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 #include <petsc/private/hashmapiv.h> 13 #include <petsc/private/hashseti.h> 14 #include <petscsf.h> 15 16 17 PetscErrorCode MatView_MPIAIJ_PtAP(Mat A,PetscViewer viewer) 18 { 19 PetscErrorCode ierr; 20 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 21 Mat_APMPI *ptap=a->ap; 22 PetscBool iascii; 23 PetscViewerFormat format; 24 25 PetscFunctionBegin; 26 if (!ptap) { 27 /* hack: MatDuplicate() sets oldmat->ops->view to newmat which is a base mat class with null ptpa! */ 28 A->ops->view = MatView_MPIAIJ; 29 ierr = (A->ops->view)(A,viewer);CHKERRQ(ierr); 30 PetscFunctionReturn(0); 31 } 32 33 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 34 if (iascii) { 35 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 36 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 37 if (ptap->algType == 0) { 38 ierr = PetscViewerASCIIPrintf(viewer,"using scalable MatPtAP() implementation\n");CHKERRQ(ierr); 39 } else if (ptap->algType == 1) { 40 ierr = PetscViewerASCIIPrintf(viewer,"using nonscalable MatPtAP() implementation\n");CHKERRQ(ierr); 41 } else if (ptap->algType == 2) { 42 ierr = PetscViewerASCIIPrintf(viewer,"using allatonce MatPtAP() implementation\n");CHKERRQ(ierr); 43 } else if (ptap->algType == 3) { 44 ierr = PetscViewerASCIIPrintf(viewer,"using merged allatonce MatPtAP() implementation\n");CHKERRQ(ierr); 45 } 46 } 47 } 48 ierr = (ptap->view)(A,viewer);CHKERRQ(ierr); 49 PetscFunctionReturn(0); 50 } 51 52 PetscErrorCode MatFreeIntermediateDataStructures_MPIAIJ_AP(Mat A) 53 { 54 PetscErrorCode ierr; 55 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 56 Mat_APMPI *ptap=a->ap; 57 Mat_Merge_SeqsToMPI *merge; 58 59 PetscFunctionBegin; 60 if (!ptap) PetscFunctionReturn(0); 61 62 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 63 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 64 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 65 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 66 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */ 67 ierr = MatDestroy(&ptap->Rd);CHKERRQ(ierr); 68 ierr = MatDestroy(&ptap->Ro);CHKERRQ(ierr); 69 if (ptap->AP_loc) { /* used by alg_rap */ 70 Mat_SeqAIJ *ap = (Mat_SeqAIJ*)(ptap->AP_loc)->data; 71 ierr = PetscFree(ap->i);CHKERRQ(ierr); 72 ierr = PetscFree2(ap->j,ap->a);CHKERRQ(ierr); 73 ierr = MatDestroy(&ptap->AP_loc);CHKERRQ(ierr); 74 } else { /* used by alg_ptap */ 75 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 76 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 77 } 78 ierr = MatDestroy(&ptap->C_loc);CHKERRQ(ierr); 79 ierr = MatDestroy(&ptap->C_oth);CHKERRQ(ierr); 80 if (ptap->apa) {ierr = PetscFree(ptap->apa);CHKERRQ(ierr);} 81 82 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 83 84 merge=ptap->merge; 85 if (merge) { /* used by alg_ptap */ 86 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 87 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 88 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 89 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 90 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 91 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 92 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 93 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 94 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 95 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 96 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 97 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 98 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 99 ierr = PetscFree(ptap->merge);CHKERRQ(ierr); 100 } 101 ierr = ISLocalToGlobalMappingDestroy(&ptap->ltog);CHKERRQ(ierr); 102 103 ierr = PetscSFDestroy(&ptap->sf);CHKERRQ(ierr); 104 ierr = PetscFree(ptap->c_othi);CHKERRQ(ierr); 105 ierr = PetscFree(ptap->c_rmti);CHKERRQ(ierr); 106 PetscFunctionReturn(0); 107 } 108 109 PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A) 110 { 111 PetscErrorCode ierr; 112 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 113 Mat_APMPI *ptap=a->ap; 114 115 PetscFunctionBegin; 116 ierr = (*A->ops->freeintermediatedatastructures)(A);CHKERRQ(ierr); 117 ierr = (*ptap->destroy)(A);CHKERRQ(ierr); /* MatDestroy_MPIAIJ(A) */ 118 ierr = PetscFree(ptap);CHKERRQ(ierr); 119 PetscFunctionReturn(0); 120 } 121 122 PETSC_INTERN PetscErrorCode MatPtAP_MPIAIJ_MPIAIJ(Mat A,Mat P,MatReuse scall,PetscReal fill,Mat *C) 123 { 124 PetscErrorCode ierr; 125 PetscBool flg; 126 MPI_Comm comm; 127 #if !defined(PETSC_HAVE_HYPRE) 128 const char *algTypes[4] = {"scalable","nonscalable","allatonce","allatonce_merged"}; 129 PetscInt nalg=4; 130 #else 131 const char *algTypes[5] = {"scalable","nonscalable","allatonce","allatonce_merged","hypre"}; 132 PetscInt nalg=5; 133 #endif 134 PetscInt pN=P->cmap->N,alg=1; /* set default algorithm */ 135 136 PetscFunctionBegin; 137 /* check if matrix local sizes are compatible */ 138 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 139 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); 140 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); 141 142 if (scall == MAT_INITIAL_MATRIX) { 143 /* pick an algorithm */ 144 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 145 ierr = PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 146 ierr = PetscOptionsEnd();CHKERRQ(ierr); 147 148 if (!flg && pN > 100000) { /* may switch to scalable algorithm as default */ 149 MatInfo Ainfo,Pinfo; 150 PetscInt nz_local; 151 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 152 153 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 154 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 155 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); 156 157 if (pN > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 158 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 159 160 if (alg_scalable) { 161 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 162 } 163 } 164 165 switch (alg) { 166 case 1: 167 /* do R=P^T locally, then C=R*A*P -- nonscalable */ 168 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 169 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);CHKERRQ(ierr); 170 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 171 break; 172 case 2: 173 /* compute C=P^T*A*P allatonce */ 174 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 175 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(A,P,fill,C);CHKERRQ(ierr); 176 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 177 break; 178 case 3: 179 /* compute C=P^T*A*P allatonce */ 180 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 181 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(A,P,fill,C);CHKERRQ(ierr); 182 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 183 break; 184 #if defined(PETSC_HAVE_HYPRE) 185 case 4: 186 /* Use boomerAMGBuildCoarseOperator */ 187 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 188 ierr = MatPtAPSymbolic_AIJ_AIJ_wHYPRE(A,P,fill,C);CHKERRQ(ierr); 189 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 190 break; 191 #endif 192 default: 193 /* do R=P^T locally, then C=R*A*P */ 194 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 195 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(A,P,fill,C);CHKERRQ(ierr); 196 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 197 break; 198 } 199 200 if (alg == 0 || alg == 1 || alg == 2 || alg == 3) { 201 Mat_MPIAIJ *c = (Mat_MPIAIJ*)(*C)->data; 202 Mat_APMPI *ap = c->ap; 203 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)(*C)),((PetscObject)(*C))->prefix,"MatFreeIntermediateDataStructures","Mat");CHKERRQ(ierr); 204 ap->freestruct = PETSC_FALSE; 205 ierr = PetscOptionsBool("-mat_freeintermediatedatastructures","Free intermediate data structures", "MatFreeIntermediateDataStructures",ap->freestruct,&ap->freestruct, NULL);CHKERRQ(ierr); 206 ierr = PetscOptionsEnd();CHKERRQ(ierr); 207 } 208 } 209 210 ierr = PetscLogEventBegin(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 211 ierr = (*(*C)->ops->ptapnumeric)(A,P,*C);CHKERRQ(ierr); 212 ierr = PetscLogEventEnd(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 213 PetscFunctionReturn(0); 214 } 215 216 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,Mat C) 217 { 218 PetscErrorCode ierr; 219 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 220 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 221 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 222 Mat_APMPI *ptap = c->ap; 223 Mat AP_loc,C_loc,C_oth; 224 PetscInt i,rstart,rend,cm,ncols,row,*api,*apj,am = A->rmap->n,apnz,nout; 225 PetscScalar *apa; 226 const PetscInt *cols; 227 const PetscScalar *vals; 228 229 PetscFunctionBegin; 230 if (!ptap->AP_loc) { 231 MPI_Comm comm; 232 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 233 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 234 } 235 236 ierr = MatZeroEntries(C);CHKERRQ(ierr); 237 238 /* 1) get R = Pd^T,Ro = Po^T */ 239 if (ptap->reuse == MAT_REUSE_MATRIX) { 240 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 241 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 242 } 243 244 /* 2) get AP_loc */ 245 AP_loc = ptap->AP_loc; 246 ap = (Mat_SeqAIJ*)AP_loc->data; 247 248 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 249 /*-----------------------------------------------------*/ 250 if (ptap->reuse == MAT_REUSE_MATRIX) { 251 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 252 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 253 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 254 } 255 256 /* 2-2) compute numeric A_loc*P - dominating part */ 257 /* ---------------------------------------------- */ 258 /* get