1 2 /* 3 Defines the basic matrix operations for the ADJ adjacency list matrix data-structure. 4 */ 5 #include <../src/mat/impls/adj/mpi/mpiadj.h> /*I "petscmat.h" I*/ 6 #include <petscsf.h> 7 8 #undef __FUNCT__ 9 #define __FUNCT__ "MatView_MPIAdj_ASCII" 10 PetscErrorCode MatView_MPIAdj_ASCII(Mat A,PetscViewer viewer) 11 { 12 Mat_MPIAdj *a = (Mat_MPIAdj*)A->data; 13 PetscErrorCode ierr; 14 PetscInt i,j,m = A->rmap->n; 15 const char *name; 16 PetscViewerFormat format; 17 18 PetscFunctionBegin; 19 ierr = PetscObjectGetName((PetscObject)A,&name);CHKERRQ(ierr); 20 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 21 if (format == PETSC_VIEWER_ASCII_INFO) { 22 PetscFunctionReturn(0); 23 } else if (format == PETSC_VIEWER_ASCII_MATLAB) { 24 SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"MATLAB format not supported"); 25 } else { 26 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 27 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);CHKERRQ(ierr); 28 for (i=0; i<m; i++) { 29 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"row %D:",i+A->rmap->rstart);CHKERRQ(ierr); 30 for (j=a->i[i]; j<a->i[i+1]; j++) { 31 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %D ",a->j[j]);CHKERRQ(ierr); 32 } 33 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 34 } 35 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 36 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 37 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_FALSE);CHKERRQ(ierr); 38 } 39 PetscFunctionReturn(0); 40 } 41 42 #undef __FUNCT__ 43 #define __FUNCT__ "MatView_MPIAdj" 44 PetscErrorCode MatView_MPIAdj(Mat A,PetscViewer viewer) 45 { 46 PetscErrorCode ierr; 47 PetscBool iascii; 48 49 PetscFunctionBegin; 50 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 51 if (iascii) { 52 ierr = MatView_MPIAdj_ASCII(A,viewer);CHKERRQ(ierr); 53 } 54 PetscFunctionReturn(0); 55 } 56 57 #undef __FUNCT__ 58 #define __FUNCT__ "MatDestroy_MPIAdj" 59 PetscErrorCode MatDestroy_MPIAdj(Mat mat) 60 { 61 Mat_MPIAdj *a = (Mat_MPIAdj*)mat->data; 62 PetscErrorCode ierr; 63 64 PetscFunctionBegin; 65 #if defined(PETSC_USE_LOG) 66 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D, NZ=%D",mat->rmap->n,mat->cmap->n,a->nz); 67 #endif 68 ierr = PetscFree(a->diag);CHKERRQ(ierr); 69 if (a->freeaij) { 70 if (a->freeaijwithfree) { 71 if (a->i) free(a->i); 72 if (a->j) free(a->j); 73 } else { 74 ierr = PetscFree(a->i);CHKERRQ(ierr); 75 ierr = PetscFree(a->j);CHKERRQ(ierr); 76 ierr = PetscFree(a->values);CHKERRQ(ierr); 77 } 78 } 79 ierr = PetscFree(a->rowvalues);CHKERRQ(ierr); 80 ierr = PetscFree(mat->data);CHKERRQ(ierr); 81 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 82 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAdjSetPreallocation_C",NULL);CHKERRQ(ierr); 83 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAdjCreateNonemptySubcommMat_C",NULL);CHKERRQ(ierr); 84 PetscFunctionReturn(0); 85 } 86 87 #undef __FUNCT__ 88 #define __FUNCT__ "MatSetOption_MPIAdj" 89 PetscErrorCode MatSetOption_MPIAdj(Mat A,MatOption op,PetscBool flg) 90 { 91 Mat_MPIAdj *a = (Mat_MPIAdj*)A->data; 92 PetscErrorCode ierr; 93 94 PetscFunctionBegin; 95 switch (op) { 96 case MAT_SYMMETRIC: 97 case MAT_STRUCTURALLY_SYMMETRIC: 98 case MAT_HERMITIAN: 99 a->symmetric = flg; 100 break; 101 case MAT_SYMMETRY_ETERNAL: 102 break; 103 default: 104 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 105 break; 106 } 107 PetscFunctionReturn(0); 108 } 109 110 111 /* 112 Adds diagonal pointers to sparse matrix structure. 