1
2 /*
3 Defines projective product routines where A is a MPIAIJ matrix
4 C = P^T * A * P
5 */
6
7 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/
8 #include <../src/mat/utils/freespace.h>
9 #include <../src/mat/impls/aij/mpi/mpiaij.h>
10 #include <petscbt.h>
11 #include <petsctime.h>
12 #include <petsc/private/hashmapiv.h>
13 #include <petsc/private/hashseti.h>
14 #include <petscsf.h>
15
MatView_MPIAIJ_PtAP(Mat A,PetscViewer viewer)16 PetscErrorCode MatView_MPIAIJ_PtAP(Mat A,PetscViewer viewer)
17 {
18 PetscErrorCode ierr;
19 PetscBool iascii;
20 PetscViewerFormat format;
21 Mat_APMPI *ptap;
22
23 PetscFunctionBegin;
24 MatCheckProduct(A,1);
25 ptap = (Mat_APMPI*)A->product->data;
26 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
27 if (iascii) {
28 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr);
29 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
30 if (ptap->algType == 0) {
31 ierr = PetscViewerASCIIPrintf(viewer,"using scalable MatPtAP() implementation\n");CHKERRQ(ierr);
32 } else if (ptap->algType == 1) {
33 ierr = PetscViewerASCIIPrintf(viewer,"using nonscalable MatPtAP() implementation\n");CHKERRQ(ierr);
34 } else if (ptap->algType == 2) {
35 ierr = PetscViewerASCIIPrintf(viewer,"using allatonce MatPtAP() implementation\n");CHKERRQ(ierr);
36 } else if (ptap->algType == 3) {
37 ierr = PetscViewerASCIIPrintf(viewer,"using merged allatonce MatPtAP() implementation\n");CHKERRQ(ierr);
38 }
39 }
40 }
41 PetscFunctionReturn(0);
42 }
43
MatDestroy_MPIAIJ_PtAP(void * data)44 PetscErrorCode MatDestroy_MPIAIJ_PtAP(void *data)
45 {
46 PetscErrorCode ierr;
47 Mat_APMPI *ptap = (Mat_APMPI*)data;
48 Mat_Merge_SeqsToMPI *merge;
49
50 PetscFunctionBegin;
51 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr);
52 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr);
53 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr);
54 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr);
55 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */
56 ierr = MatDestroy(&ptap->Rd);CHKERRQ(ierr);
57 ierr = MatDestroy(&ptap->Ro);CHKERRQ(ierr);
58 if (ptap->AP_loc) { /* used by alg_rap */
59 Mat_SeqAIJ *ap = (Mat_SeqAIJ*)(ptap->AP_loc)->data;
60 ierr = PetscFree(ap->i);CHKERRQ(ierr);
61 ierr = PetscFree2(ap->j,ap->a);CHKERRQ(ierr);
62 ierr = MatDestroy(&ptap->AP_loc);CHKERRQ(ierr);
63 } else { /* used by alg_ptap */
64 ierr = PetscFree(ptap->api);CHKERRQ(ierr);
65 ierr = PetscFree(ptap->apj);CHKERRQ(ierr);
66 }
67 ierr = MatDestroy(&ptap->C_loc);CHKERRQ(ierr);
68 ierr = MatDestroy(&ptap->C_oth);CHKERRQ(ierr);
69 if (ptap->apa) {ierr = PetscFree(ptap->apa);CHKERRQ(ierr);}
70
71 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr);
72
73 merge = ptap->merge;
74 if (merge) { /* used by alg_ptap */
75 ierr = PetscFree(merge->id_r);CHKERRQ(ierr);
76 ierr = PetscFree(merge->len_s);CHKERRQ(ierr);
77 ierr = PetscFree(merge->len_r);CHKERRQ(ierr);
78 ierr = PetscFree(merge->bi);CHKERRQ(ierr);
79 ierr = PetscFree(merge->bj);CHKERRQ(ierr);
80 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr);
81 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr);
82 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr);
83 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr);
84 ierr = PetscFree(merge->coi);CHKERRQ(ierr);
85 ierr = PetscFree(merge->coj);CHKERRQ(ierr);
86 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr);
87 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr);
88 ierr = PetscFree(ptap->merge);CHKERRQ(ierr);
89 }
90 ierr = ISLocalToGlobalMappingDestroy(&ptap->ltog);CHKERRQ(ierr);
91
92 ierr = PetscSFDestroy(&ptap->sf);CHKERRQ(ierr);
93 ierr = PetscFree(ptap->c_othi);CHKERRQ(ierr);
94 ierr = PetscFree(ptap->c_rmti);CHKERRQ(ierr);
95 ierr = PetscFree(ptap);CHKERRQ(ierr);
96 PetscFunctionReturn(0);
97 }
98
MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,Mat C)99 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,Mat C)
100 {
101 PetscErrorCode ierr;
102 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data;
103 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data;
104 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq;
105 Mat_APMPI *ptap;
106 Mat AP_loc,C_loc,C_oth;
107 PetscInt i,rstart,rend,cm,ncols,row,*api,*apj,am = A->rmap->n,apnz,nout;
108 PetscScalar *apa;
109 const PetscInt *cols;
110 const PetscScalar *vals;
111
112 PetscFunctionBegin;
113 MatCheckProduct(C,3);
114 ptap = (Mat_APMPI*)C->product->data;
115 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data");
116 if (!ptap->AP_loc) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatProductClear()");
117
118 ierr = MatZeroEntries(C);CHKERRQ(ierr);
119
120 /* 1) get R = Pd^T,Ro = Po^T */
121 if (ptap->reuse == MAT_REUSE_MATRIX) {
122 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr);
123 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr);
124 }
125
126 /* 2) get AP_loc */
127 AP_loc = ptap->AP_loc;
128 ap = (Mat_SeqAIJ*)AP_loc->data;
129
130 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */
131 /*-----------------------------------------------------*/
132 if (ptap->reuse == MAT_REUSE_MATRIX) {
133 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */
134 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr);
135 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr);
136 }
137
138 /* 2-2) compute numeric A_loc*P - dominating part */
139 /* ---------------------------------------------- */
140 /* get data from symbolic products */
141 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data;
142 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data;
143
144 api = ap->i;
145 apj = ap->j;
146 ierr = ISLocalToGlobalMappingApply(ptap->ltog,api[AP_loc->rmap->n],apj,apj);CHKERRQ(ierr);
147 for (i=0; i<am; i++) {
148 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */
149 apnz = api[i+1] - api[i];
150 apa = ap->a + api[i];
151 ierr = PetscArrayzero(apa,apnz);CHKERRQ(ierr);
152 AProw_scalable(i,ad,ao,p_loc,p_oth,api,apj,apa);
153 }
154 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,api[AP_loc->rmap->n],apj,&nout,apj);CHKERRQ(ierr);
155 if (api[AP_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",api[AP_loc->rmap->n],nout);
156
157 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */
158 /* Always use scalable version since we are in the MPI scalable version */
159 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr);
160 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr);
161
162 C_loc = ptap->C_loc;
163 C_oth = ptap->C_oth;
164
165 /* add C_loc and Co to to C */
166 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr);
167
168 /* C_loc -> C */
169 cm = C_loc->rmap->N;
170 c_seq = (Mat_SeqAIJ*)C_loc->data;
171 cols = c_seq->j;
172 vals = c_seq->a;
173 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_loc->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr);
174
175 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */
176 /* when there are no off-processor parts. */
177 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */
178 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */
179 /* a table, and other, more complex stuff has to be done. */
180 if (C->assembled) {
181 C->was_assembled = PETSC_TRUE;
182 C->assembled = PETSC_FALSE;
183 }
184 if (C->was_assembled) {
185 for (i=0; i<cm; i++) {
186 ncols = c_seq->i[i+1] - c_seq->i[i];
187 row = rstart + i;
188 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr);
189 cols += ncols; vals += ncols;
190 }
191 } else {
192 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr);
193 }
194 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_loc->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr);
195 if (c_seq->i[C_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_seq->i[C_loc->rmap->n],nout);
196
197 /* Co -> C, off-processor part */
198 cm = C_oth->rmap->N;
199 c_seq = (Mat_SeqAIJ*)C_oth->data;
200 cols = c_seq->j;
201 vals = c_seq->a;
202 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_oth->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr);
203 for (i=0; i<cm; i++) {
204 ncols = c_seq->i[i+1] - c_seq->i[i];
205 row = p->garray[i];
206 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr);
207 cols += ncols; vals += ncols;
208 }
209 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
210 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
211
212 ptap->reuse = MAT_REUSE_MATRIX;
213
214 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_oth->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr);
215 if (c_seq->i[C_oth->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_seq->i[C_loc->rmap->n],nout);
216 PetscFunctionReturn(0);
217 }
218
MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat Cmpi)219 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat Cmpi)
220 {
221 PetscErrorCode ierr;
222 Mat_APMPI *ptap;
223 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data;
224 MPI_Comm comm;
225 PetscMPIInt size,rank;
226 Mat P_loc,P_oth;
227 PetscFreeSpaceList free_space=NULL,current_space=NULL;
228 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n;
229 PetscInt *lnk,i,k,pnz,row,nsend;
230 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv;
231 PetscInt **buf_rj,**buf_ri,**buf_ri_k;
232 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble;
233 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci;
234 MPI_Request *swaits,*rwaits;
235 MPI_Status *sstatus,rstatus;
236 PetscLayout rowmap;
237 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */
238 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */
239 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,Crmax,*aj,*ai,*pi,nout;
240 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth;
241 PetscScalar *apv;
242 PetscTable ta;
243 MatType mtype;
244 const char *prefix;
245 #if defined(PETSC_USE_INFO)
246 PetscReal apfill;
247 #endif
248
249 PetscFunctionBegin;
250 MatCheckProduct(Cmpi,4);
251 if (Cmpi->product->data) SETERRQ(PetscObjectComm((PetscObject)Cmpi),PETSC_ERR_PLIB,"Product data not empty");
252 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);
253 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
254 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
255
256 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data;
257
