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 ierr = PetscTableCreate(pN,pN,&ta);CHKERRQ(ierr); 221 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 222 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 223 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 224 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 225 226 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 227 228 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 229 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 230 current_space = free_space; 231 232 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 233 for (i=0; i<am; i++) { 234 /* diagonal portion of A */ 235 nzi = adi[i+1] - adi[i]; 236 for (j=0; j<nzi; j++) { 237 row = *adj++; 238 pnz = pi_loc[row+1] - pi_loc[row]; 239 Jptr = pj_loc + pi_loc[row]; 240 /* add non-zero cols of P into the sorted linked list lnk */ 241 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 242 } 243 /* off-diagonal portion of A */ 244 nzi = aoi[i+1] - aoi[i]; 245 for (j=0; j<nzi; j++) { 246 row = *aoj++; 247 pnz = pi_oth[row+1] - pi_oth[row]; 248 Jptr = pj_oth + pi_oth[row]; 249 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 250 } 251 252 apnz = lnk[0]; 253 api[i+1] = api[i] + apnz; 254 255 /* if free space is not available, double the total space in the list */ 256 if (current_space->local_remaining<apnz) { 257 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 258 nspacedouble++; 259 } 260 261 /* Copy data into free space, then initialize lnk */ 262 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 263 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 264 265 current_space->array += apnz; 266 current_space->local_used += apnz; 267 current_space->local_remaining -= apnz; 268 } 269 270 /* Allocate space for apj, initialize apj, and */ 271 /* destroy list of free space and other temporary array(s) */ 272 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 273 apj = ptap->apj; 274 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 275 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 276 277 /* malloc apa to store dense row A[i,:]*P */ 278 ierr = PetscCalloc1(pN,&apa);CHKERRQ(ierr); 279 280 ptap->apa = apa; 281 282 /* create and assemble symbolic parallel matrix Cmpi */ 283 /*----------------------------------------------------*/ 284 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 285 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 286 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 287 288 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 289 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 290 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 291 for (i=0; i<am; i++) { 292 row = i + rstart; 293 apnz = api[i+1] - api[i]; 294 ierr = MatSetValues(Cmpi,1,&row,apnz,apj,apa,INSERT_VALUES);CHKERRQ(ierr); 295 apj += apnz; 296 } 297 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 298 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 299 300 ptap->destroy = Cmpi->ops->destroy; 301 ptap->duplicate = Cmpi->ops->duplicate; 302 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 303 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 304 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatMatMult; 305 306 /* attach the supporting struct to Cmpi for reuse */ 307 c = (Mat_MPIAIJ*)Cmpi->data; 308 c->ptap = ptap; 309 310 *C = Cmpi; 311 312 /* set MatInfo */ 313 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 314 if (afill < 1.0) afill = 1.0; 315 Cmpi->info.mallocs = nspacedouble; 316 Cmpi->info.fill_ratio_given = fill; 317 Cmpi->info.fill_ratio_needed = afill; 318 319 #if defined(PETSC_USE_INFO) 320 if (api[am]) { 321 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 322 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 323 } else { 324 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 325 } 326 #endif 327 PetscFunctionReturn(0); 328 } 329 330 #undef __FUNCT__ 331 #define __FUNCT__ "MatMatMult_MPIAIJ_MPIDense" 332 PETSC_INTERN PetscErrorCode MatMatMult_MPIAIJ_MPIDense(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 333 { 334 PetscErrorCode ierr; 335 336 PetscFunctionBegin; 337 if (scall == MAT_INITIAL_MATRIX) { 338 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 339 ierr = MatMatMultSymbolic_MPIAIJ_MPIDense(A,B,fill,C);CHKERRQ(ierr); 340 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 341 } 342 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 343 ierr = MatMatMultNumeric_MPIAIJ_MPIDense(A,B,*C);CHKERRQ(ierr); 344 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 345 PetscFunctionReturn(0); 346 } 347 348 typedef struct { 349 Mat workB; 350 PetscScalar *rvalues,*svalues; 351 MPI_Request *rwaits,*swaits; 352 } MPIAIJ_MPIDense; 353 354 #undef __FUNCT__ 355 #define __FUNCT__ "MatMPIAIJ_MPIDenseDestroy" 356 PetscErrorCode MatMPIAIJ_MPIDenseDestroy(void *ctx) 357 { 358 MPIAIJ_MPIDense *contents = (MPIAIJ_MPIDense*) ctx; 359 PetscErrorCode ierr; 360 361 PetscFunctionBegin; 362 ierr = MatDestroy(&contents->workB);CHKERRQ(ierr); 363 ierr = PetscFree4(contents->rvalues,contents->svalues,contents->rwaits,contents->swaits);CHKERRQ(ierr); 364 ierr = PetscFree(contents);CHKERRQ(ierr); 365 PetscFunctionReturn(0); 366 } 367 368 #undef __FUNCT__ 369 #define __FUNCT__ "MatMatMultNumeric_MPIDense" 370 /* 371 This is a "dummy function" that handles the case where matrix C was created as a dense matrix 372 directly by the user and passed to MatMatMult() with the MAT_REUSE_MATRIX option 373 374 It is the same as MatMatMultSymbolic_MPIAIJ_MPIDense() except does not create C 375 */ 376 PetscErrorCode MatMatMultNumeric_MPIDense(Mat A,Mat B,Mat C) 377 { 378 PetscErrorCode ierr; 379 PetscBool flg; 380 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) A->data; 381 PetscInt nz = aij->B->cmap->n; 382 PetscContainer container; 383 MPIAIJ_MPIDense *contents; 384 VecScatter ctx = aij->Mvctx; 385 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 386 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 387 388 PetscFunctionBegin; 389 ierr = PetscObjectTypeCompare((PetscObject)B,MATMPIDENSE,&flg);CHKERRQ(ierr); 390 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Second matrix must be mpidense"); 391 392 /* Handle case where where user provided the final C matrix rather than calling MatMatMult() with MAT_INITIAL_MATRIX*/ 393 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 394 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"First matrix must be MPIAIJ"); 395 396 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 397 398 ierr = PetscNew(&contents);CHKERRQ(ierr); 399 /* Create work matrix used to store off processor rows of B needed for local product */ 400 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,B->cmap->N,NULL,&contents->workB);CHKERRQ(ierr); 401 /* Create work arrays needed */ 402 ierr = PetscMalloc4(B->cmap->N*from->starts[from->n],&contents->rvalues, 403 B->cmap->N*to->starts[to->n],&contents->svalues, 404 from->n,&contents->rwaits, 405 to->n,&contents->swaits);CHKERRQ(ierr); 406 407 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)A),&container);CHKERRQ(ierr); 408 ierr = PetscContainerSetPointer(container,contents);CHKERRQ(ierr); 409 ierr = PetscContainerSetUserDestroy(container,MatMPIAIJ_MPIDenseDestroy);CHKERRQ(ierr); 410 ierr = PetscObjectCompose((PetscObject)C,"workB",(PetscObject)container);CHKERRQ(ierr); 411 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 