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 /* renumber columns */ 515 for(j=0; j<irow_n; j++){ 516 for(k=sxadj[j]; k<sxadj[j+1]; k++){ 517 ierr = PetscFindInt(sadjncy[k],nindx,indices,&loc);CHKERRQ(ierr); 518 #if PETSC_USE_DEBUG 519 if(loc<0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"can not find col %d \n",sadjncy[k]); 520 #endif 521 sadjncy[k] = loc; 522 } 523 } 524 if(scall==MAT_INITIAL_MATRIX){ 525 ierr = MatCreateMPIAdj(PETSC_COMM_SELF,irow_n,icol_n,sxadj,sadjncy,svalues,submat[i]);CHKERRQ(ierr); 526 }else{ 527 Mat sadj = *(submat[i]); 528 Mat_MPIAdj *sa = (Mat_MPIAdj*)((sadj)->data); 529 ierr = PetscMemcpy(sa->i,sxadj,sizeof(PetscInt)*(irow_n+1));CHKERRQ(ierr); 530 ierr = PetscMemcpy(sa->j,sadjncy,sizeof(PetscInt)*sxadj[irow_n]);CHKERRQ(ierr); 531 if(svalues){ierr = PetscMemcpy(sa->values,svalues,sizeof(PetscInt)*sxadj[irow_n]);CHKERRQ(ierr);} 532 ierr = PetscFree(sxadj);CHKERRQ(ierr); 533 ierr = PetscFree(sadjncy);CHKERRQ(ierr); 534 if(svalues) {ierr = PetscFree(svalues);CHKERRQ(ierr);} 535 } 536 } 537 ierr = PetscFree(indices);CHKERRQ(ierr); 538 PetscFunctionReturn(0); 539 } 540 541 542 #undef __FUNCT__ 543 #define __FUNCT__ "MatGetSubMatrix_MPIAdj_data" 544 /* 545 * The interface should be easy to use for both MatGetSubMatrix (parallel sub-matrix) and MatGetSubMatrices (sequential sub-matrices) 546 * */ 547 static PetscErrorCode MatGetSubMatrix_MPIAdj_data(Mat adj,IS irows, IS icols, PetscInt **sadj_xadj,PetscInt **sadj_adjncy,PetscInt **sadj_values) 548 { 549 PetscInt nlrows_is,icols_n,i,j,nroots,nleaves,owner,rlocalindex,*ncols_send,*ncols_recv; 550 PetscInt nlrows_mat,*adjncy_recv,Ncols_recv,Ncols_send,*xadj_recv,*values_recv; 551 PetscInt *ncols_recv_offsets,loc,rnclos,*sadjncy,*sxadj,*svalues,isvalue; 552 const PetscInt *irows_indices,*icols_indices,*xadj, *adjncy; 553 Mat_MPIAdj *a = (Mat_MPIAdj*)adj->data; 554 PetscLayout rmap; 555 MPI_Comm comm; 556 PetscSF sf; 557 PetscSFNode *iremote; 558 PetscBool done; 559 PetscErrorCode ierr; 560 561 PetscFunctionBegin; 562 /* communicator */ 563 ierr = PetscObjectGetComm((PetscObject)adj,&comm);CHKERRQ(ierr); 564 /* Layouts */ 565 ierr = MatGetLayouts(adj,&rmap,PETSC_NULL);CHKERRQ(ierr); 566 /* get rows information */ 567 ierr = ISGetLocalSize(irows,&nlrows_is);CHKERRQ(ierr); 568 ierr = ISGetIndices(irows,&irows_indices);CHKERRQ(ierr); 569 ierr = PetscCalloc1(nlrows_is,&iremote);CHKERRQ(ierr); 570 /* construct sf graph*/ 571 nleaves = nlrows_is; 572 for(i=0; i<nlrows_is; i++){ 573 ierr = PetscLayoutFindOwnerIndex(rmap,irows_indices[i],&owner,&rlocalindex);CHKERRQ(ierr); 574 iremote[i].rank = owner; 575 iremote[i].index = rlocalindex; 576 } 577 ierr = MatGetRowIJ(adj,0,PETSC_FALSE,PETSC_FALSE,&nlrows_mat,&xadj,&adjncy,&done);CHKERRQ(ierr); 578 ierr = PetscCalloc4(nlrows_mat,&ncols_send,nlrows_is,&xadj_recv,nlrows_is+1,&ncols_recv_offsets,nlrows_is,&ncols_recv);CHKERRQ(ierr); 579 nroots = nlrows_mat; 580 for(i=0; i<nlrows_mat; i++){ 581 ncols_send[i] = xadj[i+1]-xadj[i]; 582 } 583 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 584 ierr = PetscSFSetGraph(sf,nroots,nleaves,PETSC_NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 585 ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr); 586 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 587 ierr = PetscSFBcastBegin(sf,MPIU_INT,ncols_send,ncols_recv);CHKERRQ(ierr); 588 ierr = PetscSFBcastEnd(sf,MPIU_INT,ncols_send,ncols_recv);CHKERRQ(ierr); 589 ierr = PetscSFBcastBegin(sf,MPIU_INT,xadj,xadj_recv);CHKERRQ(ierr); 590 ierr = PetscSFBcastEnd(sf,MPIU_INT,xadj,xadj_recv);CHKERRQ(ierr); 591 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 592 Ncols_recv =0; 593 for(i=0; i<nlrows_is; i++){ 594 Ncols_recv += ncols_recv[i]; 595 ncols_recv_offsets[i+1] = ncols_recv[i]+ncols_recv_offsets[i]; 596 } 597 Ncols_send = 0; 598 for(i=0; i<nlrows_mat; i++){ 599 Ncols_send += ncols_send[i]; 600 } 601 ierr = PetscCalloc1(Ncols_recv,&iremote);CHKERRQ(ierr); 602 ierr = PetscCalloc1(Ncols_recv,&adjncy_recv);CHKERRQ(ierr); 603 nleaves = Ncols_recv; 604 Ncols_recv = 0; 605 for(i=0; i<nlrows_is; i++){ 606 ierr = PetscLayoutFindOwner(rmap,irows_indices[i],&owner);CHKERRQ(ierr); 607 for(j=0; j<ncols_recv[i]; j++){ 608 iremote[Ncols_recv].rank = owner; 609 iremote[Ncols_recv++].index = xadj_recv[i]+j; 610 } 611 } 612 ierr = ISRestoreIndices(irows,&irows_indices);CHKERRQ(ierr); 613 /*if we need to deal with edge weights ???*/ 614 if(a->values){isvalue=1;}else{isvalue=0;} 615 /*involve a global communication */ 616 /*ierr = MPI_Allreduce(&isvalue,&isvalue,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);*/ 617 if(isvalue){ierr = PetscCalloc1(Ncols_recv,&values_recv);CHKERRQ(ierr);} 618 nroots = Ncols_send; 619 ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr); 620 ierr = PetscSFSetGraph(sf,nroots,nleaves,PETSC_NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr); 621 ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr); 622 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 623 ierr = PetscSFBcastBegin(sf,MPIU_INT,adjncy,adjncy_recv);CHKERRQ(ierr); 624 ierr = PetscSFBcastEnd(sf,MPIU_INT,adjncy,adjncy_recv);CHKERRQ(ierr); 625 if(isvalue){ 626 ierr = PetscSFBcastBegin(sf,MPIU_INT,a->values,values_recv);CHKERRQ(ierr); 627 ierr = PetscSFBcastEnd(sf,MPIU_INT,a->values,values_recv);CHKERRQ(ierr); 628 } 629 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 630 ierr = MatRestoreRowIJ(adj,0,PETSC_FALSE,PETSC_FALSE,&nlrows_mat,&xadj,&adjncy,&done);CHKERRQ(ierr); 631 ierr = ISGetLocalSize(icols,&icols_n);CHKERRQ(ierr); 632 ierr = ISGetIndices(icols,&icols_indices);CHKERRQ(ierr); 633 rnclos = 0; 634 for(i=0; i<nlrows_is; i++){ 635 for(j=ncols_recv_offsets[i]; j<ncols_recv_offsets[i+1]; j++){ 636 ierr = PetscFindInt(adjncy_recv[j], icols_n, icols_indices, &loc);CHKERRQ(ierr); 637 if(loc<0){ 638 adjncy_recv[j] = -1; 639 if(isvalue) values_recv[j] = -1; 640 ncols_recv[i]--; 641 }else{ 642 rnclos++; 643 } 644 } 645 } 646 ierr = ISRestoreIndices(icols,&icols_indices);CHKERRQ(ierr); 647 ierr = PetscCalloc1(rnclos,&sadjncy);CHKERRQ(ierr); 648 if(isvalue) {ierr = PetscCalloc1(rnclos,&svalues);CHKERRQ(ierr);} 649 ierr = PetscCalloc1(nlrows_is+1,&sxadj);CHKERRQ(ierr); 650 rnclos = 0; 651 for(i=0; i<nlrows_is; i++){ 652 for(j=ncols_recv_offsets[i]; j<ncols_recv_offsets[i+1]; j++){ 653 if(adjncy_recv[j]<0) continue; 654 sadjncy[rnclos] = adjncy_recv[j]; 655 if(isvalue) svalues[rnclos] = values_recv[j]; 656 rnclos++; 657 } 658 } 659 for(i=0; i<nlrows_is; i++){ 660 sxadj[i+1] = sxadj[i]+ncols_recv[i]; 661 } 662 if(sadj_xadj) { *sadj_xadj = sxadj;}else { ierr = PetscFree(sxadj);CHKERRQ(ierr);} 663 if(sadj_adjncy){ *sadj_adjncy = sadjncy;}else{ ierr = PetscFree(sadjncy);CHKERRQ(ierr);} 664 if(sadj_values){ 665 if(isvalue) *sadj_values = svalues; else *sadj_values=0; 666 }else{ 667 if(isvalue) {ierr = PetscFree(svalues);CHKERRQ(ierr);} 668 } 669 ierr = PetscFree4(ncols_send,xadj_recv,ncols_recv_offsets,ncols_recv);CHKERRQ(ierr); 670 ierr = PetscFree(adjncy_recv);CHKERRQ(ierr); 671 if(isvalue) {ierr = PetscFree(values_recv);CHKERRQ(ierr);} 672 PetscFunctionReturn(0); 673 } 674 675 676 #undef __FUNCT__ 677 #define __FUNCT__ "MatMPIAdjCreateNonemptySubcommMat_MPIAdj" 678 static PetscErrorCode MatMPIAdjCreateNonemptySubcommMat_MPIAdj(Mat A,Mat *B) 679 { 680 Mat_MPIAdj *a = (Mat_MPIAdj*)A->data; 681 PetscErrorCode ierr; 682 const PetscInt *ranges; 683 MPI_Comm acomm,bcomm; 684 MPI_Group agroup,bgroup; 685 PetscMPIInt i,rank,size,nranks,*ranks; 686 687 PetscFunctionBegin; 688 *B = NULL; 689 ierr = PetscObjectGetComm((PetscObject)A,&acomm);CHKERRQ(ierr); 690 ierr = MPI_Comm_size(acomm,&size);CHKERRQ(ierr); 691 ierr = MPI_Comm_size(acomm,&rank);CHKERRQ(ierr); 692 ierr = MatGetOwnershipRanges(A,&ranges);CHKERRQ(ierr); 693 for (i=0,nranks=0; i<size; i++) { 694 if (ranges[i+1] - ranges[i] > 0) nranks++; 695 } 696 if (nranks == size) { /* All ranks have a positive number of rows, so we do not need to create a subcomm; */ 697 ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr); 698 *B = A; 699 PetscFunctionReturn(0); 700 } 701 702 ierr = PetscMalloc1(nranks,&ranks);CHKERRQ(ierr); 703 for (i=0,nranks=0; i<size; i++) { 704 if (ranges[i+1] - ranges[i] > 0) ranks[nranks++] = i; 705 } 706 ierr = MPI_Comm_group(acomm,&agroup);CHKERRQ(ierr); 707 ierr = MPI_Group_incl(agroup,nranks,ranks,&bgroup);CHKERRQ(ierr); 708 ierr = PetscFree(ranks);CHKERRQ(ierr); 709 ierr = MPI_Comm_create(acomm,bgroup,&bcomm);CHKERRQ(ierr); 710 ierr = MPI_Group_free(&agroup);CHKERRQ(ierr); 711 ierr = MPI_Group_free(&bgroup);CHKERRQ(ierr); 712 if (bcomm != MPI_COMM_NULL) { 713 PetscInt m,N; 714 Mat_MPIAdj *b; 715 ierr = MatGetLocalSize(A,&m,NULL);CHKERRQ(ierr); 716 ierr = MatGetSize(A,NULL,&N);CHKERRQ(ierr); 717 ierr = MatCreateMPIAdj(bcomm,m,N,a->i,a->j,a->values,B);CHKERRQ(ierr); 718 b = (Mat_MPIAdj*)(*B)->data; 719 b->freeaij = PETSC_FALSE; 720 ierr = MPI_Comm_free(&bcomm);CHKERRQ(ierr); 721 } 722 PetscFunctionReturn(0); 723 } 724 725 #undef __FUNCT__ 726 #define __FUNCT__ "MatMPIAdjCreateNonemptySubcommMat" 727 /*@ 728 MatMPIAdjCreateNonemptySubcommMat - create the same MPIAdj matrix on a subcommunicator containing only processes owning a positive number of rows 729 730 Collective 731 732 Input Arguments: 733 . A - original MPIAdj matrix 734 735 Output Arguments: 736 . B - matrix on subcommunicator, NULL on ranks that owned zero rows of A 737 738 Level: developer 739 740 Note: 741 This function is mostly useful for internal use by mesh partitioning packages that require that every process owns at least one row. 742 743 The matrix B should be destroyed with MatDestroy(). The arrays are not copied, so B should be destroyed before A is destroyed. 744 745 .seealso: MatCreateMPIAdj() 746 @*/ 747 PetscErrorCode MatMPIAdjCreateNonemptySubcommMat(Mat A,Mat *B) 748 { 749 PetscErrorCode ierr; 750 751 PetscFunctionBegin; 752 PetscValidHeaderSpecific(A,MAT_CLASSID,1); 753 ierr = PetscUseMethod(A,"MatMPIAdjCreateNonemptySubcommMat_C",(Mat,Mat*),(A,B));CHKERRQ(ierr); 754 PetscFunctionReturn(0); 755 } 756 757 /*MC 758 MATMPIADJ - MATMPIADJ = "mpiadj" - A matrix type to be used for distributed adjacency matrices, 759 intended for use constructing orderings and partitionings. 