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