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 if (ptap->C_loc->ops->matmultnumeric) { 257 ierr = (*ptap->C_loc->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 258 } else { 259 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 260 } 261 if (ptap->C_oth->ops->matmultnumeric) { 262 ierr = (*ptap->C_oth->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 263 } else { 264 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 265 } 266 267 C_loc = ptap->C_loc; 268 C_oth = ptap->C_oth; 269 270 /* add C_loc and Co to to C */ 271 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 272 273 /* C_loc -> C */ 274 cm = C_loc->rmap->N; 275 c_seq = (Mat_SeqAIJ*)C_loc->data; 276 cols = c_seq->j; 277 vals = c_seq->a; 278 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_loc->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 279 280 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 281 /* when there are no off-processor parts. */ 282 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 283 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 284 /* a table, and other, more complex stuff has to be done. */ 285 if (C->assembled) { 286 C->was_assembled = PETSC_TRUE; 287 C->assembled = PETSC_FALSE; 288 } 289 if (C->was_assembled) { 290 for (i=0; i<cm; i++) { 291 ncols = c_seq->i[i+1] - c_seq->i[i]; 292 row = rstart + i; 293 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 294 cols += ncols; vals += ncols; 295 } 296 } else { 297 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 298 } 299 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_loc->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 300 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); 301 302 /* Co -> C, off-processor part */ 303 cm = C_oth->rmap->N; 304 c_seq = (Mat_SeqAIJ*)C_oth->data; 305 cols = c_seq->j; 306 vals = c_seq->a; 307 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_oth->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 308 for (i=0; i<cm; i++) { 309 ncols = c_seq->i[i+1] - c_seq->i[i]; 310 row = p->garray[i]; 311 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 312 cols += ncols; vals += ncols; 313 } 314 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 315 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 316 317 ptap->reuse = MAT_REUSE_MATRIX; 318 319 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_oth->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 320 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); 321 322 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 323 if (ptap->freestruct) { 324 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 325 } 326 PetscFunctionReturn(0); 327 } 328 329 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat *C) 330 { 331 PetscErrorCode ierr; 332 Mat_APMPI *ptap; 333 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 334 MPI_Comm comm; 335 PetscMPIInt size,rank; 336 Mat Cmpi,P_loc,P_oth; 337 PetscFreeSpaceList free_space=NULL,current_space=NULL; 338 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 339 PetscInt *lnk,i,k,pnz,row,nsend; 340 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 341 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 342 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 343 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 344 MPI_Request *swaits,*rwaits; 345 MPI_Status *sstatus,rstatus; 346 PetscLayout rowmap; 347 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 348 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 349 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,Crmax,*aj,*ai,*pi,nout; 350 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 351 PetscScalar *apv; 352 PetscTable ta; 353 MatType mtype; 354 #if defined(PETSC_USE_INFO) 355 PetscReal apfill; 356 #endif 357 358 PetscFunctionBegin; 359 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 360 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 361 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 362 363 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 364 365 /* create symbolic parallel matrix Cmpi */ 366 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 367 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 368 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 369 370 /* create struct Mat_APMPI and attached it to C later */ 371 ierr = PetscNew(&ptap);CHKERRQ(ierr); 372 ptap->reuse = MAT_INITIAL_MATRIX; 373 ptap->algType = 0; 374 375 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 376 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&P_oth);CHKERRQ(ierr); 377 /* get P_loc by taking all local rows of P */ 378 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&P_loc);CHKERRQ(ierr); 379 380 ptap->P_loc = P_loc; 381 ptap->P_oth = P_oth; 382 383 /* (0) compute Rd = Pd^T, Ro = Po^T */ 384 /* --------------------------------- */ 385 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 386 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 387 388 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 389 /* ----------------------------------------------------------------- */ 390 p_loc = (Mat_SeqAIJ*)P_loc->data; 391 if (P_oth) p_oth = (Mat_SeqAIJ*)P_oth->data; 392 393 /* create and initialize a linked list */ 394 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 395 MatRowMergeMax_SeqAIJ(p_loc,P_loc->rmap->N,ta); 396 MatRowMergeMax_SeqAIJ(p_oth,P_oth->rmap->N,ta); 397 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 