1 2 /* 3 Defines projective product routines where A is a MPIAIJ matrix 4 C = P^T * A * P 5 */ 6 7 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 8 #include <../src/mat/utils/freespace.h> 9 #include <../src/mat/impls/aij/mpi/mpiaij.h> 10 #include <petscbt.h> 11 #include <petsctime.h> 12 #include <petsc/private/hashmapiv.h> 13 #include <petsc/private/hashseti.h> 14 #include <petscsf.h> 15 16 17 PetscErrorCode MatView_MPIAIJ_PtAP(Mat A,PetscViewer viewer) 18 { 19 PetscErrorCode ierr; 20 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 21 Mat_APMPI *ptap=a->ap; 22 PetscBool iascii; 23 PetscViewerFormat format; 24 25 PetscFunctionBegin; 26 if (!ptap) { 27 /* hack: MatDuplicate() sets oldmat->ops->view to newmat which is a base mat class with null ptpa! */ 28 A->ops->view = MatView_MPIAIJ; 29 ierr = (A->ops->view)(A,viewer);CHKERRQ(ierr); 30 PetscFunctionReturn(0); 31 } 32 33 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 34 if (iascii) { 35 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 36 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 37 if (ptap->algType == 0) { 38 ierr = PetscViewerASCIIPrintf(viewer,"using scalable MatPtAP() implementation\n");CHKERRQ(ierr); 39 } else if (ptap->algType == 1) { 40 ierr = PetscViewerASCIIPrintf(viewer,"using nonscalable MatPtAP() implementation\n");CHKERRQ(ierr); 41 } else if (ptap->algType == 2) { 42 ierr = PetscViewerASCIIPrintf(viewer,"using allatonce MatPtAP() implementation\n");CHKERRQ(ierr); 43 } else if (ptap->algType == 3) { 44 ierr = PetscViewerASCIIPrintf(viewer,"using merged allatonce MatPtAP() implementation\n");CHKERRQ(ierr); 45 } 46 } 47 } 48 ierr = (ptap->view)(A,viewer);CHKERRQ(ierr); 49 PetscFunctionReturn(0); 50 } 51 52 PetscErrorCode MatFreeIntermediateDataStructures_MPIAIJ_AP(Mat A) 53 { 54 PetscErrorCode ierr; 55 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 56 Mat_APMPI *ptap=a->ap; 57 Mat_Merge_SeqsToMPI *merge; 58 59 PetscFunctionBegin; 60 if (!ptap) PetscFunctionReturn(0); 61 62 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 63 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 64 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 65 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 66 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */ 67 ierr = MatDestroy(&ptap->Rd);CHKERRQ(ierr); 68 ierr = MatDestroy(&ptap->Ro);CHKERRQ(ierr); 69 if (ptap->AP_loc) { /* used by alg_rap */ 70 Mat_SeqAIJ *ap = (Mat_SeqAIJ*)(ptap->AP_loc)->data; 71 ierr = PetscFree(ap->i);CHKERRQ(ierr); 72 ierr = PetscFree2(ap->j,ap->a);CHKERRQ(ierr); 73 ierr = MatDestroy(&ptap->AP_loc);CHKERRQ(ierr); 74 } else { /* used by alg_ptap */ 75 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 76 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 77 } 78 ierr = MatDestroy(&ptap->C_loc);CHKERRQ(ierr); 79 ierr = MatDestroy(&ptap->C_oth);CHKERRQ(ierr); 80 if (ptap->apa) {ierr = PetscFree(ptap->apa);CHKERRQ(ierr);} 81 82 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 83 84 merge=ptap->merge; 85 if (merge) { /* used by alg_ptap */ 86 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 87 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 88 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 89 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 90 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 91 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 92 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 93 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 94 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 95 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 96 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 97 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 98 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 99 ierr = PetscFree(ptap->merge);CHKERRQ(ierr); 100 } 101 ierr = ISLocalToGlobalMappingDestroy(&ptap->ltog);CHKERRQ(ierr); 102 103 ierr = PetscSFDestroy(&ptap->sf);CHKERRQ(ierr); 104 ierr = PetscFree(ptap->c_othi);CHKERRQ(ierr); 105 ierr = PetscFree(ptap->c_rmti);CHKERRQ(ierr); 106 PetscFunctionReturn(0); 107 } 108 109 PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A) 110 { 111 PetscErrorCode ierr; 112 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 113 Mat_APMPI *ptap=a->ap; 114 115 PetscFunctionBegin; 116 ierr = (*A->ops->freeintermediatedatastructures)(A);CHKERRQ(ierr); 117 ierr = (*ptap->destroy)(A);CHKERRQ(ierr); /* MatDestroy_MPIAIJ(A) */ 118 ierr = PetscFree(ptap);CHKERRQ(ierr); 119 PetscFunctionReturn(0); 120 } 121 122 PETSC_INTERN PetscErrorCode MatPtAP_MPIAIJ_MPIAIJ(Mat A,Mat P,MatReuse scall,PetscReal fill,Mat *C) 123 { 124 PetscErrorCode ierr; 125 PetscBool flg; 126 MPI_Comm comm; 127 #if !defined(PETSC_HAVE_HYPRE) 128 const char *algTypes[4] = {"scalable","nonscalable","allatonce","allatonce_merged"}; 129 PetscInt nalg=4; 130 #else 131 const char *algTypes[5] = {"scalable","nonscalable","allatonce","allatonce_merged","hypre"}; 132 PetscInt nalg=5; 133 #endif 134 PetscInt pN=P->cmap->N,alg=1; /* set default algorithm */ 135 136 PetscFunctionBegin; 137 /* check if matrix local sizes are compatible */ 138 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 139 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Arow (%D, %D) != Prow (%D,%D)",A->rmap->rstart,A->rmap->rend,P->rmap->rstart,P->rmap->rend); 140 if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend) SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Acol (%D, %D) != Prow (%D,%D)",A->cmap->rstart,A->cmap->rend,P->rmap->rstart,P->rmap->rend); 141 142 if (scall == MAT_INITIAL_MATRIX) { 143 /* pick an algorithm */ 144 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 145 ierr = PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 146 ierr = PetscOptionsEnd();CHKERRQ(ierr); 147 148 if (!flg && pN > 100000) { /* may switch to scalable algorithm as default */ 149 MatInfo Ainfo,Pinfo; 150 PetscInt nz_local; 151 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 152 153 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 154 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 155 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); 156 157 if (pN > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 158 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 159 160 if (alg_scalable) { 161 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 162 } 163 } 164 165 switch (alg) { 166 case 1: 167 /* do R=P^T locally, then C=R*A*P -- nonscalable */ 168 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 169 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);CHKERRQ(ierr); 170 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 171 break; 172 case 2: 173 /* compute C=P^T*A*P allatonce */ 174 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 175 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(A,P,fill,C);CHKERRQ(ierr); 176 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 177 break; 178 case 3: 179 /* compute C=P^T*A*P allatonce */ 180 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 181 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(A,P,fill,C);CHKERRQ(ierr); 182 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 183 break; 184 #if defined(PETSC_HAVE_HYPRE) 185 case 4: 186 /* Use boomerAMGBuildCoarseOperator */ 187 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 188 ierr = MatPtAPSymbolic_AIJ_AIJ_wHYPRE(A,P,fill,C);CHKERRQ(ierr); 189 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 190 break; 191 #endif 192 default: 193 /* do R=P^T locally, then C=R*A*P */ 194 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 195 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(A,P,fill,C);CHKERRQ(ierr); 196 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 197 break; 198 } 199 200 if (alg == 0 || alg == 1 || alg == 2 || alg == 3) { 201 Mat_MPIAIJ *c = (Mat_MPIAIJ*)(*C)->data; 202 Mat_APMPI *ap = c->ap; 203 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)(*C)),((PetscObject)(*C))->prefix,"MatFreeIntermediateDataStructures","Mat");CHKERRQ(ierr); 204 ap->freestruct = PETSC_FALSE; 205 ierr = PetscOptionsBool("-mat_freeintermediatedatastructures","Free intermediate data structures", "MatFreeIntermediateDataStructures",ap->freestruct,&ap->freestruct, NULL);CHKERRQ(ierr); 206 ierr = PetscOptionsEnd();CHKERRQ(ierr); 207 } 208 } 209 210 ierr = PetscLogEventBegin(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 211 ierr = (*(*C)->ops->ptapnumeric)(A,P,*C);CHKERRQ(ierr); 212 ierr = PetscLogEventEnd(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 213 PetscFunctionReturn(0); 214 } 215 216 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,Mat C) 217 { 218 PetscErrorCode ierr; 219 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 220 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 221 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 222 Mat_APMPI *ptap = c->ap; 223 Mat AP_loc,C_loc,C_oth; 224 PetscInt i,rstart,rend,cm,ncols,row,*api,*apj,am = A->rmap->n,apnz,nout; 225 PetscScalar *apa; 226 const PetscInt *cols; 227 const PetscScalar *vals; 228 229 PetscFunctionBegin; 230 if (!ptap->AP_loc) { 231 MPI_Comm comm; 232 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 233 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 234 } 235 236 ierr = MatZeroEntries(C);CHKERRQ(ierr); 237 238 /* 1) get R = Pd^T,Ro = Po^T */ 239 if (ptap->reuse == MAT_REUSE_MATRIX) { 240 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 241 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 242 } 243 244 /* 2) get AP_loc */ 245 AP_loc = ptap->AP_loc; 246 ap = (Mat_SeqAIJ*)AP_loc->data; 247 248 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 249 /*-----------------------------------------------------*/ 250 if (ptap->reuse == MAT_REUSE_MATRIX) { 251 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 252 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 253 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 254 } 255 256 /* 2-2) compute numeric A_loc*P - dominating part */ 257 /* ---------------------------------------------- */ 258 /* get data from symbolic products */ 259 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 260 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 261 262 api = ap->i; 263 apj = ap->j; 264 ierr = ISLocalToGlobalMappingApply(ptap->ltog,api[AP_loc->rmap->n],apj,apj);CHKERRQ(ierr); 265 for (i=0; i<am; i++) { 266 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 267 apnz = api[i+1] - api[i]; 268 apa = ap->a + api[i]; 269 ierr = PetscMemzero(apa,sizeof(PetscScalar)*apnz);CHKERRQ(ierr); 270 AProw_scalable(i,ad,ao,p_loc,p_oth,api,apj,apa); 271 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 272 } 273 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,api[AP_loc->rmap->n],apj,&nout,apj);CHKERRQ(ierr); 274 if (api[AP_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",api[AP_loc->rmap->n],nout); 275 276 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 277 /* Always use scalable version since we are in the MPI scalable version */ 278 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 279 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 280 281 C_loc = ptap->C_loc; 282 C_oth = ptap->C_oth; 283 284 /* add C_loc and Co to to C */ 285 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 286 287 /* C_loc -> C */ 288 cm = C_loc->rmap->N; 289 c_seq = (Mat_SeqAIJ*)C_loc->data; 290 cols = c_seq->j; 291 vals = c_seq->a; 292 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_loc->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 293 294 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 295 /* when there are no off-processor parts. */ 296 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 297 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 298 /* a table, and other, more complex stuff has to be done. */ 299 if (C->assembled) { 300 C->was_assembled = PETSC_TRUE; 301 C->assembled = PETSC_FALSE; 302 } 303 if (C->was_assembled) { 304 for (i=0; i<cm; i++) { 305 ncols = c_seq->i[i+1] - c_seq->i[i]; 306 row = rstart + i; 307 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 308 cols += ncols; vals += ncols; 309 } 310 } else { 311 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 312 } 313 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_loc->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 314 if (c_seq->i[C_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_seq->i[C_loc->rmap->n],nout); 315 316 /* Co -> C, off-processor part */ 317 cm = C_oth->rmap->N; 318 c_seq = (Mat_SeqAIJ*)C_oth->data; 319 cols = c_seq->j; 320 vals = c_seq->a; 321 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_oth->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 322 for (i=0; i<cm; i++) { 323 ncols = c_seq->i[i+1] - c_seq->i[i]; 324 row = p->garray[i]; 325 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 326 cols += ncols; vals += ncols; 327 } 328 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 329 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 330 331 ptap->reuse = MAT_REUSE_MATRIX; 332 333 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_oth->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 334 if (c_seq->i[C_oth->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_seq->i[C_loc->rmap->n],nout); 335 336 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 337 if (ptap->freestruct) { 338 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 339 } 340 PetscFunctionReturn(0); 341 } 342 343 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat *C) 344 { 345 PetscErrorCode ierr; 346 Mat_APMPI *ptap; 347 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 348 MPI_Comm comm; 349 PetscMPIInt size,rank; 350 Mat Cmpi,P_loc,P_oth; 351 PetscFreeSpaceList free_space=NULL,current_space=NULL; 352 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 353 PetscInt *lnk,i,k,pnz,row,nsend; 354 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 355 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 356 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 357 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 358 MPI_Request *swaits,*rwaits; 359 MPI_Status *sstatus,rstatus; 360 PetscLayout rowmap; 361 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 362 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 363 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,Crmax,*aj,*ai,*pi,nout; 364 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 365 PetscScalar *apv; 366 PetscTable ta; 367 MatType mtype; 368 const char *prefix; 369 #if defined(PETSC_USE_INFO) 370 PetscReal apfill; 371 #endif 372 373 PetscFunctionBegin; 374 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 375 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 376 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 377 378 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 379 380 /* create symbolic parallel matrix Cmpi */ 381 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 382 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 383 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 384 385 /* create struct Mat_APMPI and attached it to C later */ 386 ierr = PetscNew(&ptap);CHKERRQ(ierr); 387 ptap->reuse = MAT_INITIAL_MATRIX; 388 ptap->algType = 0; 389 390 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 391 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&P_oth);CHKERRQ(ierr); 392 /* get P_loc by taking all local rows of P */ 393 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&P_loc);CHKERRQ(ierr); 394 395 ptap->P_loc = P_loc; 396 ptap->P_oth = P_oth; 397 398 /* (0) compute Rd = Pd^T, Ro = Po^T */ 399 /* --------------------------------- */ 400 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 401 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 402 403 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 404 /* ----------------------------------------------------------------- */ 405 p_loc = (Mat_SeqAIJ*)P_loc->data; 406 if (P_oth) p_oth = (Mat_SeqAIJ*)P_oth->data; 407 408 /* create and initialize a linked list */ 409 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 410 MatRowMergeMax_SeqAIJ(p_loc,P_loc->rmap->N,ta); 411 MatRowMergeMax_SeqAIJ(p_oth,P_oth->rmap->N,ta); 412 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 413 414 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 415 416 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 417 if (ao) { 418 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 419 } else { 420 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 421 } 422 current_space = free_space; 423 nspacedouble = 0; 424 425 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 426 api[0] = 0; 427 for (i=0; i<am; i++) { 428 /* diagonal portion: Ad[i,:]*P */ 429 ai = ad->i; pi = p_loc->i; 430 nzi = ai[i+1] - ai[i]; 431 aj = ad->j + ai[i]; 432 for (j=0; j<nzi; j++) { 433 row = aj[j]; 434 pnz = pi[row+1] - pi[row]; 435 Jptr = p_loc->j + pi[row]; 436 /* add non-zero cols of P into the sorted linked list lnk */ 437 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 438 } 439 /* off-diagonal portion: Ao[i,:]*P */ 440 if (ao) { 441 ai = ao->i; pi = p_oth->i; 442 nzi = ai[i+1] - ai[i]; 443 aj = ao->j + ai[i]; 444 for (j=0; j<nzi; j++) { 445 row = aj[j]; 446 pnz = pi[row+1] - pi[row]; 447 Jptr = p_oth->j + pi[row]; 448 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 449 } 450 } 451 apnz = lnk[0]; 452 api[i+1] = api[i] + apnz; 453 454 /* if free space is not available, double the total space in the list */ 455 if (current_space->local_remaining<apnz) { 456 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 457 nspacedouble++; 458 } 459 460 /* Copy data into free space, then initialize lnk */ 461 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 462 463 current_space->array += apnz; 464 current_space->local_used += apnz; 465 current_space->local_remaining -= apnz; 466 } 467 /* Allocate space for apj and apv, initialize apj, and */ 468 /* destroy list of free space and other temporary array(s) */ 469 ierr = PetscCalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 470 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 471 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 472 473 /* Create AP_loc for reuse */ 474 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 475 ierr = MatSeqAIJCompactOutExtraColumns_SeqAIJ(ptap->AP_loc, &ptap->ltog);CHKERRQ(ierr); 476 477 #if defined(PETSC_USE_INFO) 478 if (ao) { 479 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 480 } else { 481 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 482 } 483 ptap->AP_loc->info.mallocs = nspacedouble; 484 ptap->AP_loc->info.fill_ratio_given = fill; 485 ptap->AP_loc->info.fill_ratio_needed = apfill; 486 487 if (api[am]) { 488 ierr = PetscInfo3(ptap->AP_loc,"Scalable algorithm, AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);CHKERRQ(ierr); 489 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 490 } else { 491 ierr = PetscInfo(ptap->AP_loc,"Scalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 492 } 493 #endif 494 495 /* (2-1) compute symbolic Co = Ro*AP_loc */ 496 /* ------------------------------------ */ 497 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 498 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 499 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 500 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 501 502 /* (3) send coj of C_oth to other processors */ 503 /* ------------------------------------------ */ 504 /* determine row ownership */ 505 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 506 rowmap->n = pn; 507 rowmap->bs = 1; 508 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 509 owners = rowmap->range; 510 511 /* determine the number of messages to send, their lengths */ 512 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 513 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 514 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 515 516 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 517 coi = c_oth->i; coj = c_oth->j; 518 con = ptap->C_oth->rmap->n; 519 proc = 0; 520 ierr = ISLocalToGlobalMappingApply(ptap->ltog,coi[con],coj,coj);CHKERRQ(ierr); 521 for (i=0; i<con; i++) { 522 while (prmap[i] >= owners[proc+1]) proc++; 523 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 524 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 525 } 526 527 len = 0; /* max length of buf_si[], see (4) */ 528 owners_co[0] = 0; 529 nsend = 0; 530 for (proc=0; proc<size; proc++) { 531 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 532 if (len_s[proc]) { 533 nsend++; 534 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 535 len += len_si[proc]; 536 } 537 } 538 539 /* determine the number and length of messages to receive for coi and coj */ 540 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 541 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 542 543 /* post the Irecv and Isend of coj */ 544 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 545 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 546 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 547 for (proc=0, k=0; proc<size; proc++) { 548 if (!len_s[proc]) continue; 549 i = owners_co[proc]; 550 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 551 k++; 552 } 553 554 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 555 /* ---------------------------------------- */ 556 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 557 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 558 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 559 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 560 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,c_loc->j);CHKERRQ(ierr); 561 562 /* receives coj are complete */ 563 for (i=0; i<nrecv; i++) { 564 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 565 } 566 ierr = PetscFree(rwaits);CHKERRQ(ierr); 567 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 568 569 /* add received column indices into ta to update Crmax */ 570 for (k=0; k<nrecv; k++) {/* k-th received message */ 571 Jptr = buf_rj[k]; 572 for (j=0; j<len_r[k]; j++) { 573 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 574 } 575 } 576 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 577 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 578 579 /* (4) send and recv coi */ 580 /*-----------------------*/ 581 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 582 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 583 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 584 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 585 for (proc=0,k=0; proc<size; proc++) { 586 if (!len_s[proc]) continue; 587 /* form outgoing message for i-structure: 588 buf_si[0]: nrows to be sent 589 [1:nrows]: row index (global) 590 [nrows+1:2*nrows+1]: i-structure index 591 */ 592 /*-------------------------------------------*/ 593 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 594 buf_si_i = buf_si + nrows+1; 595 buf_si[0] = nrows; 596 buf_si_i[0] = 0; 597 nrows = 0; 598 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 599 nzi = coi[i+1] - coi[i]; 600 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 601 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 602 nrows++; 603 } 604 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 605 k++; 606 buf_si += len_si[proc]; 607 } 608 for (i=0; i<nrecv; i++) { 609 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 610 } 611 ierr = PetscFree(rwaits);CHKERRQ(ierr); 612 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 613 614 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 615 ierr = PetscFree(len_ri);CHKERRQ(ierr); 616 ierr = PetscFree(swaits);CHKERRQ(ierr); 617 ierr = PetscFree(buf_s);CHKERRQ(ierr); 618 619 /* (5) compute the local portion of Cmpi */ 620 /* ------------------------------------------ */ 621 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 622 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 623 current_space = free_space; 624 625 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 626 for (k=0; k<nrecv; k++) { 627 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 628 nrows = *buf_ri_k[k]; 629 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 630 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 631 } 632 633 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 634 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 635 for (i=0; i<pn; i++) { 636 /* add C_loc into Cmpi */ 637 nzi = c_loc->i[i+1] - c_loc->i[i]; 638 Jptr = c_loc->j + c_loc->i[i]; 639 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 640 641 /* add received col data into lnk */ 642 for (k=0; k<nrecv; k++) { /* k-th received message */ 643 if (i == *nextrow[k]) { /* i-th row */ 644 nzi = *(nextci[k]+1) - *nextci[k]; 645 Jptr = buf_rj[k] + *nextci[k]; 646 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 647 nextrow[k]++; nextci[k]++; 648 } 649 } 650 nzi = lnk[0]; 651 652 /* copy data into free space, then initialize lnk */ 653 ierr = PetscLLCondensedClean_Scalable(nzi,current_space->array,lnk);CHKERRQ(ierr); 654 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 655 } 656 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 657 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 658 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 659 660 /* local sizes and preallocation */ 661 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 662 if (P->cmap->bs > 0) { 663 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr); 664 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr); 665 } 666 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 667 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 668 669 /* members in merge */ 670 ierr = PetscFree(id_r);CHKERRQ(ierr); 671 ierr = PetscFree(len_r);CHKERRQ(ierr); 672 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 673 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 674 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 675 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 676 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 677 678 /* attach the supporting struct to Cmpi for reuse */ 679 c = (Mat_MPIAIJ*)Cmpi->data; 680 c->ap = ptap; 681 ptap->duplicate = Cmpi->ops->duplicate; 682 ptap->destroy = Cmpi->ops->destroy; 683 ptap->view = Cmpi->ops->view; 684 685 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 686 Cmpi->assembled = PETSC_FALSE; 687 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable; 688 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 689 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 690 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 691 *C = Cmpi; 692 693 nout = 0; 694 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_oth->i[ptap->C_oth->rmap->n],c_oth->j,&nout,c_oth->j);CHKERRQ(ierr); 695 if (c_oth->i[ptap->C_oth->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_oth->i[ptap->C_oth->rmap->n],nout); 696 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,&nout,c_loc->j);CHKERRQ(ierr); 697 if (c_loc->i[ptap->C_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_loc->i[ptap->C_loc->rmap->n],nout); 698 699 PetscFunctionReturn(0); 700 } 701 702 PETSC_STATIC_INLINE PetscErrorCode MatPtAPSymbolicComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,PetscInt i,PetscHSetI dht,PetscHSetI oht) 703 { 704 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data; 705 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_oth=(Mat_SeqAIJ*)P_oth->data,*pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data; 706 PetscInt *ai,nzi,j,*aj,row,col,*pi,*pj,pnz,nzpi,*p_othcols,k; 707 PetscInt pcstart,pcend,column; 708 PetscErrorCode ierr; 709 710 PetscFunctionBegin; 711 712 pcstart = P->cmap->rstart; 713 pcend = P->cmap->rend; 714 /* diagonal portion: Ad[i,:]*P */ 715 ai = ad->i; 716 nzi = ai[i+1] - ai[i]; 717 aj = ad->j + ai[i]; 718 for (j=0; j<nzi; j++) { 719 row = aj[j]; 720 nzpi = pd->i[row+1] - pd->i[row]; 721 pj = pd->j + pd->i[row]; 722 for (k=0; k<nzpi; k++) { 723 ierr = PetscHSetIAdd(dht,pj[k]+pcstart);CHKERRQ(ierr); 724 } 725 } 726 for (j=0; j<nzi; j++) { 727 row = aj[j]; 728 nzpi = po->i[row+1] - po->i[row]; 729 pj = po->j + po->i[row]; 730 for (k=0; k<nzpi; k++) { 731 ierr = PetscHSetIAdd(oht,p->garray[pj[k]]);CHKERRQ(ierr); 732 } 733 } 734 735 /* off diagonal part: Ao[i, :]*P_oth */ 736 if (ao) { 737 ai = ao->i; 738 pi = p_oth->i; 739 nzi = ai[i+1] - ai[i]; 740 aj = ao->j + ai[i]; 741 for (j=0; j<nzi; j++) { 742 row = aj[j]; 743 pnz = pi[row+1] - pi[row]; 744 p_othcols = p_oth->j + pi[row]; 745 for (col=0; col<pnz; col++) { 746 column = p_othcols[col]; 747 if (column>=pcstart && column<pcend) { 748 ierr = PetscHSetIAdd(dht,column);CHKERRQ(ierr); 749 } else { 750 ierr = PetscHSetIAdd(oht,column);CHKERRQ(ierr); 751 } 752 } 753 } 754 } /* end if (ao) */ 755 PetscFunctionReturn(0); 756 } 757 758 PETSC_STATIC_INLINE PetscErrorCode MatPtAPNumericComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,PetscInt i,PetscHMapIV hmap) 759 { 760 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data; 761 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_oth=(Mat_SeqAIJ*)P_oth->data,*pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data; 762 PetscInt *ai,nzi,j,*aj,row,col,*pi,pnz,*p_othcols,pcstart,*pj,k,nzpi; 763 PetscScalar ra,*aa,*pa; 764 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 } 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 } 794 795 796 /* off diagonal part: Ao[i, :]*P_oth */ 797 if (ao) { 798 ai = ao->i; 799 pi = p_oth->i; 800 nzi = ai[i+1] - ai[i]; 801 aj = ao->j + ai[i]; 802 aa = ao->a + ai[i]; 803 for (j=0; j<nzi; j++) { 804 row = aj[j]; 805 ra = aa[j]; 806 pnz = pi[row+1] - pi[row]; 807 p_othcols = p_oth->j + pi[row]; 808 pa = p_oth->a + pi[row]; 809 for (col=0; col<pnz; col++) { 810 ierr = PetscHMapIVAddValue(hmap,p_othcols[col],ra*pa[col]);CHKERRQ(ierr); 811 } 812 } 813 } /* end if (ao) */ 814 PetscFunctionReturn(0); 815 } 816 817 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,Mat C) 818 { 819 PetscErrorCode ierr; 820 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 821 Mat_SeqAIJ *cd,*co,*po,*pd; 822 Mat_APMPI *ptap = c->ap; 823 PetscHMapIV hmap; 824 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; 825 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa; 826 MPI_Comm comm; 827 828 PetscFunctionBegin; 829 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 830 if (!ptap->P_oth) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 831 832 ierr = MatZeroEntries(C);CHKERRQ(ierr); 833 834 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 835 /*-----------------------------------------------------*/ 836 if (ptap->reuse == MAT_REUSE_MATRIX) { 837 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 838 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 839 } 840 841 po = (Mat_SeqAIJ*) p->B->data; 842 pd = (Mat_SeqAIJ*) p->A->data; 843 844 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 845 846 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr); 847 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 848 cmaxr = 0; 849 for (i=0; i<pon; i++) { 850 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]); 851 } 852 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr); 853 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 854 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 855 for (i=0; i<am && pon; i++) { 856 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 857 nzi = po->i[i+1] - po->i[i]; 858 if (!nzi) continue; 859 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 860 voff = 0; 861 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 862 if (!voff) continue; 863 /*ierr = PetscMemzero(c_rmtc,sizeof(PetscInt)*pon);CHKERRQ(ierr);*/ 864 865 /* Form C(ii, :) */ 866 poj = po->j + po->i[i]; 867 poa = po->a + po->i[i]; 868 for (j=0; j<nzi; j++) { 869 c_rmtjj = c_rmtj + ptap->c_rmti[poj[j]]; 870 c_rmtaa = c_rmta + ptap->c_rmti[poj[j]]; 871 for (jj=0; jj<voff; jj++) { 872 apvaluestmp[jj] = apvalues[jj]*poa[j]; 873 /*If the row is empty */ 874 if (!c_rmtc[poj[j]]) { 875 c_rmtjj[jj] = apindices[jj]; 876 c_rmtaa[jj] = apvaluestmp[jj]; 877 c_rmtc[poj[j]]++; 878 } else { 879 ierr = PetscFindInt(apindices[jj],c_rmtc[poj[j]],c_rmtjj,&loc);CHKERRQ(ierr); 880 if (loc>=0){ /* hit */ 881 c_rmtaa[loc] += apvaluestmp[jj]; 882 } else { /* new element */ 883 loc = -(loc+1); 884 /* Move data backward */ 885 for (kk=c_rmtc[poj[j]]; kk>loc; kk--) { 886 c_rmtjj[kk] = c_rmtjj[kk-1]; 887 c_rmtaa[kk] = c_rmtaa[kk-1]; 888 }/* End kk */ 889 c_rmtjj[loc] = apindices[jj]; 890 c_rmtaa[loc] = apvaluestmp[jj]; 891 c_rmtc[poj[j]]++; 892 } 893 } 894 } /* End jj */ 895 } /* End j */ 896 } /* End i */ 897 898 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr); 899 900 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 901 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr); 902 903 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 904 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 905 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 906 cd = (Mat_SeqAIJ*)(c->A)->data; 907 co = (Mat_SeqAIJ*)(c->B)->data; 908 909 cmaxr = 0; 910 for (i=0; i<pn; i++) { 911 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i])); 912 } 913 ierr = PetscCalloc5(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pn,&dcc,pn,&occ);CHKERRQ(ierr); 914 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 915 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 916 for (i=0; i<am && pn; i++) { 917 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 918 nzi = pd->i[i+1] - pd->i[i]; 919 if (!nzi) continue; 920 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 921 voff = 0; 922 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 923 if (!voff) continue; 924 /* Form C(ii, :) */ 925 pdj = pd->j + pd->i[i]; 926 pda = pd->a + pd->i[i]; 927 for (j=0; j<nzi; j++) { 928 row = pcstart + pdj[j]; 929 for (jj=0; jj<voff; jj++) { 930 apvaluestmp[jj] = apvalues[jj]*pda[j]; 931 } 932 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr); 933 } 934 } 935 936 ierr = MatGetOwnershipRangeColumn(C,&ccstart,&ccend);CHKERRQ(ierr); 937 ierr = PetscFree5(apindices,apvalues,apvaluestmp,dcc,occ);CHKERRQ(ierr); 938 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr); 939 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPI_SUM);CHKERRQ(ierr); 940 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 941 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr); 942 943 /* Add contributions from remote */ 944 for (i = 0; i < pn; i++) { 945 row = i + pcstart; 946 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); 947 } 948 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr); 949 950 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 951 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 952 953 ptap->reuse = MAT_REUSE_MATRIX; 954 955 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 956 if (ptap->freestruct) { 957 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 958 } 959 PetscFunctionReturn(0); 960 } 961 962 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,Mat C) 963 { 964 PetscErrorCode ierr; 965 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 966 Mat_SeqAIJ *cd,*co,*po,*pd; 967 Mat_APMPI *ptap = c->ap; 968 PetscHMapIV hmap; 969 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; 970 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa; 971 MPI_Comm comm; 972 973 PetscFunctionBegin; 974 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 975 if (!ptap->P_oth) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 976 977 ierr = MatZeroEntries(C);CHKERRQ(ierr); 978 979 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 980 /*-----------------------------------------------------*/ 981 if (ptap->reuse == MAT_REUSE_MATRIX) { 982 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 983 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 984 } 985 986 po = (Mat_SeqAIJ*) p->B->data; 987 pd = (Mat_SeqAIJ*) p->A->data; 988 989 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 990 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 991 992 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr); 993 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 994 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 995 cmaxr = 0; 996 for (i=0; i<pon; i++) { 997 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]); 998 } 999 cd = (Mat_SeqAIJ*)(c->A)->data; 1000 co = (Mat_SeqAIJ*)(c->B)->data; 1001 for (i=0; i<pn; i++) { 1002 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i])); 1003 } 1004 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr); 1005 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 1006 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 1007 for (i=0; i<am && (pon || pn); i++) { 1008 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 1009 nzi = po->i[i+1] - po->i[i]; 1010 dnzi = pd->i[i+1] - pd->i[i]; 1011 if (!nzi && !dnzi) continue; 1012 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,i,hmap);CHKERRQ(ierr); 1013 voff = 0; 1014 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 1015 if (!voff) continue; 1016 1017 /* Form remote C(ii, :) */ 1018 poj = po->j + po->i[i]; 1019 poa = po->a + po->i[i]; 1020 for (j=0; j<nzi; j++) { 1021 c_rmtjj = c_rmtj + ptap->c_rmti[poj[j]]; 1022 c_rmtaa = c_rmta + ptap->c_rmti[poj[j]]; 1023 for (jj=0; jj<voff; jj++) { 1024 apvaluestmp[jj] = apvalues[jj]*poa[j]; 1025 /*If the row is empty */ 1026 if (!c_rmtc[poj[j]]) { 1027 c_rmtjj[jj] = apindices[jj]; 1028 c_rmtaa[jj] = apvaluestmp[jj]; 1029 c_rmtc[poj[j]]++; 1030 } else { 1031 ierr = PetscFindInt(apindices[jj],c_rmtc[poj[j]],c_rmtjj,&loc);CHKERRQ(ierr); 1032 if (loc>=0){ /* hit */ 1033 c_rmtaa[loc] += apvaluestmp[jj]; 1034 } else { /* new element */ 1035 loc = -(loc+1); 1036 /* Move data backward */ 1037 for (kk=c_rmtc[poj[j]]; kk>loc; kk--) { 1038 c_rmtjj[kk] = c_rmtjj[kk-1]; 1039 c_rmtaa[kk] = c_rmtaa[kk-1]; 1040 }/* End kk */ 1041 c_rmtjj[loc] = apindices[jj]; 1042 c_rmtaa[loc] = apvaluestmp[jj]; 1043 c_rmtc[poj[j]]++; 1044 } 1045 } 1046 } /* End jj */ 1047 } /* End j */ 1048 1049 /* Form local C(ii, :) */ 1050 pdj = pd->j + pd->i[i]; 1051 pda = pd->a + pd->i[i]; 