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 #undef __FUNCT__ 14 #define __FUNCT__ "MatMatMult_MPIAIJ_MPIAIJ" 15 PETSC_INTERN PetscErrorCode MatMatMult_MPIAIJ_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill, Mat *C) 16 { 17 PetscErrorCode ierr; 18 const char *algTypes[2] = {"scalable","nonscalable"}; 19 PetscInt alg=1; /* set default algorithm */ 20 MPI_Comm comm; 21 22 PetscFunctionBegin; 23 if (scall == MAT_INITIAL_MATRIX) { 24 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 25 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); 26 27 ierr = PetscObjectOptionsBegin((PetscObject)A);CHKERRQ(ierr); 28 ierr = PetscOptionsEList("-matmatmult_via","Algorithmic approach","MatMatMult",algTypes,2,algTypes[1],&alg,NULL);CHKERRQ(ierr); 29 ierr = PetscOptionsEnd();CHKERRQ(ierr); 30 31 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 32 switch (alg) { 33 case 1: 34 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(A,B,fill,C);CHKERRQ(ierr); 35 break; 36 default: 37 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 38 break; 39 } 40 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 41 } 42 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 43 ierr = (*(*C)->ops->matmultnumeric)(A,B,*C);CHKERRQ(ierr); 44 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 45 PetscFunctionReturn(0); 46 } 47 48 #undef __FUNCT__ 49 #define __FUNCT__ "MatDestroy_MPIAIJ_MatMatMult" 50 PetscErrorCode MatDestroy_MPIAIJ_MatMatMult(Mat A) 51 { 52 PetscErrorCode ierr; 53 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 54 Mat_PtAPMPI *ptap = a->ptap; 55 56 PetscFunctionBegin; 57 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 58 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 59 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 60 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 61 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 62 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 63 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 64 ierr = PetscFree(ptap->apa);CHKERRQ(ierr); 65 ierr = ptap->destroy(A);CHKERRQ(ierr); 66 ierr = PetscFree(ptap);CHKERRQ(ierr); 67 PetscFunctionReturn(0); 68 } 69 70 #undef __FUNCT__ 71 #define __FUNCT__ "MatDuplicate_MPIAIJ_MatMatMult" 72 PetscErrorCode MatDuplicate_MPIAIJ_MatMatMult(Mat A, MatDuplicateOption op, Mat *M) 73 { 74 PetscErrorCode ierr; 75 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 76 Mat_PtAPMPI *ptap = a->ptap; 77 78 PetscFunctionBegin; 79 ierr = (*ptap->duplicate)(A,op,M);CHKERRQ(ierr); 80 81 (*M)->ops->destroy = ptap->destroy; /* = MatDestroy_MPIAIJ, *M doesn't duplicate A's special structure! */ 82 (*M)->ops->duplicate = ptap->duplicate; /* = MatDuplicate_MPIAIJ */ 83 PetscFunctionReturn(0); 84 } 85 86 #undef __FUNCT__ 87 #define __FUNCT__ "MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable" 88 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,Mat C) 89 { 90 PetscErrorCode ierr; 91 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 92 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 93 Mat_SeqAIJ *cd =(Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 94 PetscScalar *cda=cd->a,*coa=co->a; 95 Mat_SeqAIJ *p_loc,*p_oth; 96 PetscScalar *apa,*ca; 97 PetscInt cm =C->rmap->n; 98 Mat_PtAPMPI *ptap=c->ptap; 99 PetscInt *api,*apj,*apJ,i,k; 100 PetscInt cstart=C->cmap->rstart; 101 PetscInt cdnz,conz,k0,k1; 102 MPI_Comm comm; 103 PetscMPIInt size; 104 105 PetscFunctionBegin; 106 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 107 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 108 109 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 110 /*-----------------------------------------------------*/ 111 /* update numerical values of P_oth and P_loc */ 112 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 113 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 114 115 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 116 /*----------------------------------------------------------*/ 117 /* get data from symbolic products */ 118 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 119 p_oth = NULL; 120 if (size >1) { 121 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 122 } 123 124 /* get apa for storing dense row A[i,:]*P */ 125 apa = ptap->apa; 126 127 api = ptap->api; 128 apj = ptap->apj; 129 for (i=0; i<cm; i++) { 130 /* compute apa = A[i,:]*P */ 131 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 132 133 /* set values in C */ 134 apJ = apj + api[i]; 135 cdnz = cd->i[i+1] - cd->i[i]; 136 conz = co->i[i+1] - co->i[i]; 137 138 /* 1st off-diagoanl part of C */ 139 ca = coa + co->i[i]; 140 k = 0; 141 for (k0=0; k0<conz; k0++) { 142 if (apJ[k] >= cstart) break; 143 ca[k0] = apa[apJ[k]]; 144 apa[apJ[k]] = 0.0; 145 k++; 146 } 147 148 /* diagonal part of C */ 149 ca = cda + cd->i[i]; 150 for (k1=0; k1<cdnz; k1++) { 151 ca[k1] = apa[apJ[k]]; 152 apa[apJ[k]] = 0.0; 153 k++; 154 } 155 156 /* 2nd off-diagoanl part of C */ 157 ca = coa + co->i[i]; 158 for (; k0<conz; k0++) { 159 ca[k0] = apa[apJ[k]]; 160 apa[apJ[k]] = 0.0; 161 k++; 162 } 163 } 164 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 165 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 166 PetscFunctionReturn(0); 167 } 168 169 #undef __FUNCT__ 170 #define __FUNCT__ "MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable" 171 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,PetscReal fill,Mat *C) 172 { 173 PetscErrorCode ierr; 174 MPI_Comm comm; 175 PetscMPIInt size; 176 Mat Cmpi; 177 Mat_PtAPMPI *ptap; 178 PetscFreeSpaceList free_space=NULL,current_space=NULL; 179 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c; 180 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 181 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 182 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 183 PetscInt *lnk,i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi; 184 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n,Crmax; 185 PetscBT lnkbt; 186 PetscScalar *apa; 187 PetscReal afill; 188 PetscTable ta; 189 190 PetscFunctionBegin; 191 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 192 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 193 194 /* create struct Mat_PtAPMPI and attached it to C later */ 195 ierr = PetscNew(&ptap);CHKERRQ(ierr); 196 197 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 198 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 199 200 /* get P_loc by taking all local rows of P */ 201 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 202 203 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 204 pi_loc = p_loc->i; pj_loc = p_loc->j; 205 if (size > 1) { 206 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 207 pi_oth = p_oth->i; pj_oth = p_oth->j; 208 } else { 209 p_oth = NULL; 210 pi_oth = NULL; pj_oth = NULL; 211 } 212 213 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 214 /*-------------------------------------------------------------------*/ 215 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 216 ptap->api = api; 217 api[0] = 0; 218 219 /* create and initialize a linked list */ 220 Crmax = 6*(p_loc->rmax + (PetscInt)(1.e-2*pN)); 221 if (Crmax > pN) Crmax = pN; 222 ierr = PetscTableCreate(Crmax,pN,&ta);CHKERRQ(ierr); 223 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 224 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 225 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 226 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 227 228 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 229 230 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 231 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 232 current_space = free_space; 233 234 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 235 for (i=0; i<am; i++) { 236 /* diagonal portion of A */ 237 nzi = adi[i+1] - adi[i]; 238 for (j=0; j<nzi; j++) { 239 row = *adj++; 240 pnz = pi_loc[row+1] - pi_loc[row]; 241 Jptr = pj_loc + pi_loc[row]; 242 /* add non-zero cols of P into the sorted linked list lnk */ 243 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 244 } 245 /* off-diagonal portion of A */ 246 nzi = aoi[i+1] - aoi[i]; 247 for (j=0; j<nzi; j++) { 248 row = *aoj++; 249 pnz = pi_oth[row+1] - pi_oth[row]; 250 Jptr = pj_oth + pi_oth[row]; 251 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 252 } 253 254 apnz = lnk[0]; 255 api[i+1] = api[i] + apnz; 256 257 /* if free space is not available, double the total space in the list */ 258 if (current_space->local_remaining<apnz) { 259 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 260 nspacedouble++; 261 } 262 263 /* Copy data into free space, then initialize lnk */ 264 