Actual source code: util.c
petsc-3.14.6 2021-03-30
1: /*
2: GAMG geometric-algebric multigrid PC - Mark Adams 2011
3: */
4: #include <petsc/private/matimpl.h>
5: #include <../src/ksp/pc/impls/gamg/gamg.h>
7: /*
8: Produces a set of block column indices of the matrix row, one for each block represented in the original row
10: n - the number of block indices in cc[]
11: cc - the block indices (must be large enough to contain the indices)
12: */
13: PETSC_STATIC_INLINE PetscErrorCode MatCollapseRow(Mat Amat,PetscInt row,PetscInt bs,PetscInt *n,PetscInt *cc)
14: {
15: PetscInt cnt = -1,nidx,j;
16: const PetscInt *idx;
20: MatGetRow(Amat,row,&nidx,&idx,NULL);
21: if (nidx) {
22: cnt = 0;
23: cc[cnt] = idx[0]/bs;
24: for (j=1; j<nidx; j++) {
25: if (cc[cnt] < idx[j]/bs) cc[++cnt] = idx[j]/bs;
26: }
27: }
28: MatRestoreRow(Amat,row,&nidx,&idx,NULL);
29: *n = cnt+1;
30: return(0);
31: }
33: /*
34: Produces a set of block column indices of the matrix block row, one for each block represented in the original set of rows
36: ncollapsed - the number of block indices
37: collapsed - the block indices (must be large enough to contain the indices)
38: */
39: PETSC_STATIC_INLINE PetscErrorCode MatCollapseRows(Mat Amat,PetscInt start,PetscInt bs,PetscInt *w0,PetscInt *w1,PetscInt *w2,PetscInt *ncollapsed,PetscInt **collapsed)
40: {
41: PetscInt i,nprev,*cprev = w0,ncur = 0,*ccur = w1,*merged = w2,*cprevtmp;
45: MatCollapseRow(Amat,start,bs,&nprev,cprev);
46: for (i=start+1; i<start+bs; i++) {
47: MatCollapseRow(Amat,i,bs,&ncur,ccur);
48: PetscMergeIntArray(nprev,cprev,ncur,ccur,&nprev,&merged);
49: cprevtmp = cprev; cprev = merged; merged = cprevtmp;
50: }
51: *ncollapsed = nprev;
52: if (collapsed) *collapsed = cprev;
53: return(0);
54: }
57: /* -------------------------------------------------------------------------- */
58: /*
59: PCGAMGCreateGraph - create simple scaled scalar graph from matrix
61: Input Parameter:
62: . Amat - matrix
63: Output Parameter:
64: . a_Gmaat - eoutput scalar graph (symmetric?)
65: */
66: PetscErrorCode PCGAMGCreateGraph(Mat Amat, Mat *a_Gmat)
67: {
69: PetscInt Istart,Iend,Ii,jj,kk,ncols,nloc,NN,MM,bs;
70: MPI_Comm comm;
71: Mat Gmat;
74: PetscObjectGetComm((PetscObject)Amat,&comm);
75: MatGetOwnershipRange(Amat, &Istart, &Iend);
76: MatGetSize(Amat, &MM, &NN);
77: MatGetBlockSize(Amat, &bs);
78: nloc = (Iend-Istart)/bs;
80: #if defined PETSC_GAMG_USE_LOG
81: PetscLogEventBegin(petsc_gamg_setup_events[GRAPH],0,0,0,0);
82: #endif
84: if (bs > 1) {
85: const PetscScalar *vals;
86: const PetscInt *idx;
87: PetscInt *d_nnz, *o_nnz,*w0,*w1,*w2;
88: PetscBool ismpiaij,isseqaij;
90: /*
91: Determine the preallocation needed for the scalar matrix derived from the vector matrix.