1052 for (j=0; j<dnzi; j++) { 1053 row = pcstart + pdj[j]; 1054 for (jj=0; jj<voff; jj++) { 1055 apvaluestmp[jj] = apvalues[jj]*pda[j]; 1056 }/* End kk */ 1057 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr); 1058 }/* End j */ 1059 } /* End i */ 1060 1061 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr); 1062 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr); 1063 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr); 1064 1065 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1066 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 1067 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPI_SUM);CHKERRQ(ierr); 1068 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 1069 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr); 1070 1071 /* Add contributions from remote */ 1072 for (i = 0; i < pn; i++) { 1073 row = i + pcstart; 1074 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); 1075 } 1076 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr); 1077 1078 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1079 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1080 1081 ptap->reuse = MAT_REUSE_MATRIX; 1082 1083 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1084 if (ptap->freestruct) { 1085 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1086 } 1087 PetscFunctionReturn(0); 1088 } 1089 1090 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,PetscReal fill,Mat *C) 1091 { 1092 Mat_APMPI *ptap; 1093 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1094 MPI_Comm comm; 1095 Mat Cmpi; 1096 Mat_SeqAIJ *pd,*po; 1097 MatType mtype; 1098 PetscSF sf; 1099 PetscSFNode *iremote; 1100 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves; 1101 const PetscInt *rootdegrees; 1102 PetscHSetI ht,oht,*hta,*hto; 1103 PetscInt pn,pon,*c_rmtc,i,j,nzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets; 1104 PetscInt owner,lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj; 1105 PetscInt nalg=2,alg=0; 1106 PetscBool flg; 1107 const char *algTypes[2] = {"overlapping","merged"}; 1108 PetscErrorCode ierr; 1109 1110 PetscFunctionBegin; 1111 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1112 1113 /* Create symbolic parallel matrix Cmpi */ 1114 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1115 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1116 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1117 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1118 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1119 1120 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1121 ptap->reuse = MAT_INITIAL_MATRIX; 1122 ptap->algType = 2; 1123 1124 /* Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1125 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1126 1127 po = (Mat_SeqAIJ*)p->B->data; 1128 pd = (Mat_SeqAIJ*)p->A->data; 1129 1130 /* This equals to the number of offdiag columns in P */ 1131 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1132 /* offsets */ 1133 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr); 1134 /* The number of columns we will send to remote ranks */ 1135 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr); 1136 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr); 1137 for (i=0; i<pon; i++) { 1138 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1139 } 1140 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1141 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr); 1142 /* Create hash table to merge all columns for C(i, :) */ 1143 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1144 1145 ptap->c_rmti[0] = 0; 1146 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */ 1147 for (i=0; i<am && pon; i++) { 1148 /* Form one row of AP */ 1149 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1150 /* If the off diag is empty, we should not do any calculation */ 1151 nzi = po->i[i+1] - po->i[i]; 1152 if (!nzi) continue; 1153 1154 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,ht);CHKERRQ(ierr); 1155 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1156 /* If AP is empty, just continue */ 1157 if (!htsize) continue; 1158 /* Form C(ii, :) */ 1159 poj = po->j + po->i[i]; 1160 for (j=0; j<nzi; j++) { 1161 ierr = PetscHSetIUpdate(hta[poj[j]],ht);CHKERRQ(ierr); 1162 } 1163 } 1164 1165 for (i=0; i<pon; i++) { 1166 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1167 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize; 1168 c_rmtc[i] = htsize; 1169 } 1170 1171 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr); 1172 1173 for (i=0; i<pon; i++) { 1174 off = 0; 1175 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr); 1176 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1177 } 1178 ierr = PetscFree(hta);CHKERRQ(ierr); 1179 1180 ierr = PetscCalloc1(pon,&iremote);CHKERRQ(ierr); 1181 for (i=0; i<pon; i++) { 1182 owner = 0; lidx = 0; 1183 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1184 iremote[i].index = lidx; 1185 iremote[i].rank = owner; 1186 } 1187 1188 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 1189 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1190 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */ 1191 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr); 1192 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1193 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1194 /* How many neighbors have contributions to my rows? */ 1195 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr); 1196 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr); 1197 rootspacesize = 0; 1198 for (i = 0; i < pn; i++) { 1199 rootspacesize += rootdegrees[i]; 1200 } 1201 ierr = PetscCalloc1(rootspacesize,&rootspace);CHKERRQ(ierr); 1202 ierr = PetscCalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr); 1203 /* Get information from leaves 1204 * Number of columns other people contribute to my rows 1205 * */ 1206 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1207 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1208 ierr = PetscFree(c_rmtc);CHKERRQ(ierr); 1209 ierr = PetscCalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr); 1210 /* The number of columns is received for each row */ 1211 ptap->c_othi[0] = 0; 1212 rootspacesize = 0; 1213 rootspaceoffsets[0] = 0; 1214 for (i = 0; i < pn; i++) { 1215 rcvncols = 0; 1216 for (j = 0; j<rootdegrees[i]; j++) { 1217 rcvncols += rootspace[rootspacesize]; 1218 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize]; 1219 rootspacesize++; 1220 } 1221 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols; 1222 } 1223 ierr = PetscFree(rootspace);CHKERRQ(ierr); 1224 1225 ierr = PetscCalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr); 1226 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1227 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1228 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1229 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr); 1230 1231 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr); 1232 nleaves = 0; 1233 for (i = 0; i<pon; i++) { 1234 owner = 0; lidx = 0; 1235 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1236 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i]; 1237 for (j=0; j<sendncols; j++) { 1238 iremote[nleaves].rank = owner; 1239 iremote[nleaves++].index = c_rmtoffsets[i] + j; 1240 } 1241 } 1242 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr); 1243 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr); 1244 1245 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr); 1246 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1247 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr); 1248 /* One to one map */ 1249 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1250 1251 ierr = PetscCalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr); 1252 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr); 1253 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1254 ierr = PetscMalloc2(pn,&hta,pn,&hto);CHKERRQ(ierr); 1255 for (i=0; i<pn; i++) { 1256 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1257 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr); 1258 } 1259 /* Work on local part */ 1260 /* 4) Pass 1: Estimate memory for C_loc */ 1261 for (i=0; i<am && pn; i++) { 1262 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1263 ierr = PetscHSetIClear(oht);CHKERRQ(ierr); 1264 nzi = pd->i[i+1] - pd->i[i]; 1265 if (!nzi) continue; 1266 1267 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,oht);CHKERRQ(ierr); 1268 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1269 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr); 1270 if (!