398 399 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 400 401 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 402 if (ao) { 403 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 404 } else { 405 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 406 } 407 current_space = free_space; 408 nspacedouble = 0; 409 410 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 411 api[0] = 0; 412 for (i=0; i<am; i++) { 413 /* diagonal portion: Ad[i,:]*P */ 414 ai = ad->i; pi = p_loc->i; 415 nzi = ai[i+1] - ai[i]; 416 aj = ad->j + ai[i]; 417 for (j=0; j<nzi; j++) { 418 row = aj[j]; 419 pnz = pi[row+1] - pi[row]; 420 Jptr = p_loc->j + pi[row]; 421 /* add non-zero cols of P into the sorted linked list lnk */ 422 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 423 } 424 /* off-diagonal portion: Ao[i,:]*P */ 425 if (ao) { 426 ai = ao->i; pi = p_oth->i; 427 nzi = ai[i+1] - ai[i]; 428 aj = ao->j + ai[i]; 429 for (j=0; j<nzi; j++) { 430 row = aj[j]; 431 pnz = pi[row+1] - pi[row]; 432 Jptr = p_oth->j + pi[row]; 433 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 434 } 435 } 436 apnz = lnk[0]; 437 api[i+1] = api[i] + apnz; 438 439 /* if free space is not available, double the total space in the list */ 440 if (current_space->local_remaining<apnz) { 441 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 442 nspacedouble++; 443 } 444 445 /* Copy data into free space, then initialize lnk */ 446 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 447 448 current_space->array += apnz; 449 current_space->local_used += apnz; 450 current_space->local_remaining -= apnz; 451 } 452 /* Allocate space for apj and apv, initialize apj, and */ 453 /* destroy list of free space and other temporary array(s) */ 454 ierr = PetscCalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 455 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 456 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 457 458 /* Create AP_loc for reuse */ 459 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 460 ierr = MatSeqAIJCompactOutExtraColumns_SeqAIJ(ptap->AP_loc, &ptap->ltog);CHKERRQ(ierr); 461 462 #if defined(PETSC_USE_INFO) 463 if (ao) { 464 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 465 } else { 466 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 467 } 468 ptap->AP_loc->info.mallocs = nspacedouble; 469 ptap->AP_loc->info.fill_ratio_given = fill; 470 ptap->AP_loc->info.fill_ratio_needed = apfill; 471 472 if (api[am]) { 473 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); 474 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 475 } else { 476 ierr = PetscInfo(ptap->AP_loc,"Scalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 477 } 478 #endif 479 480 /* (2-1) compute symbolic Co = Ro*AP_loc */ 481 /* ------------------------------------ */ 482 ierr = MatSetOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 483 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 484 485 /* (3) send coj of C_oth to other processors */ 486 /* ------------------------------------------ */ 487 /* determine row ownership */ 488 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 489 rowmap->n = pn; 490 rowmap->bs = 1; 491 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 492 owners = rowmap->range; 493 494 /* determine the number of messages to send, their lengths */ 495 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 496 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 497 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 498 499 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 500 coi = c_oth->i; coj = c_oth->j; 501 con = ptap->C_oth->rmap->n; 502 proc = 0; 503 ierr = ISLocalToGlobalMappingApply(ptap->ltog,coi[con],coj,coj);CHKERRQ(ierr); 504 for (i=0; i<con; i++) { 505 while (prmap[i] >= owners[proc+1]) proc++; 506 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 507 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 508 } 509 510 len = 0; /* max length of buf_si[], see (4) */ 511 owners_co[0] = 0; 512 nsend = 0; 513 for (proc=0; proc<size; proc++) { 514 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 515 if (len_s[proc]) { 516 nsend++; 517 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 518 len += len_si[proc]; 519 } 520 } 521 522 /* determine the number and length of messages to receive for coi and coj */ 523 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 524 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 525 526 /* post the Irecv and Isend of coj */ 527 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 528 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 529 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 530 for (proc=0, k=0; proc<size; proc++) { 531 if (!len_s[proc]) continue; 532 i = owners_co[proc]; 533 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 534 k++; 535 } 536 537 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 538 /* ---------------------------------------- */ 539 ierr = MatSetOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 540 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 541 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 542 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,c_loc->j);CHKERRQ(ierr); 543 544 /* receives coj are complete */ 545 for (i=0; i<nrecv; i++) { 546 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 547 } 548 ierr = PetscFree(rwaits);CHKERRQ(ierr); 549 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 