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 *C = NULL; 352 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 353 ierr = MatMatMultSymbolic_MPIAIJ_MPIDense(A,B,fill,C);CHKERRQ(ierr); 354 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 355 } 356 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 357 ierr = MatMatMultNumeric_MPIAIJ_MPIDense(A,B,*C);CHKERRQ(ierr); 358 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 359 PetscFunctionReturn(0); 360 } 361 362 typedef struct { 363 Mat workB,Bb,Cb,workB1,Bb1,Cb1; 364 MPI_Request *rwaits,*swaits; 365 PetscInt numBb; /* num of Bb matrices */ 366 PetscInt nsends,nrecvs; 367 MPI_Datatype *stype,*rtype; 368 } MPIAIJ_MPIDense; 369 370 PetscErrorCode MatMPIAIJ_MPIDenseDestroy(void *ctx) 371 { 372 MPIAIJ_MPIDense *contents = (MPIAIJ_MPIDense*)ctx; 373 PetscErrorCode ierr; 374 PetscInt i; 375 376 PetscFunctionBegin; 377 ierr = MatDestroy(&contents->workB);CHKERRQ(ierr); 378 379 if (contents->numBb) { 380 ierr = MatDestroy(&contents->Bb);CHKERRQ(ierr); 381 ierr = MatDestroy(&contents->Cb);CHKERRQ(ierr); 382 383 ierr = MatDestroy(&contents->workB1);CHKERRQ(ierr); 384 ierr = MatDestroy(&contents->Bb1);CHKERRQ(ierr); 385 ierr = MatDestroy(&contents->Cb1);CHKERRQ(ierr); 386 } 387 for (i=0; i<contents->nsends; i++) { 388 ierr = MPI_Type_free(&contents->stype[i]);CHKERRQ(ierr); 389 } 390 for (i=0; i<contents->nrecvs; i++) { 391 ierr = MPI_Type_free(&contents->rtype[i]);CHKERRQ(ierr); 392 } 393 ierr = PetscFree4(contents->stype,contents->rtype,contents->rwaits,contents->swaits);CHKERRQ(ierr); 394 ierr = PetscFree(contents);CHKERRQ(ierr); 395 PetscFunctionReturn(0); 396 } 397 398 /* 399 This is a "dummy function" that handles the case where matrix C was created as a dense matrix 400 directly by the user and passed to MatMatMult() with the MAT_REUSE_MATRIX option 401 402 It is the same as MatMatMultSymbolic_MPIAIJ_MPIDense() except does not create C 403 */ 404 PetscErrorCode MatMatMultNumeric_MPIDense(Mat A,Mat B,Mat C) 405 { 406 PetscErrorCode ierr; 407 408 PetscFunctionBegin; 409 ierr = MatMatMultSymbolic_MPIAIJ_MPIDense(A,B,0,&C);CHKERRQ(ierr); 410 ierr = (*C->ops->matmultnumeric)(A,B,C);CHKERRQ(ierr); 411 PetscFunctionReturn(0); 412 } 413 414 /* 415 Create Bb, Cb, Bb1 and Cb1 matrices to be used by MatMatMult_MPIAIJ_MPIDense(). 416 These matrices are used as wrappers for sub-columns of B and C, thus their own matrix operations are not used. 417 Modified from MatCreateDense(). 418 */ 419 PETSC_STATIC_INLINE PetscErrorCode MatCreateSubMPIDense_private(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,PetscInt rbs,PetscInt cbs,PetscScalar *data,Mat *A) 420 { 421 PetscErrorCode ierr; 422 423 PetscFunctionBegin; 424 ierr = MatCreate(comm,A);CHKERRQ(ierr); 425 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 426 ierr = MatSetBlockSizes(*A,rbs,cbs);CHKERRQ(ierr); 427 ierr = MatSetType(*A,MATMPIDENSE);CHKERRQ(ierr); 428 ierr = MatMPIDenseSetPreallocation(*A,data);CHKERRQ(ierr); 429 (*A)->assembled = PETSC_TRUE; 430 PetscFunctionReturn(0); 431 } 432 433 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat A,Mat B,PetscReal fill,Mat *C) 434 { 435 PetscErrorCode ierr; 436 Mat_MPIAIJ *aij=(Mat_MPIAIJ*)A->data; 437 Mat_MPIDense *b=(Mat_MPIDense*)B->data; 438 Mat_SeqDense *bseq=(Mat_SeqDense*)(b->A)->data; 439 PetscInt nz=aij->B->cmap->n,nsends,nrecvs,i,nrows_to,j,lda=bseq->lda; 440 PetscContainer container; 441 MPIAIJ_MPIDense *contents; 442 VecScatter ctx=aij->Mvctx; 443 PetscInt Am=A->rmap->n,Bm=B->rmap->n,Bn=B->cmap->n,BN=B->cmap->N,Bbn,Bbn1,bs,nrows_from; 444 MPI_Comm comm; 445 MPI_Datatype type1,*stype,*rtype; 446 const PetscInt *sindices,*sstarts,*rstarts; 447 PetscMPIInt *disp; 448 449 PetscFunctionBegin; 450 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 451 if (!(*C)) { 452 ierr = MatCreate(comm,C);CHKERRQ(ierr); 453 ierr = MatSetSizes(*C,Am,Bn,A->rmap->N,BN);CHKERRQ(ierr); 454 ierr = MatSetBlockSizesFromMats(*C,A,B);CHKERRQ(ierr); 455 ierr = MatSetType(*C,MATMPIDENSE);CHKERRQ(ierr); 456 ierr = MatMPIDenseSetPreallocation(*C,NULL);CHKERRQ(ierr); 457 ierr = MatAssemblyBegin(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 458 ierr = MatAssemblyEnd(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 459 } else { 460 /* Check matrix size */ 461 if ((*C)->rmap->n != A->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local row dimensions are incompatible, %D != %D",(*C)->rmap->n,A->rmap->n); 462 if ((*C)->cmap->n != B->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local column dimensions are incompatible, %D != %D",(*C)->cmap->n,B->cmap->n); 463 } 464 465 (*C)->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 466 467 ierr = PetscNew(&contents);CHKERRQ(ierr); 468 contents->numBb = 0; 469 470 ierr = VecScatterGetRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,NULL,NULL);CHKERRQ(ierr); 471 ierr = VecScatterGetRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,NULL,NULL);CHKERRQ(ierr); 472 473 /* Create column block of B and C for memory scalability when BN is too large */ 474 /* Estimate Bbn, column size of Bb */ 475 if (nz) { 476 Bbn1 = 2*Am*BN/nz; 477 } else Bbn1 = BN; 478 479 bs = PetscAbs(B->cmap->bs); 480 Bbn1 = Bbn1/bs *bs; /* Bbn1 is a multiple of bs */ 481 if (Bbn1 > BN) Bbn1 = BN; 482 ierr = MPI_Allreduce(&Bbn1,&Bbn,1,MPIU_INT,MPI_MAX,comm);CHKERRQ(ierr); 483 484 /* Enable runtime option for Bbn */ 485 ierr = PetscOptionsBegin(comm,((PetscObject)*C)->prefix,"MatMatMult","Mat");CHKERRQ(ierr); 486 ierr = PetscOptionsInt("-matmatmult_Bbn","Number of columns in Bb","MatMatMult",Bbn,&Bbn,NULL);CHKERRQ(ierr); 487 if (Bbn > BN) SETERRQ2(comm,PETSC_ERR_ARG_SIZ,"Bbn=%D cannot be larger than %D, column size of B",Bbn,BN); 488 ierr = PetscOptionsEnd();CHKERRQ(ierr); 489 490 if (Bbn < BN) { 491 contents->numBb = BN/Bbn; 492 Bbn1 = BN - contents->numBb*Bbn; 493 } 494 495 if (contents->numBb) { 496 PetscScalar data[1]; /* fake array for Bb and Cb */ 497 ierr = PetscInfo3(*C,"use Bb, BN=%D, Bbn=%D; numBb=%D\n",BN,Bbn,contents->numBb);CHKERRQ(ierr); 498 ierr = MatCreateSubMPIDense_private(comm,B->rmap->n,PETSC_DECIDE,A->rmap->N,Bbn,B->rmap->bs,B->cmap->bs,data,&contents->Bb);CHKERRQ(ierr); 499 ierr = MatCreateSubMPIDense_private(comm,Am,PETSC_DECIDE,A->rmap->N,Bbn,(*C)->rmap->bs,(*C)->cmap->bs,data,&contents->Cb);CHKERRQ(ierr); 500 501 if (Bbn1) { /* Create Bb1 and Cb1 for the remaining columns */ 502 ierr = PetscInfo2(*C,"use Bb1, BN=%D, Bbn1=%D\n",BN,Bbn1);CHKERRQ(ierr); 503 ierr = MatCreateSubMPIDense_private(comm,B->rmap->n,PETSC_DECIDE,A->rmap->N,Bbn1,B->rmap->bs,B->cmap->bs,data,&contents->Bb1);CHKERRQ(ierr); 504 ierr = MatCreateSubMPIDense_private(comm,Am,PETSC_DECIDE,A->rmap->N,Bbn1,(*C)->rmap->bs,(*C)->cmap->bs,data,&contents->Cb1);CHKERRQ(ierr); 505 506 /* Create work matrix used to store off processor rows of B needed for local product */ 507 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,Bbn1,NULL,&contents->workB1);CHKERRQ(ierr); 508 } 509 } 510 511 /* Create work matrix used to store off processor rows of B needed for local product */ 512 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,Bbn,NULL,&contents->workB);CHKERRQ(ierr); 513 514 /* Use MPI derived data type to reduce memory required by the send/recv buffers */ 515 ierr = PetscMalloc4(nsends,&stype,nrecvs,&rtype,nrecvs,&contents->rwaits,nsends,&contents->swaits);CHKERRQ(ierr); 516 contents->stype = stype; 517 contents->nsends = nsends; 518 519 contents->rtype = rtype; 520 contents->nrecvs = nrecvs; 521 522 ierr = PetscMalloc1(Bm+1,&disp);CHKERRQ(ierr); 523 for (i=0; i<nsends; i++) { 524 nrows_to = sstarts[i+1]-sstarts[i]; 525 for (j=0; j<nrows_to; j++){ 526 disp[j] = sindices[sstarts[i]+j]; /* rowB to be sent */ 527 } 528 ierr = MPI_Type_create_indexed_block(nrows_to,1,(const PetscMPIInt *)disp,MPIU_SCALAR,&type1);CHKERRQ(ierr); 529 530 ierr = MPI_Type_create_resized(type1,0,lda*sizeof(PetscScalar),&stype[i]);CHKERRQ(ierr); 531 ierr = MPI_Type_commit(&stype[i]);CHKERRQ(ierr); 532 ierr = MPI_Type_free(&type1);CHKERRQ(ierr); 533 } 534 535 for (i=0; i<nrecvs; i++) { 536 /* received values from a process form a (nrows_from x Bbn) row block in workB (column-wise) */ 537 nrows_from = rstarts[i+1]-rstarts[i]; 538 disp[0] = 0; 539 ierr = MPI_Type_create_indexed_block(1, nrows_from, (const PetscMPIInt *)disp, MPIU_SCALAR, &type1);CHKERRQ(ierr); 540 ierr = MPI_Type_create_resized(type1, 0, nz*sizeof(PetscScalar), &rtype[i]);CHKERRQ(ierr); 541 ierr = MPI_Type_commit(&rtype[i]);CHKERRQ(ierr); 542 ierr = MPI_Type_free(&type1);CHKERRQ(ierr); 543 } 544 545 ierr = PetscFree(disp);CHKERRQ(ierr); 546 ierr = VecScatterRestoreRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,NULL,NULL);CHKERRQ(ierr); 547 ierr = VecScatterRestoreRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,NULL,NULL);CHKERRQ(ierr); 548 549 ierr = PetscContainerCreate(comm,&container);CHKERRQ(ierr); 550 ierr = PetscContainerSetPointer(container,contents);CHKERRQ(ierr); 551 ierr = PetscContainerSetUserDestroy(container,MatMPIAIJ_MPIDenseDestroy);CHKERRQ(ierr); 552 ierr = PetscObjectCompose((PetscObject)(*C),"workB",(PetscObject)container);CHKERRQ(ierr); 553 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 554 PetscFunctionReturn(0); 555 } 556 557 extern PetscErrorCode MatMatMultNumericAdd_SeqAIJ_SeqDense(Mat,Mat,Mat); 558 /* 559 Performs an efficient scatter on the rows of B needed by this process; this is 560 a modification of the VecScatterBegin_() routines. 