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 /* TODO: Use PetscCalloc2() */ 513 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 514 ierr = PetscArrayzero(len_si,size);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 PetscErrorCode ierr; 765 766 PetscFunctionBegin; 767 pcstart = P->cmap->rstart; 768 /* diagonal portion: Ad[i,:]*P */ 769 ai = ad->i; 770 nzi = ai[i+1] - ai[i]; 771 aj = ad->j + ai[i]; 772 aa = ad->a + ai[i]; 773 774 for (j=0; j<nzi; j++) { 775 ra = aa[j]; 776 row = aj[j]; 777 nzpi = pd->i[row+1] - pd->i[row]; 778 pj = pd->j + pd->i[row]; 779 pa = pd->a + pd->i[row]; 780 for (k=0; k<nzpi; k++) { 781 ierr = PetscHMapIVAddValue(hmap,pj[k]+pcstart,ra*pa[k]);CHKERRQ(ierr); 782 } 783 ierr = PetscLogFlops(2.0*nzpi);CHKERRQ(ierr); 784 } 785 for (j=0; j<nzi; j++) { 786 ra = aa[j]; 787 row = aj[j]; 788 nzpi = po->i[row+1] - po->i[row]; 789 pj = po->j + po->i[row]; 790 pa = po->a + po->i[row]; 791 for (k=0; k<nzpi; k++) { 792 ierr = PetscHMapIVAddValue(hmap,p->garray[pj[k]],ra*pa[k]);CHKERRQ(ierr); 793 } 794 ierr = PetscLogFlops(2.0*nzpi);CHKERRQ(ierr); 795 } 796 797 798 /* off diagonal part: Ao[i, :]*P_oth */ 799 if (ao) { 800 ai = ao->i; 801 pi = p_oth->i; 802 nzi = ai[i+1] - ai[i]; 803 aj = ao->j + ai[i]; 804 aa = ao->a + ai[i]; 805 for (j=0; j<nzi; j++) { 806 row = aj[j]; 807 ra = aa[j]; 808 pnz = pi[row+1] - pi[row]; 809 p_othcols = p_oth->j + pi[row]; 810 pa = p_oth->a + pi[row]; 811 for (col=0; col<pnz; col++) { 812 ierr = PetscHMapIVAddValue(hmap,p_othcols[col],ra*pa[col]);CHKERRQ(ierr); 813 } 814 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 815 } 816 } /* end if (ao) */ 817 818 PetscFunctionReturn(0); 819 } 820 821 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,Mat C) 822 { 823 PetscErrorCode ierr; 824 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 825 Mat_SeqAIJ *cd,*co,*po,*pd; 826 Mat_APMPI *ptap = c->ap; 827 PetscHMapIV hmap; 828 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; 829 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa; 830 MPI_Comm comm; 831 832 PetscFunctionBegin; 833 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 834 if (!ptap->P_oth) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 835 836 ierr = MatZeroEntries(C);CHKERRQ(ierr); 837 838 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 839 /*-----------------------------------------------------*/ 840 if (ptap->reuse == MAT_REUSE_MATRIX) { 841 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 842 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 843 } 844 845 po = (Mat_SeqAIJ*) p->B->data; 846 pd = (Mat_SeqAIJ*) p->A->data; 847 848 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 849 850 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr); 851 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 852 cmaxr = 0; 853 for (i=0; i<pon; i++) { 854 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]); 855 } 856 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr); 857 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 858 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 859 for (i=0; i<am && pon; i++) { 860 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 861 nzi = po->i[i+1] - po->i[i]; 862 if (!nzi) continue; 863 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 864 voff = 0; 865 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 866 if (!voff) continue; 867 868 /* Form C(ii, :) */ 869 poj = po->j + po->i[i]; 870 poa = po->a + po->i[i]; 871 for (j=0; j<nzi; j++) { 872 c_rmtjj = c_rmtj + ptap->c_rmti[poj[j]]; 873 c_rmtaa = c_rmta + ptap->c_rmti[poj[j]]; 874 for (jj=0; jj<voff; jj++) { 875 apvaluestmp[jj] = apvalues[jj]*poa[j]; 876 /*If the row is empty */ 877 if (!c_rmtc[poj[j]]) { 878 c_rmtjj[jj] = apindices[jj]; 879 c_rmtaa[jj] = apvaluestmp[jj]; 880 c_rmtc[poj[j]]++; 881 } else { 882 ierr = PetscFindInt(apindices[jj],c_rmtc[poj[j]],c_rmtjj,&loc);CHKERRQ(ierr); 883 if (loc>=0){ /* hit */ 884 c_rmtaa[loc] += apvaluestmp[jj]; 885 ierr = PetscLogFlops(1.0);CHKERRQ(ierr); 886 } else { /* new element */ 887 loc = -(loc+1); 888 /* Move data backward */ 889 for (kk=c_rmtc[poj[j]]; kk>loc; kk--) { 890 c_rmtjj[kk] = c_rmtjj[kk-1]; 891 c_rmtaa[kk] = c_rmtaa[kk-1]; 892 }/* End kk */ 893 c_rmtjj[loc] = apindices[jj]; 894 c_rmtaa[loc] = apvaluestmp[jj]; 895 c_rmtc[poj[j]]++; 896 } 897 } 898 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 899 } /* End jj */ 900 } /* End j */ 901 } /* End i */ 902 903 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr); 904 905 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 906 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr); 907 908 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 909 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 910 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 911 cd = (Mat_SeqAIJ*)(c->A)->data; 912 co = (Mat_SeqAIJ*)(c->B)->data; 913 914 cmaxr = 0; 915 for (i=0; i<pn; i++) { 916 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i])); 917 } 918 ierr = PetscCalloc5(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pn,&dcc,pn,&occ);CHKERRQ(ierr); 919 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 920 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 921 for (i=0; i<am && pn; i++) { 922 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 923 nzi = pd->i[i+1] - pd->i[i]; 924 if (!nzi) continue; 925 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 926 voff = 0; 927 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 928 if (!voff) continue; 929 /* Form C(ii, :) */ 930 pdj = pd->j + pd->i[i]; 931 pda = pd->a + pd->i[i]; 932 for (j=0; j<nzi; j++) { 933 row = pcstart + pdj[j]; 934 for (jj=0; jj<voff; jj++) { 935 apvaluestmp[jj] = apvalues[jj]*pda[j]; 936 } 937 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 938 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr); 939 } 940 } 941 942 ierr = MatGetOwnershipRangeColumn(C,&ccstart,&ccend);CHKERRQ(ierr); 943 ierr = PetscFree5(apindices,apvalues,apvaluestmp,dcc,occ);CHKERRQ(ierr); 944 