550 551 /* add received column indices into ta to update Crmax */ 552 for (k=0; k<nrecv; k++) {/* k-th received message */ 553 Jptr = buf_rj[k]; 554 for (j=0; j<len_r[k]; j++) { 555 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 556 } 557 } 558 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 559 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 560 561 /* (4) send and recv coi */ 562 /*-----------------------*/ 563 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 564 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 565 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 566 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 567 for (proc=0,k=0; proc<size; proc++) { 568 if (!len_s[proc]) continue; 569 /* form outgoing message for i-structure: 570 buf_si[0]: nrows to be sent 571 [1:nrows]: row index (global) 572 [nrows+1:2*nrows+1]: i-structure index 573 */ 574 /*-------------------------------------------*/ 575 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 576 buf_si_i = buf_si + nrows+1; 577 buf_si[0] = nrows; 578 buf_si_i[0] = 0; 579 nrows = 0; 580 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 581 nzi = coi[i+1] - coi[i]; 582 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 583 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 584 nrows++; 585 } 586 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 587 k++; 588 buf_si += len_si[proc]; 589 } 590 for (i=0; i<nrecv; i++) { 591 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 592 } 593 ierr = PetscFree(rwaits);CHKERRQ(ierr); 594 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 595 596 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 597 ierr = PetscFree(len_ri);CHKERRQ(ierr); 598 ierr = PetscFree(swaits);CHKERRQ(ierr); 599 ierr = PetscFree(buf_s);CHKERRQ(ierr); 600 601 /* (5) compute the local portion of Cmpi */ 602 /* ------------------------------------------ */ 603 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 604 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 605 current_space = free_space; 606 607 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 608 for (k=0; k<nrecv; k++) { 609 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 610 nrows = *buf_ri_k[k]; 611 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 612 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 613 } 614 615 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 616 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 617 for (i=0; i<pn; i++) { 618 /* add C_loc into Cmpi */ 619 nzi = c_loc->i[i+1] - c_loc->i[i]; 620 Jptr = c_loc->j + c_loc->i[i]; 621 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 622 623 /* add received col data into lnk */ 624 for (k=0; k<nrecv; k++) { /* k-th received message */ 625 if (i == *nextrow[k]) { /* i-th row */ 626 nzi = *(nextci[k]+1) - *nextci[k]; 627 Jptr = buf_rj[k] + *nextci[k]; 628 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 629 nextrow[k]++; nextci[k]++; 630 } 631 } 632 nzi = lnk[0]; 633 634 /* copy data into free space, then initialize lnk */ 635 ierr = PetscLLCondensedClean_Scalable(nzi,current_space->array,lnk);CHKERRQ(ierr); 636 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 637 } 638 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 639 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 640 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 641 642 /* local sizes and preallocation */ 643 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 644 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 645 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 646 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 647 648 /* members in merge */ 649 ierr = PetscFree(id_r);CHKERRQ(ierr); 650 ierr = PetscFree(len_r);CHKERRQ(ierr); 651 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 652 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 653 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 654 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 655 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 656 657 /* attach the supporting struct to Cmpi for reuse */ 658 c = (Mat_MPIAIJ*)Cmpi->data; 659 c->ap = ptap; 660 ptap->duplicate = Cmpi->ops->duplicate; 661 ptap->destroy = Cmpi->ops->destroy; 662 ptap->view = Cmpi->ops->view; 663 664 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 665 Cmpi->assembled = PETSC_FALSE; 666 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable; 667 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 668 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 669 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 670 *C = Cmpi; 671 672 nout = 0; 673 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_oth->i[ptap->C_oth->rmap->n],c_oth->j,&nout,c_oth->j);CHKERRQ(ierr); 674 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); 675 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,&nout,c_loc->j);CHKERRQ(ierr); 676 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); 677 678 PetscFunctionReturn(0); 679 } 680 681 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 682 { 683 PetscErrorCode ierr; 684 Mat_APMPI *ptap; 685 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 686 MPI_Comm comm; 687 PetscMPIInt size,rank; 688 Mat Cmpi; 689 PetscFreeSpaceList free_space=NULL,current_space=NULL; 690 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 691 PetscInt *lnk,i,k,pnz,row,nsend; 692 PetscBT lnkbt; 