1 2 /* 3 Defines projective product routines where A is a MPIAIJ matrix 4 C = P^T * A * P 5 */ 6 7 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 8 #include <../src/mat/utils/freespace.h> 9 #include <../src/mat/impls/aij/mpi/mpiaij.h> 10 #include <petscbt.h> 11 #include <petsctime.h> 12 13 /* #define PTAP_PROFILE */ 14 15 PetscErrorCode MatView_MPIAIJ_PtAP(Mat A,PetscViewer viewer) 16 { 17 PetscErrorCode ierr; 18 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 19 Mat_APMPI *ptap=a->ap; 20 PetscBool iascii; 21 PetscViewerFormat format; 22 23 PetscFunctionBegin; 24 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 25 if (iascii) { 26 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 27 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 28 if (ptap->algType == 0) { 29 ierr = PetscViewerASCIIPrintf(viewer,"using scalable MatPtAP() implementation\n");CHKERRQ(ierr); 30 } else if (ptap->algType == 1) { 31 ierr = PetscViewerASCIIPrintf(viewer,"using nonscalable MatPtAP() implementation\n");CHKERRQ(ierr); 32 } 33 } 34 } 35 ierr = (ptap->view)(A,viewer);CHKERRQ(ierr); 36 PetscFunctionReturn(0); 37 } 38 39 PetscErrorCode MatFreeIntermediateDataStructures_MPIAIJ_AP(Mat A) 40 { 41 PetscErrorCode ierr; 42 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 43 Mat_APMPI *ptap=a->ap; 44 Mat_Merge_SeqsToMPI *merge; 45 46 PetscFunctionBegin; 47 if (!ptap) PetscFunctionReturn(0); 48 49 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 50 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 51 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 52 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 53 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */ 54 ierr = MatDestroy(&ptap->Rd);CHKERRQ(ierr); 55 ierr = MatDestroy(&ptap->Ro);CHKERRQ(ierr); 56 if (ptap->AP_loc) { /* used by alg_rap */ 57 Mat_SeqAIJ *ap = (Mat_SeqAIJ*)(ptap->AP_loc)->data; 58 ierr = PetscFree(ap->i);CHKERRQ(ierr); 59 ierr = PetscFree2(ap->j,ap->a);CHKERRQ(ierr); 60 ierr = MatDestroy(&ptap->AP_loc);CHKERRQ(ierr); 61 } else { /* used by alg_ptap */ 62 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 63 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 64 } 65 ierr = MatDestroy(&ptap->C_loc);CHKERRQ(ierr); 66 ierr = MatDestroy(&ptap->C_oth);CHKERRQ(ierr); 67 if (ptap->apa) {ierr = PetscFree(ptap->apa);CHKERRQ(ierr);} 68 69 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 70 71 merge=ptap->merge; 72 if (merge) { /* used by alg_ptap */ 73 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 74 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 75 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 76 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 77 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 78 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 79 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 80 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 81 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 82 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 83 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 84 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 85 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 86 ierr = PetscFree(ptap->merge);CHKERRQ(ierr); 87 } 88 89 A->ops->destroy = ptap->destroy; 90 ierr = PetscFree(a->ap);CHKERRQ(ierr); 91 PetscFunctionReturn(0); 92 } 93 94 PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A) 95 { 96 PetscErrorCode ierr; 97 98 PetscFunctionBegin; 99 ierr = (*A->ops->freeintermediatedatastructures)(A);CHKERRQ(ierr); 100 ierr = (*A->ops->destroy)(A);CHKERRQ(ierr); 101 PetscFunctionReturn(0); 102 } 103 104 PETSC_INTERN PetscErrorCode MatPtAP_MPIAIJ_MPIAIJ(Mat A,Mat P,MatReuse scall,PetscReal fill,Mat *C) 105 { 106 PetscErrorCode ierr; 107 PetscBool flg; 108 MPI_Comm comm; 109 #if !defined(PETSC_HAVE_HYPRE) 110 const char *algTypes[2] = {"scalable","nonscalable"}; 111 PetscInt nalg=2; 112 #else 113 const char *algTypes[3] = {"scalable","nonscalable","hypre"}; 114 PetscInt nalg=3; 115 #endif 116 PetscInt pN=P->cmap->N,alg=1; /* set default algorithm */ 117 118 PetscFunctionBegin; 119 /* check if matrix local sizes are compatible */ 120 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 121 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Arow (%D, %D) != Prow (%D,%D)",A->rmap->rstart,A->rmap->rend,P->rmap->rstart,P->rmap->rend); 122 if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend) SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Acol (%D, %D) != Prow (%D,%D)",A->cmap->rstart,A->cmap->rend,P->rmap->rstart,P->rmap->rend); 123 124 if (scall == MAT_INITIAL_MATRIX) { 125 /* pick an algorithm */ 126 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 127 ierr = PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 128 ierr = PetscOptionsEnd();CHKERRQ(ierr); 129 130 if (!flg && pN > 100000) { /* may switch to scalable algorithm as default */ 131 MatInfo Ainfo,Pinfo; 132 PetscInt nz_local; 133 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 