1 2 /* 3 Defines matrix-matrix product routines for pairs of MPIAIJ matrices 4 C = A * B 5 */ 6 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 7 #include <../src/mat/utils/freespace.h> 8 #include <../src/mat/impls/aij/mpi/mpiaij.h> 9 #include <petscbt.h> 10 #include <../src/mat/impls/dense/mpi/mpidense.h> 11 #include <petsc/private/vecimpl.h> 12 #include <petsc/private/vecscatterimpl.h> 13 14 #if defined(PETSC_HAVE_HYPRE) 15 PETSC_INTERN PetscErrorCode MatMatMultSymbolic_AIJ_AIJ_wHYPRE(Mat,Mat,PetscReal,Mat*); 16 #endif 17 18 PETSC_INTERN PetscErrorCode MatMatMult_MPIAIJ_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill, Mat *C) 19 { 20 PetscErrorCode ierr; 21 #if defined(PETSC_HAVE_HYPRE) 22 const char *algTypes[4] = {"scalable","nonscalable","seqmpi","hypre"}; 23 PetscInt nalg = 4; 24 #else 25 const char *algTypes[3] = {"scalable","nonscalable","seqmpi"}; 26 PetscInt nalg = 3; 27 #endif 28 PetscInt alg = 1; /* set nonscalable algorithm as default */ 29 MPI_Comm comm; 30 PetscBool flg; 31 32 PetscFunctionBegin; 33 if (scall == MAT_INITIAL_MATRIX) { 34 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 35 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); 36 37 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatMatMult","Mat");CHKERRQ(ierr); 38 ierr = PetscOptionsEList("-matmatmult_via","Algorithmic approach","MatMatMult",algTypes,nalg,algTypes[1],&alg,&flg);CHKERRQ(ierr); 39 ierr = PetscOptionsEnd();CHKERRQ(ierr); 40 41 if (!flg && B->cmap->N > 100000) { /* may switch to scalable algorithm as default */ 42 MatInfo Ainfo,Binfo; 43 PetscInt nz_local; 44 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 45 46 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 47 ierr = MatGetInfo(B,MAT_LOCAL,&Binfo);CHKERRQ(ierr); 48 nz_local = (PetscInt)(Ainfo.nz_allocated + Binfo.nz_allocated); 49 50 if (B->cmap->N > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 51 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 52 53 if (alg_scalable) { 54 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 55 ierr = PetscInfo2(B,"Use scalable algorithm, BN %D, fill*nz_allocated %g\n",B->cmap->N,fill*nz_local);CHKERRQ(ierr); 56 } 57 } 58 59 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 60 switch (alg) { 61 case 1: 62 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(A,B,fill,C);CHKERRQ(ierr); 63 break; 64 case 2: 65 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI(A,B,fill,C);CHKERRQ(ierr); 66 break; 67 #if defined(PETSC_HAVE_HYPRE) 68 case 3: 69 ierr = MatMatMultSymbolic_AIJ_AIJ_wHYPRE(A,B,fill,C);CHKERRQ(ierr); 70 break; 71 #endif 72 default: 73 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 74 break; 75 } 76 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 77 78 if (alg == 0 || alg == 1) { 79 Mat_MPIAIJ *c = (Mat_MPIAIJ*)(*C)->data; 80 Mat_APMPI *ap = c->ap; 81 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)(*C)),((PetscObject)(*C))->prefix,"MatFreeIntermediateDataStructures","Mat");CHKERRQ(ierr); 82 ap->freestruct = PETSC_FALSE; 83 ierr = PetscOptionsBool("-mat_freeintermediatedatastructures","Free intermediate data structures", "MatFreeIntermediateDataStructures",ap->freestruct,&ap->freestruct, NULL);CHKERRQ(ierr); 84 ierr = PetscOptionsEnd();CHKERRQ(ierr); 85 } 86 } 87 88 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 89 ierr = (*(*C)->ops->matmultnumeric)(A,B,*C);CHKERRQ(ierr); 90 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 91 PetscFunctionReturn(0); 92 } 93 94 PetscErrorCode MatDestroy_MPIAIJ_MatMatMult(Mat A) 95 { 96 PetscErrorCode ierr; 97 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 98 Mat_APMPI *ptap = a->ap; 99 100 PetscFunctionBegin; 101 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 102 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 103 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 104 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 105 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 106 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 107 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 108 ierr = PetscFree(ptap->apa);CHKERRQ(ierr); 109 ierr = ptap->destroy(A);CHKERRQ(ierr); 110 ierr = PetscFree(ptap);CHKERRQ(ierr); 111 PetscFunctionReturn(0); 112 } 113 114 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,Mat C) 115 { 116 PetscErrorCode ierr; 117 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 118 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 119 Mat_SeqAIJ *cd =(Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 120 PetscScalar *cda=cd->a,*coa=co->a; 121 Mat_SeqAIJ *p_loc,*p_oth; 122 PetscScalar *apa,*ca; 123 PetscInt cm =C->rmap->n; 124 Mat_APMPI *ptap=c->ap; 125 PetscInt *api,*apj,*apJ,i,k; 126 PetscInt cstart=C->cmap->rstart; 127 PetscInt cdnz,conz,k0,k1; 128 MPI_Comm comm; 129 PetscMPIInt size; 130 131 PetscFunctionBegin; 132 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 133 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 134 135 if (!ptap->P_oth && size>1) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"AP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 136 137 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 138 /*-----------------------------------------------------*/ 139 /* update numerical values of P_oth and P_loc */ 140 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 141 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 142 143 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 144 /*----------------------------------------------------------*/ 145 /* get data from symbolic products */ 146 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 147 p_oth = NULL; 148 if (size >1) { 149 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 150 } 151 152 /* get apa for storing dense row A[i,:]*P */ 153 apa = ptap->apa; 154 155 api = ptap->api; 156 apj = ptap->apj; 157 for (i=0; i<cm; i++) { 158 /* compute apa = A[i,:]*P */ 159 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 160 161 /* set values in C */ 162 apJ = apj + api[i]; 163 cdnz = cd->i[i+1] - cd->i[i]; 164 conz = co->i[i+1] - co->i[i]; 165 166 /* 1st off-diagoanl part of C */ 167 ca = coa + co->i[i]; 168 k = 0; 169 for (k0=0; k0<conz; k0++) { 170 if (apJ[k] >= cstart) break; 171 ca[k0] = apa[apJ[k]]; 172 apa[apJ[k++]] = 0.0; 173 } 174 175 /* diagonal part of C */ 176 ca = cda + cd->i[i]; 177 for (k1=0; k1<cdnz; k1++) { 178 ca[k1] = apa[apJ[k]]; 179 apa[apJ[k++]] = 0.0; 180 } 181 182 /* 2nd off-diagoanl part of C */ 183 ca = coa + co->i[i]; 184 for (; k0<conz; k0++) { 185 ca[k0] = apa[apJ[k]]; 186 apa[apJ[k++]] = 0.0; 187 } 188 } 189 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 190 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 191 192 if (ptap->freestruct) { 193 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 194 } 195 PetscFunctionReturn(0); 196 } 197 198 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,PetscReal fill,Mat *C) 199 { 200 PetscErrorCode ierr; 201 MPI_Comm comm; 202 PetscMPIInt size; 203 Mat Cmpi; 204 Mat_APMPI *ptap; 205 PetscFreeSpaceList free_space=NULL,current_space=NULL; 206 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c; 207 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 208 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 209 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 210 PetscInt *lnk,i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi; 211 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n; 212 PetscBT lnkbt; 213 PetscReal afill; 214 MatType mtype; 215 216 PetscFunctionBegin; 217 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 218 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 219 220 /* create struct Mat_APMPI and attached it to C later */ 221 ierr = PetscNew(&ptap);CHKERRQ(ierr); 222 223 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 224 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 225 226 /* get P_loc by taking all local rows of P */ 227 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 228 229 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 230 pi_loc = p_loc->i; pj_loc = p_loc->j; 231 if (size > 1) { 232 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 233 pi_oth = p_oth->i; pj_oth = p_oth->j; 234 } else { 235 p_oth = NULL; 236 pi_oth = NULL; pj_oth = NULL; 237 } 238 239 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 240 /*-------------------------------------------------------------------*/ 241 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 242 ptap->api = api; 243 api[0] = 0; 244 245 /* create and initialize a linked list */ 246 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 247 248 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 249 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 250 current_space = free_space; 251 252 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 253 for (i=0; i<am; i++) { 254 /* diagonal portion of A */ 255 nzi = adi[i+1] - adi[i]; 256 for (j=0; j<nzi; j++) { 257 row = *adj++; 258 pnz = pi_loc[row+1] - pi_loc[row]; 259 Jptr = pj_loc + pi_loc[row]; 260 /* add non-zero cols of P into the sorted linked list lnk */ 261 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 262 } 263 /* off-diagonal portion of A */ 264 nzi = aoi[i+1] - aoi[i]; 265 for (j=0; j<nzi; j++) { 