258 /* create symbolic parallel matrix Cmpi */
259 ierr = MatGetType(A,&mtype);CHKERRQ(ierr);
260 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr);
261
262 /* create struct Mat_APMPI and attached it to C later */
263 ierr = PetscNew(&ptap);CHKERRQ(ierr);
264 ptap->reuse = MAT_INITIAL_MATRIX;
265 ptap->algType = 0;
266
267 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */
268 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&P_oth);CHKERRQ(ierr);
269 /* get P_loc by taking all local rows of P */
270 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&P_loc);CHKERRQ(ierr);
271
272 ptap->P_loc = P_loc;
273 ptap->P_oth = P_oth;
274
275 /* (0) compute Rd = Pd^T, Ro = Po^T */
276 /* --------------------------------- */
277 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr);
278 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr);
279
280 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */
281 /* ----------------------------------------------------------------- */
282 p_loc = (Mat_SeqAIJ*)P_loc->data;
283 if (P_oth) p_oth = (Mat_SeqAIJ*)P_oth->data;
284
285 /* create and initialize a linked list */
286 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */
287 MatRowMergeMax_SeqAIJ(p_loc,P_loc->rmap->N,ta);
288 MatRowMergeMax_SeqAIJ(p_oth,P_oth->rmap->N,ta);
289 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */
290
291 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr);
292
293 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */
294 if (ao) {
295 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr);
296 } else {
297 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr);
298 }
299 current_space = free_space;
300 nspacedouble = 0;
301
302 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr);
303 api[0] = 0;
304 for (i=0; i<am; i++) {
305 /* diagonal portion: Ad[i,:]*P */
306 ai = ad->i; pi = p_loc->i;
307 nzi = ai[i+1] - ai[i];
308 aj = ad->j + ai[i];
309 for (j=0; j<nzi; j++) {
310 row = aj[j];
311 pnz = pi[row+1] - pi[row];
312 Jptr = p_loc->j + pi[row];
313 /* add non-zero cols of P into the sorted linked list lnk */
314 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr);
315 }
316 /* off-diagonal portion: Ao[i,:]*P */
317 if (ao) {
318 ai = ao->i; pi = p_oth->i;
319 nzi = ai[i+1] - ai[i];
320 aj = ao->j + ai[i];
321 for (j=0; j<nzi; j++) {
322 row = aj[j];
323 pnz = pi[row+1] - pi[row];
324 Jptr = p_oth->j + pi[row];
325 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr);
326 }
327 }
328 apnz = lnk[0];
329 api[i+1] = api[i] + apnz;
330
331 /* if free space is not available, double the total space in the list */
332 if (current_space->local_remaining<apnz) {
333 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr);
334 nspacedouble++;
335 }
336
337 /* Copy data into free space, then initialize lnk */
338 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr);
339
340 current_space->array += apnz;
341 current_space->local_used += apnz;
342 current_space->local_remaining -= apnz;
343 }
344 /* Allocate space for apj and apv, initialize apj, and */
345 /* destroy list of free space and other temporary array(s) */
346 ierr = PetscCalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr);
347 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr);
348 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr);
349
350 /* Create AP_loc for reuse */
351 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr);
352 ierr = MatSeqAIJCompactOutExtraColumns_SeqAIJ(ptap->AP_loc, &ptap->ltog);CHKERRQ(ierr);
353
354 #if defined(PETSC_USE_INFO)
355 if (ao) {
356 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1);
357 } else {
358 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1);
359 }
360 ptap->AP_loc->info.mallocs = nspacedouble;
361 ptap->AP_loc->info.fill_ratio_given = fill;
362 ptap->AP_loc->info.fill_ratio_needed = apfill;
363
364 if (api[am]) {
365 ierr = PetscInfo3(ptap->AP_loc,"Scalable algorithm, AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);CHKERRQ(ierr);
366 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr);
367 } else {
368 ierr = PetscInfo(ptap->AP_loc,"Scalable algorithm, AP_loc is empty \n");CHKERRQ(ierr);
369 }
370 #endif
371
372 /* (2-1) compute symbolic Co = Ro*AP_loc */
373 /* -------------------------------------- */
374 ierr = MatProductCreate(ptap->Ro,ptap->AP_loc,NULL,&ptap->C_oth);CHKERRQ(ierr);
375 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr);
376 ierr = MatSetOptionsPrefix(ptap->C_oth,prefix);CHKERRQ(ierr);
377 ierr = MatAppendOptionsPrefix(ptap->C_oth,"inner_offdiag_");CHKERRQ(ierr);
378
379 ierr = MatProductSetType(ptap->C_oth,MATPRODUCT_AB);CHKERRQ(ierr);
380 ierr = MatProductSetAlgorithm(ptap->C_oth,"sorted");CHKERRQ(ierr);
381 ierr = MatProductSetFill(ptap->C_oth,fill);CHKERRQ(ierr);
382 ierr = MatProductSetFromOptions(ptap->C_oth);CHKERRQ(ierr);
383 ierr = MatProductSymbolic(ptap->C_oth);CHKERRQ(ierr);
384
385 /* (3) send coj of C_oth to other processors */
386 /* ------------------------------------------ */
387 /* determine row ownership */
388 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr);
389 rowmap->n = pn;
390 rowmap->bs = 1;
391 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr);
392 owners = rowmap->range;
393
394 /* determine the number of messages to send, their lengths */
395 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr);
396 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr);
397 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr);
398
399 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data;
400 coi = c_oth->i; coj = c_oth->j;
401 con = ptap->C_oth->rmap->n;
402 proc = 0;
403 ierr = ISLocalToGlobalMappingApply(ptap->ltog,coi[con],coj,coj);CHKERRQ(ierr);
404 for (i=0; i<con; i++) {
405 while (prmap[i] >= owners[proc+1]) proc++;
406 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */
407 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */
408 }
409
410 len = 0; /* max length of buf_si[], see (4) */
411 owners_co[0] = 0;
412 nsend = 0;
413 for (proc=0; proc<size; proc++) {
414 owners_co[proc+1] = owners_co[proc] + len_si[proc];
415 if (len_s[proc]) {
416 nsend++;
417 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */
418 len += len_si[proc];
419 }
420 }
421
422 /* determine the number and length of messages to receive for coi and coj */
423 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr);
424 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr);
425
426 /* post the Irecv and Isend of coj */
427 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr);
428 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr);
429 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr);
430 for (proc=0, k=0; proc<size; proc++) {
431 if (!len_s[proc]) continue;
432 i = owners_co[proc];
433 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr);
434 k++;
435 }
436
437 /* (2-2) compute symbolic C_loc = Rd*AP_loc */
438 /* ---------------------------------------- */
439 ierr = MatProductCreate(ptap->Rd,ptap->AP_loc,NULL,&ptap->C_loc);CHKERRQ(ierr);
440 ierr = MatProductSetType(ptap->C_loc,MATPRODUCT_AB);CHKERRQ(ierr);
441 ierr = MatProductSetAlgorithm(ptap->C_loc,"default");CHKERRQ(ierr);
442 ierr = MatProductSetFill(ptap->C_loc,fill);CHKERRQ(ierr);
443
444 ierr = MatSetOptionsPrefix(ptap->C_loc,prefix);CHKERRQ(ierr);
445 ierr = MatAppendOptionsPrefix(ptap->C_loc,"inner_diag_");CHKERRQ(ierr);
446
447 ierr = MatProductSetFromOptions(ptap->C_loc);CHKERRQ(ierr);
448 ierr = MatProductSymbolic(ptap->C_loc);CHKERRQ(ierr);
449
450 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data;
451 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,c_loc->j);CHKERRQ(ierr);
452
453 /* receives coj are complete */
454 for (i=0; i<nrecv; i++) {
455 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr);
456 }
457 ierr = PetscFree(rwaits);CHKERRQ(ierr);
458 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);}
459
460 /* add received column indices into ta to update Crmax */
461 for (k=0; k<nrecv; k++) {/* k-th received message */
462 Jptr = buf_rj[k];
463 for (j=0; j<len_r[k]; j++) {
464 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr);
465 }
466 }
467 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr);
468 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr);
469
470 /* (4) send and recv coi */
471 /*-----------------------*/
472 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr);
473 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr);
474 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr);
475 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */
476 for (proc=0,k=0; proc<size; proc++) {
477 if (!len_s[proc]) continue;
478 /* form outgoing message for i-structure:
479 buf_si[0]: nrows to be sent
480 [1:nrows]: row index (global)
481 [nrows+1:2*nrows+1]: i-structure index
482 */
483 /*-------------------------------------------*/
484 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */
485 buf_si_i = buf_si + nrows+1;
486 buf_si[0] = nrows;
487 buf_si_i[0] = 0;
488 nrows = 0;
489 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) {
490 nzi = coi[i+1] - coi[i];
491 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */
492 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */
493 nrows++;
494 }
495 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr);
496 k++;
497 buf_si += len_si[proc];
498 }
499 for (i=0; i<nrecv; i++) {
500 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr);
501 }
502 ierr = PetscFree(rwaits);CHKERRQ(ierr);
503 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);}
504
505 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr);
506 ierr = PetscFree(len_ri);CHKERRQ(ierr);
507 ierr = PetscFree(swaits);CHKERRQ(ierr);
508 ierr = PetscFree(buf_s);CHKERRQ(ierr);
509
510 /* (5) compute the local portion of Cmpi */
511 /* ------------------------------------------ */
512 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */
513 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr);
514 current_space = free_space;
515
516 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr);
517 for (k=0; k<nrecv; k++) {
518 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */
519 nrows = *buf_ri_k[k];
520 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */
521 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */
522 }
523
524 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr);
525 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr);
526 for (i=0; i<pn; i++) {
527 /* add C_loc into Cmpi */
528 nzi = c_loc->i[i+1] - c_loc->i[i];
529 Jptr = c_loc->j + c_loc->i[i];
530 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr);
531
532 /* add received col data into lnk */
533 for (k=0; k<nrecv; k++) { /* k-th received message */
534 if (i == *nextrow[k]) { /* i-th row */
535 nzi = *(nextci[k]+1) - *nextci[k];
536 Jptr = buf_rj[k] + *nextci[k];
537 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr);
538 nextrow[k]++; nextci[k]++;
539 }
540 }
541 nzi = lnk[0];
542
543 /* copy data into free space, then initialize lnk */
544 ierr = PetscLLCondensedClean_Scalable(nzi,current_space->array,lnk);CHKERRQ(ierr);
545 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr);
546 }
547 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr);
548 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr);
549 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr);
550
551 /* local sizes and preallocation */
552 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
553 if (P->cmap->bs > 0) {
554 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr);
555 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr);
556 }
557 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr);
558 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);
559
560 /* members in merge */
561 ierr = PetscFree(id_r);CHKERRQ(ierr);
562 ierr = PetscFree(len_r);CHKERRQ(ierr);
563 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr);
564 ierr = PetscFree(buf_ri);CHKERRQ(ierr);
565 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr);
566 ierr = PetscFree(buf_rj);CHKERRQ(ierr);
567 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr);
568
569 nout = 0;
570 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_oth->i[ptap->C_oth->rmap->n],c_oth->j,&nout,c_oth->j);CHKERRQ(ierr);
571 if (c_oth->i[ptap->C_oth->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_oth->i[ptap->C_oth->rmap->n],nout);
572 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,&nout,c_loc->j);CHKERRQ(ierr);
573 if (c_loc->i[ptap->C_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_loc->i[ptap->C_loc->rmap->n],nout);
574
575 /* attach the supporting struct to Cmpi for reuse */
576 Cmpi->product->data = ptap;
577 Cmpi->product->view = MatView_MPIAIJ_PtAP;
578 Cmpi->product->destroy = MatDestroy_MPIAIJ_PtAP;
579
580 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */
581 Cmpi->assembled = PETSC_FALSE;
582 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable;
583 PetscFunctionReturn(0);
584 }
585
MatPtAPSymbolicComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,const PetscInt * map,PetscInt dof,PetscInt i,PetscHSetI dht,PetscHSetI oht)586 PETSC_STATIC_INLINE PetscErrorCode MatPtAPSymbolicComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,const PetscInt *map,PetscInt dof,PetscInt i,PetscHSetI dht,PetscHSetI oht)
587 {
588 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data;
589 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_oth=(Mat_SeqAIJ*)P_oth->data,*pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data;
590 PetscInt *ai,nzi,j,*aj,row,col,*pi,*pj,pnz,nzpi,*p_othcols,k;
591 PetscInt pcstart,pcend,column,offset;
592 PetscErrorCode ierr;
593
594 PetscFunctionBegin;
595 pcstart = P->cmap->rstart;
596 pcstart *= dof;
597 pcend = P->cmap->rend;
598 pcend *= dof;
599 /* diagonal portion: Ad[i,:]*P */
600 ai = ad->i;
601 nzi = ai[i+1] - ai[i];
602 aj = ad->j + ai[i];
603 for (j=0; j<nzi; j++) {
604 row = aj[j];
605 offset = row%dof;
606 row /= dof;
607 nzpi = pd->i[row+1] - pd->i[row];
608 pj = pd->j + pd->i[row];
609 for (k=0; k<nzpi; k++) {
610 ierr = PetscHSetIAdd(dht,pj[k]*dof+offset+pcstart);CHKERRQ(ierr);
611 }
612 }
613 /* off diag P */
614 for (j=0; j<nzi; j++) {
615 row = aj[j];
616 offset = row%dof;
617 row /= dof;
618 nzpi = po->i[row+1] - po->i[row];
619 pj = po->j + po->i[row];
620 for (k=0; k<nzpi; k++) {
621 ierr = PetscHSetIAdd(oht,p->garray[pj[k]]*dof+offset);CHKERRQ(ierr);
622 }
623 }
624
625 /* off diagonal part: Ao[i, :]*P_oth */
626 if (ao) {
627 ai = ao->i;
628 pi = p_oth->i;
629 nzi = ai[i+1] - ai[i];
630 aj = ao->j + ai[i];
631 for (j=0; j<nzi; j++) {
632 row = aj[j];
633 offset = a->garray[row]%dof;
634 row = map[row];
635 pnz = pi[row+1] - pi[row];
636 p_othcols = p_oth->j + pi[row];
637 for (col=0; col<pnz; col++) {
638 column = p_othcols[col] * dof + offset;
639 if (column>=pcstart && column<pcend) {
640 ierr = PetscHSetIAdd(dht,column);CHKERRQ(ierr);
641 } else {
642 ierr = PetscHSetIAdd(oht,column);CHKERRQ(ierr);
643 }
644 }
645 }
646 } /* end if (ao) */
647 PetscFunctionReturn(0);
648 }
649
MatPtAPNumericComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,const PetscInt * map,PetscInt dof,PetscInt i,PetscHMapIV hmap)650 PETSC_STATIC_INLINE PetscErrorCode MatPtAPNumericComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,const PetscInt *map,PetscInt dof,PetscInt i,PetscHMapIV hmap)
651 {
652 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data;
653 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_oth=(Mat_SeqAIJ*)P_oth->data,*pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data;
654 PetscInt *ai,nzi,j,*aj,row,col,*pi,pnz,*p_othcols,pcstart,*pj,k,nzpi,offset;
655 PetscScalar ra,*aa,*pa;
656 PetscErrorCode ierr;
657
658 PetscFunctionBegin;
659 pcstart = P->cmap->rstart;
660 pcstart *= dof;
661
662 /* diagonal portion: Ad[i,:]*P */
663 ai = ad->i;
664 nzi = ai[i+1] - ai[i];
665 aj = ad->j + ai[i];
666 aa = ad->a + ai[i];
667 for (j=0; j<nzi; j++) {
668 ra = aa[j];
669 row = aj[j];
670 offset = row%dof;
671 row /= dof;
672 nzpi = pd->i[row+1] - pd->i[row];
673 pj = pd->j + pd->i[row];
674 pa = pd->a + pd->i[row];
675 for (k=0; k<nzpi; k++) {
676 ierr = PetscHMapIVAddValue(hmap,pj[k]*dof+offset+pcstart,ra*pa[k]);CHKERRQ(ierr);
677 }
678 ierr = PetscLogFlops(2.0*nzpi);CHKERRQ(ierr);
679 }
680 for (j=0; j<nzi; j++) {
681 ra = aa[j];
682 row = aj[j];
683 offset = row%dof;
684 row /= dof;
685 nzpi = po->i[row+1] - po->i[row];
686 pj = po->j + po->i[row];
687 pa = po->a + po->i[row];
688 for (k=0; k<nzpi; k++) {
689 ierr = PetscHMapIVAddValue(hmap,p->garray[pj[k]]*dof+offset,ra*pa[k]);CHKERRQ(ierr);
690 }
691 ierr = PetscLogFlops(2.0*nzpi);CHKERRQ(ierr);
692 }
693
694 /* off diagonal part: Ao[i, :]*P_oth */
695 if (ao) {
696 ai = ao->i;
697 pi = p_oth->i;
698 nzi = ai[i+1] - ai[i];
699 aj = ao->j + ai[i];
700 aa = ao->a + ai[i];
701 for (j=0; j<nzi; j++) {
702 row = aj[j];
703 offset = a->garray[row]%dof;
704 row = map[row];
705 ra = aa[j];
706 pnz = pi[row+1] - pi[row];
707 p_othcols = p_oth->j + pi[row];
708 pa = p_oth->a + pi[row];
709 for (col=0; col<pnz; col++) {
710 ierr = PetscHMapIVAddValue(hmap,p_othcols[col]*dof+offset,ra*pa[col]);CHKERRQ(ierr);
711 }
712 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr);
713 }
714 } /* end if (ao) */
715
716 PetscFunctionReturn(0);
717 }
718
719 PetscErrorCode MatGetBrowsOfAcols_MPIXAIJ(Mat,Mat,PetscInt dof,MatReuse,Mat*);
720
MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce(Mat A,Mat P,PetscInt dof,Mat C)721 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce(Mat A,Mat P,PetscInt dof,Mat C)
722 {
723 PetscErrorCode ierr;
724 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data;
725 Mat_SeqAIJ *cd,*co,*po=(Mat_SeqAIJ*)p->B->data,*pd=(Mat_SeqAIJ*)p->A->data;
726 Mat_APMPI *ptap;
727 PetscHMapIV hmap;
728 PetscInt i,j,jj,kk,nzi,*c_rmtj,voff,*c_othj,pn,pon,pcstart,pcend,ccstart,ccend,row,am,*poj,*pdj,*apindices,cmaxr,*c_rmtc,*c_rmtjj,*dcc,*occ,loc;
729 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa;
730 PetscInt offset,ii,pocol;
731 const PetscInt *mappingindices;
732 IS map;
733
734 PetscFunctionBegin;
735 MatCheckProduct(C,4);
736 ptap = (Mat_APMPI*)C->product->data;
737 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data");
738 if (!ptap->P_oth) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatProductClear()");
739
740 ierr = MatZeroEntries(C);CHKERRQ(ierr);
741
742 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */
743 /*-----------------------------------------------------*/
744 if (ptap->reuse == MAT_REUSE_MATRIX) {
745 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */
746 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,dof,MAT_REUSE_MATRIX,&ptap->P_oth);CHKERRQ(ierr);
747 }
748 ierr = PetscObjectQuery((PetscObject)ptap->P_oth,"aoffdiagtopothmapping",(PetscObject*)&map);CHKERRQ(ierr);
749
750 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr);
751 pon *= dof;
752 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr);
753 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr);
754 cmaxr = 0;
755 for (i=0; i<pon; i++) {
756 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]);
757 }
758 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr);
759 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr);
760 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr);
761 ierr = ISGetIndices(map,&mappingindices);CHKERRQ(ierr);
762 for (i=0; i<am && pon; i++) {
763 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr);
764 offset = i%dof;
765 ii = i/dof;
766 nzi = po->i[ii+1] - po->i[ii];
767 if (!nzi) continue;
768 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,hmap);CHKERRQ(ierr);
769 voff = 0;
770 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr);
771 if (!voff) continue;
772
773 /* Form C(ii, :) */
774 poj = po->j + po->i[ii];
775 poa = po->a + po->i[ii];
776 for (j=0; j<nzi; j++) {
777 pocol = poj[j]*dof+offset;
778 c_rmtjj = c_rmtj + ptap->c_rmti[pocol];
779 c_rmtaa = c_rmta + ptap->c_rmti[pocol];
780 for (jj=0; jj<voff; jj++) {
781 apvaluestmp[jj] = apvalues[jj]*poa[j];
782 /*If the row is empty */
783 if (!c_rmtc[pocol]) {
784 c_rmtjj[jj] = apindices[jj];
785 c_rmtaa[jj] = apvaluestmp[jj];
786 c_rmtc[pocol]++;
787 } else {
788 ierr = PetscFindInt(apindices[jj],c_rmtc[pocol],c_rmtjj,&loc);CHKERRQ(ierr);
789 if (loc>=0){ /* hit */
790 c_rmtaa[loc] += apvaluestmp[jj];
791 ierr = PetscLogFlops(1.0);CHKERRQ(ierr);
792 } else { /* new element */
793 loc = -(loc+1);
794 /* Move data backward */
795 for (kk=c_rmtc[pocol]; kk>loc; kk--) {
