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 12 /* 13 #define DEBUG_MATPTAP 14 */ 15 16 extern PetscErrorCode MatDestroy_MPIAIJ(Mat); 17 #undef __FUNCT__ 18 #define __FUNCT__ "MatDestroy_MPIAIJ_PtAP" 19 PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A) 20 { 21 PetscErrorCode ierr; 22 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 23 Mat_PtAPMPI *ptap=a->ptap; 24 25 PetscFunctionBegin; 26 if (ptap){ 27 Mat_Merge_SeqsToMPI *merge=ptap->merge; 28 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 29 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 30 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 31 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 32 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */ 33 if (ptap->api){ierr = PetscFree(ptap->api);CHKERRQ(ierr);} 34 if (ptap->apj){ierr = PetscFree(ptap->apj);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 55 PetscFunctionReturn(0); 56 } 57 58 #undef __FUNCT__ 59 #define __FUNCT__ "MatDuplicate_MPIAIJ_MatPtAP" 60 PetscErrorCode MatDuplicate_MPIAIJ_MatPtAP(Mat A, MatDuplicateOption op, Mat *M) 61 { 62 PetscErrorCode ierr; 63 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 64 Mat_PtAPMPI *ptap = a->ptap; 65 Mat_Merge_SeqsToMPI *merge = ptap->merge; 66 67 PetscFunctionBegin; 68 ierr = (*merge->duplicate)(A,op,M);CHKERRQ(ierr); 69 (*M)->ops->destroy = merge->destroy; 70 (*M)->ops->duplicate = merge->duplicate; 71 PetscFunctionReturn(0); 72 } 73 74 #undef __FUNCT__ 75 #define __FUNCT__ "MatPtAPSymbolic_MPIAIJ" 76 PetscErrorCode MatPtAPSymbolic_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 77 { 78 PetscErrorCode ierr; 79 80 PetscFunctionBegin; 81 if (!P->ops->ptapsymbolic_mpiaij) SETERRQ2(((PetscObject)A)->comm,PETSC_ERR_SUP,"Not implemented for A=%s and P=%s",((PetscObject)A)->type_name,((PetscObject)P)->type_name); 82 ierr = (*P->ops->ptapsymbolic_mpiaij)(A,P,fill,C);CHKERRQ(ierr); 83 PetscFunctionReturn(0); 84 } 85 86 #undef __FUNCT__ 87 #define __FUNCT__ "MatPtAPNumeric_MPIAIJ" 88 PetscErrorCode MatPtAPNumeric_MPIAIJ(Mat A,Mat P,Mat C) 89 { 90 PetscErrorCode ierr; 91 92 PetscFunctionBegin; 93 if (!P->ops->ptapnumeric_mpiaij) SETERRQ2(((PetscObject)A)->comm,PETSC_ERR_SUP,"Not implemented for A=%s and P=%s",((PetscObject)A)->type_name,((PetscObject)P)->type_name); 94 ierr = (*P->ops->ptapnumeric_mpiaij)(A,P,C);CHKERRQ(ierr); 95 PetscFunctionReturn(0); 96 } 97 98 #undef __FUNCT__ 99 #define __FUNCT__ "MatPtAPSymbolic_MPIAIJ_MPIAIJ" 100 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 101 { 102 PetscErrorCode ierr; 103 Mat Cmpi; 104 Mat_PtAPMPI *ptap; 105 PetscFreeSpaceList free_space=PETSC_NULL,current_space=PETSC_NULL; 106 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 107 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 108 Mat_SeqAIJ *p_loc,*p_oth; 109 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pdti,*pdtj,*poti,*potj,*ptJ; 110 PetscInt *adi=ad->i,*aj,*aoi=ao->i,nnz; 111 PetscInt nlnk,*lnk,*owners_co,*coi,*coj,i,k,pnz,row; 112 PetscInt am=A->rmap->n,pN=P->cmap->N,pm=P->rmap->n,pn=P->cmap->n; 113 PetscBT lnkbt; 114 MPI_Comm comm=((PetscObject)A)->comm; 115 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 116 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 117 PetscInt len,proc,*dnz,*onz,*owners; 118 PetscInt nzi,*bi,*bj; 119 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 120 MPI_Request *swaits,*rwaits; 121 MPI_Status *sstatus,rstatus; 122 Mat_Merge_SeqsToMPI *merge; 123 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,pon,nspacedouble=0,j,ap_rmax=0; 124 PetscReal afill=1.0,afill_tmp; 125 PetscInt rstart = P->cmap->rstart,rmax; 126 PetscScalar *vals; 127 128 PetscFunctionBegin; 129 /* check if matrix local sizes are compatible */ 130 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend){ 131 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); 132 } 133 if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend){ 134 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); 135 } 136 137 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 138 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 139 140 /* create struct Mat_PtAPMPI and attached it to C later */ 141 ierr = PetscNew(Mat_PtAPMPI,&ptap);CHKERRQ(ierr); 142 ptap->reuse = MAT_INITIAL_MATRIX; 143 144 145 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 146 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 147 #if defined(DEBUG_MATPTAP) 148 if (!rank) ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] P_oth is done...