266 row = *aoj++; 267 pnz = pi_oth[row+1] - pi_oth[row]; 268 Jptr = pj_oth + pi_oth[row]; 269 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 270 } 271 272 apnz = lnk[0]; 273 api[i+1] = api[i] + apnz; 274 275 /* if free space is not available, double the total space in the list */ 276 if (current_space->local_remaining<apnz) { 277 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 278 nspacedouble++; 279 } 280 281 /* Copy data into free space, then initialize lnk */ 282 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 283 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 284 285 current_space->array += apnz; 286 current_space->local_used += apnz; 287 current_space->local_remaining -= apnz; 288 } 289 290 /* Allocate space for apj, initialize apj, and */ 291 /* destroy list of free space and other temporary array(s) */ 292 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 293 apj = ptap->apj; 294 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 295 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 296 297 /* malloc apa to store dense row A[i,:]*P */ 298 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 299 300 /* create and assemble symbolic parallel matrix Cmpi */ 301 /*----------------------------------------------------*/ 302 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 303 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 304 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 305 306 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 307 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 308 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 309 310 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(Cmpi, apj, api);CHKERRQ(ierr); 311 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 312 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 313 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 314 315 ptap->destroy = Cmpi->ops->destroy; 316 ptap->duplicate = Cmpi->ops->duplicate; 317 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 318 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 319 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 320 321 /* attach the supporting struct to Cmpi for reuse */ 322 c = (Mat_MPIAIJ*)Cmpi->data; 323 c->ap = ptap; 324 325 *C = Cmpi; 326 327 /* set MatInfo */ 328 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 329 if (afill < 1.0) afill = 1.0; 330 Cmpi->info.mallocs = nspacedouble; 331 Cmpi->info.fill_ratio_given = fill; 332 Cmpi->info.fill_ratio_needed = afill; 333 334 #if defined(PETSC_USE_INFO) 335 if (api[am]) { 336 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 337 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 338 } else { 339 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 340 } 341 #endif 342 PetscFunctionReturn(0); 343 } 344 345 PETSC_INTERN PetscErrorCode MatMatMult_MPIAIJ_MPIDense(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 346 { 347 PetscErrorCode ierr; 348 349 PetscFunctionBegin; 350 if (scall == MAT_INITIAL_MATRIX) { 351 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 352 ierr = MatMatMultSymbolic_MPIAIJ_MPIDense(A,B,fill,C);CHKERRQ(ierr); 353 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 354 } 355 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 356 ierr = MatMatMultNumeric_MPIAIJ_MPIDense(A,B,*C);CHKERRQ(ierr); 357 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 358 PetscFunctionReturn(0); 359 } 360 361 typedef struct { 362 Mat workB; 363 PetscScalar *rvalues,*svalues; 364 MPI_Request *rwaits,*swaits; 365 } MPIAIJ_MPIDense; 366 367 PetscErrorCode MatMPIAIJ_MPIDenseDestroy(void *ctx) 368 { 369 MPIAIJ_MPIDense *contents = (MPIAIJ_MPIDense*) ctx; 370 PetscErrorCode ierr; 371 372 PetscFunctionBegin; 373 ierr = MatDestroy(&contents->workB);CHKERRQ(ierr); 374 ierr = PetscFree4(contents->rvalues,contents->svalues,contents->rwaits,contents->swaits);CHKERRQ(ierr); 375 ierr = PetscFree(contents);CHKERRQ(ierr); 376 PetscFunctionReturn(0); 377 } 378 379 /* 380 This is a "dummy function" that handles the case where matrix C was created as a dense matrix 381 directly by the user and passed to MatMatMult() with the MAT_REUSE_MATRIX option 382 383 It is the same as MatMatMultSymbolic_MPIAIJ_MPIDense() except does not create C 384 */ 385 PetscErrorCode MatMatMultNumeric_MPIDense(Mat A,Mat B,Mat C) 386 { 387 PetscErrorCode ierr; 388 PetscBool flg; 389 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) A->data; 390 PetscInt nz = aij->B->cmap->n,to_n,to_entries,from_n,from_entries; 391 PetscContainer container; 392 MPIAIJ_MPIDense *contents; 393 VecScatter ctx = aij->Mvctx; 394 395 PetscFunctionBegin; 396 ierr = PetscObjectTypeCompare((PetscObject)B,MATMPIDENSE,&flg);CHKERRQ(ierr); 397 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Second matrix must be mpidense"); 398 399 /* Handle case where where user provided the final C matrix rather than calling MatMatMult() with MAT_INITIAL_MATRIX*/ 400 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 401 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"First matrix must be MPIAIJ"); 402 403 C->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 404 405 ierr = PetscNew(&contents);CHKERRQ(ierr); 406 /* Create work matrix used to store off processor rows of B needed for local product */ 407 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,B->cmap->N,NULL,&contents->workB);CHKERRQ(ierr); 408 /* Create work arrays needed */ 409 ierr = VecScatterGetRemoteCount_Private(ctx,PETSC_TRUE/*send*/,&to_n,&to_entries);CHKERRQ(ierr); 410 ierr = VecScatterGetRemoteCount_Private(ctx,PETSC_FALSE/*recv*/,&from_n,&from_entries);CHKERRQ(ierr); 411 ierr = PetscMalloc4(B->cmap->N*from_entries,&contents->rvalues,B->cmap->N*to_entries,&contents->svalues,from_n,&contents->rwaits,to_n,&contents->swaits);CHKERRQ(ierr); 412 413 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)A),&container);CHKERRQ(ierr); 414 ierr = PetscContainerSetPointer(container,contents);CHKERRQ(ierr); 415 ierr = PetscContainerSetUserDestroy(container,MatMPIAIJ_MPIDenseDestroy);CHKERRQ(ierr); 416 ierr = PetscObjectCompose((PetscObject)C,"workB",(PetscObject)container);CHKERRQ(ierr); 417 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 418 419 ierr = (*C->ops->matmultnumeric)(A,B,C);CHKERRQ(ierr); 420 PetscFunctionReturn(0); 421 } 422 423 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat A,Mat B,PetscReal fill,Mat *C) 424 { 425 PetscErrorCode ierr; 426 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) A->data; 427 PetscInt nz = aij->B->cmap->n,to_n,to_entries,from_n,from_entries; 428 PetscContainer container; 429 MPIAIJ_MPIDense *contents; 430 VecScatter ctx = aij->Mvctx; 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 = VecScatterGetRemoteCount_Private(ctx,PETSC_TRUE/*send*/,&to_n,&to_entries);CHKERRQ(ierr); 449 ierr = VecScatterGetRemoteCount_Private(ctx,PETSC_FALSE/*recv*/,&from_n,&from_entries);CHKERRQ(ierr); 450 ierr = PetscMalloc4(B->cmap->N*from_entries,&contents->rvalues,B->cmap->N*to_entries,&contents->svalues,from_n,&contents->rwaits,to_n,&contents->swaits);CHKERRQ(ierr); 451 452 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)A),&container);CHKERRQ(ierr); 453 ierr = PetscContainerSetPointer(container,contents);CHKERRQ(ierr); 454 ierr = PetscContainerSetUserDestroy(container,MatMPIAIJ_MPIDenseDestroy);CHKERRQ(ierr); 455 ierr = PetscObjectCompose((PetscObject)(*C),"workB",(PetscObject)container);CHKERRQ(ierr); 456 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 457 PetscFunctionReturn(0); 458 } 459 460 /* 461 Performs an efficient scatter on the rows of B needed by this process; this is 462 a modification of the VecScatterBegin_() routines. 463 */ 464 PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,Mat C,Mat *outworkB) 465 { 466 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 467 PetscErrorCode ierr; 468 const PetscScalar *b; 469 PetscScalar *w,*svalues,*rvalues; 470 VecScatter ctx = aij->Mvctx; 471 PetscInt i,j,k; 472 const PetscInt *sindices,*sstarts,*rindices,*rstarts; 473 const PetscMPIInt *sprocs,*rprocs; 474 PetscInt nsends,nrecvs,nrecvs2; 475 MPI_Request *swaits,*rwaits; 476 MPI_Comm comm; 477 PetscMPIInt tag = ((PetscObject)ctx)->tag,ncols = B->cmap->N, nrows = aij->B->cmap->n,imdex,nrowsB = B->rmap->n,nsends_mpi,nrecvs_mpi; 478 MPI_Status status; 479 MPIAIJ_MPIDense *contents; 480 PetscContainer container; 481 Mat workB; 482 483 PetscFunctionBegin; 484 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 485 ierr = PetscObjectQuery((PetscObject)C,"workB",(PetscObject*)&container);CHKERRQ(ierr); 486 if (!container) SETERRQ(comm,PETSC_ERR_PLIB,"Container does not exist"); 487 ierr = PetscContainerGetPointer(container,(void**)&contents);CHKERRQ(ierr); 488 489 workB = *outworkB = contents->workB; 490 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); 491 ierr = VecScatterGetRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,&sprocs,NULL/*bs*/);CHKERRQ(ierr); 492 ierr = VecScatterGetRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,&rindices,&rprocs,NULL/*bs*/);CHKERRQ(ierr); 493 ierr = PetscMPIIntCast(nsends,&nsends_mpi);CHKERRQ(ierr); 494 ierr = PetscMPIIntCast(nrecvs,&nrecvs_mpi);CHKERRQ(ierr); 495 svalues = contents->svalues; 496 rvalues = contents->rvalues; 497 swaits = contents->swaits; 498 rwaits = contents->rwaits; 499 500 ierr = MatDenseGetArrayRead(B,&b);CHKERRQ(ierr); 501 ierr = MatDenseGetArray(workB,&w);CHKERRQ(ierr); 502 503 for (i=0; i<nrecvs; i++) { 504 ierr = MPI_Irecv(rvalues+ncols*(rstarts[i]-rstarts[0]),ncols*(rstarts[i+1]-rstarts[i]),MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 505 } 506 507 for (i=0; i<nsends; i++) { 508 /* pack a message at a time */ 509 for (j=0; j<sstarts[i+1]-sstarts[i]; j++) { 510 for (k=0; k<ncols; k++) { 511 svalues[ncols*(sstarts[i]-sstarts[0]+j) + k] = b[sindices[sstarts[i]+j] + nrowsB*k]; 512 } 513 } 514 ierr = MPI_Isend(svalues+ncols*(sstarts[i]-sstarts[0]),ncols*(sstarts[i+1]-sstarts[i]),MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 515 } 516 517 nrecvs2 = nrecvs; 518 while (nrecvs2) { 519 ierr = MPI_Waitany(nrecvs_mpi,rwaits,&imdex,&status);CHKERRQ(ierr); 520 nrecvs2--; 521 /* unpack a message at a time */ 522 for (j=0; j<rstarts[imdex+1]-rstarts[imdex]; j++) { 523 for (k=0; k<ncols; k++) { 524 w[rindices[rstarts[imdex]+j] + nrows*k] = rvalues[ncols*(rstarts[imdex]-rstarts[0]+j) + k]; 525 } 526 } 527 } 528 if (nsends) {ierr = MPI_Waitall(nsends_mpi,swaits,MPI_STATUSES_IGNORE);CHKERRQ(ierr);} 529 530 ierr = VecScatterRestoreRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,&sprocs,NULL/*bs*/);CHKERRQ(ierr); 531 ierr = VecScatterRestoreRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,&rindices,&rprocs,NULL/*bs*/);CHKERRQ(ierr); 532 ierr = MatDenseRestoreArrayRead(B,&b);CHKERRQ(ierr); 533 ierr = MatDenseRestoreArray(workB,&w);CHKERRQ(ierr); 534 ierr = MatAssemblyBegin(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 535 ierr = MatAssemblyEnd(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 536 PetscFunctionReturn(0); 537 538 } 539 extern PetscErrorCode MatMatMultNumericAdd_SeqAIJ_SeqDense(Mat,Mat,Mat); 540 541 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat A,Mat B,Mat C) 542 { 543 PetscErrorCode ierr; 544 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 545 Mat_MPIDense *bdense = (Mat_MPIDense*)B->data; 546 Mat_MPIDense *cdense = (Mat_MPIDense*)C->data; 547 Mat workB; 548 549 PetscFunctionBegin; 550 /* diagonal block of A times all local rows of B*/ 551 ierr = MatMatMultNumeric_SeqAIJ_SeqDense(aij->A,bdense->A,cdense->A);CHKERRQ(ierr); 552 553 /* get off processor parts of B needed to complete the product */ 554 ierr = MatMPIDenseScatter(A,B,C,&workB);CHKERRQ(ierr); 555 556 /* off-diagonal block of A times nonlocal rows of B */ 557 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A);CHKERRQ(ierr); 558 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 559 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 560 PetscFunctionReturn(0); 561 } 562 563 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 564 { 565 PetscErrorCode ierr; 566 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 567 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 568 Mat_SeqAIJ *cd = (Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 569 PetscInt *adi = ad->i,*adj,*aoi=ao->i,*aoj; 570 PetscScalar *ada,*aoa,*cda=cd->a,*coa=co->a; 571 Mat_SeqAIJ *p_loc,*p_oth; 572 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pj; 573 PetscScalar *pa_loc,*pa_oth,*pa,valtmp,*ca; 574 PetscInt cm = C->rmap->n,anz,pnz; 575 Mat_APMPI *ptap = c->ap; 576 PetscScalar *apa_sparse; 577 PetscInt *api,*apj,*apJ,i,j,k,row; 578 PetscInt cstart = C->cmap->rstart; 579 PetscInt cdnz,conz,k0,k1,nextp; 580 MPI_Comm comm; 581 PetscMPIInt size; 582 583 PetscFunctionBegin; 584 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 585 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 586 587 if (!ptap->P_oth && size>1) { 588 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"AP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 589 } 590 apa_sparse = ptap->apa; 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); 687 688 if (ptap->freestruct) { 689 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 690 } 691 PetscFunctionReturn(0); 692 } 693 694 /* same as MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(), except using LLCondensed to avoid O(BN) memory requirement */ 695 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 696 { 697 PetscErrorCode ierr; 698 MPI_Comm comm; 699 PetscMPIInt size; 700 Mat Cmpi; 701 Mat_APMPI *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=0; 708 PetscInt am=A->rmap->n,pn=P->cmap->n,pm=P->rmap->n,lsize=pn+20; 709 PetscReal afill; 710 MatType mtype; 711 712 PetscFunctionBegin; 713 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 714 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 715 716 /* create struct Mat_APMPI and attached it to C later */ 717 ierr = PetscNew(&ptap);CHKERRQ(ierr); 718 719 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 720 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 721 722 /* get P_loc by taking all local rows of P */ 723 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 724 725 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 726 pi_loc = p_loc->i; pj_loc = p_loc->j; 727 if (size > 1) { 728 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 729 pi_oth = p_oth->i; pj_oth = p_oth->j; 730 } else { 731 p_oth = NULL; 732 pi_oth = NULL; pj_oth = NULL; 733 } 734 735 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 736 /*-------------------------------------------------------------------*/ 737 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 738 ptap->api = api; 739 api[0] = 0; 740 741 ierr = PetscLLCondensedCreate_Scalable(lsize,&lnk);CHKERRQ(ierr); 742 743 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 744 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 745 current_space = free_space; 746 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 747 for (i=0; i<am; i++) { 748 /* diagonal portion of A */ 749 nzi = adi[i+1] - adi[i]; 750 for (j=0; j<nzi; j++) { 751 row = *adj++; 752 pnz = pi_loc[row+1] - pi_loc[row]; 753 Jptr = pj_loc + pi_loc[row]; 754 /* Expand list if it is not long enough */ 755 if (pnz+apnz_max > lsize) { 756 lsize = pnz+apnz_max; 757 ierr = PetscLLCondensedExpand_Scalable(lsize, &lnk);CHKERRQ(ierr); 758 } 759 /* add non-zero cols of P into the sorted linked list lnk */ 760 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 761 apnz = *lnk; /* The first element in the list is the number of items in the list */ 762 api[i+1] = api[i] + apnz; 763 if (apnz > apnz_max) apnz_max = apnz; 764 } 765 /* off-diagonal portion of A */ 766 nzi = aoi[i+1] - aoi[i]; 767 for (j=0; j<nzi; j++) { 768 row = *aoj++; 769 pnz = pi_oth[row+1] - pi_oth[row]; 770 Jptr = pj_oth + pi_oth[row]; 771 /* Expand list if it is not long enough */ 772 if (pnz+apnz_max > lsize) { 773 lsize = pnz + apnz_max; 774 ierr = PetscLLCondensedExpand_Scalable(lsize, &lnk);CHKERRQ(ierr); 775 } 776 /* add non-zero cols of P into the sorted linked list lnk */ 777 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 778 apnz = *lnk; /* The first element in the list is the number of items in the list */ 779 api[i+1] = api[i] + apnz; 780 if (apnz > apnz_max) apnz_max = apnz; 781 } 782 apnz = *lnk; 783 api[i+1] = api[i] + apnz; 784 if (apnz > apnz_max) apnz_max = apnz; 785 786 /* if free space is not available, double the total space in the list */ 787 if (current_space->local_remaining<apnz) { 788 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 789 nspacedouble++; 790 } 791 792 /* Copy data into free space, then initialize lnk */ 793 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 794 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 795 796 current_space->array += apnz; 797 current_space->local_used += apnz; 798 current_space->local_remaining -= apnz; 799 } 800 801 /* Allocate space for apj, initialize apj, and */ 802 /* destroy list of free space and other temporary array(s) */ 803 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 804 apj = ptap->apj; 805 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 806 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 807 808 /* create and assemble symbolic parallel matrix Cmpi */ 809 /*----------------------------------------------------*/ 810 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 811 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 812 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 813 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 814 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 815 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 816 817 /* malloc apa for assembly Cmpi */ 818 ierr = PetscCalloc1(apnz_max,&ptap->apa);CHKERRQ(ierr); 819 820 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(Cmpi, apj, api);CHKERRQ(ierr); 821 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 822 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 823 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 824 825 ptap->destroy = Cmpi->ops->destroy; 826 ptap->duplicate = Cmpi->ops->duplicate; 827 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ; 828 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 829 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 830 831 /* attach the supporting struct to Cmpi for reuse */ 832 c = (Mat_MPIAIJ*)Cmpi->data; 833 c->ap = ptap; 834 *C = Cmpi; 835 836 /* set MatInfo */ 837 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 838 if (afill < 1.0) afill = 1.0; 839 Cmpi->info.mallocs = nspacedouble; 840 Cmpi->info.fill_ratio_given = fill; 841 Cmpi->info.fill_ratio_needed = afill; 842 843 #if defined(PETSC_USE_INFO) 844 if (api[am]) { 845 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 846 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 847 } else { 848 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 849 } 850 #endif 851 PetscFunctionReturn(0); 852 } 853 854 /* This function is needed for the seqMPI matrix-matrix multiplication. */ 855 /* Three input arrays are merged to one output array. The size of the */ 856 /* output array is also output. Duplicate entries only show up once. */ 857 static void Merge3SortedArrays(PetscInt size1, PetscInt *in1, 858 PetscInt size2, PetscInt *in2, 859 PetscInt size3, PetscInt *in3, 860 PetscInt *size4, PetscInt *out) 861 { 862 int i = 0, j = 0, k = 0, l = 0; 863 864 /* Traverse all three arrays */ 865 while (i<size1 && j<size2 && k<size3) { 866 if (in1[i] < in2[j] && in1[i] < in3[k]) { 867 out[l++] = in1[i++]; 868 } 869 else if(in2[j] < in1[i] && in2[j] < in3[k]) { 870 out[l++] = in2[j++]; 871 } 872 else if(in3[k] < in1[i] && in3[k] < in2[j]) { 873 out[l++] = in3[k++]; 874 } 875 else if(in1[i] == in2[j] && in1[i] < in3[k]) { 876 out[l++] = in1[i]; 877 i++, j++; 878 } 879 else if(in1[i] == in3[k] && in1[i] < in2[j]) { 880 out[l++] = in1[i]; 881 i++, k++; 882 } 883 else if(in3[k] == in2[j] && in2[j] < in1[i]) { 884 out[l++] = in2[j]; 885 k++, j++; 886 } 887 else if(in1[i] == in2[j] && in1[i] == in3[k]) { 888 out[l++] = in1[i]; 889 i++, j++, k++; 890 } 891 } 892 893 /* Traverse two remaining arrays */ 894 while (i<size1 && j<size2) { 895 if (in1[i] < in2[j]) { 896 out[l++] = in1[i++]; 897 } 898 else if(in1[i] > in2[j]) { 899 out[l++] = in2[j++]; 900 } 901 else { 902 out[l++] = in1[i]; 903 i++, j++; 904 } 905 } 906 907 while (i<size1 && k<size3) { 908 if (in1[i] < in3[k]) { 909 out[l++] = in1[i++]; 910 } 911 else if(in1[i] > in3[k]) { 912 out[l++] = in3[k++]; 913 } 914 else { 915 out[l++] = in1[i]; 916 i++, k++; 917 } 918 } 919 920 while (k<size3 && j<size2) { 921 if (in3[k] < in2[j]) { 922 out[l++] = in3[k++]; 923 } 924 else if(in3[k] > in2[j]) { 925 out[l++] = in2[j++]; 926 } 927 else { 928 out[l++] = in3[k]; 929 k++, j++; 930 } 931 } 932 933 /* Traverse one remaining array */ 934 while (i<size1) out[l++] = in1[i++]; 935 while (j<size2) out[l++] = in2[j++]; 936 while (k<size3) out[l++] = in3[k++]; 937 938 *size4 = l; 939 } 940 941 /* This matrix-matrix multiplication algorithm divides the multiplication into three multiplications and */ 942 /* adds up the products. Two of these three multiplications are performed with existing (sequential) */ 943 /* matrix-matrix multiplications. */ 944 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI(Mat A, Mat P, PetscReal fill, Mat *C) 945 { 946 PetscErrorCode ierr; 947 MPI_Comm comm; 948 PetscMPIInt size; 949 Mat Cmpi; 950 Mat_APMPI *ptap; 951 PetscFreeSpaceList free_space_diag=NULL, current_space=NULL; 952 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data; 953 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc; 954 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data; 955 Mat_MPIAIJ *c; 956 Mat_SeqAIJ *adpd_seq, *p_off, *aopoth_seq; 957 PetscInt adponz, adpdnz; 958 PetscInt *pi_loc,*dnz,*onz; 959 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,rstart=A->rmap->rstart; 960 PetscInt *lnk,i, i1=0,pnz,row,*adpoi,*adpoj, *api, *adpoJ, *aopJ, *apJ,*Jptr, aopnz, nspacedouble=0,j,nzi, 961 *apj,apnz, *adpdi, *adpdj, *adpdJ, *poff_i, *poff_j, *j_temp, *aopothi, *aopothj; 962 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n, p_colstart, p_colend; 963 PetscBT lnkbt; 964 PetscReal afill; 965 PetscMPIInt rank; 966 Mat adpd, aopoth; 967 MatType mtype; 968 const char *prefix; 969 970 PetscFunctionBegin; 971 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 972 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 973 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 974 ierr = MatGetOwnershipRangeColumn(P, &p_colstart, &p_colend); CHKERRQ(ierr); 975 976 /* create struct Mat_APMPI and attached it to C later */ 977 ierr = PetscNew(&ptap);CHKERRQ(ierr); 978 979 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 980 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 981 982 /* get P_loc by taking all local rows of P */ 983 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 984 985 986 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 987 pi_loc = p_loc->i; 988 989 /* Allocate memory for the i arrays of the matrices A*P, A_diag*P_off and A_offd * P */ 990 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 991 ierr = PetscMalloc1(am+2,&adpoi);CHKERRQ(ierr); 992 993 adpoi[0] = 0; 994 ptap->api = api; 995 api[0] = 0; 996 997 /* create and initialize a linked list, will be used for both A_diag * P_loc_off and A_offd * P_oth */ 998 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 999 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 1000 1001 /* Symbolic calc of A_loc_diag * P_loc_diag */ 1002 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1003 ierr = MatSetOptionsPrefix(a->A,prefix);CHKERRQ(ierr); 1004 ierr = MatAppendOptionsPrefix(a->A,"inner_diag_");CHKERRQ(ierr); 1005 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(a->A, p->A, fill, &adpd);CHKERRQ(ierr); 1006 adpd_seq = (Mat_SeqAIJ*)((adpd)->data); 1007 adpdi = adpd_seq->i; adpdj = adpd_seq->j; 1008 p_off = (Mat_SeqAIJ*)((p->B)->data); 1009 poff_i = p_off->i; poff_j = p_off->j; 1010 1011 /* j_temp stores indices of a result row before they are added to the linked list */ 1012 ierr = PetscMalloc1(pN+2,&j_temp);CHKERRQ(ierr); 1013 1014 1015 /* Symbolic calc of the A_diag * p_loc_off */ 1016 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 1017 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space_diag);CHKERRQ(ierr); 1018 current_space = free_space_diag; 1019 1020 for (i=0; i<am; i++) { 1021 /* A_diag * P_loc_off */ 1022 nzi = adi[i+1] - adi[i]; 1023 for (j=0; j<nzi; j++) { 1024 row = *adj++; 1025 pnz = poff_i[row+1] - poff_i[row]; 1026 Jptr = poff_j + poff_i[row]; 1027 for(i1 = 0; i1 < pnz; i1++) { 1028 j_temp[i1] = p->garray[Jptr[i1]]; 1029 } 1030 /* add non-zero cols of P into the sorted linked list lnk */ 1031 ierr = PetscLLCondensedAddSorted(pnz,j_temp,lnk,lnkbt);CHKERRQ(ierr); 1032 } 1033 1034 adponz = lnk[0]; 1035 adpoi[i+1] = adpoi[i] + adponz; 1036 1037 /* if free space is not available, double the total space in the list */ 1038 if (current_space->local_remaining<adponz) { 1039 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(adponz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1040 nspacedouble++; 1041 } 1042 1043 /* Copy data into free space, then initialize lnk */ 1044 ierr = PetscLLCondensedClean(pN,adponz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1045 1046 current_space->array += adponz; 1047 current_space->local_used += adponz; 1048 current_space->local_remaining -= adponz; 1049 } 1050 1051 /* Symbolic calc of A_off * P_oth */ 1052 ierr = MatSetOptionsPrefix(a->B,prefix);CHKERRQ(ierr); 1053 ierr = MatAppendOptionsPrefix(a->B,"inner_offdiag_");CHKERRQ(ierr); 1054 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(a->B, ptap->P_oth, fill, &aopoth);CHKERRQ(ierr); 1055 aopoth_seq = (Mat_SeqAIJ*)((aopoth)->data); 1056 aopothi = aopoth_seq->i; aopothj = aopoth_seq->j; 1057 1058 /* Allocate space for apj, adpj, aopj, ... */ 1059 /* destroy lists of free space and other temporary array(s) */ 1060 1061 ierr = PetscMalloc1(aopothi[am] + adpoi[am] + adpdi[am]+2, &ptap->apj);CHKERRQ(ierr); 1062 ierr = PetscMalloc1(adpoi[am]+2, &adpoj);CHKERRQ(ierr); 1063 1064 /* Copy from linked list to j-array */ 1065 ierr = PetscFreeSpaceContiguous(&free_space_diag,adpoj);CHKERRQ(ierr); 1066 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1067 1068 adpoJ = adpoj; 1069 adpdJ = adpdj; 1070 aopJ = aopothj; 1071 apj = ptap->apj; 1072 apJ = apj; /* still empty */ 1073 1074 /* Merge j-arrays of A_off * P, A_diag * P_loc_off, and */ 1075 /* A_diag * P_loc_diag to get A*P */ 1076 for (i = 0; i < am; i++) { 1077 aopnz = aopothi[i+1] - aopothi[i]; 1078 adponz = adpoi[i+1] - adpoi[i]; 1079 adpdnz = adpdi[i+1] - adpdi[i]; 1080 1081 /* Correct indices from A_diag*P_diag */ 1082 for(i1 = 0; i1 < adpdnz; i1++) { 1083 adpdJ[i1] += p_colstart; 1084 } 1085 /* Merge j-arrays of A_diag * P_loc_off and A_diag * P_loc_diag and A_off * P_oth */ 1086 Merge3SortedArrays(adponz, adpoJ, adpdnz, adpdJ, aopnz, aopJ, &apnz, apJ); 1087 ierr = MatPreallocateSet(i+rstart, apnz, apJ, dnz, onz); CHKERRQ(ierr); 1088 1089 aopJ += aopnz; 1090 adpoJ += adponz; 1091 adpdJ += adpdnz; 1092 apJ += apnz; 1093 api[i+1] = api[i] + apnz; 1094 } 1095 1096 /* malloc apa to store dense row A[i,:]*P */ 1097 ierr = PetscCalloc1(pN+2,&ptap->apa);CHKERRQ(ierr); 1098 1099 /* create and assemble symbolic parallel matrix Cmpi */ 1100 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1101 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1102 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 1103 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1104 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1105 