data from symbolic products */ 259 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 260 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 261 262 api = ap->i; 263 apj = ap->j; 264 ierr = ISLocalToGlobalMappingApply(ptap->ltog,api[AP_loc->rmap->n],apj,apj);CHKERRQ(ierr); 265 for (i=0; i<am; i++) { 266 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 267 apnz = api[i+1] - api[i]; 268 apa = ap->a + api[i]; 269 ierr = PetscMemzero(apa,sizeof(PetscScalar)*apnz);CHKERRQ(ierr); 270 AProw_scalable(i,ad,ao,p_loc,p_oth,api,apj,apa); 271 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 272 } 273 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,api[AP_loc->rmap->n],apj,&nout,apj);CHKERRQ(ierr); 274 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); 275 276 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 277 /* Always use scalable version since we are in the MPI scalable version */ 278 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 279 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 280 281 C_loc = ptap->C_loc; 282 C_oth = ptap->C_oth; 283 284 /* add C_loc and Co to to C */ 285 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 286 287 /* C_loc -> C */ 288 cm = C_loc->rmap->N; 289 c_seq = (Mat_SeqAIJ*)C_loc->data; 290 cols = c_seq->j; 291 vals = c_seq->a; 292 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_loc->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 293 294 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 295 /* when there are no off-processor parts. */ 296 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 297 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 298 /* a table, and other, more complex stuff has to be done. */ 299 if (C->assembled) { 300 C->was_assembled = PETSC_TRUE; 301 C->assembled = PETSC_FALSE; 302 } 303 if (C->was_assembled) { 304 for (i=0; i<cm; i++) { 305 ncols = c_seq->i[i+1] - c_seq->i[i]; 306 row = rstart + i; 307 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 308 cols += ncols; vals += ncols; 309 } 310 } else { 311 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 312 } 313 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_loc->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 314 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); 315 316 /* Co -> C, off-processor part */ 317 cm = C_oth->rmap->N; 318 c_seq = (Mat_SeqAIJ*)C_oth->data; 319 cols = c_seq->j; 320 vals = c_seq->a; 321 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_oth->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 322 for (i=0; i<cm; i++) { 323 ncols = c_seq->i[i+1] - c_seq->i[i]; 324 row = p->garray[i]; 325 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 326 cols += ncols; vals += ncols; 327 } 328 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 329 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 330 331 ptap->reuse = MAT_REUSE_MATRIX; 332 333 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_oth->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 334 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); 335 336 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 337 if (ptap->freestruct) { 338 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 339 } 340 PetscFunctionReturn(0); 341 } 342 343 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat *C) 344 { 345 PetscErrorCode ierr; 346 Mat_APMPI *ptap; 347 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 348 MPI_Comm comm; 349 PetscMPIInt size,rank; 350 Mat Cmpi,P_loc,P_oth; 351 PetscFreeSpaceList free_space=NULL,current_space=NULL; 352 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 353 PetscInt *lnk,i,k,pnz,row,nsend; 354 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 355 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 356 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 357 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 358 MPI_Request *swaits,*rwaits; 359 MPI_Status *sstatus,rstatus; 360 PetscLayout rowmap; 361 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 362 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 363 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,Crmax,*aj,*ai,*pi,nout; 364 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 365 PetscScalar *apv; 366 PetscTable ta; 367 MatType mtype; 368 const char *prefix; 369 #if defined(PETSC_USE_INFO) 370 PetscReal apfill; 371 #endif 372 373 PetscFunctionBegin; 374 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 375 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 376 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 377 378 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 379 380 /* create symbolic parallel matrix Cmpi */ 381 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 382 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 383 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 384 385 /* create struct Mat_APMPI and attached it to C later */ 386 ierr = PetscNew(&ptap);CHKERRQ(ierr); 387 ptap->reuse = MAT_INITIAL_MATRIX; 388 ptap->algType = 0; 389 390 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 391 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&P_oth);CHKERRQ(ierr); 392 /* get P_loc by taking all local rows of P */ 393 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&P_loc);CHKERRQ(ierr); 394 395 ptap->P_loc = P_loc; 396 ptap->P_oth = P_oth; 397 398 /* (0) compute Rd = Pd^T, Ro = Po^T */ 399 /* --------------------------------- */ 400 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 401 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 402 403 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 404 /* ----------------------------------------------------------------- */ 405 p_loc = (Mat_SeqAIJ*)P_loc->data; 406 if (P_oth) p_oth = (Mat_SeqAIJ*)P_oth->data; 407 408 /* create and initialize a linked list */ 409 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 410 MatRowMergeMax_SeqAIJ(p_loc,P_loc->rmap->N,ta); 411 MatRowMergeMax_SeqAIJ(p_oth,P_oth->rmap->N,ta); 412 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 413 414 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 415 416 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 417 if (ao) { 418 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 419 } else { 420 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 421 } 422 current_space = free_space; 423 nspacedouble = 0; 424 425 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 426 api[0] = 0; 427 for (i=0; i<am; i++) { 428 /* diagonal portion: Ad[i,:]*P */ 429 ai = ad->i; pi = p_loc->i; 430 nzi = ai[i+1] - ai[i]; 431 aj = ad->j + ai[i]; 432 for (j=0; j<nzi; j++) { 433 row = aj[j]; 434 pnz = pi[row+1] - pi[row]; 435 Jptr = p_loc->j + pi[row]; 436 /* add non-zero cols of P into the sorted linked list lnk */ 437 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 438 } 439 /* off-diagonal portion: Ao[i,:]*P */ 440 if (ao) { 441 ai = ao->i; pi = p_oth->i; 442 nzi = ai[i+1] - ai[i]; 443 aj = ao->j + ai[i]; 444 for (j=0; j<nzi; j++) { 445 row = aj[j]; 446 pnz = pi[row+1] - pi[row]; 447 Jptr = p_oth->j + pi[row]; 448 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 449 } 450 } 451 apnz = lnk[0]; 452 api[i+1] = api[i] + apnz; 453 454 /* if free space is not available, double the total space in the list */ 455 if (current_space->local_remaining<apnz) { 456 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 457 nspacedouble++; 458 } 459 460 /* Copy data into free space, then initialize lnk */ 461 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 462 463 current_space->array += apnz; 464 current_space->local_used += apnz; 465 current_space->local_remaining -= apnz; 466 } 467 /* Allocate space for apj and apv, initialize apj, and */ 468 /* destroy list of free space and other temporary array(s) */ 469 ierr = PetscCalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 470 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 471 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 472 473 /* Create AP_loc for reuse */ 474 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 475 ierr = MatSeqAIJCompactOutExtraColumns_SeqAIJ(ptap->AP_loc, &ptap->ltog);CHKERRQ(ierr); 476 477 #if defined(PETSC_USE_INFO) 478 if (ao) { 479 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 480 } else { 481 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 482 } 483 ptap->AP_loc->info.mallocs = nspacedouble; 484 ptap->AP_loc->info.fill_ratio_given = fill; 485 ptap->AP_loc->info.fill_ratio_needed = apfill; 486 487 if (api[am]) { 488 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); 489 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 490 } else { 491 ierr = PetscInfo(ptap->AP_loc,"Scalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 492 } 493 #endif 494 495 /* (2-1) compute symbolic Co = Ro*AP_loc */ 496 /* ------------------------------------ */ 497 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 498 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 499 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 500 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 501 502 /* (3) send coj of C_oth to other processors */ 503 /* ------------------------------------------ */ 504 /* determine row ownership */ 505 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 506 rowmap->n = pn; 507 rowmap->bs = 1; 508 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 509 owners = rowmap->range; 510 511 /* determine the number of messages to send, their lengths */ 512 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 513 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 514 