(htsize+htosize)) continue; 1271 /* Form C(ii, :) */ 1272 pdj = pd->j + pd->i[i]; 1273 for (j=0; j<nzi; j++) { 1274 ierr = PetscHSetIUpdate(hta[pdj[j]],ht);CHKERRQ(ierr); 1275 ierr = PetscHSetIUpdate(hto[pdj[j]],oht);CHKERRQ(ierr); 1276 } 1277 } 1278 1279 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1280 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr); 1281 1282 /* Get remote data */ 1283 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1284 ierr = PetscFree(c_rmtj);CHKERRQ(ierr); 1285 1286 for (i = 0; i < pn; i++) { 1287 nzi = ptap->c_othi[i+1] - ptap->c_othi[i]; 1288 rdj = c_othj + ptap->c_othi[i]; 1289 for (j = 0; j < nzi; j++) { 1290 col = rdj[j]; 1291 /* diag part */ 1292 if (col>=pcstart && col<pcend) { 1293 ierr = PetscHSetIAdd(hta[i],col);CHKERRQ(ierr); 1294 } else { /* off diag */ 1295 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr); 1296 } 1297 } 1298 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1299 dnz[i] = htsize; 1300 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1301 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr); 1302 onz[i] = htsize; 1303 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr); 1304 } 1305 1306 ierr = PetscFree2(hta,hto);CHKERRQ(ierr); 1307 ierr = PetscFree(c_othj);CHKERRQ(ierr); 1308 1309 /* local sizes and preallocation */ 1310 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1311 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 1312 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1313 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 1314 1315 /* attach the supporting struct to Cmpi for reuse */ 1316 c = (Mat_MPIAIJ*)Cmpi->data; 1317 c->ap = ptap; 1318 ptap->duplicate = Cmpi->ops->duplicate; 1319 ptap->destroy = Cmpi->ops->destroy; 1320 ptap->view = Cmpi->ops->view; 1321 1322 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1323 Cmpi->assembled = PETSC_FALSE; 1324 /* pick an algorithm */ 1325 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 1326 alg = 0; 1327 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 1328 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1329 switch (alg) { 1330 case 0: 1331 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce; 1332 break; 1333 case 1: 1334 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged; 1335 break; 1336 default: 1337 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n"); 1338 } 1339 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1340 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1341 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1342 *C = Cmpi; 1343 PetscFunctionReturn(0); 1344 } 1345 1346 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,PetscReal fill,Mat *C) 1347 { 1348 Mat_APMPI *ptap; 1349 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1350 MPI_Comm comm; 1351 Mat Cmpi; 1352 Mat_SeqAIJ *pd,*po; 1353 MatType mtype; 1354 PetscSF sf; 1355 PetscSFNode *iremote; 1356 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves; 1357 const PetscInt *rootdegrees; 1358 PetscHSetI ht,oht,*hta,*hto,*htd; 1359 PetscInt pn,pon,*c_rmtc,i,j,nzi,dnzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets; 1360 PetscInt owner,lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj; 1361 PetscInt nalg=2,alg=0; 1362 PetscBool flg; 1363 const char *algTypes[2] = {"merged","overlapping"}; 1364 PetscErrorCode ierr; 1365 1366 PetscFunctionBegin; 1367 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1368 1369 /* Create symbolic parallel matrix Cmpi */ 1370 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1371 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1372 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1373 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1374 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1375 1376 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1377 ptap->reuse = MAT_INITIAL_MATRIX; 1378 ptap->algType = 3; 1379 1380 /* 0) Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1381 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1382 1383 po = (Mat_SeqAIJ*)p->B->data; 1384 pd = (Mat_SeqAIJ*)p->A->data; 1385 1386 /* This equals to the number of offdiag columns in P */ 1387 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1388 /* offsets */ 1389 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr); 1390 /* The number of columns we will send to remote ranks */ 1391 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr); 1392 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr); 1393 for (i=0; i<pon; i++) { 1394 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1395 } 1396 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1397 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr); 1398 /* Create hash table to merge all columns for C(i, :) */ 1399 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1400 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr); 1401 ierr = PetscMalloc2(pn,&htd,pn,&hto);CHKERRQ(ierr); 1402 for (i=0; i<pn; i++) { 1403 ierr = PetscHSetICreate(&htd[i]);CHKERRQ(ierr); 1404 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr); 1405 } 1406 ptap->c_rmti[0] = 0; 1407 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */ 1408 for (i=0; i<am && (pon || pn); i++) { 1409 /* Form one row of AP */ 1410 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1411 ierr = PetscHSetIClear(oht);CHKERRQ(ierr); 1412 /* If the off diag is empty, we should not do any calculation */ 1413 nzi = po->i[i+1] - po->i[i]; 1414 dnzi = pd->i[i+1] - pd->i[i]; 1415 if (!nzi && !dnzi) continue; 1416 1417 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,i,ht,oht);CHKERRQ(ierr); 1418 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1419 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr); 1420 /* If AP is empty, just continue */ 1421 if (!(htsize+htosize)) continue; 1422 1423 /* Form remote C(ii, :) */ 1424 poj = po->j + po->i[i]; 1425 for (j=0; j<nzi; j++) { 1426 ierr = PetscHSetIUpdate(hta[poj[j]],ht);CHKERRQ(ierr); 1427 ierr = PetscHSetIUpdate(hta[poj[j]],oht);CHKERRQ(ierr); 1428 } 1429 1430 /* Form local C(ii, :) */ 1431 pdj = pd->j + pd->i[i]; 1432 for (j=0; j<dnzi; j++) { 1433 ierr = PetscHSetIUpdate(htd[pdj[j]],ht);CHKERRQ(ierr); 1434 ierr = PetscHSetIUpdate(hto[pdj[j]],oht);CHKERRQ(ierr); 1435 } 1436 } 1437 1438 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1439 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr); 1440 1441 for (i=0; i<pon; i++) { 1442 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1443 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize; 1444 c_rmtc[i] = htsize; 1445 } 1446 1447 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr); 1448 1449 for (i=0; i<pon; i++) { 1450 off = 0; 1451 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr); 1452 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1453 } 1454 ierr = PetscFree(hta);CHKERRQ(ierr); 1455 1456 ierr = PetscCalloc1(pon,&iremote);CHKERRQ(ierr); 1457 for (i=0; i<pon; i++) { 1458 owner = 0; lidx = 0; 1459 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1460 iremote[i].index = lidx; 1461 iremote[i].rank = owner; 1462 } 1463 1464 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 1465 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1466 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */ 1467 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr); 1468 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1469 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1470 /* How many neighbors have contributions to my rows? */ 1471 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr); 1472 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr); 1473 rootspacesize = 0; 1474 for (i = 0; i < pn; i++) { 1475 rootspacesize += rootdegrees[i]; 1476 } 1477 ierr = PetscCalloc1(rootspacesize,&rootspace);CHKERRQ(ierr); 1478 ierr = PetscCalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr); 1479 /* Get information from leaves 1480 * Number of columns other people contribute to my rows 1481 * */ 1482 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1483 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1484 ierr = PetscFree(c_rmtc);CHKERRQ(ierr); 1485 ierr = PetscCalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr); 1486 /* The number of columns is received for each row */ 1487 ptap->c_othi[0] = 0; 1488 rootspacesize = 0; 1489 rootspaceoffsets[0] = 0; 1490 for (i = 0; i < pn; i++) { 1491 rcvncols = 0; 1492 for (j = 0; j<rootdegrees[i]; j++) { 1493 rcvncols += rootspace[rootspacesize]; 1494 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize]; 1495 rootspacesize++; 1496 } 1497 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols; 1498 } 1499 ierr = PetscFree(rootspace);CHKERRQ(ierr); 1500 1501 ierr = PetscCalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr); 1502 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1503 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1504 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1505 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr); 1506 1507 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr); 1508 nleaves = 0; 1509 for (i = 0; i<pon; i++) { 1510 owner = 0; lidx = 0; 1511 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[i],&owner,&lidx);CHKERRQ(ierr); 1512 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i]; 1513 for (j=0; j<sendncols; j++) { 1514 iremote[nleaves].rank = owner; 1515 iremote[nleaves++].index = c_rmtoffsets[i] + j; 1516 } 1517 } 1518 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr); 1519 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr); 1520 1521 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr); 1522 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1523 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr); 1524 /* One to one map */ 1525 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1526 /* Get remote data */ 1527 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1528 ierr = PetscFree(c_rmtj);CHKERRQ(ierr); 1529 ierr = PetscCalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr); 1530 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1531 1532 for (i = 0; i < pn; i++) { 1533 nzi = ptap->c_othi[i+1] - ptap->c_othi[i]; 1534 rdj = c_othj + ptap->c_othi[i]; 1535 for (j = 0; j < nzi; j++) { 1536 col = rdj[j]; 1537 /* diag part */ 1538 if (col>=pcstart && col<pcend) { 1539 ierr = PetscHSetIAdd(htd[i],col);CHKERRQ(ierr); 1540 } else { /* off diag */ 1541 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr); 