796 c_rmtjj[kk] = c_rmtjj[kk-1];
797 c_rmtaa[kk] = c_rmtaa[kk-1];
798 }/* End kk */
799 c_rmtjj[loc] = apindices[jj];
800 c_rmtaa[loc] = apvaluestmp[jj];
801 c_rmtc[pocol]++;
802 }
803 }
804 ierr = PetscLogFlops(voff);CHKERRQ(ierr);
805 } /* End jj */
806 } /* End j */
807 } /* End i */
808
809 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr);
810 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr);
811
812 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr);
813 pn *= dof;
814 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr);
815
816 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr);
817 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr);
818 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr);
819 pcstart = pcstart*dof;
820 pcend = pcend*dof;
821 cd = (Mat_SeqAIJ*)(c->A)->data;
822 co = (Mat_SeqAIJ*)(c->B)->data;
823
824 cmaxr = 0;
825 for (i=0; i<pn; i++) {
826 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i]));
827 }
828 ierr = PetscCalloc5(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pn,&dcc,pn,&occ);CHKERRQ(ierr);
829 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr);
830 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr);
831 for (i=0; i<am && pn; i++) {
832 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr);
833 offset = i%dof;
834 ii = i/dof;
835 nzi = pd->i[ii+1] - pd->i[ii];
836 if (!nzi) continue;
837 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,hmap);CHKERRQ(ierr);
838 voff = 0;
839 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr);
840 if (!voff) continue;
841 /* Form C(ii, :) */
842 pdj = pd->j + pd->i[ii];
843 pda = pd->a + pd->i[ii];
844 for (j=0; j<nzi; j++) {
845 row = pcstart + pdj[j] * dof + offset;
846 for (jj=0; jj<voff; jj++) {
847 apvaluestmp[jj] = apvalues[jj]*pda[j];
848 }
849 ierr = PetscLogFlops(voff);CHKERRQ(ierr);
850 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr);
851 }
852 }
853 ierr = ISRestoreIndices(map,&mappingindices);CHKERRQ(ierr);
854 ierr = MatGetOwnershipRangeColumn(C,&ccstart,&ccend);CHKERRQ(ierr);
855 ierr = PetscFree5(apindices,apvalues,apvaluestmp,dcc,occ);CHKERRQ(ierr);
856 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr);
857 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr);
858 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr);
859 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr);
860
861 /* Add contributions from remote */
862 for (i = 0; i < pn; i++) {
863 row = i + pcstart;
864 ierr = MatSetValues(C,1,&row,ptap->c_othi[i+1]-ptap->c_othi[i],c_othj+ptap->c_othi[i],c_otha+ptap->c_othi[i],ADD_VALUES);CHKERRQ(ierr);
865 }
866 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr);
867
868 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
869 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
870
871 ptap->reuse = MAT_REUSE_MATRIX;
872 PetscFunctionReturn(0);
873 }
874
MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,Mat C)875 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,Mat C)
876 {
877 PetscErrorCode ierr;
878
879 PetscFunctionBegin;
880
881 ierr = MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce(A,P,1,C);CHKERRQ(ierr);
882 PetscFunctionReturn(0);
883 }
884
MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce_merged(Mat A,Mat P,PetscInt dof,Mat C)885 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce_merged(Mat A,Mat P,PetscInt dof,Mat C)
886 {
887 PetscErrorCode ierr;
888 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data;
889 Mat_SeqAIJ *cd,*co,*po=(Mat_SeqAIJ*)p->B->data,*pd=(Mat_SeqAIJ*)p->A->data;
890 Mat_APMPI *ptap;
891 PetscHMapIV hmap;
892 PetscInt i,j,jj,kk,nzi,dnzi,*c_rmtj,voff,*c_othj,pn,pon,pcstart,pcend,row,am,*poj,*pdj,*apindices,cmaxr,*c_rmtc,*c_rmtjj,loc;
893 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa;
894 PetscInt offset,ii,pocol;
895 const PetscInt *mappingindices;
896 IS map;
897
898 PetscFunctionBegin;
899 MatCheckProduct(C,4);
900 ptap = (Mat_APMPI*)C->product->data;
901 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data");
902 if (!ptap->P_oth) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatProductClear()");
903
904 ierr = MatZeroEntries(C);CHKERRQ(ierr);
905
906 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */
907 /*-----------------------------------------------------*/
908 if (ptap->reuse == MAT_REUSE_MATRIX) {
909 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */
910 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,dof,MAT_REUSE_MATRIX,&ptap->P_oth);CHKERRQ(ierr);
911 }
912 ierr = PetscObjectQuery((PetscObject)ptap->P_oth,"aoffdiagtopothmapping",(PetscObject*)&map);CHKERRQ(ierr);
913 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr);
914 pon *= dof;
915 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr);
916 pn *= dof;
917
918 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr);
919 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr);
920 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr);
921 pcstart *= dof;
922 pcend *= dof;
923 cmaxr = 0;
924 for (i=0; i<pon; i++) {
925 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]);
926 }
927 cd = (Mat_SeqAIJ*)(c->A)->data;
928 co = (Mat_SeqAIJ*)(c->B)->data;
929 for (i=0; i<pn; i++) {
930 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i]));
931 }
932 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr);
933 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr);
934 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr);
935 ierr = ISGetIndices(map,&mappingindices);CHKERRQ(ierr);
936 for (i=0; i<am && (pon || pn); i++) {
937 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr);
938 offset = i%dof;
939 ii = i/dof;
940 nzi = po->i[ii+1] - po->i[ii];
941 dnzi = pd->i[ii+1] - pd->i[ii];
942 if (!nzi && !dnzi) continue;
943 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,hmap);CHKERRQ(ierr);
944 voff = 0;
945 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr);
946 if (!voff) continue;
947
948 /* Form remote C(ii, :) */
949 poj = po->j + po->i[ii];
950 poa = po->a + po->i[ii];
951 for (j=0; j<nzi; j++) {
952 pocol = poj[j]*dof+offset;
953 c_rmtjj = c_rmtj + ptap->c_rmti[pocol];
954 c_rmtaa = c_rmta + ptap->c_rmti[pocol];
955 for (jj=0; jj<voff; jj++) {
956 apvaluestmp[jj] = apvalues[jj]*poa[j];
957 /*If the row is empty */
958 if (!c_rmtc[pocol]) {
959 c_rmtjj[jj] = apindices[jj];
960 c_rmtaa[jj] = apvaluestmp[jj];
961 c_rmtc[pocol]++;
962 } else {
963 ierr = PetscFindInt(apindices[jj],c_rmtc[pocol],c_rmtjj,&loc);CHKERRQ(ierr);
964 if (loc>=0){ /* hit */
965 c_rmtaa[loc] += apvaluestmp[jj];
966 ierr = PetscLogFlops(1.0);CHKERRQ(ierr);
967 } else { /* new element */
968 loc = -(loc+1);
969 /* Move data backward */
970 for (kk=c_rmtc[pocol]; kk>loc; kk--) {
971 c_rmtjj[kk] = c_rmtjj[kk-1];
972 c_rmtaa[kk] = c_rmtaa[kk-1];
973 }/* End kk */
974 c_rmtjj[loc] = apindices[jj];
975 c_rmtaa[loc] = apvaluestmp[jj];
976 c_rmtc[pocol]++;
977 }
978 }
979 } /* End jj */
980 ierr = PetscLogFlops(voff);CHKERRQ(ierr);
981 } /* End j */
982
983 /* Form local C(ii, :) */
984 pdj = pd->j + pd->i[ii];
985 pda = pd->a + pd->i[ii];
986 for (j=0; j<dnzi; j++) {
987 row = pcstart + pdj[j] * dof + offset;
988 for (jj=0; jj<voff; jj++) {
989 apvaluestmp[jj] = apvalues[jj]*pda[j];
990 }/* End kk */
991 ierr = PetscLogFlops(voff);CHKERRQ(ierr);
992 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr);
993 }/* End j */
994 } /* End i */
995
996 ierr = ISRestoreIndices(map,&mappingindices);CHKERRQ(ierr);
997 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr);
998 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr);
999 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr);
1000
1001 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr);
1002 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr);
1003 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr);
1004 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr);
1005 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr);
1006
1007 /* Add contributions from remote */
1008 for (i = 0; i < pn; i++) {
1009 row = i + pcstart;
1010 ierr = MatSetValues(C,1,&row,ptap->c_othi[i+1]-ptap->c_othi[i],c_othj+ptap->c_othi[i],c_otha+ptap->c_othi[i],ADD_VALUES);CHKERRQ(ierr);
1011 }
1012 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr);
1013
1014 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
1015 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
1016
1017 ptap->reuse = MAT_REUSE_MATRIX;
1018 PetscFunctionReturn(0);
1019 }
1020
MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,Mat C)1021 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,Mat C)
1022 {
1023 PetscErrorCode ierr;
1024
1025 PetscFunctionBegin;
1026
1027 ierr = MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce_merged(A,P,1,C);CHKERRQ(ierr);
1028 PetscFunctionReturn(0);
1029 }
1030
1031 /* TODO: move algorithm selection to MatProductSetFromOptions */
MatPtAPSymbolic_MPIAIJ_MPIXAIJ_allatonce(Mat A,Mat P,PetscInt dof,PetscReal fill,Mat Cmpi)1032 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIXAIJ_allatonce(Mat A,Mat P,PetscInt dof,PetscReal fill,Mat Cmpi)
1033 {
1034 Mat_APMPI *ptap;
1035 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data;
1036 MPI_Comm comm;
1037 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data;
1038 MatType mtype;
1039 PetscSF sf;
1040 PetscSFNode *iremote;
1041 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves;
1042 const PetscInt *rootdegrees;
1043 PetscHSetI ht,oht,*hta,*hto;
1044 PetscInt pn,pon,*c_rmtc,i,j,nzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets;
1045 PetscInt lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj;
1046 PetscInt nalg=2,alg=0,offset,ii;
1047 PetscMPIInt owner;
1048 const PetscInt *mappingindices;
1049 PetscBool flg;
1050 const char *algTypes[2] = {"overlapping","merged"};
1051 IS map;
1052 PetscErrorCode ierr;
1053
1054 PetscFunctionBegin;
1055 MatCheckProduct(Cmpi,5);
1056 if (Cmpi->product->data) SETERRQ(PetscObjectComm((PetscObject)Cmpi),PETSC_ERR_PLIB,"Product data not empty");
1057 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);
1058
1059 /* Create symbolic parallel matrix Cmpi */
1060 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr);
1061 pn *= dof;
1062 ierr = MatGetType(A,&mtype);CHKERRQ(ierr);
