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 = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3060 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3061 ierr = VecSet(lvec,-1.0);CHKERRQ(ierr); 3062 3063 /* Get start indices */ 3064 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3065 isstart -= ncols; 3066 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3067 3068 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3069 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3070 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3071 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3072 for (i=0; i<ncols; i++) { 3073 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3074 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3075 idx[i] = is_idx[i]-cstart; /* local index of iscol[i] */ 3076 } 3077 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3078 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3079 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3080 //ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3081 3082 /* Get iscol_d */ 3083 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,iscol_d);CHKERRQ(ierr); 3084 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3085 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3086 3087 /* Get isrow_d */ 3088 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3089 rstart = mat->rmap->rstart; 3090 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3091 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3092 for (i=0; i<m; i++) idx[i] = is_idx[i]-rstart; 3093 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3094 3095 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_OWN_POINTER,isrow_d);CHKERRQ(ierr); 3096 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3097 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3098 3099 /* (2) Scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3100 #if 0 3101 if (!a->Mvctx_mpi1) { 3102 /* a->Mvctx causes random 'count' in o-build? See src/mat/examples/tests/runex59_2 */ 3103 a->Mvctx_mpi1_flg = PETSC_TRUE; 3104 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 3105 } 3106 Mvctx = a->Mvctx_mpi1; 3107 #endif 3108 Mvctx = a->Mvctx; 3109 ierr = VecScatterBegin(Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3110 ierr = VecScatterEnd(Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3111 3112 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3113 ierr = VecSet(lcmap,-1.0);CHKERRQ(ierr); 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 //if (rank == 1) { 3137 printf("[%d] lvec:\n",rank); 3138 ierr = VecView(lvec,0);CHKERRQ(ierr); 3139 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"count %d != 6",count); 3140 } 3141 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr); 3142 /* cannot ensure iscol_o has same blocksize as iscol! */ 3143 3144 ierr = PetscFree(idx);CHKERRQ(ierr); 3145 3146 *garray = cmap1; 3147 3148 ierr = VecDestroy(&x);CHKERRQ(ierr); 3149 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3150 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3151 PetscFunctionReturn(0); 3152 } 3153 3154 /* isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */ 3155 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *submat) 3156 { 3157 PetscErrorCode ierr; 3158 Mat_MPIAIJ *a = (Mat_MPIAIJ*)mat->data,*asub; 3159 Mat M = NULL; 3160 MPI_Comm comm; 3161 IS iscol_d,isrow_d,iscol_o; 3162 Mat Asub = NULL,Bsub = NULL; 3163 PetscInt n; 3164 3165 PetscFunctionBegin; 3166 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3167 3168 if (call == MAT_REUSE_MATRIX) { 3169 /* Retrieve isrow_d, iscol_d and iscol_o from submat */ 3170 ierr = PetscObjectQuery((PetscObject)*submat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3171 if (!isrow_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow_d passed in was not used before, cannot reuse"); 3172 3173 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_d",(PetscObject*)&iscol_d);CHKERRQ(ierr); 3174 if (!iscol_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_d passed in was not used before, cannot reuse"); 3175 3176 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_o",(PetscObject*)&iscol_o);CHKERRQ(ierr); 3177 if (!iscol_o) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_o passed in was not used before, cannot reuse"); 3178 3179 /* Update diagonal and off-diagonal portions of submat */ 3180 asub = (Mat_MPIAIJ*)(*submat)->data; 3181 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->A);CHKERRQ(ierr); 3182 ierr = ISGetLocalSize(iscol_o,&n);CHKERRQ(ierr); 3183 if (n) { 3184 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->B);CHKERRQ(ierr); 3185 } 3186 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3187 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3188 3189 } else { /* call == MAT_INITIAL_MATRIX) */ 3190 const PetscInt *garray; 3191 PetscInt BsubN; 3192 3193 /* Create isrow_d, iscol_d, iscol_o and isgarray (replace isgarray with array?) */ 3194 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&isrow_d,&iscol_d,&iscol_o,&garray);CHKERRQ(ierr); 3195 3196 /* Create local submatrices Asub and Bsub */ 3197 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Asub);CHKERRQ(ierr); 3198 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Bsub);CHKERRQ(ierr); 3199 3200 /* Create submatrix M */ 3201 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray,&M);CHKERRQ(ierr); 3202 3203 /* If Bsub has empty columns, compress iscol_o such that it will retrieve condensed Bsub from a->B during reuse */ 3204 asub = (Mat_MPIAIJ*)M->data; 3205 3206 ierr = ISGetLocalSize(iscol_o,&BsubN);CHKERRQ(ierr); 3207 n = asub->B->cmap->N; 3208 if (BsubN > n) { 3209 /* This case can be tested using ~petsc/src/tao/bound/examples/tutorials/runplate2_3 */ 3210 const PetscInt *idx; 3211 PetscInt i,j,*idx_new,*subgarray = asub->garray; 3212 ierr = PetscInfo2(M,"submatrix Bn %D != BsubN %D, update iscol_o\n",n,BsubN);CHKERRQ(ierr); 3213 3214 ierr = PetscMalloc1(n,&idx_new);CHKERRQ(ierr); 3215 j = 0; 3216 ierr = ISGetIndices(iscol_o,&idx);CHKERRQ(ierr); 3217 for (i=0; i<n; i++) { 3218 if (j >= BsubN) break; 3219 while (subgarray[i] > garray[j]) j++; 3220 3221 if (subgarray[i] == garray[j]) { 3222 idx_new[i] = idx[j++]; 3223 } else SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"subgarray[%D]=%D cannot < garray[%D]=%D",i,subgarray[i],j,garray[j]); 3224 } 3225 ierr = ISRestoreIndices(iscol_o,&idx);CHKERRQ(ierr); 3226 3227 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3228 ierr = ISCreateGeneral(PETSC_COMM_SELF,n,idx_new,PETSC_OWN_POINTER,&iscol_o);CHKERRQ(ierr); 3229 3230 } else if (BsubN < n) { 3231 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Columns of Bsub cannot be smaller than B's",BsubN,asub->B->cmap->N); 3232 } 3233 3234 ierr = PetscFree(garray);CHKERRQ(ierr); 3235 *submat = M; 3236 3237 /* Save isrow_d, iscol_d and iscol_o used in processor for next request */ 3238 ierr = PetscObjectCompose((PetscObject)M,"isrow_d",(PetscObject)isrow_d);CHKERRQ(ierr); 3239 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3240 3241 ierr = PetscObjectCompose((PetscObject)M,"iscol_d",(PetscObject)iscol_d);CHKERRQ(ierr); 3242 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3243 3244 ierr = PetscObjectCompose((PetscObject)M,"iscol_o",(PetscObject)iscol_o);CHKERRQ(ierr); 3245 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3246 } 3247 PetscFunctionReturn(0); 3248 } 3249 3250 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3251 { 3252 PetscErrorCode ierr; 3253 IS iscol_local=NULL,isrow_d; 3254 PetscInt csize; 3255 PetscInt n,i,j,start,end; 3256 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3257 MPI_Comm comm; 3258 3259 PetscFunctionBegin; 3260 /* If isrow has same processor distribution as mat, 3261 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3262 if (call == MAT_REUSE_MATRIX) { 3263 ierr = PetscObjectQuery((PetscObject)*newmat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3264 if (isrow_d) { 3265 sameRowDist = PETSC_TRUE; 3266 tsameDist[1] = PETSC_TRUE; /* sameColDist */ 3267 } else { 3268 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3269 if (iscol_local) { 3270 sameRowDist = PETSC_TRUE; 3271 tsameDist[1] = PETSC_FALSE; /* !sameColDist */ 3272 } 3273 } 3274 } else { 3275 /* Check if isrow has same processor distribution as mat */ 3276 sameDist[0] = PETSC_FALSE; 3277 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3278 if (!n) { 3279 sameDist[0] = PETSC_TRUE; 3280 } else { 3281 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3282 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3283 if (i >= start && j < end) { 3284 sameDist[0] = PETSC_TRUE; 3285 } 3286 } 3287 3288 /* Check if iscol has same processor distribution as mat */ 3289 sameDist[1] = PETSC_FALSE; 3290 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3291 if (!n) { 3292 sameDist[1] = PETSC_TRUE; 3293 } else { 3294 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3295 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3296 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3297 } 3298 3299 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3300 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3301 sameRowDist = tsameDist[0]; 3302 } 3303 3304 if (sameRowDist) { 3305 if (tsameDist[1]) { /* sameRowDist & sameColDist */ 3306 /* isrow and iscol have same processor distribution as mat */ 3307 ierr = MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3308 PetscFunctionReturn(0); 3309 } else { /* sameRowDist */ 3310 /* isrow has same processor distribution as mat */ 3311 if (call == MAT_INITIAL_MATRIX) { 3312 PetscBool sorted; 3313 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3314 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3315 ierr = ISGetSize(iscol,&i);CHKERRQ(ierr); 3316 if (n != i) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != size of iscol %d",n,i); 3317 3318 ierr = ISSorted(iscol_local,&sorted);CHKERRQ(ierr); 3319 if (sorted) { 3320 /* MatCreateSubMatrix_MPIAIJ_SameRowDist() requires iscol_local be sorted; it can have duplicate indices */ 3321 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,iscol_local,MAT_INITIAL_MATRIX,newmat);CHKERRQ(ierr); 3322 PetscFunctionReturn(0); 3323 } 3324 } else { /* call == MAT_REUSE_MATRIX */ 3325 IS iscol_sub; 3326 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3327 if (iscol_sub) { 3328 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,NULL,call,newmat);CHKERRQ(ierr); 3329 PetscFunctionReturn(0); 3330 } 3331 } 3332 } 3333 } 3334 3335 /* General case: iscol -> iscol_local which has global size of iscol */ 3336 if (call == MAT_REUSE_MATRIX) { 3337 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3338 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3339 } else { 3340 if (!iscol_local) { 3341 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3342 } 3343 } 3344 3345 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3346 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3347 3348 if (call == MAT_INITIAL_MATRIX) { 3349 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3350 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3351 } 3352 PetscFunctionReturn(0); 3353 } 3354 3355 /*@C 3356 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3357 and "off-diagonal" part of the matrix in CSR format. 3358 3359 Collective on MPI_Comm 3360 3361 Input Parameters: 3362 + comm - MPI communicator 3363 . A - "diagonal" portion of matrix 3364 . B - "off-diagonal" portion of matrix, may have empty columns, will be destroyed by this routine 3365 - garray - global index of B columns 3366 3367 Output Parameter: 3368 . mat - the matrix, with input A as its local diagonal matrix 3369 Level: advanced 3370 3371 Notes: 3372 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3373 A becomes part of output mat, B is destroyed by this routine. The user cannot use A and B anymore. 