\n",rank); 149 #endif 150 151 /* get P_loc by taking all local rows of P */ 152 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 153 #if defined(DEBUG_MATPTAP) 154 ierr = MPI_Barrier(comm);CHKERRQ(ierr); 155 if (!rank) ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] P_loc is done...\n",rank); 156 #endif 157 158 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 159 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 160 pi_loc = p_loc->i; pj_loc = p_loc->j; 161 pi_oth = p_oth->i; pj_oth = p_oth->j; 162 163 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 164 /*-------------------------------------------------------------------*/ 165 ierr = PetscMalloc((am+1)*sizeof(PetscInt),&api);CHKERRQ(ierr); 166 api[0] = 0; 167 168 /* create and initialize a linked list */ 169 nlnk = pN+1; 170 #if defined(DEBUG_MATPTAP) 171 ierr = MPI_Barrier(comm);CHKERRQ(ierr); 172 if (!rank) ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] call PetscLLCreate(), pN %D, P_rmax %D %D; Annz %D\n",rank,pN,p_loc->rmax,p_oth->rmax,adi[am]+aoi[am]); 173 #endif 174 ierr = PetscLLCreate(pN,pN,nlnk,lnk,lnkbt);CHKERRQ(ierr); 175 #if defined(DEBUG_MATPTAP) 176 ierr = MPI_Barrier(comm);CHKERRQ(ierr); 177 if (!rank) ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] call PetscLLCreate() is done\n",rank); 178 #endif 179 180 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 181 ierr = PetscFreeSpaceGet((PetscInt)(fill*(adi[am]+aoi[am]+pi_loc[pm])),&free_space);CHKERRQ(ierr); 182 current_space = free_space; 183 184 for (i=0; i<am; i++) { 185 apnz = 0; 186 /* diagonal portion of A */ 187 nzi = adi[i+1] - adi[i]; 188 aj = ad->j + adi[i]; 189 for (j=0; j<nzi; j++){ 190 row = aj[j]; 191 pnz = pi_loc[row+1] - pi_loc[row]; 192 Jptr = pj_loc + pi_loc[row]; 193 /* add non-zero cols of P into the sorted linked list lnk */ 194 ierr = PetscLLAddSorted(pnz,Jptr,pN,nlnk,lnk,lnkbt);CHKERRQ(ierr); 195 apnz += nlnk; 196 } 197 /* off-diagonal portion of A */ 198 nzi = aoi[i+1] - aoi[i]; 199 aj = ao->j + aoi[i]; 200 for (j=0; j<nzi; j++){ 201 row = aj[j]; 202 pnz = pi_oth[row+1] - pi_oth[row]; 203 Jptr = pj_oth + pi_oth[row]; 204 ierr = PetscLLAddSorted(pnz,Jptr,pN,nlnk,lnk,lnkbt);CHKERRQ(ierr); 205 apnz += nlnk; 206 } 207 208 api[i+1] = api[i] + apnz; 209 if (ap_rmax < apnz) ap_rmax = apnz; 210 211 /* if free space is not available, double the total space in the list */ 212 if (current_space->local_remaining<apnz) { 213 ierr = PetscFreeSpaceGet(apnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 214 nspacedouble++; 215 } 216 217 /* Copy data into free space, then initialize lnk */ 218 ierr = PetscLLClean(pN,pN,apnz,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 219 current_space->array += apnz; 220 current_space->local_used += apnz; 221 current_space->local_remaining -= apnz; 222 } 223 /* Allocate space for apj, initialize apj, and */ 224 /* destroy list of free space and other temporary array(s) */ 225 ierr = PetscMalloc((api[am]+1)*sizeof(PetscInt),&apj);CHKERRQ(ierr); 226 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 227 afill_tmp = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1); 228 if (afill_tmp > afill) afill = afill_tmp; 229 230 /* determine symbolic Co=(p->B)^T*AP - send to others */ 231 /*----------------------------------------------------*/ 232 ierr = MatGetSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); 233 234 /* then, compute symbolic Co = (p->B)^T*AP */ 235 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 236 >= (num of nonzero rows of C_seq) - pn */ 237 ierr = PetscMalloc((pon+1)*sizeof(PetscInt),&coi);CHKERRQ(ierr); 238 coi[0] = 0; 239 240 /* set initial free space