92: */
94: PetscObjectBaseTypeCompare((PetscObject)Amat,MATSEQAIJ,&isseqaij);
95: PetscObjectBaseTypeCompare((PetscObject)Amat,MATMPIAIJ,&ismpiaij);
96: PetscMalloc2(nloc, &d_nnz,isseqaij ? 0 : nloc, &o_nnz);
98: if (isseqaij) {
99: PetscInt max_d_nnz;
101: /*
102: Determine exact preallocation count for (sequential) scalar matrix
103: */
104: MatSeqAIJGetMaxRowNonzeros(Amat,&max_d_nnz);
105: max_d_nnz = PetscMin(nloc,bs*max_d_nnz);
106: PetscMalloc3(max_d_nnz, &w0,max_d_nnz, &w1,max_d_nnz, &w2);
107: for (Ii = 0, jj = 0; Ii < Iend; Ii += bs, jj++) {
108: MatCollapseRows(Amat,Ii,bs,w0,w1,w2,&d_nnz[jj],NULL);
109: }
110: PetscFree3(w0,w1,w2);
112: } else if (ismpiaij) {
113: Mat Daij,Oaij;
114: const PetscInt *garray;
115: PetscInt max_d_nnz;
117: MatMPIAIJGetSeqAIJ(Amat,&Daij,&Oaij,&garray);
119: /*
120: Determine exact preallocation count for diagonal block portion of scalar matrix
121: */
122: MatSeqAIJGetMaxRowNonzeros(Daij,&max_d_nnz);
123: max_d_nnz = PetscMin(nloc,bs*max_d_nnz);
124: PetscMalloc3(max_d_nnz, &w0,max_d_nnz, &w1,max_d_nnz, &w2);
125: for (Ii = 0, jj = 0; Ii < Iend - Istart; Ii += bs, jj++) {
126: MatCollapseRows(Daij,Ii,bs,w0,w1,w2,&d_nnz[jj],NULL);
127: }
128: PetscFree3(w0,w1,w2);
130: /*
131: Over estimate (usually grossly over), preallocation count for off-diagonal portion of scalar matrix
132: */
133: for (Ii = 0, jj = 0; Ii < Iend - Istart; Ii += bs, jj++) {
134: o_nnz[jj] = 0;
135: for (kk=0; kk<bs; kk++) { /* rows that get collapsed to a single row */
136: MatGetRow(Oaij,Ii+kk,&ncols,NULL,NULL);
137: o_nnz[jj] += ncols;
138: MatRestoreRow(Oaij,Ii+kk,&ncols,NULL,NULL);
139: }
140: if (o_nnz[jj] > (NN/bs-nloc)) o_nnz[jj] = NN/bs-nloc;
141: }
143: } else SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Require AIJ matrix type");
145: /* get scalar copy (norms) of matrix */
146: MatCreate(comm, &Gmat);
147: MatSetSizes(Gmat,nloc,nloc,PETSC_DETERMINE,PETSC_DETERMINE);
148: MatSetBlockSizes(Gmat, 1, 1);
149: MatSetType(Gmat, MATAIJ);
150: MatSeqAIJSetPreallocation(Gmat,0,d_nnz);
151: MatMPIAIJSetPreallocation(Gmat,0,d_nnz,0,o_nnz);
152: PetscFree2(d_nnz,o_nnz);
154: for (Ii = Istart; Ii < Iend; Ii++) {
155: PetscInt dest_row = Ii/bs;
156: MatGetRow(Amat,Ii,&ncols,&idx,&vals);
157: for (jj=0; jj<ncols; jj++) {
158: PetscInt dest_col = idx[jj]/bs;
159: PetscScalar sv = PetscAbs(PetscRealPart(vals[jj]));
160: MatSetValues(Gmat,1,&dest_row,1,&dest_col,&sv,ADD_VALUES);
161: }
162: MatRestoreRow(Amat,Ii,&ncols,&idx,&vals);
163: }
164: MatAssemblyBegin(Gmat,MAT_FINAL_ASSEMBLY);
165: MatAssemblyEnd(Gmat,MAT_FINAL_ASSEMBLY);
166: } else {
167: /* just copy scalar matrix - abs() not taken here but scaled later */
168: MatDuplicate(Amat, MAT_COPY_VALUES, &Gmat);
169: }
170: MatPropagateSymmetryOptions(Amat, Gmat);
172: #if defined PETSC_GAMG_USE_LOG
173: PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);
174: #endif
176: *a_Gmat = Gmat;
177: return(0);
178: }
180: /* -------------------------------------------------------------------------- */
181: /*@C
182: PCGAMGFilterGraph - filter (remove zero and possibly small values from the) graph and make it symmetric if requested
184: Collective on Mat
186: Input Parameter:
187: + a_Gmat - the graph
188: . vfilter - threshold parameter [0,1)
189: - symm - make the result symmetric
191: Level: developer
193: Notes:
194: This is called before graph coarsers are called.
