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 13 /* #define PTAP_PROFILE */ 14 15 extern PetscErrorCode MatDestroy_MPIAIJ(Mat); 16 #undef __FUNCT__ 17 #define __FUNCT__ "MatDestroy_MPIAIJ_PtAP" 18 PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A) 19 { 20 PetscErrorCode ierr; 21 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data; 22 Mat_PtAPMPI *ptap=a->ptap; 23 24 PetscFunctionBegin; 25 if (ptap) { 26 Mat_Merge_SeqsToMPI *merge=ptap->merge; 27 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 28 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 29 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 30 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 31 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */ 32 if (ptap->api) {ierr = PetscFree(ptap->api);CHKERRQ(ierr);} 33 if (ptap->apj) {ierr = PetscFree(ptap->apj);CHKERRQ(ierr);} 34 if (ptap->apa) {ierr = PetscFree(ptap->apa);CHKERRQ(ierr);} 35 if (merge) { 36 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 37 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 38 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 39 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 40 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 41 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 42 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 43 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 44 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 45 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 46 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 47 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 48 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 49 ierr = merge->destroy(A);CHKERRQ(ierr); 50 ierr = PetscFree(ptap->merge);CHKERRQ(ierr); 51 } 52 ierr = PetscFree(ptap);CHKERRQ(ierr); 53 } 54 PetscFunctionReturn(0); 55 } 56 57 #undef __FUNCT__ 58 #define __FUNCT__ "MatDuplicate_MPIAIJ_MatPtAP" 59 PetscErrorCode MatDuplicate_MPIAIJ_MatPtAP(Mat A, MatDuplicateOption op, Mat *M) 60 { 61 PetscErrorCode ierr; 62 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 63 Mat_PtAPMPI *ptap = a->ptap; 64 Mat_Merge_SeqsToMPI *merge = ptap->merge; 65 66 PetscFunctionBegin; 67 ierr = (*merge->duplicate)(A,op,M);CHKERRQ(ierr); 68 69 (*M)->ops->destroy = merge->destroy; 70 (*M)->ops->duplicate = merge->duplicate; 71 PetscFunctionReturn(0); 72 } 73 74 #undef __FUNCT__ 75 #define __FUNCT__ "MatPtAP_MPIAIJ_MPIAIJ" 76 PetscErrorCode MatPtAP_MPIAIJ_MPIAIJ(Mat A,Mat P,MatReuse scall,PetscReal fill,Mat *C) 77 { 78 PetscErrorCode ierr; 79 80 PetscFunctionBegin; 81 if (scall == MAT_INITIAL_MATRIX) { 82 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 83 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);CHKERRQ(ierr); 84 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 85 } 86 ierr = PetscLogEventBegin(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 87 ierr = MatPtAPNumeric_MPIAIJ_MPIAIJ(A,P,*C);CHKERRQ(ierr); 88 ierr = PetscLogEventEnd(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 89 PetscFunctionReturn(0); 90 } 91 92 #undef __FUNCT__ 93 #define __FUNCT__ "MatPtAPSymbolic_MPIAIJ_MPIAIJ" 94 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 95 { 96 PetscErrorCode ierr; 97 Mat Cmpi; 98 Mat_PtAPMPI *ptap; 99 PetscFreeSpaceList free_space=NULL,current_space=NULL; 100 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 101 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 102 Mat_SeqAIJ *p_loc,*p_oth; 103 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pdti,*pdtj,*poti,*potj,*ptJ; 104 PetscInt *adi=ad->i,*aj,*aoi=ao->i,nnz; 105 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 106 PetscInt am=A->rmap->n,pN=P->cmap->N,pm=P->rmap->n,pn=P->cmap->n; 107 PetscBT lnkbt; 108 MPI_Comm comm; 109 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0; 110 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 111 PetscInt len,proc,*dnz,*onz,*owners; 112 PetscInt nzi,*pti,*ptj; 113 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 114 MPI_Request *swaits,*rwaits; 115 MPI_Status *sstatus,rstatus; 116 Mat_Merge_SeqsToMPI *merge; 117 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,pon,nspacedouble=0,j,ap_rmax=0; 