1 2 /* 3 Defines matrix-matrix product routines for pairs of MPIAIJ matrices 4 C = A * B 5 */ 6 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 7 #include <../src/mat/utils/freespace.h> 8 #include <../src/mat/impls/aij/mpi/mpiaij.h> 9 #include <petscbt.h> 10 #include <../src/mat/impls/dense/mpi/mpidense.h> 11 #include <petsc-private/vecimpl.h> 12 13 #undef __FUNCT__ 14 #define __FUNCT__ "MatMatMult_MPIAIJ_MPIAIJ" 15 PetscErrorCode MatMatMult_MPIAIJ_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill, Mat *C) 16 { 17 PetscErrorCode ierr; 18 const char *algTypes[2] = {"scalable","nonscalable"}; 19 PetscInt alg=0; /* set default algorithm */ 20 21 PetscFunctionBegin; 22 if (scall == MAT_INITIAL_MATRIX) { 23 ierr = PetscObjectOptionsBegin((PetscObject)A);CHKERRQ(ierr); 24 ierr = PetscOptionsEList("-matmatmult_via","Algorithmic approach","MatMatMult",algTypes,2,algTypes[0],&alg,NULL);CHKERRQ(ierr); 25 ierr = PetscOptionsEnd();CHKERRQ(ierr); 26 27 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 28 switch (alg) { 29 case 1: 30 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(A,B,fill,C);CHKERRQ(ierr); 31 break; 32 default: 33 ierr = MatMatMultSymbolic_MPIAIJ_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 34 break; 35 } 36 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 37 } 38 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 39 ierr = (*(*C)->ops->matmultnumeric)(A,B,*C);CHKERRQ(ierr); 40 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 41 PetscFunctionReturn(0); 42 } 43 44 #undef __FUNCT__ 45 #define __FUNCT__ "MatDestroy_MPIAIJ_MatMatMult" 46 PetscErrorCode MatDestroy_MPIAIJ_MatMatMult(Mat A) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 50 Mat_PtAPMPI *ptap = a->ptap; 51 52 PetscFunctionBegin; 53 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 54 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 55 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 56 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 57 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 58 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 59 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 60 ierr = PetscFree(ptap->apa);CHKERRQ(ierr); 61 ierr = ptap->destroy(A);CHKERRQ(ierr); 62 ierr = PetscFree(ptap);CHKERRQ(ierr); 63 PetscFunctionReturn(0); 64 } 65 66 #undef __FUNCT__ 67 #define __FUNCT__ "MatDuplicate_MPIAIJ_MatMatMult" 68 PetscErrorCode MatDuplicate_MPIAIJ_MatMatMult(Mat A, MatDuplicateOption op, Mat *M) 69 { 70 PetscErrorCode ierr; 71 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 72 Mat_PtAPMPI *ptap = a->ptap; 73 74 PetscFunctionBegin; 75 ierr = (*ptap->duplicate)(A,op,M);CHKERRQ(ierr); 76 77 (*M)->ops->destroy = ptap->destroy; /* = MatDestroy_MPIAIJ, *M doesn't duplicate A's special structure! */ 78 (*M)->ops->duplicate = ptap->duplicate; /* = MatDuplicate_MPIAIJ */ 79 PetscFunctionReturn(0); 80 } 81 82 #undef __FUNCT__ 83 #define __FUNCT__ "MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable" 84 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,Mat C) 85 { 86 PetscErrorCode ierr; 87 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 88 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 89 Mat_SeqAIJ *cd =(Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 90 PetscInt *adi=ad->i,*adj,*aoi=ao->i,*aoj; 91 PetscScalar *ada,*aoa,*cda=cd->a,*coa=co->a; 92 Mat_SeqAIJ *p_loc,*p_oth; 93 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pj; 94 PetscScalar *pa_loc,*pa_oth,*pa,*apa,valtmp,*ca; 95 PetscInt cm =C->rmap->n,anz,pnz; 96 Mat_PtAPMPI *ptap=c->ptap; 97 PetscInt *api,*apj,*apJ,i,j,k,row; 98 PetscInt cstart=C->cmap->rstart; 99 PetscInt cdnz,conz,k0,k1; 100 MPI_Comm comm; 101 PetscMPIInt size; 102 103 PetscFunctionBegin; 104 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 105 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 106 107 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 108 /*-----------------------------------------------------*/ 109 /* update numerical values of P_oth and P_loc */ 110 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 111 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 112 113 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 114 /*----------------------------------------------------------*/ 115 /* get data from symbolic products */ 116 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 117 pi_loc=p_loc->i; pj_loc=p_loc->j; pa_loc=p_loc->a; 118 if (size >1) { 119 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 120 pi_oth=p_oth->i; pj_oth=p_oth->j; pa_oth=p_oth->a; 121 } else { 122 pi_oth=NULL; pj_oth=NULL; pa_oth=NULL; 123 } 124 125 /* get apa for storing dense row A[i,:]*P */ 126 apa = ptap->apa; 127 128 api = ptap->api; 129 apj = ptap->apj; 130 for (i=0; i<cm; i++) { 131 /* diagonal portion of A */ 132 anz = adi[i+1] - adi[i]; 133 adj = ad->j + adi[i]; 134 ada = ad->a + adi[i]; 135 for (j=0; j<anz; j++) { 136 row = adj[j]; 137 pnz = pi_loc[row+1] - pi_loc[row]; 138 pj = pj_loc + pi_loc[row]; 139 pa = pa_loc + pi_loc[row]; 140 141 /* perform dense axpy */ 142 valtmp = ada[j]; 143 for (k=0; k<pnz; k++) { 144 apa[pj[k]] += valtmp*pa[k]; 145 } 146 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 147 } 148 149 /* off-diagonal portion of A */ 150 anz = aoi[i+1] - aoi[i]; 151 aoj = ao->j + aoi[i]; 152 aoa = ao->a + aoi[i]; 153 for (j=0; j<anz; j++) { 154 row = aoj[j]; 155 pnz = pi_oth[row+1] - pi_oth[row]; 156 pj = pj_oth + pi_oth[row]; 157 pa = pa_oth + pi_oth[row]; 158 159 /* perform dense axpy */ 160 valtmp = aoa[j]; 161 for (k=0; k<pnz; k++) { 162 apa[pj[k]] += valtmp*pa[k]; 163 } 164 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 165 } 166 167 /* set values in C */ 168 apJ = apj + api[i]; 169 cdnz = cd->i[i+1] - cd->i[i]; 170 conz = co->i[i+1] - co->i[i]; 171 172 /* 1st off-diagoanl part of C */ 173 ca = coa + co->i[i]; 174 k = 0; 175 for (k0=0; k0<conz; k0++) { 176 if (apJ[k] >= cstart) break; 177 ca[k0] = apa[apJ[k]]; 178 apa[apJ[k]] = 0.0; 179 k++; 180 } 181 182 /* diagonal part of C */ 183 ca = cda + cd->i[i]; 184 for (k1=0; k1<cdnz; k1++) { 185 ca[k1] = apa[apJ[k]]; 186 apa[apJ[k]] = 0.0; 187 k++; 188 } 189 190 /* 2nd off-diagoanl part of C */ 191 ca = coa + co->i[i]; 192 for (; k0<conz; k0++) { 193 ca[k0] = apa[apJ[k]]; 194 apa[apJ[k]] = 0.0; 195 k++; 196 } 197 } 198 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 199 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 200 PetscFunctionReturn(0); 201 } 202 203 #undef __FUNCT__ 204 #define __FUNCT__ "MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable" 205 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat A,Mat P,PetscReal fill,Mat *C) 206 { 207 PetscErrorCode ierr; 208 MPI_Comm comm; 209 PetscMPIInt size; 210 Mat Cmpi; 211 Mat_PtAPMPI *ptap; 212 PetscFreeSpaceList free_space=NULL,current_space=NULL; 213 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*c; 214 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 215 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 216 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 217 PetscInt *lnk,i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi; 218 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n; 219 PetscBT lnkbt; 220 PetscScalar *apa; 221 PetscReal afill; 222 PetscInt nlnk_max,armax,prmax; 223 224 PetscFunctionBegin; 225 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 226 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 227 228 if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend) { 229 SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%D, %D) != (%D,%D)",A->cmap->rstart,A->cmap->rend,P->rmap->rstart,P->rmap->rend); 230 } 231 232 /* create struct Mat_PtAPMPI and attached it to C later */ 233 ierr = PetscNew(&ptap);CHKERRQ(ierr); 234 235 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 236 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 237 238 /* get P_loc by taking all local rows of P */ 239 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 240 241 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 242 pi_loc = p_loc->i; pj_loc = p_loc->j; 243 if (size > 1) { 244 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 245 pi_oth = p_oth->i; pj_oth = p_oth->j; 246 } else { 247 p_oth = NULL; 248 pi_oth = NULL; pj_oth = NULL; 249 } 250 251 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 252 /*-------------------------------------------------------------------*/ 253 ierr = PetscMalloc1((am+2),&api);CHKERRQ(ierr); 254 ptap->api = api; 255 api[0] = 0; 256 257 /* create and initialize a linked list */ 258 armax = ad->rmax+ao->rmax; 259 if (size >1) { 260 prmax = PetscMax(p_loc->rmax,p_oth->rmax); 261 } else { 262 prmax = p_loc->rmax; 263 } 264 nlnk_max = armax*prmax; 265 if (!nlnk_max || nlnk_max > pN) nlnk_max = pN; 266 ierr = PetscLLCondensedCreate(nlnk_max,pN,&lnk,&lnkbt);CHKERRQ(ierr); 267 268 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 269 ierr = PetscFreeSpaceGet((PetscInt)(fill*(adi[am]+aoi[am]+pi_loc[pm])),&free_space);CHKERRQ(ierr); 270 271 current_space = free_space; 272 273 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 274 for (i=0; i<am; i++) { 275 /* diagonal portion of A */ 276 nzi = adi[i+1] - adi[i]; 277 for (j=0; j<nzi; j++) { 278 row = *adj++; 279 pnz = pi_loc[row+1] - pi_loc[row]; 280 Jptr = pj_loc + pi_loc[row]; 281 /* add non-zero cols of P into the sorted linked list lnk */ 282 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 283 } 284 /* off-diagonal portion of A */ 285 nzi = aoi[i+1] - aoi[i]; 286 for (j=0; j<nzi; j++) { 287 row = *aoj++; 288 pnz = pi_oth[row+1] - pi_oth[row]; 289 Jptr = pj_oth + pi_oth[row]; 290 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 291 } 292 293 apnz = lnk[0]; 294 api[i+1] = api[i] + apnz; 295 296 /* if free space is not available, double the total space in the list */ 297 if (current_space->local_remaining<apnz) { 298 ierr = PetscFreeSpaceGet(apnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 299 nspacedouble++; 300 } 301 302 /* Copy data into free space, then initialize lnk */ 303 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 304 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 305 306 current_space->array += apnz; 307 current_space->local_used += apnz; 308 current_space->local_remaining -= apnz; 309 } 310 311 /* Allocate space for apj, initialize apj, and */ 312 /* destroy list of free space and other temporary array(s) */ 313 ierr = PetscMalloc1((api[am]+1),&ptap->apj);CHKERRQ(ierr); 314 apj = ptap->apj; 315 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 316 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 317 318 /* malloc apa to store dense row A[i,:]*P */ 319 ierr = PetscCalloc1(pN,&apa);CHKERRQ(ierr); 320 321 ptap->apa = apa; 322 323 /* create and assemble symbolic parallel matrix Cmpi */ 324 /*----------------------------------------------------*/ 325 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 326 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 327 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 328 329 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 330 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 331 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 332 for (i=0; i<am; i++) { 333 row = i + rstart; 334 apnz = api[i+1] - api[i]; 335 ierr = MatSetValues(Cmpi,1,&row,apnz,apj,apa,INSERT_VALUES);CHKERRQ(ierr); 336 apj += apnz; 337 } 338 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 339 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 340 341 ptap->destroy = Cmpi->ops->destroy; 342 ptap->duplicate = Cmpi->ops->duplicate; 343 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 344 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 345 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatMatMult; 346 347 /* attach the supporting struct to Cmpi for reuse */ 348 c = (Mat_MPIAIJ*)Cmpi->data; 349 c->ptap = ptap; 350 351 *C = Cmpi; 352 353 /* set MatInfo */ 354 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 355 if (afill < 1.0) afill = 1.0; 356 Cmpi->info.mallocs = nspacedouble; 357 Cmpi->info.fill_ratio_given = fill; 358 Cmpi->info.fill_ratio_needed = afill; 359 360 #if defined(PETSC_USE_INFO) 361 if (api[am]) { 362 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 363 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 364 } else { 365 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 366 } 367 #endif 368 PetscFunctionReturn(0); 369 } 370 371 #undef __FUNCT__ 372 #define __FUNCT__ "MatMatMult_MPIAIJ_MPIDense" 373 PetscErrorCode MatMatMult_MPIAIJ_MPIDense(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 374 { 375 PetscErrorCode ierr; 376 377 PetscFunctionBegin; 378 if (scall == MAT_INITIAL_MATRIX) { 379 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 380 ierr = MatMatMultSymbolic_MPIAIJ_MPIDense(A,B,fill,C);CHKERRQ(ierr); 381 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 382 } 383 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 384 ierr = MatMatMultNumeric_MPIAIJ_MPIDense(A,B,*C);CHKERRQ(ierr); 385 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 386 PetscFunctionReturn(0); 387 } 388 389 typedef struct { 390 Mat workB; 391 PetscScalar *rvalues,*svalues; 392 MPI_Request *rwaits,*swaits; 393 } MPIAIJ_MPIDense; 394 395 #undef __FUNCT__ 396 #define __FUNCT__ "MatMPIAIJ_MPIDenseDestroy" 397 PetscErrorCode MatMPIAIJ_MPIDenseDestroy(void *ctx) 398 { 399 MPIAIJ_MPIDense *contents = (MPIAIJ_MPIDense*) ctx; 400 PetscErrorCode ierr; 401 402 PetscFunctionBegin; 403 ierr = MatDestroy(&contents->workB);CHKERRQ(ierr); 404 ierr = PetscFree4(contents->rvalues,contents->svalues,contents->rwaits,contents->swaits);CHKERRQ(ierr); 405 ierr = PetscFree(contents);CHKERRQ(ierr); 406 PetscFunctionReturn(0); 407 } 408 409 #undef __FUNCT__ 410 #define __FUNCT__ "MatMatMultSymbolic_MPIAIJ_MPIDense" 411 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIDense(Mat A,Mat B,PetscReal fill,Mat *C) 412 { 413 PetscErrorCode ierr; 414 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) A->data; 415 PetscInt nz = aij->B->cmap->n; 416 PetscContainer container; 417 MPIAIJ_MPIDense *contents; 418 VecScatter ctx = aij->Mvctx; 419 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 420 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 421 PetscInt m = A->rmap->n,n=B->cmap->n; 422 423 PetscFunctionBegin; 424 ierr = MatCreate(PetscObjectComm((PetscObject)B),C);CHKERRQ(ierr); 425 ierr = MatSetSizes(*C,m,n,A->rmap->N,B->cmap->N);CHKERRQ(ierr); 426 ierr = MatSetBlockSizesFromMats(*C,A,B);CHKERRQ(ierr); 427 ierr = MatSetType(*C,MATMPIDENSE);CHKERRQ(ierr); 428 ierr = MatMPIDenseSetPreallocation(*C,NULL);CHKERRQ(ierr); 429 ierr = MatAssemblyBegin(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 430 ierr = MatAssemblyEnd(*C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 431 432 (*C)->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIDense; 433 434 ierr = PetscNew(&contents);CHKERRQ(ierr); 435 /* Create work matrix used to store off processor rows of B needed for local product */ 436 ierr = MatCreateSeqDense(PETSC_COMM_SELF,nz,B->cmap->N,NULL,&contents->workB);CHKERRQ(ierr); 437 /* Create work arrays needed */ 438 ierr = PetscMalloc4(B->cmap->N*from->starts[from->n],&contents->rvalues, 439 B->cmap->N*to->starts[to->n],&contents->svalues, 440 from->n,&contents->rwaits, 441 to->n,&contents->swaits);CHKERRQ(ierr); 442 443 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)A),&container);CHKERRQ(ierr); 444 ierr = PetscContainerSetPointer(container,contents);CHKERRQ(ierr); 445 ierr = PetscContainerSetUserDestroy(container,MatMPIAIJ_MPIDenseDestroy);CHKERRQ(ierr); 446 ierr = PetscObjectCompose((PetscObject)(*C),"workB",(PetscObject)container);CHKERRQ(ierr); 447 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 448 PetscFunctionReturn(0); 449 } 450 451 #undef __FUNCT__ 452 #define __FUNCT__ "MatMPIDenseScatter" 453 /* 454 Performs an efficient scatter on the rows of B needed by this process; this is 455 a modification of the VecScatterBegin_() routines. 456 */ 457 PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,Mat C,Mat *outworkB) 458 { 459 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 460 PetscErrorCode ierr; 461 PetscScalar *b,*w,*svalues,*rvalues; 462 VecScatter ctx = aij->Mvctx; 463 VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata; 464 VecScatter_MPI_General *to = (VecScatter_MPI_General*) ctx->todata; 465 PetscInt i,j,k; 466 PetscInt *sindices,*sstarts,*rindices,*rstarts; 467 PetscMPIInt *sprocs,*rprocs,nrecvs; 468 MPI_Request *swaits,*rwaits; 469 MPI_Comm comm; 470 PetscMPIInt tag = ((PetscObject)ctx)->tag,ncols = B->cmap->N, nrows = aij->B->cmap->n,imdex,nrowsB = B->rmap->n; 471 MPI_Status status; 472 MPIAIJ_MPIDense *contents; 473 PetscContainer container; 474 Mat workB; 475 476 PetscFunctionBegin; 477 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 478 ierr = PetscObjectQuery((PetscObject)C,"workB",(PetscObject*)&container);CHKERRQ(ierr); 479 if (!container) SETERRQ(comm,PETSC_ERR_PLIB,"Container does not exist"); 480 ierr = PetscContainerGetPointer(container,(void**)&contents);CHKERRQ(ierr); 481 482 workB = *outworkB = contents->workB; 483 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); 484 sindices = to->indices; 485 sstarts = to->starts; 486 sprocs = to->procs; 487 swaits = contents->swaits; 