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 13 #if defined(PETSC_HAVE_HYPRE) 14 PETSC_INTERN PetscErrorCode MatMatMultSymbolic_AIJ_AIJ_wHYPRE(Mat,Mat,PetscReal,Mat*); 15 #endif 16 17 PETSC_INTERN PetscErrorCode MatMatMult_MPIAIJ_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill, Mat *C) 18 { 19 PetscErrorCode ierr; 20 #if defined(PETSC_HAVE_HYPRE) 21 const char *algTypes[4] = {"scalable","nonscalable","seqmpi","hypre"}; 22 PetscInt nalg = 4; 23 #else 24 const char *algTypes[3] = {"scalable","nonscalable","seqmpi"}; 25 PetscInt nalg = 3; 26 #endif 27 PetscInt alg = 1; /* set nonscalable algorithm as default */ 28 MPI_Comm comm; 29 PetscBool flg; 30 31 PetscFunctionBegin; 32 if (scall == MAT_INITIAL_MATRIX) { 33 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 34 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) SETERRQ4(comm,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); 35 36 ierr = PetscObjectOptionsBegin((PetscObject)A);CHKERRQ(ierr); 37 PetscOptionsObject->alreadyprinted = PETSC_FALSE; /* a hack to ensure the option shows in '-help' */ 38 ierr = PetscOptionsEList("-matmatmult_via","Algorithmic approach","MatMatMult",algTypes,nalg,algTypes[1],&alg,&flg);CHKERRQ(ierr); 39 ierr = PetscOptionsEnd();CHKERRQ(ierr); 40 41 if (!flg && B->cmap->N > 100000) { /* may switch to scalable algorithm as default */ 42 MatInfo Ainfo,Binfo; 43 PetscInt nz_local; 44 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 45 46 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 47 ierr = MatGetInfo(B,MAT_LOCAL,&Binfo);CHKERRQ(ierr); 48 nz_local = (PetscInt)(Ainfo.nz_allocated + Binfo.nz_allocated); 49 50 if (B->cmap->N > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 51 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 52 53 if (alg_scalable) { 54 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 55 ierr = PetscInfo2(B,"Use scalable algorithm, BN %D, fill*nz_allocated %g\n",B->cmap->N,fill*nz_local);CHKERRQ(ierr); 56 } 57 } 58 59 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 60 switch (alg) { 61 case 1: 62 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(A,B,fill,C);CHKERRQ(ierr); 63 break; 64 case 2: 65 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI(A,B,fill,C);CHKERRQ(ierr); 66 break; 67 #if defined(PETSC_HAVE_HYPRE) 68 case 3: 69 ierr = MatMatMultSymbolic_AIJ_AIJ_wHYPRE(A,B,fill,C);CHKERRQ(ierr); 70 break; 71 #endif 72 default: 73 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 74 break; 75 } 76 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 77 } 78 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 79 ierr = (*(*C)->ops->matmultnumeric)(A,B,*C);CHKERRQ(ierr); 80 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 81 PetscFunctionReturn(0); 82 } 83 84 PetscErrorCode MatDestroy_MPIAIJ_MatMatMult(Mat A) 85 { 86 PetscErrorCode ierr; 87 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 88 Mat_PtAPMPI *ptap = a->ptap; 89 90 PetscFunctionBegin; 91 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 92 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 93 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 94 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 95 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 96 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 97 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 98 ierr = PetscFree(ptap->apa);CHKERRQ(ierr); 99 ierr = ptap->destroy(A);CHKERRQ(ierr); 100 ierr = PetscFree(ptap);CHKERRQ(ierr); 101 PetscFunctionReturn(0); 102 } 103 104 PetscErrorCode MatDuplicate_MPIAIJ_MatMatMult(Mat A, MatDuplicateOption op, Mat *M) 105 { 106 PetscErrorCode ierr; 107 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 108 Mat_PtAPMPI *ptap = a->ptap; 109 110 PetscFunctionBegin; 111 ierr = (*ptap->duplicate)(A,op,M);CHKERRQ(ierr); 112 113 (*M)->ops->destroy = ptap->destroy; /* = MatDestroy_MPIAIJ, *M doesn't duplicate A's special structure! */ 114 (*M)->ops->duplicate = ptap->duplicate; /* = MatDuplicate_MPIAIJ */ 115 PetscFunctionReturn(0); 116 } 117 118 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,Mat C) 119 { 120 PetscErrorCode ierr; 121 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 122 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 123 Mat_SeqAIJ *cd =(Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 124 PetscScalar *cda=cd->a,*coa=co->a; 125 Mat_SeqAIJ *p_loc,*p_oth; 126 PetscScalar *apa,*ca; 127 PetscInt cm =C->rmap->n; 128 Mat_PtAPMPI *ptap=c->ptap; 129 PetscInt *api,*apj,*apJ,i,k; 130 PetscInt cstart=C->cmap->rstart; 131 PetscInt cdnz,conz,k0,k1; 132 MPI_Comm comm; 133 PetscMPIInt size; 134 135 PetscFunctionBegin; 136 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 137 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 138 139 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 140 /*-----------------------------------------------------*/ 141 /* update numerical values of P_oth and P_loc */ 142 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 143 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 144 145 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 146 /*----------------------------------------------------------*/ 147 /* get data from symbolic products */ 148 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 149 p_oth = NULL; 150 if (size >1) { 151 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 152 } 153 154 /* get apa for storing dense row A[i,:]*P */ 155 apa = ptap->apa; 156 157 api = ptap->api; 158 apj = ptap->apj; 159 for (i=0; i<cm; i++) { 160 /* compute apa = A[i,:]*P */ 161 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 162 163 /* set values in C */ 164 apJ = apj + api[i]; 165 cdnz = cd->i[i+1] - cd->i[i]; 166 conz = co->i[i+1] - co->i[i]; 167 168 /* 1st off-diagoanl part of C */ 169 ca = coa + co->i[i]; 170 k = 0; 171 for (k0=0; k0<conz; k0++) { 172 if (apJ[k] >= cstart) break; 173 ca[k0] = apa[apJ[k]]; 174 apa[apJ[k++]] = 0.0; 175 } 176 177 /* diagonal part of C */ 178 ca = cda + cd->i[i]; 179 for (k1=0; k1<cdnz; k1++) { 180 ca[k1] = apa[apJ[k]]; 181 apa[apJ[k++]] = 0.0; 182 } 183 184 /* 2nd off-diagoanl part of C */ 185 ca = coa + co->i[i]; 186 for (; k0<conz; k0++) { 187 ca[k0] = apa[apJ[k]]; 188 apa[apJ[k++]] = 0.0; 189 } 190 } 191 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 192 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 193 PetscFunctionReturn(0); 194 } 195 196 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,PetscReal fill,Mat *C) 197 { 198 PetscErrorCode ierr; 199 MPI_Comm comm; 200 PetscMPIInt size; 201 Mat Cmpi; 202 Mat_PtAPMPI *ptap; 203 PetscFreeSpaceList free_space=NULL,current_space=NULL; 204 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c; 205 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 206 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 207 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 208 PetscInt *lnk,i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi; 209 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n; 210 PetscBT lnkbt; 211 PetscScalar *apa; 212 PetscReal afill; 213 214 PetscFunctionBegin; 215 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 216 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 217 218 /* create struct Mat_PtAPMPI and attached it to C later */ 219 ierr = PetscNew(&ptap);CHKERRQ(ierr); 220 221 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 222 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 223 224 /* get P_loc by taking all local rows of P */ 225 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 226 227 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 228 pi_loc = p_loc->i; pj_loc = p_loc->j; 229 if (size > 1) { 230 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 231 pi_oth = p_oth->i; pj_oth = p_oth->j; 232 } else { 233 p_oth = NULL; 234 pi_oth = NULL; pj_oth = NULL; 235 } 236 237 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 238 /*-------------------------------------------------------------------*/ 239 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 240 ptap->api = api; 241 api[0] = 0; 242 243 /* create and initialize a linked list */ 244 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 