3374 3375 .seealso: MatCreateMPIAIJWithSplitArrays() 3376 @*/ 3377 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3378 { 3379 PetscErrorCode ierr; 3380 Mat_MPIAIJ *maij; 3381 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data,*bnew; 3382 PetscInt *oi=b->i,*oj=b->j,i,nz,col; 3383 PetscScalar *oa=b->a; 3384 Mat Bnew; 3385 PetscInt m,n,N; 3386 3387 PetscFunctionBegin; 3388 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3389 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3390 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %D != Bm %D",m,B->rmap->N); 3391 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); 3392 /* remove check below; When B is created using iscol_o from ISGetSeqIS_SameColDist_Private(), its bs may not be same as A */ 3393 /* 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); */ 3394 3395 /* Get global columns of mat */ 3396 ierr = MPIU_Allreduce(&n,&N,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3397 3398 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3399 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3400 ierr = MatSetBlockSizes(*mat,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 3401 maij = (Mat_MPIAIJ*)(*mat)->data; 3402 3403 (*mat)->preallocated = PETSC_TRUE; 3404 3405 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3406 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3407 3408 /* Set A as diagonal portion of *mat */ 3409 maij->A = A; 3410 3411 nz = oi[m]; 3412 for (i=0; i<nz; i++) { 3413 col = oj[i]; 3414 oj[i] = garray[col]; 3415 } 3416 3417 /* Set Bnew as off-diagonal portion of *mat */ 3418 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Bnew);CHKERRQ(ierr); 3419 bnew = (Mat_SeqAIJ*)Bnew->data; 3420 bnew->maxnz = b->maxnz; /* allocated nonzeros of B */ 3421 maij->B = Bnew; 3422 3423 if (B->rmap->N != Bnew->rmap->N) SETERRQ2(PETSC_COMM_SELF,0,"BN %d != BnewN %d",B->rmap->N,Bnew->rmap->N); 3424 3425 b->singlemalloc = PETSC_FALSE; /* B arrays are shared by Bnew */ 3426 b->free_a = PETSC_FALSE; 3427 b->free_ij = PETSC_FALSE; 3428 ierr = MatDestroy(&B);CHKERRQ(ierr); 3429 3430 bnew->singlemalloc = PETSC_TRUE; /* arrays will be freed by MatDestroy(&Bnew) */ 3431 bnew->free_a = PETSC_TRUE; 3432 bnew->free_ij = PETSC_TRUE; 3433 3434 /* condense columns of maij->B */ 3435 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3436 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3437 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3438 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3439 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3440 PetscFunctionReturn(0); 3441 } 3442 3443 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3444 3445 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,IS iscol_local,MatReuse call,Mat *newmat) 3446 { 3447 PetscErrorCode ierr; 3448 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3449 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3450 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3451 Mat M,Msub,B=a->B; 3452 MatScalar *aa; 3453 Mat_SeqAIJ *aij; 3454 PetscInt *garray = a->garray,*colsub,Ncols; 3455 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3456 IS iscol_sub,iscmap; 3457 const PetscInt *is_idx,*cmap; 3458 PetscBool allcolumns=PETSC_FALSE; 3459 MPI_Comm comm; 3460 3461 PetscFunctionBegin; 3462 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3463 3464 if (call == MAT_REUSE_MATRIX) { 3465 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3466 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3467 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3468 3469 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3470 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3471 3472 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3473 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3474 3475 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3476 3477 } else { /* call == MAT_INITIAL_MATRIX) */ 3478 PetscBool flg; 3479 3480 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3481 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3482 3483 /* (1) iscol -> nonscalable iscol_local */ 3484 /* Check for special case: each processor gets entire matrix columns */ 3485 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3486 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3487 if (allcolumns) { 3488 iscol_sub = iscol_local; 3489 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3490 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3491 3492 } else { 3493 /* (2) iscol_local -> iscol_sub and iscmap. Implementation below requires iscol_local be sorted, it can have duplicate indices */ 3494 PetscInt *idx,*cmap1,k; 3495 ierr = PetscMalloc1(Ncols,&idx);CHKERRQ(ierr); 3496 ierr = PetscMalloc1(Ncols,&cmap1);CHKERRQ(ierr); 3497 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3498 count = 0; 3499 k = 0; 3500 for (i=0; i<Ncols; i++) { 3501 j = is_idx[i]; 3502 if (j >= cstart && j < cend) { 3503 /* diagonal part of mat */ 3504 idx[count] = j; 3505 cmap1[count++] = i; /* column index in submat */ 3506 } else if (Bn) { 3507 /* off-diagonal part of mat */ 3508 if (j == garray[k]) { 3509 idx[count] = j; 3510 cmap1[count++] = i; /* column index in submat */ 3511 } else if (j > garray[k]) { 3512 while (j > garray[k] && k < Bn-1) k++; 3513 if (j == garray[k]) { 3514 idx[count] = j; 3515 cmap1[count++] = i; /* column index in submat */ 3516 } 3517 } 3518 } 3519 } 3520 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3521 3522 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_OWN_POINTER,&iscol_sub);CHKERRQ(ierr); 3523 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3524 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3525 3526 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_OWN_POINTER,&iscmap);CHKERRQ(ierr); 3527 } 3528 3529 /* (3) Create sequential Msub */ 3530 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3531 } 3532 3533 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3534 aij = (Mat_SeqAIJ*)(Msub)->data; 3535 ii = aij->i; 3536 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3537 3538 /* 3539 m - number of local rows 3540 Ncols - number of columns (same on all processors) 3541 rstart - first row in new global matrix generated 3542 */ 3543 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3544 3545 if (call == MAT_INITIAL_MATRIX) { 3546 /* (4) Create parallel newmat */ 3547 PetscMPIInt rank,size; 3548 PetscInt csize; 3549 3550 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3551 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3552 3553 /* 3554 Determine the number of non-zeros in the diagonal and off-diagonal 3555 portions of the matrix in order to do correct preallocation 3556 */ 3557 3558 /* first get start and end of "diagonal" columns */ 3559 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3560 if (csize == PETSC_DECIDE) { 3561 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3562 if (mglobal == Ncols) { /* square matrix */ 3563 nlocal = m; 3564 } else { 3565 nlocal = Ncols/size + ((Ncols % size) > rank); 3566 } 3567 } else { 3568 nlocal = csize; 3569 } 3570 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3571 rstart = rend - nlocal; 3572 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); 3573 3574 /* next, compute all the lengths */ 3575 jj = aij->j; 3576 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3577 olens = dlens + m; 3578 for (i=0; i<m; i++) { 3579 jend = ii[i+1] - ii[i]; 3580 olen = 0; 3581 dlen = 0; 3582 for (j=0; j<jend; j++) { 3583 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3584 else dlen++; 3585 jj++; 3586 } 3587 olens[i] = olen; 3588 dlens[i] = dlen; 3589 } 3590 3591 ierr = ISGetBlockSize(isrow,&bs);CHKERRQ(ierr); 3592 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3593 3594 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3595 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr); 3596 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3597 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3598 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3599 ierr = PetscFree(dlens);CHKERRQ(ierr); 3600 3601 } else { /* call == MAT_REUSE_MATRIX */ 3602 M = *newmat; 3603 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3604 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3605 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3606 /* 3607 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3608 rather than the slower MatSetValues(). 3609 */ 3610 M->was_assembled = PETSC_TRUE; 3611 M->assembled = PETSC_FALSE; 3612 } 3613 3614 /* (5) Set values of Msub to *newmat */ 3615 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3616 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3617 3618 jj = aij->j; 3619 aa = aij->a; 3620 for (i=0; i<m; i++) { 3621 row = rstart + i; 3622 nz = ii[i+1] - ii[i]; 3623 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3624 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3625 jj += nz; aa += nz; 3626 } 3627 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3628 3629 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3630 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3631 3632 ierr = PetscFree(colsub);CHKERRQ(ierr); 3633 3634 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3635 if (call == MAT_INITIAL_MATRIX) { 3636 *newmat = M; 3637 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3638 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3639 3640 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3641 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3642 3643 ierr = PetscObjectCompose((PetscObject)(*newmat),"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3644 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3645 3646 if (iscol_local) { 3647 ierr = PetscObjectCompose((PetscObject)(*newmat),"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3648 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3649 } 3650 } 3651 PetscFunctionReturn(0); 3652 } 3653 3654 /* 3655 Not great since it makes two copies of the submatrix, first an SeqAIJ 3656 in local and then by concatenating the local matrices the end result. 3657 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3658 3659 Note: This requires a sequential iscol with all indices. 3660 */ 3661 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3662 { 3663 PetscErrorCode ierr; 3664 PetscMPIInt rank,size; 3665 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3666 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3667 Mat M,Mreuse; 3668 MatScalar *aa,*vwork; 3669 MPI_Comm comm; 3670 Mat_SeqAIJ *aij; 3671 PetscBool colflag,allcolumns=PETSC_FALSE; 3672 3673 PetscFunctionBegin; 3674 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3675 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3676 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3677 3678 /* Check for special case: each processor gets entire matrix columns */ 3679 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3680 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3681 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3682 3683 if (call == MAT_REUSE_MATRIX) { 3684 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3685 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3686 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3687 } else { 3688 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3689 } 3690 3691 /* 3692 m - number of local rows 3693 n - number of columns (same on all processors) 3694 rstart - first row in new global matrix generated 3695 */ 3696 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3697 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3698 if (call == MAT_INITIAL_MATRIX) { 3699 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3700 ii = aij->i; 3701 jj = aij->j; 3702 3703 /* 3704 Determine the number of non-zeros in the diagonal and off-diagonal 3705 portions of the matrix in order to do correct preallocation 3706 */ 3707 3708 /* first get start and end of "diagonal" columns */ 3709 if (csize == PETSC_DECIDE) { 3710 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3711 if (mglobal == n) { /* square matrix */ 3712 nlocal = m; 3713 } else { 3714 nlocal = n/size + ((n % size) > rank); 3715 } 3716 } else { 3717 nlocal = csize; 3718 } 3719 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3720 rstart = rend - nlocal; 3721 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); 3722 3723 /* next, compute all the lengths */ 3724 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3725 olens = dlens + m; 3726 for (i=0; i<m; i++) { 3727 jend = ii[i+1] - ii[i]; 3728 olen = 0; 3729 dlen = 0; 3730 for (j=0; j<jend; j++) { 3731 if (*jj < rstart || *jj >= rend) olen++; 3732 else dlen++; 3733 jj++; 3734 } 3735 olens[i] = olen; 3736 dlens[i] = dlen; 3737 } 3738 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3739 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3740 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3741 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3742 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3743 ierr = PetscFree(dlens);CHKERRQ(ierr); 3744 } else { 3745 PetscInt ml,nl; 3746 3747 M = *newmat; 3748 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3749 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3750 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3751 /* 3752 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3753 rather than the slower MatSetValues(). 