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 515 516 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 517 coi = c_oth->i; coj = c_oth->j; 518 con = ptap->C_oth->rmap->n; 519 proc = 0; 520 ierr = ISLocalToGlobalMappingApply(ptap->ltog,coi[con],coj,coj);CHKERRQ(ierr); 521 for (i=0; i<con; i++) { 522 while (prmap[i] >= owners[proc+1]) proc++; 523 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 524 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 525 } 526 527 len = 0; /* max length of buf_si[], see (4) */ 528 owners_co[0] = 0; 529 nsend = 0; 530 for (proc=0; proc<size; proc++) { 531 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 532 if (len_s[proc]) { 533 nsend++; 534 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 535 len += len_si[proc]; 536 } 537 } 538 539 /* determine the number and length of messages to receive for coi and coj */ 540 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 541 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 542 543 /* post the Irecv and Isend of coj */ 544 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 545 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 546 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 547 for (proc=0, k=0; proc<size; proc++) { 548 if (!len_s[proc]) continue; 549 i = owners_co[proc]; 550 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 551 k++; 552 } 553 554 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 555 /* ---------------------------------------- */ 556 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 557 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 558 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 559 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 560 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,c_loc->j);CHKERRQ(ierr); 561 562 /* receives coj are complete */ 563 for (i=0; i<nrecv; i++) { 564 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 565 } 566 ierr = PetscFree(rwaits);CHKERRQ(ierr); 567 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 568 569 /* add received column indices into ta to update Crmax */ 570 for (k=0; k<nrecv; k++) {/* k-th received message */ 571 Jptr = buf_rj[k]; 572 for (j=0; j<len_r[k]; j++) { 573 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 574 } 575 } 576 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 577 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 578 579 /* (4) send and recv coi */ 580 /*-----------------------*/ 581 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 582 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 583 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 584 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 585 for (proc=0,k=0; proc<size; proc++) { 586 if (!len_s[proc]) continue; 587 /* form outgoing message for i-structure: 588 buf_si[0]: nrows to be sent 589 [1:nrows]: row index (global) 590 [nrows+1:2*nrows+1]: i-structure index 591 */ 592 /*-------------------------------------------*/ 593 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 594 buf_si_i = buf_si + nrows+1; 595 buf_si[0] = nrows; 596 buf_si_i[0] = 0; 597 nrows = 0; 598 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 599 nzi = coi[i+1] - coi[i]; 600 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 601 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 602 nrows++; 603 } 604 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 605 k++; 606 buf_si += len_si[proc]; 607 } 608 for (i=0; i<nrecv; i++) { 609 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 610 } 611 ierr = PetscFree(rwaits);CHKERRQ(ierr); 612 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 613 614 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 615 ierr = PetscFree(len_ri);CHKERRQ(ierr); 616 ierr = PetscFree(swaits);CHKERRQ(ierr); 617 ierr = PetscFree(buf_s);CHKERRQ(ierr); 618 619 /* (5) compute the local portion of Cmpi */ 620 /* ------------------------------------------ */ 621 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 622 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 623 current_space = free_space; 624 625 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 626 for (k=0; k<nrecv; k++) { 627 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 628 nrows = *buf_ri_k[k]; 629 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 630 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 631 } 632 633 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 634 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 635 for (i=0; i<pn; i++) { 636 /* add C_loc into Cmpi */ 637 nzi = c_loc->i[i+1] - c_loc->i[i]; 638 Jptr = c_loc->j + c_loc->i[i]; 639 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 640 641 /* add received col data into lnk */ 642 for (k=0; k<nrecv; k++) { /* k-th received message */ 643 if (i == *nextrow[k]) { /* i-th row */ 644 nzi = *(nextci[k]+1) - *nextci[k]; 645 Jptr = buf_rj[k] + *nextci[k]; 646 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 647 nextrow[k]++; nextci[k]++; 648 } 649 } 650 nzi = lnk[0]; 651 652 /* copy data into free space, then initialize lnk */ 653 ierr = PetscLLCondensedClean_Scalable(nzi,current_space->array,lnk);CHKERRQ(ierr); 654 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 655 } 656 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 657 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 658 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 659 660 /* local sizes and preallocation */ 661 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 662 if (P->cmap->bs > 0) { 663 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr); 664 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr); 665 } 666 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 667 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 668 669 /* members in merge */ 670 ierr = PetscFree(id_r);CHKERRQ(ierr); 671 ierr = PetscFree(len_r);CHKERRQ(ierr); 672 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 673 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 674 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 675 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 676 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 677 678 /* attach the supporting struct to Cmpi for reuse */ 679 c = (Mat_MPIAIJ*)Cmpi->data; 680 c->ap = ptap; 681 ptap->duplicate = Cmpi->ops->duplicate; 682 ptap->destroy = Cmpi->ops->destroy; 683 ptap->view = Cmpi->ops->view; 684 685 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 686 Cmpi->assembled = PETSC_FALSE; 687 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable; 688 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 689 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 690 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 691 *C = Cmpi; 692 693 nout = 0; 694 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_oth->i[ptap->C_oth->rmap->n],c_oth->j,&nout,c_oth->j);CHKERRQ(ierr); 695 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); 696 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,&nout,c_loc->j);CHKERRQ(ierr); 697 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); 698 699 PetscFunctionReturn(0); 700 } 701 702 PETSC_STATIC_INLINE PetscErrorCode MatPtAPSymbolicComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,PetscInt i,PetscHSetI dht,PetscHSetI oht) 703 { 704 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data; 705 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_oth=(Mat_SeqAIJ*)P_oth->data,*pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data; 706 PetscInt *ai,nzi,j,*aj,row,col,*pi,*pj,pnz,nzpi,*p_othcols,k; 707 PetscInt pcstart,pcend,column; 708 PetscErrorCode ierr; 709 710 PetscFunctionBegin; 711 712 pcstart = P->cmap->rstart; 713 pcend = P->cmap->rend; 714 /* diagonal portion: Ad[i,:]*P */ 715 ai = ad->i; 716 nzi = ai[i+1] - ai[i]; 717 aj = ad->j + ai[i]; 718 for (j=0; j<nzi; j++) { 719 row = aj[j]; 720 nzpi = pd->i[row+1] - pd->i[row]; 721 pj = pd->j + pd->i[row]; 722 for (k=0; k<nzpi; k++) { 723 ierr = PetscHSetIAdd(dht,pj[k]+pcstart);CHKERRQ(ierr); 724 } 725 } 726 for (j=0; j<nzi; j++) { 727 row = aj[j]; 728 nzpi = po->i[row+1] - po->i[row]; 729 pj = po->j + po->i[row]; 730 for (k=0; k<nzpi; k++) { 731 ierr = PetscHSetIAdd(oht,p->garray[pj[k]]);CHKERRQ(ierr); 732 } 733 } 734 735 /* off diagonal part: Ao[i, :]*P_oth */ 736 if (ao) { 737 ai = ao->i; 738 pi = p_oth->i; 739 nzi = ai[i+1] - ai[i]; 740 aj = ao->j + ai[i]; 741 for (j=0; j<nzi; j++) { 742 row = aj[j]; 743 pnz = pi[row+1] - pi[row]; 744 p_othcols = p_oth->j + pi[row]; 745 for (col=0; col<pnz; col++) { 746 column = p_othcols[col]; 747 if (column>=pcstart && column<pcend) { 748 ierr = PetscHSetIAdd(dht,column);CHKERRQ(ierr); 749 } else { 750 ierr = PetscHSetIAdd(oht,column);CHKERRQ(ierr); 751 } 752 } 753 } 754 } /* end if (ao) */ 755 PetscFunctionReturn(0); 756 } 757 758 PETSC_STATIC_INLINE PetscErrorCode MatPtAPNumericComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,PetscInt i,PetscHMapIV hmap) 759 { 760 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data; 761 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_oth=(Mat_SeqAIJ*)P_oth->data,*pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data; 762 PetscInt *ai,nzi,j,*aj,row,col,*pi,pnz,*p_othcols,pcstart,*pj,k,nzpi; 763 PetscScalar ra,*aa,*pa; 764 PetscLogDouble flops=0.0; 765 PetscErrorCode ierr; 766 767 PetscFunctionBegin; 768 pcstart = P->cmap->rstart; 769 /* diagonal portion: Ad[i,:]*P */ 770 ai = ad->i; 771 nzi = ai[i+1] - ai[i]; 772 aj = ad->j + ai[i]; 773 aa = ad->a + ai[i]; 774 775 for (j=0; j<nzi; j++) { 776 ra = aa[j]; 777 row = aj[j]; 778 nzpi = pd->i[row+1] - pd->i[row]; 779 pj = pd->j + pd->i[row]; 780 pa = pd->a + pd->i[row]; 781 for (k=0; k<nzpi; k++) { 782 ierr = PetscHMapIVAddValue(hmap,pj[k]+pcstart,ra*pa[k]);CHKERRQ(ierr); 783 } 784 flops += nzpi; 785 } 786 for (j=0; j<nzi; j++) { 787 ra = aa[j]; 788 row = aj[j]; 789 nzpi = po->i[row+1] - po->i[row]; 790 pj = po->j + po->i[row]; 791 pa = po->a + po->i[row]; 792 for (k=0; k<nzpi; k++) { 793 ierr = PetscHMapIVAddValue(hmap,p->garray[pj[k]],ra*pa[k]);CHKERRQ(ierr); 794 } 795 flops += nzpi; 796 } 797 798 799 /* off diagonal part: Ao[i, :]*P_oth */ 800 if (ao) { 801 ai = ao->i; 802 pi = p_oth->i; 803 nzi = ai[i+1] - ai[i]; 804 aj = ao->j + ai[i]; 805 aa = ao->a + ai[i]; 806 for (j=0; j<nzi; j++) { 807 row = aj[j]; 808 ra = aa[j]; 809 pnz = pi[row+1] - pi[row]; 810 p_othcols = p_oth->j + pi[row]; 811 pa = p_oth->a + pi[row]; 812 for (col=0; col<pnz; col++) { 813 ierr = PetscHMapIVAddValue(hmap,p_othcols[col],ra*pa[col]);CHKERRQ(ierr); 814 } 815 flops += pnz; 816 } 817 } /* end if (ao) */ 818 819 ierr = PetscLogFlops(flops);CHKERRQ(ierr); 820 PetscFunctionReturn(0); 821 } 822 823 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,Mat C) 824 { 825 PetscErrorCode ierr; 826 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 827 Mat_SeqAIJ *cd,*co,*po,*pd; 828 Mat_APMPI *ptap = c->ap; 829 PetscHMapIV hmap; 830 PetscInt i,j,jj,kk,nzi,*c_rmtj,voff,*c_othj,pn,pon,pcstart,pcend,ccstart,ccend,row,am,*poj,*pdj,*apindices,cmaxr,*c_rmtc,*c_rmtjj,*dcc,*occ,loc; 831 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa; 832 PetscLogDouble flops=0.0; 833 MPI_Comm comm; 834 835 PetscFunctionBegin; 836 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 837 if (!ptap->P_oth) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 838 839 ierr = MatZeroEntries(C);CHKERRQ(ierr); 840 841 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 842 /*-----------------------------------------------------*/ 843 if (ptap->reuse == MAT_REUSE_MATRIX) { 844 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 845 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 846 } 847 848 po = (Mat_SeqAIJ*) p->B->data; 849 pd = (Mat_SeqAIJ*) p->A->data; 850 851 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 852 853 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr); 854 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 855 cmaxr = 0; 856 for (i=0; i<pon; i++) { 857 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]); 858 } 859 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr); 860 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 861 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 862 for (i=0; i<am && pon; i++) { 863 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 864 nzi = po->i[i+1] - po->i[i]; 865 if (!nzi) continue; 866 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 867 voff = 0; 868 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 869 if (!voff) continue; 870 /*ierr = PetscMemzero(c_rmtc,sizeof(PetscInt)*pon);CHKERRQ(ierr);*/ 871 872 /* Form C(ii, :) */ 873 poj = po->j + po->i[i]; 874 poa = po->a + po->i[i]; 875 for (j=0; j<nzi; j++) { 876 c_rmtjj = c_rmtj + ptap->c_rmti[poj[j]]; 877 c_rmtaa = c_rmta + ptap->c_rmti[poj[j]]; 878 for (jj=0; jj<voff; jj++) { 879 apvaluestmp[jj] = apvalues[jj]*poa[j]; 880 /*If the row is empty */ 881 if (!c_rmtc[poj[j]]) { 882 c_rmtjj[jj] = apindices[jj]; 883 c_rmtaa[jj] = apvaluestmp[jj]; 884 c_rmtc[poj[j]]++; 885 } else { 886 ierr = PetscFindInt(apindices[jj],c_rmtc[poj[j]],c_rmtjj,&loc);CHKERRQ(ierr); 887 if (loc>=0){ /* hit */ 888 c_rmtaa[loc] += apvaluestmp[jj]; 889 } else { /* new element */ 890 loc = -(loc+1); 891 /* Move data backward */ 892 for (kk=c_rmtc[poj[j]]; kk>loc; kk--) { 893 c_rmtjj[kk] = c_rmtjj[kk-1]; 894 c_rmtaa[kk] = c_rmtaa[kk-1]; 895 }/* End kk */ 896 c_rmtjj[loc] = apindices[jj]; 897 c_rmtaa[loc] = apvaluestmp[jj]; 898 c_rmtc[poj[j]]++; 899 } 900 } 901 flops += voff; 902 } /* End jj */ 903 } /* End j */ 904 } /* End i */ 905 906 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr); 907 908 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 909 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr); 910 911 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 912 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 913 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 914 cd = (Mat_SeqAIJ*)(c->A)->data; 915 co = (Mat_SeqAIJ*)(c->B)->data; 916 917 cmaxr = 0; 918 for (i=0; i<pn; i++) { 919 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i])); 920 } 921 ierr = PetscCalloc5(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pn,&dcc,pn,&occ);CHKERRQ(ierr); 922 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 923 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 924 for (i=0; i<am && pn; i++) { 925 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 926 nzi = pd->i[i+1] - pd->i[i]; 927 if (!nzi) continue; 928 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 929 voff = 0; 930 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 931 if (!voff) continue; 932 /* Form C(ii, :) */ 933 pdj = pd->j + pd->i[i]; 934 pda = pd->a + pd->i[i]; 935 for (j=0; j<nzi; j++) { 936 row = pcstart + pdj[j]; 937 for (jj=0; jj<voff; jj++) { 938 apvaluestmp[jj] = apvalues[jj]*pda[j]; 939 } 940 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr); 941 flops += voff; 942 } 943 } 944 945 ierr = MatGetOwnershipRangeColumn(C,&ccstart,&ccend);CHKERRQ(ierr); 946 ierr = PetscFree5(apindices,apvalues,apvaluestmp,dcc,occ);CHKERRQ(ierr); 947 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr); 948 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPI_SUM);CHKERRQ(ierr); 949 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 950 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr); 951 952 /* Add contributions from remote */ 953 for (i = 0; i < pn; i++) { 954 row = i + pcstart; 955 ierr = MatSetValues(C,1,&row,ptap->c_othi[i+1]-ptap->c_othi[i],c_othj+ptap->c_othi[i],c_otha+ptap->c_othi[i],ADD_VALUES);CHKERRQ(ierr); 956 } 957 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr); 958 959 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 960 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 961 ierr = PetscLogFlops(flops);CHKERRQ(ierr); 962 963 ptap->reuse = MAT_REUSE_MATRIX; 964 965 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 966 if (ptap->freestruct) { 967 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 968 } 969 PetscFunctionReturn(0); 970 } 971 972 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,Mat C) 973 { 974 PetscErrorCode ierr; 975 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 976 Mat_SeqAIJ *cd,*co,*po,*pd; 977 Mat_APMPI *ptap = c->ap; 978 PetscHMapIV hmap; 979 PetscInt i,j,jj,kk,nzi,dnzi,*c_rmtj,voff,*c_othj,pn,pon,pcstart,pcend,row,am,*poj,*pdj,*apindices,cmaxr,*c_rmtc,*c_rmtjj,loc; 980 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa; 981 PetscLogDouble flops=0.0; 982 MPI_Comm comm; 983 984 PetscFunctionBegin; 985 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 986 if (!ptap->P_oth) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 987 988 ierr = MatZeroEntries(C);CHKERRQ(ierr); 989 990 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 991 /*-----------------------------------------------------*/ 992 if (ptap->reuse == MAT_REUSE_MATRIX) { 993 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 994 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 995 } 996 997 po = (Mat_SeqAIJ*) p->B->data; 998 pd = (Mat_SeqAIJ*) p->A->data; 999 1000 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1001 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1002 1003 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr); 1004 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1005 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1006 cmaxr = 0; 1007 for (i=0; i<pon; i++) { 1008 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]); 1009 } 1010 cd = (Mat_SeqAIJ*)(c->A)->data; 1011 co = (Mat_SeqAIJ*)(c->B)->data; 1012 for (i=0; i<pn; i++) { 1013 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i])); 1014 } 1015 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr); 1016 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 1017 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 1018 for (i=0; i<am && (pon || pn); i++) { 1019 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 1020 nzi = po->i[i+1] - po->i[i]; 1021 dnzi = pd->i[i+1] - pd->i[i]; 1022 if (!nzi && !dnzi) continue; 1023 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 1024 voff = 0; 1025 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 1026 if (!voff) continue; 1027 1028 /* Form remote C(ii, :) */ 1029 poj = po->j + po->i[i]; 1030 poa = po->a + po->i[i]; 1031 for (j=0; j<nzi; j++) { 1032 c_rmtjj = c_rmtj + ptap->c_rmti[poj[j]]; 1033 c_rmtaa = c_rmta + ptap->c_rmti[poj[j]]; 1034 for (jj=0; jj<voff; jj++) { 1035 apvaluestmp[jj] = apvalues[jj]*poa[j]; 1036 /*If the row is empty */ 1037 if (!c_rmtc[poj[j]]) { 1038 c_rmtjj[jj] = apindices[jj]; 1039 c_rmtaa[jj] = apvaluestmp[jj]; 1040 c_rmtc[poj[j]]++; 1041 } else { 1042 ierr = PetscFindInt(apindices[jj],c_rmtc[poj[j]],c_rmtjj,&loc);CHKERRQ(ierr); 1043 if (loc>=0){ /* hit */ 1044 c_rmtaa[loc] += apvaluestmp[jj]; 1045 } else { /* new element */ 1046 loc = -(loc+1); 1047 /* Move data backward */ 1048 for (kk=c_rmtc[poj[j]]; kk>loc; kk--) { 1049 c_rmtjj[kk] = c_rmtjj[kk-1]; 1050 c_rmtaa[kk] = c_rmtaa[kk-1]; 1051 }/* End kk */ 1052 c_rmtjj[loc] = apindices[jj]; 1053 c_rmtaa[loc] = apvaluestmp[jj]; 1054 c_rmtc[poj[j]]++; 1055 } 1056 } 1057 } /* End jj */ 1058 flops += voff; 1059 } /* End j */ 1060 1061 /* Form local C(ii, :) */ 1062 pdj = pd->j + pd->i[i]; 1063 pda = pd->a + pd->i[i]; 1064 for (j=0; j<dnzi; j++) { 1065 row = pcstart + pdj[j]; 1066 for (jj=0; jj<voff; jj++) { 1067 apvaluestmp[jj] = apvalues[jj]*pda[j]; 1068 }/* End kk */ 1069 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr); 1070 flops += voff; 1071 }/* End j */ 1072 } /* End i */ 1073 1074 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr); 1075 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr); 1076 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr); 1077 1078 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1079 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 1080 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPI_SUM);CHKERRQ(ierr); 1081 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 1082 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr); 1083 1084 /* Add contributions from remote */ 1085 for (i = 0; i < pn; i++) { 1086 row = i + pcstart; 1087 ierr = MatSetValues(C,1,&row,ptap->c_othi[i+1]-ptap->c_othi[i],c_othj+ptap->c_othi[i],c_otha+ptap->c_othi[i],ADD_VALUES);CHKERRQ(ierr); 1088 } 1089 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr); 1090 1091 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1092 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1093 ierr = PetscLogFlops(flops);CHKERRQ(ierr); 1094 1095 ptap->reuse = MAT_REUSE_MATRIX; 1096 1097 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1098 if (ptap->freestruct) { 1099 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1100 } 1101 PetscFunctionReturn(0); 1102 } 1103 1104 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,PetscReal fill,Mat *C) 1105 { 1106 Mat_APMPI *ptap; 1107 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1108 MPI_Comm comm; 1109 Mat Cmpi; 1110 Mat_SeqAIJ *pd,*po; 1111 MatType mtype; 1112 PetscSF sf; 1113 PetscSFNode *iremote; 1114 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves; 1115 const PetscInt *rootdegrees; 1116 PetscHSetI ht,oht,*hta,*hto; 1117 PetscInt pn,pon,*c_rmtc,i,j,nzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets; 1118 PetscInt owner,lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj; 1119 PetscInt nalg=2,alg=0; 1120 PetscBool flg; 1121 const char *algTypes[2] = {"overlapping","merged"}; 1122 PetscErrorCode ierr; 1123 1124 PetscFunctionBegin; 1125 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1126 1127 /* Create symbolic parallel matrix Cmpi */ 1128 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1129 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1130 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1131 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1132 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1133 1134 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1135 ptap->reuse = MAT_INITIAL_MATRIX; 1136 ptap->algType = 2; 1137 1138 /* Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1139 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1140 1141 po = (Mat_SeqAIJ*)p->B->data; 1142 pd = (Mat_SeqAIJ*)p->A->data; 1143 1144 /* This equals to the number of offdiag columns in P */ 1145 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1146 /* offsets */ 1147 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr); 1148 /* The number of columns we will send to remote ranks */ 1149 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr); 1150 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr); 1151 for (i=0; i<pon; i++) { 1152 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1153 } 1154 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1155 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr); 1156 /* Create hash table to merge all columns for C(i, :) */ 1157 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1158 1159 ptap->c_rmti[0] = 0; 1160 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */ 1161 for (i=0; i<am && pon; i++) { 1162 /* Form one row of AP */ 1163 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1164 /* If the off diag is empty, we should not do any calculation */ 1165 nzi = po->i[i+1] - po->i[i]; 1166 if (!nzi) continue; 1167 1168 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,ht);CHKERRQ(ierr); 1169 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1170 /* If AP is empty, just continue */ 1171 if (!htsize) continue; 1172 /* Form C(ii, :) */ 1173 poj = po->j + po->i[i]; 1174 for (j=0; j<nzi; j++) { 1175 ierr = PetscHSetIUpdate(hta[poj[j]],ht);CHKERRQ(ierr); 1176 } 1177 } 1178 1179 for (i=0; i<pon; i++) { 1180 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1181 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize; 1182 c_rmtc[i] = htsize; 1183 } 1184 1185 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr); 1186 1187 for (i=0; i<pon; i++) { 1188 off = 0; 1189 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr); 1190 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1191 } 1192 ierr = PetscFree(hta);CHKERRQ(ierr); 1193 1194 ierr = PetscCalloc1(pon,&iremote);CHKERRQ(ierr); 1195 for (i=0; i<pon; i++) { 1196 owner = 0; lidx = 0; 1197 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1198 iremote[i].index = lidx; 1199 iremote[i].rank = owner; 1200 } 1201 1202 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 1203 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1204 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */ 1205 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr); 1206 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1207 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1208 /* How many neighbors have contributions to my rows? */ 1209 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr); 1210 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr); 1211 rootspacesize = 0; 1212 for (i = 0; i < pn; i++) { 1213 rootspacesize += rootdegrees[i]; 1214 } 1215 ierr = PetscCalloc1(rootspacesize,&rootspace);CHKERRQ(ierr); 1216 ierr = PetscCalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr); 1217 /* Get information from leaves 1218 * Number of columns other people contribute to my rows 1219 * */ 1220 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1221 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1222 ierr = PetscFree(c_rmtc);CHKERRQ(ierr); 1223 ierr = PetscCalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr); 1224 /* The number of columns is received for each row */ 1225 ptap->c_othi[0] = 0; 1226 rootspacesize = 0; 1227 rootspaceoffsets[0] = 0; 1228 for (i = 0; i < pn; i++) { 1229 rcvncols = 0; 1230 for (j = 0; j<rootdegrees[i]; j++) { 1231 rcvncols += rootspace[rootspacesize]; 1232 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize]; 1233 rootspacesize++; 1234 } 1235 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols; 1236 } 1237 ierr = PetscFree(rootspace);CHKERRQ(ierr); 1238 1239 ierr = PetscCalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr); 1240 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1241 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1242 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1243 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr); 1244 1245 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr); 1246 nleaves = 0; 1247 for (i = 0; i<pon; i++) { 1248 owner = 0; lidx = 0; 1249 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1250 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i]; 1251 for (j=0; j<sendncols; j++) { 1252 iremote[nleaves].rank = owner; 1253 iremote[nleaves++].index = c_rmtoffsets[i] + j; 1254 } 1255 } 1256 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr); 1257 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr); 1258 1259 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr); 1260 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1261 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr); 1262 /* One to one map */ 1263 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1264 1265 ierr = PetscCalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr); 1266 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr); 1267 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1268 ierr = PetscMalloc2(pn,&hta,pn,&hto);CHKERRQ(ierr); 1269 for (i=0; i<pn; i++) { 1270 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1271 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr); 1272 } 1273 /* Work on local part */ 1274 /* 4) Pass 1: Estimate memory for C_loc */ 1275 for (i=0; i<am && pn; i++) { 1276 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1277 ierr = PetscHSetIClear(oht);CHKERRQ(ierr); 1278 nzi = pd->i[i+1] - pd->i[i]; 1279 if (!nzi) continue; 1280 1281 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,oht);CHKERRQ(ierr); 1282 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1283 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr); 1284 if (!