245 246 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 247 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 248 current_space = free_space; 249 250 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 251 for (i=0; i<am; i++) { 252 /* diagonal portion of A */ 253 nzi = adi[i+1] - adi[i]; 254 for (j=0; j<nzi; j++) { 255 row = *adj++; 256 pnz = pi_loc[row+1] - pi_loc[row]; 257 Jptr = pj_loc + pi_loc[row]; 258 /* add non-zero cols of P into the sorted linked list lnk */ 259 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 260 } 261 /* off-diagonal portion of A */ 262 nzi = aoi[i+1] - aoi[i]; 263 for (j=0; j<nzi; j++) { 264 row = *aoj++; 265 pnz = pi_oth[row+1] - pi_oth[row]; 266 Jptr = pj_oth + pi_oth[row]; 267 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 268 } 269 270 apnz = lnk[0]; 271 api[i+1] = api[i] + apnz; 272 273 /* if free space is not available, double the total space in the list */ 274 if (current_space->local_remaining<apnz) { 275 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 276 nspacedouble++; 277 } 278 279 /* Copy data into free space, then initialize lnk */ 280 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 281 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 282 283 current_space->array += apnz; 284 current_space->local_used += apnz; 285 current_space->local_remaining -= apnz; 286 } 287 288 /* Allocate space for apj, initialize apj, and */ 289 /* destroy list of free space and other temporary array(s) */ 290 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 291 apj = ptap->apj; 292 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 293 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 294 295 /* malloc apa to store dense row A[i,:]*P */ 296 ierr = PetscCalloc1(pN,&apa);CHKERRQ(ierr); 297 298 ptap->apa = apa; 299 300 /* create and assemble symbolic parallel matrix Cmpi */ 301 /*----------------------------------------------------*/ 302 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 303 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 304 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 305 306 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 307 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 308 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 309 for (i=0; i<am; i++) { 310 row = i + rstart; 311 apnz = api[i+1] - api[i]; 312 ierr = MatSetValues(Cmpi,1,&row,apnz,apj,apa,INSERT_VALUES);CHKERRQ(ierr); 313 apj += apnz; 314 } 315 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 316 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 317 318 ptap->destroy = Cmpi->ops->destroy; 319 ptap->duplicate = Cmpi->ops->duplicate; 320 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 321 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 322 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatMatMult; 323 324 /* attach the supporting struct to Cmpi for reuse */ 325 c = (Mat_MPIAIJ*)Cmpi->data; 326 c->ptap = ptap; 327 328 *C = Cmpi; 329 330 /* set MatInfo */ 331 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 332 if (afill < 1.0) afill = 1.0; 333 Cmpi->info.mallocs = nspacedouble; 334 Cmpi->info.fill_ratio_given = fill; 335 Cmpi->info.fill_ratio_needed = afill; 336 337 #if defined(PETSC_USE_INFO) 338 if (api[am]) { 339 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 340 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 341 } else { 342 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 343 } 344 #endif 345 PetscFunctionReturn(0); 346 } 347 348 PETSC_INTERN PetscErrorCode MatMatMult_MPIAIJ_MPIDense(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 349 { 350 PetscErrorCode ierr; 351 352 PetscFunctionBegin; 353 if (scall == MAT_INITIAL_MATRIX) { 354 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 355 ierr = MatMatMultSymbolic_MPIAIJ_MPIDense(A,B,fill,C);CHKERRQ(ierr); 356 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 357 } 358 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 359 ierr = MatMatMultNumeric_MPIAIJ_MPIDense(A,B,*C);CHKERRQ(ierr); 360 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 361 PetscFunctionReturn(0); 362 } 363 364 typedef struct { 365 Mat workB; 366 PetscScalar *rvalues,*svalues; 367 MPI_Request *rwaits,*swaits; 368 } MPIAIJ_MPIDense; 369 370 PetscErrorCode MatMPIAIJ_MPIDenseDestroy(void *ctx) 371 { 372 MPIAIJ_MPIDense *contents = (MPIAIJ_MPIDense*) ctx; 373 PetscErrorCode ierr; 374 375 PetscFunctionBegin; 376 ierr = MatDestroy(&contents->workB);CHKERRQ(ierr); 377 ierr = PetscFree4(contents->rvalues,contents->svalues,contents->rwaits,contents->swaits);CHKERRQ(ierr); 378 ierr = PetscFree(contents);CHKERRQ(ierr); 379 PetscFunctionReturn(0); 380 } 381 382 /* 383 This is a "dummy function" that handles the case where matrix C was created as a dense matrix 384 directly by the user and passed to MatMatMult() with the MAT_REUSE_MATRIX option 385 386 It is the same as MatMatMultSymbolic_MPIAIJ_MPIDense() except does not create C 387 */ 388 PetscErrorCode MatMatMultNumeric_MPIDense(Mat A,Mat B,Mat C) 389 { 390 PetscErrorCode ierr; 391 PetscBool flg; 392 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) A->data; 393 PetscInt nz = aij->B->cmap->n; 394 PetscContainer container; 395 MPIAIJ_MPIDense *contents; 396 VecScatter ctx = aij->Mvctx; 397 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 398 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 399 400 PetscFunctionBegin; 401 ierr = PetscObjectTypeCompare((PetscObject)B,MATMPIDENSE,&flg);CHKERRQ(ierr); 402 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Second matrix must be mpidense"); 403 404 /* Handle case where where user provided the final C matrix rather than calling MatMatMult() with MAT_INITIAL_MATRIX*/ 405 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 406 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"First matrix must be MPIAIJ"); 407 408 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 409 410 ierr = PetscNew(&contents);CHKERRQ(ierr); 411 /* Create work matrix used to store off processor rows of B needed for local product */ 412 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,B->cmap->N,NULL,&contents->workB);CHKERRQ(ierr); 413 /* Create work arrays needed */ 414 ierr = PetscMalloc4(B->cmap->N*from->starts[from->n],&contents->rvalues, 415 B->cmap->N*to->starts[to->n],&contents->svalues, 416 from->n,&contents->rwaits, 417 to->n,&contents->swaits);CHKERRQ(ierr); 418 419 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)A),&container);CHKERRQ(ierr); 420 ierr = PetscContainerSetPointer(container,contents);CHKERRQ(ierr); 421 ierr = PetscContainerSetUserDestroy(container,MatMPIAIJ_MPIDenseDestroy);CHKERRQ(ierr); 422 ierr = PetscObjectCompose((PetscObject)C,"workB",(PetscObject)container);CHKERRQ(ierr); 423 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 424 425 ierr = (*C->ops->matmultnumeric)(A,B,C);CHKERRQ(ierr); 426 PetscFunctionReturn(0); 427 } 428 429 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat A,Mat B,PetscReal fill,Mat *C) 430 { 431 PetscErrorCode ierr; 432 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) A->data; 433 PetscInt nz = aij->B->cmap->n; 434 PetscContainer container; 435 MPIAIJ_MPIDense *contents; 436 VecScatter ctx = aij->Mvctx; 437 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 438 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 439 PetscInt m = A->rmap->n,n=B->cmap->n; 440 441 PetscFunctionBegin; 442 ierr = MatCreate(PetscObjectComm((PetscObject)B),C);CHKERRQ(ierr); 443 ierr = MatSetSizes(*C,m,n,A->rmap->N,B->cmap->N);CHKERRQ(ierr); 444 ierr = MatSetBlockSizesFromMats(*C,A,B);CHKERRQ(ierr); 445 ierr = MatSetType(*C,MATMPIDENSE);CHKERRQ(ierr); 446 ierr = MatMPIDenseSetPreallocation(*C,NULL);CHKERRQ(ierr); 447 ierr = MatAssemblyBegin(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 448 ierr = MatAssemblyEnd(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 449 450 (*C)->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 451 452 ierr = PetscNew(&contents);CHKERRQ(ierr); 453 /* Create work matrix used to store off processor rows of B needed for local product */ 454 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,B->cmap->N,NULL,&contents->workB);CHKERRQ(ierr); 455 /* Create work arrays needed */ 456 ierr = PetscMalloc4(B->cmap->N*from->starts[from->n],&contents->rvalues, 457 B->cmap->N*to->starts[to->n],&contents->svalues, 458 from->n,&contents->rwaits, 459 to->n,&contents->swaits);CHKERRQ(ierr); 460 461 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)A),&container);CHKERRQ(ierr); 462 ierr = PetscContainerSetPointer(container,contents);CHKERRQ(ierr); 463 ierr = PetscContainerSetUserDestroy(container,MatMPIAIJ_MPIDenseDestroy);CHKERRQ(ierr); 464 ierr = PetscObjectCompose((PetscObject)(*C),"workB",(PetscObject)container);CHKERRQ(ierr); 465 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 466 PetscFunctionReturn(0); 467 } 468 469 /* 470 Performs an efficient scatter on the rows of B needed by this process; this is 471 a modification of the VecScatterBegin_() routines. 