1 2 /* 3 Defines projective product routines where A is a MPIAIJ matrix 4 C = P^T * A * P 5 */ 6 7 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 8 #include <../src/mat/utils/freespace.h> 9 #include <../src/mat/impls/aij/mpi/mpiaij.h> 10 #include <petscbt.h> 11 #include <petsctime.h> 12 13 /* #define PTAP_PROFILE */ 14 15 PetscErrorCode MatView_MPIAIJ_PtAP(Mat A,PetscViewer viewer) 16 { 17 PetscErrorCode ierr; 18 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 19 Mat_APMPI *ptap=a->ap; 20 PetscBool iascii; 21 PetscViewerFormat format; 22 23 PetscFunctionBegin; 24 if (!ptap) { 25 /* hack: MatDuplicate() sets oldmat->ops->view to newmat which is a base mat class with null ptpa! */ 26 A->ops->view = MatView_MPIAIJ; 27 ierr = (A->ops->view)(A,viewer);CHKERRQ(ierr); 28 PetscFunctionReturn(0); 29 } 30 31 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 32 if (iascii) { 33 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 34 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 35 if (ptap->algType == 0) { 36 ierr = PetscViewerASCIIPrintf(viewer,"using scalable MatPtAP() implementation\n");CHKERRQ(ierr); 37 } else if (ptap->algType == 1) { 38 ierr = PetscViewerASCIIPrintf(viewer,"using nonscalable MatPtAP() implementation\n");CHKERRQ(ierr); 39 } 40 } 41 } 42 ierr = (ptap->view)(A,viewer);CHKERRQ(ierr); 43 PetscFunctionReturn(0); 44 } 45 46 PetscErrorCode MatFreeIntermediateDataStructures_MPIAIJ_AP(Mat A) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 50 Mat_APMPI *ptap=a->ap; 51 Mat_Merge_SeqsToMPI *merge; 52 53 PetscFunctionBegin; 54 if (!ptap) PetscFunctionReturn(0); 55 56 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 57 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 58 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 59 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 60 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */ 61 ierr = MatDestroy(&ptap->Rd);CHKERRQ(ierr); 62 ierr = MatDestroy(&ptap->Ro);CHKERRQ(ierr); 63 if (ptap->AP_loc) { /* used by alg_rap */ 64 Mat_SeqAIJ *ap = (Mat_SeqAIJ*)(ptap->AP_loc)->data; 65 ierr = PetscFree(ap->i);CHKERRQ(ierr); 66 ierr = PetscFree2(ap->j,ap->a);CHKERRQ(ierr); 67 ierr = MatDestroy(&ptap->AP_loc);CHKERRQ(ierr); 68 } else { /* used by alg_ptap */ 69 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 70 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 71 } 72 ierr = MatDestroy(&ptap->C_loc);CHKERRQ(ierr); 73 ierr = MatDestroy(&ptap->C_oth);CHKERRQ(ierr); 74 if (ptap->apa) {ierr = PetscFree(ptap->apa);CHKERRQ(ierr);} 75 76 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 77 78 merge=ptap->merge; 79 if (merge) { /* used by alg_ptap */ 80 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 81 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 82 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 83 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 84 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 85 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 86 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 87 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 88 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 89 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 90 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 91 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 92 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 93 ierr = PetscFree(ptap->merge);CHKERRQ(ierr); 94 } 95 ierr = ISLocalToGlobalMappingDestroy(&ptap->ltog);CHKERRQ(ierr); 96 97 A->ops->destroy = ptap->destroy; 98 ierr = PetscFree(a->ap);CHKERRQ(ierr); 99 PetscFunctionReturn(0); 100 } 101 102 PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A) 103 { 104 PetscErrorCode ierr; 105 106 PetscFunctionBegin; 107 ierr = (*A->ops->freeintermediatedatastructures)(A);CHKERRQ(ierr); 108 ierr = (*A->ops->destroy)(A);CHKERRQ(ierr); 109 PetscFunctionReturn(0); 110 } 111 112 PETSC_INTERN PetscErrorCode MatPtAP_MPIAIJ_MPIAIJ(Mat A,Mat P,MatReuse scall,PetscReal fill,Mat *C) 113 { 114 PetscErrorCode ierr; 115 PetscBool flg; 116 MPI_Comm comm; 117 #if !defined(PETSC_HAVE_HYPRE) 118 const char *algTypes[2] = {"scalable","nonscalable"}; 119 PetscInt nalg=2; 120 #else 121 const char *algTypes[3] = {"scalable","nonscalable","hypre"}; 122 PetscInt nalg=3; 123 #endif 124 PetscInt pN=P->cmap->N,alg=1; /* set default algorithm */ 125 126 PetscFunctionBegin; 127 /* check if matrix local sizes are compatible */ 128 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 129 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); 130 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); 131 132 if (scall == MAT_INITIAL_MATRIX) { 133 /* pick an algorithm */ 134 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 135 ierr = PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 136 ierr = PetscOptionsEnd();CHKERRQ(ierr); 137 138 if (!flg && pN > 100000) { /* may switch to scalable algorithm as default */ 139 MatInfo Ainfo,Pinfo; 140 PetscInt nz_local; 141 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 142 143 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 144 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 145 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); 