1 2 /* 3 Defines matrix-matrix product routines for pairs of MPIAIJ matrices 4 C = A * B 5 */ 6 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 7 #include <../src/mat/utils/freespace.h> 8 #include <../src/mat/impls/aij/mpi/mpiaij.h> 9 #include <petscbt.h> 10 #include <../src/mat/impls/dense/mpi/mpidense.h> 11 #include <petsc/private/vecimpl.h> 12 #include <petsc/private/vecscatterimpl.h> 13 14 #if defined(PETSC_HAVE_HYPRE) 15 PETSC_INTERN PetscErrorCode MatMatMultSymbolic_AIJ_AIJ_wHYPRE(Mat,Mat,PetscReal,Mat); 16 #endif 17 18 PETSC_INTERN PetscErrorCode MatProductSymbolic_AB_MPIAIJ_MPIAIJ(Mat C) 19 { 20 PetscErrorCode ierr; 21 Mat_Product *product = C->product; 22 Mat A=product->A,B=product->B; 23 MatProductAlgorithm alg=product->alg; 24 PetscReal fill=product->fill; 25 PetscBool flg; 26 27 PetscFunctionBegin; 28 /* scalable */ 29 ierr = PetscStrcmp(alg,"scalable",&flg);CHKERRQ(ierr); 30 if (flg) { 31 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 32 PetscFunctionReturn(0); 33 } 34 35 /* nonscalable */ 36 ierr = PetscStrcmp(alg,"nonscalable",&flg);CHKERRQ(ierr); 37 if (flg) { 38 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(A,B,fill,C);CHKERRQ(ierr); 39 PetscFunctionReturn(0); 40 } 41 42 /* seqmpi */ 43 ierr = PetscStrcmp(alg,"seqmpi",&flg);CHKERRQ(ierr); 44 if (flg) { 45 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI(A,B,fill,C);CHKERRQ(ierr); 46 PetscFunctionReturn(0); 47 } 48 49 #if defined(PETSC_HAVE_HYPRE) 50 ierr = PetscStrcmp(alg,"hypre",&flg);CHKERRQ(ierr); 51 if (flg) { 52 ierr = MatMatMultSymbolic_AIJ_AIJ_wHYPRE(A,B,fill,C);CHKERRQ(ierr); 53 PetscFunctionReturn(0); 54 } 55 #endif 56 SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_SUP,"Mat Product Algorithm is not supported"); 57 } 58 59 PetscErrorCode MatDestroy_MPIAIJ_MatMatMult(void *data) 60 { 61 PetscErrorCode ierr; 62 Mat_APMPI *ptap = (Mat_APMPI*)data; 63 64 PetscFunctionBegin; 65 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 66 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 67 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 68 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 69 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 70 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 71 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 72 ierr = PetscFree(ptap->apa);CHKERRQ(ierr); 73 ierr = PetscFree(ptap);CHKERRQ(ierr); 74 PetscFunctionReturn(0); 75 } 76 77 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,Mat C) 78 { 79 PetscErrorCode ierr; 80 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 81 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 82 Mat_SeqAIJ *cd =(Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 83 PetscScalar *cda=cd->a,*coa=co->a; 84 Mat_SeqAIJ *p_loc,*p_oth; 85 PetscScalar *apa,*ca; 86 PetscInt cm =C->rmap->n; 87 Mat_APMPI *ptap; 88 PetscInt *api,*apj,*apJ,i,k; 89 PetscInt cstart=C->cmap->rstart; 90 PetscInt cdnz,conz,k0,k1; 91 MPI_Comm comm; 92 PetscMPIInt size; 93 94 PetscFunctionBegin; 95 MatCheckProduct(C,3); 96 ptap = (Mat_APMPI*)C->product->data; 97 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 98 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 99 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 100 101 if (!ptap->P_oth && size>1) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"AP cannot be reused. Do not call MatProductClear()"); 102 103 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 104 /*-----------------------------------------------------*/ 105 /* update numerical values of P_oth and P_loc */ 106 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 107 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 108 109 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 110 /*----------------------------------------------------------*/ 111 /* get data from symbolic products */ 112 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 113 p_oth = NULL; 114 if (size >1) { 115 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 116 } 117 118 /* get apa for storing dense row A[i,:]*P */ 119 apa = ptap->apa; 120 121 api = ptap->api; 122 apj = ptap->apj; 123 for (i=0; i<cm; i++) { 124 /* compute apa = A[i,:]*P */ 125 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 126 127 /* set values in C */ 128 apJ = apj + api[i]; 129 cdnz = cd->i[i+1] - cd->i[i]; 130 conz = co->i[i+1] - co->i[i]; 131 132 /* 1st off-diagonal part of C */ 133 ca = coa + co->i[i]; 134 k = 0; 135 for (k0=0; k0<conz; k0++) { 136 if (apJ[k] >= cstart) break; 137 ca[k0] = apa[apJ[k]]; 138 apa[apJ[k++]] = 0.0; 139 } 140 141 /* diagonal part of C */ 142 ca = cda + cd->i[i]; 143 for (k1=0; k1<cdnz; k1++) { 144 ca[k1] = apa[apJ[k]]; 145 apa[apJ[k++]] = 0.0; 146 } 147 148 /* 2nd off-diagonal part of C */ 149 ca = coa + co->i[i]; 150 for (; k0<conz; k0++) { 151 ca[k0] = apa[apJ[k]]; 152 apa[apJ[k++]] = 0.0; 153 } 154 } 155 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 156 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 157 PetscFunctionReturn(0); 158 } 159 160 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,PetscReal fill,Mat C) 161 { 162 PetscErrorCode ierr; 163 MPI_Comm comm; 164 PetscMPIInt size; 165 Mat_APMPI *ptap; 166 PetscFreeSpaceList free_space=NULL,current_space=NULL; 167 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 168 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 169 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 170 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 171 PetscInt *lnk,i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi; 172 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n; 173 PetscBT lnkbt; 174 PetscReal afill; 175 MatType mtype; 176 177 PetscFunctionBegin; 178 MatCheckProduct(C,4); 179 if (C->product->data) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Extra product struct not empty"); 180 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 181 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 182 183 /* create struct Mat_APMPI and attached it to C later */ 184 ierr = PetscNew(&ptap);CHKERRQ(ierr); 185 186 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 187 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 188 189 /* get P_loc by taking all local rows of P */ 190 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 191 192 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 193 pi_loc = p_loc->i; pj_loc = p_loc->j; 194 if (size > 1) { 195 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 196 pi_oth = p_oth->i; pj_oth = p_oth->j; 197 } else { 198 p_oth = NULL; 199 pi_oth = NULL; pj_oth = NULL; 200 } 201 202 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 203 /*-------------------------------------------------------------------*/ 204 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 205 ptap->api = api; 206 api[0] = 0; 207 208 /* create and initialize a linked list */ 209 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 210 211 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 212 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 213 current_space = free_space; 214 215 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 216 for (i=0; i<am; i++) { 217 /* diagonal portion of A */ 218 nzi = adi[i+1] - adi[i]; 219 for (j=0; j<nzi; j++) { 220 row = *adj++; 221 pnz = pi_loc[row+1] - pi_loc[row]; 222 Jptr = pj_loc + pi_loc[row]; 223 /* add non-zero cols of P into the sorted linked list lnk */ 224 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 225 } 226 /* off-diagonal portion of A */ 227 nzi = aoi[i+1] - aoi[i]; 228 for (j=0; j<nzi; j++) { 229 row = *aoj++; 230 pnz = pi_oth[row+1] - pi_oth[row]; 231 Jptr = pj_oth + pi_oth[row]; 232 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 233 } 234 235 apnz = lnk[0]; 236 api[i+1] = api[i] + apnz; 237 238 /* if free space is not available, double the total space in the list */ 239 if (current_space->local_remaining<apnz) { 240 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 241 nspacedouble++; 242 } 243 244 /* Copy data into free space, then initialize lnk */ 245 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 246 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 247 248 current_space->array += apnz; 249 current_space->local_used += apnz; 250 current_space->local_remaining -= apnz; 251 } 252 253 /* Allocate space for apj, initialize apj, and */ 254 /* destroy list of free space and other temporary array(s) */ 255 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 256 apj = ptap->apj; 257 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 258 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 259 260 /* malloc apa to store dense row A[i,:]*P */ 261 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 262 263 /* set and assemble symbolic parallel matrix C */ 264 /*---------------------------------------------*/ 265 ierr = MatSetSizes(C,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 266 ierr = MatSetBlockSizesFromMats(C,A,P);CHKERRQ(ierr); 267 268 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 269 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 270 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 271 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 272 273 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(C, apj, api);CHKERRQ(ierr); 274 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 275 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 276 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 277 278 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 279 C->ops->productnumeric = MatProductNumeric_AB; 280 281 /* attach the supporting struct to C for reuse */ 282 C->product->data = ptap; 283 C->product->destroy = MatDestroy_MPIAIJ_MatMatMult; 284 285 /* set MatInfo */ 286 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 287 if (afill < 1.0) afill = 1.0; 288 C->info.mallocs = nspacedouble; 289 C->info.fill_ratio_given = fill; 290 C->info.fill_ratio_needed = afill; 291 292 #if defined(PETSC_USE_INFO) 293 if (api[am]) { 294 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 295 ierr = PetscInfo1(C,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 296 } else { 297 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 298 } 299 #endif 300 PetscFunctionReturn(0); 301 } 302 303 /* ------------------------------------------------------- */ 304 static PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat,Mat,PetscReal,Mat); 305 static PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat,Mat,Mat); 306 307 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_MPIDense_AB(Mat C) 308 { 309 Mat_Product *product = C->product; 310 Mat A = product->A,B=product->B; 311 312 PetscFunctionBegin; 313 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) 314 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%D, %D) != (%D,%D)",A->cmap->rstart,A->cmap->rend,B->rmap->rstart,B->rmap->rend); 315 316 C->ops->matmultsymbolic = MatMatMultSymbolic_MPIAIJ_MPIDense; 317 C->ops->productsymbolic = MatProductSymbolic_AB; 318 PetscFunctionReturn(0); 319 } 320 /* -------------------------------------------------------------------- */ 321 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_MPIDense_AtB(Mat