472 */ 473 PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,Mat C,Mat *outworkB) 474 { 475 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 476 PetscErrorCode ierr; 477 PetscScalar *b,*w,*svalues,*rvalues; 478 VecScatter ctx = aij->Mvctx; 479 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 480 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 481 PetscInt i,j,k; 482 PetscInt *sindices,*sstarts,*rindices,*rstarts; 483 PetscMPIInt *sprocs,*rprocs,nrecvs; 484 MPI_Request *swaits,*rwaits; 485 MPI_Comm comm; 486 PetscMPIInt tag = ((PetscObject)ctx)->tag,ncols = B->cmap->N, nrows = aij->B->cmap->n,imdex,nrowsB = B->rmap->n; 487 MPI_Status status; 488 MPIAIJ_MPIDense *contents; 489 PetscContainer container; 490 Mat workB; 491 492 PetscFunctionBegin; 493 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 494 ierr = PetscObjectQuery((PetscObject)C,"workB",(PetscObject*)&container);CHKERRQ(ierr); 495 if (!container) SETERRQ(comm,PETSC_ERR_PLIB,"Container does not exist"); 496 ierr = PetscContainerGetPointer(container,(void**)&contents);CHKERRQ(ierr); 497 498 workB = *outworkB = contents->workB; 499 if (nrows != workB->rmap->n) SETERRQ2(comm,PETSC_ERR_PLIB,"Number of rows of workB %D not equal to columns of aij->B %D",nrows,workB->cmap->n); 500 sindices = to->indices; 501 sstarts = to->starts; 502 sprocs = to->procs; 503 swaits = contents->swaits; 504 svalues = contents->svalues; 505 506 rindices = from->indices; 507 rstarts = from->starts; 508 rprocs = from->procs; 509 rwaits = contents->rwaits; 510 rvalues = contents->rvalues; 511 512 ierr = MatDenseGetArray(B,&b);CHKERRQ(ierr); 513 ierr = MatDenseGetArray(workB,&w);CHKERRQ(ierr); 514 515 for (i=0; i<from->n; i++) { 516 ierr = MPI_Irecv(rvalues+ncols*rstarts[i],ncols*(rstarts[i+1]-rstarts[i]),MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 517 } 518 519 for (i=0; i<to->n; i++) { 520 /* pack a message at a time */ 521 for (j=0; j<sstarts[i+1]-sstarts[i]; j++) { 522 for (k=0; k<ncols; k++) { 523 svalues[ncols*(sstarts[i] + j) + k] = b[sindices[sstarts[i]+j] + nrowsB*k]; 524 } 525 } 526 ierr = MPI_Isend(svalues+ncols*sstarts[i],ncols*(sstarts[i+1]-sstarts[i]),MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 527 } 528 529 nrecvs = from->n; 530 while (nrecvs) { 531 ierr = MPI_Waitany(from->n,rwaits,&imdex,&status);CHKERRQ(ierr); 532 nrecvs--; 533 /* unpack a message at a time */ 534 for (j=0; j<rstarts[imdex+1]-rstarts[imdex]; j++) { 535 for (k=0; k<ncols; k++) { 536 w[rindices[rstarts[imdex]+j] + nrows*k] = rvalues[ncols*(rstarts[imdex] + j) + k]; 537 } 538 } 539 } 540 if (to->n) {ierr = MPI_Waitall(to->n,swaits,to->sstatus);CHKERRQ(ierr);} 541 542 ierr = MatDenseRestoreArray(B,&b);CHKERRQ(ierr); 543 ierr = MatDenseRestoreArray(workB,&w);CHKERRQ(ierr); 544 ierr = MatAssemblyBegin(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 545 ierr = MatAssemblyEnd(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 546 PetscFunctionReturn(0); 547 } 548 extern PetscErrorCode MatMatMultNumericAdd_SeqAIJ_SeqDense(Mat,Mat,Mat); 549 550 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat A,Mat B,Mat C) 551 { 552 PetscErrorCode ierr; 553 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 554 Mat_MPIDense *bdense = (Mat_MPIDense*)B->data; 555 Mat_MPIDense *cdense = (Mat_MPIDense*)C->data; 556 Mat workB; 557 558 PetscFunctionBegin; 559 /* diagonal block of A times all local rows of B*/ 560 ierr = MatMatMultNumeric_SeqAIJ_SeqDense(aij->A,bdense->A,cdense->A);CHKERRQ(ierr); 561 562 /* get off processor parts of B needed to complete the product */ 563 ierr = MatMPIDenseScatter(A,B,C,&workB);CHKERRQ(ierr); 564 565 /* off-diagonal block of A times nonlocal rows of B */ 566 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A);CHKERRQ(ierr); 567 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 568 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 569 PetscFunctionReturn(0); 570 } 571 572 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 573 { 574 PetscErrorCode ierr; 575 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 576 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 577 Mat_SeqAIJ *cd = (Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 578 PetscInt *adi = ad->i,*adj,*aoi=ao->i,*aoj; 579 PetscScalar *ada,*aoa,*cda=cd->a,*coa=co->a; 580 Mat_SeqAIJ *p_loc,*p_oth; 581 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pj; 582 PetscScalar *pa_loc,*pa_oth,*pa,valtmp,*ca; 583 PetscInt cm = C->rmap->n,anz,pnz; 584 Mat_PtAPMPI *ptap = c->ptap; 585 PetscScalar *apa_sparse = ptap->apa; 586 PetscInt *api,*apj,*apJ,i,j,k,row; 587 PetscInt cstart = C->cmap->rstart; 588 PetscInt cdnz,conz,k0,k1,nextp; 589 MPI_Comm comm; 590 PetscMPIInt size; 591 592 PetscFunctionBegin; 593 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 594 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 595 596 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 597 /*-----------------------------------------------------*/ 598 /* update numerical values of P_oth and P_loc */ 599 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 600 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 601 602 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 603 /*----------------------------------------------------------*/ 604 /* get data from symbolic products */ 605 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 606 pi_loc = p_loc->i; pj_loc = p_loc->j; pa_loc = p_loc->a; 607 if (size >1) { 608 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 609 pi_oth = p_oth->i; pj_oth = p_oth->j; pa_oth = p_oth->a; 610 } else { 611 p_oth = NULL; pi_oth = NULL; pj_oth = NULL; pa_oth = NULL; 612 } 613 614 api = ptap->api; 615 apj = ptap->apj; 616 for (i=0; i<cm; i++) { 617 apJ = apj + api[i]; 618 619 /* diagonal portion of A */ 620 anz = adi[i+1] - adi[i]; 621 adj = ad->j + adi[i]; 622 ada = ad->a + adi[i]; 623 for (j=0; j<anz; j++) { 624 row = adj[j]; 625 pnz = pi_loc[row+1] - pi_loc[row]; 626 pj = pj_loc + pi_loc[row]; 627 pa = pa_loc + pi_loc[row]; 628 /* perform sparse axpy */ 629 valtmp = ada[j]; 630 nextp = 0; 631 for (k=0; nextp<pnz; k++) { 632 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 633 apa_sparse[k] += valtmp*pa[nextp++]; 634 } 635 } 636 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 637 } 638 639 /* off-diagonal portion of A */ 640 anz = aoi[i+1] - aoi[i]; 641 aoj = ao->j + aoi[i]; 642 aoa = ao->a + aoi[i]; 643 for (j=0; j<anz; j++) { 644 row = aoj[j]; 645 pnz = pi_oth[row+1] - pi_oth[row]; 646 pj = pj_oth + pi_oth[row]; 647 pa = pa_oth + pi_oth[row]; 648 /* perform sparse axpy */ 649 valtmp = aoa[j]; 650 nextp = 0; 651 for (k=0; nextp<pnz; k++) { 652 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 653 apa_sparse[k] += valtmp*pa[nextp++]; 654 } 655 } 656 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 657 } 658 659 /* set values in C */ 660 cdnz = cd->i[i+1] - cd->i[i]; 661 conz = co->i[i+1] - co->i[i]; 662 663 /* 1st off-diagoanl part of C */ 664 ca = coa + co->i[i]; 665 k = 0; 666 for (k0=0; k0<conz; k0++) { 667 if (apJ[k] >= cstart) break; 668 ca[k0] = apa_sparse[k]; 669 apa_sparse[k] = 0.0; 670 k++; 671 } 672 673 /* diagonal part of C */ 674 ca = cda + cd->i[i]; 675 for (k1=0; k1<cdnz; k1++) { 676 ca[k1] = apa_sparse[k]; 677 apa_sparse[k] = 0.0; 678 k++; 679 } 680 681 /* 2nd off-diagoanl part of C */ 682 ca = coa + co->i[i]; 683 for (; k0<conz; k0++) { 684 ca[k0] = apa_sparse[k]; 685 apa_sparse[k] = 0.0; 686 k++; 687 } 688 } 689 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 690 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 691 PetscFunctionReturn(0); 692 } 693 694 /* same as MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(), except using LLCondensed to avoid O(BN) memory requirement */ 695 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 696 { 697 PetscErrorCode ierr; 698 MPI_Comm comm; 699 PetscMPIInt size; 700 Mat Cmpi; 701 Mat_PtAPMPI *ptap; 702 PetscFreeSpaceList free_space = NULL,current_space=NULL; 703 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c; 704 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 705 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 706 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 707 PetscInt i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi,*lnk,apnz_max; 708 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n; 709 PetscReal afill; 710 PetscScalar *apa; 711 PetscTable ta; 712 713 PetscFunctionBegin; 714 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 715 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 716 717 /* create struct Mat_PtAPMPI and attached it to C later */ 718 ierr = PetscNew(&ptap);CHKERRQ(ierr); 719 720 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 721 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 722 723 /* get P_loc by taking all local rows of P */ 724 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 725 726 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 727 pi_loc = p_loc->i; pj_loc = p_loc->j; 728 if (size > 1) { 729 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 730 pi_oth = p_oth->i; pj_oth = p_oth->j; 731 } else { 732 p_oth = NULL; 733 pi_oth = NULL; pj_oth = NULL; 734 } 735 736 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 737 /*-------------------------------------------------------------------*/ 738 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 739 ptap->api = api; 740 api[0] = 0; 741 742 /* create and initialize a linked list */ 743 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); 744 745 /* Calculate apnz_max */ 746 apnz_max = 0; 747 for (i=0; i<am; i++) { 748 ierr = PetscTableRemoveAll(ta);CHKERRQ(ierr); 749 /* diagonal portion of A */ 750 nzi = adi[i+1] - adi[i]; 751 Jptr = adj+adi[i]; /* cols of A_diag */ 752 MatMergeRows_SeqAIJ(p_loc,nzi,Jptr,ta); 753 ierr = PetscTableGetCount(ta,&apnz);CHKERRQ(ierr); 754 if (apnz_max < apnz) apnz_max = apnz; 755 756 /* off-diagonal portion of A */ 757 nzi = aoi[i+1] - aoi[i]; 758 Jptr = aoj+aoi[i]; /* cols of A_off */ 759 MatMergeRows_SeqAIJ(p_oth,nzi,Jptr,ta); 760 ierr = PetscTableGetCount(ta,&apnz);CHKERRQ(ierr); 761 if (apnz_max < apnz) apnz_max = apnz; 762 } 763 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 764 765 ierr = PetscLLCondensedCreate_Scalable(apnz_max,&lnk);CHKERRQ(ierr); 766 767 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 768 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 769 current_space = free_space; 770 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 771 for (i=0; i<am; i++) { 772 /* diagonal portion of A */ 773 nzi = adi[i+1] - adi[i]; 774 for (j=0; j<nzi; j++) { 775 row = *adj++; 776 pnz = pi_loc[row+1] - pi_loc[row]; 777 Jptr = pj_loc + pi_loc[row]; 778 /* add non-zero cols of P into the sorted linked list lnk */ 779 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 780 } 781 /* off-diagonal portion of A */ 782 nzi = aoi[i+1] - aoi[i]; 783 for (j=0; j<nzi; j++) { 784 row = *aoj++; 785 pnz = pi_oth[row+1] - pi_oth[row]; 786 Jptr = pj_oth + pi_oth[row]; 787 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 788 } 789 790 apnz = *lnk; 791 api[i+1] = api[i] + apnz; 792 793 /* if free space is not available, double the total space in the list */ 794 if (current_space->local_remaining<apnz) { 795 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 796 nspacedouble++; 797 } 798 799 /* Copy data into free space, then initialize lnk */ 800 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 801 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 802 803 current_space->array += apnz; 804 current_space->local_used += apnz; 805 current_space->local_remaining -= apnz; 806 } 807 808 /* Allocate space for apj, initialize apj, and */ 809 /* destroy list of free space and other temporary array(s) */ 810 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 811 apj = ptap->apj; 812 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 813 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 814 815 /* create and assemble symbolic parallel matrix Cmpi */ 816 /*----------------------------------------------------*/ 817 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 818 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 819 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 820 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 821 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 822 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 823 824 /* malloc apa for assembly Cmpi */ 825 ierr = PetscCalloc1(apnz_max,&apa);CHKERRQ(ierr); 826 827 ptap->apa = apa; 828 for (i=0; i<am; i++) { 829 row = i + rstart; 830 apnz = api[i+1] - api[i]; 831 ierr = MatSetValues(Cmpi,1,&row,apnz,apj,apa,INSERT_VALUES);CHKERRQ(ierr); 832 apj += apnz; 833 } 834 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 835 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 836 837 ptap->destroy = Cmpi->ops->destroy; 838 ptap->duplicate = Cmpi->ops->duplicate; 839 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ; 840 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 841 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatMatMult; 842 843 /* attach the supporting struct to Cmpi for reuse */ 844 c = (Mat_MPIAIJ*)Cmpi->data; 845 c->ptap = ptap; 846 847 *C = Cmpi; 848 849 /* set MatInfo */ 850 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 851 if (afill < 1.0) afill = 1.0; 852 Cmpi->info.mallocs = nspacedouble; 853 Cmpi->info.fill_ratio_given = fill; 854 Cmpi->info.fill_ratio_needed = afill; 855 856 #if defined(PETSC_USE_INFO) 857 if (api[am]) { 858 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 859 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 860 } else { 861 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 862 } 863 #endif 864 PetscFunctionReturn(0); 865 } 866 867 /* This function is needed for the seqMPI matrix-matrix multiplication. */ 868 /* Three input arrays are merged to one output array. The size of the */ 869 /* output array is also output. Duplicate entries only show up once. */ 870 static void Merge3SortedArrays(PetscInt size1, PetscInt *in1, 871 PetscInt size2, PetscInt *in2, 872 PetscInt size3, PetscInt *in3, 873 PetscInt *size4, PetscInt *out) 874 { 875 int i = 0, j = 0, k = 0, l = 0; 876 877 /* Traverse all three arrays */ 878 while (i<size1 && j<size2 && k<size3) { 879 if (in1[i] < in2[j] && in1[i] < in3[k]) { 880 out[l++] = in1[i++]; 881 } 882 else if(in2[j] < in1[i] && in2[j] < in3[k]) { 883 out[l++] = in2[j++]; 884 } 885 else if(in3[k] < in1[i] && in3[k] < in2[j]) { 886 out[l++] = in3[k++]; 887 } 888 else if(in1[i] == in2[j] && in1[i] < in3[k]) { 889 out[l++] = in1[i]; 890 i++, j++; 891 } 892 else if(in1[i] == in3[k] && in1[i] < in2[j]) { 893 out[l++] = in1[i]; 894 i++, k++; 895 } 896 else if(in3[k] == in2[j] && in2[j] < in1[i]) { 897 out[l++] = in2[j]; 898 k++, j++; 899 } 900 else if(in1[i] == in2[j] && in1[i] == in3[k]) { 901 out[l++] = in1[i]; 902 i++, j++, k++; 903 } 904 } 905 906 /* Traverse two remaining arrays */ 907 while (i<size1 && j<size2) { 908 if (in1[i] < in2[j]) { 909 out[l++] = in1[i++]; 910 } 911 else if(in1[i] > in2[j]) { 912 out[l++] = in2[j++]; 913 } 914 else { 915 out[l++] = in1[i]; 916 i++, j++; 917 } 918 } 919 920 while (i<size1 && k<size3) { 921 if (in1[i] < in3[k]) { 922 out[l++] = in1[i++]; 923 } 924 else if(in1[i] > in3[k]) { 925 out[l++] = in3[k++]; 926 } 927 else { 928 out[l++] = in1[i]; 929 i++, k++; 930 } 931 } 932 933 while (k<size3 && j<size2) { 934 if (in3[k] < in2[j]) { 935 out[l++] = in3[k++]; 936 } 937 else