1 2 /* 3 Defines projective product routines where A is a MPIAIJ matrix 4 C = P^T * A * P 5 */ 6 7 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 8 #include <../src/mat/utils/freespace.h> 9 #include <../src/mat/impls/aij/mpi/mpiaij.h> 10 #include <petscbt.h> 11 #include <petsctime.h> 12 #include <petsc/private/hashmapiv.h> 13 #include <petsc/private/hashseti.h> 14 #include <petscsf.h> 15 16 17 PetscErrorCode MatView_MPIAIJ_PtAP(Mat A,PetscViewer viewer) 18 { 19 PetscErrorCode ierr; 20 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 21 Mat_APMPI *ptap=a->ap; 22 PetscBool iascii; 23 PetscViewerFormat format; 24 25 PetscFunctionBegin; 26 if (!ptap) { 27 /* hack: MatDuplicate() sets oldmat->ops->view to newmat which is a base mat class with null ptpa! */ 28 A->ops->view = MatView_MPIAIJ; 29 ierr = (A->ops->view)(A,viewer);CHKERRQ(ierr); 30 PetscFunctionReturn(0); 31 } 32 33 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 34 if (iascii) { 35 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 36 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 37 if (ptap->algType == 0) { 38 ierr = PetscViewerASCIIPrintf(viewer,"using scalable MatPtAP() implementation\n");CHKERRQ(ierr); 39 } else if (ptap->algType == 1) { 40 ierr = PetscViewerASCIIPrintf(viewer,"using nonscalable MatPtAP() implementation\n");CHKERRQ(ierr); 41 } else if (ptap->algType == 2) { 42 ierr = PetscViewerASCIIPrintf(viewer,"using allatonce MatPtAP() implementation\n");CHKERRQ(ierr); 43 } else if (ptap->algType == 3) { 44 ierr = PetscViewerASCIIPrintf(viewer,"using merged allatonce MatPtAP() implementation\n");CHKERRQ(ierr); 45 } 46 } 47 } 48 ierr = (ptap->view)(A,viewer);CHKERRQ(ierr); 49 PetscFunctionReturn(0); 50 } 51 52 PetscErrorCode MatFreeIntermediateDataStructures_MPIAIJ_AP(Mat A) 53 { 54 PetscErrorCode ierr; 55 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 56 Mat_APMPI *ptap=a->ap; 57 Mat_Merge_SeqsToMPI *merge; 58 59 PetscFunctionBegin; 60 if (!ptap) PetscFunctionReturn(0); 61 62 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 63 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 64 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 65 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 66 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */ 67 ierr = MatDestroy(&ptap->Rd);CHKERRQ(ierr); 68 ierr = MatDestroy(&ptap->Ro);CHKERRQ(ierr); 69 if (ptap->AP_loc) { /* used by alg_rap */ 70 Mat_SeqAIJ *ap = (Mat_SeqAIJ*)(ptap->AP_loc)->data; 71 ierr = PetscFree(ap->i);CHKERRQ(ierr); 72 ierr = PetscFree2(ap->j,ap->a);CHKERRQ(ierr); 73 ierr = MatDestroy(&ptap->AP_loc);CHKERRQ(ierr); 74 } else { /* used by alg_ptap */ 75 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 76 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 77 } 78 ierr = MatDestroy(&ptap->C_loc);CHKERRQ(ierr); 79 ierr = MatDestroy(&ptap->C_oth);CHKERRQ(ierr); 80 if (ptap->apa) {ierr = PetscFree(ptap->apa);CHKERRQ(ierr);} 81 82 ierr = MatDestroy(&ptap->Pt);CHKERRQ(ierr); 83 84 merge=ptap->merge; 85 if (merge) { /* used by alg_ptap */ 86 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 87 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 88 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 89 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 90 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 91 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 92 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 93 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 94 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 95 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 96 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 97 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 98 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 99 ierr = PetscFree(ptap->merge);CHKERRQ(ierr); 100 } 101 ierr = ISLocalToGlobalMappingDestroy(&ptap->ltog);CHKERRQ(ierr); 102 103 ierr = PetscSFDestroy(&ptap->sf);CHKERRQ(ierr); 104 ierr = PetscFree(ptap->c_othi);CHKERRQ(ierr); 105 ierr = PetscFree(ptap->c_rmti);CHKERRQ(ierr); 106 PetscFunctionReturn(0); 107 } 108 109 PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A) 110 { 111 PetscErrorCode ierr; 112 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 113 Mat_APMPI *ptap=a->ap; 114 115 PetscFunctionBegin; 116 ierr = (*A->ops->freeintermediatedatastructures)(A);CHKERRQ(ierr); 117 ierr = (*ptap->destroy)(A);CHKERRQ(ierr); /* MatDestroy_MPIAIJ(A) */ 118 ierr = PetscFree(ptap);CHKERRQ(ierr); 119 PetscFunctionReturn(0); 120 } 121 122 PETSC_INTERN PetscErrorCode MatPtAP_MPIAIJ_MPIAIJ(Mat A,Mat P,MatReuse scall,PetscReal fill,Mat *C) 123 { 124 PetscErrorCode ierr; 125 PetscBool flg; 126 MPI_Comm comm; 127 #if !defined(PETSC_HAVE_HYPRE) 128 const char *algTypes[4] = {"scalable","nonscalable","allatonce","allatonce_merged"}; 129 PetscInt nalg=4; 130 #else 131 const char *algTypes[5] = {"scalable","nonscalable","allatonce","allatonce_merged","hypre"}; 132 PetscInt nalg=5; 133 #endif 134 PetscInt pN=P->cmap->N,alg=1; /* set default algorithm */ 135 136 PetscFunctionBegin; 137 /* check if matrix local sizes are compatible */ 138 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 139 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Arow (%D, %D) != Prow (%D,%D)",A->rmap->rstart,A->rmap->rend,P->rmap->rstart,P->rmap->rend); 140 if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend) SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Acol (%D, %D) != Prow (%D,%D)",A->cmap->rstart,A->cmap->rend,P->rmap->rstart,P->rmap->rend); 141 142 if (scall == MAT_INITIAL_MATRIX) { 143 /* pick an algorithm */ 144 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 145 ierr = PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 146 ierr = PetscOptionsEnd();CHKERRQ(ierr); 147 148 if (!flg && pN > 100000) { /* may switch to scalable algorithm as default */ 149 MatInfo Ainfo,Pinfo; 150 PetscInt nz_local; 151 PetscBool alg_scalable_loc=PETSC_FALSE,alg_scalable; 152 153 ierr = MatGetInfo(A,MAT_LOCAL,&Ainfo);CHKERRQ(ierr); 154 ierr = MatGetInfo(P,MAT_LOCAL,&Pinfo);CHKERRQ(ierr); 155 nz_local = (PetscInt)(Ainfo.nz_allocated + Pinfo.nz_allocated); 156 157 if (pN > fill*nz_local) alg_scalable_loc = PETSC_TRUE; 158 ierr = MPIU_Allreduce(&alg_scalable_loc,&alg_scalable,1,MPIU_BOOL,MPI_LOR,comm);CHKERRQ(ierr); 159 160 if (alg_scalable) { 161 alg = 0; /* scalable algorithm would 50% slower than nonscalable algorithm */ 162 } 163 } 164 165 switch (alg) { 166 case 1: 167 /* do R=P^T locally, then C=R*A*P -- nonscalable */ 168 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 169 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);CHKERRQ(ierr); 170 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 171 break; 172 case 2: 173 /* compute C=P^T*A*P allatonce */ 174 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 175 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(A,P,fill,C);CHKERRQ(ierr); 176 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 177 break; 178 case 3: 179 /* compute C=P^T*A*P allatonce */ 180 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 181 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(A,P,fill,C);CHKERRQ(ierr); 182 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 183 break; 184 #if defined(PETSC_HAVE_HYPRE) 185 case 4: 186 /* Use boomerAMGBuildCoarseOperator */ 187 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 188 ierr = MatPtAPSymbolic_AIJ_AIJ_wHYPRE(A,P,fill,C);CHKERRQ(ierr); 189 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 190 break; 191 #endif 192 default: 193 /* do R=P^T locally, then C=R*A*P */ 194 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 195 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(A,P,fill,C);CHKERRQ(ierr); 196 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 197 break; 198 } 199 200 if (alg == 0 || alg == 1 || alg == 2 || alg == 3) { 201 Mat_MPIAIJ *c = (Mat_MPIAIJ*)(*C)->data; 202 Mat_APMPI *ap = c->ap; 203 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)(*C)),((PetscObject)(*C))->prefix,"MatFreeIntermediateDataStructures","Mat");CHKERRQ(ierr); 204 ap->freestruct = PETSC_FALSE; 205 ierr = PetscOptionsBool("-mat_freeintermediatedatastructures","Free intermediate data structures", "MatFreeIntermediateDataStructures",ap->freestruct,&ap->freestruct, NULL);CHKERRQ(ierr); 206 ierr = PetscOptionsEnd();CHKERRQ(ierr); 207 } 208 } 209 210 ierr = PetscLogEventBegin(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 211 ierr = (*(*C)->ops->ptapnumeric)(A,P,*C);CHKERRQ(ierr); 212 ierr = PetscLogEventEnd(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 213 PetscFunctionReturn(0); 214 } 215 216 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,Mat C) 217 { 218 PetscErrorCode ierr; 219 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 220 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 221 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 222 Mat_APMPI *ptap = c->ap; 223 Mat AP_loc,C_loc,C_oth; 224 PetscInt i,rstart,rend,cm,ncols,row,*api,*apj,am = A->rmap->n,apnz,nout; 225 PetscScalar *apa; 226 const PetscInt *cols; 227 const PetscScalar *vals; 228 229 PetscFunctionBegin; 230 if (!ptap->AP_loc) { 231 MPI_Comm comm; 232 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 233 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 234 } 235 236 ierr = MatZeroEntries(C);CHKERRQ(ierr); 237 238 /* 1) get R = Pd^T,Ro = Po^T */ 239 if (ptap->reuse == MAT_REUSE_MATRIX) { 240 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 241 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 242 } 243 244 /* 2) get AP_loc */ 245 AP_loc = ptap->AP_loc; 246 ap = (Mat_SeqAIJ*)AP_loc->data; 247 248 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 249 /*-----------------------------------------------------*/ 250 if (ptap->reuse == MAT_REUSE_MATRIX) { 251 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 252 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 253 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 254 } 255 256 /* 2-2) compute numeric A_loc*P - dominating part */ 257 /* ---------------------------------------------- */ 258 /* get data from symbolic products */ 259 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 260 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 261 262 api = ap->i; 263 apj = ap->j; 264 ierr = ISLocalToGlobalMappingApply(ptap->ltog,api[AP_loc->rmap->n],apj,apj);CHKERRQ(ierr); 