C) 322 { 323 Mat_Product *product = C->product; 324 Mat A = product->A,B=product->B; 325 326 PetscFunctionBegin; 327 if (A->rmap->rstart != B->rmap->rstart || A->rmap->rend != B->rmap->rend) 328 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%D, %D) != (%D,%D)",A->rmap->rstart,A->rmap->rend,B->rmap->rstart,B->rmap->rend); 329 330 C->ops->transposematmultsymbolic = MatTransposeMatMultSymbolic_MPIAIJ_MPIDense; 331 C->ops->productsymbolic = MatProductSymbolic_AtB; 332 PetscFunctionReturn(0); 333 } 334 335 /* --------------------------------------------------------------------- */ 336 PETSC_INTERN PetscErrorCode MatProductSetFromOptions_MPIAIJ_MPIDense(Mat C) 337 { 338 PetscErrorCode ierr; 339 Mat_Product *product = C->product; 340 341 PetscFunctionBegin; 342 switch (product->type) { 343 case MATPRODUCT_AB: 344 ierr = MatProductSetFromOptions_MPIAIJ_MPIDense_AB(C);CHKERRQ(ierr); 345 break; 346 case MATPRODUCT_AtB: 347 ierr = MatProductSetFromOptions_MPIAIJ_MPIDense_AtB(C);CHKERRQ(ierr); 348 break; 349 default: 350 break; 351 } 352 PetscFunctionReturn(0); 353 } 354 /* ------------------------------------------------------- */ 355 356 typedef struct { 357 Mat workB,workB1; 358 MPI_Request *rwaits,*swaits; 359 PetscInt nsends,nrecvs; 360 MPI_Datatype *stype,*rtype; 361 PetscInt blda; 362 } MPIAIJ_MPIDense; 363 364 PetscErrorCode MatMPIAIJ_MPIDenseDestroy(void *ctx) 365 { 366 MPIAIJ_MPIDense *contents = (MPIAIJ_MPIDense*)ctx; 367 PetscErrorCode ierr; 368 PetscInt i; 369 370 PetscFunctionBegin; 371 ierr = MatDestroy(&contents->workB);CHKERRQ(ierr); 372 ierr = MatDestroy(&contents->workB1);CHKERRQ(ierr); 373 for (i=0; i<contents->nsends; i++) { 374 ierr = MPI_Type_free(&contents->stype[i]);CHKERRQ(ierr); 375 } 376 for (i=0; i<contents->nrecvs; i++) { 377 ierr = MPI_Type_free(&contents->rtype[i]);CHKERRQ(ierr); 378 } 379 ierr = PetscFree4(contents->stype,contents->rtype,contents->rwaits,contents->swaits);CHKERRQ(ierr); 380 ierr = PetscFree(contents);CHKERRQ(ierr); 381 PetscFunctionReturn(0); 382 } 383 384 static PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat A,Mat B,PetscReal fill,Mat C) 385 { 386 PetscErrorCode ierr; 387 Mat_MPIAIJ *aij=(Mat_MPIAIJ*)A->data; 388 PetscInt nz=aij->B->cmap->n,nsends,nrecvs,i,nrows_to,j,blda,clda; 389 MPIAIJ_MPIDense *contents; 390 VecScatter ctx=aij->Mvctx; 391 PetscInt Am=A->rmap->n,Bm=B->rmap->n,BN=B->cmap->N,Bbn,Bbn1,bs,nrows_from,numBb; 392 MPI_Comm comm; 393 MPI_Datatype type1,*stype,*rtype; 394 const PetscInt *sindices,*sstarts,*rstarts; 395 PetscMPIInt *disp; 396 PetscBool cisdense; 397 398 PetscFunctionBegin; 399 MatCheckProduct(C,4); 400 if (C->product->data) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_PLIB,"Product data not empty"); 401 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 402 ierr = PetscObjectBaseTypeCompare((PetscObject)C,MATMPIDENSE,&cisdense);CHKERRQ(ierr); 403 if (!cisdense) { 404 ierr = MatSetType(C,((PetscObject)B)->type_name);CHKERRQ(ierr); 405 } 406 ierr = MatSetSizes(C,Am,B->cmap->n,A->rmap->N,BN);CHKERRQ(ierr); 407 ierr = MatSetBlockSizesFromMats(C,A,B);CHKERRQ(ierr); 408 ierr = MatSetUp(C);CHKERRQ(ierr); 409 ierr = MatDenseGetLDA(B,&blda);CHKERRQ(ierr); 410 ierr = MatDenseGetLDA(C,&clda);CHKERRQ(ierr); 411 ierr = PetscNew(&contents);CHKERRQ(ierr); 412 413 ierr = VecScatterGetRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,NULL,NULL);CHKERRQ(ierr); 414 ierr = VecScatterGetRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,NULL,NULL);CHKERRQ(ierr); 415 416 /* Create column block of B and C for memory scalability when BN is too large */ 417 /* Estimate Bbn, column size of Bb */ 418 if (nz) { 419 Bbn1 = 2*Am*BN/nz; 420 } else Bbn1 = BN; 421 422 bs = PetscAbs(B->cmap->bs); 423 Bbn1 = Bbn1/bs *bs; /* Bbn1 is a multiple of bs */ 424 if (Bbn1 > BN) Bbn1 = BN; 425 ierr = MPI_Allreduce(&Bbn1,&Bbn,1,MPIU_INT,MPI_MAX,comm);CHKERRQ(ierr); 426 427 /* Enable runtime option for Bbn */ 428 ierr = PetscOptionsBegin(comm,((PetscObject)C)->prefix,"MatMatMult","Mat");CHKERRQ(ierr); 429 ierr = PetscOptionsInt("-matmatmult_Bbn","Number of columns in Bb","MatMatMult",Bbn,&Bbn,NULL);CHKERRQ(ierr); 430 ierr = PetscOptionsEnd();CHKERRQ(ierr); 431 Bbn = PetscMin(Bbn,BN); 432 433 if (Bbn > 0 && Bbn < BN) { 434 numBb = BN/Bbn; 435 Bbn1 = BN - numBb*Bbn; 436 } else numBb = 0; 437 438 if (numBb) { 439 ierr = PetscInfo3(C,"use Bb, BN=%D, Bbn=%D; numBb=%D\n",BN,Bbn,numBb);CHKERRQ(ierr); 440 if (Bbn1) { /* Create workB1 for the remaining columns */ 441 ierr = PetscInfo2(C,"use Bb1, BN=%D, Bbn1=%D\n",BN,Bbn1);CHKERRQ(ierr); 442 /* Create work matrix used to store off processor rows of B needed for local product */ 443 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,Bbn1,NULL,&contents->workB1);CHKERRQ(ierr); 444 } else contents->workB1 = NULL; 445 } 446 447 /* Create work matrix used to store off processor rows of B needed for local product */ 448 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,Bbn,NULL,&contents->workB);CHKERRQ(ierr); 449 450 /* Use MPI derived data type to reduce memory required by the send/recv buffers */ 451 ierr = PetscMalloc4(nsends,&stype,nrecvs,&rtype,nrecvs,&contents->rwaits,nsends,&contents->swaits);CHKERRQ(ierr); 452 contents->stype = stype; 453 contents->nsends = nsends; 454 455 contents->rtype = rtype; 456 contents->nrecvs = nrecvs; 457 contents->blda = blda; 458 459 ierr = PetscMalloc1(Bm+1,&disp);CHKERRQ(ierr); 460 for (i=0; i<nsends; i++) { 461 nrows_to = sstarts[i+1]-sstarts[i]; 462 for (j=0; j<nrows_to; j++){ 463 disp[j] = sindices[sstarts[i]+j]; /* rowB to be sent */ 464 } 465 ierr = MPI_Type_create_indexed_block(nrows_to,1,(const PetscMPIInt *)disp,MPIU_SCALAR,&type1);CHKERRQ(ierr); 466 467 ierr = MPI_Type_create_resized(type1,0,blda*sizeof(PetscScalar),&stype[i]);CHKERRQ(ierr); 468 ierr = MPI_Type_commit(&stype[i]);CHKERRQ(ierr); 469 ierr = MPI_Type_free(&type1);CHKERRQ(ierr); 470 } 471 472 for (i=0; i<nrecvs; i++) { 473 /* received values from a process form a (nrows_from x Bbn) row block in workB (column-wise) */ 474 nrows_from = rstarts[i+1]-rstarts[i]; 475 disp[0] = 0; 476 ierr = MPI_Type_create_indexed_block(1, nrows_from, (const PetscMPIInt *)disp, MPIU_SCALAR, &type1);CHKERRQ(ierr); 477 ierr = MPI_Type_create_resized(type1, 0, nz*sizeof(PetscScalar), &rtype[i]);CHKERRQ(ierr); 478 ierr = MPI_Type_commit(&rtype[i]);CHKERRQ(ierr); 479 ierr = MPI_Type_free(&type1);CHKERRQ(ierr); 480 } 481 482 ierr = PetscFree(disp);CHKERRQ(ierr); 483 ierr = VecScatterRestoreRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,NULL,NULL);CHKERRQ(ierr); 484 ierr = VecScatterRestoreRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,NULL,NULL);CHKERRQ(ierr); 485 ierr = MatSetOption(C,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 486 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 487 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 488 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 489 490 C->product->data = contents; 491 C->product->destroy = MatMPIAIJ_MPIDenseDestroy; 492 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 493 PetscFunctionReturn(0); 494 } 495 496 PETSC_INTERN PetscErrorCode MatMatMultNumericAdd_SeqAIJ_SeqDense(Mat,Mat,Mat,const PetscBool); 497 /* 498 Performs an efficient scatter on the rows of B needed by this process; this is 499 a modification of the VecScatterBegin_() routines. 500 501 Input: Bbidx = 0: B = Bb 502 = 1: B = Bb1, see MatMatMultSymbolic_MPIAIJ_MPIDense() 503 */ 504 PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,PetscInt Bbidx,Mat C,Mat *outworkB) 505 { 506 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 507 PetscErrorCode ierr; 508 const PetscScalar *b; 509 PetscScalar *rvalues; 510 VecScatter ctx = aij->Mvctx; 511 const PetscInt *sindices,*sstarts,*rstarts; 512 const PetscMPIInt *sprocs,*rprocs; 513 PetscInt i,nsends,nrecvs; 514 MPI_Request *swaits,*rwaits; 515 MPI_Comm comm; 516 PetscMPIInt tag=((PetscObject)ctx)->tag,ncols=B->cmap->N,nrows=aij->B->cmap->n,nsends_mpi,nrecvs_mpi; 517 MPIAIJ_MPIDense *contents; 518 Mat workB; 519 MPI_Datatype *stype,*rtype; 520 PetscInt blda; 521 522 PetscFunctionBegin; 523 MatCheckProduct(C,4); 524 if (!C->product->data) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_PLIB,"Product data empty"); 525 contents = (MPIAIJ_MPIDense*)C->product->data; 526 ierr = VecScatterGetRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,&sprocs,NULL/*bs*/);CHKERRQ(ierr); 527 ierr = VecScatterGetRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,&rprocs,NULL/*bs*/);CHKERRQ(ierr); 528 ierr = PetscMPIIntCast(nsends,&nsends_mpi);CHKERRQ(ierr); 529 ierr = PetscMPIIntCast(nrecvs,&nrecvs_mpi);CHKERRQ(ierr); 530 if (Bbidx == 0) { 531 workB = *outworkB = contents->workB; 532 } else { 533 workB = *outworkB = contents->workB1; 534 } 535 if (nrows != workB->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Number of rows of workB %D not equal to columns of aij->B %D",workB->cmap->n,nrows); 536 swaits = contents->swaits; 537 rwaits = contents->rwaits; 538 539 ierr = MatDenseGetArrayRead(B,&b);CHKERRQ(ierr); 540 ierr = MatDenseGetLDA(B,&blda);CHKERRQ(ierr); 541 if (blda != contents->blda) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Cannot reuse an input matrix with lda %D != %D",blda,contents->blda); 542 ierr = MatDenseGetArray(workB,&rvalues);CHKERRQ(ierr); 543 544 /* Post recv, use MPI derived data type to save memory */ 545 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 546 rtype = contents->rtype; 547 for (i=0; i<nrecvs; i++) { 548 ierr = MPI_Irecv(rvalues+(rstarts[i]-rstarts[0]),ncols,rtype[i],rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 549 } 550 551 stype = contents->stype; 552 for (i=0; i<nsends; i++) { 553 ierr = MPI_Isend(b,ncols,stype[i],sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 554 } 555 556 if (nrecvs) {ierr = MPI_Waitall(nrecvs_mpi,rwaits,MPI_STATUSES_IGNORE);CHKERRQ(ierr);} 557 if (nsends) {ierr = MPI_Waitall(nsends_mpi,swaits,MPI_STATUSES_IGNORE);CHKERRQ(ierr);} 558 559 ierr = VecScatterRestoreRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,&sprocs,NULL);CHKERRQ(ierr); 560 ierr = VecScatterRestoreRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,&rprocs,NULL);CHKERRQ(ierr); 561 ierr = MatDenseRestoreArrayRead(B,&b);CHKERRQ(ierr); 562 ierr = MatDenseRestoreArray(workB,&rvalues);CHKERRQ(ierr); 563 PetscFunctionReturn(0); 564 } 565 566 static PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat A,Mat B,Mat C) 567 { 568 PetscErrorCode ierr; 569 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 570 Mat_MPIDense *bdense = (Mat_MPIDense*)B->data; 571 Mat_MPIDense *cdense = (Mat_MPIDense*)C->data; 572 Mat workB; 573 MPIAIJ_MPIDense *contents; 574 575 PetscFunctionBegin; 576 MatCheckProduct(C,3); 577 if (!C->product->data) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_PLIB,"Product data empty"); 578 contents = (MPIAIJ_MPIDense*)C->product->data; 579 /* diagonal block of A times all local rows of B */ 580 /* TODO: this calls a symbolic multiplication every time, which could be avoided */ 581 ierr = MatMatMult(aij->A,bdense->A,MAT_REUSE_MATRIX,PETSC_DEFAULT,&cdense->A);CHKERRQ(ierr); 582 if (contents->workB->cmap->n == B->cmap->N) { 583 /* get off processor parts of B needed to complete C=A*B */ 584 ierr = MatMPIDenseScatter(A,B,0,C,&workB);CHKERRQ(ierr); 585 586 /* off-diagonal block of A times nonlocal rows of B */ 587 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A,PETSC_TRUE);CHKERRQ(ierr); 588 } else { 589 Mat Bb,Cb; 590 PetscInt BN=B->cmap->N,n=contents->workB->cmap->n,i; 591 592 for (i=0; i<BN; i+=n) { 593 ierr = MatDenseGetSubMatrix(B,i,PetscMin(i+n,BN),&Bb);CHKERRQ(ierr); 594 ierr = MatDenseGetSubMatrix(C,i,PetscMin(i+n,BN),&Cb);CHKERRQ(ierr); 595 596 /* get off processor parts of B needed to complete C=A*B */ 597 ierr = MatMPIDenseScatter(A,Bb,i+n>BN,C,&workB);CHKERRQ(ierr); 598 599 /* off-diagonal block of A times nonlocal rows of B */ 600 cdense = (Mat_MPIDense*)Cb->data; 601 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A,PETSC_TRUE);CHKERRQ(ierr); 602 603 ierr = MatDenseRestoreSubMatrix(B,&Bb);CHKERRQ(ierr); 604 ierr = MatDenseRestoreSubMatrix(C,&Cb);CHKERRQ(ierr); 605 } 606 } 607 PetscFunctionReturn(0); 608 } 609 610 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 611 { 612 PetscErrorCode ierr; 613 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 614 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 615 Mat_SeqAIJ *cd = (Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 616 PetscInt *adi = ad->i,*adj,*aoi=ao->i,*aoj; 617 PetscScalar *ada,*aoa,*cda=cd->a,*coa=co->a; 618 Mat_SeqAIJ *p_loc,*p_oth; 619 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pj; 620 PetscScalar *pa_loc,*pa_oth,*pa,valtmp,*ca; 621 PetscInt cm = C->rmap->n,anz,pnz; 622 Mat_APMPI *ptap; 623 PetscScalar *apa_sparse; 624 PetscInt *api,*apj,*apJ,i,j,k,row; 625 PetscInt cstart = C->cmap->rstart; 626 PetscInt cdnz,conz,k0,k1,nextp; 627 MPI_Comm comm; 628 PetscMPIInt size; 629 630 PetscFunctionBegin; 631 MatCheckProduct(C,3); 632 ptap = (Mat_APMPI*)C->product->data; 633 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 634 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 635 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 636 if (!ptap->P_oth && size>1) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"AP cannot be reused. Do not call MatProductClear()"); 637 638 apa_sparse = ptap->apa; 639 640 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 641 /*-----------------------------------------------------*/ 642 /* update numerical values of P_oth and P_loc */ 643 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 644 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 645 646 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 647 /*----------------------------------------------------------*/ 648 /* get data from symbolic products */ 649 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 650 pi_loc = p_loc->i; pj_loc = p_loc->j; pa_loc = p_loc->a; 651 if (size >1) { 652 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 653 pi_oth = p_oth->i; pj_oth = p_oth->j; pa_oth = p_oth->a; 654 } else { 655 p_oth = NULL; pi_oth = NULL; pj_oth = NULL; pa_oth = NULL; 656 } 657 658 api = ptap->api; 659 apj = ptap->apj; 660 for (i=0; i<cm; i++) { 661 apJ = apj + api[i]; 662 663 /* diagonal portion of A */ 664 anz = adi[i+1] - adi[i]; 665 adj = ad->j + adi[i]; 666 ada = ad->a + adi[i]; 667 for (j=0; j<anz; j++) { 668 row = adj[j]; 669 pnz = pi_loc[row+1] - pi_loc[row]; 670 pj = pj_loc + pi_loc[row]; 671 pa = pa_loc + pi_loc[row]; 672 /* perform sparse axpy */ 673 valtmp = ada[j]; 674 nextp = 0; 675 for (k=0; nextp<pnz; k++) { 676 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 677 apa_sparse[k] += valtmp*pa[nextp++]; 678 } 679 } 680 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 681 } 682 683 /* off-diagonal portion of A */ 684 anz = aoi[i+1] - aoi[i]; 685 aoj = ao->j + aoi[i]; 686 aoa = ao->a + aoi[i]; 687 for (j=0; j<anz; j++) { 688 row = aoj[j]; 689 pnz = pi_oth[row+1] - pi_oth[row]; 690 pj = pj_oth + pi_oth[row]; 691 pa = pa_oth + pi_oth[row]; 692 /* perform sparse axpy */ 693 valtmp = aoa[j]; 694 nextp = 0; 695 for (k=0; nextp<pnz; k++) { 696 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 697 apa_sparse[k] += valtmp*pa[nextp++]; 698 } 699 } 700 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 701 } 702 703 /* set values in C */ 704 cdnz = cd->i[i+1] - cd->i[i]; 705 conz = co->i[i+1] - co->i[i]; 706 707 /* 1st off-diagonal part of C */ 708 ca = coa + co->i[i]; 709 k = 0; 710 for (k0=0; k0<conz; k0++) { 711 if (apJ[k] >= cstart) break; 712 ca[k0] = apa_sparse[k]; 713 apa_sparse[k] = 0.0; 714 k++; 715 } 716 717 /* diagonal part of C */ 718 ca = cda + cd->i[i]; 719 for (k1=0; k1<cdnz; k1++) { 720 ca[k1] = apa_sparse[k]; 721 apa_sparse[k] = 0.0; 722 k++; 723 } 724 725 /* 2nd off-diagonal part of C */ 726 ca = coa + co->i[i]; 727 for (; k0<conz; k0++) { 728 ca[k0] = apa_sparse[k]; 729 apa_sparse[k] = 0.0; 730 k++; 731 } 732 } 733 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 734 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 735 PetscFunctionReturn(0); 736 } 737 738 /* same as MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(), except using LLCondensed to avoid O(BN) memory requirement */ 739 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat C) 740 { 741 PetscErrorCode ierr; 742 MPI_Comm comm; 743 PetscMPIInt size; 744 Mat_APMPI *ptap; 745 PetscFreeSpaceList free_space = NULL,current_space=NULL; 746 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 747 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 748 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 749 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 750 PetscInt i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi,*lnk,apnz_max=0; 751 PetscInt am=A->rmap->n,pn=P->cmap->n,pm=P->rmap->n,lsize=pn+20; 752 PetscReal afill; 753 MatType mtype; 754 755 PetscFunctionBegin; 756 MatCheckProduct(C,4); 757 if (C->product->data) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Extra product struct not empty"); 758 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 759 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 760 761 /* create struct Mat_APMPI and attached it to C later */ 762 ierr = PetscNew(&ptap);CHKERRQ(ierr); 763 764 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 765 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 766 767 /* get P_loc by taking all local rows of P */ 768 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 769 770 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 771 pi_loc = p_loc->i; pj_loc = p_loc->j; 772 if (size > 1) { 773 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 774 pi_oth = p_oth->i; pj_oth = p_oth->j; 775 } else { 776 p_oth = NULL; 777 pi_oth = NULL; pj_oth = NULL; 778 } 779 780 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 781 /*-------------------------------------------------------------------*/ 782 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 783 ptap->api = api; 784 api[0] = 0; 785 786 ierr = PetscLLCondensedCreate_Scalable(lsize,&lnk);CHKERRQ(ierr); 787 788 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 789 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 790 current_space = free_space; 791 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 792 for (i=0; i<am; i++) { 793 /* diagonal portion of A */ 794 nzi = adi[i+1] - adi[i]; 795 for (j=0; j<nzi; j++) { 796 row = *adj++; 797 pnz = pi_loc[row+1] - pi_loc[row]; 798 Jptr = pj_loc + pi_loc[row]; 799 /* Expand list if it is not long enough */ 800 if (pnz+apnz_max > lsize) { 801 lsize = pnz+apnz_max; 802 ierr = PetscLLCondensedExpand_Scalable(lsize, &lnk);CHKERRQ(ierr); 803 } 804 /* add non-zero cols of P into the sorted linked list lnk */ 805 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 806 apnz = *lnk; /* The first element in the list is the number of items in the list */ 807 api[i+1] = api[i] + apnz; 808 if (apnz > apnz_max) apnz_max = apnz; 809 } 810 /* off-diagonal portion of A */ 811 nzi = aoi[i+1] - aoi[i]; 812 for (j=0; j<nzi; j++) { 813 row = *aoj++; 814 pnz = pi_oth[row+1] - pi_oth[row]; 815 Jptr = pj_oth + pi_oth[row]; 816 /* Expand list if it is not long enough */ 817 if (pnz+apnz_max > lsize) { 818 lsize = pnz + apnz_max; 819 ierr = PetscLLCondensedExpand_Scalable(lsize, &lnk);CHKERRQ(ierr); 820 } 821 /* add non-zero cols of P into the sorted linked list lnk */ 822 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 823 apnz = *lnk; /* The first element in the list is the number of items in the list */ 824 api[i+1] = api[i] + apnz; 825 if (apnz > apnz_max) apnz_max = apnz; 826 } 827 apnz = *lnk; 828 api[i+1] = api[i] + apnz; 829 if (apnz > apnz_max) apnz_max = apnz; 830 831 /* if free space is not available, double the total space in the list */ 832 if (current_space->local_remaining<apnz) { 833 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 834 nspacedouble++; 835 } 836 837 /* Copy data into free space, then initialize lnk */ 838 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 839 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 840 841 current_space->array += apnz; 842 current_space->local_used += apnz; 843 current_space->local_remaining -= apnz; 844 } 845 846 /* Allocate space for apj, initialize apj, and */ 847 /* destroy list of free space and other temporary array(s) */ 848 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 849 apj = ptap->apj; 850 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 851 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 852 853 /* create and assemble symbolic parallel matrix C */ 854 /*----------------------------------------------------*/ 855 ierr = MatSetSizes(C,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 856 ierr = MatSetBlockSizesFromMats(C,A,P);CHKERRQ(ierr); 857 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 858 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 859 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 860 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 861 862 /* malloc apa for assembly C */ 863 ierr = PetscCalloc1(apnz_max,&ptap->apa);CHKERRQ(ierr); 864 865 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(C, apj, api);CHKERRQ(ierr); 866 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 867 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 868 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 869 870 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ; 871 C->ops->productnumeric = MatProductNumeric_AB; 872 873 /* attach the supporting struct to C for reuse */ 874 C->product->data = ptap; 875 C->product->destroy = MatDestroy_MPIAIJ_MatMatMult; 876 877 /* set MatInfo */ 878 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 879 if (afill < 1.0) afill = 1.0; 880 C->info.mallocs = nspacedouble; 881 C->info.fill_ratio_given = fill; 882 C->info.fill_ratio_needed = afill; 883 884 #if defined(PETSC_USE_INFO) 885 if (api[am]) { 886 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 887 ierr = PetscInfo1(C,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 888 } else { 889 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 890 } 891 #endif 892 PetscFunctionReturn(0); 893 } 894 895 /* This function is needed for the seqMPI matrix-matrix multiplication. */ 