1 2 3 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 4 #include <petsc/private/vecimpl.h> 5 #include <petsc/private/isimpl.h> 6 #include <petscblaslapack.h> 7 #include <petscsf.h> 8 9 /*MC 10 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 11 12 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 13 and MATMPIAIJ otherwise. As a result, for single process communicators, 14 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 15 for communicators controlling multiple processes. It is recommended that you call both of 16 the above preallocation routines for simplicity. 17 18 Options Database Keys: 19 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 20 21 Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJMKL, MATAIJCRL, and also automatically switches over to use inodes when 22 enough exist. 23 24 Level: beginner 25 26 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ, MATMPIAIJ 27 M*/ 28 29 /*MC 30 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 31 32 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 33 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 34 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 35 for communicators controlling multiple processes. It is recommended that you call both of 36 the above preallocation routines for simplicity. 37 38 Options Database Keys: 39 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 40 41 Level: beginner 42 43 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 44 M*/ 45 46 PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 50 51 PetscFunctionBegin; 52 if (mat->A) { 53 ierr = MatSetBlockSizes(mat->A,rbs,cbs);CHKERRQ(ierr); 54 ierr = MatSetBlockSizes(mat->B,rbs,1);CHKERRQ(ierr); 55 } 56 PetscFunctionReturn(0); 57 } 58 59 PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows) 60 { 61 PetscErrorCode ierr; 62 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 63 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data; 64 Mat_SeqAIJ *b = (Mat_SeqAIJ*)mat->B->data; 65 const PetscInt *ia,*ib; 66 const MatScalar *aa,*bb; 67 PetscInt na,nb,i,j,*rows,cnt=0,n0rows; 68 PetscInt m = M->rmap->n,rstart = M->rmap->rstart; 69 70 PetscFunctionBegin; 71 *keptrows = 0; 72 ia = a->i; 73 ib = b->i; 74 for (i=0; i<m; i++) { 75 na = ia[i+1] - ia[i]; 76 nb = ib[i+1] - ib[i]; 77 if (!na && !nb) { 78 cnt++; 79 goto ok1; 80 } 81 aa = a->a + ia[i]; 82 for (j=0; j<na; j++) { 83 if (aa[j] != 0.0) goto ok1; 84 } 85 bb = b->a + ib[i]; 86 for (j=0; j <nb; j++) { 87 if (bb[j] != 0.0) goto ok1; 88 } 89 cnt++; 90 ok1:; 91 } 92 ierr = MPIU_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr); 93 if (!n0rows) PetscFunctionReturn(0); 94 ierr = PetscMalloc1(M->rmap->n-cnt,&rows);CHKERRQ(ierr); 95 cnt = 0; 96 for (i=0; i<m; i++) { 97 na = ia[i+1] - ia[i]; 98 nb = ib[i+1] - ib[i]; 99 if (!na && !nb) continue; 100 aa = a->a + ia[i]; 101 for (j=0; j<na;j++) { 102 if (aa[j] != 0.0) { 103 rows[cnt++] = rstart + i; 104 goto ok2; 105 } 106 } 107 bb = b->a + ib[i]; 108 for (j=0; j<nb; j++) { 109 if (bb[j] != 0.0) { 110 rows[cnt++] = rstart + i; 111 goto ok2; 112 } 113 } 114 ok2:; 115 } 116 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 117 PetscFunctionReturn(0); 118 } 119 120 PetscErrorCode MatDiagonalSet_MPIAIJ(Mat Y,Vec D,InsertMode is) 121 { 122 PetscErrorCode ierr; 123 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) Y->data; 124 125 PetscFunctionBegin; 126 if (Y->assembled && Y->rmap->rstart == Y->cmap->rstart && Y->rmap->rend == Y->cmap->rend) { 127 ierr = MatDiagonalSet(aij->A,D,is);CHKERRQ(ierr); 128 } else { 129 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 130 } 131 PetscFunctionReturn(0); 132 } 133 134 PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows) 135 { 136 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)M->data; 137 PetscErrorCode ierr; 138 PetscInt i,rstart,nrows,*rows; 139 140 PetscFunctionBegin; 141 *zrows = NULL; 142 ierr = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr); 143 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 144 for (i=0; i<nrows; i++) rows[i] += rstart; 145 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 146 PetscFunctionReturn(0); 147 } 148 149 PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms) 150 { 151 PetscErrorCode ierr; 152 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 153 PetscInt i,n,*garray = aij->garray; 154 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ*) aij->A->data; 155 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ*) aij->B->data; 156 PetscReal *work; 157 158 PetscFunctionBegin; 159 ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr); 160 ierr = PetscCalloc1(n,&work);CHKERRQ(ierr); 161 if (type == NORM_2) { 162 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 163 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]); 164 } 165 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 166 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]); 167 } 168 } else if (type == NORM_1) { 169 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 170 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 171 } 172 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 173 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 174 } 175 } else if (type == NORM_INFINITY) { 176 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 177 work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 178 } 179 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 180 work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]); 181 } 182 183 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 184 if (type == NORM_INFINITY) { 185 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 186 } else { 187 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 188 } 189 ierr = PetscFree(work);CHKERRQ(ierr); 190 if (type == NORM_2) { 191 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 192 } 193 PetscFunctionReturn(0); 194 } 195 196 PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A,IS *is) 197 { 198 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 199 IS sis,gis; 200 PetscErrorCode ierr; 201 const PetscInt *isis,*igis; 202 PetscInt n,*iis,nsis,ngis,rstart,i; 203 204 PetscFunctionBegin; 205 ierr = MatFindOffBlockDiagonalEntries(a->A,&sis);CHKERRQ(ierr); 206 ierr = MatFindNonzeroRows(a->B,&gis);CHKERRQ(ierr); 207 ierr = ISGetSize(gis,&ngis);CHKERRQ(ierr); 208 ierr = ISGetSize(sis,&nsis);CHKERRQ(ierr); 209 ierr = ISGetIndices(sis,&isis);CHKERRQ(ierr); 210 ierr = ISGetIndices(gis,&igis);CHKERRQ(ierr); 211 212 ierr = PetscMalloc1(ngis+nsis,&iis);CHKERRQ(ierr); 213 ierr = PetscMemcpy(iis,igis,ngis*sizeof(PetscInt));CHKERRQ(ierr); 214 ierr = PetscMemcpy(iis+ngis,isis,nsis*sizeof(PetscInt));CHKERRQ(ierr); 215 n = ngis + nsis; 216 ierr = PetscSortRemoveDupsInt(&n,iis);CHKERRQ(ierr); 217 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 218 for (i=0; i<n; i++) iis[i] += rstart; 219 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),n,iis,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 220 221 ierr = ISRestoreIndices(sis,&isis);CHKERRQ(ierr); 222 ierr = ISRestoreIndices(gis,&igis);CHKERRQ(ierr); 223 ierr = ISDestroy(&sis);CHKERRQ(ierr); 224 ierr = ISDestroy(&gis);CHKERRQ(ierr); 225 PetscFunctionReturn(0); 226 } 227 228 /* 229 Distributes a SeqAIJ matrix across a set of processes. Code stolen from 230 MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type. 231 232 Only for square matrices 233 234 Used by a preconditioner, hence PETSC_EXTERN 235 */ 236 PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat) 237 { 238 PetscMPIInt rank,size; 239 PetscInt *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz = 0,*gmataj,cnt,row,*ld,bses[2]; 240 PetscErrorCode ierr; 241 Mat mat; 242 Mat_SeqAIJ *gmata; 243 PetscMPIInt tag; 244 MPI_Status status; 245 PetscBool aij; 246 MatScalar *gmataa,*ao,*ad,*gmataarestore=0; 247 248 PetscFunctionBegin; 249 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 250 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 251 if (!rank) { 252 ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr); 253 if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name); 254 } 255 if (reuse == MAT_INITIAL_MATRIX) { 256 ierr = MatCreate(comm,&mat);CHKERRQ(ierr); 257 ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 258 ierr = MatGetBlockSizes(gmat,&bses[0],&bses[1]);CHKERRQ(ierr); 259 ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr); 260 ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr); 261 ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr); 262 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 263 ierr = PetscMalloc2(m,&dlens,m,&olens);CHKERRQ(ierr); 264 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 265 266 rowners[0] = 0; 267 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 268 rstart = rowners[rank]; 269 rend = rowners[rank+1]; 270 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 271 if (!rank) { 272 gmata = (Mat_SeqAIJ*) gmat->data; 273 /* send row lengths to all processors */ 274 for (i=0; i<m; i++) dlens[i] = gmata->ilen[i]; 275 for (i=1; i<size; i++) { 276 ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 277 } 278 /* determine number diagonal and off-diagonal counts */ 279 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 280 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 281 jj = 0; 282 for (i=0; i<m; i++) { 283 for (j=0; j<dlens[i]; j++) { 284 if (gmata->j[jj] < rstart) ld[i]++; 285 if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++; 286 jj++; 287 } 288 } 289 /* send column indices to other processes */ 290 for (i=1; i<size; i++) { 291 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 292 ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 293 ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 294 } 295 296 /* send numerical values to other processes */ 297 for (i=1; i<size; i++) { 298 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 299 ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 300 } 301 gmataa = gmata->a; 302 gmataj = gmata->j; 303 304 } else { 305 /* receive row lengths */ 306 ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 307 /* receive column indices */ 308 ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 309 ierr = PetscMalloc2(nz,&gmataa,nz,&gmataj);CHKERRQ(ierr); 310 ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 311 /* determine number diagonal and off-diagonal counts */ 312 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 313 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 314 jj = 0; 315 for (i=0; i<m; i++) { 316 for (j=0; j<dlens[i]; j++) { 317 if (gmataj[jj] < rstart) ld[i]++; 318 if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++; 319 jj++; 320 } 321 } 322 /* receive numerical values */ 323 ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 324 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 325 } 326 /* set preallocation */ 327 for (i=0; i<m; i++) { 328 dlens[i] -= olens[i]; 329 } 330 ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr); 331 ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr); 332 333 for (i=0; i<m; i++) { 334 dlens[i] += olens[i]; 335 } 336 cnt = 0; 337 for (i=0; i<m; i++) { 338 row = rstart + i; 339 ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr); 340 cnt += dlens[i]; 341 } 342 if (rank) { 343 ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr); 344 } 345 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 346 ierr = PetscFree(rowners);CHKERRQ(ierr); 347 348 ((Mat_MPIAIJ*)(mat->data))->ld = ld; 349 350 *inmat = mat; 351 } else { /* column indices are already set; only need to move over numerical values from process 0 */ 352 Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data; 353 Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data; 354 mat = *inmat; 355 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 356 if (!rank) { 357 /* send numerical values to other processes */ 358 gmata = (Mat_SeqAIJ*) gmat->data; 359 ierr = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr); 360 gmataa = gmata->a; 361 for (i=1; i<size; i++) { 362 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 363 ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 364 } 365 nz = gmata->i[rowners[1]]-gmata->i[rowners[0]]; 366 } else { 367 /* receive numerical values from process 0*/ 368 nz = Ad->nz + Ao->nz; 369 ierr = PetscMalloc1(nz,&gmataa);CHKERRQ(ierr); gmataarestore = gmataa; 370 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 371 } 372 /* transfer numerical values into the diagonal A and off diagonal B parts of mat */ 373 ld = ((Mat_MPIAIJ*)(mat->data))->ld; 374 ad = Ad->a; 375 ao = Ao->a; 376 if (mat->rmap->n) { 377 i = 0; 378 nz = ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 379 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 380 } 381 for (i=1; i<mat->rmap->n; i++) { 382 nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 383 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 384 } 385 i--; 386 if (mat->rmap->n) { 387 nz = Ao->i[i+1] - Ao->i[i] - ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 388 } 389 if (rank) { 390 ierr = PetscFree(gmataarestore);CHKERRQ(ierr); 391 } 392 } 393 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 394 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 395 PetscFunctionReturn(0); 396 } 397 398 /* 399 Local utility routine that creates a mapping from the global column 400 number to the local number in the off-diagonal part of the local 401 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 402 a slightly higher hash table cost; without it it is not scalable (each processor 403 has an order N integer array but is fast to acess. 404 */ 405 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 406 { 407 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 408 PetscErrorCode ierr; 409 PetscInt n = aij->B->cmap->n,i; 410 411 PetscFunctionBegin; 412 if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray"); 413 #if defined(PETSC_USE_CTABLE) 414 ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 415 for (i=0; i<n; i++) { 416 ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr); 417 } 418 #else 419 ierr = PetscCalloc1(mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 420 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N+1)*sizeof(PetscInt));CHKERRQ(ierr); 421 for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1; 422 #endif 423 PetscFunctionReturn(0); 424 } 425 426 #define MatSetValues_SeqAIJ_A_Private(row,col,value,addv,orow,ocol) \ 427 { \ 428 if (col <= lastcol1) low1 = 0; \ 429 else high1 = nrow1; \ 430 lastcol1 = col;\ 431 while (high1-low1 > 5) { \ 432 t = (low1+high1)/2; \ 433 if (rp1[t] > col) high1 = t; \ 434 else low1 = t; \ 435 } \ 436 for (_i=low1; _i<high1; _i++) { \ 437 if (rp1[_i] > col) break; \ 438 if (rp1[_i] == col) { \ 439 if (addv == ADD_VALUES) ap1[_i] += value; \ 440 else ap1[_i] = value; \ 441 goto a_noinsert; \ 442 } \ 443 } \ 444 if (value == 0.0 && ignorezeroentries && row != col) {low1 = 0; high1 = nrow1;goto a_noinsert;} \ 445 if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;} \ 446 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 447 MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \ 448 N = nrow1++ - 1; a->nz++; high1++; \ 449 /* shift up all the later entries in this row */ \ 450 for (ii=N; ii>=_i; ii--) { \ 451 rp1[ii+1] = rp1[ii]; \ 452 ap1[ii+1] = ap1[ii]; \ 453 } \ 454 rp1[_i] = col; \ 455 ap1[_i] = value; \ 456 A->nonzerostate++;\ 457 a_noinsert: ; \ 458 ailen[row] = nrow1; \ 459 } 460 461 #define MatSetValues_SeqAIJ_B_Private(row,col,value,addv,orow,ocol) \ 462 { \ 463 if (col <= lastcol2) low2 = 0; \ 464 else high2 = nrow2; \ 465 lastcol2 = col; \ 466 while (high2-low2 > 5) { \ 467 t = (low2+high2)/2; \ 468 if (rp2[t] > col) high2 = t; \ 469 else low2 = t; \ 470 } \ 471 for (_i=low2; _i<high2; _i++) { \ 472 if (rp2[_i] > col) break; \ 473 if (rp2[_i] == col) { \ 474 if (addv == ADD_VALUES) ap2[_i] += value; \ 475 else ap2[_i] = value; \ 476 goto b_noinsert; \ 477 } \ 478 } \ 479 if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 480 if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 481 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 482 MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \ 483 N = nrow2++ - 1; b->nz++; high2++; \ 484 /* shift up all the later entries in this row */ \ 485 for (ii=N; ii>=_i; ii--) { \ 486 rp2[ii+1] = rp2[ii]; \ 487 ap2[ii+1] = ap2[ii]; \ 488 } \ 489 rp2[_i] = col; \ 490 ap2[_i] = value; \ 491 B->nonzerostate++; \ 492 b_noinsert: ; \ 493 bilen[row] = nrow2; \ 494 } 495 496 PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[]) 497 { 498 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)A->data; 499 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data; 500 PetscErrorCode ierr; 501 PetscInt l,*garray = mat->garray,diag; 502 503 PetscFunctionBegin; 504 /* code only works for square matrices A */ 505 506 /* find size of row to the left of the diagonal part */ 507 ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr); 508 row = row - diag; 509 for (l=0; l<b->i[row+1]-b->i[row]; l++) { 510 if (garray[b->j[b->i[row]+l]] > diag) break; 511 } 512 ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr); 513 514 /* diagonal part */ 515 ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr); 516 517 /* right of diagonal part */ 518 ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr); 519 PetscFunctionReturn(0); 520 } 521 522 PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 523 { 524 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 525 PetscScalar value; 526 PetscErrorCode ierr; 527 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 528 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 529 PetscBool roworiented = aij->roworiented; 530 531 /* Some Variables required in the macro */ 532 Mat A = aij->A; 533 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 534 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 535 MatScalar *aa = a->a; 536 PetscBool ignorezeroentries = a->ignorezeroentries; 537 Mat B = aij->B; 538 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 539 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 540 MatScalar *ba = b->a; 541 542 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 543 PetscInt nonew; 544 MatScalar *ap1,*ap2; 545 546 PetscFunctionBegin; 547 for (i=0; i<m; i++) { 548 if (im[i] < 0) continue; 549 #if defined(PETSC_USE_DEBUG) 550 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 551 #endif 552 if (im[i] >= rstart && im[i] < rend) { 553 row = im[i] - rstart; 554 lastcol1 = -1; 555 rp1 = aj + ai[row]; 556 ap1 = aa + ai[row]; 557 rmax1 = aimax[row]; 558 nrow1 = ailen[row]; 559 low1 = 0; 560 high1 = nrow1; 561 lastcol2 = -1; 562 rp2 = bj + bi[row]; 563 ap2 = ba + bi[row]; 564 rmax2 = bimax[row]; 565 nrow2 = bilen[row]; 566 low2 = 0; 567 high2 = nrow2; 568 569 for (j=0; j<n; j++) { 570 if (roworiented) value = v[i*n+j]; 571 else value = v[i+j*m]; 572 if (in[j] >= cstart && in[j] < cend) { 573 col = in[j] - cstart; 574 nonew = a->nonew; 575 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 576 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 577 } else if (in[j] < 0) continue; 578 #if defined(PETSC_USE_DEBUG) 579 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 580 #endif 581 else { 582 if (mat->was_assembled) { 583 if (!aij->colmap) { 584 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 585 } 586 #if defined(PETSC_USE_CTABLE) 587 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 588 col--; 589 #else 590 col = aij->colmap[in[j]] - 1; 591 #endif 592 if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) { 593 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 594 col = in[j]; 595 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 596 B = aij->B; 597 b = (Mat_SeqAIJ*)B->data; 598 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a; 599 rp2 = bj + bi[row]; 600 ap2 = ba + bi[row]; 601 rmax2 = bimax[row]; 602 nrow2 = bilen[row]; 603 low2 = 0; 604 high2 = nrow2; 605 bm = aij->B->rmap->n; 606 ba = b->a; 607 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", im[i], in[j]); 608 } else col = in[j]; 609 nonew = b->nonew; 610 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 611 } 612 } 613 } else { 614 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 615 if (!aij->donotstash) { 616 mat->assembled = PETSC_FALSE; 617 if (roworiented) { 618 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 619 } else { 620 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 621 } 622 } 623 } 624 } 625 PetscFunctionReturn(0); 626 } 627 628 PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 629 { 630 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 631 PetscErrorCode ierr; 632 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 633 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 634 635 PetscFunctionBegin; 636 for (i=0; i<m; i++) { 637 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 638 if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1); 639 if (idxm[i] >= rstart && idxm[i] < rend) { 640 row = idxm[i] - rstart; 641 for (j=0; j<n; j++) { 642 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 643 if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1); 644 if (idxn[j] >= cstart && idxn[j] < cend) { 645 col = idxn[j] - cstart; 646 ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 647 } else { 648 if (!aij->colmap) { 649 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 650 } 651 #if defined(PETSC_USE_CTABLE) 652 ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr); 653 col--; 654 #else 655 col = aij->colmap[idxn[j]] - 1; 656 #endif 657 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0; 658 else { 659 ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 660 } 661 } 662 } 663 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 664 } 665 PetscFunctionReturn(0); 666 } 667 668 extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec); 669 670 PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode) 671 { 672 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 673 PetscErrorCode ierr; 674 PetscInt nstash,reallocs; 675 676 PetscFunctionBegin; 677 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 678 679 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 680 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 681 ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 682 PetscFunctionReturn(0); 683 } 684 685 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode) 686 { 687 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 688 Mat_SeqAIJ *a = (Mat_SeqAIJ*)aij->A->data; 689 PetscErrorCode ierr; 690 PetscMPIInt n; 691 PetscInt i,j,rstart,ncols,flg; 692 PetscInt *row,*col; 693 PetscBool other_disassembled; 694 PetscScalar *val; 695 696 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 697 698 PetscFunctionBegin; 699 if (!aij->donotstash && !mat->nooffprocentries) { 700 while (1) { 701 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 702 if (!flg) break; 703 704 for (i=0; i<n; ) { 705 /* Now identify the consecutive vals belonging to the same row */ 706 for (j=i,rstart=row[j]; j<n; j++) { 707 if (row[j] != rstart) break; 708 } 709 if (j < n) ncols = j-i; 710 else ncols = n-i; 711 /* Now assemble all these values with a single function call */ 712 ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr); 713 714 i = j; 715 } 716 } 717 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 718 } 719 ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr); 720 ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr); 721 722 /* determine if any processor has disassembled, if so we must 723 also disassemble ourselfs, in order that we may reassemble. */ 724 /* 725 if nonzero structure of submatrix B cannot change then we know that 726 no processor disassembled thus we can skip this stuff 727 */ 728 if (!((Mat_SeqAIJ*)aij->B->data)->nonew) { 729 ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 730 if (mat->was_assembled && !other_disassembled) { 731 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 732 } 733 } 734 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 735 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 736 } 737 ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr); 738 ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr); 739 ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr); 740 741 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 742 743 aij->rowvalues = 0; 744 745 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 746 if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ; 747 748 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 749 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 750 PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate; 751 ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 752 } 753 PetscFunctionReturn(0); 754 } 755 756 PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 757 { 758 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 759 PetscErrorCode ierr; 760 761 PetscFunctionBegin; 762 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 763 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 764 PetscFunctionReturn(0); 765 } 766 767 PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 768 { 769 Mat_MPIAIJ *mat = (Mat_MPIAIJ *) A->data; 770 PetscInt *lrows; 771 PetscInt r, len; 772 PetscErrorCode ierr; 773 774 PetscFunctionBegin; 775 /* get locally owned rows */ 776 ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr); 777 /* fix right hand side if needed */ 778 if (x && b) { 779 const PetscScalar *xx; 780 PetscScalar *bb; 781 782 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 783 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 784 for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]]; 785 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 786 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 787 } 788 /* Must zero l->B before l->A because the (diag) case below may put values into l->B*/ 789 ierr = MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 790 if (A->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 791 PetscBool cong; 792 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 793 if (cong) A->congruentlayouts = 1; 794 else A->congruentlayouts = 0; 795 } 796 if ((diag != 0.0) && A->congruentlayouts) { 797 ierr = MatZeroRows(mat->A, len, lrows, diag, NULL, NULL);CHKERRQ(ierr); 798 } else if (diag != 0.0) { 799 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 800 if (((Mat_SeqAIJ *) mat->A->data)->nonew) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 801 for (r = 0; r < len; ++r) { 802 const PetscInt row = lrows[r] + A->rmap->rstart; 803 ierr = MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES);CHKERRQ(ierr); 804 } 805 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 806 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 807 } else { 808 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 809 } 810 ierr = PetscFree(lrows);CHKERRQ(ierr); 811 812 /* only change matrix nonzero state if pattern was allowed to be changed */ 813 if (!