134 135 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 136 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 137 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); 138 139 if (pN > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 140 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 141 142 if (alg_scalable) { 143 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 144 } 145 } 146 147 switch (alg) { 148 case 1: 149 /* do R=P^T locally, then C=R*A*P -- nonscalable */ 150 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 151 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);CHKERRQ(ierr); 152 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 153 break; 154 #if defined(PETSC_HAVE_HYPRE) 155 case 2: 156 /* Use boomerAMGBuildCoarseOperator */ 157 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 158 ierr = MatPtAPSymbolic_AIJ_AIJ_wHYPRE(A,P,fill,C);CHKERRQ(ierr); 159 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 160 break; 161 #endif 162 default: 163 /* do R=P^T locally, then C=R*A*P */ 164 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 165 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(A,P,fill,C);CHKERRQ(ierr); 166 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 167 break; 168 } 169 170 if (alg == 0 || alg == 1) { 171 Mat_MPIAIJ *c = (Mat_MPIAIJ*)(*C)->data; 172 Mat_APMPI *ap = c->ap; 173 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)(*C)),((PetscObject)(*C))->prefix,"MatFreeIntermediateDataStructures","Mat");CHKERRQ(ierr); 174 ap->freestruct = PETSC_FALSE; 175 ierr = PetscOptionsBool("-mat_freeintermediatedatastructures","Free intermediate data structures", "MatFreeIntermediateDataStructures",ap->freestruct,&ap->freestruct, NULL);CHKERRQ(ierr); 176 ierr = PetscOptionsEnd();CHKERRQ(ierr); 177 } 178 } 179 180 ierr = PetscLogEventBegin(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 181 ierr = (*(*C)->ops->ptapnumeric)(A,P,*C);CHKERRQ(ierr); 182 ierr = PetscLogEventEnd(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 183 PetscFunctionReturn(0); 184 } 185 186 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,Mat C) 187 { 188 PetscErrorCode ierr; 189 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 190 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 191 Mat_SeqAIJ *ap,*p_loc,*p_oth,*c_seq; 192 Mat_APMPI *ptap = c->ap; 193 Mat AP_loc,C_loc,C_oth; 194 PetscInt i,rstart,rend,cm,ncols,row,*api,*apj,am = A->rmap->n,apnz; 195 PetscScalar *apa; 196 const PetscInt *cols; 197 const PetscScalar *vals; 198 199 PetscFunctionBegin; 200 if (!ptap) { 201 MPI_Comm comm; 202 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 203 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 204 } 205 206 ierr = MatZeroEntries(C);CHKERRQ(ierr); 207 208 /* 1) get R = Pd^T,Ro = Po^T */ 209 if (ptap->reuse == MAT_REUSE_MATRIX) { 210 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 211 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 212 } 213 214 /* 2) get AP_loc */ 215 AP_loc = ptap->AP_loc; 216 ap = (Mat_SeqAIJ*)AP_loc->data; 217 218 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 219 /*-----------------------------------------------------*/ 220 if (ptap->reuse == MAT_REUSE_MATRIX) { 221 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 222 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 223 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 224 } 225 226 /* 2-2) compute numeric A_loc*P - dominating part */ 227 /* ---------------------------------------------- */ 228 /* get data from symbolic products */ 229 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 230 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 231 else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"ptap->P_oth is NULL. Cannot proceed!"); 232 233 api = ap->i; 234 apj = ap->j; 235 for (i=0; i<am; i++) { 236 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 237 apnz = api[i+1] - api[i]; 238 apa = ap->a + api[i]; 239 ierr = PetscMemzero(apa,sizeof(PetscScalar)*apnz);CHKERRQ(ierr); 240 AProw_scalable(i,ad,ao,p_loc,p_oth,api,apj,apa); 241 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 242 } 243 244 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 245 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 246 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 247 248 C_loc = ptap->C_loc; 249 C_oth = ptap->C_oth; 250 251 /* add C_loc and Co to to C */ 252 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 253 254 /* C_loc -> C */ 255 cm = C_loc->rmap->N; 256 c_seq = (Mat_SeqAIJ*)C_loc->data; 257 cols = c_seq->j; 258 vals = c_seq->a; 259 260 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 261 /* when there are no off-processor parts. */ 262 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 263 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 264 /* a table, and other, more complex stuff has to be done. */ 265 if (C->assembled) { 266 C->was_assembled = PETSC_TRUE; 267 C->assembled = PETSC_FALSE; 268 } 269 if (C->was_assembled) { 270 