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/sfimpl.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 /* backend general code */ 50 ierr = PetscStrcmp(alg,"backend",&flg);CHKERRQ(ierr); 51 if (flg) { 52 ierr = MatProductSymbolic_MPIAIJBACKEND(C);CHKERRQ(ierr); 53 PetscFunctionReturn(0); 54 } 55 56 #if defined(PETSC_HAVE_HYPRE) 57 ierr = PetscStrcmp(alg,"hypre",&flg);CHKERRQ(ierr); 58 if (flg) { 59 ierr = MatMatMultSymbolic_AIJ_AIJ_wHYPRE(A,B,fill,C);CHKERRQ(ierr); 60 PetscFunctionReturn(0); 61 } 62 #endif 63 SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_SUP,"Mat Product Algorithm is not supported"); 64 } 65 66 PetscErrorCode MatDestroy_MPIAIJ_MatMatMult(void *data) 67 { 68 PetscErrorCode ierr; 69 Mat_APMPI *ptap = (Mat_APMPI*)data; 70 71 PetscFunctionBegin; 72 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 73 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 74 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 75 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 76 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 77 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 78 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 79 ierr = PetscFree(ptap->apa);CHKERRQ(ierr); 80 ierr = PetscFree(ptap);CHKERRQ(ierr); 81 PetscFunctionReturn(0); 82 } 83 84 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,Mat C) 85 { 86 PetscErrorCode ierr; 87 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 88 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 89 Mat_SeqAIJ *cd =(Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 90 PetscScalar *cda=cd->a,*coa=co->a; 91 Mat_SeqAIJ *p_loc,*p_oth; 92 PetscScalar *apa,*ca; 93 PetscInt cm =C->rmap->n; 94 Mat_APMPI *ptap; 95 PetscInt *api,*apj,*apJ,i,k; 96 PetscInt cstart=C->cmap->rstart; 97 PetscInt cdnz,conz,k0,k1; 98 MPI_Comm comm; 99 PetscMPIInt size; 100 101 PetscFunctionBegin; 102 MatCheckProduct(C,3); 103 ptap = (Mat_APMPI*)C->product->data; 104 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 105 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 106 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 107 108 if (!ptap->P_oth && size>1) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"AP cannot be reused. Do not call MatProductClear()"); 109 110 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 111 /*-----------------------------------------------------*/ 112 /* update numerical values of P_oth and P_loc */ 113 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 114 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 115 116 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 117 /*----------------------------------------------------------*/ 118 /* get data from symbolic products */ 119 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 120 p_oth = NULL; 121 if (size >1) { 122 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 123 } 124 125 /* get apa for storing dense row A[i,:]*P */ 126 apa = ptap->apa; 127 128 api = ptap->api; 129 apj = ptap->apj; 130 for (i=0; i<cm; i++) { 131 /* compute apa = A[i,:]*P */ 132 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 133 134 /* set values in C */ 135 apJ = apj + api[i]; 136 cdnz = cd->i[i+1] - cd->i[i]; 137 conz = co->i[i+1] - co->i[i]; 138 139 /* 1st off-diagonal part of C */ 140 ca = coa + co->i[i]; 141 k = 0; 142 for (k0=0; k0<conz; k0++) { 143 if (apJ[k] >= cstart) break; 144 ca[k0] = apa[apJ[k]]; 145 apa[apJ[k++]] = 0.0; 146 } 147 148 /* diagonal part of C */ 149 ca = cda + cd->i[i]; 150 for (k1=0; k1<cdnz; k1++) { 151 ca[k1] = apa[apJ[k]]; 152 apa[apJ[k++]] = 0.0; 153 } 154 155 /* 2nd off-diagonal part of C */ 156 ca = coa + co->i[i]; 157 for (; k0<conz; k0++) { 158 ca[k0] = apa[apJ[k]]; 159 apa[apJ[k++]] = 0.0; 160 } 161 } 162 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 163 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 164 PetscFunctionReturn(0); 165 } 166 167 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,PetscReal fill,Mat C) 168 { 169 PetscErrorCode ierr; 170 MPI_Comm comm; 171 PetscMPIInt size; 172 Mat_APMPI *ptap; 173 PetscFreeSpaceList free_space=NULL,current_space=NULL; 174 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 175 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 176 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 177 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 178 PetscInt *lnk,i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi; 179 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n; 180 PetscBT lnkbt; 181 PetscReal afill; 182 MatType mtype; 183 184 PetscFunctionBegin; 185 MatCheckProduct(C,4); 186 if (C->product->data) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Extra product struct not empty"); 187 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 188 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 189 190 /* create struct Mat_APMPI and attached it to C later */ 191 ierr = PetscNew(&ptap);CHKERRQ(ierr); 192 193 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 194 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 195 196 /* get P_loc by taking all local rows of P */ 197 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 198 199 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 200 pi_loc = p_loc->i; pj_loc = p_loc->j; 201 if (size > 1) { 202 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 203 pi_oth = p_oth->i; pj_oth = p_oth->j; 204 } else { 205 p_oth = NULL; 206 pi_oth = NULL; pj_oth = NULL; 207 } 208 209 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 210 /*-------------------------------------------------------------------*/ 211 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 212 ptap->api = api; 213 api[0] = 0; 214 215 /* create and initialize a linked list */ 216 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 217 218 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 219 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 220 current_space = free_space; 221 222 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 223 for (i=0; i<am; i++) { 224 /* diagonal portion of A */ 225 nzi = adi[i+1] - adi[i]; 226 for (j=0; j<nzi; j++) { 227 row = *adj++; 228 pnz = pi_loc[row+1] - pi_loc[row]; 229 Jptr = pj_loc + pi_loc[row]; 230 /* add non-zero cols of P into the sorted linked list lnk */ 231 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 232 } 233 /* off-diagonal portion of A */ 234 nzi = aoi[i+1] - aoi[i]; 235 for (j=0; j<nzi; j++) { 236 row = *aoj++; 237 pnz = pi_oth[row+1] - pi_oth[row]; 238 Jptr = pj_oth + pi_oth[row]; 239 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 240 } 241 /* add possible missing diagonal entry */ 242 if (C->force_diagonals) { 243 j = i + rstart; /* column index */ 244 ierr = PetscLLCondensedAddSorted(1,&j,lnk,lnkbt);CHKERRQ(ierr); 245 } 246 247 apnz = lnk[0]; 248 api[i+1] = api[i] + apnz; 249 250 /* if free space is not available, double the total space in the list */ 251 if (current_space->local_remaining<apnz) { 252 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 253 nspacedouble++; 254 } 255 256 /* Copy data into free space, then initialize lnk */ 257 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 258 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 259 260 current_space->array += apnz; 261 current_space->local_used += apnz; 262 current_space->local_remaining -= apnz; 263 } 264 265 /* Allocate space for apj, initialize apj, and */ 266 /* destroy list of free space and other temporary array(s) */ 267 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 268 apj = ptap->apj; 269 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 270 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 271 272 /* malloc apa to store dense row A[i,:]*P */ 273 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 274 275 /* set and assemble symbolic parallel matrix C */ 276 /*---------------------------------------------*/ 277 ierr = MatSetSizes(C,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 278 ierr = MatSetBlockSizesFromMats(C,A,P);CHKERRQ(ierr); 279 280 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 281 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 282 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 283 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 284 285 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(C, apj, api);CHKERRQ(ierr); 286 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 287 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 288 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 289 290 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 291 C->ops->productnumeric = MatProductNumeric_AB; 292 293 /* attach the supporting struct to C for reuse */ 294 C->product->data = ptap; 295 C->product->destroy = MatDestroy_MPIAIJ_MatMatMult; 296 297 /* set MatInfo */ 298 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 299 if (afill < 1.0) afill = 1.0; 300 C->info.mallocs = nspacedouble; 301 C->info.fill_ratio_given = fill; 302 C->info.fill_ratio_needed = afill; 303 304 #if defined(PETSC_USE_INFO) 305 if (api[am]) { 306 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 307 ierr = PetscInfo1(C,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 308 } else { 309 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 310 } 311 #endif 312 PetscFunctionReturn(0); 313 } 314 315 /* ------------------------------------------------------- */ 316 static PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat,Mat,PetscReal,Mat); 317 static PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat,Mat,Mat); 318 319 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_MPIDense_AB(Mat C) 320 { 321 Mat_Product *product = C->product; 322 Mat A = product->A,B=product->B; 323 324 PetscFunctionBegin; 325 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) 326 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); 327 328 C->ops->matmultsymbolic = MatMatMultSymbolic_MPIAIJ_MPIDense; 329 C->ops->productsymbolic = MatProductSymbolic_AB; 330 PetscFunctionReturn(0); 331 } 332 /* -------------------------------------------------------------------- */ 333 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_MPIDense_AtB(Mat C) 334 { 335 Mat_Product *product = C->product; 336 Mat A = product->A,B=product->B; 337 338 PetscFunctionBegin; 339 if (A->rmap->rstart != B->rmap->rstart || A->rmap->rend != B->rmap->rend) 340 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); 341 342 C->ops->transposematmultsymbolic = MatTransposeMatMultSymbolic_MPIAIJ_MPIDense; 343 C->ops->productsymbolic = MatProductSymbolic_AtB; 344 PetscFunctionReturn(0); 345 } 346 347 /* --------------------------------------------------------------------- */ 348 PETSC_INTERN PetscErrorCode MatProductSetFromOptions_MPIAIJ_MPIDense(Mat C) 349 { 350 PetscErrorCode ierr; 351 Mat_Product *product = C->product; 352 353 PetscFunctionBegin; 354 switch (product->type) { 355 case MATPRODUCT_AB: 356 ierr = MatProductSetFromOptions_MPIAIJ_MPIDense_AB(C);CHKERRQ(ierr); 357 break; 358 case MATPRODUCT_AtB: 359 ierr = MatProductSetFromOptions_MPIAIJ_MPIDense_AtB(C);CHKERRQ(ierr); 