1 2 /* 3 Defines matrix-matrix product routines for pairs of MPIAIJ matrices 4 C = A * B 5 */ 6 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 7 #include <../src/mat/utils/freespace.h> 8 #include <../src/mat/impls/aij/mpi/mpiaij.h> 9 #include <petscbt.h> 10 #include <../src/mat/impls/dense/mpi/mpidense.h> 11 #include <petsc/private/vecimpl.h> 12 #include <petsc/private/vecscatterimpl.h> 13 14 #if defined(PETSC_HAVE_HYPRE) 15 PETSC_INTERN PetscErrorCode MatMatMultSymbolic_AIJ_AIJ_wHYPRE(Mat,Mat,PetscReal,Mat); 16 #endif 17 18 PETSC_INTERN PetscErrorCode MatProductSymbolic_AB_MPIAIJ_MPIAIJ(Mat C) 19 { 20 PetscErrorCode ierr; 21 Mat_Product *product = C->product; 22 Mat A=product->A,B=product->B; 23 MatProductAlgorithm alg=product->alg; 24 PetscReal fill=product->fill; 25 PetscBool flg; 26 27 PetscFunctionBegin; 28 /* scalable */ 29 ierr = PetscStrcmp(alg,"scalable",&flg);CHKERRQ(ierr); 30 if (flg) { 31 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 32 PetscFunctionReturn(0); 33 } 34 35 /* nonscalable */ 36 ierr = PetscStrcmp(alg,"nonscalable",&flg);CHKERRQ(ierr); 37 if (flg) { 38 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(A,B,fill,C);CHKERRQ(ierr); 39 PetscFunctionReturn(0); 40 } 41 42 /* seqmpi */ 43 ierr = PetscStrcmp(alg,"seqmpi",&flg);CHKERRQ(ierr); 44 if (flg) { 45 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI(A,B,fill,C);CHKERRQ(ierr); 46 PetscFunctionReturn(0); 47 } 48 49 #if defined(PETSC_HAVE_HYPRE) 50 ierr = PetscStrcmp(alg,"hypre",&flg);CHKERRQ(ierr); 51 if (flg) { 52 ierr = MatMatMultSymbolic_AIJ_AIJ_wHYPRE(A,B,fill,C);CHKERRQ(ierr); 53 PetscFunctionReturn(0); 54 } 55 #endif 56 SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_SUP,"Mat Product Algorithm is not supported"); 57 } 58 59 PetscErrorCode MatDestroy_MPIAIJ_MatMatMult(void *data) 60 { 61 PetscErrorCode ierr; 62 Mat_APMPI *ptap = (Mat_APMPI*)data; 63 64 PetscFunctionBegin; 65 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 66 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 67 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 68 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 69 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 70 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 71 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 72 ierr = PetscFree(ptap->apa);CHKERRQ(ierr); 73 ierr = PetscFree(ptap);CHKERRQ(ierr); 74 PetscFunctionReturn(0); 75 } 76 77 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,Mat C) 78 { 79 PetscErrorCode ierr; 80 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 81 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 82 Mat_SeqAIJ *cd =(Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 83 PetscScalar *cda=cd->a,*coa=co->a; 84 Mat_SeqAIJ *p_loc,*p_oth; 85 PetscScalar *apa,*ca; 86 PetscInt cm =C->rmap->n; 87 Mat_APMPI *ptap; 88 PetscInt *api,*apj,*apJ,i,k; 89 PetscInt cstart=C->cmap->rstart; 90 PetscInt cdnz,conz,k0,k1; 91 MPI_Comm comm; 92 PetscMPIInt size; 93 94 PetscFunctionBegin; 95 MatCheckProduct(C,3); 96 ptap = (Mat_APMPI*)C->product->data; 97 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 98 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 99 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 100 101 if (!ptap->P_oth && size>1) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"AP cannot be reused. Do not call MatProductClear()"); 102 103 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 104 /*-----------------------------------------------------*/ 105 /* update numerical values of P_oth and P_loc */ 106 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 107 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 108 109 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 110 /*----------------------------------------------------------*/ 111 /* get data from symbolic products */ 112 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 113 p_oth = NULL; 114 if (size >1) { 115 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 116 } 117 118 /* get apa for storing dense row A[i,:]*P */ 119 apa = ptap->apa; 120 121 api = ptap->api; 122 apj = ptap->apj; 123 for (i=0; i<cm; i++) { 124 /* compute apa = A[i,:]*P */ 125 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 126 127 /* set values in C */ 128 apJ = apj + api[i]; 129 cdnz = cd->i[i+1] - cd->i[i]; 130 conz = co->i[i+1] - co->i[i]; 131 132 /* 1st off-diagonal part of C */ 133 ca = coa + co->i[i]; 134 k = 0; 135 for (k0=0; k0<conz; k0++) { 136 if (apJ[k] >= cstart) break; 137 ca[k0] = apa[apJ[k]]; 138 apa[apJ[k++]] = 0.0; 139 } 140 141 /* diagonal part of C */ 142 ca = cda + cd->i[i]; 143 for (k1=0; k1<cdnz; k1++) { 144 ca[k1] = apa[apJ[k]]; 145 apa[apJ[k++]] = 0.0; 146 } 147 148 /* 2nd off-diagonal part of C */ 149 ca = coa + co->i[i]; 150 for (; k0<conz; k0++) { 151 ca[k0] = apa[apJ[k]]; 152 apa[apJ[k++]] = 0.0; 153 } 154 } 155 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 156 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 157 PetscFunctionReturn(0); 158 } 159 160 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,PetscReal fill,Mat C) 161 { 162 PetscErrorCode ierr; 163 MPI_Comm comm; 164 PetscMPIInt size; 165 Mat_APMPI *ptap; 166 PetscFreeSpaceList free_space=NULL,current_space=NULL; 167 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 168 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 169 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 170 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 171 PetscInt *lnk,i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi; 172 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n; 173 PetscBT lnkbt; 174 PetscReal afill; 175 MatType mtype; 176 177 PetscFunctionBegin; 178 MatCheckProduct(C,4); 179 if (C->product->data) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Extra product struct not empty"); 180 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 181 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 182 183 /* create struct Mat_APMPI and attached it to C later */ 184 ierr = PetscNew(&ptap);CHKERRQ(ierr); 185 186 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 187 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 188 189 /* get P_loc by taking all local rows of P */ 190 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 191 192 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 193 pi_loc = p_loc->i; pj_loc = p_loc->j; 194 if (size > 1) { 195 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 196 pi_oth = p_oth->i; pj_oth = p_oth->j; 197 } else { 198 p_oth = NULL; 199 pi_oth = NULL; pj_oth = NULL; 200 } 201 202 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 203 /*-------------------------------------------------------------------*/ 204 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 205 ptap->api = api; 206 api[0] = 0; 207 208 /* create and initialize a linked list */ 209 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 210 211 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 212 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 213 current_space = free_space; 214 215 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 216 for (i=0; i<am; i++) { 217 /* diagonal portion of A */ 218 nzi = adi[i+1] - adi[i]; 219 for (j=0; j<nzi; j++) { 220 row = *adj++; 221 pnz = pi_loc[row+1] - pi_loc[row]; 222 Jptr = pj_loc + pi_loc[row]; 223 /* add non-zero cols of P into the sorted linked list lnk */ 224 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 225 } 226 /* off-diagonal portion of A */ 227 nzi = aoi[i+1] - aoi[i]; 228 for (j=0; j<nzi; j++) { 229 row = *aoj++; 230 pnz = pi_oth[row+1] - pi_oth[row]; 231 Jptr = pj_oth + pi_oth[row]; 232 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 233 } 234 235 apnz = lnk[0]; 236 api[i+1] = api[i] + apnz; 237 238 /* if free space is not available, double the total space in the list */ 239 if (current_space->local_remaining<apnz) { 240 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 241 nspacedouble++; 242 } 243 244 /* Copy data into free space, then initialize lnk */ 245 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 246 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 247 248 current_space->array += apnz; 249 current_space->local_used += apnz; 250 current_space->local_remaining -= apnz; 251 } 252 253 /* Allocate space for apj, initialize apj, and */ 254 /* destroy list of free space and other temporary array(s) */ 255 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 256 apj = ptap->apj; 257 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 258 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 259 260 /* malloc apa to store dense row A[i,:]*P */ 261 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 262 263 /* set and assemble symbolic parallel matrix C */ 264 /*---------------------------------------------*/ 265 ierr = MatSetSizes(C,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 266 ierr = MatSetBlockSizesFromMats(C,A,P);CHKERRQ(ierr); 267 268 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 269 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 270 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 271 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 272 273 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(C, apj, api);CHKERRQ(ierr); 274 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 275 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 276 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 277 278 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 279 C->ops->productnumeric = MatProductNumeric_AB; 280 281 /* attach the supporting struct to C for reuse */ 282 C->product->data = ptap; 283 C->product->destroy = MatDestroy_MPIAIJ_MatMatMult; 284 285 /* set MatInfo */ 286 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 287 if (afill < 1.0) afill = 1.0; 288 C->info.mallocs = nspacedouble; 289 C->info.fill_ratio_given = fill; 290 C->info.fill_ratio_needed = afill; 291 292 #if defined(PETSC_USE_INFO) 293 if (api[am]) { 294 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 295 ierr = PetscInfo1(C,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 296 } else { 297 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 298 } 299 #endif 300 PetscFunctionReturn(0); 301 } 302 303 /* ------------------------------------------------------- */ 304 static PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat,Mat,PetscReal,Mat); 305 static PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat,Mat,Mat); 306 307 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_MPIDense_AB(Mat C) 308 { 309 Mat_Product *product = C->product; 310 Mat A = product->A,B=product->B; 311 312 PetscFunctionBegin; 313 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) 314 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%D, %D) != (%D,%D)",A->cmap->rstart,A->cmap->rend,B->rmap->rstart,B->rmap->rend); 315 316 C->ops->matmultsymbolic = MatMatMultSymbolic_MPIAIJ_MPIDense; 317 C->ops->productsymbolic = MatProductSymbolic_AB; 318 PetscFunctionReturn(0); 319 } 320 /* -------------------------------------------------------------------- */ 321 