for (i=0; i<cm; i++) { 271 ncols = c_seq->i[i+1] - c_seq->i[i]; 272 row = rstart + i; 273 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 274 cols += ncols; vals += ncols; 275 } 276 } else { 277 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 278 } 279 280 /* Co -> C, off-processor part */ 281 cm = C_oth->rmap->N; 282 c_seq = (Mat_SeqAIJ*)C_oth->data; 283 cols = c_seq->j; 284 vals = c_seq->a; 285 for (i=0; i<cm; i++) { 286 ncols = c_seq->i[i+1] - c_seq->i[i]; 287 row = p->garray[i]; 288 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 289 cols += ncols; vals += ncols; 290 } 291 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 292 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 293 294 ptap->reuse = MAT_REUSE_MATRIX; 295 296 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 297 if (ptap->freestruct) { 298 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 299 } 300 PetscFunctionReturn(0); 301 } 302 303 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat *C) 304 { 305 PetscErrorCode ierr; 306 Mat_APMPI *ptap; 307 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 308 MPI_Comm comm; 309 PetscMPIInt size,rank; 310 Mat Cmpi,P_loc,P_oth; 311 PetscFreeSpaceList free_space=NULL,current_space=NULL; 312 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 313 PetscInt *lnk,i,k,pnz,row,nsend; 314 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 315 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 316 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 317 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 318 MPI_Request *swaits,*rwaits; 319 MPI_Status *sstatus,rstatus; 320 PetscLayout rowmap; 321 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 322 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 323 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,Crmax,*aj,*ai,*pi; 324 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 325 PetscScalar *apv; 326 PetscTable ta; 327 MatType mtype; 328 #if defined(PETSC_USE_INFO) 329 PetscReal apfill; 330 #endif 331 332 PetscFunctionBegin; 333 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 334 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 335 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 336 337 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 338 339 /* create symbolic parallel matrix Cmpi */ 340 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 341 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 342 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 343 344 /* create struct Mat_APMPI and attached it to C later */ 345 ierr = PetscNew(&ptap);CHKERRQ(ierr); 346 ptap->reuse = MAT_INITIAL_MATRIX; 347 ptap->algType = 0; 348 349 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 350 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&P_oth);CHKERRQ(ierr); 351 /* get P_loc by taking all local rows of P */ 352 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&P_loc);CHKERRQ(ierr); 353 354 ptap->P_loc = P_loc; 355 ptap->P_oth = P_oth; 356 357 /* (0) compute Rd = Pd^T, Ro = Po^T */ 358 /* --------------------------------- */ 359 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 360 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 361 362 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 363 /* ----------------------------------------------------------------- */ 364 p_loc = (Mat_SeqAIJ*)P_loc->data; 365 if (P_oth) p_oth = (Mat_SeqAIJ*)P_oth->data; 366 367 /* create and initialize a linked list */ 368 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 369 MatRowMergeMax_SeqAIJ(p_loc,P_loc->rmap->N,ta); 370 MatRowMergeMax_SeqAIJ(p_oth,P_oth->rmap->N,ta); 371 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 372 373 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 374 375 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 376 if (ao) { 377 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 378 } else { 379 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 380 } 381 current_space = free_space; 382 nspacedouble = 0; 383 384 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 385 api[0] = 0; 386 for (i=0; i<am; i++) { 387 /* diagonal portion: Ad[i,:]*P */ 388 ai = ad->i; pi = p_loc->i; 389 nzi = ai[i+1] - ai[i]; 390 aj = ad->j + ai[i]; 391 for (j=0; j<nzi; j++) { 392 row = aj[j]; 393 pnz = pi[row+1] - pi[row]; 394 Jptr = p_loc->j + pi[row]; 395 /* add non-zero cols of P into the sorted linked list lnk */ 396 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 397 } 398 /* off-diagonal portion: Ao[i,:]*P */ 399 if (ao) { 400 ai = ao->i; pi = p_oth->i; 401 nzi = ai[i+1] - ai[i]; 402 aj = ao->j + ai[i]; 403 for (j=0; j<nzi; j++) { 404 row = aj[j]; 405 pnz = pi[row+1] - pi[row]; 406 Jptr = p_oth->j + pi[row]; 407 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 408 } 409 } 410 apnz = lnk[0]; 411 api[i+1] = api[i] + apnz; 412 413 /* if free space is not available, double the total space in the list */ 414 if (current_space->local_remaining<apnz) { 415 