(htsize+htosize)) continue; 1285 /* Form C(ii, :) */ 1286 pdj = pd->j + pd->i[i]; 1287 for (j=0; j<nzi; j++) { 1288 ierr = PetscHSetIUpdate(hta[pdj[j]],ht);CHKERRQ(ierr); 1289 ierr = PetscHSetIUpdate(hto[pdj[j]],oht);CHKERRQ(ierr); 1290 } 1291 } 1292 1293 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1294 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr); 1295 1296 /* Get remote data */ 1297 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1298 ierr = PetscFree(c_rmtj);CHKERRQ(ierr); 1299 1300 for (i = 0; i < pn; i++) { 1301 nzi = ptap->c_othi[i+1] - ptap->c_othi[i]; 1302 rdj = c_othj + ptap->c_othi[i]; 1303 for (j = 0; j < nzi; j++) { 1304 col = rdj[j]; 1305 /* diag part */ 1306 if (col>=pcstart && col<pcend) { 1307 ierr = PetscHSetIAdd(hta[i],col);CHKERRQ(ierr); 1308 } else { /* off diag */ 1309 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr); 1310 } 1311 } 1312 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1313 dnz[i] = htsize; 1314 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1315 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr); 1316 onz[i] = htsize; 1317 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr); 1318 } 1319 1320 ierr = PetscFree2(hta,hto);CHKERRQ(ierr); 1321 ierr = PetscFree(c_othj);CHKERRQ(ierr); 1322 1323 /* local sizes and preallocation */ 1324 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1325 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 1326 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1327 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 1328 1329 /* attach the supporting struct to Cmpi for reuse */ 1330 c = (Mat_MPIAIJ*)Cmpi->data; 1331 c->ap = ptap; 1332 ptap->duplicate = Cmpi->ops->duplicate; 1333 ptap->destroy = Cmpi->ops->destroy; 1334 ptap->view = Cmpi->ops->view; 1335 1336 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1337 Cmpi->assembled = PETSC_FALSE; 1338 /* pick an algorithm */ 1339 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 1340 alg = 0; 1341 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 1342 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1343 switch (alg) { 1344 case 0: 1345 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce; 1346 break; 1347 case 1: 1348 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged; 1349 break; 1350 default: 1351 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n"); 1352 } 1353 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1354 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1355 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1356 *C = Cmpi; 1357 PetscFunctionReturn(0); 1358 } 1359 1360 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,PetscReal fill,Mat *C) 1361 { 1362 Mat_APMPI *ptap; 1363 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1364 MPI_Comm comm; 1365 Mat Cmpi; 1366 Mat_SeqAIJ *pd,*po; 1367 MatType mtype; 1368 PetscSF sf; 1369 PetscSFNode *iremote; 1370 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves; 1371 const PetscInt *rootdegrees; 1372 PetscHSetI ht,oht,*hta,*hto,*htd; 1373 PetscInt pn,pon,*c_rmtc,i,j,nzi,dnzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets; 1374 PetscInt owner,lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj; 1375 PetscInt nalg=2,alg=0; 1376 PetscBool flg; 1377 const char *algTypes[2] = {"merged","overlapping"}; 1378 PetscErrorCode ierr; 1379 1380 PetscFunctionBegin; 1381 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1382 1383 /* Create symbolic parallel matrix Cmpi */ 1384 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1385 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1386 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1387 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1388 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1389 1390 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1391 ptap->reuse = MAT_INITIAL_MATRIX; 1392 ptap->algType = 3; 1393 1394 /* 0) Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1395 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1396 1397 po = (Mat_SeqAIJ*)p->B->data; 1398 pd = (Mat_SeqAIJ*)p->A->data; 1399 1400 /* This equals to the number of offdiag columns in P */ 1401 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1402 /* offsets */ 1403 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr); 1404 /* The number of columns we will send to remote ranks */ 1405 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr); 1406 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr); 1407 for (i=0; i<pon; i++) { 1408 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1409 } 1410 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1411 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr); 1412 /* Create hash table to merge all columns for C(i, :) */ 1413 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1414 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr); 1415 ierr = PetscMalloc2(pn,&htd,pn,&hto);CHKERRQ(ierr); 1416 for (i=0; i<pn; i++) { 1417 ierr = PetscHSetICreate(&htd[i]);CHKERRQ(ierr); 1418 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr); 1419 } 1420 ptap->c_rmti[0] = 0; 1421 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */ 1422 for (i=0; i<am && (pon || pn); i++) { 1423 /* Form one row of AP */ 1424 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1425 ierr = PetscHSetIClear(oht);CHKERRQ(ierr); 1426 /* If the off diag is empty, we should not do any calculation */ 1427 nzi = po->i[i+1] - po->i[i]; 1428 dnzi = pd->i[i+1] - pd->i[i]; 1429 if (!nzi && !dnzi) continue; 1430 1431 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,oht);CHKERRQ(ierr); 1432 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1433 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr); 1434 /* If AP is empty, just continue */ 1435 if (!(htsize+htosize)) continue; 1436 1437 /* Form remote C(ii, :) */ 1438 poj = po->j + po->i[i]; 1439 for (j=0; j<nzi; j++) { 1440 ierr = PetscHSetIUpdate(hta[poj[j]],ht);CHKERRQ(ierr); 1441 ierr = PetscHSetIUpdate(hta[poj[j]],oht);CHKERRQ(ierr); 1442 } 1443 1444 /* Form local C(ii, :) */ 1445 pdj = pd->j + pd->i[i]; 1446 for (j=0; j<dnzi; j++) { 1447 ierr = PetscHSetIUpdate(htd[pdj[j]],ht);CHKERRQ(ierr); 1448 ierr = PetscHSetIUpdate(hto[pdj[j]],oht);CHKERRQ(ierr); 1449 } 1450 } 1451 1452 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1453 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr); 1454 1455 for (i=0; i<pon; i++) { 1456 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1457 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize; 1458 c_rmtc[i] = htsize; 1459 } 1460 1461 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr); 1462 1463 for (i=0; i<pon; i++) { 1464 off = 0; 1465 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr); 1466 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1467 } 1468 ierr = PetscFree(hta);CHKERRQ(ierr); 1469 1470 ierr = PetscCalloc1(pon,&iremote);CHKERRQ(ierr); 1471 for (i=0; i<pon; i++) { 1472 owner = 0; lidx = 0; 1473 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1474 iremote[i].index = lidx; 1475 iremote[i].rank = owner; 1476 } 1477 1478 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 1479 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1480 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */ 1481 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr); 1482 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1483 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1484 /* How many neighbors have contributions to my rows? */ 1485 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr); 1486 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr); 1487 rootspacesize = 0; 1488 for (i = 0; i < pn; i++) { 1489 rootspacesize += rootdegrees[i]; 1490 } 1491 ierr = PetscCalloc1(rootspacesize,&rootspace);CHKERRQ(ierr); 1492 ierr = PetscCalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr); 1493 /* Get information from leaves 1494 * Number of columns other people contribute to my rows 1495 * */ 1496 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1497 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1498 ierr = PetscFree(c_rmtc);CHKERRQ(ierr); 1499 ierr = PetscCalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr); 1500 /* The number of columns is received for each row */ 1501 ptap->c_othi[0] = 0; 1502 rootspacesize = 0; 1503 rootspaceoffsets[0] = 0; 1504 for (i = 0; i < pn; i++) { 1505 rcvncols = 0; 1506 for (j = 0; j<rootdegrees[i]; j++) { 1507 rcvncols += rootspace[rootspacesize]; 1508 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize]; 1509 rootspacesize++; 1510 } 1511 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols; 1512 } 1513 ierr = PetscFree(rootspace);CHKERRQ(ierr); 1514 1515 ierr = PetscCalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr); 1516 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1517 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1518 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1519 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr); 1520 1521 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr); 1522 nleaves = 0; 1523 for (i = 0; i<pon; i++) { 1524 owner = 0; lidx = 0; 1525 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1526 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i]; 1527 for (j=0; j<sendncols; j++) { 1528 iremote[nleaves].rank = owner; 1529 iremote[nleaves++].index = c_rmtoffsets[i] + j; 1530 } 1531 } 1532 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr); 1533 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr); 1534 1535 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr); 1536 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1537 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr); 1538 /* One to one map */ 1539 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1540 /* Get remote data */ 1541 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1542 ierr = PetscFree(c_rmtj);CHKERRQ(ierr); 1543 ierr = PetscCalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr); 1544 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1545 1546 for (i = 0; i < pn; i++) { 1547 nzi = ptap->c_othi[i+1] - ptap->c_othi[i]; 1548 rdj = c_othj + ptap->c_othi[i]; 1549 for (j = 0; j < nzi; j++) { 1550 col = rdj[j]; 1551 /* diag part */ 1552 if (col>=pcstart && col<pcend) { 1553 ierr = PetscHSetIAdd(htd[i],col);CHKERRQ(ierr); 1554 } else { /* off diag */ 1555 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr); 1556 } 1557 } 1558 ierr = PetscHSetIGetSize(htd[i],&htsize);CHKERRQ(ierr); 1559 dnz[i] = htsize; 1560 ierr = PetscHSetIDestroy(&htd[i]);CHKERRQ(ierr); 1561 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr); 1562 onz[i] = htsize; 1563 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr); 1564 } 1565 1566 ierr = PetscFree2(htd,hto);CHKERRQ(ierr); 1567 ierr = PetscFree(c_othj);CHKERRQ(ierr); 1568 1569 /* local sizes and preallocation */ 1570 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1571 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 1572 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1573 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 1574 1575 /* attach the supporting struct to Cmpi for reuse */ 1576 c = (Mat_MPIAIJ*)Cmpi->data; 1577 c->ap = ptap; 1578 ptap->duplicate = Cmpi->ops->duplicate; 1579 ptap->destroy = Cmpi->ops->destroy; 1580 ptap->view = Cmpi->ops->view; 1581 1582 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1583 Cmpi->assembled = PETSC_FALSE; 1584 /* pick an algorithm */ 1585 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 1586 alg = 0; 1587 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 1588 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1589 switch (alg) { 1590 case 0: 1591 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged; 1592 break; 1593 case 1: 1594 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce; 1595 break; 1596 default: 1597 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n"); 1598 } 1599 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1600 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1601 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1602 *C = Cmpi; 1603 PetscFunctionReturn(0); 1604 } 1605 1606 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 1607 { 1608 PetscErrorCode ierr; 1609 Mat_APMPI *ptap; 1610 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 1611 MPI_Comm comm; 1612 PetscMPIInt size,rank; 1613 Mat Cmpi; 1614 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1615 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 1616 PetscInt *lnk,i,k,pnz,row,nsend; 1617 PetscBT lnkbt; 1618 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 1619 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1620 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 1621 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1622 MPI_Request *swaits,*rwaits; 1623 MPI_Status *sstatus,rstatus; 1624 PetscLayout rowmap; 1625 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1626 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1627 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 1628 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 1629 PetscScalar *apv; 1630 PetscTable ta; 1631 MatType mtype; 1632 const char *prefix; 1633 #if defined(PETSC_USE_INFO) 1634 PetscReal apfill; 1635 #endif 1636 1637 PetscFunctionBegin; 1638 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1639 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1640 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1641 1642 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 1643 1644 /* create symbolic parallel matrix Cmpi */ 1645 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1646 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1647 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1648 1649 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 1650 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 1651 1652 /* create struct Mat_APMPI and attached it to C later */ 1653 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1654 ptap->reuse = MAT_INITIAL_MATRIX; 1655 ptap->algType = 1; 1656 1657 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1658 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1659 /* get P_loc by taking all local rows of P */ 1660 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1661 1662 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1663 /* --------------------------------- */ 1664 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1665 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1666 1667 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 1668 /* ----------------------------------------------------------------- */ 1669 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1670 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1671 1672 /* create and initialize a linked list */ 1673 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 1674 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 1675 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 1676 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 1677 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 1678 1679 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1680 1681 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 1682 if (ao) { 1683 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 1684 } else { 1685 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 1686 } 1687 current_space = free_space; 1688 nspacedouble = 0; 1689 1690 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 1691 api[0] = 0; 1692 for (i=0; i<am; i++) { 1693 /* diagonal portion: Ad[i,:]*P */ 1694 ai = ad->i; pi = p_loc->i; 1695 nzi = ai[i+1] - ai[i]; 1696 aj = ad->j + ai[i]; 1697 for (j=0; j<nzi; j++) { 1698 row = aj[j]; 1699 pnz = pi[row+1] - pi[row]; 1700 Jptr = p_loc->j + pi[row]; 1701 /* add non-zero cols of P into the sorted linked list lnk */ 1702 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1703 } 1704 /* off-diagonal portion: Ao[i,:]*P */ 1705 if (ao) { 1706 ai = ao->i; pi = p_oth->i; 1707 nzi = ai[i+1] - ai[i]; 1708 aj = ao->j + ai[i]; 1709 for (j=0; j<nzi; j++) { 1710 row = aj[j]; 1711 pnz = pi[row+1] - pi[row]; 1712 Jptr = p_oth->j + pi[row]; 1713 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1714 } 1715 } 1716 apnz = lnk[0]; 1717 api[i+1] = api[i] + apnz; 1718 if (ap_rmax < apnz) ap_rmax = apnz; 1719 1720 /* if free space is not available, double the total space in the list */ 1721 if (current_space->local_remaining<apnz) { 1722 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1723 nspacedouble++; 1724 } 1725 1726 /* Copy data into free space, then initialize lnk */ 1727 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1728 1729 current_space->array += apnz; 1730 current_space->local_used += apnz; 1731 current_space->local_remaining -= apnz; 1732 } 1733 /* Allocate space for apj and apv, initialize apj, and */ 1734 /* destroy list of free space and other temporary array(s) */ 1735 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 1736 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 1737 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1738 1739 /* Create AP_loc for reuse */ 1740 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 1741 1742 #if defined(PETSC_USE_INFO) 1743 if (ao) { 1744 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 1745 } else { 1746 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 1747 } 1748 ptap->AP_loc->info.mallocs = nspacedouble; 1749 ptap->AP_loc->info.fill_ratio_given = fill; 1750 ptap->AP_loc->info.fill_ratio_needed = apfill; 1751 1752 if (api[am]) { 1753 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); 1754 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 1755 } else { 1756 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 1757 } 1758 #endif 1759 1760 /* (2-1) compute symbolic Co = Ro*AP_loc */ 1761 /* ------------------------------------ */ 1762 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1763 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 1764 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 1765 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 1766 1767 /* (3) send coj of C_oth to other processors */ 1768 /* ------------------------------------------ */ 1769 /* determine row ownership */ 1770 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1771 rowmap->n = pn; 1772 rowmap->bs = 1; 1773 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1774 owners = rowmap->range; 1775 1776 /* determine the number of messages to send, their lengths */ 1777 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1778 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1779 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1780 1781 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1782 coi = c_oth->i; coj = c_oth->j; 1783 con = ptap->C_oth->rmap->n; 1784 proc = 0; 1785 for (i=0; i<con; i++) { 1786 while (prmap[i] >= owners[proc+1]) proc++; 1787 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 1788 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1789 } 1790 1791 len = 0; /* max length of buf_si[], see (4) */ 1792 owners_co[0] = 0; 1793 nsend = 0; 1794 for (proc=0; proc<size; proc++) { 1795 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1796 if (len_s[proc]) { 1797 nsend++; 1798 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1799 len += len_si[proc]; 1800 } 1801 } 1802 1803 /* determine the number and length of messages to receive for coi and coj */ 1804 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1805 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1806 1807 /* post the Irecv and Isend of coj */ 1808 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1809 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1810 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1811 for (proc=0, k=0; proc<size; proc++) { 1812 if (!len_s[proc]) continue; 