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 = PetscArrayzero(apa,apnz);CHKERRQ(ierr); 270 AProw_scalable(i,ad,ao,p_loc,p_oth,api,apj,apa); 271 } 272 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,api[AP_loc->rmap->n],apj,&nout,apj);CHKERRQ(ierr); 273 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); 274 275 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 276 /* Always use scalable version since we are in the MPI scalable version */ 277 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 278 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 279 280 C_loc = ptap->C_loc; 281 C_oth = ptap->C_oth; 282 283 /* add C_loc and Co to to C */ 284 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 285 286 /* C_loc -> C */ 287 cm = C_loc->rmap->N; 288 c_seq = (Mat_SeqAIJ*)C_loc->data; 289 cols = c_seq->j; 290 vals = c_seq->a; 291 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_loc->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 292 293 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 294 /* when there are no off-processor parts. */ 295 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 296 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 297 /* a table, and other, more complex stuff has to be done. */ 298 if (C->assembled) { 299 C->was_assembled = PETSC_TRUE; 300 C->assembled = PETSC_FALSE; 301 } 302 if (C->was_assembled) { 303 for (i=0; i<cm; i++) { 304 ncols = c_seq->i[i+1] - c_seq->i[i]; 305 row = rstart + i; 306 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 307 cols += ncols; vals += ncols; 308 } 309 } else { 310 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 311 } 312 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_loc->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 313 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); 314 315 /* Co -> C, off-processor part */ 316 cm = C_oth->rmap->N; 317 c_seq = (Mat_SeqAIJ*)C_oth->data; 318 cols = c_seq->j; 319 vals = c_seq->a; 320 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_oth->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 321 for (i=0; i<cm; i++) { 322 ncols = c_seq->i[i+1] - c_seq->i[i]; 323 row = p->garray[i]; 324 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 325 cols += ncols; vals += ncols; 326 } 327 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 328 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 329 330 ptap->reuse = MAT_REUSE_MATRIX; 331 332 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_oth->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 333 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); 334 335 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 336 if (ptap->freestruct) { 337 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 338 } 339 PetscFunctionReturn(0); 340 } 341 342 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat *C) 343 { 344 PetscErrorCode ierr; 345 Mat_APMPI *ptap; 346 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 347 MPI_Comm comm; 348 PetscMPIInt size,rank; 349 Mat Cmpi,P_loc,P_oth; 350 PetscFreeSpaceList free_space=NULL,current_space=NULL; 351 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 352 PetscInt *lnk,i,k,pnz,row,nsend; 353 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 354 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 355 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 356 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 357 MPI_Request *swaits,*rwaits; 358 MPI_Status *sstatus,rstatus; 359 PetscLayout rowmap; 360 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 361 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 362 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,Crmax,*aj,*ai,*pi,nout; 363 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 364 PetscScalar *apv; 365 PetscTable ta; 366 MatType mtype; 367 const char *prefix; 368 #if defined(PETSC_USE_INFO) 369 PetscReal apfill; 370 #endif 371 372 PetscFunctionBegin; 373 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 374 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 375 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 376 377 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 378 379 /* create symbolic parallel matrix Cmpi */ 380 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 381 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 382 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 383 384 /* create struct Mat_APMPI and attached it to C later */ 385 ierr = PetscNew(&ptap);CHKERRQ(ierr); 386 ptap->reuse = MAT_INITIAL_MATRIX; 387 ptap->algType = 0; 388 389 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 390 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&P_oth);CHKERRQ(ierr); 391 /* get P_loc by taking all local rows of P */ 392 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&P_loc);CHKERRQ(ierr); 393 394 ptap->P_loc = P_loc; 395 ptap->P_oth = P_oth; 396 397 /* (0) compute Rd = Pd^T, Ro = Po^T */ 398 /* --------------------------------- */ 399 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 400 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 401 402 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 403 /* ----------------------------------------------------------------- */ 404 p_loc = (Mat_SeqAIJ*)P_loc->data; 405 if (P_oth) p_oth = (Mat_SeqAIJ*)P_oth->data; 406 407 /* create and initialize a linked list */ 408 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 409 MatRowMergeMax_SeqAIJ(p_loc,P_loc->rmap->N,ta); 410 MatRowMergeMax_SeqAIJ(p_oth,P_oth->rmap->N,ta); 411 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 412 413 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 414 415 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 416 if (ao) { 417 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 418 } else { 419 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 420 } 421 current_space = free_space; 422 nspacedouble = 0; 423 424 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 425 api[0] = 0; 426 for (i=0; i<am; i++) { 427 /* diagonal portion: Ad[i,:]*P */ 428 ai = ad->i; pi = p_loc->i; 429 nzi = ai[i+1] - ai[i]; 430 aj = ad->j + ai[i]; 431 for (j=0; j<nzi; j++) { 432 row = aj[j]; 433 pnz = pi[row+1] - pi[row]; 434 Jptr = p_loc->j + pi[row]; 435 /* add non-zero cols of P into the sorted linked list lnk */ 436 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 437 } 438 /* off-diagonal portion: Ao[i,:]*P */ 439 if (ao) { 440 ai = ao->i; pi = p_oth->i; 441 nzi = ai[i+1] - ai[i]; 442 aj = ao->j + ai[i]; 443 for (j=0; j<nzi; j++) { 444 row = aj[j]; 445 pnz = pi[row+1] - pi[row]; 446 Jptr = p_oth->j + pi[row]; 447 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 448 } 449 } 450 apnz = lnk[0]; 451 api[i+1] = api[i] + apnz; 452 453 /* if free space is not available, double the total space in the list */ 454 if (current_space->local_remaining<apnz) { 455 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 456 nspacedouble++; 457 } 458 459 /* Copy data into free space, then initialize lnk */ 460 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 461 462 current_space->array += apnz; 463 current_space->local_used += apnz; 464 current_space->local_remaining -= apnz; 465 } 466 /* Allocate space for apj and apv, initialize apj, and */ 467 /* destroy list of free space and other temporary array(s) */ 468 ierr = PetscCalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 469 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 470 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 471 472 /* Create AP_loc for reuse */ 473 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 474 ierr = MatSeqAIJCompactOutExtraColumns_SeqAIJ(ptap->AP_loc, &ptap->ltog);CHKERRQ(ierr); 475 476 #if defined(PETSC_USE_INFO) 477 if (ao) { 478 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 479 } else { 480 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 481 } 482 ptap->AP_loc->info.mallocs = nspacedouble; 483 ptap->AP_loc->info.fill_ratio_given = fill; 484 ptap->AP_loc->info.fill_ratio_needed = apfill; 485 486 if (api[am]) { 487 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); 488 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 489 } else { 490 ierr = PetscInfo(ptap->AP_loc,"Scalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 491 } 492 #endif 493 