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 416 nspacedouble++; 417 } 418 419 /* Copy data into free space, then initialize lnk */ 420 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 421 422 current_space->array += apnz; 423 current_space->local_used += apnz; 424 current_space->local_remaining -= apnz; 425 } 426 /* Allocate space for apj and apv, initialize apj, and */ 427 /* destroy list of free space and other temporary array(s) */ 428 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 429 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 430 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 431 432 /* Create AP_loc for reuse */ 433 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 434 435 #if defined(PETSC_USE_INFO) 436 if (ao) { 437 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 438 } else { 439 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 440 } 441 ptap->AP_loc->info.mallocs = nspacedouble; 442 ptap->AP_loc->info.fill_ratio_given = fill; 443 ptap->AP_loc->info.fill_ratio_needed = apfill; 444 445 if (api[am]) { 446 ierr = PetscInfo3(ptap->AP_loc,"Scalable algorithm, AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);CHKERRQ(ierr); 447 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 448 } else { 449 ierr = PetscInfo(ptap->AP_loc,"Scalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 450 } 451 #endif 452 453 /* (2-1) compute symbolic Co = Ro*AP_loc */ 454 /* ------------------------------------ */ 455 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 456 457 /* (3) send coj of C_oth to other processors */ 458 /* ------------------------------------------ */ 459 /* determine row ownership */ 460 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 461 rowmap->n = pn; 462 rowmap->bs = 1; 463 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 464 owners = rowmap->range; 465 466 /* determine the number of messages to send, their lengths */ 467 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 468 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 469 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 470 471 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 472 coi = c_oth->i; coj = c_oth->j; 473 con = ptap->C_oth->rmap->n; 474 proc = 0; 475 for (i=0; i<con; i++) { 476 while (prmap[i] >= owners[proc+1]) proc++; 477 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 478 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 479 } 480 481 len = 0; /* max length of buf_si[], see (4) */ 482 owners_co[0] = 0; 483 nsend = 0; 484 for (proc=0; proc<size; proc++) { 485 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 486 if (len_s[proc]) { 487 nsend++; 488 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 489 len += len_si[proc]; 490 } 491 } 492 493 /* determine the number and length of messages to receive for coi and coj */ 494 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 495 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 496 497 /* post the Irecv and Isend of coj */ 498 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 499 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 500 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 501 for (proc=0, k=0; proc<size; proc++) { 502 if (!len_s[proc]) continue; 503 i = owners_co[proc]; 504 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 505 k++; 506 } 507 508 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 509 /* ---------------------------------------- */ 510 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 511 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 512 513 /* receives coj are complete */ 514 for (i=0; i<nrecv; i++) { 515 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 516 } 517 ierr = PetscFree(rwaits);CHKERRQ(ierr); 518 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 519 520 /* add received column indices into ta to update Crmax */ 521 for (k=0; k<nrecv; k++) {/* k-th received message */ 522 Jptr = buf_rj[k]; 523 for (j=0; j<len_r[k]; j++) { 524 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 525 } 526 } 527 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 528 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 529 530 /* (4) send and recv coi */ 531 /*-----------------------*/ 532 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 533 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 534 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 535 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 536 for (proc=0,k=0; proc<size; proc++) { 537 if (!len_s[proc]) continue; 538 /* form outgoing message for i-structure: 539 buf_si[0]: nrows to be sent 540 [1:nrows]: row index (global) 541 [nrows+1:2*nrows+1]: i-structure index 542 */ 543 /*-------------------------------------------*/ 544 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 545 buf_si_i = buf_si + nrows+1; 546 buf_si[0] = nrows; 547 buf_si_i[0] = 0; 548 nrows = 0; 549 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 550 nzi = coi[i+1] - coi[i]; 551 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 