1063 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr);
1064 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
1065
1066 ierr = PetscNew(&ptap);CHKERRQ(ierr);
1067 ptap->reuse = MAT_INITIAL_MATRIX;
1068 ptap->algType = 2;
1069
1070 /* Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */
1071 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,dof,MAT_INITIAL_MATRIX,&ptap->P_oth);CHKERRQ(ierr);
1072 ierr = PetscObjectQuery((PetscObject)ptap->P_oth,"aoffdiagtopothmapping",(PetscObject*)&map);CHKERRQ(ierr);
1073 /* This equals to the number of offdiag columns in P */
1074 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr);
1075 pon *= dof;
1076 /* offsets */
1077 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr);
1078 /* The number of columns we will send to remote ranks */
1079 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr);
1080 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr);
1081 for (i=0; i<pon; i++) {
1082 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr);
1083 }
1084 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr);
1085 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr);
1086 /* Create hash table to merge all columns for C(i, :) */
1087 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr);
1088
1089 ierr = ISGetIndices(map,&mappingindices);CHKERRQ(ierr);
1090 ptap->c_rmti[0] = 0;
1091 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */
1092 for (i=0; i<am && pon; i++) {
1093 /* Form one row of AP */
1094 ierr = PetscHSetIClear(ht);CHKERRQ(ierr);
1095 offset = i%dof;
1096 ii = i/dof;
1097 /* If the off diag is empty, we should not do any calculation */
1098 nzi = po->i[ii+1] - po->i[ii];
1099 if (!nzi) continue;
1100
1101 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,ht,ht);CHKERRQ(ierr);
1102 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr);
1103 /* If AP is empty, just continue */
1104 if (!htsize) continue;
1105 /* Form C(ii, :) */
1106 poj = po->j + po->i[ii];
1107 for (j=0; j<nzi; j++) {
1108 ierr = PetscHSetIUpdate(hta[poj[j]*dof+offset],ht);CHKERRQ(ierr);
1109 }
1110 }
1111
1112 for (i=0; i<pon; i++) {
1113 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr);
1114 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize;
1115 c_rmtc[i] = htsize;
1116 }
1117
1118 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr);
1119
1120 for (i=0; i<pon; i++) {
1121 off = 0;
1122 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr);
1123 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr);
1124 }
1125 ierr = PetscFree(hta);CHKERRQ(ierr);
1126
1127 ierr = PetscMalloc1(pon,&iremote);CHKERRQ(ierr);
1128 for (i=0; i<pon; i++) {
1129 owner = 0; lidx = 0;
1130 offset = i%dof;
1131 ii = i/dof;
1132 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[ii],&owner,&lidx);CHKERRQ(ierr);
1133 iremote[i].index = lidx*dof + offset;
1134 iremote[i].rank = owner;
1135 }
1136
1137 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr);
1138 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr);
1139 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */
1140 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr);
1141 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr);
1142 ierr = PetscSFSetUp(sf);CHKERRQ(ierr);
1143 /* How many neighbors have contributions to my rows? */
1144 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr);
1145 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr);
1146 rootspacesize = 0;
1147 for (i = 0; i < pn; i++) {
1148 rootspacesize += rootdegrees[i];
1149 }
1150 ierr = PetscMalloc1(rootspacesize,&rootspace);CHKERRQ(ierr);
1151 ierr = PetscMalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr);
1152 /* Get information from leaves
1153 * Number of columns other people contribute to my rows
1154 * */
1155 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr);
1156 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr);
1157 ierr = PetscFree(c_rmtc);CHKERRQ(ierr);
1158 ierr = PetscCalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr);
1159 /* The number of columns is received for each row */
1160 ptap->c_othi[0] = 0;
1161 rootspacesize = 0;
1162 rootspaceoffsets[0] = 0;
1163 for (i = 0; i < pn; i++) {
1164 rcvncols = 0;
1165 for (j = 0; j<rootdegrees[i]; j++) {
1166 rcvncols += rootspace[rootspacesize];
1167 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize];
1168 rootspacesize++;
1169 }
1170 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols;
1171 }
1172 ierr = PetscFree(rootspace);CHKERRQ(ierr);
1173
1174 ierr = PetscMalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr);
1175 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr);
1176 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr);
1177 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);
1178 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr);
1179
1180 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr);
1181 nleaves = 0;
1182 for (i = 0; i<pon; i++) {
1183 owner = 0;
1184 ii = i/dof;
1185 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[ii],&owner,NULL);CHKERRQ(ierr);
1186 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i];
1187 for (j=0; j<sendncols; j++) {
1188 iremote[nleaves].rank = owner;
1189 iremote[nleaves++].index = c_rmtoffsets[i] + j;
1190 }
1191 }
1192 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr);
1193 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr);
1194
1195 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr);
1196 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr);
1197 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr);
1198 /* One to one map */
1199 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr);
1200
1201 ierr = PetscMalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr);
1202 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr);
1203 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr);
1204 pcstart *= dof;
1205 pcend *= dof;
1206 ierr = PetscMalloc2(pn,&hta,pn,&hto);CHKERRQ(ierr);
1207 for (i=0; i<pn; i++) {
1208 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr);
1209 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr);
1210 }
1211 /* Work on local part */
1212 /* 4) Pass 1: Estimate memory for C_loc */
1213 for (i=0; i<am && pn; i++) {
1214 ierr = PetscHSetIClear(ht);CHKERRQ(ierr);
1215 ierr = PetscHSetIClear(oht);CHKERRQ(ierr);
1216 offset = i%dof;
1217 ii = i/dof;
1218 nzi = pd->i[ii+1] - pd->i[ii];
1219 if (!nzi) continue;
1220
1221 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,ht,oht);CHKERRQ(ierr);
1222 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr);
1223 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr);
1224 if (!(htsize+htosize)) continue;
1225 /* Form C(ii, :) */
1226 pdj = pd->j + pd->i[ii];
1227 for (j=0; j<nzi; j++) {
1228 ierr = PetscHSetIUpdate(hta[pdj[j]*dof+offset],ht);CHKERRQ(ierr);
1229 ierr = PetscHSetIUpdate(hto[pdj[j]*dof+offset],oht);CHKERRQ(ierr);
1230 }
1231 }
1232
1233 ierr = ISRestoreIndices(map,&mappingindices);CHKERRQ(ierr);
1234
1235 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr);
1236 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr);
1237
1238 /* Get remote data */
1239 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr);
1240 ierr = PetscFree(c_rmtj);CHKERRQ(ierr);
1241
1242 for (i = 0; i < pn; i++) {
1243 nzi = ptap->c_othi[i+1] - ptap->c_othi[i];
1244 rdj = c_othj + ptap->c_othi[i];
1245 for (j = 0; j < nzi; j++) {
1246 col = rdj[j];
1247 /* diag part */
1248 if (col>=pcstart && col<pcend) {
1249 ierr = PetscHSetIAdd(hta[i],col);CHKERRQ(ierr);
1250 } else { /* off diag */
1251 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr);
1252 }
1253 }
1254 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr);
1255 dnz[i] = htsize;
1256 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr);
1257 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr);
1258 onz[i] = htsize;
1259 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr);
1260 }
1261
1262 ierr = PetscFree2(hta,hto);CHKERRQ(ierr);
1263 ierr = PetscFree(c_othj);CHKERRQ(ierr);
1264
1265 /* local sizes and preallocation */
1266 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
1267 ierr = MatSetBlockSizes(Cmpi,dof>1? dof: P->cmap->bs,dof>1? dof: P->cmap->bs);CHKERRQ(ierr);
1268 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr);
1269 ierr = MatSetUp(Cmpi);CHKERRQ(ierr);
1270 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr);
1271
1272 /* attach the supporting struct to Cmpi for reuse */
1273 Cmpi->product->data = ptap;
1274 Cmpi->product->destroy = MatDestroy_MPIAIJ_PtAP;
1275 Cmpi->product->view = MatView_MPIAIJ_PtAP;
1276
1277 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */
1278 Cmpi->assembled = PETSC_FALSE;
1279 /* pick an algorithm */
1280 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr);
1281 alg = 0;
1282 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr);
1283 ierr = PetscOptionsEnd();CHKERRQ(ierr);
1284 switch (alg) {
1285 case 0:
1286 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce;
1287 break;
1288 case 1:
1289 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged;
1290 break;
1291 default:
1292 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n");
1293 }
1294 PetscFunctionReturn(0);
1295 }
1296
MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,PetscReal fill,Mat C)1297 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,PetscReal fill,Mat C)
1298 {
1299 PetscErrorCode ierr;
1300
1301 PetscFunctionBegin;
1302 ierr = MatPtAPSymbolic_MPIAIJ_MPIXAIJ_allatonce(A,P,1,fill,C);CHKERRQ(ierr);
1303 PetscFunctionReturn(0);
1304 }
1305
MatPtAPSymbolic_MPIAIJ_MPIXAIJ_allatonce_merged(Mat A,Mat P,PetscInt dof,PetscReal fill,Mat Cmpi)1306 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIXAIJ_allatonce_merged(Mat A,Mat P,PetscInt dof,PetscReal fill,Mat Cmpi)
1307 {
1308 Mat_APMPI *ptap;
1309 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data;
1310 MPI_Comm comm;
1311 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data;
1312 MatType mtype;
1313 PetscSF sf;
1314 PetscSFNode *iremote;
1315 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves;
1316 const PetscInt *rootdegrees;
1317 PetscHSetI ht,oht,*hta,*hto,*htd;