494 /* (2-1) compute symbolic Co = Ro*AP_loc */ 495 /* ------------------------------------ */ 496 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 497 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 498 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 499 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 500 501 /* (3) send coj of C_oth to other processors */ 502 /* ------------------------------------------ */ 503 /* determine row ownership */ 504 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 505 rowmap->n = pn; 506 rowmap->bs = 1; 507 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 508 owners = rowmap->range; 509 510 /* determine the number of messages to send, their lengths */ 511 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 512 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 513 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr); 514 515 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 516 coi = c_oth->i; coj = c_oth->j; 517 con = ptap->C_oth->rmap->n; 518 proc = 0; 519 ierr = ISLocalToGlobalMappingApply(ptap->ltog,coi[con],coj,coj);CHKERRQ(ierr); 520 for (i=0; i<con; i++) { 521 while (prmap[i] >= owners[proc+1]) proc++; 522 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 523 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 524 } 525 526 len = 0; /* max length of buf_si[], see (4) */ 527 owners_co[0] = 0; 528 nsend = 0; 529 for (proc=0; proc<size; proc++) { 530 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 531 if (len_s[proc]) { 532 nsend++; 533 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 534 len += len_si[proc]; 535 } 536 } 537 538 /* determine the number and length of messages to receive for coi and coj */ 539 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 540 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 541 542 /* post the Irecv and Isend of coj */ 543 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 544 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 545 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 546 for (proc=0, k=0; proc<size; proc++) { 547 if (!len_s[proc]) continue; 548 i = owners_co[proc]; 549 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 550 k++; 551 } 552 553 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 554 /* ---------------------------------------- */ 555 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 556 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 557 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 558 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 559 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,c_loc->j);CHKERRQ(ierr); 560 561 /* receives coj are complete */ 562 for (i=0; i<nrecv; i++) { 563 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 564 } 565 ierr = PetscFree(rwaits);CHKERRQ(ierr); 566 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 567 568 /* add received column indices into ta to update Crmax */ 569 for (k=0; k<nrecv; k++) {/* k-th received message */ 570 Jptr = buf_rj[k]; 571 for (j=0; j<len_r[k]; j++) { 572 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 573 } 574 } 575 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 576 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 577 578 /* (4) send and recv coi */ 579 /*-----------------------*/ 580 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 581 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 582 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 583 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 584 for (proc=0,k=0; proc<size; proc++) { 585 if (!len_s[proc]) continue; 586 /* form outgoing message for i-structure: 587 buf_si[0]: nrows to be sent 588 [1:nrows]: row index (global) 589 [nrows+1:2*nrows+1]: i-structure index 590 */ 591 /*-------------------------------------------*/ 592 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 593 buf_si_i = buf_si + nrows+1; 594 buf_si[0] = nrows; 595 buf_si_i[0] = 0; 596 nrows = 0; 597 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 598 nzi = coi[i+1] - coi[i]; 599 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 600 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 601 nrows++; 602 } 603 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 604 k++; 605 buf_si += len_si[proc]; 606 } 607 for (i=0; i<nrecv; i++) { 608 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 609 } 610 ierr = PetscFree(rwaits);CHKERRQ(ierr); 611 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 612 613 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 614 ierr = PetscFree(len_ri);CHKERRQ(ierr); 615 ierr = PetscFree(swaits);CHKERRQ(ierr); 616 ierr = PetscFree(buf_s);CHKERRQ(ierr); 617 618 /* (5) compute the local portion of Cmpi */ 619 /* ------------------------------------------ */ 620 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 621 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 622 current_space = free_space; 623 624 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 625 for (k=0; k<nrecv; k++) { 626 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 627 nrows = *buf_ri_k[k]; 628 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 629 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 630 } 631 632 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 633 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 634 for (i=0; i<pn; i++) { 635 /* add C_loc into Cmpi */ 636 nzi = c_loc->i[i+1] - c_loc->i[i]; 637 Jptr = c_loc->j + c_loc->i[i]; 638 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 639 640 /* add received col data into lnk */ 641 for (k=0; k<nrecv; k++) { /* k-th received message */ 642 if (i == *nextrow[k]) { /* i-th row */ 643 nzi = *(nextci[k]+1) - *nextci[k]; 644 Jptr = buf_rj[k] + *nextci[k]; 645 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 646 nextrow[k]++; nextci[k]++; 647 } 648 } 649 nzi = lnk[0]; 650 651 /* copy data into free space, then initialize lnk */ 652 ierr = PetscLLCondensedClean_Scalable(nzi,current_space->array,lnk);CHKERRQ(ierr); 653 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 654 } 655 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 656 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 657 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 658 659 /* local sizes and preallocation */ 660 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 661 if (P->cmap->bs > 0) { 662 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr); 663 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr); 664 } 665 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 666 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 667 668 /* members in merge */ 669 ierr = PetscFree(id_r);CHKERRQ(ierr); 670 ierr = PetscFree(len_r);CHKERRQ(ierr); 671 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 672 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 673 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 674 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 675 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 676 677 /* attach the supporting struct to Cmpi for reuse */ 678 c = (Mat_MPIAIJ*)Cmpi->data; 679 c->ap = ptap; 680 ptap->duplicate = Cmpi->ops->duplicate; 681 ptap->destroy = Cmpi->ops->destroy; 682 ptap->view = Cmpi->ops->view; 683 684 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 685 Cmpi->assembled = PETSC_FALSE; 686 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable; 687 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 688 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 689 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 690 *C = Cmpi; 691 692 nout = 0; 693 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_oth->i[ptap->C_oth->rmap->n],c_oth->j,&nout,c_oth->j);CHKERRQ(ierr); 694 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); 695 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,&nout,c_loc->j);CHKERRQ(ierr); 696 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); 697 698 PetscFunctionReturn(0); 699 } 700 701 PETSC_STATIC_INLINE PetscErrorCode MatPtAPSymbolicComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,PetscInt i,PetscHSetI dht,PetscHSetI oht) 702 { 703 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data; 704 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; 705 