488 svalues = contents->svalues; 489 490 rindices = from->indices; 491 rstarts = from->starts; 492 rprocs = from->procs; 493 rwaits = contents->rwaits; 494 rvalues = contents->rvalues; 495 496 ierr = MatDenseGetArray(B,&b);CHKERRQ(ierr); 497 ierr = MatDenseGetArray(workB,&w);CHKERRQ(ierr); 498 499 for (i=0; i<from->n; i++) { 500 ierr = MPI_Irecv(rvalues+ncols*rstarts[i],ncols*(rstarts[i+1]-rstarts[i]),MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 501 } 502 503 for (i=0; i<to->n; i++) { 504 /* pack a message at a time */ 505 for (j=0; j<sstarts[i+1]-sstarts[i]; j++) { 506 for (k=0; k<ncols; k++) { 507 svalues[ncols*(sstarts[i] + j) + k] = b[sindices[sstarts[i]+j] + nrowsB*k]; 508 } 509 } 510 ierr = MPI_Isend(svalues+ncols*sstarts[i],ncols*(sstarts[i+1]-sstarts[i]),MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 511 } 512 513 nrecvs = from->n; 514 while (nrecvs) { 515 ierr = MPI_Waitany(from->n,rwaits,&imdex,&status);CHKERRQ(ierr); 516 nrecvs--; 517 /* unpack a message at a time */ 518 for (j=0; j<rstarts[imdex+1]-rstarts[imdex]; j++) { 519 for (k=0; k<ncols; k++) { 520 w[rindices[rstarts[imdex]+j] + nrows*k] = rvalues[ncols*(rstarts[imdex] + j) + k]; 521 } 522 } 523 } 524 if (to->n) {ierr = MPI_Waitall(to->n,swaits,to->sstatus);CHKERRQ(ierr);} 525 526 ierr = MatDenseRestoreArray(B,&b);CHKERRQ(ierr); 527 ierr = MatDenseRestoreArray(workB,&w);CHKERRQ(ierr); 528 ierr = MatAssemblyBegin(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 529 ierr = MatAssemblyEnd(workB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 530 PetscFunctionReturn(0); 531 } 532 extern PetscErrorCode MatMatMultNumericAdd_SeqAIJ_SeqDense(Mat,Mat,Mat); 533 534 #undef __FUNCT__ 535 #define __FUNCT__ "MatMatMultNumeric_MPIAIJ_MPIDense" 536 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIDense(Mat A,Mat B,Mat C) 537 { 538 PetscErrorCode ierr; 539 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 540 Mat_MPIDense *bdense = (Mat_MPIDense*)B->data; 541 Mat_MPIDense *cdense = (Mat_MPIDense*)C->data; 542 Mat workB; 543 544 PetscFunctionBegin; 545 /* diagonal block of A times all local rows of B*/ 546 ierr = MatMatMultNumeric_SeqAIJ_SeqDense(aij->A,bdense->A,cdense->A);CHKERRQ(ierr); 547 548 /* get off processor parts of B needed to complete the product */ 549 ierr = MatMPIDenseScatter(A,B,C,&workB);CHKERRQ(ierr); 550 551 /* off-diagonal block of A times nonlocal rows of B */ 552 ierr = MatMatMultNumericAdd_SeqAIJ_SeqDense(aij->B,workB,cdense->A);CHKERRQ(ierr); 553 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 554 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 555 PetscFunctionReturn(0); 556 } 557 558 #undef __FUNCT__ 559 #define __FUNCT__ "MatMatMultNumeric_MPIAIJ_MPIAIJ" 560 PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 561 { 562 PetscErrorCode ierr; 563 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c=(Mat_MPIAIJ*)C->data; 564 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 565 Mat_SeqAIJ *cd = (Mat_SeqAIJ*)(c->A)->data,*co=(Mat_SeqAIJ*)(c->B)->data; 566 PetscInt *adi = ad->i,*adj,*aoi=ao->i,*aoj; 567 PetscScalar *ada,*aoa,*cda=cd->a,*coa=co->a; 568 Mat_SeqAIJ *p_loc,*p_oth; 569 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pj; 570 PetscScalar *pa_loc,*pa_oth,*pa,valtmp,*ca; 571 PetscInt cm = C->rmap->n,anz,pnz; 572 Mat_PtAPMPI *ptap = c->ptap; 573 PetscScalar *apa_sparse = ptap->apa; 574 PetscInt *api,*apj,*apJ,i,j,k,row; 575 PetscInt cstart = C->cmap->rstart; 576 PetscInt cdnz,conz,k0,k1,nextp; 577 MPI_Comm comm; 578 PetscMPIInt size; 579 580 PetscFunctionBegin; 581 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 582 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 583 584 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 585 /*-----------------------------------------------------*/ 586 /* update numerical values of P_oth and P_loc */ 587 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 588 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 589 590 /* 2) compute numeric C_loc = A_loc*P = Ad*P_loc + Ao*P_oth */ 591 /*----------------------------------------------------------*/ 592 /* get data from symbolic products */ 593 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 594 pi_loc = p_loc->i; pj_loc = p_loc->j; pa_loc = p_loc->a; 595 if (size >1) { 596 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 597 pi_oth = p_oth->i; pj_oth = p_oth->j; pa_oth = p_oth->a; 598 } else { 599 p_oth = NULL; pi_oth = NULL; pj_oth = NULL; pa_oth = NULL; 600 } 601 602 api = ptap->api; 603 apj = ptap->apj; 604 for (i=0; i<cm; i++) { 605 apJ = apj + api[i]; 606 607 /* diagonal portion of A */ 608 anz = adi[i+1] - adi[i]; 609 adj = ad->j + adi[i]; 610 ada = ad->a + adi[i]; 611 for (j=0; j<anz; j++) { 612 row = adj[j]; 613 pnz = pi_loc[row+1] - pi_loc[row]; 614 pj = pj_loc + pi_loc[row]; 615 pa = pa_loc + pi_loc[row]; 616 /* perform sparse axpy */ 617 valtmp = ada[j]; 618 nextp = 0; 619 for (k=0; nextp<pnz; k++) { 620 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 621 apa_sparse[k] += valtmp*pa[nextp++]; 622 } 623 } 624 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 625 } 626 627 /* off-diagonal portion of A */ 628 anz = aoi[i+1] - aoi[i]; 629 aoj = ao->j + aoi[i]; 630 aoa = ao->a + aoi[i]; 631 for (j=0; j<anz; j++) { 632 row = aoj[j]; 633 pnz = pi_oth[row+1] - pi_oth[row]; 634 pj = pj_oth + pi_oth[row]; 635 pa = pa_oth + pi_oth[row]; 636 /* perform sparse axpy */ 637 valtmp = aoa[j]; 638 nextp = 0; 639 for (k=0; nextp<pnz; k++) { 640 if (apJ[k] == pj[nextp]) { /* column of AP == column of P */ 641 apa_sparse[k] += valtmp*pa[nextp++]; 642 } 643 } 644 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 645 } 646 647 /* set values in C */ 648 cdnz = cd->i[i+1] - cd->i[i]; 649 conz = co->i[i+1] - co->i[i]; 650 651 /* 1st off-diagoanl part of C */ 652 ca = coa + co->i[i]; 653 k = 0; 654 for (k0=0; k0<conz; k0++) { 655 if (apJ[k] >= cstart) break; 656 ca[k0] = apa_sparse[k]; 657 apa_sparse[k] = 0.0; 658 k++; 659 } 660 661 /* diagonal part of C */ 662 ca = cda + cd->i[i]; 663 for (k1=0; k1<cdnz; k1++) { 664 ca[k1] = apa_sparse[k]; 665 apa_sparse[k] = 0.0; 666 k++; 667 } 668 669 /* 2nd off-diagoanl part of C */ 670 ca = coa + co->i[i]; 671 for (; k0<conz; k0++) { 672 ca[k0] = apa_sparse[k]; 673 apa_sparse[k] = 0.0; 674 k++; 675 } 676 } 677 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 678 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 679 PetscFunctionReturn(0); 680 } 681 682 /* same as MatMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(), except using LLCondensed to avoid O(BN) memory requirement */ 683 #undef __FUNCT__ 684 #define __FUNCT__ "MatMatMultSymbolic_MPIAIJ_MPIAIJ" 685 PetscErrorCode MatMatMultSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 686 { 687 PetscErrorCode ierr; 688 MPI_Comm comm; 689 PetscMPIInt size; 690 Mat Cmpi; 691 Mat_PtAPMPI *ptap; 692 PetscFreeSpaceList free_space = NULL,current_space=NULL; 693 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data,*c; 694 Mat_SeqAIJ *ad = (Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_loc,*p_oth; 695 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*dnz,*onz; 696 PetscInt *adi=ad->i,*adj=ad->j,*aoi=ao->i,*aoj=ao->j,rstart=A->rmap->rstart; 697 PetscInt i,pnz,row,*api,*apj,*Jptr,apnz,nspacedouble=0,j,nzi,*lnk,apnz_max=0; 698 PetscInt am=A->rmap->n,pN=P->cmap->N,pn=P->cmap->n,pm=P->rmap->n; 699 PetscInt nlnk_max,armax,prmax; 700 PetscReal afill; 701 PetscScalar *apa; 702 703 PetscFunctionBegin; 704 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 705 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 706 707 /* create struct Mat_PtAPMPI and attached it to C later */ 708 ierr = PetscNew(&ptap);CHKERRQ(ierr); 709 710 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 711 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 712 713 /* get P_loc by taking all local rows of P */ 714 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 715 716 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 717 pi_loc = p_loc->i; pj_loc = p_loc->j; 718 if (size > 1) { 719 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 720 pi_oth = p_oth->i; pj_oth = p_oth->j; 721 } else { 722 p_oth = NULL; 723 pi_oth = NULL; pj_oth = NULL; 724 } 725 726 /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ 727 /*-------------------------------------------------------------------*/ 728 ierr = PetscMalloc1((am+2),&api);CHKERRQ(ierr); 729 ptap->api = api; 730 api[0] = 0; 731 732 /* create and initialize a linked list */ 733 armax = ad->rmax+ao->rmax; 734 if (size >1) { 735 prmax = PetscMax(p_loc->rmax,p_oth->rmax); 736 } else { 737 prmax = p_loc->rmax; 738 } 739 nlnk_max = armax*prmax; 740 if (!nlnk_max || nlnk_max > pN) nlnk_max = pN; 741 ierr = PetscLLCondensedCreate_Scalable(nlnk_max,&lnk);CHKERRQ(ierr); 742 743 /* Initial FreeSpace size is fill*(nnz(A)+nnz(P)) */ 744 ierr = PetscFreeSpaceGet((PetscInt)(fill*(adi[am]+aoi[am]+pi_loc[pm])),&free_space);CHKERRQ(ierr); 745 746 current_space = free_space; 747 748 ierr = MatPreallocateInitialize(comm,am,pn,dnz,onz);CHKERRQ(ierr); 749 for (i=0; i<am; i++) { 750 /* diagonal portion of A */ 751 nzi = adi[i+1] - adi[i]; 752 for (j=0; j<nzi; j++) { 753 row = *adj++; 754 pnz = pi_loc[row+1] - pi_loc[row]; 755 Jptr = pj_loc + pi_loc[row]; 756 /* add non-zero cols of P into the sorted linked list lnk */ 757 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 758 } 759 /* off-diagonal portion of A */ 760 nzi = aoi[i+1] - aoi[i]; 761 for (j=0; j<nzi; j++) { 762 row = *aoj++; 763 pnz = pi_oth[row+1] - pi_oth[row]; 764 Jptr = pj_oth + pi_oth[row]; 765 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 766 } 767 768 apnz = *lnk; 769 api[i+1] = api[i] + apnz; 770 if (apnz > apnz_max) apnz_max = apnz; 771 772 /* if free space is not available, double the total space in the list */ 773 if (current_space->local_remaining<apnz) { 774 ierr = PetscFreeSpaceGet(apnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 775 nspacedouble++; 776 } 777 778 /* Copy data into free space, then initialize lnk */ 779 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 780 ierr = MatPreallocateSet(i+rstart,apnz,current_space->array,dnz,onz);CHKERRQ(ierr); 781 782 current_space->array += apnz; 783 current_space->local_used += apnz; 784 current_space->local_remaining -= apnz; 785 } 786 787 /* Allocate space for apj, initialize apj, and */ 788 /* destroy list of free space and other temporary array(s) */ 789 ierr = PetscMalloc1((api[am]+1),&ptap->apj);CHKERRQ(ierr); 790 apj = ptap->apj; 791 ierr = PetscFreeSpaceContiguous(&free_space,ptap->apj);CHKERRQ(ierr); 792 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 793 794 /* create and assemble symbolic parallel matrix Cmpi */ 795 /*----------------------------------------------------*/ 796 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 797 ierr = MatSetSizes(Cmpi,am,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 798 ierr = MatSetBlockSizesFromMats(Cmpi,A,P);CHKERRQ(ierr); 799 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 800 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 801 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 802 803 /* malloc apa for assembly Cmpi */ 804 ierr = PetscCalloc1(apnz_max,&apa);CHKERRQ(ierr); 805 806 ptap->apa = apa; 807 for (i=0; i<am; i++) { 808 row = i + rstart; 809 apnz = api[i+1] - api[i]; 810 ierr = MatSetValues(Cmpi,1,&row,apnz,apj,apa,INSERT_VALUES);CHKERRQ(ierr); 811 apj += apnz; 812 } 813 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 814 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 815 816 ptap->destroy = Cmpi->ops->destroy; 817 ptap->duplicate = Cmpi->ops->duplicate; 818 Cmpi->ops->matmultnumeric = MatMatMultNumeric_MPIAIJ_MPIAIJ; 819 Cmpi->ops->destroy = MatDestroy_MPIAIJ_MatMatMult; 820 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatMatMult; 821 822 /* attach the supporting struct to Cmpi for reuse */ 823 c = (Mat_MPIAIJ*)Cmpi->data; 824 c->ptap = ptap; 825 826 *C = Cmpi; 827 828 /* set MatInfo */ 829 afill = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1) + 1.e-5; 830 if (afill < 1.0) afill = 1.0; 831 Cmpi->info.mallocs = nspacedouble; 832 Cmpi->info.fill_ratio_given = fill; 833 Cmpi->info.fill_ratio_needed = afill; 834 835 #if defined(PETSC_USE_INFO) 836 if (api[am]) { 837 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 838 ierr = PetscInfo1(Cmpi,"Use MatMatMult(A,B,MatReuse,%g,&C) for best performance.;\n",(double)afill);CHKERRQ(ierr); 839 } else { 840 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 841 } 842 #endif 843 PetscFunctionReturn(0); 844 } 845 846 /*-------------------------------------------------------------------------*/ 847 #undef __FUNCT__ 848 #define __FUNCT__ "MatTransposeMatMult_MPIAIJ_MPIAIJ" 849 PetscErrorCode MatTransposeMatMult_MPIAIJ_MPIAIJ(Mat P,Mat A,MatReuse scall,PetscReal fill,Mat *C) 850 { 851 PetscErrorCode ierr; 852 const char *algTypes[3] = {"scalable","nonscalable","matmatmult"}; 853 PetscInt alg=0; /* set default algorithm */ 854 855 PetscFunctionBegin; 856 if (scall == MAT_INITIAL_MATRIX) { 857 ierr = PetscObjectOptionsBegin((PetscObject)A);CHKERRQ(ierr); 858 ierr = PetscOptionsEList("-mattransposematmult_via","Algorithmic approach","MatTransposeMatMult",algTypes,3,algTypes[0],&alg,NULL);CHKERRQ(ierr); 859 ierr = PetscOptionsEnd();CHKERRQ(ierr); 860 861 ierr = PetscLogEventBegin(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 862 switch (alg) { 863 case 1: 864 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(P,A,fill,C);CHKERRQ(ierr); 865 break; 866 case 2: 867 { 868 Mat Pt; 869 Mat_PtAPMPI *ptap; 870 Mat_MPIAIJ *c; 871 ierr = MatTranspose(P,MAT_INITIAL_MATRIX,&Pt);CHKERRQ(ierr); 872 ierr = MatMatMult(Pt,A,MAT_INITIAL_MATRIX,fill,C);CHKERRQ(ierr); 873 c = (Mat_MPIAIJ*)(*C)->data; 874 ptap = c->ptap; 875 ptap->Pt = Pt; 876 (*C)->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult; 877 PetscFunctionReturn(0); 878 } 879 break; 880 default: 881 ierr = MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(P,A,fill,C);CHKERRQ(ierr); 882 break; 883 } 884 ierr = PetscLogEventEnd(MAT_TransposeMatMultSymbolic,P,A,0,0);CHKERRQ(ierr); 885 } 886 ierr = PetscLogEventBegin(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 887 ierr = (*(*C)->ops->mattransposemultnumeric)(P,A,*C);CHKERRQ(ierr); 888 ierr = PetscLogEventEnd(MAT_TransposeMatMultNumeric,P,A,0,0);CHKERRQ(ierr); 889 PetscFunctionReturn(0); 890 } 891 892 /* This routine only works when scall=MAT_REUSE_MATRIX! */ 893 #undef __FUNCT__ 894 #define __FUNCT__ "MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult" 895 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_matmatmult(Mat P,Mat A,Mat C) 896 { 897 PetscErrorCode ierr; 898 Mat_MPIAIJ *c=(Mat_MPIAIJ*)C->data; 899 Mat_PtAPMPI *ptap= c->ptap; 900 Mat Pt=ptap->Pt; 901 902 PetscFunctionBegin; 903 ierr = MatTranspose(P,MAT_REUSE_MATRIX,&Pt);CHKERRQ(ierr); 904 ierr = MatMatMultNumeric(Pt,A,C);CHKERRQ(ierr); 905 PetscFunctionReturn(0); 906 } 907 908 /* Non-scalable version, use dense axpy */ 909 #undef __FUNCT__ 910 #define __FUNCT__ "MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable" 911 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,Mat C) 912 { 913 PetscErrorCode ierr; 914 Mat_Merge_SeqsToMPI *merge; 915 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 916 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 917 Mat_PtAPMPI *ptap; 918 PetscInt *adj,*aJ; 919 PetscInt i,j,k,anz,pnz,row,*cj; 920 MatScalar *ada,*aval,*ca,valtmp; 921 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 922 MPI_Comm comm; 923 PetscMPIInt size,rank,taga,*len_s; 924 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 925 PetscInt **buf_ri,**buf_rj; 926 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 927 MPI_Request *s_waits,*r_waits; 928 MPI_Status *status; 929 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 930 PetscInt *ai,*aj,*coi,*coj; 931 PetscInt *poJ,*pdJ; 932 Mat A_loc; 933 Mat_SeqAIJ *a_loc; 934 935 PetscFunctionBegin; 936 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 937 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 938 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 939 940 ptap = c->ptap; 941 merge = ptap->merge; 942 943 /* 2) compute numeric C_seq = P_loc^T*A_loc*P - dominating part */ 944 /*--------------------------------------------------------------*/ 945 /* get data from symbolic products */ 946 coi = merge->coi; coj = merge->coj; 947 ierr = PetscCalloc1((coi[pon]+1),&coa);CHKERRQ(ierr); 948 949 bi = merge->bi; bj = merge->bj; 950 owners = merge->rowmap->range; 951 ierr = PetscCalloc1((bi[cm]+1),&ba);CHKERRQ(ierr); 952 953 /* get A_loc by taking all local rows of A */ 954 A_loc = ptap->A_loc; 955 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 956 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 957 ai = a_loc->i; 958 aj = a_loc->j; 959 960 ierr = PetscCalloc1((A->cmap->N),&aval);CHKERRQ(ierr); /* non-scalable!!! */ 961 962 for (i=0; i<am; i++) { 963 /* 2-a) put A[i,:] to dense array aval */ 964 anz = ai[i+1] - ai[i]; 965 adj = aj + ai[i]; 966 ada = a_loc->a + ai[i]; 967 for (j=0; j<anz; j++) { 968 aval[adj[j]] = ada[j]; 969 } 970 971 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 972 /*--------------------------------------------------------------*/ 973 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 974 