360 break; 361 default: 362 break; 363 } 364 PetscFunctionReturn(0); 365 } 366 /* ------------------------------------------------------- */ 367 368 typedef struct { 369 Mat workB,workB1; 370 MPI_Request *rwaits,*swaits; 371 PetscInt nsends,nrecvs; 372 MPI_Datatype *stype,*rtype; 373 PetscInt blda; 374 } MPIAIJ_MPIDense; 375 376 PetscErrorCode MatMPIAIJ_MPIDenseDestroy(void *ctx) 377 { 378 MPIAIJ_MPIDense *contents = (MPIAIJ_MPIDense*)ctx; 379 PetscErrorCode ierr; 380 PetscInt i; 381 382 PetscFunctionBegin; 383 ierr = MatDestroy(&contents->workB);CHKERRQ(ierr); 384 ierr = MatDestroy(&contents->workB1);CHKERRQ(ierr); 385 for (i=0; i<contents->nsends; i++) { 386 ierr = MPI_Type_free(&contents->stype[i]);CHKERRMPI(ierr); 387 } 388 for (i=0; i<contents->nrecvs; i++) { 389 ierr = MPI_Type_free(&contents->rtype[i]);CHKERRMPI(ierr); 390 } 391 ierr = PetscFree4(contents->stype,contents->rtype,contents->rwaits,contents->swaits);CHKERRQ(ierr); 392 ierr = PetscFree(contents);CHKERRQ(ierr); 393 PetscFunctionReturn(0); 394 } 395 396 static PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat A,Mat B,PetscReal fill,Mat C) 397 { 398 PetscErrorCode ierr; 399 Mat_MPIAIJ *aij=(Mat_MPIAIJ*)A->data; 400 PetscInt nz=aij->B->cmap->n,nsends,nrecvs,i,nrows_to,j,blda,clda; 401 MPIAIJ_MPIDense *contents; 402 VecScatter ctx=aij->Mvctx; 403 PetscInt Am=A->rmap->n,Bm=B->rmap->n,BN=B->cmap->N,Bbn,Bbn1,bs,nrows_from,numBb; 404 MPI_Comm comm; 405 MPI_Datatype type1,*stype,*rtype; 406 const PetscInt *sindices,*sstarts,*rstarts; 407 PetscMPIInt *disp; 408 PetscBool cisdense; 409 410 PetscFunctionBegin; 411 MatCheckProduct(C,4); 412 if (C->product->data) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_PLIB,"Product data not empty"); 413 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 414 ierr = PetscObjectBaseTypeCompare((PetscObject)C,MATMPIDENSE,&cisdense);CHKERRQ(ierr); 415 if (!cisdense) { 416 ierr = MatSetType(C,((PetscObject)B)->type_name);CHKERRQ(ierr); 417 } 418 ierr = MatSetSizes(C,Am,B->cmap->n,A->rmap->N,BN);CHKERRQ(ierr); 419 ierr = MatSetBlockSizesFromMats(C,A,B);CHKERRQ(ierr); 420 ierr = MatSetUp(C);CHKERRQ(ierr); 421 ierr = MatDenseGetLDA(B,&blda);CHKERRQ(ierr); 422 ierr = MatDenseGetLDA(C,&clda);CHKERRQ(ierr); 423 ierr = PetscNew(&contents);CHKERRQ(ierr); 424 425 ierr = VecScatterGetRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,NULL,NULL);CHKERRQ(ierr); 426 ierr = VecScatterGetRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,NULL,NULL);CHKERRQ(ierr); 427 428 /* Create column block of B and C for memory scalability when BN is too large */ 429 /* Estimate Bbn, column size of Bb */ 430 if (nz) { 431 Bbn1 = 2*Am*BN/nz; 432 } else Bbn1 = BN; 433 434 bs = PetscAbs(B->cmap->bs); 435 Bbn1 = Bbn1/bs *bs; /* Bbn1 is a multiple of bs */ 436 if (Bbn1 > BN) Bbn1 = BN; 437 ierr = MPI_Allreduce(&Bbn1,&Bbn,1,MPIU_INT,MPI_MAX,comm);CHKERRMPI(ierr); 438 439 /* Enable runtime option for Bbn */ 440 ierr = PetscOptionsBegin(comm,((PetscObject)C)->prefix,"MatMatMult","Mat");CHKERRQ(ierr); 441 ierr = PetscOptionsInt("-matmatmult_Bbn","Number of columns in Bb","MatMatMult",Bbn,&Bbn,NULL);CHKERRQ(ierr); 442 ierr = PetscOptionsEnd();CHKERRQ(ierr); 443 Bbn = PetscMin(Bbn,BN); 444 445 if (Bbn > 0 && Bbn < BN) { 446 numBb = BN/Bbn; 447 Bbn1 = BN - numBb*Bbn; 448 } else numBb = 0; 449 450 if (numBb) { 451 ierr = PetscInfo3(C,"use Bb, BN=%D, Bbn=%D; numBb=%D\n",BN,Bbn,numBb);CHKERRQ(ierr); 452 if (Bbn1) { /* Create workB1 for the remaining columns */ 453 ierr = PetscInfo2(C,"use Bb1, BN=%D, Bbn1=%D\n",BN,Bbn1);CHKERRQ(ierr); 454 /* Create work matrix used to store off processor rows of B needed for local product */ 455 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,Bbn1,NULL,&contents->workB1);CHKERRQ(ierr); 456 } else contents->workB1 = NULL; 457 } 458 459 /* Create work matrix used to store off processor rows of B needed for local product */ 460 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,Bbn,NULL,&contents->workB);CHKERRQ(ierr); 461 462 /* Use MPI derived data type to reduce memory required by the send/recv buffers */ 463 ierr = PetscMalloc4(nsends,&stype,nrecvs,&rtype,nrecvs,&contents->rwaits,nsends,&contents->swaits);CHKERRQ(ierr); 464 contents->stype = stype; 465 contents->nsends = nsends; 466 467 contents->rtype = rtype; 468 contents->nrecvs = nrecvs; 469 contents->blda = blda; 470 471 ierr = PetscMalloc1(Bm+1,&disp);CHKERRQ(ierr); 472 for (i=0; i<nsends; i++) { 473 nrows_to = sstarts[i+1]-sstarts[i]; 474 for (j=0; j<nrows_to; j++){ 475 disp[j] = sindices[sstarts[i]+j]; /* rowB to be sent */ 476 } 477 ierr = MPI_Type_create_indexed_block(nrows_to,1,(const PetscMPIInt *)disp,MPIU_SCALAR,&type1);CHKERRMPI(ierr); 478 479 ierr = MPI_Type_create_resized(type1,0,blda*sizeof(PetscScalar),&stype[i]);CHKERRMPI(ierr); 480 ierr = MPI_Type_commit(&stype[i]);CHKERRMPI(ierr); 481 ierr = MPI_Type_free(&type1);CHKERRMPI(ierr); 482 } 483 484 for (i=0; i<nrecvs; i++) { 485 /* received values from a process form a (nrows_from x Bbn) row block in workB (column-wise) */ 486 nrows_from = rstarts[i+1]-rstarts[i]; 487 disp[0] = 0; 488 ierr = MPI_Type_create_indexed_block(1, nrows_from, (const PetscMPIInt *)disp, MPIU_SCALAR, &type1);CHKERRMPI(ierr); 489 ierr = MPI_Type_create_resized(type1, 0, nz*sizeof(PetscScalar), &rtype[i]);CHKERRMPI(ierr); 490 ierr = MPI_Type_commit(&rtype[i]);CHKERRMPI(ierr); 491 ierr = MPI_Type_free(&type1);CHKERRMPI(ierr); 492 } 493 494 ierr = PetscFree(disp);CHKERRQ(ierr); 495 ierr = VecScatterRestoreRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,NULL,NULL);CHKERRQ(ierr); 496 ierr = VecScatterRestoreRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,NULL,NULL);CHKERRQ(ierr); 497 ierr = MatSetOption(C,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 498 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 499 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 500 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 501 502 C->product->data = contents; 503 C->product->destroy = MatMPIAIJ_MPIDenseDestroy; 504 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 505 PetscFunctionReturn(0); 506 } 507 508 PETSC_INTERN PetscErrorCode MatMatMultNumericAdd_SeqAIJ_SeqDense(Mat,Mat,Mat,const PetscBool); 509 /* 510 Performs an efficient scatter on the rows of B needed by this process; this is 511 a modification of the VecScatterBegin_() routines. 512 513 Input: Bbidx = 0: B = Bb 514 = 1: B = Bb1, see MatMatMultSymbolic_MPIAIJ_MPIDense() 515 */ 516 PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,PetscInt Bbidx,Mat C,Mat *outworkB) 517 { 518 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 519 PetscErrorCode ierr; 520 const PetscScalar *b; 521 PetscScalar *rvalues; 522 VecScatter ctx = aij->Mvctx; 523 const PetscInt *sindices,*sstarts,*rstarts; 524 const PetscMPIInt *sprocs,*rprocs; 525 PetscInt i,nsends,nrecvs; 526 MPI_Request *swaits,*rwaits; 527 MPI_Comm comm; 528 PetscMPIInt tag=((PetscObject)ctx)->tag,ncols=B->cmap->N,nrows=aij->B->cmap->n,nsends_mpi,nrecvs_mpi; 529 MPIAIJ_MPIDense *contents; 530 Mat workB; 531 MPI_Datatype *stype,*rtype; 532 PetscInt blda; 533 534 PetscFunctionBegin; 535 MatCheckProduct(C,4); 536 if (!C->product->data) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_PLIB,"Product data empty"); 537 contents = (MPIAIJ_MPIDense*)C->product->data; 538 ierr = VecScatterGetRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,&sprocs,NULL/*bs*/);CHKERRQ(ierr); 539 ierr = VecScatterGetRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,&rprocs,NULL/*bs*/);CHKERRQ(ierr); 540 ierr = PetscMPIIntCast(nsends,&nsends_mpi);CHKERRQ(ierr); 541 ierr = PetscMPIIntCast(nrecvs,&nrecvs_mpi);CHKERRQ(ierr); 542 if (Bbidx == 0) { 543 workB = *outworkB = contents->workB; 544 } else { 545 workB = *outworkB = contents->workB1; 546 } 547 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); 548 swaits = contents->swaits; 549 rwaits = contents->rwaits; 550 551 ierr = MatDenseGetArrayRead(B,&b);CHKERRQ(ierr); 552 ierr = MatDenseGetLDA(B,&blda);CHKERRQ(ierr); 553 if (blda != contents->blda) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Cannot reuse an input matrix with lda %D != %D",blda,contents->blda); 554 ierr = MatDenseGetArray(workB,&rvalues);CHKERRQ(ierr); 555 556 /* Post recv, use MPI derived data type to save memory */ 557 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 558 rtype = contents->rtype; 559 for (i=0; i<nrecvs; i++) { 560 ierr = MPI_Irecv(rvalues+(rstarts[i]-rstarts[0]),ncols,rtype[i],rprocs[i],tag,comm,rwaits+i);CHKERRMPI(ierr); 561 } 562 563 stype = contents->stype; 564 for (i=0; i<nsends; i++) { 565 ierr = MPI_Isend(b,ncols,stype[i],sprocs[i],tag,comm,swaits+i);CHKERRMPI(ierr); 566 } 567 568 if (nrecvs) {ierr = MPI_Waitall(nrecvs_mpi,rwaits,MPI_STATUSES_IGNORE);CHKERRMPI(ierr);} 569 if (nsends) {ierr = MPI_Waitall(nsends_mpi,swaits,MPI_STATUSES_IGNORE);CHKERRMPI(ierr);} 570 571 ierr = VecScatterRestoreRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,&sprocs,NULL);CHKERRQ(ierr); 572 ierr = VecScatterRestoreRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,&rprocs,NULL);CHKERRQ(ierr); 573 ierr = MatDenseRestoreArrayRead(B,&b);CHKERRQ(ierr); 574 ierr = MatDenseRestoreArray(workB,&rvalues);CHKERRQ(ierr); 575 PetscFunctionReturn(0); 576 } 577 578 static PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat A,Mat B,Mat C) 579 { 580 PetscErrorCode ierr; 581 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 582 Mat_MPIDense *bdense = (Mat_MPIDense*)B->data; 583 Mat_MPIDense *cdense = (Mat_MPIDense*)C->data; 584 Mat workB; 585 MPIAIJ_MPIDense *contents; 586 587 PetscFunctionBegin; 588 MatCheckProduct(C,3); 589 if (!C->product->data) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_PLIB,"Product data empty"); 590 contents = (MPIAIJ_MPIDense*)C->product->data; 591 /* diagonal block of A times all local rows of B */ 592 /* TODO: this calls a symbolic multiplication every time, which could be avoided */ 593 ierr = MatMatMult(aij->A,bdense->A,MAT_REUSE_MATRIX,PETSC_DEFAULT,&cdense->A);CHKERRQ(ierr); 594 if (contents->workB->cmap->n == B->cmap->N) { 595 /* get off processor parts of B needed to complete C=A*B */ 596 ierr = MatMPIDenseScatter(A,B,0,C,&workB);CHKERRQ(ierr); 597 598 /* off-diagonal block of A times nonlocal rows of B */ 599 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A,PETSC_TRUE);CHKERRQ(ierr); 600 } else { 601 Mat Bb,Cb; 602 PetscInt BN=B->cmap->N,n=contents->workB->cmap->n,i; 603 604 for (i=0; i<BN; i+=n) { 605 ierr = MatDenseGetSubMatrix(B,i,PetscMin(i+n,BN),&Bb);CHKERRQ(ierr); 606 ierr = MatDenseGetSubMatrix(C,i,PetscMin(i+n,BN),&Cb);CHKERRQ(ierr); 607 608 /* get off processor parts of B needed to complete C=A*B */ 609 ierr = MatMPIDenseScatter(A,Bb,i+n>BN,C,&workB);CHKERRQ(ierr); 610 611 /* off-diagonal block of A times nonlocal rows of B */ 612 cdense = (Mat_MPIDense*)Cb->data; 613 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A,PETSC_TRUE);CHKERRQ(ierr); 614 615 ierr = MatDenseRestoreSubMatrix(B,&Bb);CHKERRQ(ierr); 616 ierr = MatDenseRestoreSubMatrix(C,&Cb);CHKERRQ(ierr); 617 } 618 } 619 PetscFunctionReturn(0); 