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(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 196 ierr = MatTranspose(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; 244 245 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 246 /* when there are no off-processor parts. */ 247 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 248 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 249 /* a table, and other, more complex stuff has to be done. */ 250 if (C->assembled) { 251 C->was_assembled = PETSC_TRUE; 252 C->assembled = PETSC_FALSE; 253 } 254 if (C->was_assembled) { 255 for (i=0; i<cm; i++) { 256 ncols = c_seq->i[i+1] - c_seq->i[i]; 257 row = rstart + i; 258 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 259 cols += ncols; vals += ncols; 260 } 261 } else { 262 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 263 } 264 265 /* Co -> C, off-processor part */ 266 cm = C_oth->rmap->N; 267 c_seq = (Mat_SeqAIJ*)C_oth->data; 268 cols = c_seq->j; 269 vals = c_seq->a; 270 for (i=0; i<cm; i++) { 271 ncols = c_seq->i[i+1] - c_seq->i[i]; 272 row = p->garray[i]; 273 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 274 cols += ncols; vals += ncols; 275 } 276 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 277 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 278 279 ptap->reuse = MAT_REUSE_MATRIX; 280 PetscFunctionReturn(0); 281 } 282 283 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat *C) 284 { 285 PetscErrorCode ierr; 286 Mat_PtAPMPI *ptap; 287 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 288 MPI_Comm comm; 289 PetscMPIInt size,rank; 290 Mat Cmpi,P_loc,P_oth; 291 PetscFreeSpaceList free_space=NULL,current_space=NULL; 292 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 293 PetscInt *lnk,i,k,pnz,row,nsend; 294 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 295 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 296 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 297 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 298 MPI_Request *swaits,*rwaits; 299 MPI_Status *sstatus,rstatus; 300 PetscLayout rowmap; 301 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 302 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 303 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,Crmax,*aj,*ai,*pi; 304 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 305 PetscScalar *apv; 306 PetscTable ta; 307 MatType mtype; 308 #if defined(PETSC_USE_INFO) 309 PetscReal apfill; 310 #endif 311 312 PetscFunctionBegin; 313 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 314 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 315 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 316 317 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 318 319 /* create symbolic parallel matrix Cmpi */ 320 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 321 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 322 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 323 324 /* create struct Mat_PtAPMPI and attached it to C later */ 325 ierr = PetscNew(&ptap);CHKERRQ(ierr); 326 ptap->reuse = MAT_INITIAL_MATRIX; 327 ptap->algType = 0; 328 329 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 330 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&P_oth);CHKERRQ(ierr); 331 /* get P_loc by taking all local rows of P */ 332 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&P_loc);CHKERRQ(ierr); 333 334 ptap->P_loc = P_loc; 335 ptap->P_oth = P_oth; 336 337 /* (0) compute Rd = Pd^T, Ro = Po^T */ 338 /* --------------------------------- */ 339 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 340 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 341 342 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 343 /* ----------------------------------------------------------------- */ 344 p_loc = (Mat_SeqAIJ*)P_loc->data; 345 if (P_oth) p_oth = (Mat_SeqAIJ*)P_oth->data; 346 347 /* create and initialize a linked list */ 348 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 349 MatRowMergeMax_SeqAIJ(p_loc,P_loc->rmap->N,ta); 350 MatRowMergeMax_SeqAIJ(p_oth,P_oth->rmap->N,ta); 351 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 352 353 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 354 355 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 356 if (ao) { 357 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 358 } else { 359 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 360 } 361 current_space = free_space; 362 nspacedouble = 0; 363 364 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 365 api[0] = 0; 366 for (i=0; i<am; i++) { 367 /* diagonal portion: Ad[i,:]*P */ 368 ai = ad->i; pi = p_loc->i; 369 nzi = ai[i+1] - ai[i]; 370 aj = ad->j + ai[i]; 371 for (j=0; j<nzi; j++) { 372 row = aj[j]; 373 pnz = pi[row+1] - pi[row]; 374 Jptr = p_loc->j + pi[row]; 375 /* add non-zero cols of P into the sorted linked list lnk */ 376 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 377 } 378 /* off-diagonal portion: Ao[i,:]*P */ 379 if (ao) { 380 ai = ao->i; pi = p_oth->i; 381 nzi = ai[i+1] - ai[i]; 382 aj = ao->j + ai[i]; 383 for (j=0; j<nzi; j++) { 384 row = aj[j]; 385 pnz = pi[row+1] - pi[row]; 386 Jptr = p_oth->j + pi[row]; 387 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 388 } 389 } 390 apnz = lnk[0]; 391 api[i+1] = api[i] + apnz; 392 393 /* if free space is not available, double the total space in the list */ 394 if (current_space->local_remaining<apnz) { 395 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 396 nspacedouble++; 397 } 398 399 /* Copy data into free space, then initialize lnk */ 400 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 401 402 current_space->array += apnz; 403 current_space->local_used += apnz; 404 current_space->local_remaining -= apnz; 405 } 406 /* Allocate space for apj and apv, initialize apj, and */ 407 /* destroy list of free space and other temporary array(s) */ 408 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 409 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 410 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 411 412 /* Create AP_loc for reuse */ 413 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 414 415 #if defined(PETSC_USE_INFO) 416 if (ao) { 417 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 418 } else { 419 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 420 } 421 ptap->AP_loc->info.mallocs = nspacedouble; 422 ptap->AP_loc->info.fill_ratio_given = fill; 423 ptap->AP_loc->info.fill_ratio_needed = apfill; 424 425 if (api[am]) { 426 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); 427 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 428 } else { 429 ierr = PetscInfo(ptap->AP_loc,"Scalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 430 } 431 #endif 432 433 /* (2-1) compute symbolic Co = Ro*AP_loc */ 434 /* ------------------------------------ */ 435 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 436 437 /* (3) send coj of C_oth to other processors */ 438 /* ------------------------------------------ */ 439 /* determine row ownership */ 440 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 441 rowmap->n = pn; 442 rowmap->bs = 1; 443 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 444 owners = rowmap->range; 445 446 /* determine the number of messages to send, their lengths */ 447 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 448 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 449 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 450 451 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 452 coi = c_oth->i; coj = c_oth->j; 453 con = ptap->C_oth->rmap->n; 454 proc = 0; 455 for (i=0; i<con; i++) { 456 while (prmap[i] >= owners[proc+1]) proc++; 457 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 458 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 459 } 460 461 len = 0; /* max length of buf_si[], see (4) */ 462 owners_co[0] = 0; 463 nsend = 0; 464 for (proc=0; proc<size; proc++) { 465 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 466 if (len_s[proc]) { 467 nsend++; 468 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 469 len += len_si[proc]; 470 } 471 } 472 473 /* determine the number and length of messages to receive for coi and coj */ 474 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 475 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 476 477 /* post the Irecv and Isend of coj */ 478 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 479 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 480 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 481 for (proc=0, k=0; proc<size; proc++) { 482 if (!len_s[proc]) continue; 483 i = owners_co[proc]; 484 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 485 k++; 486 } 487 488 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 489 /* ---------------------------------------- */ 490 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 491 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 492 493 /* receives coj are complete */ 494 for (i=0; i<nrecv; i++) { 495 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 496 } 497 ierr = PetscFree(rwaits);CHKERRQ(ierr); 498 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 499 500 /* add received column indices into ta to update Crmax */ 501 for (k=0; k<nrecv; k++) {/* k-th received message */ 502 Jptr = buf_rj[k]; 503 for (j=0; j<len_r[k]; j++) { 504 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 505 } 506 } 507 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 508 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 509 510 /* (4) send and recv coi */ 511 /*-----------------------*/ 512 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 513 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 514 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 515 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 516 for (proc=0,k=0; proc<size; proc++) { 517 if (!len_s[proc]) continue; 518 /* form outgoing message for i-structure: 519 buf_si[0]: nrows to be sent 520 [1:nrows]: row