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr); 945 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPI_SUM);CHKERRQ(ierr); 946 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 947 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr); 948 949 /* Add contributions from remote */ 950 for (i = 0; i < pn; i++) { 951 row = i + pcstart; 952 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); 953 } 954 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr); 955 956 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 957 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 958 959 ptap->reuse = MAT_REUSE_MATRIX; 960 961 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 962 if (ptap->freestruct) { 963 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 964 } 965 PetscFunctionReturn(0); 966 } 967 968 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,Mat C) 969 { 970 PetscErrorCode ierr; 971 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 972 Mat_SeqAIJ *cd,*co,*po,*pd; 973 Mat_APMPI *ptap = c->ap; 974 PetscHMapIV hmap; 975 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; 976 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa; 977 MPI_Comm comm; 978 979 PetscFunctionBegin; 980 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 981 if (!ptap->P_oth) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 982 983 ierr = MatZeroEntries(C);CHKERRQ(ierr); 984 985 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 986 /*-----------------------------------------------------*/ 987 if (ptap->reuse == MAT_REUSE_MATRIX) { 988 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 989 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 990 } 991 992 po = (Mat_SeqAIJ*) p->B->data; 993 pd = (Mat_SeqAIJ*) p->A->data; 994 995 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 996 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 997 998 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr); 999 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1000 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1001 cmaxr = 0; 1002 for (i=0; i<pon; i++) { 1003 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]); 1004 } 1005 cd = (Mat_SeqAIJ*)(c->A)->data; 1006 co = (Mat_SeqAIJ*)(c->B)->data; 1007 for (i=0; i<pn; i++) { 1008 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i])); 1009 } 1010 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr); 1011 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 1012 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 1013 for (i=0; i<am && (pon || pn); i++) { 1014 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 1015 nzi = po->i[i+1] - po->i[i]; 1016 dnzi = pd->i[i+1] - pd->i[i]; 1017 if (!nzi && !dnzi) continue; 1018 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 1019 voff = 0; 1020 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 1021 if (!voff) continue; 1022 1023 /* Form remote C(ii, :) */ 1024 poj = po->j + po->i[i]; 1025 poa = po->a + po->i[i]; 1026 for (j=0; j<nzi; j++) { 1027 c_rmtjj = c_rmtj + ptap->c_rmti[poj[j]]; 1028 c_rmtaa = c_rmta + ptap->c_rmti[poj[j]]; 1029 for (jj=0; jj<voff; jj++) { 1030 apvaluestmp[jj] = apvalues[jj]*poa[j]; 1031 /*If the row is empty */ 1032 if (!c_rmtc[poj[j]]) { 1033 c_rmtjj[jj] = apindices[jj]; 1034 c_rmtaa[jj] = apvaluestmp[jj]; 1035 c_rmtc[poj[j]]++; 1036 } else { 1037 ierr = PetscFindInt(apindices[jj],c_rmtc[poj[j]],c_rmtjj,&loc);CHKERRQ(ierr); 1038 if (loc>=0){ /* hit */ 1039 c_rmtaa[loc] += apvaluestmp[jj]; 1040 ierr = PetscLogFlops(1.0);CHKERRQ(ierr); 1041 } else { /* new element */ 1042 loc = -(loc+1); 1043 /* Move data backward */ 1044 for (kk=c_rmtc[poj[j]]; kk>loc; kk--) { 1045 c_rmtjj[kk] = c_rmtjj[kk-1]; 1046 c_rmtaa[kk] = c_rmtaa[kk-1]; 1047 }/* End kk */ 1048 c_rmtjj[loc] = apindices[jj]; 1049 c_rmtaa[loc] = apvaluestmp[jj]; 1050 c_rmtc[poj[j]]++; 1051 } 1052 } 1053 } /* End jj */ 1054 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 1055 } /* End j */ 1056 1057 /* Form local C(ii, :) */ 1058 pdj = pd->j + pd->i[i]; 1059 pda = pd->a + pd->i[i]; 1060 for (j=0; j<dnzi; j++) { 1061 row = pcstart + pdj[j]; 1062 for (jj=0; jj<voff; jj++) { 1063 apvaluestmp[jj] = apvalues[jj]*pda[j]; 1064 }/* End kk */ 1065 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 1066 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr); 1067 }/* End j */ 1068 } /* End i */ 1069 1070 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr); 1071 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr); 1072 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr); 1073 1074 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1075 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 1076 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPI_SUM);CHKERRQ(ierr); 1077 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 1078 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr); 1079 1080 /* Add contributions from remote */ 1081 for (i = 0; i < pn; i++) { 1082 row = i + pcstart; 1083 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); 1084 } 1085 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr); 1086 1087 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1088 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1089 1090 ptap->reuse = MAT_REUSE_MATRIX; 1091 1092 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1093 if (ptap->freestruct) { 1094 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1095 } 1096 PetscFunctionReturn(0); 1097 } 1098 1099 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,PetscReal fill,Mat *C) 1100 { 1101 Mat_APMPI *ptap; 1102 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1103 MPI_Comm comm; 1104 Mat Cmpi; 1105 Mat_SeqAIJ *pd,*po; 1106 MatType mtype; 1107 PetscSF sf; 1108 PetscSFNode *iremote; 1109 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves; 1110 const PetscInt *rootdegrees; 1111 PetscHSetI ht,oht,*hta,*hto; 1112 PetscInt pn,pon,*c_rmtc,i,j,nzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets; 1113 PetscInt owner,lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj; 