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 265 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 266 267 current_space->array += apnz; 268 current_space->local_used += apnz; 269 current_space->local_remaining -= apnz; 270 } 271 272 /* Allocate space for apj, initialize apj, and */ 273 /* destroy list of free space and other temporary array(s) */ 274 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 275 apj = ptap->apj; 276 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 277 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 278 279 /* malloc apa to store dense row A[i,:]*P */ 280 ierr = PetscCalloc1(pN,&apa);CHKERRQ(ierr); 281 282 ptap->apa = apa; 283 284 /* create and assemble symbolic parallel matrix Cmpi */ 285 /*----------------------------------------------------*/ 286 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 287 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 288 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 289 290 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 291 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 292 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 293 for (i=0; i<am; i++) { 294 row = i + rstart; 295 apnz = api[i+1] - api[i]; 296 ierr = MatSetValues(Cmpi,1,&row,apnz,apj,apa,INSERT_VALUES);CHKERRQ(ierr); 297 apj += apnz; 298 } 299 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 300 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 301 302 ptap->destroy = Cmpi->ops->destroy; 303 ptap->duplicate = Cmpi->ops->duplicate; 304 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 305 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 306 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatMatMult; 307 308 /* attach the supporting struct to Cmpi for reuse */ 309 c = (Mat_MPIAIJ*)Cmpi->data; 310 c->ptap = ptap; 311 312 *C = Cmpi; 313 314 /* set MatInfo */ 315 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 316 if (afill < 1.0) afill = 1.0; 317 Cmpi->info.mallocs = nspacedouble; 318 Cmpi->info.fill_ratio_given = fill; 319 Cmpi->info.fill_ratio_needed = afill; 320 321 #if defined(PETSC_USE_INFO) 322 if (api[am]) { 323 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 324 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 325 } else { 326 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 327 } 328 #endif 329 PetscFunctionReturn(0); 330 } 331 332 #undef __FUNCT__ 333 #define __FUNCT__ "MatMatMult_MPIAIJ_MPIDense" 334 PETSC_INTERN PetscErrorCode MatMatMult_MPIAIJ_MPIDense(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 335 { 336 PetscErrorCode ierr; 337 338 PetscFunctionBegin; 339 if (scall == MAT_INITIAL_MATRIX) { 340 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 341 ierr = MatMatMultSymbolic_MPIAIJ_MPIDense(A,B,fill,C);CHKERRQ(ierr); 342 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 343 } 344 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 345 ierr = MatMatMultNumeric_MPIAIJ_MPIDense(A,B,*C);CHKERRQ(ierr); 346 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 347 PetscFunctionReturn(0); 348 } 349 350 typedef struct { 351 Mat workB; 352 PetscScalar *rvalues,*svalues; 353 MPI_Request *rwaits,*swaits; 354 } MPIAIJ_MPIDense; 355 356 #undef __FUNCT__ 357 #define __FUNCT__ "MatMPIAIJ_MPIDenseDestroy" 358 PetscErrorCode MatMPIAIJ_MPIDenseDestroy(void *ctx) 359 { 360 MPIAIJ_MPIDense *contents = (MPIAIJ_MPIDense*) ctx; 361 PetscErrorCode ierr; 362 363 PetscFunctionBegin; 364 ierr = MatDestroy(&contents->workB);CHKERRQ(ierr); 365 ierr = PetscFree4(contents->rvalues,contents->svalues,contents->rwaits,contents->swaits);CHKERRQ(ierr); 366 ierr = PetscFree(contents);CHKERRQ(ierr); 367 PetscFunctionReturn(0); 368 } 369 370 #undef __FUNCT__ 371 #define __FUNCT__ "MatMatMultNumeric_MPIDense" 372 /* 373 This is a "dummy function" that handles the case where matrix C was created as a dense matrix 374 directly by the user and passed to MatMatMult() with the MAT_REUSE_MATRIX option 375 376 It is the same as MatMatMultSymbolic_MPIAIJ_MPIDense() except does not create C 377 */ 378 PetscErrorCode MatMatMultNumeric_MPIDense(Mat A,Mat B,Mat C) 379 { 380 PetscErrorCode ierr; 381 PetscBool flg; 382 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) A->data; 383 PetscInt nz = aij->B->cmap->n; 384 PetscContainer container; 385 MPIAIJ_MPIDense *contents; 386 VecScatter ctx = aij->Mvctx; 387 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 388 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 389 390 PetscFunctionBegin; 391 ierr = PetscObjectTypeCompare((PetscObject)B,MATMPIDENSE,&flg);CHKERRQ(ierr); 392 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Second matrix must be mpidense"); 393 394 /* Handle case where where user provided the final C matrix rather than calling MatMatMult() with MAT_INITIAL_MATRIX*/ 395 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 396 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"First matrix must be MPIAIJ"); 397 398 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 399 400 ierr = PetscNew(&contents);CHKERRQ(ierr); 401 /* Create work matrix used to store off processor rows of B needed for local product */ 402 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,B->cmap->N,NULL,&contents->workB);CHKERRQ(ierr); 403 /* Create work arrays needed */ 404 ierr = PetscMalloc4(B->cmap->N*from->starts[from->n],&contents->rvalues, 405 B->cmap->N*to->starts[to->n],&contents->svalues, 406 from->n,&contents->rwaits, 407 to->n,&contents->swaits);CHKERRQ(ierr); 408 409 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)A),&container);CHKERRQ(ierr); 410 ierr = PetscContainerSetPointer(container,contents);CHKERRQ(ierr); 411 ierr = PetscContainerSetUserDestroy(container,MatMPIAIJ_MPIDenseDestroy);CHKERRQ(ierr); 412 ierr = PetscObjectCompose((PetscObject)C,"workB",(PetscObject)container);CHKERRQ(ierr); 413 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 414 415 ierr = (*C->ops->matmultnumeric)(A,B,C);CHKERRQ(ierr); 416 PetscFunctionReturn(0); 417 } 418 419 #undef __FUNCT__ 420 #define __FUNCT__ "MatMatMultSymbolic_MPIAIJ_MPIDense" 421 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat A,Mat B,PetscReal fill,Mat *C) 422 { 423 PetscErrorCode ierr; 424 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) A->data; 425 PetscInt nz = aij->B->cmap->n; 426 PetscContainer container; 427 MPIAIJ_MPIDense *contents; 428 VecScatter ctx = aij->Mvctx; 429 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 430 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 431 PetscInt m = A->rmap->n,n=B->cmap->n; 432 433 PetscFunctionBegin; 434 ierr = MatCreate(PetscObjectComm((PetscObject)B),C);CHKERRQ(ierr); 435 ierr = MatSetSizes(*C,m,n,A->rmap->N,B->cmap->N);CHKERRQ(ierr); 436 ierr = MatSetBlockSizesFromMats(*C,A,B);CHKERRQ(ierr); 437 ierr = MatSetType(*C,MATMPIDENSE);CHKERRQ(ierr); 438 ierr = MatMPIDenseSetPreallocation(*C,NULL);CHKERRQ(ierr); 439 ierr = MatAssemblyBegin(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 440 ierr = MatAssemblyEnd(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 441 442 (*C)->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 443 444 ierr = PetscNew(&contents);CHKERRQ(ierr); 445 /* Create work matrix used to store off processor rows of B needed for local product */ 446 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,B->cmap->N,NULL,&contents->workB);CHKERRQ(ierr); 447 /* Create work arrays needed */ 448 ierr = PetscMalloc4(B->cmap->N*from->starts[from->n],&contents->rvalues, 449 B->cmap->N*to->starts[to->n],&contents->svalues, 450 from->n,&contents->rwaits, 451 to->n,&contents->swaits);CHKERRQ(ierr); 452 453 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)A),&container);CHKERRQ(ierr); 454 ierr = PetscContainerSetPointer(container,contents);CHKERRQ(ierr); 455 ierr = PetscContainerSetUserDestroy(container,MatMPIAIJ_MPIDenseDestroy);CHKERRQ(ierr); 456 ierr = PetscObjectCompose((PetscObject)(*C),"workB",(PetscObject)container);CHKERRQ(ierr); 457 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 458 PetscFunctionReturn(0); 459 } 460 461 #undef __FUNCT__ 462 #define __FUNCT__ "MatMPIDenseScatter" 463 /* 464 Performs an efficient scatter on the rows of B needed by this process; this is 465 a modification of the VecScatterBegin_() routines. 