((Mat_SeqAIJ*)(mat->A->data))->keepnonzeropattern) { 814 PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate; 815 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 816 } 817 PetscFunctionReturn(0); 818 } 819 820 PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 821 { 822 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 823 PetscErrorCode ierr; 824 PetscMPIInt n = A->rmap->n; 825 PetscInt i,j,r,m,p = 0,len = 0; 826 PetscInt *lrows,*owners = A->rmap->range; 827 PetscSFNode *rrows; 828 PetscSF sf; 829 const PetscScalar *xx; 830 PetscScalar *bb,*mask; 831 Vec xmask,lmask; 832 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)l->B->data; 833 const PetscInt *aj, *ii,*ridx; 834 PetscScalar *aa; 835 836 PetscFunctionBegin; 837 /* Create SF where leaves are input rows and roots are owned rows */ 838 ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr); 839 for (r = 0; r < n; ++r) lrows[r] = -1; 840 ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr); 841 for (r = 0; r < N; ++r) { 842 const PetscInt idx = rows[r]; 843 if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N); 844 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */ 845 ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr); 846 } 847 rrows[r].rank = p; 848 rrows[r].index = rows[r] - owners[p]; 849 } 850 ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr); 851 ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr); 852 /* Collect flags for rows to be zeroed */ 853 ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 854 ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 855 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 856 /* Compress and put in row numbers */ 857 for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r; 858 /* zero diagonal part of matrix */ 859 ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr); 860 /* handle off diagonal part of matrix */ 861 ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr); 862 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 863 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 864 for (i=0; i<len; i++) bb[lrows[i]] = 1; 865 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 866 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 867 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 868 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 869 if (x) { 870 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 871 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 872 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 873 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 874 } 875 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 876 /* remove zeroed rows of off diagonal matrix */ 877 ii = aij->i; 878 for (i=0; i<len; i++) { 879 ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr); 880 } 881 /* loop over all elements of off process part of matrix zeroing removed columns*/ 882 if (aij->compressedrow.use) { 883 m = aij->compressedrow.nrows; 884 ii = aij->compressedrow.i; 885 ridx = aij->compressedrow.rindex; 886 for (i=0; i<m; i++) { 887 n = ii[i+1] - ii[i]; 888 aj = aij->j + ii[i]; 889 aa = aij->a + ii[i]; 890 891 for (j=0; j<n; j++) { 892 if (PetscAbsScalar(mask[*aj])) { 893 if (b) bb[*ridx] -= *aa*xx[*aj]; 894 *aa = 0.0; 895 } 896 aa++; 897 aj++; 898 } 899 ridx++; 900 } 901 } else { /* do not use compressed row format */ 902 m = l->B->rmap->n; 903 for (i=0; i<m; i++) { 904 n = ii[i+1] - ii[i]; 905 aj = aij->j + ii[i]; 906 aa = aij->a + ii[i]; 907 for (j=0; j<n; j++) { 908 if (PetscAbsScalar(mask[*aj])) { 909 if (b) bb[i] -= *aa*xx[*aj]; 910 *aa = 0.0; 911 } 912 aa++; 913 aj++; 914 } 915 } 916 } 917 if (x) { 918 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 919 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 920 } 921 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 922 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 923 ierr = PetscFree(lrows);CHKERRQ(ierr); 924 925 /* only change matrix nonzero state if pattern was allowed to be changed */ 926 if (!((Mat_SeqAIJ*)(l->A->data))->keepnonzeropattern) { 927 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 928 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 929 } 930 PetscFunctionReturn(0); 931 } 932 933 PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy) 934 { 935 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 936 PetscErrorCode ierr; 937 PetscInt nt; 938 939 PetscFunctionBegin; 940 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 941 if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt); 942 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 943 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 944 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 945 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 946 PetscFunctionReturn(0); 947 } 948 949 PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx) 950 { 951 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 952 PetscErrorCode ierr; 953 954 PetscFunctionBegin; 955 ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr); 956 PetscFunctionReturn(0); 957 } 958 959 PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 960 { 961 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 962 PetscErrorCode ierr; 963 964 PetscFunctionBegin; 965 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 966 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 967 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 968 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 969 PetscFunctionReturn(0); 970 } 971 972 PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy) 973 { 974 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 975 PetscErrorCode ierr; 976 PetscBool merged; 977 978 PetscFunctionBegin; 979 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 980 /* do nondiagonal part */ 981 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 982 if (!merged) { 983 /* send it on its way */ 984 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 985 /* do local part */ 986 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 987 /* receive remote parts: note this assumes the values are not actually */ 988 /* added in yy until the next line, */ 989 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 990 } else { 991 /* do local part */ 992 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 993 /* send it on its way */ 994 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 995 /* values actually were received in the Begin() but we need to call this nop */ 996 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 997 } 998 PetscFunctionReturn(0); 999 } 1000 1001 PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool *f) 1002 { 1003 MPI_Comm comm; 1004 Mat_MPIAIJ *Aij = (Mat_MPIAIJ*) Amat->data, *Bij; 1005 Mat Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs; 1006 IS Me,Notme; 1007 PetscErrorCode ierr; 1008 PetscInt M,N,first,last,*notme,i; 1009 PetscMPIInt size; 1010 1011 PetscFunctionBegin; 1012 /* Easy test: symmetric diagonal block */ 1013 Bij = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A; 1014 ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr); 1015 if (!*f) PetscFunctionReturn(0); 1016 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1017 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1018 if (size == 1) PetscFunctionReturn(0); 1019 1020 /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */ 1021 ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr); 1022 ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr); 1023 ierr = PetscMalloc1(N-last+first,¬me);CHKERRQ(ierr); 1024 for (i=0; i<first; i++) notme[i] = i; 1025 for (i=last; i<M; i++) notme[i-last+first] = i; 1026 ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr); 1027 ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr); 1028 ierr = MatCreateSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr); 1029 Aoff = Aoffs[0]; 1030 ierr = MatCreateSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr); 1031 Boff = Boffs[0]; 1032 ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr); 1033 ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr); 1034 ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr); 1035 ierr = ISDestroy(&Me);CHKERRQ(ierr); 1036 ierr = ISDestroy(&Notme);CHKERRQ(ierr); 1037 ierr = PetscFree(notme);CHKERRQ(ierr); 1038 PetscFunctionReturn(0); 1039 } 1040 1041 PetscErrorCode MatIsSymmetric_MPIAIJ(Mat A,PetscReal tol,PetscBool *f) 1042 { 1043 PetscErrorCode ierr; 1044 1045 PetscFunctionBegin; 1046 ierr = MatIsTranspose_MPIAIJ(A,A,tol,f);CHKERRQ(ierr); 1047 PetscFunctionReturn(0); 1048 } 1049 1050 PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1051 { 1052 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1053 PetscErrorCode ierr; 1054 1055 PetscFunctionBegin; 1056 /* do nondiagonal part */ 1057 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1058 /* send it on its way */ 1059 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1060 /* do local part */ 1061 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1062 /* receive remote parts */ 1063 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1064 PetscFunctionReturn(0); 1065 } 1066 1067 /* 1068 This only works correctly for square matrices where the subblock A->A is the 1069 diagonal block 1070 */ 1071 PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v) 1072 { 1073 PetscErrorCode ierr; 1074 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1075 1076 PetscFunctionBegin; 1077 if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1078 if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition"); 1079 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1080 PetscFunctionReturn(0); 1081 } 1082 1083 PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa) 1084 { 1085 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1086 PetscErrorCode ierr; 1087 1088 PetscFunctionBegin; 1089 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1090 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1091 PetscFunctionReturn(0); 1092 } 1093 1094 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 1095 { 1096 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1097 PetscErrorCode ierr; 1098 1099 PetscFunctionBegin; 1100 #if defined(PETSC_USE_LOG) 1101 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N); 1102 #endif 1103 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1104 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 1105 ierr = MatDestroy(&aij->A);CHKERRQ(ierr); 1106 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 1107 #if defined(PETSC_USE_CTABLE) 1108 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 1109 #else 1110 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 1111 #endif 1112 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 1113 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 1114 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 1115 if (aij->Mvctx_mpi1) {ierr = VecScatterDestroy(&aij->Mvctx_mpi1);CHKERRQ(ierr);} 1116 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 1117 ierr = PetscFree(aij->ld);CHKERRQ(ierr); 1118 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1119 1120 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1121 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1122 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1123 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1124 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1125 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatResetPreallocation_C",NULL);CHKERRQ(ierr); 1126 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1127 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1128 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1129 #if defined(PETSC_HAVE_ELEMENTAL) 1130 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_elemental_C",NULL);CHKERRQ(ierr); 1131 #endif 1132 #if defined(PETSC_HAVE_HYPRE) 1133 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_hypre_C",NULL);CHKERRQ(ierr); 1134 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMatMatMult_transpose_mpiaij_mpiaij_C",NULL);CHKERRQ(ierr); 1135 #endif 1136 PetscFunctionReturn(0); 1137 } 1138 1139 PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer) 1140 { 1141 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1142 Mat_SeqAIJ *A = (Mat_SeqAIJ*)aij->A->data; 1143 Mat_SeqAIJ *B = (Mat_SeqAIJ*)aij->B->data; 1144 PetscErrorCode ierr; 1145 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1146 int fd; 1147 PetscInt nz,header[4],*row_lengths,*range=0,rlen,i; 1148 PetscInt nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz = 0; 1149 PetscScalar *column_values; 1150 PetscInt message_count,flowcontrolcount; 1151 FILE *file; 1152 1153 PetscFunctionBegin; 1154 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1155 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1156 nz = A->nz + B->nz; 1157 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1158 if (!rank) { 1159 header[0] = MAT_FILE_CLASSID; 1160 header[1] = mat->rmap->N; 1161 header[2] = mat->cmap->N; 1162 1163 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1164 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1165 /* get largest number of rows any processor has */ 1166 rlen = mat->rmap->n; 1167 range = mat->rmap->range; 1168 for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]); 1169 } else { 1170 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1171 rlen = mat->rmap->n; 1172 } 1173 1174 /* load up the local row counts */ 1175 ierr = PetscMalloc1(rlen+1,&row_lengths);CHKERRQ(ierr); 1176 for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1177 1178 /* store the row lengths to the file */ 1179 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1180 if (!rank) { 1181 ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1182 for (i=1; i<size; i++) { 1183 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1184 rlen = range[i+1] - range[i]; 1185 ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1186 ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1187 } 1188 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1189 } else { 1190 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1191 ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1192 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1193 } 1194 ierr = PetscFree(row_lengths);CHKERRQ(ierr); 1195 1196 /* load up the local column indices */ 1197 nzmax = nz; /* th processor needs space a largest processor needs */ 1198 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1199 ierr = PetscMalloc1(nzmax+1,&column_indices);CHKERRQ(ierr); 1200 cnt = 0; 1201 for (i=0; i<mat->rmap->n; i++) { 1202 for (j=B->i[i]; j<B->i[i+1]; j++) { 1203 if ((col = garray[B->j[j]]) > cstart) break; 1204 column_indices[cnt++] = col; 1205 } 1206 for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart; 1207 for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]]; 1208 } 1209 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1210 1211 /* store the column indices to the file */ 1212 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1213 if (!rank) { 1214 MPI_Status status; 1215 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1216 for (i=1; i<size; i++) { 1217 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1218 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1219 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1220 ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1221 ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1222 } 1223 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1224 } else { 1225 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1226 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1227 ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1228 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1229 } 1230 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1231 1232 /* load up the local column values */ 1233 ierr = PetscMalloc1(nzmax+1,&column_values);CHKERRQ(ierr); 1234 cnt = 0; 1235 for (i=0; i<mat->rmap->n; i++) { 1236 for (j=B->i[i]; j<B->i[i+1]; j++) { 1237 if (garray[B->j[j]] > cstart) break; 1238 column_values[cnt++] = B->a[j]; 1239 } 1240 for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k]; 1241 for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j]; 1242 } 1243 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1244 1245 /* store the column values to the file */ 1246 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1247 if (!rank) { 1248 MPI_Status status; 1249 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1250 for (i=1; i<size; i++) { 1251 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1252 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1253 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1254 ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1255 ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1256 } 1257 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1258 } else { 1259 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1260 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1261 ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1262 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1263 } 1264 ierr = PetscFree(column_values);CHKERRQ(ierr); 1265 1266 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1267 if (file) fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(mat->rmap->bs)); 1268 PetscFunctionReturn(0); 1269 } 1270 1271 #include <petscdraw.h> 1272 PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 1273 { 1274 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1275 PetscErrorCode ierr; 1276 PetscMPIInt rank = aij->rank,size = aij->size; 1277 PetscBool isdraw,iascii,isbinary; 1278 PetscViewer sviewer; 1279 PetscViewerFormat format; 1280 1281 PetscFunctionBegin; 1282 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1283 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1284 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1285 if (iascii) { 1286 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1287 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1288 MatInfo info; 1289 PetscBool inodes; 1290 1291 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1292 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 1293 ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr); 1294 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 1295 if (!inodes) { 1296 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n", 1297 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1298 } else { 1299 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n", 1300 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1301 } 1302 ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1303 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1304 ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1305 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1306 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1307 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 1308 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1309 ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr); 1310 PetscFunctionReturn(0); 1311 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1312 PetscInt inodecount,inodelimit,*inodes; 1313 ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr); 1314 if (inodes) { 1315 ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr); 1316 } else { 1317 ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr); 1318 } 1319 PetscFunctionReturn(0); 1320 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1321 PetscFunctionReturn(0); 1322 } 1323 } else if (isbinary) { 1324 if (size == 1) { 1325 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1326 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1327 } else { 1328 ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1329 } 1330 PetscFunctionReturn(0); 1331 } else if (isdraw) { 1332 PetscDraw draw; 1333 PetscBool isnull; 1334 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1335 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 1336 if (isnull) PetscFunctionReturn(0); 1337 } 1338 1339 { 1340 /* assemble the entire matrix onto first processor. */ 1341 Mat A; 1342 Mat_SeqAIJ *Aloc; 1343 PetscInt M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct; 1344 MatScalar *a; 1345 1346 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1347 if (!rank) { 1348 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1349 } else { 1350 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1351 } 1352 /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */ 1353 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 1354 ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr); 1355 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1356 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1357 1358 /* copy over the A part */ 1359 Aloc = (Mat_SeqAIJ*)aij->A->data; 1360 m = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1361 row = mat->rmap->rstart; 1362 for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart; 1363 for (i=0; i<m; i++) { 1364 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr); 1365 row++; 1366 a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i]; 1367 } 1368 aj = Aloc->j; 1369 for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart; 1370 1371 /* copy over the B part */ 1372 Aloc = (Mat_SeqAIJ*)aij->B->data; 1373 m = aij->B->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1374 row = mat->rmap->rstart; 1375 ierr = PetscMalloc1(ai[m]+1,&cols);CHKERRQ(ierr); 1376 ct = cols; 1377 for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]]; 1378 for (i=0; i<m; i++) { 1379 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr); 1380 row++; 1381 a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i]; 1382 } 1383 ierr = PetscFree(ct);CHKERRQ(ierr); 1384 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1385 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1386 /* 1387 Everyone has to call to draw the matrix since the graphics waits are 1388 synchronized across all processors that share the PetscDraw object 1389 */ 1390 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1391 if (!rank) { 1392 ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1393 ierr = MatView_SeqAIJ(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1394 } 1395 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1396 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1397 ierr = MatDestroy(&A);CHKERRQ(ierr); 1398 } 1399 PetscFunctionReturn(0); 1400 } 1401 1402 PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer) 1403 { 1404 PetscErrorCode ierr; 1405 PetscBool iascii,isdraw,issocket,isbinary; 1406 1407 PetscFunctionBegin; 1408 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1409 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1410 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1411 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1412 if (iascii || isdraw || isbinary || issocket) { 1413 ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1414 } 1415 PetscFunctionReturn(0); 1416 } 1417 1418 PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1419 { 1420 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1421 PetscErrorCode ierr; 1422 Vec bb1 = 0; 1423 PetscBool hasop; 1424 1425 PetscFunctionBegin; 1426 if (flag == SOR_APPLY_UPPER) { 1427 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1428 PetscFunctionReturn(0); 1429 } 1430 1431 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) { 1432 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 1433 } 1434 1435 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1436 if (flag & SOR_ZERO_INITIAL_GUESS) { 1437 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1438 its--; 1439 } 1440 1441 while (its--) { 1442 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1443 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1444 1445 /* update rhs: bb1 = bb - B*x */ 1446 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1447 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1448 1449 /* local sweep */ 1450 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1451 } 1452 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1453 if (flag & SOR_ZERO_INITIAL_GUESS) { 1454 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1455 