PetscInt *ai,nzi,j,*aj,row,col,*pi,*pj,pnz,nzpi,*p_othcols,k; 706 PetscInt pcstart,pcend,column; 707 PetscErrorCode ierr; 708 709 PetscFunctionBegin; 710 711 pcstart = P->cmap->rstart; 712 pcend = P->cmap->rend; 713 /* diagonal portion: Ad[i,:]*P */ 714 ai = ad->i; 715 nzi = ai[i+1] - ai[i]; 716 aj = ad->j + ai[i]; 717 for (j=0; j<nzi; j++) { 718 row = aj[j]; 719 nzpi = pd->i[row+1] - pd->i[row]; 720 pj = pd->j + pd->i[row]; 721 for (k=0; k<nzpi; k++) { 722 ierr = PetscHSetIAdd(dht,pj[k]+pcstart);CHKERRQ(ierr); 723 } 724 } 725 for (j=0; j<nzi; j++) { 726 row = aj[j]; 727 nzpi = po->i[row+1] - po->i[row]; 728 pj = po->j + po->i[row]; 729 for (k=0; k<nzpi; k++) { 730 ierr = PetscHSetIAdd(oht,p->garray[pj[k]]);CHKERRQ(ierr); 731 } 732 } 733 734 /* off diagonal part: Ao[i, :]*P_oth */ 735 if (ao) { 736 ai = ao->i; 737 pi = p_oth->i; 738 nzi = ai[i+1] - ai[i]; 739 aj = ao->j + ai[i]; 740 for (j=0; j<nzi; j++) { 741 row = aj[j]; 742 pnz = pi[row+1] - pi[row]; 743 p_othcols = p_oth->j + pi[row]; 744 for (col=0; col<pnz; col++) { 745 column = p_othcols[col]; 746 if (column>=pcstart && column<pcend) { 747 ierr = PetscHSetIAdd(dht,column);CHKERRQ(ierr); 748 } else { 749 ierr = PetscHSetIAdd(oht,column);CHKERRQ(ierr); 750 } 751 } 752 } 753 } /* end if (ao) */ 754 PetscFunctionReturn(0); 755 } 756 757 PETSC_STATIC_INLINE PetscErrorCode MatPtAPNumericComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,PetscInt i,PetscHMapIV hmap) 758 { 759 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data; 760 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; 761 PetscInt *ai,nzi,j,*aj,row,col,*pi,pnz,*p_othcols,pcstart,*pj,k,nzpi; 762 PetscScalar ra,*aa,*pa; 763 PetscErrorCode ierr; 764 765 PetscFunctionBegin; 766 pcstart = P->cmap->rstart; 767 /* diagonal portion: Ad[i,:]*P */ 768 ai = ad->i; 769 nzi = ai[i+1] - ai[i]; 770 aj = ad->j + ai[i]; 771 aa = ad->a + ai[i]; 772 773 for (j=0; j<nzi; j++) { 774 ra = aa[j]; 775 row = aj[j]; 776 nzpi = pd->i[row+1] - pd->i[row]; 777 pj = pd->j + pd->i[row]; 778 pa = pd->a + pd->i[row]; 779 for (k=0; k<nzpi; k++) { 780 ierr = PetscHMapIVAddValue(hmap,pj[k]+pcstart,ra*pa[k]);CHKERRQ(ierr); 781 } 782 ierr = PetscLogFlops(2.0*nzpi);CHKERRQ(ierr); 783 } 784 for (j=0; j<nzi; j++) { 785 ra = aa[j]; 786 row = aj[j]; 787 nzpi = po->i[row+1] - po->i[row]; 788 pj = po->j + po->i[row]; 789 pa = po->a + po->i[row]; 790 for (k=0; k<nzpi; k++) { 791 ierr = PetscHMapIVAddValue(hmap,p->garray[pj[k]],ra*pa[k]);CHKERRQ(ierr); 792 } 793 ierr = PetscLogFlops(2.0*nzpi);CHKERRQ(ierr); 794 } 795 796 797 /* off diagonal part: Ao[i, :]*P_oth */ 798 if (ao) { 799 ai = ao->i; 800 pi = p_oth->i; 801 nzi = ai[i+1] - ai[i]; 802 aj = ao->j + ai[i]; 803 aa = ao->a + ai[i]; 804 for (j=0; j<nzi; j++) { 805 row = aj[j]; 806 ra = aa[j]; 807 pnz = pi[row+1] - pi[row]; 808 p_othcols = p_oth->j + pi[row]; 809 pa = p_oth->a + pi[row]; 810 for (col=0; col<pnz; col++) { 811 ierr = PetscHMapIVAddValue(hmap,p_othcols[col],ra*pa[col]);CHKERRQ(ierr); 812 } 813 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 814 } 815 } /* end if (ao) */ 816 817 PetscFunctionReturn(0); 818 } 819 820 PetscErrorCode MatGetBrowsOfAcols_MPIXAIJ(Mat,Mat,MatReuse,Mat*); 821 822 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,Mat C) 823 { 824 PetscErrorCode ierr; 825 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 826 Mat_SeqAIJ *cd,*co,*po,*pd; 827 Mat_APMPI *ptap = c->ap; 828 PetscHMapIV hmap; 829 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; 830 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa; 831 MPI_Comm comm; 832 833 PetscFunctionBegin; 834 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 835 if (!ptap->P_oth) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 836 837 ierr = MatZeroEntries(C);CHKERRQ(ierr); 838 839 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 840 /*-----------------------------------------------------*/ 841 if (ptap->reuse == MAT_REUSE_MATRIX) { 842 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 843 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,MAT_REUSE_MATRIX,&ptap->P_oth);CHKERRQ(ierr); 844 } 845 846 po = (Mat_SeqAIJ*) p->B->data; 847 pd = (Mat_SeqAIJ*) p->A->data; 848 849 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 850 851 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr); 852 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 853 cmaxr = 0; 854 for (i=0; i<pon; i++) { 855 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]); 856 } 857 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr); 858 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 859 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 860 for (i=0; i<am && pon; i++) { 861 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 862 nzi = po->i[i+1] - po->i[i]; 863 if (!nzi) continue; 864 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 865 voff = 0; 866 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 867 if (!voff) continue; 868 869 /* Form C(ii, :) */ 870 poj = po->j + po->i[i]; 871 poa = po->a + po->i[i]; 872 for (j=0; j<nzi; j++) { 873 c_rmtjj = c_rmtj + ptap->c_rmti[poj[j]]; 874 c_rmtaa = c_rmta + ptap->c_rmti[poj[j]]; 875 for (jj=0; jj<voff; jj++) { 876 apvaluestmp[jj] = apvalues[jj]*poa[j]; 877 /*If the row is empty */ 878 if (!c_rmtc[poj[j]]) { 879 c_rmtjj[jj] = apindices[jj]; 880 c_rmtaa[jj] = apvaluestmp[jj]; 881 c_rmtc[poj[j]]++; 882 } else { 883 ierr = PetscFindInt(apindices[jj],c_rmtc[poj[j]],c_rmtjj,&loc);CHKERRQ(ierr); 884 if (loc>=0){ /* hit */ 885 c_rmtaa[loc] += apvaluestmp[jj]; 886 ierr = PetscLogFlops(1.0);CHKERRQ(ierr); 887 } else { /* new element */ 888 loc = -(loc+1); 889 /* Move data backward */ 890 for (kk=c_rmtc[poj[j]]; kk>loc; kk--) { 891 c_rmtjj[kk] = c_rmtjj[kk-1]; 892 c_rmtaa[kk] = c_rmtaa[kk-1]; 893 }/* End kk */ 894 c_rmtjj[loc] = apindices[jj]; 895 c_rmtaa[loc] = apvaluestmp[jj]; 896 c_rmtc[poj[j]]++; 897 } 898 } 899 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 900 } /* End jj */ 901 } /* End j */ 902 } /* End i */ 903 904 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr); 905 906 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 907 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr); 908 909 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 910 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 911 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 912 cd = (Mat_SeqAIJ*)(c->A)->data; 913 co = (Mat_SeqAIJ*)(c->B)->data; 914 915 cmaxr = 0; 916 for (i=0; i<pn; i++) { 917 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i])); 918 } 919 ierr = PetscCalloc5(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pn,&dcc,pn,&occ);CHKERRQ(ierr); 920 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 921 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 922 for (i=0; i<am && pn; i++) { 923 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 924 nzi = pd->i[i+1] - pd->i[i]; 925 if (!nzi) continue; 926 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 927 voff = 0; 928 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 929 if (!voff) continue; 930 /* Form C(ii, :) */ 931 pdj = pd->j + pd->i[i]; 932 pda = pd->a + pd->i[i]; 933 for (j=0; j<nzi; j++) { 934 row = pcstart + pdj[j]; 935 for (jj=0; jj<voff; jj++) { 936 apvaluestmp[jj] = apvalues[jj]*pda[j]; 937 } 938 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 939 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr); 940 } 941 } 942 943 ierr = MatGetOwnershipRangeColumn(C,&ccstart,&ccend);CHKERRQ(ierr); 944 ierr = PetscFree5(apindices,apvalues,apvaluestmp,dcc,occ);CHKERRQ(ierr); 945 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr); 946 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPI_SUM);CHKERRQ(ierr); 947 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 948 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr); 949 950 /* Add contributions from remote */ 951 for (i = 0; i < pn; i++) { 952 row = i + pcstart; 953 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); 954 } 955 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr); 956 957 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 958 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 959 960 ptap->reuse = MAT_REUSE_MATRIX; 961 962 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 963 if (ptap->freestruct) { 964 