552 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 553 nrows++; 554 } 555 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 556 k++; 557 buf_si += len_si[proc]; 558 } 559 for (i=0; i<nrecv; i++) { 560 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 561 } 562 ierr = PetscFree(rwaits);CHKERRQ(ierr); 563 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 564 565 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 566 ierr = PetscFree(len_ri);CHKERRQ(ierr); 567 ierr = PetscFree(swaits);CHKERRQ(ierr); 568 ierr = PetscFree(buf_s);CHKERRQ(ierr); 569 570 /* (5) compute the local portion of Cmpi */ 571 /* ------------------------------------------ */ 572 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 573 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 574 current_space = free_space; 575 576 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 577 for (k=0; k<nrecv; k++) { 578 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 579 nrows = *buf_ri_k[k]; 580 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 581 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 582 } 583 584 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 585 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 586 for (i=0; i<pn; i++) { 587 /* add C_loc into Cmpi */ 588 nzi = c_loc->i[i+1] - c_loc->i[i]; 589 Jptr = c_loc->j + c_loc->i[i]; 590 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 591 592 /* add received col data into lnk */ 593 for (k=0; k<nrecv; k++) { /* k-th received message */ 594 if (i == *nextrow[k]) { /* i-th row */ 595 nzi = *(nextci[k]+1) - *nextci[k]; 596 Jptr = buf_rj[k] + *nextci[k]; 597 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 598 nextrow[k]++; nextci[k]++; 599 } 600 } 601 nzi = lnk[0]; 602 603 /* copy data into free space, then initialize lnk */ 604 ierr = PetscLLCondensedClean_Scalable(nzi,current_space->array,lnk);CHKERRQ(ierr); 605 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 606 } 607 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 608 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 609 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 610 611 /* local sizes and preallocation */ 612 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 613 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 614 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 615 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 616 617 /* members in merge */ 618 ierr = PetscFree(id_r);CHKERRQ(ierr); 619 ierr = PetscFree(len_r);CHKERRQ(ierr); 620 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 621 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 622 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 623 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 624 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 625 626 /* attach the supporting struct to Cmpi for reuse */ 627 c = (Mat_MPIAIJ*)Cmpi->data; 628 c->ap = ptap; 629 ptap->duplicate = Cmpi->ops->duplicate; 630 ptap->destroy = Cmpi->ops->destroy; 631 ptap->view = Cmpi->ops->view; 632 633 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 634 Cmpi->assembled = PETSC_FALSE; 635 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable; 636 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 637 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 638 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 639 *C = Cmpi; 640 PetscFunctionReturn(0); 641 } 642 643 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 644 { 645 PetscErrorCode ierr; 646 Mat_APMPI *ptap; 647 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 648 MPI_Comm comm; 649 PetscMPIInt size,rank; 650 Mat Cmpi; 651 PetscFreeSpaceList free_space=NULL,current_space=NULL; 652 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 653 PetscInt *lnk,i,k,pnz,row,nsend; 654 PetscBT lnkbt; 655 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 656 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 657 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 658 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 659 MPI_Request *swaits,*rwaits; 660 MPI_Status *sstatus,rstatus; 661 PetscLayout rowmap; 662 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 663 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 664 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 665 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 666 PetscScalar *apv; 667 PetscTable ta; 668 MatType mtype; 669 #if defined(PETSC_USE_INFO) 670 PetscReal apfill; 671 #endif 672 673 PetscFunctionBegin; 674 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 675 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 676 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 677 678 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 679 680 /* create symbolic parallel matrix Cmpi */ 681 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 682 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 683 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 684 