1318 PetscInt pn,pon,*c_rmtc,i,j,nzi,dnzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets;
1319 PetscInt lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj;
1320 PetscInt nalg=2,alg=0,offset,ii;
1321 PetscMPIInt owner;
1322 PetscBool flg;
1323 const char *algTypes[2] = {"merged","overlapping"};
1324 const PetscInt *mappingindices;
1325 IS map;
1326 PetscErrorCode ierr;
1327
1328 PetscFunctionBegin;
1329 MatCheckProduct(Cmpi,5);
1330 if (Cmpi->product->data) SETERRQ(PetscObjectComm((PetscObject)Cmpi),PETSC_ERR_PLIB,"Product data not empty");
1331 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);
1332
1333 /* Create symbolic parallel matrix Cmpi */
1334 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr);
1335 pn *= dof;
1336 ierr = MatGetType(A,&mtype);CHKERRQ(ierr);
1337 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr);
1338 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
1339
1340 ierr = PetscNew(&ptap);CHKERRQ(ierr);
1341 ptap->reuse = MAT_INITIAL_MATRIX;
1342 ptap->algType = 3;
1343
1344 /* 0) Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */
1345 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,dof,MAT_INITIAL_MATRIX,&ptap->P_oth);CHKERRQ(ierr);
1346 ierr = PetscObjectQuery((PetscObject)ptap->P_oth,"aoffdiagtopothmapping",(PetscObject*)&map);CHKERRQ(ierr);
1347
1348 /* This equals to the number of offdiag columns in P */
1349 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr);
1350 pon *= dof;
1351 /* offsets */
1352 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr);
1353 /* The number of columns we will send to remote ranks */
1354 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr);
1355 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr);
1356 for (i=0; i<pon; i++) {
1357 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr);
1358 }
1359 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr);
1360 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr);
1361 /* Create hash table to merge all columns for C(i, :) */
1362 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr);
1363 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr);
1364 ierr = PetscMalloc2(pn,&htd,pn,&hto);CHKERRQ(ierr);
1365 for (i=0; i<pn; i++) {
1366 ierr = PetscHSetICreate(&htd[i]);CHKERRQ(ierr);
1367 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr);
1368 }
1369
1370 ierr = ISGetIndices(map,&mappingindices);CHKERRQ(ierr);
1371 ptap->c_rmti[0] = 0;
1372 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */
1373 for (i=0; i<am && (pon || pn); i++) {
1374 /* Form one row of AP */
1375 ierr = PetscHSetIClear(ht);CHKERRQ(ierr);
1376 ierr = PetscHSetIClear(oht);CHKERRQ(ierr);
1377 offset = i%dof;
1378 ii = i/dof;
1379 /* If the off diag is empty, we should not do any calculation */
1380 nzi = po->i[ii+1] - po->i[ii];
1381 dnzi = pd->i[ii+1] - pd->i[ii];
1382 if (!nzi && !dnzi) continue;
1383
1384 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,ht,oht);CHKERRQ(ierr);
1385 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr);
1386 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr);
1387 /* If AP is empty, just continue */
1388 if (!(htsize+htosize)) continue;
1389
1390 /* Form remote C(ii, :) */
1391 poj = po->j + po->i[ii];
1392 for (j=0; j<nzi; j++) {
1393 ierr = PetscHSetIUpdate(hta[poj[j]*dof+offset],ht);CHKERRQ(ierr);
1394 ierr = PetscHSetIUpdate(hta[poj[j]*dof+offset],oht);CHKERRQ(ierr);
1395 }
1396
1397 /* Form local C(ii, :) */
1398 pdj = pd->j + pd->i[ii];
1399 for (j=0; j<dnzi; j++) {
1400 ierr = PetscHSetIUpdate(htd[pdj[j]*dof+offset],ht);CHKERRQ(ierr);
1401 ierr = PetscHSetIUpdate(hto[pdj[j]*dof+offset],oht);CHKERRQ(ierr);
1402 }
1403 }
1404
1405 ierr = ISRestoreIndices(map,&mappingindices);CHKERRQ(ierr);
1406
1407 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr);
1408 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr);
1409
1410 for (i=0; i<pon; i++) {
1411 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr);
1412 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize;
1413 c_rmtc[i] = htsize;
1414 }
1415
1416 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr);
1417
1418 for (i=0; i<pon; i++) {
1419 off = 0;
1420 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr);
1421 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr);
1422 }
1423 ierr = PetscFree(hta);CHKERRQ(ierr);
1424
1425 ierr = PetscMalloc1(pon,&iremote);CHKERRQ(ierr);
1426 for (i=0; i<pon; i++) {
1427 owner = 0; lidx = 0;
1428 offset = i%dof;
1429 ii = i/dof;
1430 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[ii],&owner,&lidx);CHKERRQ(ierr);
1431 iremote[i].index = lidx*dof+offset;
1432 iremote[i].rank = owner;
1433 }
1434
1435 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr);
1436 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr);
1437 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */
1438 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr);
1439 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr);
1440 ierr = PetscSFSetUp(sf);CHKERRQ(ierr);
1441 /* How many neighbors have contributions to my rows? */
1442 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr);
1443 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr);
1444 rootspacesize = 0;
1445 for (i = 0; i < pn; i++) {
1446 rootspacesize += rootdegrees[i];
1447 }
1448 ierr = PetscMalloc1(rootspacesize,&rootspace);CHKERRQ(ierr);
1449 ierr = PetscMalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr);
1450 /* Get information from leaves
1451 * Number of columns other people contribute to my rows
1452 * */
1453 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr);
1454 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr);
1455 ierr = PetscFree(c_rmtc);CHKERRQ(ierr);
1456 ierr = PetscMalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr);
1457 /* The number of columns is received for each row */
1458 ptap->c_othi[0] = 0;
1459 rootspacesize = 0;
1460 rootspaceoffsets[0] = 0;
1461 for (i = 0; i < pn; i++) {
1462 rcvncols = 0;
1463 for (j = 0; j<rootdegrees[i]; j++) {
1464 rcvncols += rootspace[rootspacesize];
1465 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize];
1466 rootspacesize++;
1467 }
1468 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols;
1469 }
1470 ierr = PetscFree(rootspace);CHKERRQ(ierr);
1471
1472 ierr = PetscMalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr);
1473 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr);
1474 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr);
1475 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);
1476 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr);
1477
1478 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr);
1479 nleaves = 0;
1480 for (i = 0; i<pon; i++) {
1481 owner = 0;
1482 ii = i/dof;
1483 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[ii],&owner,NULL);CHKERRQ(ierr);
1484 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i];
1485 for (j=0; j<sendncols; j++) {
1486 iremote[nleaves].rank = owner;
1487 iremote[nleaves++].index = c_rmtoffsets[i] + j;
1488 }
1489 }
1490 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr);
1491 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr);
1492
1493 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr);
1494 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr);
1495 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr);
1496 /* One to one map */
1497 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr);
1498 /* Get remote data */
1499 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr);
1500 ierr = PetscFree(c_rmtj);CHKERRQ(ierr);
1501 ierr = PetscMalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr);
1502 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr);
1503 pcstart *= dof;
1504 pcend *= dof;
1505 for (i = 0; i < pn; i++) {
1506 nzi = ptap->c_othi[i+1] - ptap->c_othi[i];
1507 rdj = c_othj + ptap->c_othi[i];
1508 for (j = 0; j < nzi; j++) {
1509 col = rdj[j];
1510 /* diag part */
1511 if (col>=pcstart && col<pcend) {
1512 ierr = PetscHSetIAdd(htd[i],col);CHKERRQ(ierr);
1513 } else { /* off diag */
1514 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr);
1515 }
1516 }
1517 ierr = PetscHSetIGetSize(htd[i],&htsize);CHKERRQ(ierr);
1518 dnz[i] = htsize;
1519 ierr = PetscHSetIDestroy(&htd[i]);CHKERRQ(ierr);
1520 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr);
1521 onz[i] = htsize;
1522 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr);
1523 }
1524
1525 ierr = PetscFree2(htd,hto);CHKERRQ(ierr);
1526 ierr = PetscFree(c_othj);CHKERRQ(ierr);
1527
1528 /* local sizes and preallocation */
1529 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
1530 ierr = MatSetBlockSizes(Cmpi, dof>1? dof: P->cmap->bs,dof>1? dof: P->cmap->bs);CHKERRQ(ierr);
1531 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr);
1532 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr);
1533
1534 /* attach the supporting struct to Cmpi for reuse */
1535 Cmpi->product->data = ptap;
1536 Cmpi->product->destroy = MatDestroy_MPIAIJ_PtAP;
1537 Cmpi->product->view = MatView_MPIAIJ_PtAP;
1538
1539 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */
1540 Cmpi->assembled = PETSC_FALSE;
1541 /* pick an algorithm */
1542 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr);
1543 alg = 0;
1544 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr);
1545 ierr = PetscOptionsEnd();CHKERRQ(ierr);
1546 switch (alg) {
1547 case 0:
1548 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged;
1549 break;
1550 case 1:
1551 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce;
1552 break;
1553 default:
1554 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n");
1555 }
1556 PetscFunctionReturn(0);
1557 }
1558
MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,PetscReal fill,Mat C)1559 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,PetscReal fill,Mat C)
1560 {
1561 PetscErrorCode ierr;
1562
1563 PetscFunctionBegin;
1564 ierr = MatPtAPSymbolic_MPIAIJ_MPIXAIJ_allatonce_merged(A,P,1,fill,C);CHKERRQ(ierr);
1565 PetscFunctionReturn(0);
1566 }
1567
MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat Cmpi)1568 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat Cmpi)
1569 {
1570 PetscErrorCode ierr;
1571 Mat_APMPI *ptap;
1572 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data;