113 */ 114 115 #undef __FUNCT__ 116 #define __FUNCT__ "MatMarkDiagonal_MPIAdj" 117 PetscErrorCode MatMarkDiagonal_MPIAdj(Mat A) 118 { 119 Mat_MPIAdj *a = (Mat_MPIAdj*)A->data; 120 PetscErrorCode ierr; 121 PetscInt i,j,m = A->rmap->n; 122 123 PetscFunctionBegin; 124 ierr = PetscMalloc1(m,&a->diag);CHKERRQ(ierr); 125 ierr = PetscLogObjectMemory((PetscObject)A,m*sizeof(PetscInt));CHKERRQ(ierr); 126 for (i=0; i<A->rmap->n; i++) { 127 for (j=a->i[i]; j<a->i[i+1]; j++) { 128 if (a->j[j] == i) { 129 a->diag[i] = j; 130 break; 131 } 132 } 133 } 134 PetscFunctionReturn(0); 135 } 136 137 #undef __FUNCT__ 138 #define __FUNCT__ "MatGetRow_MPIAdj" 139 PetscErrorCode MatGetRow_MPIAdj(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 140 { 141 Mat_MPIAdj *a = (Mat_MPIAdj*)A->data; 142 PetscErrorCode ierr; 143 144 PetscFunctionBegin; 145 row -= A->rmap->rstart; 146 147 if (row < 0 || row >= A->rmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row out of range"); 148 149 *nz = a->i[row+1] - a->i[row]; 150 if (v) { 151 PetscInt j; 152 if (a->rowvalues_alloc < *nz) { 153 ierr = PetscFree(a->rowvalues);CHKERRQ(ierr); 154 a->rowvalues_alloc = PetscMax(a->rowvalues_alloc*2, *nz); 155 ierr = PetscMalloc1(a->rowvalues_alloc,&a->rowvalues);CHKERRQ(ierr); 156 } 157 for (j=0; j<*nz; j++) a->rowvalues[j] = a->values[a->i[row]+j]; 158 *v = (*nz) ? a->rowvalues : NULL; 159 } 160 if (idx) *idx = (*nz) ? a->j + a->i[row] : NULL; 161 PetscFunctionReturn(0); 162 } 163 164 #undef __FUNCT__ 165 #define __FUNCT__ "MatRestoreRow_MPIAdj" 166 PetscErrorCode MatRestoreRow_MPIAdj(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 167 { 168 PetscFunctionBegin; 169 PetscFunctionReturn(0); 170 } 171 172 #undef __FUNCT__ 173 #define __FUNCT__ "MatEqual_MPIAdj" 174 PetscErrorCode MatEqual_MPIAdj(Mat A,Mat B,PetscBool * flg) 175 { 176 Mat_MPIAdj *a = (Mat_MPIAdj*)A->data,*b = (Mat_MPIAdj*)B->data; 177 PetscErrorCode ierr; 178 PetscBool flag; 179 180 PetscFunctionBegin; 181 /* If the matrix dimensions are not equal,or no of nonzeros */ 182 if ((A->rmap->n != B->rmap->n) ||(a->nz != b->nz)) { 183 flag = PETSC_FALSE; 184 } 185 186 /* if the a->i are the same */ 187 ierr = PetscMemcmp(a->i,b->i,(A->rmap->n+1)*sizeof(PetscInt),&flag);CHKERRQ(ierr); 188 189 /* if a->j are the same */ 190 ierr = PetscMemcmp(a->j,b->j,(a->nz)*sizeof(PetscInt),&flag);CHKERRQ(ierr); 191 192 ierr = MPI_Allreduce(&flag,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 193 PetscFunctionReturn(0); 194 } 195 196 #undef __FUNCT__ 197 #define __FUNCT__ "MatGetRowIJ_MPIAdj" 198 PetscErrorCode MatGetRowIJ_MPIAdj(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *m,const PetscInt *inia[],const PetscInt *inja[],PetscBool *done) 199 { 200 PetscInt i; 201 Mat_MPIAdj *a = (Mat_MPIAdj*)A->data; 202 PetscInt **ia = (PetscInt**)inia,**ja = (PetscInt**)inja; 203 204 PetscFunctionBegin; 205 *m = A->rmap->n; 206 *ia = a->i; 207 *ja = a->j; 208 *done = PETSC_TRUE; 209 if (oshift) { 210 for (i=0; i<(*ia)[*m]; i++) { 211 (*ja)[i]++; 212 } 213 for (i=0; i<=(*m); i++) (*ia)[i]++; 214 } 215 PetscFunctionReturn(0); 216 } 217 218 #undef __FUNCT__ 219 #define __FUNCT__ "MatRestoreRowIJ_MPIAdj" 220 PetscErrorCode MatRestoreRowIJ_MPIAdj(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *m,const PetscInt *inia[],const PetscInt *inja[],PetscBool *done) 221 { 222 PetscInt i; 223 Mat_MPIAdj *a = (Mat_MPIAdj*)A->data; 224 PetscInt **ia = (PetscInt**)inia,**ja = (PetscInt**)inja; 225 226 PetscFunctionBegin; 227 if (ia && a->i != *ia) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"ia passed back is not one obtained with MatGetRowIJ()"); 228 if (ja && a->j != *ja) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"ja passed back is not one obtained with MatGetRowIJ()"); 229 if (oshift) { 230 for (i=0; i<=(*m); i++) (*ia)[i]--; 231 for (i=0; i<(*ia)[*m]; i++) { 232 (*ja)[i]--; 233 } 234 } 235 PetscFunctionReturn(0); 236 } 237 238 #undef __FUNCT__ 239 #define __FUNCT__ "MatConvertFrom_MPIAdj" 240 PetscErrorCode MatConvertFrom_MPIAdj(Mat A,MatType type,MatReuse reuse,Mat *newmat) 241 { 242 Mat B; 243 PetscErrorCode ierr; 244 PetscInt i,m,N,nzeros = 0,*ia,*ja,len,rstart,cnt,j,*a; 245 const PetscInt *rj; 246 const PetscScalar *ra; 247 MPI_Comm comm; 248 249 PetscFunctionBegin; 250 ierr = MatGetSize(A,NULL,&N);CHKERRQ(ierr); 251 ierr = MatGetLocalSize(A,&m,NULL);CHKERRQ(ierr); 252 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 253 254 /* count the number of nonzeros per row */ 255 for (i=0; i<m; i++) { 256 ierr = MatGetRow(A,i+rstart,&len,&rj,NULL);CHKERRQ(ierr); 257 for (j=0; j<len; j++) { 258 if (rj[j] == i+rstart) {len--; break;} /* don't count diagonal */ 259 } 260 nzeros += len; 261 ierr = MatRestoreRow(A,i+rstart,&len,&rj,NULL);CHKERRQ(ierr); 262 } 263 264 /* malloc space for nonzeros */ 265 ierr = PetscMalloc1(nzeros+1,&a);CHKERRQ(ierr); 266 ierr = PetscMalloc1(N+1,&ia);CHKERRQ(ierr); 267 ierr = PetscMalloc1(nzeros+1,&ja);CHKERRQ(ierr); 268 269 nzeros = 0; 270 ia[0] = 0; 271 for (i=0; i<m; i++) { 272 ierr = MatGetRow(A,i+rstart,&len,&rj,&ra);CHKERRQ(ierr); 273 cnt = 0; 274 for (j=0; j<len; j++) { 275 if (rj[j] != i+rstart) { /* if not diagonal */ 276 a[nzeros+cnt] = (PetscInt) PetscAbsScalar(ra[j]); 277 ja[nzeros+cnt++] = rj[j]; 278 } 279 } 280 ierr = MatRestoreRow(A,i+rstart,&len,&rj,&ra);CHKERRQ(ierr); 281 nzeros += cnt; 282 ia[i+1] = nzeros; 283 } 284 285 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 286 ierr = MatCreate(comm,&B);CHKERRQ(ierr); 287 ierr = MatSetSizes(B,m,PETSC_DETERMINE,PETSC_DETERMINE,N);CHKERRQ(ierr); 288 ierr = MatSetType(B,type);CHKERRQ(ierr); 289 ierr = MatMPIAdjSetPreallocation(B,ia,ja,a);CHKERRQ(ierr); 290 291 if (reuse == MAT_REUSE_MATRIX) { 292 ierr = MatHeaderReplace(A,B);CHKERRQ(ierr); 293 } else { 294 *newmat = B; 295 } 296 PetscFunctionReturn(0); 297 } 298 299 /* -------------------------------------------------------------------*/ 300 static struct _MatOps MatOps_Values = {0, 301 MatGetRow_MPIAdj, 302 MatRestoreRow_MPIAdj, 303 0, 304 /* 4*/ 0, 305 0, 306 0, 307 0, 308 0, 309 0, 310 /*10*/ 0, 311 0, 312 0, 313 0, 314 0, 315 /*15*/ 0, 316 MatEqual_MPIAdj, 317 0, 318 0, 319 0, 320 /*20*/ 0, 321 0, 322 MatSetOption_MPIAdj, 323 0, 324 /*24*/ 0, 325 0, 326 0, 327 0, 328 0, 329 /*29*/ 0, 330 0, 331 0, 332 0, 333 0, 334 /*34*/ 0, 335 0, 336 0, 337 0, 338 0, 339 /*39*/ 0, 340 MatGetSubMatrices_MPIAdj, 341 0, 342 0, 343 0, 344 /*44*/ 0, 345 0, 346 MatShift_Basic, 347 0, 348 0, 349 /*49*/ 0, 350 MatGetRowIJ_MPIAdj, 351 MatRestoreRowIJ_MPIAdj, 352 0, 353 0, 354 /*54*/ 0, 355 0, 356 0, 357 0, 358 0, 359 /*59*/ 0, 360 MatDestroy_MPIAdj, 361 MatView_MPIAdj, 362 MatConvertFrom_MPIAdj, 363 0, 364 /*64*/ 0, 365 0, 366 0, 367 0, 368 0, 369 /*69*/ 0, 370 0, 371 0, 372 0, 373 0, 374 /*74*/ 0, 375 0, 376 0, 377 0, 378 0, 379 /*79*/ 0, 