685 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 686 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 687 688 /* create struct Mat_APMPI and attached it to C later */ 689 ierr = PetscNew(&ptap);CHKERRQ(ierr); 690 ptap->reuse = MAT_INITIAL_MATRIX; 691 ptap->algType = 1; 692 693 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 694 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 695 /* get P_loc by taking all local rows of P */ 696 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 697 698 /* (0) compute Rd = Pd^T, Ro = Po^T */ 699 /* --------------------------------- */ 700 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 701 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 702 703 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 704 /* ----------------------------------------------------------------- */ 705 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 706 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 707 708 /* create and initialize a linked list */ 709 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 710 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 711 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 712 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 713 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 714 715 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 716 717 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 718 if (ao) { 719 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 720 } else { 721 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 722 } 723 current_space = free_space; 724 nspacedouble = 0; 725 726 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 727 api[0] = 0; 728 for (i=0; i<am; i++) { 729 /* diagonal portion: Ad[i,:]*P */ 730 ai = ad->i; pi = p_loc->i; 731 nzi = ai[i+1] - ai[i]; 732 aj = ad->j + ai[i]; 733 for (j=0; j<nzi; j++) { 734 row = aj[j]; 735 pnz = pi[row+1] - pi[row]; 736 Jptr = p_loc->j + pi[row]; 737 /* add non-zero cols of P into the sorted linked list lnk */ 738 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 739 } 740 /* off-diagonal portion: Ao[i,:]*P */ 741 if (ao) { 742 ai = ao->i; pi = p_oth->i; 743 nzi = ai[i+1] - ai[i]; 744 aj = ao->j + ai[i]; 745 for (j=0; j<nzi; j++) { 746 row = aj[j]; 747 pnz = pi[row+1] - pi[row]; 748 Jptr = p_oth->j + pi[row]; 749 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 750 } 751 } 752 apnz = lnk[0]; 753 api[i+1] = api[i] + apnz; 754 if (ap_rmax < apnz) ap_rmax = apnz; 755 756 /* if free space is not available, double the total space in the list */ 757 if (current_space->local_remaining<apnz) { 758 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 759 nspacedouble++; 760 } 761 762 /* Copy data into free space, then initialize lnk */ 763 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 764 765 current_space->array += apnz; 766 current_space->local_used += apnz; 767 current_space->local_remaining -= apnz; 768 } 769 /* Allocate space for apj and apv, initialize apj, and */ 770 /* destroy list of free space and other temporary array(s) */ 771 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 772 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 773 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 774 775 /* Create AP_loc for reuse */ 776 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 777 778 #if defined(PETSC_USE_INFO) 779 if (ao) { 780 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 781 } else { 782 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 783 } 784 ptap->AP_loc->info.mallocs = nspacedouble; 785 ptap->AP_loc->info.fill_ratio_given = fill; 786 ptap->AP_loc->info.fill_ratio_needed = apfill; 787 788 if (api[am]) { 789 ierr = PetscInfo3(ptap->AP_loc,"Nonscalable algorithm, AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);CHKERRQ(ierr); 790 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 791 } else { 792 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 793 } 794 #endif 795 796 /* (2-1) compute symbolic Co = Ro*AP_loc */ 797 /* ------------------------------------ */ 798 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 799 800 /* (3) send coj of C_oth to other processors */ 801 /* ------------------------------------------ */ 802 /* determine row ownership */ 803 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 804 rowmap->n = pn; 805 rowmap->bs = 1; 806 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 807 owners = rowmap->range; 808 809 /* determine the number of messages to send, their lengths */ 810 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 811 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 812 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 813 814 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 815 coi = c_oth->i; coj = c_oth->j; 816 con = ptap->C_oth->rmap->n; 817 proc = 0; 818 for (i=0; i<con; i++) { 819 while (prmap[i] >= owners[proc+1]) proc++; 820 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 821 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 