index (global) 521 [nrows+1:2*nrows+1]: i-structure index 522 */ 523 /*-------------------------------------------*/ 524 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 525 buf_si_i = buf_si + nrows+1; 526 buf_si[0] = nrows; 527 buf_si_i[0] = 0; 528 nrows = 0; 529 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 530 nzi = coi[i+1] - coi[i]; 531 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 532 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 533 nrows++; 534 } 535 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 536 k++; 537 buf_si += len_si[proc]; 538 } 539 for (i=0; i<nrecv; i++) { 540 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 541 } 542 ierr = PetscFree(rwaits);CHKERRQ(ierr); 543 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 544 545 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 546 ierr = PetscFree(len_ri);CHKERRQ(ierr); 547 ierr = PetscFree(swaits);CHKERRQ(ierr); 548 ierr = PetscFree(buf_s);CHKERRQ(ierr); 549 550 /* (5) compute the local portion of Cmpi */ 551 /* ------------------------------------------ */ 552 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 553 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 554 current_space = free_space; 555 556 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 557 for (k=0; k<nrecv; k++) { 558 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 559 nrows = *buf_ri_k[k]; 560 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 561 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 562 } 563 564 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 565 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 566 for (i=0; i<pn; i++) { 567 /* add C_loc into Cmpi */ 568 nzi = c_loc->i[i+1] - c_loc->i[i]; 569 Jptr = c_loc->j + c_loc->i[i]; 570 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 571 572 /* add received col data into lnk */ 573 for (k=0; k<nrecv; k++) { /* k-th received message */ 574 if (i == *nextrow[k]) { /* i-th row */ 575 nzi = *(nextci[k]+1) - *nextci[k]; 576 Jptr = buf_rj[k] + *nextci[k]; 577 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 578 nextrow[k]++; nextci[k]++; 579 } 580 } 581 nzi = lnk[0]; 582 583 /* copy data into free space, then initialize lnk */ 584 ierr = PetscLLCondensedClean_Scalable(nzi,current_space->array,lnk);CHKERRQ(ierr); 585 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 586 } 587 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 588 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 589 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 590 591 /* local sizes and preallocation */ 592 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 593 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 594 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 595 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 596 597 /* members in merge */ 598 ierr = PetscFree(id_r);CHKERRQ(ierr); 599 ierr = PetscFree(len_r);CHKERRQ(ierr); 600 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 601 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 602 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 603 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 604 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 605 606 /* attach the supporting struct to Cmpi for reuse */ 607 c = (Mat_MPIAIJ*)Cmpi->data; 608 c->ptap = ptap; 609 ptap->duplicate = Cmpi->ops->duplicate; 610 ptap->destroy = Cmpi->ops->destroy; 611 ptap->view = Cmpi->ops->view; 612 613 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 614 Cmpi->assembled = PETSC_FALSE; 615 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable; 616 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 617 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 618 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 619 *C = Cmpi; 620 PetscFunctionReturn(0); 621 } 622 623 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 624 { 625 PetscErrorCode ierr; 626 Mat_PtAPMPI *ptap; 627 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 628 MPI_Comm comm; 629 PetscMPIInt size,rank; 630 Mat Cmpi; 631 PetscFreeSpaceList free_space=NULL,current_space=NULL; 632 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 633 PetscInt *lnk,i,k,pnz,row,nsend; 634 PetscBT lnkbt; 635 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 636 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 637 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 638 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 639 MPI_Request *swaits,*rwaits; 640 MPI_Status *sstatus,rstatus; 641 PetscLayout rowmap; 642 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 643 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 644 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 645 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 646 PetscScalar *apv; 647 PetscTable ta; 648 MatType mtype; 649 #if defined(PETSC_USE_INFO) 650 PetscReal apfill; 651 #endif 652 653 PetscFunctionBegin; 654 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 655 