118 PetscReal afill=1.0,afill_tmp; 119 PetscInt rmax; 120 121 PetscFunctionBegin; 122 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 123 124 /* check if matrix local sizes are compatible */ 125 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) { 126 SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Arow (%D, %D) != Prow (%D,%D)",A->rmap->rstart,A->rmap->rend,P->rmap->rstart,P->rmap->rend); 127 } 128 if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend) { 129 SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Acol (%D, %D) != Prow (%D,%D)",A->cmap->rstart,A->cmap->rend,P->rmap->rstart,P->rmap->rend); 130 } 131 132 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 133 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 134 135 /* create struct Mat_PtAPMPI and attached it to C later */ 136 ierr = PetscNew(&ptap);CHKERRQ(ierr); 137 ierr = PetscNew(&merge);CHKERRQ(ierr); 138 ptap->merge = merge; 139 ptap->reuse = MAT_INITIAL_MATRIX; 140 141 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 142 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 143 144 /* get P_loc by taking all local rows of P */ 145 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 146 147 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 148 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 149 pi_loc = p_loc->i; pj_loc = p_loc->j; 150 pi_oth = p_oth->i; pj_oth = p_oth->j; 151 152 /* (1) compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth (api,apj) */ 153 /*--------------------------------------------------------------------------*/ 154 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 155 api[0] = 0; 156 157 /* create and initialize a linked list */ 158 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 159 160 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) -OOM for ex56, np=8k on Intrepid! */ 161 ierr = PetscFreeSpaceGet((PetscInt)(fill*(adi[am]+aoi[am]+pi_loc[pm])),&free_space);CHKERRQ(ierr); 162 163 current_space = free_space; 164 165 for (i=0; i<am; i++) { 166 /* diagonal portion of A */ 167 nzi = adi[i+1] - adi[i]; 168 aj = ad->j + adi[i]; 169 for (j=0; j<nzi; j++) { 170 row = aj[j]; 171 pnz = pi_loc[row+1] - pi_loc[row]; 172 Jptr = pj_loc + pi_loc[row]; 173 /* add non-zero cols of P into the sorted linked list lnk */ 174 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 175 } 176 /* off-diagonal portion of A */ 177 nzi = aoi[i+1] - aoi[i]; 178 aj = ao->j + aoi[i]; 179 for (j=0; j<nzi; j++) { 180 row = aj[j]; 181 pnz = pi_oth[row+1] - pi_oth[row]; 182 Jptr = pj_oth + pi_oth[row]; 183 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 184 } 185 apnz = lnk[0]; 186 api[i+1] = api[i] + apnz; 187 if (ap_rmax < apnz) ap_rmax = apnz; 188 189 /* if free space is not available, double the total space in the list */ 190 if (current_space->local_remaining<apnz) { 191 ierr = PetscFreeSpaceGet(apnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 192 nspacedouble++; 193 } 194 195 /* Copy data into free space, then initialize lnk */ 196 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 197 198 current_space->array += apnz; 199 current_space->local_used += apnz; 200 current_space->local_remaining -= apnz; 201 } 202 203 /* Allocate space for apj, initialize apj, and */ 204 /* destroy list of free space and other temporary array(s) */ 205 ierr = PetscMalloc1(api[am]+1,&apj);CHKERRQ(ierr); 206 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 207 afill_tmp = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1); 208 if (afill_tmp > afill) afill = afill_tmp; 209 210 /* (2) determine symbolic Co=(p->B)^T*AP - send to others (coi,coj)*/ 211 /*-----------------------------------------------------------------*/ 212 ierr = MatGetSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); 213 214 /* then, compute symbolic Co = (p->B)^T*AP */ 215 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 216 >= (num of nonzero rows of C_seq) - pn */ 217 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 218 coi[0] = 0; 219 220 /* set initial free space to be fill*(nnz(p->B) + nnz(AP)) */ 221 nnz = fill*(poti[pon] + api[am]); 222 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 