380 0, 381 0, 382 0, 383 0, 384 /*84*/ 0, 385 0, 386 0, 387 0, 388 0, 389 /*89*/ 0, 390 0, 391 0, 392 0, 393 0, 394 /*94*/ 0, 395 0, 396 0, 397 0, 398 0, 399 /*99*/ 0, 400 0, 401 0, 402 0, 403 0, 404 /*104*/ 0, 405 0, 406 0, 407 0, 408 0, 409 /*109*/ 0, 410 0, 411 0, 412 0, 413 0, 414 /*114*/ 0, 415 0, 416 0, 417 0, 418 0, 419 /*119*/ 0, 420 0, 421 0, 422 0, 423 0, 424 /*124*/ 0, 425 0, 426 0, 427 0, 428 0, 429 /*129*/ 0, 430 0, 431 0, 432 0, 433 0, 434 /*134*/ 0, 435 0, 436 0, 437 0, 438 0, 439 /*139*/ 0, 440 0, 441 0 442 }; 443 444 #undef __FUNCT__ 445 #define __FUNCT__ "MatMPIAdjSetPreallocation_MPIAdj" 446 static PetscErrorCode MatMPIAdjSetPreallocation_MPIAdj(Mat B,PetscInt *i,PetscInt *j,PetscInt *values) 447 { 448 Mat_MPIAdj *b = (Mat_MPIAdj*)B->data; 449 PetscErrorCode ierr; 450 #if defined(PETSC_USE_DEBUG) 451 PetscInt ii; 452 #endif 453 454 PetscFunctionBegin; 455 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 456 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 457 458 #if defined(PETSC_USE_DEBUG) 459 if (i[0] != 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"First i[] index must be zero, instead it is %D\n",i[0]); 460 for (ii=1; ii<B->rmap->n; ii++) { 461 if (i[ii] < 0 || i[ii] < i[ii-1]) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i[%D]=%D index is out of range: i[%D]=%D",ii,i[ii],ii-1,i[ii-1]); 462 } 463 for (ii=0; ii<i[B->rmap->n]; ii++) { 464 if (j[ii] < 0 || j[ii] >= B->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column index %D out of range %D\n",ii,j[ii]); 465 } 466 #endif 467 B->preallocated = PETSC_TRUE; 468 469 b->j = j; 470 b->i = i; 471 b->values = values; 472 473 b->nz = i[B->rmap->n]; 474 b->diag = 0; 475 b->symmetric = PETSC_FALSE; 476 b->freeaij = PETSC_TRUE; 477 478 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 479 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 480 PetscFunctionReturn(0); 481 } 482 483 static PetscErrorCode MatGetSubMatrix_MPIAdj_data(Mat adj,IS irows, IS icols, PetscInt **sadj_xadj,PetscInt **sadj_adjncy,PetscInt **sadj_values); 484 485 #undef __FUNCT__ 486 #define __FUNCT__ "MatGetSubMatrices_MPIAdj" 487 PetscErrorCode MatGetSubMatrices_MPIAdj(Mat mat,PetscInt n,const IS irow[],const IS icol[],MatReuse scall,Mat *submat[]) 488 { 489 PetscInt i,irow_n,icol_n,*sxadj,*sadjncy,*svalues; 490 PetscInt *indices,nindx,j,k,loc; 491 const PetscInt *irow_indices,*icol_indices; 492 PetscErrorCode ierr; 493 494 PetscFunctionBegin; 495 nindx = 0; 496 for(i=0; i<n; i++){ 497 ierr = ISGetLocalSize(irow[i],&irow_n);CHKERRQ(ierr); 498 ierr = ISGetLocalSize(icol[i],&icol_n);CHKERRQ(ierr); 499 nindx = nindx>(irow_n+icol_n)? nindx:(irow_n+icol_n); 500 } 501 ierr = PetscCalloc1(nindx,&indices);CHKERRQ(ierr); 502 for(i=0; i<n; i++){ 503 ierr = MatGetSubMatrix_MPIAdj_data(mat,irow[i],icol[i],&sxadj,&sadjncy,&svalues);CHKERRQ(ierr); 504 ierr = ISGetLocalSize(irow[i],&irow_n);CHKERRQ(ierr); 505 ierr = ISGetLocalSize(icol[i],&icol_n);CHKERRQ(ierr); 506 ierr = ISGetIndices(irow[i],&irow_indices);CHKERRQ(ierr); 507 ierr = PetscMemcpy(indices,irow_indices,sizeof(PetscInt)*irow_n);CHKERRQ(ierr); 508 ierr = ISRestoreIndices(irow[i],&irow_indices);CHKERRQ(ierr); 509 ierr = ISGetIndices(icol[i],&icol_indices);CHKERRQ(ierr); 510 ierr = PetscMemcpy(indices+irow_n,icol_indices,sizeof(PetscInt)*icol_n);CHKERRQ(ierr); 511 ierr = ISRestoreIndices(icol[i],&icol_indices);CHKERRQ(ierr); 512 nindx = irow_n+icol_n; 513 ierr = PetscSortRemoveDupsInt(&nindx,indices);CHKERRQ(ierr); 514 for(j=0; j<irow_n; j++){ 515 for(k=sxadj[j]; k<sxadj[j]; k++){ 516 ierr = PetscFindInt(sadjncy[k],nindx,indices,&loc);CHKERRQ(ierr); 517 #if PETSC_USE_DEBUG 518 if(loc<0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"can not find col %d \n",sadjncy[k]); 519 #endif 520 sadjncy[k] = loc; 521 } 522 } 523 if(scall==MAT_INITIAL_MATRIX){ 524 ierr = MatCreateMPIAdj(PETSC_COMM_SELF,irow_n,icol_n,sxadj,sadjncy,svalues,submat[i]);CHKERRQ(ierr); 525 }else{ 526 Mat sadj = *(submat[i]); 527 Mat_MPIAdj *sa = (Mat_MPIAdj*)((sadj)->data); 528 ierr = PetscMemcpy(sa->i,sxadj,sizeof(PetscInt)*(irow_n+1));CHKERRQ(ierr); 529 ierr = PetscMemcpy(sa->j,sadjncy,sizeof(PetscInt)*sxadj[irow_n]);CHKERRQ(ierr); 530 if(svalues){ierr = PetscMemcpy(sa->values,svalues,sizeof(PetscInt)*sxadj[irow_n]);CHKERRQ(ierr);} 531 ierr = PetscFree(sxadj);CHKERRQ(ierr); 532 ierr = PetscFree(sadjncy);CHKERRQ(ierr); 533 if(svalues) {ierr = PetscFree(svalues);CHKERRQ(ierr);} 534 } 535 } 536 ierr = PetscFree(indices);CHKERRQ(ierr); 537 PetscFunctionReturn(0); 538 } 539 540 541 #undef __FUNCT__ 542 #define __FUNCT__ "MatGetSubMatrix_MPIAdj_data" 543 /* 544 * The interface should be easy to use for both MatGetSubMatrix (parallel sub-matrix) and MatGetSubMatrices (sequential sub-matrices) 545 * */ 546 static PetscErrorCode MatGetSubMatrix_MPIAdj_data(Mat adj,IS irows, IS icols, PetscInt **sadj_xadj,PetscInt **sadj_adjncy,PetscInt **sadj_values) 547 { 548 PetscInt nlrows_is,icols_n,i,j,nroots,nleaves,owner,rlocalindex,*ncols_send,*ncols_recv; 549 PetscInt nlrows_mat,*adjncy_recv,Ncols_recv,Ncols_send,*xadj_recv,*values_recv; 550 PetscInt *ncols_recv_offsets,loc,rnclos,*sadjncy,*sxadj,*svalues,isvalue; 551 const PetscInt *irows_indices,*icols_indices,*xadj, *adjncy; 552 Mat_MPIAdj *a = (Mat_MPIAdj*)adj->data; 553 PetscLayout rmap; 554 MPI_Comm comm; 555 PetscSF sf; 556 PetscSFNode *iremote; 557 PetscBool done; 558 PetscErrorCode ierr; 559 560 PetscFunctionBegin; 561 /* communicator */ 562 ierr = PetscObjectGetComm((PetscObject)adj,&comm);CHKERRQ(ierr); 563 /* Layouts */ 564 ierr = MatGetLayouts(adj,&rmap,PETSC_NULL);CHKERRQ(ierr); 565 /* get rows information */ 566 ierr = ISGetLocalSize(irows,&nlrows_is);CHKERRQ(ierr); 567 ierr = ISGetIndices(irows,&irows_indices);CHKERRQ(ierr); 568 ierr = PetscCalloc1(nlrows_is,&iremote);CHKERRQ(ierr); 569 /* construct sf graph*/ 570 nleaves = nlrows_is; 571 for(i=0; i<nlrows_is; i++){ 572 ierr = PetscLayoutFindOwnerIndex(rmap,irows_indices[i],&owner,&rlocalindex);CHKERRQ(ierr); 573 iremote[i].rank = owner; 574 iremote[i].index = rlocalindex; 575 } 576 ierr = MatGetRowIJ(adj,0,PETSC_FALSE,PETSC_FALSE,&nlrows_mat,&xadj,&adjncy,&done);CHKERRQ(ierr); 577 ierr = PetscCalloc4(nlrows_mat,&ncols_send,nlrows_is,&xadj_recv,nlrows_is+1,&ncols_recv_offsets,nlrows_is,&ncols_recv);CHKERRQ(ierr); 578 nroots = nlrows_mat; 579 for(i=0; i<nlrows_mat; i++){ 580 ncols_send[i] = xadj[i+1]-xadj[i]; 581 } 582 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 583 ierr = PetscSFSetGraph(sf,nroots,nleaves,PETSC_NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 584 ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr); 585 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 586 ierr = PetscSFBcastBegin(sf,MPIU_INT,ncols_send,ncols_recv);CHKERRQ(ierr); 587 ierr = PetscSFBcastEnd(sf,MPIU_INT,ncols_send,ncols_recv);CHKERRQ(ierr); 588 ierr = PetscSFBcastBegin(sf,MPIU_INT,xadj,xadj_recv);CHKERRQ(ierr); 589 ierr = PetscSFBcastEnd(sf,MPIU_INT,xadj,xadj_recv);CHKERRQ(ierr); 590 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 591 Ncols_recv =0; 592 for(i=0; i<nlrows_is; i++){ 593 Ncols_recv += ncols_recv[i]; 594 ncols_recv_offsets[i+1] = ncols_recv[i]+ncols_recv_offsets[i]; 595 } 596 Ncols_send = 0; 597 for(i=0; i<nlrows_mat; i++){ 598 Ncols_send += ncols_send[i]; 599 } 600 ierr = PetscCalloc1(Ncols_recv,&iremote);CHKERRQ(ierr); 601 ierr = PetscCalloc1(Ncols_recv,&adjncy_recv);CHKERRQ(ierr); 602 nleaves = Ncols_recv; 603 Ncols_recv = 0; 604 for(i=0; i<nlrows_is; i++){ 605 ierr = PetscLayoutFindOwner(rmap,irows_indices[i],&owner);CHKERRQ(ierr); 606 for(j=0; j<ncols_recv[i]; j++){ 607 iremote[Ncols_recv].rank = owner; 608 iremote[Ncols_recv++].index = xadj_recv[i]+j; 609 } 610 } 611 ierr = ISRestoreIndices(irows,&irows_indices);CHKERRQ(ierr); 612 /*if we need to deal with edge weights */ 613 if(a->values){isvalue=1;}else{isvalue=0;} 614 /*involve a global communication */ 615 ierr = MPI_Allreduce(&isvalue,&isvalue,1,MPIU_INT,MPIU_SUM,comm);CHKERRQ(ierr); 616 if(isvalue){ierr = PetscCalloc1(Ncols_recv,&values_recv);CHKERRQ(ierr);} 617 nroots = Ncols_send; 618 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 619 ierr = PetscSFSetGraph(sf,nroots,nleaves,PETSC_NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 620 ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr); 621 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 622 ierr = PetscSFBcastBegin(sf,MPIU_INT,adjncy,adjncy_recv);CHKERRQ(ierr); 623 ierr = PetscSFBcastEnd(sf,MPIU_INT,adjncy,adjncy_recv);CHKERRQ(ierr); 624 if(isvalue){ 625 ierr = PetscSFBcastBegin(sf,MPIU_INT,a->values,values_recv);CHKERRQ(ierr); 626 ierr = PetscSFBcastEnd(sf,MPIU_INT,a->values,values_recv);CHKERRQ(ierr); 627 } 628 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 629 ierr = MatRestoreRowIJ(adj,0,PETSC_FALSE,PETSC_FALSE,&nlrows_mat,&xadj,&adjncy,&done);CHKERRQ(ierr); 630 ierr = ISGetLocalSize(icols,&icols_n);CHKERRQ(ierr); 631 ierr = ISGetIndices(icols,&icols_indices);CHKERRQ(ierr); 632 rnclos = 0; 633 for(i=0; i<nlrows_is; i++){ 634 for(j=ncols_recv_offsets[i]; j<ncols_recv_offsets[i+1]; j++){ 635 ierr = PetscFindInt(adjncy_recv[j], icols_n, icols_indices, &loc);CHKERRQ(ierr); 636 if(loc<0){ 637 adjncy_recv[j] = -1; 638 if(isvalue) values_recv[j] = -1; 639 ncols_recv[i]--; 640 }else{ 641 rnclos++; 642 } 643 } 644 } 645 ierr = ISRestoreIndices(icols,&icols_indices);CHKERRQ(ierr); 646 ierr = PetscCalloc1(rnclos,&sadjncy);CHKERRQ(ierr); 647 if(isvalue) {ierr = PetscCalloc1(rnclos,&svalues);CHKERRQ(ierr);} 648 ierr = PetscCalloc1(nlrows_is+1,&sxadj);CHKERRQ(ierr); 649 rnclos = 0; 650 for(i=0; i<nlrows_is; i++){ 651 for(j=ncols_recv_offsets[i]; j<ncols_recv_offsets[i+1]; j++){ 652 if(adjncy_recv[j]<0) continue; 653 sadjncy[rnclos] = adjncy_recv[j]; 654 if(isvalue) svalues[rnclos] = values_recv[j]; 655 rnclos++; 656 } 657 } 658 for(i=0; i<nlrows_is; i++){ 659 sxadj[i+1] = sxadj[i]+ncols_recv[i]; 660 } 661 if(sadj_xadj) { *sadj_xadj = sxadj;}else { ierr = PetscFree(sxadj);CHKERRQ(ierr);} 662 if(sadj_adjncy){ *sadj_adjncy = sadjncy;}else{ ierr = PetscFree(sadjncy);CHKERRQ(ierr);} 663 if(sadj_values){ 664 if(isvalue) *sadj_values = svalues; else *sadj_values=0; 665 }else{ 666 if(isvalue) {ierr = PetscFree(svalues);CHKERRQ(ierr);} 667 } 668 ierr = PetscFree4(ncols_send,xadj_recv,ncols_recv_offsets,ncols_recv);CHKERRQ(ierr); 