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1106 1107 1108 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(Cmpi, apj, api);CHKERRQ(ierr); 1109 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1110 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1111 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1112 1113 1114 ptap->destroy = Cmpi->ops->destroy; 1115 ptap->duplicate = Cmpi->ops->duplicate; 1116 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1117 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 1118 1119 /* attach the supporting struct to Cmpi for reuse */ 1120 c = (Mat_MPIAIJ*)Cmpi->data; 1121 c->ap = ptap; 1122 *C = Cmpi; 1123 1124 /* set MatInfo */ 1125 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 1126 if (afill < 1.0) afill = 1.0; 1127 Cmpi->info.mallocs = nspacedouble; 1128 Cmpi->info.fill_ratio_given = fill; 1129 Cmpi->info.fill_ratio_needed = afill; 1130 1131 #if defined(PETSC_USE_INFO) 1132 if (api[am]) { 1133 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1134 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 1135 } else { 1136 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1137 } 1138 #endif 1139 1140 ierr = MatDestroy(&aopoth);CHKERRQ(ierr); 1141 ierr = MatDestroy(&adpd);CHKERRQ(ierr); 1142 ierr = PetscFree(j_temp);CHKERRQ(ierr); 1143 ierr = PetscFree(adpoj);CHKERRQ(ierr); 1144 ierr = PetscFree(adpoi);CHKERRQ(ierr); 1145 PetscFunctionReturn(0); 1146 } 1147 1148 1149 /*-------------------------------------------------------------------------*/ 1150 PetscErrorCode MatTransposeMatMult_MPIAIJ_MPIAIJ(Mat P,Mat A,MatReuse scall,PetscReal fill,Mat *C) 1151 { 1152 PetscErrorCode ierr; 1153 const char *algTypes[3] = {"scalable","nonscalable","matmatmult"}; 1154 PetscInt aN=A->cmap->N,alg=1; /* set default algorithm */ 1155 PetscBool flg; 1156 1157 PetscFunctionBegin; 1158 if (scall == MAT_INITIAL_MATRIX) { 1159 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatTransposeMatMult","Mat");CHKERRQ(ierr); 1160 ierr = PetscOptionsEList("-mattransposematmult_via","Algorithmic approach","MatTransposeMatMult",algTypes,3,algTypes[1],&alg,&flg);CHKERRQ(ierr); 1161 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1162 1163 ierr = PetscLogEventBegin(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 1164 switch (alg) { 1165 case 1: 1166 if (!flg && aN > 100000) { /* may switch to scalable algorithm as default */ 1167 MatInfo Ainfo,Pinfo; 1168 PetscInt nz_local; 1169 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 1170 MPI_Comm comm; 1171 1172 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 1173 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 1174 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); /* estimated local nonzero entries */ 1175 1176 if (aN > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 1177 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1178 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 1179 1180 if (alg_scalable) { 1181 alg = 0; /* scalable algorithm would slower than nonscalable algorithm */ 1182 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(P,A,fill,C);CHKERRQ(ierr); 1183 break; 1184 } 1185 } 1186 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(P,A,fill,C);CHKERRQ(ierr); 1187 break; 1188 case 2: 1189 { 1190 Mat Pt; 1191 Mat_APMPI *ptap; 1192 Mat_MPIAIJ *c; 1193 ierr = MatTranspose(P,MAT_INITIAL_MATRIX,&Pt);CHKERRQ(ierr); 1194 ierr = MatMatMult(Pt,A,MAT_INITIAL_MATRIX,fill,C);CHKERRQ(ierr); 1195 c = (Mat_MPIAIJ*)(*C)->data; 1196 ptap = c->ap; 1197 if (ptap) { 1198 ptap->Pt = Pt; 1199 (*C)->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1200 } 1201 (*C)->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult; 1202 PetscFunctionReturn(0); 1203 } 1204 break; 1205 default: /* scalable algorithm */ 1206 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(P,A,fill,C);CHKERRQ(ierr); 1207 break; 1208 } 1209 ierr = PetscLogEventEnd(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 1210 1211 { 1212 Mat_MPIAIJ *c = (Mat_MPIAIJ*)(*C)->data; 1213 Mat_APMPI *ap = c->ap; 1214 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)(*C)),((PetscObject)(*C))->prefix,"MatFreeIntermediateDataStructures","Mat");CHKERRQ(ierr); 1215 ap->freestruct = PETSC_FALSE; 1216 ierr = PetscOptionsBool("-mat_freeintermediatedatastructures","Free intermediate data structures", "MatFreeIntermediateDataStructures",ap->freestruct,&ap->freestruct, NULL);CHKERRQ(ierr); 1217 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1218 } 1219 } 1220 1221 ierr = PetscLogEventBegin(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 1222 ierr = (*(*C)->ops->mattransposemultnumeric)(P,A,*C);CHKERRQ(ierr); 1223 ierr = PetscLogEventEnd(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 1224 PetscFunctionReturn(0); 1225 } 1226 1227 /* This routine only works when scall=MAT_REUSE_MATRIX! */ 1228 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult(Mat P,Mat A,Mat C) 1229 { 1230 PetscErrorCode ierr; 1231 Mat_MPIAIJ *c=(Mat_MPIAIJ*)C->data; 1232 Mat_APMPI *ptap= c->ap; 1233 Mat Pt; 1234 1235 PetscFunctionBegin; 1236 if (!ptap->Pt) { 1237 MPI_Comm comm; 1238 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1239 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1240 } 1241 1242 Pt=ptap->Pt; 1243 ierr = MatTranspose(P,MAT_REUSE_MATRIX,&Pt);CHKERRQ(ierr); 1244 ierr = MatMatMultNumeric(Pt,A,C);CHKERRQ(ierr); 1245 1246 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1247 if (ptap->freestruct) { 1248 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1249 } 1250 PetscFunctionReturn(0); 1251 } 1252 1253 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ() */ 1254 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,PetscReal fill,Mat *C) 1255 { 1256 PetscErrorCode ierr; 1257 Mat_APMPI *ptap; 1258 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1259 MPI_Comm comm; 1260 PetscMPIInt size,rank; 1261 Mat Cmpi; 1262 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1263 PetscInt pn=P->cmap->n,aN=A->cmap->N,an=A->cmap->n; 1264 PetscInt *lnk,i,k,nsend; 1265 PetscBT lnkbt; 1266 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 1267 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1268 PetscInt len,proc,*dnz,*onz,*owners,nzi; 1269 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1270 MPI_Request *swaits,*rwaits; 1271 MPI_Status *sstatus,rstatus; 1272 PetscLayout rowmap; 1273 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1274 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1275 PetscInt *Jptr,*prmap=p->garray,con,j,Crmax; 1276 Mat_SeqAIJ *a_loc,*c_loc,*c_oth; 1277 PetscTable ta; 1278 MatType mtype; 1279 const char *prefix; 1280 1281 PetscFunctionBegin; 1282 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1283 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1284 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1285 1286 /* create symbolic parallel matrix Cmpi */ 1287 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1288 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1289 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1290 1291 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1292 1293 /* create struct Mat_APMPI and attached it to C later */ 1294 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1295 ptap->reuse = MAT_INITIAL_MATRIX; 1296 1297 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1298 /* --------------------------------- */ 1299 ierr = MatTranspose_SeqAIJ(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1300 ierr = MatTranspose_SeqAIJ(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1301 1302 /* (1) compute symbolic A_loc */ 1303 /* ---------------------------*/ 1304 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1305 1306 /* (2-1) compute symbolic C_oth = Ro*A_loc */ 1307 /* ------------------------------------ */ 1308 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1309 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 1310 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 1311 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->A_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 1312 1313 /* (3) send coj of C_oth to other processors */ 1314 /* ------------------------------------------ */ 1315 /* determine row ownership */ 1316 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1317 rowmap->n = pn; 1318 rowmap->bs = 1; 1319 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1320 owners = rowmap->range; 1321 1322 /* determine the number of messages to send, their lengths */ 1323 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1324 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 1325 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr); 1326 1327 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1328 coi = c_oth->i; coj = c_oth->j; 1329 con = ptap->C_oth->rmap->n; 1330 proc = 0; 1331 for (i=0; i<con; i++) { 1332 while (prmap[i] >= owners[proc+1]) proc++; 1333 len_si[proc]++; /* num of rows in Co(=Pt*A) to be sent to [proc] */ 1334 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1335 } 1336 1337 len = 0; /* max length of buf_si[], see (4) */ 1338 owners_co[0] = 0; 1339 nsend = 0; 1340 for (proc=0; proc<size; proc++) { 1341 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1342 