if(in3[k] > in2[j]) { 938 out[l++] = in2[j++]; 939 } 940 else { 941 out[l++] = in3[k]; 942 k++, j++; 943 } 944 } 945 946 /* Traverse one remaining array */ 947 while (i<size1) out[l++] = in1[i++]; 948 while (j<size2) out[l++] = in2[j++]; 949 while (k<size3) out[l++] = in3[k++]; 950 951 *size4 = l; 952 } 953 954 #undef __FUNCT__ 955 #define __FUNCT__ "MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI" 956 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI(Mat A, Mat P, PetscReal fill, Mat *C) 957 { 958 PetscErrorCode ierr; 959 MPI_Comm comm; 960 PetscMPIInt size; 961 Mat Cmpi; 962 Mat_PtAPMPI *ptap; 963 PetscFreeSpaceList free_space_diag=NULL, current_space=NULL; 964 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data; 965 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc; 966 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data; 967 Mat_MPIAIJ *c; 968 Mat_SeqAIJ *adpd_seq, *p_off, *aopoth_seq; 969 PetscInt adponz, adpdnz; 970 PetscInt *pi_loc,*dnz,*onz; 971 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,rstart=A->rmap->rstart; 972 PetscInt *lnk,i, i1=0,pnz,row,*adpoi,*adpoj, *api, *adpoJ, *aopJ, *apJ,*Jptr, aopnz, nspacedouble=0,j,nzi, 973 *apj,apnz, *adpdi, *adpdj, *adpdJ, *poff_i, *poff_j, *j_temp, *aopothi, *aopothj; 974 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n, p_rowstart, p_rowend; 975 PetscBT lnkbt; 976 PetscScalar *apa; 977 PetscReal afill; 978 PetscMPIInt rank; 979 Mat adpd, aopoth; 980 981 PetscFunctionBegin; 982 983 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 984 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 985 MPI_Comm_rank(comm, &rank); 986 ierr = MatGetOwnershipRange(P, &p_rowstart, &p_rowend); CHKERRQ(ierr); 987 988 /* create struct Mat_PtAPMPI and attached it to C later */ 989 ierr = PetscNew(&ptap);CHKERRQ(ierr); 990 991 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 992 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 993 994 /* get P_loc by taking all local rows of P */ 995 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 996 997 998 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 999 pi_loc = p_loc->i; 1000 1001 /* Allocate memory for the i arrays of the matrices A*P, A_diag*P_off and A_offd * P */ 1002 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 1003 ierr = PetscMalloc1(am+2,&adpoi);CHKERRQ(ierr); 1004 1005 adpoi[0] = 0; 1006 ptap->api = api; 1007 api[0] = 0; 1008 1009 /* create and initialize a linked list, will be used for both A_diag * P_loc_off and A_offd * P_oth */ 1010 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1011 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 1012 1013 /* Symbolic calc of A_loc_diag * P_loc_diag */ 1014 MatMatMultSymbolic_SeqAIJ_SeqAIJ(a->A, p->A, fill, &adpd); 1015 adpd_seq = (Mat_SeqAIJ*)((adpd)->data); 1016 adpdi = adpd_seq->i; adpdj = adpd_seq->j; 1017 p_off = (Mat_SeqAIJ*)((p->B)->data); 1018 poff_i = p_off->i; poff_j = p_off->j; 1019 1020 /* j_temp stores indices of a result row before they added to the linked list */ 1021 ierr = PetscMalloc1(pN+2,&j_temp);CHKERRQ(ierr); 1022 1023 1024 /* Symbolic calc of the A_diag * p_loc_off */ 1025 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 1026 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space_diag);CHKERRQ(ierr); 1027 current_space = free_space_diag; 1028 1029 for (i=0; i<am; i++) { 1030 /* A_diag * P_loc_off */ 1031 nzi = adi[i+1] - adi[i]; 1032 for (j=0; j<nzi; j++) { 1033 row = *adj++; 1034 pnz = poff_i[row+1] - poff_i[row]; 1035 Jptr = poff_j + poff_i[row]; 1036 for(i1 = 0; i1 < pnz; i1++) { 1037 j_temp[i1] = p->garray[Jptr[i1]]; 1038 } 1039 /* add non-zero cols of P into the sorted linked list lnk */ 1040 ierr = PetscLLCondensedAddSorted(pnz,j_temp,lnk,lnkbt);CHKERRQ(ierr); 1041 } 1042 1043 adponz = lnk[0]; 1044 adpoi[i+1] = adpoi[i] + adponz; 1045 1046 /* if free space is not available, double the total space in the list */ 1047 if (current_space->local_remaining<adponz) { 1048 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(adponz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1049 nspacedouble++; 1050 } 1051 1052 /* Copy data into free space, then initialize lnk */ 1053 ierr = PetscLLCondensedClean(pN,adponz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1054 1055 current_space->array += adponz; 1056 current_space->local_used += adponz; 1057 current_space->local_remaining -= adponz; 1058 } 1059 1060 /* Symbolic calc of A_off * P_oth */ 1061 MatMatMultSymbolic_SeqAIJ_SeqAIJ(a->B, ptap->P_oth, fill, &aopoth); 1062 aopoth_seq = (Mat_SeqAIJ*)((aopoth)->data); 1063 aopothi = aopoth_seq->i; aopothj = aopoth_seq->j; 1064 1065 /* Allocate space for apj, adpj, aopj, ... */ 1066 /* destroy lists of free space and other temporary array(s) */ 1067 1068 ierr = PetscMalloc1(aopothi[am] + adpoi[am] + adpdi[am]+2, &ptap->apj);CHKERRQ(ierr); 1069 ierr = PetscMalloc1(adpoi[am]+2, &adpoj);CHKERRQ(ierr); 1070 1071 /* Copy from linked list to j-array */ 1072 ierr = PetscFreeSpaceContiguous(&free_space_diag,adpoj);CHKERRQ(ierr); 1073 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1074 1075 adpoJ = adpoj; 1076 adpdJ = adpdj; 1077 aopJ = aopothj; 1078 apj = ptap->apj; 1079 apJ = apj; /* still empty */ 1080 1081 /* Merge j-arrays of A_off * P, A_diag * P_loc_off, and */ 1082 /* A_diag * P_loc_diag to get A*P */ 1083 for (i = 0; i < am; i++) { 1084 aopnz = aopothi[i+1] - aopothi[i]; 1085 adponz = adpoi[i+1] - adpoi[i]; 1086 adpdnz = adpdi[i+1] - adpdi[i]; 1087 1088 /* Correct indices from A_diag*P_diag */ 1089 for(i1 = 0; i1 < adpdnz; i1++) { 1090 adpdJ[i1] += p_rowstart; 1091 } 1092 /* Merge j-arrays of A_diag * P_loc_off and A_diag * P_loc_diag and A_off * P_oth */ 1093 Merge3SortedArrays(adponz, adpoJ, adpdnz, adpdJ, aopnz, aopJ, &apnz, apJ); 1094 ierr = MatPreallocateSet(i+rstart, apnz, apJ, dnz, onz); CHKERRQ(ierr); 1095 1096 aopJ += aopnz; 1097 adpoJ += adponz; 1098 adpdJ += adpdnz; 1099 apJ += apnz; 1100 api[i+1] = api[i] + apnz; 1101 } 1102 1103 /* malloc apa to store dense row A[i,:]*P */ 1104 ierr = PetscCalloc1(pN+2,&apa);CHKERRQ(ierr); 1105 1106 ptap->apa = apa; 1107 /* create and assemble symbolic parallel matrix Cmpi */ 1108 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1109 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1110 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 1111 1112 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 1113 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1114 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1115 for (i=0; i<am; i++) { 1116 row = i + rstart; 1117 apnz = api[i+1] - api[i]; 1118 ierr = MatSetValues(Cmpi, 1, &row, apnz, apj, apa, INSERT_VALUES);CHKERRQ(ierr); 1119 apj += apnz; 1120 } 1121 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1122 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1123 1124 ptap->destroy = Cmpi->ops->destroy; 1125 ptap->duplicate = Cmpi->ops->duplicate; 1126 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1127 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 1128 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatMatMult; 1129 1130 /* attach the supporting struct to Cmpi for reuse */ 1131 c = (Mat_MPIAIJ*)Cmpi->data; 1132 c->ptap = ptap; 1133 *C = Cmpi; 1134 1135 /* set MatInfo */ 1136 /* afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; */ 1137 /* if (afill < 1.0) afill = 1.0; */ 1138 afill = 1.0; 1139 Cmpi->info.mallocs = nspacedouble; 1140 Cmpi->info.fill_ratio_given = fill; 1141 Cmpi->info.fill_ratio_needed = afill; 1142 1143 #if defined(PETSC_USE_INFO) 1144 if (api[am]) { 1145 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1146 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 1147 } else { 1148 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1149 } 1150 #endif 1151 1152 MatDestroy(&aopoth); 1153 MatDestroy(&adpd); 1154 PetscFree(j_temp); 1155 PetscFree(adpoj); 1156 PetscFree(adpoi); 1157 PetscFunctionReturn(0); 1158 } 1159 1160 1161 /*-------------------------------------------------------------------------*/ 1162 PetscErrorCode MatTransposeMatMult_MPIAIJ_MPIAIJ(Mat P,Mat A,MatReuse scall,PetscReal fill,Mat *C) 1163 { 1164 PetscErrorCode ierr; 1165 const char *algTypes[3] = {"scalable","nonscalable","matmatmult"}; 1166 PetscInt aN=A->cmap->N,alg=1; /* set default algorithm */ 1167 PetscBool flg; 1168 1169 PetscFunctionBegin; 1170 if (scall == MAT_INITIAL_MATRIX) { 1171 ierr = PetscObjectOptionsBegin((PetscObject)A);CHKERRQ(ierr); 1172 PetscOptionsObject->alreadyprinted = PETSC_FALSE; /* a hack to ensure the option shows in '-help' */ 1173 ierr = PetscOptionsEList("-mattransposematmult_via","Algorithmic approach","MatTransposeMatMult",algTypes,3,algTypes[1],&alg,&flg);CHKERRQ(ierr); 1174 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1175 1176 ierr = PetscLogEventBegin(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 1177 switch (alg) { 1178 case 1: 1179 if (!flg && aN > 100000) { /* may switch to scalable algorithm as default */ 1180 MatInfo Ainfo,Pinfo; 1181 PetscInt nz_local; 1182 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 1183 MPI_Comm comm; 1184 1185 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 1186 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 1187 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); /* estimated local nonzero entries */ 1188 1189 if (aN > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 1190 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1191 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 1192 1193 if (alg_scalable) { 1194 alg = 0; /* scalable algorithm would slower than nonscalable algorithm */ 1195 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(P,A,fill,C);CHKERRQ(ierr); 1196 break; 1197 } 1198 } 1199 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(P,A,fill,C);CHKERRQ(ierr); 1200 break; 1201 case 2: 1202 { 1203 Mat Pt; 1204 Mat_PtAPMPI *ptap; 1205 Mat_MPIAIJ *c; 1206 ierr = MatTranspose(P,MAT_INITIAL_MATRIX,&Pt);CHKERRQ(ierr); 1207 ierr = MatMatMult(Pt,A,MAT_INITIAL_MATRIX,fill,C);CHKERRQ(ierr); 1208 c = (Mat_MPIAIJ*)(*C)->data; 1209 ptap = c->ptap; 1210 ptap->Pt = Pt; 1211 (*C)->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult; 1212 PetscFunctionReturn(0); 1213 } 1214 break; 1215 default: /* scalable algorithm */ 1216 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(P,A,fill,C);CHKERRQ(ierr); 1217 break; 1218 } 1219 ierr = PetscLogEventEnd(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 1220 } 1221 ierr = PetscLogEventBegin(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 1222 ierr = (*(*C)->ops->mattransposemultnumeric)(P,A,*C);CHKERRQ(ierr); 1223 ierr = PetscLogEventEnd(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 1224 PetscFunctionReturn(0); 1225 } 1226 1227 /* This routine only works when scall=MAT_REUSE_MATRIX! */ 1228 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult(Mat P,Mat A,Mat C) 1229 { 1230 PetscErrorCode ierr; 1231 Mat_MPIAIJ *c=(Mat_MPIAIJ*)C->data; 1232 Mat_PtAPMPI *ptap= c->ptap; 1233 Mat Pt=ptap->Pt; 1234 1235 PetscFunctionBegin; 1236 ierr = MatTranspose(P,MAT_REUSE_MATRIX,&Pt);CHKERRQ(ierr); 1237 ierr = MatMatMultNumeric(Pt,A,C);CHKERRQ(ierr); 1238 PetscFunctionReturn(0); 1239 } 1240 1241 PetscErrorCode MatDuplicate_MPIAIJ_MatPtAP(Mat,MatDuplicateOption,Mat*); 1242 1243 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ() */ 1244 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,PetscReal fill,Mat *C) 1245 { 1246 PetscErrorCode ierr; 1247 Mat_PtAPMPI *ptap; 1248 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1249 MPI_Comm comm; 1250 PetscMPIInt size,rank; 1251 Mat Cmpi; 1252 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1253 PetscInt pn=P->cmap->n,aN=A->cmap->N,an=A->cmap->n; 1254 PetscInt *lnk,i,k,nsend; 1255 PetscBT lnkbt; 1256 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 1257 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1258 PetscInt len,proc,*dnz,*onz,*owners,nzi; 1259 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1260 MPI_Request *swaits,*rwaits; 1261 MPI_Status *sstatus,rstatus; 1262 PetscLayout rowmap; 1263 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1264 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1265 PetscInt *Jptr,*prmap=p->garray,con,j,Crmax; 1266 Mat_SeqAIJ *a_loc,*c_loc,*c_oth; 1267 PetscTable ta; 1268 1269 PetscFunctionBegin; 1270 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1271 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1272 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1273 1274 /* create symbolic parallel matrix Cmpi */ 1275 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1276 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 1277 1278 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1279 1280 /* create struct Mat_PtAPMPI and attached it to C later */ 1281 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1282 ptap->reuse = MAT_INITIAL_MATRIX; 1283 1284 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1285 /* --------------------------------- */ 1286 ierr = MatTranspose_SeqAIJ(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1287 ierr = MatTranspose_SeqAIJ(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1288 1289 /* (1) compute symbolic A_loc */ 1290 /* ---------------------------*/ 1291 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1292 1293 /* (2-1) compute symbolic C_oth = Ro*A_loc */ 1294 /* ------------------------------------ */ 1295 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->A_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 1296 1297 /* (3) send coj of C_oth to other processors */ 1298 /* ------------------------------------------ */ 1299 /* determine row ownership */ 1300 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1301 rowmap->n = pn; 1302 rowmap->bs = 1; 1303 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1304 owners = rowmap->range; 1305 1306 /* determine the number of messages to send, their lengths */ 1307 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1308 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1309 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1310 1311 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1312 coi = c_oth->i; coj = c_oth->j; 1313 con = ptap->C_oth->rmap->n; 1314 proc = 0; 1315 for (i=0; i<con; i++) { 1316 while (prmap[i] >= owners[proc+1]) proc++; 1317 len_si[proc]++; /* num of rows in Co(=Pt*A) to be sent to [proc] */ 1318 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1319 } 1320 1321 len = 0; /* max length of buf_si[], see (4) */ 1322 owners_co[0] = 0; 1323 nsend = 0; 1324 for (proc=0; proc<size; proc++) { 1325 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1326 if (len_s[proc]) { 1327 nsend++; 1328 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1329 len += len_si[proc]; 1330 } 1331 } 1332 1333 /* determine the number and length of messages to receive for coi and coj */ 1334 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1335 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1336 1337 /* post the Irecv and Isend of coj */ 1338 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1339 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1340 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1341 for (proc=0, k=0; proc<size; proc++) { 1342 if (!len_s[proc]) continue; 1343 i = owners_co[proc]; 1344 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1345 k++; 1346 } 1347 1348 /* (2-2) compute symbolic C_loc = Rd*A_loc */ 1349 /* ---------------------------------------- */ 1350 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->A_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 1351 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1352 1353 /* receives coj are complete */ 1354 for (i=0; i<nrecv; i++) { 1355 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1356 } 1357 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1358 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1359 1360 /* add received column indices into ta to update Crmax */ 1361 a_loc = (Mat_SeqAIJ*)(ptap->A_loc)->data; 1362 1363 /* create and initialize a linked list */ 1364 ierr = PetscTableCreate(an,aN,&ta);CHKERRQ(ierr); /* for compute Crmax */ 1365 MatRowMergeMax_SeqAIJ(a_loc,ptap->A_loc->rmap->N,ta); 1366 1367 for (k=0; k<nrecv; k++) {/* k-th received message */ 1368 Jptr = buf_rj[k]; 1369 for (j=0; j<len_r[k]; j++) { 1370 