196: .seealso: PCGAMGSetThreshold()
197: @*/
198: PetscErrorCode PCGAMGFilterGraph(Mat *a_Gmat,PetscReal vfilter,PetscBool symm)
199: {
200: PetscErrorCode ierr;
201: PetscInt Istart,Iend,Ii,jj,ncols,nnz0,nnz1, NN, MM, nloc;
202: PetscMPIInt rank;
203: Mat Gmat = *a_Gmat, tGmat, matTrans;
204: MPI_Comm comm;
205: const PetscScalar *vals;
206: const PetscInt *idx;
207: PetscInt *d_nnz, *o_nnz;
208: Vec diag;
211: #if defined PETSC_GAMG_USE_LOG
212: PetscLogEventBegin(petsc_gamg_setup_events[GRAPH],0,0,0,0);
213: #endif
214: /* scale Gmat for all values between -1 and 1 */
215: MatCreateVecs(Gmat, &diag, NULL);
216: MatGetDiagonal(Gmat, diag);
217: VecReciprocal(diag);
218: VecSqrtAbs(diag);
219: MatDiagonalScale(Gmat, diag, diag);
220: VecDestroy(&diag);
222: if (vfilter < 0.0 && !symm) {
223: /* Just use the provided matrix as the graph but make all values positive */
224: MatInfo info;
225: PetscScalar *avals;
226: PetscBool isaij,ismpiaij;
227: PetscObjectBaseTypeCompare((PetscObject)Gmat,MATSEQAIJ,&isaij);
228: PetscObjectBaseTypeCompare((PetscObject)Gmat,MATMPIAIJ,&ismpiaij);
229: if (!isaij && !ismpiaij) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Require (MPI)AIJ matrix type");
230: if (isaij) {
231: MatGetInfo(Gmat,MAT_LOCAL,&info);
232: MatSeqAIJGetArray(Gmat,&avals);
233: for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]);
234: MatSeqAIJRestoreArray(Gmat,&avals);
235: } else {
236: Mat_MPIAIJ *aij = (Mat_MPIAIJ*)Gmat->data;
237: MatGetInfo(aij->A,MAT_LOCAL,&info);
238: MatSeqAIJGetArray(aij->A,&avals);
239: for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]);
240: MatSeqAIJRestoreArray(aij->A,&avals);
241: MatGetInfo(aij->B,MAT_LOCAL,&info);
242: MatSeqAIJGetArray(aij->B,&avals);
243: for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]);
244: MatSeqAIJRestoreArray(aij->B,&avals);
245: }
246: #if defined PETSC_GAMG_USE_LOG
247: PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);
248: #endif
249: return(0);
250: }
252: PetscObjectGetComm((PetscObject)Gmat,&comm);
253: MPI_Comm_rank(comm,&rank);
254: MatGetOwnershipRange(Gmat, &Istart, &Iend);
255: nloc = Iend - Istart;
256: MatGetSize(Gmat, &MM, &NN);
258: if (symm) {
259: MatTranspose(Gmat, MAT_INITIAL_MATRIX, &matTrans);
260: }
262: /* Determine upper bound on nonzeros needed in new filtered matrix */
263: PetscMalloc2(nloc, &d_nnz,nloc, &o_nnz);
264: for (Ii = Istart, jj = 0; Ii < Iend; Ii++, jj++) {
265: MatGetRow(Gmat,Ii,&ncols,NULL,NULL);
266: d_nnz[jj] = ncols;
267: o_nnz[jj] = ncols;
268: MatRestoreRow(Gmat,Ii,&ncols,NULL,NULL);
269: if (symm) {
270: MatGetRow(matTrans,Ii,&ncols,NULL,NULL);
271: d_nnz[jj] += ncols;
272: o_nnz[jj] += ncols;
273: MatRestoreRow(matTrans,Ii,&ncols,NULL,NULL);
274: }
275: if (d_nnz[jj] > nloc) d_nnz[jj] = nloc;