896 /* Three input arrays are merged to one output array. The size of the */ 897 /* output array is also output. Duplicate entries only show up once. */ 898 static void Merge3SortedArrays(PetscInt size1, PetscInt *in1, 899 PetscInt size2, PetscInt *in2, 900 PetscInt size3, PetscInt *in3, 901 PetscInt *size4, PetscInt *out) 902 { 903 int i = 0, j = 0, k = 0, l = 0; 904 905 /* Traverse all three arrays */ 906 while (i<size1 && j<size2 && k<size3) { 907 if (in1[i] < in2[j] && in1[i] < in3[k]) { 908 out[l++] = in1[i++]; 909 } 910 else if (in2[j] < in1[i] && in2[j] < in3[k]) { 911 out[l++] = in2[j++]; 912 } 913 else if (in3[k] < in1[i] && in3[k] < in2[j]) { 914 out[l++] = in3[k++]; 915 } 916 else if (in1[i] == in2[j] && in1[i] < in3[k]) { 917 out[l++] = in1[i]; 918 i++, j++; 919 } 920 else if (in1[i] == in3[k] && in1[i] < in2[j]) { 921 out[l++] = in1[i]; 922 i++, k++; 923 } 924 else if (in3[k] == in2[j] && in2[j] < in1[i]) { 925 out[l++] = in2[j]; 926 k++, j++; 927 } 928 else if (in1[i] == in2[j] && in1[i] == in3[k]) { 929 out[l++] = in1[i]; 930 i++, j++, k++; 931 } 932 } 933 934 /* Traverse two remaining arrays */ 935 while (i<size1 && j<size2) { 936 if (in1[i] < in2[j]) { 937 out[l++] = in1[i++]; 938 } 939 else if (in1[i] > in2[j]) { 940 out[l++] = in2[j++]; 941 } 942 else { 943 out[l++] = in1[i]; 944 i++, j++; 945 } 946 } 947 948 while (i<size1 && k<size3) { 949 if (in1[i] < in3[k]) { 950 out[l++] = in1[i++]; 951 } 952 else if (in1[i] > in3[k]) { 953 out[l++] = in3[k++]; 954 } 955 else { 956 out[l++] = in1[i]; 957 i++, k++; 958 } 959 } 960 961 while (k<size3 && j<size2) { 962 if (in3[k] < in2[j]) { 963 out[l++] = in3[k++]; 964 } 965 else if (in3[k] > in2[j]) { 966 out[l++] = in2[j++]; 967 } 968 else { 969 out[l++] = in3[k]; 970 k++, j++; 971 } 972 } 973 974 /* Traverse one remaining array */ 975 while (i<size1) out[l++] = in1[i++]; 976 while (j<size2) out[l++] = in2[j++]; 977 while (k<size3) out[l++] = in3[k++]; 978 979 *size4 = l; 980 } 981 982 /* This matrix-matrix multiplication algorithm divides the multiplication into three multiplications and */ 983 /* adds up the products. Two of these three multiplications are performed with existing (sequential) */ 984 /* matrix-matrix multiplications. */ 985 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI(Mat A, Mat P, PetscReal fill, Mat C) 986 { 987 PetscErrorCode ierr; 988 MPI_Comm comm; 989 PetscMPIInt size; 990 Mat_APMPI *ptap; 991 PetscFreeSpaceList free_space_diag=NULL, current_space=NULL; 992 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data; 993 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc; 994 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data; 995 Mat_SeqAIJ *adpd_seq, *p_off, *aopoth_seq; 996 PetscInt adponz, adpdnz; 997 PetscInt *pi_loc,*dnz,*onz; 998 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,rstart=A->rmap->rstart; 999 PetscInt *lnk,i, i1=0,pnz,row,*adpoi,*adpoj, *api, *adpoJ, *aopJ, *apJ,*Jptr, aopnz, nspacedouble=0,j,nzi, 1000 *apj,apnz, *adpdi, *adpdj, *adpdJ, *poff_i, *poff_j, *j_temp, *aopothi, *aopothj; 1001 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n, p_colstart, p_colend; 1002 PetscBT lnkbt; 1003 PetscReal afill; 1004 PetscMPIInt rank; 1005 Mat adpd, aopoth; 1006 MatType mtype; 1007 const char *prefix; 1008 1009 PetscFunctionBegin; 1010 MatCheckProduct(C,4); 1011 if (C->product->data) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Extra product struct not empty"); 1012 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1013 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1014 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1015 ierr = MatGetOwnershipRangeColumn(P, &p_colstart, &p_colend);CHKERRQ(ierr); 1016 1017 /* create struct Mat_APMPI and attached it to C later */ 1018 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1019 1020 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1021 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1022 1023 /* get P_loc by taking all local rows of P */ 1024 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1025 1026 1027 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1028 pi_loc = p_loc->i; 1029 1030 /* Allocate memory for the i arrays of the matrices A*P, A_diag*P_off and A_offd * P */ 1031 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 1032 ierr = PetscMalloc1(am+2,&adpoi);CHKERRQ(ierr); 1033 1034 adpoi[0] = 0; 1035 ptap->api = api; 1036 api[0] = 0; 1037 1038 /* create and initialize a linked list, will be used for both A_diag * P_loc_off and A_offd * P_oth */ 1039 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1040 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 1041 1042 /* Symbolic calc of A_loc_diag * P_loc_diag */ 1043 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1044 ierr = MatProductCreate(a->A,p->A,NULL,&adpd);CHKERRQ(ierr); 1045 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1046 ierr = MatSetOptionsPrefix(adpd,prefix);CHKERRQ(ierr); 1047 ierr = MatAppendOptionsPrefix(adpd,"inner_diag_");CHKERRQ(ierr); 1048 1049 ierr = MatProductSetType(adpd,MATPRODUCT_AB);CHKERRQ(ierr); 1050 ierr = MatProductSetAlgorithm(adpd,"sorted");CHKERRQ(ierr); 1051 ierr = MatProductSetFill(adpd,fill);CHKERRQ(ierr); 1052 ierr = MatProductSetFromOptions(adpd);CHKERRQ(ierr); 1053 ierr = MatProductSymbolic(adpd);CHKERRQ(ierr); 1054 1055 adpd_seq = (Mat_SeqAIJ*)((adpd)->data); 1056 adpdi = adpd_seq->i; adpdj = adpd_seq->j; 1057 p_off = (Mat_SeqAIJ*)((p->B)->data); 1058 poff_i = p_off->i; poff_j = p_off->j; 1059 1060 /* j_temp stores indices of a result row before they are added to the linked list */ 1061 ierr = PetscMalloc1(pN+2,&j_temp);CHKERRQ(ierr); 1062 1063 1064 /* Symbolic calc of the A_diag * p_loc_off */ 1065 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 1066 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space_diag);CHKERRQ(ierr); 1067 current_space = free_space_diag; 1068 1069 for (i=0; i<am; i++) { 1070 /* A_diag * P_loc_off */ 1071 nzi = adi[i+1] - adi[i]; 1072 for (j=0; j<nzi; j++) { 1073 row = *adj++; 1074 pnz = poff_i[row+1] - poff_i[row]; 1075 Jptr = poff_j + poff_i[row]; 1076 for (i1 = 0; i1 < pnz; i1++) { 1077 j_temp[i1] = p->garray[Jptr[i1]]; 1078 } 1079 /* add non-zero cols of P into the sorted linked list lnk */ 1080 ierr = PetscLLCondensedAddSorted(pnz,j_temp,lnk,lnkbt);CHKERRQ(ierr); 1081 } 1082 1083 adponz = lnk[0]; 1084 adpoi[i+1] = adpoi[i] + adponz; 1085 1086 /* if free space is not available, double the total space in the list */ 1087 if (current_space->local_remaining<adponz) { 1088 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(adponz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1089 nspacedouble++; 1090 } 1091 1092 /* Copy data into free space, then initialize lnk */ 1093 ierr = PetscLLCondensedClean(pN,adponz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1094 1095 current_space->array += adponz; 1096 current_space->local_used += adponz; 1097 current_space->local_remaining -= adponz; 1098 } 1099 1100 /* Symbolic calc of A_off * P_oth */ 1101 ierr = MatSetOptionsPrefix(a->B,prefix);CHKERRQ(ierr); 1102 ierr = MatAppendOptionsPrefix(a->B,"inner_offdiag_");CHKERRQ(ierr); 1103 ierr = MatCreate(PETSC_COMM_SELF,&aopoth);CHKERRQ(ierr); 1104 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(a->B, ptap->P_oth, fill, aopoth);CHKERRQ(ierr); 1105 aopoth_seq = (Mat_SeqAIJ*)((aopoth)->data); 1106 aopothi = aopoth_seq->i; aopothj = aopoth_seq->j; 1107 1108 /* Allocate space for apj, adpj, aopj, ... */ 1109 /* destroy lists of free space and other temporary array(s) */ 1110 1111 ierr = PetscMalloc1(aopothi[am] + adpoi[am] + adpdi[am]+2, &ptap->apj);CHKERRQ(ierr); 1112 ierr = PetscMalloc1(adpoi[am]+2, &adpoj);CHKERRQ(ierr); 1113 1114 /* Copy from linked list to j-array */ 1115 ierr = PetscFreeSpaceContiguous(&free_space_diag,adpoj);CHKERRQ(ierr); 1116 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1117 1118 adpoJ = adpoj; 1119 adpdJ = adpdj; 1120 aopJ = aopothj; 1121 apj = ptap->apj; 1122 apJ = apj; /* still empty */ 1123 1124 /* Merge j-arrays of A_off * P, A_diag * P_loc_off, and */ 1125 /* A_diag * P_loc_diag to get A*P */ 1126 for (i = 0; i < am; i++) { 1127 aopnz = aopothi[i+1] - aopothi[i]; 1128 adponz = adpoi[i+1] - adpoi[i]; 1129 adpdnz = adpdi[i+1] - adpdi[i]; 1130 1131 /* Correct indices from A_diag*P_diag */ 1132 for (i1 = 0; i1 < adpdnz; i1++) { 1133 adpdJ[i1] += p_colstart; 1134 } 1135 /* Merge j-arrays of A_diag * P_loc_off and A_diag * P_loc_diag and A_off * P_oth */ 1136 Merge3SortedArrays(adponz, adpoJ, adpdnz, adpdJ, aopnz, aopJ, &apnz, apJ); 1137 ierr = MatPreallocateSet(i+rstart, apnz, apJ, dnz, onz);CHKERRQ(ierr); 1138 1139 aopJ += aopnz; 1140 adpoJ += adponz; 1141 adpdJ += adpdnz; 1142 apJ += apnz; 1143 api[i+1] = api[i] + apnz; 1144 } 1145 1146 /* malloc apa to store dense row A[i,:]*P */ 1147 ierr = PetscCalloc1(pN+2,&ptap->apa);CHKERRQ(ierr); 1148 1149 /* create and assemble symbolic parallel matrix C */ 1150 ierr = MatSetSizes(C,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1151 ierr = MatSetBlockSizesFromMats(C,A,P);CHKERRQ(ierr); 1152 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1153 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 1154 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 1155 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1156 1157 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(C, apj, api);CHKERRQ(ierr); 1158 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1159 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1160 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1161 1162 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1163 C->ops->productnumeric = MatProductNumeric_AB; 1164 1165 /* attach the supporting struct to C for reuse */ 1166 C->product->data = ptap; 1167 C->product->destroy = MatDestroy_MPIAIJ_MatMatMult; 1168 1169 /* set MatInfo */ 1170 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 1171 if (afill < 1.0) afill = 1.0; 1172 C->info.mallocs = nspacedouble; 1173 C->info.fill_ratio_given = fill; 1174 C->info.fill_ratio_needed = afill; 1175 1176 #if defined(PETSC_USE_INFO) 1177 if (api[am]) { 1178 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1179 ierr = PetscInfo1(C,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 1180 } else { 1181 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 1182 } 1183 #endif 1184 1185 ierr = MatDestroy(&aopoth);CHKERRQ(ierr); 1186 ierr = MatDestroy(&adpd);CHKERRQ(ierr); 1187 ierr = PetscFree(j_temp);CHKERRQ(ierr); 1188 ierr = PetscFree(adpoj);CHKERRQ(ierr); 1189 ierr = PetscFree(adpoi);CHKERRQ(ierr); 1190 PetscFunctionReturn(0); 1191 } 1192 1193 /*-------------------------------------------------------------------------*/ 1194 /* This routine only works when scall=MAT_REUSE_MATRIX! */ 1195 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult(Mat P,Mat A,Mat C) 1196 { 1197 PetscErrorCode ierr; 1198 Mat_APMPI *ptap; 1199 Mat Pt; 1200 1201 PetscFunctionBegin; 1202 MatCheckProduct(C,3); 1203 ptap = (Mat_APMPI*)C->product->data; 1204 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 1205 if (!ptap->Pt) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatProductClear()"); 1206 1207 Pt = ptap->Pt; 1208 ierr = MatTranspose(P,MAT_REUSE_MATRIX,&Pt);CHKERRQ(ierr); 1209 ierr = MatMatMultNumeric_MPIAIJ_MPIAIJ(Pt,A,C);CHKERRQ(ierr); 1210 PetscFunctionReturn(0); 1211 } 1212 1213 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ() */ 1214 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,PetscReal fill,Mat C) 1215 { 1216 PetscErrorCode ierr; 1217 Mat_APMPI *ptap; 1218 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data; 1219 MPI_Comm comm; 1220 PetscMPIInt size,rank; 1221 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1222 PetscInt pn=P->cmap->n,aN=A->cmap->N,an=A->cmap->n; 1223 PetscInt *lnk,i,k,nsend,rstart; 1224 PetscBT lnkbt; 1225 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 1226 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1227 PetscInt len,proc,*dnz,*onz,*owners,nzi; 1228 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1229 MPI_Request *swaits,*rwaits; 1230 MPI_Status *sstatus,rstatus; 1231 PetscLayout rowmap; 1232 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1233 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1234 PetscInt *Jptr,*prmap=p->garray,con,j,Crmax; 1235 Mat_SeqAIJ *a_loc,*c_loc,*c_oth; 1236 PetscTable ta; 1237 MatType mtype; 1238 const char *prefix; 1239 1240 PetscFunctionBegin; 1241 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1242 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1243 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1244 1245 /* create symbolic parallel matrix C */ 1246 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1247 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 1248 1249 C->ops->transposematmultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1250 1251 /* create struct Mat_APMPI and attached it to C later */ 1252 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1253 ptap->reuse = MAT_INITIAL_MATRIX; 1254 1255 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1256 /* --------------------------------- */ 1257 ierr = MatTranspose_SeqAIJ(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1258 ierr = MatTranspose_SeqAIJ(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1259 1260 /* (1) compute symbolic A_loc */ 1261 /* ---------------------------*/ 1262 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1263 1264 /* (2-1) compute symbolic C_oth = Ro*A_loc */ 1265 /* ------------------------------------ */ 1266 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1267 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 1268 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 1269 ierr = MatCreate(PETSC_COMM_SELF,&ptap->C_oth);CHKERRQ(ierr); 1270 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->A_loc,fill,ptap->C_oth);CHKERRQ(ierr); 1271 1272 /* (3) send coj of C_oth to other processors */ 1273 /* ------------------------------------------ */ 1274 /* determine row ownership */ 1275 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1276 rowmap->n = pn; 1277 rowmap->bs = 1; 1278 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1279 owners = rowmap->range; 1280 1281 /* determine the number of messages to send, their lengths */ 1282 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1283 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 1284 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr); 1285 1286 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1287 coi = c_oth->i; coj = c_oth->j; 1288 con = ptap->C_oth->rmap->n; 1289 proc = 0; 1290 for (i=0; i<con; i++) { 1291 while (prmap[i] >= owners[proc+1]) proc++; 1292 len_si[proc]++; /* num of rows in Co(=Pt*A) to be sent to [proc] */ 1293 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1294 } 1295 1296 len = 0; /* max length of buf_si[], see (4) */ 1297 owners_co[0] = 0; 1298 nsend = 0; 1299 for (proc=0; proc<size; proc++) { 1300 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1301 if (len_s[proc]) { 1302 nsend++; 1303 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1304 len += len_si[proc]; 1305 } 1306 } 1307 1308 /* determine the number and length of messages to receive for coi and coj */ 1309 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1310 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1311 1312 /* post the Irecv and Isend of coj */ 1313 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1314 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1315 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1316 for (proc=0, k=0; proc<size; proc++) { 1317 if (!len_s[proc]) continue; 1318 i = owners_co[proc]; 1319 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1320 k++; 1321 } 1322 1323 /* (2-2) compute symbolic C_loc = Rd*A_loc */ 1324 /* ---------------------------------------- */ 1325 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 1326 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 1327 ierr = MatCreate(PETSC_COMM_SELF,&ptap->C_loc);CHKERRQ(ierr); 1328 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->A_loc,fill,ptap->C_loc);CHKERRQ(ierr); 1329 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1330 1331 /* receives coj are complete */ 1332 for (i=0; i<nrecv; i++) { 1333 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1334 } 1335 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1336 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1337 1338 /* add received column indices into ta to update Crmax */ 1339 a_loc = (Mat_SeqAIJ*)(ptap->A_loc)->data; 1340 1341 /* create and initialize a linked list */ 1342 ierr = PetscTableCreate(an,aN,&ta);CHKERRQ(ierr); /* for compute Crmax */ 1343 MatRowMergeMax_SeqAIJ(a_loc,ptap->A_loc->rmap->N,ta); 1344 1345 for (k=0; k<nrecv; k++) {/* k-th received message */ 1346 Jptr = buf_rj[k]; 1347 for (j=0; j<len_r[k]; j++) { 1348 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1349 } 1350 } 1351 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1352 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1353 1354 /* (4) send and recv coi */ 1355 /*-----------------------*/ 1356 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1357 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1358 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1359 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1360 for (proc=0,k=0; proc<size; proc++) { 1361 if (!len_s[proc]) continue; 1362 /* form outgoing message for i-structure: 1363 buf_si[0]: nrows to be sent 1364 [1:nrows]: row index (global) 1365 [nrows+1:2*nrows+1]: i-structure index 1366 */ 1367 /*-------------------------------------------*/ 1368 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1369 buf_si_i = buf_si + nrows+1; 1370 buf_si[0] = nrows; 1371 buf_si_i[0] = 0; 1372 nrows = 0; 1373 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1374 nzi = coi[i+1] - coi[i]; 1375 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1376 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1377 nrows++; 1378 } 1379 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1380 k++; 1381 buf_si += len_si[proc]; 1382 } 1383 for (i=0; i<nrecv; i++) { 1384 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1385 } 1386 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1387 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1388 1389 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1390 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1391 ierr = PetscFree(swaits);CHKERRQ(ierr); 1392 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1393 1394 /* (5) compute the local portion of C */ 1395 /* ------------------------------------------ */ 1396 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of C */ 1397 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1398 current_space = free_space; 1399 1400 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1401 for (k=0; k<nrecv; k++) { 1402 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1403 nrows = *buf_ri_k[k]; 1404 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1405 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1406 } 1407 1408 ierr = MatPreallocateInitialize(comm,pn,an,dnz,onz);CHKERRQ(ierr); 1409 ierr = PetscLLCondensedCreate(Crmax,aN,&lnk,&lnkbt);CHKERRQ(ierr); 1410 for (i=0; i<pn; i++) { 1411 /* add C_loc into C */ 1412 nzi = c_loc->i[i+1] - c_loc->i[i]; 1413 Jptr = c_loc->j + c_loc->i[i]; 1414 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1415 1416 /* add received col data into lnk */ 1417 for (k=0; k<nrecv; k++) { /* k-th received message */ 1418 if (i == *nextrow[k]) { /* i-th row */ 1419 nzi = *(nextci[k]+1) - *nextci[k]; 1420 Jptr = buf_rj[k] + *nextci[k]; 1421 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1422 nextrow[k]++; nextci[k]++; 1423 } 1424 } 1425 nzi = lnk[0]; 1426 1427 /* copy data into free space, then initialize lnk */ 1428 ierr = PetscLLCondensedClean(aN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1429 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 1430 } 1431 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1432 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1433 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 1434 1435 /* local sizes and preallocation */ 1436 ierr = MatSetSizes(C,pn,an,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1437 if (P->cmap->bs > 0) {ierr = PetscLayoutSetBlockSize(C->rmap,P->cmap->bs);CHKERRQ(ierr);} 1438 if (A->cmap->bs > 0) {ierr = PetscLayoutSetBlockSize(C->cmap,A->cmap->bs);CHKERRQ(ierr);} 1439 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 1440 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1441 1442 /* add C_loc and C_oth to C */ 1443 ierr = MatGetOwnershipRange(C,&rstart,NULL);CHKERRQ(ierr); 1444 for (i=0; i<pn; i++) { 1445 const PetscInt ncols = c_loc->i[i+1] - c_loc->i[i]; 1446 const PetscInt *cols = c_loc->j + c_loc->i[i]; 1447 const PetscInt row = rstart + i; 1448 ierr = MatSetValues(C,1,&row,ncols,cols,NULL,INSERT_VALUES);CHKERRQ(ierr); 1449 } 1450 for (i=0; i<con; i++) { 1451 const PetscInt ncols = c_oth->i[i+1] - c_oth->i[i]; 1452 const PetscInt *cols = c_oth->j + c_oth->i[i]; 1453 const PetscInt row = prmap[i]; 1454 ierr = MatSetValues(C,1,&row,ncols,cols,NULL,INSERT_VALUES);CHKERRQ(ierr); 1455 } 1456 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1457 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1458 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1459 1460 /* members in merge */ 1461 ierr = PetscFree(id_r);CHKERRQ(ierr); 1462 ierr = PetscFree(len_r);CHKERRQ(ierr); 1463 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 1464 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 1465 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 1466 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 1467 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 1468 1469 /* attach the supporting struct to C for reuse */ 1470 C->product->data = ptap; 1471 C->product->destroy = MatDestroy_MPIAIJ_PtAP; 1472 PetscFunctionReturn(0); 1473 } 1474 1475 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,Mat C) 1476 { 1477 PetscErrorCode ierr; 1478 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data; 1479 Mat_SeqAIJ *c_seq; 1480 Mat_APMPI *ptap; 1481 Mat A_loc,C_loc,C_oth; 1482 PetscInt i,rstart,rend,cm,ncols,row; 