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1371 } 1372 } 1373 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1374 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1375 1376 /* (4) send and recv coi */ 1377 /*-----------------------*/ 1378 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1379 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1380 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1381 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1382 for (proc=0,k=0; proc<size; proc++) { 1383 if (!len_s[proc]) continue; 1384 /* form outgoing message for i-structure: 1385 buf_si[0]: nrows to be sent 1386 [1:nrows]: row index (global) 1387 [nrows+1:2*nrows+1]: i-structure index 1388 */ 1389 /*-------------------------------------------*/ 1390 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1391 buf_si_i = buf_si + nrows+1; 1392 buf_si[0] = nrows; 1393 buf_si_i[0] = 0; 1394 nrows = 0; 1395 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1396 nzi = coi[i+1] - coi[i]; 1397 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1398 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1399 nrows++; 1400 } 1401 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1402 k++; 1403 buf_si += len_si[proc]; 1404 } 1405 for (i=0; i<nrecv; i++) { 1406 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1407 } 1408 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1409 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1410 1411 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1412 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1413 ierr = PetscFree(swaits);CHKERRQ(ierr); 1414 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1415 1416 /* (5) compute the local portion of Cmpi */ 1417 /* ------------------------------------------ */ 1418 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 1419 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1420 current_space = free_space; 1421 1422 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1423 for (k=0; k<nrecv; k++) { 1424 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1425 nrows = *buf_ri_k[k]; 1426 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1427 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1428 } 1429 1430 ierr = MatPreallocateInitialize(comm,pn,an,dnz,onz);CHKERRQ(ierr); 1431 ierr = PetscLLCondensedCreate(Crmax,aN,&lnk,&lnkbt);CHKERRQ(ierr); 1432 for (i=0; i<pn; i++) { 1433 /* add C_loc into Cmpi */ 1434 nzi = c_loc->i[i+1] - c_loc->i[i]; 1435 Jptr = c_loc->j + c_loc->i[i]; 1436 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1437 1438 /* add received col data into lnk */ 1439 for (k=0; k<nrecv; k++) { /* k-th received message */ 1440 if (i == *nextrow[k]) { /* i-th row */ 1441 nzi = *(nextci[k]+1) - *nextci[k]; 1442 Jptr = buf_rj[k] + *nextci[k]; 1443 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1444 nextrow[k]++; nextci[k]++; 1445 } 1446 } 1447 nzi = lnk[0]; 1448 1449 /* copy data into free space, then initialize lnk */ 1450 ierr = PetscLLCondensedClean(aN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1451 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 1452 } 1453 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1454 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1455 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 1456 1457 /* local sizes and preallocation */ 1458 ierr = MatSetSizes(Cmpi,pn,an,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1459 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 1460 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1461 ierr = MatPreallocateFinalize(dnz,onz);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 Cmpi for reuse */ 1473 c = (Mat_MPIAIJ*)Cmpi->data; 1474 c->ptap = ptap; 1475 ptap->duplicate = Cmpi->ops->duplicate; 1476 ptap->destroy = Cmpi->ops->destroy; 1477 1478 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1479 Cmpi->assembled = PETSC_FALSE; 1480 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1481 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 1482 *C = Cmpi; 1483 PetscFunctionReturn(0); 1484 } 1485 1486 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,Mat C) 1487 { 1488 PetscErrorCode ierr; 1489 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1490 Mat_SeqAIJ *c_seq; 1491 Mat_PtAPMPI *ptap = c->ptap; 1492 Mat A_loc,C_loc,C_oth; 1493 PetscInt i,rstart,rend,cm,ncols,row; 1494 const PetscInt *cols; 1495 const PetscScalar *vals; 1496 1497 PetscFunctionBegin; 1498 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1499 1500 if (ptap->reuse == MAT_REUSE_MATRIX) { 1501 /* These matrices are obtained in MatTransposeMatMultSymbolic() */ 1502 /* 1) get R = Pd^T, Ro = Po^T */ 1503 /*----------------------------*/ 1504 ierr = MatTranspose_SeqAIJ(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1505 ierr = MatTranspose_SeqAIJ(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1506 1507 /* 2) compute numeric A_loc */ 1508 /*--------------------------*/ 1509 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1510 } 1511 1512 /* 3) C_loc = Rd*A_loc, C_oth = Ro*A_loc */ 1513 A_loc = ptap->A_loc; 1514 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,A_loc,ptap->C_loc);CHKERRQ(ierr); 1515 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,A_loc,ptap->C_oth);CHKERRQ(ierr); 1516 C_loc = ptap->C_loc; 1517 C_oth = ptap->C_oth; 1518 1519 /* add C_loc and Co to to C */ 1520 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1521 1522 /* C_loc -> C */ 1523 cm = C_loc->rmap->N; 1524 c_seq = (Mat_SeqAIJ*)C_loc->data; 1525 cols = c_seq->j; 1526 vals = c_seq->a; 1527 for (i=0; i<cm; i++) { 1528 ncols = c_seq->i[i+1] - c_seq->i[i]; 1529 row = rstart + i; 1530 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1531 cols += ncols; vals += ncols; 1532 } 1533 1534 /* Co -> C, off-processor part */ 1535 cm = C_oth->rmap->N; 1536 c_seq = (Mat_SeqAIJ*)C_oth->data; 1537 cols = c_seq->j; 1538 vals = c_seq->a; 1539 for (i=0; i<cm; i++) { 1540 ncols = c_seq->i[i+1] - c_seq->i[i]; 1541 row = p->garray[i]; 1542 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1543 cols += ncols; vals += ncols; 1544 } 1545 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1546 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1547 1548 ptap->reuse = MAT_REUSE_MATRIX; 1549 PetscFunctionReturn(0); 1550 } 1551 1552 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ(Mat P,Mat A,Mat C) 1553 { 1554 PetscErrorCode ierr; 1555 Mat_Merge_SeqsToMPI *merge; 1556 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1557 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1558 Mat_PtAPMPI *ptap; 1559 PetscInt *adj; 1560 PetscInt i,j,k,anz,pnz,row,*cj,nexta; 1561 MatScalar *ada,*ca,valtmp; 1562 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1563 MPI_Comm comm; 1564 PetscMPIInt size,rank,taga,*len_s; 1565 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1566 PetscInt **buf_ri,**buf_rj; 1567 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1568 MPI_Request *s_waits,*r_waits; 1569 MPI_Status *status; 1570 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1571 PetscInt *ai,*aj,*coi,*coj,*poJ,*pdJ; 1572 Mat A_loc; 1573 Mat_SeqAIJ *a_loc; 1574 1575 PetscFunctionBegin; 1576 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1577 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1578 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1579 1580 ptap = c->ptap; 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 Cmpi,A_loc,POt,PDt; 1717 Mat_PtAPMPI *ptap; 1718 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1719 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*a=(Mat_MPIAIJ*)A->data,*c; 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 PetscScalar *vals; 1737 Mat_SeqAIJ *a_loc,*pdt,*pot; 1738 PetscTable ta; 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_PtAPMPI 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 = PetscMalloc1(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 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1843 1844 proc = 0; 1845 for (i=0; i<pon; i++) { 1846 while (prmap[i] >= owners[proc+1]) proc++; 1847 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1848 len_s[proc] += coi[i+1] - coi[i]; 