL, MPIU_MAX, comm);
756: if (tm > 1.) { /* needs to be globalized - should not happen */
757: PetscInfo1(pc," failed metric for coarse grid %e\n",(double)tm);
758: MatDestroy(&Prol);
759: } else if (metric > .0) {
760: PetscInfo1(pc,"worst metric for coarse grid = %e\n",(double)metric);
761: }
762: } else SETERRQ(comm,PETSC_ERR_PLIB,"3D not implemented for 'geo' AMG");
763: { /* create next coords - output */
764: PetscReal *crs_crds;
765: PetscMalloc1(dim*nLocalSelected, &crs_crds);
766: for (kk=0; kk<nLocalSelected; kk++) { /* grab local select nodes to promote - output */
767: PetscInt lid = clid_flid[kk];
768: for (jj=0; jj<dim; jj++) crs_crds[jj*nLocalSelected + kk] = pc_gamg->data[jj*nloc + lid];
769: }
771: PetscFree(pc_gamg->data);
772: pc_gamg->data = crs_crds; /* out */
773: pc_gamg->data_sz = dim*nLocalSelected;
774: }
775: ISDestroy(&selected_2);
776: }
778: *a_P_out = Prol; /* out */
779: PetscFree(clid_flid);
780: PetscLogEventEnd(PC_GAMGProlongator_GEO,0,0,0,0);
781: return(0);
782: }
784: static PetscErrorCode PCDestroy_GAMG_GEO(PC pc)
785: {
789: PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",NULL);
790: return(0);
791: }
793: /* -------------------------------------------------------------------------- */
794: /*
795: PCCreateGAMG_GEO
797: Input Parameter:
798: . pc -
799: */
800: PetscErrorCode PCCreateGAMG_GEO(PC pc)
801: {
803: PC_MG *mg = (PC_MG*)pc->data;
804: PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx;
807: pc_gamg->ops->setfromoptions = PCSetFromOptions_GEO;
808: pc_gamg->ops->destroy = PCDestroy_GAMG_GEO;
809: /* reset does not do anything; setup not virtual */
811: /* set internal function pointers */
812: pc_gamg->ops->graph = PCGAMGGraph_GEO;
813: pc_gamg->ops->coarsen = PCGAMGCoarsen_GEO;
814: pc_gamg->ops->prolongator = PCGAMGProlongator_GEO;
815: pc_gamg->ops->optprolongator = NULL;
816: pc_gamg->ops->createdefaultdata = PCSetData_GEO;
818: PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",PCSetCoordinates_GEO);
819: return(0);
820: }