1542 } 1543 } 1544 ierr = PetscHSetIGetSize(htd[i],&htsize);CHKERRQ(ierr); 1545 dnz[i] = htsize; 1546 ierr = PetscHSetIDestroy(&htd[i]);CHKERRQ(ierr); 1547 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr); 1548 onz[i] = htsize; 1549 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr); 1550 } 1551 1552 ierr = PetscFree2(htd,hto);CHKERRQ(ierr); 1553 ierr = PetscFree(c_othj);CHKERRQ(ierr); 1554 1555 /* local sizes and preallocation */ 1556 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1557 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 1558 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1559 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 1560 1561 /* attach the supporting struct to Cmpi for reuse */ 1562 c = (Mat_MPIAIJ*)Cmpi->data; 1563 c->ap = ptap; 1564 ptap->duplicate = Cmpi->ops->duplicate; 1565 ptap->destroy = Cmpi->ops->destroy; 1566 ptap->view = Cmpi->ops->view; 1567 1568 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1569 Cmpi->assembled = PETSC_FALSE; 1570 /* pick an algorithm */ 1571 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 1572 alg = 0; 1573 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 1574 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1575 switch (alg) { 1576 case 0: 1577 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged; 1578 break; 1579 case 1: 1580 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce; 1581 break; 1582 default: 1583 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n"); 1584 } 1585 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1586 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1587 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1588 *C = Cmpi; 1589 PetscFunctionReturn(0); 1590 } 1591 1592 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 1593 { 1594 PetscErrorCode ierr; 1595 Mat_APMPI *ptap; 1596 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 1597 MPI_Comm comm; 1598 PetscMPIInt size,rank; 1599 Mat Cmpi; 1600 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1601 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 1602 PetscInt *lnk,i,k,pnz,row,nsend; 1603 PetscBT lnkbt; 1604 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 1605 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1606 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 1607 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1608 MPI_Request *swaits,*rwaits; 1609 MPI_Status *sstatus,rstatus; 1610 PetscLayout rowmap; 1611 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1612 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1613 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 1614 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 1615 PetscScalar *apv; 1616 PetscTable ta; 1617 MatType mtype; 1618 const char *prefix; 1619 #if defined(PETSC_USE_INFO) 1620 PetscReal apfill; 1621 #endif 1622 1623 PetscFunctionBegin; 1624 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1625 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1626 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1627 1628 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 1629 1630 /* create symbolic parallel matrix Cmpi */ 1631 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1632 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1633 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1634 1635 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 1636 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 1637 1638 /* create struct Mat_APMPI and attached it to C later */ 1639 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1640 ptap->reuse = MAT_INITIAL_MATRIX; 1641 ptap->algType = 1; 1642 1643 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1644 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1645 /* get P_loc by taking all local rows of P */ 1646 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1647 1648 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1649 /* --------------------------------- */ 1650 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1651 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1652 1653 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 1654 /* ----------------------------------------------------------------- */ 1655 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1656 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1657 1658 /* create and initialize a linked list */ 1659 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 1660 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 1661 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 1662 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 1663 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 1664 1665 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1666 1667 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 1668 if (ao) { 1669 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 1670 } else { 1671 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 1672 } 1673 current_space = free_space; 1674 nspacedouble = 0; 1675 1676 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 1677 api[0] = 0; 1678 for (i=0; i<am; i++) { 1679 /* diagonal portion: Ad[i,:]*P */ 1680 ai = ad->i; pi = p_loc->i; 1681 nzi = ai[i+1] - ai[i]; 1682 aj = ad->j + ai[i]; 1683 for (j=0; j<nzi; j++) { 1684 row = aj[j]; 1685 pnz = pi[row+1] - pi[row]; 1686 Jptr = p_loc->j + pi[row]; 1687 /* add non-zero cols of P into the sorted linked list lnk */ 1688 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1689 } 1690 /* off-diagonal portion: Ao[i,:]*P */ 1691 if (ao) { 1692 ai = ao->i; pi = p_oth->i; 1693 nzi = ai[i+1] - ai[i]; 1694 aj = ao->j + ai[i]; 1695 for (j=0; j<nzi; j++) { 1696 row = aj[j]; 1697 pnz = pi[row+1] - pi[row]; 1698 Jptr = p_oth->j + pi[row]; 1699 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1700 } 1701 } 1702 apnz = lnk[0]; 1703 api[i+1] = api[i] + apnz; 1704 if (ap_rmax < apnz) ap_rmax = apnz; 1705 1706 /* if free space is not available, double the total space in the list */ 1707 if (current_space->local_remaining<apnz) { 1708 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1709 nspacedouble++; 1710 } 1711 1712 /* Copy data into free space, then initialize lnk */ 1713 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1714 1715 current_space->array += apnz; 1716 current_space->local_used += apnz; 1717 current_space->local_remaining -= apnz; 1718 } 1719 /* Allocate space for apj and apv, initialize apj, and */ 1720 /* destroy list of free space and other temporary array(s) */ 1721 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 1722 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 1723 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1724 1725 /* Create AP_loc for reuse */ 1726 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 1727 1728 #if defined(PETSC_USE_INFO) 1729 if (ao) { 1730 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 1731 } else { 1732 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 1733 } 1734 ptap->AP_loc->info.mallocs = nspacedouble; 1735 ptap->AP_loc->info.fill_ratio_given = fill; 1736 ptap->AP_loc->info.fill_ratio_needed = apfill; 1737 1738 if (api[am]) { 1739 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); 1740 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 1741 } else { 1742 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 1743 } 1744 #endif 1745 1746 /* (2-1) compute symbolic Co = Ro*AP_loc */ 1747 /* ------------------------------------ */ 1748 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1749 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 1750 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 1751 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 1752 1753 /* (3) send coj of C_oth to other processors */ 1754 /* ------------------------------------------ */ 1755 /* determine row ownership */ 1756 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1757 rowmap->n = pn; 1758 rowmap->bs = 1; 1759 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1760 owners = rowmap->range; 1761 1762 /* determine the number of messages to send, their lengths */ 1763 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1764 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1765 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 1766 1767 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1768 coi = c_oth->i; coj = c_oth->j; 1769 con = ptap->C_oth->rmap->n; 1770 proc = 0; 1771 for (i=0; i<con; i++) { 1772 while (prmap[i] >= owners[proc+1]) proc++; 1773 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 1774 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1775 } 1776 1777 len = 0; /* max length of buf_si[], see (4) */ 1778 owners_co[0] = 0; 1779 nsend = 0; 1780 for (proc=0; proc<size; proc++) { 1781 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1782 if (len_s[proc]) { 1783 nsend++; 1784 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1785 len += len_si[proc]; 1786 } 1787 } 1788 1789 /* determine the number and length of messages to receive for coi and coj */ 1790 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1791 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1792 1793 /* post the Irecv and Isend of coj */ 1794 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1795 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1796 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1797 for (proc=0, k=0; proc<size; proc++) { 1798 if (!len_s[proc]) continue; 1799 i = owners_co[proc]; 1800 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1801 