pnz = po->i[i+1] - po->i[i]; 975 poJ = po->j + po->i[i]; 976 pA = po->a + po->i[i]; 977 for (j=0; j<pnz; j++) { 978 row = poJ[j]; 979 cnz = coi[row+1] - coi[row]; 980 cj = coj + coi[row]; 981 ca = coa + coi[row]; 982 /* perform dense axpy */ 983 valtmp = pA[j]; 984 for (k=0; k<cnz; k++) { 985 ca[k] += valtmp*aval[cj[k]]; 986 } 987 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 988 } 989 990 /* put the value into Cd (diagonal part) */ 991 pnz = pd->i[i+1] - pd->i[i]; 992 pdJ = pd->j + pd->i[i]; 993 pA = pd->a + pd->i[i]; 994 for (j=0; j<pnz; j++) { 995 row = pdJ[j]; 996 cnz = bi[row+1] - bi[row]; 997 cj = bj + bi[row]; 998 ca = ba + bi[row]; 999 /* perform dense axpy */ 1000 valtmp = pA[j]; 1001 for (k=0; k<cnz; k++) { 1002 ca[k] += valtmp*aval[cj[k]]; 1003 } 1004 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1005 } 1006 1007 /* zero the current row of Pt*A */ 1008 aJ = aj + ai[i]; 1009 for (k=0; k<anz; k++) aval[aJ[k]] = 0.0; 1010 } 1011 1012 /* 3) send and recv matrix values coa */ 1013 /*------------------------------------*/ 1014 buf_ri = merge->buf_ri; 1015 buf_rj = merge->buf_rj; 1016 len_s = merge->len_s; 1017 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1018 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1019 1020 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1021 for (proc=0,k=0; proc<size; proc++) { 1022 if (!len_s[proc]) continue; 1023 i = merge->owners_co[proc]; 1024 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1025 k++; 1026 } 1027 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1028 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1029 1030 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1031 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1032 ierr = PetscFree(coa);CHKERRQ(ierr); 1033 1034 /* 4) insert local Cseq and received values into Cmpi */ 1035 /*----------------------------------------------------*/ 1036 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1037 for (k=0; k<merge->nrecv; k++) { 1038 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1039 nrows = *(buf_ri_k[k]); 1040 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1041 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1042 } 1043 1044 for (i=0; i<cm; i++) { 1045 row = owners[rank] + i; /* global row index of C_seq */ 1046 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1047 ba_i = ba + bi[i]; 1048 bnz = bi[i+1] - bi[i]; 1049 /* add received vals into ba */ 1050 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1051 /* i-th row */ 1052 if (i == *nextrow[k]) { 1053 cnz = *(nextci[k]+1) - *nextci[k]; 1054 cj = buf_rj[k] + *(nextci[k]); 1055 ca = abuf_r[k] + *(nextci[k]); 1056 nextcj = 0; 1057 for (j=0; nextcj<cnz; j++) { 1058 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1059 ba_i[j] += ca[nextcj++]; 1060 } 1061 } 1062 nextrow[k]++; nextci[k]++; 1063 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1064 } 1065 } 1066 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1067 } 1068 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1069 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1070 1071 ierr = PetscFree(ba);CHKERRQ(ierr); 1072 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1073 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1074 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1075 ierr = PetscFree(aval);CHKERRQ(ierr); 1076 PetscFunctionReturn(0); 1077 } 1078 1079 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ() */ 1080 #undef __FUNCT__ 1081 #define __FUNCT__ "MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable" 1082 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable(Mat P,Mat A,PetscReal fill,Mat *C) 1083 { 1084 PetscErrorCode ierr; 1085 Mat Cmpi,A_loc,POt,PDt; 1086 Mat_PtAPMPI *ptap; 1087 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1088 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c; 1089 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1090 PetscInt nnz; 1091 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1092 PetscInt am=A->rmap->n,pn=P->cmap->n; 1093 PetscBT lnkbt; 1094 MPI_Comm comm; 1095 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1096 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1097 PetscInt len,proc,*dnz,*onz,*owners; 1098 PetscInt nzi,*bi,*bj; 1099 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1100 MPI_Request *swaits,*rwaits; 1101 MPI_Status *sstatus,rstatus; 1102 Mat_Merge_SeqsToMPI *merge; 1103 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1104 PetscReal afill =1.0,afill_tmp; 1105 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N,Crmax; 1106 PetscScalar *vals; 1107 Mat_SeqAIJ *a_loc, *pdt,*pot; 1108 1109 PetscFunctionBegin; 1110 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1111 /* check if matrix local sizes are compatible */ 1112 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) { 1113 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); 1114 } 1115 1116 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1117 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1118 1119 /* create struct Mat_PtAPMPI and attached it to C later */ 1120 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1121 1122 /* get A_loc by taking all local rows of A */ 1123 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1124 1125 ptap->A_loc = A_loc; 1126 1127 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1128 ai = a_loc->i; 1129 aj = a_loc->j; 1130 1131 /* determine symbolic Co=(p->B)^T*A - send to others */ 1132 /*----------------------------------------------------*/ 1133 ierr = MatTransposeSymbolic_SeqAIJ(p->A,&PDt);CHKERRQ(ierr); 1134 pdt = (Mat_SeqAIJ*)PDt->data; 1135 pdti = pdt->i; pdtj = pdt->j; 1136 1137 ierr = MatTransposeSymbolic_SeqAIJ(p->B,&POt);CHKERRQ(ierr); 1138 pot = (Mat_SeqAIJ*)POt->data; 1139 poti = pot->i; potj = pot->j; 1140 1141 /* then, compute symbolic Co = (p->B)^T*A */ 1142 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors >= (num of nonzero rows of C_seq) - pn */ 1143 ierr = PetscMalloc1((pon+1),&coi);CHKERRQ(ierr); 1144 coi[0] = 0; 1145 1146 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1147 nnz = fill*(poti[pon] + ai[am]); 1148 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1149 current_space = free_space; 1150 1151 /* create and initialize a linked list */ 1152 i = PetscMax(pdt->rmax,pot->rmax); 1153 Crmax = i*a_loc->rmax*size; 1154 if (!Crmax || Crmax > aN) Crmax = aN; 1155 ierr = PetscLLCondensedCreate(Crmax,aN,&lnk,&lnkbt);CHKERRQ(ierr); 1156 1157 for (i=0; i<pon; i++) { 1158 pnz = poti[i+1] - poti[i]; 1159 ptJ = potj + poti[i]; 1160 for (j=0; j<pnz; j++) { 1161 row = ptJ[j]; /* row of A_loc == col of Pot */ 1162 anz = ai[row+1] - ai[row]; 1163 Jptr = aj + ai[row]; 1164 /* add non-zero cols of AP into the sorted linked list lnk */ 1165 ierr = PetscLLCondensedAddSorted(anz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1166 } 1167 nnz = lnk[0]; 1168 1169 /* If free space is not available, double the total space in the list */ 1170 if (current_space->local_remaining<nnz) { 1171 ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 1172 nspacedouble++; 1173 } 1174 1175 /* Copy data into free space, and zero out denserows */ 1176 ierr = PetscLLCondensedClean(aN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1177 1178 current_space->array += nnz; 1179 current_space->local_used += nnz; 1180 current_space->local_remaining -= nnz; 1181 1182 coi[i+1] = coi[i] + nnz; 1183 } 1184 1185 ierr = PetscMalloc1((coi[pon]+1),&coj);CHKERRQ(ierr); 1186 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 1187 1188 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 1189 if (afill_tmp > afill) afill = afill_tmp; 1190 1191 /* send j-array (coj) of Co to other processors */ 1192 /*----------------------------------------------*/ 1193 /* determine row ownership */ 1194 ierr = PetscNew(&merge);CHKERRQ(ierr); 1195 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 1196 1197 merge->rowmap->n = pn; 1198 merge->rowmap->bs = 1; 1199 1200 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 1201 owners = merge->rowmap->range; 1202 1203 /* determine the number of messages to send, their lengths */ 1204 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 1205 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 1206 1207 len_s = merge->len_s; 1208 merge->nsend = 0; 1209 1210 ierr = PetscMalloc1((size+2),&owners_co);CHKERRQ(ierr); 1211 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1212 1213 proc = 0; 1214 for (i=0; i<pon; i++) { 1215 while (prmap[i] >= owners[proc+1]) proc++; 1216 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1217 len_s[proc] += coi[i+1] - coi[i]; 1218 } 1219 1220 len = 0; /* max length of buf_si[] */ 1221 owners_co[0] = 0; 1222 for (proc=0; proc<size; proc++) { 1223 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1224 if (len_si[proc]) { 1225 merge->nsend++; 1226 len_si[proc] = 2*(len_si[proc] + 1); 1227 len += len_si[proc]; 1228 } 1229 } 1230 1231 /* determine the number and length of messages to receive for coi and coj */ 1232 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1233 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1234 1235 /* post the Irecv and Isend of coj */ 1236 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1237 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1238 ierr = PetscMalloc1((merge->nsend+1),&swaits);CHKERRQ(ierr); 1239 for (proc=0, k=0; proc<size; proc++) { 1240 if (!len_s[proc]) continue; 1241 i = owners_co[proc]; 1242 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1243 k++; 1244 } 1245 1246 /* receives and sends of coj are complete */ 1247 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1248 for (i=0; i<merge->nrecv; i++) { 1249 PetscMPIInt icompleted; 1250 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1251 } 1252 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1253 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1254 1255 /* send and recv coi */ 1256 /*-------------------*/ 1257 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1258 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1259 ierr = PetscMalloc1((len+1),&buf_s);CHKERRQ(ierr); 1260 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1261 for (proc=0,k=0; proc<size; proc++) { 1262 if (!len_s[proc]) continue; 1263 /* form outgoing message for i-structure: 1264 buf_si[0]: nrows to be sent 1265 [1:nrows]: row index (global) 1266 [nrows+1:2*nrows+1]: i-structure index 1267 */ 1268 /*-------------------------------------------*/ 1269 nrows = len_si[proc]/2 - 1; 1270 buf_si_i = buf_si + nrows+1; 1271 buf_si[0] = nrows; 1272 buf_si_i[0] = 0; 1273 nrows = 0; 1274 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1275 nzi = coi[i+1] - coi[i]; 1276 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1277 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1278 nrows++; 1279 } 1280 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1281 k++; 1282 buf_si += len_si[proc]; 1283 } 1284 i = merge->nrecv; 1285 while (i--) { 1286 PetscMPIInt icompleted; 1287 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1288 } 1289 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1290 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1291 ierr = PetscFree(len_si);CHKERRQ(ierr); 1292 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1293 ierr = PetscFree(swaits);CHKERRQ(ierr); 1294 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1295 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1296 1297 /* compute the local portion of C (mpi mat) */ 1298 /*------------------------------------------*/ 1299 /* allocate bi array and free space for accumulating nonzero column info */ 1300 ierr = PetscMalloc1((pn+1),&bi);CHKERRQ(ierr); 1301 bi[0] = 0; 1302 1303 /* set initial free space to be fill*(nnz(P) + nnz(A)) */ 1304 nnz = fill*(pdti[pn] + poti[pon] + ai[am]); 1305 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1306 current_space = free_space; 1307 1308 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1309 for (k=0; k<merge->nrecv; k++) { 1310 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1311 nrows = *buf_ri_k[k]; 1312 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1313 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1314 } 1315 1316 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1317 rmax = 0; 1318 for (i=0; i<pn; i++) { 1319 /* add pdt[i,:]*AP into lnk */ 1320 pnz = pdti[i+1] - pdti[i]; 1321 ptJ = pdtj + pdti[i]; 1322 for (j=0; j<pnz; j++) { 1323 row = ptJ[j]; /* row of AP == col of Pt */ 1324 anz = ai[row+1] - ai[row]; 1325 Jptr = aj + ai[row]; 1326 /* add non-zero cols of AP into the sorted linked list lnk */ 1327 ierr = PetscLLCondensedAddSorted(anz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1328 } 1329 1330 /* add received col data into lnk */ 1331 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1332 if (i == *nextrow[k]) { /* i-th row */ 1333 nzi = *(nextci[k]+1) - *nextci[k]; 1334 Jptr = buf_rj[k] + *nextci[k]; 1335 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1336 nextrow[k]++; nextci[k]++; 1337 } 1338 } 1339 nnz = lnk[0]; 1340 1341 /* if free space is not available, make more free space */ 1342 if (current_space->local_remaining<nnz) { 1343 ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 1344 nspacedouble++; 1345 } 1346 /* copy data into free space, then initialize lnk */ 1347 ierr = PetscLLCondensedClean(aN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1348 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 1349 1350 current_space->array += nnz; 1351 current_space->local_used += nnz; 1352 current_space->local_remaining -= nnz; 1353 1354 bi[i+1] = bi[i] + nnz; 1355 if (nnz > rmax) rmax = nnz; 1356 } 1357 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1358 1359 ierr = PetscMalloc1((bi[pn]+1),&bj);CHKERRQ(ierr); 1360 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 1361 1362 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 1363 if (afill_tmp > afill) afill = afill_tmp; 1364 ierr = PetscLLCondensedDestroy(lnk,lnkbt);CHKERRQ(ierr); 1365 ierr = MatDestroy(&POt);CHKERRQ(ierr); 1366 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 1367 1368 /* create symbolic parallel matrix Cmpi - why cannot be assembled in Numeric part */ 1369 /*----------------------------------------------------------------------------------*/ 1370 ierr = PetscCalloc1(rmax+1,&vals);CHKERRQ(ierr); 1371 1372 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1373 ierr = MatSetSizes(Cmpi,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1374 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 1375 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 1376 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1377 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1378 ierr = MatSetBlockSize(Cmpi,1);CHKERRQ(ierr); 1379 for (i=0; i<pn; i++) { 1380 row = i + rstart; 1381 nnz = bi[i+1] - bi[i]; 1382 Jptr = bj + bi[i]; 1383 ierr = MatSetValues(Cmpi,1,&row,nnz,Jptr,vals,INSERT_VALUES);CHKERRQ(ierr); 1384 } 1385 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1386 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1387 ierr = PetscFree(vals);CHKERRQ(ierr); 1388 1389 merge->bi = bi; 1390 merge->bj = bj; 1391 merge->coi = coi; 1392 merge->coj = coj; 1393 merge->buf_ri = buf_ri; 1394 merge->buf_rj = buf_rj; 1395 merge->owners_co = owners_co; 1396 merge->destroy = Cmpi->ops->destroy; 1397 merge->duplicate = Cmpi->ops->duplicate; 1398 1399 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ_nonscalable; 1400 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1401 1402 /* attach the supporting struct to Cmpi for reuse */ 1403 c = (Mat_MPIAIJ*)Cmpi->data; 1404 c->ptap = ptap; 1405 ptap->api = NULL; 1406 ptap->apj = NULL; 1407 ptap->merge = merge; 1408 ptap->rmax = rmax; 1409 1410 *C = Cmpi; 1411 #if defined(PETSC_USE_INFO) 1412 if (bi[pn] != 0) { 1413 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1414 ierr = PetscInfo1(Cmpi,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 1415 } else { 1416 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1417 } 1418 #endif 1419 PetscFunctionReturn(0); 1420 } 1421 1422 #undef __FUNCT__ 1423 #define __FUNCT__ "MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ" 1424 PetscErrorCode MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ(Mat P,Mat A,Mat C) 1425 { 1426 PetscErrorCode ierr; 1427 Mat_Merge_SeqsToMPI *merge; 1428 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1429 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1430 Mat_PtAPMPI *ptap; 1431 PetscInt *adj; 1432 PetscInt i,j,k,anz,pnz,row,*cj,nexta; 1433 MatScalar *ada,*ca,valtmp; 1434 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1435 MPI_Comm comm; 1436 PetscMPIInt size,rank,taga,*len_s; 1437 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1438 PetscInt **buf_ri,**buf_rj; 1439 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1440 MPI_Request *s_waits,*r_waits; 1441 MPI_Status *status; 1442 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1443 PetscInt *ai,*aj,*coi,*coj; 1444 PetscInt *poJ,*pdJ; 1445 Mat A_loc; 1446 Mat_SeqAIJ *a_loc; 1447 1448 PetscFunctionBegin; 1449 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1450 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1451 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1452 1453 ptap = c->ptap; 