412 413 ierr = (*C->ops->matmultnumeric)(A,B,C);CHKERRQ(ierr); 414 PetscFunctionReturn(0); 415 } 416 417 #undef __FUNCT__ 418 #define __FUNCT__ "MatMatMultSymbolic_MPIAIJ_MPIDense" 419 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat A,Mat B,PetscReal fill,Mat *C) 420 { 421 PetscErrorCode ierr; 422 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) A->data; 423 PetscInt nz = aij->B->cmap->n; 424 PetscContainer container; 425 MPIAIJ_MPIDense *contents; 426 VecScatter ctx = aij->Mvctx; 427 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 428 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 429 PetscInt m = A->rmap->n,n=B->cmap->n; 430 431 PetscFunctionBegin; 432 ierr = MatCreate(PetscObjectComm((PetscObject)B),C);CHKERRQ(ierr); 433 ierr = MatSetSizes(*C,m,n,A->rmap->N,B->cmap->N);CHKERRQ(ierr); 434 ierr = MatSetBlockSizesFromMats(*C,A,B);CHKERRQ(ierr); 435 ierr = MatSetType(*C,MATMPIDENSE);CHKERRQ(ierr); 436 ierr = MatMPIDenseSetPreallocation(*C,NULL);CHKERRQ(ierr); 437 ierr = MatAssemblyBegin(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 438 ierr = MatAssemblyEnd(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 439 440 (*C)->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 441 442 ierr = PetscNew(&contents);CHKERRQ(ierr); 443 /* Create work matrix used to store off processor rows of B needed for local product */ 444 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,B->cmap->N,NULL,&contents->workB);CHKERRQ(ierr); 445 /* Create work arrays needed */ 446 ierr = PetscMalloc4(B->cmap->N*from->starts[from->n],&contents->rvalues, 447 B->cmap->N*to->starts[to->n],&contents->svalues, 448 from->n,&contents->rwaits, 449 to->n,&contents->swaits);CHKERRQ(ierr); 450 451 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)A),&container);CHKERRQ(ierr); 452 ierr = PetscContainerSetPointer(container,contents);CHKERRQ(ierr); 453 ierr = PetscContainerSetUserDestroy(container,MatMPIAIJ_MPIDenseDestroy);CHKERRQ(ierr); 454 ierr = PetscObjectCompose((PetscObject)(*C),"workB",(PetscObject)container);CHKERRQ(ierr); 455 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 456 PetscFunctionReturn(0); 457 } 458 459 #undef __FUNCT__ 460 #define __FUNCT__ "MatMPIDenseScatter" 461 /* 462 Performs an efficient scatter on the rows of B needed by this process; this is 463 a modification of the VecScatterBegin_() routines. 464 */ 465 PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,Mat C,Mat *outworkB) 466 { 467 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 468 PetscErrorCode ierr; 469 PetscScalar *b,*w,*svalues,*rvalues; 470 VecScatter ctx = aij->Mvctx; 471 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 472 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 473 PetscInt i,j,k; 474 PetscInt *sindices,*sstarts,*rindices,*rstarts; 475 PetscMPIInt *sprocs,*rprocs,nrecvs; 476 MPI_Request *swaits,*rwaits; 477 MPI_Comm comm; 478 PetscMPIInt tag = ((PetscObject)ctx)->tag,ncols = B->cmap->N, nrows = aij->B->cmap->n,imdex,nrowsB = B->rmap->n; 479 MPI_Status status; 480 MPIAIJ_MPIDense *contents; 481 PetscContainer container; 482 Mat workB; 483 484 PetscFunctionBegin; 485 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 486 ierr = PetscObjectQuery((PetscObject)C,"workB",(PetscObject*)&container);CHKERRQ(ierr); 487 if (!container) SETERRQ(comm,PETSC_ERR_PLIB,"Container does not exist"); 488 ierr = PetscContainerGetPointer(container,(void**)&contents);CHKERRQ(ierr); 489 490 workB = *outworkB = contents->workB; 491 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); 492 sindices = to->indices; 493 sstarts = to->starts; 494 sprocs = to->procs; 495 swaits = contents->swaits; 496 svalues = contents->svalues; 497 498 rindices = from->indices; 499 rstarts = from->starts; 500 rprocs = from->procs; 501 rwaits = contents->rwaits; 502 rvalues = contents->rvalues; 503 504 ierr = MatDenseGetArray(B,&b);CHKERRQ(ierr); 505 ierr = MatDenseGetArray(workB,&w);CHKERRQ(ierr); 506 507 for (i=0; i<from->n; i++) { 508 ierr = MPI_Irecv(rvalues+ncols*rstarts[i],ncols*(rstarts[i+1]-rstarts[i]),MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 509 } 510 511 for (i=0; i<to->n; i++) { 512 /* pack a message at a time */ 513 for (j=0; j<sstarts[i+1]-sstarts[i]; j++) { 514 for (k=0; k<ncols; k++) { 515 svalues[ncols*(sstarts[i] + j) + k] = b[sindices[sstarts[i]+j] + nrowsB*k]; 516 } 517 } 518 ierr = MPI_Isend(svalues+ncols*sstarts[i],ncols*(sstarts[i+1]-sstarts[i]),MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 519 } 520 521 nrecvs = from->n; 522 while (nrecvs) { 523 ierr = MPI_Waitany(from->n,rwaits,&imdex,&status);CHKERRQ(ierr); 524 nrecvs--; 525 /* unpack a message at a time */ 526 for (j=0; j<rstarts[imdex+1]-rstarts[imdex]; j++) { 527 for (k=0; k<ncols; k++) { 528 w[rindices[rstarts[imdex]+j] + nrows*k] = rvalues[ncols*(rstarts[imdex] + j) + k]; 529 } 530 } 531 } 532 if (to->n) {ierr = MPI_Waitall(to->n,swaits,to->sstatus);CHKERRQ(ierr);} 533 534 ierr = MatDenseRestoreArray(B,&b);CHKERRQ(ierr); 535 ierr = MatDenseRestoreArray(workB,&w);CHKERRQ(ierr); 536 ierr = MatAssemblyBegin(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 537 ierr = MatAssemblyEnd(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 538 PetscFunctionReturn(0); 539 } 540 extern PetscErrorCode MatMatMultNumericAdd_SeqAIJ_SeqDense(Mat,Mat,Mat); 541 542 #undef __FUNCT__ 543 #define __FUNCT__ "MatMatMultNumeric_MPIAIJ_MPIDense" 544 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat A,Mat B,Mat C) 545 { 546 PetscErrorCode ierr; 547 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 548 Mat_MPIDense *bdense = (Mat_MPIDense*)B->data; 549 Mat_MPIDense *cdense = (Mat_MPIDense*)C->data; 550 Mat workB; 551 552 PetscFunctionBegin; 553 /* diagonal block of A times all local rows of B*/ 554 ierr = MatMatMultNumeric_SeqAIJ_SeqDense(aij->A,bdense->A,cdense->A);CHKERRQ(ierr); 555 556 /* get off processor parts of B needed to complete the product */ 557 ierr = MatMPIDenseScatter(A,B,C,&workB);CHKERRQ(ierr); 558 559 /* off-diagonal block of A times nonlocal rows of B */ 560 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A);CHKERRQ(ierr); 561 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 562 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 563 PetscFunctionReturn(0); 564 } 565 566 #undef __FUNCT__ 567 #define __FUNCT__ "MatMatMultNumeric_MPIAIJ_MPIAIJ" 568 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 569 { 570 PetscErrorCode ierr; 571 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 572 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 573 Mat_SeqAIJ *cd = (Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 574 PetscInt *adi = ad->i,*adj,*aoi=ao->i,*aoj; 575 PetscScalar *ada,*aoa,*cda=cd->a,*coa=co->a; 576 Mat_SeqAIJ *p_loc,*p_oth; 577 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pj; 578 PetscScalar *pa_loc,*pa_oth,*pa,valtmp,*ca; 579 PetscInt cm = C->rmap->n,anz,pnz; 580 Mat_PtAPMPI *ptap = c->ptap; 581 PetscScalar *apa_sparse = ptap->apa; 582 PetscInt *api,*apj,*apJ,i,j,k,row; 583 PetscInt cstart = C->cmap->rstart; 584 PetscInt cdnz,conz,k0,k1,nextp; 585 MPI_Comm comm; 586 PetscMPIInt size; 587 588 PetscFunctionBegin; 589 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 590 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 591 592 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 593 /*-----------------------------------------------------*/ 594 /* update numerical