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 965 } 966 PetscFunctionReturn(0); 967 } 968 969 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,Mat C) 970 { 971 PetscErrorCode ierr; 972 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 973 Mat_SeqAIJ *cd,*co,*po,*pd; 974 Mat_APMPI *ptap = c->ap; 975 PetscHMapIV hmap; 976 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; 977 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa; 978 MPI_Comm comm; 979 980 PetscFunctionBegin; 981 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 982 if (!ptap->P_oth) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 983 984 ierr = MatZeroEntries(C);CHKERRQ(ierr); 985 986 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 987 /*-----------------------------------------------------*/ 988 if (ptap->reuse == MAT_REUSE_MATRIX) { 989 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 990 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,MAT_REUSE_MATRIX,&ptap->P_oth);CHKERRQ(ierr); 991 } 992 993 po = (Mat_SeqAIJ*) p->B->data; 994 pd = (Mat_SeqAIJ*) p->A->data; 995 996 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 997 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 998 999 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr); 1000 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1001 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1002 cmaxr = 0; 1003 for (i=0; i<pon; i++) { 1004 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]); 1005 } 1006 cd = (Mat_SeqAIJ*)(c->A)->data; 1007 co = (Mat_SeqAIJ*)(c->B)->data; 1008 for (i=0; i<pn; i++) { 1009 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i])); 1010 } 1011 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr); 1012 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 1013 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 1014 for (i=0; i<am && (pon || pn); i++) { 1015 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 1016 nzi = po->i[i+1] - po->i[i]; 1017 dnzi = pd->i[i+1] - pd->i[i]; 1018 if (!nzi && !dnzi) continue; 1019 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 1020 voff = 0; 1021 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 1022 if (!voff) continue; 1023 1024 /* Form remote C(ii, :) */ 1025 poj = po->j + po->i[i]; 1026 poa = po->a + po->i[i]; 1027 for (j=0; j<nzi; j++) { 1028 c_rmtjj = c_rmtj + ptap->c_rmti[poj[j]]; 1029 c_rmtaa = c_rmta + ptap->c_rmti[poj[j]]; 1030 for (jj=0; jj<voff; jj++) { 1031 apvaluestmp[jj] = apvalues[jj]*poa[j]; 1032 /*If the row is empty */ 1033 if (!c_rmtc[poj[j]]) { 1034 c_rmtjj[jj] = apindices[jj]; 1035 c_rmtaa[jj] = apvaluestmp[jj]; 1036 c_rmtc[poj[j]]++; 1037 } else { 1038 ierr = PetscFindInt(apindices[jj],c_rmtc[poj[j]],c_rmtjj,&loc);CHKERRQ(ierr); 1039 if (loc>=0){ /* hit */ 1040 c_rmtaa[loc] += apvaluestmp[jj]; 1041 ierr = PetscLogFlops(1.0);CHKERRQ(ierr); 1042 } else { /* new element */ 1043 loc = -(loc+1); 1044 /* Move data backward */ 1045 for (kk=c_rmtc[poj[j]]; kk>loc; kk--) { 1046 c_rmtjj[kk] = c_rmtjj[kk-1]; 1047 c_rmtaa[kk] = c_rmtaa[kk-1]; 1048 }/* End kk */ 1049 c_rmtjj[loc] = apindices[jj]; 1050 c_rmtaa[loc] = apvaluestmp[jj]; 1051 c_rmtc[poj[j]]++; 1052 } 1053 } 1054 } /* End jj */ 1055 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 1056 } /* End j */ 1057 1058 /* Form local C(ii, :) */ 1059 pdj = pd->j + pd->i[i]; 1060 pda = pd->a + pd->i[i]; 1061 for (j=0; j<dnzi; j++) { 1062 row = pcstart + pdj[j]; 1063 for (jj=0; jj<voff; jj++) { 1064 apvaluestmp[jj] = apvalues[jj]*pda[j]; 1065 }/* End kk */ 1066 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 1067 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr); 1068 }/* End j */ 1069 } /* End i */ 1070 1071 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr); 1072 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr); 1073 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr); 1074 1075 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1076 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 1077 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPI_SUM);CHKERRQ(ierr); 1078 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 1079 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr); 1080 1081 /* Add contributions from remote */ 1082 for (i = 0; i < pn; i++) { 1083 row = i + pcstart; 1084 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); 1085 } 1086 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr); 1087 1088 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1089 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1090 1091 ptap->reuse = MAT_REUSE_MATRIX; 1092 1093 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1094 if (ptap->freestruct) { 1095 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1096 } 1097 PetscFunctionReturn(0); 1098 } 1099 1100 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,PetscReal fill,Mat *C) 1101 { 1102 Mat_APMPI *ptap; 1103 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1104 MPI_Comm comm; 1105 Mat Cmpi; 1106 Mat_SeqAIJ *pd,*po; 1107 MatType mtype; 1108 PetscSF sf; 1109 PetscSFNode *iremote; 1110 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves; 1111 const PetscInt *rootdegrees; 1112 PetscHSetI ht,oht,*hta,*hto; 1113 PetscInt pn,pon,*c_rmtc,i,j,nzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets; 1114 PetscInt owner,lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj; 1115 PetscInt nalg=2,alg=0; 1116 PetscBool flg; 1117 const char *algTypes[2] = {"overlapping","merged"}; 1118 PetscErrorCode ierr; 1119 1120 PetscFunctionBegin; 1121 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1122 1123 /* Create symbolic parallel matrix Cmpi */ 1124 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1125 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1126 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1127 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1128 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1129 1130 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1131 ptap->reuse = MAT_INITIAL_MATRIX; 1132 ptap->algType = 2; 1133 1134 /* Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1135 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->P_oth);CHKERRQ(ierr); 1136 1137 po = (Mat_SeqAIJ*)p->B->data; 1138 pd = (Mat_SeqAIJ*)p->A->data; 1139 1140 /* This equals to the number of offdiag columns in P */ 1141 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1142 /* offsets */ 1143 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr); 1144 /* The number of columns we will send to remote ranks */ 1145 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr); 1146 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr); 1147 for (i=0; i<pon; i++) { 1148 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1149 } 1150 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1151 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr); 1152 /* Create hash table to merge all columns for C(i, :) */ 1153 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1154 1155 ptap->c_rmti[0] = 0; 1156 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */ 1157 for (i=0; i<am && pon; i++) { 1158 /* Form one row of AP */ 1159 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1160 /* If the off diag is empty, we should not do any calculation */ 1161 nzi = po->i[i+1] - po->i[i]; 1162 if (!nzi) continue; 1163 1164 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,ht);CHKERRQ(ierr); 1165 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1166 /* If AP is empty, just continue */ 1167 if (!htsize) continue; 1168 /* Form C(ii, :) */ 1169 poj = po->j + po->i[i]; 1170 for (j=0; j<nzi; j++) { 1171 ierr = PetscHSetIUpdate(hta[poj[j]],ht);CHKERRQ(ierr); 1172 } 1173 } 1174 1175 for (i=0; i<pon; i++) { 1176 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1177 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize; 1178 c_rmtc[i] = htsize; 1179 } 1180 1181 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr); 1182 1183 for (i=0; i<pon; i++) { 1184 off = 0; 1185 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr); 1186 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1187 } 1188 ierr = PetscFree(hta);CHKERRQ(ierr); 1189 1190 ierr = PetscMalloc1(pon,&iremote);CHKERRQ(ierr); 1191 for (i=0; i<pon; i++) { 1192 owner = 0; lidx = 0; 1193 