265 for (i=0; i<am; i++) { 266 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 267 apnz = api[i+1] - api[i]; 268 apa = ap->a + api[i]; 269 ierr = PetscArrayzero(apa,apnz);CHKERRQ(ierr); 270 AProw_scalable(i,ad,ao,p_loc,p_oth,api,apj,apa); 271 } 272 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,api[AP_loc->rmap->n],apj,&nout,apj);CHKERRQ(ierr); 273 if (api[AP_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",api[AP_loc->rmap->n],nout); 274 275 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 276 /* Always use scalable version since we are in the MPI scalable version */ 277 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 278 ierr = MatMatMultNumeric_SeqAIJ_SeqAIJ_Scalable(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 279 280 C_loc = ptap->C_loc; 281 C_oth = ptap->C_oth; 282 283 /* add C_loc and Co to to C */ 284 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 285 286 /* C_loc -> C */ 287 cm = C_loc->rmap->N; 288 c_seq = (Mat_SeqAIJ*)C_loc->data; 289 cols = c_seq->j; 290 vals = c_seq->a; 291 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_loc->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 292 293 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 294 /* when there are no off-processor parts. */ 295 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 296 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 297 /* a table, and other, more complex stuff has to be done. */ 298 if (C->assembled) { 299 C->was_assembled = PETSC_TRUE; 300 C->assembled = PETSC_FALSE; 301 } 302 if (C->was_assembled) { 303 for (i=0; i<cm; i++) { 304 ncols = c_seq->i[i+1] - c_seq->i[i]; 305 row = rstart + i; 306 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 307 cols += ncols; vals += ncols; 308 } 309 } else { 310 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 311 } 312 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_loc->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 313 if (c_seq->i[C_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_seq->i[C_loc->rmap->n],nout); 314 315 /* Co -> C, off-processor part */ 316 cm = C_oth->rmap->N; 317 c_seq = (Mat_SeqAIJ*)C_oth->data; 318 cols = c_seq->j; 319 vals = c_seq->a; 320 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_seq->i[C_oth->rmap->n],c_seq->j,c_seq->j);CHKERRQ(ierr); 321 for (i=0; i<cm; i++) { 322 ncols = c_seq->i[i+1] - c_seq->i[i]; 323 row = p->garray[i]; 324 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 325 cols += ncols; vals += ncols; 326 } 327 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 328 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 329 330 ptap->reuse = MAT_REUSE_MATRIX; 331 332 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_seq->i[C_oth->rmap->n],c_seq->j,&nout,c_seq->j);CHKERRQ(ierr); 333 if (c_seq->i[C_oth->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_seq->i[C_loc->rmap->n],nout); 334 335 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 336 if (ptap->freestruct) { 337 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 338 } 339 PetscFunctionReturn(0); 340 } 341 342 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_scalable(Mat A,Mat P,PetscReal fill,Mat *C) 343 { 344 PetscErrorCode ierr; 345 Mat_APMPI *ptap; 346 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 347 MPI_Comm comm; 348 PetscMPIInt size,rank; 349 Mat Cmpi,P_loc,P_oth; 350 PetscFreeSpaceList free_space=NULL,current_space=NULL; 351 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 352 PetscInt *lnk,i,k,pnz,row,nsend; 353 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 354 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 355 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 356 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 357 MPI_Request *swaits,*rwaits; 358 MPI_Status *sstatus,rstatus; 359 PetscLayout rowmap; 360 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 361 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 362 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,Crmax,*aj,*ai,*pi,nout; 363 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 364 PetscScalar *apv; 365 PetscTable ta; 366 MatType mtype; 367 const char *prefix; 368 #if defined(PETSC_USE_INFO) 369 PetscReal apfill; 370 #endif 371 372 PetscFunctionBegin; 373 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 374 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 375 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 376 377 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 378 379 /* create symbolic parallel matrix Cmpi */ 380 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 381 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 382 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 383 384 /* create struct Mat_APMPI and attached it to C later */ 385 ierr = PetscNew(&ptap);CHKERRQ(ierr); 386 ptap->reuse = MAT_INITIAL_MATRIX; 387 ptap->algType = 0; 388 389 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 390 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&P_oth);CHKERRQ(ierr); 391 /* get P_loc by taking all local rows of P */ 392 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&P_loc);CHKERRQ(ierr); 393 394 ptap->P_loc = P_loc; 395 ptap->P_oth = P_oth; 396 397 /* (0) compute Rd = Pd^T, Ro = Po^T */ 398 /* --------------------------------- */ 399 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 400 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 401 402 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 403 /* ----------------------------------------------------------------- */ 404 p_loc = (Mat_SeqAIJ*)P_loc->data; 405 if (P_oth) p_oth = (Mat_SeqAIJ*)P_oth->data; 406 407 /* create and initialize a linked list */ 408 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 409 MatRowMergeMax_SeqAIJ(p_loc,P_loc->rmap->N,ta); 410 MatRowMergeMax_SeqAIJ(p_oth,P_oth->rmap->N,ta); 411 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 412 413 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 414 415 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 416 if (ao) { 417 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 418 } else { 419 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 420 } 421 current_space = free_space; 422 nspacedouble = 0; 423 424 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 425 api[0] = 0; 426 for (i=0; i<am; i++) { 427 /* diagonal portion: Ad[i,:]*P */ 428 ai = ad->i; pi = p_loc->i; 429 nzi = ai[i+1] - ai[i]; 430 aj = ad->j + ai[i]; 431 for (j=0; j<nzi; j++) { 432 row = aj[j]; 433 pnz = pi[row+1] - pi[row]; 434 Jptr = p_loc->j + pi[row]; 435 /* add non-zero cols of P into the sorted linked list lnk */ 436 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 437 } 438 /* off-diagonal portion: Ao[i,:]*P */ 439 if (ao) { 440 ai = ao->i; pi = p_oth->i; 441 nzi = ai[i+1] - ai[i]; 442 aj = ao->j + ai[i]; 443 for (j=0; j<nzi; j++) { 444 row = aj[j]; 445 pnz = pi[row+1] - pi[row]; 446 Jptr = p_oth->j + pi[row]; 447 ierr = PetscLLCondensedAddSorted_Scalable(pnz,Jptr,lnk);CHKERRQ(ierr); 448 } 449 } 450 apnz = lnk[0]; 451 api[i+1] = api[i] + apnz; 452 453 /* if free space is not available, double the total space in the list */ 454 if (current_space->local_remaining<apnz) { 455 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 456 nspacedouble++; 457 } 458 459 /* Copy data into free space, then initialize lnk */ 460 ierr = PetscLLCondensedClean_Scalable(apnz,current_space->array,lnk);CHKERRQ(ierr); 461 462 current_space->array += apnz; 463 current_space->local_used += apnz; 464 current_space->local_remaining -= apnz; 465 } 466 /* Allocate space for apj and apv, initialize apj, and */ 467 /* destroy list of free space and other temporary array(s) */ 468 ierr = PetscCalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 469 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 470 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 471 472 /* Create AP_loc for reuse */ 473 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 474 ierr = MatSeqAIJCompactOutExtraColumns_SeqAIJ(ptap->AP_loc, &ptap->ltog);CHKERRQ(ierr); 475 476 #if defined(PETSC_USE_INFO) 477 if (ao) { 478 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 479 } else { 480 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 481 } 482 ptap->AP_loc->info.mallocs = nspacedouble; 483 ptap->AP_loc->info.fill_ratio_given = fill; 484 ptap->AP_loc->info.fill_ratio_needed = apfill; 485 486 if (api[am]) { 487 ierr = PetscInfo3(ptap->AP_loc,"Scalable algorithm, AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);CHKERRQ(ierr); 488 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 489 } else { 490 ierr = PetscInfo(ptap->AP_loc,"Scalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 491 } 492 #endif 493 494 /* (2-1) compute symbolic Co = Ro*AP_loc */ 495 /* ------------------------------------ */ 496 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 497 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 498 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 499 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 500 501 /* (3) send coj of C_oth to other processors */ 502 /* ------------------------------------------ */ 503 /* determine row ownership */ 504 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 505 rowmap->n = pn; 506 rowmap->bs = 1; 507 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 508 owners = rowmap->range; 509 510 /* determine the number of messages to send, their lengths */ 511 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 512 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 513 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr); 514 515 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 516 coi = c_oth->i; coj = c_oth->j; 517 con = ptap->C_oth->rmap->n; 518 proc = 0; 519 ierr = ISLocalToGlobalMappingApply(ptap->ltog,coi[con],coj,coj);CHKERRQ(ierr); 520 for (i=0; i<con; i++) { 521 while (prmap[i] >= owners[proc+1]) proc++; 522 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 523 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 524 } 525 526 len = 0; /* max length of buf_si[], see (4) */ 527 owners_co[0] = 0; 528 nsend = 0; 529 for (proc=0; proc<size; proc++) { 530 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 531 if (len_s[proc]) { 532 nsend++; 533 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 534 len += len_si[proc]; 535 } 536 } 537 538 /* determine the