values of P_oth and P_loc */ 595 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 596 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 597 598 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 599 /*----------------------------------------------------------*/ 600 /* get data from symbolic products */ 601 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 602 pi_loc = p_loc->i; pj_loc = p_loc->j; pa_loc = p_loc->a; 603 if (size >1) { 604 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 605 pi_oth = p_oth->i; pj_oth = p_oth->j; pa_oth = p_oth->a; 606 } else { 607 p_oth = NULL; pi_oth = NULL; pj_oth = NULL; pa_oth = NULL; 608 } 609 610 api = ptap->api; 611 apj = ptap->apj; 612 for (i=0; i<cm; i++) { 613 apJ = apj + api[i]; 614 615 /* diagonal portion of A */ 616 anz = adi[i+1] - adi[i]; 617 adj = ad->j + adi[i]; 618 ada = ad->a + adi[i]; 619 for (j=0; j<anz; j++) { 620 row = adj[j]; 621 pnz = pi_loc[row+1] - pi_loc[row]; 622 pj = pj_loc + pi_loc[row]; 623 pa = pa_loc + pi_loc[row]; 624 /* perform sparse axpy */ 625 valtmp = ada[j]; 626 nextp = 0; 627 for (k=0; nextp<pnz; k++) { 628 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 629 apa_sparse[k] += valtmp*pa[nextp++]; 630 } 631 } 632 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 633 } 634 635 /* off-diagonal portion of A */ 636 anz = aoi[i+1] - aoi[i]; 637 aoj = ao->j + aoi[i]; 638 aoa = ao->a + aoi[i]; 639 for (j=0; j<anz; j++) { 640 row = aoj[j]; 641 pnz = pi_oth[row+1] - pi_oth[row]; 642 pj = pj_oth + pi_oth[row]; 643 pa = pa_oth + pi_oth[row]; 644 /* perform sparse axpy */ 645 valtmp = aoa[j]; 646 nextp = 0; 647 for (k=0; nextp<pnz; k++) { 648 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 649 apa_sparse[k] += valtmp*pa[nextp++]; 650 } 651 } 652 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 653 } 654 655 /* set values in C */ 656 cdnz = cd->i[i+1] - cd->i[i]; 657 conz = co->i[i+1] - co->i[i]; 658 659 /* 1st off-diagoanl part of C */ 660 ca = coa + co->i[i]; 661 k = 0; 662 for (k0=0; k0<conz; k0++) { 663 if (apJ[k] >= cstart) break; 664 ca[k0] = apa_sparse[k]; 665 apa_sparse[k] = 0.0; 666 k++; 667 } 668 669 /* diagonal part of C */ 670 ca = cda + cd->i[i]; 671 for (k1=0; k1<cdnz; k1++) { 672 ca[k1] = apa_sparse[k]; 673 apa_sparse[k] = 0.0; 674 k++; 675 } 676 677 /* 2nd off-diagoanl part of C */ 678 ca = coa + co->i[i]; 679 for (; k0<conz; k0++) { 680 ca[k0] = apa_sparse[k]; 681 apa_sparse[k] = 0.0; 682 k++; 683 } 684 } 685 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 686 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 687 PetscFunctionReturn(0); 688 } 689 690 /* same as MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(), except using LLCondensed to avoid O(BN) memory requirement */ 691 #undef __FUNCT__ 692 #define __FUNCT__ "MatMatMultSymbolic_MPIAIJ_MPIAIJ" 693 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 694 { 695 PetscErrorCode ierr; 696 MPI_Comm comm; 697 PetscMPIInt size; 698 Mat Cmpi; 699 Mat_PtAPMPI *ptap; 700 PetscFreeSpaceList free_space = NULL,current_space=NULL; 701 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c; 702 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 703 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 704 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 705 PetscInt i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi,*lnk,apnz_max; 706 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n; 707 PetscReal afill; 708 PetscScalar *apa; 709 PetscTable ta; 710 711 PetscFunctionBegin; 712 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 713 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 714 715 /* create struct Mat_PtAPMPI and attached it to C later */ 716 ierr = PetscNew(&ptap);CHKERRQ(ierr); 717 718 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 719 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 720 721 /* get P_loc by taking all local rows of P */ 722 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 723 724 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 725 pi_loc = p_loc->i; pj_loc = p_loc->j; 726 if (size > 1) { 727 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 728 pi_oth = p_oth->i; pj_oth = p_oth->j; 729 } else { 730 p_oth = NULL; 731 pi_oth = NULL; pj_oth = NULL; 732 } 733 734 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 735 /*-------------------------------------------------------------------*/ 736 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 737 ptap->api = api; 738 api[0] = 0; 739 740 /* create and initialize a linked list */ 741 apnz_max = 6*(p_loc->rmax + (PetscInt)(1.e-2*pN)); /* expected apnz_max */ 742 if (apnz_max > pN) apnz_max = pN; 743 ierr = PetscTableCreate(apnz_max,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 /*-------------------------------------------------------------------------*/ 868 #undef __FUNCT__ 869 #define __FUNCT__ "MatTransposeMatMult_MPIAIJ_MPIAIJ" 870 PetscErrorCode MatTransposeMatMult_MPIAIJ_MPIAIJ(Mat P,Mat A,MatReuse scall,PetscReal fill,Mat *C) 871 { 872 PetscErrorCode ierr; 873 const char *algTypes[3] = {"scalable","nonscalable","matmatmult"}; 874 PetscInt alg=0; /* set default algorithm */ 875 876 PetscFunctionBegin; 877 if (scall == MAT_INITIAL_MATRIX) { 878 ierr = PetscObjectOptionsBegin((PetscObject)A);CHKERRQ(ierr); 879 ierr = PetscOptionsEList("-mattransposematmult_via","Algorithmic approach","MatTransposeMatMult",algTypes,3,algTypes[0],&alg,NULL);CHKERRQ(ierr); 880 ierr = PetscOptionsEnd();CHKERRQ(ierr); 881 882 ierr = PetscLogEventBegin(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 883 switch (alg) { 884 case 1: 885 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(P,A,fill,C);CHKERRQ(ierr); 886 break; 887 case 2: 888 { 889 Mat Pt; 890 Mat_PtAPMPI *ptap; 891 Mat_MPIAIJ *c; 892 ierr = MatTranspose(P,MAT_INITIAL_MATRIX,&Pt);CHKERRQ(ierr); 893 ierr = MatMatMult(Pt,A,MAT_INITIAL_MATRIX,fill,C);CHKERRQ(ierr); 894 c = (Mat_MPIAIJ*)(*C)->data; 895 ptap = c->ptap; 896 ptap->Pt = Pt; 897 (*C)->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult; 898 PetscFunctionReturn(0); 899 } 900 break; 901 default: 902 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(P,A,fill,C);CHKERRQ(ierr); 903 break; 904 } 905 ierr = PetscLogEventEnd(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 906 } 907 ierr = PetscLogEventBegin(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 908 ierr = (*(*C)->ops->mattransposemultnumeric)(P,A,*C);CHKERRQ(ierr); 909 ierr = PetscLogEventEnd(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 910 PetscFunctionReturn(0); 911 } 912 913 /* This routine only works when scall=MAT_REUSE_MATRIX! */ 914 #undef __FUNCT__ 915 #define __FUNCT__ "MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult" 916 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult(Mat P,Mat A,Mat C) 917 { 918 PetscErrorCode ierr; 919 Mat_MPIAIJ *c=(Mat_MPIAIJ*)C->data; 920 Mat_PtAPMPI *ptap= c->ptap; 921 Mat Pt=ptap->Pt; 922 923 PetscFunctionBegin; 924 ierr = MatTranspose(P,MAT_REUSE_MATRIX,&Pt);CHKERRQ(ierr); 925 ierr = MatMatMultNumeric(Pt,A,C);CHKERRQ(ierr); 926 PetscFunctionReturn(0); 927 } 928 929 /* Non-scalable version, use dense axpy */ 930 #undef __FUNCT__ 931 #define __FUNCT__ "MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable" 932 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,Mat C) 933 { 934 PetscErrorCode ierr; 935 Mat_Merge_SeqsToMPI *merge; 936 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 