1114 PetscInt nalg=2,alg=0; 1115 PetscBool flg; 1116 const char *algTypes[2] = {"overlapping","merged"}; 1117 PetscErrorCode ierr; 1118 1119 PetscFunctionBegin; 1120 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1121 1122 /* Create symbolic parallel matrix Cmpi */ 1123 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1124 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1125 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1126 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1127 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1128 1129 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1130 ptap->reuse = MAT_INITIAL_MATRIX; 1131 ptap->algType = 2; 1132 1133 /* Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1134 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1135 1136 po = (Mat_SeqAIJ*)p->B->data; 1137 pd = (Mat_SeqAIJ*)p->A->data; 1138 1139 /* This equals to the number of offdiag columns in P */ 1140 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1141 /* offsets */ 1142 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr); 1143 /* The number of columns we will send to remote ranks */ 1144 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr); 1145 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr); 1146 for (i=0; i<pon; i++) { 1147 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1148 } 1149 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1150 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr); 1151 /* Create hash table to merge all columns for C(i, :) */ 1152 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1153 1154 ptap->c_rmti[0] = 0; 1155 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */ 1156 for (i=0; i<am && pon; i++) { 1157 /* Form one row of AP */ 1158 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1159 /* If the off diag is empty, we should not do any calculation */ 1160 nzi = po->i[i+1] - po->i[i]; 1161 if (!nzi) continue; 1162 1163 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,ht);CHKERRQ(ierr); 1164 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1165 /* If AP is empty, just continue */ 1166 if (!htsize) continue; 1167 /* Form C(ii, :) */ 1168 poj = po->j + po->i[i]; 1169 for (j=0; j<nzi; j++) { 1170 ierr = PetscHSetIUpdate(hta[poj[j]],ht);CHKERRQ(ierr); 1171 } 1172 } 1173 1174 for (i=0; i<pon; i++) { 1175 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1176 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize; 1177 c_rmtc[i] = htsize; 1178 } 1179 1180 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr); 1181 1182 for (i=0; i<pon; i++) { 1183 off = 0; 1184 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr); 1185 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1186 } 1187 ierr = PetscFree(hta);CHKERRQ(ierr); 1188 1189 ierr = PetscCalloc1(pon,&iremote);CHKERRQ(ierr); 1190 for (i=0; i<pon; i++) { 1191 owner = 0; lidx = 0; 1192 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1193 iremote[i].index = lidx; 1194 iremote[i].rank = owner; 1195 } 1196 1197 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 1198 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1199 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */ 1200 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr); 1201 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1202 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1203 /* How many neighbors have contributions to my rows? */ 1204 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr); 1205 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr); 1206 rootspacesize = 0; 1207 for (i = 0; i < pn; i++) { 1208 rootspacesize += rootdegrees[i]; 1209 } 1210 ierr = PetscCalloc1(rootspacesize,&rootspace);CHKERRQ(ierr); 1211 ierr = PetscCalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr); 1212 /* Get information from leaves 1213 * Number of columns other people contribute to my rows 1214 * */ 1215 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1216 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1217 ierr = PetscFree(c_rmtc);CHKERRQ(ierr); 1218 ierr = PetscCalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr); 1219 /* The number of columns is received for each row */ 1220 ptap->c_othi[0] = 0; 1221 rootspacesize = 0; 1222 rootspaceoffsets[0] = 0; 1223 for (i = 0; i < pn; i++) { 1224 rcvncols = 0; 1225 for (j = 0; j<rootdegrees[i]; j++) { 1226 rcvncols += rootspace[rootspacesize]; 1227 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize]; 1228 rootspacesize++; 1229 } 1230 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols; 1231 } 1232 ierr = PetscFree(rootspace);CHKERRQ(ierr); 1233 1234 ierr = PetscCalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr); 1235 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1236 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1237 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1238 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr); 1239 1240 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr); 1241 nleaves = 0; 1242 for (i = 0; i<pon; i++) { 1243 owner = 0; lidx = 0; 1244 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1245 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i]; 1246 for (j=0; j<sendncols; j++) { 1247 iremote[nleaves].rank = owner; 1248 iremote[nleaves++].index = c_rmtoffsets[i] + j; 1249 } 1250 } 1251 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr); 1252 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr); 1253 1254 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr); 1255 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1256 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr); 1257 /* One to one map */ 1258 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1259 1260 ierr = PetscCalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr); 1261 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr); 1262 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1263 ierr = PetscMalloc2(pn,&hta,pn,&hto);CHKERRQ(ierr); 1264 for (i=0; i<pn; i++) { 1265 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1266 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr); 1267 } 1268 /* Work on local part */ 1269 /* 4) Pass 1: Estimate memory for C_loc */ 1270 for (i=0; i<am && pn; i++) { 1271 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1272 ierr = PetscHSetIClear(oht);CHKERRQ(ierr); 1273 nzi = pd->i[i+1] - pd->i[i]; 1274 if (!nzi) continue; 1275 1276 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,oht);CHKERRQ(ierr); 1277 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1278 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr); 1279 if (!