1483 const PetscInt *cols; 1484 const PetscScalar *vals; 1485 1486 PetscFunctionBegin; 1487 MatCheckProduct(C,3); 1488 ptap = (Mat_APMPI*)C->product->data; 1489 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 1490 if (!ptap->A_loc) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatProductClear()"); 1491 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1492 1493 if (ptap->reuse == MAT_REUSE_MATRIX) { 1494 /* These matrices are obtained in MatTransposeMatMultSymbolic() */ 1495 /* 1) get R = Pd^T, Ro = Po^T */ 1496 /*----------------------------*/ 1497 ierr = MatTranspose_SeqAIJ(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1498 ierr = MatTranspose_SeqAIJ(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1499 1500 /* 2) compute numeric A_loc */ 1501 /*--------------------------*/ 1502 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1503 } 1504 1505 /* 3) C_loc = Rd*A_loc, C_oth = Ro*A_loc */ 1506 A_loc = ptap->A_loc; 1507 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,A_loc,ptap->C_loc);CHKERRQ(ierr); 1508 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,A_loc,ptap->C_oth);CHKERRQ(ierr); 1509 C_loc = ptap->C_loc; 1510 C_oth = ptap->C_oth; 1511 1512 /* add C_loc and C_oth to C */ 1513 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1514 1515 /* C_loc -> C */ 1516 cm = C_loc->rmap->N; 1517 c_seq = (Mat_SeqAIJ*)C_loc->data; 1518 cols = c_seq->j; 1519 vals = c_seq->a; 1520 for (i=0; i<cm; i++) { 1521 ncols = c_seq->i[i+1] - c_seq->i[i]; 1522 row = rstart + i; 1523 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1524 cols += ncols; vals += ncols; 1525 } 1526 1527 /* Co -> C, off-processor part */ 1528 cm = C_oth->rmap->N; 1529 c_seq = (Mat_SeqAIJ*)C_oth->data; 1530 cols = c_seq->j; 1531 vals = c_seq->a; 1532 for (i=0; i<cm; i++) { 1533 ncols = c_seq->i[i+1] - c_seq->i[i]; 1534 row = p->garray[i]; 1535 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1536 cols += ncols; vals += ncols; 1537 } 1538 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1539 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1540 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1541 1542 ptap->reuse = MAT_REUSE_MATRIX; 1543 PetscFunctionReturn(0); 1544 } 1545 1546 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ(Mat P,Mat A,Mat C) 1547 { 1548 PetscErrorCode ierr; 1549 Mat_Merge_SeqsToMPI *merge; 1550 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data; 1551 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1552 Mat_APMPI *ptap; 1553 PetscInt *adj; 1554 PetscInt i,j,k,anz,pnz,row,*cj,nexta; 1555 MatScalar *ada,*ca,valtmp; 1556 PetscInt am=A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1557 MPI_Comm comm; 1558 PetscMPIInt size,rank,taga,*len_s; 1559 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1560 PetscInt **buf_ri,**buf_rj; 1561 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1562 MPI_Request *s_waits,*r_waits; 1563 MPI_Status *status; 1564 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1565 PetscInt *ai,*aj,*coi,*coj,*poJ,*pdJ; 1566 Mat A_loc; 1567 Mat_SeqAIJ *a_loc; 1568 1569 PetscFunctionBegin; 1570 MatCheckProduct(C,3); 1571 ptap = (Mat_APMPI*)C->product->data; 1572 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 1573 if (!ptap->A_loc) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatProductClear()"); 1574 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1575 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1576 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1577 1578 merge = ptap->merge; 1579 1580 /* 2) compute numeric C_seq = P_loc^T*A_loc */ 1581 /*------------------------------------------*/ 1582 /* get data from symbolic products */ 1583 coi = merge->coi; coj = merge->coj; 1584 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 1585 bi = merge->bi; bj = merge->bj; 1586 owners = merge->rowmap->range; 1587 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); 1588 1589 /* get A_loc by taking all local rows of A */ 1590 A_loc = ptap->A_loc; 1591 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 1592 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1593 ai = a_loc->i; 1594 aj = a_loc->j; 1595 1596 for (i=0; i<am; i++) { 1597 anz = ai[i+1] - ai[i]; 1598 adj = aj + ai[i]; 1599 ada = a_loc->a + ai[i]; 1600 1601 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 1602 /*-------------------------------------------------------------*/ 1603 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 1604 pnz = po->i[i+1] - po->i[i]; 1605 poJ = po->j + po->i[i]; 1606 pA = po->a + po->i[i]; 1607 for (j=0; j<pnz; j++) { 1608 row = poJ[j]; 1609 cj = coj + coi[row]; 1610 ca = coa + coi[row]; 1611 /* perform sparse axpy */ 1612 nexta = 0; 1613 valtmp = pA[j]; 1614 for (k=0; nexta<anz; k++) { 1615 if (cj[k] == adj[nexta]) { 1616 ca[k] += valtmp*ada[nexta]; 1617 nexta++; 1618 } 1619 } 1620 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1621 } 1622 1623 /* put the value into Cd (diagonal part) */ 1624 pnz = pd->i[i+1] - pd->i[i]; 1625 pdJ = pd->j + pd->i[i]; 1626 pA = pd->a + pd->i[i]; 1627 for (j=0; j<pnz; j++) { 1628 row = pdJ[j]; 1629 cj = bj + bi[row]; 1630 ca = ba + bi[row]; 1631 /* perform sparse axpy */ 1632 nexta = 0; 1633 valtmp = pA[j]; 1634 for (k=0; nexta<anz; k++) { 1635 if (cj[k] == adj[nexta]) { 1636 ca[k] += valtmp*ada[nexta]; 1637 nexta++; 1638 } 1639 } 1640 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1641 } 1642 } 1643 1644 /* 3) send and recv matrix values coa */ 1645 /*------------------------------------*/ 1646 buf_ri = merge->buf_ri; 1647 buf_rj = merge->buf_rj; 1648 len_s = merge->len_s; 1649 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1650 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1651 1652 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1653 for (proc=0,k=0; proc<size; proc++) { 1654 if (!len_s[proc]) continue; 1655 i = merge->owners_co[proc]; 1656 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1657 k++; 1658 } 1659 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1660 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1661 1662 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1663 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1664 ierr = PetscFree(coa);CHKERRQ(ierr); 1665 1666 /* 4) insert local Cseq and received values into Cmpi */ 1667 /*----------------------------------------------------*/ 1668 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1669 for (k=0; k<merge->nrecv; k++) { 1670 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1671 nrows = *(buf_ri_k[k]); 1672 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1673 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1674 } 1675 1676 for (i=0; i<cm; i++) { 1677 row = owners[rank] + i; /* global row index of C_seq */ 1678 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1679 ba_i = ba + bi[i]; 1680 bnz = bi[i+1] - bi[i]; 1681 /* add received vals into ba */ 1682 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1683 /* i-th row */ 1684 if (i == *nextrow[k]) { 1685 cnz = *(nextci[k]+1) - *nextci[k]; 1686 cj = buf_rj[k] + *(nextci[k]); 1687 ca = abuf_r[k] + *(nextci[k]); 1688 nextcj = 0; 1689 for (j=0; nextcj<cnz; j++) { 1690 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1691 ba_i[j] += ca[nextcj++]; 1692 } 1693 } 1694 nextrow[k]++; nextci[k]++; 1695 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1696 } 1697 } 1698 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1699 } 1700 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1701 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1702 1703 ierr = PetscFree(ba);CHKERRQ(ierr); 1704 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1705 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1706 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1707 PetscFunctionReturn(0); 1708 } 1709 1710 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(Mat P,Mat A,PetscReal fill,Mat C) 1711 { 1712 PetscErrorCode ierr; 1713 Mat A_loc,POt,PDt; 1714 Mat_APMPI *ptap; 1715 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1716 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*a=(Mat_MPIAIJ*)A->data; 1717 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1718 PetscInt nnz; 1719 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1720 PetscInt am =A->rmap->n,pn=P->cmap->n; 1721 MPI_Comm comm; 1722 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1723 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1724 PetscInt len,proc,*dnz,*onz,*owners; 1725 PetscInt nzi,*bi,*bj; 1726 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1727 MPI_Request *swaits,*rwaits; 1728 MPI_Status *sstatus,rstatus; 1729 Mat_Merge_SeqsToMPI *merge; 1730 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1731 PetscReal afill =1.0,afill_tmp; 1732 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N,Armax; 1733 Mat_SeqAIJ *a_loc,*pdt,*pot; 1734 PetscTable ta; 1735 MatType mtype; 1736 1737 PetscFunctionBegin; 1738 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1739 /* check if matrix local sizes are compatible */ 1740 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, A (%D, %D) != P (%D,%D)",A->rmap->rstart,A->rmap->rend,P->rmap->rstart,P->rmap->rend); 1741 1742 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1743 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1744 1745 /* create struct Mat_APMPI and attached it to C later */ 1746 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1747 1748 /* get A_loc by taking all local rows of A */ 1749 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1750 1751 ptap->A_loc = A_loc; 1752 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1753 ai = a_loc->i; 1754 aj = a_loc->j; 1755 1756 /* determine symbolic Co=(p->B)^T*A - send to others */ 1757 /*----------------------------------------------------*/ 1758 ierr = MatTransposeSymbolic_SeqAIJ(p->A,&PDt);CHKERRQ(ierr); 1759 pdt = (Mat_SeqAIJ*)PDt->data; 1760 pdti = pdt->i; pdtj = pdt->j; 1761 1762 ierr = MatTransposeSymbolic_SeqAIJ(p->B,&POt);CHKERRQ(ierr); 1763 pot = (Mat_SeqAIJ*)POt->data; 1764 poti = pot->i; potj = pot->j; 1765 1766 /* then, compute symbolic Co = (p->B)^T*A */ 1767 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 1768 >= (num of nonzero rows of C_seq) - pn */ 1769 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 1770 coi[0] = 0; 1771 1772 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1773 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],ai[am])); 1774 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1775 current_space = free_space; 1776 1777 /* create and initialize a linked list */ 1778 ierr = PetscTableCreate(A->cmap->n + a->B->cmap->N,aN,&ta);CHKERRQ(ierr); 1779 MatRowMergeMax_SeqAIJ(a_loc,am,ta); 1780 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1781 1782 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1783 1784 for (i=0; i<pon; i++) { 1785 pnz = poti[i+1] - poti[i]; 1786 ptJ = potj + poti[i]; 1787 for (j=0; j<pnz; j++) { 1788 row = ptJ[j]; /* row of A_loc == col of Pot */ 1789 anz = ai[row+1] - ai[row]; 1790 Jptr = aj + ai[row]; 1791 /* add non-zero cols of AP into the sorted linked list lnk */ 1792 