466 */ 467 PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,Mat C,Mat *outworkB) 468 { 469 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 470 PetscErrorCode ierr; 471 PetscScalar *b,*w,*svalues,*rvalues; 472 VecScatter ctx = aij->Mvctx; 473 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 474 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 475 PetscInt i,j,k; 476 PetscInt *sindices,*sstarts,*rindices,*rstarts; 477 PetscMPIInt *sprocs,*rprocs,nrecvs; 478 MPI_Request *swaits,*rwaits; 479 MPI_Comm comm; 480 PetscMPIInt tag = ((PetscObject)ctx)->tag,ncols = B->cmap->N, nrows = aij->B->cmap->n,imdex,nrowsB = B->rmap->n; 481 MPI_Status status; 482 MPIAIJ_MPIDense *contents; 483 PetscContainer container; 484 Mat workB; 485 486 PetscFunctionBegin; 487 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 488 ierr = PetscObjectQuery((PetscObject)C,"workB",(PetscObject*)&container);CHKERRQ(ierr); 489 if (!container) SETERRQ(comm,PETSC_ERR_PLIB,"Container does not exist"); 490 ierr = PetscContainerGetPointer(container,(void**)&contents);CHKERRQ(ierr); 491 492 workB = *outworkB = contents->workB; 493 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); 494 sindices = to->indices; 495 sstarts = to->starts; 496 sprocs = to->procs; 497 swaits = contents->swaits; 498 svalues = contents->svalues; 499 500 rindices = from->indices; 501 rstarts = from->starts; 502 rprocs = from->procs; 503 rwaits = contents->rwaits; 504 rvalues = contents->rvalues; 505 506 ierr = MatDenseGetArray(B,&b);CHKERRQ(ierr); 507 ierr = MatDenseGetArray(workB,&w);CHKERRQ(ierr); 508 509 for (i=0; i<from->n; i++) { 510 ierr = MPI_Irecv(rvalues+ncols*rstarts[i],ncols*(rstarts[i+1]-rstarts[i]),MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 511 } 512 513 for (i=0; i<to->n; i++) { 514 /* pack a message at a time */ 515 for (j=0; j<sstarts[i+1]-sstarts[i]; j++) { 516 for (k=0; k<ncols; k++) { 517 svalues[ncols*(sstarts[i] + j) + k] = b[sindices[sstarts[i]+j] + nrowsB*k]; 518 } 519 } 520 ierr = MPI_Isend(svalues+ncols*sstarts[i],ncols*(sstarts[i+1]-sstarts[i]),MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 521 } 522 523 nrecvs = from->n; 524 while (nrecvs) { 525 ierr = MPI_Waitany(from->n,rwaits,&imdex,&status);CHKERRQ(ierr); 526 nrecvs--; 527 /* unpack a message at a time */ 528 for (j=0; j<rstarts[imdex+1]-rstarts[imdex]; j++) { 529 for (k=0; k<ncols; k++) { 530 w[rindices[rstarts[imdex]+j] + nrows*k] = rvalues[ncols*(rstarts[imdex] + j) + k]; 531 } 532 } 533 } 534 if (to->n) {ierr = MPI_Waitall(to->n,swaits,to->sstatus);CHKERRQ(ierr);} 535 536 ierr = MatDenseRestoreArray(B,&b);CHKERRQ(ierr); 537 ierr = MatDenseRestoreArray(workB,&w);CHKERRQ(ierr); 538 ierr = MatAssemblyBegin(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 539 ierr = MatAssemblyEnd(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 540 PetscFunctionReturn(0); 541 } 542 extern PetscErrorCode MatMatMultNumericAdd_SeqAIJ_SeqDense(Mat,Mat,Mat); 543 544 #undef __FUNCT__ 545 #define __FUNCT__ "MatMatMultNumeric_MPIAIJ_MPIDense" 546 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat A,Mat B,Mat C) 547 { 548 PetscErrorCode ierr; 549 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 550 Mat_MPIDense *bdense = (Mat_MPIDense*)B->data; 551 Mat_MPIDense *cdense = (Mat_MPIDense*)C->data; 552 Mat workB; 553 554 PetscFunctionBegin; 555 /* diagonal block of A times all local rows of B*/ 556 ierr = MatMatMultNumeric_SeqAIJ_SeqDense(aij->A,bdense->A,cdense->A);CHKERRQ(ierr); 557 558 /* get off processor parts of B needed to complete the product */ 559 ierr = MatMPIDenseScatter(A,B,C,&workB);CHKERRQ(ierr); 560 561 /* off-diagonal block of A times nonlocal rows of B */ 562 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A);CHKERRQ(ierr); 563 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 564 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 565 PetscFunctionReturn(0); 566 } 567 568 #undef __FUNCT__ 569 #define __FUNCT__ "MatMatMultNumeric_MPIAIJ_MPIAIJ" 570 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 571 { 572 PetscErrorCode ierr; 573 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 574 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 575 Mat_SeqAIJ *cd = (Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 576 PetscInt *adi = ad->i,*adj,*aoi=ao->i,*aoj; 577 PetscScalar *ada,*aoa,*cda=cd->a,*coa=co->a; 578 Mat_SeqAIJ *p_loc,*p_oth; 579 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pj; 580 PetscScalar *pa_loc,*pa_oth,*pa,valtmp,*ca; 581 PetscInt cm = C->rmap->n,anz,pnz; 582 Mat_PtAPMPI *ptap = c->ptap; 583 PetscScalar *apa_sparse = ptap->apa; 584 PetscInt *api,*apj,*apJ,i,j,k,row; 585 PetscInt cstart = C->cmap->rstart; 586 PetscInt cdnz,conz,k0,k1,nextp; 587 MPI_Comm comm; 588 PetscMPIInt size; 589 590 PetscFunctionBegin; 591 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 592 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 593 594 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 595 /*-----------------------------------------------------*/ 596 /* update numerical values of P_oth and P_loc */ 597 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 598 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 599 600 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 601 /*----------------------------------------------------------*/ 602 /* get data from symbolic products */ 603 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 604 pi_loc = p_loc->i; pj_loc = p_loc->j; pa_loc = p_loc->a; 605 if (size >1) { 606 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 607 pi_oth = p_oth->i; pj_oth = p_oth->j; pa_oth = p_oth->a; 608 } else { 609 p_oth = NULL; pi_oth = NULL; pj_oth = NULL; pa_oth = NULL; 610 } 611 612 api = ptap->api; 613 apj = ptap->apj; 614 for (i=0; i<cm; i++) { 615 apJ = apj + api[i]; 616 617 /* diagonal portion of A */ 618 anz = adi[i+1] - adi[i]; 619 adj = ad->j + adi[i]; 620 ada = ad->a + adi[i]; 621 for (j=0; j<anz; j++) { 622 row = adj[j]; 623 pnz = pi_loc[row+1] - pi_loc[row]; 624 pj = pj_loc + pi_loc[row]; 625 pa = pa_loc + pi_loc[row]; 626 /* perform sparse axpy */ 627 valtmp = ada[j]; 628 nextp = 0; 629 for (k=0; nextp<pnz; k++) { 630 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 631 apa_sparse[k] += valtmp*pa[nextp++]; 632 } 633 } 634 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 635 } 636 637 /* off-diagonal portion of A */ 638 anz = aoi[i+1] - aoi[i]; 639 aoj = ao->j + aoi[i]; 640 aoa = ao->a + aoi[i]; 641 for (j=0; j<anz; j++) { 642 row = aoj[j]; 643 pnz = pi_oth[row+1] - pi_oth[row]; 644 pj = pj_oth + pi_oth[row]; 645 pa = pa_oth + pi_oth[row]; 646 /* perform sparse axpy */ 647 valtmp = aoa[j]; 648 nextp = 0; 649 for (k=0; nextp<pnz; k++) { 650 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 651 apa_sparse[k] += valtmp*pa[nextp++]; 652 } 653 } 654 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 655 } 656 657 /* set values in C */ 658 cdnz = cd->i[i+1] - cd->i[i]; 659 conz = co->i[i+1] - co->i[i]; 660 661 /* 1st off-diagoanl part of C */ 662 ca = coa + co->i[i]; 663 k = 0; 664 for (k0=0; k0<conz; k0++) { 665 if (apJ[k] >= cstart) break; 666 ca[k0] = apa_sparse[k]; 667 apa_sparse[k] = 0.0; 668 k++; 669 } 670 671 /* diagonal part of C */ 672 ca = cda + cd->i[i]; 673 for (k1=0; k1<cdnz; k1++) { 674 ca[k1] = apa_sparse[k]; 675 apa_sparse[k] = 0.0; 676 k++; 677 } 678 679 /* 2nd off-diagoanl part of C */ 680 ca = coa + co->i[i]; 681 for (; k0<conz; k0++) { 682 ca[k0] = apa_sparse[k]; 683 apa_sparse[k] = 0.0; 684 k++; 685 } 686 } 687 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 688 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 689 PetscFunctionReturn(0); 690 } 691 692 /* same as MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(), except using LLCondensed to avoid O(BN) memory requirement */ 693 #undef __FUNCT__ 694 #define __FUNCT__ "MatMatMultSymbolic_MPIAIJ_MPIAIJ" 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 apnz_max = 6*(p_loc->rmax + (PetscInt)(1.e-2*pN)); /* expected apnz_max */ 744 if (apnz_max > pN) apnz_max = pN; 745 ierr = PetscTableCreate(apnz_max,pN,&ta);CHKERRQ(ierr); 746 747 /* Calculate apnz_max */ 748 apnz_max = 0; 749 for (i=0; i<am; i++) { 750 ierr = PetscTableRemoveAll(ta);CHKERRQ(ierr); 751 /* diagonal portion of A */ 752 nzi = adi[i+1] - adi[i]; 753 Jptr = adj+adi[i]; /* cols of A_diag */ 754 MatMergeRows_SeqAIJ(p_loc,nzi,Jptr,ta); 755 ierr = PetscTableGetCount(ta,&apnz);CHKERRQ(ierr); 756 if (apnz_max < apnz) apnz_max = apnz; 757 758 /* off-diagonal portion of A */ 759 nzi = aoi[i+1] - aoi[i]; 760 Jptr = aoj+aoi[i]; /* cols of A_off */ 761 MatMergeRows_SeqAIJ(p_oth,nzi,Jptr,ta); 762 ierr = PetscTableGetCount(ta,&apnz);CHKERRQ(ierr); 763 if (apnz_max < apnz) apnz_max = apnz; 764 } 765 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 766 767 ierr = PetscLLCondensedCreate_Scalable(apnz_max,&lnk);CHKERRQ(ierr); 768 769 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 770 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 771 current_space = free_space; 772 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 773 for (i=0; i<am; i++) { 774 /* diagonal portion of A */ 775 nzi = adi[i+1] - adi[i]; 776 for (j=0; j<nzi; j++) { 777 row = *adj++; 778 pnz = pi_loc[row+1] - pi_loc[row]; 779 Jptr = pj_loc + pi_loc[row]; 780 /* add non-zero cols of P into the sorted linked list lnk */ 781 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 782 } 783 /* off-diagonal portion of A */ 784 nzi = aoi[i+1] - aoi[i]; 785 for (j=0; j<nzi; j++) { 786 row = *aoj++; 787 pnz = pi_oth[row+1] - pi_oth[row]; 788 Jptr = pj_oth + pi_oth[row]; 789 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 790 } 791 792 apnz = *lnk; 793 api[i+1] = api[i] + apnz; 794 795 /* if free space is not available, double the total space in the list */ 796 if (current_space->local_remaining<apnz) { 797 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 798 nspacedouble++; 799 } 800 801 /* Copy data into free space, then initialize lnk */ 802 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 803 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 804 805 current_space->array += apnz; 806 current_space->local_used += apnz; 807 current_space->local_remaining -= apnz; 808 } 809 810 /* Allocate space for apj, initialize apj, and */ 811 /* destroy list of free space and other temporary array(s) */ 812 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 813 apj = ptap->apj; 814 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 815 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 816 817 /* create and assemble symbolic parallel matrix Cmpi */ 818 /*----------------------------------------------------*/ 819 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 820 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 821 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 822 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 823 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 824 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 825 826 /* malloc apa for assembly Cmpi */ 827 ierr = PetscCalloc1(apnz_max,&apa);CHKERRQ(ierr); 828 829 ptap->apa = apa; 830 for (i=0; i<am; i++) { 831 row = i + rstart; 832 apnz = api[i+1] - api[i]; 833 ierr = MatSetValues(Cmpi,1,&row,apnz,apj,apa,INSERT_VALUES);CHKERRQ(ierr); 834 apj += apnz; 835 } 836 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 837 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 838 839 ptap->destroy = Cmpi->ops->destroy; 840 ptap->duplicate = Cmpi->ops->duplicate; 841 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ; 842 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 843 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatMatMult; 844 845 /* attach the supporting struct to Cmpi for reuse */ 846 c = (Mat_MPIAIJ*)Cmpi->data; 847 c->ptap = ptap; 848 849 *C = Cmpi; 850 851 /* set MatInfo */ 852 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 853 if (afill < 1.0) afill = 1.0; 854 Cmpi->info.mallocs = nspacedouble; 855 Cmpi->info.fill_ratio_given = fill; 856 Cmpi->info.fill_ratio_needed = afill; 857 858 #if defined(PETSC_USE_INFO) 859 if (api[am]) { 860 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 861 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 862 } else { 863 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 864 } 865 #endif 866 PetscFunctionReturn(0); 867 } 868 869 /*-------------------------------------------------------------------------*/ 870 #undef __FUNCT__ 871 #define __FUNCT__ "MatTransposeMatMult_MPIAIJ_MPIAIJ" 872 PetscErrorCode MatTransposeMatMult_MPIAIJ_MPIAIJ(Mat P,Mat A,MatReuse scall,PetscReal fill,Mat *C) 873 { 874 PetscErrorCode ierr; 875 const char *algTypes[3] = {"scalable","nonscalable","matmatmult"}; 876 PetscInt alg=0; /* set default algorithm */ 877 878 PetscFunctionBegin; 879 if (scall == MAT_INITIAL_MATRIX) { 880 ierr = PetscObjectOptionsBegin((PetscObject)A);CHKERRQ(ierr); 881 ierr = PetscOptionsEList("-mattransposematmult_via","Algorithmic approach","MatTransposeMatMult",algTypes,3,algTypes[0],&alg,NULL);CHKERRQ(ierr); 882 ierr = PetscOptionsEnd();CHKERRQ(ierr); 883 884 ierr = PetscLogEventBegin(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 885 switch (alg) { 886 case 1: 887 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(P,A,fill,C);CHKERRQ(ierr); 888 break; 889 case 2: 890 { 891 Mat Pt; 892 Mat_PtAPMPI *ptap; 893 Mat_MPIAIJ *c; 894 ierr = MatTranspose(P,MAT_INITIAL_MATRIX,&Pt);CHKERRQ(ierr); 895 ierr = MatMatMult(Pt,A,MAT_INITIAL_MATRIX,fill,C);CHKERRQ(ierr); 896 c = (Mat_MPIAIJ*)(*C)->data; 897 ptap = c->ptap; 898 ptap->Pt = Pt; 899 (*C)->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult; 900 PetscFunctionReturn(0); 901 } 902 break; 903 default: 904 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(P,A,fill,C);CHKERRQ(ierr); 905 break; 906 } 907 ierr = PetscLogEventEnd(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 908 } 909 ierr = PetscLogEventBegin(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 910 ierr = (*(*C)->ops->mattransposemultnumeric)(P,A,*C);CHKERRQ(ierr); 911 ierr = PetscLogEventEnd(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 912 PetscFunctionReturn(0); 913 } 914 915 /* This routine only works when scall=MAT_REUSE_MATRIX! */ 916 #undef __FUNCT__ 917 #define __FUNCT__ "MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult" 918 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult(Mat P,Mat A,Mat C) 919 { 920 PetscErrorCode ierr; 921 Mat_MPIAIJ *c=(Mat_MPIAIJ*)C->data; 922 Mat_PtAPMPI *ptap= c->ptap; 923 Mat Pt=ptap->Pt; 924 925 PetscFunctionBegin; 926 ierr = MatTranspose(P,MAT_REUSE_MATRIX,&Pt);CHKERRQ(ierr); 927 ierr = MatMatMultNumeric(Pt,A,C);CHKERRQ(ierr); 928 PetscFunctionReturn(0); 929 } 930 931 /* Non-scalable version, use dense axpy */ 932 #undef __FUNCT__ 933 #define __FUNCT__ "MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable" 934 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,Mat C) 935 { 936 PetscErrorCode ierr; 937 Mat_Merge_SeqsToMPI *merge; 938 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 939 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 940 Mat_PtAPMPI *ptap; 941 PetscInt *adj,*aJ; 942 PetscInt i,j,k,anz,pnz,row,*cj; 943 MatScalar *ada,*aval,*ca,valtmp; 944 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 945 MPI_Comm comm; 946 PetscMPIInt size,rank,taga,*len_s; 947 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 948 PetscInt **buf_ri,**buf_rj; 949 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 950 MPI_Request *s_waits,*r_waits; 951 MPI_Status *status; 952 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 953 PetscInt *ai,*aj,*coi,*coj; 954 PetscInt *poJ,*pdJ; 955 Mat A_loc; 956 Mat_SeqAIJ *a_loc; 957 958 PetscFunctionBegin; 959 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 960 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 961 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 962 963 ptap = c->ptap; 964 merge = ptap->merge; 965 966 /* 2) compute numeric C_seq = P_loc^T*A_loc*P - dominating part */ 967 /*--------------------------------------------------------------*/ 968 /* get data from symbolic products */ 969 coi = merge->coi; coj = merge->coj; 970 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 971 972 bi = merge->bi; bj = merge->bj; 973 owners = merge->rowmap->range; 974 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); 975 976 /* get A_loc by taking all local rows of A */ 977 A_loc = ptap->A_loc; 978 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 979 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 980 ai = a_loc->i; 981 aj = a_loc->j; 982 983 ierr = PetscCalloc1(A->cmap->N,&aval);CHKERRQ(ierr); /* non-scalable!!! */ 984 985 for (i=0; i<am; i++) { 986 /* 2-a) put A[i,:] to dense array aval */ 987 anz = ai[i+1] - ai[i]; 988 adj = aj + ai[i]; 989 ada = a_loc->a + ai[i]; 990 for (j=0; j<anz; j++) { 991 aval[adj[j]] = ada[j]; 992 } 993 994 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 995 /*--------------------------------------------------------------*/ 996 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 997 pnz = po->i[i+1] - po->i[i]; 998 poJ = po->j + po->i[i]; 999 pA = po->a + po->i[i]; 1000 for (j=0; j<pnz; j++) { 1001 row = poJ[j]; 1002 cnz = coi[row+1] - coi[row]; 1003 cj = coj + coi[row]; 1004 ca = coa + coi[row]; 1005 /* perform dense axpy */ 1006 valtmp = pA[j]; 1007 for (k=0; k<cnz; k++) { 1008 ca[k] += valtmp*aval[cj[k]]; 1009 } 1010 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1011 } 1012 1013 /* put the value into Cd (diagonal part) */ 1014 pnz = pd->i[i+1] - pd->i[i]; 1015 pdJ = pd->j + pd->i[i]; 1016 pA = pd->a + pd->i[i]; 1017 for (j=0; j<pnz; j++) { 1018 row = pdJ[j]; 1019 cnz = bi[row+1] - bi[row]; 1020 cj = bj + bi[row]; 1021 ca = ba + bi[row]; 1022 /* perform dense axpy */ 1023 valtmp = pA[j]; 1024 for (k=0; k<cnz; k++) { 1025 ca[k] += valtmp*aval[cj[k]]; 1026 } 1027 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1028 } 1029 1030 /* zero the current row of Pt*A */ 1031 aJ = aj + ai[i]; 1032 for (k=0; k<anz; k++) aval[aJ[k]] = 0.0; 1033 } 1034 1035 /* 3) send and recv matrix values coa */ 1036 /*------------------------------------*/ 1037 buf_ri = merge->buf_ri; 1038 buf_rj = merge->buf_rj; 1039 len_s = merge->len_s; 1040 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1041 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1042 1043 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1044 for (proc=0,k=0; proc<size; proc++) { 1045 if (!len_s[proc]) continue; 1046 i = merge->owners_co[proc]; 1047 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1048 k++; 1049 } 1050 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1051 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1052 1053 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1054 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1055 ierr = PetscFree(coa);CHKERRQ(ierr); 1056 1057 /* 4) insert local Cseq and received values into Cmpi */ 1058 /*----------------------------------------------------*/ 1059 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1060 for (k=0; k<merge->nrecv; k++) { 1061 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1062 nrows = *(buf_ri_k[k]); 1063 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1064 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1065 } 1066 1067 for (i=0; i<cm; i++) { 1068 row = owners[rank] + i; /* global row index of C_seq */ 1069 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1070 ba_i = ba + bi[i]; 1071 bnz = bi[i+1] - bi[i]; 1072 /* add received vals into ba */ 1073 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1074 /* i-th row */ 1075 if (i == *nextrow[k]) { 1076 cnz = *(nextci[k]+1) - *nextci[k]; 1077 cj = buf_rj[k] + *(nextci[k]); 1078 ca = abuf_r[k] + *(nextci[k]); 1079 nextcj = 0; 1080 for (j=0; nextcj<cnz; j++) { 1081 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1082 ba_i[j] += ca[nextcj++]; 1083 } 1084 } 1085 nextrow[k]++; nextci[k]++; 1086 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1087 } 1088 } 1089 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1090 } 1091 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1092 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1093 1094 ierr = PetscFree(ba);CHKERRQ(ierr); 1095 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1096 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1097 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1098 ierr = PetscFree(aval);CHKERRQ(ierr); 1099 PetscFunctionReturn(0); 1100 } 1101 1102 PetscErrorCode MatDuplicate_MPIAIJ_MatPtAP(Mat, MatDuplicateOption,Mat*); 1103 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ() */ 1104 #undef __FUNCT__ 1105 #define __FUNCT__ "MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable" 1106 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,PetscReal fill,Mat *C) 1107 { 1108 PetscErrorCode ierr; 1109 Mat Cmpi,A_loc,POt,PDt; 1110 Mat_PtAPMPI *ptap; 1111 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1112 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c; 1113 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1114 PetscInt nnz; 1115 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1116 PetscInt am=A->rmap->n,pn=P->cmap->n; 1117 PetscBT lnkbt; 1118 MPI_Comm comm; 1119 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1120 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1121 PetscInt len,proc,*dnz,*onz,*owners; 1122 PetscInt nzi,*bi,*bj; 1123 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1124 MPI_Request *swaits,*rwaits; 1125 MPI_Status *sstatus,rstatus; 1126 Mat_Merge_SeqsToMPI *merge; 1127 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1128 PetscReal afill =1.0,afill_tmp; 1129 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N; 1130 PetscScalar *vals; 1131 Mat_SeqAIJ *a_loc, *pdt,*pot; 1132 1133 PetscFunctionBegin; 1134 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1135 /* check if matrix local sizes are compatible */ 1136 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); 1137 1138 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1139 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1140 1141 /* create struct Mat_PtAPMPI and attached it to C later */ 1142 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1143 1144 /* get A_loc by taking all local rows of A */ 1145 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1146 1147 ptap->A_loc = A_loc; 1148 1149 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1150 ai = a_loc->i; 1151 aj = a_loc->j; 1152 1153 /* determine symbolic Co=(p->B)^T*A - send to others */ 1154 /*----------------------------------------------------*/ 1155 ierr = MatTransposeSymbolic_SeqAIJ(p->A,&PDt);CHKERRQ(ierr); 1156 pdt = (Mat_SeqAIJ*)PDt->data; 1157 pdti = pdt->i; pdtj = pdt->j; 1158 1159 ierr = MatTransposeSymbolic_SeqAIJ(p->B,&POt);CHKERRQ(ierr); 1160 pot = (Mat_SeqAIJ*)POt->data; 1161 poti = pot->i; potj = pot->j; 1162 1163 /* then, compute symbolic Co = (p->B)^T*A */ 1164 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors >= (num of nonzero rows of C_seq) - pn */ 1165 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 1166 coi[0] = 0; 1167 1168 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1169 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],ai[am])); 1170 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1171 current_space = free_space; 1172 1173 /* create and initialize a linked list */ 1174 ierr = PetscLLCondensedCreate(aN,aN,&lnk,&lnkbt);CHKERRQ(ierr); 1175 1176 for (i=0; i<pon; i++) { 1177 pnz = poti[i+1] - poti[i]; 1178 ptJ = potj + poti[i]; 1179 for (j=0; j<pnz; j++) { 1180 row = ptJ[j]; /* row of A_loc == col of Pot */ 1181 anz = ai[row+1] - ai[row]; 1182 Jptr = aj + ai[row]; 1183 /* add non-zero cols of AP into the sorted linked list lnk */ 1184 ierr = PetscLLCondensedAddSorted(anz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1185 } 1186 nnz = lnk[0]; 1187 1188 /* If free space is not available, double the total space in the list */ 1189 if (current_space->local_remaining<nnz) { 1190 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1191 nspacedouble++; 1192 } 1193 1194 /* Copy data into free space, and zero out denserows */ 1195 ierr = PetscLLCondensedClean(aN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1196 1197 current_space->array += nnz; 1198 current_space->local_used += nnz; 1199 current_space->local_remaining -= nnz; 1200 1201 coi[i+1] = coi[i] + nnz; 1202 } 1203 1204 ierr = PetscMalloc1(coi[pon]+1,&coj);CHKERRQ(ierr); 1205 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 1206 1207 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 1208 if (afill_tmp > afill) afill = afill_tmp; 1209 1210 /* send j-array (coj) of Co to other processors */ 1211 /*----------------------------------------------*/ 1212 /* determine row ownership */ 1213 ierr = PetscNew(&merge);CHKERRQ(ierr); 1214 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 1215 1216 merge->rowmap->n = pn; 1217 merge->rowmap->bs = 1; 1218 1219 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 1220 owners = merge->rowmap->range; 1221 1222 /* determine the number of messages to send, their lengths */ 1223 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 1224 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 1225 1226 len_s = merge->len_s; 1227 merge->nsend = 0; 1228 1229 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 1230 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1231 1232 proc = 0; 1233 for (i=0; i<pon; i++) { 1234 while (prmap[i] >= owners[proc+1]) proc++; 1235 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1236 len_s[proc] += coi[i+1] - coi[i]; 1237 } 1238 1239 len = 0; /* max length of buf_si[] */ 1240 owners_co[0] = 0; 1241 for (proc=0; proc<size; proc++) { 1242 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1243 if (len_si[proc]) { 1244 merge->nsend++; 1245 len_si[proc] = 2*(len_si[proc] + 1); 1246 len += len_si[proc]; 1247 } 1248 } 1249 1250 /* determine the number and length of messages to receive for coi and coj */ 1251 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1252 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1253 1254 /* post the Irecv and Isend of coj */ 1255 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1256 