(htsize+htosize)) continue; 1280 /* Form C(ii, :) */ 1281 pdj = pd->j + pd->i[i]; 1282 for (j=0; j<nzi; j++) { 1283 ierr = PetscHSetIUpdate(hta[pdj[j]],ht);CHKERRQ(ierr); 1284 ierr = PetscHSetIUpdate(hto[pdj[j]],oht);CHKERRQ(ierr); 1285 } 1286 } 1287 1288 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1289 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr); 1290 1291 /* Get remote data */ 1292 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1293 ierr = PetscFree(c_rmtj);CHKERRQ(ierr); 1294 1295 for (i = 0; i < pn; i++) { 1296 nzi = ptap->c_othi[i+1] - ptap->c_othi[i]; 1297 rdj = c_othj + ptap->c_othi[i]; 1298 for (j = 0; j < nzi; j++) { 1299 col = rdj[j]; 1300 /* diag part */ 1301 if (col>=pcstart && col<pcend) { 1302 ierr = PetscHSetIAdd(hta[i],col);CHKERRQ(ierr); 1303 } else { /* off diag */ 1304 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr); 1305 } 1306 } 1307 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1308 dnz[i] = htsize; 1309 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1310 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr); 1311 onz[i] = htsize; 1312 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr); 1313 } 1314 1315 ierr = PetscFree2(hta,hto);CHKERRQ(ierr); 1316 ierr = PetscFree(c_othj);CHKERRQ(ierr); 1317 1318 /* local sizes and preallocation */ 1319 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1320 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 1321 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1322 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 1323 1324 /* attach the supporting struct to Cmpi for reuse */ 1325 c = (Mat_MPIAIJ*)Cmpi->data; 1326 c->ap = ptap; 1327 ptap->duplicate = Cmpi->ops->duplicate; 1328 ptap->destroy = Cmpi->ops->destroy; 1329 ptap->view = Cmpi->ops->view; 1330 1331 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1332 Cmpi->assembled = PETSC_FALSE; 1333 /* pick an algorithm */ 1334 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 1335 alg = 0; 1336 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 1337 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1338 switch (alg) { 1339 case 0: 1340 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce; 1341 break; 1342 case 1: 1343 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged; 1344 break; 1345 default: 1346 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n"); 1347 } 1348 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1349 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1350 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1351 *C = Cmpi; 1352 PetscFunctionReturn(0); 1353 } 1354 1355 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,PetscReal fill,Mat *C) 1356 { 1357 Mat_APMPI *ptap; 1358 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1359 MPI_Comm comm; 1360 Mat Cmpi; 1361 Mat_SeqAIJ *pd,*po; 1362 MatType mtype; 1363 PetscSF sf; 1364 PetscSFNode *iremote; 1365 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves; 1366 const PetscInt *rootdegrees; 1367 PetscHSetI ht,oht,*hta,*hto,*htd; 1368 PetscInt pn,pon,*c_rmtc,i,j,nzi,dnzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets; 1369 PetscInt owner,lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj; 1370 PetscInt nalg=2,alg=0; 1371 PetscBool flg; 1372 const char *algTypes[2] = {"merged","overlapping"}; 1373 PetscErrorCode ierr; 1374 1375 PetscFunctionBegin; 1376 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1377 1378 /* Create symbolic parallel matrix Cmpi */ 1379 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1380 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1381 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1382 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1383 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1384 1385 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1386 ptap->reuse = MAT_INITIAL_MATRIX; 1387 ptap->algType = 3; 1388 1389 /* 0) Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1390 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1391 1392 po = (Mat_SeqAIJ*)p->B->data; 1393 pd = (Mat_SeqAIJ*)p->A->data; 1394 1395 /* This equals to the number of offdiag columns in P */ 1396 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1397 /* offsets */ 1398 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr); 1399 /* The number of columns we will send to remote ranks */ 1400 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr); 1401 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr); 1402 for (i=0; i<pon; i++) { 1403 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1404 } 1405 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1406 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr); 1407 /* Create hash table to merge all columns for C(i, :) */ 1408 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1409 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr); 1410 ierr = PetscMalloc2(pn,&htd,pn,&hto);CHKERRQ(ierr); 1411 for (i=0; i<pn; i++) { 1412 ierr = PetscHSetICreate(&htd[i]);CHKERRQ(ierr); 1413 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr); 1414 } 1415 ptap->c_rmti[0] = 0; 1416 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */ 1417 for (i=0; i<am && (pon || pn); i++) { 1418 /* Form one row of AP */ 1419 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1420 ierr = PetscHSetIClear(oht);CHKERRQ(ierr); 1421 /* If the off diag is empty, we should not do any calculation */ 1422 nzi = po->i[i+1] - po->i[i]; 1423 dnzi = pd->i[i+1] - pd->i[i]; 1424 if (!nzi && !dnzi) continue; 1425 1426 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,oht);CHKERRQ(ierr); 1427 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1428 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr); 1429 /* If AP is empty, just continue */ 1430 if (!