to be fill*(nnz(p->B) + nnz(AP)) */ 241 nnz = fill*(poti[pon] + api[am]); 242 ierr = PetscFreeSpaceGet(nnz,&free_space); 243 current_space = free_space; 244 245 for (i=0; i<pon; i++) { 246 nnz = 0; 247 pnz = poti[i+1] - poti[i]; 248 ptJ = potj + poti[i]; 249 for (j=0; j<pnz; j++){ 250 row = ptJ[j]; /* row of AP == col of Pot */ 251 apnz = api[row+1] - api[row]; 252 Jptr = apj + api[row]; 253 /* add non-zero cols of AP into the sorted linked list lnk */ 254 ierr = PetscLLAddSorted(apnz,Jptr,pN,nlnk,lnk,lnkbt);CHKERRQ(ierr); 255 nnz += nlnk; 256 } 257 258 /* If free space is not available, double the total space in the list */ 259 if (current_space->local_remaining<nnz) { 260 ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 261 nspacedouble++; 262 } 263 264 /* Copy data into free space, and zero out denserows */ 265 ierr = PetscLLClean(pN,pN,nnz,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 266 current_space->array += nnz; 267 current_space->local_used += nnz; 268 current_space->local_remaining -= nnz; 269 coi[i+1] = coi[i] + nnz; 270 } 271 ierr = PetscMalloc((coi[pon]+1)*sizeof(PetscInt),&coj);CHKERRQ(ierr); 272 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 273 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + api[am]+1); 274 if (afill_tmp > afill) afill = afill_tmp; 275 ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); 276 277 #if defined(DEBUG_MATPTAP) 278 ierr = MPI_Barrier(comm);CHKERRQ(ierr); 279 if (!rank) ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] local Co is done\n",rank); 280 #endif 281 282 /* send j-array (coj) of Co to other processors */ 283 /*----------------------------------------------*/ 284 /* determine row ownership */ 285 ierr = PetscNew(Mat_Merge_SeqsToMPI,&merge);CHKERRQ(ierr); 286 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 287 merge->rowmap->n = pn; 288 merge->rowmap->bs = 1; 289 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 290 owners = merge->rowmap->range; 291 292 /* determine the number of messages to send, their lengths */ 293 ierr = PetscMalloc(size*sizeof(PetscMPIInt),&len_si);CHKERRQ(ierr); 294 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 295 ierr = PetscMalloc(size*sizeof(PetscMPIInt),&merge->len_s);CHKERRQ(ierr); 296 len_s = merge->len_s; 297 merge->nsend = 0; 298 299 ierr = PetscMalloc((size+2)*sizeof(PetscInt),&owners_co);CHKERRQ(ierr); 300 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 301 302 proc = 0; 303 for (i=0; i<pon; i++){ 304 while (prmap[i] >= owners[proc+1]) proc++; 305 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 306 len_s[proc] += coi[i+1] - coi[i]; 307 } 308 309 len = 0; /* max length of buf_si[] */ 310 owners_co[0] = 0; 311 for (proc=0; proc<size; proc++){ 312 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 313 if (len_si[proc]){ 314 merge->nsend++; 315 len_si[proc] = 2*(len_si[proc] + 1); 316 len += len_si[proc]; 317 } 318 } 319 320 /* determine the number and length of messages to receive for coi and coj */ 321 ierr = PetscGatherNumberOfMessages(comm,PETSC_NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 322 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 323 324 /* post the Irecv and Isend of coj */ 325 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 326 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 327 ierr = PetscMalloc((merge->nsend+1)*sizeof(MPI_Request),&swaits);CHKERRQ(ierr); 328 for (proc=0, k=0; proc<size; proc++){ 329 if (!len_s[proc]) continue; 330 i = owners_co[proc]; 331 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 332 k++; 333 } 334 335 /* receives and sends of coj are complete */ 336 ierr = PetscMalloc(size*sizeof(MPI_Status),&sstatus);CHKERRQ(ierr); 337 for (i=0; i<merge->nrecv; i++){ 338 PetscMPIInt icompleted; 339 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 340 } 341 ierr = PetscFree(rwaits);CHKERRQ(ierr); 342 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 343 344 /* send and recv coi */ 345 /*-------------------*/ 346 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 347 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 