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_MPIDense_AtB(Mat C) 322 { 323 Mat_Product *product = C->product; 324 Mat A = product->A,B=product->B; 325 326 PetscFunctionBegin; 327 if (A->rmap->rstart != B->rmap->rstart || A->rmap->rend != B->rmap->rend) 328 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%D, %D) != (%D,%D)",A->rmap->rstart,A->rmap->rend,B->rmap->rstart,B->rmap->rend); 329 330 C->ops->transposematmultsymbolic = MatTransposeMatMultSymbolic_MPIAIJ_MPIDense; 331 C->ops->productsymbolic = MatProductSymbolic_AtB; 332 PetscFunctionReturn(0); 333 } 334 335 /* --------------------------------------------------------------------- */ 336 PETSC_INTERN PetscErrorCode MatProductSetFromOptions_MPIAIJ_MPIDense(Mat C) 337 { 338 PetscErrorCode ierr; 339 Mat_Product *product = C->product; 340 341 PetscFunctionBegin; 342 switch (product->type) { 343 case MATPRODUCT_AB: 344 ierr = MatProductSetFromOptions_MPIAIJ_MPIDense_AB(C);CHKERRQ(ierr); 345 break; 346 case MATPRODUCT_AtB: 347 ierr = MatProductSetFromOptions_MPIAIJ_MPIDense_AtB(C);CHKERRQ(ierr); 348 break; 349 default: 350 break; 351 } 352 PetscFunctionReturn(0); 353 } 354 /* ------------------------------------------------------- */ 355 356 typedef struct { 357 Mat workB,workB1; 358 MPI_Request *rwaits,*swaits; 359 PetscInt nsends,nrecvs; 360 MPI_Datatype *stype,*rtype; 361 PetscInt blda; 362 } MPIAIJ_MPIDense; 363 364 PetscErrorCode MatMPIAIJ_MPIDenseDestroy(void *ctx) 365 { 366 MPIAIJ_MPIDense *contents = (MPIAIJ_MPIDense*)ctx; 367 PetscErrorCode ierr; 368 PetscInt i; 369 370 PetscFunctionBegin; 371 ierr = MatDestroy(&contents->workB);CHKERRQ(ierr); 372 ierr = MatDestroy(&contents->workB1);CHKERRQ(ierr); 373 for (i=0; i<contents->nsends; i++) { 374 ierr = MPI_Type_free(&contents->stype[i]);CHKERRQ(ierr); 375 } 376 for (i=0; i<contents->nrecvs; i++) { 377 ierr = MPI_Type_free(&contents->rtype[i]);CHKERRQ(ierr); 378 } 379 ierr = PetscFree4(contents->stype,contents->rtype,contents->rwaits,contents->swaits);CHKERRQ(ierr); 380 ierr = PetscFree(contents);CHKERRQ(ierr); 381 PetscFunctionReturn(0); 382 } 383 384 static PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat A,Mat B,PetscReal fill,Mat C) 385 { 386 PetscErrorCode ierr; 387 Mat_MPIAIJ *aij=(Mat_MPIAIJ*)A->data; 388 PetscInt nz=aij->B->cmap->n,nsends,nrecvs,i,nrows_to,j,blda,clda; 389 MPIAIJ_MPIDense *contents; 390 VecScatter ctx=aij->Mvctx; 391 PetscInt Am=A->rmap->n,Bm=B->rmap->n,BN=B->cmap->N,Bbn,Bbn1,bs,nrows_from,numBb; 392 MPI_Comm comm; 393 MPI_Datatype type1,*stype,*rtype; 394 const PetscInt *sindices,*sstarts,*rstarts; 395 PetscMPIInt *disp; 396 PetscBool cisdense; 397 398 PetscFunctionBegin; 399 MatCheckProduct(C,4); 400 if (C->product->data) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_PLIB,"Product data not empty"); 401 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 402 ierr = PetscObjectBaseTypeCompare((PetscObject)C,MATMPIDENSE,&cisdense);CHKERRQ(ierr); 403 if (!cisdense) { 404 ierr = MatSetType(C,((PetscObject)B)->type_name);CHKERRQ(ierr); 405 } 406 ierr = MatSetSizes(C,Am,B->cmap->n,A->rmap->N,BN);CHKERRQ(ierr); 407 ierr = MatSetBlockSizesFromMats(C,A,B);CHKERRQ(ierr); 408 ierr = MatSetUp(C);CHKERRQ(ierr); 409 ierr = MatDenseGetLDA(B,&blda);CHKERRQ(ierr); 410 ierr = MatDenseGetLDA(C,&clda);CHKERRQ(ierr); 411 ierr = PetscNew(&contents);CHKERRQ(ierr); 412 413 ierr = VecScatterGetRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,NULL,NULL);CHKERRQ(ierr); 414 ierr = VecScatterGetRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,NULL,NULL);CHKERRQ(ierr); 415 416 /* Create column block of B and C for memory scalability when BN is too large */ 417 /* Estimate Bbn, column size of Bb */ 418 if (nz) { 419 Bbn1 = 2*Am*BN/nz; 420 if (!Bbn1) Bbn1 = 1; 421 } else Bbn1 = BN; 422 423 bs = PetscAbs(B->cmap->bs); 424 Bbn1 = Bbn1/bs *bs; /* Bbn1 is a multiple of bs */ 425 if (Bbn1 > BN) Bbn1 = BN; 426 ierr = MPI_Allreduce(&Bbn1,&Bbn,1,MPIU_INT,MPI_MAX,comm);CHKERRQ(ierr); 427 428 /* Enable runtime option for Bbn */ 429 ierr = PetscOptionsBegin(comm,((PetscObject)C)->prefix,"MatMatMult","Mat");CHKERRQ(ierr); 430 ierr = PetscOptionsInt("-matmatmult_Bbn","Number of columns in Bb","MatMatMult",Bbn,&Bbn,NULL);CHKERRQ(ierr); 431 ierr = PetscOptionsEnd();CHKERRQ(ierr); 432 Bbn = PetscMin(Bbn,BN); 433 434 if (Bbn > 0 && Bbn < BN) { 435 numBb = BN/Bbn; 436 Bbn1 = BN - numBb*Bbn; 437 } else numBb = 0; 438 439 if (numBb) { 440 ierr = PetscInfo3(C,"use Bb, BN=%D, Bbn=%D; numBb=%D\n",BN,Bbn,numBb);CHKERRQ(ierr); 441 if (Bbn1) { /* Create workB1 for the remaining columns */ 442 ierr = PetscInfo2(C,"use Bb1, BN=%D, Bbn1=%D\n",BN,Bbn1);CHKERRQ(ierr); 443 /* Create work matrix used to store off processor rows of B needed for local product */ 444 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,Bbn1,NULL,&contents->workB1);CHKERRQ(ierr); 445 } else contents->workB1 = NULL; 446 } 447 448 /* Create work matrix used to store off processor rows of B needed for local product */ 449 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,Bbn,NULL,&contents->workB);CHKERRQ(ierr); 450 451 /* Use MPI derived data type to reduce memory required by the send/recv buffers */ 452 ierr = PetscMalloc4(nsends,&stype,nrecvs,&rtype,nrecvs,&contents->rwaits,nsends,&contents->swaits);CHKERRQ(ierr); 453 contents->stype = stype; 454 contents->nsends = nsends; 455 456 contents->rtype = rtype; 457 contents->nrecvs = nrecvs; 458 contents->blda = blda; 459 460 ierr = PetscMalloc1(Bm+1,&disp);CHKERRQ(ierr); 461 for (i=0; i<nsends; i++) { 462 nrows_to = sstarts[i+1]-sstarts[i]; 463 for (j=0; j<nrows_to; j++){ 464 disp[j] = sindices[sstarts[i]+j]; /* rowB to be sent */ 465 } 466 ierr = MPI_Type_create_indexed_block(nrows_to,1,(const PetscMPIInt *)disp,MPIU_SCALAR,&type1);CHKERRQ(ierr); 467 468 ierr = MPI_Type_create_resized(type1,0,blda*sizeof(PetscScalar),&stype[i]);CHKERRQ(ierr); 469 ierr = MPI_Type_commit(&stype[i]);CHKERRQ(ierr); 470 ierr = MPI_Type_free(&type1);CHKERRQ(ierr); 471 } 472 473 for (i=0; i<nrecvs; i++) { 474 /* received values from a process form a (nrows_from x Bbn) row block in workB (column-wise) */ 475 nrows_from = rstarts[i+1]-rstarts[i]; 476 disp[0] = 0; 477 ierr = MPI_Type_create_indexed_block(1, nrows_from, (const PetscMPIInt *)disp, MPIU_SCALAR, &type1);CHKERRQ(ierr); 478 ierr = MPI_Type_create_resized(type1, 0, nz*sizeof(PetscScalar), &rtype[i]);CHKERRQ(ierr); 479 ierr = MPI_Type_commit(&rtype[i]);CHKERRQ(ierr); 480 ierr = MPI_Type_free(&type1);CHKERRQ(ierr); 481 } 482 483 ierr = PetscFree(disp);CHKERRQ(ierr); 484 ierr = VecScatterRestoreRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,NULL,NULL);CHKERRQ(ierr); 485 ierr = VecScatterRestoreRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,NULL,NULL);CHKERRQ(ierr); 486 ierr = MatSetOption(C,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 487 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 488 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 489 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 490 491 C->product->data = contents; 492 C->product->destroy = MatMPIAIJ_MPIDenseDestroy; 493 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 494 PetscFunctionReturn(0); 495 } 496 497 PETSC_INTERN PetscErrorCode MatMatMultNumericAdd_SeqAIJ_SeqDense(Mat,Mat,Mat,const PetscBool); 498 /* 499 Performs an efficient scatter on the rows of B needed by this process; this is 500 a modification of the VecScatterBegin_() routines. 501 502 Input: Bbidx = 0: B = Bb 503 = 1: B = Bb1, see MatMatMultSymbolic_MPIAIJ_MPIDense() 504 */ 505 PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,PetscInt Bbidx,Mat C,Mat *outworkB) 506 { 507 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 508 PetscErrorCode ierr; 509 const PetscScalar *b; 510 PetscScalar *rvalues; 511 VecScatter ctx = aij->Mvctx; 512 const PetscInt *sindices,*sstarts,*rstarts; 513 const PetscMPIInt *sprocs,*rprocs; 514 PetscInt i,nsends,nrecvs; 515 MPI_Request *swaits,*rwaits; 516 MPI_Comm comm; 517 PetscMPIInt tag=((PetscObject)ctx)->tag,ncols=B->cmap->N,nrows=aij->B->cmap->n,nsends_mpi,nrecvs_mpi; 518 MPIAIJ_MPIDense *contents; 519 Mat workB; 520 MPI_Datatype *stype,*rtype; 521 PetscInt blda; 522 523 PetscFunctionBegin; 524 MatCheckProduct(C,4); 525 if (!C->product->data) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_PLIB,"Product data empty"); 526 contents = (MPIAIJ_MPIDense*)C->product->data; 527 ierr = VecScatterGetRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,&sprocs,NULL/*bs*/);CHKERRQ(ierr); 528 ierr = VecScatterGetRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,&rprocs,NULL/*bs*/);CHKERRQ(ierr); 529 ierr = PetscMPIIntCast(nsends,&nsends_mpi);CHKERRQ(ierr); 530 ierr = PetscMPIIntCast(nrecvs,&nrecvs_mpi);CHKERRQ(ierr); 531 if (Bbidx == 0) { 532 workB = *outworkB = contents->workB; 533 } else { 534 workB = *outworkB = contents->workB1; 535 } 536 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); 537 swaits = contents->swaits; 538 rwaits = contents->rwaits; 539 540 ierr = MatDenseGetArrayRead(B,&b);CHKERRQ(ierr); 541 ierr = MatDenseGetLDA(B,&blda);CHKERRQ(ierr); 542 if (blda != contents->blda) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Cannot reuse an input matrix with lda %D != %D",blda,contents->blda); 543 ierr = MatDenseGetArray(workB,&rvalues);CHKERRQ(ierr); 544 545 /* Post recv, use MPI derived data type to save memory */ 546 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 547 rtype = contents->rtype; 548 for (i=0; i<nrecvs; i++) { 549 ierr = MPI_Irecv(rvalues+(rstarts[i]-rstarts[0]),ncols,rtype[i],rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 550 } 551 552 stype = contents->stype; 553 for (i=0; i<nsends; i++) { 554 ierr = MPI_Isend(b,ncols,stype[i],sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 555 } 556 557 if (nrecvs) {ierr = MPI_Waitall(nrecvs_mpi,rwaits,MPI_STATUSES_IGNORE);CHKERRQ(ierr);} 558 if (nsends) {ierr = MPI_Waitall(nsends_mpi,swaits,MPI_STATUSES_IGNORE);CHKERRQ(ierr);} 559 560 ierr = VecScatterRestoreRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,&sprocs,NULL);CHKERRQ(ierr); 561 ierr = VecScatterRestoreRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,&rprocs,NULL);CHKERRQ(ierr); 562 ierr = MatDenseRestoreArrayRead(B,&b);CHKERRQ(ierr); 563 ierr = MatDenseRestoreArray(workB,&rvalues);CHKERRQ(ierr); 564 PetscFunctionReturn(0); 565 } 566 567 static PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat A,Mat B,Mat C) 568 { 569 PetscErrorCode ierr; 570 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 571 Mat_MPIDense *bdense = (Mat_MPIDense*)B->data; 572 Mat_MPIDense *cdense = (Mat_MPIDense*)C->data; 573 Mat workB; 574 MPIAIJ_MPIDense *contents; 575 576 PetscFunctionBegin; 577 MatCheckProduct(C,3); 578 if (!C->product->data) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_PLIB,"Product data empty"); 579 contents = (MPIAIJ_MPIDense*)C->product->data; 580 /* diagonal block of A times all local rows of B */ 581 /* TODO: this calls a symbolic multiplication every time, which could be avoided */ 582 ierr = MatMatMult(aij->A,bdense->A,MAT_REUSE_MATRIX,PETSC_DEFAULT,&cdense->A);CHKERRQ(ierr); 583 if (contents->workB->cmap->n == B->cmap->N) { 584 /* get off processor parts of B needed to complete C=A*B */ 585 ierr = MatMPIDenseScatter(A,B,0,C,&workB);CHKERRQ(ierr); 586 587 /* off-diagonal block of A times nonlocal rows of B */ 588 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A,PETSC_TRUE);CHKERRQ(ierr); 589 } else { 590 Mat Bb,Cb; 591 PetscInt BN=B->cmap->N,n=contents->workB->cmap->n,i; 592 if (n <= 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Column block size %D must be positive",n); 593 594 for (i=0; i<BN; i+=n) { 595 ierr = MatDenseGetSubMatrix(B,i,PetscMin(i+n,BN),&Bb);CHKERRQ(ierr); 596 ierr = MatDenseGetSubMatrix(C,i,PetscMin(i+n,BN),&Cb);CHKERRQ(ierr); 597 598 /* get off processor parts of B needed to complete C=A*B */ 599 ierr = MatMPIDenseScatter(A,Bb,i+n>BN,C,&workB);CHKERRQ(ierr); 600 601 /* off-diagonal block of A times nonlocal rows of B */ 602 cdense = (Mat_MPIDense*)Cb->data; 603 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A,PETSC_TRUE);CHKERRQ(ierr); 604 605 ierr = MatDenseRestoreSubMatrix(B,&Bb);CHKERRQ(ierr); 606 ierr = MatDenseRestoreSubMatrix(C,&Cb);CHKERRQ(ierr); 607 } 608 } 609 PetscFunctionReturn(0); 610 } 611 612 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 613 { 614 PetscErrorCode ierr; 615 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 616 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 617 Mat_SeqAIJ *cd = (Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 618 PetscInt *adi = ad->i,*adj,*aoi=ao->i,*aoj; 619 PetscScalar *ada,*aoa,*cda=cd->a,*coa=co->a; 620 Mat_SeqAIJ *p_loc,*p_oth; 621 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pj; 622 PetscScalar *pa_loc,*pa_oth,*pa,valtmp,*ca; 623 PetscInt cm = C->rmap->n,anz,pnz; 624 Mat_APMPI *ptap; 625 PetscScalar *apa_sparse; 626 PetscInt *api,*apj,*apJ,i,j,k,row; 627 PetscInt cstart = C->cmap->rstart; 628 PetscInt cdnz,conz,k0,k1,nextp; 629 MPI_Comm comm; 630 PetscMPIInt size; 631 632 PetscFunctionBegin; 633 MatCheckProduct(C,3); 634 ptap = (Mat_APMPI*)C->product->data; 635 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 636 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 637 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 638 if (!ptap->P_oth && size>1) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"AP cannot be reused. Do not call MatProductClear()"); 639 640 apa_sparse = ptap->apa; 641 642 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 643 /*-----------------------------------------------------*/ 644 /* update numerical values of P_oth and P_loc */ 645 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 646 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 647 648 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 649 /*----------------------------------------------------------*/ 650 /* get data from symbolic products */ 651 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 652 pi_loc = p_loc->i; pj_loc = p_loc->j; pa_loc = p_loc->a; 653 if (size >1) { 654 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 655 pi_oth = p_oth->i; pj_oth = p_oth->j; pa_oth = p_oth->a; 656 } else { 657 p_oth = NULL; pi_oth = NULL; pj_oth = NULL; pa_oth = NULL; 658 } 659 660 api = ptap->api; 661 apj = ptap->apj; 662 for (i=0; i<cm; i++) { 663 apJ = apj + api[i]; 664 665 /* diagonal portion of A */ 666 anz = adi[i+1] - adi[i]; 667 adj = ad->j + adi[i]; 668 ada = ad->a + adi[i]; 669 for (j=0; j<anz; j++) { 670 row = adj[j]; 671 pnz = pi_loc[row+1] - pi_loc[row]; 672 pj = pj_loc + pi_loc[row]; 673 pa = pa_loc + pi_loc[row]; 674 /* perform sparse axpy */ 675 valtmp = ada[j]; 676 nextp = 0; 677 for (k=0; nextp<pnz; k++) { 678 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 679 apa_sparse[k] += valtmp*pa[nextp++]; 680 } 681 } 682 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 683 } 684 685 /* off-diagonal portion of A */ 686 anz = aoi[i+1] - aoi[i]; 687 aoj = ao->j + aoi[i]; 688 aoa = ao->a + aoi[i]; 689 for (j=0; j<anz; j++) { 690 row = aoj[j]; 691 pnz = pi_oth[row+1] - pi_oth[row]; 692 pj = pj_oth + pi_oth[row]; 693 pa = pa_oth + pi_oth[row]; 694 /* perform sparse axpy */ 695 valtmp = aoa[j]; 696 nextp = 0; 697 for (k=0; nextp<pnz; k++) { 698 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 699 apa_sparse[k] += valtmp*pa[nextp++]; 700 } 701 } 702 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 703 } 704 705 /* set values in C */ 706 cdnz = cd->i[i+1] - cd->i[i]; 707 conz = co->i[i+1] - co->i[i]; 708 709 /* 1st off-diagonal part of C */ 710 ca = coa + co->i[i]; 711 k = 0; 712 for (k0=0; k0<conz; k0++) { 713 if (apJ[k] >= cstart) break; 714 ca[k0] = apa_sparse[k]; 715 apa_sparse[k] = 0.0; 716 k++; 717 } 718 719 /* diagonal part of C */ 720 ca = cda + cd->i[i]; 721 for (k1=0; k1<cdnz; k1++) { 722 ca[k1] = apa_sparse[k]; 723 apa_sparse[k] = 0.0; 724 k++; 725 } 726 727 /* 2nd off-diagonal part of C */ 728 ca = coa + co->i[i]; 729 for (; k0<conz; k0++) { 730 ca[k0] = apa_sparse[k]; 731 apa_sparse[k] = 0.0; 732 k++; 733 } 734 } 735 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 736 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 737 PetscFunctionReturn(0); 738 } 739 740 /* same as MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(), except using LLCondensed to avoid O(BN) memory requirement */ 741 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat C) 742 { 743 PetscErrorCode ierr; 744 MPI_Comm comm; 745 PetscMPIInt size; 746 Mat_APMPI *ptap; 747 PetscFreeSpaceList free_space = NULL,current_space=NULL; 748 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 749 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 750 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 751 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 752 PetscInt i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi,*lnk,apnz_max=0; 753 PetscInt am=A->rmap->n,pn=P->cmap->n,pm=P->rmap->n,lsize=pn+20; 754 PetscReal afill; 755 MatType mtype; 756 757 PetscFunctionBegin; 758 MatCheckProduct(C,4); 759 if (C->product->data) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Extra product struct not empty"); 760 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 761 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 762 763 /* create struct Mat_APMPI and attached it to C later */ 764 ierr = PetscNew(&ptap);CHKERRQ(ierr); 765 766 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 767 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 768 769 /* get P_loc by taking all local rows of P */ 770 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 771 772 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 773 pi_loc = p_loc->i; pj_loc = p_loc->j; 774 if (size > 1) { 775 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 776 pi_oth = p_oth->i; pj_oth = p_oth->j; 777 } else { 778 p_oth = NULL; 779 pi_oth = NULL; pj_oth = NULL; 780 } 781 782 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 783 /*-------------------------------------------------------------------*/ 784 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 785 ptap->api = api; 786 api[0] = 0; 787 788 ierr = PetscLLCondensedCreate_Scalable(lsize,&lnk);CHKERRQ(ierr); 789 790 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 791 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 792 current_space = free_space; 793 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 794 for (i=0; i<am; i++) { 795 /* diagonal portion of A */ 796 nzi = adi[i+1] - adi[i]; 797 for (j=0; j<nzi; j++) { 798 row = *adj++; 799 pnz = pi_loc[row+1] - pi_loc[row]; 800 Jptr = pj_loc + pi_loc[row]; 801 /* Expand list if it is not long enough */ 802 if (pnz+apnz_max > lsize) { 803 lsize = pnz+apnz_max; 804 ierr = PetscLLCondensedExpand_Scalable(lsize, &lnk);CHKERRQ(ierr); 805 } 806 /* add non-zero cols of P into the sorted linked list lnk */ 807 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 808 apnz = *lnk; /* The first element in the list is the number of items in the list */ 809 api[i+1] = api[i] + apnz; 810 if (apnz > apnz_max) apnz_max = apnz; 811 } 812 /* off-diagonal portion of A */ 813 nzi = aoi[i+1] - aoi[i]; 814 for (j=0; j<nzi; j++) { 815 row = *aoj++; 816 pnz = pi_oth[row+1] - pi_oth[row]; 817 Jptr = pj_oth + pi_oth[row]; 818 /* Expand list if it is not long enough */ 819 if (pnz+apnz_max > lsize) { 820 lsize = pnz + apnz_max; 821 ierr = PetscLLCondensedExpand_Scalable(lsize, &lnk);CHKERRQ(ierr); 822 } 823 /* add non-zero cols of P into the sorted linked list lnk */ 824 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 825 apnz = *lnk; /* The first element in the list is the number of items in the list */ 826 api[i+1] = api[i] + apnz; 827 if (apnz > apnz_max) apnz_max = apnz; 828 } 829 apnz = *lnk; 830 api[i+1] = api[i] + apnz; 831 if (apnz > apnz_max) apnz_max = apnz; 832 833 /* if free space is not available, double the total space in the list */ 834 if (current_space->local_remaining<apnz) { 835 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 836 nspacedouble++; 837 } 838 839 /* Copy data into free space, then initialize lnk */ 840 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 841 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 842 843 current_space->array += apnz; 844 current_space->local_used += apnz; 845 current_space->local_remaining -= apnz; 846 } 847 848 /* Allocate space for apj, initialize apj, and */ 849 /* destroy list of free space and other temporary array(s) */ 850 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 851 apj = ptap->apj; 852 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 853 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 854 855 /* create and assemble symbolic parallel matrix C */ 856 /*----------------------------------------------------*/ 857 ierr = MatSetSizes(C,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 858 ierr = MatSetBlockSizesFromMats(C,A,P);CHKERRQ(ierr); 859 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 860 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 861 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 862 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 863 864 /* malloc apa for assembly C */ 865 ierr = PetscCalloc1(apnz_max,&ptap->apa);CHKERRQ(ierr); 866 867 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(C, apj, api);CHKERRQ(ierr); 868 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 869 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 870 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 871 872 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ; 873 C->ops->productnumeric = MatProductNumeric_AB; 874 875 /* attach the supporting struct to C for reuse */ 876 C->product->data = ptap; 877 C->product->destroy = MatDestroy_MPIAIJ_MatMatMult; 878 879 /* set MatInfo */ 880 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 881 if (afill < 1.0) afill = 1.0; 882 C->info.mallocs = nspacedouble; 883 C->info.fill_ratio_given = fill; 884 C->info.fill_ratio_needed = afill; 885 886 #if defined(PETSC_USE_INFO) 887 if (api[am]) { 888 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 889 ierr = PetscInfo1(C,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 890 } else { 891 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 892 } 893 #endif 894 PetscFunctionReturn(0); 895 } 896 897 /* This function is needed for the seqMPI matrix-matrix multiplication. */ 898 /* Three input arrays are merged to one output array. The size of the */ 899 /* output array is also output. Duplicate entries only show up once. */ 900 static void Merge3SortedArrays(PetscInt size1, PetscInt *in1, 901 PetscInt size2, PetscInt *in2, 902 PetscInt size3, PetscInt *in3, 903 PetscInt *size4, PetscInt *out) 904 { 905 int i = 0, j = 0, k = 0, l = 0; 906 907 /* Traverse all three arrays */ 908 while (i<size1 && j<size2 && k<size3) { 909 if (in1[i] < in2[j] && in1[i] < in3[k]) { 910 out[l++] = in1[i++]; 911 } 912 else if (in2[j] < in1[i] && in2[j] < in3[k]) { 913 out[l++] = in2[j++]; 914 } 915 else if (in3[k] < in1[i] && in3[k] < in2[j]) { 916 out[l++] = in3[k++]; 917 } 918 else if (in1[i] == in2[j] && in1[i] < in3[k]) { 919 out[l++] = in1[i]; 920 i++, j++; 921 } 922 else if (in1[i] == in3[k] && in1[i] < in2[j]) { 923 out[l++] = in1[i]; 924 i++, k++; 925 } 926 else if (in3[k] == in2[j] && in2[j] < in1[i]) { 927 out[l++] = in2[j]; 928 k++, j++; 929 } 930 else if (in1[i] == in2[j] && in1[i] == in3[k]) { 931 out[l++] = in1[i]; 932 i++, j++, k++; 933 } 934 } 935 936 /* Traverse two remaining arrays */ 937 while (i<size1 && j<size2) { 938 if (in1[i] < in2[j]) { 939 out[l++] = in1[i++]; 940 } 941 else if (in1[i] > in2[j]) { 942 out[l++] = in2[j++]; 943 } 944 else { 945 out[l++] = in1[i]; 946 i++, j++; 947 } 948 } 949 950 while (i<size1 && k<size3) { 951 if (in1[i] < in3[k]) { 952 out[l++] = in1[i++]; 953 } 954 else if (in1[i] > in3[k]) { 955 out[l++] = in3[k++]; 956 } 957 else { 958 out[l++] = in1[i]; 959 i++, k++; 960 } 961 } 962 963 while (k<size3 && j<size2) { 964 if (in3[k] < in2[j]) { 965 out[l++] = in3[k++]; 966 } 967 else if (in3[k] > in2[j]) { 968 out[l++] = in2[j++]; 969 } 970 else { 971 out[l++] = in3[k]; 972 k++, j++; 973 } 974 } 975 976 /* Traverse one remaining array */ 977 while (i<size1) out[l++] = in1[i++]; 978 while (j<size2) out[l++] = in2[j++]; 979 while (k<size3) out[l++] = in3[k++]; 980 981 *size4 = l; 982 } 983 984 /* This matrix-matrix multiplication algorithm divides the multiplication into three multiplications and */ 985 /* adds up the products. Two of these three multiplications are performed with existing (sequential) */ 986 /* matrix-matrix multiplications. */ 987 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI(Mat A, Mat P, PetscReal fill, Mat C) 988 { 989 PetscErrorCode ierr; 990 MPI_Comm comm; 991 PetscMPIInt size; 992 Mat_APMPI *ptap; 993 PetscFreeSpaceList free_space_diag=NULL, current_space=NULL; 994 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data; 995 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc; 996 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data; 997 Mat_SeqAIJ *adpd_seq, *p_off, *aopoth_seq; 998 PetscInt adponz, adpdnz; 999 PetscInt *pi_loc,*dnz,*onz; 1000 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,rstart=A->rmap->rstart; 1001 PetscInt *lnk,i, i1=0,pnz,row,*adpoi,*adpoj, *api, *adpoJ, *aopJ, *apJ,*Jptr, aopnz, nspacedouble=0,j,nzi, 1002 *apj,apnz, *adpdi, *adpdj, *adpdJ, *poff_i, *poff_j, *j_temp, *aopothi, *aopothj; 1003 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n, p_colstart, p_colend; 1004 PetscBT lnkbt; 1005 PetscReal afill; 1006 PetscMPIInt rank; 1007 Mat adpd, aopoth; 1008 MatType mtype; 1009 const char *prefix; 1010 1011 PetscFunctionBegin; 1012 MatCheckProduct(C,4); 1013 if (C->product->data) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Extra product struct not empty"); 1014 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1015 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1016 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1017 ierr = MatGetOwnershipRangeColumn(P, &p_colstart, &p_colend);CHKERRQ(ierr); 1018 1019 /* create struct Mat_APMPI and attached it to C later */ 1020 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1021 1022 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1023 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1024 1025 /* get P_loc by taking all local rows of P */ 1026 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1027 1028 1029 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1030 pi_loc = p_loc->i; 1031 1032 /* Allocate memory for the i arrays of the matrices A*P, A_diag*P_off and A_offd * P */ 1033 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 1034 ierr = PetscMalloc1(am+2,&adpoi);CHKERRQ(ierr); 1035 1036 adpoi[0] = 0; 1037 ptap->api = api; 1038 api[0] = 0; 1039 1040 /* create and initialize a linked list, will be used for both A_diag * P_loc_off and A_offd * P_oth */ 1041 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1042 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 1043 1044 /* Symbolic calc of A_loc_diag * P_loc_diag */ 1045 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1046 ierr = MatProductCreate(a->A,p->A,NULL,&adpd);CHKERRQ(ierr); 1047 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1048 ierr = MatSetOptionsPrefix(adpd,prefix);CHKERRQ(ierr); 1049 ierr = MatAppendOptionsPrefix(adpd,"inner_diag_");CHKERRQ(ierr); 1050 1051 ierr = MatProductSetType(adpd,MATPRODUCT_AB);CHKERRQ(ierr); 1052 ierr = MatProductSetAlgorithm(adpd,"sorted");CHKERRQ(ierr); 1053 ierr = MatProductSetFill(adpd,fill);CHKERRQ(ierr); 1054 ierr = MatProductSetFromOptions(adpd);CHKERRQ(ierr); 1055 ierr = MatProductSymbolic(adpd);CHKERRQ(ierr); 1056 1057 adpd_seq = (Mat_SeqAIJ*)((adpd)->data); 1058 adpdi = adpd_seq->i; adpdj = adpd_seq->j; 1059 p_off = (Mat_SeqAIJ*)((p->B)->data); 1060 poff_i = p_off->i; poff_j = p_off->j; 1061 1062 /* j_temp stores indices of a result row before they are added to the linked list */ 1063 ierr = PetscMalloc1(pN+2,&j_temp);CHKERRQ(ierr); 1064 1065 1066 /* Symbolic calc of the A_diag * p_loc_off */ 1067 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 1068 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space_diag);CHKERRQ(ierr); 1069 current_space = free_space_diag; 1070 1071 for (i=0; i<am; i++) { 1072 /* A_diag * P_loc_off */ 1073 nzi = adi[i+1] - adi[i]; 1074 for (j=0; j<nzi; j++) { 1075 row = *adj++; 1076 pnz = poff_i[row+1] - poff_i[row]; 1077 Jptr = poff_j + poff_i[row]; 1078 for (i1 = 0; i1 < pnz; i1++) { 1079 j_temp[i1] = p->garray[Jptr[i1]]; 1080 } 1081 /* add non-zero cols of P into the sorted linked list lnk */ 1082 ierr = PetscLLCondensedAddSorted(pnz,j_temp,lnk,lnkbt);CHKERRQ(ierr); 1083 } 1084 1085 adponz = lnk[0]; 1086 adpoi[i+1] = adpoi[i] + adponz; 1087 1088 /* if free space is not available, double the total space in the list */ 1089 if (current_space->local_remaining<adponz) { 1090 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(adponz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1091 nspacedouble++; 1092 } 1093 1094 /* Copy data into free space, then initialize lnk */ 1095 ierr = PetscLLCondensedClean(pN,adponz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1096 1097 current_space->array += adponz; 1098 current_space->local_used += adponz; 1099 current_space->local_remaining -= adponz; 1100 } 1101 1102 /* Symbolic calc of A_off * P_oth */ 1103 ierr = MatSetOptionsPrefix(a->B,prefix);CHKERRQ(ierr); 1104 ierr = MatAppendOptionsPrefix(a->B,"inner_offdiag_");CHKERRQ(ierr); 1105 ierr = MatCreate(PETSC_COMM_SELF,&aopoth);CHKERRQ(ierr); 1106 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(a->B, ptap->P_oth, fill, aopoth);CHKERRQ(ierr); 1107 aopoth_seq = (Mat_SeqAIJ*)((aopoth)->data); 1108 aopothi = aopoth_seq->i; aopothj = aopoth_seq->j; 1109 1110 /* Allocate space for apj, adpj, aopj, ... */ 1111 /* destroy lists of free space and other temporary array(s) */ 1112 1113 ierr = PetscMalloc1(aopothi[am] + adpoi[am] + adpdi[am]+2, &ptap->apj);CHKERRQ(ierr); 1114 ierr = PetscMalloc1(adpoi[am]+2, &adpoj);CHKERRQ(ierr); 1115 1116 /* Copy from linked list to j-array */ 1117 ierr = PetscFreeSpaceContiguous(&free_space_diag,adpoj);CHKERRQ(ierr); 1118 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1119 1120 adpoJ = adpoj; 1121 adpdJ = adpdj; 1122 aopJ = aopothj; 1123 apj = ptap->apj; 1124 apJ = apj; /* still empty */ 1125 1126 /* Merge j-arrays of A_off * P, A_diag * P_loc_off, and */ 1127 /* A_diag * P_loc_diag to get A*P */ 1128 for (i = 0; i < am; i++) { 1129 aopnz = aopothi[i+1] - aopothi[i]; 1130 adponz = adpoi[i+1] - adpoi[i]; 1131 adpdnz = adpdi[i+1] - adpdi[i]; 1132 1133 /* Correct indices from A_diag*P_diag */ 1134 for (i1 = 0; i1 < adpdnz; i1++) { 1135 adpdJ[i1] += p_colstart; 1136 } 1137 /* Merge j-arrays of A_diag * P_loc_off and A_diag * P_loc_diag and A_off * P_oth */ 1138 Merge3SortedArrays(adponz, adpoJ, adpdnz, adpdJ, aopnz, aopJ, &apnz, apJ); 1139 ierr = MatPreallocateSet(i+rstart, apnz, apJ, dnz, onz);CHKERRQ(ierr); 1140 1141 aopJ += aopnz; 1142 adpoJ += adponz; 1143 adpdJ += adpdnz; 1144 apJ += apnz; 1145 api[i+1] = api[i] + apnz; 1146 } 1147 1148 /* malloc apa to store dense row A[i,:]*P */ 1149 ierr = PetscCalloc1(pN+2,&ptap->apa);CHKERRQ(ierr); 1150 1151 /* create and assemble symbolic parallel matrix C */ 1152 ierr = MatSetSizes(C,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1153 ierr = MatSetBlockSizesFromMats(C,A,P);CHKERRQ(ierr); 1154 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1155 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 1156 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 1157 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1158 1159 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(C, apj, api);CHKERRQ(ierr); 1160 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1161 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1162 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1163 1164 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1165 C->ops->productnumeric = MatProductNumeric_AB; 1166 1167 /* attach the supporting struct to C for reuse */ 1168 C->product->data = ptap; 1169 C->product->destroy = MatDestroy_MPIAIJ_MatMatMult; 1170 1171 /* set MatInfo */ 1172 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 1173 if (afill < 1.0) afill = 1.0; 1174 C->info.mallocs = nspacedouble; 1175 C->info.fill_ratio_given = fill; 1176 C->info.fill_ratio_needed = afill; 1177 1178 #if defined(PETSC_USE_INFO) 1179 if (api[am]) { 1180 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1181 ierr = PetscInfo1(C,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 1182 } else { 1183 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 1184 } 1185 #endif 1186 1187 ierr = MatDestroy(&aopoth);CHKERRQ(ierr); 1188 ierr = MatDestroy(&adpd);CHKERRQ(ierr); 1189 ierr = PetscFree(j_temp);CHKERRQ(ierr); 1190 ierr = PetscFree(adpoj);CHKERRQ(ierr); 1191 ierr = PetscFree(adpoi);CHKERRQ(ierr); 1192 PetscFunctionReturn(0); 1193 } 1194 1195 /*-------------------------------------------------------------------------*/ 1196 /* This routine only works when scall=MAT_REUSE_MATRIX! */ 1197 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult(Mat P,Mat A,Mat C) 1198 { 1199 PetscErrorCode ierr; 1200 Mat_APMPI *ptap; 1201 Mat Pt; 1202 1203 