561 562 Input: Bbidx = 0: B = Bb 563 = 1: B = Bb1, see MatMatMultSymbolic_MPIAIJ_MPIDense() 564 */ 565 PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,PetscInt Bbidx,Mat C,Mat *outworkB) 566 { 567 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 568 PetscErrorCode ierr; 569 const PetscScalar *b; 570 PetscScalar *rvalues; 571 VecScatter ctx = aij->Mvctx; 572 const PetscInt *sindices,*sstarts,*rstarts; 573 const PetscMPIInt *sprocs,*rprocs; 574 PetscInt i,nsends,nrecvs,nrecvs2; 575 MPI_Request *swaits,*rwaits; 576 MPI_Comm comm; 577 PetscMPIInt tag=((PetscObject)ctx)->tag,ncols=B->cmap->N,nrows=aij->B->cmap->n,imdex,nsends_mpi,nrecvs_mpi; 578 MPI_Status status; 579 MPIAIJ_MPIDense *contents; 580 PetscContainer container; 581 Mat workB; 582 MPI_Datatype *stype,*rtype; 583 584 PetscFunctionBegin; 585 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 586 ierr = PetscObjectQuery((PetscObject)C,"workB",(PetscObject*)&container);CHKERRQ(ierr); 587 if (!container) SETERRQ(comm,PETSC_ERR_PLIB,"Container does not exist"); 588 ierr = PetscContainerGetPointer(container,(void**)&contents);CHKERRQ(ierr); 589 590 ierr = VecScatterGetRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,&sprocs,NULL/*bs*/);CHKERRQ(ierr); 591 ierr = VecScatterGetRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,&rprocs,NULL/*bs*/);CHKERRQ(ierr); 592 ierr = PetscMPIIntCast(nsends,&nsends_mpi);CHKERRQ(ierr); 593 ierr = PetscMPIIntCast(nrecvs,&nrecvs_mpi);CHKERRQ(ierr); 594 if (Bbidx == 0) { 595 workB = *outworkB = contents->workB; 596 } else { 597 workB = *outworkB = contents->workB1; 598 } 599 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); 600 swaits = contents->swaits; 601 rwaits = contents->rwaits; 602 603 ierr = MatDenseGetArrayRead(B,&b);CHKERRQ(ierr); 604 ierr = MatDenseGetArray(workB,&rvalues);CHKERRQ(ierr); 605 606 /* Post recv, use MPI derived data type to save memory */ 607 rtype = contents->rtype; 608 for (i=0; i<nrecvs; i++) { 609 ierr = MPI_Irecv(rvalues+(rstarts[i]-rstarts[0]),ncols,rtype[i],rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 610 } 611 612 stype = contents->stype; 613 for (i=0; i<nsends; i++) { 614 ierr = MPI_Isend(b,ncols,stype[i],sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 615 } 616 617 nrecvs2 = nrecvs; 618 while (nrecvs2) { 619 ierr = MPI_Waitany(nrecvs_mpi,rwaits,&imdex,&status);CHKERRQ(ierr); 620 nrecvs2--; 621 } 622 if (nsends) {ierr = MPI_Waitall(nsends_mpi,swaits,MPI_STATUSES_IGNORE);CHKERRQ(ierr);} 623 624 ierr = VecScatterRestoreRemote_Private(ctx,PETSC_TRUE/*send*/,&nsends,&sstarts,&sindices,&sprocs,NULL);CHKERRQ(ierr); 625 ierr = VecScatterRestoreRemoteOrdered_Private(ctx,PETSC_FALSE/*recv*/,&nrecvs,&rstarts,NULL,&rprocs,NULL);CHKERRQ(ierr); 626 ierr = MatDenseRestoreArrayRead(B,&b);CHKERRQ(ierr); 627 ierr = MatDenseRestoreArray(workB,&rvalues);CHKERRQ(ierr); 628 ierr = MatAssemblyBegin(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 629 ierr = MatAssemblyEnd(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 630 PetscFunctionReturn(0); 631 } 632 633 /* 634 Compute Cb = A*Bb 635 */ 636 PETSC_STATIC_INLINE PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense_private(Mat A,Mat Bb,PetscInt Bbidx,PetscInt start,Mat C,const PetscScalar *barray,PetscScalar *carray,Mat Cb) 637 { 638 PetscErrorCode ierr; 639 PetscInt start1; 640 Mat workB; 641 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 642 Mat_MPIDense *cbdense = (Mat_MPIDense*)Cb->data; 643 644 PetscFunctionBegin; 645 /* Place barray to Bb */ 646 start1 = start*Bb->rmap->n; 647 ierr = MatDensePlaceArray(Bb,barray+start1);CHKERRQ(ierr); 648 649 /* get off processor parts of Bb needed to complete Cb=A*Bb */ 650 ierr = MatMPIDenseScatter(A,Bb,Bbidx,C,&workB);CHKERRQ(ierr); 651 ierr = MatDenseResetArray(Bb);CHKERRQ(ierr); 652 653 /* off-diagonal block of A times nonlocal rows of Bb */ 654 /* Place carray to Cb */ 655 start1 = start*Cb->rmap->n; 656 ierr = MatDensePlaceArray(Cb,carray+start1);CHKERRQ(ierr); 657 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cbdense->A);CHKERRQ(ierr); 658 ierr = MatDenseResetArray(Cb);CHKERRQ(ierr); 659 PetscFunctionReturn(0); 660 } 661 662 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat A,Mat B,Mat C) 663 { 664 PetscErrorCode ierr; 665 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 666 Mat_MPIDense *bdense = (Mat_MPIDense*)B->data; 667 Mat_MPIDense *cdense = (Mat_MPIDense*)C->data; 668 Mat workB; 669 MPIAIJ_MPIDense *contents; 670 PetscContainer container; 671 MPI_Comm comm; 672 PetscInt numBb; 673 674 PetscFunctionBegin; 675 /* diagonal block of A times all local rows of B*/ 676 ierr = MatMatMultNumeric_SeqAIJ_SeqDense(aij->A,bdense->A,cdense->A);CHKERRQ(ierr); 677 678 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 679 ierr = PetscObjectQuery((PetscObject)C,"workB",(PetscObject*)&container);CHKERRQ(ierr); 680 if (!container) SETERRQ(comm,PETSC_ERR_PLIB,"Container does not exist"); 681 ierr = PetscContainerGetPointer(container,(void**)&contents);CHKERRQ(ierr); 682 numBb = contents->numBb; 683 684 if (!numBb) { 685 /* get off processor parts of B needed to complete C=A*B */ 686 ierr = MatMPIDenseScatter(A,B,0,C,&workB);CHKERRQ(ierr); 687 688 /* off-diagonal block of A times nonlocal rows of B */ 689 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A);CHKERRQ(ierr); 690 691 } else { 692 const PetscScalar *barray; 693 PetscScalar *carray; 694 Mat Bb=contents->Bb,Cb=contents->Cb; 695 PetscInt BbN=Bb->cmap->N,start,i; 696 697 ierr = MatDenseGetArrayRead(B,&barray);CHKERRQ(ierr); 698 ierr = MatDenseGetArray(C,&carray);CHKERRQ(ierr); 699 for (i=0; i<numBb; i++) { 700 start = i*BbN; 701 ierr = MatMatMultNumeric_MPIAIJ_MPIDense_private(A,Bb,0,start,C,barray,carray,Cb);CHKERRQ(ierr); 702 } 703 704 if (contents->Bb1) { 705 Bb = contents->Bb1; Cb = contents->Cb1; 706 start = i*BbN; 707 ierr = MatMatMultNumeric_MPIAIJ_MPIDense_private(A,Bb,1,start,C,barray,carray,Cb);CHKERRQ(ierr); 708 } 709 ierr = MatDenseRestoreArrayRead(B,&barray);CHKERRQ(ierr); 710 ierr = MatDenseRestoreArray(C,&carray);CHKERRQ(ierr); 711 } 712 PetscFunctionReturn(0); 713 } 714 715 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 716 { 717 PetscErrorCode ierr; 718 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 719 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 720 Mat_SeqAIJ *cd = (Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 721 PetscInt *adi = ad->i,*adj,*aoi=ao->i,*aoj; 722 PetscScalar *ada,*aoa,*cda=cd->a,*coa=co->a; 723 Mat_SeqAIJ *p_loc,*p_oth; 724 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pj; 725 PetscScalar *pa_loc,*pa_oth,*pa,valtmp,*ca; 726 PetscInt cm = C->rmap->n,anz,pnz; 727 Mat_APMPI *ptap = c->ap; 728 PetscScalar *apa_sparse; 729 PetscInt *api,*apj,*apJ,i,j,k,row; 730 PetscInt cstart = C->cmap->rstart; 731 PetscInt cdnz,conz,k0,k1,nextp; 732 MPI_Comm comm; 733 PetscMPIInt size; 734 735 PetscFunctionBegin; 736 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 737 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 738 739 if (!ptap->P_oth && size>1) { 740 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"AP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 741 } 742 apa_sparse = ptap->apa; 743 744 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 745 /*-----------------------------------------------------*/ 746 /* update numerical values of P_oth and P_loc */ 747 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 748 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 749 750 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 751 /*----------------------------------------------------------*/ 752 /* get data from symbolic products */ 753 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 754 pi_loc = p_loc->i; pj_loc = p_loc->j; pa_loc = p_loc->a; 755 if (size >1) { 756 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 757 pi_oth = p_oth->i; pj_oth = p_oth->j; pa_oth = p_oth->a; 758 } else { 759 p_oth = NULL; pi_oth = NULL; pj_oth = NULL; pa_oth = NULL; 760 } 761 762 api = ptap->api; 763 apj = ptap->apj; 764 for (i=0; i<cm; i++) { 765 apJ = apj + api[i]; 766 767 /* diagonal portion of A */ 768 anz = adi[i+1] - adi[i]; 769 adj = ad->j + adi[i]; 770 ada = ad->a + adi[i]; 771 for (j=0; j<anz; j++) { 772 row = adj[j]; 773 pnz = pi_loc[row+1] - pi_loc[row]; 774 pj = pj_loc + pi_loc[row]; 775 pa = pa_loc + pi_loc[row]; 776 /* perform sparse axpy */ 777 valtmp = ada[j]; 778 nextp = 0; 779 for (k=0; nextp<pnz; k++) { 