its--; 1456 } 1457 while (its--) { 1458 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1459 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1460 1461 /* update rhs: bb1 = bb - B*x */ 1462 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1463 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1464 1465 /* local sweep */ 1466 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1467 } 1468 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1469 if (flag & SOR_ZERO_INITIAL_GUESS) { 1470 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1471 its--; 1472 } 1473 while (its--) { 1474 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1475 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1476 1477 /* update rhs: bb1 = bb - B*x */ 1478 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1479 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1480 1481 /* local sweep */ 1482 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1483 } 1484 } else if (flag & SOR_EISENSTAT) { 1485 Vec xx1; 1486 1487 ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr); 1488 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr); 1489 1490 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1491 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1492 if (!mat->diag) { 1493 ierr = MatCreateVecs(matin,&mat->diag,NULL);CHKERRQ(ierr); 1494 ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr); 1495 } 1496 ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr); 1497 if (hasop) { 1498 ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr); 1499 } else { 1500 ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr); 1501 } 1502 ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr); 1503 1504 ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr); 1505 1506 /* local sweep */ 1507 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr); 1508 ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr); 1509 ierr = VecDestroy(&xx1);CHKERRQ(ierr); 1510 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported"); 1511 1512 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 1513 1514 matin->factorerrortype = mat->A->factorerrortype; 1515 PetscFunctionReturn(0); 1516 } 1517 1518 PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B) 1519 { 1520 Mat aA,aB,Aperm; 1521 const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj; 1522 PetscScalar *aa,*ba; 1523 PetscInt i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest; 1524 PetscSF rowsf,sf; 1525 IS parcolp = NULL; 1526 PetscBool done; 1527 PetscErrorCode ierr; 1528 1529 PetscFunctionBegin; 1530 ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); 1531 ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr); 1532 ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr); 1533 ierr = PetscMalloc3(PetscMax(m,n),&work,m,&rdest,n,&cdest);CHKERRQ(ierr); 1534 1535 /* Invert row permutation to find out where my rows should go */ 1536 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr); 1537 ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr); 1538 ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr); 1539 for (i=0; i<m; i++) work[i] = A->rmap->rstart + i; 1540 ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1541 ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1542 1543 /* Invert column permutation to find out where my columns should go */ 1544 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1545 ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr); 1546 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1547 for (i=0; i<n; i++) work[i] = A->cmap->rstart + i; 1548 ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1549 ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1550 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1551 1552 ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr); 1553 ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr); 1554 ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr); 1555 1556 /* Find out where my gcols should go */ 1557 ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr); 1558 ierr = PetscMalloc1(ng,&gcdest);CHKERRQ(ierr); 1559 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1560 ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr); 1561 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1562 ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1563 ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1564 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1565 1566 ierr = PetscCalloc4(m,&dnnz,m,&onnz,m,&tdnnz,m,&tonnz);CHKERRQ(ierr); 1567 ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1568 ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1569 for (i=0; i<m; i++) { 1570 PetscInt row = rdest[i],rowner; 1571 ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr); 1572 for (j=ai[i]; j<ai[i+1]; j++) { 1573 PetscInt cowner,col = cdest[aj[j]]; 1574 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */ 1575 if (rowner == cowner) dnnz[i]++; 1576 else onnz[i]++; 1577 } 1578 for (j=bi[i]; j<bi[i+1]; j++) { 1579 PetscInt cowner,col = gcdest[bj[j]]; 1580 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); 1581 if (rowner == cowner) dnnz[i]++; 1582 else onnz[i]++; 1583 } 1584 } 1585 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1586 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1587 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1588 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1589 ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr); 1590 1591 ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr); 1592 ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr); 1593 ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr); 1594 for (i=0; i<m; i++) { 1595 PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */ 1596 PetscInt j0,rowlen; 1597 rowlen = ai[i+1] - ai[i]; 1598 for (j0=j=0; j<rowlen; j0=j) { /* rowlen could be larger than number of rows m, so sum in batches */ 1599 for ( ; j<PetscMin(rowlen,j0+m); j++) acols[j-j0] = cdest[aj[ai[i]+j]]; 1600 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,acols,aa+ai[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1601 } 1602 rowlen = bi[i+1] - bi[i]; 1603 for (j0=j=0; j<rowlen; j0=j) { 1604 for ( ; j<PetscMin(rowlen,j0+m); j++) bcols[j-j0] = gcdest[bj[bi[i]+j]]; 1605 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,bcols,ba+bi[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1606 } 1607 } 1608 ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1609 ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1610 ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1611 ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1612 ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr); 1613 ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr); 1614 ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr); 1615 ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr); 1616 ierr = PetscFree(gcdest);CHKERRQ(ierr); 1617 if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);} 1618 *B = Aperm; 1619 PetscFunctionReturn(0); 1620 } 1621 1622 PetscErrorCode MatGetGhosts_MPIAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 1623 { 1624 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1625 PetscErrorCode ierr; 1626 1627 PetscFunctionBegin; 1628 ierr = MatGetSize(aij->B,NULL,nghosts);CHKERRQ(ierr); 1629 if (ghosts) *ghosts = aij->garray; 1630 PetscFunctionReturn(0); 1631 } 1632 1633 PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1634 { 1635 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1636 Mat A = mat->A,B = mat->B; 1637 PetscErrorCode ierr; 1638 PetscReal isend[5],irecv[5]; 1639 1640 PetscFunctionBegin; 1641 info->block_size = 1.0; 1642 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1643 1644 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1645 isend[3] = info->memory; isend[4] = info->mallocs; 1646 1647 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1648 1649 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1650 isend[3] += info->memory; isend[4] += info->mallocs; 1651 if (flag == MAT_LOCAL) { 1652 info->nz_used = isend[0]; 1653 info->nz_allocated = isend[1]; 1654 info->nz_unneeded = isend[2]; 1655 info->memory = isend[3]; 1656 info->mallocs = isend[4]; 1657 } else if (flag == MAT_GLOBAL_MAX) { 1658 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1659 1660 info->nz_used = irecv[0]; 1661 info->nz_allocated = irecv[1]; 1662 info->nz_unneeded = irecv[2]; 1663 info->memory = irecv[3]; 1664 info->mallocs = irecv[4]; 1665 } else if (flag == MAT_GLOBAL_SUM) { 1666 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1667 1668 info->nz_used = irecv[0]; 1669 info->nz_allocated = irecv[1]; 1670 info->nz_unneeded = irecv[2]; 1671 info->memory = irecv[3]; 1672 info->mallocs = irecv[4]; 1673 } 1674 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1675 info->fill_ratio_needed = 0; 1676 info->factor_mallocs = 0; 1677 PetscFunctionReturn(0); 1678 } 1679 1680 PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg) 1681 { 1682 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1683 PetscErrorCode ierr; 1684 1685 PetscFunctionBegin; 1686 switch (op) { 1687 case MAT_NEW_NONZERO_LOCATIONS: 1688 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1689 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1690 case MAT_KEEP_NONZERO_PATTERN: 1691 case MAT_NEW_NONZERO_LOCATION_ERR: 1692 case MAT_USE_INODES: 1693 case MAT_IGNORE_ZERO_ENTRIES: 1694 MatCheckPreallocated(A,1); 1695 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1696 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1697 break; 1698 case MAT_ROW_ORIENTED: 1699 MatCheckPreallocated(A,1); 1700 a->roworiented = flg; 1701 1702 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1703 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1704 break; 1705 case MAT_NEW_DIAGONALS: 1706 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1707 break; 1708 case MAT_IGNORE_OFF_PROC_ENTRIES: 1709 a->donotstash = flg; 1710 break; 1711 case MAT_SPD: 1712 A->spd_set = PETSC_TRUE; 1713 A->spd = flg; 1714 if (flg) { 1715 A->symmetric = PETSC_TRUE; 1716 A->structurally_symmetric = PETSC_TRUE; 1717 A->symmetric_set = PETSC_TRUE; 1718 A->structurally_symmetric_set = PETSC_TRUE; 1719 } 1720 break; 1721 case MAT_SYMMETRIC: 1722 MatCheckPreallocated(A,1); 1723 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1724 break; 1725 case MAT_STRUCTURALLY_SYMMETRIC: 1726 MatCheckPreallocated(A,1); 1727 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1728 break; 1729 case MAT_HERMITIAN: 1730 MatCheckPreallocated(A,1); 1731 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1732 break; 1733 case MAT_SYMMETRY_ETERNAL: 1734 MatCheckPreallocated(A,1); 1735 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1736 break; 1737 case MAT_SUBMAT_SINGLEIS: 1738 A->submat_singleis = flg; 1739 break; 1740 case MAT_STRUCTURE_ONLY: 1741 /* The option is handled directly by MatSetOption() */ 1742 break; 1743 default: 1744 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1745 } 1746 PetscFunctionReturn(0); 1747 } 1748 1749 PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1750 { 1751 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1752 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1753 PetscErrorCode ierr; 1754 PetscInt i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart; 1755 PetscInt nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend; 1756 PetscInt *cmap,*idx_p; 1757 1758 PetscFunctionBegin; 1759 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1760 mat->getrowactive = PETSC_TRUE; 1761 1762 if (!mat->rowvalues && (idx || v)) { 1763 /* 1764 allocate enough space to hold information from the longest row. 1765 */ 1766 Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data; 1767 PetscInt max = 1,tmp; 1768 for (i=0; i<matin->rmap->n; i++) { 1769 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1770 if (max < tmp) max = tmp; 1771 } 1772 ierr = PetscMalloc2(max,&mat->rowvalues,max,&mat->rowindices);CHKERRQ(ierr); 1773 } 1774 1775 if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows"); 1776 lrow = row - rstart; 1777 1778 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1779 if (!v) {pvA = 0; pvB = 0;} 1780 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1781 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1782 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1783 nztot = nzA + nzB; 1784 1785 cmap = mat->garray; 1786 if (v || idx) { 1787 if (nztot) { 1788 /* Sort by increasing column numbers, assuming A and B already sorted */ 1789 PetscInt imark = -1; 1790 if (v) { 1791 *v = v_p = mat->rowvalues; 1792 for (i=0; i<nzB; i++) { 1793 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1794 else break; 1795 } 1796 imark = i; 1797 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1798 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1799 } 1800 if (idx) { 1801 *idx = idx_p = mat->rowindices; 1802 if (imark > -1) { 1803 for (i=0; i<imark; i++) { 1804 idx_p[i] = cmap[cworkB[i]]; 1805 } 1806 } else { 1807 for (i=0; i<nzB; i++) { 1808 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1809 else break; 1810 } 1811 imark = i; 1812 } 1813 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart + cworkA[i]; 1814 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]]; 1815 } 1816 } else { 1817 if (idx) *idx = 0; 1818 if (v) *v = 0; 1819 } 1820 } 1821 *nz = nztot; 1822 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1823 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1824 PetscFunctionReturn(0); 1825 } 1826 1827 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1828 { 1829 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1830 1831 PetscFunctionBegin; 1832 if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first"); 1833 aij->getrowactive = PETSC_FALSE; 1834 PetscFunctionReturn(0); 1835 } 1836 1837 PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm) 1838 { 1839 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1840 Mat_SeqAIJ *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data; 1841 PetscErrorCode ierr; 1842 PetscInt i,j,cstart = mat->cmap->rstart; 1843 PetscReal sum = 0.0; 1844 MatScalar *v; 1845 1846 PetscFunctionBegin; 1847 if (aij->size == 1) { 1848 ierr = MatNorm(aij->A,type,norm);CHKERRQ(ierr); 1849 } else { 1850 if (type == NORM_FROBENIUS) { 1851 v = amat->a; 1852 for (i=0; i<amat->nz; i++) { 1853 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1854 } 1855 v = bmat->a; 1856 for (i=0; i<bmat->nz; i++) { 1857 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1858 } 1859 ierr = MPIU_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1860 *norm = PetscSqrtReal(*norm); 1861 ierr = PetscLogFlops(2*amat->nz+2*bmat->nz);CHKERRQ(ierr); 1862 } else if (type == NORM_1) { /* max column norm */ 1863 PetscReal *tmp,*tmp2; 1864 PetscInt *jj,*garray = aij->garray; 1865 ierr = PetscCalloc1(mat->cmap->N+1,&tmp);CHKERRQ(ierr); 1866 ierr = PetscMalloc1(mat->cmap->N+1,&tmp2);CHKERRQ(ierr); 1867 *norm = 0.0; 1868 v = amat->a; jj = amat->j; 1869 for (j=0; j<amat->nz; j++) { 1870 tmp[cstart + *jj++] += PetscAbsScalar(*v); v++; 1871 } 1872 v = bmat->a; jj = bmat->j; 1873 for (j=0; j<bmat->nz; j++) { 1874 tmp[garray[*jj++]] += PetscAbsScalar(*v); v++; 1875 } 1876 ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1877 for (j=0; j<mat->cmap->N; j++) { 1878 if (tmp2[j] > *norm) *norm = tmp2[j]; 1879 } 1880 ierr = PetscFree(tmp);CHKERRQ(ierr); 1881 ierr = PetscFree(tmp2);CHKERRQ(ierr); 1882 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1883 } else if (type == NORM_INFINITY) { /* max row norm */ 1884 PetscReal ntemp = 0.0; 1885 for (j=0; j<aij->A->rmap->n; j++) { 1886 v = amat->a + amat->i[j]; 1887 sum = 0.0; 1888 for (i=0; i<amat->i[j+1]-amat->i[j]; i++) { 1889 sum += PetscAbsScalar(*v); v++; 1890 } 1891 v = bmat->a + bmat->i[j]; 1892 for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) { 1893 sum += PetscAbsScalar(*v); v++; 1894 } 1895 if (sum > ntemp) ntemp = sum; 1896 } 1897 ierr = MPIU_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1898 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1899 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm"); 1900 } 1901 PetscFunctionReturn(0); 1902 } 1903 1904 PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout) 1905 { 1906 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1907 Mat_SeqAIJ *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data; 1908 PetscErrorCode ierr; 1909 PetscInt M = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i; 1910 PetscInt cstart = A->cmap->rstart,ncol; 1911 Mat B; 1912 MatScalar *array; 1913 1914 PetscFunctionBegin; 1915 if (reuse == MAT_INPLACE_MATRIX && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1916 1917 ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n; 1918 ai = Aloc->i; aj = Aloc->j; 1919 bi = Bloc->i; bj = Bloc->j; 1920 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1921 PetscInt *d_nnz,*g_nnz,*o_nnz; 1922 PetscSFNode *oloc; 1923 PETSC_UNUSED PetscSF sf; 1924 1925 ierr = PetscMalloc4(na,&d_nnz,na,&o_nnz,nb,&g_nnz,nb,&oloc);CHKERRQ(ierr); 1926 /* compute d_nnz for preallocation */ 1927 ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1928 for (i=0; i<ai[ma]; i++) { 1929 d_nnz[aj[i]]++; 1930 aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1931 } 1932 /* compute local off-diagonal contributions */ 1933 ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr); 1934 for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++; 1935 /* map those to global */ 1936 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1937 ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr); 1938 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1939 ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1940 ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1941 ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1942 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1943 1944 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1945 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1946 ierr = MatSetBlockSizes(B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 1947 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1948 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 1949 ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr); 1950 } else { 1951 B = *matout; 1952 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1953 for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1954 } 1955 1956 /* copy over the A part */ 1957 array = Aloc->a; 1958 row = A->rmap->rstart; 1959 for (i=0; i<ma; i++) { 1960 ncol = ai[i+1]-ai[i]; 1961 ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1962 row++; 1963 array += ncol; aj += ncol; 1964 } 1965 aj = Aloc->j; 1966 for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */ 1967 1968 /* copy over the B part */ 1969 ierr = PetscCalloc1(bi[mb],&cols);CHKERRQ(ierr); 1970 array = Bloc->a; 1971 row = A->rmap->rstart; 1972 for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]]; 1973 cols_tmp = cols; 1974 for (i=0; i<mb; i++) { 1975 ncol = bi[i+1]-bi[i]; 1976 ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1977 row++; 1978 array += ncol; cols_tmp += ncol; 1979 } 1980 ierr = PetscFree(cols);CHKERRQ(ierr); 1981 1982 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1983 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1984 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 1985 *matout = B; 1986 } else { 1987 ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr); 1988 } 1989 PetscFunctionReturn(0); 1990 } 1991 1992 PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr) 1993 { 1994 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1995 Mat a = aij->A,b = aij->B; 1996 PetscErrorCode ierr; 1997 PetscInt s1,s2,s3; 1998 1999 PetscFunctionBegin; 2000 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 2001 if (rr) { 2002 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 2003 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 2004 /* Overlap communication with computation. */ 2005 ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2006 } 2007 if (ll) { 2008 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 2009 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 2010 ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr); 2011 } 2012 /* scale the diagonal block */ 2013 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 2014 2015 if (rr) { 2016 /* Do a scatter end and then right scale the off-diagonal block */ 2017 ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2018 ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr); 2019 } 2020 PetscFunctionReturn(0); 2021 } 2022 2023 PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2024 { 2025 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2026 PetscErrorCode ierr; 2027 2028 PetscFunctionBegin; 2029 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 2030 PetscFunctionReturn(0); 2031 } 2032 2033 PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool *flag) 2034 { 2035 Mat_MPIAIJ *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data; 2036 Mat a,b,c,d; 2037 PetscBool flg; 2038 PetscErrorCode ierr; 2039 2040 PetscFunctionBegin; 2041 a = matA->A; b = matA->B; 2042 c = matB->A; d = matB->B; 2043 2044 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 2045 if (flg) { 2046 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 2047 } 2048 ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2049 PetscFunctionReturn(0); 2050 } 2051 2052 PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str) 2053 { 2054 PetscErrorCode ierr; 2055 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2056 Mat_MPIAIJ *b = (Mat_MPIAIJ*)B->data; 2057 2058 PetscFunctionBegin; 2059 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2060 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2061 /* because of the column compression in the off-processor part of the matrix a->B, 2062 the number of columns in a->B and b->B may be different, hence we cannot call 2063 the MatCopy() directly on the two parts. If need be, we can provide a more 2064 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2065 then copying the submatrices */ 2066 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2067 } else { 2068 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 2069 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 2070 } 2071 ierr = PetscObjectStateIncrease((PetscObject)B);CHKERRQ(ierr); 2072 PetscFunctionReturn(0); 2073 } 2074 2075 PetscErrorCode MatSetUp_MPIAIJ(Mat A) 2076 { 2077 PetscErrorCode ierr; 2078 2079 PetscFunctionBegin; 2080 ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 2081 PetscFunctionReturn(0); 2082 } 2083 2084 /* 2085 Computes the number of nonzeros per row needed for preallocation when X and Y 2086 have different nonzero structure. 