693 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 694 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 695 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 696 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 697 MPI_Request *swaits,*rwaits; 698 MPI_Status *sstatus,rstatus; 699 PetscLayout rowmap; 700 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 701 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 702 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 703 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 704 PetscScalar *apv; 705 PetscTable ta; 706 MatType mtype; 707 #if defined(PETSC_USE_INFO) 708 PetscReal apfill; 709 #endif 710 711 PetscFunctionBegin; 712 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 713 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 714 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 715 716 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 717 718 /* create symbolic parallel matrix Cmpi */ 719 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 720 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 721 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 722 723 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 724 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 725 726 /* create struct Mat_APMPI and attached it to C later */ 727 ierr = PetscNew(&ptap);CHKERRQ(ierr); 728 ptap->reuse = MAT_INITIAL_MATRIX; 729 ptap->algType = 1; 730 731 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 732 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 733 /* get P_loc by taking all local rows of P */ 734 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 735 736 /* (0) compute Rd = Pd^T, Ro = Po^T */ 737 /* --------------------------------- */ 738 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 739 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 740 741 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 742 /* ----------------------------------------------------------------- */ 743 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 744 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 745 746 /* create and initialize a linked list */ 747 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 748 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 749 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 750 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 751 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 752 753 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 754 755 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 756 if (ao) { 757 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 758 } else { 759 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 760 } 761 current_space = free_space; 762 nspacedouble = 0; 763 764 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 765 api[0] = 0; 766 for (i=0; i<am; i++) { 767 /* diagonal portion: Ad[i,:]*P */ 768 ai = ad->i; pi = p_loc->i; 769 nzi = ai[i+1] - ai[i]; 770 aj = ad->j + ai[i]; 771 for (j=0; j<nzi; j++) { 772 row = aj[j]; 773 pnz = pi[row+1] - pi[row]; 774 Jptr = p_loc->j + pi[row]; 775 /* add non-zero cols of P into the sorted linked list lnk */ 776 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 777 } 778 /* off-diagonal portion: Ao[i,:]*P */ 779 if (ao) { 780 ai = ao->i; pi = p_oth->i; 781 nzi = ai[i+1] - ai[i]; 782 aj = ao->j + ai[i]; 783 for (j=0; j<nzi; j++) { 784 row = aj[j]; 785 pnz = pi[row+1] - pi[row]; 786 Jptr = p_oth->j + pi[row]; 787 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 788 } 789 } 790 apnz = lnk[0]; 791 api[i+1] = api[i] + apnz; 792 if (ap_rmax < apnz) ap_rmax = apnz; 793 794 /* if free space is not available, double the total space in the list */ 795 if (current_space->local_remaining<apnz) { 796 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 797 nspacedouble++; 798 } 799 800 /* Copy data into free space, then initialize lnk */ 801 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 802 803 current_space->array += apnz; 804 current_space->local_used += apnz; 805 current_space->local_remaining -= apnz; 806 } 807 /* Allocate space for apj and apv, initialize apj, and */ 808 /* destroy list of free space and other temporary array(s) */ 809 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 810 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 811 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 812 813 /* Create AP_loc for reuse */ 814 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 815 816 #if defined(PETSC_USE_INFO) 817 if (ao) { 818 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 819 } else { 820 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 821 } 822 ptap->AP_loc->info.mallocs = nspacedouble; 823 ptap->AP_loc->info.fill_ratio_given = fill; 824 ptap->AP_loc->info.fill_ratio_needed = apfill; 825 826 if (api[am]) { 827 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); 828 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 829 } else { 830 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 831 } 832 #endif 833 834 /* (2-1) compute symbolic Co = Ro*AP_loc */ 835 /* ------------------------------------ */ 836 ierr = MatSetOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 837 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 838 839 /* (3) send coj of C_oth to other processors */ 840 /* ------------------------------------------ */ 841 /* determine row ownership */ 