780 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 781 apa_sparse[k] += valtmp*pa[nextp++]; 782 } 783 } 784 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 785 } 786 787 /* off-diagonal portion of A */ 788 anz = aoi[i+1] - aoi[i]; 789 aoj = ao->j + aoi[i]; 790 aoa = ao->a + aoi[i]; 791 for (j=0; j<anz; j++) { 792 row = aoj[j]; 793 pnz = pi_oth[row+1] - pi_oth[row]; 794 pj = pj_oth + pi_oth[row]; 795 pa = pa_oth + pi_oth[row]; 796 /* perform sparse axpy */ 797 valtmp = aoa[j]; 798 nextp = 0; 799 for (k=0; nextp<pnz; k++) { 800 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 801 apa_sparse[k] += valtmp*pa[nextp++]; 802 } 803 } 804 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 805 } 806 807 /* set values in C */ 808 cdnz = cd->i[i+1] - cd->i[i]; 809 conz = co->i[i+1] - co->i[i]; 810 811 /* 1st off-diagoanl part of C */ 812 ca = coa + co->i[i]; 813 k = 0; 814 for (k0=0; k0<conz; k0++) { 815 if (apJ[k] >= cstart) break; 816 ca[k0] = apa_sparse[k]; 817 apa_sparse[k] = 0.0; 818 k++; 819 } 820 821 /* diagonal part of C */ 822 ca = cda + cd->i[i]; 823 for (k1=0; k1<cdnz; k1++) { 824 ca[k1] = apa_sparse[k]; 825 apa_sparse[k] = 0.0; 826 k++; 827 } 828 829 /* 2nd off-diagoanl part of C */ 830 ca = coa + co->i[i]; 831 for (; k0<conz; k0++) { 832 ca[k0] = apa_sparse[k]; 833 apa_sparse[k] = 0.0; 834 k++; 835 } 836 } 837 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 838 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 839 840 if (ptap->freestruct) { 841 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 842 } 843 PetscFunctionReturn(0); 844 } 845 846 /* same as MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(), except using LLCondensed to avoid O(BN) memory requirement */ 847 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 848 { 849 PetscErrorCode ierr; 850 MPI_Comm comm; 851 PetscMPIInt size; 852 Mat Cmpi; 853 Mat_APMPI *ptap; 854 PetscFreeSpaceList free_space = NULL,current_space=NULL; 855 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c; 856 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 857 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 858 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 859 PetscInt i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi,*lnk,apnz_max=0; 860 PetscInt am=A->rmap->n,pn=P->cmap->n,pm=P->rmap->n,lsize=pn+20; 861 PetscReal afill; 862 MatType mtype; 863 864 PetscFunctionBegin; 865 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 866 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 867 868 /* create struct Mat_APMPI and attached it to C later */ 869 ierr = PetscNew(&ptap);CHKERRQ(ierr); 870 871 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 872 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 873 874 /* get P_loc by taking all local rows of P */ 875 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 876 877 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 878 pi_loc = p_loc->i; pj_loc = p_loc->j; 879 if (size > 1) { 880 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 881 pi_oth = p_oth->i; pj_oth = p_oth->j; 882 } else { 883 p_oth = NULL; 884 pi_oth = NULL; pj_oth = NULL; 885 } 886 887 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 888 /*-------------------------------------------------------------------*/ 889 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 890 ptap->api = api; 891 api[0] = 0; 892 893 ierr = PetscLLCondensedCreate_Scalable(lsize,&lnk);CHKERRQ(ierr); 894 895 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 896 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);CHKERRQ(ierr); 897 current_space = free_space; 898 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 899 for (i=0; i<am; i++) { 900 /* diagonal portion of A */ 901 nzi = adi[i+1] - adi[i]; 902 for (j=0; j<nzi; j++) { 903 row = *adj++; 904 pnz = pi_loc[row+1] - pi_loc[row]; 905 Jptr = pj_loc + pi_loc[row]; 906 /* Expand list if it is not long enough */ 907 if (pnz+apnz_max > lsize) { 908 lsize = pnz+apnz_max; 909 ierr = PetscLLCondensedExpand_Scalable(lsize, &lnk);CHKERRQ(ierr); 910 } 911 /* add non-zero cols of P into the sorted linked list lnk */ 912 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 913 apnz = *lnk; /* The first element in the list is the number of items in the list */ 914 api[i+1] = api[i] + apnz; 915 if (apnz > apnz_max) apnz_max = apnz; 916 } 917 /* off-diagonal portion of A */ 918 nzi = aoi[i+1] - aoi[i]; 919 for (j=0; j<nzi; j++) { 920 row = *aoj++; 921 pnz = pi_oth[row+1] - pi_oth[row]; 922 Jptr = pj_oth + pi_oth[row]; 923 /* Expand list if it is not long enough */ 924 if (pnz+apnz_max > lsize) { 925 lsize = pnz + apnz_max; 926 ierr = PetscLLCondensedExpand_Scalable(lsize, &lnk);CHKERRQ(ierr); 927 } 928 /* add non-zero cols of P into the sorted linked list lnk */ 929 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 930 apnz = *lnk; /* The first element in the list is the number of items in the list */ 931 api[i+1] = api[i] + apnz; 932 if (apnz > apnz_max) apnz_max = apnz; 933 } 934 apnz = *lnk; 935 api[i+1] = api[i] + apnz; 936 if (apnz > apnz_max) apnz_max = apnz; 937 938 /* if free space is not available, double the total space in the list */ 939 if (current_space->local_remaining<apnz) { 940 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 941 nspacedouble++; 942 } 943 944 /* Copy data into free space, then initialize lnk */ 945 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 946 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 947 948 current_space->array += apnz; 949 current_space->local_used += apnz; 950 current_space->local_remaining -= apnz; 951 } 952 953 /* Allocate space for apj, initialize apj, and */ 954 /* destroy list of free space and other temporary array(s) */ 955 ierr = PetscMalloc1(api[am]+1,&ptap->apj);CHKERRQ(ierr); 956 apj = ptap->apj; 957 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 958 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 959 960 /* create and assemble symbolic parallel matrix Cmpi */ 961 /*----------------------------------------------------*/ 962 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 963 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 964 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 965 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 966 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 967 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 968 969 /* malloc apa for assembly Cmpi */ 970 ierr = PetscCalloc1(apnz_max,&ptap->apa);CHKERRQ(ierr); 971 972 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(Cmpi, apj, api);CHKERRQ(ierr); 973 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 974 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 975 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 976 977 ptap->destroy = Cmpi->ops->destroy; 978 ptap->duplicate = Cmpi->ops->duplicate; 979 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ; 980 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 981 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 982 983 /* attach the supporting struct to Cmpi for reuse */ 984 c = (Mat_MPIAIJ*)Cmpi->data; 985 c->ap = ptap; 986 *C = Cmpi; 987 988 /* set MatInfo */ 989 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 990 if (afill < 1.0) afill = 1.0; 991 Cmpi->info.mallocs = nspacedouble; 992 Cmpi->info.fill_ratio_given = fill; 993 Cmpi->info.fill_ratio_needed = afill; 994 995 #if defined(PETSC_USE_INFO) 996 if (api[am]) { 997 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 998 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 999 } else { 1000 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1001 } 1002 #endif 1003 PetscFunctionReturn(0); 1004 } 1005 1006 /* This function is needed for the seqMPI matrix-matrix multiplication. */ 1007 /* Three input arrays are merged to one output array. The size of the */ 1008 /* output array is also output. Duplicate entries only show up once. */ 1009 static void Merge3SortedArrays(PetscInt size1, PetscInt *in1, 1010 PetscInt size2, PetscInt *in2, 1011 PetscInt size3, PetscInt *in3, 1012 PetscInt *size4, PetscInt *out) 1013 { 1014 int i = 0, j = 0, k = 0, l = 0; 1015 1016 /* Traverse all three arrays */ 1017 while (i<size1 && j<size2 && k<size3) { 1018 if (in1[i] < in2[j] && in1[i] < in3[k]) { 1019 out[l++] = in1[i++]; 1020 } 1021 else if(in2[j] < in1[i] && in2[j] < in3[k]) { 1022 out[l++] = in2[j++]; 1023 } 1024 else if(in3[k] < in1[i] && in3[k] < in2[j]) { 1025 out[l++] = in3[k++]; 1026 } 1027 else if(in1[i] == in2[j] && in1[i] < in3[k]) { 1028 out[l++] = in1[i]; 1029 i++, j++; 1030 } 1031 else if(in1[i] == in3[k] && in1[i] < in2[j]) { 1032 out[l++] = in1[i]; 1033 i++, k++; 1034 } 1035 else if(in3[k] == in2[j] && in2[j] < in1[i]) { 1036 out[l++] = in2[j]; 1037 k++, j++; 1038 } 1039 else if(in1[i] == in2[j] && in1[i] == in3[k]) { 1040 out[l++] = in1[i]; 1041 i++, j++, k++; 1042 } 1043 } 1044 1045 /* Traverse two remaining arrays */ 1046 while (i<size1 && j<size2) { 1047 if (in1[i] < in2[j]) { 1048 out[l++] = in1[i++]; 1049 } 1050 else if(in1[i] > in2[j]) { 1051 out[l++] = in2[j++]; 1052 } 1053 else { 1054 out[l++] = in1[i]; 1055 i++, j++; 1056 } 1057 } 1058 1059 while (i<size1 && k<size3) { 1060 if (in1[i] < in3[k]) { 1061 out[l++] = in1[i++]; 1062 } 1063 else if(in1[i] > in3[k]) { 1064 out[l++] = in3[k++]; 1065 } 1066 else { 1067 out[l++] = in1[i]; 1068 i++, k++; 1069 } 1070 } 1071 1072 while (k<size3 && j<size2) { 1073 if (in3[k] < in2[j]) { 1074 out[l++] = in3[k++]; 1075 } 1076 else if(in3[k] > in2[j]) { 1077 out[l++] = in2[j++]; 1078 } 1079 else { 1080 out[l++] = in3[k]; 1081 k++, j++; 1082 } 1083 } 1084 1085 /* Traverse one remaining array */ 1086 while (i<size1) out[l++] = in1[i++]; 1087 while (j<size2) out[l++] = in2[j++]; 1088 while (k<size3) out[l++] = in3[k++]; 1089 1090 *size4 = l; 1091 } 1092 1093 /* This matrix-matrix multiplication algorithm divides the multiplication into three multiplications and */ 1094 /* adds up the products. Two of these three multiplications are performed with existing (sequential) */ 1095 /* matrix-matrix multiplications. */ 1096 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_seqMPI(Mat A, Mat P, PetscReal fill, Mat *C) 1097 { 1098 PetscErrorCode ierr; 1099 MPI_Comm comm; 1100 PetscMPIInt size; 1101 Mat Cmpi; 1102 Mat_APMPI *ptap; 1103 PetscFreeSpaceList free_space_diag=NULL, current_space=NULL; 1104 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data; 1105 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc; 1106 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data; 1107 Mat_MPIAIJ *c; 1108 Mat_SeqAIJ *adpd_seq, *p_off, *aopoth_seq; 1109 PetscInt adponz, adpdnz; 1110 PetscInt *pi_loc,*dnz,*onz; 1111 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,rstart=A->rmap->rstart; 1112 PetscInt *lnk,i, i1=0,pnz,row,*adpoi,*adpoj, *api, *adpoJ, *aopJ, *apJ,*Jptr, aopnz, nspacedouble=0,j,nzi, 1113 *apj,apnz, *adpdi, *adpdj, *adpdJ, *poff_i, *poff_j, *j_temp, *aopothi, *aopothj; 1114 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n, p_colstart, p_colend; 1115 PetscBT lnkbt; 1116 PetscReal afill; 1117 PetscMPIInt rank; 1118 Mat adpd, aopoth; 1119 MatType mtype; 1120 const char *prefix; 1121 1122 PetscFunctionBegin; 1123 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1124 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1125 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1126 ierr = MatGetOwnershipRangeColumn(P, &p_colstart, &p_colend); CHKERRQ(ierr); 1127 1128 /* create struct Mat_APMPI and attached it to C later */ 1129 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1130 1131 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1132 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1133 1134 /* get P_loc by taking all local rows of P */ 1135 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1136 1137 1138 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1139 pi_loc = p_loc->i; 1140 1141 /* Allocate memory for the i arrays of the matrices A*P, A_diag*P_off and A_offd * P */ 1142 ierr = PetscMalloc1(am+2,&api);CHKERRQ(ierr); 1143 ierr = PetscMalloc1(am+2,&adpoi);CHKERRQ(ierr); 1144 1145 adpoi[0] = 0; 1146 ptap->api = api; 1147 api[0] = 0; 1148 1149 /* create and initialize a linked list, will be used for both A_diag * P_loc_off and A_offd * P_oth */ 1150 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1151 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 1152 1153 /* Symbolic calc of A_loc_diag * P_loc_diag */ 1154 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1155 ierr = MatSetOptionsPrefix(a->A,prefix);CHKERRQ(ierr); 1156 ierr = MatAppendOptionsPrefix(a->A,"inner_diag_");CHKERRQ(ierr); 1157 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(a->A, p->A, fill, &adpd);CHKERRQ(ierr); 1158 adpd_seq = (Mat_SeqAIJ*)((adpd)->data); 1159 adpdi = adpd_seq->i; adpdj = adpd_seq->j; 1160 p_off = (Mat_SeqAIJ*)((p->B)->data); 1161 poff_i = p_off->i; poff_j = p_off->j; 1162 1163 /* j_temp stores indices of a result row before they are added to the linked list */ 1164 ierr = PetscMalloc1(pN+2,&j_temp);CHKERRQ(ierr); 1165 1166 1167 /* Symbolic calc of the A_diag * p_loc_off */ 1168 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 1169 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space_diag);CHKERRQ(ierr); 1170 current_space = free_space_diag; 1171 1172 for (i=0; i<am; i++) { 1173 /* A_diag * P_loc_off */ 1174 nzi = adi[i+1] - adi[i]; 1175 for (j=0; j<nzi; j++) { 1176 row = *adj++; 1177 pnz = poff_i[row+1] - poff_i[row]; 1178 Jptr = poff_j + poff_i[row]; 1179 for(i1 = 0; i1 < pnz; i1++) { 1180 j_temp[i1] = p->garray[Jptr[i1]]; 1181 } 1182 /* add non-zero cols of P into the sorted linked list lnk */ 1183 ierr = PetscLLCondensedAddSorted(pnz,j_temp,lnk,lnkbt);CHKERRQ(ierr); 1184 } 1185 1186 adponz = lnk[0]; 1187 adpoi[i+1] = adpoi[i] + adponz; 1188 1189 /* if free space is not available, double the total space in the list */ 1190 if (current_space->local_remaining<adponz) { 1191 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(adponz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1192 nspacedouble++; 1193 } 1194 1195 /* Copy data into free space, then initialize lnk */ 1196 ierr = PetscLLCondensedClean(pN,adponz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1197 1198 current_space->array += adponz; 1199 current_space->local_used += adponz; 1200 current_space->local_remaining -= adponz; 1201 } 1202 1203 /* Symbolic calc of A_off * P_oth */ 1204 ierr = MatSetOptionsPrefix(a->B,prefix);CHKERRQ(ierr); 1205 ierr = MatAppendOptionsPrefix(a->B,"inner_offdiag_");CHKERRQ(ierr); 1206 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(a->B, ptap->P_oth, fill, &aopoth);CHKERRQ(ierr); 1207 aopoth_seq = (Mat_SeqAIJ*)((aopoth)->data); 1208 aopothi = aopoth_seq->i; aopothj = aopoth_seq->j; 1209 1210 /* Allocate space for apj, adpj, aopj, ... */ 1211 /* destroy lists of free space and other temporary array(s) */ 1212 1213 ierr = PetscMalloc1(aopothi[am] + adpoi[am] + adpdi[am]+2, &ptap->apj);CHKERRQ(ierr); 1214 ierr = PetscMalloc1(adpoi[am]+2, &adpoj);CHKERRQ(ierr); 1215 1216 /* Copy from linked list to j-array */ 1217 ierr = PetscFreeSpaceContiguous(&free_space_diag,adpoj);CHKERRQ(ierr); 1218 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1219 1220 adpoJ = adpoj; 1221 adpdJ = adpdj; 1222 aopJ = aopothj; 1223 apj = ptap->apj; 1224 apJ = apj; /* still empty */ 1225 1226 /* Merge j-arrays of A_off * P, A_diag * P_loc_off, and */ 1227 /* A_diag * P_loc_diag to get A*P */ 1228 for (i = 0; i < am; i++) { 1229 aopnz = aopothi[i+1] - aopothi[i]; 1230 adponz = adpoi[i+1] - adpoi[i]; 1231 adpdnz = adpdi[i+1] - adpdi[i]; 1232 1233 /* Correct indices from A_diag*P_diag */ 1234 for(i1 = 0; i1 < adpdnz; i1++) { 1235 adpdJ[i1] += p_colstart; 1236 } 1237 /* Merge j-arrays of A_diag * P_loc_off and A_diag * P_loc_diag and A_off * P_oth */ 1238 Merge3SortedArrays(adponz, adpoJ, adpdnz, adpdJ, aopnz, aopJ, &apnz, apJ); 1239 ierr = MatPreallocateSet(i+rstart, apnz, apJ, dnz, onz); CHKERRQ(ierr); 1240 1241 aopJ += aopnz; 1242 adpoJ += adponz; 1243 adpdJ += adpdnz; 1244 apJ += apnz; 1245 api[i+1] = api[i] + apnz; 1246 } 1247 1248 /* malloc apa to store dense row A[i,:]*P */ 1249 ierr = PetscCalloc1(pN+2,&ptap->apa);CHKERRQ(ierr); 1250 1251 /* create and assemble symbolic parallel matrix Cmpi */ 1252 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1253 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1254 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 1255 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1256 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1257 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1258 1259 1260 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(Cmpi, apj, api);CHKERRQ(ierr); 1261 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1262 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1263 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1264 1265 1266 ptap->destroy = Cmpi->ops->destroy; 1267 ptap->duplicate = Cmpi->ops->duplicate; 1268 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1269 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 1270 1271 /* attach the supporting struct to Cmpi for reuse */ 1272 c = (Mat_MPIAIJ*)Cmpi->data; 1273 c->ap = ptap; 1274 *C = Cmpi; 1275 1276 /* set MatInfo */ 1277 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 1278 if (afill < 1.0) afill = 1.0; 1279 Cmpi->info.mallocs = nspacedouble; 1280 Cmpi->info.fill_ratio_given = fill; 1281 Cmpi->info.fill_ratio_needed = afill; 1282 1283 #if defined(PETSC_USE_INFO) 1284 if (api[am]) { 1285 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1286 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 1287 } else { 1288 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1289 } 1290 #endif 1291 1292 ierr = MatDestroy(&aopoth);CHKERRQ(ierr); 1293 ierr = MatDestroy(&adpd);CHKERRQ(ierr); 