PetscFunctionBegin; 1204 MatCheckProduct(C,3); 1205 ptap = (Mat_APMPI*)C->product->data; 1206 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 1207 if (!ptap->Pt) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatProductClear()"); 1208 1209 Pt = ptap->Pt; 1210 ierr = MatTranspose(P,MAT_REUSE_MATRIX,&Pt);CHKERRQ(ierr); 1211 ierr = MatMatMultNumeric_MPIAIJ_MPIAIJ(Pt,A,C);CHKERRQ(ierr); 1212 PetscFunctionReturn(0); 1213 } 1214 1215 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ() */ 1216 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,PetscReal fill,Mat C) 1217 { 1218 PetscErrorCode ierr; 1219 Mat_APMPI *ptap; 1220 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data; 1221 MPI_Comm comm; 1222 PetscMPIInt size,rank; 1223 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1224 PetscInt pn=P->cmap->n,aN=A->cmap->N,an=A->cmap->n; 1225 PetscInt *lnk,i,k,nsend,rstart; 1226 PetscBT lnkbt; 1227 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,nrecv; 1228 PETSC_UNUSED PetscMPIInt icompleted=0; 1229 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1230 PetscInt len,proc,*dnz,*onz,*owners,nzi; 1231 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1232 MPI_Request *swaits,*rwaits; 1233 MPI_Status *sstatus,rstatus; 1234 PetscLayout rowmap; 1235 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1236 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1237 PetscInt *Jptr,*prmap=p->garray,con,j,Crmax; 1238 Mat_SeqAIJ *a_loc,*c_loc,*c_oth; 1239 PetscTable ta; 1240 MatType mtype; 1241 const char *prefix; 1242 1243 PetscFunctionBegin; 1244 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1245 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1246 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1247 1248 /* create symbolic parallel matrix C */ 1249 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1250 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 1251 1252 C->ops->transposematmultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1253 1254 /* create struct Mat_APMPI and attached it to C later */ 1255 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1256 ptap->reuse = MAT_INITIAL_MATRIX; 1257 1258 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1259 /* --------------------------------- */ 1260 ierr = MatTranspose_SeqAIJ(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1261 ierr = MatTranspose_SeqAIJ(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1262 1263 /* (1) compute symbolic A_loc */ 1264 /* ---------------------------*/ 1265 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1266 1267 /* (2-1) compute symbolic C_oth = Ro*A_loc */ 1268 /* ------------------------------------ */ 1269 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1270 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 1271 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 1272 ierr = MatCreate(PETSC_COMM_SELF,&ptap->C_oth);CHKERRQ(ierr); 1273 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->A_loc,fill,ptap->C_oth);CHKERRQ(ierr); 1274 1275 /* (3) send coj of C_oth to other processors */ 1276 /* ------------------------------------------ */ 1277 /* determine row ownership */ 1278 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1279 rowmap->n = pn; 1280 rowmap->bs = 1; 1281 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1282 owners = rowmap->range; 1283 1284 /* determine the number of messages to send, their lengths */ 1285 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1286 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 1287 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr); 1288 1289 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1290 coi = c_oth->i; coj = c_oth->j; 1291 con = ptap->C_oth->rmap->n; 1292 proc = 0; 1293 for (i=0; i<con; i++) { 1294 while (prmap[i] >= owners[proc+1]) proc++; 1295 len_si[proc]++; /* num of rows in Co(=Pt*A) to be sent to [proc] */ 1296 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1297 } 1298 1299 len = 0; /* max length of buf_si[], see (4) */ 1300 owners_co[0] = 0; 1301 nsend = 0; 1302 for (proc=0; proc<size; proc++) { 1303 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1304 if (len_s[proc]) { 1305 nsend++; 1306 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1307 len += len_si[proc]; 1308 } 1309 } 1310 1311 /* determine the number and length of messages to receive for coi and coj */ 1312 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1313 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1314 1315 /* post the Irecv and Isend of coj */ 1316 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1317 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1318 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1319 for (proc=0, k=0; proc<size; proc++) { 1320 if (!len_s[proc]) continue; 1321 i = owners_co[proc]; 1322 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1323 k++; 1324 } 1325 1326 /* (2-2) compute symbolic C_loc = Rd*A_loc */ 1327 /* ---------------------------------------- */ 1328 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 1329 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 1330 ierr = MatCreate(PETSC_COMM_SELF,&ptap->C_loc);CHKERRQ(ierr); 1331 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->A_loc,fill,ptap->C_loc);CHKERRQ(ierr); 1332 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1333 1334 /* receives coj are complete */ 1335 for (i=0; i<nrecv; i++) { 1336 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1337 } 1338 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1339 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1340 1341 /* add received column indices into ta to update Crmax */ 1342 a_loc = (Mat_SeqAIJ*)(ptap->A_loc)->data; 1343 1344 /* create and initialize a linked list */ 1345 ierr = PetscTableCreate(an,aN,&ta);CHKERRQ(ierr); /* for compute Crmax */ 1346 MatRowMergeMax_SeqAIJ(a_loc,ptap->A_loc->rmap->N,ta); 1347 1348 for (k=0; k<nrecv; k++) {/* k-th received message */ 1349 Jptr = buf_rj[k]; 1350 for (j=0; j<len_r[k]; j++) { 1351 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1352 } 1353 } 1354 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1355 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1356 1357 /* (4) send and recv coi */ 1358 /*-----------------------*/ 1359 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1360 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1361 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1362 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1363 for (proc=0,k=0; proc<size; proc++) { 1364 if (!len_s[proc]) continue; 1365 /* form outgoing message for i-structure: 1366 buf_si[0]: nrows to be sent 1367 [1:nrows]: row index (global) 1368 [nrows+1:2*nrows+1]: i-structure index 1369 */ 1370 /*-------------------------------------------*/ 1371 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1372 buf_si_i = buf_si + nrows+1; 1373 buf_si[0] = nrows; 1374 buf_si_i[0] = 0; 1375 nrows = 0; 1376 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1377 nzi = coi[i+1] - coi[i]; 1378 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1379 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1380 nrows++; 1381 } 1382 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1383 k++; 1384 buf_si += len_si[proc]; 1385 } 1386 for (i=0; i<nrecv; i++) { 1387 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1388 } 1389 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1390 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1391 1392 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1393 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1394 ierr = PetscFree(swaits);CHKERRQ(ierr); 1395 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1396 1397 /* (5) compute the local portion of C */ 1398 /* ------------------------------------------ */ 1399 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of C */ 1400 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1401 current_space = free_space; 1402 1403 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1404 for (k=0; k<nrecv; k++) { 1405 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1406 nrows = *buf_ri_k[k]; 1407 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1408 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1409 } 1410 1411 ierr = MatPreallocateInitialize(comm,pn,an,dnz,onz);CHKERRQ(ierr); 1412 ierr = PetscLLCondensedCreate(Crmax,aN,&lnk,&lnkbt);CHKERRQ(ierr); 1413 for (i=0; i<pn; i++) { 1414 /* add C_loc into C */ 1415 nzi = c_loc->i[i+1] - c_loc->i[i]; 1416 Jptr = c_loc->j + c_loc->i[i]; 1417 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1418 1419 /* add received col data into lnk */ 1420 for (k=0; k<nrecv; k++) { /* k-th received message */ 1421 if (i == *nextrow[k]) { /* i-th row */ 1422 nzi = *(nextci[k]+1) - *nextci[k]; 1423 Jptr = buf_rj[k] + *nextci[k]; 1424 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1425 nextrow[k]++; nextci[k]++; 1426 } 1427 } 1428 nzi = lnk[0]; 1429 1430 /* copy data into free space, then initialize lnk */ 1431 ierr = PetscLLCondensedClean(aN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1432 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 1433 } 1434 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1435 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1436 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 1437 1438 /* local sizes and preallocation */ 1439 ierr = MatSetSizes(C,pn,an,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1440 if (P->cmap->bs > 0) {ierr = PetscLayoutSetBlockSize(C->rmap,P->cmap->bs);CHKERRQ(ierr);} 1441 if (A->cmap->bs > 0) {ierr = PetscLayoutSetBlockSize(C->cmap,A->cmap->bs);CHKERRQ(ierr);} 1442 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 1443 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1444 1445 /* add C_loc and C_oth to C */ 1446 ierr = MatGetOwnershipRange(C,&rstart,NULL);CHKERRQ(ierr); 1447 for (i=0; i<pn; i++) { 1448 const PetscInt ncols = c_loc->i[i+1] - c_loc->i[i]; 1449 const PetscInt *cols = c_loc->j + c_loc->i[i]; 1450 const PetscInt row = rstart + i; 1451 ierr = MatSetValues(C,1,&row,ncols,cols,NULL,INSERT_VALUES);CHKERRQ(ierr); 1452 } 1453 for (i=0; i<con; i++) { 1454 const PetscInt ncols = c_oth->i[i+1] - c_oth->i[i]; 1455 const PetscInt *cols = c_oth->j + c_oth->i[i]; 1456 const PetscInt row = prmap[i]; 1457 ierr = MatSetValues(C,1,&row,ncols,cols,NULL,INSERT_VALUES);CHKERRQ(ierr); 1458 } 1459 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1460 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1461 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1462 1463 /* members in merge */ 1464 ierr = PetscFree(id_r);CHKERRQ(ierr); 1465 ierr = PetscFree(len_r);CHKERRQ(ierr); 1466 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 1467 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 1468 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 1469 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 1470 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 1471 1472 /* attach the supporting struct to C for reuse */ 1473 C->product->data = ptap; 1474 C->product->destroy = MatDestroy_MPIAIJ_PtAP; 1475 PetscFunctionReturn(0); 1476 } 1477 1478 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,Mat C) 1479 { 1480 PetscErrorCode ierr; 1481 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data; 1482 Mat_SeqAIJ *c_seq; 1483 Mat_APMPI *ptap; 1484 Mat A_loc,C_loc,C_oth; 1485 PetscInt i,rstart,rend,cm,ncols,row; 1486 const PetscInt *cols; 1487 const PetscScalar *vals; 1488 1489 PetscFunctionBegin; 1490 MatCheckProduct(C,3); 1491 ptap = (Mat_APMPI*)C->product->data; 1492 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 1493 if (!ptap->A_loc) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatProductClear()"); 1494 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1495 1496 if (ptap->reuse == MAT_REUSE_MATRIX) { 1497 /* These matrices are obtained in MatTransposeMatMultSymbolic() */ 1498 /* 1) get R = Pd^T, Ro = Po^T */ 1499 /*----------------------------*/ 1500 ierr = MatTranspose_SeqAIJ(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1501 ierr = MatTranspose_SeqAIJ(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1502 1503 /* 2) compute numeric A_loc */ 1504 /*--------------------------*/ 1505 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1506 } 1507 1508 /* 3) C_loc = Rd*A_loc, C_oth = Ro*A_loc */ 1509 A_loc = ptap->A_loc; 1510 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,A_loc,ptap->C_loc);CHKERRQ(ierr); 1511 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,A_loc,ptap->C_oth);CHKERRQ(ierr); 1512 C_loc = ptap->C_loc; 1513 C_oth = ptap->C_oth; 1514 1515 /* add C_loc and C_oth to C */ 1516 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1517 1518 /* C_loc -> C */ 1519 cm = C_loc->rmap->N; 1520 c_seq = (Mat_SeqAIJ*)C_loc->data; 1521 cols = c_seq->j; 1522 vals = c_seq->a; 1523 for (i=0; i<cm; i++) { 1524 ncols = c_seq->i[i+1] - c_seq->i[i]; 1525 row = rstart + i; 1526 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1527 cols += ncols; vals += ncols; 1528 } 1529 1530 /* Co -> C, off-processor part */ 1531 cm = C_oth->rmap->N; 1532 c_seq = (Mat_SeqAIJ*)C_oth->data; 1533 cols = c_seq->j; 1534 vals = c_seq->a; 1535 for (i=0; i<cm; i++) { 1536 ncols = c_seq->i[i+1] - c_seq->i[i]; 1537 row = p->garray[i]; 1538 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1539 cols += ncols; vals += ncols; 1540 } 1541 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1542 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1543 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1544 1545 ptap->reuse = MAT_REUSE_MATRIX; 1546 PetscFunctionReturn(0); 1547 } 1548 1549 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ(Mat P,Mat A,Mat C) 1550 { 1551 PetscErrorCode ierr; 1552 Mat_Merge_SeqsToMPI *merge; 1553 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data; 1554 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1555 Mat_APMPI *ptap; 1556 PetscInt *adj; 1557 PetscInt i,j,k,anz,pnz,row,*cj,nexta; 1558 MatScalar *ada,*ca,valtmp; 1559 PetscInt am=A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1560 MPI_Comm comm; 1561 PetscMPIInt size,rank,taga,*len_s; 1562 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1563 PetscInt **buf_ri,**buf_rj; 1564 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1565 MPI_Request *s_waits,*r_waits; 1566 MPI_Status *status; 1567 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1568 PetscInt *ai,*aj,*coi,*coj,*poJ,*pdJ; 1569 Mat A_loc; 1570 Mat_SeqAIJ *a_loc; 1571 1572 PetscFunctionBegin; 1573 MatCheckProduct(C,3); 1574 ptap = (Mat_APMPI*)C->product->data; 1575 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be computed. Missing data"); 1576 if (!ptap->A_loc) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatProductClear()"); 1577 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1578 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1579 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1580 1581 merge = ptap->merge; 1582 1583 /* 2) compute numeric C_seq = P_loc^T*A_loc */ 1584 /*------------------------------------------*/ 1585 /* get data from symbolic products */ 1586 coi = merge->coi; coj = merge->coj; 1587 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 1588 bi = merge->bi; bj = merge->bj; 1589 owners = merge->rowmap->range; 1590 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); 1591 1592 /* get A_loc by taking all local rows of A */ 1593 A_loc = ptap->A_loc; 1594 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 1595 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1596 ai = a_loc->i; 1597 aj = a_loc->j; 1598 1599 for (i=0; i<am; i++) { 1600 anz = ai[i+1] - ai[i]; 1601 adj = aj + ai[i]; 1602 ada = a_loc->a + ai[i]; 1603 1604 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 1605 /*-------------------------------------------------------------*/ 1606 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 1607 pnz = po->i[i+1] - po->i[i]; 1608 poJ = po->j + po->i[i]; 1609 pA = po->a + po->i[i]; 1610 for (j=0; j<pnz; j++) { 1611 row = poJ[j]; 1612 cj = coj + coi[row]; 1613 ca = coa + coi[row]; 1614 /* perform sparse axpy */ 1615 nexta = 0; 1616 valtmp = pA[j]; 1617 for (k=0; nexta<anz; k++) { 1618 if (cj[k] == adj[nexta]) { 1619 ca[k] += valtmp*ada[nexta]; 1620 nexta++; 1621 } 1622 } 1623 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1624 } 1625 1626 /* put the value into Cd (diagonal part) */ 1627 pnz = pd->i[i+1] - pd->i[i]; 1628 pdJ = pd->j + pd->i[i]; 1629 pA = pd->a + pd->i[i]; 1630 for (j=0; j<pnz; j++) { 1631 row = pdJ[j]; 1632 cj = bj + bi[row]; 1633 ca = ba + bi[row]; 1634 /* perform sparse axpy */ 1635 nexta = 0; 1636 valtmp = pA[j]; 1637 for (k=0; nexta<anz; k++) { 1638 if (cj[k] == adj[nexta]) { 1639 ca[k] += valtmp*ada[nexta]; 1640 nexta++; 1641 } 1642 } 1643 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1644 } 1645 } 1646 1647 /* 3) send and recv matrix values coa */ 1648 /*------------------------------------*/ 1649 buf_ri = merge->buf_ri; 1650 buf_rj = merge->buf_rj; 1651 len_s = merge->len_s; 1652 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1653 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1654 1655 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1656 for (proc=0,k=0; proc<size; proc++) { 1657 if (!len_s[proc]) continue; 1658 i = merge->owners_co[proc]; 1659 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1660 k++; 1661 } 1662 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1663 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1664 1665 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1666 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1667 ierr = PetscFree(coa);CHKERRQ(ierr); 1668 1669 /* 4) insert local Cseq and received values into Cmpi */ 1670 /*----------------------------------------------------*/ 1671 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1672 for (k=0; k<merge->nrecv; k++) { 1673 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1674 nrows = *(buf_ri_k[k]); 1675 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1676 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1677 } 1678 1679 for (i=0; i<cm; i++) { 1680 row = owners[rank] + i; /* global row index of C_seq */ 1681 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1682 ba_i = ba + bi[i]; 1683 bnz = bi[i+1] - bi[i]; 1684 /* add received vals into ba */ 1685 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1686 /* i-th row */ 1687 if (i == *nextrow[k]) { 1688 cnz = *(nextci[k]+1) - *nextci[k]; 1689 cj = buf_rj[k] + *(nextci[k]); 1690 ca = abuf_r[k] + *(nextci[k]); 1691 nextcj = 0; 1692 for (j=0; nextcj<cnz; j++) { 1693 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1694 ba_i[j] += ca[nextcj++]; 1695 } 1696 } 1697 nextrow[k]++; nextci[k]++; 1698 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1699 } 1700 } 1701 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1702 } 1703 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1704 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1705 1706 ierr = PetscFree(ba);CHKERRQ(ierr); 1707 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1708 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1709 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1710 PetscFunctionReturn(0); 1711 } 1712 1713 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(Mat P,Mat A,PetscReal fill,Mat C) 1714 { 1715 PetscErrorCode ierr; 1716 Mat A_loc,POt,PDt; 1717 Mat_APMPI *ptap; 1718 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1719 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*a=(Mat_MPIAIJ*)A->data; 1720 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1721 PetscInt nnz; 1722 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1723 PetscInt am =A->rmap->n,pn=P->cmap->n; 1724 MPI_Comm comm; 1725 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1726 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1727 PetscInt len,proc,*dnz,*onz,*owners; 1728 PetscInt nzi,*bi,*bj; 1729 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1730 MPI_Request *swaits,*rwaits; 1731 MPI_Status *sstatus,rstatus; 1732 Mat_Merge_SeqsToMPI *merge; 1733 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1734 PetscReal afill =1.0,afill_tmp; 1735 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N,Armax; 1736 Mat_SeqAIJ *a_loc,*pdt,*pot; 1737 PetscTable ta; 1738 MatType mtype; 1739 1740 PetscFunctionBegin; 1741 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1742 /* check if matrix local sizes are compatible */ 1743 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); 1744 1745 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1746 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1747 1748 /* create struct Mat_APMPI and attached it to C later */ 1749 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1750 1751 /* get A_loc by taking all local rows of A */ 1752 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1753 1754 ptap->A_loc = A_loc; 1755 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1756 ai = a_loc->i; 1757 aj = a_loc->j; 1758 1759 /* determine symbolic Co=(p->B)^T*A - send to others */ 1760 /*----------------------------------------------------*/ 1761 ierr = MatTransposeSymbolic_SeqAIJ(p->A,&PDt);CHKERRQ(ierr); 1762 pdt = (Mat_SeqAIJ*)PDt->data; 1763 pdti = pdt->i; pdtj = pdt->j; 1764 1765 ierr = MatTransposeSymbolic_SeqAIJ(p->B,&POt);CHKERRQ(ierr); 1766 pot = (Mat_SeqAIJ*)POt->data; 1767 poti = pot->i; potj = pot->j; 1768 1769 /* then, compute symbolic Co = (p->B)^T*A */ 1770 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 1771 >= (num of nonzero rows of C_seq) - pn */ 1772 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 1773 coi[0] = 0; 1774 1775 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1776 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],ai[am])); 1777 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1778 current_space = free_space; 1779 1780 /* create and initialize a linked list */ 1781 ierr = PetscTableCreate(A->cmap->n + a->B->cmap->N,aN,&ta);CHKERRQ(ierr); 1782 MatRowMergeMax_SeqAIJ(a_loc,am,ta); 1783 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1784 1785 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1786 