276: if (o_nnz[jj] > (MM-nloc)) o_nnz[jj] = MM - nloc;
277: }
278: MatCreate(comm, &tGmat);
279: MatSetSizes(tGmat,nloc,nloc,MM,MM);
280: MatSetBlockSizes(tGmat, 1, 1);
281: MatSetType(tGmat, MATAIJ);
282: MatSeqAIJSetPreallocation(tGmat,0,d_nnz);
283: MatMPIAIJSetPreallocation(tGmat,0,d_nnz,0,o_nnz);
284: PetscFree2(d_nnz,o_nnz);
285: if (symm) {
286: MatDestroy(&matTrans);
287: } else {
288: /* all entries are generated locally so MatAssembly will be slightly faster for large process counts */
289: MatSetOption(tGmat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);
290: }
292: for (Ii = Istart, nnz0 = nnz1 = 0; Ii < Iend; Ii++) {
293: MatGetRow(Gmat,Ii,&ncols,&idx,&vals);
294: for (jj=0; jj<ncols; jj++,nnz0++) {
295: PetscScalar sv = PetscAbs(PetscRealPart(vals[jj]));
296: if (PetscRealPart(sv) > vfilter) {
297: nnz1++;
298: if (symm) {
299: sv *= 0.5;
300: MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);
301: MatSetValues(tGmat,1,&idx[jj],1,&Ii,&sv,ADD_VALUES);
302: } else {
303: MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);
304: }
305: }
306: }
307: MatRestoreRow(Gmat,Ii,&ncols,&idx,&vals);
308: }
309: MatAssemblyBegin(tGmat,MAT_FINAL_ASSEMBLY);
310: MatAssemblyEnd(tGmat,MAT_FINAL_ASSEMBLY);
311: if (symm) {
312: MatSetOption(tGmat,MAT_SYMMETRIC,PETSC_TRUE);
313: } else {
314: MatPropagateSymmetryOptions(Gmat,tGmat);
315: }
316: #if defined PETSC_GAMG_USE_LOG
317: PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);
318: #endif
320: #if defined(PETSC_USE_INFO)
321: {
322: double t1 = (!nnz0) ? 1. : 100.*(double)nnz1/(double)nnz0, t2 = (!nloc) ? 1. : (double)nnz0/(double)nloc;
323: PetscInfo4(*a_Gmat,"\t %g%% nnz after filtering, with threshold %g, %g nnz ave. (N=%D)\n",t1,vfilter,t2,MM);
324: }
325: #endif
326: MatDestroy(&Gmat);
327: *a_Gmat = tGmat;
328: return(0);
329: }
331: /* -------------------------------------------------------------------------- */
332: /*
333: PCGAMGGetDataWithGhosts - hacks into Mat MPIAIJ so this must have size > 1
335: Input Parameter:
336: . Gmat - MPIAIJ matrix for scattters
337: . data_sz - number of data terms per node (# cols in output)
338: . data_in[nloc*data_sz] - column oriented data
339: Output Parameter:
340: . a_stride - numbrt of rows of output
341: . a_data_out[stride*data_sz] - output data with ghosts
342: */
343: PetscErrorCode PCGAMGGetDataWithGhosts(Mat Gmat,PetscInt data_sz,PetscReal data_in[],PetscInt *a_stride,PetscReal **a_data_out)
344: {
346: Vec tmp_crds;
347: Mat_MPIAIJ *mpimat = (Mat_MPIAIJ*)Gmat->data;
348: PetscInt nnodes,num_ghosts,dir,kk,jj,my0,Iend,nloc;
349: PetscScalar *data_arr;
350: PetscReal *datas;
351: PetscBool isMPIAIJ;
354: PetscObjectBaseTypeCompare((PetscObject)Gmat, MATMPIAIJ, &isMPIAIJ);