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 656 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 657 658 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 659 660 /* create symbolic parallel matrix Cmpi */ 661 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 662 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 663 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 664 665 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 666 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 667 668 /* create struct Mat_PtAPMPI and attached it to C later */ 669 ierr = PetscNew(&ptap);CHKERRQ(ierr); 670 ptap->reuse = MAT_INITIAL_MATRIX; 671 ptap->algType = 1; 672 673 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 674 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 675 /* get P_loc by taking all local rows of P */ 676 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 677 678 /* (0) compute Rd = Pd^T, Ro = Po^T */ 679 /* --------------------------------- */ 680 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 681 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 682 683 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 684 /* ----------------------------------------------------------------- */ 685 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 686 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 687 688 /* create and initialize a linked list */ 689 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 690 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 691 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 692 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 693 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 694 695 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 696 697 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 698 if (ao) { 699 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 700 } else { 701 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 702 } 703 current_space = free_space; 704 nspacedouble = 0; 705 706 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 707 api[0] = 0; 708 for (i=0; i<am; i++) { 709 /* diagonal portion: Ad[i,:]*P */ 710 ai = ad->i; pi = p_loc->i; 711 nzi = ai[i+1] - ai[i]; 712 aj = ad->j + ai[i]; 713 for (j=0; j<nzi; j++) { 714 row = aj[j]; 715 pnz = pi[row+1] - pi[row]; 716 Jptr = p_loc->j + pi[row]; 717 /* add non-zero cols of P into the sorted linked list lnk */ 718 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 719 } 720 /* off-diagonal portion: Ao[i,:]*P */ 721 if (ao) { 722 ai = ao->i; pi = p_oth->i; 723 nzi = ai[i+1] - ai[i]; 724 aj = ao->j + ai[i]; 725 for (j=0; j<nzi; j++) { 726 row = aj[j]; 727 pnz = pi[row+1] - pi[row]; 728 Jptr = p_oth->j + pi[row]; 729 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 730 } 731 } 732 apnz = lnk[0]; 733 api[i+1] = api[i] + apnz; 734 if (ap_rmax < apnz) ap_rmax = apnz; 735 736 /* if free space is not available, double the total space in the list */ 737 if (current_space->local_remaining<apnz) { 738 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 739 nspacedouble++; 740 } 741 742 /* Copy data into free space, then initialize lnk */ 743 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 744 745 current_space->array += apnz; 746 current_space->local_used += apnz; 747 current_space->local_remaining -= apnz; 748 } 749 /* Allocate space for apj and apv, initialize apj, and */ 750 /* destroy list of free space and other temporary array(s) */ 751 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 752 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 753 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 754 755 /* Create AP_loc for reuse */ 756 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 757 758 #if defined(PETSC_USE_INFO) 759 if (ao) { 760 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 761 } else { 762 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 763 } 764 ptap->AP_loc->info.mallocs = nspacedouble; 765 ptap->AP_loc->info.fill_ratio_given = fill; 766 ptap->AP_loc->info.fill_ratio_needed = apfill; 767 768 if (api[am]) { 769 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); 770 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 771 } else { 772 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 773 } 774 #endif 775 776 /* (2-1) compute symbolic Co = Ro*AP_loc */ 777 /* ------------------------------------ */ 778 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 779 780 /* (3) send coj of C_oth to other processors */ 781 /* ------------------------------------------ */ 782 /* determine row ownership */ 783 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 784 rowmap->n = pn; 785 rowmap->bs = 1; 786 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 787 owners = rowmap->range; 788 789 /* determine the number of messages to send, their lengths */ 790 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 791 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 792 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 