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1194 iremote[i].index = lidx; 1195 iremote[i].rank = owner; 1196 } 1197 1198 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 1199 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1200 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */ 1201 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr); 1202 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1203 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1204 /* How many neighbors have contributions to my rows? */ 1205 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr); 1206 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr); 1207 rootspacesize = 0; 1208 for (i = 0; i < pn; i++) { 1209 rootspacesize += rootdegrees[i]; 1210 } 1211 ierr = PetscMalloc1(rootspacesize,&rootspace);CHKERRQ(ierr); 1212 ierr = PetscMalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr); 1213 /* Get information from leaves 1214 * Number of columns other people contribute to my rows 1215 * */ 1216 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1217 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1218 ierr = PetscFree(c_rmtc);CHKERRQ(ierr); 1219 ierr = PetscCalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr); 1220 /* The number of columns is received for each row */ 1221 ptap->c_othi[0] = 0; 1222 rootspacesize = 0; 1223 rootspaceoffsets[0] = 0; 1224 for (i = 0; i < pn; i++) { 1225 rcvncols = 0; 1226 for (j = 0; j<rootdegrees[i]; j++) { 1227 rcvncols += rootspace[rootspacesize]; 1228 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize]; 1229 rootspacesize++; 1230 } 1231 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols; 1232 } 1233 ierr = PetscFree(rootspace);CHKERRQ(ierr); 1234 1235 ierr = PetscMalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr); 1236 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1237 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1238 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1239 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr); 1240 1241 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr); 1242 nleaves = 0; 1243 for (i = 0; i<pon; i++) { 1244 owner = 0; lidx = 0; 1245 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1246 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i]; 1247 for (j=0; j<sendncols; j++) { 1248 iremote[nleaves].rank = owner; 1249 iremote[nleaves++].index = c_rmtoffsets[i] + j; 1250 } 1251 } 1252 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr); 1253 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr); 1254 1255 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr); 1256 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1257 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr); 1258 /* One to one map */ 1259 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1260 1261 ierr = PetscMalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr); 1262 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr); 1263 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1264 ierr = PetscMalloc2(pn,&hta,pn,&hto);CHKERRQ(ierr); 1265 for (i=0; i<pn; i++) { 1266 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1267 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr); 1268 } 1269 /* Work on local part */ 1270 /* 4) Pass 1: Estimate memory for C_loc */ 1271 for (i=0; i<am && pn; i++) { 1272 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1273 ierr = PetscHSetIClear(oht);CHKERRQ(ierr); 1274 nzi = pd->i[i+1] - pd->i[i]; 1275 if (!nzi) continue; 1276 1277 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,oht);CHKERRQ(ierr); 1278 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1279 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr); 1280 if (!(htsize+htosize)) continue; 1281 /* Form C(ii, :) */ 1282 pdj = pd->j + pd->i[i]; 1283 for (j=0; j<nzi; j++) { 1284 ierr = PetscHSetIUpdate(hta[pdj[j]],ht);CHKERRQ(ierr); 1285 ierr = PetscHSetIUpdate(hto[pdj[j]],oht);CHKERRQ(ierr); 1286 } 1287 } 1288 1289 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1290 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr); 1291 1292 /* Get remote data */ 1293 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1294 ierr = PetscFree(c_rmtj);CHKERRQ(ierr); 1295 1296 for (i = 0; i < pn; i++) { 1297 nzi = ptap->c_othi[i+1] - ptap->c_othi[i]; 1298 rdj = c_othj + ptap->c_othi[i]; 1299 for (j = 0; j < nzi; j++) { 1300 col = rdj[j]; 1301 /* diag part */ 1302 if (col>=pcstart && col<pcend) { 1303 ierr = PetscHSetIAdd(hta[i],col);CHKERRQ(ierr); 1304 } else { /* off diag */ 1305 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr); 1306 } 1307 } 1308 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1309 dnz[i] = htsize; 1310 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1311 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr); 1312 onz[i] = htsize; 1313 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr); 1314 } 1315 1316 ierr = PetscFree2(hta,hto);CHKERRQ(ierr); 1317 ierr = PetscFree(c_othj);CHKERRQ(ierr); 1318 1319 /* local sizes and preallocation */ 1320 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1321 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 1322 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1323 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 1324 1325 /* attach the supporting struct to Cmpi for reuse */ 1326 c = (Mat_MPIAIJ*)Cmpi->data; 1327 c->ap = ptap; 1328 ptap->duplicate = Cmpi->ops->duplicate; 1329 ptap->destroy = Cmpi->ops->destroy; 1330 ptap->view = Cmpi->ops->view; 1331 1332 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1333 Cmpi->assembled = PETSC_FALSE; 1334 /* pick an algorithm */ 1335 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 1336 alg = 0; 1337 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 1338 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1339 switch (alg) { 1340 case 0: 1341 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce; 1342 break; 1343 case 1: 1344 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged; 1345 break; 1346 default: 1347 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n"); 1348 } 1349 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1350 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1351 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1352 *C = Cmpi; 1353 PetscFunctionReturn(0); 1354 } 1355 1356 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,PetscReal fill,Mat *C) 1357 { 1358 Mat_APMPI *ptap; 1359 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1360 MPI_Comm comm; 1361 Mat Cmpi; 1362 Mat_SeqAIJ *pd,*po; 1363 MatType mtype; 1364 PetscSF sf; 1365 PetscSFNode *iremote; 1366 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves; 1367 const PetscInt *rootdegrees; 1368 PetscHSetI ht,oht,*hta,*hto,*htd; 1369 PetscInt pn,pon,*c_rmtc,i,j,nzi,dnzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets; 1370 PetscInt owner,lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj; 1371 PetscInt nalg=2,alg=0; 1372 PetscBool flg; 1373 const char *algTypes[2] = {"merged","overlapping"}; 1374 PetscErrorCode ierr; 1375 1376 PetscFunctionBegin; 1377 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1378 1379 /* Create symbolic parallel matrix Cmpi */ 1380 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1381 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1382 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1383 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1384 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1385 1386 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1387 ptap->reuse = MAT_INITIAL_MATRIX; 1388 ptap->algType = 3; 1389 1390 /* 0) Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1391 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->P_oth);CHKERRQ(ierr); 1392 1393 po = (Mat_SeqAIJ*)p->B->data; 1394 pd = (Mat_SeqAIJ*)p->A->data; 1395 1396 /* This equals to the number of offdiag columns in P */ 1397 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1398 /* offsets */ 1399 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr); 1400 /* The number of columns we will send to remote ranks */ 1401 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr); 1402 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr); 1403 for (i=0; i<pon; i++) { 1404 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1405 } 1406 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1407 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr); 1408 /* Create hash table to merge all columns for C(i, :) */ 1409 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1410 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr); 1411 ierr = PetscMalloc2(pn,&htd,pn,&hto);CHKERRQ(ierr); 1412 for (i=0; i<pn; i++) { 1413 ierr = PetscHSetICreate(&htd[i]);CHKERRQ(ierr); 1414 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr); 1415 } 1416 ptap->c_rmti[0] = 0; 1417 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */ 1418 for (i=0; i<am && (pon || pn); i++) { 1419 /* Form one row of AP */ 1420 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1421 ierr = PetscHSetIClear(oht);CHKERRQ(ierr); 1422 /* If the off diag is empty, we should not do any calculation */ 1423 nzi = po->i[i+1] - po->i[i]; 1424 dnzi = pd->i[i+1] - pd->i[i]; 1425 if (!nzi && !dnzi) continue; 1426 1427 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,oht);CHKERRQ(ierr); 1428 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1429 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr); 1430 /* If AP is empty, just continue */ 1431 if (!