822 } 823 824 len = 0; /* max length of buf_si[], see (4) */ 825 owners_co[0] = 0; 826 nsend = 0; 827 for (proc=0; proc<size; proc++) { 828 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 829 if (len_s[proc]) { 830 nsend++; 831 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 832 len += len_si[proc]; 833 } 834 } 835 836 /* determine the number and length of messages to receive for coi and coj */ 837 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 838 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 839 840 /* post the Irecv and Isend of coj */ 841 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 842 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 843 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 844 for (proc=0, k=0; proc<size; proc++) { 845 if (!len_s[proc]) continue; 846 i = owners_co[proc]; 847 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 848 k++; 849 } 850 851 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 852 /* ---------------------------------------- */ 853 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 854 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 855 856 /* receives coj are complete */ 857 for (i=0; i<nrecv; i++) { 858 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 859 } 860 ierr = PetscFree(rwaits);CHKERRQ(ierr); 861 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 862 863 /* add received column indices into ta to update Crmax */ 864 for (k=0; k<nrecv; k++) {/* k-th received message */ 865 Jptr = buf_rj[k]; 866 for (j=0; j<len_r[k]; j++) { 867 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 868 } 869 } 870 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 871 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 872 873 /* (4) send and recv coi */ 874 /*-----------------------*/ 875 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 876 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 877 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 878 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 879 for (proc=0,k=0; proc<size; proc++) { 880 if (!len_s[proc]) continue; 881 /* form outgoing message for i-structure: 882 buf_si[0]: nrows to be sent 883 [1:nrows]: row index (global) 884 [nrows+1:2*nrows+1]: i-structure index 885 */ 886 /*-------------------------------------------*/ 887 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 888 buf_si_i = buf_si + nrows+1; 889 buf_si[0] = nrows; 890 buf_si_i[0] = 0; 891 nrows = 0; 892 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 893 nzi = coi[i+1] - coi[i]; 894 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 895 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 896 nrows++; 897 } 898 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 899 k++; 900 buf_si += len_si[proc]; 901 } 902 for (i=0; i<nrecv; i++) { 903 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 904 } 905 ierr = PetscFree(rwaits);CHKERRQ(ierr); 906 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 907 908 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 909 ierr = PetscFree(len_ri);CHKERRQ(ierr); 910 ierr = PetscFree(swaits);CHKERRQ(ierr); 911 ierr = PetscFree(buf_s);CHKERRQ(ierr); 912 913 /* (5) compute the local portion of Cmpi */ 914 /* ------------------------------------------ */ 915 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 916 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 917 current_space = free_space; 918 919 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 920 for (k=0; k<nrecv; k++) { 921 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 922 nrows = *buf_ri_k[k]; 923 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 924 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 925 } 926 927 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 928 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 929 for (i=0; i<pn; i++) { 930 /* add C_loc into Cmpi */ 931 nzi = c_loc->i[i+1] - c_loc->i[i]; 932 Jptr = c_loc->j + c_loc->i[i]; 933 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 934 935 /* add received col data into lnk */ 936 for (k=0; k<nrecv; k++) { /* k-th received message */ 937 if (i == *nextrow[k]) { /* i-th row */ 938 nzi = *(nextci[k]+1) - *nextci[k]; 939 Jptr = buf_rj[k] + *nextci[k]; 940 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 941 nextrow[k]++; nextci[k]++; 942 } 943 } 944 nzi = lnk[0]; 945 946 /* copy data into free space, then initialize lnk */ 947 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 948 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 949 } 950 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 951 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 952 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 953 954 /* local sizes and preallocation */ 955 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 956 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 957 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 958 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 