2087 */ 2088 PetscErrorCode MatAXPYGetPreallocation_MPIX_private(PetscInt m,const PetscInt *xi,const PetscInt *xj,const PetscInt *xltog,const PetscInt *yi,const PetscInt *yj,const PetscInt *yltog,PetscInt *nnz) 2089 { 2090 PetscInt i,j,k,nzx,nzy; 2091 2092 PetscFunctionBegin; 2093 /* Set the number of nonzeros in the new matrix */ 2094 for (i=0; i<m; i++) { 2095 const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i]; 2096 nzx = xi[i+1] - xi[i]; 2097 nzy = yi[i+1] - yi[i]; 2098 nnz[i] = 0; 2099 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2100 for (; k<nzy && yltog[yjj[k]]<xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */ 2101 if (k<nzy && yltog[yjj[k]]==xltog[xjj[j]]) k++; /* Skip duplicate */ 2102 nnz[i]++; 2103 } 2104 for (; k<nzy; k++) nnz[i]++; 2105 } 2106 PetscFunctionReturn(0); 2107 } 2108 2109 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2110 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 2111 { 2112 PetscErrorCode ierr; 2113 PetscInt m = Y->rmap->N; 2114 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2115 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2116 2117 PetscFunctionBegin; 2118 ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr); 2119 PetscFunctionReturn(0); 2120 } 2121 2122 PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2123 { 2124 PetscErrorCode ierr; 2125 Mat_MPIAIJ *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data; 2126 PetscBLASInt bnz,one=1; 2127 Mat_SeqAIJ *x,*y; 2128 2129 PetscFunctionBegin; 2130 if (str == SAME_NONZERO_PATTERN) { 2131 PetscScalar alpha = a; 2132 x = (Mat_SeqAIJ*)xx->A->data; 2133 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2134 y = (Mat_SeqAIJ*)yy->A->data; 2135 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2136 x = (Mat_SeqAIJ*)xx->B->data; 2137 y = (Mat_SeqAIJ*)yy->B->data; 2138 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2139 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2140 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 2141 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2142 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 2143 } else { 2144 Mat B; 2145 PetscInt *nnz_d,*nnz_o; 2146 ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr); 2147 ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr); 2148 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2149 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2150 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2151 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 2152 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2153 ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 2154 ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 2155 ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 2156 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2157 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 2158 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 2159 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 2160 } 2161 PetscFunctionReturn(0); 2162 } 2163 2164 extern PetscErrorCode MatConjugate_SeqAIJ(Mat); 2165 2166 PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2167 { 2168 #if defined(PETSC_USE_COMPLEX) 2169 PetscErrorCode ierr; 2170 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2171 2172 PetscFunctionBegin; 2173 ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr); 2174 ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr); 2175 #else 2176 PetscFunctionBegin; 2177 #endif 2178 PetscFunctionReturn(0); 2179 } 2180 2181 PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2182 { 2183 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2184 PetscErrorCode ierr; 2185 2186 PetscFunctionBegin; 2187 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2188 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2189 PetscFunctionReturn(0); 2190 } 2191 2192 PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2193 { 2194 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2195 PetscErrorCode ierr; 2196 2197 PetscFunctionBegin; 2198 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2199 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2200 PetscFunctionReturn(0); 2201 } 2202 2203 PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2204 { 2205 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2206 PetscErrorCode ierr; 2207 PetscInt i,*idxb = 0; 2208 PetscScalar *va,*vb; 2209 Vec vtmp; 2210 2211 PetscFunctionBegin; 2212 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 2213 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2214 if (idx) { 2215 for (i=0; i<A->rmap->n; i++) { 2216 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2217 } 2218 } 2219 2220 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2221 if (idx) { 2222 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2223 } 2224 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2225 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2226 2227 for (i=0; i<A->rmap->n; i++) { 2228 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 2229 va[i] = vb[i]; 2230 if (idx) idx[i] = a->garray[idxb[i]]; 2231 } 2232 } 2233 2234 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2235 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2236 ierr = PetscFree(idxb);CHKERRQ(ierr); 2237 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2238 PetscFunctionReturn(0); 2239 } 2240 2241 PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2242 { 2243 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2244 PetscErrorCode ierr; 2245 PetscInt i,*idxb = 0; 2246 PetscScalar *va,*vb; 2247 Vec vtmp; 2248 2249 PetscFunctionBegin; 2250 ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr); 2251 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2252 if (idx) { 2253 for (i=0; i<A->cmap->n; i++) { 2254 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2255 } 2256 } 2257 2258 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2259 if (idx) { 2260 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2261 } 2262 ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2263 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2264 2265 for (i=0; i<A->rmap->n; i++) { 2266 if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) { 2267 va[i] = vb[i]; 2268 if (idx) idx[i] = a->garray[idxb[i]]; 2269 } 2270 } 2271 2272 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2273 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2274 ierr = PetscFree(idxb);CHKERRQ(ierr); 2275 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2276 PetscFunctionReturn(0); 2277 } 2278 2279 PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2280 { 2281 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2282 PetscInt n = A->rmap->n; 2283 PetscInt cstart = A->cmap->rstart; 2284 PetscInt *cmap = mat->garray; 2285 PetscInt *diagIdx, *offdiagIdx; 2286 Vec diagV, offdiagV; 2287 PetscScalar *a, *diagA, *offdiagA; 2288 PetscInt r; 2289 PetscErrorCode ierr; 2290 2291 PetscFunctionBegin; 2292 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2293 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr); 2294 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr); 2295 ierr = MatGetRowMin(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2296 ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2297 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2298 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2299 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2300 for (r = 0; r < n; ++r) { 2301 if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) { 2302 a[r] = diagA[r]; 2303 idx[r] = cstart + diagIdx[r]; 2304 } else { 2305 a[r] = offdiagA[r]; 2306 idx[r] = cmap[offdiagIdx[r]]; 2307 } 2308 } 2309 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2310 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2311 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2312 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2313 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2314 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2315 PetscFunctionReturn(0); 2316 } 2317 2318 PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2319 { 2320 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2321 PetscInt n = A->rmap->n; 2322 PetscInt cstart = A->cmap->rstart; 2323 PetscInt *cmap = mat->garray; 2324 PetscInt *diagIdx, *offdiagIdx; 2325 Vec diagV, offdiagV; 2326 PetscScalar *a, *diagA, *offdiagA; 2327 PetscInt r; 2328 PetscErrorCode ierr; 2329 2330 PetscFunctionBegin; 2331 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2332 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr); 2333 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr); 2334 ierr = MatGetRowMax(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2335 ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2336 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2337 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2338 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2339 for (r = 0; r < n; ++r) { 2340 if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) { 2341 a[r] = diagA[r]; 2342 idx[r] = cstart + diagIdx[r]; 2343 } else { 2344 a[r] = offdiagA[r]; 2345 idx[r] = cmap[offdiagIdx[r]]; 2346 } 2347 } 2348 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2349 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2350 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2351 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2352 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2353 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2354 PetscFunctionReturn(0); 2355 } 2356 2357 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat) 2358 { 2359 PetscErrorCode ierr; 2360 Mat *dummy; 2361 2362 PetscFunctionBegin; 2363 ierr = MatCreateSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr); 2364 *newmat = *dummy; 2365 ierr = PetscFree(dummy);CHKERRQ(ierr); 2366 PetscFunctionReturn(0); 2367 } 2368 2369 PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values) 2370 { 2371 Mat_MPIAIJ *a = (Mat_MPIAIJ*) A->data; 2372 PetscErrorCode ierr; 2373 2374 PetscFunctionBegin; 2375 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2376 A->factorerrortype = a->A->factorerrortype; 2377 PetscFunctionReturn(0); 2378 } 2379 2380 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx) 2381 { 2382 PetscErrorCode ierr; 2383 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)x->data; 2384 2385 PetscFunctionBegin; 2386 ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr); 2387 ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr); 2388 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2389 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2390 PetscFunctionReturn(0); 2391 } 2392 2393 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A,PetscBool sc) 2394 { 2395 PetscFunctionBegin; 2396 if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable; 2397 else A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ; 2398 PetscFunctionReturn(0); 2399 } 2400 2401 /*@ 2402 MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap 2403 2404 Collective on Mat 2405 2406 Input Parameters: 2407 + A - the matrix 2408 - sc - PETSC_TRUE indicates use the scalable algorithm (default is not to use the scalable algorithm) 2409 2410 Level: advanced 2411 2412 @*/ 2413 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A,PetscBool sc) 2414 { 2415 PetscErrorCode ierr; 2416 2417 PetscFunctionBegin; 2418 ierr = PetscTryMethod(A,"MatMPIAIJSetUseScalableIncreaseOverlap_C",(Mat,PetscBool),(A,sc));CHKERRQ(ierr); 2419 PetscFunctionReturn(0); 2420 } 2421 2422 PetscErrorCode MatSetFromOptions_MPIAIJ(PetscOptionItems *PetscOptionsObject,Mat A) 2423 { 2424 PetscErrorCode ierr; 2425 PetscBool sc = PETSC_FALSE,flg; 2426 2427 PetscFunctionBegin; 2428 ierr = PetscOptionsHead(PetscOptionsObject,"MPIAIJ options");CHKERRQ(ierr); 2429 ierr = PetscObjectOptionsBegin((PetscObject)A); 2430 if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE; 2431 ierr = PetscOptionsBool("-mat_increase_overlap_scalable","Use a scalable algorithm to compute the overlap","MatIncreaseOverlap",sc,&sc,&flg);CHKERRQ(ierr); 2432 if (flg) { 2433 ierr = MatMPIAIJSetUseScalableIncreaseOverlap(A,sc);CHKERRQ(ierr); 2434 } 2435 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2436 PetscFunctionReturn(0); 2437 } 2438 2439 PetscErrorCode MatShift_MPIAIJ(Mat Y,PetscScalar a) 2440 { 2441 PetscErrorCode ierr; 2442 Mat_MPIAIJ *maij = (Mat_MPIAIJ*)Y->data; 2443 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)maij->A->data; 2444 2445 PetscFunctionBegin; 2446 if (!Y->preallocated) { 2447 ierr = MatMPIAIJSetPreallocation(Y,1,NULL,0,NULL);CHKERRQ(ierr); 2448 } else if (!aij->nz) { 2449 PetscInt nonew = aij->nonew; 2450 ierr = MatSeqAIJSetPreallocation(maij->A,1,NULL);CHKERRQ(ierr); 2451 aij->nonew = nonew; 2452 } 2453 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2454 PetscFunctionReturn(0); 2455 } 2456 2457 PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A,PetscBool *missing,PetscInt *d) 2458 { 2459 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2460 PetscErrorCode ierr; 2461 2462 PetscFunctionBegin; 2463 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2464 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2465 if (d) { 2466 PetscInt rstart; 2467 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2468 *d += rstart; 2469 2470 } 2471 PetscFunctionReturn(0); 2472 } 2473 2474 2475 /* -------------------------------------------------------------------*/ 2476 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 2477 MatGetRow_MPIAIJ, 2478 MatRestoreRow_MPIAIJ, 2479 MatMult_MPIAIJ, 2480 /* 4*/ MatMultAdd_MPIAIJ, 2481 MatMultTranspose_MPIAIJ, 2482 MatMultTransposeAdd_MPIAIJ, 2483 0, 2484 0, 2485 0, 2486 /*10*/ 0, 2487 0, 2488 0, 2489 MatSOR_MPIAIJ, 2490 MatTranspose_MPIAIJ, 2491 /*15*/ MatGetInfo_MPIAIJ, 2492 MatEqual_MPIAIJ, 2493 MatGetDiagonal_MPIAIJ, 2494 MatDiagonalScale_MPIAIJ, 2495 MatNorm_MPIAIJ, 2496 /*20*/ MatAssemblyBegin_MPIAIJ, 2497 MatAssemblyEnd_MPIAIJ, 2498 MatSetOption_MPIAIJ, 2499 MatZeroEntries_MPIAIJ, 2500 /*24*/ MatZeroRows_MPIAIJ, 2501 0, 2502 0, 2503 0, 2504 0, 2505 /*29*/ MatSetUp_MPIAIJ, 2506 0, 2507 0, 2508 MatGetDiagonalBlock_MPIAIJ, 2509 0, 2510 /*34*/ MatDuplicate_MPIAIJ, 2511 0, 2512 0, 2513 0, 2514 0, 2515 /*39*/ MatAXPY_MPIAIJ, 2516 MatCreateSubMatrices_MPIAIJ, 2517 MatIncreaseOverlap_MPIAIJ, 2518 MatGetValues_MPIAIJ, 2519 MatCopy_MPIAIJ, 2520 /*44*/ MatGetRowMax_MPIAIJ, 2521 MatScale_MPIAIJ, 2522 MatShift_MPIAIJ, 2523 MatDiagonalSet_MPIAIJ, 2524 MatZeroRowsColumns_MPIAIJ, 2525 /*49*/ MatSetRandom_MPIAIJ, 2526 0, 2527 0, 2528 0, 2529 0, 2530 /*54*/ MatFDColoringCreate_MPIXAIJ, 2531 0, 2532 MatSetUnfactored_MPIAIJ, 2533 MatPermute_MPIAIJ, 2534 0, 2535 /*59*/ MatCreateSubMatrix_MPIAIJ, 2536 MatDestroy_MPIAIJ, 2537 MatView_MPIAIJ, 2538 0, 2539 MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ, 2540 /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ, 2541 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 2542 0, 2543 0, 2544 0, 2545 /*69*/ MatGetRowMaxAbs_MPIAIJ, 2546 MatGetRowMinAbs_MPIAIJ, 2547 0, 2548 0, 2549 0, 2550 0, 2551 /*75*/ MatFDColoringApply_AIJ, 2552 MatSetFromOptions_MPIAIJ, 2553 0, 2554 0, 2555 MatFindZeroDiagonals_MPIAIJ, 2556 /*80*/ 0, 2557 0, 2558 0, 2559 /*83*/ MatLoad_MPIAIJ, 2560 MatIsSymmetric_MPIAIJ, 2561 0, 2562 0, 2563 0, 2564 0, 2565 /*89*/ MatMatMult_MPIAIJ_MPIAIJ, 2566 MatMatMultSymbolic_MPIAIJ_MPIAIJ, 2567 MatMatMultNumeric_MPIAIJ_MPIAIJ, 2568 MatPtAP_MPIAIJ_MPIAIJ, 2569 MatPtAPSymbolic_MPIAIJ_MPIAIJ, 2570 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 2571 0, 2572 0, 2573 0, 2574 0, 2575 /*99*/ 0, 2576 0, 2577 0, 2578 MatConjugate_MPIAIJ, 2579 0, 2580 /*104*/MatSetValuesRow_MPIAIJ, 2581 MatRealPart_MPIAIJ, 2582 MatImaginaryPart_MPIAIJ, 2583 0, 2584 0, 2585 /*109*/0, 2586 0, 2587 MatGetRowMin_MPIAIJ, 2588 0, 2589 MatMissingDiagonal_MPIAIJ, 2590 /*114*/MatGetSeqNonzeroStructure_MPIAIJ, 2591 0, 2592 MatGetGhosts_MPIAIJ, 2593 0, 2594 0, 2595 /*119*/0, 2596 0, 2597 0, 2598 0, 2599 MatGetMultiProcBlock_MPIAIJ, 2600 /*124*/MatFindNonzeroRows_MPIAIJ, 2601 MatGetColumnNorms_MPIAIJ, 2602 MatInvertBlockDiagonal_MPIAIJ, 2603 0, 2604 MatCreateSubMatricesMPI_MPIAIJ, 2605 /*129*/0, 2606 MatTransposeMatMult_MPIAIJ_MPIAIJ, 2607 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ, 2608 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 2609 0, 2610 /*134*/0, 2611 0, 2612 MatRARt_MPIAIJ_MPIAIJ, 2613 0, 2614 0, 2615 /*139*/MatSetBlockSizes_MPIAIJ, 2616 0, 2617 0, 2618 MatFDColoringSetUp_MPIXAIJ, 2619 MatFindOffBlockDiagonalEntries_MPIAIJ, 2620 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIAIJ 2621 }; 2622 2623 /* ----------------------------------------------------------------------------------------*/ 2624 2625 PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 2626 { 2627 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2628 PetscErrorCode ierr; 2629 2630 PetscFunctionBegin; 2631 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 2632 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 2633 PetscFunctionReturn(0); 2634 } 2635 2636 PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 2637 { 2638 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2639 PetscErrorCode ierr; 2640 2641 PetscFunctionBegin; 2642 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 2643 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 2644 PetscFunctionReturn(0); 2645 } 2646 2647 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 2648 { 2649 Mat_MPIAIJ *b; 2650 PetscErrorCode ierr; 2651 2652 PetscFunctionBegin; 2653 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2654 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2655 b = (Mat_MPIAIJ*)B->data; 2656 2657 #if defined(PETSC_USE_CTABLE) 2658 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2659 #else 2660 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2661 #endif 2662 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2663 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2664 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2665 2666 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2667 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2668 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2669 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 2670 ierr = MatSetBlockSizesFromMats(b->B,B,B);CHKERRQ(ierr); 2671 ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr); 2672 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2673 2674 if (!B->preallocated) { 2675 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2676 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2677 ierr = MatSetBlockSizesFromMats(b->A,B,B);CHKERRQ(ierr); 2678 ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr); 2679 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2680 } 2681 2682 ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr); 2683 ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr); 2684 B->preallocated = PETSC_TRUE; 2685 B->was_assembled = PETSC_FALSE; 2686 B->assembled = PETSC_FALSE;; 2687 PetscFunctionReturn(0); 2688 } 2689 2690 PetscErrorCode MatResetPreallocation_MPIAIJ(Mat B) 2691 { 2692 Mat_MPIAIJ *b; 2693 PetscErrorCode ierr; 2694 2695 PetscFunctionBegin; 2696 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2697 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2698 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2699 b = (Mat_MPIAIJ*)B->data; 2700 2701 #if defined(PETSC_USE_CTABLE) 2702 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2703 #else 2704 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2705 #endif 2706 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2707 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2708 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2709 2710 ierr = MatResetPreallocation(b->A);CHKERRQ(ierr); 2711 ierr = MatResetPreallocation(b->B);CHKERRQ(ierr); 2712 B->preallocated = PETSC_TRUE; 2713 B->was_assembled = PETSC_FALSE; 2714 B->assembled = PETSC_FALSE; 2715 PetscFunctionReturn(0); 2716 } 2717 2718 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 2719 { 2720 Mat mat; 2721 Mat_MPIAIJ *a,*oldmat = (Mat_MPIAIJ*)matin->data; 2722 PetscErrorCode ierr; 2723 2724 PetscFunctionBegin; 2725 *newmat = 0; 2726 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 2727 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 2728 ierr = MatSetBlockSizesFromMats(mat,matin,matin);CHKERRQ(ierr); 2729 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 2730 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2731 a = (Mat_MPIAIJ*)mat->data; 2732 2733 mat->factortype = matin->factortype; 2734 mat->assembled = PETSC_TRUE; 2735 mat->insertmode = NOT_SET_VALUES; 2736 mat->preallocated = PETSC_TRUE; 2737 2738 a->size = oldmat->size; 2739 a->rank = oldmat->rank; 2740 a->donotstash = oldmat->donotstash; 2741 a->roworiented = oldmat->roworiented; 2742 a->rowindices = 0; 2743 a->rowvalues = 0; 2744 a->getrowactive = PETSC_FALSE; 2745 2746 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 2747 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 2748 2749 if (oldmat->colmap) { 2750 #if defined(PETSC_USE_CTABLE) 2751 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 2752 #else 2753 ierr = PetscMalloc1(mat->cmap->N,&a->colmap);CHKERRQ(ierr); 2754 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2755 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2756 #endif 2757 } else a->colmap = 0; 2758 if (oldmat->garray) { 2759 PetscInt len; 2760 len = oldmat->B->cmap->n; 2761 ierr = PetscMalloc1(len+1,&a->garray);CHKERRQ(ierr); 2762 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 2763 if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); } 2764 } else a->garray = 0; 2765 2766 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 2767 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 2768 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 2769 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 2770 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 2771 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 2772 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 2773 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 2774 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 2775 *newmat = mat; 2776 PetscFunctionReturn(0); 2777 } 2778 2779 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 2780 { 2781 PetscScalar *vals,*svals; 2782 MPI_Comm comm; 2783 PetscErrorCode ierr; 2784 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 2785 PetscInt i,nz,j,rstart,rend,mmax,maxnz = 0; 2786 PetscInt header[4],*rowlengths = 0,M,N,m,*cols; 2787 PetscInt *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols; 2788 PetscInt cend,cstart,n,*rowners; 2789 int fd; 2790 PetscInt bs = newMat->rmap->bs; 2791 2792 PetscFunctionBegin; 2793 /* force binary viewer to load .info file if it has not yet done so */ 2794 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 2795 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2796 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2797 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2798 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2799 if (!rank) { 2800 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 2801 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 2802 if (header[3] < 0) SETERRQ(PetscObjectComm((PetscObject)newMat),PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as MATMPIAIJ"); 2803 } 2804 2805 ierr = PetscOptionsBegin(comm,NULL,"Options for loading MATMPIAIJ matrix","Mat");CHKERRQ(ierr); 2806 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 2807 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2808 if (bs < 0) bs = 1; 2809 2810 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 2811 M = header[1]; N = header[2]; 2812 2813 /* If global sizes are set, check if they are consistent with that given in the file */ 2814 if (newMat->rmap->N >= 0 && newMat->rmap->N != M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of rows:Matrix in file has (%D) and input matrix has (%D)",newMat->rmap->N,M); 2815 if (newMat->cmap->N >=0 && newMat->cmap->N != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of cols:Matrix in file has (%D) and input matrix has (%D)",newMat->cmap->N,N); 2816 2817 /* determine ownership of all (block) rows */ 2818 if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs); 2819 if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank)); /* PETSC_DECIDE */ 2820 else m = newMat->rmap->n; /* Set by user */ 2821 2822 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 2823 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 2824 2825 /* First process needs enough room for process with most rows */ 2826 if (!rank) { 2827 mmax = rowners[1]; 2828 for (i=2; i<=size; i++) { 2829 mmax = PetscMax(mmax, rowners[i]); 2830 } 2831 } else mmax = -1; /* unused, but compilers complain */ 2832 2833 rowners[0] = 0; 2834 for (i=2; i<=size; i++) { 2835 rowners[i] += rowners[i-1]; 2836 } 2837 rstart = rowners[rank]; 2838 rend = rowners[rank+1]; 2839 2840 /* distribute row lengths to all processors */ 2841 ierr = PetscMalloc2(m,&ourlens,m,&offlens);CHKERRQ(ierr); 2842 if (!rank) { 2843 ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr); 2844 ierr = PetscMalloc1(mmax,&rowlengths);CHKERRQ(ierr); 2845 ierr = PetscCalloc1(size,&procsnz);CHKERRQ(ierr); 2846 for (j=0; j<m; j++) { 2847 procsnz[0] += ourlens[j]; 2848 } 2849 for (i=1; i<size; i++) { 2850 ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr); 2851 /* calculate the number of nonzeros on each processor */ 2852 for (j=0; j<rowners[i+1]-rowners[i]; j++) { 2853 procsnz[i] += rowlengths[j]; 2854 } 2855 ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2856 } 2857 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2858 } else { 2859 ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2860 } 2861 2862 if (!rank) { 2863 /* determine max buffer needed and allocate it */ 2864 maxnz = 0; 2865 for (i=0; i<size; i++) { 2866 maxnz = PetscMax(maxnz,procsnz[i]); 2867 } 2868 ierr = PetscMalloc1(maxnz,&cols);CHKERRQ(ierr); 2869 2870 /* read in my part of the matrix column indices */ 2871 nz = procsnz[0]; 2872 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2873 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 2874 2875 /* read in every one elses and ship off */ 2876 for (i=1; i<size; i++) { 2877 nz = procsnz[i]; 2878 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 2879 ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2880 } 2881 ierr = PetscFree(cols);CHKERRQ(ierr); 2882 } else { 2883 /* determine buffer space needed for message */ 2884 nz = 0; 2885 for (i=0; i<m; i++) { 2886 nz += ourlens[i]; 2887 } 2888 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2889 2890 /* receive message of column indices*/ 2891 ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2892 } 2893 2894 /* determine column ownership if matrix is not square */ 2895 if (N != M) { 2896 if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank); 2897 else n = newMat->cmap->n; 2898 ierr = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2899 cstart = cend - n; 2900 } else { 2901 cstart = rstart; 2902 cend = rend; 2903 n = cend - cstart; 2904 } 2905 2906 /* loop over local rows, determining number of off diagonal entries */ 2907 ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr); 2908 jj = 0; 2909 for (i=0; i<m; i++) { 2910 for (j=0; j<ourlens[i]; j++) { 2911 if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++; 2912 jj++; 2913 } 2914 } 2915 2916 for (i=0; i<m; i++) { 2917 ourlens[i] -= offlens[i]; 2918 } 2919 ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr); 2920 2921 if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);} 2922 2923 ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr); 2924 2925 for (i=0; i<m; i++) { 2926 ourlens[i] += offlens[i]; 2927 } 2928 2929 if (!rank) { 2930 ierr = PetscMalloc1(maxnz+1,&vals);CHKERRQ(ierr); 2931 2932 /* read in my part of the matrix numerical values */ 2933 nz = procsnz[0]; 2934 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2935 2936 /* insert into matrix */ 2937 jj = rstart; 2938 smycols = mycols; 2939 svals = vals; 2940 for (i=0; i<m; i++) { 2941 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2942 smycols += ourlens[i]; 2943 svals += ourlens[i]; 2944 jj++; 2945 } 2946 2947 /* read in other processors and ship out */ 2948 for (i=1; i<size; i++) { 2949 nz = procsnz[i]; 2950 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2951 