937 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 938 Mat_PtAPMPI *ptap; 939 PetscInt *adj,*aJ; 940 PetscInt i,j,k,anz,pnz,row,*cj; 941 MatScalar *ada,*aval,*ca,valtmp; 942 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 943 MPI_Comm comm; 944 PetscMPIInt size,rank,taga,*len_s; 945 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 946 PetscInt **buf_ri,**buf_rj; 947 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 948 MPI_Request *s_waits,*r_waits; 949 MPI_Status *status; 950 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 951 PetscInt *ai,*aj,*coi,*coj; 952 PetscInt *poJ,*pdJ; 953 Mat A_loc; 954 Mat_SeqAIJ *a_loc; 955 956 PetscFunctionBegin; 957 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 958 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 959 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 960 961 ptap = c->ptap; 962 merge = ptap->merge; 963 964 /* 2) compute numeric C_seq = P_loc^T*A_loc*P - dominating part */ 965 /*--------------------------------------------------------------*/ 966 /* get data from symbolic products */ 967 coi = merge->coi; coj = merge->coj; 968 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 969 970 bi = merge->bi; bj = merge->bj; 971 owners = merge->rowmap->range; 972 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); 973 974 /* get A_loc by taking all local rows of A */ 975 A_loc = ptap->A_loc; 976 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 977 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 978 ai = a_loc->i; 979 aj = a_loc->j; 980 981 ierr = PetscCalloc1(A->cmap->N,&aval);CHKERRQ(ierr); /* non-scalable!!! */ 982 983 for (i=0; i<am; i++) { 984 /* 2-a) put A[i,:] to dense array aval */ 985 anz = ai[i+1] - ai[i]; 986 adj = aj + ai[i]; 987 ada = a_loc->a + ai[i]; 988 for (j=0; j<anz; j++) { 989 aval[adj[j]] = ada[j]; 990 } 991 992 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 993 /*--------------------------------------------------------------*/ 994 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 995 pnz = po->i[i+1] - po->i[i]; 996 poJ = po->j + po->i[i]; 997 pA = po->a + po->i[i]; 998 for (j=0; j<pnz; j++) { 999 row = poJ[j]; 1000 cnz = coi[row+1] - coi[row]; 1001 cj = coj + coi[row]; 1002 ca = coa + coi[row]; 1003 /* perform dense axpy */ 1004 valtmp = pA[j]; 1005 for (k=0; k<cnz; k++) { 1006 ca[k] += valtmp*aval[cj[k]]; 1007 } 1008 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1009 } 1010 1011 /* put the value into Cd (diagonal part) */ 1012 pnz = pd->i[i+1] - pd->i[i]; 1013 pdJ = pd->j + pd->i[i]; 1014 pA = pd->a + pd->i[i]; 1015 for (j=0; j<pnz; j++) { 1016 row = pdJ[j]; 1017 cnz = bi[row+1] - bi[row]; 1018 cj = bj + bi[row]; 1019 ca = ba + bi[row]; 1020 /* perform dense axpy */ 1021 valtmp = pA[j]; 1022 for (k=0; k<cnz; k++) { 1023 ca[k] += valtmp*aval[cj[k]]; 1024 } 1025 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1026 } 1027 1028 /* zero the current row of Pt*A */ 1029 aJ = aj + ai[i]; 1030 for (k=0; k<anz; k++) aval[aJ[k]] = 0.0; 1031 } 1032 1033 /* 3) send and recv matrix values coa */ 1034 /*------------------------------------*/ 1035 buf_ri = merge->buf_ri; 1036 buf_rj = merge->buf_rj; 1037 len_s = merge->len_s; 1038 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1039 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1040 1041 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1042 for (proc=0,k=0; proc<size; proc++) { 1043 if (!len_s[proc]) continue; 1044 i = merge->owners_co[proc]; 1045 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1046 k++; 1047 } 1048 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1049 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1050 1051 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1052 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1053 ierr = PetscFree(coa);CHKERRQ(ierr); 1054 1055 /* 4) insert local Cseq and received values into Cmpi */ 1056 /*----------------------------------------------------*/ 1057 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1058 for (k=0; k<merge->nrecv; k++) { 1059 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1060 nrows = *(buf_ri_k[k]); 1061 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1062 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1063 } 1064 1065 for (i=0; i<cm; i++) { 1066 row = owners[rank] + i; /* global row index of C_seq */ 1067 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1068 ba_i = ba + bi[i]; 1069 bnz = bi[i+1] - bi[i]; 1070 /* add received vals into ba */ 1071 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1072 /* i-th row */ 1073 if (i == *nextrow[k]) { 1074 cnz = *(nextci[k]+1) - *nextci[k]; 1075 cj = buf_rj[k] + *(nextci[k]); 1076 ca = abuf_r[k] + *(nextci[k]); 1077 nextcj = 0; 1078 for (j=0; nextcj<cnz; j++) { 1079 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1080 ba_i[j] += ca[nextcj++]; 1081 } 1082 } 1083 nextrow[k]++; nextci[k]++; 1084 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1085 } 1086 } 1087 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1088 } 1089 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1090 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1091 1092 ierr = PetscFree(ba);CHKERRQ(ierr); 1093 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1094 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1095 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1096 ierr = PetscFree(aval);CHKERRQ(ierr); 1097 PetscFunctionReturn(0); 1098 } 1099 1100 PetscErrorCode MatDuplicate_MPIAIJ_MatPtAP(Mat, MatDuplicateOption,Mat*); 1101 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ() */ 1102 #undef __FUNCT__ 1103 #define __FUNCT__ "MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable" 1104 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,PetscReal fill,Mat *C) 1105 { 1106 PetscErrorCode ierr; 1107 Mat Cmpi,A_loc,POt,PDt; 1108 Mat_PtAPMPI *ptap; 1109 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1110 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c; 1111 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1112 PetscInt nnz; 1113 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1114 PetscInt am=A->rmap->n,pn=P->cmap->n; 1115 PetscBT lnkbt; 1116 MPI_Comm comm; 1117 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1118 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1119 PetscInt len,proc,*dnz,*onz,*owners; 1120 PetscInt nzi,*bi,*bj; 1121 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1122 MPI_Request *swaits,*rwaits; 1123 MPI_Status *sstatus,rstatus; 1124 Mat_Merge_SeqsToMPI *merge; 1125 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1126 PetscReal afill =1.0,afill_tmp; 1127 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N; 1128 PetscScalar *vals; 1129 Mat_SeqAIJ *a_loc, *pdt,*pot; 1130 1131 PetscFunctionBegin; 1132 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1133 /* check if matrix local sizes are compatible */ 1134 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); 1135 1136 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1137 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1138 1139 /* create struct Mat_PtAPMPI and attached it to C later */ 1140 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1141 1142 /* get A_loc by taking all local rows of A */ 1143 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1144 1145 ptap->A_loc = A_loc; 1146 1147 