1294 ierr = PetscFree(j_temp);CHKERRQ(ierr); 1295 ierr = PetscFree(adpoj);CHKERRQ(ierr); 1296 ierr = PetscFree(adpoi);CHKERRQ(ierr); 1297 PetscFunctionReturn(0); 1298 } 1299 1300 1301 /*-------------------------------------------------------------------------*/ 1302 PetscErrorCode MatTransposeMatMult_MPIAIJ_MPIAIJ(Mat P,Mat A,MatReuse scall,PetscReal fill,Mat *C) 1303 { 1304 PetscErrorCode ierr; 1305 const char *algTypes[3] = {"scalable","nonscalable","matmatmult"}; 1306 PetscInt aN=A->cmap->N,alg=1; /* set default algorithm */ 1307 PetscBool flg; 1308 1309 PetscFunctionBegin; 1310 if (scall == MAT_INITIAL_MATRIX) { 1311 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatTransposeMatMult","Mat");CHKERRQ(ierr); 1312 ierr = PetscOptionsEList("-mattransposematmult_via","Algorithmic approach","MatTransposeMatMult",algTypes,3,algTypes[1],&alg,&flg);CHKERRQ(ierr); 1313 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1314 1315 ierr = PetscLogEventBegin(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 1316 switch (alg) { 1317 case 1: 1318 if (!flg && aN > 100000) { /* may switch to scalable algorithm as default */ 1319 MatInfo Ainfo,Pinfo; 1320 PetscInt nz_local; 1321 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 1322 MPI_Comm comm; 1323 1324 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 1325 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 1326 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); /* estimated local nonzero entries */ 1327 1328 if (aN > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 1329 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1330 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 1331 1332 if (alg_scalable) { 1333 alg = 0; /* scalable algorithm would slower than nonscalable algorithm */ 1334 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(P,A,fill,C);CHKERRQ(ierr); 1335 break; 1336 } 1337 } 1338 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(P,A,fill,C);CHKERRQ(ierr); 1339 break; 1340 case 2: 1341 { 1342 Mat Pt; 1343 Mat_APMPI *ptap; 1344 Mat_MPIAIJ *c; 1345 ierr = MatTranspose(P,MAT_INITIAL_MATRIX,&Pt);CHKERRQ(ierr); 1346 ierr = MatMatMult(Pt,A,MAT_INITIAL_MATRIX,fill,C);CHKERRQ(ierr); 1347 c = (Mat_MPIAIJ*)(*C)->data; 1348 ptap = c->ap; 1349 if (ptap) { 1350 ptap->Pt = Pt; 1351 (*C)->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1352 } 1353 (*C)->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult; 1354 PetscFunctionReturn(0); 1355 } 1356 break; 1357 default: /* scalable algorithm */ 1358 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(P,A,fill,C);CHKERRQ(ierr); 1359 break; 1360 } 1361 ierr = PetscLogEventEnd(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 1362 1363 { 1364 Mat_MPIAIJ *c = (Mat_MPIAIJ*)(*C)->data; 1365 Mat_APMPI *ap = c->ap; 1366 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)(*C)),((PetscObject)(*C))->prefix,"MatFreeIntermediateDataStructures","Mat");CHKERRQ(ierr); 1367 ap->freestruct = PETSC_FALSE; 1368 ierr = PetscOptionsBool("-mat_freeintermediatedatastructures","Free intermediate data structures", "MatFreeIntermediateDataStructures",ap->freestruct,&ap->freestruct, NULL);CHKERRQ(ierr); 1369 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1370 } 1371 } 1372 1373 ierr = PetscLogEventBegin(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 1374 ierr = (*(*C)->ops->mattransposemultnumeric)(P,A,*C);CHKERRQ(ierr); 1375 ierr = PetscLogEventEnd(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 1376 PetscFunctionReturn(0); 1377 } 1378 1379 /* This routine only works when scall=MAT_REUSE_MATRIX! */ 1380 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult(Mat P,Mat A,Mat C) 1381 { 1382 PetscErrorCode ierr; 1383 Mat_MPIAIJ *c=(Mat_MPIAIJ*)C->data; 1384 Mat_APMPI *ptap= c->ap; 1385 Mat Pt; 1386 1387 PetscFunctionBegin; 1388 if (!ptap->Pt) { 1389 MPI_Comm comm; 1390 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1391 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1392 } 1393 1394 Pt=ptap->Pt; 1395 ierr = MatTranspose(P,MAT_REUSE_MATRIX,&Pt);CHKERRQ(ierr); 1396 ierr = MatMatMultNumeric(Pt,A,C);CHKERRQ(ierr); 1397 1398 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1399 if (ptap->freestruct) { 1400 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1401 } 1402 PetscFunctionReturn(0); 1403 } 1404 1405 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ() */ 1406 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,PetscReal fill,Mat *C) 1407 { 1408 PetscErrorCode ierr; 1409 Mat_APMPI *ptap; 1410 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1411 MPI_Comm comm; 1412 PetscMPIInt size,rank; 1413 Mat Cmpi; 1414 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1415 PetscInt pn=P->cmap->n,aN=A->cmap->N,an=A->cmap->n; 1416 PetscInt *lnk,i,k,nsend; 1417 PetscBT lnkbt; 1418 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 1419 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1420 PetscInt len,proc,*dnz,*onz,*owners,nzi; 1421 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1422 MPI_Request *swaits,*rwaits; 1423 MPI_Status *sstatus,rstatus; 1424 PetscLayout rowmap; 1425 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1426 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1427 PetscInt *Jptr,*prmap=p->garray,con,j,Crmax; 1428 Mat_SeqAIJ *a_loc,*c_loc,*c_oth; 1429 PetscTable ta; 1430 MatType mtype; 1431 const char *prefix; 1432 1433 PetscFunctionBegin; 1434 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1435 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1436 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1437 1438 /* create symbolic parallel matrix Cmpi */ 1439 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1440 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1441 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1442 1443 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1444 1445 /* create struct Mat_APMPI and attached it to C later */ 1446 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1447 ptap->reuse = MAT_INITIAL_MATRIX; 1448 1449 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1450 /* --------------------------------- */ 1451 ierr = MatTranspose_SeqAIJ(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1452 ierr = MatTranspose_SeqAIJ(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1453 1454 /* (1) compute symbolic A_loc */ 1455 /* ---------------------------*/ 1456 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1457 1458 /* (2-1) compute symbolic C_oth = Ro*A_loc */ 1459 /* ------------------------------------ */ 1460 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1461 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 1462 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 1463 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->A_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 1464 1465 /* (3) send coj of C_oth to other processors */ 1466 /* ------------------------------------------ */ 1467 /* determine row ownership */ 1468 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1469 rowmap->n = pn; 1470 rowmap->bs = 1; 1471 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1472 owners = rowmap->range; 1473 1474 /* determine the number of messages to send, their lengths */ 1475 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1476 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 1477 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr); 1478 1479 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1480 coi = c_oth->i; coj = c_oth->j; 1481 con = ptap->C_oth->rmap->n; 1482 proc = 0; 1483 for (i=0; i<con; i++) { 1484 while (prmap[i] >= owners[proc+1]) proc++; 1485 len_si[proc]++; /* num of rows in Co(=Pt*A) to be sent to [proc] */ 1486 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1487 } 1488 1489 len = 0; /* max length of buf_si[], see (4) */ 1490 owners_co[0] = 0; 1491 nsend = 0; 1492 for (proc=0; proc<size; proc++) { 1493 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1494 if (len_s[proc]) { 1495 nsend++; 1496 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1497 len += len_si[proc]; 1498 } 1499 } 1500 1501 /* determine the number and length of messages to receive for coi and coj */ 1502 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1503 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1504 1505 /* post the Irecv and Isend of coj */ 1506 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1507 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1508 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1509 for (proc=0, k=0; proc<size; proc++) { 1510 if (!len_s[proc]) continue; 1511 i = owners_co[proc]; 1512 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1513 k++; 1514 } 1515 1516 /* (2-2) compute symbolic C_loc = Rd*A_loc */ 1517 /* ---------------------------------------- */ 1518 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 1519 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 1520 