1573 MPI_Comm comm;
1574 PetscMPIInt size,rank;
1575 PetscFreeSpaceList free_space=NULL,current_space=NULL;
1576 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n;
1577 PetscInt *lnk,i,k,pnz,row,nsend;
1578 PetscBT lnkbt;
1579 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv;
1580 PetscInt **buf_rj,**buf_ri,**buf_ri_k;
1581 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble;
1582 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci;
1583 MPI_Request *swaits,*rwaits;
1584 MPI_Status *sstatus,rstatus;
1585 PetscLayout rowmap;
1586 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */
1587 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */
1588 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi;
1589 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth;
1590 PetscScalar *apv;
1591 PetscTable ta;
1592 MatType mtype;
1593 const char *prefix;
1594 #if defined(PETSC_USE_INFO)
1595 PetscReal apfill;
1596 #endif
1597
1598 PetscFunctionBegin;
1599 MatCheckProduct(Cmpi,4);
1600 if (Cmpi->product->data) SETERRQ(PetscObjectComm((PetscObject)Cmpi),PETSC_ERR_PLIB,"Product data not empty");
1601 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr);
1602 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
1603 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
1604
1605 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data;
1606
1607 /* create symbolic parallel matrix Cmpi */
1608 ierr = MatGetType(A,&mtype);CHKERRQ(ierr);
1609 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr);
1610
1611 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */
1612 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ;
1613
1614 /* create struct Mat_APMPI and attached it to C later */
1615 ierr = PetscNew(&ptap);CHKERRQ(ierr);
1616 ptap->reuse = MAT_INITIAL_MATRIX;
1617 ptap->algType = 1;
1618
1619 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */
1620 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr);
1621 /* get P_loc by taking all local rows of P */
1622 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr);
1623
1624 /* (0) compute Rd = Pd^T, Ro = Po^T */
1625 /* --------------------------------- */
1626 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr);
1627 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr);
1628
1629 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */
1630 /* ----------------------------------------------------------------- */
1631 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data;
1632 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data;
1633
1634 /* create and initialize a linked list */
1635 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */
1636 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta);
1637 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta);
1638 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */
1639 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */
1640
1641 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr);
1642
1643 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */
1644 if (ao) {
1645 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr);
1646 } else {
1647 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr);
1648 }
1649 current_space = free_space;
1650 nspacedouble = 0;
1651
1652 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr);
1653 api[0] = 0;
1654 for (i=0; i<am; i++) {
1655 /* diagonal portion: Ad[i,:]*P */
1656 ai = ad->i; pi = p_loc->i;
1657 nzi = ai[i+1] - ai[i];
1658 aj = ad->j + ai[i];
1659 for (j=0; j<nzi; j++) {
1660 row = aj[j];
1661 pnz = pi[row+1] - pi[row];
1662 Jptr = p_loc->j + pi[row];
1663 /* add non-zero cols of P into the sorted linked list lnk */
1664 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr);
1665 }
1666 /* off-diagonal portion: Ao[i,:]*P */
1667 if (ao) {
1668 ai = ao->i; pi = p_oth->i;
1669 nzi = ai[i+1] - ai[i];
1670 aj = ao->j + ai[i];
1671 for (j=0; j<nzi; j++) {
1672 row = aj[j];
1673 pnz = pi[row+1] - pi[row];
1674 Jptr = p_oth->j + pi[row];
1675 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr);
1676 }
1677 }
1678 apnz = lnk[0];
1679 api[i+1] = api[i] + apnz;
1680 if (ap_rmax < apnz) ap_rmax = apnz;
1681
1682 /* if free space is not available, double the total space in the list */
1683 if (current_space->local_remaining<apnz) {
1684 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr);
1685 nspacedouble++;
1686 }
1687
1688 /* Copy data into free space, then initialize lnk */
1689 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr);
1690
1691 current_space->array += apnz;
1692 current_space->local_used += apnz;
1693 current_space->local_remaining -= apnz;
1694 }
1695 /* Allocate space for apj and apv, initialize apj, and */
1696 /* destroy list of free space and other temporary array(s) */
1697 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr);
1698 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr);
1699 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr);
1700
1701 /* Create AP_loc for reuse */
1702 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr);
1703
1704 #if defined(PETSC_USE_INFO)
1705 if (ao) {
1706 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1);
1707 } else {
1708 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1);
1709 }
1710 ptap->AP_loc->info.mallocs = nspacedouble;
1711 ptap->AP_loc->info.fill_ratio_given = fill;
1712 ptap->AP_loc->info.fill_ratio_needed = apfill;
1713
1714 if (api[am]) {
1715 ierr = PetscInfo3(ptap->AP_loc,"Nonscalable algorithm, AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);CHKERRQ(ierr);
1716 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr);
1717 } else {
1718 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr);
1719 }
1720 #endif
1721
1722 /* (2-1) compute symbolic Co = Ro*AP_loc */
1723 /* ------------------------------------ */
1724 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr);
1725 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr);
1726 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr);
1727
1728 ierr = MatProductCreate(ptap->Ro,ptap->AP_loc,NULL,&ptap->C_oth);CHKERRQ(ierr);
1729 ierr = MatGetOptionsPrefix(Cmpi,&prefix);CHKERRQ(ierr);
1730 ierr = MatSetOptionsPrefix(ptap->C_oth,prefix);CHKERRQ(ierr);
1731 ierr = MatAppendOptionsPrefix(ptap->C_oth,"inner_C_oth_");CHKERRQ(ierr);
1732
1733 ierr = MatProductSetType(ptap->C_oth,MATPRODUCT_AB);CHKERRQ(ierr);
1734 ierr = MatProductSetAlgorithm(ptap->C_oth,"default");CHKERRQ(ierr);
1735 ierr = MatProductSetFill(ptap->C_oth,fill);CHKERRQ(ierr);
1736 ierr = MatProductSetFromOptions(ptap->C_oth);CHKERRQ(ierr);
1737 ierr = MatProductSymbolic(ptap->C_oth);CHKERRQ(ierr);
1738
1739 /* (3) send coj of C_oth to other processors */
1740 /* ------------------------------------------ */
1741 /* determine row ownership */
1742 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr);
1743 rowmap->n = pn;
1744 rowmap->bs = 1;
1745 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr);
1746 owners = rowmap->range;
1747
1748 /* determine the number of messages to send, their lengths */
1749 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr);
1750 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr);
1751 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr);
1752
1753 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data;
1754 coi = c_oth->i; coj = c_oth->j;
1755 con = ptap->C_oth->rmap->n;
1756 proc = 0;
1757 for (i=0; i<con; i++) {
1758 while (prmap[i] >= owners[proc+1]) proc++;
1759 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */
1760 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */
1761 }
1762
1763 len = 0; /* max length of buf_si[], see (4) */
1764 owners_co[0] = 0;
1765 nsend = 0;
1766 for (proc=0; proc<size; proc++) {
1767 owners_co[proc+1] = owners_co[proc] + len_si[proc];
1768 if (len_s[proc]) {
1769 nsend++;
1770 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */
1771 len += len_si[proc];
1772 }
1773 }
1774
1775 /* determine the number and length of messages to receive for coi and coj */
1776 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr);
1777 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr);
1778
1779 /* post the Irecv and Isend of coj */
1780 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr);
1781 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr);
1782 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr);
1783 for (proc=0, k=0; proc<size; proc++) {
1784 if (!len_s[proc]) continue;
1785 i = owners_co[proc];
1786 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr);
1787 k++;
1788 }
1789
1790 /* (2-2) compute symbolic C_loc = Rd*AP_loc */
1791 /* ---------------------------------------- */
1792 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr);
1793 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr);
1794
1795 ierr = MatProductCreate(ptap->Rd,ptap->AP_loc,NULL,&ptap->C_loc);CHKERRQ(ierr);
1796 ierr = MatGetOptionsPrefix(Cmpi,&prefix);CHKERRQ(ierr);
1797 ierr = MatSetOptionsPrefix(ptap->C_loc,prefix);CHKERRQ(ierr);
1798 ierr = MatAppendOptionsPrefix(ptap->C_loc,"inner_C_loc_");CHKERRQ(ierr);
1799
1800 ierr = MatProductSetType(ptap->C_loc,MATPRODUCT_AB);CHKERRQ(ierr);
1801 ierr = MatProductSetAlgorithm(ptap->C_loc,"default");CHKERRQ(ierr);
1802 ierr = MatProductSetFill(ptap->C_loc,fill);CHKERRQ(ierr);
1803 ierr = MatProductSetFromOptions(ptap->C_loc);CHKERRQ(ierr);
1804 ierr = MatProductSymbolic(ptap->C_loc);CHKERRQ(ierr);
1805
1806 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data;
1807
1808 /* receives coj are complete */
1809 for (i=0; i<nrecv; i++) {
1810 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr);
1811 }
1812 ierr = PetscFree(rwaits);CHKERRQ(ierr);
1813 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);}
1814
1815 /* add received column indices into ta to update Crmax */
1816 for (k=0; k<nrecv; k++) {/* k-th received message */
1817 Jptr = buf_rj[k];
1818 for (j=0; j<len_r[k]; j++) {
1819 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr);
1820 }
1821 }
1822 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr);
1823 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr);
1824
1825 /* (4) send and recv coi */
1826 /*-----------------------*/
1827 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr);