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1148 ai = a_loc->i; 1149 aj = a_loc->j; 1150 1151 /* determine symbolic Co=(p->B)^T*A - send to others */ 1152 /*----------------------------------------------------*/ 1153 ierr = MatTransposeSymbolic_SeqAIJ(p->A,&PDt);CHKERRQ(ierr); 1154 pdt = (Mat_SeqAIJ*)PDt->data; 1155 pdti = pdt->i; pdtj = pdt->j; 1156 1157 ierr = MatTransposeSymbolic_SeqAIJ(p->B,&POt);CHKERRQ(ierr); 1158 pot = (Mat_SeqAIJ*)POt->data; 1159 poti = pot->i; potj = pot->j; 1160 1161 /* then, compute symbolic Co = (p->B)^T*A */ 1162 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors >= (num of nonzero rows of C_seq) - pn */ 1163 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 1164 coi[0] = 0; 1165 1166 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1167 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],ai[am])); 1168 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1169 current_space = free_space; 1170 1171 /* create and initialize a linked list */ 1172 ierr = PetscLLCondensedCreate(aN,aN,&lnk,&lnkbt);CHKERRQ(ierr); 1173 1174 for (i=0; i<pon; i++) { 1175 pnz = poti[i+1] - poti[i]; 1176 ptJ = potj + poti[i]; 1177 for (j=0; j<pnz; j++) { 1178 row = ptJ[j]; /* row of A_loc == col of Pot */ 1179 anz = ai[row+1] - ai[row]; 1180 Jptr = aj + ai[row]; 1181 /* add non-zero cols of AP into the sorted linked list lnk */ 1182 ierr = PetscLLCondensedAddSorted(anz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1183 } 1184 nnz = lnk[0]; 1185 1186 /* If free space is not available, double the total space in the list */ 1187 if (current_space->local_remaining<nnz) { 1188 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1189 nspacedouble++; 1190 } 1191 1192 /* Copy data into free space, and zero out denserows */ 1193 ierr = PetscLLCondensedClean(aN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1194 1195 current_space->array += nnz; 1196 current_space->local_used += nnz; 1197 current_space->local_remaining -= nnz; 1198 1199 coi[i+1] = coi[i] + nnz; 1200 } 1201 1202 ierr = PetscMalloc1(coi[pon]+1,&coj);CHKERRQ(ierr); 1203 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 1204 1205 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 1206 if (afill_tmp > afill) afill = afill_tmp; 1207 1208 /* send j-array (coj) of Co to other processors */ 1209 /*----------------------------------------------*/ 1210 /* determine row ownership */ 1211 ierr = PetscNew(&merge);CHKERRQ(ierr); 1212 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 1213 1214 merge->rowmap->n = pn; 1215 merge->rowmap->bs = 1; 1216 1217 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 1218 owners = merge->rowmap->range; 1219 1220 /* determine the number of messages to send, their lengths */ 1221 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 1222 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 1223 1224 len_s = merge->len_s; 1225 merge->nsend = 0; 1226 1227 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 1228 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1229 1230 proc = 0; 1231 for (i=0; i<pon; i++) { 1232 while (prmap[i] >= owners[proc+1]) proc++; 1233 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1234 len_s[proc] += coi[i+1] - coi[i]; 1235 } 1236 1237 len = 0; /* max length of buf_si[] */ 1238 owners_co[0] = 0; 1239 for (proc=0; proc<size; proc++) { 1240 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1241 if (len_si[proc]) { 1242 merge->nsend++; 1243 len_si[proc] = 2*(len_si[proc] + 1); 1244 len += len_si[proc]; 1245 } 1246 } 1247 1248 /* determine the number and length of messages to receive for coi and coj */ 1249 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1250 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1251 1252 /* post the Irecv and Isend of coj */ 1253 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1254 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1255 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 1256 for (proc=0, k=0; proc<size; proc++) { 1257 if (!len_s[proc]) continue; 1258 i = owners_co[proc]; 1259 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1260 k++; 1261 } 1262 1263 /* receives and sends of coj are complete */ 1264 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1265 for (i=0; i<merge->nrecv; i++) { 1266 PetscMPIInt icompleted; 1267 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1268 } 1269 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1270 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1271 1272 /* send and recv coi */ 1273 /*-------------------*/ 1274 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1275 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1276 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1277 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1278 for (proc=0,k=0; proc<size; proc++) { 1279 if (!len_s[proc]) continue; 1280 /* form outgoing message for i-structure: 1281 buf_si[0]: nrows to be sent 1282 [1:nrows]: row index (global) 1283 [nrows+1:2*nrows+1]: i-structure index 1284 */ 1285 /*-------------------------------------------*/ 1286 nrows = len_si[proc]/2 - 1; 1287 buf_si_i = buf_si + nrows+1; 1288 buf_si[0] = nrows; 1289 buf_si_i[0] = 0; 1290 nrows = 0; 1291 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1292 nzi = coi[i+1] - coi[i]; 1293 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1294 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1295 nrows++; 1296 } 1297 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1298 k++; 1299 buf_si += len_si[proc]; 1300 } 1301 i = merge->nrecv; 1302 while (i--) { 1303 PetscMPIInt icompleted; 1304 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1305 } 1306 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1307 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1308 ierr = PetscFree(len_si);CHKERRQ(ierr); 1309 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1310 ierr = PetscFree(swaits);CHKERRQ(ierr); 1311 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1312 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1313 1314 /* compute the local portion of C (mpi mat) */ 1315 /*------------------------------------------*/ 1316 /* allocate bi array and free space for accumulating nonzero column info */ 1317 ierr = PetscMalloc1(pn+1,&bi);CHKERRQ(ierr); 1318 bi[0] = 0; 1319 1320 /* set initial free space to be fill*(nnz(P) + nnz(A)) */ 1321 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pdti[pn],PetscIntSumTruncate(poti[pon],ai[am]))); 1322 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1323 current_space = free_space; 1324 1325 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1326 for (k=0; k<merge->nrecv; k++) { 1327 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1328 nrows = *buf_ri_k[k]; 1329 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1330 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1331 } 1332 1333 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1334 rmax = 0; 1335 for (i=0; i<pn; i++) { 1336 /* add pdt[i,:]*AP into lnk */ 1337 pnz = pdti[i+1] - pdti[i]; 1338 ptJ = pdtj + pdti[i]; 1339 for (j=0; j<pnz; j++) { 1340 row = ptJ[j]; /* row of AP == col of Pt */ 1341 anz = ai[row+1] - ai[row]; 1342 Jptr = aj + ai[row]; 1343 /* add non-zero cols of AP into the sorted linked list lnk */ 1344 ierr = PetscLLCondensedAddSorted(anz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1345 } 1346 1347 /* add received col data into lnk */ 1348 