348 ierr = PetscMalloc((len+1)*sizeof(PetscInt),&buf_s);CHKERRQ(ierr); 349 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 350 for (proc=0,k=0; proc<size; proc++){ 351 if (!len_s[proc]) continue; 352 /* form outgoing message for i-structure: 353 buf_si[0]: nrows to be sent 354 [1:nrows]: row index (global) 355 [nrows+1:2*nrows+1]: i-structure index 356 */ 357 /*-------------------------------------------*/ 358 nrows = len_si[proc]/2 - 1; 359 buf_si_i = buf_si + nrows+1; 360 buf_si[0] = nrows; 361 buf_si_i[0] = 0; 362 nrows = 0; 363 for (i=owners_co[proc]; i<owners_co[proc+1]; i++){ 364 nzi = coi[i+1] - coi[i]; 365 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 366 buf_si[nrows+1] =prmap[i] -owners[proc]; /* local row index */ 367 nrows++; 368 } 369 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 370 k++; 371 buf_si += len_si[proc]; 372 } 373 i = merge->nrecv; 374 while (i--) { 375 PetscMPIInt icompleted; 376 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 377 } 378 ierr = PetscFree(rwaits);CHKERRQ(ierr); 379 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 380 /* 381 ierr = PetscInfo2(A,"nsend: %d, nrecv: %d\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 382 for (i=0; i<merge->nrecv; i++){ 383 ierr = PetscInfo3(A,"recv len_ri=%d, len_rj=%d from [%d]\n",len_ri[i],merge->len_r[i],merge->id_r[i]);CHKERRQ(ierr); 384 } 385 */ 386 ierr = PetscFree(len_si);CHKERRQ(ierr); 387 ierr = PetscFree(len_ri);CHKERRQ(ierr); 388 ierr = PetscFree(swaits);CHKERRQ(ierr); 389 ierr = PetscFree(sstatus);CHKERRQ(ierr); 390 ierr = PetscFree(buf_s);CHKERRQ(ierr); 391 392 #if defined(DEBUG_MATPTAP) 393 ierr = MPI_Barrier(comm);CHKERRQ(ierr); 394 if (!rank) ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] Co is done\n",rank); 395 #endif 396 397 /* compute the local portion of C (mpi mat) */ 398 /*------------------------------------------*/ 399 ierr = MatGetSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); 400 401 /* allocate bi array and free space for accumulating nonzero column info */ 402 ierr = PetscMalloc((pn+1)*sizeof(PetscInt),&bi);CHKERRQ(ierr); 403 bi[0] = 0; 404 405 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 406 nnz = fill*(pi_loc[pm] + api[am]); 407 ierr = PetscFreeSpaceGet(nnz,&free_space); 408 current_space = free_space; 409 410 ierr = PetscMalloc3(merge->nrecv,PetscInt**,&buf_ri_k,merge->nrecv,PetscInt*,&nextrow,merge->nrecv,PetscInt*,&nextci);CHKERRQ(ierr); 411 for (k=0; k<merge->nrecv; k++){ 412 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 413 nrows = *buf_ri_k[k]; 414 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 415 nextci[k] = buf_ri_k[k] + (nrows + 1);/* poins to the next i-structure of k-th recved i-structure */ 416 } 417 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 418 rmax = 0; 419 for (i=0; i<pn; i++) { 420 /* add pdt[i,:]*AP into lnk */ 421 nnz = 0; 422 pnz = pdti[i+1] - pdti[i]; 423 ptJ = pdtj + pdti[i]; 424 for (j=0; j<pnz; j++){ 425 row = ptJ[j]; /* row of AP == col of Pt */ 426 apnz = api[row+1] - api[row]; 427 Jptr = apj + api[row]; 428 /* add non-zero cols of AP into the sorted linked list lnk */ 429 ierr = PetscLLAddSorted(apnz,Jptr,pN,nlnk,lnk,lnkbt);CHKERRQ(ierr); 430 nnz += nlnk; 431 } 432 /* add received col data into lnk */ 433 for (k=0; k<merge->nrecv; k++){ /* k-th received message */ 434 if (i == *nextrow[k]) { /* i-th row */ 435 nzi = *(nextci[k]+1) - *nextci[k]; 436 Jptr = buf_rj[k] + *nextci[k]; 437 ierr = PetscLLAddSorted(nzi,Jptr,pN,nlnk,lnk,lnkbt);CHKERRQ(ierr); 438 nnz += nlnk; 439 nextrow[k]++; nextci[k]++; 440 } 441 } 442 443 /* if free space is not available, make more free space */ 444 if (current_space->local_remaining<nnz) { 445 ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 446 nspacedouble++; 447 } 448 /* copy data into free space, then initialize lnk */ 449 ierr = PetscLLClean(pN,pN,nnz,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 450 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 451 current_space->array += nnz; 452 current_space->local_used += nnz; 453 current_space->local_remaining -= nnz; 454 bi[i+1] = bi[i] + nnz; 455 if (nnz > rmax) rmax = nnz; 456 } 457 ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); 458 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 459 460 ierr = PetscMalloc((bi[pn]+1)*sizeof(PetscInt),&bj);CHKERRQ(ierr); 461 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 462 afill_tmp = (PetscReal)bi[pn]/(pi_loc[pm] + api[am]+1); 463 if (afill_tmp > afill) afill = afill_tmp; 464 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 465 466 /* create symbolic parallel matrix Cmpi - why cannot be assembled in Numeric part - check runex55_SA ? */ 467 /*------------------------------------------------------------------------------------------------------*/ 468 ierr = PetscMalloc((rmax+1)*sizeof(PetscScalar),&vals);CHKERRQ(ierr); 469 ierr = PetscMemzero(vals,rmax*sizeof(PetscScalar));CHKERRQ(ierr); 470 471 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 472 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 473 ierr = MatSetBlockSizes(Cmpi,P->cmap->bs,P->cmap->bs);CHKERRQ(ierr); 474 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 475 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 476 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 477 478 for (i=0; i<pn; i++){ 479 row = i + rstart; 480 nnz = bi[i+1] - bi[i]; 481 Jptr = bj + bi[i]; 482 ierr = MatSetValues(Cmpi,1,&row,nnz,Jptr,vals,INSERT_VALUES);CHKERRQ(ierr); 483 } 484 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 485 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 486 ierr = PetscFree(vals);CHKERRQ(ierr); 487 488 merge->bi = bi; 489 merge->bj = bj; 490 merge->coi = coi; 491 merge->coj = coj; 492 merge->buf_ri = buf_ri; 493 merge->buf_rj = buf_rj; 494 merge->owners_co = owners_co; 495 merge->destroy = Cmpi->ops->destroy; 496 merge->duplicate = Cmpi->ops->duplicate; 497 498 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 499 /* Cmpi->assembled = PETSC_FALSE; */ 500 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 501 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 502 503 /* attach the supporting struct to Cmpi for reuse */ 504 c = (Mat_MPIAIJ*)Cmpi->data; 505 c->ptap = ptap; 506 ptap->api = api; 507 ptap->apj = apj; 508 ptap->merge = merge; 509 ptap->rmax = ap_rmax; 510 511 *C = Cmpi; 512 #if defined(PETSC_USE_INFO) 513 if (bi[pn] != 0) { 514 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %G needed %G.\n",nspacedouble,fill,afill);CHKERRQ(ierr); 515 ierr = PetscInfo1(Cmpi,"Use MatPtAP(A,P,MatReuse,%G,&C) for best performance.\n",afill);CHKERRQ(ierr); 516 } else { 517 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 518 } 519 #endif 520 PetscFunctionReturn(0); 521 } 522 523 #undef __FUNCT__ 524 #define __FUNCT__ "MatPtAPNumeric_MPIAIJ_MPIAIJ" 525 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 526 { 527 PetscErrorCode ierr; 528 Mat_Merge_SeqsToMPI *merge; 529 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 530 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 531 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 532 Mat_SeqAIJ *p_loc,*p_oth; 533 Mat_PtAPMPI *ptap; 534 PetscInt *adi=ad->i,*aoi=ao->i,*adj,*aoj,*apJ,nextp; 535 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pJ,*pj; 536 PetscInt i,j,k,anz,pnz,apnz,nextap,row,*cj; 537 MatScalar *ada,*aoa,*apa,*pa,*ca,*pa_loc,*pa_oth,valtmp; 538 PetscInt am=A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 539 MPI_Comm comm=((PetscObject)C)->comm; 540 PetscMPIInt size,rank,taga,*len_s; 541 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 542 PetscInt **buf_ri,**buf_rj; 543 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 544 MPI_Request *s_waits,*r_waits; 545 MPI_Status *status; 546 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 547 PetscInt *api,*apj,*coi,*coj; 548 PetscInt *poJ=po->j,*pdJ=pd->j,pcstart=P->cmap->rstart,pcend=P->cmap->rend; 549 PetscInt sparse_axpy; 550 551 PetscFunctionBegin; 552 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 553 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 554 555 ptap = c->ptap; 556 if (!ptap) SETERRQ(((PetscObject)C)->comm,PETSC_ERR_ARG_INCOMP,"MatPtAP() has not been called to create matrix C yet, cannot use MAT_REUSE_MATRIX"); 557 merge = ptap->merge; 558 559 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 560 /*--------------------------------------------------*/ 561 if (ptap->reuse == MAT_INITIAL_MATRIX){ 562 ptap->reuse = MAT_REUSE_MATRIX; 563 } else { /* update numerical values of P_oth and P_loc */ 564 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 565 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 566 } 567 568 /* 2) compute numeric C_seq = P_loc^T*A_loc*P - dominating part */ 569 /*--------------------------------------------------------------*/ 570 /* get data from symbolic products */ 571 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 572 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 573 pi_loc=p_loc->i; pj_loc=p_loc->j; pJ=pj_loc; pa_loc=p_loc->a; 574 pi_oth=p_oth->i; pj_oth=p_oth->j; pa_oth=p_oth->a; 575 576 coi = merge->coi; coj = merge->coj; 577 ierr = PetscMalloc((coi[pon]+1)*sizeof(MatScalar),&coa);CHKERRQ(ierr); 578 ierr = PetscMemzero(coa,coi[pon]*sizeof(MatScalar));CHKERRQ(ierr); 579 580 bi = merge->bi; bj = merge->bj; 581 owners = merge->rowmap->range; 582 ierr = PetscMalloc((bi[cm]+1)*sizeof(MatScalar),&ba);CHKERRQ(ierr); 583 ierr = PetscMemzero(ba,bi[cm]*sizeof(MatScalar));CHKERRQ(ierr); 584 585 api = ptap->api; apj = ptap->apj; 586 /* flag 'sparse_axpy' determines which implementations to be used: 587 0: do dense axpy in MatPtAPNumeric() - fastest, but requires storage of a dense array apa; (default) 588 1: do one sparse axpy - uses same memory as sparse_axpy=0 and might execute less flops 589 (apnz vs. cnz in the outerproduct), slower than case '0' when cnz is not too large than apnz; 590 2: do two sparse axpy in MatPtAPNumeric() - slowest, uses a sparse array apa */ 591 /* set default sparse_axpy */ 592 sparse_axpy = 0; 593 ierr = PetscOptionsGetInt(PETSC_NULL,"-matptap_sparseaxpy",&sparse_axpy,PETSC_NULL);CHKERRQ(ierr); 594 if (sparse_axpy == 0){ /* Do not perform sparse axpy */ 595 /*--------------------------------------------------*/ 596 /* malloc apa to store dense row A[i,:]*P */ 597 ierr = PetscMalloc((P->cmap->N)*sizeof(PetscScalar),&apa);CHKERRQ(ierr); 598 ierr = PetscMemzero(apa,P->cmap->N*sizeof(PetscScalar));CHKERRQ(ierr); 599 600 for (i=0; i<am; i++) { 601 /* 2-a) form i-th sparse row of A_loc*P = Ad*P_loc + Ao*P_oth */ 602 /*------------------------------------------------------------*/ 603 apJ = apj + api[i]; 604 605 /* diagonal portion of A */ 606 anz = adi[i+1] - adi[i]; 607 adj = ad->j + adi[i]; 608 ada = ad->a + adi[i]; 609 for (j=0; j<anz; j++) { 610 row = adj[j]; 611 pnz = pi_loc[row+1] - pi_loc[row]; 612 pj = pj_loc + pi_loc[row]; 613 pa = pa_loc + pi_loc[row]; 614 615 /* perform dense axpy */ 616 valtmp = ada[j]; 617 for (k=0; k<pnz; k++){ 618 apa[pj[k]] += valtmp*pa[k]; 619 } 620 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 621 } 622 623 /* off-diagonal portion of A */ 624 anz = aoi[i+1] - aoi[i]; 625 aoj = ao->j + aoi[i]; 626 aoa = ao->a + aoi[i]; 627 for (j=0; j<anz; j++) { 628 row = aoj[j]; 629 pnz = pi_oth[row+1] - pi_oth[row]; 630 pj = pj_oth + pi_oth[row]; 631 pa = pa_oth + pi_oth[row]; 632 633 /* perform dense axpy */ 634 valtmp = aoa[j]; 635 for (k=0; k<pnz; k++){ 636 apa[pj[k]] += valtmp*pa[k]; 637 } 638 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 639 } 640 641 /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */ 642 /*--------------------------------------------------------------*/ 643 apnz = api[i+1] - api[i]; 644 /* put the value into Co=(p->B)^T*AP (off-diagonal part, send to others) */ 645 pnz = po->i[i+1] - po->i[i]; 646 poJ = po->j + po->i[i]; 647 pA = po->a + po->i[i]; 648 for (j=0; j<pnz; j++){ 649 row = poJ[j]; 650 cnz = coi[row+1] - coi[row]; 651 cj = coj + coi[row]; 652 ca = coa + coi[row]; 653 /* perform dense axpy */ 654 valtmp = pA[j]; 655 for (k=0; k<cnz; k++) { 656 ca[k] += valtmp*apa[cj[k]]; 657 } 658 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 659 } 660 661 /* put the value into Cd (diagonal