1828 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr);
1829 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr);
1830 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */
1831 for (proc=0,k=0; proc<size; proc++) {
1832 if (!len_s[proc]) continue;
1833 /* form outgoing message for i-structure:
1834 buf_si[0]: nrows to be sent
1835 [1:nrows]: row index (global)
1836 [nrows+1:2*nrows+1]: i-structure index
1837 */
1838 /*-------------------------------------------*/
1839 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */
1840 buf_si_i = buf_si + nrows+1;
1841 buf_si[0] = nrows;
1842 buf_si_i[0] = 0;
1843 nrows = 0;
1844 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) {
1845 nzi = coi[i+1] - coi[i];
1846 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */
1847 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */
1848 nrows++;
1849 }
1850 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr);
1851 k++;
1852 buf_si += len_si[proc];
1853 }
1854 for (i=0; i<nrecv; i++) {
1855 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr);
1856 }
1857 ierr = PetscFree(rwaits);CHKERRQ(ierr);
1858 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);}
1859
1860 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr);
1861 ierr = PetscFree(len_ri);CHKERRQ(ierr);
1862 ierr = PetscFree(swaits);CHKERRQ(ierr);
1863 ierr = PetscFree(buf_s);CHKERRQ(ierr);
1864
1865 /* (5) compute the local portion of Cmpi */
1866 /* ------------------------------------------ */
1867 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */
1868 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr);
1869 current_space = free_space;
1870
1871 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr);
1872 for (k=0; k<nrecv; k++) {
1873 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */
1874 nrows = *buf_ri_k[k];
1875 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */
1876 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */
1877 }
1878
1879 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr);
1880 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr);
1881 for (i=0; i<pn; i++) {
1882 /* add C_loc into Cmpi */
1883 nzi = c_loc->i[i+1] - c_loc->i[i];
1884 Jptr = c_loc->j + c_loc->i[i];
1885 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr);
1886
1887 /* add received col data into lnk */
1888 for (k=0; k<nrecv; k++) { /* k-th received message */
1889 if (i == *nextrow[k]) { /* i-th row */
1890 nzi = *(nextci[k]+1) - *nextci[k];
1891 Jptr = buf_rj[k] + *nextci[k];
1892 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr);
1893 nextrow[k]++; nextci[k]++;
1894 }
1895 }
1896 nzi = lnk[0];
1897
1898 /* copy data into free space, then initialize lnk */
1899 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr);
1900 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr);
1901 }
1902 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr);
1903 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr);
1904 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr);
1905
1906 /* local sizes and preallocation */
1907 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
1908 if (P->cmap->bs > 0) {
1909 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr);
1910 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr);
1911 }
1912 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr);
1913 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr);
1914
1915 /* members in merge */
1916 ierr = PetscFree(id_r);CHKERRQ(ierr);
1917 ierr = PetscFree(len_r);CHKERRQ(ierr);
1918 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr);
1919 ierr = PetscFree(buf_ri);CHKERRQ(ierr);
1920 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr);
1921 ierr = PetscFree(buf_rj);CHKERRQ(ierr);
1922 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr);
1923
1924 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr);
1925
1926 /* attach the supporting struct to Cmpi for reuse */
1927 Cmpi->product->data = ptap;
1928 Cmpi->product->destroy = MatDestroy_MPIAIJ_PtAP;
1929 Cmpi->product->view = MatView_MPIAIJ_PtAP;
1930
1931 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */
1932 Cmpi->assembled = PETSC_FALSE;
1933 PetscFunctionReturn(0);
1934 }
1935
MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C)1936 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C)
1937 {
1938 PetscErrorCode ierr;
1939 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data;
1940 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data;
1941 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq;
1942 Mat_APMPI *ptap;
1943 Mat AP_loc,C_loc,C_oth;
1944 PetscInt i,rstart,rend,cm,ncols,row;
1945 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz;
1946 PetscScalar *apa;
1947 const PetscInt *cols;
1948 const PetscScalar *vals;
1949
1950 PetscFunctionBegin;
1951 MatCheckProduct(C,3);
1952 ptap = (Mat_APMPI*)C->product->data;
1953 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data");
1954 if (!ptap->AP_loc) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatProductClear()");
1955
1956 ierr = MatZeroEntries(C);CHKERRQ(ierr);
1957 /* 1) get R = Pd^T,Ro = Po^T */
1958 if (ptap->reuse == MAT_REUSE_MATRIX) {
1959 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr);
1960 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr);
1961 }
1962
1963 /* 2) get AP_loc */
1964 AP_loc = ptap->AP_loc;
1965 ap = (Mat_SeqAIJ*)AP_loc->data;
1966
1967 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */
1968 /*-----------------------------------------------------*/
1969 if (ptap->reuse == MAT_REUSE_MATRIX) {
1970 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */
1971 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr);
1972 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr);
1973 }
1974
1975 /* 2-2) compute numeric A_loc*P - dominating part */
1976 /* ---------------------------------------------- */
1977 /* get data from symbolic products */
1978 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data;
1979 if (ptap->P_oth) {
1980 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data;
1981 }
1982 apa = ptap->apa;
1983 api = ap->i;
1984 apj = ap->j;
1985 for (i=0; i<am; i++) {
1986 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */
1987 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa);
1988 apnz = api[i+1] - api[i];
1989 for (j=0; j<apnz; j++) {
1990 col = apj[j+api[i]];
1991 ap->a[j+ap->i[i]] = apa[col];
1992 apa[col] = 0.0;
1993 }
1994 }
1995 /* We have modified the contents of local matrix AP_loc and must increase its ObjectState, since we are not doing AssemblyBegin/End on it. */
1996 ierr = PetscObjectStateIncrease((PetscObject)AP_loc);CHKERRQ(ierr);
1997
1998 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */
1999 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr);
2000 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr);
2001 C_loc = ptap->C_loc;
2002 C_oth = ptap->C_oth;
2003
2004 /* add C_loc and Co to to C */
2005 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr);
2006
2007 /* C_loc -> C */
2008 cm = C_loc->rmap->N;
2009 c_seq = (Mat_SeqAIJ*)C_loc->data;
2010 cols = c_seq->j;
2011 vals = c_seq->a;
2012
2013
2014 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */
2015 /* when there are no off-processor parts. */
2016 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */
2017 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */
2018 /* a table, and other, more complex stuff has to be done. */
2019 if (C->assembled) {
2020 C->was_assembled = PETSC_TRUE;
2021 C->assembled = PETSC_FALSE;
2022 }
2023 if (C->was_assembled) {
2024 for (i=0; i<cm; i++) {
2025 ncols = c_seq->i[i+1] - c_seq->i[i];
2026 row = rstart + i;
2027 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr);
2028 cols += ncols; vals += ncols;
2029 }
2030 } else {
2031 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr);
2032 }
2033
2034 /* Co -> C, off-processor part */
2035 cm = C_oth->rmap->N;
2036 c_seq = (Mat_SeqAIJ*)C_oth->data;
2037 cols = c_seq->j;
2038 vals = c_seq->a;
2039 for (i=0; i<cm; i++) {
2040 ncols = c_seq->i[i+1] - c_seq->i[i];
2041 row = p->garray[i];
2042 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr);
2043 cols += ncols; vals += ncols;
2044 }
2045
2046 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2047 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
2048
2049 ptap->reuse = MAT_REUSE_MATRIX;
2050 PetscFunctionReturn(0);
2051 }
2052
MatProductSymbolic_PtAP_MPIAIJ_MPIAIJ(Mat C)2053 PETSC_INTERN PetscErrorCode MatProductSymbolic_PtAP_MPIAIJ_MPIAIJ(Mat C)
2054 {
2055 PetscErrorCode ierr;
2056 Mat_Product *product = C->product;
2057 Mat A=product->A,P=product->B;
2058 MatProductAlgorithm alg=product->alg;
2059 PetscReal fill=product->fill;
2060 PetscBool flg;
2061
2062 PetscFunctionBegin;
2063 /* scalable: do R=P^T locally, then C=R*A*P */
2064 ierr = PetscStrcmp(alg,"scalable",&flg);CHKERRQ(ierr);
2065 if (flg) {
2066 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(A,P,product->fill,C);CHKERRQ(ierr);
2067 C->ops->productnumeric = MatProductNumeric_PtAP;
2068 goto next;
2069 }
2070
2071 /* nonscalable: do R=P^T locally, then C=R*A*P */
2072 ierr = PetscStrcmp(alg,"nonscalable",&flg);CHKERRQ(ierr);
2073 if (flg) {
2074 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);CHKERRQ(ierr);
2075 goto next;
2076 }
2077
2078 /* allatonce */
2079 ierr = PetscStrcmp(alg,"allatonce",&flg);CHKERRQ(ierr);
2080 if (flg) {
2081 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(A,P,fill,C);CHKERRQ(ierr);
2082 goto next;
2083 }
2084
2085 /* allatonce_merged */
2086 ierr = PetscStrcmp(alg,"allatonce_merged",&flg);CHKERRQ(ierr);
2087 if (flg) {
2088 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(A,P,fill,C);CHKERRQ(ierr);
2089 goto next;
2090 }
2091
2092 /* hypre */
2093 #if defined(PETSC_HAVE_HYPRE)
2094 ierr = PetscStrcmp(alg,"hypre",&flg);CHKERRQ(ierr);
2095 if (flg) {
2096 ierr = MatPtAPSymbolic_AIJ_AIJ_wHYPRE(A,P,fill,C);CHKERRQ(ierr);
2097 C->ops->productnumeric = MatProductNumeric_PtAP;
2098 PetscFunctionReturn(0);
2099 }
2100 #endif
2101 SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_SUP,"Mat Product Algorithm is not supported");
2102
2103 next:
2104 C->ops->productnumeric = MatProductNumeric_PtAP;
2105 PetscFunctionReturn(0);
2106 }
2107