number and length of messages to receive for coi and coj */ 539 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 540 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 541 542 /* post the Irecv and Isend of coj */ 543 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 544 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 545 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 546 for (proc=0, k=0; proc<size; proc++) { 547 if (!len_s[proc]) continue; 548 i = owners_co[proc]; 549 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 550 k++; 551 } 552 553 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 554 /* ---------------------------------------- */ 555 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 556 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 557 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 558 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 559 ierr = ISLocalToGlobalMappingApply(ptap->ltog,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,c_loc->j);CHKERRQ(ierr); 560 561 /* receives coj are complete */ 562 for (i=0; i<nrecv; i++) { 563 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 564 } 565 ierr = PetscFree(rwaits);CHKERRQ(ierr); 566 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 567 568 /* add received column indices into ta to update Crmax */ 569 for (k=0; k<nrecv; k++) {/* k-th received message */ 570 Jptr = buf_rj[k]; 571 for (j=0; j<len_r[k]; j++) { 572 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 573 } 574 } 575 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 576 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 577 578 /* (4) send and recv coi */ 579 /*-----------------------*/ 580 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 581 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 582 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 583 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 584 for (proc=0,k=0; proc<size; proc++) { 585 if (!len_s[proc]) continue; 586 /* form outgoing message for i-structure: 587 buf_si[0]: nrows to be sent 588 [1:nrows]: row index (global) 589 [nrows+1:2*nrows+1]: i-structure index 590 */ 591 /*-------------------------------------------*/ 592 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 593 buf_si_i = buf_si + nrows+1; 594 buf_si[0] = nrows; 595 buf_si_i[0] = 0; 596 nrows = 0; 597 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 598 nzi = coi[i+1] - coi[i]; 599 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 600 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 601 nrows++; 602 } 603 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 604 k++; 605 buf_si += len_si[proc]; 606 } 607 for (i=0; i<nrecv; i++) { 608 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 609 } 610 ierr = PetscFree(rwaits);CHKERRQ(ierr); 611 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 612 613 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 614 ierr = PetscFree(len_ri);CHKERRQ(ierr); 615 ierr = PetscFree(swaits);CHKERRQ(ierr); 616 ierr = PetscFree(buf_s);CHKERRQ(ierr); 617 618 /* (5) compute the local portion of Cmpi */ 619 /* ------------------------------------------ */ 620 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 621 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 622 current_space = free_space; 623 624 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 625 for (k=0; k<nrecv; k++) { 626 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 627 nrows = *buf_ri_k[k]; 628 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 629 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 630 } 631 632 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 633 ierr = PetscLLCondensedCreate_Scalable(Crmax,&lnk);CHKERRQ(ierr); 634 for (i=0; i<pn; i++) { 635 /* add C_loc into Cmpi */ 636 nzi = c_loc->i[i+1] - c_loc->i[i]; 637 Jptr = c_loc->j + c_loc->i[i]; 638 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 639 640 /* add received col data into lnk */ 641 for (k=0; k<nrecv; k++) { /* k-th received message */ 642 if (i == *nextrow[k]) { /* i-th row */ 643 nzi = *(nextci[k]+1) - *nextci[k]; 644 Jptr = buf_rj[k] + *nextci[k]; 645 ierr = PetscLLCondensedAddSorted_Scalable(nzi,Jptr,lnk);CHKERRQ(ierr); 646 nextrow[k]++; nextci[k]++; 647 } 648 } 649 nzi = lnk[0]; 650 651 /* copy data into free space, then initialize lnk */ 652 ierr = PetscLLCondensedClean_Scalable(nzi,current_space->array,lnk);CHKERRQ(ierr); 653 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 654 } 655 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 656 ierr = PetscLLCondensedDestroy_Scalable(lnk);CHKERRQ(ierr); 657 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 658 659 /* local sizes and preallocation */ 660 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 661 if (P->cmap->bs > 0) { 662 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr); 663 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr); 664 } 665 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 666 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 667 668 /* members in merge */ 669 ierr = PetscFree(id_r);CHKERRQ(ierr); 670 ierr = PetscFree(len_r);CHKERRQ(ierr); 671 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 672 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 673 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 674 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 675 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 676 677 /* attach the supporting struct to Cmpi for reuse */ 678 c = (Mat_MPIAIJ*)Cmpi->data; 679 c->ap = ptap; 680 ptap->duplicate = Cmpi->ops->duplicate; 681 ptap->destroy = Cmpi->ops->destroy; 682 ptap->view = Cmpi->ops->view; 683 684 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 685 Cmpi->assembled = PETSC_FALSE; 686 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_scalable; 687 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 688 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 689 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 690 *C = Cmpi; 691 692 nout = 0; 693 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_oth->i[ptap->C_oth->rmap->n],c_oth->j,&nout,c_oth->j);CHKERRQ(ierr); 694 if (c_oth->i[ptap->C_oth->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_oth->i[ptap->C_oth->rmap->n],nout); 695 ierr = ISGlobalToLocalMappingApply(ptap->ltog,IS_GTOLM_DROP,c_loc->i[ptap->C_loc->rmap->n],c_loc->j,&nout,c_loc->j);CHKERRQ(ierr); 696 if (c_loc->i[ptap->C_loc->rmap->n] != nout) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Incorrect mapping %D != %D\n",c_loc->i[ptap->C_loc->rmap->n],nout); 697 698 PetscFunctionReturn(0); 699 } 700 701 PETSC_STATIC_INLINE PetscErrorCode MatPtAPSymbolicComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,const PetscInt *map,PetscInt dof,PetscInt i,PetscHSetI dht,PetscHSetI oht) 702 { 703 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data; 704 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*p_oth=(Mat_SeqAIJ*)P_oth->data,*pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data; 705 PetscInt *ai,nzi,j,*aj,row,col,*pi,*pj,pnz,nzpi,*p_othcols,k; 706 PetscInt pcstart,pcend,column,offset; 707 PetscErrorCode ierr; 708 709 PetscFunctionBegin; 710 pcstart = P->cmap->rstart; 711 pcstart *= dof; 712 pcend = P->cmap->rend; 713 pcend *= dof; 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 offset = row%dof; 721 row /= dof; 722 nzpi = pd->i[row+1] - pd->i[row]; 723 pj = pd->j + pd->i[row]; 724 for (k=0; k<nzpi; k++) { 725 ierr = PetscHSetIAdd(dht,pj[k]*dof+offset+pcstart);CHKERRQ(ierr); 726 } 727 } 728 /* off diag P */ 729 for (j=0; j<nzi; j++) { 730 row = aj[j]; 731 offset = row%dof; 732 row /= dof; 733 nzpi = po->i[row+1] - po->i[row]; 734 pj = po->j + po->i[row]; 735 for (k=0; k<nzpi; k++) { 736 ierr = PetscHSetIAdd(oht,p->garray[pj[k]]*dof+offset);CHKERRQ(ierr); 737 } 738 } 739 740 /* off diagonal part: Ao[i, :]*P_oth */ 741 if (ao) { 742 ai = ao->i; 743 pi = p_oth->i; 744 nzi = ai[i+1] - ai[i]; 745 aj = ao->j + ai[i]; 746 for (j=0; j<nzi; j++) { 747 row = aj[j]; 748 offset = a->garray[row]%dof; 749 row = map[row]; 750 pnz = pi[row+1] - pi[row]; 751 p_othcols = p_oth->j + pi[row]; 752 for (col=0; col<pnz; col++) { 753 column = p_othcols[col] * dof + offset; 754 if (column>=pcstart && column<pcend) { 755 ierr = PetscHSetIAdd(dht,column);CHKERRQ(ierr); 756 } else { 757 ierr = PetscHSetIAdd(oht,column);CHKERRQ(ierr); 758 } 759 } 760 } 761 } /* end if (ao) */ 762 PetscFunctionReturn(0); 763 } 764 765 PETSC_STATIC_INLINE PetscErrorCode MatPtAPNumericComputeOneRowOfAP_private(Mat A,Mat P,Mat P_oth,const PetscInt *map,PetscInt dof,PetscInt i,PetscHMapIV hmap) 766 { 767 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data; 768 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; 769 PetscInt *ai,nzi,j,*aj,row,col,*pi,pnz,*p_othcols,pcstart,*pj,k,nzpi,offset; 770 PetscScalar ra,*aa,*pa; 771 PetscErrorCode ierr; 772 773 PetscFunctionBegin; 774 pcstart = P->cmap->rstart; 775 pcstart *= dof; 776 777 /* diagonal portion: Ad[i,:]*P */ 778 ai = ad->i; 779 nzi = ai[i+1] - ai[i]; 780 aj = ad->j + ai[i]; 781 aa = ad->a + ai[i]; 782 for (j=0; j<nzi; j++) { 783 ra = aa[j]; 784 row = aj[j]; 785 offset = row%dof; 786 row /= dof; 787 nzpi = pd->i[row+1] - pd->i[row]; 788 pj = pd->j + pd->i[row]; 789 pa = pd->a + pd->i[row]; 790 for (k=0; k<nzpi; k++) { 791 ierr = PetscHMapIVAddValue(hmap,pj[k]*dof+offset+pcstart,ra*pa[k]);CHKERRQ(ierr); 792 } 793 ierr = PetscLogFlops(2.0*nzpi);CHKERRQ(ierr); 794 } 795 for (j=0; j<nzi; j++) { 796 ra = aa[j]; 797 row = aj[j]; 798 offset = row%dof; 799 row /= dof; 800 nzpi = po->i[row+1] - po->i[row]; 801 pj = po->j + po->i[row]; 802 pa = po->a + po->i[row]; 803 for (k=0; k<nzpi; k++) { 804 ierr = PetscHMapIVAddValue(hmap,p->garray[pj[k]]*dof+offset,ra*pa[k]);CHKERRQ(ierr); 805 } 806 ierr = PetscLogFlops(2.0*nzpi);CHKERRQ(ierr); 807 } 808 809 /* off diagonal part: Ao[i, :]*P_oth */ 810 if (ao) { 811 ai = ao->i; 812 pi = p_oth->i; 813 nzi = ai[i+1] - ai[i]; 814 aj = ao->j + ai[i]; 815 aa = ao->a + ai[i]; 816 for (j=0; j<nzi; j++) { 817 row = aj[j]; 818 offset = a->garray[row]%dof; 819 row = map[row]; 820 ra = aa[j]; 821 pnz = pi[row+1] - pi[row]; 822 p_othcols = p_oth->j + pi[row]; 823 pa = p_oth->a + pi[row]; 824 for (col=0; col<pnz; col++) { 825 ierr = PetscHMapIVAddValue(hmap,p_othcols[col]*dof+offset,ra*pa[col]);CHKERRQ(ierr); 826 } 827 