k++; 1802 } 1803 1804 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 1805 /* ---------------------------------------- */ 1806 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 1807 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 1808 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 1809 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1810 1811 /* receives coj are complete */ 1812 for (i=0; i<nrecv; i++) { 1813 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1814 } 1815 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1816 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1817 1818 /* add received column indices into ta to update Crmax */ 1819 for (k=0; k<nrecv; k++) {/* k-th received message */ 1820 Jptr = buf_rj[k]; 1821 for (j=0; j<len_r[k]; j++) { 1822 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1823 } 1824 } 1825 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1826 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1827 1828 /* (4) send and recv coi */ 1829 /*-----------------------*/ 1830 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1831 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1832 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1833 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1834 for (proc=0,k=0; proc<size; proc++) { 1835 if (!len_s[proc]) continue; 1836 /* form outgoing message for i-structure: 1837 buf_si[0]: nrows to be sent 1838 [1:nrows]: row index (global) 1839 [nrows+1:2*nrows+1]: i-structure index 1840 */ 1841 /*-------------------------------------------*/ 1842 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1843 buf_si_i = buf_si + nrows+1; 1844 buf_si[0] = nrows; 1845 buf_si_i[0] = 0; 1846 nrows = 0; 1847 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1848 nzi = coi[i+1] - coi[i]; 1849 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1850 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1851 nrows++; 1852 } 1853 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1854 k++; 1855 buf_si += len_si[proc]; 1856 } 1857 for (i=0; i<nrecv; i++) { 1858 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1859 } 1860 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1861 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1862 1863 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1864 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1865 ierr = PetscFree(swaits);CHKERRQ(ierr); 1866 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1867 1868 /* (5) compute the local portion of Cmpi */ 1869 /* ------------------------------------------ */ 1870 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 1871 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1872 current_space = free_space; 1873 1874 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1875 for (k=0; k<nrecv; k++) { 1876 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1877 nrows = *buf_ri_k[k]; 1878 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1879 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1880 } 1881 1882 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 1883 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1884 for (i=0; i<pn; i++) { 1885 /* add C_loc into Cmpi */ 1886 nzi = c_loc->i[i+1] - c_loc->i[i]; 1887 Jptr = c_loc->j + c_loc->i[i]; 1888 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1889 1890 /* add received col data into lnk */ 1891 for (k=0; k<nrecv; k++) { /* k-th received message */ 1892 if (i == *nextrow[k]) { /* i-th row */ 1893 nzi = *(nextci[k]+1) - *nextci[k]; 1894 Jptr = buf_rj[k] + *nextci[k]; 1895 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1896 nextrow[k]++; nextci[k]++; 1897 } 1898 } 1899 nzi = lnk[0]; 1900 1901 /* copy data into free space, then initialize lnk */ 1902 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1903 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 1904 } 1905 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1906 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1907 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 1908 1909 /* local sizes and preallocation */ 1910 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1911 if (P->cmap->bs > 0) { 1912 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr); 1913 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr); 1914 } 1915 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1916 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1917 1918 /* members in merge */ 1919 ierr = PetscFree(id_r);CHKERRQ(ierr); 1920 ierr = PetscFree(len_r);CHKERRQ(ierr); 1921 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 1922 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 1923 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 1924 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 1925 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 1926 1927 /* attach the supporting struct to Cmpi for reuse */ 1928 c = (Mat_MPIAIJ*)Cmpi->data; 1929 c->ap = ptap; 1930 ptap->duplicate = Cmpi->ops->duplicate; 1931 ptap->destroy = Cmpi->ops->destroy; 1932 ptap->view = Cmpi->ops->view; 1933 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 1934 1935 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1936 Cmpi->assembled = PETSC_FALSE; 1937 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1938 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1939 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1940 *C = Cmpi; 1941 PetscFunctionReturn(0); 1942 } 1943 1944 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 1945 { 1946 PetscErrorCode ierr; 1947 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1948 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 1949 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 1950 Mat_APMPI *ptap = c->ap; 1951 Mat AP_loc,C_loc,C_oth; 1952 PetscInt i,rstart,rend,cm,ncols,row; 1953 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 1954 PetscScalar *apa; 1955 const PetscInt *cols; 1956 const PetscScalar *vals; 1957 1958 PetscFunctionBegin; 1959 if (!ptap->AP_loc) { 1960 MPI_Comm comm; 1961 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1962 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1963 } 1964 1965 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1966 /* 1) get R = Pd^T,Ro = Po^T */ 1967 if (ptap->reuse == MAT_REUSE_MATRIX) { 1968 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1969 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1970 } 1971 1972 /* 2) get AP_loc */ 1973 AP_loc = ptap->AP_loc; 1974 ap = (Mat_SeqAIJ*)AP_loc->data; 1975 1976 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 1977 /*-----------------------------------------------------*/ 1978 if (ptap->reuse == MAT_REUSE_MATRIX) { 1979 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 1980 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1981 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1982 } 1983 1984 /* 2-2) compute numeric A_loc*P - dominating part */ 1985 /* ---------------------------------------------- */ 1986 /* get data from symbolic products */ 1987 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1988 if (ptap->P_oth) { 1989 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1990 } 1991 apa = ptap->apa; 1992 api = ap->i; 1993 apj = ap->j; 1994 for (i=0; i<am; i++) { 1995 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 1996 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 1997 apnz = api[i+1] - api[i]; 1998 for (j=0; j<apnz; j++) { 1999 col = apj[j+api[i]]; 2000 ap->a[j+ap->i[i]] = apa[col]; 2001 apa[col] = 0.0; 2002 } 2003 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 2004 } 2005 2006 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 2007 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 2008 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 2009 C_loc = ptap->C_loc; 2010 C_oth = ptap->C_oth; 2011 2012 /* add C_loc and Co to to C */ 2013 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 2014 2015 /* C_loc -> C */ 2016 cm = C_loc->rmap->N; 2017 c_seq = (Mat_SeqAIJ*)C_loc->data; 2018 cols = c_seq->j; 2019 vals = c_seq->a; 2020 2021 2022 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 2023 /* when there are no off-processor parts. */ 2024 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 2025 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 2026 /* a table, and other, more complex stuff has to be done. */ 2027 if (C->assembled) { 2028 C->was_assembled = PETSC_TRUE; 2029 C->assembled = PETSC_FALSE; 2030 } 2031 if (C->was_assembled) { 2032 for (i=0; i<cm; i++) { 2033 ncols = c_seq->i[i+1] - c_seq->i[i]; 2034 row = rstart + i; 2035 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 2036 cols += ncols; vals += ncols; 2037 } 2038 } else { 2039 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 2040 } 2041 2042 /* Co -> C, off-processor part */ 2043 cm = C_oth->rmap->N; 2044 c_seq = (Mat_SeqAIJ*)C_oth->data; 2045 cols = c_seq->j; 2046 vals = c_seq->a; 2047 for (i=0; i<cm; i++) { 2048 ncols = c_seq->i[i+1] - c_seq->i[i]; 2049 row = p->garray[i]; 2050 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 2051 cols += ncols; vals += ncols; 2052 } 2053 2054 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2055 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2056 2057 ptap->reuse = MAT_REUSE_MATRIX; 2058 2059 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 2060 if (ptap->freestruct) { 2061 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 2062 } 2063 PetscFunctionReturn(0); 2064 } 2065