(htsize+htosize)) continue; 1432 1433 /* Form remote C(ii, :) */ 1434 poj = po->j + po->i[i]; 1435 for (j=0; j<nzi; j++) { 1436 ierr = PetscHSetIUpdate(hta[poj[j]],ht);CHKERRQ(ierr); 1437 ierr = PetscHSetIUpdate(hta[poj[j]],oht);CHKERRQ(ierr); 1438 } 1439 1440 /* Form local C(ii, :) */ 1441 pdj = pd->j + pd->i[i]; 1442 for (j=0; j<dnzi; j++) { 1443 ierr = PetscHSetIUpdate(htd[pdj[j]],ht);CHKERRQ(ierr); 1444 ierr = PetscHSetIUpdate(hto[pdj[j]],oht);CHKERRQ(ierr); 1445 } 1446 } 1447 1448 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1449 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr); 1450 1451 for (i=0; i<pon; i++) { 1452 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1453 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize; 1454 c_rmtc[i] = htsize; 1455 } 1456 1457 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr); 1458 1459 for (i=0; i<pon; i++) { 1460 off = 0; 1461 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr); 1462 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1463 } 1464 ierr = PetscFree(hta);CHKERRQ(ierr); 1465 1466 ierr = PetscMalloc1(pon,&iremote);CHKERRQ(ierr); 1467 for (i=0; i<pon; i++) { 1468 owner = 0; lidx = 0; 1469 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1470 iremote[i].index = lidx; 1471 iremote[i].rank = owner; 1472 } 1473 1474 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 1475 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1476 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */ 1477 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr); 1478 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1479 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1480 /* How many neighbors have contributions to my rows? */ 1481 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr); 1482 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr); 1483 rootspacesize = 0; 1484 for (i = 0; i < pn; i++) { 1485 rootspacesize += rootdegrees[i]; 1486 } 1487 ierr = PetscMalloc1(rootspacesize,&rootspace);CHKERRQ(ierr); 1488 ierr = PetscMalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr); 1489 /* Get information from leaves 1490 * Number of columns other people contribute to my rows 1491 * */ 1492 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1493 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1494 ierr = PetscFree(c_rmtc);CHKERRQ(ierr); 1495 ierr = PetscMalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr); 1496 /* The number of columns is received for each row */ 1497 ptap->c_othi[0] = 0; 1498 rootspacesize = 0; 1499 rootspaceoffsets[0] = 0; 1500 for (i = 0; i < pn; i++) { 1501 rcvncols = 0; 1502 for (j = 0; j<rootdegrees[i]; j++) { 1503 rcvncols += rootspace[rootspacesize]; 1504 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize]; 1505 rootspacesize++; 1506 } 1507 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols; 1508 } 1509 ierr = PetscFree(rootspace);CHKERRQ(ierr); 1510 1511 ierr = PetscMalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr); 1512 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1513 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1514 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1515 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr); 1516 1517 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr); 1518 nleaves = 0; 1519 for (i = 0; i<pon; i++) { 1520 owner = 0; 1521 lidx = 0; 1522 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1523 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i]; 1524 for (j=0; j<sendncols; j++) { 1525 iremote[nleaves].rank = owner; 1526 iremote[nleaves++].index = c_rmtoffsets[i] + j; 1527 } 1528 } 1529 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr); 1530 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr); 1531 1532 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr); 1533 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1534 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr); 1535 /* One to one map */ 1536 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1537 /* Get remote data */ 1538 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1539 ierr = PetscFree(c_rmtj);CHKERRQ(ierr); 1540 ierr = PetscMalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr); 1541 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1542 1543 for (i = 0; i < pn; i++) { 1544 nzi = ptap->c_othi[i+1] - ptap->c_othi[i]; 1545 rdj = c_othj + ptap->c_othi[i]; 1546 for (j = 0; j < nzi; j++) { 1547 col = rdj[j]; 1548 /* diag part */ 1549 if (col>=pcstart && col<pcend) { 1550 ierr = PetscHSetIAdd(htd[i],col);CHKERRQ(ierr); 1551 } else { /* off diag */ 1552 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr); 1553 } 1554 } 1555 ierr = PetscHSetIGetSize(htd[i],&htsize);CHKERRQ(ierr); 1556 dnz[i] = htsize; 1557 ierr = PetscHSetIDestroy(&htd[i]);CHKERRQ(ierr); 1558 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr); 1559 onz[i] = htsize; 1560 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr); 1561 } 1562 1563 ierr = PetscFree2(htd,hto);CHKERRQ(ierr); 1564 ierr = PetscFree(c_othj);CHKERRQ(ierr); 1565 1566 /* local sizes and preallocation */ 1567 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1568 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 1569 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1570 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 1571 1572 /* attach the supporting struct to Cmpi for reuse */ 1573 c = (Mat_MPIAIJ*)Cmpi->data; 1574 c->ap = ptap; 1575 ptap->duplicate = Cmpi->ops->duplicate; 1576 ptap->destroy = Cmpi->ops->destroy; 1577 ptap->view = Cmpi->ops->view; 1578 1579 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1580 Cmpi->assembled = PETSC_FALSE; 1581 /* pick an algorithm */ 1582 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 1583 alg = 0; 1584 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 1585 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1586 switch (alg) { 1587 case 0: 1588 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged; 1589 break; 1590 case 1: 1591 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce; 1592 break; 1593 default: 1594 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n"); 1595 } 1596 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1597 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1598 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1599 *C = Cmpi; 1600 PetscFunctionReturn(0); 1601 } 1602 1603 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 1604 { 1605 PetscErrorCode ierr; 1606 Mat_APMPI *ptap; 1607 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 1608 MPI_Comm comm; 1609 PetscMPIInt size,rank; 1610 Mat Cmpi; 1611 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1612 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 1613 PetscInt *lnk,i,k,pnz,row,nsend; 1614 PetscBT lnkbt; 1615 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 1616 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1617 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 1618 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1619 MPI_Request *swaits,*rwaits; 1620 MPI_Status *sstatus,rstatus; 1621 PetscLayout rowmap; 1622 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1623 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1624 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 1625 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 1626 PetscScalar *apv; 1627 PetscTable ta; 1628 MatType mtype; 1629 const char *prefix; 1630 #if defined(PETSC_USE_INFO) 1631 PetscReal apfill; 1632 #endif 1633 1634 PetscFunctionBegin; 1635 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1636 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1637 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1638 1639 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 1640 1641 /* create symbolic parallel matrix Cmpi */ 1642 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1643 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1644 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1645 1646 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 1647 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 1648 1649 /* create struct Mat_APMPI and attached it to C later */ 1650 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1651 ptap->reuse = MAT_INITIAL_MATRIX; 1652 ptap->algType = 1; 1653 1654 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1655 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1656 /* get P_loc by taking all local rows of P */ 1657 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1658 1659 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1660 /* --------------------------------- */ 1661 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1662 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1663 1664 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 1665 /* ----------------------------------------------------------------- */ 1666 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1667 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1668 1669 /* create and initialize a linked list */ 1670 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 1671 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 1672 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 1673 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 1674 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 1675 1676 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1677 1678 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 1679 if (ao) { 1680 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 1681 } else { 1682 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 1683 } 1684 current_space = free_space; 1685 nspacedouble = 0; 1686 1687 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 1688 api[0] = 0; 1689 for (i=0; i<am; i++) { 1690 /* diagonal portion: Ad[i,:]*P */ 1691 ai = ad->i; pi = p_loc->i; 1692 nzi = ai[i+1] - ai[i]; 1693 aj = ad->j + ai[i]; 1694 for (j=0; j<nzi; j++) { 1695 row = aj[j]; 1696 pnz = pi[row+1] - pi[row]; 1697 Jptr = p_loc->j + pi[row]; 1698 /* add non-zero cols of P into the sorted linked list lnk */ 1699 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1700 } 1701 /* off-diagonal portion: Ao[i,:]*P */ 1702 if (ao) { 1703 ai = ao->i; pi = p_oth->i; 1704 nzi = ai[i+1] - ai[i]; 1705 aj = ao->j + ai[i]; 1706 for (j=0; j<nzi; j++) { 1707 row = aj[j]; 1708 pnz = pi[row+1] - pi[row]; 1709 Jptr = p_oth->j + pi[row]; 1710 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1711 } 1712 } 1713 apnz = lnk[0]; 1714 api[i+1] = api[i] + apnz; 1715 if (ap_rmax < apnz) ap_rmax = apnz; 1716 1717 /* if free space is not available, double the total space in the list */ 1718 if (current_space->local_remaining<apnz) { 1719 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1720 nspacedouble++; 1721 } 1722 1723 /* Copy data into free space, then initialize lnk */ 1724 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1725 1726 current_space->array += apnz; 1727 current_space->local_used += apnz; 1728 current_space->local_remaining -= apnz; 1729 } 1730 /* Allocate space for apj and apv, initialize apj, and */ 1731 /* destroy list of free space and other temporary array(s) */ 1732 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 1733 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 1734 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1735 1736 /* Create AP_loc for reuse */ 1737 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 1738 1739 #if defined(PETSC_USE_INFO) 1740 if (ao) { 1741 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 1742 } else { 1743 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 1744 } 1745 ptap->AP_loc->info.mallocs = nspacedouble; 1746 ptap->AP_loc->info.fill_ratio_given = fill; 1747 ptap->AP_loc->info.fill_ratio_needed = apfill; 1748 1749 if (api[am]) { 1750 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); 1751 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 1752 } else { 1753 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 1754 } 1755 #endif 1756 1757 /* (2-1) compute symbolic Co = Ro*AP_loc */ 1758 /* ------------------------------------ */ 1759 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1760 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 1761 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 1762 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 1763 1764 /* (3) send coj of C_oth to other processors */ 1765 /* ------------------------------------------ */ 1766 /* determine row ownership */ 1767 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1768 rowmap->n = pn; 1769 rowmap->bs = 1; 1770 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1771 owners = rowmap->range; 1772 1773 /* determine the number of messages to send, their lengths */ 1774 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1775 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 1776 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr); 1777 1778 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1779 coi = c_oth->i; coj = c_oth->j; 1780 con = ptap->C_oth->rmap->n; 1781 proc = 0; 1782 for (i=0; i<con; i++) { 1783 while (prmap[i] >= owners[proc+1]) proc++; 1784 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 1785 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1786 } 1787 1788 len = 0; /* max length of buf_si[], see (4) */ 1789 owners_co[0] = 0; 1790 nsend = 0; 1791 for (proc=0; proc<size; proc++) { 1792 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1793 if (len_s[proc]) { 1794 nsend++; 1795 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1796 len += len_si[proc]; 1797 } 1798 } 1799 1800 /* determine the number and length of messages to receive for coi and coj */ 1801 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1802 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1803 1804 /* post the Irecv and Isend of coj */ 1805 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1806 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1807 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1808 for (proc=0, k=0; proc<size; proc++) { 1809 if (!len_s[proc]) continue; 1810 i = owners_co[proc]; 1811 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1812 k++; 1813 } 1814 1815 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 1816 /* ---------------------------------------- */ 1817 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 1818 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 1819 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 1820 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1821 1822 /* receives coj are complete */ 1823 for (i=0; i<nrecv; i++) { 1824 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1825 } 1826 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1827 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1828 1829 /* add received column indices into ta to update Crmax */ 1830 for (k=0; k<nrecv; k++) {/* k-th received message */ 1831 Jptr = buf_rj[k]; 1832 for (j=0; j<len_r[k]; j++) { 1833 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1834 } 1835 } 1836 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1837 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1838 1839 /* (4) send and recv coi */ 1840 /*-----------------------*/ 1841 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1842 