3754 */ 3755 M->was_assembled = PETSC_TRUE; 3756 M->assembled = PETSC_FALSE; 3757 } 3758 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3759 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3760 ii = aij->i; 3761 jj = aij->j; 3762 aa = aij->a; 3763 for (i=0; i<m; i++) { 3764 row = rstart + i; 3765 nz = ii[i+1] - ii[i]; 3766 cwork = jj; jj += nz; 3767 vwork = aa; aa += nz; 3768 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3769 } 3770 3771 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3772 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3773 *newmat = M; 3774 3775 /* save submatrix used in processor for next request */ 3776 if (call == MAT_INITIAL_MATRIX) { 3777 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3778 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3779 } 3780 PetscFunctionReturn(0); 3781 } 3782 3783 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3784 { 3785 PetscInt m,cstart, cend,j,nnz,i,d; 3786 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3787 const PetscInt *JJ; 3788 PetscScalar *values; 3789 PetscErrorCode ierr; 3790 PetscBool nooffprocentries; 3791 3792 PetscFunctionBegin; 3793 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3794 3795 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3796 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3797 m = B->rmap->n; 3798 cstart = B->cmap->rstart; 3799 cend = B->cmap->rend; 3800 rstart = B->rmap->rstart; 3801 3802 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3803 3804 #if defined(PETSC_USE_DEBUGGING) 3805 for (i=0; i<m; i++) { 3806 nnz = Ii[i+1]- Ii[i]; 3807 JJ = J + Ii[i]; 3808 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3809 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3810 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); 3811 } 3812 #endif 3813 3814 for (i=0; i<m; i++) { 3815 nnz = Ii[i+1]- Ii[i]; 3816 JJ = J + Ii[i]; 3817 nnz_max = PetscMax(nnz_max,nnz); 3818 d = 0; 3819 for (j=0; j<nnz; j++) { 3820 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3821 } 3822 d_nnz[i] = d; 3823 o_nnz[i] = nnz - d; 3824 } 3825 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3826 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3827 3828 if (v) values = (PetscScalar*)v; 3829 else { 3830 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3831 } 3832 3833 for (i=0; i<m; i++) { 3834 ii = i + rstart; 3835 nnz = Ii[i+1]- Ii[i]; 3836 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3837 } 3838 nooffprocentries = B->nooffprocentries; 3839 B->nooffprocentries = PETSC_TRUE; 3840 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3841 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3842 B->nooffprocentries = nooffprocentries; 3843 3844 if (!v) { 3845 ierr = PetscFree(values);CHKERRQ(ierr); 3846 } 3847 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3848 PetscFunctionReturn(0); 3849 } 3850 3851 /*@ 3852 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3853 (the default parallel PETSc format). 3854 3855 Collective on MPI_Comm 3856 3857 Input Parameters: 3858 + B - the matrix 3859 . i - the indices into j for the start of each local row (starts with zero) 3860 . j - the column indices for each local row (starts with zero) 3861 - v - optional values in the matrix 3862 3863 Level: developer 3864 3865 Notes: 3866 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3867 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3868 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3869 3870 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3871 3872 The format which is used for the sparse matrix input, is equivalent to a 3873 row-major ordering.. i.e for the following matrix, the input data expected is 3874 as shown 3875 3876 $ 1 0 0 3877 $ 2 0 3 P0 3878 $ ------- 3879 $ 4 5 6 P1 3880 $ 3881 $ Process0 [P0]: rows_owned=[0,1] 3882 $ i = {0,1,3} [size = nrow+1 = 2+1] 3883 $ j = {0,0,2} [size = 3] 3884 $ v = {1,2,3} [size = 3] 3885 $ 3886 $ Process1 [P1]: rows_owned=[2] 3887 $ i = {0,3} [size = nrow+1 = 1+1] 3888 $ j = {0,1,2} [size = 3] 3889 $ v = {4,5,6} [size = 3] 3890 3891 .keywords: matrix, aij, compressed row, sparse, parallel 3892 3893 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3894 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3895 @*/ 3896 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3897 { 3898 PetscErrorCode ierr; 3899 3900 PetscFunctionBegin; 3901 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3902 PetscFunctionReturn(0); 3903 } 3904 3905 /*@C 3906 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3907 (the default parallel PETSc format). For good matrix assembly performance 3908 the user should preallocate the matrix storage by setting the parameters 3909 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3910 performance can be increased by more than a factor of 50. 3911 3912 Collective on MPI_Comm 3913 3914 Input Parameters: 3915 + B - the matrix 3916 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3917 (same value is used for all local rows) 3918 . d_nnz - array containing the number of nonzeros in the various rows of the 3919 DIAGONAL portion of the local submatrix (possibly different for each row) 3920 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3921 The size of this array is equal to the number of local rows, i.e 'm'. 3922 For matrices that will be factored, you must leave room for (and set) 3923 the diagonal entry even if it is zero. 3924 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3925 submatrix (same value is used for all local rows). 3926 - o_nnz - array containing the number of nonzeros in the various rows of the 3927 OFF-DIAGONAL portion of the local submatrix (possibly different for 3928 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3929 structure. The size of this array is equal to the number 3930 of local rows, i.e 'm'. 3931 3932 If the *_nnz parameter is given then the *_nz parameter is ignored 3933 3934 The AIJ format (also called the Yale sparse matrix format or 3935 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3936 storage. The stored row and column indices begin with zero. 3937 See Users-Manual: ch_mat for details. 3938 3939 The parallel matrix is partitioned such that the first m0 rows belong to 3940 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3941 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3942 3943 The DIAGONAL portion of the local submatrix of a processor can be defined 3944 as the submatrix which is obtained by extraction the part corresponding to 3945 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3946 first row that belongs to the processor, r2 is the last row belonging to 3947 the this processor, and c1-c2 is range of indices of the local part of a 3948 vector suitable for applying the matrix to. This is an mxn matrix. In the 3949 common case of a square matrix, the row and column ranges are the same and 3950 the DIAGONAL part is also square. The remaining portion of the local 3951 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3952 3953 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3954 3955 You can call MatGetInfo() to get information on how effective the preallocation was; 3956 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3957 You can also run with the option -info and look for messages with the string 3958 malloc in them to see if additional memory allocation was needed. 3959 3960 Example usage: 3961 3962 Consider the following 8x8 matrix with 34 non-zero values, that is 3963 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3964 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3965 as follows: 3966 3967 .vb 3968 1 2 0 | 0 3 0 | 0 4 3969 Proc0 0 5 6 | 7 0 0 | 8 0 3970 9 0 10 | 11 0 0 | 12 0 3971 ------------------------------------- 3972 13 0 14 | 15 16 17 | 0 0 3973 Proc1 0 18 0 | 19 20 21 | 0 0 3974 0 0 0 | 22 23 0 | 24 0 3975 ------------------------------------- 3976 Proc2 25 26 27 | 0 0 28 | 29 0 3977 30 0 0 | 31 32 33 | 0 34 3978 .ve 3979 3980 This can be represented as a collection of submatrices as: 3981 3982 .vb 3983 A B C 3984 D E F 3985 G H I 3986 .ve 3987 3988 Where the submatrices A,B,C are owned by proc0, D,E,F are 3989 owned by proc1, G,H,I are owned by proc2. 3990 3991 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3992 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3993 The 'M','N' parameters are 8,8, and have the same values on all procs. 3994 3995 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3996 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3997 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3998 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3999 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4000 matrix, ans [DF] as another SeqAIJ matrix. 4001 4002 When d_nz, o_nz parameters are specified, d_nz storage elements are 4003 allocated for every row of the local diagonal submatrix, and o_nz 4004 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4005 One way to choose d_nz and o_nz is to use the max nonzerors per local 4006 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4007 In this case, the values of d_nz,o_nz are: 4008 .vb 4009 proc0 : dnz = 2, o_nz = 2 4010 proc1 : dnz = 3, o_nz = 2 4011 proc2 : dnz = 1, o_nz = 4 4012 .ve 4013 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4014 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4015 for proc3. i.e we are using 12+15+10=37 storage locations to store 4016 34 values. 4017 4018 When d_nnz, o_nnz parameters are specified, the storage is specified 4019 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4020 In the above case the values for d_nnz,o_nnz are: 4021 .vb 4022 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4023 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4024 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4025 .ve 4026 Here the space allocated is sum of all the above values i.e 34, and 4027 hence pre-allocation is perfect. 