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