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