if (len_s[proc]) { 1343 nsend++; 1344 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1345 len += len_si[proc]; 1346 } 1347 } 1348 1349 /* determine the number and length of messages to receive for coi and coj */ 1350 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1351 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1352 1353 /* post the Irecv and Isend of coj */ 1354 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1355 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1356 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1357 for (proc=0, k=0; proc<size; proc++) { 1358 if (!len_s[proc]) continue; 1359 i = owners_co[proc]; 1360 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1361 k++; 1362 } 1363 1364 /* (2-2) compute symbolic C_loc = Rd*A_loc */ 1365 /* ---------------------------------------- */ 1366 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 1367 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 1368 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->A_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 1369 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1370 1371 /* receives coj are complete */ 1372 for (i=0; i<nrecv; i++) { 1373 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1374 } 1375 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1376 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1377 1378 /* add received column indices into ta to update Crmax */ 1379 a_loc = (Mat_SeqAIJ*)(ptap->A_loc)->data; 1380 1381 /* create and initialize a linked list */ 1382 ierr = PetscTableCreate(an,aN,&ta);CHKERRQ(ierr); /* for compute Crmax */ 1383 MatRowMergeMax_SeqAIJ(a_loc,ptap->A_loc->rmap->N,ta); 1384 1385 for (k=0; k<nrecv; k++) {/* k-th received message */ 1386 Jptr = buf_rj[k]; 1387 for (j=0; j<len_r[k]; j++) { 1388 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1389 } 1390 } 1391 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1392 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1393 1394 /* (4) send and recv coi */ 1395 /*-----------------------*/ 1396 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1397 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1398 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1399 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1400 for (proc=0,k=0; proc<size; proc++) { 1401 if (!len_s[proc]) continue; 1402 /* form outgoing message for i-structure: 1403 buf_si[0]: nrows to be sent 1404 [1:nrows]: row index (global) 1405 [nrows+1:2*nrows+1]: i-structure index 1406 */ 1407 /*-------------------------------------------*/ 1408 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1409 buf_si_i = buf_si + nrows+1; 1410 buf_si[0] = nrows; 1411 buf_si_i[0] = 0; 1412 nrows = 0; 1413 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1414 nzi = coi[i+1] - coi[i]; 1415 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1416 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1417 nrows++; 1418 } 1419 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1420 k++; 1421 buf_si += len_si[proc]; 1422 } 1423 for (i=0; i<nrecv; i++) { 1424 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1425 } 1426 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1427 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1428 1429 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1430 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1431 ierr = PetscFree(swaits);CHKERRQ(ierr); 1432 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1433 1434 /* (5) compute the local portion of Cmpi */ 1435 /* ------------------------------------------ */ 1436 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 1437 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1438 current_space = free_space; 1439 1440 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1441 for (k=0; k<nrecv; k++) { 1442 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1443 nrows = *buf_ri_k[k]; 1444 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1445 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1446 } 1447 1448 ierr = MatPreallocateInitialize(comm,pn,an,dnz,onz);CHKERRQ(ierr); 1449 ierr = PetscLLCondensedCreate(Crmax,aN,&lnk,&lnkbt);CHKERRQ(ierr); 1450 for (i=0; i<pn; i++) { 1451 /* add C_loc into Cmpi */ 1452 nzi = c_loc->i[i+1] - c_loc->i[i]; 1453 Jptr = c_loc->j + c_loc->i[i]; 1454 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1455 1456 /* add received col data into lnk */ 1457 for (k=0; k<nrecv; k++) { /* k-th received message */ 1458 if (i == *nextrow[k]) { /* i-th row */ 1459 nzi = *(nextci[k]+1) - *nextci[k]; 1460 Jptr = buf_rj[k] + *nextci[k]; 1461 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1462 nextrow[k]++; nextci[k]++; 1463 } 1464 } 1465 nzi = lnk[0]; 1466 1467 /* copy data into free space, then initialize lnk */ 1468 ierr = PetscLLCondensedClean(aN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1469 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 1470 } 1471 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1472 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1473 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 1474 1475 /* local sizes and preallocation */ 1476 ierr = MatSetSizes(Cmpi,pn,an,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1477 if (P->cmap->bs > 0) {ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr);} 1478 if (A->cmap->bs > 0) {ierr = PetscLayoutSetBlockSize(Cmpi->cmap,A->cmap->bs);CHKERRQ(ierr);} 1479 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1480 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1481 1482 /* members in merge */ 1483 ierr = PetscFree(id_r);CHKERRQ(ierr); 1484 ierr = PetscFree(len_r);CHKERRQ(ierr); 1485 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 1486 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 1487 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 1488 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 1489 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 1490 1491 /* attach the supporting struct to Cmpi for reuse */ 1492 c = (Mat_MPIAIJ*)Cmpi->data; 1493 c->ap = ptap; 1494 ptap->destroy = Cmpi->ops->destroy; 1495 1496 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1497 Cmpi->assembled = PETSC_FALSE; 1498 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1499 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1500 1501 *C = Cmpi; 1502 PetscFunctionReturn(0); 1503 } 1504 1505 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,Mat C) 1506 { 1507 PetscErrorCode ierr; 1508 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1509 Mat_SeqAIJ *c_seq; 1510 Mat_APMPI *ptap = c->ap; 1511 Mat A_loc,C_loc,C_oth; 1512 PetscInt i,rstart,rend,cm,ncols,row; 1513 const PetscInt *cols; 1514 const PetscScalar *vals; 1515 1516 PetscFunctionBegin; 1517 if (!ptap->A_loc) { 1518 MPI_Comm comm; 1519 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1520 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1521 } 1522 1523 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1524 1525 if (ptap->reuse == MAT_REUSE_MATRIX) { 1526 /* These matrices are obtained in MatTransposeMatMultSymbolic() */ 1527 /* 1) get R = Pd^T, Ro = Po^T */ 1528 /*----------------------------*/ 1529 ierr = MatTranspose_SeqAIJ(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1530 ierr = MatTranspose_SeqAIJ(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1531 1532 /* 2) compute numeric A_loc */ 1533 /*--------------------------*/ 1534 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1535 } 1536 1537 /* 3) C_loc = Rd*A_loc, C_oth = Ro*A_loc */ 1538 A_loc = ptap->A_loc; 1539 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,A_loc,ptap->C_loc);CHKERRQ(ierr); 1540 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,A_loc,ptap->C_oth);CHKERRQ(ierr); 1541 C_loc = ptap->C_loc; 1542 C_oth = ptap->C_oth; 1543 1544 /* add C_loc and Co to to C */ 1545 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1546 1547 /* C_loc -> C */ 1548 cm = C_loc->rmap->N; 1549 c_seq = (Mat_SeqAIJ*)C_loc->data; 1550 cols = c_seq->j; 1551 vals = c_seq->a; 1552 for (i=0; i<cm; i++) { 1553 ncols = c_seq->i[i+1] - c_seq->i[i]; 1554 row = rstart + i; 1555 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1556 cols += ncols; vals += ncols; 1557 } 1558 1559 /* Co -> C, off-processor part */ 1560 cm = C_oth->rmap->N; 1561 c_seq = (Mat_SeqAIJ*)C_oth->data; 1562 cols = c_seq->j; 1563 vals = c_seq->a; 1564 for (i=0; i<cm; i++) { 1565 ncols = c_seq->i[i+1] - c_seq->i[i]; 1566 row = p->garray[i]; 1567 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1568 cols += ncols; vals += ncols; 1569 } 1570 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1571 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1572 1573 ptap->reuse = MAT_REUSE_MATRIX; 1574 1575 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1576 if (ptap->freestruct) { 1577 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1578 } 1579 PetscFunctionReturn(0); 1580 } 1581 1582 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ(Mat P,Mat A,Mat C) 1583 { 1584 PetscErrorCode ierr; 1585 Mat_Merge_SeqsToMPI *merge; 1586 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1587 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1588 Mat_APMPI *ptap; 1589 