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1349 if (i == *nextrow[k]) { /* i-th row */ 1350 nzi = *(nextci[k]+1) - *nextci[k]; 1351 Jptr = buf_rj[k] + *nextci[k]; 1352 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1353 nextrow[k]++; nextci[k]++; 1354 } 1355 } 1356 nnz = lnk[0]; 1357 1358 /* if free space is not available, make more free space */ 1359 if (current_space->local_remaining<nnz) { 1360 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1361 nspacedouble++; 1362 } 1363 /* copy data into free space, then initialize lnk */ 1364 ierr = PetscLLCondensedClean(aN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1365 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 1366 1367 current_space->array += nnz; 1368 current_space->local_used += nnz; 1369 current_space->local_remaining -= nnz; 1370 1371 bi[i+1] = bi[i] + nnz; 1372 if (nnz > rmax) rmax = nnz; 1373 } 1374 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1375 1376 ierr = PetscMalloc1(bi[pn]+1,&bj);CHKERRQ(ierr); 1377 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 1378 1379 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 1380 if (afill_tmp > afill) afill = afill_tmp; 1381 ierr = PetscLLCondensedDestroy(lnk,lnkbt);CHKERRQ(ierr); 1382 ierr = MatDestroy(&POt);CHKERRQ(ierr); 1383 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 1384 1385 /* create symbolic parallel matrix Cmpi - why cannot be assembled in Numeric part */ 1386 /*----------------------------------------------------------------------------------*/ 1387 ierr = PetscCalloc1(rmax+1,&vals);CHKERRQ(ierr); 1388 1389 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1390 ierr = MatSetSizes(Cmpi,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1391 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 1392 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 1393 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1394 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1395 ierr = MatSetBlockSize(Cmpi,1);CHKERRQ(ierr); 1396 for (i=0; i<pn; i++) { 1397 row = i + rstart; 1398 nnz = bi[i+1] - bi[i]; 1399 Jptr = bj + bi[i]; 1400 ierr = MatSetValues(Cmpi,1,&row,nnz,Jptr,vals,INSERT_VALUES);CHKERRQ(ierr); 1401 } 1402 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1403 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1404 ierr = PetscFree(vals);CHKERRQ(ierr); 1405 1406 merge->bi = bi; 1407 merge->bj = bj; 1408 merge->coi = coi; 1409 merge->coj = coj; 1410 merge->buf_ri = buf_ri; 1411 merge->buf_rj = buf_rj; 1412 merge->owners_co = owners_co; 1413 1414 /* attach the supporting struct to Cmpi for reuse */ 1415 c = (Mat_MPIAIJ*)Cmpi->data; 1416 c->ptap = ptap; 1417 ptap->api = NULL; 1418 ptap->apj = NULL; 1419 ptap->merge = merge; 1420 ptap->destroy = Cmpi->ops->destroy; 1421 ptap->duplicate = Cmpi->ops->duplicate; 1422 1423 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1424 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1425 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 1426 1427 *C = Cmpi; 1428 #if defined(PETSC_USE_INFO) 1429 if (bi[pn] != 0) { 1430 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1431 ierr = PetscInfo1(Cmpi,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 1432 } else { 1433 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1434 } 1435 #endif 1436 PetscFunctionReturn(0); 1437 } 1438 1439 #undef __FUNCT__ 1440 #define __FUNCT__ "MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ" 1441 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ(Mat P,Mat A,Mat C) 1442 { 1443 PetscErrorCode ierr; 1444 Mat_Merge_SeqsToMPI *merge; 1445 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1446 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1447 Mat_PtAPMPI *ptap; 1448 PetscInt *adj; 1449 PetscInt i,j,k,anz,pnz,row,*cj,nexta; 1450 MatScalar *ada,*ca,valtmp; 1451 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1452 MPI_Comm comm; 1453 PetscMPIInt size,rank,taga,*len_s; 1454 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1455 PetscInt **buf_ri,**buf_rj; 1456 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1457 MPI_Request *s_waits,*r_waits; 1458 MPI_Status *status; 1459 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1460 PetscInt *ai,*aj,*coi,*coj; 1461 PetscInt *poJ,*pdJ; 1462 Mat A_loc; 1463 Mat_SeqAIJ *a_loc; 1464 1465 PetscFunctionBegin; 1466 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1467 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1468 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1469 1470 ptap = c->ptap; 1471 merge = ptap->merge; 1472 1473 /* 2) compute numeric C_seq = P_loc^T*A_loc */ 1474 /*------------------------------------------*/ 1475 /* get data from symbolic products */ 1476 coi = merge->coi; coj = merge->coj; 1477 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 1478 bi = merge->bi; bj = merge->bj; 1479 owners = merge->rowmap->range; 1480 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); 1481 1482 /* get A_loc by taking all local rows of A */ 1483 A_loc = ptap->A_loc; 1484 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 1485 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1486 ai = a_loc->i; 1487 aj = a_loc->j; 1488 1489 for (i=0; i<am; i++) { 1490 anz = ai[i+1] - ai[i]; 1491 adj = aj + ai[i]; 1492 ada = a_loc->a + ai[i]; 1493 1494 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 1495 /*-------------------------------------------------------------*/ 1496 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 1497 pnz = po->i[i+1] - po->i[i]; 1498 poJ = po->j + po->i[i]; 1499 pA = po->a + po->i[i]; 1500 for (j=0; j<pnz; j++) { 1501 row = poJ[j]; 1502 cj = coj + coi[row]; 1503 ca = coa + coi[row]; 1504 /* perform sparse axpy */ 1505 nexta = 0; 1506 valtmp = pA[j]; 1507 for (k=0; nexta<anz; k++) { 1508 if (cj[k] == adj[nexta]) { 1509 ca[k] += valtmp*ada[nexta]; 1510 nexta++; 1511 } 1512 } 1513 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1514 } 1515 1516 /* put the value into Cd (diagonal part) */ 1517 pnz = pd->i[i+1] - pd->i[i]; 1518 pdJ = pd->j + pd->i[i]; 1519 pA = pd->a + pd->i[i]; 1520 for (j=0; j<pnz; j++) { 1521 row = pdJ[j]; 1522 cj = bj + bi[row]; 1523 ca = ba + bi[row]; 1524 /* perform sparse axpy */ 1525 nexta = 0; 1526 valtmp = pA[j]; 1527 for (k=0; nexta<anz; k++) { 1528 if (cj[k] == adj[nexta]) { 1529 ca[k] += valtmp*ada[nexta]; 1530 nexta++; 1531 } 1532 } 1533 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1534 } 1535 } 1536 1537 /* 3) send and recv matrix values coa */ 1538 /*------------------------------------*/ 1539 buf_ri = merge->buf_ri; 1540 buf_rj = merge->buf_rj; 1541 len_s = merge->len_s; 1542 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1543 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1544 1545 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1546 for (proc=0,k=0; proc<size; proc++) { 1547 if (!len_s[proc]) continue; 1548 i = merge->owners_co[proc]; 1549 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1550 k++; 1551 } 1552 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1553 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1554 1555 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1556 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1557 ierr = PetscFree(coa);CHKERRQ(ierr); 1558 1559 /* 4) insert local Cseq and received values into Cmpi */ 1560 /*----------------------------------------------------*/ 1561 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1562 