146 147 if (pN > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 148 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 149 150 if (alg_scalable) { 151 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 152 } 153 } 154 155 switch (alg) { 156 case 1: 157 /* do R=P^T locally, then C=R*A*P -- nonscalable */ 158 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 159 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);CHKERRQ(ierr); 160 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 161 break; 162 #if defined(PETSC_HAVE_HYPRE) 163 case 2: 164 /* Use boomerAMGBuildCoarseOperator */ 165 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 166 ierr = MatPtAPSymbolic_AIJ_AIJ_wHYPRE(A,P,fill,C);CHKERRQ(ierr); 167 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 168 break; 169 #endif 170 default: 171 /* do R=P^T locally, then C=R*A*P */ 172 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 173 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(A,P,fill,C);CHKERRQ(ierr); 174 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 175 break; 176 } 177 178 if (alg == 0 || alg == 1) { 179 Mat_MPIAIJ *c = (Mat_MPIAIJ*)(*C)->data; 180 Mat_APMPI *ap = c->ap; 181 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)(*C)),((PetscObject)(*C))->prefix,"MatFreeIntermediateDataStructures","Mat");CHKERRQ(ierr); 182 ap->freestruct = PETSC_FALSE; 183 ierr = PetscOptionsBool("-mat_freeintermediatedatastructures","Free intermediate data structures", "MatFreeIntermediateDataStructures",ap->freestruct,&ap->freestruct, NULL);CHKERRQ(ierr); 184 ierr = PetscOptionsEnd();CHKERRQ(ierr); 185 } 186 } 187 188 ierr = PetscLogEventBegin(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 189 ierr = (*(*C)->ops->ptapnumeric)(A,P,*C);CHKERRQ(ierr); 190 ierr = PetscLogEventEnd(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 191 PetscFunctionReturn(0); 192 } 193 194 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,Mat C) 195 { 196 PetscErrorCode ierr; 197 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 198 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 199 Mat_SeqAIJ *ap,*p_loc,*p_oth,*c_seq; 200 Mat_APMPI *ptap = c->ap; 201 Mat AP_loc,C_loc,C_oth; 202 PetscInt i,rstart,rend,cm,ncols,row,*api,*apj,am = A->rmap->n,apnz,nout; 203 PetscScalar *apa; 204 const PetscInt *cols; 205 const PetscScalar *vals; 206 207 PetscFunctionBegin; 208 if (!ptap) { 209 MPI_Comm comm; 210 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 211 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 212 } 213 214 ierr = MatZeroEntries(C);CHKERRQ(ierr); 215 216 /* 1) get R = Pd^T,Ro = Po^T */ 217 if (ptap->reuse == MAT_REUSE_MATRIX) { 218 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 219 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 220 } 221 222 /* 2) get AP_loc */ 223 AP_loc = ptap->AP_loc; 224 ap = (Mat_SeqAIJ*)AP_loc->data; 225 226 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 227 /*-----------------------------------------------------*/ 228 if (ptap->reuse == MAT_REUSE_MATRIX) { 229 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 230 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 231 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 232 } 233 234 /* 2-2) compute numeric A_loc*P - dominating part */ 235 /* ---------------------------------------------- */ 236 /* get data from symbolic products */ 237 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 238 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 239 else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"ptap->P_oth is NULL. Cannot proceed!"); 240 241 api = ap->i; 242 apj = ap->j; 243 ierr = ISLocalToGlobalMappingApply(ptap->ltog,api[AP_loc->rmap->n],apj,apj);CHKERRQ(ierr); 244 for (i=0; i<am; i++) { 245 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 246 apnz = api[i+1] - api[i]; 247 apa = ap->a + api[i]; 248 ierr = PetscMemzero(apa,sizeof(PetscScalar)*apnz);CHKERRQ(ierr); 249 AProw_scalable(i,ad,ao,p_loc,p_oth,api,apj,apa); 250 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 251 } 252 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,api[AP_loc->rmap->n],apj,&nout,apj);CHKERRQ(ierr); 253 if (api[AP_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",api[AP_loc->rmap->n],nout); 254 255 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 256 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 257 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 258 259 C_loc = ptap->C_loc; 260 C_oth = ptap->C_oth; 261 262 /* add C_loc and Co to to C */ 263 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 264 265 /* C_loc -> C */ 266 cm = C_loc->rmap->N; 267 c_seq = (Mat_SeqAIJ*)C_loc->data; 268 cols = c_seq->j; 269 vals = c_seq->a; 270 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_loc->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 271 272 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 273 /* when there are no off-processor parts. */ 274 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 275 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 276 /* a table, and other, more complex stuff has to be done. */ 277 if (C->assembled) { 278 C->was_assembled = PETSC_TRUE; 279 C->assembled = PETSC_FALSE; 280 } 281 if (C->was_assembled) { 282 for (i=0; i<cm; i++) { 283 ncols = c_seq->i[i+1] - c_seq->i[i]; 284 row = rstart + i; 285 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 286 cols += ncols; vals += ncols; 287 } 288 } else { 289 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 290 } 291 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_loc->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 292 if (c_seq->i[C_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_seq->i[C_loc->rmap->n],nout); 293 294 /* Co -> C, off-processor part */ 295 cm = C_oth->rmap->N; 296 c_seq = (Mat_SeqAIJ*)C_oth->data; 297 cols = c_seq->j; 298 vals = c_seq->a; 299 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_oth->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 300 for (i=0; i<cm; i++) { 301 ncols = c_seq->i[i+1] - c_seq->i[i]; 302 row = p->garray[i]; 303 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 304 cols += ncols; vals += ncols; 305 } 306 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 307 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 308 309 ptap->reuse = MAT_REUSE_MATRIX; 310 311 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_oth->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 312 if (c_seq->i[C_oth->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_seq->i[C_loc->rmap->n],nout); 313 314 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 315 if (ptap->freestruct) { 316 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 317 } 318 PetscFunctionReturn(0); 319 } 320 321 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat *C) 322 { 323 PetscErrorCode ierr; 324 Mat_APMPI *ptap; 325 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 326 MPI_Comm comm; 327 PetscMPIInt size,rank; 328 Mat Cmpi,P_loc,P_oth; 329 PetscFreeSpaceList free_space=NULL,current_space=NULL; 330 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 331 PetscInt *lnk,i,k,pnz,row,nsend; 332 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 333 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 334 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 335 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 336 MPI_Request *swaits,*rwaits; 337 MPI_Status *sstatus,rstatus; 338 PetscLayout rowmap; 339 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 340 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 341 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,Crmax,*aj,*ai,*pi,nout; 342 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 343 PetscScalar *apv; 344 PetscTable ta; 345 MatType mtype; 346 #if defined(PETSC_USE_INFO) 347 PetscReal apfill; 348 #endif 349 350 PetscFunctionBegin; 351 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 352 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 353 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 354 355 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 356 357 /* create symbolic parallel matrix Cmpi */ 358 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 359 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 360 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 361 362 /* create struct Mat_APMPI and attached it to C later */ 363 ierr = PetscNew(&ptap);CHKERRQ(ierr); 364 ptap->reuse = MAT_INITIAL_MATRIX; 365 ptap->algType = 0; 366 367 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 368 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&P_oth);CHKERRQ(ierr); 369 /* get P_loc by taking all local rows of P */ 370 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&P_loc);CHKERRQ(ierr); 371 372 ptap->P_loc = P_loc; 373 ptap->P_oth = P_oth; 374 375 /* (0) compute Rd = Pd^T, Ro = Po^T */ 376 /* --------------------------------- */ 377 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 378 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 379 380 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 381 /* ----------------------------------------------------------------- */ 382 p_loc = (Mat_SeqAIJ*)P_loc->data; 383 if (P_oth) p_oth = (Mat_SeqAIJ*)P_oth->data; 384 385 /* create and initialize a linked list */ 386 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 387 MatRowMergeMax_SeqAIJ(p_loc,P_loc->rmap->N,ta); 388 MatRowMergeMax_SeqAIJ(p_oth,P_oth->rmap->N,ta); 389 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 390 391 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 392 393 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 394 if (ao) { 395 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 396 } else { 397 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 398 } 399 current_space = free_space; 400 nspacedouble = 0; 401 402 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 403 api[0] = 0; 404 for (i=0; i<am; i++) { 405 /* diagonal portion: Ad[i,:]*P */ 406 ai = ad->i; pi = p_loc->i; 407 nzi = ai[i+1] - ai[i]; 408 aj = ad->j + ai[i]; 409 for (j=0; j<nzi; j++) { 410 row = aj[j]; 411 pnz = pi[row+1] - pi[row]; 412 Jptr = p_loc->j + pi[row]; 413 /* add non-zero cols of P into the sorted linked list lnk */ 414 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 415 } 416 /* off-diagonal portion: Ao[i,:]*P */ 417 if (ao) { 418 ai = ao->i; pi = p_oth->i; 419 nzi = ai[i+1] - ai[i]; 