4028 4029 Level: intermediate 4030 4031 .keywords: matrix, aij, compressed row, sparse, parallel 4032 4033 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 4034 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 4035 @*/ 4036 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 4037 { 4038 PetscErrorCode ierr; 4039 4040 PetscFunctionBegin; 4041 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 4042 PetscValidType(B,1); 4043 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 4044 PetscFunctionReturn(0); 4045 } 4046 4047 /*@ 4048 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 4049 CSR format the local rows. 4050 4051 Collective on MPI_Comm 4052 4053 Input Parameters: 4054 + comm - MPI communicator 4055 . m - number of local rows (Cannot be PETSC_DECIDE) 4056 . n - This value should be the same as the local size used in creating the 4057 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4058 calculated if N is given) For square matrices n is almost always m. 4059 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4060 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4061 . i - row indices 4062 . j - column indices 4063 - a - matrix values 4064 4065 Output Parameter: 4066 . mat - the matrix 4067 4068 Level: intermediate 4069 4070 Notes: 4071 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 4072 thus you CANNOT change the matrix entries by changing the values of a[] after you have 4073 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 4074 4075 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4076 4077 The format which is used for the sparse matrix input, is equivalent to a 4078 row-major ordering.. i.e for the following matrix, the input data expected is 4079 as shown 4080 4081 $ 1 0 0 4082 $ 2 0 3 P0 4083 $ ------- 4084 $ 4 5 6 P1 4085 $ 4086 $ Process0 [P0]: rows_owned=[0,1] 4087 $ i = {0,1,3} [size = nrow+1 = 2+1] 4088 $ j = {0,0,2} [size = 3] 4089 $ v = {1,2,3} [size = 3] 4090 $ 4091 $ Process1 [P1]: rows_owned=[2] 4092 $ i = {0,3} [size = nrow+1 = 1+1] 4093 $ j = {0,1,2} [size = 3] 4094 $ v = {4,5,6} [size = 3] 4095 4096 .keywords: matrix, aij, compressed row, sparse, parallel 4097 4098 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4099 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4100 @*/ 4101 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 4102 { 4103 PetscErrorCode ierr; 4104 4105 PetscFunctionBegin; 4106 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4107 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4108 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4109 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4110 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 4111 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 4112 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 4113 PetscFunctionReturn(0); 4114 } 4115 4116 /*@C 4117 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 4118 (the default parallel PETSc format). For good matrix assembly performance 4119 the user should preallocate the matrix storage by setting the parameters 4120 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4121 performance can be increased by more than a factor of 50. 4122 4123 Collective on MPI_Comm 4124 4125 Input Parameters: 4126 + comm - MPI communicator 4127 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 4128 This value should be the same as the local size used in creating the 4129 y vector for the matrix-vector product y = Ax. 4130 . n - This value should be the same as the local size used in creating the 4131 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4132 calculated if N is given) For square matrices n is almost always m. 4133 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4134 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4135 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4136 (same value is used for all local rows) 4137 . d_nnz - array containing the number of nonzeros in the various rows of the 4138 DIAGONAL portion of the local submatrix (possibly different for each row) 4139 or NULL, if d_nz is used to specify the nonzero structure. 4140 The size of this array is equal to the number of local rows, i.e 'm'. 4141 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4142 submatrix (same value is used for all local rows). 4143 - o_nnz - array containing the number of nonzeros in the various rows of the 4144 OFF-DIAGONAL portion of the local submatrix (possibly different for 4145 each row) or NULL, if o_nz is used to specify the nonzero 4146 structure. The size of this array is equal to the number 4147 of local rows, i.e 'm'. 4148 4149 Output Parameter: 4150 . A - the matrix 4151 4152 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4153 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4154 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4155 4156 Notes: 4157 If the *_nnz parameter is given then the *_nz parameter is ignored 4158 4159 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4160 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4161 storage requirements for this matrix. 4162 4163 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4164 processor than it must be used on all processors that share the object for 4165 that argument. 4166 4167 The user MUST specify either the local or global matrix dimensions 4168 (possibly both). 4169 4170 The parallel matrix is partitioned across processors such that the 4171 first m0 rows belong to process 0, the next m1 rows belong to 4172 process 1, the next m2 rows belong to process 2 etc.. where 4173 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4174 values corresponding to [m x N] submatrix. 4175 4176 The columns are logically partitioned with the n0 columns belonging 4177 to 0th partition, the next n1 columns belonging to the next 4178 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4179 4180 The DIAGONAL portion of the local submatrix on any given processor 4181 is the submatrix corresponding to the rows and columns m,n 4182 corresponding to the given processor. i.e diagonal matrix on 4183 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4184 etc. The remaining portion of the local submatrix [m x (N-n)] 4185 constitute the OFF-DIAGONAL portion. The example below better 4186 illustrates this concept. 4187 4188 For a square global matrix we define each processor's diagonal portion 4189 to be its local rows and the corresponding columns (a square submatrix); 4190 each processor's off-diagonal portion encompasses the remainder of the 4191 local matrix (a rectangular submatrix). 4192 4193 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4194 4195 When calling this routine with a single process communicator, a matrix of 4196 type SEQAIJ is returned. If a matrix of type MPIAIJ is desired for this 4197 type of communicator, use the construction mechanism 4198 .vb 4199 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4200 .ve 4201 4202 $ MatCreate(...,&A); 4203 $ MatSetType(A,MATMPIAIJ); 4204 $ MatSetSizes(A, m,n,M,N); 4205 $ MatMPIAIJSetPreallocation(A,...); 4206 4207 By default, this format uses inodes (identical nodes) when possible. 4208 We search for consecutive rows with the same nonzero structure, thereby 4209 reusing matrix information to achieve increased efficiency. 4210 4211 Options Database Keys: 4212 + -mat_no_inode - Do not use inodes 4213 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4214 - -mat_aij_oneindex - Internally use indexing starting at 1 4215 rather than 0. Note that when calling MatSetValues(), 4216 the user still MUST index entries starting at 0! 4217 4218 4219 Example usage: 4220 4221 Consider the following 8x8 matrix with 34 non-zero values, that is 4222 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4223 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4224 as follows 4225 4226 .vb 4227 1 2 0 | 0 3 0 | 0 4 4228 Proc0 0 5 6 | 7 0 0 | 8 0 4229 9 0 10 | 11 0 0 | 12 0 4230 ------------------------------------- 4231 13 0 14 | 15 16 17 | 0 0 4232 Proc1 0 18 0 | 19 20 21 | 0 0 4233 0 0 0 | 22 23 0 | 24 0 4234 ------------------------------------- 4235 Proc2 25 26 27 | 0 0 28 | 29 0 4236 30 0 0 | 31 32 33 | 0 34 4237 .ve 4238 4239 This can be represented as a collection of submatrices as 4240 4241 .vb 4242 A B C 4243 D E F 4244 G H I 4245 .ve 4246 4247 Where the submatrices A,B,C are owned by proc0, D,E,F are 4248 owned by proc1, G,H,I are owned by proc2. 4249 4250 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4251 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4252 The 'M','N' parameters are 8,8, and have the same values on all procs. 4253 4254 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4255 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4256 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4257 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4258 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4259 matrix, ans [DF] as another SeqAIJ matrix. 4260 4261 When d_nz, o_nz parameters are specified, d_nz storage elements are 4262 allocated for every row of the local diagonal submatrix, and o_nz 4263 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4264 One way to choose d_nz and o_nz is to use the max nonzerors per local 4265 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4266 In this case, the values of d_nz,o_nz are 4267 .vb 4268 proc0 : dnz = 2, o_nz = 2 4269 proc1 : dnz = 3, o_nz = 2 4270 proc2 : dnz = 1, o_nz = 4 4271 .ve 4272 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4273 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4274 for proc3. i.e we are using 12+15+10=37 storage locations to store 4275 34 values. 4276 4277 When d_nnz, o_nnz parameters are specified, the storage is specified 4278 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4279 In the above case the values for d_nnz,o_nnz are 4280 .vb 4281 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4282 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4283 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4284 .ve 4285 Here the space allocated is sum of all the above values i.e 34, and 4286 hence pre-allocation is perfect. 4287 4288 Level: intermediate 4289 4290 .keywords: matrix, aij, compressed row, sparse, parallel 4291 4292 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4293 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4294 @*/ 4295 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) 4296 { 4297 PetscErrorCode ierr; 4298 PetscMPIInt size; 4299 4300 PetscFunctionBegin; 4301 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4302 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4303 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4304 if (size > 1) { 4305 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4306 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4307 } else { 4308 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4309 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4310 } 4311 PetscFunctionReturn(0); 4312 } 4313 4314 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4315 { 4316 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4317 PetscBool flg; 4318 PetscErrorCode ierr; 4319 4320 PetscFunctionBegin; 4321 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4322 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4323 if (Ad) *Ad = a->A; 4324 if (Ao) *Ao = a->B; 4325 if (colmap) *colmap = a->garray; 4326 PetscFunctionReturn(0); 4327 } 4328 4329 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4330 { 4331 PetscErrorCode ierr; 4332 PetscInt m,N,i,rstart,nnz,Ii; 4333 PetscInt *indx; 4334 PetscScalar *values; 4335 4336 PetscFunctionBegin; 4337 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4338 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4339 PetscInt *dnz,*onz,sum,bs,cbs; 4340 4341 if (n == PETSC_DECIDE) { 4342 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4343 } 4344 /* Check sum(n) = N */ 4345 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4346 if (sum != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns %D != global columns %D",sum,N); 4347 4348 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4349 rstart -= m; 4350 4351 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4352 for (i=0; i<m; i++) { 4353 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4354 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4355 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4356 } 4357 4358 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4359 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4360 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4361 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4362 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4363 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4364 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4365 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4366 } 4367 4368 /* numeric phase */ 4369 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4370 for (i=0; i<m; i++) { 4371 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4372 Ii = i + rstart; 4373 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4374 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4375 } 4376 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4377 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4378 PetscFunctionReturn(0); 4379 } 4380 4381 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4382 { 4383 PetscErrorCode ierr; 4384 PetscMPIInt rank; 4385 PetscInt m,N,i,rstart,nnz; 4386 size_t len; 4387 const PetscInt *indx; 4388 PetscViewer out; 4389 char *name; 4390 Mat B; 4391 const PetscScalar *values; 4392 4393 PetscFunctionBegin; 4394 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4395 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4396 /* Should this be the type of the diagonal block of A? */ 4397 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4398 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4399 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4400 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4401 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4402 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4403 for (i=0; i<m; i++) { 4404 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4405 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4406 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4407 } 4408 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4409 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4410 4411 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4412 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4413 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4414 sprintf(name,"%s.%d",outfile,rank); 4415 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4416 ierr = PetscFree(name);CHKERRQ(ierr); 4417 ierr = MatView(B,out);CHKERRQ(ierr); 4418 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4419 ierr = MatDestroy(&B);CHKERRQ(ierr); 4420 PetscFunctionReturn(0); 4421 } 4422 4423 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4424 { 4425 PetscErrorCode ierr; 4426 Mat_Merge_SeqsToMPI *merge; 4427 PetscContainer container; 4428 4429 PetscFunctionBegin; 4430 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4431 if (container) { 4432 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4433 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4434 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4435 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4436 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4437 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4438 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4439 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4440 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4441 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4442 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4443 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4444 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4445 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4446 ierr = PetscFree(merge);CHKERRQ(ierr); 4447 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4448 } 4449 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4450 PetscFunctionReturn(0); 4451 } 4452 4453 #include <../src/mat/utils/freespace.h> 4454 #include <petscbt.h> 4455 4456 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4457 { 4458 PetscErrorCode ierr; 4459 MPI_Comm comm; 4460 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4461 PetscMPIInt size,rank,taga,*len_s; 4462 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4463 PetscInt proc,m; 4464 PetscInt **buf_ri,**buf_rj; 4465 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4466 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4467 MPI_Request *s_waits,*r_waits; 4468 MPI_Status *status; 4469 MatScalar *aa=a->a; 4470 MatScalar **abuf_r,*ba_i; 4471 Mat_Merge_SeqsToMPI *merge; 4472 PetscContainer container; 4473 4474 PetscFunctionBegin; 4475 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4476 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4477 4478 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4479 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4480 4481 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4482 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4483 4484 bi = merge->bi; 4485 bj = merge->bj; 4486 buf_ri = merge->buf_ri; 4487 buf_rj = merge->buf_rj; 4488 4489 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4490 owners = merge->rowmap->range; 4491 len_s = merge->len_s; 4492 4493 /* send and recv matrix values */ 4494 /*-----------------------------*/ 4495 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4496 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4497 4498 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4499 for (proc=0,k=0; proc<size; proc++) { 4500 if (!len_s[proc]) continue; 4501 i = owners[proc]; 4502 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4503 k++; 4504 } 4505 4506 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4507 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4508 ierr = PetscFree(status);CHKERRQ(ierr); 4509 4510 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4511 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4512 4513 /* insert mat values of mpimat */ 4514 /*----------------------------*/ 4515 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4516 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4517 4518 for (k=0; k<merge->nrecv; k++) { 4519 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4520 nrows = *(buf_ri_k[k]); 4521 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4522 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4523 } 4524 4525 /* set values of ba */ 4526 m = merge->rowmap->n; 4527 for (i=0; i<m; i++) { 4528 arow = owners[rank] + i; 4529 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4530 bnzi = bi[i+1] - bi[i]; 4531 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4532 4533 /* add local non-zero vals of this proc's seqmat into ba */ 4534 anzi = ai[arow+1] - ai[arow]; 4535 aj = a->j + ai[arow]; 4536 aa = a->a + ai[arow]; 4537 nextaj = 0; 4538 for (j=0; nextaj<anzi; j++) { 4539 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4540 ba_i[j] += aa[nextaj++]; 4541 } 4542 } 4543 4544 /* add received vals into ba */ 4545 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4546 /* i-th row */ 4547 if (i == *nextrow[k]) { 4548 anzi = *(nextai[k]+1) - *nextai[k]; 4549 aj = buf_rj[k] + *(nextai[k]); 4550 aa = abuf_r[k] + *(nextai[k]); 4551 nextaj = 0; 4552 for (j=0; nextaj<anzi; j++) { 4553 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4554 ba_i[j] += aa[nextaj++]; 4555 } 4556 } 4557 nextrow[k]++; nextai[k]++; 4558 } 4559 } 4560 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4561 } 4562 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4563 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4564 4565 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4566 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4567 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4568 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4569 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4570 PetscFunctionReturn(0); 4571 } 4572 4573 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4574 { 4575 PetscErrorCode ierr; 4576 Mat B_mpi; 4577 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4578 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4579 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4580 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4581 PetscInt len,proc,*dnz,*onz,bs,cbs; 4582 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4583 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4584 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4585 MPI_Status *status; 4586 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4587 PetscBT lnkbt; 4588 Mat_Merge_SeqsToMPI *merge; 4589 PetscContainer container; 4590 4591 PetscFunctionBegin; 4592 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4593 4594 /* make sure it is a PETSc comm */ 4595 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4596 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4597 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4598 4599 ierr = PetscNew(&merge);CHKERRQ(ierr); 4600 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4601 4602 /* determine row ownership */ 4603 /*---------------------------------------------------------*/ 4604 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4605 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4606 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4607 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4608 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4609 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4610 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4611 4612 m = merge->rowmap->n; 4613 owners = merge->rowmap->range; 4614 4615 /* determine the number of messages to send, their lengths */ 4616 /*---------------------------------------------------------*/ 4617 len_s = merge->len_s; 4618 4619 len = 0; /* length of buf_si[] */ 4620 merge->nsend = 0; 4621 for (proc=0; proc<size; proc++) { 4622 len_si[proc] = 0; 4623 if (proc == rank) { 4624 len_s[proc] = 0; 4625 } else { 4626 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4627 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4628 } 4629 if (len_s[proc]) { 4630 merge->nsend++; 4631 nrows = 0; 4632 for (i=owners[proc]; i<owners[proc+1]; i++) { 4633 if (ai[i+1] > ai[i]) nrows++; 4634 } 4635 len_si[proc] = 2*(nrows+1); 4636 len += len_si[proc]; 4637 } 4638 } 4639 4640 /* determine the number and length of messages to receive for ij-structure */ 4641 /*-------------------------------------------------------------------------*/ 4642 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4643 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4644 4645 /* post the Irecv of j-structure */ 4646 /*-------------------------------*/ 4647 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4648 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4649 4650 /* post the Isend of j-structure */ 4651 /*--------------------------------*/ 4652 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4653 4654 for (proc=0, k=0; proc<size; proc++) { 4655 if (!len_s[proc]) continue; 4656 i = owners[proc]; 4657 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4658 k++; 4659 } 4660 4661 /* receives and sends of j-structure are complete */ 4662 /*------------------------------------------------*/ 4663 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4664 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4665 4666 /* send and recv i-structure */ 4667 /*---------------------------*/ 4668 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4669 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4670 4671 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4672 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4673 for (proc=0,k=0; proc<size; proc++) { 4674 if (!len_s[proc]) continue; 4675 /* form outgoing message for i-structure: 4676 buf_si[0]: nrows to be sent 4677 [1:nrows]: row index (global) 4678 [nrows+1:2*nrows+1]: i-structure index 4679 */ 4680 /*-------------------------------------------*/ 4681 nrows = len_si[proc]/2 - 1; 4682 buf_si_i = buf_si + nrows+1; 4683 buf_si[0] = nrows; 4684 buf_si_i[0] = 0; 4685 nrows = 0; 4686 for (i=owners[proc]; i<owners[proc+1]; i++) { 4687 anzi = ai[i+1] - ai[i]; 4688 if (anzi) { 4689 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4690 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4691 nrows++; 4692 } 4693 } 4694 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4695 k++; 4696 buf_si += len_si[proc]; 4697 } 4698 4699 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4700 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4701 4702 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4703 for (i=0; i<merge->nrecv; i++) { 4704 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); 4705 } 4706 4707 ierr = PetscFree(len_si);CHKERRQ(ierr); 4708 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4709 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4710 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4711 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4712 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4713 ierr = PetscFree(status);CHKERRQ(ierr); 4714 4715 /* compute a local seq matrix in each processor */ 4716 /*----------------------------------------------*/ 4717 /* allocate bi array and free space for accumulating nonzero column info */ 4718 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4719 bi[0] = 0; 4720 4721 /* create and initialize a linked list */ 4722 nlnk = N+1; 4723 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4724 4725 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4726 len = ai[owners[rank+1]] - ai[owners[rank]]; 4727 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4728 4729 current_space = free_space; 4730 4731 /* determine symbolic info for each local row */ 4732 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4733 4734 for (k=0; k<merge->nrecv; k++) { 4735 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4736 nrows = *buf_ri_k[k]; 4737 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4738 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4739 } 4740 4741 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4742 len = 0; 4743 for (i=0; i<m; i++) { 4744 bnzi = 0; 4745 /* add local non-zero cols of this proc's seqmat into lnk */ 4746 arow = owners[rank] + i; 4747 anzi = ai[arow+1] - ai[arow]; 4748 aj = a->j + ai[arow]; 4749 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4750 bnzi += nlnk; 4751 /* add received col data into lnk */ 4752 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4753 if (i == *nextrow[k]) { /* i-th row */ 4754 anzi = *(nextai[k]+1) - *nextai[k]; 4755 aj = buf_rj[k] + *nextai[k]; 4756 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4757 bnzi += nlnk; 4758 nextrow[k]++; nextai[k]++; 4759 } 4760 } 4761 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4762 4763 /* if free space is not available, make more free space */ 4764 if (current_space->local_remaining<bnzi) { 4765 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4766 nspacedouble++; 4767 } 4768 /* copy data into free space, then initialize lnk */ 4769 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4770 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4771 4772 current_space->array += bnzi; 4773 current_space->local_used += bnzi; 4774 current_space->local_remaining -= bnzi; 4775 4776 bi[i+1] = bi[i] + bnzi; 4777 } 4778 4779 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4780 4781 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4782 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4783 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4784 4785 /* create symbolic parallel matrix B_mpi */ 4786 /*---------------------------------------*/ 4787 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4788 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4789 if (n==PETSC_DECIDE) { 4790 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4791 } else { 4792 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4793 } 4794 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4795 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4796 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4797 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4798 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4799 4800 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4801 B_mpi->assembled = PETSC_FALSE; 4802 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4803 merge->bi = bi; 4804 merge->bj = bj; 4805 merge->buf_ri = buf_ri; 4806 merge->buf_rj = buf_rj; 4807 merge->coi = NULL; 4808 merge->coj = NULL; 4809 merge->owners_co = NULL; 4810 4811 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4812 4813 /* attach the supporting struct to B_mpi for reuse */ 4814 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4815 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4816 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4817 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4818 *mpimat = B_mpi; 4819 4820 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4821 PetscFunctionReturn(0); 4822 } 4823 4824 /*@C 4825 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4826 matrices from each processor 4827 4828 Collective on MPI_Comm 4829 4830 Input Parameters: 4831 + comm - the communicators the parallel matrix will live on 4832 . seqmat - the input sequential matrices 4833 . m - number of local rows (or PETSC_DECIDE) 4834 . n - number of local columns (or PETSC_DECIDE) 4835 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4836 4837 Output Parameter: 4838 . mpimat - the parallel matrix generated 4839 4840 Level: advanced 4841 4842 Notes: 4843 The dimensions of the sequential matrix in each processor MUST be the same. 4844 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4845 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4846 @*/ 4847 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4848 { 4849 PetscErrorCode ierr; 4850 PetscMPIInt size; 4851 4852 PetscFunctionBegin; 4853 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4854 if (size == 1) { 4855 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4856 if (scall == MAT_INITIAL_MATRIX) { 4857 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4858 } else { 4859 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4860 } 4861 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4862 PetscFunctionReturn(0); 4863 } 4864 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4865 if (scall == MAT_INITIAL_MATRIX) { 4866 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4867 } 4868 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4869 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4870 PetscFunctionReturn(0); 4871 } 4872 4873 /*@ 4874 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential matrix with 4875 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4876 with MatGetSize() 4877 4878 Not Collective 4879 4880 Input Parameters: 4881 + A - the matrix 4882 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4883 4884 Output Parameter: 4885 . A_loc - the local sequential matrix generated 4886 4887 Level: developer 4888 4889 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4890 4891 @*/ 4892 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4893 { 4894 PetscErrorCode ierr; 4895 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4896 Mat_SeqAIJ *mat,*a,*b; 4897 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4898 MatScalar *aa,*ba,*cam; 4899 PetscScalar *ca; 4900 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4901 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4902 PetscBool match; 4903 MPI_Comm comm; 4904 PetscMPIInt size; 4905 4906 PetscFunctionBegin; 4907 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4908 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4909 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4910 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4911 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4912 4913 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4914 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4915 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4916 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4917 aa = a->a; ba = b->a; 4918 if (scall == MAT_INITIAL_MATRIX) { 4919 if (size == 1) { 4920 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4921 PetscFunctionReturn(0); 4922 } 4923 4924 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4925 ci[0] = 0; 4926 for (i=0; i<am; i++) { 4927 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4928 } 4929 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4930 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4931 k = 0; 4932 for (i=0; i<am; i++) { 4933 ncols_o = bi[i+1] - bi[i]; 4934 ncols_d = ai[i+1] - ai[i]; 4935 /* off-diagonal portion of A */ 4936 for (jo=0; jo<ncols_o; jo++) { 4937 col = cmap[*bj]; 4938 if (col >= cstart) break; 4939 cj[k] = col; bj++; 4940 ca[k++] = *ba++; 4941 } 4942 /* diagonal portion of A */ 4943 for (j=0; j<ncols_d; j++) { 4944 cj[k] = cstart + *aj++; 4945 ca[k++] = *aa++; 4946 } 4947 /* off-diagonal portion of A */ 4948 for (j=jo; j<ncols_o; j++) { 4949 cj[k] = cmap[*bj++]; 4950 ca[k++] = *ba++; 4951 } 4952 } 4953 /* put together the new matrix */ 4954 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4955 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4956 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4957 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4958 mat->free_a = PETSC_TRUE; 4959 mat->free_ij = PETSC_TRUE; 4960 mat->nonew = 0; 4961 } else if (scall == MAT_REUSE_MATRIX) { 4962 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4963 ci = mat->i; cj = mat->j; cam = mat->a; 4964 for (i=0; i<am; i++) { 4965 /* off-diagonal portion of A */ 4966 ncols_o = bi[i+1] - bi[i]; 4967 for (jo=0; jo<ncols_o; jo++) { 4968 col = cmap[*bj]; 4969 if (col >= cstart) break; 4970 *cam++ = *ba++; bj++; 4971 } 4972 /* diagonal portion of A */ 4973 ncols_d = ai[i+1] - ai[i]; 4974 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4975 /* off-diagonal portion of A */ 4976 for (j=jo; j<ncols_o; j++) { 4977 *cam++ = *ba++; bj++; 4978 } 4979 } 4980 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4981 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4982 PetscFunctionReturn(0); 4983 } 4984 4985 /*@C 4986 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4987 4988 Not Collective 4989 4990 Input Parameters: 4991 + A - the matrix 4992 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4993 - row, col - index sets of rows and columns to extract (or NULL) 4994 4995 Output Parameter: 4996 . A_loc - the local sequential matrix generated 4997 4998 Level: developer 4999 5000 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 5001 5002 @*/ 5003 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 5004 { 5005 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5006 PetscErrorCode ierr; 5007 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 5008 IS isrowa,iscola; 5009 Mat *aloc; 5010 PetscBool match; 5011 5012 PetscFunctionBegin; 5013 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 5014 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 5015 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 5016 if (!row) { 5017 start = A->rmap->rstart; end = A->rmap->rend; 5018 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 5019 } else { 5020 isrowa = *row; 5021 } 5022 if (!col) { 5023 start = A->cmap->rstart; 5024 cmap = a->garray; 5025 nzA = a->A->cmap->n; 5026 nzB = a->B->cmap->n; 5027 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5028 ncols = 0; 5029 for (i=0; i<nzB; i++) { 5030 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5031 else break; 5032 } 5033 imark = i; 5034 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 5035 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 5036 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 5037 } else { 5038 iscola = *col; 5039 } 5040 if (scall != MAT_INITIAL_MATRIX) { 5041 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 5042 aloc[0] = *A_loc; 5043 } 5044 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 5045 *A_loc = aloc[0]; 5046 ierr = PetscFree(aloc);CHKERRQ(ierr); 5047 if (!row) { 5048 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 5049 } 5050 if (!col) { 5051 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 5052 } 5053 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 5054 PetscFunctionReturn(0); 5055 } 5056 5057 /*@C 5058 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 5059 5060 Collective on Mat 5061 5062 Input Parameters: 5063 + A,B - the matrices in mpiaij format 5064 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5065 