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1257 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 1258 for (proc=0, k=0; proc<size; proc++) { 1259 if (!len_s[proc]) continue; 1260 i = owners_co[proc]; 1261 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1262 k++; 1263 } 1264 1265 /* receives and sends of coj are complete */ 1266 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1267 for (i=0; i<merge->nrecv; i++) { 1268 PetscMPIInt icompleted; 1269 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1270 } 1271 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1272 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1273 1274 /* send and recv coi */ 1275 /*-------------------*/ 1276 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1277 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1278 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1279 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1280 for (proc=0,k=0; proc<size; proc++) { 1281 if (!len_s[proc]) continue; 1282 /* form outgoing message for i-structure: 1283 buf_si[0]: nrows to be sent 1284 [1:nrows]: row index (global) 1285 [nrows+1:2*nrows+1]: i-structure index 1286 */ 1287 /*-------------------------------------------*/ 1288 nrows = len_si[proc]/2 - 1; 1289 buf_si_i = buf_si + nrows+1; 1290 buf_si[0] = nrows; 1291 buf_si_i[0] = 0; 1292 nrows = 0; 1293 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1294 nzi = coi[i+1] - coi[i]; 1295 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1296 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1297 nrows++; 1298 } 1299 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1300 k++; 1301 buf_si += len_si[proc]; 1302 } 1303 i = merge->nrecv; 1304 while (i--) { 1305 PetscMPIInt icompleted; 1306 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1307 } 1308 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1309 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1310 ierr = PetscFree(len_si);CHKERRQ(ierr); 1311 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1312 ierr = PetscFree(swaits);CHKERRQ(ierr); 1313 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1314 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1315 1316 /* compute the local portion of C (mpi mat) */ 1317 /*------------------------------------------*/ 1318 /* allocate bi array and free space for accumulating nonzero column info */ 1319 ierr = PetscMalloc1(pn+1,&bi);CHKERRQ(ierr); 1320 bi[0] = 0; 1321 1322 /* set initial free space to be fill*(nnz(P) + nnz(A)) */ 1323 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pdti[pn],PetscIntSumTruncate(poti[pon],ai[am]))); 1324 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1325 current_space = free_space; 1326 1327 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1328 for (k=0; k<merge->nrecv; k++) { 1329 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1330 nrows = *buf_ri_k[k]; 1331 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1332 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1333 } 1334 1335 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1336 rmax = 0; 1337 for (i=0; i<pn; i++) { 1338 /* add pdt[i,:]*AP into lnk */ 1339 pnz = pdti[i+1] - pdti[i]; 1340 ptJ = pdtj + pdti[i]; 1341 for (j=0; j<pnz; j++) { 1342 row = ptJ[j]; /* row of AP == col of Pt */ 1343 anz = ai[row+1] - ai[row]; 1344 Jptr = aj + ai[row]; 1345 /* add non-zero cols of AP into the sorted linked list lnk */ 1346 ierr = PetscLLCondensedAddSorted(anz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1347 } 1348 1349 /* add received col data into lnk */ 1350 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1351 if (i == *nextrow[k]) { /* i-th row */ 1352 nzi = *(nextci[k]+1) - *nextci[k]; 1353 Jptr = buf_rj[k] + *nextci[k]; 1354 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1355 nextrow[k]++; nextci[k]++; 1356 } 1357 } 1358 nnz = lnk[0]; 1359 1360 /* if free space is not available, make more free space */ 1361 if (current_space->local_remaining<nnz) { 1362 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1363 nspacedouble++; 1364 } 1365 /* copy data into free space, then initialize lnk */ 1366 ierr = PetscLLCondensedClean(aN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1367 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 1368 1369 current_space->array += nnz; 1370 current_space->local_used += nnz; 1371 current_space->local_remaining -= nnz; 1372 1373 bi[i+1] = bi[i] + nnz; 1374 if (nnz > rmax) rmax = nnz; 1375 } 1376 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1377 1378 ierr = PetscMalloc1(bi[pn]+1,&bj);CHKERRQ(ierr); 1379 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 1380 1381 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 1382 if (afill_tmp > afill) afill = afill_tmp; 1383 ierr = PetscLLCondensedDestroy(lnk,lnkbt);CHKERRQ(ierr); 1384 ierr = MatDestroy(&POt);CHKERRQ(ierr); 1385 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 1386 1387 /* create symbolic parallel matrix Cmpi - why cannot be assembled in Numeric part */ 1388 /*----------------------------------------------------------------------------------*/ 1389 ierr = PetscCalloc1(rmax+1,&vals);CHKERRQ(ierr); 1390 1391 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1392 ierr = MatSetSizes(Cmpi,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1393 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 1394 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 1395 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1396 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1397 ierr = MatSetBlockSize(Cmpi,1);CHKERRQ(ierr); 1398 for (i=0; i<pn; i++) { 1399 row = i + rstart; 1400 nnz = bi[i+1] - bi[i]; 1401 Jptr = bj + bi[i]; 1402 ierr = MatSetValues(Cmpi,1,&row,nnz,Jptr,vals,INSERT_VALUES);CHKERRQ(ierr); 1403 } 1404 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1405 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1406 ierr = PetscFree(vals);CHKERRQ(ierr); 1407 1408 merge->bi = bi; 1409 merge->bj = bj; 1410 merge->coi = coi; 1411 merge->coj = coj; 1412 merge->buf_ri = buf_ri; 1413 merge->buf_rj = buf_rj; 1414 merge->owners_co = owners_co; 1415 merge->destroy = Cmpi->ops->destroy; 1416 merge->duplicate = Cmpi->ops->duplicate; 1417 1418 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1419 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1420 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 1421 1422 /* attach the supporting struct to Cmpi for reuse */ 1423 c = (Mat_MPIAIJ*)Cmpi->data; 1424 c->ptap = ptap; 1425 ptap->api = NULL; 1426 ptap->apj = NULL; 1427 ptap->merge = merge; 1428 1429 *C = Cmpi; 1430 #if defined(PETSC_USE_INFO) 1431 if (bi[pn] != 0) { 1432 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1433 ierr = PetscInfo1(Cmpi,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 1434 } else { 1435 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1436 } 1437 #endif 1438 PetscFunctionReturn(0); 1439 } 1440 1441 #undef __FUNCT__ 1442 #define __FUNCT__ "MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ" 1443 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ(Mat P,Mat A,Mat C) 1444 { 1445 PetscErrorCode ierr; 1446 Mat_Merge_SeqsToMPI *merge; 1447 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1448 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1449 Mat_PtAPMPI *ptap; 1450 PetscInt *adj; 1451 PetscInt i,j,k,anz,pnz,row,*cj,nexta; 1452 MatScalar *ada,*ca,valtmp; 1453 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1454 MPI_Comm comm; 1455 PetscMPIInt size,rank,taga,*len_s; 1456 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1457 PetscInt **buf_ri,**buf_rj; 1458 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1459 MPI_Request *s_waits,*r_waits; 1460 MPI_Status *status; 1461 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1462 PetscInt *ai,*aj,*coi,*coj; 1463 PetscInt *poJ,*pdJ; 1464 Mat A_loc; 1465 Mat_SeqAIJ *a_loc; 1466 1467 PetscFunctionBegin; 1468 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1469 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1470 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1471 1472 ptap = c->ptap; 1473 merge = ptap->merge; 1474 1475 /* 2) compute numeric C_seq = P_loc^T*A_loc */ 1476 /*------------------------------------------*/ 1477 /* get data from symbolic products */ 1478 coi = merge->coi; coj = merge->coj; 1479 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 1480 bi = merge->bi; bj = merge->bj; 1481 owners = merge->rowmap->range; 1482 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); 1483 1484 /* get A_loc by taking all local rows of A */ 1485 A_loc = ptap->A_loc; 