420 aj = ao->j + ai[i]; 421 for (j=0; j<nzi; j++) { 422 row = aj[j]; 423 pnz = pi[row+1] - pi[row]; 424 Jptr = p_oth->j + pi[row]; 425 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 426 } 427 } 428 apnz = lnk[0]; 429 api[i+1] = api[i] + apnz; 430 431 /* if free space is not available, double the total space in the list */ 432 if (current_space->local_remaining<apnz) { 433 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 434 nspacedouble++; 435 } 436 437 /* Copy data into free space, then initialize lnk */ 438 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 439 440 current_space->array += apnz; 441 current_space->local_used += apnz; 442 current_space->local_remaining -= apnz; 443 } 444 /* Allocate space for apj and apv, initialize apj, and */ 445 /* destroy list of free space and other temporary array(s) */ 446 ierr = PetscCalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 447 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 448 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 449 450 /* Create AP_loc for reuse */ 451 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 452 ierr = MatSeqAIJCompactOutExtraColumns_SeqAIJ(ptap->AP_loc, &ptap->ltog);CHKERRQ(ierr); 453 454 #if defined(PETSC_USE_INFO) 455 if (ao) { 456 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 457 } else { 458 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 459 } 460 ptap->AP_loc->info.mallocs = nspacedouble; 461 ptap->AP_loc->info.fill_ratio_given = fill; 462 ptap->AP_loc->info.fill_ratio_needed = apfill; 463 464 if (api[am]) { 465 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); 466 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 467 } else { 468 ierr = PetscInfo(ptap->AP_loc,"Scalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 469 } 470 #endif 471 472 /* (2-1) compute symbolic Co = Ro*AP_loc */ 473 /* ------------------------------------ */ 474 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 475 476 477 /* (3) send coj of C_oth to other processors */ 478 /* ------------------------------------------ */ 479 /* determine row ownership */ 480 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 481 rowmap->n = pn; 482 rowmap->bs = 1; 483 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 484 owners = rowmap->range; 485 486 /* determine the number of messages to send, their lengths */ 487 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 488 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 489 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 490 491 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 492 coi = c_oth->i; coj = c_oth->j; 493 con = ptap->C_oth->rmap->n; 494 proc = 0; 495 ierr = ISLocalToGlobalMappingApply(ptap->ltog,coi[con],coj,coj);CHKERRQ(ierr); 496 for (i=0; i<con; i++) { 497 while (prmap[i] >= owners[proc+1]) proc++; 498 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 499 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 500 } 501 502 len = 0; /* max length of buf_si[], see (4) */ 503 owners_co[0] = 0; 504 nsend = 0; 505 for (proc=0; proc<size; proc++) { 506 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 507 if (len_s[proc]) { 508 nsend++; 509 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 510 len += len_si[proc]; 511 } 512 } 513 514 /* determine the number and length of messages to receive for coi and coj */ 515 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 516 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 517 518 /* post the Irecv and Isend of coj */ 519 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 520 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 521 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 522 for (proc=0, k=0; proc<size; proc++) { 523 if (!len_s[proc]) continue; 524 i = owners_co[proc]; 525 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 526 k++; 527 } 528 529 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 530 /* ---------------------------------------- */ 531 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 532 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 533 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,c_loc->j);CHKERRQ(ierr); 534 535 /* receives coj are complete */ 536 for (i=0; i<nrecv; i++) { 537 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 538 } 539 ierr = PetscFree(rwaits);CHKERRQ(ierr); 540 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 541 542 /* add received column indices into ta to update Crmax */ 543 for (k=0; k<nrecv; k++) {/* k-th received message */ 544 Jptr = buf_rj[k]; 545 for (j=0; j<len_r[k]; j++) { 546 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 547 } 548 } 549 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 550 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 551 552 /* (4) send and recv coi */ 553 /*-----------------------*/ 554 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 555 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 556 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 557 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 558 for (proc=0,k=0; proc<size; proc++) { 559 if (!len_s[proc]) continue; 560 /* form outgoing message for i-structure: 561 buf_si[0]: nrows to be sent 562 [1:nrows]: row index (global) 563 [nrows+1:2*nrows+1]: i-structure index 564 */ 565 /*-------------------------------------------*/ 566 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 567 buf_si_i = buf_si + nrows+1; 568 buf_si[0] = nrows; 569 buf_si_i[0] = 0; 570 nrows = 0; 571 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 572 nzi = coi[i+1] - coi[i]; 573 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 574 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 575 nrows++; 576 } 577 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 578 k++; 579 buf_si += len_si[proc]; 580 } 581 for (i=0; i<nrecv; i++) { 582 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 583 } 584 ierr = PetscFree(rwaits);CHKERRQ(ierr); 585 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 586 587 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 588 ierr = PetscFree(len_ri);CHKERRQ(ierr); 589 ierr = PetscFree(swaits);CHKERRQ(ierr); 590 ierr = PetscFree(buf_s);CHKERRQ(ierr); 591 592 /* (5) compute the local portion of Cmpi */ 593 /* ------------------------------------------ */ 594 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 595 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 596 current_space = free_space; 597 598 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 599 for (k=0; k<nrecv; k++) { 600 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 601 nrows = *buf_ri_k[k]; 602 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 603 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 604 } 605 606 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 607 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 608 for (i=0; i<pn; i++) { 609 /* add C_loc into Cmpi */ 610 nzi = c_loc->i[i+1] - c_loc->i[i]; 611 Jptr = c_loc->j + c_loc->i[i]; 612 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 613 614 /* add received col data into lnk */ 615 for (k=0; k<nrecv; k++) { /* k-th received message */ 616 if (i == *nextrow[k]) { /* i-th row */ 617 nzi = *(nextci[k]+1) - *nextci[k]; 618 Jptr = buf_rj[k] + *nextci[k]; 619 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 620 nextrow[k]++; nextci[k]++; 621 } 622 } 623 nzi = lnk[0]; 624 625 /* copy data into free space, then initialize lnk */ 626 ierr = PetscLLCondensedClean_Scalable(nzi,current_space->array,lnk);CHKERRQ(ierr); 627 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 628 } 629 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 630 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 631 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 632 633 /* local sizes and preallocation */ 634 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 635 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 636 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 637 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 638 639 /* members in merge */ 640 ierr = PetscFree(id_r);CHKERRQ(ierr); 641 ierr = PetscFree(len_r);CHKERRQ(ierr); 642 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 643 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 644 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 645 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 646 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 647 648 /* attach the supporting struct to Cmpi for reuse */ 649 c = (Mat_MPIAIJ*)Cmpi->data; 650 c->ap = ptap; 651 ptap->duplicate = Cmpi->ops->duplicate; 652 ptap->destroy = Cmpi->ops->destroy; 653 ptap->view = Cmpi->ops->view; 654 655 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 656 Cmpi->assembled = PETSC_FALSE; 657 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable; 658 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 659 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 660 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 661 *C = Cmpi; 662 663 nout = 0; 664 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_oth->i[ptap->C_oth->rmap->n],c_oth->j,&nout,c_oth->j);CHKERRQ(ierr); 665 if (c_oth->i[ptap->C_oth->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_oth->i[ptap->C_oth->rmap->n],nout); 666 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,&nout,c_loc->j);CHKERRQ(ierr); 667 if (c_loc->i[ptap->C_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_loc->i[ptap->C_loc->rmap->n],nout); 668 669 PetscFunctionReturn(0); 670 } 671 672 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 673 { 674 PetscErrorCode ierr; 675 Mat_APMPI *ptap; 676 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 677 MPI_Comm comm; 678 PetscMPIInt size,rank; 679 Mat Cmpi; 680 PetscFreeSpaceList free_space=NULL,current_space=NULL; 681 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 682 PetscInt *lnk,i,k,pnz,row,nsend; 683 PetscBT lnkbt; 684 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 685 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 686 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 687 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 688 MPI_Request *swaits,*rwaits; 689 MPI_Status *sstatus,rstatus; 690 PetscLayout rowmap; 691 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 692 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 693 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 694 