1454 merge = ptap->merge; 1455 1456 /* 2) compute numeric C_seq = P_loc^T*A_loc */ 1457 /*------------------------------------------*/ 1458 /* get data from symbolic products */ 1459 coi = merge->coi; coj = merge->coj; 1460 ierr = PetscCalloc1((coi[pon]+1),&coa);CHKERRQ(ierr); 1461 bi = merge->bi; bj = merge->bj; 1462 owners = merge->rowmap->range; 1463 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); 1464 1465 /* get A_loc by taking all local rows of A */ 1466 A_loc = ptap->A_loc; 1467 ierr = MatMPIAIJGetLocalMat(A,MAT_REUSE_MATRIX,&A_loc);CHKERRQ(ierr); 1468 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1469 ai = a_loc->i; 1470 aj = a_loc->j; 1471 1472 for (i=0; i<am; i++) { 1473 anz = ai[i+1] - ai[i]; 1474 adj = aj + ai[i]; 1475 ada = a_loc->a + ai[i]; 1476 1477 /* 2-b) Compute Cseq = P_loc[i,:]^T*A[i,:] using outer product */ 1478 /*-------------------------------------------------------------*/ 1479 /* put the value into Co=(p->B)^T*A (off-diagonal part, send to others) */ 1480 pnz = po->i[i+1] - po->i[i]; 1481 poJ = po->j + po->i[i]; 1482 pA = po->a + po->i[i]; 1483 for (j=0; j<pnz; j++) { 1484 row = poJ[j]; 1485 cj = coj + coi[row]; 1486 ca = coa + coi[row]; 1487 /* perform sparse axpy */ 1488 nexta = 0; 1489 valtmp = pA[j]; 1490 for (k=0; nexta<anz; k++) { 1491 if (cj[k] == adj[nexta]) { 1492 ca[k] += valtmp*ada[nexta]; 1493 nexta++; 1494 } 1495 } 1496 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1497 } 1498 1499 /* put the value into Cd (diagonal part) */ 1500 pnz = pd->i[i+1] - pd->i[i]; 1501 pdJ = pd->j + pd->i[i]; 1502 pA = pd->a + pd->i[i]; 1503 for (j=0; j<pnz; j++) { 1504 row = pdJ[j]; 1505 cj = bj + bi[row]; 1506 ca = ba + bi[row]; 1507 /* perform sparse axpy */ 1508 nexta = 0; 1509 valtmp = pA[j]; 1510 for (k=0; nexta<anz; k++) { 1511 if (cj[k] == adj[nexta]) { 1512 ca[k] += valtmp*ada[nexta]; 1513 nexta++; 1514 } 1515 } 1516 ierr = PetscLogFlops(2.0*anz);CHKERRQ(ierr); 1517 } 1518 } 1519 1520 /* 3) send and recv matrix values coa */ 1521 /*------------------------------------*/ 1522 buf_ri = merge->buf_ri; 1523 buf_rj = merge->buf_rj; 1524 len_s = merge->len_s; 1525 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1526 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1527 1528 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1529 for (proc=0,k=0; proc<size; proc++) { 1530 if (!len_s[proc]) continue; 1531 i = merge->owners_co[proc]; 1532 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1533 k++; 1534 } 1535 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1536 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1537 1538 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1539 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1540 ierr = PetscFree(coa);CHKERRQ(ierr); 1541 1542 /* 4) insert local Cseq and received values into Cmpi */ 1543 /*----------------------------------------------------*/ 1544 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1545 for (k=0; k<merge->nrecv; k++) { 1546 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1547 nrows = *(buf_ri_k[k]); 1548 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1549 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1550 } 1551 1552 for (i=0; i<cm; i++) { 1553 row = owners[rank] + i; /* global row index of C_seq */ 1554 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1555 ba_i = ba + bi[i]; 1556 bnz = bi[i+1] - bi[i]; 1557 /* add received vals into ba */ 1558 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1559 /* i-th row */ 1560 if (i == *nextrow[k]) { 1561 cnz = *(nextci[k]+1) - *nextci[k]; 1562 cj = buf_rj[k] + *(nextci[k]); 1563 ca = abuf_r[k] + *(nextci[k]); 1564 nextcj = 0; 1565 for (j=0; nextcj<cnz; j++) { 1566 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1567 ba_i[j] += ca[nextcj++]; 1568 } 1569 } 1570 nextrow[k]++; nextci[k]++; 1571 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1572 } 1573 } 1574 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1575 } 1576 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1577 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1578 1579 ierr = PetscFree(ba);CHKERRQ(ierr); 1580 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1581 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1582 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1583 PetscFunctionReturn(0); 1584 } 1585 1586 /* This routine is modified from MatPtAPSymbolic_MPIAIJ_MPIAIJ(); 1587 differ from MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable in using LLCondensedCreate_Scalable() */ 1588 #undef __FUNCT__ 1589 #define __FUNCT__ "MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ" 1590 PetscErrorCode MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ(Mat P,Mat A,PetscReal fill,Mat *C) 1591 { 1592 PetscErrorCode ierr; 1593 Mat Cmpi,A_loc,POt,PDt; 1594 Mat_PtAPMPI *ptap; 1595 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1596 Mat_MPIAIJ *p =(Mat_MPIAIJ*)P->data,*c; 1597 PetscInt *pdti,*pdtj,*poti,*potj,*ptJ; 1598 PetscInt nnz; 1599 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 1600 PetscInt am =A->rmap->n,pn=P->cmap->n; 1601 MPI_Comm comm; 1602 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri; 1603 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1604 PetscInt len,proc,*dnz,*onz,*owners; 1605 PetscInt nzi,*bi,*bj; 1606 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1607 MPI_Request *swaits,*rwaits; 1608 MPI_Status *sstatus,rstatus; 1609 Mat_Merge_SeqsToMPI *merge; 1610 PetscInt *ai,*aj,*Jptr,anz,*prmap=p->garray,pon,nspacedouble=0,j; 1611 PetscReal afill =1.0,afill_tmp; 1612 PetscInt rstart = P->cmap->rstart,rmax,aN=A->cmap->N,Crmax; 1613 PetscScalar *vals; 1614 Mat_SeqAIJ *a_loc, *pdt,*pot; 1615 1616 PetscFunctionBegin; 1617 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1618 /* check if matrix local sizes are compatible */ 1619 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) { 1620 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); 1621 } 1622 1623 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1624 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1625 1626 /* create struct Mat_PtAPMPI and attached it to C later */ 1627 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1628 1629 /* get A_loc by taking all local rows of A */ 1630 ierr = MatMPIAIJGetLocalMat(A,MAT_INITIAL_MATRIX,&A_loc);CHKERRQ(ierr); 1631 1632 ptap->A_loc = A_loc; 1633 a_loc = (Mat_SeqAIJ*)(A_loc)->data; 1634 ai = a_loc->i; 1635 aj = a_loc->j; 1636 1637 /* determine symbolic Co=(p->B)^T*A - send to others */ 1638 /*----------------------------------------------------*/ 1639 ierr = MatTransposeSymbolic_SeqAIJ(p->A,&PDt);CHKERRQ(ierr); 1640 pdt = (Mat_SeqAIJ*)PDt->data; 1641 pdti = pdt->i; pdtj = pdt->j; 1642 1643 ierr = MatTransposeSymbolic_SeqAIJ(p->B,&POt);CHKERRQ(ierr); 1644 pot = (Mat_SeqAIJ*)POt->data; 1645 poti = pot->i; potj = pot->j; 1646 1647 /* then, compute symbolic Co = (p->B)^T*A */ 1648 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 1649 >= (num of nonzero rows of C_seq) - pn */ 1650 ierr = PetscMalloc1((pon+1),&coi);CHKERRQ(ierr); 1651 coi[0] = 0; 1652 1653 /* set initial free space to be fill*(nnz(p->B) + nnz(A)) */ 1654 nnz = fill*(poti[pon] + ai[am]); 1655 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1656 current_space = free_space; 1657 1658 /* create and initialize a linked list */ 1659 i = PetscMax(pdt->rmax,pot->rmax); 1660 Crmax = i*a_loc->rmax*size; /* non-scalable! */ 1661 if (!Crmax || Crmax > aN) Crmax = aN; 1662 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 1663 1664 for (i=0; i<pon; i++) { 1665 pnz = poti[i+1] - poti[i]; 1666 ptJ = potj + poti[i]; 1667 for (j=0; j<pnz; j++) { 1668 row = ptJ[j]; /* row of A_loc == col of Pot */ 1669 anz = ai[row+1] - ai[row]; 1670 Jptr = aj + ai[row]; 1671 /* add non-zero cols of AP into the sorted linked list lnk */ 1672 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1673 } 1674 nnz = lnk[0]; 1675 1676 /* If free space is not available, double the total space in the list */ 1677 if (current_space->local_remaining<nnz) { 1678 ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 1679 nspacedouble++; 1680 } 1681 1682 /* Copy data into free space, and zero out denserows */ 1683 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1684 1685 current_space->array += nnz; 1686 current_space->local_used += nnz; 1687 current_space->local_remaining -= nnz; 1688 1689 coi[i+1] = coi[i] + nnz; 1690 } 1691 1692 ierr = PetscMalloc1((coi[pon]+1),&coj);CHKERRQ(ierr); 1693 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 1694 1695 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + ai[am]+1); 1696 if (afill_tmp > afill) afill = afill_tmp; 1697 1698 /* send j-array (coj) of Co to other processors */ 1699 /*----------------------------------------------*/ 1700 /* determine row ownership */ 1701 ierr = PetscNew(&merge);CHKERRQ(ierr); 1702 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 1703 1704 merge->rowmap->n = pn; 1705 merge->rowmap->bs = 1; 1706 1707 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 1708 owners = merge->rowmap->range; 1709 1710 /* determine the number of messages to send, their lengths */ 1711 ierr = PetscCalloc1(size,&len_si);CHKERRQ(ierr); 1712 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 1713 1714 len_s = merge->len_s; 1715 merge->nsend = 0; 1716 1717 ierr = PetscMalloc1((size+2),&owners_co);CHKERRQ(ierr); 1718 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1719 1720 proc = 0; 1721 for (i=0; i<pon; i++) { 1722 while (prmap[i] >= owners[proc+1]) proc++; 1723 len_si[proc]++; /* num of rows in Co to be sent to [proc] */ 1724 len_s[proc] += coi[i+1] - coi[i]; 1725 } 1726 1727 len = 0; /* max length of buf_si[] */ 1728 owners_co[0] = 0; 1729 for (proc=0; proc<size; proc++) { 1730 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1731 if (len_si[proc]) { 1732 merge->nsend++; 1733 len_si[proc] = 2*(len_si[proc] + 1); 1734 len += len_si[proc]; 1735 } 1736 } 1737 1738 /* determine the number and length of messages to receive for coi and coj */ 1739 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 1740 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 1741 1742 /* post the Irecv and Isend of coj */ 1743 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1744 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1745 ierr = PetscMalloc1((merge->nsend+1),&swaits);CHKERRQ(ierr); 1746 for (proc=0, k=0; proc<size; proc++) { 1747 if (!len_s[proc]) continue; 1748 i = owners_co[proc]; 1749 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1750 k++; 1751 } 1752 1753 /* receives and sends of coj are complete */ 1754 ierr = PetscMalloc1(size,&sstatus);CHKERRQ(ierr); 1755 for (i=0; i<merge->nrecv; i++) { 1756 PetscMPIInt icompleted; 1757 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1758 } 1759 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1760 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1761 1762 /* send and recv coi */ 1763 /*-------------------*/ 1764 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1765 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1766 ierr = PetscMalloc1((len+1),&buf_s);CHKERRQ(ierr); 1767 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1768 for (proc=0,k=0; proc<size; proc++) { 1769 if (!len_s[proc]) continue; 1770 /* form outgoing message for i-structure: 1771 buf_si[0]: nrows to be sent 1772 [1:nrows]: row index (global) 1773 [nrows+1:2*nrows+1]: i-structure index 1774 */ 1775 /*-------------------------------------------*/ 1776 nrows = len_si[proc]/2 - 1; 1777 buf_si_i = buf_si + nrows+1; 1778 buf_si[0] = nrows; 1779 buf_si_i[0] = 0; 1780 nrows = 0; 1781 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1782 nzi = coi[i+1] - coi[i]; 1783 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1784 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1785 nrows++; 1786 } 1787 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1788 k++; 1789 buf_si += len_si[proc]; 1790 } 1791 i = merge->nrecv; 1792 while (i--) { 1793 PetscMPIInt icompleted; 1794 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1795 } 1796 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1797 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 1798 ierr = PetscFree(len_si);CHKERRQ(ierr); 1799 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1800 ierr = PetscFree(swaits);CHKERRQ(ierr); 1801 ierr = PetscFree(sstatus);CHKERRQ(ierr); 1802 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1803 1804 /* compute the local portion of C (mpi mat) */ 1805 /*------------------------------------------*/ 1806 /* allocate bi array and free space for accumulating nonzero column info */ 1807 ierr = PetscMalloc1((pn+1),&bi);CHKERRQ(ierr); 1808 bi[0] = 0; 1809 1810 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 1811 nnz = fill*(pdti[pn] + poti[pon] + ai[am]); 1812 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 1813 current_space = free_space; 1814 1815 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1816 for (k=0; k<merge->nrecv; k++) { 1817 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1818 nrows = *buf_ri_k[k]; 1819 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1820 nextci[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th recieved i-structure */ 1821 } 1822 1823 ierr = MatPreallocateInitialize(comm,pn,A->cmap->n,dnz,onz);CHKERRQ(ierr); 1824 rmax = 0; 1825 for (i=0; i<pn; i++) { 1826 /* add pdt[i,:]*AP into lnk */ 1827 pnz = pdti[i+1] - pdti[i]; 1828 ptJ = pdtj + pdti[i]; 1829 for (j=0; j<pnz; j++) { 1830 row = ptJ[j]; /* row of AP == col of Pt */ 1831 anz = ai[row+1] - ai[row]; 1832 Jptr = aj + ai[row]; 1833 /* add non-zero cols of AP into the sorted linked list lnk */ 1834 ierr = PetscLLCondensedAddSorted_Scalable(anz,Jptr,lnk);CHKERRQ(ierr); 1835 } 1836 1837 /* add received col data into lnk */ 1838 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1839 if (i == *nextrow[k]) { /* i-th row */ 1840 nzi = *(nextci[k]+1) - *nextci[k]; 1841 Jptr = buf_rj[k] + *nextci[k]; 1842 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 1843 nextrow[k]++; nextci[k]++; 1844 } 1845 } 1846 nnz = lnk[0]; 1847 1848 /* if free space is not available, make more free space */ 1849 if (current_space->local_remaining<nnz) { 1850 ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 1851 nspacedouble++; 1852 } 1853 /* copy data into free space, then initialize lnk */ 1854 ierr = PetscLLCondensedClean_Scalable(nnz,current_space->array,lnk);CHKERRQ(ierr); 1855 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 1856 1857 current_space->array += nnz; 1858 current_space->local_used += nnz; 1859 current_space->local_remaining -= nnz; 1860 1861 bi[i+1] = bi[i] + nnz; 1862 if (nnz > rmax) rmax = nnz; 1863 } 1864 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1865 1866 ierr = PetscMalloc1((bi[pn]+1),&bj);CHKERRQ(ierr); 1867 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 1868 afill_tmp = (PetscReal)bi[pn]/(pdti[pn] + poti[pon] + ai[am]+1); 1869 if (afill_tmp > afill) afill = afill_tmp; 1870 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 1871 ierr = MatDestroy(&POt);CHKERRQ(ierr); 1872 ierr = MatDestroy(&PDt);CHKERRQ(ierr); 1873 1874 /* create symbolic parallel matrix Cmpi - why cannot be assembled in Numeric part */ 1875 /*----------------------------------------------------------------------------------*/ 1876 ierr = PetscCalloc1(rmax+1,&vals);CHKERRQ(ierr); 1877 1878 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1879 ierr = MatSetSizes(Cmpi,pn,A->cmap->n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1880 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(A->cmap->bs));CHKERRQ(ierr); 1881 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 1882 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1883 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1884 ierr = MatSetBlockSize(Cmpi,1);CHKERRQ(ierr); 1885 for (i=0; i<pn; i++) { 1886 row = i + rstart; 1887 nnz = bi[i+1] - bi[i]; 1888 Jptr = bj + bi[i]; 1889 ierr = MatSetValues(Cmpi,1,&row,nnz,Jptr,vals,INSERT_VALUES);CHKERRQ(ierr); 1890 } 1891 ierr = MatAssemblyBegin(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1892 ierr = MatAssemblyEnd(Cmpi,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1893 ierr = PetscFree(vals);CHKERRQ(ierr); 1894 1895 merge->bi = bi; 1896 merge->bj = bj; 1897 merge->coi = coi; 1898 merge->coj = coj; 1899 merge->buf_ri = buf_ri; 1900 merge->buf_rj = buf_rj; 1901 merge->owners_co = owners_co; 1902 merge->destroy = Cmpi->ops->destroy; 1903 merge->duplicate = Cmpi->ops->duplicate; 1904 1905 Cmpi->ops->mattransposemultnumeric = MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ; 1906 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1907 1908 /* attach the supporting struct to Cmpi for reuse */ 1909 c = (Mat_MPIAIJ*)Cmpi->data; 1910 1911 c->ptap = ptap; 1912 ptap->api = NULL; 1913 ptap->apj = NULL; 1914 ptap->merge = merge; 1915 ptap->rmax = rmax; 1916 ptap->apa = NULL; 1917 1918 *C = Cmpi; 1919 #if defined(PETSC_USE_INFO) 1920 if (bi[pn] != 0) { 1921 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1922 ierr = PetscInfo1(Cmpi,"Use MatTransposeMatMult(A,B,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 1923 } else { 1924 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1925 } 1926 #endif 1927 PetscFunctionReturn(0); 1928 } 1929