1486 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 1487 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1488 ai = a_loc->i; 1489 aj = a_loc->j; 1490 1491 for (i=0; i<am; i++) { 1492 anz = ai[i+1] - ai[i]; 1493 adj = aj + ai[i]; 1494 ada = a_loc->a + ai[i]; 1495 1496 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 1497 /*-------------------------------------------------------------*/ 1498 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 1499 pnz = po->i[i+1] - po->i[i]; 1500 poJ = po->j + po->i[i]; 1501 pA = po->a + po->i[i]; 1502 for (j=0; j<pnz; j++) { 1503 row = poJ[j]; 1504 cj = coj + coi[row]; 1505 ca = coa + coi[row]; 1506 /* perform sparse axpy */ 1507 nexta = 0; 1508 valtmp = pA[j]; 1509 for (k=0; nexta<anz; k++) { 1510 if (cj[k] == adj[nexta]) { 1511 ca[k] += valtmp*ada[nexta]; 1512 nexta++; 1513 } 1514 } 1515 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1516 } 1517 1518 /* put the value into Cd (diagonal part) */ 1519 pnz = pd->i[i+1] - pd->i[i]; 1520 pdJ = pd->j + pd->i[i]; 1521 pA = pd->a + pd->i[i]; 1522 for (j=0; j<pnz; j++) { 1523 row = pdJ[j]; 1524 cj = bj + bi[row]; 1525 ca = ba + bi[row]; 1526 /* perform sparse axpy */ 1527 nexta = 0; 1528 valtmp = pA[j]; 1529 for (k=0; nexta<anz; k++) { 1530 if (cj[k] == adj[nexta]) { 1531 ca[k] += valtmp*ada[nexta]; 1532 nexta++; 1533 } 1534 } 1535 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1536 } 1537 } 1538 1539 /* 3) send and recv matrix values coa */ 1540 /*------------------------------------*/ 1541 buf_ri = merge->buf_ri; 1542 buf_rj = merge->buf_rj; 1543 len_s = merge->len_s; 1544 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1545 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1546 1547 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1548 for (proc=0,k=0; proc<size; proc++) { 1549 if (!len_s[proc]) continue; 1550 i = merge->owners_co[proc]; 1551 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1552 k++; 1553 } 1554 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1555 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1556 1557 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1558 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1559 ierr = PetscFree(coa);CHKERRQ(ierr); 1560 1561 /* 4) insert local Cseq and received values into Cmpi */ 1562 /*----------------------------------------------------*/ 1563 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1564 for (k=0; k<merge->nrecv; k++) { 1565 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1566 nrows = *(buf_ri_k[k]); 1567 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1568 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1569 } 1570 1571 for (i=0; i<cm; i++) { 1572 row = owners[rank] + i; /* global row index of C_seq */ 1573 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1574 ba_i = ba + bi[i]; 1575 bnz = bi[i+1] - bi[i]; 1576 /* add received vals into ba */ 1577 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1578 /* i-th row */ 1579 if (i == *nextrow[k]) { 1580 cnz = *(nextci[k]+1) - *nextci[k]; 1581 cj = buf_rj[k] + *(nextci[k]); 1582 ca = abuf_r[k] + *(nextci[k]); 1583 nextcj = 0; 1584 for (j=0; nextcj<cnz; j++) { 1585 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1586 ba_i[j] += ca[nextcj++]; 1587 } 1588 } 1589 nextrow[k]++; nextci[k]++; 1590 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1591 } 1592 } 1593 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1594 } 1595 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1596 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1597 1598 ierr = PetscFree(ba);CHKERRQ(ierr); 1599 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1600 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1601 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1602 PetscFunctionReturn(0); 1603 } 1604 1605 PetscErrorCode MatDuplicate_MPIAIJ_MatPtAP(Mat, MatDuplicateOption,Mat*); 1606 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ(); 1607 differ from MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable in using LLCondensedCreate_Scalable() */ 1608 #undef __FUNCT__ 1609 #define __FUNCT__ "MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ" 1610 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(Mat P,Mat A,PetscReal fill,Mat *C) 1611 { 1612 PetscErrorCode ierr; 1613 Mat Cmpi,A_loc,POt,PDt; 1614 Mat_PtAPMPI *ptap; 1615 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1616 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c; 1617 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1618 PetscInt nnz; 1619 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1620 PetscInt am =A->rmap->n,pn=P->cmap->n; 1621 MPI_Comm comm; 1622 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1623 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1624 PetscInt len,proc,*dnz,*onz,*owners; 1625 PetscInt nzi,*bi,*bj; 1626 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1627 MPI_Request *swaits,*rwaits; 1628 MPI_Status *sstatus,rstatus; 1629 Mat_Merge_SeqsToMPI *merge; 1630 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1631 PetscReal afill =1.0,afill_tmp; 1632 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N,Armax; 1633 PetscScalar *vals; 1634 Mat_SeqAIJ *a_loc,*pdt,*pot; 1635 PetscTable ta; 1636 1637 PetscFunctionBegin; 1638 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1639 /* check if matrix local sizes are compatible */ 1640 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); 1641 1642 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1643 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1644 1645 /* create struct Mat_PtAPMPI and attached it to C later */ 1646 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1647 1648 /* get A_loc by taking all local rows of A */ 1649 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1650 1651 ptap->A_loc = A_loc; 1652 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1653 ai = a_loc->i; 1654 aj = a_loc->j; 1655 1656 /* determine symbolic Co=(p->B)^T*A - send to others */ 1657 /*----------------------------------------------------*/ 1658 ierr = MatTransposeSymbolic_SeqAIJ(p->A,&PDt);CHKERRQ(ierr); 1659 pdt = (Mat_SeqAIJ*)PDt->data; 1660 pdti = pdt->i; pdtj = pdt->j; 1661 1662 ierr = MatTransposeSymbolic_SeqAIJ(p->B,&POt);CHKERRQ(ierr); 1663 pot = (Mat_SeqAIJ*)POt->data; 1664 poti = pot->i; potj = pot->j; 1665 1666 /* then, compute symbolic Co = (p->B)^T*A */ 1667 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 1668 >= (num of nonzero rows of C_seq) - pn */ 1669 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 1670 coi[0] = 0; 1671 1672 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1673 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],ai[am])); 1674 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1675 current_space = free_space; 1676 1677 /* create and initialize a linked list */ 1678 ierr = PetscTableCreate(2*a_loc->rmax,aN,&ta);CHKERRQ(ierr); 1679 MatRowMergeMax_SeqAIJ(a_loc,am,ta); 1680 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1681 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1682 1683 for (i=0; i<pon; i++) { 1684 pnz = poti[i+1] - poti[i]; 1685 ptJ = potj + poti[i]; 1686 for (j=0; j<pnz; j++) { 1687 row = ptJ[j]; /* row of A_loc == col of Pot */ 1688 anz = ai[row+1] - ai[row]; 1689 Jptr = aj + ai[row]; 1690 /* add non-zero cols of AP into the sorted linked list lnk */ 1691 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1692 } 1693 nnz = lnk[0]; 1694 1695 /* If free space is not available, double the total space in the list */ 1696 if (current_space->local_remaining<nnz) { 1697 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1698 nspacedouble++; 1699 } 1700 1701 /* Copy data into free space, and zero out denserows */ 1702 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1703 1704 current_space->array += nnz; 1705 current_space->local_used += nnz; 1706 current_space->local_remaining -= nnz; 1707 1708 coi[i+1] = coi[i] + nnz; 1709 } 1710 1711 ierr = PetscMalloc1(coi[pon]+1,&coj);CHKERRQ(ierr); 1712 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 1713 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); /* must destroy to get a new one for C */ 1714 1715 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 1716 if (afill_tmp > afill) afill = afill_tmp; 1717 1718 /* send j-array (coj) of Co to other processors */ 1719 /*----------------------------------------------*/ 1720 /* determine row ownership */ 1721 ierr = PetscNew(&merge);CHKERRQ(ierr); 1722 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 1723 1724 merge->rowmap->n = pn; 1725 merge->rowmap->bs = 1; 1726 1727 