1849 } 1850 1851 len = 0; /* max length of buf_si[] */ 1852 owners_co[0] = 0; 1853 for (proc=0; proc<size; proc++) { 1854 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1855 if (len_si[proc]) { 1856 merge->nsend++; 1857 len_si[proc] = 2*(len_si[proc] + 1); 1858 len += len_si[proc]; 1859 } 1860 } 1861 1862 /* determine the number and length of messages to receive for coi and coj */ 1863 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1864 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1865 1866 /* post the Irecv and Isend of coj */ 1867 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1868 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1869 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 1870 for (proc=0, k=0; proc<size; proc++) { 1871 if (!len_s[proc]) continue; 1872 i = owners_co[proc]; 1873 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1874 k++; 1875 } 1876 1877 /* receives and sends of coj are complete */ 1878 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1879 for (i=0; i<merge->nrecv; i++) { 1880 PetscMPIInt icompleted; 1881 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1882 } 1883 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1884 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1885 1886 /* add received column indices into table to update Armax */ 1887 /* Armax can be as large as aN if a P[row,:] is dense, see src/ksp/ksp/examples/tutorials/ex56.c! */ 1888 for (k=0; k<merge->nrecv; k++) {/* k-th received message */ 1889 Jptr = buf_rj[k]; 1890 for (j=0; j<merge->len_r[k]; j++) { 1891 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1892 } 1893 } 1894 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1895 /* 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); */ 1896 1897 /* send and recv coi */ 1898 /*-------------------*/ 1899 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1900 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1901 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1902 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1903 for (proc=0,k=0; proc<size; proc++) { 1904 if (!len_s[proc]) continue; 1905 /* form outgoing message for i-structure: 1906 buf_si[0]: nrows to be sent 1907 [1:nrows]: row index (global) 1908 [nrows+1:2*nrows+1]: i-structure index 1909 */ 1910 /*-------------------------------------------*/ 1911 nrows = len_si[proc]/2 - 1; 1912 buf_si_i = buf_si + nrows+1; 1913 buf_si[0] = nrows; 1914 buf_si_i[0] = 0; 1915 nrows = 0; 1916 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1917 nzi = coi[i+1] - coi[i]; 1918 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1919 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1920 nrows++; 1921 } 1922 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1923 k++; 1924 buf_si += len_si[proc]; 1925 } 1926 i = merge->nrecv; 1927 while (i--) { 1928 PetscMPIInt icompleted; 1929 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1930 } 1931 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1932 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1933 ierr = PetscFree(len_si);CHKERRQ(ierr); 1934 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1935 ierr = PetscFree(swaits);CHKERRQ(ierr); 1936 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1937 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1938 1939 /* compute the local portion of C (mpi mat) */ 1940 /*------------------------------------------*/ 1941 /* allocate bi array and free space for accumulating nonzero column info */ 1942 ierr = PetscMalloc1(pn+1,&bi);CHKERRQ(ierr); 1943 bi[0] = 0; 1944 1945 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 1946 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pdti[pn],PetscIntSumTruncate(poti[pon],ai[am]))); 1947 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1948 current_space = free_space; 1949 1950 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1951 for (k=0; k<merge->nrecv; k++) { 1952 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1953 nrows = *buf_ri_k[k]; 1954 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1955 nextci[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th recieved i-structure */ 1956 } 1957 1958 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1959 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1960 rmax = 0; 1961 for (i=0; i<pn; i++) { 1962 /* add pdt[i,:]*AP into lnk */ 1963 pnz = pdti[i+1] - pdti[i]; 1964 ptJ = pdtj + pdti[i]; 1965 for (j=0; j<pnz; j++) { 1966 row = ptJ[j]; /* row of AP == col of Pt */ 1967 anz = ai[row+1] - ai[row]; 1968 Jptr = aj + ai[row]; 1969 /* add non-zero cols of AP into the sorted linked list lnk */ 1970 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1971 } 1972 1973 /* add received col data into lnk */ 1974 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1975 if (i == *nextrow[k]) { /* i-th row */ 1976 nzi = *(nextci[k]+1) - *nextci[k]; 1977 Jptr = buf_rj[k] + *nextci[k]; 1978 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 1979 nextrow[k]++; nextci[k]++; 1980 } 1981 } 1982 nnz = lnk[0]; 1983 1984 /* if free space is not available, make more free space */ 1985 if (current_space->local_remaining<nnz) { 1986 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1987 nspacedouble++; 1988 } 1989 /* copy data into free space, then initialize lnk */ 1990 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1991 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 1992 1993 current_space->array += nnz; 1994 current_space->local_used += nnz; 1995 current_space->local_remaining -= nnz; 1996 1997 bi[i+1] = bi[i] + nnz; 1998 if (nnz > rmax) rmax = nnz; 1999 } 2000 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 2001 2002 ierr = PetscMalloc1(bi[pn]+1,&bj);CHKERRQ(ierr); 2003 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 2004 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 2005 if (afill_tmp > afill) afill = afill_tmp; 2006 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 2007 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 2008 2009 ierr = MatDestroy(&POt);CHKERRQ(ierr); 2010 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 2011 2012 /* create symbolic parallel matrix Cmpi - why cannot be assembled in Numeric part */ 2013 /*----------------------------------------------------------------------------------*/ 2014 ierr = PetscCalloc1(rmax+1,&vals);CHKERRQ(ierr); 2015 2016 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 2017 ierr = MatSetSizes(Cmpi,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2018 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 2019 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 2020 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 2021 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 2022 ierr = MatSetBlockSize(Cmpi,1);CHKERRQ(ierr); 2023 for (i=0; i<pn; i++) { 2024 row = i + rstart; 2025 nnz = bi[i+1] - bi[i]; 2026 Jptr = bj + bi[i]; 2027 ierr = MatSetValues(Cmpi,1,&row,nnz,Jptr,vals,INSERT_VALUES);CHKERRQ(ierr); 2028 } 2029 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2030 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2031 ierr = PetscFree(vals);CHKERRQ(ierr); 2032 2033 merge->bi = bi; 2034 merge->bj = bj; 2035 merge->coi = coi; 2036 merge->coj = coj; 2037 merge->buf_ri = buf_ri; 2038 merge->buf_rj = buf_rj; 2039 merge->owners_co = owners_co; 2040 2041 /* attach the supporting struct to Cmpi for reuse */ 2042 c = (Mat_MPIAIJ*)Cmpi->data; 2043 2044 c->ptap = ptap; 2045 ptap->api = NULL; 2046 ptap->apj = NULL; 2047 ptap->merge = merge; 2048 ptap->apa = NULL; 2049 ptap->destroy = Cmpi->ops->destroy; 2050 ptap->duplicate = Cmpi->ops->duplicate; 2051 2052 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ; 2053 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 2054 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 2055 2056 *C = Cmpi; 2057 #if defined(PETSC_USE_INFO) 2058 if (bi[pn] != 0) { 2059 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 2060 ierr = PetscInfo1(Cmpi,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 2061 } else { 2062 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 2063 } 2064 #endif 2065 PetscFunctionReturn(0); 2066 } 2067