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 5066 5067 Output Parameter: 5068 + rowb, colb - index sets of rows and columns of B to extract 5069 - B_seq - the sequential matrix generated 5070 5071 Level: developer 5072 5073 @*/ 5074 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 5075 { 5076 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5077 PetscErrorCode ierr; 5078 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 5079 IS isrowb,iscolb; 5080 Mat *bseq=NULL; 5081 5082 PetscFunctionBegin; 5083 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5084 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); 5085 } 5086 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5087 5088 if (scall == MAT_INITIAL_MATRIX) { 5089 start = A->cmap->rstart; 5090 cmap = a->garray; 5091 nzA = a->A->cmap->n; 5092 nzB = a->B->cmap->n; 5093 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5094 ncols = 0; 5095 for (i=0; i<nzB; i++) { /* row < local row index */ 5096 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5097 else break; 5098 } 5099 imark = i; 5100 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 5101 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5102 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 5103 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 5104 } else { 5105 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5106 isrowb = *rowb; iscolb = *colb; 5107 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 5108 bseq[0] = *B_seq; 5109 } 5110 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 5111 *B_seq = bseq[0]; 5112 ierr = PetscFree(bseq);CHKERRQ(ierr); 5113 if (!rowb) { 5114 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 5115 } else { 5116 *rowb = isrowb; 5117 } 5118 if (!colb) { 5119 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 5120 } else { 5121 *colb = iscolb; 5122 } 5123 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5124 PetscFunctionReturn(0); 5125 } 5126 5127 /* 5128 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 5129 of the OFF-DIAGONAL portion of local A 5130 5131 Collective on Mat 5132 5133 Input Parameters: 5134 + A,B - the matrices in mpiaij format 5135 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5136 5137 Output Parameter: 5138 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5139 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5140 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5141 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5142 5143 Level: developer 5144 5145 */ 5146 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5147 { 5148 VecScatter_MPI_General *gen_to,*gen_from; 5149 PetscErrorCode ierr; 5150 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5151 Mat_SeqAIJ *b_oth; 5152 VecScatter ctx; 5153 MPI_Comm comm; 5154 PetscMPIInt *rprocs,*sprocs,tag,rank; 5155 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5156 PetscInt *rvalues,*svalues; 5157 MatScalar *b_otha,*bufa,*bufA; 5158 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5159 MPI_Request *rwaits = NULL,*swaits = NULL; 5160 MPI_Status *sstatus,rstatus; 5161 PetscMPIInt jj,size; 5162 PetscInt *cols,sbs,rbs; 5163 PetscScalar *vals; 5164 5165 PetscFunctionBegin; 5166 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5167 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5168 5169 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5170 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); 5171 } 5172 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5173 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5174 5175 if (size == 1) { 5176 startsj_s = NULL; 5177 bufa_ptr = NULL; 5178 *B_oth = NULL; 5179 PetscFunctionReturn(0); 5180 } 5181 5182 if (!a->Mvctx_mpi1) { /* create a->Mvctx_mpi1 to be used for Mat-Mat ops */ 5183 a->Mvctx_mpi1_flg = PETSC_TRUE; 5184 ierr = MatSetUpMultiply_MPIAIJ(A);CHKERRQ(ierr); 5185 } 5186 ctx = a->Mvctx_mpi1; 5187 tag = ((PetscObject)ctx)->tag; 5188 5189 gen_to = (VecScatter_MPI_General*)ctx->todata; 5190 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5191 nrecvs = gen_from->n; 5192 nsends = gen_to->n; 5193 5194 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 5195 srow = gen_to->indices; /* local row index to be sent */ 5196 sstarts = gen_to->starts; 5197 sprocs = gen_to->procs; 5198 sstatus = gen_to->sstatus; 5199 sbs = gen_to->bs; 5200 rstarts = gen_from->starts; 5201 rprocs = gen_from->procs; 5202 rbs = gen_from->bs; 5203 5204 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5205 if (scall == MAT_INITIAL_MATRIX) { 5206 /* i-array */ 5207 /*---------*/ 5208 /* post receives */ 5209 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 5210 for (i=0; i<nrecvs; i++) { 5211 rowlen = rvalues + rstarts[i]*rbs; 5212 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5213 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5214 } 5215 5216 /* pack the outgoing message */ 5217 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 5218 5219 sstartsj[0] = 0; 5220 rstartsj[0] = 0; 5221 len = 0; /* total length of j or a array to be sent */ 5222 k = 0; 5223 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 5224 for (i=0; i<nsends; i++) { 5225 rowlen = svalues + sstarts[i]*sbs; 5226 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5227 for (j=0; j<nrows; j++) { 5228 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5229 for (l=0; l<sbs; l++) { 5230 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5231 5232 rowlen[j*sbs+l] = ncols; 5233 5234 len += ncols; 5235 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5236 } 5237 k++; 5238 } 5239 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5240 5241 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5242 } 5243 /* recvs and sends of i-array are completed */ 5244 i = nrecvs; 5245 while (i--) { 5246 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5247 } 5248 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5249 ierr = PetscFree(svalues);CHKERRQ(ierr); 5250 5251 /* allocate buffers for sending j and a arrays */ 5252 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5253 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5254 5255 /* create i-array of B_oth */ 5256 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5257 5258 b_othi[0] = 0; 5259 len = 0; /* total length of j or a array to be received */ 5260 k = 0; 5261 for (i=0; i<nrecvs; i++) { 5262 rowlen = rvalues + rstarts[i]*rbs; 5263 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5264 for (j=0; j<nrows; j++) { 5265 b_othi[k+1] = b_othi[k] + rowlen[j]; 5266 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5267 k++; 5268 } 5269 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5270 } 5271 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5272 5273 /* allocate space for j and a arrrays of B_oth */ 5274 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5275 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5276 5277 /* j-array */ 5278 /*---------*/ 5279 /* post receives of j-array */ 5280 for (i=0; i<nrecvs; i++) { 5281 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5282 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5283 } 5284 5285 /* pack the outgoing message j-array */ 5286 k = 0; 5287 for (i=0; i<nsends; i++) { 5288 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5289 bufJ = bufj+sstartsj[i]; 5290 for (j=0; j<nrows; j++) { 5291 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5292 for (ll=0; ll<sbs; ll++) { 5293 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5294 for (l=0; l<ncols; l++) { 5295 *bufJ++ = cols[l]; 5296 } 5297 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5298 } 5299 } 5300 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5301 } 5302 5303 /* recvs and sends of j-array are completed */ 5304 i = nrecvs; 5305 while (i--) { 5306 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5307 } 5308 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5309 } else if (scall == MAT_REUSE_MATRIX) { 5310 sstartsj = *startsj_s; 5311 rstartsj = *startsj_r; 5312 bufa = *bufa_ptr; 5313 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5314 b_otha = b_oth->a; 5315 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5316 5317 /* a-array */ 5318 /*---------*/ 5319 /* post receives of a-array */ 5320 for (i=0; i<nrecvs; i++) { 5321 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5322 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5323 } 5324 5325 /* pack the outgoing message a-array */ 5326 k = 0; 5327 for (i=0; i<nsends; i++) { 5328 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5329 bufA = bufa+sstartsj[i]; 5330 for (j=0; j<nrows; j++) { 5331 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5332 for (ll=0; ll<sbs; ll++) { 5333 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5334 for (l=0; l<ncols; l++) { 5335 *bufA++ = vals[l]; 5336 } 5337 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5338 } 5339 } 5340 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5341 } 5342 /* recvs and sends of a-array are completed */ 5343 i = nrecvs; 5344 while (i--) { 5345 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5346 } 5347 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5348 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5349 5350 if (scall == MAT_INITIAL_MATRIX) { 5351 /* put together the new matrix */ 5352 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5353 5354 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5355 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5356 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5357 b_oth->free_a = PETSC_TRUE; 5358 b_oth->free_ij = PETSC_TRUE; 5359 b_oth->nonew = 0; 5360 5361 ierr = PetscFree(bufj);CHKERRQ(ierr); 5362 if (!startsj_s || !bufa_ptr) { 5363 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5364 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5365 } else { 5366 *startsj_s = sstartsj; 5367 *startsj_r = rstartsj; 5368 *bufa_ptr = bufa; 5369 } 5370 } 5371 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5372 PetscFunctionReturn(0); 5373 } 5374 5375 /*@C 5376 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5377 5378 Not Collective 5379 5380 Input Parameters: 5381 . A - The matrix in mpiaij format 5382 5383 Output Parameter: 5384 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5385 . colmap - A map from global column index to local index into lvec 5386 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5387 5388 Level: developer 5389 5390 @*/ 5391 #if defined(PETSC_USE_CTABLE) 5392 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5393 #else 5394 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5395 #endif 5396 { 5397 Mat_MPIAIJ *a; 5398 5399 PetscFunctionBegin; 5400 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5401 PetscValidPointer(lvec, 2); 5402 PetscValidPointer(colmap, 3); 5403 PetscValidPointer(multScatter, 4); 5404 a = (Mat_MPIAIJ*) A->data; 5405 if (lvec) *lvec = a->lvec; 5406 if (colmap) *colmap = a->colmap; 5407 if (multScatter) *multScatter = a->Mvctx; 5408 PetscFunctionReturn(0); 5409 } 5410 5411 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5412 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5413 #if defined(PETSC_HAVE_MKL_SPARSE) 5414 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJMKL(Mat,MatType,MatReuse,Mat*); 5415 #endif 5416 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5417 #if defined(PETSC_HAVE_ELEMENTAL) 5418 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5419 #endif 5420 #if defined(PETSC_HAVE_HYPRE) 5421 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5422 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5423 #endif 5424 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5425 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISELL(Mat,MatType,MatReuse,Mat*); 5426 5427 /* 5428 Computes (B'*A')' since computing B*A directly is untenable 5429 5430 n p p 5431 ( ) ( ) ( ) 5432 m ( A ) * n ( B ) = m ( C ) 5433 ( ) ( ) ( ) 5434 5435 */ 5436 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5437 { 5438 PetscErrorCode ierr; 5439 Mat At,Bt,Ct; 