355: MatGetOwnershipRange(Gmat, &my0, &Iend);
356: nloc = Iend - my0;
357: VecGetLocalSize(mpimat->lvec, &num_ghosts);
358: nnodes = num_ghosts + nloc;
359: *a_stride = nnodes;
360: MatCreateVecs(Gmat, &tmp_crds, NULL);
362: PetscMalloc1(data_sz*nnodes, &datas);
363: for (dir=0; dir<data_sz; dir++) {
364: /* set local, and global */
365: for (kk=0; kk<nloc; kk++) {
366: PetscInt gid = my0 + kk;
367: PetscScalar crd = (PetscScalar)data_in[dir*nloc + kk]; /* col oriented */
368: datas[dir*nnodes + kk] = PetscRealPart(crd);
370: VecSetValues(tmp_crds, 1, &gid, &crd, INSERT_VALUES);
371: }
372: VecAssemblyBegin(tmp_crds);
373: VecAssemblyEnd(tmp_crds);
374: /* get ghost datas */
375: VecScatterBegin(mpimat->Mvctx,tmp_crds,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);
376: VecScatterEnd(mpimat->Mvctx,tmp_crds,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);
377: VecGetArray(mpimat->lvec, &data_arr);
378: for (kk=nloc,jj=0;jj<num_ghosts;kk++,jj++) datas[dir*nnodes + kk] = PetscRealPart(data_arr[jj]);
379: VecRestoreArray(mpimat->lvec, &data_arr);
380: }
381: VecDestroy(&tmp_crds);
382: *a_data_out = datas;
383: return(0);
384: }
386: PetscErrorCode PCGAMGHashTableCreate(PetscInt a_size, PCGAMGHashTable *a_tab)
387: {
389: PetscInt kk;
392: a_tab->size = a_size;
393: PetscMalloc2(a_size, &a_tab->table,a_size, &a_tab->data);
394: for (kk=0; kk<a_size; kk++) a_tab->table[kk] = -1;
395: return(0);
396: }
398: PetscErrorCode PCGAMGHashTableDestroy(PCGAMGHashTable *a_tab)
399: {
403: PetscFree2(a_tab->table,a_tab->data);
404: return(0);
405: }
407: PetscErrorCode PCGAMGHashTableAdd(PCGAMGHashTable *a_tab, PetscInt a_key, PetscInt a_data)
408: {
409: PetscInt kk,idx;
412: if (a_key<0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Negative key %D.",a_key);
413: for (kk = 0, idx = GAMG_HASH(a_key); kk < a_tab->size; kk++, idx = (idx==(a_tab->size-1)) ? 0 : idx + 1) {
414: if (a_tab->table[idx] == a_key) {
415: /* exists */
416: a_tab->data[idx] = a_data;
417: break;
418: } else if (a_tab->table[idx] == -1) {
419: /* add */
420: a_tab->table[idx] = a_key;
421: a_tab->data[idx] = a_data;
422: break;
423: }
424: }
425: if (kk==a_tab->size) {
426: /* this is not to efficient, waiting until completely full */
427: PetscInt oldsize = a_tab->size, new_size = 2*a_tab->size + 5, *oldtable = a_tab->table, *olddata = a_tab->data;
430: a_tab->size = new_size;
431: PetscMalloc2(a_tab->size, &a_tab->table,a_tab->size, &a_tab->data);
432: for (kk=0;kk<a_tab->size;kk++) a_tab->table[kk] = -1;
433: for (kk=0;kk<oldsize;kk++) {
434: if (oldtable[kk] != -1) {
435: PCGAMGHashTableAdd(a_tab, oldtable[kk], olddata[kk]);
436: }
437: }
438: PetscFree2(oldtable,olddata);
439: PCGAMGHashTableAdd(a_tab, a_key, a_data);
440: }
441: return(0);
442: }