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 PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A) 17 { 18 PetscErrorCode ierr; 19 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 20 Mat_PtAPMPI *ptap=a->ptap; 21 22 PetscFunctionBegin; 23 if (ptap) { 24 Mat_Merge_SeqsToMPI *merge=ptap->merge; 25 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 26 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 27 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 28 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 29 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */ 30 ierr = MatDestroy(&ptap->Rd);CHKERRQ(ierr); 31 ierr = MatDestroy(&ptap->Ro);CHKERRQ(ierr); 32 if (ptap->AP_loc) { /* used by alg_rap */ 33 Mat_SeqAIJ *ap = (Mat_SeqAIJ*)(ptap->AP_loc)->data; 34 ierr = PetscFree(ap->i);CHKERRQ(ierr); 35 ierr = PetscFree2(ap->j,ap->a);CHKERRQ(ierr); 36 ierr = MatDestroy(&ptap->AP_loc);CHKERRQ(ierr); 37 } else { /* used by alg_ptap */ 38 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 39 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 40 } 41 ierr = MatDestroy(&ptap->C_loc);CHKERRQ(ierr); 42 ierr = MatDestroy(&ptap->C_oth);CHKERRQ(ierr); 43 if (ptap->apa) {ierr = PetscFree(ptap->apa);CHKERRQ(ierr);} 44 45 if (merge) { /* used by alg_ptap */ 46 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 47 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 48 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 49 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 50 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 51 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 52 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 53 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 54 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 55 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 56 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 57 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 58 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 59 ierr = PetscFree(ptap->merge);CHKERRQ(ierr); 60 } 61 62 ierr = ptap->destroy(A);CHKERRQ(ierr); 63 ierr = PetscFree(ptap);CHKERRQ(ierr); 64 } 65 PetscFunctionReturn(0); 66 } 67 68 PetscErrorCode MatDuplicate_MPIAIJ_MatPtAP(Mat A, MatDuplicateOption op, Mat *M) 69 { 70 PetscErrorCode ierr; 71 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 72 Mat_PtAPMPI *ptap = a->ptap; 73 74 PetscFunctionBegin; 75 ierr = (*ptap->duplicate)(A,op,M);CHKERRQ(ierr); 76 (*M)->ops->destroy = ptap->destroy; 77 (*M)->ops->duplicate = ptap->duplicate; 78 PetscFunctionReturn(0); 79 } 80 81 PETSC_INTERN PetscErrorCode MatPtAP_MPIAIJ_MPIAIJ(Mat A,Mat P,MatReuse scall,PetscReal fill,Mat *C) 82 { 83 PetscErrorCode ierr; 84 PetscBool rap=PETSC_TRUE; /* do R=P^T locally, then C=R*A*P */ 85 MPI_Comm comm; 86 87 PetscFunctionBegin; 88 /* check if matrix local sizes are compatible */ 89 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 90 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) 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); 91 if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend) 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); 92 93 ierr = PetscOptionsGetBool(NULL,NULL,"-matrap",&rap,NULL);CHKERRQ(ierr); 94 if (scall == MAT_INITIAL_MATRIX) { 95 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 96 if (rap) { /* do R=P^T locally, then C=R*A*P */ 97 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);CHKERRQ(ierr); 98 } else { /* do P^T*A*P */ 99 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_ptap(A,P,fill,C);CHKERRQ(ierr); 100 } 101 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 102 } 103 ierr = PetscLogEventBegin(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 104 ierr = (*(*C)->ops->ptapnumeric)(A,P,*C);CHKERRQ(ierr); 105 ierr = PetscLogEventEnd(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 106 PetscFunctionReturn(0); 107 } 108 109 #if defined(PETSC_HAVE_HYPRE) 110 PETSC_INTERN PetscErrorCode MatPtAPSymbolic_AIJ_AIJ_wHYPRE(Mat,Mat,PetscReal,Mat*); 111 #endif 112 113 #undef __FUNCT__ 114 #define __FUNCT__ "MatPtAPSymbolic_MPIAIJ_MPIAIJ" 115 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 116 { 117 PetscErrorCode ierr; 118 Mat_PtAPMPI *ptap; 119 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 120 MPI_Comm comm; 121 PetscMPIInt size,rank; 122 Mat Cmpi; 123 PetscFreeSpaceList free_space=NULL,current_space=NULL; 124 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 125 PetscInt *lnk,i,k,pnz,row,nsend; 126 PetscBT lnkbt; 127 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 128 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 129 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 130 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 131 MPI_Request *swaits,*rwaits; 132 MPI_Status *sstatus,rstatus; 133 PetscLayout rowmap; 134 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 135 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 136 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 137 Mat_SeqAIJ *p_loc,*p_oth,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*c_loc,*c_oth; 138 PetscScalar *apv; 139 PetscTable ta; 140 #if defined(PETSC_HAVE_HYPRE) 141 const char *algTypes[3] = {"scalable","nonscalable","hypre"}; 142 PetscInt nalg = 3; 143 #else 144 const char *algTypes[2] = {"scalable","nonscalable"}; 145 PetscInt nalg = 2; 146 #endif 147 PetscInt alg = 1; /* set default algorithm */ 148 #if defined(PETSC_USE_INFO) 149 PetscReal apfill; 150 #endif 151 #if defined(PTAP_PROFILE) 152 PetscLogDouble t0,t1,t11,t12,t2,t3,t4; 153 #endif 154 155 PetscFunctionBegin; 156 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 157 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 158 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 159 160 /* create symbolic parallel matrix Cmpi */ 161 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 162 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 163 164 ierr = PetscObjectOptionsBegin((PetscObject)A);CHKERRQ(ierr); 165 ierr = PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[1],&alg,NULL);CHKERRQ(ierr); 166 ierr = PetscOptionsEnd();CHKERRQ(ierr); 167 168 if (alg == 1) { 169 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 170 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 171 } else if (alg == 0) { 172 Cmpi->ops->ptapnumeric = 0; /* not done yet */ 173 SETERRQ(comm,PETSC_ERR_ARG_SIZ,"Not done yet"); 174 #if defined(PETSC_HAVE_HYPRE) 175 } else if (alg == 2) { 176 /* Use boomerAMGBuildCoarseOperator */ 177 ierr = MatDestroy(&Cmpi);CHKERRQ(ierr); 178 ierr = MatPtAPSymbolic_AIJ_AIJ_wHYPRE(A,P,fill,C);CHKERRQ(ierr); 179 PetscFunctionReturn(0); 180 #endif 181 } else { 182 SETERRQ1(comm,PETSC_ERR_PLIB,"Unknown algorithm number %D\n",alg); 183 } 184 185 #if defined(PTAP_PROFILE) 186 ierr = PetscTime(&t0);CHKERRQ(ierr); 187 #endif 188 189 /* create struct Mat_PtAPMPI and attached it to C later */ 190 ierr = PetscNew(&ptap);CHKERRQ(ierr); 191 ptap->reuse = MAT_INITIAL_MATRIX; 192 193 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 194 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 195 /* get P_loc by taking all local rows of P */ 196 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 197 198 /* (0) compute Rd = Pd^T, Ro = Po^T */ 199 /* --------------------------------- */ 200 ierr = MatTranspose_SeqAIJ(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 201 ierr = MatTranspose_SeqAIJ(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 202 #if defined(PTAP_PROFILE) 203 ierr = PetscTime(&t11);CHKERRQ(ierr); 204 #endif 205 206 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 207 /* ----------------------------------------------------------------- */ 208 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 209 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 210 211 /* create and initialize a linked list */ 212 ierr = PetscTableCreate(pN,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 213 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 214 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 215 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 216 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 217 218 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 219 220 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 221 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 222 current_space = free_space; 223 nspacedouble = 0; 224 225 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 226 api[0] = 0; 227 for (i=0; i<am; i++) { 228 /* diagonal portion: Ad[i,:]*P */ 229 ai = ad->i; pi = p_loc->i; 230 nzi = ai[i+1] - ai[i]; 231 aj = ad->j + ai[i]; 232 for (j=0; j<nzi; j++) { 233 row = aj[j]; 234 pnz = pi[row+1] - pi[row]; 235 Jptr = p_loc->j + pi[row]; 236 /* add non-zero cols of P into the sorted linked list lnk */ 237 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 238 } 239 /* off-diagonal portion: Ao[i,:]*P */ 240 ai = ao->i; pi = p_oth->i; 241 nzi = ai[i+1] - ai[i]; 242 aj = ao->j + ai[i]; 243 for (j=0; j<nzi; j++) { 244 row = aj[j]; 245 pnz = pi[row+1] - pi[row]; 246 Jptr = p_oth->j + pi[row]; 247 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 248 } 249 apnz = lnk[0]; 250 api[i+1] = api[i] + apnz; 251 if (ap_rmax < apnz) ap_rmax = apnz; 252 253 /* if free space is not available, double the total space in the list */ 254 if (current_space->local_remaining<apnz) { 255 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 256 nspacedouble++; 257 } 258 259 /* Copy data into free space, then initialize lnk */ 260 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 261 262 current_space->array += apnz; 263 current_space->local_used += apnz; 264 current_space->local_remaining -= apnz; 265 } 266 /* Allocate space for apj and apv, initialize apj, and */ 267 /* destroy list of free space and other temporary array(s) */ 268 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 269 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 270 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 271 272 /* Create AP_loc for reuse */ 273 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 274 275 #if defined(PETSC_USE_INFO) 276 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 277 ptap->AP_loc->info.mallocs = nspacedouble; 278 ptap->AP_loc->info.fill_ratio_given = fill; 279 ptap->AP_loc->info.fill_ratio_needed = apfill; 280 281 if (api[am]) { 282 ierr = PetscInfo3(ptap->AP_loc,"AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);CHKERRQ(ierr); 283 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 284 } else { 285 ierr = PetscInfo(ptap->AP_loc,"AP_loc is empty \n");CHKERRQ(ierr); 286 } 287 #endif 288 289 #if defined(PTAP_PROFILE) 290 ierr = PetscTime(&t12);CHKERRQ(ierr); 291 #endif 292 293 /* (2-1) compute symbolic Co = Ro*AP_loc */ 294 /* ------------------------------------ */ 295 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 296 #if defined(PTAP_PROFILE) 297 ierr = PetscTime(&t1);CHKERRQ(ierr); 298 #endif 299 300 /* (3) send coj of C_oth to other processors */ 301 /* ------------------------------------------ */ 302 /* determine row ownership */ 303 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 304 rowmap->n = pn; 305 rowmap->bs = 1; 306 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 307 owners = rowmap->range; 308 309 /* determine the number of messages to send, their lengths */ 310 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 311 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 312 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 313 314 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 315 coi = c_oth->i; coj = c_oth->j; 316 con = ptap->C_oth->rmap->n; 317 proc = 0; 318 for (i=0; i<con; i++) { 319 while (prmap[i] >= owners[proc+1]) proc++; 320 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 321 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 322 } 323 324 len = 0; /* max length of buf_si[], see (4) */ 325 owners_co[0] = 0; 326 nsend = 0; 327 for (proc=0; proc<size; proc++) { 328 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 329 if (len_s[proc]) { 330 nsend++; 331 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 332 len += len_si[proc]; 333 } 334 } 335 336 /* determine the number and length of messages to receive for coi and coj */ 337 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 338 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 339 340 /* post the Irecv and Isend of coj */ 341 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 342 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 343 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 344 for (proc=0, k=0; proc<size; proc++) { 345 if (!len_s[proc]) continue; 346 i = owners_co[proc]; 347 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 348 k++; 349 } 350 351 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 352 /* ---------------------------------------- */ 353 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 354 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 355 356 /* receives coj are complete */ 357 for (i=0; i<nrecv; i++) { 358 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 359 } 360 ierr = PetscFree(rwaits);CHKERRQ(ierr); 361 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 362 363 /* add received column indices into ta to update Crmax */ 364 for (k=0; k<nrecv; k++) {/* k-th received message */ 365 Jptr = buf_rj[k]; 366 for (j=0; j<len_r[k]; j++) { 367 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 368 } 369 } 370 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 371 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 372 373 /* (4) send and recv coi */ 374 /*-----------------------*/ 375 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 376 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 377 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 378 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 379 for (proc=0,k=0; proc<size; proc++) { 380 if (!len_s[proc]) continue; 381 /* form outgoing message for i-structure: 382 buf_si[0]: nrows to be sent 383 [1:nrows]: row index (global) 384 [nrows+1:2*nrows+1]: i-structure index 385 */ 386 /*-------------------------------------------*/ 387 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 388 buf_si_i = buf_si + nrows+1; 389 buf_si[0] = nrows; 390 buf_si_i[0] = 0; 391 nrows = 0; 392 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 393 nzi = coi[i+1] - coi[i]; 394 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 395 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 396 nrows++; 397 } 398 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 399 k++; 400 buf_si += len_si[proc]; 401 } 402 for (i=0; i<nrecv; i++) { 403 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 404 } 405 ierr = PetscFree(rwaits);CHKERRQ(ierr); 406 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 407 408 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 409 ierr = PetscFree(len_ri);CHKERRQ(ierr); 410 ierr = PetscFree(swaits);CHKERRQ(ierr); 411 ierr = PetscFree(buf_s);CHKERRQ(ierr); 412 #if defined(PTAP_PROFILE) 413 ierr = PetscTime(&t2);CHKERRQ(ierr); 414 #endif 415 /* (5) compute the local portion of Cmpi */ 416 /* ------------------------------------------ */ 417 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 418 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 419 current_space = free_space; 420 421 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 422 for (k=0; k<nrecv; k++) { 423 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 424 nrows = *buf_ri_k[k]; 425 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 426 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 427 } 428 429 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 430 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 431 for (i=0; i<pn; i++) { 432 /* add C_loc into Cmpi */ 433 nzi = c_loc->i[i+1] - c_loc->i[i]; 434 Jptr = c_loc->j + c_loc->i[i]; 435 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 436 437 /* add received col data into lnk */ 438 for (k=0; k<nrecv; k++) { /* k-th received message */ 439 if (i == *nextrow[k]) { /* i-th row */ 440 nzi = *(nextci[k]+1) - *nextci[k]; 441 Jptr = buf_rj[k] + *nextci[k]; 442 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 443 nextrow[k]++; nextci[k]++; 444 } 445 } 446 nzi = lnk[0]; 447 448 /* copy data into free space, then initialize lnk */ 449 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 450 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 451 } 452 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 453 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 454 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 455 #if defined(PTAP_PROFILE) 456 ierr = PetscTime(&t3);CHKERRQ(ierr); 457 #endif 458 459 /* local sizes and preallocation */ 460 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 461 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 462 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 463 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 464 465 /* members in merge */ 466 ierr = PetscFree(id_r);CHKERRQ(ierr); 467 ierr = PetscFree(len_r);CHKERRQ(ierr); 468 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 469 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 470 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 471 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 472 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 473 474 /* attach the supporting struct to Cmpi for reuse */ 475 c = (Mat_MPIAIJ*)Cmpi->data; 476 c->ptap = ptap; 477 ptap->duplicate = Cmpi->ops->duplicate; 478 ptap->destroy = Cmpi->ops->destroy; 479 480 if (alg == 1) { 481 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 482 } 483 484 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 485 Cmpi->assembled = PETSC_FALSE; 486 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 487 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 488 *C = Cmpi; 489 490 #if defined(PTAP_PROFILE) 491 ierr = PetscTime(&t4);CHKERRQ(ierr); 492 if (rank == 1) { 493 printf("PtAPSym: %g + %g + %g + %g + %g + %g = %g\n",t11-t0,t1-t11,t12-t11,t2-t2,t3-t2,t4-t3,t4-t0); 494 } 495 #endif 496 PetscFunctionReturn(0); 497 } 498 499 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 500 { 501 PetscErrorCode ierr; 502 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 503 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 504 Mat_SeqAIJ *ap,*p_loc,*p_oth,*c_seq; 505 Mat_PtAPMPI *ptap = c->ptap; 506 Mat AP_loc,C_loc,C_oth; 507 PetscInt i,rstart,rend,cm,ncols,row; 508 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 509 PetscScalar *apa; 510 const PetscInt *cols; 511 const PetscScalar *vals; 512 #if defined(PTAP_PROFILE) 513 PetscMPIInt rank; 514 MPI_Comm comm; 515 PetscLogDouble t0,t1,t2,t3,t4,eR,eAP,eCseq,eCmpi; 516 #endif 517 518 PetscFunctionBegin; 519 ierr = MatZeroEntries(C);CHKERRQ(ierr); 520 521 /* 1) get R = Pd^T,Ro = Po^T */ 522 #if defined(PTAP_PROFILE) 523 ierr = PetscTime(&t0);CHKERRQ(ierr); 524 #endif 525 if (ptap->reuse == MAT_REUSE_MATRIX) { 526 ierr = MatTranspose_SeqAIJ(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 527 ierr = MatTranspose_SeqAIJ(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 528 } 529 #if defined(PTAP_PROFILE) 530 ierr = PetscTime(&t1);CHKERRQ(ierr); 531 eR = t1 - t0; 532 #endif 533 534 /* 2) get AP_loc */ 535 AP_loc = ptap->AP_loc; 536 ap = (Mat_SeqAIJ*)AP_loc->data; 537 538 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 539 /*-----------------------------------------------------*/ 540 if (ptap->reuse == MAT_REUSE_MATRIX) { 541 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 542 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 543 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 544 } 545 546 /* 2-2) compute numeric A_loc*P - dominating part */ 547 /* ---------------------------------------------- */ 548 /* get data from symbolic products */ 549 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 550 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 551 apa = ptap->apa; 552 api = ap->i; 553 apj = ap->j; 554 for (i=0; i<am; i++) { 555 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 556 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 557 apnz = api[i+1] - api[i]; 558 for (j=0; j<apnz; j++) { 559 col = apj[j+api[i]]; 560 ap->a[j+ap->i[i]] = apa[col]; 561 apa[col] = 0.0; 562 } 563 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 564 } 565 #if defined(PTAP_PROFILE) 566 ierr = PetscTime(&t2);CHKERRQ(ierr); 567 eAP = t2 - t1; 568 #endif 569 570 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 571 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 572 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 573 C_loc = ptap->C_loc; 574 C_oth = ptap->C_oth; 575 #if defined(PTAP_PROFILE) 576 ierr = PetscTime(&t3);CHKERRQ(ierr); 577 eCseq = t3 - t2; 578 #endif 579 580 /* add C_loc and Co to to C */ 581 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 582 583 /* C_loc -> C */ 584 cm = C_loc->rmap->N; 585 c_seq = (Mat_SeqAIJ*)C_loc->data; 586 cols = c_seq->j; 587 vals = c_seq->a; 588 for (i=0; i<cm; i++) { 589 ncols = c_seq->i[i+1] - c_seq->i[i]; 590 row = rstart + i; 591 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 592 cols += ncols; vals += ncols; 593 } 594 595 /* Co -> C, off-processor part */ 596 cm = C_oth->rmap->N; 597 c_seq = (Mat_SeqAIJ*)C_oth->data; 598 cols = c_seq->j; 599 vals = c_seq->a; 600 for (i=0; i<cm; i++) { 601 ncols = c_seq->i[i+1] - c_seq->i[i]; 602 row = p->garray[i]; 603 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 604 cols += ncols; vals += ncols; 605 } 606 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 607 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 608 #if defined(PTAP_PROFILE) 609 ierr = PetscTime(&t4);CHKERRQ(ierr); 610 eCmpi = t4 - t3; 611 612 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 613 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 614 if (rank==1) { 615 ierr = PetscPrintf(MPI_COMM_SELF," R %g, AP %g, Cseq %g, Cmpi %g = %g\n", eR,eAP,eCseq,eCmpi,eR+eAP+eCseq+eCmpi);CHKERRQ(ierr); 616 } 617 #endif 618 ptap->reuse = MAT_REUSE_MATRIX; 619 PetscFunctionReturn(0); 620 } 621 622 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_ptap(Mat A,Mat P,PetscReal fill,Mat *C) 623 { 624 PetscErrorCode ierr; 625 Mat Cmpi; 626 Mat_PtAPMPI *ptap; 627 PetscFreeSpaceList free_space=NULL,current_space=NULL; 628 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 629 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 630 Mat_SeqAIJ *p_loc,*p_oth; 631 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pdti,*pdtj,*poti,*potj,*ptJ; 632 PetscInt *adi=ad->i,*aj,*aoi=ao->i,nnz; 633 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 634 PetscInt am=A->rmap->n,pN=P->cmap->N,pm=P->rmap->n,pn=P->cmap->n; 635 PetscBT lnkbt; 636 MPI_Comm comm; 637 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0; 638 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 639 PetscInt len,proc,*dnz,*onz,*owners; 640 PetscInt nzi,*pti,*ptj; 641 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 642 MPI_Request *swaits,*rwaits; 643 MPI_Status *sstatus,rstatus; 644 Mat_Merge_SeqsToMPI *merge; 645 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,pon,nspacedouble=0,j,ap_rmax=0; 646 PetscReal afill=1.0,afill_tmp; 647 648 PetscFunctionBegin; 649 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 650 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 651 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 652 653 /* create struct Mat_PtAPMPI and attached it to C later */ 654 ierr = PetscNew(&ptap);CHKERRQ(ierr); 655 ierr = PetscNew(&merge);CHKERRQ(ierr); 656 ptap->merge = merge; 657 ptap->reuse = MAT_INITIAL_MATRIX; 658 659 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 660 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 661 662 /* get P_loc by taking all local rows of P */ 663 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 664 665 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 666 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 667 pi_loc = p_loc->i; pj_loc = p_loc->j; 668 pi_oth = p_oth->i; pj_oth = p_oth->j; 669 670 /* (1) compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth (api,apj) */ 671 /*--------------------------------------------------------------------------*/ 672 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 673 api[0] = 0; 674 675 /* create and initialize a linked list */ 676 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 677 678 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) -OOM for ex56, np=8k on Intrepid! */ 679 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 680 current_space = free_space; 681 682 for (i=0; i<am; i++) { 683 /* diagonal portion of A */ 684 nzi = adi[i+1] - adi[i]; 685 aj = ad->j + adi[i]; 686 for (j=0; j<nzi; j++) { 687 row = aj[j]; 688 pnz = pi_loc[row+1] - pi_loc[row]; 689 Jptr = pj_loc + pi_loc[row]; 690 /* add non-zero cols of P into the sorted linked list lnk */ 691 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 692 } 693 /* off-diagonal portion of A */ 694 nzi = aoi[i+1] - aoi[i]; 695 aj = ao->j + aoi[i]; 696 for (j=0; j<nzi; j++) { 697 row = aj[j]; 698 pnz = pi_oth[row+1] - pi_oth[row]; 699 Jptr = pj_oth + pi_oth[row]; 700 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 701 } 702 apnz = lnk[0]; 703 api[i+1] = api[i] + apnz; 704 if (ap_rmax < apnz) ap_rmax = apnz; 705 706 /* if free space is not available, double the total space in the list */ 707 if (current_space->local_remaining<apnz) { 708 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 709 nspacedouble++; 710 } 711 712 /* Copy data into free space, then initialize lnk */ 713 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 714 715 current_space->array += apnz; 716 current_space->local_used += apnz; 717 current_space->local_remaining -= apnz; 718 } 719 720 /* Allocate space for apj, initialize apj, and */ 721 /* destroy list of free space and other temporary array(s) */ 722 ierr = PetscMalloc1(api[am]+1,&apj);CHKERRQ(ierr); 723 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 724 afill_tmp = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1); 725 if (afill_tmp > afill) afill = afill_tmp; 726 727 /* (2) determine symbolic Co=(p->B)^T*AP - send to others (coi,coj)*/ 728 /*-----------------------------------------------------------------*/ 729 ierr = MatGetSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); 730 731 /* then, compute symbolic Co = (p->B)^T*AP */ 732 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 733 >= (num of nonzero rows of C_seq) - pn */ 734 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 735 coi[0] = 0; 736 737 /* set initial free space to be fill*(nnz(p->B) + nnz(AP)) */ 738 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],api[am])); 739 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 740 current_space = free_space; 741 742 for (i=0; i<pon; i++) { 743 pnz = poti[i+1] - poti[i]; 744 ptJ = potj + poti[i]; 745 for (j=0; j<pnz; j++) { 746 row = ptJ[j]; /* row of AP == col of Pot */ 747 apnz = api[row+1] - api[row]; 748 Jptr = apj + api[row]; 749 /* add non-zero cols of AP into the sorted linked list lnk */ 750 ierr = PetscLLCondensedAddSorted(apnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 751 } 752 nnz = lnk[0]; 753 754 /* If free space is not available, double the total space in the list */ 755 if (current_space->local_remaining<nnz) { 756 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 757 nspacedouble++; 758 } 759 760 /* Copy data into free space, and zero out denserows */ 761 ierr = PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 762 763 current_space->array += nnz; 764 current_space->local_used += nnz; 765 current_space->local_remaining -= nnz; 766 767 coi[i+1] = coi[i] + nnz; 768 } 769 770 ierr = PetscMalloc1(coi[pon],&coj);CHKERRQ(ierr); 771 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 772 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + api[am]+1); 773 if (afill_tmp > afill) afill = afill_tmp; 774 ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); 775 776 /* (3) send j-array (coj) of Co to other processors */ 777 /*--------------------------------------------------*/ 778 ierr = PetscCalloc1(size,&merge->len_s);CHKERRQ(ierr); 779 len_s = merge->len_s; 780 merge->nsend = 0; 781 782 783 /* determine row ownership */ 784 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 785 merge->rowmap->n = pn; 786 merge->rowmap->bs = 1; 787 788 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 789 owners = merge->rowmap->range; 790 791 /* determine the number of messages to send, their lengths */ 792 ierr = PetscMalloc2(size,&len_si,size,&sstatus);CHKERRQ(ierr); 793 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 794 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 795 796 proc = 0; 797 for (i=0; i<pon; i++) { 798 while (prmap[i] >= owners[proc+1]) proc++; 799 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 800 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 801 } 802 803 len = 0; /* max length of buf_si[], see (4) */ 804 owners_co[0] = 0; 805 for (proc=0; proc<size; proc++) { 806 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 807 if (len_s[proc]) { 808 merge->nsend++; 809 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 810 len += len_si[proc]; 811 } 812 } 813 814 /* determine the number and length of messages to receive for coi and coj */ 815 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 816 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 817 818 /* post the Irecv and Isend of coj */ 819 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 820 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 821 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 822 for (proc=0, k=0; proc<size; proc++) { 823 if (!len_s[proc]) continue; 824 i = owners_co[proc]; 825 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 826 k++; 827 } 828 829 /* receives and sends of coj are complete */ 830 for (i=0; i<merge->nrecv; i++) { 831 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 832 } 833 ierr = PetscFree(rwaits);CHKERRQ(ierr); 834 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 