223 current_space = free_space; 224 225 for (i=0; i<pon; i++) { 226 pnz = poti[i+1] - poti[i]; 227 ptJ = potj + poti[i]; 228 for (j=0; j<pnz; j++) { 229 row = ptJ[j]; /* row of AP == col of Pot */ 230 apnz = api[row+1] - api[row]; 231 Jptr = apj + api[row]; 232 /* add non-zero cols of AP into the sorted linked list lnk */ 233 ierr = PetscLLCondensedAddSorted(apnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 234 } 235 nnz = lnk[0]; 236 237 /* If free space is not available, double the total space in the list */ 238 if (current_space->local_remaining<nnz) { 239 ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 240 nspacedouble++; 241 } 242 243 /* Copy data into free space, and zero out denserows */ 244 ierr = PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 245 246 current_space->array += nnz; 247 current_space->local_used += nnz; 248 current_space->local_remaining -= nnz; 249 250 coi[i+1] = coi[i] + nnz; 251 } 252 253 ierr = PetscMalloc1(coi[pon],&coj);CHKERRQ(ierr); 254 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 255 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + api[am]+1); 256 if (afill_tmp > afill) afill = afill_tmp; 257 ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); 258 259 /* (3) send j-array (coj) of Co to other processors */ 260 /*--------------------------------------------------*/ 261 ierr = PetscCalloc1(size,&merge->len_s);CHKERRQ(ierr); 262 len_s = merge->len_s; 263 merge->nsend = 0; 264 265 266 /* determine row ownership */ 267 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 268 merge->rowmap->n = pn; 269 merge->rowmap->bs = 1; 270 271 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 272 owners = merge->rowmap->range; 273 274 /* determine the number of messages to send, their lengths */ 275 ierr = PetscMalloc2(size,&len_si,size,&sstatus);CHKERRQ(ierr); 276 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 277 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 278 279 proc = 0; 280 for (i=0; i<pon; i++) { 281 while (prmap[i] >= owners[proc+1]) proc++; 282 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 283 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 284 } 285 286 len = 0; /* max length of buf_si[], see (4) */ 287 owners_co[0] = 0; 288 for (proc=0; proc<size; proc++) { 289 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 290 if (len_s[proc]) { 291 merge->nsend++; 292 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 293 len += len_si[proc]; 294 } 295 } 296 297 /* determine the number and length of messages to receive for coi and coj */ 298 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 299 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 300 301 /* post the Irecv and Isend of coj */ 302 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 303 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 304 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 305 for (proc=0, k=0; proc<size; proc++) { 306 if (!len_s[proc]) continue; 307 i = owners_co[proc]; 308 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 309 k++; 310 } 311 312 /* receives and sends of coj are complete */ 313 for (i=0; i<merge->nrecv; i++) { 314 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 315 } 316 ierr = PetscFree(rwaits);CHKERRQ(ierr); 317 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 318 319 /* (4) send and recv coi */ 320 /*-----------------------*/ 321 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 322 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 323 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 324 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 325 for (proc=0,k=0; proc<size; proc++) { 326 if (!len_s[proc]) continue; 327 /* form outgoing message for i-structure: 328 buf_si[0]: nrows to be sent 329 [1:nrows]: row index (global) 330 [nrows+1:2*nrows+1]: i-structure index 331 */ 332 /*-------------------------------------------*/ 333 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 334 buf_si_i = buf_si + nrows+1; 335 buf_si[0] = nrows; 336 buf_si_i[0] = 0; 337 nrows = 0; 338 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 339 nzi = coi[i+1] - coi[i]; 340 