842 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 843 rowmap->n = pn; 844 rowmap->bs = 1; 845 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 846 owners = rowmap->range; 847 848 /* determine the number of messages to send, their lengths */ 849 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 850 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 851 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 852 853 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 854 coi = c_oth->i; coj = c_oth->j; 855 con = ptap->C_oth->rmap->n; 856 proc = 0; 857 for (i=0; i<con; i++) { 858 while (prmap[i] >= owners[proc+1]) proc++; 859 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 860 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 861 } 862 863 len = 0; /* max length of buf_si[], see (4) */ 864 owners_co[0] = 0; 865 nsend = 0; 866 for (proc=0; proc<size; proc++) { 867 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 868 if (len_s[proc]) { 869 nsend++; 870 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 871 len += len_si[proc]; 872 } 873 } 874 875 /* determine the number and length of messages to receive for coi and coj */ 876 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 877 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 878 879 /* post the Irecv and Isend of coj */ 880 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 881 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 882 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 883 for (proc=0, k=0; proc<size; proc++) { 884 if (!len_s[proc]) continue; 885 i = owners_co[proc]; 886 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 887 k++; 888 } 889 890 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 891 /* ---------------------------------------- */ 892 ierr = MatSetOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 893 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 894 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 895 896 /* receives coj are complete */ 897 for (i=0; i<nrecv; i++) { 898 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 899 } 900 ierr = PetscFree(rwaits);CHKERRQ(ierr); 901 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 902 903 /* add received column indices into ta to update Crmax */ 904 for (k=0; k<nrecv; k++) {/* k-th received message */ 905 Jptr = buf_rj[k]; 906 for (j=0; j<len_r[k]; j++) { 907 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 908 } 909 } 910 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 911 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 912 913 /* (4) send and recv coi */ 914 /*-----------------------*/ 915 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 916 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 917 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 918 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 919 for (proc=0,k=0; proc<size; proc++) { 920 if (!len_s[proc]) continue; 921 /* form outgoing message for i-structure: 922 buf_si[0]: nrows to be sent 923 [1:nrows]: row index (global) 924 [nrows+1:2*nrows+1]: i-structure index 925 */ 926 /*-------------------------------------------*/ 927 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 928 buf_si_i = buf_si + nrows+1; 929 buf_si[0] = nrows; 930 buf_si_i[0] = 0; 931 nrows = 0; 932 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 933 nzi = coi[i+1] - coi[i]; 934 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 935 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 936 nrows++; 937 } 938 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 939 k++; 940 buf_si += len_si[proc]; 941 } 942 for (i=0; i<nrecv; i++) { 943 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 944 } 945 ierr = PetscFree(rwaits);CHKERRQ(ierr); 946 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 947 948 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 949 ierr = PetscFree(len_ri);CHKERRQ(ierr); 950 ierr = PetscFree(swaits);CHKERRQ(ierr); 951 ierr = PetscFree(buf_s);CHKERRQ(ierr); 952 953 /* (5) compute the local portion of Cmpi */ 954 /* ------------------------------------------ */ 955 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 956 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 957 current_space = free_space; 958 959 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 960 for (k=0; k<nrecv; k++) { 961 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 962 nrows = *buf_ri_k[k]; 963 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 964 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 965 } 966 967 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 968 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 969 for (i=0; i<pn; i++) { 970 /* add C_loc into Cmpi */ 971 nzi = c_loc->i[i+1] - c_loc->i[i]; 972 Jptr = c_loc->j + c_loc->i[i]; 973 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 974 975 /* add received col data into lnk */ 976 for (k=0; k<nrecv; k++) { /* k-th received message */ 977 if (i == *nextrow[k]) { /* i-th row */ 978 nzi = *(nextci[k]+1) - *nextci[k]; 979 Jptr = buf_rj[k] + *nextci[k]; 980 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 981 nextrow[k]++; nextci[k]++; 982 } 983 } 984 nzi = lnk[0]; 985 986 /* copy data into free space, then initialize lnk */ 987 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 988 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 989 } 990 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 