part) */ 662 pnz = pd->i[i+1] - pd->i[i]; 663 pdJ = pd->j + pd->i[i]; 664 pA = pd->a + pd->i[i]; 665 for (j=0; j<pnz; j++){ 666 row = pdJ[j]; 667 cnz = bi[row+1] - bi[row]; 668 cj = bj + bi[row]; 669 ca = ba + bi[row]; 670 /* perform dense axpy */ 671 valtmp = pA[j]; 672 for (k=0; k<cnz; k++) { 673 ca[k] += valtmp*apa[cj[k]]; 674 } 675 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 676 } 677 678 /* zero the current row of A*P */ 679 for (k=0; k<apnz; k++) apa[apJ[k]] = 0.0; 680 } 681 } else if (sparse_axpy == 1){ /* Perform one sparse axpy */ 682 /*------------------------------------------------------*/ 683 /* malloc apa to store dense row A[i,:]*P */ 684 ierr = PetscMalloc((P->cmap->N)*sizeof(PetscScalar),&apa);CHKERRQ(ierr); 685 ierr = PetscMemzero(apa,P->cmap->N*sizeof(PetscScalar));CHKERRQ(ierr); 686 687 for (i=0; i<am; i++) { 688 /* 2-a) form i-th sparse row of A_loc*P = Ad*P_loc + Ao*P_oth */ 689 /*------------------------------------------------------------*/ 690 apJ = apj + api[i]; 691 692 /* diagonal portion of A */ 693 anz = adi[i+1] - adi[i]; 694 adj = ad->j + adi[i]; 695 ada = ad->a + adi[i]; 696 for (j=0; j<anz; j++) { 697 row = adj[j]; 698 pnz = pi_loc[row+1] - pi_loc[row]; 699 pj = pj_loc + pi_loc[row]; 700 pa = pa_loc + pi_loc[row]; 701 702 /* perform dense axpy */ 703 valtmp = ada[j]; 704 for (k=0; k<pnz; k++){ 705 apa[pj[k]] += valtmp*pa[k]; 706 } 707 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 708 } 709 710 /* off-diagonal portion of A */ 711 anz = aoi[i+1] - aoi[i]; 712 aoj = ao->j + aoi[i]; 713 aoa = ao->a + aoi[i]; 714 for (j=0; j<anz; j++) { 715 row = aoj[j]; 716 pnz = pi_oth[row+1] - pi_oth[row]; 717 pj = pj_oth + pi_oth[row]; 718 pa = pa_oth + pi_oth[row]; 719 720 /* perform dense axpy */ 721 valtmp = aoa[j]; 722 for (k=0; k<pnz; k++){ 723 apa[pj[k]] += valtmp*pa[k]; 724 } 725 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 726 } 727 728 /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */ 729 /*--------------------------------------------------------------*/ 730 apnz = api[i+1] - api[i]; 731 /* put the value into Co=(p->B)^T*AP (off-diagonal part, send to others) */ 732 pnz = po->i[i+1] - po->i[i]; 733 poJ = po->j + po->i[i]; 734 pA = po->a + po->i[i]; 735 for (j=0; j<pnz; j++){ 736 row = poJ[j]; 737 cj = coj + coi[row]; 738 ca = coa + coi[row]; 739 valtmp = pA[j]; 740 /* perform sparse axpy */ 741 nextap = 0; 742 for (k=0; nextap<apnz; k++) { 743 if (cj[k]==apJ[nextap]) { /* global column index */ 744 ca[k] += valtmp*apa[cj[k]]; nextap++; 745 } 746 } 747 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 748 } 749 750 /* put the value into Cd (diagonal part) */ 751 pnz = pd->i[i+1] - pd->i[i]; 752 pdJ = pd->j + pd->i[i]; 753 pA = pd->a + pd->i[i]; 754 for (j=0; j<pnz; j++){ 755 row = pdJ[j]; 756 cj = bj + bi[row]; 757 ca = ba + bi[row]; 758 valtmp = pA[j]; 759 /* perform sparse axpy */ 760 nextap = 0; 761 for (k=0; nextap<apnz; k++) { 762 if (cj[k]==apJ[nextap]) { /* global column index */ 763 ca[k] += valtmp*apa[cj[k]]; 764 nextap++; 765 } 766 } 767 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 768 } 769 770 /* zero the current row of A*P */ 771 for (k=0; k<apnz; k++) apa[apJ[k]] = 0.0; 772 } 773 } else if (sparse_axpy == 2){/* Perform two sparse axpy */ 774 /*----------------------------------------------------*/ 775 /* malloc apa to store sparse row A[i,:]*P */ 776 ierr = PetscMalloc((ptap->rmax+1)*sizeof(MatScalar),&apa);CHKERRQ(ierr); 777 ierr = PetscMemzero(apa,ptap->rmax*sizeof(MatScalar));CHKERRQ(ierr); 778 779 pA=pa_loc; 780 for (i=0; i<am; i++) { 781 /* form i-th sparse row of A*P */ 782 apnz = api[i+1] - api[i]; 783 apJ = apj + api[i]; 784 /* diagonal portion of A */ 785 anz = adi[i+1] - adi[i]; 786 adj = ad->j + adi[i]; 787 ada = ad->a + adi[i]; 788 for (j=0; j<anz; j++) { 789 row = adj[j]; 790 pnz = pi_loc[row+1] - pi_loc[row]; 791 pj = pj_loc + pi_loc[row]; 792 pa = pa_loc + pi_loc[row]; 793 valtmp = ada[j]; 794 nextp = 0; 795 for (k=0; nextp<pnz; k++) { 796 if (apJ[k] == pj[nextp]) { /* col of AP == col of P */ 797 apa[k] += valtmp*pa[nextp++]; 