620 } 621 622 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 623 { 624 PetscErrorCode ierr; 625 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 626 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 627 Mat_SeqAIJ *cd = (Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 628 PetscInt *adi = ad->i,*adj,*aoi=ao->i,*aoj; 629 PetscScalar *ada,*aoa,*cda=cd->a,*coa=co->a; 630 Mat_SeqAIJ *p_loc,*p_oth; 631 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pj; 632 PetscScalar *pa_loc,*pa_oth,*pa,valtmp,*ca; 633 PetscInt cm = C->rmap->n,anz,pnz; 634 Mat_APMPI *ptap; 635 PetscScalar *apa_sparse; 636 PetscInt *api,*apj,*apJ,i,j,k,row; 637 PetscInt cstart = C->cmap->rstart; 638 PetscInt cdnz,conz,k0,k1,nextp; 639 MPI_Comm comm; 640 PetscMPIInt size; 641 642 PetscFunctionBegin; 643 MatCheckProduct(C,3); 644 ptap = (Mat_APMPI*)C->product->data; 645 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 646 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 647 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 648 if (!ptap->P_oth && size>1) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"AP cannot be reused. Do not call MatProductClear()"); 649 650 apa_sparse = ptap->apa; 651 652 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 653 /*-----------------------------------------------------*/ 654 /* update numerical values of P_oth and P_loc */ 655 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 656 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 657 658 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 659 /*----------------------------------------------------------*/ 660 /* get data from symbolic products */ 661 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 662 pi_loc = p_loc->i; pj_loc = p_loc->j; pa_loc = p_loc->a; 663 if (size >1) { 664 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 665 pi_oth = p_oth->i; pj_oth = p_oth->j; pa_oth = p_oth->a; 666 } else { 667 p_oth = NULL; pi_oth = NULL; pj_oth = NULL; pa_oth = NULL; 668 } 669 670 api = ptap->api; 671 apj = ptap->apj; 672 for (i=0; i<cm; i++) { 673 apJ = apj + api[i]; 674 675 /* diagonal portion of A */ 676 anz = adi[i+1] - adi[i]; 677 adj = ad->j + adi[i]; 678 ada = ad->a + adi[i]; 679 for (j=0; j<anz; j++) { 680 row = adj[j]; 681 pnz = pi_loc[row+1] - pi_loc[row]; 682 pj = pj_loc + pi_loc[row]; 683 pa = pa_loc + pi_loc[row]; 684 /* perform sparse axpy */ 685 valtmp = ada[j]; 686 nextp = 0; 687 for (k=0; nextp<pnz; k++) { 688 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 689 apa_sparse[k] += valtmp*pa[nextp++]; 690 } 691 } 692 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 693 } 694 695 /* off-diagonal portion of A */ 696 anz = aoi[i+1] - aoi[i]; 697 aoj = ao->j + aoi[i]; 698 aoa = ao->a + aoi[i]; 699 for (j=0; j<anz; j++) { 700 row = aoj[j]; 701 pnz = pi_oth[row+1] - pi_oth[row]; 702 pj = pj_oth + pi_oth[row]; 703 pa = pa_oth + pi_oth[row]; 704 /* perform sparse axpy */ 705 valtmp = aoa[j]; 706 nextp = 0; 707 for (k=0; nextp<pnz; k++) { 708 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 709 apa_sparse[k] += valtmp*pa[nextp++]; 710 } 711 } 712 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 713 } 714 715 /* set values in C */ 716 cdnz = cd->i[i+1] - cd->i[i]; 717 conz = co->i[i+1] - co->i[i]; 718 719 /* 1st off-diagonal part of C */ 720 ca = coa + co->i[i]; 721 k = 0; 722 for (k0=0; k0<conz; k0++) { 723 if (apJ[k] >= cstart) break; 724 ca[k0] = apa_sparse[k]; 725 apa_sparse[k] = 0.0; 726 k++; 727 } 728 729 /* diagonal part of C */ 730 ca = cda + cd->i[i]; 731 for (k1=0; k1<cdnz; k1++) { 732 ca[k1] = apa_sparse[k]; 733 apa_sparse[k] = 0.0; 734 k++; 735 } 736 737 /* 2nd off-diagonal part of C */ 738 ca = coa + co->i[i]; 739 for (; k0<conz; k0++) { 740 ca[k0] = apa_sparse[k]; 741 apa_sparse[k] = 0.0; 742 k++; 743 } 744 } 745 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 746 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 747 PetscFunctionReturn(0); 748 } 749 750 /* same as MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(), except using LLCondensed to avoid O(BN) memory requirement */ 751 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat C) 752 { 753 PetscErrorCode ierr; 754 MPI_Comm comm; 755 PetscMPIInt size; 756 Mat_APMPI *ptap; 757 PetscFreeSpaceList free_space = NULL,current_space=NULL; 758 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 759 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 760 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 761 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 762 PetscInt i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi,*lnk,apnz_max=1; 763 PetscInt am=A->rmap->n,pn=P->cmap->n,pm=P->rmap->n,lsize=pn+20; 764 PetscReal afill; 765 MatType mtype; 766 767 PetscFunctionBegin; 768 MatCheckProduct(C,4); 769 if (C->product->data) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Extra product struct not empty"); 770 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 771 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 772 773 /* create struct Mat_APMPI and attached it to C later */ 774 ierr = PetscNew(&ptap);CHKERRQ(ierr); 775 776 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 777 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 778 779 /* get P_loc by taking all local rows of P */ 780 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 781 782 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 783 pi_loc = p_loc->i; pj_loc = p_loc->j; 784 if (size > 1) { 785 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 786 pi_oth = p_oth->i; pj_oth = p_oth->j; 787 } else { 788 p_oth = NULL; 789 pi_oth = NULL; pj_oth = NULL; 790 } 791 792 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 793 /*-------------------------------------------------------------------*/ 794 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 795 ptap->api = api; 796 api[0] = 0; 797 798 ierr = PetscLLCondensedCreate_Scalable(lsize,&lnk);CHKERRQ(ierr); 799 800 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 801 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 802 current_space = free_space; 803 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 804 for (i=0; i<am; i++) { 805 /* diagonal portion of A */ 806 nzi = adi[i+1] - adi[i]; 807 for (j=0; j<nzi; j++) { 808 row = *adj++; 809 pnz = pi_loc[row+1] - pi_loc[row]; 810 Jptr = pj_loc + pi_loc[row]; 811 /* Expand list if it is not long enough */ 812 if (pnz+apnz_max > lsize) { 813 lsize = pnz+apnz_max; 814 ierr = PetscLLCondensedExpand_Scalable(lsize, &lnk);CHKERRQ(ierr); 815 } 816 /* add non-zero cols of P into the sorted linked list lnk */ 817 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 818 apnz = *lnk; /* The first element in the list is the number of items in the list */ 819 api[i+1] = api[i] + apnz; 820 if (apnz > apnz_max) apnz_max = apnz + 1; /* '1' for diagonal entry */ 821 } 822 /* off-diagonal portion of A */ 823 nzi = aoi[i+1] - aoi[i]; 824 for (j=0; j<nzi; j++) { 825 row = *aoj++; 826 pnz = pi_oth[row+1] - pi_oth[row]; 827 Jptr = pj_oth + pi_oth[row]; 828 /* Expand list if it is not long enough */ 829 if (pnz+apnz_max > lsize) { 830 lsize = pnz + apnz_max; 831 ierr = PetscLLCondensedExpand_Scalable(lsize, &lnk);CHKERRQ(ierr); 832 } 833 /* add non-zero cols of P into the sorted linked list lnk */ 834 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 835 apnz = *lnk; /* The first element in the list is the number of items in the list */ 836 api[i+1] = api[i] + apnz; 837 if (apnz > apnz_max) apnz_max = apnz + 1; /* '1' for diagonal entry */ 838 } 839 840 /* add missing diagonal entry */ 841 if (C->force_diagonals) { 842 j = i + rstart; /* column index */ 843 ierr = PetscLLCondensedAddSorted_Scalable(1,&j,lnk);CHKERRQ(ierr); 844 } 845 846 apnz = *lnk; 847 api[i+1] = api[i] + apnz; 848 if (apnz > apnz_max) apnz_max = apnz; 849 850 /* if free space is not available, double the total space in the list */ 851 if (current_space->local_remaining<apnz) { 852 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 853 nspacedouble++; 854 } 855 856 /* Copy data into free space, then initialize lnk */ 857 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 858 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 859 860 current_space->array += apnz; 861 current_space->local_used += apnz; 862 current_space->local_remaining -= apnz; 863 } 864 865 /* Allocate space for apj, initialize apj, and */ 866 /* destroy list of free space and other temporary array(s) */ 867 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 868 apj = ptap->apj; 869 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 870 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 871 872 /* create and assemble symbolic parallel matrix C */ 873 /*----------------------------------------------------*/ 874 ierr = MatSetSizes(C,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 875 ierr = MatSetBlockSizesFromMats(C,A,P);CHKERRQ(ierr); 876 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 877 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 878 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 879 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 880 881 /* malloc apa for assembly C */ 882 ierr = PetscCalloc1(apnz_max,&ptap->apa);CHKERRQ(ierr); 883 884 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(C, apj, api);CHKERRQ(ierr); 885 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 886 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 887 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 888 889 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ; 890 C->ops->productnumeric = MatProductNumeric_AB; 891 892 /* attach the supporting struct to C for reuse */ 893 C->product->data = ptap; 894 C->product->destroy = MatDestroy_MPIAIJ_MatMatMult; 895 896 /* set MatInfo */ 897 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 898 if (afill < 1.0) afill = 1.0; 899 C->info.mallocs = nspacedouble; 900 C->info.fill_ratio_given = fill; 901 C->info.fill_ratio_needed = afill; 902 903 #if defined(PETSC_USE_INFO) 904 if (api[am]) { 905 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 906 ierr = PetscInfo1(C,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 907 } else { 908 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 909 } 910 #endif 911 PetscFunctionReturn(0); 912 } 913 914 /* This function is needed for the seqMPI matrix-matrix multiplication. */ 915 /* Three input arrays are merged to one output array. The size of the */ 916 /* output array is also output. Duplicate entries only show up once. */ 917 static void Merge3SortedArrays(PetscInt size1, PetscInt *in1, 918 PetscInt size2, PetscInt *in2, 919 PetscInt size3, PetscInt *in3, 920 PetscInt *size4, PetscInt *out) 921 { 922 int i = 0, j = 0, k = 0, l = 0; 923 924 /* Traverse all three arrays */ 925 while (i<size1 && j<size2 && k<size3) { 926 if (in1[i] < in2[j] && in1[i] < in3[k]) { 927 out[l++] = in1[i++]; 928 } 929 else if (in2[j] < in1[i] && in2[j] < in3[k]) { 930 out[l++] = in2[j++]; 931 } 932 else if (in3[k] < in1[i] && in3[k] < in2[j]) { 933 out[l++] = in3[k++]; 934 } 935 else if (in1[i] == in2[j] && in1[i] < in3[k]) { 936 out[l++] = in1[i]; 937 i++, j++; 938 } 939 else if (in1[i] == in3[k] && in1[i] < in2[j]) { 940 out[l++] = in1[i]; 941 i++, k++; 942 } 943 else if (in3[k] == in2[j] && in2[j] < in1[i]) { 944 out[l++] = in2[j]; 945 k++, j++; 946 } 947 else if (in1[i] == in2[j] && in1[i] == in3[k]) { 948 out[l++] = in1[i]; 949 i++, j++, k++; 950 } 951 } 952 953 /* Traverse two remaining arrays */ 954 while (i<size1 && j<size2) { 955 if (in1[i] < in2[j]) { 956 out[l++] = in1[i++]; 957 } 958 else if (in1[i] > in2[j]) { 959 out[l++] = in2[j++]; 960 } 961 else { 962 out[l++] = in1[i]; 963 i++, j++; 964 } 965 } 966 967 while (i<size1 && k<size3) { 968 if (in1[i] < in3[k]) { 969 out[l++] = in1[i++]; 970 } 971 else if (in1[i] > in3[k]) { 972 out[l++] = in3[k++]; 973 } 974 else { 975 out[l++] = in1[i]; 976 i++, k++; 977 } 978 } 979 980 while (k<size3 && j<size2) { 981 if (in3[k] < in2[j]) { 982 out[l++] = in3[k++]; 983 } 984 else if (in3[k] > in2[j]) { 985 out[l++] = in2[j++]; 986 } 987 else { 988 out[l++] = in3[k]; 989 k++, j++; 990 } 991 } 992 993 /* Traverse one remaining array */ 994 while (i<size1) out[l++] = in1[i++]; 995 while (j<size2) out[l++] = in2[j++]; 996 while (k<size3) out[l++] = in3[k++]; 997 998 *size4 = l; 999 } 1000 1001 /* This matrix-matrix multiplication algorithm divides the multiplication into three multiplications and */ 1002 /* adds up the products. Two of these three multiplications are performed with existing (sequential) */ 1003 /* matrix-matrix multiplications. */ 1004 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI(Mat A, Mat P, PetscReal fill, Mat C) 1005 { 1006 PetscErrorCode ierr; 1007 MPI_Comm comm; 1008 PetscMPIInt size; 1009 Mat_APMPI *ptap; 1010 PetscFreeSpaceList free_space_diag=NULL, current_space=NULL; 1011 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data; 1012 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc; 1013 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data; 1014 Mat_SeqAIJ *adpd_seq, *p_off, *aopoth_seq; 1015 PetscInt adponz, adpdnz; 1016 PetscInt *pi_loc,*dnz,*onz; 1017 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,rstart=A->rmap->rstart; 1018 PetscInt *lnk,i, i1=0,pnz,row,*adpoi,*adpoj, *api, *adpoJ, *aopJ, *apJ,*Jptr, aopnz, nspacedouble=0,j,nzi, 1019 *apj,apnz, *adpdi, *adpdj, *adpdJ, *poff_i, *poff_j, *j_temp, *aopothi, *aopothj; 1020 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n, p_colstart, p_colend; 1021 PetscBT lnkbt; 1022 PetscReal afill; 1023 PetscMPIInt rank; 1024 Mat adpd, aopoth; 1025 MatType mtype; 1026 const char *prefix; 1027 1028 PetscFunctionBegin; 1029 MatCheckProduct(C,4); 1030 if (C->product->data) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Extra product struct not empty"); 1031 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1032 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 1033 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 1034 ierr = MatGetOwnershipRangeColumn(P, &p_colstart, &p_colend);CHKERRQ(ierr); 1035 1036 /* create struct Mat_APMPI and attached it to C later */ 1037 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1038 1039 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1040 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1041 1042 /* get P_loc by taking all local rows of P */ 1043 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1044 1045 1046 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1047 pi_loc = p_loc->i; 1048 1049 /* Allocate memory for the i arrays of the matrices A*P, A_diag*P_off and A_offd * P */ 1050 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 1051 ierr = PetscMalloc1(am+2,&adpoi);CHKERRQ(ierr); 1052 1053 adpoi[0] = 0; 1054 ptap->api = api; 1055 api[0] = 0; 1056 1057 /* create and initialize a linked list, will be used for both A_diag * P_loc_off and A_offd * P_oth */ 1058 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1059 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 1060 1061 /* Symbolic calc of A_loc_diag * P_loc_diag */ 1062 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1063 ierr = MatProductCreate(a->A,p->A,NULL,&adpd);CHKERRQ(ierr); 1064 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1065 ierr = MatSetOptionsPrefix(adpd,prefix);CHKERRQ(ierr); 1066 ierr = MatAppendOptionsPrefix(adpd,"inner_diag_");CHKERRQ(ierr); 1067 1068 ierr = MatProductSetType(adpd,MATPRODUCT_AB);CHKERRQ(ierr); 1069 ierr = MatProductSetAlgorithm(adpd,"sorted");CHKERRQ(ierr); 1070 ierr = MatProductSetFill(adpd,fill);CHKERRQ(ierr); 1071 ierr = MatProductSetFromOptions(adpd);CHKERRQ(ierr); 1072 1073 adpd->force_diagonals = C->force_diagonals; 1074 ierr = MatProductSymbolic(adpd);CHKERRQ(ierr); 1075 1076 adpd_seq = (Mat_SeqAIJ*)((adpd)->data); 1077 adpdi = adpd_seq->i; adpdj = adpd_seq->j; 1078 p_off = (Mat_SeqAIJ*)((p->B)->data); 1079 poff_i = p_off->i; poff_j = p_off->j; 1080 1081 /* j_temp stores indices of a result row before they are added to the linked list */ 1082 ierr = PetscMalloc1(pN+2,&j_temp);CHKERRQ(ierr); 1083 1084 1085 /* Symbolic calc of the A_diag * p_loc_off */ 1086 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 1087 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space_diag);CHKERRQ(ierr); 1088 current_space = free_space_diag; 1089 1090 for (i=0; i<am; i++) { 1091 /* A_diag * P_loc_off */ 1092 nzi = adi[i+1] - adi[i]; 1093 for (j=0; j<nzi; j++) { 1094 row = *adj++; 1095 pnz = poff_i[row+1] - poff_i[row]; 1096 Jptr = poff_j + poff_i[row]; 1097 for (i1 = 0; i1 < pnz; i1++) { 1098 j_temp[i1] = p->garray[Jptr[i1]]; 1099 } 1100 /* add non-zero cols of P into the sorted linked list lnk */ 1101 ierr = PetscLLCondensedAddSorted(pnz,j_temp,lnk,lnkbt);CHKERRQ(ierr); 1102 } 1103 1104 adponz = lnk[0]; 1105 adpoi[i+1] = adpoi[i] + adponz; 1106 1107 /* if free space is not available, double the total space in the list */ 1108 if (current_space->local_remaining<adponz) { 1109 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(adponz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1110 nspacedouble++; 1111 } 1112 1113 /* Copy data into free space, then initialize lnk */ 1114 ierr = PetscLLCondensedClean(pN,adponz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1115 1116 current_space->array += adponz; 1117 current_space->local_used += adponz; 1118 current_space->local_remaining -= adponz; 1119 } 1120 1121 /* Symbolic calc of A_off * P_oth */ 1122 ierr = MatSetOptionsPrefix(a->B,prefix);CHKERRQ(ierr); 1123 ierr = MatAppendOptionsPrefix(a->B,"inner_offdiag_");CHKERRQ(ierr); 1124 ierr = MatCreate(PETSC_COMM_SELF,&aopoth);CHKERRQ(ierr); 1125 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(a->B, ptap->P_oth, fill, aopoth);CHKERRQ(ierr); 1126 aopoth_seq = (Mat_SeqAIJ*)((aopoth)->data); 1127 aopothi = aopoth_seq->i; aopothj = aopoth_seq->j; 1128 1129 /* Allocate space for apj, adpj, aopj, ... */ 1130 /* destroy lists of free space and other temporary array(s) */ 1131 1132 ierr = PetscMalloc1(aopothi[am] + adpoi[am] + adpdi[am]+2, &ptap->apj);CHKERRQ(ierr); 1133 ierr = PetscMalloc1(adpoi[am]+2, &adpoj);CHKERRQ(ierr); 1134 1135 /* Copy from linked list to j-array */ 1136 ierr = PetscFreeSpaceContiguous(&free_space_diag,adpoj);CHKERRQ(ierr); 1137 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1138 1139 adpoJ = adpoj; 1140 adpdJ = adpdj; 1141 aopJ = aopothj; 1142 apj = ptap->apj; 1143 apJ = apj; /* still empty */ 1144 1145 /* Merge j-arrays of A_off * P, A_diag * P_loc_off, and */ 1146 /* A_diag * P_loc_diag to get A*P */ 1147 for (i = 0; i < am; i++) { 1148 aopnz = aopothi[i+1] - aopothi[i]; 1149 adponz = adpoi[i+1] - adpoi[i]; 1150 adpdnz = adpdi[i+1] - adpdi[i]; 1151 1152 /* Correct indices from A_diag*P_diag */ 1153 for (i1 = 0; i1 < adpdnz; i1++) { 1154 adpdJ[i1] += p_colstart; 1155 } 1156 /* Merge j-arrays of A_diag * P_loc_off and A_diag * P_loc_diag and A_off * P_oth */ 1157 Merge3SortedArrays(adponz, adpoJ, adpdnz, adpdJ, aopnz, aopJ, &apnz, apJ); 1158 ierr = MatPreallocateSet(i+rstart, apnz, apJ, dnz, onz);CHKERRQ(ierr); 1159 1160 aopJ += aopnz; 1161 adpoJ += adponz; 1162 adpdJ += adpdnz; 1163 apJ += apnz; 1164 api[i+1] = api[i] + apnz; 1165 } 1166 1167 /* malloc apa to store dense row A[i,:]*P */ 1168 ierr = PetscCalloc1(pN+2,&ptap->apa);CHKERRQ(ierr); 1169 1170 /* create and assemble symbolic parallel matrix C */ 1171 ierr = MatSetSizes(C,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1172 ierr = MatSetBlockSizesFromMats(C,A,P);CHKERRQ(ierr); 1173 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1174 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 1175 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 1176 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1177 1178 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(C, apj, api);CHKERRQ(ierr); 1179 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1180 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1181 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1182 1183 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1184 C->ops->productnumeric = MatProductNumeric_AB; 1185 1186 /* attach the supporting struct to C for reuse */ 1187 C->product->data = ptap; 1188 C->product->destroy = MatDestroy_MPIAIJ_MatMatMult; 1189 1190 /* set MatInfo */ 1191 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 1192 if (afill < 1.0) afill = 1.0; 1193 C->info.mallocs = nspacedouble; 1194 C->info.fill_ratio_given = fill; 1195 C->info.fill_ratio_needed = afill; 1196 1197 #if defined(PETSC_USE_INFO) 1198 if (api[am]) { 1199 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1200 ierr = PetscInfo1(C,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 1201 } else { 1202 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 1203 } 1204 #endif 1205 1206 ierr = MatDestroy(&aopoth);CHKERRQ(ierr); 1207 ierr = MatDestroy(&adpd);CHKERRQ(ierr); 1208 ierr = PetscFree(j_temp);CHKERRQ(ierr); 1209 ierr = PetscFree(adpoj);CHKERRQ(ierr); 1210 ierr = PetscFree(adpoi);CHKERRQ(ierr); 1211 PetscFunctionReturn(0); 1212 } 1213 1214 /*-------------------------------------------------------------------------*/ 1215 /* This routine only works when scall=MAT_REUSE_MATRIX! */ 1216 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult(Mat P,Mat A,Mat C) 1217 { 1218 PetscErrorCode ierr; 1219 Mat_APMPI *ptap; 1220 Mat Pt; 1221 1222 PetscFunctionBegin; 1223 MatCheckProduct(C,3); 1224 ptap = (Mat_APMPI*)C->product->data; 1225 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 1226 if (!ptap->Pt) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatProductClear()"); 1227 1228 Pt = ptap->Pt; 1229 ierr = MatTranspose(P,MAT_REUSE_MATRIX,&Pt);CHKERRQ(ierr); 1230 ierr = MatMatMultNumeric_MPIAIJ_MPIAIJ(Pt,A,C);CHKERRQ(ierr); 1231 PetscFunctionReturn(0); 1232 } 1233 1234 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ() */ 1235 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,PetscReal fill,Mat C) 1236 { 1237 PetscErrorCode ierr; 1238 Mat_APMPI *ptap; 1239 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data; 1240 MPI_Comm comm; 1241 PetscMPIInt size,rank; 1242 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1243 