1787 for (i=0; i<pon; i++) { 1788 pnz = poti[i+1] - poti[i]; 1789 ptJ = potj + poti[i]; 1790 for (j=0; j<pnz; j++) { 1791 row = ptJ[j]; /* row of A_loc == col of Pot */ 1792 anz = ai[row+1] - ai[row]; 1793 Jptr = aj + ai[row]; 1794 /* add non-zero cols of AP into the sorted linked list lnk */ 1795 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1796 } 1797 nnz = lnk[0]; 1798 1799 /* If free space is not available, double the total space in the list */ 1800 if (current_space->local_remaining<nnz) { 1801 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1802 nspacedouble++; 1803 } 1804 1805 /* Copy data into free space, and zero out denserows */ 1806 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1807 1808 current_space->array += nnz; 1809 current_space->local_used += nnz; 1810 current_space->local_remaining -= nnz; 1811 1812 coi[i+1] = coi[i] + nnz; 1813 } 1814 1815 ierr = PetscMalloc1(coi[pon]+1,&coj);CHKERRQ(ierr); 1816 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 1817 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); /* must destroy to get a new one for C */ 1818 1819 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 1820 if (afill_tmp > afill) afill = afill_tmp; 1821 1822 /* send j-array (coj) of Co to other processors */ 1823 /*----------------------------------------------*/ 1824 /* determine row ownership */ 1825 ierr = PetscNew(&merge);CHKERRQ(ierr); 1826 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 1827 1828 merge->rowmap->n = pn; 1829 merge->rowmap->bs = 1; 1830 1831 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 1832 owners = merge->rowmap->range; 1833 1834 /* determine the number of messages to send, their lengths */ 1835 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 1836 ierr = PetscCalloc1(size,&merge->len_s);CHKERRQ(ierr); 1837 1838 len_s = merge->len_s; 1839 merge->nsend = 0; 1840 1841 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 1842 1843 proc = 0; 1844 for (i=0; i<pon; i++) { 1845 while (prmap[i] >= owners[proc+1]) proc++; 1846 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1847 len_s[proc] += coi[i+1] - coi[i]; 1848 } 1849 1850 len = 0; /* max length of buf_si[] */ 1851 owners_co[0] = 0; 1852 for (proc=0; proc<size; proc++) { 1853 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1854 if (len_si[proc]) { 1855 merge->nsend++; 1856 len_si[proc] = 2*(len_si[proc] + 1); 1857 len += len_si[proc]; 1858 } 1859 } 1860 1861 /* determine the number and length of messages to receive for coi and coj */ 1862 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1863 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1864 1865 /* post the Irecv and Isend of coj */ 1866 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1867 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1868 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 1869 for (proc=0, k=0; proc<size; proc++) { 1870 if (!len_s[proc]) continue; 1871 i = owners_co[proc]; 1872 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1873 k++; 1874 } 1875 1876 /* receives and sends of coj are complete */ 1877 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1878 for (i=0; i<merge->nrecv; i++) { 1879 PETSC_UNUSED PetscMPIInt icompleted; 1880 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1881 } 1882 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1883 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1884 1885 /* add received column indices into table to update Armax */ 1886 /* Armax can be as large as aN if a P[row,:] is dense, see src/ksp/ksp/tutorials/ex56.c! */ 1887 for (k=0; k<merge->nrecv; k++) {/* k-th received message */ 1888 Jptr = buf_rj[k]; 1889 for (j=0; j<merge->len_r[k]; j++) { 1890 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1891 } 1892 } 1893 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1894 /* 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); */ 1895 1896 /* send and recv coi */ 1897 /*-------------------*/ 1898 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1899 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1900 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1901 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1902 for (proc=0,k=0; proc<size; proc++) { 1903 if (!len_s[proc]) continue; 1904 /* form outgoing message for i-structure: 1905 buf_si[0]: nrows to be sent 1906 [1:nrows]: row index (global) 1907 [nrows+1:2*nrows+1]: i-structure index 1908 */ 1909 /*-------------------------------------------*/ 1910 nrows = len_si[proc]/2 - 1; 1911 buf_si_i = buf_si + nrows+1; 1912 buf_si[0] = nrows; 1913 buf_si_i[0] = 0; 1914 nrows = 0; 1915 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1916 nzi = coi[i+1] - coi[i]; 1917 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1918 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1919 nrows++; 1920 } 1921 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1922 k++; 1923 buf_si += len_si[proc]; 1924 } 1925 i = merge->nrecv; 1926 while (i--) { 1927 PETSC_UNUSED PetscMPIInt icompleted; 1928 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1929 } 1930 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1931 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1932 ierr = PetscFree(len_si);CHKERRQ(ierr); 1933 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1934 ierr = PetscFree(swaits);CHKERRQ(ierr); 1935 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1936 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1937 1938 /* compute the local portion of C (mpi mat) */ 1939 /*------------------------------------------*/ 1940 /* allocate bi array and free space for accumulating nonzero column info */ 1941 ierr = PetscMalloc1(pn+1,&bi);CHKERRQ(ierr); 1942 bi[0] = 0; 1943 1944 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 1945 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pdti[pn],PetscIntSumTruncate(poti[pon],ai[am]))); 1946 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1947 current_space = free_space; 1948 1949 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1950 for (k=0; k<merge->nrecv; k++) { 1951 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1952 nrows = *buf_ri_k[k]; 1953 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1954 nextci[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th received i-structure */ 1955 } 1956 1957 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1958 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1959 rmax = 0; 1960 for (i=0; i<pn; i++) { 1961 /* add pdt[i,:]*AP into lnk */ 1962 pnz = pdti[i+1] - pdti[i]; 1963 ptJ = pdtj + pdti[i]; 1964 for (j=0; j<pnz; j++) { 1965 row = ptJ[j]; /* row of AP == col of Pt */ 1966 anz = ai[row+1] - ai[row]; 1967 Jptr = aj + ai[row]; 1968 /* add non-zero cols of AP into the sorted linked list lnk */ 1969 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1970 } 1971 1972 /* add received col data into lnk */ 1973 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1974 if (i == *nextrow[k]) { /* i-th row */ 1975 nzi = *(nextci[k]+1) - *nextci[k]; 1976 Jptr = buf_rj[k] + *nextci[k]; 1977 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 1978 nextrow[k]++; nextci[k]++; 1979 } 1980 } 1981 nnz = lnk[0]; 1982 1983 /* if free space is not available, make more free space */ 1984 if (current_space->local_remaining<nnz) { 1985 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1986 nspacedouble++; 1987 } 1988 /* copy data into free space, then initialize lnk */ 1989 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1990 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 1991 1992 current_space->array += nnz; 1993 current_space->local_used += nnz; 1994 current_space->local_remaining -= nnz; 1995 1996 bi[i+1] = bi[i] + nnz; 1997 if (nnz > rmax) rmax = nnz; 1998 } 1999 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 2000 2001 ierr = PetscMalloc1(bi[pn]+1,&bj);CHKERRQ(ierr); 2002 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 2003 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 2004 if (afill_tmp > afill) afill = afill_tmp; 2005 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 2006 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 2007 2008 ierr = MatDestroy(&POt);CHKERRQ(ierr); 2009 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 2010 2011 /* create symbolic parallel matrix C - why cannot be assembled in Numeric part */ 2012 /*-------------------------------------------------------------------------------*/ 2013 ierr = MatSetSizes(C,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2014 ierr = MatSetBlockSizes(C,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 2015 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 2016 ierr = MatSetType(C,mtype);CHKERRQ(ierr); 2017 ierr = MatMPIAIJSetPreallocation(C,0,dnz,0,onz);CHKERRQ(ierr); 2018 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 2019 ierr = MatSetBlockSize(C,1);CHKERRQ(ierr); 2020 ierr = MatSetOption(C,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 2021 for (i=0; i<pn; i++) { 2022 row = i + rstart; 2023 nnz = bi[i+1] - bi[i]; 2024 Jptr = bj + bi[i]; 2025 ierr = MatSetValues(C,1,&row,nnz,Jptr,NULL,INSERT_VALUES);CHKERRQ(ierr); 2026 } 2027 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2028 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2029 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2030 merge->bi = bi; 2031 merge->bj = bj; 2032 merge->coi = coi; 2033 merge->coj = coj; 2034 merge->buf_ri = buf_ri; 2035 merge->buf_rj = buf_rj; 2036 merge->owners_co = owners_co; 2037 2038 /* attach the supporting struct to C for reuse */ 2039 C->product->data = ptap; 2040 C->product->destroy = MatDestroy_MPIAIJ_PtAP; 2041 ptap->merge = merge; 2042 2043 C->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ; 2044 2045 #if defined(PETSC_USE_INFO) 2046 if (bi[pn] != 0) { 2047 ierr = PetscInfo3(C,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 2048 ierr = PetscInfo1(C,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 2049 } else { 2050 ierr = PetscInfo(C,"Empty matrix product\n");CHKERRQ(ierr); 2051 } 2052 #endif 2053 PetscFunctionReturn(0); 2054 } 2055 2056 /* ---------------------------------------------------------------- */ 2057 static PetscErrorCode MatProductSymbolic_AtB_MPIAIJ_MPIAIJ(Mat C) 2058 { 2059 PetscErrorCode ierr; 2060 Mat_Product *product = C->product; 2061 Mat A=product->A,B=product->B; 2062 PetscReal fill=product->fill; 2063 PetscBool flg; 2064 2065 PetscFunctionBegin; 2066 /* scalable */ 2067 ierr = PetscStrcmp(product->alg,"scalable",&flg);CHKERRQ(ierr); 2068 if (flg) { 2069 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 2070 goto next; 2071 } 2072 2073 /* nonscalable */ 2074 ierr = PetscStrcmp(product->alg,"nonscalable",&flg);CHKERRQ(ierr); 2075 if (flg) { 2076 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(A,B,fill,C);CHKERRQ(ierr); 2077 goto next; 2078 } 2079 2080 /* matmatmult */ 2081 ierr = PetscStrcmp(product->alg,"at*b",&flg);CHKERRQ(ierr); 2082 if (flg) { 2083 Mat At; 2084 Mat_APMPI *ptap; 2085 2086 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 2087 