for (k=0; k<merge->nrecv; k++) { 1563 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1564 nrows = *(buf_ri_k[k]); 1565 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1566 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1567 } 1568 1569 for (i=0; i<cm; i++) { 1570 row = owners[rank] + i; /* global row index of C_seq */ 1571 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1572 ba_i = ba + bi[i]; 1573 bnz = bi[i+1] - bi[i]; 1574 /* add received vals into ba */ 1575 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1576 /* i-th row */ 1577 if (i == *nextrow[k]) { 1578 cnz = *(nextci[k]+1) - *nextci[k]; 1579 cj = buf_rj[k] + *(nextci[k]); 1580 ca = abuf_r[k] + *(nextci[k]); 1581 nextcj = 0; 1582 for (j=0; nextcj<cnz; j++) { 1583 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1584 ba_i[j] += ca[nextcj++]; 1585 } 1586 } 1587 nextrow[k]++; nextci[k]++; 1588 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1589 } 1590 } 1591 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1592 } 1593 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1594 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1595 1596 ierr = PetscFree(ba);CHKERRQ(ierr); 1597 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1598 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1599 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1600 PetscFunctionReturn(0); 1601 } 1602 1603 PetscErrorCode MatDuplicate_MPIAIJ_MatPtAP(Mat, MatDuplicateOption,Mat*); 1604 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ(); 1605 differ from MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable in using LLCondensedCreate_Scalable() */ 1606 #undef __FUNCT__ 1607 #define __FUNCT__ "MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ" 1608 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(Mat P,Mat A,PetscReal fill,Mat *C) 1609 { 1610 PetscErrorCode ierr; 1611 Mat Cmpi,A_loc,POt,PDt; 1612 Mat_PtAPMPI *ptap; 1613 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1614 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c; 1615 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1616 PetscInt nnz; 1617 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1618 PetscInt am =A->rmap->n,pn=P->cmap->n; 1619 MPI_Comm comm; 1620 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1621 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1622 PetscInt len,proc,*dnz,*onz,*owners; 1623 PetscInt nzi,*bi,*bj; 1624 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1625 MPI_Request *swaits,*rwaits; 1626 MPI_Status *sstatus,rstatus; 1627 Mat_Merge_SeqsToMPI *merge; 1628 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1629 PetscReal afill =1.0,afill_tmp; 1630 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N,Armax; 1631 PetscScalar *vals; 1632 Mat_SeqAIJ *a_loc,*pdt,*pot; 1633 PetscTable ta; 1634 1635 PetscFunctionBegin; 1636 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1637 /* check if matrix local sizes are compatible */ 1638 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); 1639 1640 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1641 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1642 1643 /* create struct Mat_PtAPMPI and attached it to C later */ 1644 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1645 1646 /* get A_loc by taking all local rows of A */ 1647 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1648 1649 ptap->A_loc = A_loc; 1650 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1651 ai = a_loc->i; 1652 aj = a_loc->j; 1653 1654 /* determine symbolic Co=(p->B)^T*A - send to others */ 1655 /*----------------------------------------------------*/ 1656 ierr = MatTransposeSymbolic_SeqAIJ(p->A,&PDt);CHKERRQ(ierr); 1657 pdt = (Mat_SeqAIJ*)PDt->data; 1658 pdti = pdt->i; pdtj = pdt->j; 1659 1660 ierr = MatTransposeSymbolic_SeqAIJ(p->B,&POt);CHKERRQ(ierr); 1661 pot = (Mat_SeqAIJ*)POt->data; 1662 poti = pot->i; potj = pot->j; 1663 1664 /* then, compute symbolic Co = (p->B)^T*A */ 1665 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 1666 >= (num of nonzero rows of C_seq) - pn */ 1667 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 1668 coi[0] = 0; 1669 1670 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1671 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],ai[am])); 1672 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1673 current_space = free_space; 1674 1675 /* create and initialize a linked list */ 1676 ierr = PetscTableCreate(aN,aN,&ta);CHKERRQ(ierr); 1677 MatRowMergeMax_SeqAIJ(a_loc,am,ta); 1678 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1679 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1680 1681 for (i=0; i<pon; i++) { 1682 pnz = poti[i+1] - poti[i]; 1683 ptJ = potj + poti[i]; 1684 for (j=0; j<pnz; j++) { 1685 row = ptJ[j]; /* row of A_loc == col of Pot */ 1686 anz = ai[row+1] - ai[row]; 1687 Jptr = aj + ai[row]; 1688 /* add non-zero cols of AP into the sorted linked list lnk */ 1689 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1690 } 1691 nnz = lnk[0]; 1692 1693 /* If free space is not available, double the total space in the list */ 1694 if (current_space->local_remaining<nnz) { 1695 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1696 nspacedouble++; 1697 } 1698 1699 /* Copy data into free space, and zero out denserows */ 1700 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1701 1702 current_space->array += nnz; 1703 current_space->local_used += nnz; 1704 current_space->local_remaining -= nnz; 1705 1706 coi[i+1] = coi[i] + nnz; 1707 } 1708 1709 ierr = PetscMalloc1(coi[pon]+1,&coj);CHKERRQ(ierr); 1710 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 1711 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); /* must destroy to get a new one for C */ 1712 1713 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 1714 if (afill_tmp > afill) afill = afill_tmp; 1715 1716 /* send j-array (coj) of Co to other processors */ 1717 /*----------------------------------------------*/ 1718 /* determine row ownership */ 1719 ierr = PetscNew(&merge);CHKERRQ(ierr); 1720 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 1721 1722 merge->rowmap->n = pn; 1723 merge->rowmap->bs = 1; 1724 1725 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 1726 owners = merge->rowmap->range; 1727 1728 /* determine the number of messages to send, their lengths */ 1729 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 1730 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 1731 1732 len_s = merge->len_s; 1733 merge->nsend = 0; 1734 1735 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 1736 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1737 1738 proc = 0; 1739 for (i=0; i<pon; i++) { 1740 while (prmap[i] >= owners[proc+1]) proc++; 1741 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1742 len_s[proc] += coi[i+1] - coi[i]; 1743 } 1744 1745 len = 0; /* max length of buf_si[] */ 1746 owners_co[0] = 0; 1747 for (proc=0; proc<size; proc++) { 1748 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1749 if (len_si[proc]) { 1750 merge->nsend++; 1751 len_si[proc] = 2*(len_si[proc] + 1); 1752 len += len_si[proc]; 1753 } 1754 } 1755 1756 /* determine the number and length of messages to receive for coi and coj */ 1757 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1758 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1759 1760 /* post the Irecv and Isend of coj */ 1761 