PetscInt pn=P->cmap->n,aN=A->cmap->N,an=A->cmap->n; 1244 PetscInt *lnk,i,k,nsend,rstart; 1245 PetscBT lnkbt; 1246 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,nrecv; 1247 PETSC_UNUSED PetscMPIInt icompleted=0; 1248 PetscInt **buf_rj,**buf_ri,**buf_ri_k,row,ncols,*cols; 1249 PetscInt len,proc,*dnz,*onz,*owners,nzi; 1250 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1251 MPI_Request *swaits,*rwaits; 1252 MPI_Status *sstatus,rstatus; 1253 PetscLayout rowmap; 1254 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1255 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1256 PetscInt *Jptr,*prmap=p->garray,con,j,Crmax; 1257 Mat_SeqAIJ *a_loc,*c_loc,*c_oth; 1258 PetscTable ta; 1259 MatType mtype; 1260 const char *prefix; 1261 1262 PetscFunctionBegin; 1263 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1264 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 1265 ierr = MPI_Comm_rank(comm,&rank);CHKERRMPI(ierr); 1266 1267 /* create symbolic parallel matrix C */ 1268 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1269 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 1270 1271 C->ops->transposematmultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1272 1273 /* create struct Mat_APMPI and attached it to C later */ 1274 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1275 ptap->reuse = MAT_INITIAL_MATRIX; 1276 1277 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1278 /* --------------------------------- */ 1279 ierr = MatTranspose_SeqAIJ(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1280 ierr = MatTranspose_SeqAIJ(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1281 1282 /* (1) compute symbolic A_loc */ 1283 /* ---------------------------*/ 1284 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1285 1286 /* (2-1) compute symbolic C_oth = Ro*A_loc */ 1287 /* ------------------------------------ */ 1288 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1289 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 1290 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 1291 ierr = MatCreate(PETSC_COMM_SELF,&ptap->C_oth);CHKERRQ(ierr); 1292 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->A_loc,fill,ptap->C_oth);CHKERRQ(ierr); 1293 1294 /* (3) send coj of C_oth to other processors */ 1295 /* ------------------------------------------ */ 1296 /* determine row ownership */ 1297 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1298 rowmap->n = pn; 1299 rowmap->bs = 1; 1300 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1301 owners = rowmap->range; 1302 1303 /* determine the number of messages to send, their lengths */ 1304 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1305 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 1306 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr); 1307 1308 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1309 coi = c_oth->i; coj = c_oth->j; 1310 con = ptap->C_oth->rmap->n; 1311 proc = 0; 1312 for (i=0; i<con; i++) { 1313 while (prmap[i] >= owners[proc+1]) proc++; 1314 len_si[proc]++; /* num of rows in Co(=Pt*A) to be sent to [proc] */ 1315 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1316 } 1317 1318 len = 0; /* max length of buf_si[], see (4) */ 1319 owners_co[0] = 0; 1320 nsend = 0; 1321 for (proc=0; proc<size; proc++) { 1322 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1323 if (len_s[proc]) { 1324 nsend++; 1325 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1326 len += len_si[proc]; 1327 } 1328 } 1329 1330 /* determine the number and length of messages to receive for coi and coj */ 1331 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1332 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1333 1334 /* post the Irecv and Isend of coj */ 1335 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1336 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1337 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1338 for (proc=0, k=0; proc<size; proc++) { 1339 if (!len_s[proc]) continue; 1340 i = owners_co[proc]; 1341 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRMPI(ierr); 1342 k++; 1343 } 1344 1345 /* (2-2) compute symbolic C_loc = Rd*A_loc */ 1346 /* ---------------------------------------- */ 1347 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 1348 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 1349 ierr = MatCreate(PETSC_COMM_SELF,&ptap->C_loc);CHKERRQ(ierr); 1350 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->A_loc,fill,ptap->C_loc);CHKERRQ(ierr); 1351 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1352 1353 /* receives coj are complete */ 1354 for (i=0; i<nrecv; i++) { 1355 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRMPI(ierr); 1356 } 1357 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1358 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRMPI(ierr);} 1359 1360 /* add received column indices into ta to update Crmax */ 1361 a_loc = (Mat_SeqAIJ*)(ptap->A_loc)->data; 1362 1363 /* create and initialize a linked list */ 1364 ierr = PetscTableCreate(an,aN,&ta);CHKERRQ(ierr); /* for compute Crmax */ 1365 MatRowMergeMax_SeqAIJ(a_loc,ptap->A_loc->rmap->N,ta); 1366 1367 for (k=0; k<nrecv; k++) {/* k-th received message */ 1368 Jptr = buf_rj[k]; 1369 for (j=0; j<len_r[k]; j++) { 1370 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1371 } 1372 } 1373 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1374 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1375 1376 /* (4) send and recv coi */ 1377 /*-----------------------*/ 1378 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1379 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1380 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1381 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1382 for (proc=0,k=0; proc<size; proc++) { 1383 if (!len_s[proc]) continue; 1384 /* form outgoing message for i-structure: 1385 buf_si[0]: nrows to be sent 1386 [1:nrows]: row index (global) 1387 [nrows+1:2*nrows+1]: i-structure index 1388 */ 1389 /*-------------------------------------------*/ 1390 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1391 buf_si_i = buf_si + nrows+1; 1392 buf_si[0] = nrows; 1393 buf_si_i[0] = 0; 1394 nrows = 0; 1395 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1396 nzi = coi[i+1] - coi[i]; 1397 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1398 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1399 nrows++; 1400 } 1401 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRMPI(ierr); 1402 k++; 1403 buf_si += len_si[proc]; 1404 } 1405 for (i=0; i<nrecv; i++) { 1406 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRMPI(ierr); 1407 } 1408 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1409 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRMPI(ierr);} 1410 1411 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1412 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1413 ierr = PetscFree(swaits);CHKERRQ(ierr); 1414 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1415 1416 /* (5) compute the local portion of C */ 1417 /* ------------------------------------------ */ 1418 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of C */ 1419 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1420 current_space = free_space; 1421 1422 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1423 for (k=0; k<nrecv; k++) { 1424 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1425 nrows = *buf_ri_k[k]; 1426 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1427 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1428 } 1429 1430 ierr = MatPreallocateInitialize(comm,pn,an,dnz,onz);CHKERRQ(ierr); 1431 ierr = PetscLLCondensedCreate(Crmax,aN,&lnk,&lnkbt);CHKERRQ(ierr); 1432 for (i=0; i<pn; i++) { /* for each local row of C */ 1433 /* add C_loc into C */ 1434 nzi = c_loc->i[i+1] - c_loc->i[i]; 1435 Jptr = c_loc->j + c_loc->i[i]; 1436 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1437 1438 /* add received col data into lnk */ 1439 for (k=0; k<nrecv; k++) { /* k-th received message */ 1440 if (i == *nextrow[k]) { /* i-th row */ 1441 nzi = *(nextci[k]+1) - *nextci[k]; 1442 Jptr = buf_rj[k] + *nextci[k]; 1443 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1444 nextrow[k]++; nextci[k]++; 1445 } 1446 } 1447 1448 /* add missing diagonal entry */ 1449 if (C->force_diagonals) { 1450 k = i + owners[rank]; /* column index */ 1451 ierr = PetscLLCondensedAddSorted(1,&k,lnk,lnkbt);CHKERRQ(ierr); 1452 } 1453 1454 nzi = lnk[0]; 1455 1456 /* copy data into free space, then initialize lnk */ 1457 ierr = PetscLLCondensedClean(aN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1458 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 1459 } 1460 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1461 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1462 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 1463 1464 /* local sizes and preallocation */ 1465 ierr = MatSetSizes(C,pn,an,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1466 if (P->cmap->bs > 0) {ierr = PetscLayoutSetBlockSize(C->rmap,P->cmap->bs);CHKERRQ(ierr);} 1467 if (A->cmap->bs > 0) {ierr = PetscLayoutSetBlockSize(C->cmap,A->cmap->bs);CHKERRQ(ierr);} 1468 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 1469 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1470 1471 /* add C_loc and C_oth to C */ 1472 ierr = MatGetOwnershipRange(C,&rstart,NULL);CHKERRQ(ierr); 1473 for (i=0; i<pn; i++) { 1474 ncols = c_loc->i[i+1] - c_loc->i[i]; 1475 cols = c_loc->j + c_loc->i[i]; 1476 row = rstart + i; 1477 ierr = MatSetValues(C,1,(const PetscInt*)&row,ncols,(const PetscInt*)cols,NULL,INSERT_VALUES);CHKERRQ(ierr); 1478 1479 if (C->force_diagonals) { 1480 ierr = MatSetValues(C,1,(const PetscInt*)&row,1,(const PetscInt*)&row,NULL,INSERT_VALUES);CHKERRQ(ierr); 1481 } 1482 } 1483 for (i=0; i<con; i++) { 1484 ncols = c_oth->i[i+1] - c_oth->i[i]; 1485 cols = c_oth->j + c_oth->i[i]; 1486 row = prmap[i]; 1487 ierr = MatSetValues(C,1,(const PetscInt*)&row,ncols,(const PetscInt*)cols,NULL,INSERT_VALUES);CHKERRQ(ierr); 1488 } 1489 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1490 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1491 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1492 1493 /* members in merge */ 1494 ierr = PetscFree(id_r);CHKERRQ(ierr); 1495 ierr = PetscFree(len_r);CHKERRQ(ierr); 1496 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 1497 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 1498 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 1499 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 1500 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 1501 1502 /* attach the supporting struct to C for reuse */ 1503 C->product->data = ptap; 1504 C->product->destroy = MatDestroy_MPIAIJ_PtAP; 1505 PetscFunctionReturn(0); 1506 } 1507 1508 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,Mat C) 1509 { 1510 PetscErrorCode ierr; 1511 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data; 1512 Mat_SeqAIJ *c_seq; 1513 Mat_APMPI *ptap; 1514 Mat A_loc,C_loc,C_oth; 1515 PetscInt