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 828 } 829 } /* end if (ao) */ 830 831 PetscFunctionReturn(0); 832 } 833 834 PetscErrorCode MatGetBrowsOfAcols_MPIXAIJ(Mat,Mat,PetscInt dof,MatReuse,Mat*); 835 836 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce(Mat A,Mat P,PetscInt dof,Mat C) 837 { 838 PetscErrorCode ierr; 839 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 840 Mat_SeqAIJ *cd,*co,*po=(Mat_SeqAIJ*)p->B->data,*pd=(Mat_SeqAIJ*)p->A->data; 841 Mat_APMPI *ptap = c->ap; 842 PetscHMapIV hmap; 843 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; 844 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa; 845 PetscInt offset,ii,pocol; 846 const PetscInt *mappingindices; 847 IS map; 848 MPI_Comm comm; 849 850 PetscFunctionBegin; 851 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 852 if (!ptap->P_oth) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 853 854 ierr = MatZeroEntries(C);CHKERRQ(ierr); 855 856 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 857 /*-----------------------------------------------------*/ 858 if (ptap->reuse == MAT_REUSE_MATRIX) { 859 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 860 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,dof,MAT_REUSE_MATRIX,&ptap->P_oth);CHKERRQ(ierr); 861 } 862 ierr = PetscObjectQuery((PetscObject)ptap->P_oth,"aoffdiagtopothmapping",(PetscObject*)&map);CHKERRQ(ierr); 863 864 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 865 pon *= dof; 866 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr); 867 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 868 cmaxr = 0; 869 for (i=0; i<pon; i++) { 870 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]); 871 } 872 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr); 873 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 874 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 875 ierr = ISGetIndices(map,&mappingindices);CHKERRQ(ierr); 876 for (i=0; i<am && pon; i++) { 877 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 878 offset = i%dof; 879 ii = i/dof; 880 nzi = po->i[ii+1] - po->i[ii]; 881 if (!nzi) continue; 882 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,hmap);CHKERRQ(ierr); 883 voff = 0; 884 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 885 if (!voff) continue; 886 887 /* Form C(ii, :) */ 888 poj = po->j + po->i[ii]; 889 poa = po->a + po->i[ii]; 890 for (j=0; j<nzi; j++) { 891 pocol = poj[j]*dof+offset; 892 c_rmtjj = c_rmtj + ptap->c_rmti[pocol]; 893 c_rmtaa = c_rmta + ptap->c_rmti[pocol]; 894 for (jj=0; jj<voff; jj++) { 895 apvaluestmp[jj] = apvalues[jj]*poa[j]; 896 /*If the row is empty */ 897 if (!c_rmtc[pocol]) { 898 c_rmtjj[jj] = apindices[jj]; 899 c_rmtaa[jj] = apvaluestmp[jj]; 900 c_rmtc[pocol]++; 901 } else { 902 ierr = PetscFindInt(apindices[jj],c_rmtc[pocol],c_rmtjj,&loc);CHKERRQ(ierr); 903 if (loc>=0){ /* hit */ 904 c_rmtaa[loc] += apvaluestmp[jj]; 905 ierr = PetscLogFlops(1.0);CHKERRQ(ierr); 906 } else { /* new element */ 907 loc = -(loc+1); 908 /* Move data backward */ 909 for (kk=c_rmtc[pocol]; kk>loc; kk--) { 910 c_rmtjj[kk] = c_rmtjj[kk-1]; 911 c_rmtaa[kk] = c_rmtaa[kk-1]; 912 }/* End kk */ 913 c_rmtjj[loc] = apindices[jj]; 914 c_rmtaa[loc] = apvaluestmp[jj]; 915 c_rmtc[pocol]++; 916 } 917 } 918 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 919 } /* End jj */ 920 } /* End j */ 921 } /* End i */ 922 923 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr); 924 925 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 926 pn *= dof; 927 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr); 928 929 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 930 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 931 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 932 pcstart = pcstart*dof; 933 pcend = pcend*dof; 934 cd = (Mat_SeqAIJ*)(c->A)->data; 935 co = (Mat_SeqAIJ*)(c->B)->data; 936 937 cmaxr = 0; 938 for (i=0; i<pn; i++) { 939 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i])); 940 } 941 ierr = PetscCalloc5(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pn,&dcc,pn,&occ);CHKERRQ(ierr); 942 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 943 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 944 for (i=0; i<am && pn; i++) { 945 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 946 offset = i%dof; 947 ii = i/dof; 948 nzi = pd->i[ii+1] - pd->i[ii]; 949 if (!nzi) continue; 950 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,hmap);CHKERRQ(ierr); 951 voff = 0; 952 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 953 if (!voff) continue; 954 /* Form C(ii, :) */ 955 pdj = pd->j + pd->i[ii]; 956 pda = pd->a + pd->i[ii]; 957 for (j=0; j<nzi; j++) { 958 row = pcstart + pdj[j] * dof + offset; 959 for (jj=0; jj<voff; jj++) { 960 apvaluestmp[jj] = apvalues[jj]*pda[j]; 961 } 962 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 963 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr); 964 } 965 } 966 ierr = ISRestoreIndices(map,&mappingindices);CHKERRQ(ierr); 967 ierr = MatGetOwnershipRangeColumn(C,&ccstart,&ccend);CHKERRQ(ierr); 968 ierr = PetscFree5(apindices,apvalues,apvaluestmp,dcc,occ);CHKERRQ(ierr); 969 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr); 970 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 971 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 972 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr); 973 974 /* Add contributions from remote */ 975 for (i = 0; i < pn; i++) { 976 row = i + pcstart; 977 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); 978 } 979 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr); 980 981 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 982 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 983 984 ptap->reuse = MAT_REUSE_MATRIX; 985 986 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 987 if (ptap->freestruct) { 988 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 989 } 990 PetscFunctionReturn(0); 991 } 992 993 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,Mat C) 994 { 995 PetscErrorCode ierr; 996 997 PetscFunctionBegin; 998 999 ierr = MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce(A,P,1,C);CHKERRQ(ierr); 1000 PetscFunctionReturn(0); 1001 } 1002 1003 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce_merged(Mat A,Mat P,PetscInt dof,Mat C) 1004 { 1005 PetscErrorCode ierr; 1006 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1007 Mat_SeqAIJ *cd,*co,*po=(Mat_SeqAIJ*)p->B->data,*pd=(Mat_SeqAIJ*)p->A->data; 1008 Mat_APMPI *ptap = c->ap; 1009 PetscHMapIV hmap; 1010 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; 1011 PetscScalar *c_rmta,*c_otha,*poa,*pda,*apvalues,*apvaluestmp,*c_rmtaa; 1012 PetscInt offset,ii,pocol; 1013 const PetscInt *mappingindices; 1014 IS map; 1015 MPI_Comm comm; 1016 1017 PetscFunctionBegin; 1018 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1019 if (!ptap->P_oth) SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 1020 1021 ierr = MatZeroEntries(C);CHKERRQ(ierr); 1022 1023 /* Get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 1024 /*-----------------------------------------------------*/ 1025 if (ptap->reuse == MAT_REUSE_MATRIX) { 1026 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 1027 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,dof,MAT_REUSE_MATRIX,&ptap->P_oth);CHKERRQ(ierr); 1028 } 1029 ierr = PetscObjectQuery((PetscObject)ptap->P_oth,"aoffdiagtopothmapping",(PetscObject*)&map);CHKERRQ(ierr); 1030 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1031 pon *= dof; 1032 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1033 pn *= dof; 1034 1035 ierr = PetscCalloc2(ptap->c_rmti[pon],&c_rmtj,ptap->c_rmti[pon],&c_rmta);CHKERRQ(ierr); 1036 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1037 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1038 pcstart *= dof; 1039 pcend *= dof; 1040 cmaxr = 0; 1041 for (i=0; i<pon; i++) { 1042 cmaxr = PetscMax(cmaxr,ptap->c_rmti[i+1]-ptap->c_rmti[i]); 1043 } 1044 cd = (Mat_SeqAIJ*)(c->A)->data; 1045 co = (Mat_SeqAIJ*)(c->B)->data; 1046 for (i=0; i<pn; i++) { 1047 cmaxr = PetscMax(cmaxr,(cd->i[i+1]-cd->i[i])+(co->i[i+1]-co->i[i])); 1048 } 1049 ierr = PetscCalloc4(cmaxr,&apindices,cmaxr,&apvalues,cmaxr,&apvaluestmp,pon,&c_rmtc);CHKERRQ(ierr); 1050 ierr = PetscHMapIVCreate(&hmap);CHKERRQ(ierr); 1051 ierr = PetscHMapIVResize(hmap,cmaxr);CHKERRQ(ierr); 1052 ierr = ISGetIndices(map,&mappingindices);CHKERRQ(ierr); 1053 for (i=0; i<am && (pon || pn); i++) { 1054 ierr = PetscHMapIVClear(hmap);CHKERRQ(ierr); 1055 offset = i%dof; 1056 ii = i/dof; 1057 nzi = po->i[ii+1] - po->i[ii]; 1058 dnzi = pd->i[ii+1] - pd->i[ii]; 1059 if (!nzi && !dnzi) continue; 1060 ierr = MatPtAPNumericComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,hmap);CHKERRQ(ierr); 1061 voff = 0; 1062 ierr = PetscHMapIVGetPairs(hmap,&voff,apindices,apvalues);CHKERRQ(ierr); 1063 if (!voff) continue; 1064 1065 /* Form remote C(ii, :) */ 1066 poj = po->j + po->i[ii]; 1067 poa = po->a + po->i[ii]; 1068 for (j=0; j<nzi; j++) { 1069 pocol = poj[j]*dof+offset; 1070 c_rmtjj = c_rmtj + ptap->c_rmti[pocol]; 1071 c_rmtaa = c_rmta + ptap->c_rmti[pocol]; 1072 for (jj=0; jj<voff; jj++) { 1073 apvaluestmp[jj] = apvalues[jj]*poa[j]; 1074 /*If the row is empty */ 1075 if (!c_rmtc[pocol]) { 1076 c_rmtjj[jj] = apindices[jj]; 1077 c_rmtaa[jj] = apvaluestmp[jj]; 1078 c_rmtc[pocol]++; 1079 } else { 1080 ierr = PetscFindInt(apindices[jj],c_rmtc[pocol],c_rmtjj,&loc);CHKERRQ(ierr); 1081 if (loc>=0){ /* hit */ 1082 c_rmtaa[loc] += apvaluestmp[jj]; 1083 ierr = PetscLogFlops(1.0);CHKERRQ(ierr); 1084 } else { /* new element */ 1085 loc = -(loc+1); 1086 /* Move data backward */ 1087 for (kk=c_rmtc[pocol]; kk>loc; kk--) { 1088 c_rmtjj[kk] = c_rmtjj[kk-1]; 1089 c_rmtaa[kk] = c_rmtaa[kk-1]; 1090 }/* End kk */ 1091 c_rmtjj[loc] = apindices[jj]; 1092 c_rmtaa[loc] = apvaluestmp[jj]; 1093 c_rmtc[pocol]++; 1094 } 1095 } 1096 } /* End jj */ 1097 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 1098 } /* End j */ 1099 1100 /* Form local C(ii, :) */ 1101 pdj = pd->j + pd->i[ii]; 1102 pda = pd->a + pd->i[ii]; 1103 for (j=0; j<dnzi; j++) { 1104 row = pcstart + pdj[j] * dof + offset; 1105 for (jj=0; jj<voff; jj++) { 1106 apvaluestmp[jj] = apvalues[jj]*pda[j]; 1107 }/* End kk */ 1108 ierr = PetscLogFlops(voff);CHKERRQ(ierr); 1109 ierr = MatSetValues(C,1,&row,voff,apindices,apvaluestmp,ADD_VALUES);CHKERRQ(ierr); 1110 }/* End j */ 1111 } /* End i */ 1112 1113 