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1793 } 1794 nnz = lnk[0]; 1795 1796 /* If free space is not available, double the total space in the list */ 1797 if (current_space->local_remaining<nnz) { 1798 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1799 nspacedouble++; 1800 } 1801 1802 /* Copy data into free space, and zero out denserows */ 1803 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1804 1805 current_space->array += nnz; 1806 current_space->local_used += nnz; 1807 current_space->local_remaining -= nnz; 1808 1809 coi[i+1] = coi[i] + nnz; 1810 } 1811 1812 ierr = PetscMalloc1(coi[pon]+1,&coj);CHKERRQ(ierr); 1813 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 1814 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); /* must destroy to get a new one for C */ 1815 1816 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 1817 if (afill_tmp > afill) afill = afill_tmp; 1818 1819 /* send j-array (coj) of Co to other processors */ 1820 /*----------------------------------------------*/ 1821 /* determine row ownership */ 1822 ierr = PetscNew(&merge);CHKERRQ(ierr); 1823 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 1824 1825 merge->rowmap->n = pn; 1826 merge->rowmap->bs = 1; 1827 1828 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 1829 owners = merge->rowmap->range; 1830 1831 /* determine the number of messages to send, their lengths */ 1832 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 1833 ierr = PetscCalloc1(size,&merge->len_s);CHKERRQ(ierr); 1834 1835 len_s = merge->len_s; 1836 merge->nsend = 0; 1837 1838 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 1839 1840 proc = 0; 1841 for (i=0; i<pon; i++) { 1842 while (prmap[i] >= owners[proc+1]) proc++; 1843 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1844 len_s[proc] += coi[i+1] - coi[i]; 1845 } 1846 1847 len = 0; /* max length of buf_si[] */ 1848 owners_co[0] = 0; 1849 for (proc=0; proc<size; proc++) { 1850 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1851 if (len_si[proc]) { 1852 merge->nsend++; 1853 len_si[proc] = 2*(len_si[proc] + 1); 1854 len += len_si[proc]; 1855 } 1856 } 1857 1858 /* determine the number and length of messages to receive for coi and coj */ 1859 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1860 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1861 1862 /* post the Irecv and Isend of coj */ 1863 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1864 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1865 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 1866 for (proc=0, k=0; proc<size; proc++) { 1867 if (!len_s[proc]) continue; 1868 i = owners_co[proc]; 1869 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1870 k++; 1871 } 1872 1873 /* receives and sends of coj are complete */ 1874 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1875 for (i=0; i<merge->nrecv; i++) { 1876 PetscMPIInt icompleted; 1877 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1878 } 1879 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1880 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1881 1882 /* add received column indices into table to update Armax */ 1883 /* Armax can be as large as aN if a P[row,:] is dense, see src/ksp/ksp/tutorials/ex56.c! */ 1884 for (k=0; k<merge->nrecv; k++) {/* k-th received message */ 1885 Jptr = buf_rj[k]; 1886 for (j=0; j<merge->len_r[k]; j++) { 1887 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1888 } 1889 } 1890 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1891 /* printf("Armax %d, an %d + Bn %d = %d, aN %d\n",Armax,A->cmap->n,a->B->cmap->N,A->cmap->n+a->B->cmap->N,aN); */ 1892 1893 /* send and recv coi */ 1894 /*-------------------*/ 1895 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1896 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1897 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1898 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1899 for (proc=0,k=0; proc<size; proc++) { 1900 if (!len_s[proc]) continue; 1901 /* form outgoing message for i-structure: 1902 buf_si[0]: nrows to be sent 1903 [1:nrows]: row index (global) 1904 [nrows+1:2*nrows+1]: i-structure index 1905 */ 1906 /*-------------------------------------------*/ 1907 nrows = len_si[proc]/2 - 1; 1908 buf_si_i = buf_si + nrows+1; 1909 buf_si[0] = nrows; 1910 buf_si_i[0] = 0; 1911 nrows = 0; 1912 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1913 nzi = coi[i+1] - coi[i]; 1914 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1915 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1916 nrows++; 1917 } 1918 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1919 k++; 1920 buf_si += len_si[proc]; 1921 } 1922 i = merge->nrecv; 1923 while (i--) { 1924 PetscMPIInt icompleted; 1925 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1926 } 1927 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1928 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1929 ierr = PetscFree(len_si);CHKERRQ(ierr); 1930 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1931 ierr = PetscFree(swaits);CHKERRQ(ierr); 1932 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1933 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1934 1935 /* compute the local portion of C (mpi mat) */ 1936 /*------------------------------------------*/ 1937 /* allocate bi array and free space for accumulating nonzero column info */ 1938 ierr = PetscMalloc1(pn+1,&bi);CHKERRQ(ierr); 1939 bi[0] = 0; 1940 1941 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 1942 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pdti[pn],PetscIntSumTruncate(poti[pon],ai[am]))); 1943 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1944 current_space = free_space; 1945 1946 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1947 for (k=0; k<merge->nrecv; k++) { 1948 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1949 nrows = *buf_ri_k[k]; 1950 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1951 nextci[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th received i-structure */ 1952 } 1953 1954 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1955 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1956 rmax = 0; 1957 for (i=0; i<pn; i++) { 1958 /* add pdt[i,:]*AP into lnk */ 1959 pnz = pdti[i+1] - pdti[i]; 1960 ptJ = pdtj + pdti[i]; 1961 for (j=0; j<pnz; j++) { 1962 row = ptJ[j]; /* row of AP == col of Pt */ 1963 anz = ai[row+1] - ai[row]; 1964 Jptr = aj + ai[row]; 1965 /* add non-zero cols of AP into the sorted linked list lnk */ 1966 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1967 } 1968 1969 /* add received col data into lnk */ 1970 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1971 if (i == *nextrow[k]) { /* i-th row */ 1972 nzi = *(nextci[k]+1) - *nextci[k]; 1973 Jptr = buf_rj[k] + *nextci[k]; 1974 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 1975 nextrow[k]++; nextci[k]++; 1976 } 1977 } 1978 nnz = lnk[0]; 1979 1980 /* if free space is not available, make more free space */ 1981 if (current_space->local_remaining<nnz) { 1982 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1983 nspacedouble++; 1984 } 1985 /* copy data into free space, then initialize lnk */ 1986 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1987 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 1988 1989 current_space->array += nnz; 1990 current_space->local_used += nnz; 1991 current_space->local_remaining -= nnz; 1992 1993 bi[i+1] = bi[i] + nnz; 1994 if (nnz > rmax) rmax = nnz; 1995 } 1996 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1997 1998 ierr = PetscMalloc1(bi[pn]+1,&bj);CHKERRQ(ierr); 1999 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 2000 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 2001 if (afill_tmp > afill) afill = afill_tmp; 2002 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 2003 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 2004 2005 ierr = MatDestroy(&POt);CHKERRQ(ierr); 2006 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 2007 2008 /* create symbolic parallel matrix C - why cannot be assembled in Numeric part */ 2009 /*-------------------------------------------------------------------------------*/ 2010 ierr = MatSetSizes(C,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2011 ierr = MatSetBlockSizes(C,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 2012 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 2013 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 2014 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 2015 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 2016 ierr = MatSetBlockSize(C,1);CHKERRQ(ierr); 2017 ierr = MatSetOption(C,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 2018 for (i=0; i<pn; i++) { 2019 row = i + rstart; 2020 nnz = bi[i+1] - bi[i]; 2021 Jptr = bj + bi[i]; 2022 ierr = MatSetValues(C,1,&row,nnz,Jptr,NULL,INSERT_VALUES);CHKERRQ(ierr); 2023 } 2024 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2025 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2026 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2027 merge->bi = bi; 2028 merge->bj = bj; 2029 merge->coi = coi; 2030 merge->coj = coj; 2031 merge->buf_ri = buf_ri; 2032 merge->buf_rj = buf_rj; 2033 merge->owners_co = owners_co; 2034 2035 /* attach the supporting struct to C for reuse */ 2036 C->product->data = ptap; 2037 C->product->destroy = MatDestroy_MPIAIJ_PtAP; 2038 ptap->merge = merge; 2039 2040 C->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ; 2041 2042 #if defined(PETSC_USE_INFO) 2043 if (bi[pn] != 0) { 2044 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 2045 ierr = PetscInfo1(C,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 2046 } else { 2047 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 2048 } 2049 #endif 2050 PetscFunctionReturn(0); 2051 } 2052 2053 /* ---------------------------------------------------------------- */ 2054 static PetscErrorCode MatProductSymbolic_AtB_MPIAIJ_MPIAIJ(Mat C) 2055 { 2056 PetscErrorCode ierr; 2057 Mat_Product *product = C->product; 2058 Mat A=product->A,B=product->B; 2059 PetscReal fill=product->fill; 2060 PetscBool flg; 2061 2062 PetscFunctionBegin; 2063 /* scalable */ 2064 ierr = PetscStrcmp(product->alg,"scalable",&flg);CHKERRQ(ierr); 2065 if (flg) { 2066 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 2067 goto next; 2068 } 2069 2070 /* nonscalable */ 2071 ierr = PetscStrcmp(product->alg,"nonscalable",&flg);CHKERRQ(ierr); 2072 if (flg) { 2073 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(A,B,fill,C);CHKERRQ(ierr); 2074 goto next; 2075 } 2076 2077 /* matmatmult */ 2078 ierr = PetscStrcmp(product->alg,"at*b",&flg);CHKERRQ(ierr); 2079 if (flg) { 2080 Mat At; 2081 Mat_APMPI *ptap; 2082 2083 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 2084 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ(At,B,fill,C);CHKERRQ(ierr); 2085 ptap = (Mat_APMPI*)C->product->data; 2086 if (ptap) { 2087 ptap->Pt = At; 2088 C->product->destroy = MatDestroy_MPIAIJ_PtAP; 2089 } 2090 C->ops->transposematmultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult; 2091 goto next; 2092 } 2093 2094 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MatProduct type is not