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2952 } 2953 ierr = PetscFree(procsnz);CHKERRQ(ierr); 2954 } else { 2955 /* receive numeric values */ 2956 ierr = PetscMalloc1(nz+1,&vals);CHKERRQ(ierr); 2957 2958 /* receive message of values*/ 2959 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2960 2961 /* insert into matrix */ 2962 jj = rstart; 2963 smycols = mycols; 2964 svals = vals; 2965 for (i=0; i<m; i++) { 2966 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2967 smycols += ourlens[i]; 2968 svals += ourlens[i]; 2969 jj++; 2970 } 2971 } 2972 ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr); 2973 ierr = PetscFree(vals);CHKERRQ(ierr); 2974 ierr = PetscFree(mycols);CHKERRQ(ierr); 2975 ierr = PetscFree(rowners);CHKERRQ(ierr); 2976 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2977 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2978 PetscFunctionReturn(0); 2979 } 2980 2981 /* Not scalable because of ISAllGather() unless getting all columns. */ 2982 PetscErrorCode ISGetSeqIS_Private(Mat mat,IS iscol,IS *isseq) 2983 { 2984 PetscErrorCode ierr; 2985 IS iscol_local; 2986 PetscBool isstride; 2987 PetscMPIInt lisstride=0,gisstride; 2988 2989 PetscFunctionBegin; 2990 /* check if we are grabbing all columns*/ 2991 ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&isstride);CHKERRQ(ierr); 2992 2993 if (isstride) { 2994 PetscInt start,len,mstart,mlen; 2995 ierr = ISStrideGetInfo(iscol,&start,NULL);CHKERRQ(ierr); 2996 ierr = ISGetLocalSize(iscol,&len);CHKERRQ(ierr); 2997 ierr = MatGetOwnershipRangeColumn(mat,&mstart,&mlen);CHKERRQ(ierr); 2998 if (mstart == start && mlen-mstart == len) lisstride = 1; 2999 } 3000 3001 ierr = MPIU_Allreduce(&lisstride,&gisstride,1,MPI_INT,MPI_MIN,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 3002 if (gisstride) { 3003 PetscInt N; 3004 ierr = MatGetSize(mat,NULL,&N);CHKERRQ(ierr); 3005 ierr = ISCreateStride(PetscObjectComm((PetscObject)mat),N,0,1,&iscol_local);CHKERRQ(ierr); 3006 ierr = ISSetIdentity(iscol_local);CHKERRQ(ierr); 3007 ierr = PetscInfo(mat,"Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n");CHKERRQ(ierr); 3008 } else { 3009 PetscInt cbs; 3010 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3011 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 3012 ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr); 3013 } 3014 3015 *isseq = iscol_local; 3016 PetscFunctionReturn(0); 3017 } 3018 3019 /* 3020 Used by MatCreateSubMatrix_MPIAIJ_SameRowColDist() to avoid ISAllGather() and global size of iscol_local 3021 (see MatCreateSubMatrix_MPIAIJ_nonscalable) 3022 3023 Input Parameters: 3024 mat - matrix 3025 isrow - parallel row index set; its local indices are a subset of local columns of mat, 3026 i.e., mat->rstart <= isrow[i] < mat->rend 3027 iscol - parallel column index set; its local indices are a subset of local columns of mat, 3028 i.e., mat->cstart <= iscol[i] < mat->cend 3029 Output Parameter: 3030 isrow_d,iscol_d - sequential row and column index sets for retrieving mat->A 3031 iscol_o - sequential column index set for retrieving mat->B 3032 garray - column map; garray[i] indicates global location of iscol_o[i] in iscol 3033 */ 3034 PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat,IS isrow,IS iscol,IS *isrow_d,IS *iscol_d,IS *iscol_o,const PetscInt *garray[]) 3035 { 3036 PetscErrorCode ierr; 3037 Vec x,cmap; 3038 const PetscInt *is_idx; 3039 PetscScalar *xarray,*cmaparray; 3040 PetscInt ncols,isstart,*idx,m,rstart,*cmap1,count; 3041 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3042 Mat B=a->B; 3043 Vec lvec=a->lvec,lcmap; 3044 PetscInt i,cstart,cend,Bn=B->cmap->N; 3045 MPI_Comm comm; 3046 PetscMPIInt rank; 3047 VecScatter Mvctx; 3048 3049 PetscFunctionBegin; 3050 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3051 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3052 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 3053 3054 //ierr = MatView(mat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3055 //ierr = ISView(iscol,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3056 3057 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3058 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3059 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3060 ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3061 ierr = VecSet(cmap,-1.0);CHKERRQ(ierr); 3062 3063 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3064 3065 /* Get start indices */ 3066 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3067 isstart -= ncols; 3068 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3069 3070 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3071 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3072 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3073 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3074 for (i=0; i<ncols; i++) { 3075 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3076 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3077 idx[i] = is_idx[i]-cstart; /* local index of iscol[i] */ 3078 } 3079 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3080 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3081 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3082 //ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3083 3084 /* Get iscol_d */ 3085 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,iscol_d);CHKERRQ(ierr); 3086 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3087 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3088 3089 /* Get isrow_d */ 3090 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3091 rstart = mat->rmap->rstart; 3092 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3093 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3094 for (i=0; i<m; i++) idx[i] = is_idx[i]-rstart; 3095 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3096 3097 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_OWN_POINTER,isrow_d);CHKERRQ(ierr); 3098 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3099 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3100 3101 /* (2) Scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3102 #if 0 3103 if (!a->Mvctx_mpi1) { 3104 /* a->Mvctx causes random 'count' in o-build? See src/mat/examples/tests/runex59_2 */ 3105 a->Mvctx_mpi1_flg = PETSC_TRUE; 3106 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 3107 } 3108 Mvctx = a->Mvctx_mpi1; 3109 #endif 3110 Mvctx = a->Mvctx; 3111 ierr = VecScatterBegin(Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3112 ierr = VecScatterEnd(Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3113 3114 ierr = VecScatterBegin(Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3115 ierr = VecScatterEnd(Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3116 3117 /* (3) create sequential iscol_o (a subset of iscol) and isgarray */ 3118 /* off-process column indices */ 3119 count = 0; 3120 ierr = PetscMalloc1(Bn,&idx);CHKERRQ(ierr); 3121 ierr = PetscMalloc1(Bn,&cmap1);CHKERRQ(ierr); 3122 3123 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3124 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3125 for (i=0; i<Bn; i++) { 3126 if (PetscRealPart(xarray[i]) > -1.0) { 3127 idx[count] = i; /* local column index in off-diagonal part B */ 3128 cmap1[count] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3129 count++; 3130 } 3131 } 3132 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3133 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3134 //printf("[%d] count %d, nlvec %d\n",rank,count,lvec->map->N); 3135 if (count != 6) { 3136 printf("[%d] lvec:\n",rank); 3137 ierr = VecView(lvec,0);CHKERRQ(ierr); 3138 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"count %d != 6",count); 3139 } 3140 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr); 3141 /* cannot ensure iscol_o has same blocksize as iscol! */ 3142 3143 ierr = PetscFree(idx);CHKERRQ(ierr); 3144 3145 *garray = cmap1; 3146 3147 ierr = VecDestroy(&x);CHKERRQ(ierr); 3148 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3149 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3150 PetscFunctionReturn(0); 3151 } 3152 3153 /* isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */ 3154 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *submat) 3155 { 3156 PetscErrorCode ierr; 3157 Mat_MPIAIJ *a = (Mat_MPIAIJ*)mat->data,*asub; 3158 Mat M = NULL; 3159 MPI_Comm comm; 3160 IS iscol_d,isrow_d,iscol_o; 3161 Mat Asub = NULL,Bsub = NULL; 3162 PetscInt n; 3163 3164 PetscFunctionBegin; 3165 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3166 3167 if (call == MAT_REUSE_MATRIX) { 3168 /* Retrieve isrow_d, iscol_d and iscol_o from submat */ 3169 ierr = PetscObjectQuery((PetscObject)*submat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3170 if (!isrow_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow_d passed in was not used before, cannot reuse"); 3171 3172 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_d",(PetscObject*)&iscol_d);CHKERRQ(ierr); 3173 if (!iscol_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_d passed in was not used before, cannot reuse"); 3174 3175 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_o",(PetscObject*)&iscol_o);CHKERRQ(ierr); 3176 if (!iscol_o) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_o passed in was not used before, cannot reuse"); 3177 3178 /* Update diagonal and off-diagonal portions of submat */ 3179 asub = (Mat_MPIAIJ*)(*submat)->data; 3180 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->A);CHKERRQ(ierr); 3181 ierr = ISGetLocalSize(iscol_o,&n);CHKERRQ(ierr); 3182 if (n) { 3183 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->B);CHKERRQ(ierr); 3184 } 3185 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3186 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3187 3188 } else { /* call == MAT_INITIAL_MATRIX) */ 3189 const PetscInt *garray; 3190 PetscInt BsubN; 3191 3192 /* Create isrow_d, iscol_d, iscol_o and isgarray (replace isgarray with array?) */ 3193 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&isrow_d,&iscol_d,&iscol_o,&garray);CHKERRQ(ierr); 3194 3195 /* Create local submatrices Asub and Bsub */ 3196 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Asub);CHKERRQ(ierr); 3197 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Bsub);CHKERRQ(ierr); 3198 3199 /* Create submatrix M */ 3200 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray,&M);CHKERRQ(ierr); 3201 3202 /* If Bsub has empty columns, compress iscol_o such that it will retrieve condensed Bsub from a->B during reuse */ 3203 asub = (Mat_MPIAIJ*)M->data; 3204 3205 ierr = ISGetLocalSize(iscol_o,&BsubN);CHKERRQ(ierr); 3206 n = asub->B->cmap->N; 3207 if (BsubN > n) { 3208 /* This case can be tested using ~petsc/src/tao/bound/examples/tutorials/runplate2_3 */ 3209 const PetscInt *idx; 3210 PetscInt i,j,*idx_new,*subgarray = asub->garray; 3211 ierr = PetscInfo2(M,"submatrix Bn %D != BsubN %D, update iscol_o\n",n,BsubN);CHKERRQ(ierr); 3212 3213 ierr = PetscMalloc1(n,&idx_new);CHKERRQ(ierr); 3214 j = 0; 3215 ierr = ISGetIndices(iscol_o,&idx);CHKERRQ(ierr); 3216 for (i=0; i<n; i++) { 3217 if (j >= BsubN) break; 3218 while (subgarray[i] > garray[j]) j++; 3219 3220 if (subgarray[i] == garray[j]) { 3221 idx_new[i] = idx[j++]; 3222 } else SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"subgarray[%D]=%D cannot < garray[%D]=%D",i,subgarray[i],j,garray[j]); 3223 } 3224 ierr = ISRestoreIndices(iscol_o,&idx);CHKERRQ(ierr); 3225 3226 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3227 ierr = ISCreateGeneral(PETSC_COMM_SELF,n,idx_new,PETSC_OWN_POINTER,&iscol_o);CHKERRQ(ierr); 3228 3229 } else if (BsubN < n) { 3230 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Columns of Bsub cannot be smaller than B's",BsubN,asub->B->cmap->N); 3231 } 3232 3233 ierr = PetscFree(garray);CHKERRQ(ierr); 3234 *submat = M; 3235 3236 /* Save isrow_d, iscol_d and iscol_o used in processor for next request */ 3237 ierr = PetscObjectCompose((PetscObject)M,"isrow_d",(PetscObject)isrow_d);CHKERRQ(ierr); 3238 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3239 3240 ierr = PetscObjectCompose((PetscObject)M,"iscol_d",(PetscObject)iscol_d);CHKERRQ(ierr); 3241 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3242 3243 ierr = PetscObjectCompose((PetscObject)M,"iscol_o",(PetscObject)iscol_o);CHKERRQ(ierr); 3244 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3245 } 3246 PetscFunctionReturn(0); 3247 } 3248 3249 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3250 { 3251 PetscErrorCode ierr; 3252 IS iscol_local=NULL,isrow_d; 3253 PetscInt csize; 3254 PetscInt n,i,j,start,end; 3255 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3256 MPI_Comm comm; 3257 3258 PetscFunctionBegin; 3259 /* If isrow has same processor distribution as mat, 3260 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3261 if (call == MAT_REUSE_MATRIX) { 3262 ierr = PetscObjectQuery((PetscObject)*newmat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3263 if (isrow_d) { 3264 sameRowDist = PETSC_TRUE; 3265 tsameDist[1] = PETSC_TRUE; /* sameColDist */ 3266 } else { 3267 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3268 if (iscol_local) { 3269 sameRowDist = PETSC_TRUE; 3270 tsameDist[1] = PETSC_FALSE; /* !sameColDist */ 3271 } 3272 } 3273 } else { 3274 /* Check if isrow has same processor distribution as mat */ 3275 sameDist[0] = PETSC_FALSE; 3276 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3277 if (!n) { 3278 sameDist[0] = PETSC_TRUE; 3279 } else { 3280 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3281 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3282 if (i >= start && j < end) { 3283 sameDist[0] = PETSC_TRUE; 3284 } 3285 } 3286 3287 /* Check if iscol has same processor distribution as mat */ 3288 sameDist[1] = PETSC_FALSE; 3289 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3290 if (!n) { 3291 sameDist[1] = PETSC_TRUE; 3292 } else { 3293 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3294 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3295 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3296 } 3297 3298 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3299 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3300 sameRowDist = tsameDist[0]; 3301 } 3302 3303 if (sameRowDist) { 3304 if (tsameDist[1]) { /* sameRowDist & sameColDist */ 3305 /* isrow and iscol have same processor distribution as mat */ 3306 ierr = MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3307 PetscFunctionReturn(0); 3308 } else { /* sameRowDist */ 3309 /* isrow has same processor distribution as mat */ 3310 if (call == MAT_INITIAL_MATRIX) { 3311 PetscBool sorted; 3312 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3313 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3314 ierr = ISGetSize(iscol,&i);CHKERRQ(ierr); 3315 if (n != i) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != size of iscol %d",n,i); 3316 3317 ierr = ISSorted(iscol_local,&sorted);CHKERRQ(ierr); 3318 if (sorted) { 3319 /* MatCreateSubMatrix_MPIAIJ_SameRowDist() requires iscol_local be sorted; it can have duplicate indices */ 3320 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,iscol_local,MAT_INITIAL_MATRIX,newmat);CHKERRQ(ierr); 3321 PetscFunctionReturn(0); 3322 } 3323 } else { /* call == MAT_REUSE_MATRIX */ 3324 IS iscol_sub; 3325 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3326 if (iscol_sub) { 3327 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,NULL,call,newmat);CHKERRQ(ierr); 3328 PetscFunctionReturn(0); 3329 } 3330 } 3331 } 3332 } 3333 3334 /* General case: iscol -> iscol_local which has global size of iscol */ 3335 if (call == MAT_REUSE_MATRIX) { 3336 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3337 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3338 } else { 3339 if (!iscol_local) { 3340 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3341 } 3342 } 3343 3344 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3345 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3346 3347 if (call == MAT_INITIAL_MATRIX) { 3348 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3349 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3350 } 3351 PetscFunctionReturn(0); 3352 } 3353 3354 /*@C 3355 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3356 and "off-diagonal" part of the matrix in CSR format. 3357 3358 Collective on MPI_Comm 3359 3360 Input Parameters: 3361 + comm - MPI communicator 3362 . A - "diagonal" portion of matrix 3363 . B - "off-diagonal" portion of matrix, may have empty columns, will be destroyed by this routine 3364 - garray - global index of B columns 3365 3366 Output Parameter: 3367 . mat - the matrix, with input A as its local diagonal matrix 3368 Level: advanced 3369 3370 Notes: 3371 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3372 A becomes part of output mat, B is destroyed by this routine. The user cannot use A and B anymore. 3373 3374 .seealso: MatCreateMPIAIJWithSplitArrays() 3375 @*/ 3376 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3377 { 3378 PetscErrorCode ierr; 3379 Mat_MPIAIJ *maij; 3380 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data,*bnew; 3381 PetscInt *oi=b->i,*oj=b->j,i,nz,col; 3382 PetscScalar *oa=b->a; 3383 Mat Bnew; 3384 PetscInt m,n,N; 3385 3386 PetscFunctionBegin; 3387 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3388 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3389 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %D != Bm %D",m,B->rmap->N); 3390 if (A->rmap->bs != B->rmap->bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"A row bs %D != B row bs %D",A->rmap->bs,B->rmap->bs); 3391 /* remove check below; When B is created using iscol_o from ISGetSeqIS_SameColDist_Private(), its bs may not be same as A */ 3392 /* if (A->cmap->bs != B->cmap->bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"A column bs %D != B column bs %D",A->cmap->bs,B->cmap->bs); */ 3393 3394 /* Get global columns of mat */ 3395 ierr = MPIU_Allreduce(&n,&N,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3396 3397 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3398 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3399 ierr = MatSetBlockSizes(*mat,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 3400 maij = (Mat_MPIAIJ*)(*mat)->data; 3401 3402 (*mat)->preallocated = PETSC_TRUE; 3403 3404 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3405 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3406 3407 /* Set A as diagonal portion of *mat */ 3408 maij->A = A; 3409 3410 nz = oi[m]; 3411 for (i=0; i<nz; i++) { 3412 col = oj[i]; 3413 oj[i] = garray[col]; 3414 } 3415 3416 /* Set Bnew as off-diagonal portion of *mat */ 3417 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Bnew);CHKERRQ(ierr); 3418 bnew = (Mat_SeqAIJ*)Bnew->data; 3419 bnew->maxnz = b->maxnz; /* allocated nonzeros of B */ 3420 maij->B = Bnew; 3421 3422 if (B->rmap->N != Bnew->rmap->N) SETERRQ2(PETSC_COMM_SELF,0,"BN %d != BnewN %d",B->rmap->N,Bnew->rmap->N); 3423 3424 b->singlemalloc = PETSC_FALSE; /* B arrays are shared by Bnew */ 3425 b->free_a = PETSC_FALSE; 3426 b->free_ij = PETSC_FALSE; 3427 ierr = MatDestroy(&B);CHKERRQ(ierr); 3428 3429 bnew->singlemalloc = PETSC_TRUE; /* arrays will be freed by MatDestroy(&Bnew) */ 3430 bnew->free_a = PETSC_TRUE; 3431 bnew->free_ij = PETSC_TRUE; 3432 3433 /* condense columns of maij->B */ 3434 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3435 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3436 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3437 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3438 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3439 PetscFunctionReturn(0); 3440 } 3441 3442 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3443 3444 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,IS iscol_local,MatReuse call,Mat *newmat) 3445 { 3446 PetscErrorCode ierr; 3447 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3448 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3449 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3450 Mat M,Msub,B=a->B; 3451 MatScalar *aa; 3452 Mat_SeqAIJ *aij; 3453 PetscInt *garray = a->garray,*colsub,Ncols; 3454 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3455 IS iscol_sub,iscmap; 3456 const PetscInt *is_idx,*cmap; 3457 PetscBool allcolumns=PETSC_FALSE; 3458 MPI_Comm comm; 3459 3460 PetscFunctionBegin; 3461 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3462 3463 if (call == MAT_REUSE_MATRIX) { 3464 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3465 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3466 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3467 3468 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3469 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3470 3471 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3472 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3473 3474 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3475 3476 } else { /* call == MAT_INITIAL_MATRIX) */ 3477 PetscBool flg; 3478 3479 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3480 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3481 3482 /* (1) iscol -> nonscalable iscol_local */ 3483 /* Check for special case: each processor gets entire matrix columns */ 3484 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3485 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3486 if (allcolumns) { 3487 iscol_sub = iscol_local; 3488 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3489 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3490 3491 } else { 3492 /* (2) iscol_local -> iscol_sub and iscmap. Implementation below requires iscol_local be sorted, it can have duplicate indices */ 3493 PetscInt *idx,*cmap1,k; 3494 ierr = PetscMalloc1(Ncols,&idx);CHKERRQ(ierr); 3495 ierr = PetscMalloc1(Ncols,&cmap1);CHKERRQ(ierr); 3496 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3497 count = 0; 3498 k = 0; 3499 for (i=0; i<Ncols; i++) { 3500 j = is_idx[i]; 3501 if (j >= cstart && j < cend) { 3502 /* diagonal part of mat */ 3503 idx[count] = j; 3504 cmap1[count++] = i; /* column index in submat */ 3505 } else if (Bn) { 3506 /* off-diagonal part of mat */ 3507 if (j == garray[k]) { 3508 idx[count] = j; 3509 cmap1[count++] = i; /* column index in submat */ 3510 } else if (j > garray[k]) { 3511 while (j > garray[k] && k < Bn-1) k++; 3512 if (j == garray[k]) { 3513 idx[count] = j; 3514 cmap1[count++] = i; /* column index in submat */ 3515 } 3516 } 3517 } 3518 } 3519 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3520 3521 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_OWN_POINTER,&iscol_sub);CHKERRQ(ierr); 3522 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3523 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3524 3525 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_OWN_POINTER,&iscmap);CHKERRQ(ierr); 3526 } 3527 3528 /* (3) Create sequential Msub */ 3529 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3530 } 3531 3532 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3533 aij = (Mat_SeqAIJ*)(Msub)->data; 3534 ii = aij->i; 3535 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3536 3537 /* 3538 m - number of local rows 3539 Ncols - number of columns (same on all processors) 3540 rstart - first row in new global matrix generated 3541 */ 3542 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3543 3544 if (call == MAT_INITIAL_MATRIX) { 3545 /* (4) Create parallel newmat */ 3546 PetscMPIInt rank,size; 3547 PetscInt csize; 3548 3549 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3550 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3551 3552 /* 3553 Determine the number of non-zeros in the diagonal and off-diagonal 3554 portions of the matrix in order to do correct preallocation 3555 */ 3556 3557 /* first get start and end of "diagonal" columns */ 3558 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3559 if (csize == PETSC_DECIDE) { 3560 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3561 if (mglobal == Ncols) { /* square matrix */ 3562 nlocal = m; 3563 } else { 3564 nlocal = Ncols/size + ((Ncols % size) > rank); 3565 } 3566 } else { 3567 nlocal = csize; 3568 } 3569 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3570 rstart = rend - nlocal; 3571 if (rank == size - 1 && rend != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local column sizes %D do not add up to total number of columns %D",rend,Ncols); 3572 3573 /* next, compute all the lengths */ 3574 jj = aij->j; 3575 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3576 olens = dlens + m; 3577 for (i=0; i<m; i++) { 3578 jend = ii[i+1] - ii[i]; 3579 olen = 0; 3580 dlen = 0; 3581 for (j=0; j<jend; j++) { 3582 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3583 else dlen++; 3584 jj++; 3585 } 3586 olens[i] = olen; 3587 dlens[i] = dlen; 3588 } 3589 3590 ierr = ISGetBlockSize(isrow,&bs);CHKERRQ(ierr); 3591 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3592 3593 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3594 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr); 3595 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3596 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3597 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3598 ierr = PetscFree(dlens);CHKERRQ(ierr); 3599 3600 } else { /* call == MAT_REUSE_MATRIX */ 3601 M = *newmat; 3602 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3603 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3604 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3605 /* 3606 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3607 rather than the slower MatSetValues(). 