669 ierr = PetscFree(adjncy_recv);CHKERRQ(ierr); 670 if(isvalue) {ierr = PetscFree(values_recv);CHKERRQ(ierr);} 671 PetscFunctionReturn(0); 672 } 673 674 675 #undef __FUNCT__ 676 #define __FUNCT__ "MatMPIAdjCreateNonemptySubcommMat_MPIAdj" 677 static PetscErrorCode MatMPIAdjCreateNonemptySubcommMat_MPIAdj(Mat A,Mat *B) 678 { 679 Mat_MPIAdj *a = (Mat_MPIAdj*)A->data; 680 PetscErrorCode ierr; 681 const PetscInt *ranges; 682 MPI_Comm acomm,bcomm; 683 MPI_Group agroup,bgroup; 684 PetscMPIInt i,rank,size,nranks,*ranks; 685 686 PetscFunctionBegin; 687 *B = NULL; 688 ierr = PetscObjectGetComm((PetscObject)A,&acomm);CHKERRQ(ierr); 689 ierr = MPI_Comm_size(acomm,&size);CHKERRQ(ierr); 690 ierr = MPI_Comm_size(acomm,&rank);CHKERRQ(ierr); 691 ierr = MatGetOwnershipRanges(A,&ranges);CHKERRQ(ierr); 692 for (i=0,nranks=0; i<size; i++) { 693 if (ranges[i+1] - ranges[i] > 0) nranks++; 694 } 695 if (nranks == size) { /* All ranks have a positive number of rows, so we do not need to create a subcomm; */ 696 ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr); 697 *B = A; 698 PetscFunctionReturn(0); 699 } 700 701 ierr = PetscMalloc1(nranks,&ranks);CHKERRQ(ierr); 702 for (i=0,nranks=0; i<size; i++) { 703 if (ranges[i+1] - ranges[i] > 0) ranks[nranks++] = i; 704 } 705 ierr = MPI_Comm_group(acomm,&agroup);CHKERRQ(ierr); 706 ierr = MPI_Group_incl(agroup,nranks,ranks,&bgroup);CHKERRQ(ierr); 707 ierr = PetscFree(ranks);CHKERRQ(ierr); 708 ierr = MPI_Comm_create(acomm,bgroup,&bcomm);CHKERRQ(ierr); 709 ierr = MPI_Group_free(&agroup);CHKERRQ(ierr); 710 ierr = MPI_Group_free(&bgroup);CHKERRQ(ierr); 711 if (bcomm != MPI_COMM_NULL) { 712 PetscInt m,N; 713 Mat_MPIAdj *b; 714 ierr = MatGetLocalSize(A,&m,NULL);CHKERRQ(ierr); 715 ierr = MatGetSize(A,NULL,&N);CHKERRQ(ierr); 716 ierr = MatCreateMPIAdj(bcomm,m,N,a->i,a->j,a->values,B);CHKERRQ(ierr); 717 b = (Mat_MPIAdj*)(*B)->data; 718 b->freeaij = PETSC_FALSE; 719 ierr = MPI_Comm_free(&bcomm);CHKERRQ(ierr); 720 } 721 PetscFunctionReturn(0); 722 } 723 724 #undef __FUNCT__ 725 #define __FUNCT__ "MatMPIAdjCreateNonemptySubcommMat" 726 /*@ 727 MatMPIAdjCreateNonemptySubcommMat - create the same MPIAdj matrix on a subcommunicator containing only processes owning a positive number of rows 728 729 Collective 730 731 Input Arguments: 732 . A - original MPIAdj matrix 733 734 Output Arguments: 735 . B - matrix on subcommunicator, NULL on ranks that owned zero rows of A 736 737 Level: developer 738 739 Note: 740 This function is mostly useful for internal use by mesh partitioning packages that require that every process owns at least one row. 741 742 The matrix B should be destroyed with MatDestroy(). The arrays are not copied, so B should be destroyed before A is destroyed. 743 744 .seealso: MatCreateMPIAdj() 745 @*/ 746 PetscErrorCode MatMPIAdjCreateNonemptySubcommMat(Mat A,Mat *B) 747 { 748 PetscErrorCode ierr; 749 750 PetscFunctionBegin; 751 PetscValidHeaderSpecific(A,MAT_CLASSID,1); 752 ierr = PetscUseMethod(A,"MatMPIAdjCreateNonemptySubcommMat_C",(Mat,Mat*),(A,B));CHKERRQ(ierr); 753 PetscFunctionReturn(0); 754 } 755 756 /*MC 757 MATMPIADJ - MATMPIADJ = "mpiadj" - A matrix type to be used for distributed adjacency matrices, 758 intended for use constructing orderings and partitionings. 