ierr = ISRestoreIndices(map,&mappingindices);CHKERRQ(ierr); 1114 ierr = PetscFree4(apindices,apvalues,apvaluestmp,c_rmtc);CHKERRQ(ierr); 1115 ierr = PetscHMapIVDestroy(&hmap);CHKERRQ(ierr); 1116 ierr = PetscCalloc2(ptap->c_othi[pn],&c_othj,ptap->c_othi[pn],&c_otha);CHKERRQ(ierr); 1117 1118 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1119 ierr = PetscSFReduceBegin(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 1120 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1121 ierr = PetscSFReduceEnd(ptap->sf,MPIU_SCALAR,c_rmta,c_otha,MPIU_REPLACE);CHKERRQ(ierr); 1122 ierr = PetscFree2(c_rmtj,c_rmta);CHKERRQ(ierr); 1123 1124 /* Add contributions from remote */ 1125 for (i = 0; i < pn; i++) { 1126 row = i + pcstart; 1127 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); 1128 } 1129 ierr = PetscFree2(c_othj,c_otha);CHKERRQ(ierr); 1130 1131 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1132 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1133 1134 ptap->reuse = MAT_REUSE_MATRIX; 1135 1136 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 1137 if (ptap->freestruct) { 1138 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 1139 } 1140 PetscFunctionReturn(0); 1141 } 1142 1143 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,Mat C) 1144 { 1145 PetscErrorCode ierr; 1146 1147 PetscFunctionBegin; 1148 1149 ierr = MatPtAPNumeric_MPIAIJ_MPIXAIJ_allatonce_merged(A,P,1,C);CHKERRQ(ierr); 1150 PetscFunctionReturn(0); 1151 } 1152 1153 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIXAIJ_allatonce(Mat A,Mat P,PetscInt dof,PetscReal fill,Mat *C) 1154 { 1155 Mat_APMPI *ptap; 1156 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1157 MPI_Comm comm; 1158 Mat Cmpi; 1159 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data; 1160 MatType mtype; 1161 PetscSF sf; 1162 PetscSFNode *iremote; 1163 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves; 1164 const PetscInt *rootdegrees; 1165 PetscHSetI ht,oht,*hta,*hto; 1166 PetscInt pn,pon,*c_rmtc,i,j,nzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets; 1167 PetscInt owner,lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj; 1168 PetscInt nalg=2,alg=0,offset,ii; 1169 const PetscInt *mappingindices; 1170 PetscBool flg; 1171 const char *algTypes[2] = {"overlapping","merged"}; 1172 IS map; 1173 PetscErrorCode ierr; 1174 1175 PetscFunctionBegin; 1176 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1177 1178 /* Create symbolic parallel matrix Cmpi */ 1179 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1180 pn *= dof; 1181 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1182 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1183 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1184 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1185 1186 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1187 ptap->reuse = MAT_INITIAL_MATRIX; 1188 ptap->algType = 2; 1189 1190 /* Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1191 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,dof,MAT_INITIAL_MATRIX,&ptap->P_oth);CHKERRQ(ierr); 1192 ierr = PetscObjectQuery((PetscObject)ptap->P_oth,"aoffdiagtopothmapping",(PetscObject*)&map);CHKERRQ(ierr); 1193 /* This equals to the number of offdiag columns in P */ 1194 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1195 pon *= dof; 1196 /* offsets */ 1197 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr); 1198 /* The number of columns we will send to remote ranks */ 1199 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr); 1200 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr); 1201 for (i=0; i<pon; i++) { 1202 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1203 } 1204 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1205 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr); 1206 /* Create hash table to merge all columns for C(i, :) */ 1207 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1208 1209 ierr = ISGetIndices(map,&mappingindices);CHKERRQ(ierr); 1210 ptap->c_rmti[0] = 0; 1211 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */ 1212 for (i=0; i<am && pon; i++) { 1213 /* Form one row of AP */ 1214 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1215 offset = i%dof; 1216 ii = i/dof; 1217 /* If the off diag is empty, we should not do any calculation */ 1218 nzi = po->i[ii+1] - po->i[ii]; 1219 if (!nzi) continue; 1220 1221 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,ht,ht);CHKERRQ(ierr); 1222 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1223 /* If AP is empty, just continue */ 1224 if (!htsize) continue; 1225 /* Form C(ii, :) */ 1226 poj = po->j + po->i[ii]; 1227 for (j=0; j<nzi; j++) { 1228 ierr = PetscHSetIUpdate(hta[poj[j]*dof+offset],ht);CHKERRQ(ierr); 1229 } 1230 } 1231 1232 for (i=0; i<pon; i++) { 1233 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1234 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize; 1235 c_rmtc[i] = htsize; 1236 } 1237 1238 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr); 1239 1240 for (i=0; i<pon; i++) { 1241 off = 0; 1242 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr); 1243 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1244 } 1245 ierr = PetscFree(hta);CHKERRQ(ierr); 1246 1247 ierr = PetscMalloc1(pon,&iremote);CHKERRQ(ierr); 1248 for (i=0; i<pon; i++) { 1249 owner = 0; lidx = 0; 1250 offset = i%dof; 1251 ii = i/dof; 1252 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[ii],&owner,&lidx);CHKERRQ(ierr); 1253 iremote[i].index = lidx*dof + offset; 1254 iremote[i].rank = owner; 1255 } 1256 1257 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 1258 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1259 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */ 1260 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr); 1261 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1262 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1263 /* How many neighbors have contributions to my rows? */ 1264 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr); 1265 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr); 1266 rootspacesize = 0; 1267 for (i = 0; i < pn; i++) { 1268 rootspacesize += rootdegrees[i]; 1269 } 1270 ierr = PetscMalloc1(rootspacesize,&rootspace);CHKERRQ(ierr); 1271 ierr = PetscMalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr); 1272 /* Get information from leaves 1273 * Number of columns other people contribute to my rows 1274 * */ 1275 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1276 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1277 ierr = PetscFree(c_rmtc);CHKERRQ(ierr); 1278 ierr = PetscCalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr); 1279 /* The number of columns is received for each row */ 1280 ptap->c_othi[0] = 0; 1281 rootspacesize = 0; 1282 rootspaceoffsets[0] = 0; 1283 for (i = 0; i < pn; i++) { 1284 rcvncols = 0; 1285 for (j = 0; j<rootdegrees[i]; j++) { 1286 rcvncols += rootspace[rootspacesize]; 1287 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize]; 1288 rootspacesize++; 1289 } 1290 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols; 1291 } 1292 ierr = PetscFree(rootspace);CHKERRQ(ierr); 1293 1294 ierr = PetscMalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr); 1295 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1296 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1297 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1298 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr); 1299 1300 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr); 1301 nleaves = 0; 1302 for (i = 0; i<pon; i++) { 1303 owner = 0; 1304 ii = i/dof; 1305 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[ii],&owner,NULL);CHKERRQ(ierr); 1306 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i]; 1307 for (j=0; j<sendncols; j++) { 1308 iremote[nleaves].rank = owner; 1309 iremote[nleaves++].index = c_rmtoffsets[i] + j; 1310 } 1311 } 1312 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr); 1313 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr); 1314 1315 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr); 1316 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1317 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr); 1318 /* One to one map */ 1319 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1320 1321 ierr = PetscMalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr); 1322 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr); 1323 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1324 pcstart *= dof; 1325 pcend *= dof; 1326 ierr = PetscMalloc2(pn,&hta,pn,&hto);CHKERRQ(ierr); 1327 for (i=0; i<pn; i++) { 1328 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1329 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr); 1330 } 1331 /* Work on local part */ 1332 /* 4) Pass 1: Estimate memory for C_loc */ 1333 for (i=0; i<am && pn; i++) { 1334 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1335 ierr = PetscHSetIClear(oht);CHKERRQ(ierr); 1336 offset = i%dof; 1337 ii = i/dof; 1338 nzi = pd->i[ii+1] - pd->i[ii]; 1339 if (!nzi) continue; 1340 1341 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,ht,oht);CHKERRQ(ierr); 1342 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1343 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr); 1344 if (!