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1843 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1844 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1845 for (proc=0,k=0; proc<size; proc++) { 1846 if (!len_s[proc]) continue; 1847 /* form outgoing message for i-structure: 1848 buf_si[0]: nrows to be sent 1849 [1:nrows]: row index (global) 1850 [nrows+1:2*nrows+1]: i-structure index 1851 */ 1852 /*-------------------------------------------*/ 1853 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1854 buf_si_i = buf_si + nrows+1; 1855 buf_si[0] = nrows; 1856 buf_si_i[0] = 0; 1857 nrows = 0; 1858 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1859 nzi = coi[i+1] - coi[i]; 1860 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1861 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1862 nrows++; 1863 } 1864 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1865 k++; 1866 buf_si += len_si[proc]; 1867 } 1868 for (i=0; i<nrecv; i++) { 1869 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1870 } 1871 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1872 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1873 1874 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1875 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1876 ierr = PetscFree(swaits);CHKERRQ(ierr); 1877 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1878 1879 /* (5) compute the local portion of Cmpi */ 1880 /* ------------------------------------------ */ 1881 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 1882 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1883 current_space = free_space; 1884 1885 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1886 for (k=0; k<nrecv; k++) { 1887 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1888 nrows = *buf_ri_k[k]; 1889 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1890 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1891 } 1892 1893 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 1894 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1895 for (i=0; i<pn; i++) { 1896 /* add C_loc into Cmpi */ 1897 nzi = c_loc->i[i+1] - c_loc->i[i]; 1898 Jptr = c_loc->j + c_loc->i[i]; 1899 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1900 1901 /* add received col data into lnk */ 1902 for (k=0; k<nrecv; k++) { /* k-th received message */ 1903 if (i == *nextrow[k]) { /* i-th row */ 1904 nzi = *(nextci[k]+1) - *nextci[k]; 1905 Jptr = buf_rj[k] + *nextci[k]; 1906 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1907 nextrow[k]++; nextci[k]++; 1908 } 1909 } 1910 nzi = lnk[0]; 1911 1912 /* copy data into free space, then initialize lnk */ 1913 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1914 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 1915 } 1916 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1917 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1918 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 1919 1920 /* local sizes and preallocation */ 1921 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1922 if (P->cmap->bs > 0) { 1923 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr); 1924 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr); 1925 } 1926 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1927 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1928 1929 /* members in merge */ 1930 ierr = PetscFree(id_r);CHKERRQ(ierr); 1931 ierr = PetscFree(len_r);CHKERRQ(ierr); 1932 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 1933 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 1934 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 1935 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 1936 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 1937 1938 /* attach the supporting struct to Cmpi for reuse */ 1939 c = (Mat_MPIAIJ*)Cmpi->data; 1940 c->ap = ptap; 1941 ptap->duplicate = Cmpi->ops->duplicate; 1942 ptap->destroy = Cmpi->ops->destroy; 1943 ptap->view = Cmpi->ops->view; 1944 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 1945 1946 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1947 Cmpi->assembled = PETSC_FALSE; 1948 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1949 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1950 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1951 *C = Cmpi; 1952 PetscFunctionReturn(0); 1953 } 1954 1955 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 1956 { 1957 PetscErrorCode ierr; 1958 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1959 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 1960 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 1961 Mat_APMPI *ptap = c->ap; 1962 Mat AP_loc,C_loc,C_oth; 1963 PetscInt i,rstart,rend,cm,ncols,row; 1964 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 1965 PetscScalar *apa; 1966 const PetscInt *cols; 1967 const PetscScalar *vals; 1968 1969 PetscFunctionBegin; 1970 if (!ptap->AP_loc) { 1971 MPI_Comm comm; 1972 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1973 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1974 } 1975 1976 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1977 /* 1) get R = Pd^T,Ro = Po^T */ 1978 if (ptap->reuse == MAT_REUSE_MATRIX) { 1979 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1980 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1981 } 1982 1983 /* 2) get AP_loc */ 1984 AP_loc = ptap->AP_loc; 1985 ap = (Mat_SeqAIJ*)AP_loc->data; 1986 1987 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 1988 /*-----------------------------------------------------*/ 1989 if (ptap->reuse == MAT_REUSE_MATRIX) { 1990 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 1991 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1992 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1993 } 1994 1995 /* 2-2) compute numeric A_loc*P - dominating part */ 1996 /* ---------------------------------------------- */ 1997 /* get data from symbolic products */ 1998 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1999 if (ptap->P_oth) { 2000 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 2001 } 2002 apa = ptap->apa; 2003 api = ap->i; 2004 apj = ap->j; 2005 for (i=0; i<am; i++) { 2006 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 2007 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 2008 apnz = api[i+1] - api[i]; 2009 for (j=0; j<apnz; j++) { 2010 col = apj[j+api[i]]; 2011 ap->a[j+ap->i[i]] = apa[col]; 2012 apa[col] = 0.0; 2013 } 2014 } 2015 2016 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 2017 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 2018 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 2019 C_loc = ptap->C_loc; 2020 C_oth = ptap->C_oth; 2021 2022 /* add C_loc and Co to to C */ 2023 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 2024 2025 /* C_loc -> C */ 2026 cm = C_loc->rmap->N; 2027 c_seq = (Mat_SeqAIJ*)C_loc->data; 2028 cols = c_seq->j; 2029 vals = c_seq->a; 2030 2031 2032 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 2033 /* when there are no off-processor parts. */ 2034 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 2035 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 2036 /* a table, and other, more complex stuff has to be done. */ 2037 if (C->assembled) { 2038 C->was_assembled = PETSC_TRUE; 2039 C->assembled = PETSC_FALSE; 2040 } 2041 if (C->was_assembled) { 2042 for (i=0; i<cm; i++) { 2043 ncols = c_seq->i[i+1] - c_seq->i[i]; 2044 row = rstart + i; 2045 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 2046 cols += ncols; vals += ncols; 2047 } 2048 } else { 2049 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 2050 } 2051 2052 /* Co -> C, off-processor part */ 2053 cm = C_oth->rmap->N; 2054 c_seq = (Mat_SeqAIJ*)C_oth->data; 2055 cols = c_seq->j; 2056 vals = c_seq->a; 2057 for (i=0; i<cm; i++) { 2058 ncols = c_seq->i[i+1] - c_seq->i[i]; 2059 row = p->garray[i]; 2060 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 2061 cols += ncols; vals += ncols; 2062 } 2063 2064 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2065 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2066 2067 ptap->reuse = MAT_REUSE_MATRIX; 2068 2069 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 2070 if (ptap->freestruct) { 2071 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 2072 } 2073 PetscFunctionReturn(0); 2074 } 2075