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ(At,B,fill,C);CHKERRQ(ierr); 2088 ptap = (Mat_APMPI*)C->product->data; 2089 if (ptap) { 2090 ptap->Pt = At; 2091 C->product->destroy = MatDestroy_MPIAIJ_PtAP; 2092 } 2093 C->ops->transposematmultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult; 2094 goto next; 2095 } 2096 2097 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MatProduct type is not supported"); 2098 2099 next: 2100 C->ops->productnumeric = MatProductNumeric_AtB; 2101 PetscFunctionReturn(0); 2102 } 2103 2104 /* ---------------------------------------------------------------- */ 2105 /* Set options for MatMatMultxxx_MPIAIJ_MPIAIJ */ 2106 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_AB(Mat C) 2107 { 2108 PetscErrorCode ierr; 2109 Mat_Product *product = C->product; 2110 Mat A=product->A,B=product->B; 2111 #if defined(PETSC_HAVE_HYPRE) 2112 const char *algTypes[4] = {"scalable","nonscalable","seqmpi","hypre"}; 2113 PetscInt nalg = 4; 2114 #else 2115 const char *algTypes[3] = {"scalable","nonscalable","seqmpi"}; 2116 PetscInt nalg = 3; 2117 #endif 2118 PetscInt alg = 1; /* set nonscalable algorithm as default */ 2119 PetscBool flg; 2120 MPI_Comm comm; 2121 2122 PetscFunctionBegin; 2123 /* Check matrix local sizes */ 2124 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2125 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); 2126 2127 /* Set "nonscalable" as default algorithm */ 2128 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2129 if (flg) { 2130 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2131 2132 /* Set "scalable" as default if BN and local nonzeros of A and B are large */ 2133 if (B->cmap->N > 100000) { /* may switch to scalable algorithm as default */ 2134 MatInfo Ainfo,Binfo; 2135 PetscInt nz_local; 2136 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 2137 2138 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 2139 ierr = MatGetInfo(B,MAT_LOCAL,&Binfo);CHKERRQ(ierr); 2140 nz_local = (PetscInt)(Ainfo.nz_allocated + Binfo.nz_allocated); 2141 2142 if (B->cmap->N > product->fill*nz_local) alg_scalable_loc = PETSC_TRUE; 2143 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 2144 2145 if (alg_scalable) { 2146 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 2147 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2148 ierr = PetscInfo2(B,"Use scalable algorithm, BN %D, fill*nz_allocated %g\n",B->cmap->N,product->fill*nz_local);CHKERRQ(ierr); 2149 } 2150 } 2151 } 2152 2153 /* Get runtime option */ 2154 if (product->api_user) { 2155 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatMatMult","Mat");CHKERRQ(ierr); 2156 ierr = PetscOptionsEList("-matmatmult_via","Algorithmic approach","MatMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2157 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2158 } else { 2159 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_AB","Mat");CHKERRQ(ierr); 2160 ierr = PetscOptionsEList("-matproduct_ab_via","Algorithmic approach","MatMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2161 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2162 } 2163 if (flg) { 2164 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2165 } 2166 2167 C->ops->productsymbolic = MatProductSymbolic_AB_MPIAIJ_MPIAIJ; 2168 PetscFunctionReturn(0); 2169 } 2170 2171 /* Set options for MatTransposeMatMultXXX_MPIAIJ_MPIAIJ */ 2172 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_AtB(Mat C) 2173 { 2174 PetscErrorCode ierr; 2175 Mat_Product *product = C->product; 2176 Mat A=product->A,B=product->B; 2177 const char *algTypes[3] = {"scalable","nonscalable","at*b"}; 2178 PetscInt nalg = 3; 2179 PetscInt alg = 1; /* set default algorithm */ 2180 PetscBool flg; 2181 MPI_Comm comm; 2182 2183 PetscFunctionBegin; 2184 /* Check matrix local sizes */ 2185 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2186 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); 2187 2188 /* Set default algorithm */ 2189 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2190 if (flg) { 2191 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2192 } 2193 2194 /* Set "scalable" as default if BN and local nonzeros of A and B are large */ 2195 if (alg && B->cmap->N > 100000) { /* may switch to scalable algorithm as default */ 2196 MatInfo Ainfo,Binfo; 2197 PetscInt nz_local; 2198 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 2199 2200 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 2201 ierr = MatGetInfo(B,MAT_LOCAL,&Binfo);CHKERRQ(ierr); 2202 nz_local = (PetscInt)(Ainfo.nz_allocated + Binfo.nz_allocated); 2203 2204 if (B->cmap->N > product->fill*nz_local) alg_scalable_loc = PETSC_TRUE; 2205 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 2206 2207 if (alg_scalable) { 2208 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 2209 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2210 ierr = PetscInfo2(B,"Use scalable algorithm, BN %D, fill*nz_allocated %g\n",B->cmap->N,product->fill*nz_local);CHKERRQ(ierr); 2211 } 2212 } 2213 2214 /* Get runtime option */ 2215 if (product->api_user) { 2216 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatTransposeMatMult","Mat");CHKERRQ(ierr); 2217 ierr = PetscOptionsEList("-mattransposematmult_via","Algorithmic approach","MatTransposeMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2218 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2219 } else { 2220 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_AtB","Mat");CHKERRQ(ierr); 2221 ierr = PetscOptionsEList("-matproduct_atb_via","Algorithmic approach","MatTransposeMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2222 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2223 } 2224 if (flg) { 2225 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2226 } 2227 2228 C->ops->productsymbolic = MatProductSymbolic_AtB_MPIAIJ_MPIAIJ; 2229 PetscFunctionReturn(0); 2230 } 2231 2232 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_PtAP(Mat C) 2233 { 2234 PetscErrorCode ierr; 2235 Mat_Product *product = C->product; 2236 Mat A=product->A,P=product->B; 2237 MPI_Comm comm; 2238 PetscBool flg; 2239 PetscInt alg=1; /* set default algorithm */ 2240 #if !defined(PETSC_HAVE_HYPRE) 2241 const char *algTypes[4] = {"scalable","nonscalable","allatonce","allatonce_merged"}; 2242 PetscInt nalg=4; 2243 #else 2244 const char *algTypes[5] = {"scalable","nonscalable","allatonce","allatonce_merged","hypre"}; 2245 PetscInt nalg=5; 2246 #endif 2247 PetscInt pN=P->cmap->N; 2248 2249 PetscFunctionBegin; 2250 /* Check matrix local sizes */ 2251 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2252 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); 2253 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); 2254 2255 /* Set "nonscalable" as default algorithm */ 2256 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2257 if (flg) { 2258 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2259 2260 /* Set "scalable" as default if BN and local nonzeros of A and B are large */ 2261 if (pN > 100000) { 2262 MatInfo Ainfo,Pinfo; 2263 PetscInt nz_local; 2264 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 2265 2266 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 2267 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 2268 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); 2269 2270 if (pN > product->fill*nz_local) alg_scalable_loc = PETSC_TRUE; 2271 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 2272 2273 if (alg_scalable) { 2274 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 2275 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2276 } 2277 } 2278 } 2279 2280 /* Get runtime option */ 2281 if (product->api_user) { 2282 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 2283 ierr = PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2284 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2285 } else { 2286 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_PtAP","Mat");CHKERRQ(ierr); 2287 ierr = PetscOptionsEList("-matproduct_ptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2288 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2289 } 2290 if (flg) { 2291 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2292 } 2293 2294 C->ops->productsymbolic = MatProductSymbolic_PtAP_MPIAIJ_MPIAIJ; 2295 PetscFunctionReturn(0); 2296 } 2297 2298 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_RARt(Mat C) 2299 { 2300 Mat_Product *product = C->product; 2301 Mat A = product->A,R=product->B; 2302 2303 PetscFunctionBegin; 2304 /* Check matrix local sizes */ 2305 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); 2306 2307 C->ops->productsymbolic = MatProductSymbolic_RARt_MPIAIJ_MPIAIJ; 2308 PetscFunctionReturn(0); 2309 } 2310 2311 /* 2312 Set options for ABC = A*B*C = A*(B*C); ABC's algorithm must be chosen from AB's algorithm 2313 */ 2314 static PetscErrorCode MatProductSetFromOptions_MPIAIJ_ABC(Mat C) 2315 { 2316 PetscErrorCode ierr; 2317 Mat_Product *product = C->product; 2318 PetscBool flg = PETSC_FALSE; 2319 PetscInt alg = 1; /* default algorithm */ 2320 const char *algTypes[3] = {"scalable","nonscalable","seqmpi"}; 2321 PetscInt nalg = 3; 2322 2323 PetscFunctionBegin; 2324 /* Set default algorithm */ 2325 ierr = PetscStrcmp(C->product->alg,"default",&flg);CHKERRQ(ierr); 2326 if (flg) { 2327 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2328 } 2329 2330 /* Get runtime option */ 2331 if (product->api_user) { 2332 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatMatMatMult","Mat");CHKERRQ(ierr); 2333 ierr = PetscOptionsEList("-matmatmatmult_via","Algorithmic approach","MatMatMatMult",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2334 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2335 } else { 2336 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)C),((PetscObject)C)->prefix,"MatProduct_ABC","Mat");CHKERRQ(ierr); 2337 ierr = PetscOptionsEList("-matproduct_abc_via","Algorithmic approach","MatProduct_ABC",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 2338 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2339 } 2340 if (flg) { 2341 ierr = MatProductSetAlgorithm(C,(MatProductAlgorithm)algTypes[alg]);CHKERRQ(ierr); 2342 } 2343 2344 C->ops->matmatmultsymbolic = MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ; 2345 C->ops->productsymbolic = MatProductSymbolic_ABC; 2346 PetscFunctionReturn(0); 2347 } 2348 2349 PETSC_INTERN PetscErrorCode MatProductSetFromOptions_MPIAIJ(Mat C) 2350 { 2351 PetscErrorCode ierr; 2352 Mat_Product *product = C->product; 2353 2354 PetscFunctionBegin; 2355 switch (product->type) { 2356 case MATPRODUCT_AB: 2357 ierr = MatProductSetFromOptions_MPIAIJ_AB(C);CHKERRQ(ierr); 2358 break; 2359 case MATPRODUCT_AtB: 2360 ierr = MatProductSetFromOptions_MPIAIJ_AtB(C);CHKERRQ(ierr); 2361 break; 2362 case MATPRODUCT_PtAP: 2363 ierr = MatProductSetFromOptions_MPIAIJ_PtAP(C);CHKERRQ(ierr); 2364 break; 2365 case MATPRODUCT_RARt: 2366 ierr = MatProductSetFromOptions_MPIAIJ_RARt(C);CHKERRQ(ierr); 2367 break; 2368 case MATPRODUCT_ABC: 2369 ierr = MatProductSetFromOptions_MPIAIJ_ABC(C);CHKERRQ(ierr); 2370 break; 2371 default: 2372 break; 2373 } 2374 PetscFunctionReturn(0); 2375 } 2376