PetscInt *adj; 1590 PetscInt i,j,k,anz,pnz,row,*cj,nexta; 1591 MatScalar *ada,*ca,valtmp; 1592 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1593 MPI_Comm comm; 1594 PetscMPIInt size,rank,taga,*len_s; 1595 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1596 PetscInt **buf_ri,**buf_rj; 1597 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1598 MPI_Request *s_waits,*r_waits; 1599 MPI_Status *status; 1600 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1601 PetscInt *ai,*aj,*coi,*coj,*poJ,*pdJ; 1602 Mat A_loc; 1603 Mat_SeqAIJ *a_loc; 1604 1605 PetscFunctionBegin; 1606 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1607 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1608 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1609 1610 ptap = c->ap; 1611 if (!ptap->A_loc) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1612 merge = ptap->merge; 1613 1614 /* 2) compute numeric C_seq = P_loc^T*A_loc */ 1615 /*------------------------------------------*/ 1616 /* get data from symbolic products */ 1617 coi = merge->coi; coj = merge->coj; 1618 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 1619 bi = merge->bi; bj = merge->bj; 1620 owners = merge->rowmap->range; 1621 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); 1622 1623 /* get A_loc by taking all local rows of A */ 1624 A_loc = ptap->A_loc; 1625 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 1626 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1627 ai = a_loc->i; 1628 aj = a_loc->j; 1629 1630 for (i=0; i<am; i++) { 1631 anz = ai[i+1] - ai[i]; 1632 adj = aj + ai[i]; 1633 ada = a_loc->a + ai[i]; 1634 1635 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 1636 /*-------------------------------------------------------------*/ 1637 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 1638 pnz = po->i[i+1] - po->i[i]; 1639 poJ = po->j + po->i[i]; 1640 pA = po->a + po->i[i]; 1641 for (j=0; j<pnz; j++) { 1642 row = poJ[j]; 1643 cj = coj + coi[row]; 1644 ca = coa + coi[row]; 1645 /* perform sparse axpy */ 1646 nexta = 0; 1647 valtmp = pA[j]; 1648 for (k=0; nexta<anz; k++) { 1649 if (cj[k] == adj[nexta]) { 1650 ca[k] += valtmp*ada[nexta]; 1651 nexta++; 1652 } 1653 } 1654 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1655 } 1656 1657 /* put the value into Cd (diagonal part) */ 1658 pnz = pd->i[i+1] - pd->i[i]; 1659 pdJ = pd->j + pd->i[i]; 1660 pA = pd->a + pd->i[i]; 1661 for (j=0; j<pnz; j++) { 1662 row = pdJ[j]; 1663 cj = bj + bi[row]; 1664 ca = ba + bi[row]; 1665 /* perform sparse axpy */ 1666 nexta = 0; 1667 valtmp = pA[j]; 1668 for (k=0; nexta<anz; k++) { 1669 if (cj[k] == adj[nexta]) { 1670 ca[k] += valtmp*ada[nexta]; 1671 nexta++; 1672 } 1673 } 1674 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1675 } 1676 } 1677 1678 /* 3) send and recv matrix values coa */ 1679 /*------------------------------------*/ 1680 buf_ri = merge->buf_ri; 1681 buf_rj = merge->buf_rj; 1682 len_s = merge->len_s; 1683 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1684 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1685 1686 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1687 for (proc=0,k=0; proc<size; proc++) { 1688 if (!len_s[proc]) continue; 1689 i = merge->owners_co[proc]; 1690 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1691 k++; 1692 } 1693 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1694 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1695 1696 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1697 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1698 ierr = PetscFree(coa);CHKERRQ(ierr); 1699 1700 /* 4) insert local Cseq and received values into Cmpi */ 1701 /*----------------------------------------------------*/ 1702 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1703 for (k=0; k<merge->nrecv; k++) { 1704 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1705 nrows = *(buf_ri_k[k]); 1706 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1707 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1708 } 1709 1710 for (i=0; i<cm; i++) { 1711 row = owners[rank] + i; /* global row index of C_seq */ 1712 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1713 ba_i = ba + bi[i]; 1714 bnz = bi[i+1] - bi[i]; 1715 /* add received vals into ba */ 1716 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1717 /* i-th row */ 1718 if (i == *nextrow[k]) { 1719 cnz = *(nextci[k]+1) - *nextci[k]; 1720 cj = buf_rj[k] + *(nextci[k]); 1721 ca = abuf_r[k] + *(nextci[k]); 1722 nextcj = 0; 1723 for (j=0; nextcj<cnz; j++) { 1724 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1725 ba_i[j] += ca[nextcj++]; 1726 } 1727 } 1728 nextrow[k]++; nextci[k]++; 1729 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1730 } 1731 } 1732 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1733 } 1734 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1735 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1736 1737 ierr = PetscFree(ba);CHKERRQ(ierr); 1738 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1739 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1740 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1741 1742 if (ptap->freestruct) { 1743 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1744 } 1745 PetscFunctionReturn(0); 1746 } 1747 1748 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(Mat P,Mat A,PetscReal fill,Mat *C) 1749 { 1750 PetscErrorCode ierr; 1751 Mat Cmpi,A_loc,POt,PDt; 1752 Mat_APMPI *ptap; 1753 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1754 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*a=(Mat_MPIAIJ*)A->data,*c; 1755 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1756 PetscInt nnz; 1757 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1758 PetscInt am =A->rmap->n,pn=P->cmap->n; 1759 MPI_Comm comm; 1760 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1761 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1762 PetscInt len,proc,*dnz,*onz,*owners; 1763 PetscInt nzi,*bi,*bj; 1764 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1765 MPI_Request *swaits,*rwaits; 1766 MPI_Status *sstatus,rstatus; 1767 Mat_Merge_SeqsToMPI *merge; 1768 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1769 PetscReal afill =1.0,afill_tmp; 1770 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N,Armax; 1771 Mat_SeqAIJ *a_loc,*pdt,*pot; 1772 PetscTable ta; 1773 MatType mtype; 1774 1775 PetscFunctionBegin; 1776 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1777 /* check if matrix local sizes are compatible */ 1778 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); 1779 1780 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1781 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1782 1783 /* create struct Mat_APMPI and attached it to C later */ 1784 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1785 1786 /* get A_loc by taking all local rows of A */ 1787 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1788 1789 ptap->A_loc = A_loc; 1790 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1791 ai = a_loc->i; 1792 aj = a_loc->j; 1793 1794 /* determine symbolic Co=(p->B)^T*A - send to others */ 1795 /*----------------------------------------------------*/ 1796 ierr = MatTransposeSymbolic_SeqAIJ(p->A,&PDt);CHKERRQ(ierr); 1797 pdt = (Mat_SeqAIJ*)PDt->data; 1798 pdti = pdt->i; pdtj = pdt->j; 1799 1800 ierr = MatTransposeSymbolic_SeqAIJ(p->B,&POt);CHKERRQ(ierr); 1801 pot = (Mat_SeqAIJ*)POt->data; 1802 poti = pot->i; potj = pot->j; 1803 1804 /* then, compute symbolic Co = (p->B)^T*A */ 1805 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 1806 >= (num of nonzero rows of C_seq) - pn */ 1807 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 1808 coi[0] = 0; 1809 1810 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1811 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],ai[am])); 1812 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1813 current_space = free_space; 1814 1815 /* create and initialize a linked list */ 1816 ierr = PetscTableCreate(A->cmap->n + a->B->cmap->N,aN,&ta);CHKERRQ(ierr); 1817 MatRowMergeMax_SeqAIJ(a_loc,am,ta); 1818 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1819 1820 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1821 1822 for (i=0; i<pon; i++) { 1823 pnz = poti[i+1] - poti[i]; 1824 ptJ = potj + poti[i]; 1825 for (j=0; j<pnz; j++) { 1826 row = ptJ[j]; /* row of A_loc == col of Pot */ 1827 anz = ai[row+1] - ai[row]; 1828 Jptr = aj + ai[row]; 1829 /* add non-zero cols of AP into the sorted linked list lnk */ 1830 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1831 } 1832 nnz = lnk[0]; 1833 1834 /* If free space is not available, double the total space in the list */ 1835 if (current_space->local_remaining<nnz) { 1836 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1837 nspacedouble++; 1838 } 1839 1840 /* Copy data into free space, and zero out denserows */ 1841 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1842 1843 current_space->array += nnz; 1844 current_space->local_used += nnz; 1845 current_space->local_remaining -= nnz; 1846 1847 coi[i+1] = coi[i] + nnz; 1848 } 1849 1850 ierr = PetscMalloc1(coi[pon]+1,&coj);CHKERRQ(ierr); 1851 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 1852 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); /* must