1813 i = owners_co[proc]; 1814 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1815 k++; 1816 } 1817 1818 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 1819 /* ---------------------------------------- */ 1820 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 1821 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 1822 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 1823 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1824 1825 /* receives coj are complete */ 1826 for (i=0; i<nrecv; i++) { 1827 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1828 } 1829 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1830 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1831 1832 /* add received column indices into ta to update Crmax */ 1833 for (k=0; k<nrecv; k++) {/* k-th received message */ 1834 Jptr = buf_rj[k]; 1835 for (j=0; j<len_r[k]; j++) { 1836 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1837 } 1838 } 1839 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1840 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1841 1842 /* (4) send and recv coi */ 1843 /*-----------------------*/ 1844 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1845 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1846 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1847 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1848 for (proc=0,k=0; proc<size; proc++) { 1849 if (!len_s[proc]) continue; 1850 /* form outgoing message for i-structure: 1851 buf_si[0]: nrows to be sent 1852 [1:nrows]: row index (global) 1853 [nrows+1:2*nrows+1]: i-structure index 1854 */ 1855 /*-------------------------------------------*/ 1856 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1857 buf_si_i = buf_si + nrows+1; 1858 buf_si[0] = nrows; 1859 buf_si_i[0] = 0; 1860 nrows = 0; 1861 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1862 nzi = coi[i+1] - coi[i]; 1863 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1864 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1865 nrows++; 1866 } 1867 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1868 k++; 1869 buf_si += len_si[proc]; 1870 } 1871 for (i=0; i<nrecv; i++) { 1872 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1873 } 1874 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1875 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1876 1877 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1878 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1879 ierr = PetscFree(swaits);CHKERRQ(ierr); 1880 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1881 1882 /* (5) compute the local portion of Cmpi */ 1883 /* ------------------------------------------ */ 1884 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 1885 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1886 current_space = free_space; 1887 1888 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1889 for (k=0; k<nrecv; k++) { 1890 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1891 nrows = *buf_ri_k[k]; 1892 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1893 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1894 } 1895 1896 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 1897 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1898 for (i=0; i<pn; i++) { 1899 /* add C_loc into Cmpi */ 1900 nzi = c_loc->i[i+1] - c_loc->i[i]; 1901 Jptr = c_loc->j + c_loc->i[i]; 1902 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1903 1904 /* add received col data into lnk */ 1905 for (k=0; k<nrecv; k++) { /* k-th received message */ 1906 if (i == *nextrow[k]) { /* i-th row */ 1907 nzi = *(nextci[k]+1) - *nextci[k]; 1908 Jptr = buf_rj[k] + *nextci[k]; 1909 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1910 nextrow[k]++; nextci[k]++; 1911 } 1912 } 1913 nzi = lnk[0]; 1914 1915 /* copy data into free space, then initialize lnk */ 1916 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1917 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 1918 } 1919 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1920 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1921 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 1922 1923 /* local sizes and preallocation */ 1924 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1925 if (P->cmap->bs > 0) { 1926 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr); 1927 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr); 1928 } 1929 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1930 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1931 1932 /* members in merge */ 1933 ierr = PetscFree(id_r);CHKERRQ(ierr); 1934 ierr = PetscFree(len_r);CHKERRQ(ierr); 1935 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 1936 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 1937 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 1938 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 1939 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 1940 1941 /* attach the supporting struct to Cmpi for reuse */ 1942 c = (Mat_MPIAIJ*)Cmpi->data; 1943 c->ap = ptap; 1944 ptap->duplicate = Cmpi->ops->duplicate; 1945 ptap->destroy = Cmpi->ops->destroy; 1946 ptap->view = Cmpi->ops->view; 1947 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 1948 1949 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1950 Cmpi->assembled = PETSC_FALSE; 1951 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1952 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1953 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1954 *C = Cmpi; 1955 PetscFunctionReturn(0); 1956 } 1957 1958 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 1959 { 1960 PetscErrorCode ierr; 1961 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1962 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 1963 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 1964 Mat_APMPI *ptap = c->ap; 1965 Mat AP_loc,C_loc,C_oth; 1966 PetscInt i,rstart,rend,cm,ncols,row; 1967 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 1968 PetscScalar *apa; 1969 const PetscInt *cols; 1970 const PetscScalar *vals; 1971 1972 PetscFunctionBegin; 1973 if (!ptap->AP_loc) { 1974 MPI_Comm comm; 1975 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1976 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1977 } 1978 1979 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1980 /* 1) get R = Pd^T,Ro = Po^T */ 1981 if (ptap->reuse == MAT_REUSE_MATRIX) { 1982 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1983 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1984 } 1985 1986 /* 2) get AP_loc */ 1987 AP_loc = ptap->AP_loc; 1988 ap = (Mat_SeqAIJ*)AP_loc->data; 1989 1990 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 1991 /*-----------------------------------------------------*/ 1992 if (ptap->reuse == MAT_REUSE_MATRIX) { 1993 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 1994 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1995 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1996 } 1997 1998 /* 2-2) compute numeric A_loc*P - dominating part */ 1999 /* ---------------------------------------------- */ 2000 /* get data from symbolic products */ 2001 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 2002 if (ptap->P_oth) { 2003 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 2004 } 2005 apa = ptap->apa; 2006 api = ap->i; 2007 apj = ap->j; 2008 for (i=0; i<am; i++) { 2009 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 2010 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 2011 apnz = api[i+1] - api[i]; 2012 for (j=0; j<apnz; j++) { 2013 col = apj[j+api[i]]; 2014 ap->a[j+ap->i[i]] = apa[col]; 2015 apa[col] = 0.0; 2016 } 2017 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 2018 } 2019 2020 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 2021 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 2022 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 2023 C_loc = ptap->C_loc; 2024 C_oth = ptap->C_oth; 2025 2026 /* add C_loc and Co to to C */ 2027 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 2028 2029 /* C_loc -> C */ 2030 cm = C_loc->rmap->N; 2031 c_seq = (Mat_SeqAIJ*)C_loc->data; 2032 cols = c_seq->j; 2033 vals = c_seq->a; 2034 2035 2036 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 2037 /* when there are no off-processor parts. */ 2038 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 2039 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 2040 /* a table, and other, more complex stuff has to be done. */ 2041 if (C->assembled) { 2042 C->was_assembled = PETSC_TRUE; 2043 C->assembled = PETSC_FALSE; 2044 } 2045 if (C->was_assembled) { 2046 for (i=0; i<cm; i++) { 2047 ncols = c_seq->i[i+1] - c_seq->i[i]; 2048 row = rstart + i; 2049 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 2050 cols += ncols; vals += ncols; 2051 } 2052 } else { 2053 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 2054 } 2055 2056 /* Co -> C, off-processor part */ 2057 cm = C_oth->rmap->N; 2058 c_seq = (Mat_SeqAIJ*)C_oth->data; 2059 cols = c_seq->j; 2060 vals = c_seq->a; 2061 for (i=0; i<cm; i++) { 2062 ncols = c_seq->i[i+1] - c_seq->i[i]; 2063 row = p->garray[i]; 2064 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 2065 cols += ncols; vals += ncols; 2066 } 2067 2068 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2069 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2070 2071 ptap->reuse = MAT_REUSE_MATRIX; 2072 2073 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 2074 if (ptap->freestruct) { 2075 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 2076 } 2077 PetscFunctionReturn(0); 2078 } 2079