3608 */ 3609 M->was_assembled = PETSC_TRUE; 3610 M->assembled = PETSC_FALSE; 3611 } 3612 3613 /* (5) Set values of Msub to *newmat */ 3614 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3615 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3616 3617 jj = aij->j; 3618 aa = aij->a; 3619 for (i=0; i<m; i++) { 3620 row = rstart + i; 3621 nz = ii[i+1] - ii[i]; 3622 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3623 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3624 jj += nz; aa += nz; 3625 } 3626 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3627 3628 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3629 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3630 3631 ierr = PetscFree(colsub);CHKERRQ(ierr); 3632 3633 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3634 if (call == MAT_INITIAL_MATRIX) { 3635 *newmat = M; 3636 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3637 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3638 3639 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3640 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3641 3642 ierr = PetscObjectCompose((PetscObject)(*newmat),"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3643 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3644 3645 if (iscol_local) { 3646 ierr = PetscObjectCompose((PetscObject)(*newmat),"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3647 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3648 } 3649 } 3650 PetscFunctionReturn(0); 3651 } 3652 3653 /* 3654 Not great since it makes two copies of the submatrix, first an SeqAIJ 3655 in local and then by concatenating the local matrices the end result. 3656 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3657 3658 Note: This requires a sequential iscol with all indices. 3659 */ 3660 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3661 { 3662 PetscErrorCode ierr; 3663 PetscMPIInt rank,size; 3664 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3665 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3666 Mat M,Mreuse; 3667 MatScalar *aa,*vwork; 3668 MPI_Comm comm; 3669 Mat_SeqAIJ *aij; 3670 PetscBool colflag,allcolumns=PETSC_FALSE; 3671 3672 PetscFunctionBegin; 3673 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3674 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3675 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3676 3677 /* Check for special case: each processor gets entire matrix columns */ 3678 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3679 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3680 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3681 3682 if (call == MAT_REUSE_MATRIX) { 3683 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3684 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3685 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3686 } else { 3687 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3688 } 3689 3690 /* 3691 m - number of local rows 3692 n - number of columns (same on all processors) 3693 rstart - first row in new global matrix generated 3694 */ 3695 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3696 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3697 if (call == MAT_INITIAL_MATRIX) { 3698 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3699 ii = aij->i; 3700 jj = aij->j; 3701 3702 /* 3703 Determine the number of non-zeros in the diagonal and off-diagonal 3704 portions of the matrix in order to do correct preallocation 3705 */ 3706 3707 /* first get start and end of "diagonal" columns */ 3708 if (csize == PETSC_DECIDE) { 3709 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3710 if (mglobal == n) { /* square matrix */ 3711 nlocal = m; 3712 } else { 3713 nlocal = n/size + ((n % size) > rank); 3714 } 3715 } else { 3716 nlocal = csize; 3717 } 3718 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3719 rstart = rend - nlocal; 3720 if (rank == size - 1 && rend != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local column sizes %D do not add up to total number of columns %D",rend,n); 3721 3722 /* next, compute all the lengths */ 3723 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3724 olens = dlens + m; 3725 for (i=0; i<m; i++) { 3726 jend = ii[i+1] - ii[i]; 3727 olen = 0; 3728 dlen = 0; 3729 for (j=0; j<jend; j++) { 3730 if (*jj < rstart || *jj >= rend) olen++; 3731 else dlen++; 3732 jj++; 3733 } 3734 olens[i] = olen; 3735 dlens[i] = dlen; 3736 } 3737 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3738 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3739 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3740 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3741 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3742 ierr = PetscFree(dlens);CHKERRQ(ierr); 3743 } else { 3744 PetscInt ml,nl; 3745 3746 M = *newmat; 3747 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3748 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3749 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3750 /* 3751 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3752 rather than the slower MatSetValues(). 3753 */ 3754 M->was_assembled = PETSC_TRUE; 3755 M->assembled = PETSC_FALSE; 3756 } 3757 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3758 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3759 ii = aij->i; 3760 jj = aij->j; 3761 aa = aij->a; 3762 for (i=0; i<m; i++) { 3763 row = rstart + i; 3764 nz = ii[i+1] - ii[i]; 3765 cwork = jj; jj += nz; 3766 vwork = aa; aa += nz; 3767 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3768 } 3769 3770 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3771 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3772 *newmat = M; 3773 3774 /* save submatrix used in processor for next request */ 3775 if (call == MAT_INITIAL_MATRIX) { 3776 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3777 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3778 } 3779 PetscFunctionReturn(0); 3780 } 3781 3782 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3783 { 3784 PetscInt m,cstart, cend,j,nnz,i,d; 3785 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3786 const PetscInt *JJ; 3787 PetscScalar *values; 3788 PetscErrorCode ierr; 3789 PetscBool nooffprocentries; 3790 3791 PetscFunctionBegin; 3792 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3793 3794 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3795 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3796 m = B->rmap->n; 3797 cstart = B->cmap->rstart; 3798 cend = B->cmap->rend; 3799 rstart = B->rmap->rstart; 3800 3801 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3802 3803 #if defined(PETSC_USE_DEBUGGING) 3804 for (i=0; i<m; i++) { 3805 nnz = Ii[i+1]- Ii[i]; 3806 JJ = J + Ii[i]; 3807 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3808 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3809 if (nnz && (JJ[nnz-1] >= B->cmap->N) SETERRRQ3(PETSC_ERR_ARG_WRONGSTATE,"Row %D ends with too large a column index %D (max allowed %D)",i,JJ[nnz-1],B->cmap->N); 3810 } 3811 #endif 3812 3813 for (i=0; i<m; i++) { 3814 nnz = Ii[i+1]- Ii[i]; 3815 JJ = J + Ii[i]; 3816 nnz_max = PetscMax(nnz_max,nnz); 3817 d = 0; 3818 for (j=0; j<nnz; j++) { 3819 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3820 } 3821 d_nnz[i] = d; 3822 o_nnz[i] = nnz - d; 3823 } 3824 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3825 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3826 3827 if (v) values = (PetscScalar*)v; 3828 else { 3829 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3830 } 3831 3832 for (i=0; i<m; i++) { 3833 ii = i + rstart; 3834 nnz = Ii[i+1]- Ii[i]; 3835 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3836 } 3837 nooffprocentries = B->nooffprocentries; 3838 B->nooffprocentries = PETSC_TRUE; 3839 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3840 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3841 B->nooffprocentries = nooffprocentries; 3842 3843 if (!v) { 3844 ierr = PetscFree(values);CHKERRQ(ierr); 3845 } 3846 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3847 PetscFunctionReturn(0); 3848 } 3849 3850 /*@ 3851 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3852 (the default parallel PETSc format). 3853 3854 Collective on MPI_Comm 3855 3856 Input Parameters: 3857 + B - the matrix 3858 . i - the indices into j for the start of each local row (starts with zero) 3859 . j - the column indices for each local row (starts with zero) 3860 - v - optional values in the matrix 3861 3862 Level: developer 3863 3864 Notes: 3865 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3866 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3867 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3868 3869 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3870 3871 The format which is used for the sparse matrix input, is equivalent to a 3872 row-major ordering.. i.e for the following matrix, the input data expected is 3873 as shown 3874 3875 $ 1 0 0 3876 $ 2 0 3 P0 3877 $ ------- 3878 $ 4 5 6 P1 3879 $ 3880 $ Process0 [P0]: rows_owned=[0,1] 3881 $ i = {0,1,3} [size = nrow+1 = 2+1] 3882 $ j = {0,0,2} [size = 3] 3883 $ v = {1,2,3} [size = 3] 3884 $ 3885 $ Process1 [P1]: rows_owned=[2] 3886 $ i = {0,3} [size = nrow+1 = 1+1] 3887 $ j = {0,1,2} [size = 3] 3888 $ v = {4,5,6} [size = 3] 3889 3890 .keywords: matrix, aij, compressed row, sparse, parallel 3891 3892 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3893 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3894 @*/ 3895 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3896 { 3897 PetscErrorCode ierr; 3898 3899 PetscFunctionBegin; 3900 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3901 PetscFunctionReturn(0); 3902 } 3903 3904 /*@C 3905 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3906 (the default parallel PETSc format). For good matrix assembly performance 3907 the user should preallocate the matrix storage by setting the parameters 3908 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3909 performance can be increased by more than a factor of 50. 3910 3911 Collective on MPI_Comm 3912 3913 Input Parameters: 3914 + B - the matrix 3915 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3916 (same value is used for all local rows) 3917 . d_nnz - array containing the number of nonzeros in the various rows of the 3918 DIAGONAL portion of the local submatrix (possibly different for each row) 3919 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3920 The size of this array is equal to the number of local rows, i.e 'm'. 3921 For matrices that will be factored, you must leave room for (and set) 3922 the diagonal entry even if it is zero. 3923 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3924 submatrix (same value is used for all local rows). 3925 - o_nnz - array containing the number of nonzeros in the various rows of the 3926 OFF-DIAGONAL portion of the local submatrix (possibly different for 3927 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3928 structure. The size of this array is equal to the number 3929 of local rows, i.e 'm'. 3930 3931 If the *_nnz parameter is given then the *_nz parameter is ignored 3932 3933 The AIJ format (also called the Yale sparse matrix format or 3934 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3935 storage. The stored row and column indices begin with zero. 3936 See Users-Manual: ch_mat for details. 3937 3938 The parallel matrix is partitioned such that the first m0 rows belong to 3939 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3940 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3941 3942 The DIAGONAL portion of the local submatrix of a processor can be defined 3943 as the submatrix which is obtained by extraction the part corresponding to 3944 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3945 first row that belongs to the processor, r2 is the last row belonging to 3946 the this processor, and c1-c2 is range of indices of the local part of a 3947 vector suitable for applying the matrix to. This is an mxn matrix. In the 3948 common case of a square matrix, the row and column ranges are the same and 3949 the DIAGONAL part is also square. The remaining portion of the local 3950 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3951 3952 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3953 3954 You can call MatGetInfo() to get information on how effective the preallocation was; 3955 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3956 You can also run with the option -info and look for messages with the string 3957 malloc in them to see if additional memory allocation was needed. 3958 3959 Example usage: 3960 3961 Consider the following 8x8 matrix with 34 non-zero values, that is 3962 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3963 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3964 as follows: 3965 3966 .vb 3967 1 2 0 | 0 3 0 | 0 4 3968 Proc0 0 5 6 | 7 0 0 | 8 0 3969 9 0 10 | 11 0 0 | 12 0 3970 ------------------------------------- 3971 13 0 14 | 15 16 17 | 0 0 3972 Proc1 0 18 0 | 19 20 21 | 0 0 3973 0 0 0 | 22 23 0 | 24 0 3974 ------------------------------------- 3975 Proc2 25 26 27 | 0 0 28 | 29 0 3976 30 0 0 | 31 32 33 | 0 34 3977 .ve 3978 3979 This can be represented as a collection of submatrices as: 3980 3981 .vb 3982 A B C 3983 D E F 3984 G H I 3985 .ve 3986 3987 Where the submatrices A,B,C are owned by proc0, D,E,F are 3988 owned by proc1, G,H,I are owned by proc2. 3989 3990 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3991 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3992 The 'M','N' parameters are 8,8, and have the same values on all procs. 3993 3994 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3995 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3996 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3997 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3998 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3999 matrix, ans [DF] as another SeqAIJ matrix. 4000 4001 When d_nz, o_nz parameters are specified, d_nz storage elements are 4002 allocated for every row of the local diagonal submatrix, and o_nz 4003 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4004 One way to choose d_nz and o_nz is to use the max nonzerors per local 4005 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4006 In this case, the values of d_nz,o_nz are: 4007 .vb 4008 proc0 : dnz = 2, o_nz = 2 4009 proc1 : dnz = 3, o_nz = 2 4010 proc2 : dnz = 1, o_nz = 4 4011 .ve 4012 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4013 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4014 for proc3. i.e we are using 12+15+10=37 storage locations to store 4015 34 values. 4016 4017 When d_nnz, o_nnz parameters are specified, the storage is specified 4018 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4019 In the above case the values for d_nnz,o_nnz are: 4020 .vb 4021 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4022 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4023 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4024 .ve 4025 Here the space allocated is sum of all the above values i.e 34, and 4026 hence pre-allocation is perfect. 4027 4028 Level: intermediate 4029 4030 .keywords: matrix, aij, compressed row, sparse, parallel 4031 4032 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 4033 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 4034 @*/ 4035 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 4036 { 4037 PetscErrorCode ierr; 4038 4039 PetscFunctionBegin; 4040 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 4041 PetscValidType(B,1); 4042 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 4043 PetscFunctionReturn(0); 4044 } 4045 4046 /*@ 4047 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 4048 CSR format the local rows. 4049 4050 Collective on MPI_Comm 4051 4052 Input Parameters: 4053 + comm - MPI communicator 4054 . m - number of local rows (Cannot be PETSC_DECIDE) 4055 . n - This value should be the same as the local size used in creating the 4056 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4057 calculated if N is given) For square matrices n is almost always m. 4058 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4059 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4060 . i - row indices 4061 . j - column indices 4062 - a - matrix values 4063 4064 Output Parameter: 4065 . mat - the matrix 4066 4067 Level: intermediate 4068 4069 Notes: 4070 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 4071 thus you CANNOT change the matrix entries by changing the values of a[] after you have 4072 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 4073 4074 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4075 4076 The format which is used for the sparse matrix input, is equivalent to a 4077 row-major ordering.. i.e for the following matrix, the input data expected is 4078 as shown 4079 4080 $ 1 0 0 4081 $ 2 0 3 P0 4082 $ ------- 4083 $ 4 5 6 P1 4084 $ 4085 $ Process0 [P0]: rows_owned=[0,1] 4086 $ i = {0,1,3} [size = nrow+1 = 2+1] 4087 $ j = {0,0,2} [size = 3] 4088 $ v = {1,2,3} [size = 3] 4089 $ 4090 $ Process1 [P1]: rows_owned=[2] 4091 $ i = {0,3} [size = nrow+1 = 1+1] 4092 $ j = {0,1,2} [size = 3] 4093 $ v = {4,5,6} [size = 3] 4094 4095 .keywords: matrix, aij, compressed row, sparse, parallel 4096 4097 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4098 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4099 @*/ 4100 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 4101 { 4102 PetscErrorCode ierr; 4103 4104 PetscFunctionBegin; 4105 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4106 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4107 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4108 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4109 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 4110 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 4111 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 4112 PetscFunctionReturn(0); 4113 } 4114 4115 /*@C 4116 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 4117 (the default parallel PETSc format). For good matrix assembly performance 4118 the user should preallocate the matrix storage by setting the parameters 4119 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4120 performance can be increased by more than a factor of 50. 4121 4122 Collective on MPI_Comm 4123 4124 Input Parameters: 4125 + comm - MPI communicator 4126 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 4127 This value should be the same as the local size used in creating the 4128 y vector for the matrix-vector product y = Ax. 4129 . n - This value should be the same as the local size used in creating the 4130 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4131 calculated if N is given) For square matrices n is almost always m. 4132 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4133 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4134 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4135 (same value is used for all local rows) 4136 . d_nnz - array containing the number of nonzeros in the various rows of the 4137 DIAGONAL portion of the local submatrix (possibly different for each row) 4138 or NULL, if d_nz is used to specify the nonzero structure. 4139 The size of this array is equal to the number of local rows, i.e 'm'. 4140 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4141 submatrix (same value is used for all local rows). 4142 - o_nnz - array containing the number of nonzeros in the various rows of the 4143 OFF-DIAGONAL portion of the local submatrix (possibly different for 4144 each row) or NULL, if o_nz is used to specify the nonzero 4145 structure. The size of this array is equal to the number 4146 of local rows, i.e 'm'. 4147 4148 Output Parameter: 4149 . A - the matrix 4150 4151 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4152 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4153 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4154 4155 Notes: 4156 If the *_nnz parameter is given then the *_nz parameter is ignored 4157 4158 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4159 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4160 storage requirements for this matrix. 4161 4162 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4163 processor than it must be used on all processors that share the object for 4164 that argument. 4165 4166 The user MUST specify either the local or global matrix dimensions 4167 (possibly both). 4168 4169 The parallel matrix is partitioned across processors such that the 4170 first m0 rows belong to process 0, the next m1 rows belong to 4171 process 1, the next m2 rows belong to process 2 etc.. where 4172 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4173 values corresponding to [m x N] submatrix. 4174 4175 The columns are logically partitioned with the n0 columns belonging 4176 to 0th partition, the next n1 columns belonging to the next 4177 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4178 4179 The DIAGONAL portion of the local submatrix on any given processor 4180 is the submatrix corresponding to the rows and columns m,n 4181 corresponding to the given processor. i.e diagonal matrix on 4182 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4183 etc. The remaining portion of the local submatrix [m x (N-n)] 4184 constitute the OFF-DIAGONAL portion. The example below better 4185 illustrates this concept. 4186 4187 For a square global matrix we define each processor's diagonal portion 4188 to be its local rows and the corresponding columns (a square submatrix); 4189 each processor's off-diagonal portion encompasses the remainder of the 4190 local matrix (a rectangular submatrix). 4191 4192 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4193 4194 When calling this routine with a single process communicator, a matrix of 4195 type SEQAIJ is returned. If a matrix of type MPIAIJ is desired for this 4196 type of communicator, use the construction mechanism 4197 .vb 4198 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4199 .ve 4200 4201 $ MatCreate(...,&A); 4202 $ MatSetType(A,MATMPIAIJ); 4203 $ MatSetSizes(A, m,n,M,N); 4204 $ MatMPIAIJSetPreallocation(A,...); 4205 4206 By default, this format uses inodes (identical nodes) when possible. 4207 We search for consecutive rows with the same nonzero structure, thereby 4208 reusing matrix information to achieve increased efficiency. 4209 4210 Options Database Keys: 4211 + -mat_no_inode - Do not use inodes 4212 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4213 - -mat_aij_oneindex - Internally use indexing starting at 1 4214 rather than 0. Note that when calling MatSetValues(), 4215 the user still MUST index entries starting at 0! 4216 4217 4218 Example usage: 4219 4220 Consider the following 8x8 matrix with 34 non-zero values, that is 4221 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4222 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4223 as follows 4224 4225 .vb 4226 1 2 0 | 0 3 0 | 0 4 4227 Proc0 0 5 6 | 7 0 0 | 8 0 4228 9 0 10 | 11 0 0 | 12 0 4229 ------------------------------------- 4230 13 0 14 | 15 16 17 | 0 0 4231 Proc1 0 18 0 | 19 20 21 | 0 0 4232 0 0 0 | 22 23 0 | 24 0 4233 ------------------------------------- 4234 Proc2 25 26 27 | 0 0 28 | 29 0 4235 30 0 0 | 31 32 33 | 0 34 4236 .ve 4237 4238 This can be represented as a collection of submatrices as 4239 4240 .vb 4241 A B C 4242 D E F 4243 G H I 4244 .ve 4245 4246 Where the submatrices A,B,C are owned by proc0, D,E,F are 4247 owned by proc1, G,H,I are owned by proc2. 4248 4249 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4250 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4251 The 'M','N' parameters are 8,8, and have the same values on all procs. 4252 4253 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4254 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4255 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4256 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4257 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4258 matrix, ans [DF] as another SeqAIJ matrix. 4259 4260 When d_nz, o_nz parameters are specified, d_nz storage elements are 4261 allocated for every row of the local diagonal submatrix, and o_nz 4262 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4263 One way to choose d_nz and o_nz is to use the max nonzerors per local 4264 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4265 In this case, the values of d_nz,o_nz are 4266 .vb 4267 proc0 : dnz = 2, o_nz = 2 4268 proc1 : dnz = 3, o_nz = 2 4269 proc2 : dnz = 1, o_nz = 4 4270 .ve 4271 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4272 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4273 for proc3. i.e we are using 12+15+10=37 storage locations to store 4274 34 values. 4275 4276 When d_nnz, o_nnz parameters are specified, the storage is specified 4277 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4278 In the above case the values for d_nnz,o_nnz are 4279 .vb 4280 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4281 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4282 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4283 .ve 4284 Here the space allocated is sum of all the above values i.e 34, and 4285 hence pre-allocation is perfect. 