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1762 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1763 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 1764 for (proc=0, k=0; proc<size; proc++) { 1765 if (!len_s[proc]) continue; 1766 i = owners_co[proc]; 1767 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1768 k++; 1769 } 1770 1771 /* receives and sends of coj are complete */ 1772 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1773 for (i=0; i<merge->nrecv; i++) { 1774 PetscMPIInt icompleted; 1775 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1776 } 1777 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1778 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1779 1780 /* add received column indices into table to update Armax */ 1781 for (k=0; k<merge->nrecv; k++) {/* k-th received message */ 1782 Jptr = buf_rj[k]; 1783 for (j=0; j<merge->len_r[k]; j++) { 1784 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1785 } 1786 } 1787 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1788 1789 /* send and recv coi */ 1790 /*-------------------*/ 1791 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1792 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1793 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1794 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1795 for (proc=0,k=0; proc<size; proc++) { 1796 if (!len_s[proc]) continue; 1797 /* form outgoing message for i-structure: 1798 buf_si[0]: nrows to be sent 1799 [1:nrows]: row index (global) 1800 [nrows+1:2*nrows+1]: i-structure index 1801 */ 1802 /*-------------------------------------------*/ 1803 nrows = len_si[proc]/2 - 1; 1804 buf_si_i = buf_si + nrows+1; 1805 buf_si[0] = nrows; 1806 buf_si_i[0] = 0; 1807 nrows = 0; 1808 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1809 nzi = coi[i+1] - coi[i]; 1810 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1811 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1812 nrows++; 1813 } 1814 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1815 k++; 1816 buf_si += len_si[proc]; 1817 } 1818 i = merge->nrecv; 1819 while (i--) { 1820 PetscMPIInt icompleted; 1821 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1822 } 1823 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1824 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1825 ierr = PetscFree(len_si);CHKERRQ(ierr); 1826 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1827 ierr = PetscFree(swaits);CHKERRQ(ierr); 1828 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1829 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1830 1831 /* compute the local portion of C (mpi mat) */ 1832 /*------------------------------------------*/ 1833 /* allocate bi array and free space for accumulating nonzero column info */ 1834 ierr = PetscMalloc1(pn+1,&bi);CHKERRQ(ierr); 1835 bi[0] = 0; 1836 1837 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 1838 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pdti[pn],PetscIntSumTruncate(poti[pon],ai[am]))); 1839 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1840 current_space = free_space; 1841 1842 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1843 for (k=0; k<merge->nrecv; k++) { 1844 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1845 nrows = *buf_ri_k[k]; 1846 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1847 nextci[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th recieved i-structure */ 1848 } 1849 1850 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1851 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1852 rmax = 0; 1853 for (i=0; i<pn; i++) { 1854 /* add pdt[i,:]*AP into lnk */ 1855 pnz = pdti[i+1] - pdti[i]; 1856 ptJ = pdtj + pdti[i]; 1857 for (j=0; j<pnz; j++) { 1858 row = ptJ[j]; /* row of AP == col of Pt */ 1859 anz = ai[row+1] - ai[row]; 1860 Jptr = aj + ai[row]; 1861 /* add non-zero cols of AP into the sorted linked list lnk */ 1862 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1863 } 1864 1865 /* add received col data into lnk */ 1866 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1867 if (i == *nextrow[k]) { /* i-th row */ 1868 nzi = *(nextci[k]+1) - *nextci[k]; 1869 Jptr = buf_rj[k] + *nextci[k]; 1870 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 1871 nextrow[k]++; nextci[k]++; 1872 } 1873 } 1874 nnz = lnk[0]; 1875 1876 /* if free space is not available, make more free space */ 1877 if (current_space->local_remaining<nnz) { 1878 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1879 nspacedouble++; 1880 } 1881 /* copy data into free space, then initialize lnk */ 1882 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1883 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 1884 1885 current_space->array += nnz; 1886 current_space->local_used += nnz; 1887 current_space->local_remaining -= nnz; 1888 1889 bi[i+1] = bi[i] + nnz; 1890 if (nnz > rmax) rmax = nnz; 1891 } 1892 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1893 1894 ierr = PetscMalloc1(bi[pn]+1,&bj);CHKERRQ(ierr); 1895 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 1896 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 1897 if (afill_tmp > afill) afill = afill_tmp; 1898 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 1899 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1900 1901 ierr = MatDestroy(&POt);CHKERRQ(ierr); 1902 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 1903 1904 /* create symbolic parallel matrix Cmpi - why cannot be assembled in Numeric part */ 1905 /*----------------------------------------------------------------------------------*/ 1906 ierr = PetscCalloc1(rmax+1,&vals);CHKERRQ(ierr); 1907 1908 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1909 ierr = MatSetSizes(Cmpi,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1910 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 1911 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 1912 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1913 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1914 ierr = MatSetBlockSize(Cmpi,1);CHKERRQ(ierr); 1915 for (i=0; i<pn; i++) { 1916 row = i + rstart; 1917 nnz = bi[i+1] - bi[i]; 1918 Jptr = bj + bi[i]; 1919 ierr = MatSetValues(Cmpi,1,&row,nnz,Jptr,vals,INSERT_VALUES);CHKERRQ(ierr); 1920 } 1921 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1922 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1923 ierr = PetscFree(vals);CHKERRQ(ierr); 1924 1925 merge->bi = bi; 1926 merge->bj = bj; 1927 merge->coi = coi; 1928 merge->coj = coj; 1929 merge->buf_ri = buf_ri; 1930 merge->buf_rj = buf_rj; 1931 merge->owners_co = owners_co; 1932 1933 /* attach the supporting struct to Cmpi for reuse */ 1934 c = (Mat_MPIAIJ*)Cmpi->data; 1935 1936 c->ptap = ptap; 1937 ptap->api = NULL; 1938 ptap->apj = NULL; 1939 ptap->merge = merge; 1940 ptap->apa = NULL; 1941 ptap->destroy = Cmpi->ops->destroy; 1942 ptap->duplicate = Cmpi->ops->duplicate; 1943 1944 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ; 1945 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1946 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 1947 1948 *C = Cmpi; 1949 #if defined(PETSC_USE_INFO) 1950 if (bi[pn] != 0) { 1951 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1952 ierr = PetscInfo1(Cmpi,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 1953 } else { 1954 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1955 } 1956 #endif 1957 PetscFunctionReturn(0); 1958 } 1959