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 1728 owners = merge->rowmap->range; 1729 1730 /* determine the number of messages to send, their lengths */ 1731 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 1732 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 1733 1734 len_s = merge->len_s; 1735 merge->nsend = 0; 1736 1737 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 1738 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1739 1740 proc = 0; 1741 for (i=0; i<pon; i++) { 1742 while (prmap[i] >= owners[proc+1]) proc++; 1743 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1744 len_s[proc] += coi[i+1] - coi[i]; 1745 } 1746 1747 len = 0; /* max length of buf_si[] */ 1748 owners_co[0] = 0; 1749 for (proc=0; proc<size; proc++) { 1750 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1751 if (len_si[proc]) { 1752 merge->nsend++; 1753 len_si[proc] = 2*(len_si[proc] + 1); 1754 len += len_si[proc]; 1755 } 1756 } 1757 1758 /* determine the number and length of messages to receive for coi and coj */ 1759 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1760 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1761 1762 /* post the Irecv and Isend of coj */ 1763 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1764 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1765 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 1766 for (proc=0, k=0; proc<size; proc++) { 1767 if (!len_s[proc]) continue; 1768 i = owners_co[proc]; 1769 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1770 k++; 1771 } 1772 1773 /* receives and sends of coj are complete */ 1774 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1775 for (i=0; i<merge->nrecv; i++) { 1776 PetscMPIInt icompleted; 1777 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1778 } 1779 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1780 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1781 1782 /* add received column indices into table to update Armax */ 1783 for (k=0; k<merge->nrecv; k++) {/* k-th received message */ 1784 Jptr = buf_rj[k]; 1785 for (j=0; j<merge->len_r[k]; j++) { 1786 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1787 } 1788 } 1789 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1790 1791 /* send and recv coi */ 1792 /*-------------------*/ 1793 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1794 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1795 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1796 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1797 for (proc=0,k=0; proc<size; proc++) { 1798 if (!len_s[proc]) continue; 1799 /* form outgoing message for i-structure: 1800 buf_si[0]: nrows to be sent 1801 [1:nrows]: row index (global) 1802 [nrows+1:2*nrows+1]: i-structure index 1803 */ 1804 /*-------------------------------------------*/ 1805 nrows = len_si[proc]/2 - 1; 1806 buf_si_i = buf_si + nrows+1; 1807 buf_si[0] = nrows; 1808 buf_si_i[0] = 0; 1809 nrows = 0; 1810 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1811 nzi = coi[i+1] - coi[i]; 1812 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1813 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1814 nrows++; 1815 } 1816 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1817 k++; 1818 buf_si += len_si[proc]; 1819 } 1820 i = merge->nrecv; 1821 while (i--) { 1822 PetscMPIInt icompleted; 1823 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1824 } 1825 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1826 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1827 ierr = PetscFree(len_si);CHKERRQ(ierr); 1828 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1829 ierr = PetscFree(swaits);CHKERRQ(ierr); 1830 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1831 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1832 1833 /* compute the local portion of C (mpi mat) */ 1834 /*------------------------------------------*/ 1835 /* allocate bi array and free space for accumulating nonzero column info */ 1836 ierr = PetscMalloc1(pn+1,&bi);CHKERRQ(ierr); 1837 bi[0] = 0; 1838 1839 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 1840 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pdti[pn],PetscIntSumTruncate(poti[pon],ai[am]))); 1841 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1842 current_space = free_space; 1843 1844 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1845 for (k=0; k<merge->nrecv; k++) { 1846 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1847 nrows = *buf_ri_k[k]; 1848 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1849 nextci[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th recieved i-structure */ 1850 } 1851 1852 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1853 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1854 rmax = 0; 1855 for (i=0; i<pn; i++) { 1856 /* add pdt[i,:]*AP into lnk */ 1857 pnz = pdti[i+1] - pdti[i]; 1858 ptJ = pdtj + pdti[i]; 1859 for (j=0; j<pnz; j++) { 1860 row = ptJ[j]; /* row of AP == col of Pt */ 1861 anz = ai[row+1] - ai[row]; 1862 Jptr = aj + ai[row]; 1863 /* add non-zero cols of AP into the sorted linked list lnk */ 1864 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1865 } 1866 1867 /* add received col data into lnk */ 1868 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1869 if (i == *nextrow[k]) { /* i-th row */ 1870 nzi = *(nextci[k]+1) - *nextci[k]; 1871 Jptr = buf_rj[k] + *nextci[k]; 1872 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 1873 nextrow[k]++; nextci[k]++; 1874 } 1875 } 1876 nnz = lnk[0]; 1877 1878 /* if free space is not available, make more free space */ 1879 if (current_space->local_remaining<nnz) { 1880 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1881 nspacedouble++; 1882 } 1883 /* copy data into free space, then initialize lnk */ 1884 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1885 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 1886 1887 current_space->array += nnz; 1888 current_space->local_used += nnz; 1889 current_space->local_remaining -= nnz; 1890 1891 bi[i+1] = bi[i] + nnz; 1892 if (nnz > rmax) rmax = nnz; 1893 } 1894 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1895 1896 ierr = PetscMalloc1(bi[pn]+1,&bj);CHKERRQ(ierr); 1897 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 1898 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 1899 if (afill_tmp > afill) afill = afill_tmp; 1900 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 1901 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1902 1903 ierr = MatDestroy(&POt);CHKERRQ(ierr); 1904 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 1905 1906 /* create symbolic parallel matrix Cmpi - why cannot be assembled in Numeric part */ 1907 /*----------------------------------------------------------------------------------*/ 1908 ierr = PetscCalloc1(rmax+1,&vals);CHKERRQ(ierr); 1909 1910 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1911 ierr = MatSetSizes(Cmpi,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1912 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 1913 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 1914 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1915 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1916 ierr = MatSetBlockSize(Cmpi,1);CHKERRQ(ierr); 1917 for (i=0; i<pn; i++) { 1918 row = i + rstart; 1919 nnz = bi[i+1] - bi[i]; 1920 Jptr = bj + bi[i]; 1921 ierr = MatSetValues(Cmpi,1,&row,nnz,Jptr,vals,INSERT_VALUES);CHKERRQ(ierr); 1922 } 1923 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1924 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1925 ierr = PetscFree(vals);CHKERRQ(ierr); 1926 1927 merge->bi = bi; 1928 merge->bj = bj; 1929 merge->coi = coi; 1930 merge->coj = coj; 1931 merge->buf_ri = buf_ri; 1932 merge->buf_rj = buf_rj; 1933 merge->owners_co = owners_co; 1934 merge->destroy = Cmpi->ops->destroy; 1935 merge->duplicate = Cmpi->ops->duplicate; 1936 1937 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ; 1938 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1939 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 1940 1941 /* attach the supporting struct to Cmpi for reuse */ 1942 c = (Mat_MPIAIJ*)Cmpi->data; 1943 1944 c->ptap = ptap; 1945 ptap->api = NULL; 1946 ptap->apj = NULL; 1947 ptap->merge = merge; 1948 ptap->apa = NULL; 1949 1950 *C = Cmpi; 1951 #if defined(PETSC_USE_INFO) 1952 if (bi[pn] != 0) { 1953 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1954 ierr = PetscInfo1(Cmpi,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 1955 } else { 1956 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1957 } 1958 #endif 1959 PetscFunctionReturn(0); 1960 } 1961