5440 5441 PetscFunctionBegin; 5442 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5443 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5444 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5445 ierr = MatDestroy(&At);CHKERRQ(ierr); 5446 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5447 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5448 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5449 PetscFunctionReturn(0); 5450 } 5451 5452 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5453 { 5454 PetscErrorCode ierr; 5455 PetscInt m=A->rmap->n,n=B->cmap->n; 5456 Mat Cmat; 5457 5458 PetscFunctionBegin; 5459 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); 5460 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5461 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5462 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5463 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5464 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5465 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5466 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5467 5468 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5469 5470 *C = Cmat; 5471 PetscFunctionReturn(0); 5472 } 5473 5474 /* ----------------------------------------------------------------*/ 5475 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5476 { 5477 PetscErrorCode ierr; 5478 5479 PetscFunctionBegin; 5480 if (scall == MAT_INITIAL_MATRIX) { 5481 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5482 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5483 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5484 } 5485 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5486 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5487 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5488 PetscFunctionReturn(0); 5489 } 5490 5491 /*MC 5492 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5493 5494 Options Database Keys: 5495 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5496 5497 Level: beginner 5498 5499 .seealso: MatCreateAIJ() 5500 M*/ 5501 5502 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5503 { 5504 Mat_MPIAIJ *b; 5505 PetscErrorCode ierr; 5506 PetscMPIInt size; 5507 5508 PetscFunctionBegin; 5509 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5510 5511 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5512 B->data = (void*)b; 5513 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5514 B->assembled = PETSC_FALSE; 5515 B->insertmode = NOT_SET_VALUES; 5516 b->size = size; 5517 5518 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5519 5520 /* build cache for off array entries formed */ 5521 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5522 5523 b->donotstash = PETSC_FALSE; 5524 b->colmap = 0; 5525 b->garray = 0; 5526 b->roworiented = PETSC_TRUE; 5527 5528 /* stuff used for matrix vector multiply */ 5529 b->lvec = NULL; 5530 b->Mvctx = NULL; 5531 5532 /* stuff for MatGetRow() */ 5533 b->rowindices = 0; 5534 b->rowvalues = 0; 5535 b->getrowactive = PETSC_FALSE; 5536 5537 /* flexible pointer used in CUSP/CUSPARSE classes */ 5538 b->spptr = NULL; 5539 5540 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5541 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5542 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5543 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5544 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5545 ierr = PetscObjectComposeFunction((PetscObject)B,"MatResetPreallocation_C",MatResetPreallocation_MPIAIJ);CHKERRQ(ierr); 5546 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5547 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5548 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5549 #if defined(PETSC_HAVE_MKL_SPARSE) 5550 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijmkl_C",MatConvert_MPIAIJ_MPIAIJMKL);CHKERRQ(ierr); 5551 #endif 5552 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5553 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5554 #if defined(PETSC_HAVE_ELEMENTAL) 5555 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5556 #endif 5557 #if defined(PETSC_HAVE_HYPRE) 5558 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5559 #endif 5560 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5561 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisell_C",MatConvert_MPIAIJ_MPISELL);CHKERRQ(ierr); 5562 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5563 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5564 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5565 #if defined(PETSC_HAVE_HYPRE) 5566 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5567 #endif 5568 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5569 PetscFunctionReturn(0); 5570 } 5571 5572 /*@C 5573 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5574 and "off-diagonal" part of the matrix in CSR format. 5575 5576 Collective on MPI_Comm 5577 5578 Input Parameters: 5579 + comm - MPI communicator 5580 . m - number of local rows (Cannot be PETSC_DECIDE) 5581 . n - This value should be the same as the local size used in creating the 5582 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5583 calculated if N is given) For square matrices n is almost always m. 5584 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5585 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5586 . i - row indices for "diagonal" portion of matrix 5587 . j - column indices 5588 . a - matrix values 5589 . oi - row indices for "off-diagonal" portion of matrix 5590 . oj - column indices 5591 - oa - matrix values 5592 5593 Output Parameter: 5594 . mat - the matrix 5595 5596 Level: advanced 5597 5598 Notes: 5599 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5600 must free the arrays once the matrix has been destroyed and not before. 5601 5602 The i and j indices are 0 based 5603 5604 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5605 5606 This sets local rows and cannot be used to set off-processor values. 5607 5608 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5609 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5610 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5611 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5612 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5613 communication if it is known that only local entries will be set. 5614 5615 .keywords: matrix, aij, compressed row, sparse, parallel 5616 5617 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5618 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5619 @*/ 5620 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) 5621 { 5622 PetscErrorCode ierr; 5623 Mat_MPIAIJ *maij; 5624 5625 PetscFunctionBegin; 5626 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5627 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5628 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5629 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5630 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5631 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5632 maij = (Mat_MPIAIJ*) (*mat)->data; 5633 5634 (*mat)->preallocated = PETSC_TRUE; 5635 5636 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5637 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5638 5639 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5640 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5641 5642 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5643 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5644 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5645 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5646 5647 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5648 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5649 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5650 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5651 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5652 PetscFunctionReturn(0); 5653 } 5654 5655 /* 5656 Special version for direct calls from Fortran 5657 */ 5658 #include <petsc/private/fortranimpl.h> 5659 5660 /* Change these macros so can be used in void function */ 5661 #undef CHKERRQ 5662 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5663 #undef SETERRQ2 5664 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5665 #undef SETERRQ3 5666 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5667 #undef SETERRQ 5668 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5669 5670 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5671 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5672 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5673 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5674 #else 5675 #endif 5676 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) 5677 { 5678 Mat mat = *mmat; 5679 PetscInt m = *mm, n = *mn; 5680 InsertMode addv = *maddv; 5681 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5682 PetscScalar value; 5683 PetscErrorCode ierr; 5684 5685 MatCheckPreallocated(mat,1); 5686 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5687 5688 #if defined(PETSC_USE_DEBUG) 5689 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5690 #endif 5691 { 5692 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5693 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5694 PetscBool roworiented = aij->roworiented; 5695 5696 /* Some Variables required in the macro */ 5697 Mat A = aij->A; 5698 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5699 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5700 MatScalar *aa = a->a; 5701 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5702 Mat B = aij->B; 5703 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5704 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5705 MatScalar *ba = b->a; 5706 5707 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5708 PetscInt nonew = a->nonew; 5709 MatScalar *ap1,*ap2; 5710 5711 PetscFunctionBegin; 5712 for (i=0; i<m; i++) { 5713 if (im[i] < 0) continue; 5714 #if defined(PETSC_USE_DEBUG) 5715 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); 5716 #endif 5717 if (im[i] >= rstart && im[i] < rend) { 5718 row = im[i] - rstart; 5719 lastcol1 = -1; 5720 rp1 = aj + ai[row]; 5721 ap1 = aa + ai[row]; 5722 rmax1 = aimax[row]; 5723 nrow1 = ailen[row]; 5724 low1 = 0; 5725 high1 = nrow1; 5726 lastcol2 = -1; 5727 rp2 = bj + bi[row]; 5728 ap2 = ba + bi[row]; 5729 rmax2 = bimax[row]; 5730 nrow2 = bilen[row]; 5731 low2 = 0; 5732 high2 = nrow2; 5733 5734 for (j=0; j<n; j++) { 5735 if (roworiented) value = v[i*n+j]; 5736 else value = v[i+j*m]; 5737 if (in[j] >= cstart && in[j] < cend) { 5738 col = in[j] - cstart; 5739 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5740 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5741 } else if (in[j] < 0) continue; 5742 #if defined(PETSC_USE_DEBUG) 5743 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); 5744 #endif 5745 else { 5746 if (mat->was_assembled) { 5747 if (!aij->colmap) { 5748 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5749 } 5750 #if defined(PETSC_USE_CTABLE) 5751 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5752 col--; 5753 #else 5754 col = aij->colmap[in[j]] - 1; 5755 #endif 5756 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5757 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5758 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5759 col = in[j]; 5760 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5761 B = aij->B; 5762 b = (Mat_SeqAIJ*)B->data; 5763 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5764 rp2 = bj + bi[row]; 5765 ap2 = ba + bi[row]; 5766 rmax2 = bimax[row]; 5767 nrow2 = bilen[row]; 5768 low2 = 0; 5769 high2 = nrow2; 5770 bm = aij->B->rmap->n; 5771 ba = b->a; 5772 } 5773 } else col = in[j]; 5774 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5775 } 5776 } 5777 } else if (!aij->donotstash) { 5778 if (roworiented) { 5779 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5780 } else { 5781 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5782 } 5783 } 5784 } 5785 } 5786 PetscFunctionReturnVoid(); 5787 } 5788 5789