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 341 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 342 nrows++; 343 } 344 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 345 k++; 346 buf_si += len_si[proc]; 347 } 348 i = merge->nrecv; 349 while (i--) { 350 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 351 } 352 ierr = PetscFree(rwaits);CHKERRQ(ierr); 353 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 354 355 ierr = PetscFree2(len_si,sstatus);CHKERRQ(ierr); 356 ierr = PetscFree(len_ri);CHKERRQ(ierr); 357 ierr = PetscFree(swaits);CHKERRQ(ierr); 358 ierr = PetscFree(buf_s);CHKERRQ(ierr); 359 360 /* (5) compute the local portion of C (mpi mat) */ 361 /*----------------------------------------------*/ 362 ierr = MatGetSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); 363 364 /* allocate pti array and free space for accumulating nonzero column info */ 365 ierr = PetscMalloc1(pn+1,&pti);CHKERRQ(ierr); 366 pti[0] = 0; 367 368 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 369 nnz = fill*(pi_loc[pm] + api[am]); 370 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 371 current_space = free_space; 372 373 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 374 for (k=0; k<merge->nrecv; k++) { 375 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 376 nrows = *buf_ri_k[k]; 377 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 378 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 379 } 380 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 381 rmax = 0; 382 for (i=0; i<pn; i++) { 383 /* add pdt[i,:]*AP into lnk */ 384 pnz = pdti[i+1] - pdti[i]; 385 ptJ = pdtj + pdti[i]; 386 for (j=0; j<pnz; j++) { 387 row = ptJ[j]; /* row of AP == col of Pt */ 388 apnz = api[row+1] - api[row]; 389 Jptr = apj + api[row]; 390 /* add non-zero cols of AP into the sorted linked list lnk */ 391 ierr = PetscLLCondensedAddSorted(apnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 392 } 393 394 /* add received col data into lnk */ 395 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 396 if (i == *nextrow[k]) { /* i-th row */ 397 nzi = *(nextci[k]+1) - *nextci[k]; 398 Jptr = buf_rj[k] + *nextci[k]; 399 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 400 nextrow[k]++; nextci[k]++; 401 } 402 } 403 nnz = lnk[0]; 404 405 /* if free space is not available, make more free space */ 406 if (current_space->local_remaining<nnz) { 407 ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 408 nspacedouble++; 409 } 410 /* copy data into free space, then initialize lnk */ 411 ierr = PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 412 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 413 414 current_space->array += nnz; 415 current_space->local_used += nnz; 416 current_space->local_remaining -= nnz; 417 418 pti[i+1] = pti[i] + nnz; 419 if (nnz > rmax) rmax = nnz; 420 } 421 ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); 422 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 423 424 ierr = PetscMalloc1(pti[pn]+1,&ptj);CHKERRQ(ierr); 425 ierr = PetscFreeSpaceContiguous(&free_space,ptj);CHKERRQ(ierr); 426 afill_tmp = (PetscReal)pti[pn]/(pi_loc[pm] + api[am]+1); 427 if (afill_tmp > afill) afill = afill_tmp; 428 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 429 430 /* (6) create symbolic parallel matrix Cmpi */ 431 /*------------------------------------------*/ 432 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 433 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 434 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 435 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 436 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 437 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 438 439 merge->bi = pti; /* Cseq->i */ 440 merge->bj = ptj; /* Cseq->j */ 441 merge->coi = coi; /* Co->i */ 442 merge->coj = coj; /* Co->j */ 443 merge->buf_ri = buf_ri; 444 merge->buf_rj = buf_rj; 445 merge->owners_co = owners_co; 446 merge->destroy = Cmpi->ops->destroy; 447 merge->duplicate = Cmpi->ops->duplicate; 448 449 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 450 Cmpi->assembled = PETSC_FALSE; 451 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 