835 836 /* (4) send and recv coi */ 837 /*-----------------------*/ 838 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 839 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 840 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 841 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 842 for (proc=0,k=0; proc<size; proc++) { 843 if (!len_s[proc]) continue; 844 /* form outgoing message for i-structure: 845 buf_si[0]: nrows to be sent 846 [1:nrows]: row index (global) 847 [nrows+1:2*nrows+1]: i-structure index 848 */ 849 /*-------------------------------------------*/ 850 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 851 buf_si_i = buf_si + nrows+1; 852 buf_si[0] = nrows; 853 buf_si_i[0] = 0; 854 nrows = 0; 855 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 856 nzi = coi[i+1] - coi[i]; 857 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 858 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 859 nrows++; 860 } 861 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 862 k++; 863 buf_si += len_si[proc]; 864 } 865 i = merge->nrecv; 866 while (i--) { 867 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 868 } 869 ierr = PetscFree(rwaits);CHKERRQ(ierr); 870 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 871 872 ierr = PetscFree2(len_si,sstatus);CHKERRQ(ierr); 873 ierr = PetscFree(len_ri);CHKERRQ(ierr); 874 ierr = PetscFree(swaits);CHKERRQ(ierr); 875 ierr = PetscFree(buf_s);CHKERRQ(ierr); 876 877 /* (5) compute the local portion of C (mpi mat) */ 878 /*----------------------------------------------*/ 879 ierr = MatGetSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); 880 881 /* allocate pti array and free space for accumulating nonzero column info */ 882 ierr = PetscMalloc1(pn+1,&pti);CHKERRQ(ierr); 883 pti[0] = 0; 884 885 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 886 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pi_loc[pm],api[am])); 887 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 888 current_space = free_space; 889 890 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 891 for (k=0; k<merge->nrecv; k++) { 892 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 893 nrows = *buf_ri_k[k]; 894 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 895 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 896 } 897 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 898 899 for (i=0; i<pn; i++) { 900 /* add pdt[i,:]*AP into lnk */ 901 pnz = pdti[i+1] - pdti[i]; 902 ptJ = pdtj + pdti[i]; 903 for (j=0; j<pnz; j++) { 904 row = ptJ[j]; /* row of AP == col of Pt */ 905 apnz = api[row+1] - api[row]; 906 Jptr = apj + api[row]; 907 /* add non-zero cols of AP into the sorted linked list lnk */ 908 ierr = PetscLLCondensedAddSorted(apnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 909 } 910 911 /* add received col data into lnk */ 912 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 913 if (i == *nextrow[k]) { /* i-th row */ 914 nzi = *(nextci[k]+1) - *nextci[k]; 915 Jptr = buf_rj[k] + *nextci[k]; 916 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 917 nextrow[k]++; nextci[k]++; 918 } 919 } 920 nnz = lnk[0]; 921 922 /* if free space is not available, make more free space */ 923 if (current_space->local_remaining<nnz) { 924 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 925 nspacedouble++; 926 } 927 /* copy data into free space, then initialize lnk */ 928 ierr = PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 929 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 930 931 current_space->array += nnz; 932 current_space->local_used += nnz; 933 current_space->local_remaining -= nnz; 934 935 pti[i+1] = pti[i] + nnz; 936 } 937 ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); 938 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 939 940 ierr = PetscMalloc1(pti[pn]+1,&ptj);CHKERRQ(ierr); 941 ierr = PetscFreeSpaceContiguous(&free_space,ptj);CHKERRQ(ierr); 942 afill_tmp = (PetscReal)pti[pn]/(pi_loc[pm] + api[am]+1); 943 if (afill_tmp > afill) afill = afill_tmp; 944 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 945 946 /* (6) create symbolic parallel matrix Cmpi */ 947 /*------------------------------------------*/ 948 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 949 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 950 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 951 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 952 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 953 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 954 955 merge->bi = pti; /* Cseq->i */ 956 merge->bj = ptj; /* Cseq->j */ 957 merge->coi = coi; /* Co->i */ 958 merge->coj = coj; /* Co->j */ 959 merge->buf_ri = buf_ri; 960 merge->buf_rj = buf_rj; 961 merge->owners_co = owners_co; 962 merge->destroy = Cmpi->ops->destroy; 963 964 /* attach the supporting struct to Cmpi for reuse */ 965 c = (Mat_MPIAIJ*)Cmpi->data; 966 c->ptap = ptap; 967 ptap->api = api; 968 ptap->apj = apj; 969 ptap->duplicate = Cmpi->ops->duplicate; 970 ptap->destroy = Cmpi->ops->destroy; 971 972 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 973 Cmpi->assembled = PETSC_FALSE; 974 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 975 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 976 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_ptap; 977 *C = Cmpi; 978 979 /* flag 'scalable' determines which implementations to be used: 980 0: do dense axpy in MatPtAPNumeric() - fast, but requires storage of a nonscalable dense array apa; 981 1: do sparse axpy in MatPtAPNumeric() - might slow, uses a sparse array apa */ 982 /* set default scalable */ 983 ptap->scalable = PETSC_FALSE; /* PETSC_TRUE; */ 984 985 ierr = PetscOptionsGetBool(((PetscObject)Cmpi)->options,((PetscObject)Cmpi)->prefix,"-matptap_scalable",&ptap->scalable,NULL);CHKERRQ(ierr); 986 if (!ptap->scalable) { /* Do dense axpy */ 987 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 988 } else { 989 ierr = PetscCalloc1(ap_rmax+1,&ptap->apa);CHKERRQ(ierr); 990 } 991 992 #if