(htsize+htosize)) continue; 1431 1432 /* Form remote C(ii, :) */ 1433 poj = po->j + po->i[i]; 1434 for (j=0; j<nzi; j++) { 1435 ierr = PetscHSetIUpdate(hta[poj[j]],ht);CHKERRQ(ierr); 1436 ierr = PetscHSetIUpdate(hta[poj[j]],oht);CHKERRQ(ierr); 1437 } 1438 1439 /* Form local C(ii, :) */ 1440 pdj = pd->j + pd->i[i]; 1441 for (j=0; j<dnzi; j++) { 1442 ierr = PetscHSetIUpdate(htd[pdj[j]],ht);CHKERRQ(ierr); 1443 ierr = PetscHSetIUpdate(hto[pdj[j]],oht);CHKERRQ(ierr); 1444 } 1445 } 1446 1447 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1448 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr); 1449 1450 for (i=0; i<pon; i++) { 1451 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1452 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize; 1453 c_rmtc[i] = htsize; 1454 } 1455 1456 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr); 1457 1458 for (i=0; i<pon; i++) { 1459 off = 0; 1460 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr); 1461 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1462 } 1463 ierr = PetscFree(hta);CHKERRQ(ierr); 1464 1465 ierr = PetscCalloc1(pon,&iremote);CHKERRQ(ierr); 1466 for (i=0; i<pon; i++) { 1467 owner = 0; lidx = 0; 1468 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1469 iremote[i].index = lidx; 1470 iremote[i].rank = owner; 1471 } 1472 1473 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 1474 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1475 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */ 1476 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr); 1477 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1478 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1479 /* How many neighbors have contributions to my rows? */ 1480 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr); 1481 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr); 1482 rootspacesize = 0; 1483 for (i = 0; i < pn; i++) { 1484 rootspacesize += rootdegrees[i]; 1485 } 1486 ierr = PetscCalloc1(rootspacesize,&rootspace);CHKERRQ(ierr); 1487 ierr = PetscCalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr); 1488 /* Get information from leaves 1489 * Number of columns other people contribute to my rows 1490 * */ 1491 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1492 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1493 ierr = PetscFree(c_rmtc);CHKERRQ(ierr); 1494 ierr = PetscCalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr); 1495 /* The number of columns is received for each row */ 1496 ptap->c_othi[0] = 0; 1497 rootspacesize = 0; 1498 rootspaceoffsets[0] = 0; 1499 for (i = 0; i < pn; i++) { 1500 rcvncols = 0; 1501 for (j = 0; j<rootdegrees[i]; j++) { 1502 rcvncols += rootspace[rootspacesize]; 1503 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize]; 1504 rootspacesize++; 1505 } 1506 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols; 1507 } 1508 ierr = PetscFree(rootspace);CHKERRQ(ierr); 1509 1510 ierr = PetscCalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr); 1511 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1512 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1513 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1514 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr); 1515 1516 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr); 1517 nleaves = 0; 1518 for (i = 0; i<pon; i++) { 1519 owner = 0; lidx = 0; 1520 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1521 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i]; 1522 for (j=0; j<sendncols; j++) { 1523 iremote[nleaves].rank = owner; 1524 iremote[nleaves++].index = c_rmtoffsets[i] + j; 1525 } 1526 } 1527 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr); 1528 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr); 1529 1530 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr); 1531 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1532 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr); 1533 /* One to one map */ 1534 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1535 /* Get remote data */ 1536 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1537 ierr = PetscFree(c_rmtj);CHKERRQ(ierr); 1538 ierr = PetscCalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr); 1539 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1540 1541 for (i = 0; i < pn; i++) { 1542 nzi = ptap->c_othi[i+1] - ptap->c_othi[i]; 1543 rdj = c_othj + ptap->c_othi[i]; 1544 for (j = 0; j < nzi; j++) { 1545 col = rdj[j]; 1546 /* diag part */ 1547 if (col>=pcstart && col<pcend) { 1548 ierr = PetscHSetIAdd(htd[i],col);CHKERRQ(ierr); 1549 } else { /* off diag */ 1550 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr); 1551 } 1552 } 1553 ierr = PetscHSetIGetSize(htd[i],&htsize);CHKERRQ(ierr); 1554 dnz[i] = htsize; 1555 ierr = PetscHSetIDestroy(&htd[i]);CHKERRQ(ierr); 1556 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr); 1557 onz[i] = htsize; 1558 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr); 1559 } 1560 1561 ierr = PetscFree2(htd,hto);CHKERRQ(ierr); 1562 ierr = PetscFree(c_othj);CHKERRQ(ierr); 1563 1564 /* local sizes and preallocation */ 1565 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1566 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 1567 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1568 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 1569 1570 /* attach the supporting struct to Cmpi for reuse */ 1571 c = (Mat_MPIAIJ*)Cmpi->data; 1572 c->ap = ptap; 1573 ptap->duplicate = Cmpi->ops->duplicate; 1574 ptap->destroy = Cmpi->ops->destroy; 1575 ptap->view = Cmpi->ops->view; 1576 1577 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1578 