452 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 453 454 /* attach the supporting struct to Cmpi for reuse */ 455 c = (Mat_MPIAIJ*)Cmpi->data; 456 c->ptap = ptap; 457 ptap->api = api; 458 ptap->apj = apj; 459 ptap->rmax = ap_rmax; 460 *C = Cmpi; 461 462 /* flag 'scalable' determines which implementations to be used: 463 0: do dense axpy in MatPtAPNumeric() - fast, but requires storage of a nonscalable dense array apa; 464 1: do sparse axpy in MatPtAPNumeric() - might slow, uses a sparse array apa */ 465 /* set default scalable */ 466 ptap->scalable = PETSC_TRUE; 467 468 ierr = PetscOptionsGetBool(((PetscObject)Cmpi)->prefix,"-matptap_scalable",&ptap->scalable,NULL);CHKERRQ(ierr); 469 if (!ptap->scalable) { /* Do dense axpy */ 470 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 471 } else { 472 ierr = PetscCalloc1(ap_rmax+1,&ptap->apa);CHKERRQ(ierr); 473 } 474 475 #if defined(PETSC_USE_INFO) 476 if (pti[pn] != 0) { 477 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 478 ierr = PetscInfo1(Cmpi,"Use MatPtAP(A,P,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 479 } else { 480 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 481 } 482 #endif 483 PetscFunctionReturn(0); 484 } 485 486 #undef __FUNCT__ 487 #define __FUNCT__ "MatPtAPNumeric_MPIAIJ_MPIAIJ" 488 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 489 { 490 PetscErrorCode ierr; 491 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 492 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 493 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 494 Mat_SeqAIJ *p_loc,*p_oth; 495 Mat_PtAPMPI *ptap; 496 Mat_Merge_SeqsToMPI *merge; 497 PetscInt *adi=ad->i,*aoi=ao->i,*adj,*aoj,*apJ,nextp; 498 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pJ,*pj; 499 PetscInt i,j,k,anz,pnz,apnz,nextap,row,*cj; 500 MatScalar *ada,*aoa,*apa,*pa,*ca,*pa_loc,*pa_oth,valtmp; 501 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 502 MPI_Comm comm; 503 PetscMPIInt size,rank,taga,*len_s; 504 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 505 PetscInt **buf_ri,**buf_rj; 506 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 507 MPI_Request *s_waits,*r_waits; 508 MPI_Status *status; 509 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 510 PetscInt *api,*apj,*coi,*coj; 511 PetscInt *poJ=po->j,*pdJ=pd->j,pcstart=P->cmap->rstart,pcend=P->cmap->rend; 512 PetscBool scalable; 513 #if defined(PTAP_PROFILE) 514 PetscLogDouble t0,t1,t2,t3,t4,et2_AP=0.0,et2_PtAP=0.0,t2_0,t2_1,t2_2; 515 #endif 516 517 PetscFunctionBegin; 518 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 519 #if defined(PTAP_PROFILE) 520 ierr = PetscTime(&t0);CHKERRQ(ierr); 521 #endif 522 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 523 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 524 525 ptap = c->ptap; 526 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_INCOMP,"MatPtAP() has not been called to create matrix C yet, cannot use MAT_REUSE_MATRIX"); 527 merge = ptap->merge; 528 apa = ptap->apa; 529 scalable = ptap->scalable; 530 531 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 532 /*-----------------------------------------------------*/ 533 if (ptap->reuse == MAT_INITIAL_MATRIX) { 534 /* P_oth and P_loc are obtained in MatPtASymbolic(), skip calling MatGetBrowsOfAoCols() and MatMPIAIJGetLocalMat() */ 535 ptap->reuse = MAT_REUSE_MATRIX; 536 } else { /* update numerical values of P_oth and P_loc */ 537 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 538 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 539 } 540 #if defined(PTAP_PROFILE) 541 ierr = PetscTime(&t1);CHKERRQ(ierr); 542 #endif 543 544 /* 2) compute numeric C_seq = P_loc^T*A_loc*P - dominating part */ 545 /*--------------------------------------------------------------*/ 546 /* get data from symbolic products */ 547 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 548 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 549 pi_loc=p_loc->i; pj_loc=p_loc->j; pJ=pj_loc; pa_loc=p_loc->a; 550 pi_oth=p_oth->i; pj_oth=p_oth->j; pa_oth=p_oth->a; 551 552 coi = merge->coi; coj = merge->coj; 553 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 554 555 bi = merge->bi; bj = merge->bj; 556 owners = merge->rowmap->range; 557 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); /* ba: Cseq->a */ 558 559 api = ptap->api; apj = ptap->apj; 560 561 if (!scalable) { /* Do dense axpy on apa (length of pN, stores A[i,:]*P) - nonscalable, but fast */ 562 ierr = PetscInfo(C,"Using non-scalable dense axpy\n");CHKERRQ(ierr); 563 /*-----------------------------------------------------------------------------------------------------*/ 564 for (i=0; i<am; i++) { 565 #if defined(PTAP_PROFILE) 566 ierr = PetscTime(&t2_0);CHKERRQ(ierr); 567 #endif 568 /* 2-a) form i-th sparse row of A_loc*P = Ad*P_loc + Ao*P_oth */ 569 /*------------------------------------------------------------*/ 570 apJ = apj + api[i]; 571 572 /* diagonal portion of A */ 573 anz = adi[i+1] - adi[i]; 574 adj = ad->j + adi[i]; 575 ada = ad->a + adi[i]; 576 for (j=0; j<anz; j++) { 577 row = adj[j]; 578 pnz = pi_loc[row+1] - pi_loc[row]; 579 pj = pj_loc + pi_loc[row]; 580 pa = pa_loc + pi_loc[row]; 581 582 /* perform dense axpy */ 583 valtmp = ada[j]; 584 for (k=0; k<pnz; k++) { 585 apa[pj[k]] += valtmp*pa[k]; 586 } 587 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 588 } 589 590 /* off-diagonal portion of A */ 591 anz = aoi[i+1] - aoi[i]; 592 aoj = ao->j + aoi[i]; 593 aoa = ao->a + aoi[i]; 594 for (j=0; j<anz; j++) { 595 row = aoj[j]; 596 pnz = pi_oth[row+1] - pi_oth[row]; 597 pj = pj_oth + pi_oth[row]; 598 pa = pa_oth + pi_oth[row]; 599 600 /* perform dense axpy */ 601 valtmp = aoa[j]; 602 for (k=0; k<pnz; k++) { 603 apa[pj[k]] += valtmp*pa[k]; 604 } 605 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 606 } 607 #if defined(PTAP_PROFILE) 608 ierr = PetscTime(&t2_1);CHKERRQ(ierr); 609 et2_AP += t2_1 - t2_0; 610 #endif 611 612 /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */ 613 /*--------------------------------------------------------------*/ 614 apnz = api[i+1] - api[i]; 615 /* put the value into Co=(p->B)^T*AP (off-diagonal part, send to others) */ 616 pnz = po->i[i+1] - po->i[i]; 617 poJ = po->j + po->i[i]; 618 pA = po->a + po->i[i]; 619 for (j=0; j<pnz; j++) { 620 row = poJ[j]; 621 cnz = coi[row+1] - coi[row]; 622 cj = coj + coi[row]; 623 ca = coa + coi[row]; 624 /* perform dense axpy */ 625 valtmp = pA[j]; 626 for (k=0; k<cnz; k++) { 627 ca[k] += valtmp*apa[cj[k]]; 628 } 629 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 630 } 631 632 /* put the value into Cd (diagonal part) */ 633 pnz = pd->i[i+1] - pd->i[i]; 634 pdJ = pd->j + pd->i[i]; 635 pA = pd->a + pd->i[i]; 636 for (j=0; j<pnz; j++) { 637 row = pdJ[j]; 638 cnz = bi[row+1] - bi[row]; 639 cj = bj + bi[row]; 640 ca = ba + bi[row]; 641 /* perform dense axpy */ 642 valtmp = pA[j]; 643 for (k=0; k<cnz; k++) { 644 ca[k] += valtmp*apa[cj[k]]; 645 } 646 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 647 } 648 649 /* zero the current row of A*P */ 650 for (k=0; k<apnz; k++) apa[apJ[k]] = 0.0; 651 #if defined(PTAP_PROFILE) 652 ierr = PetscTime(&t2_2);CHKERRQ(ierr); 653 et2_PtAP += t2_2 - t2_1; 654 #endif 655 } 656 } else { /* Do sparse axpy on apa (length of ap_rmax, stores A[i,:]*P) - scalable, but slower */ 657 ierr = PetscInfo(C,"Using scalable sparse axpy\n");CHKERRQ(ierr); 658 /*-----------------------------------------------------------------------------------------*/ 659 pA=pa_loc; 660 for (i=0; i<am; i++) { 661 #if defined(PTAP_PROFILE) 662 ierr = PetscTime(&t2_0);CHKERRQ(ierr); 663 #endif 664 /* form i-th sparse row of A*P */ 665 apnz = api[i+1] - api[i]; 666 apJ = apj + api[i]; 667 /* diagonal portion of A */ 668 anz = adi[i+1] - adi[i]; 669 adj = ad->j + adi[i]; 670 ada = ad->a + adi[i]; 671 for (j=0; j<anz; j++) { 672 row = adj[j]; 673 pnz = pi_loc[row+1] - pi_loc[row]; 674 pj = pj_loc + pi_loc[row]; 675 pa = pa_loc + pi_loc[row]; 676 valtmp = ada[j]; 677 nextp = 0; 678 for (k=0; nextp<pnz; k++) { 679 if (apJ[k] == pj[nextp]) { /* col of AP == col of P */ 680 apa[k] += valtmp*pa[nextp++]; 681 } 682 } 683 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 684 } 685 /* off-diagonal portion of A */ 686 anz = aoi[i+1] - aoi[i]; 687 aoj = ao->j + aoi[i]; 688 aoa = ao->a + aoi[i]; 689 for (j=0; j<anz; j++) { 690 row = aoj[j]; 691 pnz = pi_oth[row+1] - pi_oth[row]; 692 pj = pj_oth + pi_oth[row]; 693 pa = pa_oth + pi_oth[row]; 694 valtmp = aoa[j]; 695 nextp = 0; 696 for (k=0; nextp<pnz; k++) { 697 if (apJ[k] == pj[nextp]) { /* col of AP == col of P */ 698 apa[k] += valtmp*pa[nextp++]; 699 } 700 } 701 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 702 } 703 #if defined(PTAP_PROFILE) 704 ierr = PetscTime(&t2_1);CHKERRQ(ierr); 705 et2_AP += t2_1 - t2_0; 706 #endif 707 708 /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */ 709 /*--------------------------------------------------------------*/ 710 pnz = pi_loc[i+1] - pi_loc[i]; 711 pJ = pj_loc + pi_loc[i]; 712 for (j=0; j<pnz; j++) { 713 nextap = 0; 714 row = pJ[j]; /* global index */ 715 if (row < pcstart || row >=pcend) { /* put the value into Co */ 716 row = *poJ; 717 cj = coj + coi[row]; 718 ca = coa + coi[row]; poJ++; 719 } else { /* put the value into Cd */ 720 row = *pdJ; 721 cj = bj + bi[row]; 722 ca = ba + bi[row]; pdJ++; 723 } 724 valtmp = pA[j]; 725 for (k=0; nextap<apnz; k++) { 726 if (cj[k]==apJ[nextap]) ca[k] += valtmp*apa[nextap++]; 727 } 728 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 729 } 730 pA += pnz; 731 /* zero the current row info for A*P */ 732 ierr = PetscMemzero(apa,apnz*sizeof(MatScalar));CHKERRQ(ierr); 733 #if defined(PTAP_PROFILE) 734 ierr = PetscTime(&t2_2);CHKERRQ(ierr); 735 et2_PtAP += t2_2 - t2_1; 736 #endif 737 } 738 } 739 #if defined(PTAP_PROFILE) 740 ierr = PetscTime(&t2);CHKERRQ(ierr); 741 #endif 742 743 /* 3) send and recv matrix values coa */ 744 /*------------------------------------*/ 745 buf_ri = merge->buf_ri; 746 buf_rj = merge->buf_rj; 747 len_s = merge->len_s; 748 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 749 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 750 751 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 752 for (proc=0,k=0; proc<size; proc++) { 753 if (!len_s[proc]) continue; 754 i = merge->owners_co[proc]; 755 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 756 k++; 757 } 758 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 759 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 760 761 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 762 ierr = PetscFree(r_waits);CHKERRQ(ierr); 763 ierr = PetscFree(coa);CHKERRQ(ierr); 764 #if defined(PTAP_PROFILE) 765 ierr = PetscTime(&t3);CHKERRQ(ierr); 766 #endif 767 768 /* 4) insert local Cseq and received values into Cmpi */ 769 /*------------------------------------------------------*/ 770 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 771 for (k=0; k<merge->nrecv; k++) { 772 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 773 nrows = *(buf_ri_k[k]); 774 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 775 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 776 } 777 778 for (i=0; i<cm; i++) { 779 row = owners[rank] + i; /* global row index of C_seq */ 780 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 781 ba_i = ba + bi[i]; 782 bnz = bi[i+1] - bi[i]; 783 /* add received vals into ba */ 784 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 785 /* i-th row */ 786 if (i == *nextrow[k]) { 787 cnz = *(nextci[k]+1) - *nextci[k]; 788 cj = buf_rj[k] + *(nextci[k]); 789 ca = abuf_r[k] + *(nextci[k]); 790 nextcj = 0; 791 for (j=0; nextcj<cnz; j++) { 792 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 793 ba_i[j] += ca[nextcj++]; 794 } 795 } 796 nextrow[k]++; nextci[k]++; 797 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 798 } 799 } 800 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 801 } 802 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 803 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 804 805 ierr = PetscFree(ba);CHKERRQ(ierr); 806 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 807 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 808 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 809 #if defined(PTAP_PROFILE) 810 ierr = PetscTime(&t4);CHKERRQ(ierr); 811 if (rank==1) PetscPrintf(MPI_COMM_SELF," [%d] PtAPNum %g/P + %g/PtAP( %g + %g ) + %g/comm + %g/Cloc = %g\n\n",rank,t1-t0,t2-t1,et2_AP,et2_PtAP,t3-t2,t4-t3,t4-t0);CHKERRQ(ierr); 812 #endif 813 PetscFunctionReturn(0); 814 } 815