4286 4287 Level: intermediate 4288 4289 .keywords: matrix, aij, compressed row, sparse, parallel 4290 4291 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4292 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4293 @*/ 4294 PetscErrorCode MatCreateAIJ(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[],Mat *A) 4295 { 4296 PetscErrorCode ierr; 4297 PetscMPIInt size; 4298 4299 PetscFunctionBegin; 4300 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4301 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4302 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4303 if (size > 1) { 4304 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4305 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4306 } else { 4307 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4308 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4309 } 4310 PetscFunctionReturn(0); 4311 } 4312 4313 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4314 { 4315 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4316 PetscBool flg; 4317 PetscErrorCode ierr; 4318 4319 PetscFunctionBegin; 4320 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4321 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4322 if (Ad) *Ad = a->A; 4323 if (Ao) *Ao = a->B; 4324 if (colmap) *colmap = a->garray; 4325 PetscFunctionReturn(0); 4326 } 4327 4328 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4329 { 4330 PetscErrorCode ierr; 4331 PetscInt m,N,i,rstart,nnz,Ii; 4332 PetscInt *indx; 4333 PetscScalar *values; 4334 4335 PetscFunctionBegin; 4336 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4337 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4338 PetscInt *dnz,*onz,sum,bs,cbs; 4339 4340 if (n == PETSC_DECIDE) { 4341 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4342 } 4343 /* Check sum(n) = N */ 4344 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4345 if (sum != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns %D != global columns %D",sum,N); 4346 4347 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4348 rstart -= m; 4349 4350 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4351 for (i=0; i<m; i++) { 4352 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4353 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4354 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4355 } 4356 4357 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4358 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4359 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4360 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4361 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4362 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4363 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4364 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4365 } 4366 4367 /* numeric phase */ 4368 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4369 for (i=0; i<m; i++) { 4370 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4371 Ii = i + rstart; 4372 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4373 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4374 } 4375 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4376 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4377 PetscFunctionReturn(0); 4378 } 4379 4380 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4381 { 4382 PetscErrorCode ierr; 4383 PetscMPIInt rank; 4384 PetscInt m,N,i,rstart,nnz; 4385 size_t len; 4386 const PetscInt *indx; 4387 PetscViewer out; 4388 char *name; 4389 Mat B; 4390 const PetscScalar *values; 4391 4392 PetscFunctionBegin; 4393 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4394 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4395 /* Should this be the type of the diagonal block of A? */ 4396 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4397 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4398 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4399 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4400 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4401 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4402 for (i=0; i<m; i++) { 4403 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4404 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4405 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4406 } 4407 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4408 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4409 4410 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4411 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4412 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4413 sprintf(name,"%s.%d",outfile,rank); 4414 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4415 ierr = PetscFree(name);CHKERRQ(ierr); 4416 ierr = MatView(B,out);CHKERRQ(ierr); 4417 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4418 ierr = MatDestroy(&B);CHKERRQ(ierr); 4419 PetscFunctionReturn(0); 4420 } 4421 4422 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4423 { 4424 PetscErrorCode ierr; 4425 Mat_Merge_SeqsToMPI *merge; 4426 PetscContainer container; 4427 4428 PetscFunctionBegin; 4429 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4430 if (container) { 4431 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4432 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4433 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4434 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4435 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4436 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4437 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4438 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4439 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4440 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4441 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4442 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4443 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4444 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4445 ierr = PetscFree(merge);CHKERRQ(ierr); 4446 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4447 } 4448 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4449 PetscFunctionReturn(0); 4450 } 4451 4452 #include <../src/mat/utils/freespace.h> 4453 #include <petscbt.h> 4454 4455 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4456 { 4457 PetscErrorCode ierr; 4458 MPI_Comm comm; 4459 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4460 PetscMPIInt size,rank,taga,*len_s; 4461 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4462 PetscInt proc,m; 4463 PetscInt **buf_ri,**buf_rj; 4464 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4465 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4466 MPI_Request *s_waits,*r_waits; 4467 MPI_Status *status; 4468 MatScalar *aa=a->a; 4469 MatScalar **abuf_r,*ba_i; 4470 Mat_Merge_SeqsToMPI *merge; 4471 PetscContainer container; 4472 4473 PetscFunctionBegin; 4474 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4475 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4476 4477 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4478 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4479 4480 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4481 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4482 4483 bi = merge->bi; 4484 bj = merge->bj; 4485 buf_ri = merge->buf_ri; 4486 buf_rj = merge->buf_rj; 4487 4488 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4489 owners = merge->rowmap->range; 4490 len_s = merge->len_s; 4491 4492 /* send and recv matrix values */ 4493 /*-----------------------------*/ 4494 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4495 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4496 4497 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4498 for (proc=0,k=0; proc<size; proc++) { 4499 if (!len_s[proc]) continue; 4500 i = owners[proc]; 4501 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4502 k++; 4503 } 4504 4505 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4506 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4507 ierr = PetscFree(status);CHKERRQ(ierr); 4508 4509 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4510 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4511 4512 /* insert mat values of mpimat */ 4513 /*----------------------------*/ 4514 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4515 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4516 4517 for (k=0; k<merge->nrecv; k++) { 4518 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4519 nrows = *(buf_ri_k[k]); 4520 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4521 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4522 } 4523 4524 /* set values of ba */ 4525 m = merge->rowmap->n; 4526 for (i=0; i<m; i++) { 4527 arow = owners[rank] + i; 4528 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4529 bnzi = bi[i+1] - bi[i]; 4530 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4531 4532 /* add local non-zero vals of this proc's seqmat into ba */ 4533 anzi = ai[arow+1] - ai[arow]; 4534 aj = a->j + ai[arow]; 4535 aa = a->a + ai[arow]; 4536 nextaj = 0; 4537 for (j=0; nextaj<anzi; j++) { 4538 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4539 ba_i[j] += aa[nextaj++]; 4540 } 4541 } 4542 4543 /* add received vals into ba */ 4544 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4545 /* i-th row */ 4546 if (i == *nextrow[k]) { 4547 anzi = *(nextai[k]+1) - *nextai[k]; 4548 aj = buf_rj[k] + *(nextai[k]); 4549 aa = abuf_r[k] + *(nextai[k]); 4550 nextaj = 0; 4551 for (j=0; nextaj<anzi; j++) { 4552 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4553 ba_i[j] += aa[nextaj++]; 4554 } 4555 } 4556 nextrow[k]++; nextai[k]++; 4557 } 4558 } 4559 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4560 } 4561 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4562 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4563 4564 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4565 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4566 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4567 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4568 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4569 PetscFunctionReturn(0); 4570 } 4571 4572 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4573 { 4574 PetscErrorCode ierr; 4575 Mat B_mpi; 4576 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4577 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4578 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4579 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4580 PetscInt len,proc,*dnz,*onz,bs,cbs; 4581 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4582 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4583 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4584 MPI_Status *status; 4585 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4586 PetscBT lnkbt; 4587 Mat_Merge_SeqsToMPI *merge; 4588 PetscContainer container; 4589 4590 PetscFunctionBegin; 4591 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4592 4593 /* make sure it is a PETSc comm */ 4594 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4595 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4596 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4597 4598 ierr = PetscNew(&merge);CHKERRQ(ierr); 4599 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4600 4601 /* determine row ownership */ 4602 /*---------------------------------------------------------*/ 4603 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4604 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4605 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4606 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4607 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4608 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4609 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4610 4611 m = merge->rowmap->n; 4612 owners = merge->rowmap->range; 4613 4614 /* determine the number of messages to send, their lengths */ 4615 /*---------------------------------------------------------*/ 4616 len_s = merge->len_s; 4617 4618 len = 0; /* length of buf_si[] */ 4619 merge->nsend = 0; 4620 for (proc=0; proc<size; proc++) { 4621 len_si[proc] = 0; 4622 if (proc == rank) { 4623 len_s[proc] = 0; 4624 } else { 4625 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4626 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4627 } 4628 if (len_s[proc]) { 4629 merge->nsend++; 4630 nrows = 0; 4631 for (i=owners[proc]; i<owners[proc+1]; i++) { 4632 if (ai[i+1] > ai[i]) nrows++; 4633 } 4634 len_si[proc] = 2*(nrows+1); 4635 len += len_si[proc]; 4636 } 4637 } 4638 4639 /* determine the number and length of messages to receive for ij-structure */ 4640 /*-------------------------------------------------------------------------*/ 4641 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4642 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4643 4644 /* post the Irecv of j-structure */ 4645 /*-------------------------------*/ 4646 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4647 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4648 4649 /* post the Isend of j-structure */ 4650 /*--------------------------------*/ 4651 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4652 4653 for (proc=0, k=0; proc<size; proc++) { 4654 if (!len_s[proc]) continue; 4655 i = owners[proc]; 4656 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4657 k++; 4658 } 4659 4660 /* receives and sends of j-structure are complete */ 4661 /*------------------------------------------------*/ 4662 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4663 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4664 4665 /* send and recv i-structure */ 4666 /*---------------------------*/ 4667 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4668 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4669 4670 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4671 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4672 for (proc=0,k=0; proc<size; proc++) { 4673 if (!len_s[proc]) continue; 4674 /* form outgoing message for i-structure: 4675 buf_si[0]: nrows to be sent 4676 [1:nrows]: row index (global) 4677 [nrows+1:2*nrows+1]: i-structure index 4678 */ 4679 /*-------------------------------------------*/ 4680 nrows = len_si[proc]/2 - 1; 4681 buf_si_i = buf_si + nrows+1; 4682 buf_si[0] = nrows; 4683 buf_si_i[0] = 0; 4684 nrows = 0; 4685 for (i=owners[proc]; i<owners[proc+1]; i++) { 4686 anzi = ai[i+1] - ai[i]; 4687 if (anzi) { 4688 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4689 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4690 nrows++; 4691 } 4692 } 4693 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4694 k++; 4695 buf_si += len_si[proc]; 4696 } 4697 4698 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4699 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4700 4701 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4702 for (i=0; i<merge->nrecv; i++) { 4703 ierr = PetscInfo3(seqmat,"recv len_ri=%D, len_rj=%D from [%D]\n",len_ri[i],merge->len_r[i],merge->id_r[i]);CHKERRQ(ierr); 4704 } 4705 4706 ierr = PetscFree(len_si);CHKERRQ(ierr); 4707 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4708 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4709 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4710 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4711 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4712 ierr = PetscFree(status);CHKERRQ(ierr); 4713 4714 /* compute a local seq matrix in each processor */ 4715 /*----------------------------------------------*/ 4716 /* allocate bi array and free space for accumulating nonzero column info */ 4717 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4718 bi[0] = 0; 4719 4720 /* create and initialize a linked list */ 4721 nlnk = N+1; 4722 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4723 4724 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4725 len = ai[owners[rank+1]] - ai[owners[rank]]; 4726 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4727 4728 current_space = free_space; 4729 4730 /* determine symbolic info for each local row */ 4731 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4732 4733 for (k=0; k<merge->nrecv; k++) { 4734 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4735 nrows = *buf_ri_k[k]; 4736 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4737 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4738 } 4739 4740 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4741 len = 0; 4742 for (i=0; i<m; i++) { 4743 bnzi = 0; 4744 /* add local non-zero cols of this proc's seqmat into lnk */ 4745 arow = owners[rank] + i; 4746 anzi = ai[arow+1] - ai[arow]; 4747 aj = a->j + ai[arow]; 4748 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4749 bnzi += nlnk; 4750 /* add received col data into lnk */ 4751 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4752 if (i == *nextrow[k]) { /* i-th row */ 4753 anzi = *(nextai[k]+1) - *nextai[k]; 4754 aj = buf_rj[k] + *nextai[k]; 4755 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4756 bnzi += nlnk; 4757 nextrow[k]++; nextai[k]++; 4758 } 4759 } 4760 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4761 4762 /* if free space is not available, make more free space */ 4763 if (current_space->local_remaining<bnzi) { 4764 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4765 nspacedouble++; 4766 } 4767 /* copy data into free space, then initialize lnk */ 4768 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4769 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4770 4771 current_space->array += bnzi; 4772 current_space->local_used += bnzi; 4773 current_space->local_remaining -= bnzi; 4774 4775 bi[i+1] = bi[i] + bnzi; 4776 } 4777 4778 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4779 4780 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4781 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4782 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4783 4784 /* create symbolic parallel matrix B_mpi */ 4785 /*---------------------------------------*/ 4786 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4787 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4788 if (n==PETSC_DECIDE) { 4789 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4790 } else { 4791 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4792 } 4793 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4794 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4795 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4796 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4797 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4798 4799 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4800 B_mpi->assembled = PETSC_FALSE; 4801 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4802 merge->bi = bi; 4803 merge->bj = bj; 4804 merge->buf_ri = buf_ri; 4805 merge->buf_rj = buf_rj; 4806 merge->coi = NULL; 4807 merge->coj = NULL; 4808 merge->owners_co = NULL; 4809 4810 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4811 4812 /* attach the supporting struct to B_mpi for reuse */ 4813 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4814 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4815 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4816 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4817 *mpimat = B_mpi; 4818 4819 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4820 PetscFunctionReturn(0); 4821 } 4822 4823 /*@C 4824 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4825 matrices from each processor 4826 4827 Collective on MPI_Comm 4828 4829 Input Parameters: 4830 + comm - the communicators the parallel matrix will live on 4831 . seqmat - the input sequential matrices 4832 . m - number of local rows (or PETSC_DECIDE) 4833 . n - number of local columns (or PETSC_DECIDE) 4834 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4835 4836 Output Parameter: 4837 . mpimat - the parallel matrix generated 4838 4839 Level: advanced 4840 4841 Notes: 4842 The dimensions of the sequential matrix in each processor MUST be the same. 4843 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4844 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4845 @*/ 4846 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4847 { 4848 PetscErrorCode ierr; 4849 PetscMPIInt size; 4850 4851 PetscFunctionBegin; 4852 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4853 if (size == 1) { 4854 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4855 if (scall == MAT_INITIAL_MATRIX) { 4856 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4857 } else { 4858 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4859 } 4860 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4861 PetscFunctionReturn(0); 4862 } 4863 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4864 if (scall == MAT_INITIAL_MATRIX) { 4865 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4866 } 4867 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4868 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4869 PetscFunctionReturn(0); 4870 } 4871 4872 /*@ 4873 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential matrix with 4874 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4875 with MatGetSize() 4876 4877 Not Collective 4878 4879 Input Parameters: 4880 + A - the matrix 4881 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4882 4883 Output Parameter: 4884 . A_loc - the local sequential matrix generated 4885 4886 Level: developer 4887 4888 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4889 4890 @*/ 4891 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4892 { 4893 PetscErrorCode ierr; 4894 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4895 Mat_SeqAIJ *mat,*a,*b; 4896 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4897 MatScalar *aa,*ba,*cam; 4898 PetscScalar *ca; 4899 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4900 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4901 PetscBool match; 4902 MPI_Comm comm; 4903 PetscMPIInt size; 4904 4905 PetscFunctionBegin; 4906 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4907 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4908 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4909 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4910 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4911 4912 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4913 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4914 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4915 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4916 aa = a->a; ba = b->a; 4917 if (scall == MAT_INITIAL_MATRIX) { 4918 if (size == 1) { 4919 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4920 PetscFunctionReturn(0); 4921 } 4922 4923 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4924 ci[0] = 0; 4925 for (i=0; i<am; i++) { 4926 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4927 } 4928 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4929 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4930 k = 0; 4931 for (i=0; i<am; i++) { 4932 ncols_o = bi[i+1] - bi[i]; 4933 ncols_d = ai[i+1] - ai[i]; 4934 /* off-diagonal portion of A */ 4935 for (jo=0; jo<ncols_o; jo++) { 4936 col = cmap[*bj]; 4937 if (col >= cstart) break; 4938 cj[k] = col; bj++; 4939 ca[k++] = *ba++; 4940 } 4941 /* diagonal portion of A */ 4942 for (j=0; j<ncols_d; j++) { 4943 cj[k] = cstart + *aj++; 4944 ca[k++] = *aa++; 4945 } 4946 /* off-diagonal portion of A */ 4947 for (j=jo; j<ncols_o; j++) { 4948 cj[k] = cmap[*bj++]; 4949 ca[k++] = *ba++; 4950 } 4951 } 4952 /* put together the new matrix */ 4953 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4954 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4955 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4956 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4957 mat->free_a = PETSC_TRUE; 4958 mat->free_ij = PETSC_TRUE; 4959 mat->nonew = 0; 4960 } else if (scall == MAT_REUSE_MATRIX) { 4961 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4962 ci = mat->i; cj = mat->j; cam = mat->a; 4963 for (i=0; i<am; i++) { 4964 /* off-diagonal portion of A */ 4965 ncols_o = bi[i+1] - bi[i]; 4966 for (jo=0; jo<ncols_o; jo++) { 4967 col = cmap[*bj]; 4968 if (col >= cstart) break; 4969 *cam++ = *ba++; bj++; 4970 } 4971 /* diagonal portion of A */ 4972 ncols_d = ai[i+1] - ai[i]; 4973 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4974 /* off-diagonal portion of A */ 4975 for (j=jo; j<ncols_o; j++) { 4976 *cam++ = *ba++; bj++; 4977 } 4978 } 4979 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4980 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4981 PetscFunctionReturn(0); 4982 } 4983 4984 /*@C 4985 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4986 4987 Not Collective 4988 4989 Input Parameters: 4990 + A - the matrix 4991 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4992 - row, col - index sets of rows and columns to extract (or NULL) 4993 4994 Output Parameter: 4995 . A_loc - the local sequential matrix generated 4996 4997 Level: developer 4998 4999 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 5000 5001 @*/ 5002 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 5003 { 5004 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5005 PetscErrorCode ierr; 5006 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 5007 IS isrowa,iscola; 5008 Mat *aloc; 5009 PetscBool match; 5010 5011 PetscFunctionBegin; 5012 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 5013 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 5014 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 5015 if (!row) { 5016 start = A->rmap->rstart; end = A->rmap->rend; 5017 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 5018 } else { 5019 isrowa = *row; 5020 } 5021 if (!col) { 5022 start = A->cmap->rstart; 5023 cmap = a->garray; 5024 nzA = a->A->cmap->n; 5025 nzB = a->B->cmap->n; 5026 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5027 ncols = 0; 5028 for (i=0; i<nzB; i++) { 5029 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5030 