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 695 PetscScalar *apv; 696 PetscTable ta; 697 MatType mtype; 698 #if defined(PETSC_USE_INFO) 699 PetscReal apfill; 700 #endif 701 702 PetscFunctionBegin; 703 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 704 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 705 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 706 707 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 708 709 /* create symbolic parallel matrix Cmpi */ 710 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 711 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 712 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 713 714 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 715 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 716 717 /* create struct Mat_APMPI and attached it to C later */ 718 ierr = PetscNew(&ptap);CHKERRQ(ierr); 719 ptap->reuse = MAT_INITIAL_MATRIX; 720 ptap->algType = 1; 721 722 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 723 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 724 /* get P_loc by taking all local rows of P */ 725 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 726 727 /* (0) compute Rd = Pd^T, Ro = Po^T */ 728 /* --------------------------------- */ 729 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 730 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 731 732 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 733 /* ----------------------------------------------------------------- */ 734 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 735 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 736 737 /* create and initialize a linked list */ 738 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 739 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 740 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 741 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 742 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 743 744 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 745 746 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 747 if (ao) { 748 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 749 } else { 750 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 751 } 752 current_space = free_space; 753 nspacedouble = 0; 754 755 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 756 api[0] = 0; 757 for (i=0; i<am; i++) { 758 /* diagonal portion: Ad[i,:]*P */ 759 ai = ad->i; pi = p_loc->i; 760 nzi = ai[i+1] - ai[i]; 761 aj = ad->j + ai[i]; 762 for (j=0; j<nzi; j++) { 763 row = aj[j]; 764 pnz = pi[row+1] - pi[row]; 765 Jptr = p_loc->j + pi[row]; 766 /* add non-zero cols of P into the sorted linked list lnk */ 767 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 768 } 769 /* off-diagonal portion: Ao[i,:]*P */ 770 if (ao) { 771 ai = ao->i; pi = p_oth->i; 772 nzi = ai[i+1] - ai[i]; 773 aj = ao->j + ai[i]; 774 for (j=0; j<nzi; j++) { 775 row = aj[j]; 776 pnz = pi[row+1] - pi[row]; 777 Jptr = p_oth->j + pi[row]; 778 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 779 } 780 } 781 apnz = lnk[0]; 782 api[i+1] = api[i] + apnz; 783 if (ap_rmax < apnz) ap_rmax = apnz; 784 785 /* if free space is not available, double the total space in the list */ 786 if (current_space->local_remaining<apnz) { 787 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 788 nspacedouble++; 789 } 790 791 /* Copy data into free space, then initialize lnk */ 792 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 793 794 current_space->array += apnz; 795 current_space->local_used += apnz; 796 current_space->local_remaining -= apnz; 797 } 798 /* Allocate space for apj and apv, initialize apj, and */ 799 /* destroy list of free space and other temporary array(s) */ 800 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 801 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 802 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 803 804 /* Create AP_loc for reuse */ 805 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 806 807 #if defined(PETSC_USE_INFO) 808 if (ao) { 809 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 810 } else { 811 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 812 } 813 ptap->AP_loc->info.mallocs = nspacedouble; 814 ptap->AP_loc->info.fill_ratio_given = fill; 815 ptap->AP_loc->info.fill_ratio_needed = apfill; 816 817 if (api[am]) { 818 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); 819 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 820 } else { 821 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 822 } 823 #endif 824 825 /* (2-1) compute symbolic Co = Ro*AP_loc */ 826 /* ------------------------------------ */ 827 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 828 829 /* (3) send coj of C_oth to other processors */ 830 /* ------------------------------------------ */ 831 /* determine row ownership */ 832 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 833 rowmap->n = pn; 834 rowmap->bs = 1; 835 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 836 owners = rowmap->range; 837 838 /* determine the number of messages to send, their lengths */ 839 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 840 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 