(htsize+htosize)) continue; 1345 /* Form C(ii, :) */ 1346 pdj = pd->j + pd->i[ii]; 1347 for (j=0; j<nzi; j++) { 1348 ierr = PetscHSetIUpdate(hta[pdj[j]*dof+offset],ht);CHKERRQ(ierr); 1349 ierr = PetscHSetIUpdate(hto[pdj[j]*dof+offset],oht);CHKERRQ(ierr); 1350 } 1351 } 1352 1353 ierr = ISRestoreIndices(map,&mappingindices);CHKERRQ(ierr); 1354 1355 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1356 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr); 1357 1358 /* Get remote data */ 1359 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1360 ierr = PetscFree(c_rmtj);CHKERRQ(ierr); 1361 1362 for (i = 0; i < pn; i++) { 1363 nzi = ptap->c_othi[i+1] - ptap->c_othi[i]; 1364 rdj = c_othj + ptap->c_othi[i]; 1365 for (j = 0; j < nzi; j++) { 1366 col = rdj[j]; 1367 /* diag part */ 1368 if (col>=pcstart && col<pcend) { 1369 ierr = PetscHSetIAdd(hta[i],col);CHKERRQ(ierr); 1370 } else { /* off diag */ 1371 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr); 1372 } 1373 } 1374 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1375 dnz[i] = htsize; 1376 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1377 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr); 1378 onz[i] = htsize; 1379 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr); 1380 } 1381 1382 ierr = PetscFree2(hta,hto);CHKERRQ(ierr); 1383 ierr = PetscFree(c_othj);CHKERRQ(ierr); 1384 1385 /* local sizes and preallocation */ 1386 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1387 ierr = MatSetBlockSizes(Cmpi,dof>1? dof: P->cmap->bs,dof>1? dof: P->cmap->bs);CHKERRQ(ierr); 1388 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1389 ierr = MatSetUp(Cmpi);CHKERRQ(ierr); 1390 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 1391 1392 /* attach the supporting struct to Cmpi for reuse */ 1393 c = (Mat_MPIAIJ*)Cmpi->data; 1394 c->ap = ptap; 1395 ptap->duplicate = Cmpi->ops->duplicate; 1396 ptap->destroy = Cmpi->ops->destroy; 1397 ptap->view = Cmpi->ops->view; 1398 1399 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1400 Cmpi->assembled = PETSC_FALSE; 1401 /* pick an algorithm */ 1402 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 1403 alg = 0; 1404 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 1405 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1406 switch (alg) { 1407 case 0: 1408 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce; 1409 break; 1410 case 1: 1411 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged; 1412 break; 1413 default: 1414 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n"); 1415 } 1416 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1417 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1418 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1419 *C = Cmpi; 1420 PetscFunctionReturn(0); 1421 } 1422 1423 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce(Mat A,Mat P,PetscReal fill,Mat *C) 1424 { 1425 PetscErrorCode ierr; 1426 1427 PetscFunctionBegin; 1428 1429 ierr = MatPtAPSymbolic_MPIAIJ_MPIXAIJ_allatonce(A,P,1,fill,C);CHKERRQ(ierr); 1430 PetscFunctionReturn(0); 1431 } 1432 1433 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIXAIJ_allatonce_merged(Mat A,Mat P,PetscInt dof,PetscReal fill,Mat *C) 1434 { 1435 Mat_APMPI *ptap; 1436 Mat_MPIAIJ *p=(Mat_MPIAIJ*)P->data,*c; 1437 MPI_Comm comm; 1438 Mat Cmpi; 1439 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)p->A->data,*po=(Mat_SeqAIJ*)p->B->data; 1440 MatType mtype; 1441 PetscSF sf; 1442 PetscSFNode *iremote; 1443 PetscInt rootspacesize,*rootspace,*rootspaceoffsets,nleaves; 1444 const PetscInt *rootdegrees; 1445 PetscHSetI ht,oht,*hta,*hto,*htd; 1446 PetscInt pn,pon,*c_rmtc,i,j,nzi,dnzi,htsize,htosize,*c_rmtj,off,*c_othj,rcvncols,sendncols,*c_rmtoffsets; 1447 PetscInt owner,lidx,*rdj,col,pcstart,pcend,*dnz,*onz,am,arstart,arend,*poj,*pdj; 1448 PetscInt nalg=2,alg=0,offset,ii; 1449 PetscBool flg; 1450 const char *algTypes[2] = {"merged","overlapping"}; 1451 const PetscInt *mappingindices; 1452 IS map; 1453 PetscErrorCode ierr; 1454 1455 PetscFunctionBegin; 1456 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1457 1458 /* Create symbolic parallel matrix Cmpi */ 1459 ierr = MatGetLocalSize(P,NULL,&pn);CHKERRQ(ierr); 1460 pn *= dof; 1461 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1462 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1463 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1464 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1465 1466 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1467 ptap->reuse = MAT_INITIAL_MATRIX; 1468 ptap->algType = 3; 1469 1470 /* 0) Get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1471 ierr = MatGetBrowsOfAcols_MPIXAIJ(A,P,dof,MAT_INITIAL_MATRIX,&ptap->P_oth);CHKERRQ(ierr); 1472 ierr = PetscObjectQuery((PetscObject)ptap->P_oth,"aoffdiagtopothmapping",(PetscObject*)&map);CHKERRQ(ierr); 1473 1474 /* This equals to the number of offdiag columns in P */ 1475 ierr = MatGetLocalSize(p->B,NULL,&pon);CHKERRQ(ierr); 1476 pon *= dof; 1477 /* offsets */ 1478 ierr = PetscMalloc1(pon+1,&ptap->c_rmti);CHKERRQ(ierr); 1479 /* The number of columns we will send to remote ranks */ 1480 ierr = PetscMalloc1(pon,&c_rmtc);CHKERRQ(ierr); 1481 ierr = PetscMalloc1(pon,&hta);CHKERRQ(ierr); 1482 for (i=0; i<pon; i++) { 1483 ierr = PetscHSetICreate(&hta[i]);CHKERRQ(ierr); 1484 } 1485 ierr = MatGetLocalSize(A,&am,NULL);CHKERRQ(ierr); 1486 ierr = MatGetOwnershipRange(A,&arstart,&arend);CHKERRQ(ierr); 1487 /* Create hash table to merge all columns for C(i, :) */ 1488 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1489 ierr = PetscHSetICreate(&oht);CHKERRQ(ierr); 1490 ierr = PetscMalloc2(pn,&htd,pn,&hto);CHKERRQ(ierr); 1491 for (i=0; i<pn; i++) { 1492 ierr = PetscHSetICreate(&htd[i]);CHKERRQ(ierr); 1493 ierr = PetscHSetICreate(&hto[i]);CHKERRQ(ierr); 1494 } 1495 1496 ierr = ISGetIndices(map,&mappingindices);CHKERRQ(ierr); 1497 ptap->c_rmti[0] = 0; 1498 /* 2) Pass 1: calculate the size for C_rmt (a matrix need to be sent to other processors) */ 1499 for (i=0; i<am && (pon || pn); i++) { 1500 /* Form one row of AP */ 1501 ierr = PetscHSetIClear(ht);CHKERRQ(ierr); 1502 ierr = PetscHSetIClear(oht);CHKERRQ(ierr); 1503 offset = i%dof; 1504 ii = i/dof; 1505 /* If the off diag is empty, we should not do any calculation */ 1506 nzi = po->i[ii+1] - po->i[ii]; 1507 dnzi = pd->i[ii+1] - pd->i[ii]; 1508 if (!nzi && !dnzi) continue; 1509 1510 ierr = MatPtAPSymbolicComputeOneRowOfAP_private(A,P,ptap->P_oth,mappingindices,dof,i,ht,oht);CHKERRQ(ierr); 1511 ierr = PetscHSetIGetSize(ht,&htsize);CHKERRQ(ierr); 1512 ierr = PetscHSetIGetSize(oht,&htosize);CHKERRQ(ierr); 1513 /* If AP is empty, just continue */ 1514 if (!(htsize+htosize)) continue; 1515 1516 /* Form remote C(ii, :) */ 1517 poj = po->j + po->i[ii]; 1518 for (j=0; j<nzi; j++) { 1519 ierr = PetscHSetIUpdate(hta[poj[j]*dof+offset],ht);CHKERRQ(ierr); 1520 ierr = PetscHSetIUpdate(hta[poj[j]*dof+offset],oht);CHKERRQ(ierr); 1521 } 1522 1523 /* Form local C(ii, :) */ 1524 pdj = pd->j + pd->i[ii]; 1525 for (j=0; j<dnzi; j++) { 1526 ierr = PetscHSetIUpdate(htd[pdj[j]*dof+offset],ht);CHKERRQ(ierr); 1527 ierr = PetscHSetIUpdate(hto[pdj[j]*dof+offset],oht);CHKERRQ(ierr); 1528 } 1529 } 1530 1531 ierr = ISRestoreIndices(map,&mappingindices);CHKERRQ(ierr); 1532 1533 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1534 ierr = PetscHSetIDestroy(&oht);CHKERRQ(ierr); 1535 1536 for (i=0; i<pon; i++) { 1537 ierr = PetscHSetIGetSize(hta[i],&htsize);CHKERRQ(ierr); 1538 ptap->c_rmti[i+1] = ptap->c_rmti[i] + htsize; 1539 c_rmtc[i] = htsize; 1540 } 1541 1542 ierr = PetscMalloc1(ptap->c_rmti[pon],&c_rmtj);CHKERRQ(ierr); 1543 1544 for (i=0; i<pon; i++) { 1545 off = 0; 1546 ierr = PetscHSetIGetElems(hta[i],&off,c_rmtj+ptap->c_rmti[i]);CHKERRQ(ierr); 1547 ierr = PetscHSetIDestroy(&hta[i]);CHKERRQ(ierr); 1548 } 1549 ierr = PetscFree(hta);CHKERRQ(ierr); 1550 1551 ierr = PetscMalloc1(pon,&iremote);CHKERRQ(ierr); 1552 for (i=0; i<pon; i++) { 1553 owner = 0; lidx = 0; 1554 offset = i%dof; 1555 ii = i/dof; 1556 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[ii],&owner,&lidx);CHKERRQ(ierr); 1557 iremote[i].index = lidx*dof+offset; 1558 iremote[i].rank = owner; 1559 } 1560 1561 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 1562 ierr = PetscSFSetGraph(sf,pn,pon,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1563 /* Reorder ranks properly so that the data handled by gather and scatter have the same order */ 1564 ierr = PetscSFSetRankOrder(sf,PETSC_TRUE);CHKERRQ(ierr); 1565 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1566 ierr = PetscSFSetUp(sf);CHKERRQ(ierr); 1567 /* How many neighbors have contributions to my rows? */ 1568 ierr = PetscSFComputeDegreeBegin(sf,&rootdegrees);CHKERRQ(ierr); 1569 ierr = PetscSFComputeDegreeEnd(sf,&rootdegrees);CHKERRQ(ierr); 1570 rootspacesize = 0; 1571 for (i = 0; i < pn; i++) { 1572 rootspacesize += rootdegrees[i]; 1573 } 1574 ierr = PetscMalloc1(rootspacesize,&rootspace);CHKERRQ(ierr); 1575 ierr = PetscMalloc1(rootspacesize+1,&rootspaceoffsets);CHKERRQ(ierr); 1576 /* Get information from leaves 1577 * Number of columns other people contribute to my rows 1578 * */ 1579 ierr = PetscSFGatherBegin(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1580 ierr = PetscSFGatherEnd(sf,MPIU_INT,c_rmtc,rootspace);CHKERRQ(ierr); 1581 ierr = PetscFree(c_rmtc);CHKERRQ(ierr); 1582 ierr = PetscMalloc1(pn+1,&ptap->c_othi);CHKERRQ(ierr); 1583 /* The number of columns is received for each row */ 1584 ptap->c_othi[0] = 0; 1585 rootspacesize = 0; 1586 rootspaceoffsets[0] = 0; 1587 for (i = 0; i < pn; i++) { 1588 rcvncols = 0; 1589 for (j = 0; j<rootdegrees[i]; j++) { 1590 rcvncols += rootspace[rootspacesize]; 1591 rootspaceoffsets[rootspacesize+1] = rootspaceoffsets[rootspacesize] + rootspace[rootspacesize]; 1592 rootspacesize++; 1593 } 1594 ptap->c_othi[i+1] = ptap->c_othi[i] + rcvncols; 1595 } 1596 ierr = PetscFree(rootspace);CHKERRQ(ierr); 1597 1598 ierr = PetscMalloc1(pon,&c_rmtoffsets);CHKERRQ(ierr); 1599 ierr = PetscSFScatterBegin(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1600 ierr = PetscSFScatterEnd(sf,MPIU_INT,rootspaceoffsets,c_rmtoffsets);CHKERRQ(ierr); 1601 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1602 ierr = PetscFree(rootspaceoffsets);CHKERRQ(ierr); 1603 1604 ierr = PetscCalloc1(ptap->c_rmti[pon],&iremote);CHKERRQ(ierr); 1605 nleaves = 0; 1606 for (i = 0; i<pon; i++) { 1607 owner = 0; 1608 ii = i/dof; 1609 ierr = PetscLayoutFindOwnerIndex(P->cmap,p->garray[ii],&owner,NULL);CHKERRQ(ierr); 1610 sendncols = ptap->c_rmti[i+1] - ptap->c_rmti[i]; 1611 for (j=0; j<sendncols; j++) { 1612 iremote[nleaves].rank = owner; 1613 iremote[nleaves++].index = c_rmtoffsets[i] + j; 1614 } 1615 } 1616 ierr = PetscFree(c_rmtoffsets);CHKERRQ(ierr); 1617 ierr = PetscCalloc1(ptap->c_othi[pn],&c_othj);CHKERRQ(ierr); 1618 1619 ierr = PetscSFCreate(comm,&ptap->sf);CHKERRQ(ierr); 1620 ierr = PetscSFSetGraph(ptap->sf,ptap->c_othi[pn],nleaves,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 1621 ierr = PetscSFSetFromOptions(ptap->sf);CHKERRQ(ierr); 1622 /* One to one map */ 1623 ierr = PetscSFReduceBegin(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1624 /* Get remote data */ 1625 ierr = PetscSFReduceEnd(ptap->sf,MPIU_INT,c_rmtj,c_othj,MPIU_REPLACE);CHKERRQ(ierr); 1626 ierr = PetscFree(c_rmtj);CHKERRQ(ierr); 1627 ierr = PetscMalloc2(pn,&dnz,pn,&onz);CHKERRQ(ierr); 1628 ierr = MatGetOwnershipRangeColumn(P,&pcstart,&pcend);CHKERRQ(ierr); 1629 pcstart *= dof; 1630 pcend *= dof; 1631 for (i = 0; i < pn; i++) { 1632 nzi = ptap->c_othi[i+1] - ptap->c_othi[i]; 1633 rdj = c_othj + ptap->c_othi[i]; 1634 for (j = 0; j < nzi; j++) { 1635 col = rdj[j]; 1636 /* diag part */ 1637 if (col>=pcstart && col<pcend) { 1638 ierr = PetscHSetIAdd(htd[i],col);CHKERRQ(ierr); 1639 } else { /* off diag */ 1640 ierr = PetscHSetIAdd(hto[i],col);CHKERRQ(ierr); 1641 } 1642 } 1643 ierr = PetscHSetIGetSize(htd[i],&htsize);CHKERRQ(ierr); 1644 dnz[i] = htsize; 1645 ierr = PetscHSetIDestroy(&htd[i]);CHKERRQ(ierr); 1646 ierr = PetscHSetIGetSize(hto[i],&htsize);CHKERRQ(ierr); 1647 onz[i] = htsize; 1648 ierr = PetscHSetIDestroy(&hto[i]);CHKERRQ(ierr); 1649 } 1650 1651 ierr = PetscFree2(htd,hto);CHKERRQ(ierr); 1652 ierr = PetscFree(c_othj);CHKERRQ(ierr); 1653 1654 /* local sizes and preallocation */ 1655 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1656 ierr = MatSetBlockSizes(Cmpi, dof>1? dof: P->cmap->bs,dof>1? dof: P->cmap->bs);CHKERRQ(ierr); 1657 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 1658 ierr = PetscFree2(dnz,onz);CHKERRQ(ierr); 1659 1660 /* attach the supporting struct to Cmpi for reuse */ 1661 c = (Mat_MPIAIJ*)Cmpi->data; 1662 c->ap = ptap; 1663 ptap->duplicate = Cmpi->ops->duplicate; 1664 ptap->destroy = Cmpi->ops->destroy; 1665 ptap->view = Cmpi->ops->view; 1666 1667 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 1668 Cmpi->assembled = PETSC_FALSE; 1669 /* pick an algorithm */ 1670 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)A),((PetscObject)A)->prefix,"MatPtAP","Mat");CHKERRQ(ierr); 1671 alg = 0; 1672 ierr = PetscOptionsEList("-matptap_allatonce_via","PtAP allatonce numeric approach","MatPtAP",algTypes,nalg,algTypes[alg],&alg,&flg);CHKERRQ(ierr); 1673 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1674 switch (alg) { 1675 case 0: 1676 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce_merged; 1677 break; 1678 case 1: 1679 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_allatonce; 1680 break; 1681 default: 1682 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," Unsupported allatonce numerical algorithm \n"); 1683 } 1684 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 1685 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 1686 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 1687 *C = Cmpi; 1688 PetscFunctionReturn(0); 1689 } 1690 1691 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_allatonce_merged(Mat A,Mat P,PetscReal fill,Mat *C) 1692 { 1693 PetscErrorCode ierr; 1694 1695 PetscFunctionBegin; 1696 1697 ierr = MatPtAPSymbolic_MPIAIJ_MPIXAIJ_allatonce_merged(A,P,1,fill,C);CHKERRQ(ierr); 1698 PetscFunctionReturn(0); 1699 } 1700 1701 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 1702 { 1703 PetscErrorCode ierr; 1704 Mat_APMPI *ptap; 1705 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 1706 MPI_Comm comm; 1707 PetscMPIInt size,rank; 1708 Mat Cmpi; 1709 PetscFreeSpaceList free_space=NULL,current_space=NULL; 1710 PetscInt am=A->rmap->n,pm=P->rmap->n,pN=P->cmap->N,pn=P->cmap->n; 1711 PetscInt *lnk,i,k,pnz,row,nsend; 1712 PetscBT lnkbt; 1713 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 1714 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 1715 PetscInt len,proc,*dnz,*onz,*owners,nzi,nspacedouble; 1716 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 1717 MPI_Request *swaits,*rwaits; 1718 MPI_Status *sstatus,rstatus; 1719 PetscLayout rowmap; 1720 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 1721 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 1722 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Crmax,*aj,*ai,*pi; 1723 Mat_SeqAIJ *p_loc,*p_oth=NULL,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=NULL,*c_loc,*c_oth; 1724 PetscScalar *apv; 1725 PetscTable ta; 1726 MatType mtype; 1727 const char *prefix; 1728 #if defined(PETSC_USE_INFO) 1729 PetscReal apfill; 1730 #endif 1731 1732 PetscFunctionBegin; 1733 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 1734 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1735 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1736 1737 if (size > 1) ao = (Mat_SeqAIJ*)(a->B)->data; 1738 1739 /* create symbolic parallel matrix Cmpi */ 1740 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 1741 ierr = MatGetType(A,&mtype);CHKERRQ(ierr); 1742 ierr = MatSetType(Cmpi,mtype);CHKERRQ(ierr); 1743 1744 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */ 1745 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 1746 1747 /* create struct Mat_APMPI and attached it to C later */ 1748 ierr = PetscNew(&ptap);CHKERRQ(ierr); 1749 ptap->reuse = MAT_INITIAL_MATRIX; 1750 ptap->algType = 1; 1751 1752 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 1753 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1754 /* get P_loc by taking all local rows of P */ 1755 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1756 1757 /* (0) compute Rd = Pd^T, Ro = Po^T */ 1758 /* --------------------------------- */ 1759 ierr = MatTranspose(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 1760 ierr = MatTranspose(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 1761 1762 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 1763 /* ----------------------------------------------------------------- */ 1764 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1765 if (ptap->P_oth) p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1766 1767 /* create and initialize a linked list */ 1768 ierr = PetscTableCreate(pn,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc and Cmpi */ 1769 MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta); 1770 MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta); 1771 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); /* Crmax = nnz(sum of Prows) */ 1772 /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */ 1773 1774 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1775 1776 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 1777 if (ao) { 1778 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);CHKERRQ(ierr); 1779 } else { 1780 ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],p_loc->i[pm])),&free_space);CHKERRQ(ierr); 1781 } 1782 current_space = free_space; 1783 nspacedouble = 0; 1784 1785 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 1786 api[0] = 0; 1787 for (i=0; i<am; i++) { 1788 /* diagonal portion: Ad[i,:]*P */ 1789 ai = ad->i; pi = p_loc->i; 1790 nzi = ai[i+1] - ai[i]; 1791 aj = ad->j + ai[i]; 1792 for (j=0; j<nzi; j++) { 1793 row = aj[j]; 1794 pnz = pi[row+1] - pi[row]; 1795 Jptr = p_loc->j + pi[row]; 1796 /* add non-zero cols of P into the sorted linked list lnk */ 1797 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1798 } 1799 /* off-diagonal portion: Ao[i,:]*P */ 1800 if (ao) { 1801 ai = ao->i; pi = p_oth->i; 1802 nzi = ai[i+1] - ai[i]; 1803 aj = ao->j + ai[i]; 1804 for (j=0; j<nzi; j++) { 1805 row = aj[j]; 1806 pnz = pi[row+1] - pi[row]; 1807 Jptr = p_oth->j + pi[row]; 1808 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1809 } 1810 } 1811 apnz = lnk[0]; 1812 api[i+1] = api[i] + apnz; 1813 if (ap_rmax < apnz) ap_rmax = apnz; 1814 1815 /* if free space is not available, double the total space in the list */ 1816 if (current_space->local_remaining<apnz) { 1817 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 1818 nspacedouble++; 1819 } 1820 1821 /* Copy data into free space, then initialize lnk */ 1822 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 1823 1824 current_space->array += apnz; 1825 current_space->local_used += apnz; 1826 current_space->local_remaining -= apnz; 1827 } 1828 /* Allocate space for apj and apv, initialize apj, and */ 1829 /* destroy list of free space and other temporary array(s) */ 1830 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 1831 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 1832 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 1833 1834 /* Create AP_loc for reuse */ 1835 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 1836 1837 #if defined(PETSC_USE_INFO) 1838 if (ao) { 1839 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 1840 } else { 1841 apfill = (PetscReal)api[am]/(ad->i[am]+p_loc->i[pm]+1); 1842 } 1843 ptap->AP_loc->info.mallocs = nspacedouble; 1844 ptap->AP_loc->info.fill_ratio_given = fill; 1845 ptap->AP_loc->info.fill_ratio_needed = apfill; 1846 1847 if (api[am]) { 1848 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); 1849 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 1850 } else { 1851 ierr = PetscInfo(ptap->AP_loc,"Nonscalable algorithm, AP_loc is empty \n");CHKERRQ(ierr); 1852 } 1853 #endif 1854 1855 /* (2-1) compute symbolic Co = Ro*AP_loc */ 1856 /* ------------------------------------ */ 1857 ierr = MatGetOptionsPrefix(A,&prefix);CHKERRQ(ierr); 1858 ierr = MatSetOptionsPrefix(ptap->Ro,prefix);CHKERRQ(ierr); 1859 ierr = MatAppendOptionsPrefix(ptap->Ro,"inner_offdiag_");CHKERRQ(ierr); 1860 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 1861 1862 /* (3) send coj of C_oth to other processors */ 1863 /* ------------------------------------------ */ 1864 /* determine row ownership */ 1865 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 1866 rowmap->n = pn; 1867 rowmap->bs = 1; 1868 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 1869 owners = rowmap->range; 1870 1871 /* determine the number of messages to send, their lengths */ 1872 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 1873 ierr = PetscArrayzero(len_s,size);CHKERRQ(ierr); 1874 ierr = PetscArrayzero(len_si,size);CHKERRQ(ierr); 1875 1876 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 1877 coi = c_oth->i; coj = c_oth->j; 1878 con = ptap->C_oth->rmap->n; 1879 proc = 0; 1880 for (i=0; i<con; i++) { 1881 while (prmap[i] >= owners[proc+1]) proc++; 1882 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 1883 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 1884 } 1885 1886 len = 0; /* max length of buf_si[], see (4) */ 1887 owners_co[0] = 0; 1888 nsend = 0; 1889 for (proc=0; proc<size; proc++) { 1890 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 1891 if (len_s[proc]) { 1892 nsend++; 1893 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 1894 len += len_si[proc]; 1895 } 1896 } 1897 1898 /* determine the number and length of messages to receive for coi and coj */ 1899 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 1900 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 1901 1902 /* post the Irecv and Isend of coj */ 1903 