else break; 5031 } 5032 imark = i; 5033 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 5034 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 5035 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 5036 } else { 5037 iscola = *col; 5038 } 5039 if (scall != MAT_INITIAL_MATRIX) { 5040 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 5041 aloc[0] = *A_loc; 5042 } 5043 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 5044 *A_loc = aloc[0]; 5045 ierr = PetscFree(aloc);CHKERRQ(ierr); 5046 if (!row) { 5047 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 5048 } 5049 if (!col) { 5050 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 5051 } 5052 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 5053 PetscFunctionReturn(0); 5054 } 5055 5056 /*@C 5057 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 5058 5059 Collective on Mat 5060 5061 Input Parameters: 5062 + A,B - the matrices in mpiaij format 5063 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5064 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 5065 5066 Output Parameter: 5067 + rowb, colb - index sets of rows and columns of B to extract 5068 - B_seq - the sequential matrix generated 5069 5070 Level: developer 5071 5072 @*/ 5073 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 5074 { 5075 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5076 PetscErrorCode ierr; 5077 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 5078 IS isrowb,iscolb; 5079 Mat *bseq=NULL; 5080 5081 PetscFunctionBegin; 5082 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5083 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%D, %D) != (%D,%D)",A->cmap->rstart,A->cmap->rend,B->rmap->rstart,B->rmap->rend); 5084 } 5085 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5086 5087 if (scall == MAT_INITIAL_MATRIX) { 5088 start = A->cmap->rstart; 5089 cmap = a->garray; 5090 nzA = a->A->cmap->n; 5091 nzB = a->B->cmap->n; 5092 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5093 ncols = 0; 5094 for (i=0; i<nzB; i++) { /* row < local row index */ 5095 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5096 else break; 5097 } 5098 imark = i; 5099 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 5100 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5101 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 5102 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 5103 } else { 5104 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5105 isrowb = *rowb; iscolb = *colb; 5106 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 5107 bseq[0] = *B_seq; 5108 } 5109 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 5110 *B_seq = bseq[0]; 5111 ierr = PetscFree(bseq);CHKERRQ(ierr); 5112 if (!rowb) { 5113 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 5114 } else { 5115 *rowb = isrowb; 5116 } 5117 if (!colb) { 5118 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 5119 } else { 5120 *colb = iscolb; 5121 } 5122 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5123 PetscFunctionReturn(0); 5124 } 5125 5126 /* 5127 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 5128 of the OFF-DIAGONAL portion of local A 5129 5130 Collective on Mat 5131 5132 Input Parameters: 5133 + A,B - the matrices in mpiaij format 5134 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5135 5136 Output Parameter: 5137 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5138 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5139 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5140 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5141 5142 Level: developer 5143 5144 */ 5145 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5146 { 5147 VecScatter_MPI_General *gen_to,*gen_from; 5148 PetscErrorCode ierr; 5149 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5150 Mat_SeqAIJ *b_oth; 5151 VecScatter ctx; 5152 MPI_Comm comm; 5153 PetscMPIInt *rprocs,*sprocs,tag,rank; 5154 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5155 PetscInt *rvalues,*svalues; 5156 MatScalar *b_otha,*bufa,*bufA; 5157 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5158 MPI_Request *rwaits = NULL,*swaits = NULL; 5159 MPI_Status *sstatus,rstatus; 5160 PetscMPIInt jj,size; 5161 PetscInt *cols,sbs,rbs; 5162 PetscScalar *vals; 5163 5164 PetscFunctionBegin; 5165 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5166 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5167 5168 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5169 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%d, %d) != (%d,%d)",A->cmap->rstart,A->cmap->rend,B->rmap->rstart,B->rmap->rend); 5170 } 5171 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5172 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5173 5174 if (size == 1) { 5175 startsj_s = NULL; 5176 bufa_ptr = NULL; 5177 *B_oth = NULL; 5178 PetscFunctionReturn(0); 5179 } 5180 5181 if (!a->Mvctx_mpi1) { /* create a->Mvctx_mpi1 to be used for Mat-Mat ops */ 5182 a->Mvctx_mpi1_flg = PETSC_TRUE; 5183 ierr = MatSetUpMultiply_MPIAIJ(A);CHKERRQ(ierr); 5184 } 5185 ctx = a->Mvctx_mpi1; 5186 tag = ((PetscObject)ctx)->tag; 5187 5188 gen_to = (VecScatter_MPI_General*)ctx->todata; 5189 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5190 nrecvs = gen_from->n; 5191 nsends = gen_to->n; 5192 5193 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 5194 srow = gen_to->indices; /* local row index to be sent */ 5195 sstarts = gen_to->starts; 5196 sprocs = gen_to->procs; 5197 sstatus = gen_to->sstatus; 5198 sbs = gen_to->bs; 5199 rstarts = gen_from->starts; 5200 rprocs = gen_from->procs; 5201 rbs = gen_from->bs; 5202 5203 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5204 if (scall == MAT_INITIAL_MATRIX) { 5205 /* i-array */ 5206 /*---------*/ 5207 /* post receives */ 5208 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 5209 for (i=0; i<nrecvs; i++) { 5210 rowlen = rvalues + rstarts[i]*rbs; 5211 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5212 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5213 } 5214 5215 /* pack the outgoing message */ 5216 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 5217 5218 sstartsj[0] = 0; 5219 rstartsj[0] = 0; 5220 len = 0; /* total length of j or a array to be sent */ 5221 k = 0; 5222 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 5223 for (i=0; i<nsends; i++) { 5224 rowlen = svalues + sstarts[i]*sbs; 5225 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5226 for (j=0; j<nrows; j++) { 5227 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5228 for (l=0; l<sbs; l++) { 5229 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5230 5231 rowlen[j*sbs+l] = ncols; 5232 5233 len += ncols; 5234 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5235 } 5236 k++; 5237 } 5238 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5239 5240 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5241 } 5242 /* recvs and sends of i-array are completed */ 5243 i = nrecvs; 5244 while (i--) { 5245 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5246 } 5247 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5248 ierr = PetscFree(svalues);CHKERRQ(ierr); 5249 5250 /* allocate buffers for sending j and a arrays */ 5251 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5252 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5253 5254 /* create i-array of B_oth */ 5255 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5256 5257 b_othi[0] = 0; 5258 len = 0; /* total length of j or a array to be received */ 5259 k = 0; 5260 for (i=0; i<nrecvs; i++) { 5261 rowlen = rvalues + rstarts[i]*rbs; 5262 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5263 for (j=0; j<nrows; j++) { 5264 b_othi[k+1] = b_othi[k] + rowlen[j]; 5265 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5266 k++; 5267 } 5268 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5269 } 5270 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5271 5272 /* allocate space for j and a arrrays of B_oth */ 5273 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5274 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5275 5276 /* j-array */ 5277 /*---------*/ 5278 /* post receives of j-array */ 5279 for (i=0; i<nrecvs; i++) { 5280 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5281 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5282 } 5283 5284 /* pack the outgoing message j-array */ 5285 k = 0; 5286 for (i=0; i<nsends; i++) { 5287 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5288 bufJ = bufj+sstartsj[i]; 5289 for (j=0; j<nrows; j++) { 5290 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5291 for (ll=0; ll<sbs; ll++) { 5292 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5293 for (l=0; l<ncols; l++) { 5294 *bufJ++ = cols[l]; 5295 } 5296 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5297 } 5298 } 5299 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5300 } 5301 5302 /* recvs and sends of j-array are completed */ 5303 i = nrecvs; 5304 while (i--) { 5305 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5306 } 5307 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5308 } else if (scall == MAT_REUSE_MATRIX) { 5309 sstartsj = *startsj_s; 5310 rstartsj = *startsj_r; 5311 bufa = *bufa_ptr; 5312 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5313 b_otha = b_oth->a; 5314 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5315 5316 /* a-array */ 5317 /*---------*/ 5318 /* post receives of a-array */ 5319 for (i=0; i<nrecvs; i++) { 5320 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5321 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5322 } 5323 5324 /* pack the outgoing message a-array */ 5325 k = 0; 5326 for (i=0; i<nsends; i++) { 5327 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5328 bufA = bufa+sstartsj[i]; 5329 for (j=0; j<nrows; j++) { 5330 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5331 for (ll=0; ll<sbs; ll++) { 5332 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5333 for (l=0; l<ncols; l++) { 5334 *bufA++ = vals[l]; 5335 } 5336 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5337 } 5338 } 5339 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5340 } 5341 /* recvs and sends of a-array are completed */ 5342 i = nrecvs; 5343 while (i--) { 5344 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5345 } 5346 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5347 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5348 5349 if (scall == MAT_INITIAL_MATRIX) { 5350 /* put together the new matrix */ 5351 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5352 5353 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5354 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5355 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5356 b_oth->free_a = PETSC_TRUE; 5357 b_oth->free_ij = PETSC_TRUE; 5358 b_oth->nonew = 0; 5359 5360 ierr = PetscFree(bufj);CHKERRQ(ierr); 5361 if (!startsj_s || !bufa_ptr) { 5362 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5363 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5364 } else { 5365 *startsj_s = sstartsj; 5366 *startsj_r = rstartsj; 5367 *bufa_ptr = bufa; 5368 } 5369 } 5370 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5371 PetscFunctionReturn(0); 5372 } 5373 5374 /*@C 5375 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5376 5377 Not Collective 5378 5379 Input Parameters: 5380 . A - The matrix in mpiaij format 5381 5382 Output Parameter: 5383 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5384 . colmap - A map from global column index to local index into lvec 5385 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5386 5387 Level: developer 5388 5389 @*/ 5390 #if defined(PETSC_USE_CTABLE) 5391 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5392 #else 5393 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5394 #endif 5395 { 5396 Mat_MPIAIJ *a; 5397 5398 PetscFunctionBegin; 5399 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5400 PetscValidPointer(lvec, 2); 5401 PetscValidPointer(colmap, 3); 5402 PetscValidPointer(multScatter, 4); 5403 a = (Mat_MPIAIJ*) A->data; 5404 if (lvec) *lvec = a->lvec; 5405 if (colmap) *colmap = a->colmap; 5406 if (multScatter) *multScatter = a->Mvctx; 5407 PetscFunctionReturn(0); 5408 } 5409 5410 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5411 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5412 #if defined(PETSC_HAVE_MKL_SPARSE) 5413 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJMKL(Mat,MatType,MatReuse,Mat*); 5414 #endif 5415 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5416 #if defined(PETSC_HAVE_ELEMENTAL) 5417 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5418 #endif 5419 #if defined(PETSC_HAVE_HYPRE) 5420 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5421 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5422 #endif 5423 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5424 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISELL(Mat,MatType,MatReuse,Mat*); 5425 5426 /* 5427 Computes (B'*A')' since computing B*A directly is untenable 5428 5429 n p p 5430 ( ) ( ) ( ) 5431 m ( A ) * n ( B ) = m ( C ) 5432 ( ) ( ) ( ) 5433 5434 */ 5435 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5436 { 5437 PetscErrorCode ierr; 5438 Mat At,Bt,Ct; 5439 5440 PetscFunctionBegin; 5441 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5442 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5443 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5444 ierr = MatDestroy(&At);CHKERRQ(ierr); 5445 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5446 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5447 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5448 PetscFunctionReturn(0); 5449 } 5450 5451 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5452 { 5453 PetscErrorCode ierr; 5454 PetscInt m=A->rmap->n,n=B->cmap->n; 5455 Mat Cmat; 5456 5457 PetscFunctionBegin; 5458 if (A->cmap->n != B->rmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"A->cmap->n %d != B->rmap->n %d\n",A->cmap->n,B->rmap->n); 5459 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5460 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5461 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5462 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5463 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5464 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5465 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5466 5467 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5468 5469 *C = Cmat; 5470 PetscFunctionReturn(0); 5471 } 5472 5473 /* ----------------------------------------------------------------*/ 5474 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5475 { 5476 PetscErrorCode ierr; 5477 5478 PetscFunctionBegin; 5479 if (scall == MAT_INITIAL_MATRIX) { 5480 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5481 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5482 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5483 } 5484 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5485 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5486 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5487 PetscFunctionReturn(0); 5488 } 5489 5490 /*MC 5491 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5492 5493 Options Database Keys: 5494 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5495 5496 Level: beginner 5497 5498 .seealso: MatCreateAIJ() 5499 M*/ 5500 5501 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5502 { 5503 Mat_MPIAIJ *b; 5504 PetscErrorCode ierr; 5505 PetscMPIInt size; 5506 5507 PetscFunctionBegin; 5508 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5509 5510 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5511 B->data = (void*)b; 5512 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5513 B->assembled = PETSC_FALSE; 5514 B->insertmode = NOT_SET_VALUES; 5515 b->size = size; 5516 5517 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5518 5519 /* build cache for off array entries formed */ 5520 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5521 5522 b->donotstash = PETSC_FALSE; 5523 b->colmap = 0; 5524 b->garray = 0; 5525 b->roworiented = PETSC_TRUE; 5526 5527 /* stuff used for matrix vector multiply */ 5528 b->lvec = NULL; 5529 b->Mvctx = NULL; 5530 5531 /* stuff for MatGetRow() */ 5532 b->rowindices = 0; 5533 b->rowvalues = 0; 5534 b->getrowactive = PETSC_FALSE; 5535 5536 /* flexible pointer used in CUSP/CUSPARSE classes */ 5537 b->spptr = NULL; 5538 5539 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5540 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5541 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5542 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5543 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5544 ierr = PetscObjectComposeFunction((PetscObject)B,"MatResetPreallocation_C",MatResetPreallocation_MPIAIJ);CHKERRQ(ierr); 5545 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5546 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5547 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5548 #if defined(PETSC_HAVE_MKL_SPARSE) 5549 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijmkl_C",MatConvert_MPIAIJ_MPIAIJMKL);CHKERRQ(ierr); 5550 #endif 5551 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5552 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5553 #if defined(PETSC_HAVE_ELEMENTAL) 5554 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5555 #endif 5556 #if defined(PETSC_HAVE_HYPRE) 5557 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5558 #endif 5559 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5560 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisell_C",MatConvert_MPIAIJ_MPISELL);CHKERRQ(ierr); 5561 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5562 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5563 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5564 #if defined(PETSC_HAVE_HYPRE) 5565 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5566 #endif 5567 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5568 PetscFunctionReturn(0); 5569 } 5570 5571 /*@C 5572 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5573 and "off-diagonal" part of the matrix in CSR format. 5574 5575 Collective on MPI_Comm 5576 5577 Input Parameters: 5578 + comm - MPI communicator 5579 . m - number of local rows (Cannot be PETSC_DECIDE) 5580 . n - This value should be the same as the local size used in creating the 5581 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5582 calculated if N is given) For square matrices n is almost always m. 5583 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5584 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5585 . i - row indices for "diagonal" portion of matrix 5586 . j - column indices 5587 . a - matrix values 5588 . oi - row indices for "off-diagonal" portion of matrix 5589 . oj - column indices 5590 - oa - matrix values 5591 5592 Output Parameter: 5593 . mat - the matrix 5594 5595 Level: advanced 5596 5597 Notes: 5598 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5599 must free the arrays once the matrix has been destroyed and not before. 5600 5601 The i and j indices are 0 based 5602 5603 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5604 5605 This sets local rows and cannot be used to set off-processor values. 5606 5607 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5608 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5609 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5610 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5611 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5612 communication if it is known that only local entries will be set. 5613 5614 .keywords: matrix, aij, compressed row, sparse, parallel 5615 5616 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5617 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5618 @*/ 5619 PetscErrorCode MatCreateMPIAIJWithSplitArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,PetscInt i[],PetscInt j[],PetscScalar a[],PetscInt oi[], PetscInt oj[],PetscScalar oa[],Mat *mat) 5620 { 5621 PetscErrorCode ierr; 5622 Mat_MPIAIJ *maij; 5623 5624 PetscFunctionBegin; 5625 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5626 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5627 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5628 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5629 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5630 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5631 maij = (Mat_MPIAIJ*) (*mat)->data; 5632 5633 (*mat)->preallocated = PETSC_TRUE; 5634 5635 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5636 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5637 5638 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5639 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5640 5641 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5642 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5643 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5644 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5645 5646 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5647 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5648 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5649 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5650 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5651 PetscFunctionReturn(0); 5652 } 5653 5654 /* 5655 Special version for direct calls from Fortran 5656 */ 5657 #include <petsc/private/fortranimpl.h> 5658 5659 /* Change these macros so can be used in void function */ 5660 #undef CHKERRQ 5661 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5662 #undef SETERRQ2 5663 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5664 #undef SETERRQ3 5665 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5666 #undef SETERRQ 5667 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5668 5669 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5670 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5671 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5672 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5673 #else 5674 #endif 5675 PETSC_EXTERN void PETSC_STDCALL matsetvaluesmpiaij_(Mat *mmat,PetscInt *mm,const PetscInt im[],PetscInt *mn,const PetscInt in[],const PetscScalar v[],InsertMode *maddv,PetscErrorCode *_ierr) 5676 { 5677 Mat mat = *mmat; 5678 PetscInt m = *mm, n = *mn; 5679 InsertMode addv = *maddv; 5680 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5681 PetscScalar value; 5682 PetscErrorCode ierr; 5683 5684 MatCheckPreallocated(mat,1); 5685 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5686 5687 #if defined(PETSC_USE_DEBUG) 5688 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5689 #endif 5690 { 5691 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5692 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5693 PetscBool roworiented = aij->roworiented; 5694 5695 /* Some Variables required in the macro */ 5696 Mat A = aij->A; 5697 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5698 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5699 MatScalar *aa = a->a; 5700 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5701 Mat B = aij->B; 5702 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5703 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5704 MatScalar *ba = b->a; 5705 5706 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5707 PetscInt nonew = a->nonew; 5708 MatScalar *ap1,*ap2; 5709 5710 PetscFunctionBegin; 5711 for (i=0; i<m; i++) { 5712 if (im[i] < 0) continue; 5713 #if defined(PETSC_USE_DEBUG) 5714 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 5715 #endif 5716 if (im[i] >= rstart && im[i] < rend) { 5717 row = im[i] - rstart; 5718 lastcol1 = -1; 5719 rp1 = aj + ai[row]; 5720 ap1 = aa + ai[row]; 5721 rmax1 = aimax[row]; 5722 nrow1 = ailen[row]; 5723 low1 = 0; 5724 high1 = nrow1; 5725 lastcol2 = -1; 5726 rp2 = bj + bi[row]; 5727 ap2 = ba + bi[row]; 5728 rmax2 = bimax[row]; 5729 nrow2 = bilen[row]; 5730 low2 = 0; 5731 high2 = nrow2; 5732 5733 for (j=0; j<n; j++) { 5734 if (roworiented) value = v[i*n+j]; 5735 else value = v[i+j*m]; 5736 if (in[j] >= cstart && in[j] < cend) { 5737 col = in[j] - cstart; 5738 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5739 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5740 } else if (in[j] < 0) continue; 5741 #if defined(PETSC_USE_DEBUG) 5742 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 5743 #endif 5744 else { 5745 if (mat->was_assembled) { 5746 if (!aij->colmap) { 5747 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5748 } 5749 #if defined(PETSC_USE_CTABLE) 5750 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5751 col--; 5752 #else 5753 col = aij->colmap[in[j]] - 1; 5754 #endif 5755 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5756 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5757 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5758 col = in[j]; 5759 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5760 B = aij->B; 5761 b = (Mat_SeqAIJ*)B->data; 5762 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5763 rp2 = bj + bi[row]; 5764 ap2 = ba + bi[row]; 5765 rmax2 = bimax[row]; 5766 nrow2 = bilen[row]; 5767 low2 = 0; 5768 high2 = nrow2; 5769 bm = aij->B->rmap->n; 5770 ba = b->a; 5771 } 5772 } else col = in[j]; 5773 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5774 } 5775 } 5776 } else if (!aij->donotstash) { 5777 if (roworiented) { 5778 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5779 } else { 5780 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5781 } 5782 } 5783 } 5784 } 5785 PetscFunctionReturnVoid(); 5786 } 5787 5788