841 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 842 843 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 844 coi = c_oth->i; coj = c_oth->j; 845 con = ptap->C_oth->rmap->n; 846 proc = 0; 847 for (i=0; i<con; i++) { 848 while (prmap[i] >= owners[proc+1]) proc++; 849 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 850 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 851 } 852 853 len = 0; /* max length of buf_si[], see (4) */ 854 owners_co[0] = 0; 855 nsend = 0; 856 for (proc=0; proc<size; proc++) { 857 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 858 if (len_s[proc]) { 859 nsend++; 860 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 861 len += len_si[proc]; 862 } 863 } 864 865 /* determine the number and length of messages to receive for coi and coj */ 866 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 867 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 868 869 /* post the Irecv and Isend of coj */ 870 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 871 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 872 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 873 for (proc=0, k=0; proc<size; proc++) { 874 if (!len_s[proc]) continue; 875 i = owners_co[proc]; 876 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 877 k++; 878 } 879 880 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 881 /* ---------------------------------------- */ 882 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 883 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 884 885 /* receives coj are complete */ 886 for (i=0; i<nrecv; i++) { 887 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 888 } 889 ierr = PetscFree(rwaits);CHKERRQ(ierr); 890 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 891 892 /* add received column indices into ta to update Crmax */ 893 for (k=0; k<nrecv; k++) {/* k-th received message */ 894 Jptr = buf_rj[k]; 895 for (j=0; j<len_r[k]; j++) { 896 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 897 } 898 } 899 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 900 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 901 902 /* (4) send and recv coi */ 903 /*-----------------------*/ 904 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 905 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 906 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 907 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 908 for (proc=0,k=0; proc<size; proc++) { 909 if (!len_s[proc]) continue; 910 /* form outgoing message for i-structure: 911 buf_si[0]: nrows to be sent 912 [1:nrows]: row index (global) 913 [nrows+1:2*nrows+1]: i-structure index 914 */ 915 /*-------------------------------------------*/ 916 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 917 buf_si_i = buf_si + nrows+1; 918 buf_si[0] = nrows; 919 buf_si_i[0] = 0; 920 nrows = 0; 921 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 922 nzi = coi[i+1] - coi[i]; 923 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 924 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 925 nrows++; 926 } 927 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 928 k++; 929 buf_si += len_si[proc]; 930 } 931 for (i=0; i<nrecv; i++) { 932 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 933 } 934 ierr = PetscFree(rwaits);CHKERRQ(ierr); 935 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 936 937 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 938 ierr = PetscFree(len_ri);CHKERRQ(ierr); 939 ierr = PetscFree(swaits);CHKERRQ(ierr); 940 ierr = PetscFree(buf_s);CHKERRQ(ierr); 941 942 /* (5) compute the local portion of Cmpi */ 943 /* ------------------------------------------ */ 944 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 945 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 946 current_space = free_space; 947 948 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 949 for (k=0; k<nrecv; k++) { 950 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 951 nrows = *buf_ri_k[k]; 952 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 953 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 954 } 955 956 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 957 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 958 for (i=0; i<pn; i++) { 959 /* add C_loc into Cmpi */ 960 nzi = c_loc->i[i+1] - c_loc->i[i]; 961 Jptr = c_loc->j + c_loc->i[i]; 962 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 963 964 /* add received col data into lnk */ 965 for (k=0; k<nrecv; k++) { /* k-th received message */ 966 if (i == *nextrow[k]) { /* i-th row */ 967 nzi = *(nextci[k]+1) - *nextci[k]; 968 Jptr = buf_rj[k] + *nextci[k]; 969 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 970 nextrow[k]++; nextci[k]++; 971 } 972 } 973 nzi = lnk[0]; 974 975 /* copy data into free space, then initialize lnk */ 976 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 977 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 978 } 979 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 980 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 981 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 982 983 /* local sizes and preallocation */ 984 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 