759 760 Level: beginner 761 762 .seealso: MatCreateMPIAdj 763 M*/ 764 765 #undef __FUNCT__ 766 #define __FUNCT__ "MatCreate_MPIAdj" 767 PETSC_EXTERN PetscErrorCode MatCreate_MPIAdj(Mat B) 768 { 769 Mat_MPIAdj *b; 770 PetscErrorCode ierr; 771 772 PetscFunctionBegin; 773 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 774 B->data = (void*)b; 775 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 776 B->assembled = PETSC_FALSE; 777 778 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjSetPreallocation_C",MatMPIAdjSetPreallocation_MPIAdj);CHKERRQ(ierr); 779 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjCreateNonemptySubcommMat_C",MatMPIAdjCreateNonemptySubcommMat_MPIAdj);CHKERRQ(ierr); 780 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIADJ);CHKERRQ(ierr); 781 PetscFunctionReturn(0); 782 } 783 784 #undef __FUNCT__ 785 #define __FUNCT__ "MatMPIAdjSetPreallocation" 786 /*@C 787 MatMPIAdjSetPreallocation - Sets the array used for storing the matrix elements 788 789 Logically Collective on MPI_Comm 790 791 Input Parameters: 792 + A - the matrix 793 . i - the indices into j for the start of each row 794 . j - the column indices for each row (sorted for each row). 795 The indices in i and j start with zero (NOT with one). 796 - values - [optional] edge weights 797 798 Level: intermediate 799 800 .seealso: MatCreate(), MatCreateMPIAdj(), MatSetValues() 801 @*/ 802 PetscErrorCode MatMPIAdjSetPreallocation(Mat B,PetscInt *i,PetscInt *j,PetscInt *values) 803 { 804 PetscErrorCode ierr; 805 806 PetscFunctionBegin; 807 ierr = PetscTryMethod(B,"MatMPIAdjSetPreallocation_C",(Mat,PetscInt*,PetscInt*,PetscInt*),(B,i,j,values));CHKERRQ(ierr); 808 PetscFunctionReturn(0); 809 } 810 811 #undef __FUNCT__ 812 #define __FUNCT__ "MatCreateMPIAdj" 813 /*@C 814 MatCreateMPIAdj - Creates a sparse matrix representing an adjacency list. 815 The matrix does not have numerical values associated with it, but is 816 intended for ordering (to reduce bandwidth etc) and partitioning. 817 818 Collective on MPI_Comm 819 820 Input Parameters: 821 + comm - MPI communicator 822 . m - number of local rows 823 . N - number of global columns 824 . i - the indices into j for the start of each row 825 . j - the column indices for each row (sorted for each row). 826 The indices in i and j start with zero (NOT with one). 827 - values -[optional] edge weights 828 829 Output Parameter: 830 . A - the matrix 831 832 Level: intermediate 833 834 Notes: This matrix object does not support most matrix operations, include 835 MatSetValues(). 836 You must NOT free the ii, values and jj arrays yourself. PETSc will free them 837 when the matrix is destroyed; you must allocate them with PetscMalloc(). If you 838 call from Fortran you need not create the arrays with PetscMalloc(). 839 Should not include the matrix diagonals. 840 841 If you already have a matrix, you can create its adjacency matrix by a call 842 to MatConvert, specifying a type of MATMPIADJ. 843 844 Possible values for MatSetOption() - MAT_STRUCTURALLY_SYMMETRIC 845 846 .seealso: MatCreate(), MatConvert(), MatGetOrdering() 847 @*/ 848 PetscErrorCode MatCreateMPIAdj(MPI_Comm comm,PetscInt m,PetscInt N,PetscInt *i,PetscInt *j,PetscInt *values,Mat *A) 849 { 850 PetscErrorCode ierr; 851 852 PetscFunctionBegin; 853 ierr = MatCreate(comm,A);CHKERRQ(ierr); 854 ierr = MatSetSizes(*A,m,PETSC_DETERMINE,PETSC_DETERMINE,N);CHKERRQ(ierr); 855 ierr = MatSetType(*A,MATMPIADJ);CHKERRQ(ierr); 856 ierr = MatMPIAdjSetPreallocation(*A,i,j,values);CHKERRQ(ierr); 857 PetscFunctionReturn(0); 858 } 859 860 861 862 863 864 865 866