i,rstart,rend,cm,ncols,row; 1516 const PetscInt *cols; 1517 const PetscScalar *vals; 1518 1519 PetscFunctionBegin; 1520 MatCheckProduct(C,3); 1521 ptap = (Mat_APMPI*)C->product->data; 1522 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 1523 if (!ptap->A_loc) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatProductClear()"); 1524 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1525 1526 if (ptap->reuse == MAT_REUSE_MATRIX) { 1527 /* These matrices are obtained in MatTransposeMatMultSymbolic() */ 1528 /* 1) get R = Pd^T, Ro = Po^T */ 1529 /*----------------------------*/ 1530 ierr = MatTranspose_SeqAIJ(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1531 ierr = MatTranspose_SeqAIJ(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1532 1533 /* 2) compute numeric A_loc */ 1534 /*--------------------------*/ 1535 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1536 } 1537 1538 /* 3) C_loc = Rd*A_loc, C_oth = Ro*A_loc */ 1539 A_loc = ptap->A_loc; 1540 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,A_loc,ptap->C_loc);CHKERRQ(ierr); 1541 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,A_loc,ptap->C_oth);CHKERRQ(ierr); 1542 C_loc = ptap->C_loc; 1543 C_oth = ptap->C_oth; 1544 1545 /* add C_loc and C_oth to C */ 1546 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1547 1548 /* C_loc -> C */ 1549 cm = C_loc->rmap->N; 1550 c_seq = (Mat_SeqAIJ*)C_loc->data; 1551 cols = c_seq->j; 1552 vals = c_seq->a; 1553 for (i=0; i<cm; i++) { 1554 ncols = c_seq->i[i+1] - c_seq->i[i]; 1555 row = rstart + i; 1556 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1557 cols += ncols; vals += ncols; 1558 } 1559 1560 /* Co -> C, off-processor part */ 1561 cm = C_oth->rmap->N; 1562 c_seq = (Mat_SeqAIJ*)C_oth->data; 1563 cols = c_seq->j; 1564 vals = c_seq->a; 1565 for (i=0; i<cm; i++) { 1566 ncols = c_seq->i[i+1] - c_seq->i[i]; 1567 row = p->garray[i]; 1568 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1569 cols += ncols; vals += ncols; 1570 } 1571 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1572 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1573 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1574 1575 ptap->reuse = MAT_REUSE_MATRIX; 1576 PetscFunctionReturn(0); 1577 } 1578 1579 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ(Mat P,Mat A,Mat C) 1580 { 1581 PetscErrorCode ierr; 1582 Mat_Merge_SeqsToMPI *merge; 1583 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data; 1584 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1585 Mat_APMPI *ptap; 1586 PetscInt *adj; 1587 PetscInt i,j,k,anz,pnz,row,*cj,nexta; 1588 MatScalar *ada,*ca,valtmp; 1589 PetscInt am=A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1590 MPI_Comm comm; 1591 PetscMPIInt size,rank,taga,*len_s; 1592 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1593 PetscInt **buf_ri,**buf_rj; 1594 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1595 MPI_Request *s_waits,*r_waits; 1596 MPI_Status *status; 1597 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1598 PetscInt *ai,*aj,*coi,*coj,*poJ,*pdJ; 1599 Mat A_loc; 1600 Mat_SeqAIJ *a_loc; 1601 1602 PetscFunctionBegin; 1603 MatCheckProduct(C,3); 1604 ptap = (Mat_APMPI*)C->product->data; 1605 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 1606 if (!ptap->A_loc) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatProductClear()"); 1607 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1608 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 1609 ierr = MPI_Comm_rank(comm,&rank);CHKERRMPI(ierr); 1610 1611 merge = ptap->merge; 1612 1613 /* 2) compute numeric C_seq = P_loc^T*A_loc */ 1614 /*------------------------------------------*/ 1615 /* get data from symbolic products */ 1616 coi = merge->coi; coj = merge->coj; 1617 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 1618 bi = merge->bi; bj = merge->bj; 1619 owners = merge->rowmap->range; 1620 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); 1621 1622 /* get A_loc by taking all local rows of A */ 1623 A_loc = ptap->A_loc; 1624 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 1625 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1626 ai = a_loc->i; 1627 aj = a_loc->j; 1628 1629 for (i=0; i<am; i++) { 1630 anz = ai[i+1] - ai[i]; 1631 adj = aj + ai[i]; 1632 ada = a_loc->a + ai[i]; 1633 1634 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 1635 /*-------------------------------------------------------------*/ 1636 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 1637 pnz = po->i[i+1] - po->i[i]; 1638 poJ = po->j + po->i[i]; 1639 pA = po->a + po->i[i]; 1640 for (j=0; j<pnz; j++) { 1641 row = poJ[j]; 1642 cj = coj + coi[row]; 1643 ca = coa + coi[row]; 1644 /* perform sparse axpy */ 1645 nexta = 0; 1646 valtmp = pA[j]; 1647 for (k=0; nexta<anz; k++) { 1648 if (cj[k] == adj[nexta]) { 1649 ca[k] += valtmp*ada[nexta]; 1650 nexta++; 1651 } 1652 } 1653 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1654 } 1655 1656 /* put the value into Cd (diagonal part) */ 1657 pnz = pd->i[i+1] - pd->i[i]; 1658 pdJ = pd->j + pd->i[i]; 1659 pA = pd->a + pd->i[i]; 1660 for (j=0; j<pnz; j++) { 1661 row = pdJ[j]; 1662 cj = bj + bi[row]; 1663 ca = ba + bi[row]; 1664 /* perform sparse axpy */ 1665 nexta = 0; 1666 valtmp = pA[j]; 1667 for (k=0; nexta<anz; k++) { 1668 if (cj[k] == adj[nexta]) { 1669 ca[k] += valtmp*ada[nexta]; 1670 nexta++; 1671 } 1672 } 1673 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1674 } 1675 } 1676 1677 /* 3) send and recv matrix values coa */ 1678 /*------------------------------------*/ 1679 buf_ri = merge->buf_ri; 1680 buf_rj = merge->buf_rj; 1681 len_s = merge->len_s; 1682 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1683 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1684 1685 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1686 for (proc=0,k=0; proc<size; proc++) { 1687 if (!len_s[proc]) continue; 1688 i = merge->owners_co[proc]; 1689 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRMPI(ierr); 1690 k++; 1691 } 1692 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRMPI(ierr);} 1693 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRMPI(ierr);} 1694 1695 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1696 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1697 ierr = PetscFree(coa);CHKERRQ(ierr); 1698 1699 /* 4) insert local Cseq and received values into Cmpi */ 1700 /*----------------------------------------------------*/ 1701 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1702 for (k=0; k<merge->nrecv; k++) { 1703 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1704 nrows = *(buf_ri_k[k]); 1705 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1706 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1707 } 1708 1709 for (i=0; i<cm; i++) { 1710 row = owners[rank] + i; /* global row index of C_seq */ 1711 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1712 ba_i = ba + bi[i]; 1713 bnz = bi[i+1] - bi[i]; 1714 /* add received vals into ba */ 1715 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1716 /* i-th row */ 1717 if (i == *nextrow[k]) { 1718 cnz = *(nextci[k]+1) - *nextci[k]; 1719 cj = buf_rj[k] + *(nextci[k]); 1720 ca = abuf_r[k] + *(nextci[k]); 1721 nextcj = 0; 1722 for (j=0; nextcj<cnz; j++) { 1723 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1724 ba_i[j] += ca[nextcj++]; 1725 } 1726 } 1727 nextrow[k]++; nextci[k]++; 1728 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1729 } 1730 } 1731 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1732 } 1733 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1734 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1735 1736 ierr = PetscFree(ba);CHKERRQ(ierr); 1737 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1738 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1739 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1740 PetscFunctionReturn(0); 1741 } 1742 1743 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(Mat P,Mat A,PetscReal fill,Mat C) 1744 { 1745 PetscErrorCode ierr; 1746 Mat A_loc; 1747 Mat_APMPI *ptap; 1748 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1749 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*a=(Mat_MPIAIJ*)A->data; 1750 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1751 PetscInt nnz; 1752 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1753 PetscInt am =A->rmap->n,pn=P->cmap->n; 1754 MPI_Comm comm; 1755 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1756 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1757 PetscInt len,proc,*dnz,*onz,*owners; 1758 PetscInt nzi,*bi,*bj; 1759 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1760 MPI_Request *swaits,*rwaits; 1761 MPI_Status *sstatus,rstatus; 1762 Mat_Merge_SeqsToMPI *merge; 1763 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1764 PetscReal afill =1.0,afill_tmp; 1765 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N,Armax; 1766 Mat_SeqAIJ *a_loc; 1767 PetscTable ta; 1768 MatType mtype; 1769 1770 PetscFunctionBegin; 1771 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1772 /* check if matrix local sizes are compatible */ 1773 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); 1774 1775 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 1776 ierr = MPI_Comm_rank(comm,&rank);CHKERRMPI(ierr); 1777 1778 /* create struct Mat_APMPI and attached it to C later */ 1779 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1780 1781 /* get A_loc by taking all local rows of A */ 1782 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1783 1784 ptap->A_loc = A_loc; 1785 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1786 ai = a_loc->i; 1787 aj = a_loc->j; 1788 1789 /* determine symbolic Co=(p->B)^T*A - send to others */ 1790 /*----------------------------------------------------*/ 1791 ierr = MatGetSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); 1792 ierr = MatGetSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); 1793 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 1794 >= (num of nonzero rows of C_seq) - pn */ 1795 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 1796 coi[0] = 0; 1797 1798 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1799 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],ai[am])); 1800 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1801 current_space = free_space; 1802 1803 /* create and initialize a linked list */ 1804 ierr = PetscTableCreate(A->cmap->n + a->B->cmap->N,aN,&ta);CHKERRQ(ierr); 1805 MatRowMergeMax_SeqAIJ(a_loc,am,ta); 1806 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1807 1808 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1809 1810 for (i=0; i<pon; i++) { 1811 pnz = poti[i+1] - poti[i]; 1812 ptJ = potj + poti[i]; 1813 for (j=0; j<pnz; j++) { 1814 row = ptJ[j]; /* row of A_loc == col of Pot */ 1815 anz = ai[row+1] - ai[row]; 1816 Jptr = aj + ai[row]; 1817 /* add non-zero cols of AP into the sorted linked list lnk */ 1818 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1819 } 1820 nnz = lnk[0]; 1821 1822 /* If free space is not available, double the total space in the list */ 1823 if (current_space->local_remaining<nnz) { 1824 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1825 nspacedouble++; 1826 } 1827 1828 /* Copy data into free space, and zero out denserows */ 1829 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1830 1831 current_space->array += nnz; 1832 current_space->local_used += nnz; 1833 current_space->local_remaining -= nnz; 1834 1835 coi[i+1] = coi[i] + nnz; 1836 } 1837 1838 ierr = PetscMalloc1(coi[pon]+1,&coj);CHKERRQ(ierr); 1839 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 1840 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); /* must destroy to get a new one for C */ 1841 1842 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 1843 if (afill_tmp > afill) afill = afill_tmp; 1844 1845 /* send j-array (coj) of Co to other processors */ 1846 /*----------------------------------------------*/ 1847 /* determine row ownership */ 1848 ierr = PetscNew(&merge);CHKERRQ(ierr); 1849 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 1850 1851 merge->rowmap->n = pn; 1852 merge->rowmap->bs = 1; 1853 1854 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 1855 owners = merge->rowmap->range; 1856 1857 /* determine the number of messages to send, their lengths */ 1858 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 1859 ierr = PetscCalloc1(size,&merge->len_s);CHKERRQ(ierr); 1860 1861 len_s = merge->len_s; 1862 merge->nsend = 0; 1863 1864 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 1865 1866 proc = 0; 1867 for (i=0; i<pon; i++) { 1868 while (prmap[i] >= owners[proc+1]) proc++; 1869 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1870 len_s[proc] += coi[i+1] - coi[i]; 1871 } 1872 1873 len = 0; /* max length of buf_si[] */ 1874 owners_co[0] = 0; 1875 for (proc=0; proc<size; proc++) { 1876 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1877 if (len_si[proc]) { 1878 merge->nsend++; 1879 len_si[proc] = 2*(len_si[proc] + 1); 1880 len += len_si[proc]; 1881 } 1882 } 1883 1884 /* determine the number and length of messages to receive for coi and coj */ 1885 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1886 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1887 1888 /* post the Irecv and Isend of coj */ 1889 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1890 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1891 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 1892 for (proc=0, k=0; proc<size; proc++) { 1893 if (!len_s[proc]) continue; 1894 i = owners_co[proc]; 1895 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRMPI(ierr); 1896 k++; 1897 } 1898 1899 /* receives and sends of coj are complete */ 1900 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1901 for (i=0; i<merge->nrecv; i++) { 1902 PETSC_UNUSED PetscMPIInt icompleted; 1903 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRMPI(ierr); 1904 } 1905 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1906 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRMPI(ierr);} 1907 1908 /* add received column indices into table to update Armax */ 1909 /* Armax can be as large as aN if a P[row,:] is dense, see src/ksp/ksp/tutorials/ex56.c! */ 1910 for (k=0; k<merge->nrecv; k++) {/* k-th received message */ 1911 Jptr = buf_rj[k]; 1912 for (j=0; j<merge->len_r[k]; j++) { 1913 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1914 } 1915 } 1916 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1917 /* 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); */ 1918 1919 /* send and recv coi */ 1920 /*-------------------*/ 1921 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1922 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1923 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1924 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1925 for (proc=0,k=0; proc<size; proc++) { 1926 if (!len_s[proc]) continue; 1927 /* form outgoing message for i-structure: 1928 buf_si[0]: nrows to be sent 1929 [1:nrows]: row index (global) 1930 [nrows+1:2*nrows+1]: i-structure index 1931 */ 1932 /*-------------------------------------------*/ 1933 nrows = len_si[proc]/2 - 1; 1934 buf_si_i = buf_si + nrows+1; 1935 buf_si[0] = nrows; 1936 buf_si_i[0] = 0; 1937 nrows = 0; 1938 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1939 nzi = coi[i+1] - coi[i]; 1940 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1941 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1942 nrows++; 1943 } 1944 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRMPI(ierr); 1945 k++; 1946 buf_si += len_si[proc]; 1947 } 1948 i = merge->nrecv; 1949 while (i--) { 1950 PETSC_UNUSED PetscMPIInt icompleted; 1951 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRMPI(ierr); 1952 } 1953 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1954 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRMPI(ierr);} 1955 ierr = PetscFree(len_si);CHKERRQ(ierr); 1956 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1957 ierr = PetscFree(swaits);CHKERRQ(ierr); 1958 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1959 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1960 1961 /* compute the local portion of C (mpi mat) */ 1962 /*------------------------------------------*/ 1963 /* allocate bi array and free space for accumulating nonzero column info */ 1964 ierr = PetscMalloc1(pn+1,&bi);CHKERRQ(ierr); 1965 bi[0] = 0; 1966 1967 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 1968 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pdti[pn],PetscIntSumTruncate(poti[pon],ai[am]))); 1969 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1970 current_space = free_space; 1971 1972 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1973 for (k=0; k<merge->nrecv; k++) { 1974 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1975 nrows = *buf_ri_k[k]; 1976 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1977 nextci[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th received i-structure */ 1978 } 1979 1980 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1981 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1982 rmax = 0; 1983 for (i=0; i<pn; i++) { 1984 /* add pdt[i,:]*AP into lnk */ 1985 pnz = pdti[i+1] - pdti[i]; 1986 ptJ = pdtj + pdti[i]; 1987 for (j=0; j<pnz; j++) { 1988 row = ptJ[j]; /* row of AP == col of Pt */ 1989 anz = ai[row+1] - ai[row]; 1990 Jptr = aj + ai[row]; 1991 /* add non-zero cols of AP into the sorted linked list lnk */ 1992 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1993 } 1994 1995 /* add received col data into lnk */ 1996 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1997 if (i == *nextrow[k]) { /* i-th row */ 1998 nzi = *(nextci[k]+1) - *nextci[k]; 1999 Jptr = buf_rj[k] + *nextci[k]; 2000 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 2001 nextrow[k]++; nextci[k]++; 2002 } 2003 } 2004 2005 /* add missing diagonal entry */ 2006 if (C->force_diagonals) { 2007 k = i + owners[rank]; /* column index */ 2008 ierr = PetscLLCondensedAddSorted_Scalable(1,&k,lnk);CHKERRQ(ierr); 2009 } 2010 2011 nnz = lnk[0]; 2012 2013 /* if free space is not available, make more free space */ 2014 if (current_space->local_remaining<nnz) { 2015 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 2016 nspacedouble++; 2017 } 2018 /* copy data into free space, then initialize lnk */ 2019 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 2020 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 2021 2022 current_space->array += nnz; 2023 current_space->local_used += nnz; 2024 current_space->local_remaining -= nnz; 2025 2026 bi[i+1] = bi[i] + nnz; 2027 if (nnz > rmax) rmax = nnz; 2028 } 2029 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 2030 2031 ierr = PetscMalloc1(bi[pn]+1,&bj);CHKERRQ(ierr); 2032 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 2033 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 2034 if (afill_tmp > afill) afill = afill_tmp; 2035 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 2036 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 2037 ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); 2038 ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); 2039 2040 /* create symbolic parallel matrix C - why cannot be assembled in Numeric part */ 2041 /*-------------------------------------------------------------------------------*/ 2042 ierr = MatSetSizes(C,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2043 ierr = MatSetBlockSizes(C,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 2044 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 2045 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 2046 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 2047 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 2048 ierr = MatSetBlockSize(C,1);CHKERRQ(ierr); 2049 ierr = MatSetOption(C,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 2050 for (i=0; i<pn; i++) { 2051 row = i + rstart; 2052 nnz = bi[i+1] - bi[i]; 2053 Jptr = bj + bi[i]; 2054 ierr = MatSetValues(C,1,&row,nnz,Jptr,NULL,INSERT_VALUES);CHKERRQ(ierr); 2055 } 2056 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2057 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2058 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2059 merge->bi = bi; 2060 merge->bj = bj; 2061 merge->coi = coi; 2062 merge->coj = coj; 2063 merge->buf_ri = buf_ri; 2064 merge->buf_rj = buf_rj; 2065 merge->owners_co = owners_co; 2066 2067 /* attach the supporting struct to C for reuse */ 2068 C->product->data = ptap; 2069 C->product->destroy = MatDestroy_MPIAIJ_PtAP; 2070 ptap->merge = merge; 2071 2072 C->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ; 2073 2074 #if defined(PETSC_USE_INFO) 2075 if (bi[pn] != 0) { 2076 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 2077 ierr = PetscInfo1(C,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 2078 } else { 2079 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 2080 } 2081 #endif 2082 PetscFunctionReturn(0); 2083 } 2084 2085 /* ---------------------------------------------------------------- */ 2086 static PetscErrorCode MatProductSymbolic_AtB_MPIAIJ_MPIAIJ(Mat C) 2087 { 2088 PetscErrorCode ierr; 2089 Mat_Product *product = C->product; 2090 Mat A=product->A,B=product->B; 2091 PetscReal fill=product->fill; 2092 PetscBool flg; 2093 2094 PetscFunctionBegin; 2095 /* scalable */ 2096 ierr = PetscStrcmp(product->alg,"scalable",&flg);CHKERRQ(ierr); 2097 if (flg) { 2098 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 2099 goto next; 2100 } 2101 2102 /* nonscalable */ 2103 ierr = PetscStrcmp(product->alg,"nonscalable",&flg);CHKERRQ(ierr); 2104 if (flg) { 2105 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(A,B,fill,C);CHKERRQ(ierr); 2106 goto next; 2107 } 2108 2109 /* matmatmult */ 2110 ierr = PetscStrcmp(product->alg,"at*b",&flg);CHKERRQ(ierr); 2111 if (flg) { 2112 Mat At; 2113 Mat_APMPI *ptap; 2114 2115 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 2116 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ(At,B,fill,C);CHKERRQ(ierr); 2117 ptap = (Mat_APMPI*)C->product->data; 2118 if (ptap) { 2119 ptap->Pt = At; 2120 C->product->destroy = MatDestroy_MPIAIJ_PtAP; 2121 } 2122 