defined(PETSC_USE_INFO) 993 if (pti[pn] != 0) { 994 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 995 ierr = PetscInfo1(Cmpi,"Use MatPtAP(A,P,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 996 } else { 997 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 998 } 999 #endif 1000 PetscFunctionReturn(0); 1001 } 1002 1003 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_ptap(Mat A,Mat P,Mat C) 1004 { 1005 PetscErrorCode ierr; 1006 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1007 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 1008 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1009 Mat_SeqAIJ *p_loc,*p_oth; 1010 Mat_PtAPMPI *ptap; 1011 Mat_Merge_SeqsToMPI *merge; 1012 PetscInt *adi=ad->i,*aoi=ao->i,*adj,*aoj,*apJ,nextp; 1013 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pJ,*pj; 1014 PetscInt i,j,k,anz,pnz,apnz,nextap,row,*cj; 1015 MatScalar *ada,*aoa,*apa,*pa,*ca,*pa_loc,*pa_oth,valtmp; 1016 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1017 MPI_Comm comm; 1018 PetscMPIInt size,rank,taga,*len_s; 1019 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1020 PetscInt **buf_ri,**buf_rj; 1021 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1022 MPI_Request *s_waits,*r_waits; 1023 MPI_Status *status; 1024 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1025 PetscInt *api,*apj,*coi,*coj; 1026 PetscInt *poJ=po->j,*pdJ=pd->j,pcstart=P->cmap->rstart,pcend=P->cmap->rend; 1027 PetscBool scalable; 1028 #if defined(PTAP_PROFILE) 1029 PetscLogDouble t0,t1,t2,eP,t3,t4,et2_AP=0.0,ePtAP=0.0,t2_0,t2_1,t2_2; 1030 #endif 1031 1032 PetscFunctionBegin; 1033 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1034 #if defined(PTAP_PROFILE) 1035 ierr = PetscTime(&t0);CHKERRQ(ierr); 1036 #endif 1037 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1038 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1039 1040 ptap = c->ptap; 1041 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"); 1042 merge = ptap->merge; 1043 apa = ptap->apa; 1044 scalable = ptap->scalable; 1045 1046 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 1047 /*-----------------------------------------------------*/ 1048 if (ptap->reuse == MAT_INITIAL_MATRIX) { 1049 /* P_oth and P_loc are obtained in MatPtASymbolic(), skip calling MatGetBrowsOfAoCols() and MatMPIAIJGetLocalMat() */ 1050 ptap->reuse = MAT_REUSE_MATRIX; 1051 } else { /* update numerical values of P_oth and P_loc */ 1052 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1053 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1054 } 1055 #if defined(PTAP_PROFILE) 1056 ierr = PetscTime(&t1);CHKERRQ(ierr); 1057 eP = t1-t0; 1058 #endif 1059 /* 1060 printf("[%d] Ad: %d, %d; Ao: %d, %d; P_loc: %d, %d; P_oth %d, %d;\n",rank, 1061 a->A->rmap->N,a->A->cmap->N,a->B->rmap->N,a->B->cmap->N, 1062 ptap->P_loc->rmap->N,ptap->P_loc->cmap->N, 1063 ptap->P_oth->rmap->N,ptap->P_oth->cmap->N); 1064 */ 1065 1066 /* 2) compute numeric C_seq = P_loc^T*A_loc*P - dominating part */ 1067 /*--------------------------------------------------------------*/ 1068 /* get data from symbolic products */ 1069 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1070 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1071 pi_loc=p_loc->i; pj_loc=p_loc->j; pa_loc=p_loc->a; 1072 pi_oth=p_oth->i; pj_oth=p_oth->j; pa_oth=p_oth->a; 1073 1074 coi = merge->coi; coj = merge->coj; 1075 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 1076 1077 bi = merge->bi; bj = merge->bj; 1078 owners = merge->rowmap->range; 1079 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); /* ba: Cseq->a */ 1080 1081 api = ptap->api; apj = ptap->apj; 1082 1083 if (!scalable) { /* Do dense axpy on apa (length of pN, stores A[i,:]*P) - nonscalable, but faster (could take 1/3 scalable time) */ 1084 ierr = PetscInfo(C,"Using non-scalable dense axpy\n");CHKERRQ(ierr); 1085 #if defined(PTAP_PROFILE) 1086 ierr = PetscTime(&t1);CHKERRQ(ierr); 1087 #endif 1088 for (i=0; i<am; i++) { 1089 #if defined(PTAP_PROFILE) 1090 ierr = PetscTime(&t2_0);CHKERRQ(ierr); 1091 #endif 1092 /* 2-a) form i-th sparse row of A_loc*P = Ad*P_loc + Ao*P_oth */ 1093 /*------------------------------------------------------------*/ 1094 apJ = apj + api[i]; 1095 1096 /* diagonal portion of A */ 1097 anz = adi[i+1] - adi[i]; 1098 adj = ad->j + adi[i]; 1099 ada = ad->a + adi[i]; 1100 for (j=0; j<anz; j++) { 1101 row = adj[j]; 1102 pnz = pi_loc[row+1] - pi_loc[row]; 1103 pj = pj_loc + pi_loc[row]; 1104 pa = pa_loc + pi_loc[row]; 1105 1106 /* perform dense axpy */ 1107 valtmp = ada[j]; 1108 for (k=0; k<pnz; k++) { 1109 apa[pj[k]] += valtmp*pa[k]; 1110 } 1111 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 1112 } 1113 1114 /* off-diagonal portion of A */ 1115 anz = aoi[i+1] - aoi[i]; 1116 aoj = ao->j + aoi[i]; 1117 aoa = ao->a + aoi[i]; 1118 for (j=0; j<anz; j++) { 1119 row = aoj[j]; 1120 pnz = pi_oth[row+1] - pi_oth[row]; 1121 pj = pj_oth + pi_oth[row]; 1122 pa = pa_oth + pi_oth[row]; 1123 1124 /* perform dense axpy */ 1125 valtmp = aoa[j]; 1126 for (k=0; k<pnz; k++) { 1127 apa[pj[k]] += valtmp*pa[k]; 1128 } 1129 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 1130 } 1131 #if defined(PTAP_PROFILE) 1132 ierr = PetscTime(&t2_1);CHKERRQ(ierr); 1133 et2_AP += t2_1 - t2_0; 1134 #endif 1135 1136 /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */ 1137 /*--------------------------------------------------------------*/ 1138 apnz = api[i+1] - api[i]; 1139 /* put the value into Co=(p->B)^T*AP (off-diagonal part, send to others) */ 1140 pnz = po->i[i+1] - po->i[i]; 1141 poJ = po->j + po->i[i]; 1142 pA = po->a + po->i[i]; 1143 for (j=0; j<pnz; j++) { 1144 row = poJ[j]; 1145 cnz = coi[row+1] - coi[row]; 1146 cj = coj + coi[row]; 1147 ca = coa + coi[row]; 1148 /* perform dense axpy */ 1149 valtmp = pA[j]; 1150 for (k=0; k<cnz; k++) { 1151 ca[k] += valtmp*apa[cj[k]]; 1152 } 1153 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1154 } 1155 /* put the value into Cd (diagonal part) */ 1156 pnz = pd->i[i+1] - pd->i[i]; 1157 pdJ = pd->j + pd->i[i]; 1158 pA = pd->a + pd->i[i]; 1159 for (j=0; j<pnz; j++) { 1160 row = pdJ[j]; 1161 cnz = bi[row+1] - bi[row]; 1162 cj = bj + bi[row]; 1163 ca = ba + bi[row]; 1164 /* perform dense axpy */ 1165 valtmp = pA[j]; 1166 for (k=0; k<cnz; k++) { 1167 ca[k] += valtmp*apa[cj[k]]; 1168 } 1169 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1170 } 1171 1172 /* zero the current row of A*P */ 1173 for (k=0; k<apnz; k++) apa[apJ[k]] = 0.0; 1174 #if defined(PTAP_PROFILE) 1175 ierr = PetscTime(&t2_2);CHKERRQ(ierr); 1176 ePtAP += t2_2 - t2_1; 1177 #endif 1178 } 1179 } else { /* Do sparse axpy on apa (length of ap_rmax, stores A[i,:]*P) - scalable, but slower */ 1180 ierr = PetscInfo(C,"Using scalable sparse axpy\n");CHKERRQ(ierr); 1181 /*-----------------------------------------------------------------------------------------*/ 1182 pA=pa_loc; 1183 for (i=0; i<am; i++) { 1184 #if defined(PTAP_PROFILE) 1185 ierr = PetscTime(&t2_0);CHKERRQ(ierr); 1186 #endif 1187 /* form i-th sparse row of A*P */ 1188 apnz = api[i+1] - api[i]; 1189 apJ = apj + api[i]; 1190 /* diagonal portion of A */ 1191 anz = adi[i+1] - adi[i]; 1192 adj = ad->j + adi[i]; 1193 ada = ad->a + adi[i]; 1194 for (j=0; j<anz; j++) { 1195 row = adj[j]; 1196 pnz = pi_loc[row+1] - pi_loc[row]; 1197 pj = pj_loc + pi_loc[row]; 1198 pa = pa_loc + pi_loc[row]; 1199 valtmp = ada[j]; 1200 nextp = 0; 1201 for (k=0; nextp<pnz; k++) { 1202 if (apJ[k] == pj[nextp]) { /* col of AP == col of P */ 1203 apa[k] += valtmp*pa[nextp++]; 1204 } 1205 } 1206 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 1207 } 1208 /* off-diagonal portion of A */ 1209 anz = aoi[i+1] - aoi[i]; 1210 aoj = ao->j + aoi[i]; 1211 aoa = ao->a + aoi[i]; 1212 for (j=0; j<anz; j++) { 1213 row = aoj[j]; 1214 pnz = pi_oth[row+1] - pi_oth[row]; 1215 pj = pj_oth + pi_oth[row]; 1216 pa = pa_oth + pi_oth[row]; 1217 valtmp = aoa[j]; 1218 nextp = 0; 1219 for (k=0; nextp<pnz; k++) { 1220 if (apJ[k] == pj[nextp]) { /* col of AP == col of P */ 1221 apa[k] += valtmp*pa[nextp++]; 1222 } 1223 } 1224 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 1225 } 1226 #if defined(PTAP_PROFILE) 1227 ierr = PetscTime(&t2_1);CHKERRQ(ierr); 1228 et2_AP += t2_1 - t2_0; 1229 #endif 1230 1231 /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */ 1232 /*--------------------------------------------------------------*/ 1233 pnz = pi_loc[i+1] - pi_loc[i]; 1234 pJ = pj_loc + pi_loc[i]; 1235 for (j=0; j<pnz; j++) { 1236 nextap = 0; 1237 row = pJ[j]; /* global index */ 1238 if (row < pcstart || row >=pcend) { /* put the value into Co */ 1239 row = *poJ; 1240 cj = coj + coi[row]; 1241 ca = coa + coi[row]; poJ++; 1242 } else { /* put the value into Cd */ 1243 row = *pdJ; 1244 cj = bj + bi[row]; 1245 ca = ba + bi[row]; pdJ++; 1246 } 1247 valtmp = pA[j]; 1248 for (k=0; nextap<apnz; k++) { 1249 if (cj[k]==apJ[nextap]) ca[k] += valtmp*apa[nextap++]; 1250 } 1251 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 1252 } 1253 pA += pnz; 1254 /* zero the current row info for A*P */ 1255 ierr = PetscMemzero(apa,apnz*sizeof(MatScalar));CHKERRQ(ierr); 1256 #if defined(PTAP_PROFILE) 1257 ierr = PetscTime(&t2_2);CHKERRQ(ierr); 1258 ePtAP += t2_2 - t2_1; 1259 #endif 1260 } 1261 } 1262 #if defined(PTAP_PROFILE) 1263 ierr = PetscTime(&t2);CHKERRQ(ierr); 1264 #endif 1265 1266 /* 3) send and recv matrix values coa */ 1267 /*------------------------------------*/ 1268 buf_ri = merge->buf_ri; 1269 buf_rj = merge->buf_rj; 1270 len_s = merge->len_s; 1271 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1272 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1273 1274 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1275 for (proc=0,k=0; proc<size; proc++) { 1276 if (!len_s[proc]) continue; 1277 i = merge->owners_co[proc]; 1278 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1279 k++; 1280 } 1281 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1282 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1283 1284 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1285 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1286 ierr = PetscFree(coa);CHKERRQ(ierr); 1287 #if defined(PTAP_PROFILE) 1288 ierr = PetscTime(&t3);CHKERRQ(ierr); 1289 #endif 1290 1291 /* 4) insert local Cseq and received values into Cmpi */ 1292 /*------------------------------------------------------*/ 1293 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1294 for (k=0; k<merge->nrecv; k++) { 1295 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1296 nrows = *(buf_ri_k[k]); 1297 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1298 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1299 } 1300 1301 for (i=0; i<cm; i++) { 1302 row = owners[rank] + i; /* global row index of C_seq */ 1303 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1304 ba_i = ba + bi[i]; 1305 bnz = bi[i+1] - bi[i]; 1306 /* add received vals into ba */ 1307 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1308 /* i-th row */ 1309 if (i == *nextrow[k]) { 1310 cnz = *(nextci[k]+1) - *nextci[k]; 1311 cj = buf_rj[k] + *(nextci[k]); 1312 ca = abuf_r[k] + *(nextci[k]); 1313 nextcj = 0; 1314 for (j=0; nextcj<cnz; j++) { 1315 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1316 ba_i[j] += ca[nextcj++]; 1317 } 1318 } 1319 nextrow[k]++; nextci[k]++; 1320 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1321 } 1322 } 1323 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1324 } 1325 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1326 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1327 1328 ierr = PetscFree(ba);CHKERRQ(ierr); 1329 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1330 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1331 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1332 #if defined(PTAP_PROFILE) 1333 ierr = PetscTime(&t4);CHKERRQ(ierr); 1334 if (rank==1) { 1335 ierr = PetscPrintf(MPI_COMM_SELF," [%d] PtAPNum %g/P + %g/PtAP( %g/A*P + %g/Pt*AP ) + %g/comm + %g/Cloc = %g\n\n",rank,eP,t2-t1,et2_AP,ePtAP,t3-t2,t4-t3,t4-t0);CHKERRQ(ierr); 1336 } 1337 #endif 1338 PetscFunctionReturn(0); 1339 } 1340