Cmpi->assembled = PETSC_FALSE; 1579 /* pick an algorithm */ 1580 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 1581 alg = 0; 1582 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 1583 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1584 switch (alg) { 1585 case 0: 1586 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged; 1587 break; 1588 case 1: 1589 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce; 1590 break; 1591 default: 1592 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n"); 1593 } 1594 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1595 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1596 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1597 *C = Cmpi; 1598 PetscFunctionReturn(0); 1599 } 1600 1601 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 1602 { 1603 PetscErrorCode ierr; 1604 Mat_APMPI *ptap; 1605 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 1606 MPI_Comm comm; 1607 PetscMPIInt size,rank; 1608 Mat Cmpi; 1609 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1610 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 1611 PetscInt *lnk,i,k,pnz,row,nsend; 1612 PetscBT lnkbt; 1613 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 1614 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1615 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 1616 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1617 MPI_Request *swaits,*rwaits; 1618 MPI_Status *sstatus,rstatus; 1619 PetscLayout rowmap; 1620 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1621 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1622 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 1623 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 1624 PetscScalar *apv; 1625 PetscTable ta; 1626 MatType mtype; 1627 const char *prefix; 1628 #if defined(PETSC_USE_INFO) 1629 PetscReal apfill; 1630 #endif 1631 1632 PetscFunctionBegin; 1633 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1634 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1635 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1636 1637 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 1638 1639 /* create symbolic parallel matrix Cmpi */ 1640 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1641 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1642 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1643 1644 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 1645 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 1646 1647 /* create struct Mat_APMPI and attached it to C later */ 1648 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1649 ptap->reuse = MAT_INITIAL_MATRIX; 1650 ptap->algType = 1; 1651 1652 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1653 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1654 /* get P_loc by taking all local rows of P */ 1655 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1656 1657 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1658 /* --------------------------------- */ 1659 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1660 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1661 1662 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 1663 /* ----------------------------------------------------------------- */ 1664 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1665 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1666 1667 /* create and initialize a linked list */ 1668 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 1669 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 1670 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 1671 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 1672 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 1673 1674 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1675 1676 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 1677 if (ao) { 1678 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 1679 } else { 1680 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 1681 } 1682 current_space = free_space; 1683 nspacedouble = 0; 1684 1685 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 1686 api[0] = 0; 1687 for (i=0; i<am; i++) { 1688 /* diagonal portion: Ad[i,:]*P */ 1689 ai = ad->i; pi = p_loc->i; 1690 nzi = ai[i+1] - ai[i]; 1691 aj = ad->j + ai[i]; 1692 for (j=0; j<nzi; j++) { 1693 row = aj[j]; 1694 pnz = pi[row+1] - pi[row]; 1695 Jptr = p_loc->j + pi[row]; 1696 /* add non-zero cols of P into the sorted linked list lnk */ 1697 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1698 } 1699 /* off-diagonal portion: Ao[i,:]*P */ 1700 if (ao) { 1701 ai = ao->i; pi = p_oth->i; 1702 nzi = ai[i+1] - ai[i]; 1703 aj = ao->j + ai[i]; 1704 for (j=0; j<nzi; j++) { 1705 row = aj[j]; 1706 pnz = pi[row+1] - pi[row]; 1707 Jptr = p_oth->j + pi[row]; 1708 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1709 } 1710 } 1711 apnz = lnk[0]; 1712 api[i+1] = api[i] + apnz; 1713 if (ap_rmax < apnz) ap_rmax = apnz; 1714 1715 /* if free space is not available, double the total space in the list */ 1716 if (current_space->local_remaining<apnz) { 1717 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1718 nspacedouble++; 1719 } 1720 1721 /* Copy data into free space, then initialize lnk */ 1722 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1723 1724 current_space->array += apnz; 1725 current_space->local_used += apnz; 1726 current_space->local_remaining -= apnz; 1727 } 1728 /* Allocate space for apj and apv, initialize apj, and */ 1729 /* destroy list of free space and other temporary array(s) */ 1730 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 1731 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 1732 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1733 1734 /* Create AP_loc for reuse */ 1735 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 1736 1737 #if defined(PETSC_USE_INFO) 1738 if (ao) { 1739 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 1740 } else { 1741 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 1742 } 1743 ptap->AP_loc->info.mallocs = nspacedouble; 1744 ptap->AP_loc->info.fill_ratio_given = fill; 1745 ptap->AP_loc->info.fill_ratio_needed = apfill; 1746 1747 if (api[am]) { 1748 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); 1749 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 1750 } else { 1751 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 1752 } 1753 #endif 1754 1755 /* (2-1) compute symbolic Co = Ro*AP_loc */ 1756 /* ------------------------------------ */ 1757 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1758 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 1759 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 1760 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 1761 1762 /* (3) send coj of C_oth to other processors */ 1763 /* ------------------------------------------ */ 1764 /* determine row ownership */ 1765 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1766 rowmap->n = pn; 1767 rowmap->bs = 1; 1768 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1769 owners = rowmap->range; 1770 1771 /* determine the number of messages to send, their lengths */ 1772 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1773 /* TODO: Use PetscCalloc2() */ 1774 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 1775 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr); 1776 1777 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1778 coi = c_oth->i; coj = c_oth->j; 1779 con = ptap->C_oth->rmap->n; 1780 proc = 0; 1781 for (i=0; i<con; i++) { 1782 while (prmap[i] >= owners[proc+1]) proc++; 1783 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 1784 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1785 } 1786 1787 len = 0; /* max length of buf_si[], see (4) */ 1788 owners_co[0] = 0; 1789 nsend = 0; 1790 for (proc=0; proc<size; proc++) { 1791 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1792 if (len_s[proc]) { 1793 nsend++; 1794 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1795 len += len_si[proc]; 1796 } 1797 } 1798 1799 /* determine the number and length of messages to receive for coi and coj */ 1800 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1801 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1802 1803 /* post the Irecv and Isend of coj */ 1804 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1805 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1806 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1807 for (proc=0, k=0; proc<size; proc++) { 1808 if (!len_s[proc]) continue; 1809 i = owners_co[proc]; 1810 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1811 k++; 1812 } 1813 1814 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 1815 /* ---------------------------------------- */ 1816 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 1817 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 1818 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 1819 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1820 1821 /* receives coj are complete */ 1822 for (i=0; i<nrecv; i++) { 1823 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1824 } 1825 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1826 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1827 1828 /* add received column indices into ta to update Crmax */ 1829 for (k=0; k<nrecv; k++) {/* k-th received message */ 1830 Jptr = buf_rj[k]; 1831 for (j=0; j<len_r[k]; j++) { 1832 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1833 } 1834 } 1835 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1836 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1837 1838 /* (4) send and recv coi */ 1839 /*-----------------------*/ 1840 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1841 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1842 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1843 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1844 for (proc=0,k=0; proc<size; proc++) { 1845 if (!len_s[proc]) continue; 1846 /* form outgoing message for i-structure: 1847 buf_si[0]: nrows to be sent 1848 [1:nrows]: row index (global) 1849 [nrows+1:2*nrows+1]: i-structure index 1850 */ 1851 /*-------------------------------------------*/ 1852 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1853 buf_si_i = buf_si + nrows+1; 1854 buf_si[0] = nrows; 1855 buf_si_i[0] = 0; 1856 nrows = 0; 1857 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1858 nzi = coi[i+1] - coi[i]; 1859 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1860 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1861 nrows++; 1862 } 1863 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1864 k++; 1865 buf_si += len_si[proc]; 1866 } 1867 for (i=0; i<nrecv; i++) { 1868 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1869 } 1870 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1871 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1872 1873 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1874 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1875 ierr = PetscFree(swaits);CHKERRQ(ierr); 1876 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1877 1878 /* (5) compute the local portion of Cmpi */ 1879 /* ------------------------------------------ */ 1880 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 1881 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1882 current_space = free_space; 1883 1884 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1885 for (k=0; k<nrecv; k++) { 1886 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1887 nrows = *buf_ri_k[k]; 1888 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1889 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1890 } 1891 1892 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 1893 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1894 for (i=0; i<pn; i++) { 1895 /* add C_loc into Cmpi */ 1896 nzi = c_loc->i[i+1] - c_loc->i[i]; 1897 Jptr = c_loc->j + c_loc->i[i]; 1898 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1899 1900 /* add received col data into lnk */ 1901 for (k=0; k<nrecv; k++) { /* k-th received message */ 1902 if (i == *nextrow[k]) { /* i-th row */ 1903 nzi = *(nextci[k]+1) - *nextci[k]; 1904 Jptr = buf_rj[k] + *nextci[k]; 1905 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1906 nextrow[k]++; nextci[k]++; 1907 } 1908 } 1909 nzi = lnk[0]; 1910 1911 /* copy data into free space, then initialize lnk */ 1912 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1913 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 1914 } 1915 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1916 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1917 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 1918 1919 /* local sizes and preallocation */ 1920 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1921 if (P->cmap->bs > 0) { 1922 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr); 1923 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr); 1924 } 1925 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1926 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1927 1928 /* members in merge */ 1929 ierr = PetscFree(id_r);CHKERRQ(ierr); 1930 ierr = PetscFree(len_r);CHKERRQ(ierr); 1931 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 1932 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 1933 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 1934 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 1935 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 1936 1937 /* attach the supporting struct to Cmpi for reuse */ 1938 c = (Mat_MPIAIJ*)Cmpi->data; 1939 c->ap = ptap; 1940 ptap->duplicate = Cmpi->ops->duplicate; 1941 ptap->destroy = Cmpi->ops->destroy; 1942 ptap->view = Cmpi->ops->view; 1943 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 1944 1945 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1946 Cmpi->assembled = PETSC_FALSE; 1947 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1948 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1949 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1950 *C = Cmpi; 1951 PetscFunctionReturn(0); 1952 } 1953 1954 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 1955 { 1956 PetscErrorCode ierr; 1957 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1958 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 1959 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 1960 Mat_APMPI *ptap = c->ap; 1961 Mat AP_loc,C_loc,C_oth; 1962 PetscInt i,rstart,rend,cm,ncols,row; 1963 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 1964 PetscScalar *apa; 1965 const PetscInt *cols; 1966 const PetscScalar *vals; 1967 1968 PetscFunctionBegin; 1969 if (!ptap->AP_loc) { 1970 MPI_Comm comm; 1971 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1972 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1973 } 1974 1975 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1976 /* 1) get R = Pd^T,Ro = Po^T */ 1977 if (ptap->reuse == MAT_REUSE_MATRIX) { 1978 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1979 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1980 } 1981 1982 /* 2) get AP_loc */ 1983 AP_loc = ptap->AP_loc; 1984 ap = (Mat_SeqAIJ*)AP_loc->data; 1985 1986 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 1987 /*-----------------------------------------------------*/ 1988 if (ptap->reuse == MAT_REUSE_MATRIX) { 1989 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 1990 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1991 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1992 } 1993 1994 /* 2-2) compute numeric A_loc*P - dominating part */ 1995 /* ---------------------------------------------- */ 1996 /* get data from symbolic products */ 1997 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1998 if (ptap->P_oth) { 1999 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 2000 } 2001 apa = ptap->apa; 2002 api = ap->i; 2003 apj = ap->j; 2004 for (i=0; i<am; i++) { 2005 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 2006 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 2007 apnz = api[i+1] - api[i]; 2008 for (j=0; j<apnz; j++) { 2009 col = apj[j+api[i]]; 2010 ap->a[j+ap->i[i]] = apa[col]; 2011 apa[col] = 0.0; 2012 } 2013 } 2014 2015 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 2016 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 2017 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 2018 C_loc = ptap->C_loc; 2019 C_oth = ptap->C_oth; 2020 2021 /* add C_loc and Co to to C */ 2022 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 2023 2024 /* C_loc -> C */ 2025 cm = C_loc->rmap->N; 2026 c_seq = (Mat_SeqAIJ*)C_loc->data; 2027 cols = c_seq->j; 2028 vals = c_seq->a; 2029 2030 2031 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 2032 /* when there are no off-processor parts. */ 2033 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 2034 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 2035 /* a table, and other, more complex stuff has to be done. */ 2036 if (C->assembled) { 2037 C->was_assembled = PETSC_TRUE; 2038 C->assembled = PETSC_FALSE; 2039 } 2040 if (C->was_assembled) { 2041 for (i=0; i<cm; i++) { 2042 ncols = c_seq->i[i+1] - c_seq->i[i]; 2043 row = rstart + i; 2044 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 2045 cols += ncols; vals += ncols; 2046 } 2047 } else { 2048 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 2049 } 2050 2051 /* Co -> C, off-processor part */ 2052 cm = C_oth->rmap->N; 2053 c_seq = (Mat_SeqAIJ*)C_oth->data; 2054 cols = c_seq->j; 2055 vals = c_seq->a; 2056 for (i=0; i<cm; i++) { 2057 ncols = c_seq->i[i+1] - c_seq->i[i]; 2058 row = p->garray[i]; 2059 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 2060 cols += ncols; vals += ncols; 2061 } 2062 2063 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2064 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2065 2066 ptap->reuse = MAT_REUSE_MATRIX; 2067 2068 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 2069 if (ptap->freestruct) { 2070 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 2071 } 2072 PetscFunctionReturn(0); 2073 } 2074