C->ops->transposematmultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult; 2123 goto next; 2124 } 2125 2126 /* backend general code */ 2127 ierr = PetscStrcmp(product->alg,"backend",&flg);CHKERRQ(ierr); 2128 if (flg) { 2129 ierr = MatProductSymbolic_MPIAIJBACKEND(C);CHKERRQ(ierr); 2130 PetscFunctionReturn(0); 2131 } 2132 2133 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MatProduct type is not supported"); 2134 2135 next: 2136 C->ops->productnumeric = MatProductNumeric_AtB; 2137 PetscFunctionReturn(0); 2138 } 2139 2140 /* ---------------------------------------------------------------- */ 2141 /* Set options for MatMatMultxxx_MPIAIJ_MPIAIJ */ 2142 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_AB(Mat C) 2143 { 2144 PetscErrorCode ierr; 2145 Mat_Product *product = C->product; 2146 Mat A=product->A,B=product->B; 2147 #if defined(PETSC_HAVE_HYPRE) 2148 const char *algTypes[5] = {"scalable","nonscalable","seqmpi","backend","hypre"}; 2149 PetscInt nalg = 5; 2150 #else 2151 const char *algTypes[4] = {"scalable","nonscalable","seqmpi","backend",}; 2152 PetscInt nalg = 4; 2153 #endif 2154 PetscInt alg = 1; /* set nonscalable algorithm as default */ 2155 PetscBool flg; 2156 MPI_Comm comm; 2157 2158 PetscFunctionBegin; 2159 /* Check matrix local sizes */ 2160 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2161 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); 2162 2163 /* Set "nonscalable" as default algorithm */ 2164 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2165 if (flg) { 2166 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2167 2168 /* Set "scalable" as default if BN and local nonzeros of A and B are large */ 2169 if (B->cmap->N > 100000) { /* may switch to scalable algorithm as default */ 2170 MatInfo Ainfo,Binfo; 2171 PetscInt nz_local; 2172 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 2173 2174 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 2175 ierr = MatGetInfo(B,MAT_LOCAL,&Binfo);CHKERRQ(ierr); 2176 nz_local = (PetscInt)(Ainfo.nz_allocated + Binfo.nz_allocated); 2177 2178 if (B->cmap->N > product->fill*nz_local) alg_scalable_loc = PETSC_TRUE; 2179 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 2180 2181 if (alg_scalable) { 2182 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 2183 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2184 ierr = PetscInfo2(B,"Use scalable algorithm, BN %D, fill*nz_allocated %g\n",B->cmap->N,product->fill*nz_local);CHKERRQ(ierr); 2185 } 2186 } 2187 } 2188 2189 /* Get runtime option */ 2190 if (product->api_user) { 2191 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatMatMult","Mat");CHKERRQ(ierr); 2192 ierr = PetscOptionsEList("-matmatmult_via","Algorithmic approach","MatMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2193 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2194 } else { 2195 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_AB","Mat");CHKERRQ(ierr); 2196 ierr = PetscOptionsEList("-matproduct_ab_via","Algorithmic approach","MatMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2197 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2198 } 2199 if (flg) { 2200 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2201 } 2202 2203 C->ops->productsymbolic = MatProductSymbolic_AB_MPIAIJ_MPIAIJ; 2204 PetscFunctionReturn(0); 2205 } 2206 2207 /* Set options for MatTransposeMatMultXXX_MPIAIJ_MPIAIJ */ 2208 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_AtB(Mat C) 2209 { 2210 PetscErrorCode ierr; 2211 Mat_Product *product = C->product; 2212 Mat A=product->A,B=product->B; 2213 const char *algTypes[4] = {"scalable","nonscalable","at*b","backend"}; 2214 PetscInt nalg = 4; 2215 PetscInt alg = 1; /* set default algorithm */ 2216 PetscBool flg; 2217 MPI_Comm comm; 2218 2219 PetscFunctionBegin; 2220 /* Check matrix local sizes */ 2221 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2222 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); 2223 2224 /* Set default algorithm */ 2225 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2226 if (flg) { 2227 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2228 } 2229 2230 /* Set "scalable" as default if BN and local nonzeros of A and B are large */ 2231 if (alg && B->cmap->N > 100000) { /* may switch to scalable algorithm as default */ 2232 MatInfo Ainfo,Binfo; 2233 PetscInt nz_local; 2234 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 2235 2236 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 2237 ierr = MatGetInfo(B,MAT_LOCAL,&Binfo);CHKERRQ(ierr); 2238 nz_local = (PetscInt)(Ainfo.nz_allocated + Binfo.nz_allocated); 2239 2240 if (B->cmap->N > product->fill*nz_local) alg_scalable_loc = PETSC_TRUE; 2241 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 2242 2243 if (alg_scalable) { 2244 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 2245 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2246 ierr = PetscInfo2(B,"Use scalable algorithm, BN %D, fill*nz_allocated %g\n",B->cmap->N,product->fill*nz_local);CHKERRQ(ierr); 2247 } 2248 } 2249 2250 /* Get runtime option */ 2251 if (product->api_user) { 2252 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatTransposeMatMult","Mat");CHKERRQ(ierr); 2253 ierr = PetscOptionsEList("-mattransposematmult_via","Algorithmic approach","MatTransposeMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2254 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2255 } else { 2256 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_AtB","Mat");CHKERRQ(ierr); 2257 ierr = PetscOptionsEList("-matproduct_atb_via","Algorithmic approach","MatTransposeMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2258 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2259 } 2260 if (flg) { 2261 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2262 } 2263 2264 C->ops->productsymbolic = MatProductSymbolic_AtB_MPIAIJ_MPIAIJ; 2265 PetscFunctionReturn(0); 2266 } 2267 2268 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_PtAP(Mat C) 2269 { 2270 PetscErrorCode ierr; 2271 Mat_Product *product = C->product; 2272 Mat A=product->A,P=product->B; 2273 MPI_Comm comm; 2274 PetscBool flg; 2275 PetscInt alg=1; /* set default algorithm */ 2276 #if !defined(PETSC_HAVE_HYPRE) 2277 const char *algTypes[5] = {"scalable","nonscalable","allatonce","allatonce_merged","backend"}; 2278 PetscInt nalg=5; 2279 #else 2280 const char *algTypes[6] = {"scalable","nonscalable","allatonce","allatonce_merged","backend","hypre"}; 2281 PetscInt nalg=6; 2282 #endif 2283 PetscInt pN=P->cmap->N; 2284 2285 PetscFunctionBegin; 2286 /* Check matrix local sizes */ 2287 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2288 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); 2289 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); 2290 2291 /* Set "nonscalable" as default algorithm */ 2292 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2293 if (flg) { 2294 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2295 2296 /* Set "scalable" as default if BN and local nonzeros of A and B are large */ 2297 if (pN > 100000) { 2298 MatInfo Ainfo,Pinfo; 2299 PetscInt nz_local; 2300 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 2301 2302 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 2303 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 2304 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); 2305 2306 if (pN > product->fill*nz_local) alg_scalable_loc = PETSC_TRUE; 2307 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 2308 2309 if (alg_scalable) { 2310 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 2311 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2312 } 2313 } 2314 } 2315 2316 /* Get runtime option */ 2317 if (product->api_user) { 2318 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 2319 ierr = PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2320 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2321 } else { 2322 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_PtAP","Mat");CHKERRQ(ierr); 2323 ierr = PetscOptionsEList("-matproduct_ptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2324 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2325 } 2326 if (flg) { 2327 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2328 } 2329 2330 C->ops->productsymbolic = MatProductSymbolic_PtAP_MPIAIJ_MPIAIJ; 2331 PetscFunctionReturn(0); 2332 } 2333 2334 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_RARt(Mat C) 2335 { 2336 Mat_Product *product = C->product; 2337 Mat A = product->A,R=product->B; 2338 2339 PetscFunctionBegin; 2340 /* Check matrix local sizes */ 2341 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); 2342 2343 C->ops->productsymbolic = MatProductSymbolic_RARt_MPIAIJ_MPIAIJ; 2344 PetscFunctionReturn(0); 2345 } 2346 2347 /* 2348 Set options for ABC = A*B*C = A*(B*C); ABC's algorithm must be chosen from AB's algorithm 2349 */ 2350 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_ABC(Mat C) 2351 { 2352 PetscErrorCode ierr; 2353 Mat_Product *product = C->product; 2354 PetscBool flg = PETSC_FALSE; 2355 PetscInt alg = 1; /* default algorithm */ 2356 const char *algTypes[3] = {"scalable","nonscalable","seqmpi"}; 2357 PetscInt nalg = 3; 2358 2359 PetscFunctionBegin; 2360 /* Set default algorithm */ 2361 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2362 if (flg) { 2363 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2364 } 2365 2366 /* Get runtime option */ 2367 if (product->api_user) { 2368 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatMatMatMult","Mat");CHKERRQ(ierr); 2369 ierr = PetscOptionsEList("-matmatmatmult_via","Algorithmic approach","MatMatMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2370 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2371 } else { 2372 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_ABC","Mat");CHKERRQ(ierr); 2373 ierr = PetscOptionsEList("-matproduct_abc_via","Algorithmic approach","MatProduct_ABC",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2374 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2375 } 2376 if (flg) { 2377 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2378 } 2379 2380 C->ops->matmatmultsymbolic = MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ; 2381 C->ops->productsymbolic = MatProductSymbolic_ABC; 2382 PetscFunctionReturn(0); 2383 } 2384 2385 PETSC_INTERN PetscErrorCode MatProductSetFromOptions_MPIAIJ(Mat C) 2386 { 2387 PetscErrorCode ierr; 2388 Mat_Product *product = C->product; 2389 2390 PetscFunctionBegin; 2391 switch (product->type) { 2392 case MATPRODUCT_AB: 2393 ierr = MatProductSetFromOptions_MPIAIJ_AB(C);CHKERRQ(ierr); 2394 break; 2395 case MATPRODUCT_AtB: 2396 ierr = MatProductSetFromOptions_MPIAIJ_AtB(C);CHKERRQ(ierr); 2397 break; 2398 case MATPRODUCT_PtAP: 2399 ierr = MatProductSetFromOptions_MPIAIJ_PtAP(C);CHKERRQ(ierr); 2400 break; 2401 case MATPRODUCT_RARt: 2402 ierr = MatProductSetFromOptions_MPIAIJ_RARt(C);CHKERRQ(ierr); 2403 break; 2404 case MATPRODUCT_ABC: 2405 ierr = MatProductSetFromOptions_MPIAIJ_ABC(C);CHKERRQ(ierr); 2406 break; 2407 default: 2408 break; 2409 } 2410 PetscFunctionReturn(0); 2411 } 2412