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 1904 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 1905 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 1906 for (proc=0, k=0; proc<size; proc++) { 1907 if (!len_s[proc]) continue; 1908 i = owners_co[proc]; 1909 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 1910 k++; 1911 } 1912 1913 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 1914 /* ---------------------------------------- */ 1915 ierr = MatSetOptionsPrefix(ptap->Rd,prefix);CHKERRQ(ierr); 1916 ierr = MatAppendOptionsPrefix(ptap->Rd,"inner_diag_");CHKERRQ(ierr); 1917 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 1918 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 1919 1920 /* receives coj are complete */ 1921 for (i=0; i<nrecv; i++) { 1922 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1923 } 1924 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1925 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1926 1927 /* add received column indices into ta to update Crmax */ 1928 for (k=0; k<nrecv; k++) {/* k-th received message */ 1929 Jptr = buf_rj[k]; 1930 for (j=0; j<len_r[k]; j++) { 1931 ierr = PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);CHKERRQ(ierr); 1932 } 1933 } 1934 ierr = PetscTableGetCount(ta,&Crmax);CHKERRQ(ierr); 1935 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 1936 1937 /* (4) send and recv coi */ 1938 /*-----------------------*/ 1939 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 1940 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 1941 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 1942 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 1943 for (proc=0,k=0; proc<size; proc++) { 1944 if (!len_s[proc]) continue; 1945 /* form outgoing message for i-structure: 1946 buf_si[0]: nrows to be sent 1947 [1:nrows]: row index (global) 1948 [nrows+1:2*nrows+1]: i-structure index 1949 */ 1950 /*-------------------------------------------*/ 1951 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 1952 buf_si_i = buf_si + nrows+1; 1953 buf_si[0] = nrows; 1954 buf_si_i[0] = 0; 1955 nrows = 0; 1956 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 1957 nzi = coi[i+1] - coi[i]; 1958 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 1959 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 1960 nrows++; 1961 } 1962 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 1963 k++; 1964 buf_si += len_si[proc]; 1965 } 1966 for (i=0; i<nrecv; i++) { 1967 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 1968 } 1969 ierr = PetscFree(rwaits);CHKERRQ(ierr); 1970 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 1971 1972 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 1973 ierr = PetscFree(len_ri);CHKERRQ(ierr); 1974 ierr = PetscFree(swaits);CHKERRQ(ierr); 1975 ierr = PetscFree(buf_s);CHKERRQ(ierr); 1976 1977 /* (5) compute the local portion of Cmpi */ 1978 /* ------------------------------------------ */ 1979 /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */ 1980 ierr = PetscFreeSpaceGet(Crmax,&free_space);CHKERRQ(ierr); 1981 current_space = free_space; 1982 1983 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 1984 for (k=0; k<nrecv; k++) { 1985 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1986 nrows = *buf_ri_k[k]; 1987 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 1988 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1989 } 1990 1991 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 1992 ierr = PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 1993 for (i=0; i<pn; i++) { 1994 /* add C_loc into Cmpi */ 1995 nzi = c_loc->i[i+1] - c_loc->i[i]; 1996 Jptr = c_loc->j + c_loc->i[i]; 1997 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 1998 1999 /* add received col data into lnk */ 2000 for (k=0; k<nrecv; k++) { /* k-th received message */ 2001 if (i == *nextrow[k]) { /* i-th row */ 2002 nzi = *(nextci[k]+1) - *nextci[k]; 2003 Jptr = buf_rj[k] + *nextci[k]; 2004 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 2005 nextrow[k]++; nextci[k]++; 2006 } 2007 } 2008 nzi = lnk[0]; 2009 2010 /* copy data into free space, then initialize lnk */ 2011 ierr = PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 2012 ierr = MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);CHKERRQ(ierr); 2013 } 2014 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 2015 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 2016 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 2017 2018 /* local sizes and preallocation */ 2019 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 2020 if (P->cmap->bs > 0) { 2021 ierr = PetscLayoutSetBlockSize(Cmpi->rmap,P->cmap->bs);CHKERRQ(ierr); 2022 ierr = PetscLayoutSetBlockSize(Cmpi->cmap,P->cmap->bs);CHKERRQ(ierr); 2023 } 2024 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 2025 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 2026 2027 /* members in merge */ 2028 ierr = PetscFree(id_r);CHKERRQ(ierr); 2029 ierr = PetscFree(len_r);CHKERRQ(ierr); 2030 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 2031 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 2032 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 2033 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 2034 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 2035 2036 /* attach the supporting struct to Cmpi for reuse */ 2037 c = (Mat_MPIAIJ*)Cmpi->data; 2038 c->ap = ptap; 2039 ptap->duplicate = Cmpi->ops->duplicate; 2040 ptap->destroy = Cmpi->ops->destroy; 2041 ptap->view = Cmpi->ops->view; 2042 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 2043 2044 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 2045 Cmpi->assembled = PETSC_FALSE; 2046 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 2047 Cmpi->ops->view = MatView_MPIAIJ_PtAP; 2048 Cmpi->ops->freeintermediatedatastructures = MatFreeIntermediateDataStructures_MPIAIJ_AP; 2049 *C = Cmpi; 2050 PetscFunctionReturn(0); 2051 } 2052 2053 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 2054 { 2055 PetscErrorCode ierr; 2056 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 2057 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 2058 Mat_SeqAIJ *ap,*p_loc,*p_oth=NULL,*c_seq; 2059 Mat_APMPI *ptap = c->ap; 2060 Mat AP_loc,C_loc,C_oth; 2061 PetscInt i,rstart,rend,cm,ncols,row; 2062 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 2063 PetscScalar *apa; 2064 const PetscInt *cols; 2065 const PetscScalar *vals; 2066 2067 PetscFunctionBegin; 2068 if (!ptap->AP_loc) { 2069 MPI_Comm comm; 2070 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 2071 SETERRQ(comm,PETSC_ERR_ARG_WRONGSTATE,"PtAP cannot be reused. Do not call MatFreeIntermediateDataStructures() or use '-mat_freeintermediatedatastructures'"); 2072 } 2073 2074 ierr = MatZeroEntries(C);CHKERRQ(ierr); 2075 /* 1) get R = Pd^T,Ro = Po^T */ 2076 if (ptap->reuse == MAT_REUSE_MATRIX) { 2077 ierr = MatTranspose(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 2078 ierr = MatTranspose(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 2079 } 2080 2081 /* 2) get AP_loc */ 2082 AP_loc = ptap->AP_loc; 2083 ap = (Mat_SeqAIJ*)AP_loc->data; 2084 2085 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 2086 /*-----------------------------------------------------*/ 2087 if (ptap->reuse == MAT_REUSE_MATRIX) { 2088 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 2089 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 2090 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 2091 } 2092 2093 /* 2-2) compute numeric A_loc*P - dominating part */ 2094 /* ---------------------------------------------- */ 2095 /* get data from symbolic products */ 2096 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 2097 if (ptap->P_oth) { 2098 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 2099 } 2100 apa = ptap->apa; 2101 api = ap->i; 2102 apj = ap->j; 2103 for (i=0; i<am; i++) { 2104 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 2105 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 2106 apnz = api[i+1] - api[i]; 2107 for (j=0; j<apnz; j++) { 2108 col = apj[j+api[i]]; 2109 ap->a[j+ap->i[i]] = apa[col]; 2110 apa[col] = 0.0; 2111 } 2112 } 2113 2114 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 2115 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 2116 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 2117 C_loc = ptap->C_loc; 2118 C_oth = ptap->C_oth; 2119 2120 /* add C_loc and Co to to C */ 2121 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 2122 2123 /* C_loc -> C */ 2124 cm = C_loc->rmap->N; 2125 c_seq = (Mat_SeqAIJ*)C_loc->data; 2126 cols = c_seq->j; 2127 vals = c_seq->a; 2128 2129 2130 /* The (fast) MatSetValues_MPIAIJ_CopyFromCSRFormat function can only be used when C->was_assembled is PETSC_FALSE and */ 2131 /* when there are no off-processor parts. */ 2132 /* If was_assembled is true, then the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; in MatSetValues_MPIAIJ_CopyFromCSRFormat */ 2133 /* is no longer true. Then the more complex function MatSetValues_MPIAIJ() has to be used, where the column index is looked up from */ 2134 /* a table, and other, more complex stuff has to be done. */ 2135 if (C->assembled) { 2136 C->was_assembled = PETSC_TRUE; 2137 C->assembled = PETSC_FALSE; 2138 } 2139 if (C->was_assembled) { 2140 for (i=0; i<cm; i++) { 2141 ncols = c_seq->i[i+1] - c_seq->i[i]; 2142 row = rstart + i; 2143 ierr = MatSetValues_MPIAIJ(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 2144 cols += ncols; vals += ncols; 2145 } 2146 } else { 2147 ierr = MatSetValues_MPIAIJ_CopyFromCSRFormat(C,c_seq->j,c_seq->i,c_seq->a);CHKERRQ(ierr); 2148 } 2149 2150 /* Co -> C, off-processor part */ 2151 cm = C_oth->rmap->N; 2152 c_seq = (Mat_SeqAIJ*)C_oth->data; 2153 cols = c_seq->j; 2154 vals = c_seq->a; 2155 for (i=0; i<cm; i++) { 2156 ncols = c_seq->i[i+1] - c_seq->i[i]; 2157 row = p->garray[i]; 2158 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 2159 cols += ncols; vals += ncols; 2160 } 2161 2162 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2163 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2164 2165 ptap->reuse = MAT_REUSE_MATRIX; 2166 2167 /* supporting struct ptap consumes almost same amount of memory as C=PtAP, release it if C will not be updated by A and P */ 2168 if (ptap->freestruct) { 2169 ierr = MatFreeIntermediateDataStructures(C);CHKERRQ(ierr); 2170 } 2171 PetscFunctionReturn(0); 2172 } 2173