959 960 /* members in merge */ 961 ierr = PetscFree(id_r);CHKERRQ(ierr); 962 ierr = PetscFree(len_r);CHKERRQ(ierr); 963 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 964 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 965 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 966 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 967 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 968 969 /* attach the supporting struct to Cmpi for reuse */ 970 c = (Mat_MPIAIJ*)Cmpi->data; 971 c->ap = ptap; 972 ptap->duplicate = Cmpi->ops->duplicate; 973 ptap->destroy = Cmpi->ops->destroy; 974 ptap->view = Cmpi->ops->view; 975 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 976 977 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 978 Cmpi->assembled = PETSC_FALSE; 979 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 980 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 981 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 982 *C = Cmpi; 983 PetscFunctionReturn(0); 984 } 985 986 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 987 { 988 PetscErrorCode ierr; 989 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 990 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 991 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 992 Mat_APMPI *ptap = c->ap; 993 Mat AP_loc,C_loc,C_oth; 994 PetscInt i,rstart,rend,cm,ncols,row; 995 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 996 PetscScalar *apa; 997 const PetscInt *cols; 998 const PetscScalar *vals; 999 1000 PetscFunctionBegin; 1001 if (!ptap) { 1002 MPI_Comm comm; 1003 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1004 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1005 } 1006 1007 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1008 /* 1) get R = Pd^T,Ro = Po^T */ 1009 if (ptap->reuse == MAT_REUSE_MATRIX) { 1010 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1011 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1012 } 1013 1014 /* 2) get AP_loc */ 1015 AP_loc = ptap->AP_loc; 1016 ap = (Mat_SeqAIJ*)AP_loc->data; 1017 1018 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 1019 /*-----------------------------------------------------*/ 1020 if (ptap->reuse == MAT_REUSE_MATRIX) { 1021 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 1022 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1023 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1024 } 1025 1026 /* 2-2) compute numeric A_loc*P - dominating part */ 1027 /* ---------------------------------------------- */ 1028 /* get data from symbolic products */ 1029 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1030 if (ptap->P_oth) { 1031 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1032 } 1033 apa = ptap->apa; 1034 api = ap->i; 1035 apj = ap->j; 1036 for (i=0; i<am; i++) { 1037 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 1038 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 1039 apnz = api[i+1] - api[i]; 1040 for (j=0; j<apnz; j++) { 1041 col = apj[j+api[i]]; 1042 ap->a[j+ap->i[i]] = apa[col]; 1043 apa[col] = 0.0; 1044 } 1045 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 1046 } 1047 1048 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 1049 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 1050 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 1051 C_loc = ptap->C_loc; 1052 C_oth = ptap->C_oth; 1053 1054 /* add C_loc and Co to to C */ 1055 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1056 1057 /* C_loc -> C */ 1058 cm = C_loc->rmap->N; 1059 c_seq = (Mat_SeqAIJ*)C_loc->data; 1060 cols = c_seq->j; 1061 vals = c_seq->a; 1062 1063 1064 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 1065 /* when there are no off-processor parts. */ 1066 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 1067 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 1068 /* a table, and other, more complex stuff has to be done. */ 1069 if (C->assembled) { 1070 C->was_assembled = PETSC_TRUE; 1071 C->assembled = PETSC_FALSE; 1072 } 1073 if (C->was_assembled) { 1074 for (i=0; i<cm; i++) { 1075 ncols = c_seq->i[i+1] - c_seq->i[i]; 1076 row = rstart + i; 1077 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1078 cols += ncols; vals += ncols; 1079 } 1080 } else { 1081 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 1082 } 1083 1084 /* Co -> C, off-processor part */ 1085 cm = C_oth->rmap->N; 1086 c_seq = (Mat_SeqAIJ*)C_oth->data; 1087 cols = c_seq->j; 1088 vals = c_seq->a; 1089 for (i=0; i<cm; i++) { 1090 ncols = c_seq->i[i+1] - c_seq->i[i]; 1091 row = p->garray[i]; 1092 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1093 cols += ncols; vals += ncols; 1094 } 1095 1096 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1097 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1098 1099 ptap->reuse = MAT_REUSE_MATRIX; 1100 1101 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1102 if (ptap->freestruct) { 1103 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1104 } 1105 PetscFunctionReturn(0); 1106 } 1107