destroy to get a new one for C */ 1853 1854 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 1855 if (afill_tmp > afill) afill = afill_tmp; 1856 1857 /* send j-array (coj) of Co to other processors */ 1858 /*----------------------------------------------*/ 1859 /* determine row ownership */ 1860 ierr = PetscNew(&merge);CHKERRQ(ierr); 1861 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 1862 1863 merge->rowmap->n = pn; 1864 merge->rowmap->bs = 1; 1865 1866 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 1867 owners = merge->rowmap->range; 1868 1869 /* determine the number of messages to send, their lengths */ 1870 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 1871 ierr = PetscCalloc1(size,&merge->len_s);CHKERRQ(ierr); 1872 1873 len_s = merge->len_s; 1874 merge->nsend = 0; 1875 1876 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 1877 1878 proc = 0; 1879 for (i=0; i<pon; i++) { 1880 while (prmap[i] >= owners[proc+1]) proc++; 1881 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1882 len_s[proc] += coi[i+1] - coi[i]; 1883 } 1884 1885 len = 0; /* max length of buf_si[] */ 1886 owners_co[0] = 0; 1887 for (proc=0; proc<size; proc++) { 1888 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1889 if (len_si[proc]) { 1890 merge->nsend++; 1891 len_si[proc] = 2*(len_si[proc] + 1); 1892 len += len_si[proc]; 1893 } 1894 } 1895 1896 /* determine the number and length of messages to receive for coi and coj */ 1897 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1898 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1899 1900 /* post the Irecv and Isend of coj */ 1901 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1902 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1903 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 1904 for (proc=0, k=0; proc<size; proc++) { 1905 if (!len_s[proc]) continue; 1906 i = owners_co[proc]; 1907 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1908 k++; 1909 } 1910 1911 /* receives and sends of coj are complete */ 1912 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1913 for (i=0; i<merge->nrecv; i++) { 1914 PetscMPIInt icompleted; 1915 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1916 } 1917 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1918 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1919 1920 /* add received column indices into table to update Armax */ 1921 /* Armax can be as large as aN if a P[row,:] is dense, see src/ksp/ksp/examples/tutorials/ex56.c! */ 1922 for (k=0; k<merge->nrecv; k++) {/* k-th received message */ 1923 Jptr = buf_rj[k]; 1924 for (j=0; j<merge->len_r[k]; j++) { 1925 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1926 } 1927 } 1928 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1929 /* printf("Armax %d, an %d + Bn %d = %d, aN %d\n",Armax,A->cmap->n,a->B->cmap->N,A->cmap->n+a->B->cmap->N,aN); */ 1930 1931 /* send and recv coi */ 1932 /*-------------------*/ 1933 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1934 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1935 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1936 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1937 for (proc=0,k=0; proc<size; proc++) { 1938 if (!len_s[proc]) continue; 1939 /* form outgoing message for i-structure: 1940 buf_si[0]: nrows to be sent 1941 [1:nrows]: row index (global) 1942 [nrows+1:2*nrows+1]: i-structure index 1943 */ 1944 /*-------------------------------------------*/ 1945 nrows = len_si[proc]/2 - 1; 1946 buf_si_i = buf_si + nrows+1; 1947 buf_si[0] = nrows; 1948 buf_si_i[0] = 0; 1949 nrows = 0; 1950 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1951 nzi = coi[i+1] - coi[i]; 1952 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1953 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1954 nrows++; 1955 } 1956 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1957 k++; 1958 buf_si += len_si[proc]; 1959 } 1960 i = merge->nrecv; 1961 while (i--) { 1962 PetscMPIInt icompleted; 1963 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1964 } 1965 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1966 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1967 ierr = PetscFree(len_si);CHKERRQ(ierr); 1968 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1969 ierr = PetscFree(swaits);CHKERRQ(ierr); 1970 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1971 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1972 1973 /* compute the local portion of C (mpi mat) */ 1974 /*------------------------------------------*/ 1975 /* allocate bi array and free space for accumulating nonzero column info */ 1976 ierr = PetscMalloc1(pn+1,&bi);CHKERRQ(ierr); 1977 bi[0] = 0; 1978 1979 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 1980 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pdti[pn],PetscIntSumTruncate(poti[pon],ai[am]))); 1981 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1982 current_space = free_space; 1983 1984 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1985 for (k=0; k<merge->nrecv; k++) { 1986 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1987 nrows = *buf_ri_k[k]; 1988 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1989 nextci[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th recieved i-structure */ 1990 } 1991 1992 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1993 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1994 rmax = 0; 1995 for (i=0; i<pn; i++) { 1996 /* add pdt[i,:]*AP into lnk */ 1997 pnz = pdti[i+1] - pdti[i]; 1998 ptJ = pdtj + pdti[i]; 1999 for (j=0; j<pnz; j++) { 2000 row = ptJ[j]; /* row of AP == col of Pt */ 2001 anz = ai[row+1] - ai[row]; 2002 Jptr = aj + ai[row]; 2003 /* add non-zero cols of AP into the sorted linked list lnk */ 2004 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 2005 } 2006 2007 /* add received col data into lnk */ 2008 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 2009 if (i == *nextrow[k]) { /* i-th row */ 2010 nzi = *(nextci[k]+1) - *nextci[k]; 2011 Jptr = buf_rj[k] + *nextci[k]; 2012 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 2013 nextrow[k]++; nextci[k]++; 2014 } 2015 } 2016 nnz = lnk[0]; 2017 2018 /* if free space is not available, make more free space */ 2019 if (current_space->local_remaining<nnz) { 2020 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 2021 nspacedouble++; 2022 } 2023 /* copy data into free space, then initialize lnk */ 2024 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 2025 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 2026 2027 current_space->array += nnz; 2028 current_space->local_used += nnz; 2029 current_space->local_remaining -= nnz; 2030 2031 bi[i+1] = bi[i] + nnz; 2032 if (nnz > rmax) rmax = nnz; 2033 } 2034 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 2035 2036 ierr = PetscMalloc1(bi[pn]+1,&bj);CHKERRQ(ierr); 2037 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 2038 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 2039 if (afill_tmp > afill) afill = afill_tmp; 2040 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 2041 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 2042 2043 ierr = MatDestroy(&POt);CHKERRQ(ierr); 2044 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 2045 2046 /* create symbolic parallel matrix Cmpi - why cannot be assembled in Numeric part */ 2047 /*----------------------------------------------------------------------------------*/ 2048 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 2049 ierr = MatSetSizes(Cmpi,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2050 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 2051 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 2052 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 2053 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 2054 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 2055 ierr = MatSetBlockSize(Cmpi,1);CHKERRQ(ierr); 2056 for (i=0; i<pn; i++) { 2057 row = i + rstart; 2058 nnz = bi[i+1] - bi[i]; 2059 Jptr = bj + bi[i]; 2060 ierr = MatSetValues(Cmpi,1,&row,nnz,Jptr,NULL,INSERT_VALUES);CHKERRQ(ierr); 2061 } 2062 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2063 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2064 merge->bi = bi; 2065 merge->bj = bj; 2066 merge->coi = coi; 2067 merge->coj = coj; 2068 merge->buf_ri = buf_ri; 2069 merge->buf_rj = buf_rj; 2070 merge->owners_co = owners_co; 2071 2072 /* attach the supporting struct to Cmpi for reuse */ 2073 c = (Mat_MPIAIJ*)Cmpi->data; 2074 2075 c->ap = ptap; 2076 ptap->api = NULL; 2077 ptap->apj = NULL; 2078 ptap->merge = merge; 2079 ptap->apa = NULL; 2080 ptap->destroy = Cmpi->ops->destroy; 2081 ptap->duplicate = Cmpi->ops->duplicate; 2082 2083 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ; 2084 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 2085 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 2086 2087 *C = Cmpi; 2088 #if defined(PETSC_USE_INFO) 2089 if (bi[pn] != 0) { 2090 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 2091 ierr = PetscInfo1(Cmpi,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 2092 } else { 2093 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 2094 } 2095 #endif 2096 PetscFunctionReturn(0); 2097 } 2098