991 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 992 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 993 994 /* local sizes and preallocation */ 995 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 996 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 997 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 998 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 999 1000 /* members in merge */ 1001 ierr = PetscFree(id_r);CHKERRQ(ierr); 1002 ierr = PetscFree(len_r);CHKERRQ(ierr); 1003 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 1004 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 1005 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 1006 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 1007 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 1008 1009 /* attach the supporting struct to Cmpi for reuse */ 1010 c = (Mat_MPIAIJ*)Cmpi->data; 1011 c->ap = ptap; 1012 ptap->duplicate = Cmpi->ops->duplicate; 1013 ptap->destroy = Cmpi->ops->destroy; 1014 ptap->view = Cmpi->ops->view; 1015 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 1016 1017 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1018 Cmpi->assembled = PETSC_FALSE; 1019 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1020 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1021 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1022 *C = Cmpi; 1023 PetscFunctionReturn(0); 1024 } 1025 1026 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 1027 { 1028 PetscErrorCode ierr; 1029 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1030 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 1031 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 1032 Mat_APMPI *ptap = c->ap; 1033 Mat AP_loc,C_loc,C_oth; 1034 PetscInt i,rstart,rend,cm,ncols,row; 1035 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 1036 PetscScalar *apa; 1037 const PetscInt *cols; 1038 const PetscScalar *vals; 1039 1040 PetscFunctionBegin; 1041 if (!ptap) { 1042 MPI_Comm comm; 1043 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1044 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1045 } 1046 1047 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1048 /* 1) get R = Pd^T,Ro = Po^T */ 1049 if (ptap->reuse == MAT_REUSE_MATRIX) { 1050 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1051 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1052 } 1053 1054 /* 2) get AP_loc */ 1055 AP_loc = ptap->AP_loc; 1056 ap = (Mat_SeqAIJ*)AP_loc->data; 1057 1058 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 1059 /*-----------------------------------------------------*/ 1060 if (ptap->reuse == MAT_REUSE_MATRIX) { 1061 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 1062 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1063 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1064 } 1065 1066 /* 2-2) compute numeric A_loc*P - dominating part */ 1067 /* ---------------------------------------------- */ 1068 /* get data from symbolic products */ 1069 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1070 if (ptap->P_oth) { 1071 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1072 } 1073 apa = ptap->apa; 1074 api = ap->i; 1075 apj = ap->j; 1076 for (i=0; i<am; i++) { 1077 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 1078 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 1079 apnz = api[i+1] - api[i]; 1080 for (j=0; j<apnz; j++) { 1081 col = apj[j+api[i]]; 1082 ap->a[j+ap->i[i]] = apa[col]; 1083 apa[col] = 0.0; 1084 } 1085 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 1086 } 1087 1088 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 1089 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 1090 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 1091 C_loc = ptap->C_loc; 1092 C_oth = ptap->C_oth; 1093 1094 /* add C_loc and Co to to C */ 1095 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 1096 1097 /* C_loc -> C */ 1098 cm = C_loc->rmap->N; 1099 c_seq = (Mat_SeqAIJ*)C_loc->data; 1100 cols = c_seq->j; 1101 vals = c_seq->a; 1102 1103 1104 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 1105 /* when there are no off-processor parts. */ 1106 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 1107 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 1108 /* a table, and other, more complex stuff has to be done. */ 1109 if (C->assembled) { 1110 C->was_assembled = PETSC_TRUE; 1111 C->assembled = PETSC_FALSE; 1112 } 1113 if (C->was_assembled) { 1114 for (i=0; i<cm; i++) { 1115 ncols = c_seq->i[i+1] - c_seq->i[i]; 1116 row = rstart + i; 1117 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1118 cols += ncols; vals += ncols; 1119 } 1120 } else { 1121 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 1122 } 1123 1124 /* Co -> C, off-processor part */ 1125 cm = C_oth->rmap->N; 1126 c_seq = (Mat_SeqAIJ*)C_oth->data; 1127 cols = c_seq->j; 1128 vals = c_seq->a; 1129 for (i=0; i<cm; i++) { 1130 ncols = c_seq->i[i+1] - c_seq->i[i]; 1131 row = p->garray[i]; 1132 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 1133 cols += ncols; vals += ncols; 1134 } 1135 1136 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1137 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1138 1139 ptap->reuse = MAT_REUSE_MATRIX; 1140 1141 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1142 if (ptap->freestruct) { 1143 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1144 } 1145 PetscFunctionReturn(0); 1146 } 1147