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