supported"); 2095 2096 next: 2097 C->ops->productnumeric = MatProductNumeric_AtB; 2098 PetscFunctionReturn(0); 2099 } 2100 2101 /* ---------------------------------------------------------------- */ 2102 /* Set options for MatMatMultxxx_MPIAIJ_MPIAIJ */ 2103 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_AB(Mat C) 2104 { 2105 PetscErrorCode ierr; 2106 Mat_Product *product = C->product; 2107 Mat A=product->A,B=product->B; 2108 #if defined(PETSC_HAVE_HYPRE) 2109 const char *algTypes[4] = {"scalable","nonscalable","seqmpi","hypre"}; 2110 PetscInt nalg = 4; 2111 #else 2112 const char *algTypes[3] = {"scalable","nonscalable","seqmpi"}; 2113 PetscInt nalg = 3; 2114 #endif 2115 PetscInt alg = 1; /* set nonscalable algorithm as default */ 2116 PetscBool flg; 2117 MPI_Comm comm; 2118 2119 PetscFunctionBegin; 2120 /* Check matrix local sizes */ 2121 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2122 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%D, %D) != (%D,%D)",A->cmap->rstart,A->cmap->rend,B->rmap->rstart,B->rmap->rend); 2123 2124 /* Set "nonscalable" as default algorithm */ 2125 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2126 if (flg) { 2127 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2128 2129 /* Set "scalable" as default if BN and local nonzeros of A and B are large */ 2130 if (B->cmap->N > 100000) { /* may switch to scalable algorithm as default */ 2131 MatInfo Ainfo,Binfo; 2132 PetscInt nz_local; 2133 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 2134 2135 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 2136 ierr = MatGetInfo(B,MAT_LOCAL,&Binfo);CHKERRQ(ierr); 2137 nz_local = (PetscInt)(Ainfo.nz_allocated + Binfo.nz_allocated); 2138 2139 if (B->cmap->N > product->fill*nz_local) alg_scalable_loc = PETSC_TRUE; 2140 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 2141 2142 if (alg_scalable) { 2143 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 2144 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2145 ierr = PetscInfo2(B,"Use scalable algorithm, BN %D, fill*nz_allocated %g\n",B->cmap->N,product->fill*nz_local);CHKERRQ(ierr); 2146 } 2147 } 2148 } 2149 2150 /* Get runtime option */ 2151 if (product->api_user) { 2152 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatMatMult","Mat");CHKERRQ(ierr); 2153 ierr = PetscOptionsEList("-matmatmult_via","Algorithmic approach","MatMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2154 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2155 } else { 2156 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_AB","Mat");CHKERRQ(ierr); 2157 ierr = PetscOptionsEList("-matproduct_ab_via","Algorithmic approach","MatMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2158 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2159 } 2160 if (flg) { 2161 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2162 } 2163 2164 C->ops->productsymbolic = MatProductSymbolic_AB_MPIAIJ_MPIAIJ; 2165 PetscFunctionReturn(0); 2166 } 2167 2168 /* Set options for MatTransposeMatMultXXX_MPIAIJ_MPIAIJ */ 2169 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_AtB(Mat C) 2170 { 2171 PetscErrorCode ierr; 2172 Mat_Product *product = C->product; 2173 Mat A=product->A,B=product->B; 2174 const char *algTypes[3] = {"scalable","nonscalable","at*b"}; 2175 PetscInt nalg = 3; 2176 PetscInt alg = 1; /* set default algorithm */ 2177 PetscBool flg; 2178 MPI_Comm comm; 2179 2180 PetscFunctionBegin; 2181 /* Check matrix local sizes */ 2182 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2183 if (A->rmap->rstart != B->rmap->rstart || A->rmap->rend != B->rmap->rend) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, A (%D, %D) != B (%D,%D)",A->rmap->rstart,A->rmap->rend,B->rmap->rstart,B->rmap->rend); 2184 2185 /* Set default algorithm */ 2186 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2187 if (flg) { 2188 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2189 } 2190 2191 /* Set "scalable" as default if BN and local nonzeros of A and B are large */ 2192 if (alg && B->cmap->N > 100000) { /* may switch to scalable algorithm as default */ 2193 MatInfo Ainfo,Binfo; 2194 PetscInt nz_local; 2195 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 2196 2197 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 2198 ierr = MatGetInfo(B,MAT_LOCAL,&Binfo);CHKERRQ(ierr); 2199 nz_local = (PetscInt)(Ainfo.nz_allocated + Binfo.nz_allocated); 2200 2201 if (B->cmap->N > product->fill*nz_local) alg_scalable_loc = PETSC_TRUE; 2202 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 2203 2204 if (alg_scalable) { 2205 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 2206 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2207 ierr = PetscInfo2(B,"Use scalable algorithm, BN %D, fill*nz_allocated %g\n",B->cmap->N,product->fill*nz_local);CHKERRQ(ierr); 2208 } 2209 } 2210 2211 /* Get runtime option */ 2212 if (product->api_user) { 2213 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatTransposeMatMult","Mat");CHKERRQ(ierr); 2214 ierr = PetscOptionsEList("-mattransposematmult_via","Algorithmic approach","MatTransposeMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2215 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2216 } else { 2217 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_AtB","Mat");CHKERRQ(ierr); 2218 ierr = PetscOptionsEList("-matproduct_atb_via","Algorithmic approach","MatTransposeMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2219 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2220 } 2221 if (flg) { 2222 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2223 } 2224 2225 C->ops->productsymbolic = MatProductSymbolic_AtB_MPIAIJ_MPIAIJ; 2226 PetscFunctionReturn(0); 2227 } 2228 2229 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_PtAP(Mat C) 2230 { 2231 PetscErrorCode ierr; 2232 Mat_Product *product = C->product; 2233 Mat A=product->A,P=product->B; 2234 MPI_Comm comm; 2235 PetscBool flg; 2236 PetscInt alg=1; /* set default algorithm */ 2237 #if !defined(PETSC_HAVE_HYPRE) 2238 const char *algTypes[4] = {"scalable","nonscalable","allatonce","allatonce_merged"}; 2239 PetscInt nalg=4; 2240 #else 2241 const char *algTypes[5] = {"scalable","nonscalable","allatonce","allatonce_merged","hypre"}; 2242 PetscInt nalg=5; 2243 #endif 2244 PetscInt pN=P->cmap->N; 2245 2246 PetscFunctionBegin; 2247 /* Check matrix local sizes */ 2248 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2249 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) SETERRQ4(PETSC_COMM_SELF,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); 2250 if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend) SETERRQ4(PETSC_COMM_SELF,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); 2251 2252 /* Set "nonscalable" as default algorithm */ 2253 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2254 if (flg) { 2255 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2256 2257 /* Set "scalable" as default if BN and local nonzeros of A and B are large */ 2258 if (pN > 100000) { 2259 MatInfo Ainfo,Pinfo; 2260 PetscInt nz_local; 2261 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 2262 2263 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 2264 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 2265 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); 2266 2267 if (pN > product->fill*nz_local) alg_scalable_loc = PETSC_TRUE; 2268 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 2269 2270 if (alg_scalable) { 2271 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 2272 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2273 } 2274 } 2275 } 2276 2277 /* Get runtime option */ 2278 if (product->api_user) { 2279 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 2280 ierr = PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2281 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2282 } else { 2283 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_PtAP","Mat");CHKERRQ(ierr); 2284 ierr = PetscOptionsEList("-matproduct_ptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2285 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2286 } 2287 if (flg) { 2288 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2289 } 2290 2291 C->ops->productsymbolic = MatProductSymbolic_PtAP_MPIAIJ_MPIAIJ; 2292 PetscFunctionReturn(0); 2293 } 2294 2295 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_RARt(Mat C) 2296 { 2297 Mat_Product *product = C->product; 2298 Mat A = product->A,R=product->B; 2299 2300 PetscFunctionBegin; 2301 /* Check matrix local sizes */ 2302 if (A->cmap->n != R->cmap->n || A->rmap->n != R->cmap->n) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, A local (%D, %D), R local (%D,%D)",A->rmap->n,A->rmap->n,R->rmap->n,R->cmap->n); 2303 2304 C->ops->productsymbolic = MatProductSymbolic_RARt_MPIAIJ_MPIAIJ; 2305 PetscFunctionReturn(0); 2306 } 2307 2308 /* 2309 Set options for ABC = A*B*C = A*(B*C); ABC's algorithm must be chosen from AB's algorithm 2310 */ 2311 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_ABC(Mat C) 2312 { 2313 PetscErrorCode ierr; 2314 Mat_Product *product = C->product; 2315 PetscBool flg = PETSC_FALSE; 2316 PetscInt alg = 1; /* default algorithm */ 2317 const char *algTypes[3] = {"scalable","nonscalable","seqmpi"}; 2318 PetscInt nalg = 3; 2319 2320 PetscFunctionBegin; 2321 /* Set default algorithm */ 2322 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2323 if (flg) { 2324 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2325 } 2326 2327 /* Get runtime option */ 2328 if (product->api_user) { 2329 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatMatMatMult","Mat");CHKERRQ(ierr); 2330 ierr = PetscOptionsEList("-matmatmatmult_via","Algorithmic approach","MatMatMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2331 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2332 } else { 2333 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_ABC","Mat");CHKERRQ(ierr); 2334 ierr = PetscOptionsEList("-matproduct_abc_via","Algorithmic approach","MatProduct_ABC",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2335 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2336 } 2337 if (flg) { 2338 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2339 } 2340 2341 C->ops->matmatmultsymbolic = MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ; 2342 C->ops->productsymbolic = MatProductSymbolic_ABC; 2343 PetscFunctionReturn(0); 2344 } 2345 2346 PETSC_INTERN PetscErrorCode MatProductSetFromOptions_MPIAIJ(Mat C) 2347 { 2348 PetscErrorCode ierr; 2349 Mat_Product *product = C->product; 2350 2351 PetscFunctionBegin; 2352 switch (product->type) { 2353 case MATPRODUCT_AB: 2354 ierr = MatProductSetFromOptions_MPIAIJ_AB(C);CHKERRQ(ierr); 2355 break; 2356 case MATPRODUCT_AtB: 2357 ierr = MatProductSetFromOptions_MPIAIJ_AtB(C);CHKERRQ(ierr); 2358 break; 2359 case MATPRODUCT_PtAP: 2360 ierr = MatProductSetFromOptions_MPIAIJ_PtAP(C);CHKERRQ(ierr); 2361 break; 2362 case MATPRODUCT_RARt: 2363 ierr = MatProductSetFromOptions_MPIAIJ_RARt(C);CHKERRQ(ierr); 2364 break; 2365 case MATPRODUCT_ABC: 2366 ierr = MatProductSetFromOptions_MPIAIJ_ABC(C);CHKERRQ(ierr); 2367 break; 2368 default: 2369 break; 2370 } 2371 PetscFunctionReturn(0); 2372 } 2373