793 794 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 795 coi = c_oth->i; coj = c_oth->j; 796 con = ptap->C_oth->rmap->n; 797 proc = 0; 798 for (i=0; i<con; i++) { 799 while (prmap[i] >= owners[proc+1]) proc++; 800 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 801 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 802 } 803 804 len = 0; /* max length of buf_si[], see (4) */ 805 owners_co[0] = 0; 806 nsend = 0; 807 for (proc=0; proc<size; proc++) { 808 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 809 if (len_s[proc]) { 810 nsend++; 811 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 812 len += len_si[proc]; 813 } 814 } 815 816 /* determine the number and length of messages to receive for coi and coj */ 817 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 818 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 819 820 /* post the Irecv and Isend of coj */ 821 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 822 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 823 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 824 for (proc=0, k=0; proc<size; proc++) { 825 if (!len_s[proc]) continue; 826 i = owners_co[proc]; 827 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 828 k++; 829 } 830 831 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 832 /* ---------------------------------------- */ 833 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 834 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 835 836 /* receives coj are complete */ 837 for (i=0; i<nrecv; i++) { 838 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 839 } 840 ierr = PetscFree(rwaits);CHKERRQ(ierr); 841 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 842 843 /* add received column indices into ta to update Crmax */ 844 for (k=0; k<nrecv; k++) {/* k-th received message */ 845 Jptr = buf_rj[k]; 846 for (j=0; j<len_r[k]; j++) { 847 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 848 } 849 } 850 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 851 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 852 853 /* (4) send and recv coi */ 854 /*-----------------------*/ 855 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 856 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 857 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 858 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 859 for (proc=0,k=0; proc<size; proc++) { 860 if (!len_s[proc]) continue; 861 /* form outgoing message for i-structure: 862 buf_si[0]: nrows to be sent 863 [1:nrows]: row index (global) 864 [nrows+1:2*nrows+1]: i-structure index 865 */ 866 /*-------------------------------------------*/ 867 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 868 buf_si_i = buf_si + nrows+1; 869 buf_si[0] = nrows; 870 buf_si_i[0] = 0; 871 nrows = 0; 872 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 873 nzi = coi[i+1] - coi[i]; 874 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 875 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 876 nrows++; 877 } 878 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 879 k++; 880 buf_si += len_si[proc]; 881 } 882 for (i=0; i<nrecv; i++) { 883 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 884 } 885 ierr = PetscFree(rwaits);CHKERRQ(ierr); 886 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 887 888 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 889 ierr = PetscFree(len_ri);CHKERRQ(ierr); 890 ierr = PetscFree(swaits);CHKERRQ(ierr); 891 ierr = PetscFree(buf_s);CHKERRQ(ierr); 892 893 /* (5) compute the local portion of Cmpi */ 894 /* ------------------------------------------ */ 895 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 896 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 897 current_space = free_space; 898 899 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 900 for (k=0; k<nrecv; k++) { 901 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 902 nrows = *buf_ri_k[k]; 903 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 904 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 905 } 906 907 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 908 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 909 for (i=0; i<pn; i++) { 910 /* add C_loc into Cmpi */ 911 nzi = c_loc->i[i+1] - c_loc->i[i]; 912 Jptr = c_loc->j + c_loc->i[i]; 913 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 914 915 /* add received col data into lnk */ 916 for (k=0; k<nrecv; k++) { /* k-th received message */ 917 if (i == *nextrow[k]) { /* i-th row */ 918 nzi = *(nextci[k]+1) - *nextci[k]; 919 Jptr = buf_rj[k] + *nextci[k]; 920 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 921 nextrow[k]++; nextci[k]++; 922 } 923 } 924 nzi = lnk[0]; 925 926 /* copy data into free space, then initialize lnk */ 927 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 928 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 929 } 930 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 931 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 