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->A_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 1521 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1522 1523 /* receives coj are complete */ 1524 for (i=0; i<nrecv; i++) { 1525 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1526 } 1527 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1528 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1529 1530 /* add received column indices into ta to update Crmax */ 1531 a_loc = (Mat_SeqAIJ*)(ptap->A_loc)->data; 1532 1533 /* create and initialize a linked list */ 1534 ierr = PetscTableCreate(an,aN,&ta);CHKERRQ(ierr); /* for compute Crmax */ 1535 MatRowMergeMax_SeqAIJ(a_loc,ptap->A_loc->rmap->N,ta); 1536 1537 for (k=0; k<nrecv; k++) {/* k-th received message */ 1538 Jptr = buf_rj[k]; 1539 for (j=0; j<len_r[k]; j++) { 1540 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1541 } 1542 } 1543 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1544 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1545 1546 /* (4) send and recv coi */ 1547 /*-----------------------*/ 1548 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1549 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1550 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1551 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1552 for (proc=0,k=0; proc<size; proc++) { 1553 if (!len_s[proc]) continue; 1554 /* form outgoing message for i-structure: 1555 buf_si[0]: nrows to be sent 1556 [1:nrows]: row index (global) 1557 [nrows+1:2*nrows+1]: i-structure index 1558 */ 1559 /*-------------------------------------------*/ 1560 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1561 buf_si_i = buf_si + nrows+1; 1562 buf_si[0] = nrows; 1563 buf_si_i[0] = 0; 1564 nrows = 0; 1565 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1566 nzi = coi[i+1] - coi[i]; 1567 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1568 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1569 nrows++; 1570 } 1571 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1572 k++; 1573 buf_si += len_si[proc]; 1574 } 1575 for (i=0; i<nrecv; i++) { 1576 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1577 } 1578 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1579 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1580 1581 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1582 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1583 ierr = PetscFree(swaits);CHKERRQ(ierr); 1584 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1585 1586 /* (5) compute the local portion of Cmpi */ 1587 /* ------------------------------------------ */ 1588 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 1589 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1590 current_space = free_space; 1591 1592 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1593 for (k=0; k<nrecv; k++) { 1594 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1595 nrows = *buf_ri_k[k]; 1596 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1597 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1598 } 1599 1600 ierr = MatPreallocateInitialize(comm,pn,an,dnz,onz);CHKERRQ(ierr); 1601 ierr = PetscLLCondensedCreate(Crmax,aN,&lnk,&lnkbt);CHKERRQ(ierr); 1602 for (i=0; i<pn; i++) { 1603 /* add C_loc into Cmpi */ 1604 nzi = c_loc->i[i+1] - c_loc->i[i]; 1605 Jptr = c_loc->j + c_loc->i[i]; 1606 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1607 1608 /* add received col data into lnk */ 1609 for (k=0; k<nrecv; k++) { /* k-th received message */ 1610 if (i == *nextrow[k]) { /* i-th row */ 1611 nzi = *(nextci[k]+1) - *nextci[k]; 1612 Jptr = buf_rj[k] + *nextci[k]; 1613 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1614 nextrow[k]++; nextci[k]++; 1615 } 1616 } 1617 nzi = lnk[0]; 1618 1619 /* copy data into free space, then initialize lnk */ 1620 ierr = PetscLLCondensedClean(aN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1621 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 1622 } 1623 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1624 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1625 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 1626 1627 /* local sizes and preallocation */ 1628 ierr = MatSetSizes(Cmpi,pn,an,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1629 if (P->cmap->bs > 0) {ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr);} 1630 if (A->cmap->bs > 0) {ierr = PetscLayoutSetBlockSize(Cmpi->cmap,A->cmap->bs);CHKERRQ(ierr);} 1631 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1632 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1633 1634 /* members in merge */ 1635 ierr = PetscFree(id_r);CHKERRQ(ierr); 1636 ierr = PetscFree(len_r);CHKERRQ(ierr); 1637 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 1638 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 1639 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 1640 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 1641 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 1642 1643 /* attach the supporting struct to Cmpi for reuse */ 1644 c = (Mat_MPIAIJ*)Cmpi->data; 1645 c->ap = ptap; 1646 ptap->destroy = Cmpi->ops->destroy; 1647 1648 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1649 Cmpi->assembled = PETSC_FALSE; 1650 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1651 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1652 1653 *C = Cmpi; 1654 PetscFunctionReturn(0); 1655 } 1656 1657 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,Mat C) 1658 { 1659 PetscErrorCode ierr; 1660 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1661 Mat_SeqAIJ *c_seq; 1662 Mat_APMPI *ptap = c->ap; 1663 Mat A_loc,C_loc,C_oth; 1664 PetscInt i,rstart,rend,cm,ncols,row; 1665 const PetscInt *cols; 1666 const PetscScalar *vals; 1667 1668 PetscFunctionBegin; 1669 if (!ptap->A_loc) { 1670 MPI_Comm comm; 1671 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1672 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1673 } 1674 1675 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1676 1677 if (ptap->reuse == MAT_REUSE_MATRIX) { 1678 /* These matrices are obtained in MatTransposeMatMultSymbolic() */ 1679 /* 1) get R = Pd^T, Ro = Po^T */ 1680 /*----------------------------*/ 1681 ierr = MatTranspose_SeqAIJ(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1682 ierr = MatTranspose_SeqAIJ(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1683 1684 /* 2) compute numeric A_loc */ 1685 /*--------------------------*/ 1686 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&ptap->A_loc);CHKERRQ(ierr); 1687 } 1688 1689 /* 3) C_loc = Rd*A_loc, C_oth = Ro*A_loc */ 1690 A_loc = ptap->A_loc; 1691 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,A_loc,ptap->C_loc);CHKERRQ(ierr); 1692 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,A_loc,ptap->C_oth);CHKERRQ(ierr); 1693 C_loc = ptap->C_loc; 1694 C_oth = ptap->C_oth; 1695 1696 /* add C_loc and Co to to C */ 1697 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1698 1699 /* C_loc -> C */ 1700 cm = C_loc->rmap->N; 1701 c_seq = (Mat_SeqAIJ*)C_loc->data; 1702 cols = c_seq->j; 1703 vals = c_seq->a; 1704 for (i=0; i<cm; i++) { 1705 ncols = c_seq->i[i+1] - c_seq->i[i]; 1706 row = rstart + i; 1707 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1708 cols += ncols; vals += ncols; 1709 } 1710 1711 /* Co -> C, off-processor part */ 1712 cm = C_oth->rmap->N; 1713 c_seq = (Mat_SeqAIJ*)C_oth->data; 1714 cols = c_seq->j; 1715 vals = c_seq->a; 1716 for (i=0; i<cm; i++) { 1717 ncols = c_seq->i[i+1] - c_seq->i[i]; 1718 row = p->garray[i]; 1719 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1720 cols += ncols; vals += ncols; 1721 } 1722 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1723 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1724 1725 ptap->reuse = MAT_REUSE_MATRIX; 1726 1727 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1728 if (ptap->freestruct) { 1729 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1730 } 1731 PetscFunctionReturn(0); 1732 } 1733 1734 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ(Mat P,Mat A,Mat C) 1735 { 1736 PetscErrorCode ierr; 1737 Mat_Merge_SeqsToMPI *merge; 1738 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1739 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1740 Mat_APMPI *ptap; 1741 PetscInt *adj; 1742 PetscInt i,j,k,anz,pnz,row,*cj,nexta; 1743 MatScalar *ada,*ca,valtmp; 1744 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1745 MPI_Comm comm; 1746 PetscMPIInt size,rank,taga,*len_s; 1747 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1748 PetscInt **buf_ri,**buf_rj; 1749 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1750 MPI_Request *s_waits,*r_waits; 1751 MPI_Status *status; 1752 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1753 PetscInt *ai,*aj,*coi,*coj,*poJ,*pdJ; 1754 Mat A_loc; 1755 Mat_SeqAIJ *a_loc; 1756 1757 PetscFunctionBegin; 1758 