985 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 986 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 987 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 988 989 /* members in merge */ 990 ierr = PetscFree(id_r);CHKERRQ(ierr); 991 ierr = PetscFree(len_r);CHKERRQ(ierr); 992 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 993 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 994 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 995 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 996 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 997 998 /* attach the supporting struct to Cmpi for reuse */ 999 c = (Mat_MPIAIJ*)Cmpi->data; 1000 c->ap = ptap; 1001 ptap->duplicate = Cmpi->ops->duplicate; 1002 ptap->destroy = Cmpi->ops->destroy; 1003 ptap->view = Cmpi->ops->view; 1004 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 1005 1006 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1007 Cmpi->assembled = PETSC_FALSE; 1008 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1009 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1010 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1011 *C = Cmpi; 1012 PetscFunctionReturn(0); 1013 } 1014 1015 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 1016 { 1017 PetscErrorCode ierr; 1018 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1019 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 1020 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 1021 Mat_APMPI *ptap = c->ap; 1022 Mat AP_loc,C_loc,C_oth; 1023 PetscInt i,rstart,rend,cm,ncols,row; 1024 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 1025 PetscScalar *apa; 1026 const PetscInt *cols; 1027 const PetscScalar *vals; 1028 1029 PetscFunctionBegin; 1030 if (!ptap) { 1031 MPI_Comm comm; 1032 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1033 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1034 } 1035 1036 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1037 /* 1) get R = Pd^T,Ro = Po^T */ 1038 if (ptap->reuse == MAT_REUSE_MATRIX) { 1039 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1040 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1041 } 1042 1043 /* 2) get AP_loc */ 1044 AP_loc = ptap->AP_loc; 1045 ap = (Mat_SeqAIJ*)AP_loc->data; 1046 1047 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 1048 /*-----------------------------------------------------*/ 1049 if (ptap->reuse == MAT_REUSE_MATRIX) { 1050 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 1051 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1052 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1053 } 1054 1055 /* 2-2) compute numeric A_loc*P - dominating part */ 1056 /* ---------------------------------------------- */ 1057 /* get data from symbolic products */ 1058 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1059 if (ptap->P_oth) { 1060 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1061 } 1062 apa = ptap->apa; 1063 api = ap->i; 1064 apj = ap->j; 1065 for (i=0; i<am; i++) { 1066 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 1067 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 1068 apnz = api[i+1] - api[i]; 1069 for (j=0; j<apnz; j++) { 1070 col = apj[j+api[i]]; 1071 ap->a[j+ap->i[i]] = apa[col]; 1072 apa[col] = 0.0; 1073 } 1074 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 1075 } 1076 1077 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 1078 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 1079 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 1080 C_loc = ptap->C_loc; 1081 C_oth = ptap->C_oth; 1082 1083 /* add C_loc and Co to to C */ 1084 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1085 1086 /* C_loc -> C */ 1087 cm = C_loc->rmap->N; 1088 c_seq = (Mat_SeqAIJ*)C_loc->data; 1089 cols = c_seq->j; 1090 vals = c_seq->a; 1091 1092 1093 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 1094 /* when there are no off-processor parts. */ 1095 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 1096 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 1097 /* a table, and other, more complex stuff has to be done. */ 1098 if (C->assembled) { 1099 C->was_assembled = PETSC_TRUE; 1100 C->assembled = PETSC_FALSE; 1101 } 1102 if (C->was_assembled) { 1103 for (i=0; i<cm; i++) { 1104 ncols = c_seq->i[i+1] - c_seq->i[i]; 1105 row = rstart + i; 1106 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1107 cols += ncols; vals += ncols; 1108 } 1109 } else { 1110 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 1111 } 1112 1113 /* Co -> C, off-processor part */ 1114 cm = C_oth->rmap->N; 1115 c_seq = (Mat_SeqAIJ*)C_oth->data; 1116 cols = c_seq->j; 1117 vals = c_seq->a; 1118 for (i=0; i<cm; i++) { 1119 ncols = c_seq->i[i+1] - c_seq->i[i]; 1120 row = p->garray[i]; 1121 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1122 cols += ncols; vals += ncols; 1123 } 1124 1125 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1126 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1127 1128 ptap->reuse = MAT_REUSE_MATRIX; 1129 1130 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1131 if (ptap->freestruct) { 1132 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1133 } 1134 PetscFunctionReturn(0); 1135 } 1136