932 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 933 934 /* local sizes and preallocation */ 935 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 936 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 937 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 938 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 939 940 /* members in merge */ 941 ierr = PetscFree(id_r);CHKERRQ(ierr); 942 ierr = PetscFree(len_r);CHKERRQ(ierr); 943 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 944 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 945 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 946 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 947 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 948 949 /* attach the supporting struct to Cmpi for reuse */ 950 c = (Mat_MPIAIJ*)Cmpi->data; 951 c->ptap = ptap; 952 ptap->duplicate = Cmpi->ops->duplicate; 953 ptap->destroy = Cmpi->ops->destroy; 954 ptap->view = Cmpi->ops->view; 955 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 956 957 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 958 Cmpi->assembled = PETSC_FALSE; 959 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 960 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 961 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 962 *C = Cmpi; 963 PetscFunctionReturn(0); 964 } 965 966 967 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 968 { 969 PetscErrorCode ierr; 970 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 971 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 972 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 973 Mat_PtAPMPI *ptap = c->ptap; 974 Mat AP_loc,C_loc,C_oth; 975 PetscInt i,rstart,rend,cm,ncols,row; 976 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 977 PetscScalar *apa; 978 const PetscInt *cols; 979 const PetscScalar *vals; 980 981 PetscFunctionBegin; 982 ierr = MatZeroEntries(C);CHKERRQ(ierr); 983 /* 1) get R = Pd^T,Ro = Po^T */ 984 if (ptap->reuse == MAT_REUSE_MATRIX) { 985 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 986 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 987 } 988 989 /* 2) get AP_loc */ 990 AP_loc = ptap->AP_loc; 991 ap = (Mat_SeqAIJ*)AP_loc->data; 992 993 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 994 /*-----------------------------------------------------*/ 995 if (ptap->reuse == MAT_REUSE_MATRIX) { 996 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 997 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 998 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 999 } 1000 1001 /* 2-2) compute numeric A_loc*P - dominating part */ 1002 /* ---------------------------------------------- */ 1003 /* get data from symbolic products */ 1004 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1005 if (ptap->P_oth) { 1006 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1007 } 1008 apa = ptap->apa; 1009 api = ap->i; 1010 apj = ap->j; 1011 for (i=0; i<am; i++) { 1012 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 1013 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 1014 apnz = api[i+1] - api[i]; 1015 for (j=0; j<apnz; j++) { 1016 col = apj[j+api[i]]; 1017 ap->a[j+ap->i[i]] = apa[col]; 1018 apa[col] = 0.0; 1019 } 1020 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 1021 } 1022 1023 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 1024 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 1025 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 1026 C_loc = ptap->C_loc; 1027 C_oth = ptap->C_oth; 1028 1029 /* add C_loc and Co to to C */ 1030 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1031 1032 /* C_loc -> C */ 1033 cm = C_loc->rmap->N; 1034 c_seq = (Mat_SeqAIJ*)C_loc->data; 1035 cols = c_seq->j; 1036 vals = c_seq->a; 1037 1038 1039 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 1040 /* when there are no off-processor parts. */ 1041 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 1042 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 1043 /* a table, and other, more complex stuff has to be done. */ 1044 if (C->assembled) { 1045 C->was_assembled = PETSC_TRUE; 1046 C->assembled = PETSC_FALSE; 1047 } 1048 if (C->was_assembled) { 1049 for (i=0; i<cm; i++) { 1050 ncols = c_seq->i[i+1] - c_seq->i[i]; 1051 row = rstart + i; 1052 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1053 cols += ncols; vals += ncols; 1054 } 1055 } else { 1056 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 1057 } 1058 1059 /* Co -> C, off-processor part */ 1060 cm = C_oth->rmap->N; 1061 c_seq = (Mat_SeqAIJ*)C_oth->data; 1062 cols = c_seq->j; 1063 vals = c_seq->a; 1064 for (i=0; i<cm; i++) { 1065 ncols = c_seq->i[i+1] - c_seq->i[i]; 1066 row = p->garray[i]; 1067 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1068 cols += ncols; vals += ncols; 1069 } 1070 1071 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1072 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1073 1074 ptap->reuse = MAT_REUSE_MATRIX; 1075 PetscFunctionReturn(0); 1076 } 1077