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1759 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1760 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1761 1762 ptap = c->ap; 1763 if (!ptap->A_loc) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtA cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1764 merge = ptap->merge; 1765 1766 /* 2) compute numeric C_seq = P_loc^T*A_loc */ 1767 /*------------------------------------------*/ 1768 /* get data from symbolic products */ 1769 coi = merge->coi; coj = merge->coj; 1770 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 1771 bi = merge->bi; bj = merge->bj; 1772 owners = merge->rowmap->range; 1773 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); 1774 1775 /* get A_loc by taking all local rows of A */ 1776 A_loc = ptap->A_loc; 1777 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 1778 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1779 ai = a_loc->i; 1780 aj = a_loc->j; 1781 1782 for (i=0; i<am; i++) { 1783 anz = ai[i+1] - ai[i]; 1784 adj = aj + ai[i]; 1785 ada = a_loc->a + ai[i]; 1786 1787 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 1788 /*-------------------------------------------------------------*/ 1789 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 1790 pnz = po->i[i+1] - po->i[i]; 1791 poJ = po->j + po->i[i]; 1792 pA = po->a + po->i[i]; 1793 for (j=0; j<pnz; j++) { 1794 row = poJ[j]; 1795 cj = coj + coi[row]; 1796 ca = coa + coi[row]; 1797 /* perform sparse axpy */ 1798 nexta = 0; 1799 valtmp = pA[j]; 1800 for (k=0; nexta<anz; k++) { 1801 if (cj[k] == adj[nexta]) { 1802 ca[k] += valtmp*ada[nexta]; 1803 nexta++; 1804 } 1805 } 1806 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1807 } 1808 1809 /* put the value into Cd (diagonal part) */ 1810 pnz = pd->i[i+1] - pd->i[i]; 1811 pdJ = pd->j + pd->i[i]; 1812 pA = pd->a + pd->i[i]; 1813 for (j=0; j<pnz; j++) { 1814 row = pdJ[j]; 1815 cj = bj + bi[row]; 1816 ca = ba + bi[row]; 1817 /* perform sparse axpy */ 1818 nexta = 0; 1819 valtmp = pA[j]; 1820 for (k=0; nexta<anz; k++) { 1821 if (cj[k] == adj[nexta]) { 1822 ca[k] += valtmp*ada[nexta]; 1823 nexta++; 1824 } 1825 } 1826 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1827 } 1828 } 1829 1830 /* 3) send and recv matrix values coa */ 1831 /*------------------------------------*/ 1832 buf_ri = merge->buf_ri; 1833 buf_rj = merge->buf_rj; 1834 len_s = merge->len_s; 1835 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1836 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1837 1838 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1839 for (proc=0,k=0; proc<size; proc++) { 1840 if (!len_s[proc]) continue; 1841 i = merge->owners_co[proc]; 1842 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1843 k++; 1844 } 1845 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1846 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1847 1848 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1849 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1850 ierr = PetscFree(coa);CHKERRQ(ierr); 1851 1852 /* 4) insert local Cseq and received values into Cmpi */ 1853 /*----------------------------------------------------*/ 1854 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1855 for (k=0; k<merge->nrecv; k++) { 1856 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1857 nrows = *(buf_ri_k[k]); 1858 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1859 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1860 } 1861 1862 for (i=0; i<cm; i++) { 1863 row = owners[rank] + i; /* global row index of C_seq */ 1864 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1865 ba_i = ba + bi[i]; 1866 bnz = bi[i+1] - bi[i]; 1867 /* add received vals into ba */ 1868 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1869 /* i-th row */ 1870 if (i == *nextrow[k]) { 1871 cnz = *(nextci[k]+1) - *nextci[k]; 1872 cj = buf_rj[k] + *(nextci[k]); 1873 ca = abuf_r[k] + *(nextci[k]); 1874 nextcj = 0; 1875 for (j=0; nextcj<cnz; j++) { 1876 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1877 ba_i[j] += ca[nextcj++]; 1878 } 1879 } 1880 nextrow[k]++; nextci[k]++; 1881 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1882 } 1883 } 1884 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1885 } 1886 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1887 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1888 1889 ierr = PetscFree(ba);CHKERRQ(ierr); 1890 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1891 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1892 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1893 1894 if (ptap->freestruct) { 1895 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1896 } 1897 PetscFunctionReturn(0); 1898 } 1899 1900 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(Mat P,Mat A,PetscReal fill,Mat *C) 1901 { 1902 PetscErrorCode ierr; 1903 Mat Cmpi,A_loc,POt,PDt; 1904 Mat_APMPI *ptap; 1905 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1906 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*a=(Mat_MPIAIJ*)A->data,*c; 1907 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1908 PetscInt nnz; 1909 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1910 PetscInt am =A->rmap->n,pn=P->cmap->n; 1911 MPI_Comm comm; 1912 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1913 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1914 PetscInt len,proc,*dnz,*onz,*owners; 1915 PetscInt nzi,*bi,*bj; 1916 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1917 MPI_Request *swaits,*rwaits; 1918 MPI_Status *sstatus,rstatus; 1919 Mat_Merge_SeqsToMPI *merge; 1920 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1921 PetscReal afill =1.0,afill_tmp; 1922 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N,Armax; 1923 Mat_SeqAIJ *a_loc,*pdt,*pot; 1924 PetscTable ta; 1925 MatType mtype; 1926 1927 PetscFunctionBegin; 1928 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1929 /* check if matrix local sizes are compatible */ 1930 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); 1931 1932 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1933 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1934 1935 /* create struct Mat_APMPI and attached it to C later */ 1936 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1937 1938 /* get A_loc by taking all local rows of A */ 1939 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1940 1941 ptap->A_loc = A_loc; 1942 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1943 ai = a_loc->i; 1944 aj = a_loc->j; 1945 1946 /* determine symbolic Co=(p->B)^T*A - send to others */ 1947 /*----------------------------------------------------*/ 1948 ierr = MatTransposeSymbolic_SeqAIJ(p->A,&PDt);CHKERRQ(ierr); 1949 pdt = (Mat_SeqAIJ*)PDt->data; 1950 pdti = pdt->i; pdtj = pdt->j; 1951 1952 ierr = MatTransposeSymbolic_SeqAIJ(p->B,&POt);CHKERRQ(ierr); 1953 pot = (Mat_SeqAIJ*)POt->data; 1954 poti = pot->i; potj = pot->j; 1955 1956 /* then, compute symbolic Co = (p->B)^T*A */ 1957 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 1958 >= (num of nonzero rows of C_seq) - pn */ 1959 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 1960 coi[0] = 0; 1961 1962 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1963 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],ai[am])); 1964 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1965 current_space = free_space; 1966 1967 /* create and initialize a linked list */ 1968 ierr = PetscTableCreate(A->cmap->n + a->B->cmap->N,aN,&ta);CHKERRQ(ierr); 1969 MatRowMergeMax_SeqAIJ(a_loc,am,ta); 1970 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 1971 1972 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 1973 1974 for (i=0; i<pon; i++) { 1975 pnz = poti[i+1] - poti[i]; 1976 ptJ = potj + poti[i]; 1977 for (j=0; j<pnz; j++) { 1978 row = ptJ[j]; /* row of A_loc == col of Pot */ 1979 anz = ai[row+1] - ai[row]; 1980 Jptr = aj + ai[row]; 1981 /* add non-zero cols of AP into the sorted linked list lnk */ 1982 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1983 } 1984 nnz = lnk[0]; 1985 1986 /* If free space is not available, double the total space in the list */ 1987 if (current_space->local_remaining<nnz) { 1988 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1989 nspacedouble++; 1990 } 1991 1992 /* Copy data into free space, and zero out denserows */ 1993 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1994 1995 current_space->array += nnz; 1996 current_space->local_used += nnz; 1997 current_space->local_remaining -= nnz; 1998 1999 coi[i+1] = coi[i] + nnz; 2000 } 2001 2002 ierr = PetscMalloc1(coi[pon]+1,&coj);CHKERRQ(ierr); 2003 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 2004 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); /* must destroy to get a new one for C */ 2005 2006 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 2007 if (afill_tmp > afill) afill = afill_tmp; 2008 2009 /* send j-array (coj) of Co to other processors */ 2010 /*----------------------------------------------*/ 2011 /* determine row ownership */ 2012 ierr = PetscNew(&merge);CHKERRQ(ierr); 2013 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 2014 2015 merge->rowmap->n = pn; 2016 merge->rowmap->bs = 1; 2017 2018 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 2019 owners = merge->rowmap->range; 2020 2021 /* determine the number of messages to send, their lengths */ 2022 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 2023 ierr = PetscCalloc1(size,&merge->len_s);CHKERRQ(ierr); 2024 2025 len_s = merge->len_s; 2026 merge->nsend = 0; 2027 2028 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 2029 2030 proc = 0; 2031 for (i=0; i<pon; i++) { 2032 while (prmap[i] >= owners[proc+1]) proc++; 2033 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 2034 len_s[proc] += coi[i+1] - coi[i]; 2035 } 2036 2037 len = 0; /* max length of buf_si[] */ 2038 owners_co[0] = 0; 2039 for (proc=0; proc<size; proc++) { 2040 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 2041 if (len_si[proc]) { 2042 merge->nsend++; 2043 len_si[proc] = 2*(len_si[proc] + 1); 2044 len += len_si[proc]; 2045 } 2046 } 2047 2048 /* determine the number and length of messages to receive for coi and coj */ 2049 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 2050 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 2051 2052 /* post the Irecv and Isend of coj */ 2053 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 2054 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 2055 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 2056 for (proc=0, k=0; proc<size; proc++) { 2057 if (!len_s[proc]) continue; 2058 i = owners_co[proc]; 2059 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 2060 k++; 2061 } 2062 2063 /* receives and sends of coj are complete */ 2064 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 2065 for (i=0; i<merge->nrecv; i++) { 2066 PetscMPIInt icompleted; 2067 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 2068 } 2069 ierr = PetscFree(rwaits);CHKERRQ(ierr); 2070 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 2071 2072 /* add received column indices into table to update Armax */ 2073 /* Armax can be as large as aN if a P[row,:] is dense, see src/ksp/ksp/examples/tutorials/ex56.c! */ 2074 for (k=0; k<merge->nrecv; k++) {/* k-th received message */ 2075 Jptr = buf_rj[k]; 2076 for (j=0; j<merge->len_r[k]; j++) { 2077 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 2078 } 2079 } 2080 ierr = PetscTableGetCount(ta,&Armax);CHKERRQ(ierr); 2081 /* 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); */ 2082 2083 /* send and recv coi */ 2084 /*-------------------*/ 2085 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 2086 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 2087 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 2088 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 2089 for (proc=0,k=0; proc<size; proc++) { 2090 if (!len_s[proc]) continue; 2091 /* form outgoing message for i-structure: 2092 buf_si[0]: nrows to be sent 2093 [1:nrows]: row index (global) 2094 [nrows+1:2*nrows+1]: i-structure index 2095 */ 2096 /*-------------------------------------------*/ 2097 nrows = len_si[proc]/2 - 1; 2098 buf_si_i = buf_si + nrows+1; 2099 buf_si[0] = nrows; 2100 buf_si_i[0] = 0; 2101 nrows = 0; 2102 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 2103 nzi = coi[i+1] - coi[i]; 2104 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 2105 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 2106 nrows++; 2107 } 2108 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 2109 k++; 2110 buf_si += len_si[proc]; 2111 } 2112 i = merge->nrecv; 2113 while (i--) { 2114 PetscMPIInt icompleted; 2115 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 2116 } 2117 ierr = PetscFree(rwaits);CHKERRQ(ierr); 2118 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 2119 ierr = PetscFree(len_si);CHKERRQ(ierr); 2120 ierr = PetscFree(len_ri);CHKERRQ(ierr); 2121 ierr = PetscFree(swaits);CHKERRQ(ierr); 2122 ierr = PetscFree(sstatus);CHKERRQ(ierr); 2123 ierr = PetscFree(buf_s);CHKERRQ(ierr); 2124 2125 /* compute the local portion of C (mpi mat) */ 2126 /*------------------------------------------*/ 2127 /* allocate bi array and free space for accumulating nonzero column info */ 2128 ierr = PetscMalloc1(pn+1,&bi);CHKERRQ(ierr); 2129 bi[0] = 0; 2130 2131 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 2132 nnz = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pdti[pn],PetscIntSumTruncate(poti[pon],ai[am]))); 2133 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 2134 current_space = free_space; 2135 2136 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 2137 for (k=0; k<merge->nrecv; k++) { 2138 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 2139 nrows = *buf_ri_k[k]; 2140 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 2141 nextci[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th recieved i-structure */ 2142 } 2143 2144 ierr = PetscLLCondensedCreate_Scalable(Armax,&lnk);CHKERRQ(ierr); 2145 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 2146 rmax = 0; 2147 for (i=0; i<pn; i++) { 2148 /* add pdt[i,:]*AP into lnk */ 2149 pnz = pdti[i+1] - pdti[i]; 2150 ptJ = pdtj + pdti[i]; 2151 for (j=0; j<pnz; j++) { 2152 row = ptJ[j]; /* row of AP == col of Pt */ 2153 anz = ai[row+1] - ai[row]; 2154 Jptr = aj + ai[row]; 2155 /* add non-zero cols of AP into the sorted linked list lnk */ 2156 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 2157 } 2158 2159 /* add received col data into lnk */ 2160 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 2161 if (i == *nextrow[k]) { /* i-th row */ 2162 nzi = *(nextci[k]+1) - *nextci[k]; 2163 Jptr = buf_rj[k] + *nextci[k]; 2164 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 2165 nextrow[k]++; nextci[k]++; 2166 } 2167 } 2168 nnz = lnk[0]; 2169 2170 /* if free space is not available, make more free space */ 2171 if (current_space->local_remaining<nnz) { 2172 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 2173 nspacedouble++; 2174 } 2175 /* copy data into free space, then initialize lnk */ 2176 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 2177 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 2178 2179 current_space->array += nnz; 2180 current_space->local_used += nnz; 2181 current_space->local_remaining -= nnz; 2182 2183 bi[i+1] = bi[i] + nnz; 2184 if (nnz > rmax) rmax = nnz; 2185 } 2186 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 2187 2188 ierr = PetscMalloc1(bi[pn]+1,&bj);CHKERRQ(ierr); 2189 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 2190 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 2191 if (afill_tmp > afill) afill = afill_tmp; 2192 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 2193 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 2194 2195 ierr = MatDestroy(&POt);CHKERRQ(ierr); 2196 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 2197 2198 /* create symbolic parallel matrix Cmpi - why cannot be assembled in Numeric part */ 2199 /*----------------------------------------------------------------------------------*/ 2200 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 2201 ierr = MatSetSizes(Cmpi,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2202 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 2203 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 2204 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 2205 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 2206 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 2207 ierr = MatSetBlockSize(Cmpi,1);CHKERRQ(ierr); 2208 for (i=0; i<pn; i++) { 2209 row = i + rstart; 2210 nnz = bi[i+1] - bi[i]; 2211 Jptr = bj + bi[i]; 2212 ierr = MatSetValues(Cmpi,1,&row,nnz,Jptr,NULL,INSERT_VALUES);CHKERRQ(ierr); 2213 } 2214 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2215 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2216 merge->bi = bi; 2217 merge->bj = bj; 2218 merge->coi = coi; 2219 merge->coj = coj; 2220 merge->buf_ri = buf_ri; 2221 merge->buf_rj = buf_rj; 2222 merge->owners_co = owners_co; 2223 2224 /* attach the supporting struct to Cmpi for reuse */ 2225 c = (Mat_MPIAIJ*)Cmpi->data; 2226 2227 c->ap = ptap; 2228 ptap->api = NULL; 2229 ptap->apj = NULL; 2230 ptap->merge = merge; 2231 ptap->apa = NULL; 2232 ptap->destroy = Cmpi->ops->destroy; 2233 ptap->duplicate = Cmpi->ops->duplicate; 2234 2235 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ; 2236 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 2237 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 2238 2239 *C = Cmpi; 2240 #if defined(PETSC_USE_INFO) 2241 if (bi[pn] != 0) { 2242 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 2243 ierr = PetscInfo1(Cmpi,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 2244 } else { 2245 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 2246 } 2247 #endif 2248 PetscFunctionReturn(0); 2249 } 2250