798 } 799 } 800 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 801 } 802 /* off-diagonal portion of A */ 803 anz = aoi[i+1] - aoi[i]; 804 aoj = ao->j + aoi[i]; 805 aoa = ao->a + aoi[i]; 806 for (j=0; j<anz; j++) { 807 row = aoj[j]; 808 pnz = pi_oth[row+1] - pi_oth[row]; 809 pj = pj_oth + pi_oth[row]; 810 pa = pa_oth + pi_oth[row]; 811 valtmp = aoa[j]; 812 nextp = 0; 813 for (k=0; nextp<pnz; k++) { 814 if (apJ[k] == pj[nextp]) { /* col of AP == col of P */ 815 apa[k] += valtmp*pa[nextp++]; 816 } 817 } 818 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 819 } 820 821 /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */ 822 /*--------------------------------------------------------------*/ 823 pnz = pi_loc[i+1] - pi_loc[i]; 824 pJ = pj_loc + pi_loc[i]; 825 for (j=0; j<pnz; j++) { 826 nextap = 0; 827 row = pJ[j]; /* global index */ 828 if (row < pcstart || row >=pcend) { /* put the value into Co */ 829 row = *poJ; 830 cj = coj + coi[row]; 831 ca = coa + coi[row]; poJ++; 832 } else { /* put the value into Cd */ 833 row = *pdJ; 834 cj = bj + bi[row]; 835 ca = ba + bi[row]; pdJ++; 836 } 837 valtmp = pA[j]; 838 for (k=0; nextap<apnz; k++) { 839 if (cj[k]==apJ[nextap]) ca[k] += valtmp*apa[nextap++]; 840 } 841 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 842 } 843 pA += pnz; 844 /* zero the current row info for A*P */ 845 ierr = PetscMemzero(apa,apnz*sizeof(MatScalar));CHKERRQ(ierr); 846 } 847 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"sparse_axpy only takes values 0, 1 and 2"); 848 ierr = PetscFree(apa);CHKERRQ(ierr); 849 850 /* 3) send and recv matrix values coa */ 851 /*------------------------------------*/ 852 buf_ri = merge->buf_ri; 853 buf_rj = merge->buf_rj; 854 len_s = merge->len_s; 855 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 856 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 857 858 ierr = PetscMalloc2(merge->nsend+1,MPI_Request,&s_waits,size,MPI_Status,&status);CHKERRQ(ierr); 859 for (proc=0,k=0; proc<size; proc++){ 860 if (!len_s[proc]) continue; 861 i = merge->owners_co[proc]; 862 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 863 k++; 864 } 865 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 866 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 867 868 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 869 ierr = PetscFree(r_waits);CHKERRQ(ierr); 870 ierr = PetscFree(coa);CHKERRQ(ierr); 871 872 /* 4) insert local Cseq and received values into Cmpi */ 873 /*------------------------------------------------------*/ 874 ierr = PetscMalloc3(merge->nrecv,PetscInt**,&buf_ri_k,merge->nrecv,PetscInt*,&nextrow,merge->nrecv,PetscInt*,&nextci);CHKERRQ(ierr); 875 for (k=0; k<merge->nrecv; k++){ 876 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 877 nrows = *(buf_ri_k[k]); 878 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 879 nextci[k] = buf_ri_k[k] + (nrows + 1);/* poins to the next i-structure of k-th recved i-structure */ 880 } 881 882 for (i=0; i<cm; i++) { 883 row = owners[rank] + i; /* global row index of C_seq */ 884 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 885 ba_i = ba + bi[i]; 886 bnz = bi[i+1] - bi[i]; 887 /* add received vals into ba */ 888 for (k=0; k<merge->nrecv; k++){ /* k-th received message */ 889 /* i-th row */ 890 if (i == *nextrow[k]) { 891 cnz = *(nextci[k]+1) - *nextci[k]; 892 cj = buf_rj[k] + *(nextci[k]); 893 ca = abuf_r[k] + *(nextci[k]); 894 nextcj = 0; 895 for (j=0; nextcj<cnz; j++){ 896 if (bj_i[j] == cj[nextcj]){ /* bcol == ccol */ 897 ba_i[j] += ca[nextcj++]; 898 } 899 } 900 nextrow[k]++; nextci[k]++; 901 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 902 } 903 } 904 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 905 } 906 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 907 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 908 909 ierr = PetscFree(ba);CHKERRQ(ierr); 910 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 911 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 912 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 913 PetscFunctionReturn(0); 914 } 915