760 761 Level: beginner 762 763 .seealso: MatCreateMPIAdj 764 M*/ 765 766 #undef __FUNCT__ 767 #define __FUNCT__ "MatCreate_MPIAdj" 768 PETSC_EXTERN PetscErrorCode MatCreate_MPIAdj(Mat B) 769 { 770 Mat_MPIAdj *b; 771 PetscErrorCode ierr; 772 773 PetscFunctionBegin; 774 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 775 B->data = (void*)b; 776 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 777 B->assembled = PETSC_FALSE; 778 779 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjSetPreallocation_C",MatMPIAdjSetPreallocation_MPIAdj);CHKERRQ(ierr); 780 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAdjCreateNonemptySubcommMat_C",MatMPIAdjCreateNonemptySubcommMat_MPIAdj);CHKERRQ(ierr); 781 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIADJ);CHKERRQ(ierr); 782 PetscFunctionReturn(0); 783 } 784 785 #undef __FUNCT__ 786 #define __FUNCT__ "MatMPIAdjSetPreallocation" 787 /*@C 788 MatMPIAdjSetPreallocation - Sets the array used for storing the matrix elements 789 790 Logically Collective on MPI_Comm 791 792 Input Parameters: 793 + A - the matrix 794 . i - the indices into j for the start of each row 795 . j - the column indices for each row (sorted for each row). 796 The indices in i and j start with zero (NOT with one). 797 - values - [optional] edge weights 798 799 Level: intermediate 800 801 .seealso: MatCreate(), MatCreateMPIAdj(), MatSetValues() 802 @*/ 803 PetscErrorCode MatMPIAdjSetPreallocation(Mat B,PetscInt *i,PetscInt *j,PetscInt *values) 804 { 805 PetscErrorCode ierr; 806 807 PetscFunctionBegin; 808 ierr = PetscTryMethod(B,"MatMPIAdjSetPreallocation_C",(Mat,PetscInt*,PetscInt*,PetscInt*),(B,i,j,values));CHKERRQ(ierr); 809 PetscFunctionReturn(0); 810 } 811 812 #undef __FUNCT__ 813 #define __FUNCT__ "MatCreateMPIAdj" 814 /*@C 815 MatCreateMPIAdj - Creates a sparse matrix representing an adjacency list. 816 The matrix does not have numerical values associated with it, but is 817 intended for ordering (to reduce bandwidth etc) and partitioning. 818 819 Collective on MPI_Comm 820 821 Input Parameters: 822 + comm - MPI communicator 823 . m - number of local rows 824 . N - number of global columns 825 . i - the indices into j for the start of each row 826 . j - the column indices for each row (sorted for each row). 827 The indices in i and j start with zero (NOT with one). 828 - values -[optional] edge weights 829 830 Output Parameter: 831 . A - the matrix 832 833 Level: intermediate 834 835 Notes: This matrix object does not support most matrix operations, include 836 MatSetValues(). 837 You must NOT free the ii, values and jj arrays yourself. PETSc will free them 838 when the matrix is destroyed; you must allocate them with PetscMalloc(). If you 839 call from Fortran you need not create the arrays with PetscMalloc(). 840 Should not include the matrix diagonals. 841 842 If you already have a matrix, you can create its adjacency matrix by a call 843 to MatConvert, specifying a type of MATMPIADJ. 844 845 Possible values for MatSetOption() - MAT_STRUCTURALLY_SYMMETRIC 846 847 .seealso: MatCreate(), MatConvert(), MatGetOrdering() 848 @*/ 849 PetscErrorCode MatCreateMPIAdj(MPI_Comm comm,PetscInt m,PetscInt N,PetscInt *i,PetscInt *j,PetscInt *values,Mat *A) 850 { 851 PetscErrorCode ierr; 852 853 PetscFunctionBegin; 854 ierr = MatCreate(comm,A);CHKERRQ(ierr); 855 ierr = MatSetSizes(*A,m,PETSC_DETERMINE,PETSC_DETERMINE,N);CHKERRQ(ierr); 856 ierr = MatSetType(*A,MATMPIADJ);CHKERRQ(ierr); 857 ierr = MatMPIAdjSetPreallocation(*A,i,j,values);CHKERRQ(ierr); 858 PetscFunctionReturn(0); 859 } 860 861 862 863 864 865 866 867