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 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3055 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3056 ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3057 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3058 3059 /* Get start indices */ 3060 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3061 isstart -= ncols; 3062 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3063 3064 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3065 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3066 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3067 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3068 for (i=0; i<ncols; i++) { 3069 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3070 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3071 idx[i] = is_idx[i]-cstart; /* local index of iscol[i] */ 3072 } 3073 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3074 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3075 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3076 3077 /* Get iscol_d */ 3078 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,iscol_d);CHKERRQ(ierr); 3079 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3080 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3081 3082 /* Get isrow_d */ 3083 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3084 rstart = mat->rmap->rstart; 3085 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3086 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3087 for (i=0; i<m; i++) idx[i] = is_idx[i]-rstart; 3088 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3089 3090 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_OWN_POINTER,isrow_d);CHKERRQ(ierr); 3091 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3092 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3093 3094 /* (2) Scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3095 if (!a->Mvctx_mpi1) { 3096 /* a->Mvctx causes random 'count' in o-build? See src/mat/examples/tests/runex59_2 */ 3097 a->Mvctx_mpi1_flg = PETSC_TRUE; 3098 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 3099 } 3100 Mvctx = a->Mvctx_mpi1; 3101 ierr = VecScatterBegin(Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3102 3103 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3104 3105 ierr = VecScatterEnd(Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3106 ierr = VecScatterBegin(Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3107 ierr = VecScatterEnd(Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3108 3109 /* (3) create sequential iscol_o (a subset of iscol) and isgarray */ 3110 /* off-process column indices */ 3111 count = 0; 3112 ierr = PetscMalloc1(Bn,&idx);CHKERRQ(ierr); 3113 ierr = PetscMalloc1(Bn,&cmap1);CHKERRQ(ierr); 3114 3115 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3116 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3117 for (i=0; i<Bn; i++) { 3118 if (PetscRealPart(xarray[i]) > -1.0) { 3119 idx[count] = i; /* local column index in off-diagonal part B */ 3120 cmap1[count++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3121 } 3122 } 3123 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3124 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3125 /* printf("[%d] count %d\n",rank,count); */ 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 3131 *garray = cmap1; 3132 3133 ierr = VecDestroy(&x);CHKERRQ(ierr); 3134 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3135 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3136 PetscFunctionReturn(0); 3137 } 3138 3139 /* isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */ 3140 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *submat) 3141 { 3142 PetscErrorCode ierr; 3143 Mat_MPIAIJ *a = (Mat_MPIAIJ*)mat->data,*asub; 3144 Mat M = NULL; 3145 MPI_Comm comm; 3146 IS iscol_d,isrow_d,iscol_o; 3147 Mat Asub = NULL,Bsub = NULL; 3148 PetscInt n; 3149 3150 PetscFunctionBegin; 3151 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3152 3153 if (call == MAT_REUSE_MATRIX) { 3154 /* Retrieve isrow_d, iscol_d and iscol_o from submat */ 3155 ierr = PetscObjectQuery((PetscObject)*submat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3156 if (!isrow_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow_d passed in was not used before, cannot reuse"); 3157 3158 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_d",(PetscObject*)&iscol_d);CHKERRQ(ierr); 3159 if (!iscol_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_d passed in was not used before, cannot reuse"); 3160 3161 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_o",(PetscObject*)&iscol_o);CHKERRQ(ierr); 3162 if (!iscol_o) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_o passed in was not used before, cannot reuse"); 3163 3164 /* Update diagonal and off-diagonal portions of submat */ 3165 asub = (Mat_MPIAIJ*)(*submat)->data; 3166 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->A);CHKERRQ(ierr); 3167 ierr = ISGetLocalSize(iscol_o,&n);CHKERRQ(ierr); 3168 if (n) { 3169 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->B);CHKERRQ(ierr); 3170 } 3171 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3172 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3173 3174 } else { /* call == MAT_INITIAL_MATRIX) */ 3175 const PetscInt *garray; 3176 PetscInt BsubN; 3177 3178 /* Create isrow_d, iscol_d, iscol_o and isgarray (replace isgarray with array?) */ 3179 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&isrow_d,&iscol_d,&iscol_o,&garray);CHKERRQ(ierr); 3180 3181 /* Create local submatrices Asub and Bsub */ 3182 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Asub);CHKERRQ(ierr); 3183 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Bsub);CHKERRQ(ierr); 3184 3185 /* Create submatrix M */ 3186 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray,&M);CHKERRQ(ierr); 3187 3188 /* If Bsub has empty columns, compress iscol_o such that it will retrieve condensed Bsub from a->B during reuse */ 3189 asub = (Mat_MPIAIJ*)M->data; 3190 3191 ierr = ISGetLocalSize(iscol_o,&BsubN);CHKERRQ(ierr); 3192 n = asub->B->cmap->N; 3193 if (BsubN > n) { 3194 /* This case can be tested using ~petsc/src/tao/bound/examples/tutorials/runplate2_3 */ 3195 const PetscInt *idx; 3196 PetscInt i,j,*idx_new,*subgarray = asub->garray; 3197 ierr = PetscInfo2(M,"submatrix Bn %D != BsubN %D, update iscol_o\n",n,BsubN);CHKERRQ(ierr); 3198 3199 ierr = PetscMalloc1(n,&idx_new);CHKERRQ(ierr); 3200 j = 0; 3201 ierr = ISGetIndices(iscol_o,&idx);CHKERRQ(ierr); 3202 for (i=0; i<n; i++) { 3203 if (j >= BsubN) break; 3204 while (subgarray[i] > garray[j]) j++; 3205 3206 if (subgarray[i] == garray[j]) { 3207 idx_new[i] = idx[j++]; 3208 } else SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"subgarray[%D]=%D cannot < garray[%D]=%D",i,subgarray[i],j,garray[j]); 3209 } 3210 ierr = ISRestoreIndices(iscol_o,&idx);CHKERRQ(ierr); 3211 3212 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3213 ierr = ISCreateGeneral(PETSC_COMM_SELF,n,idx_new,PETSC_OWN_POINTER,&iscol_o);CHKERRQ(ierr); 3214 3215 } else if (BsubN < n) { 3216 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Columns of Bsub cannot be smaller than B's",BsubN,asub->B->cmap->N); 3217 } 3218 3219 ierr = PetscFree(garray);CHKERRQ(ierr); 3220 *submat = M; 3221 3222 /* Save isrow_d, iscol_d and iscol_o used in processor for next request */ 3223 ierr = PetscObjectCompose((PetscObject)M,"isrow_d",(PetscObject)isrow_d);CHKERRQ(ierr); 3224 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3225 3226 ierr = PetscObjectCompose((PetscObject)M,"iscol_d",(PetscObject)iscol_d);CHKERRQ(ierr); 3227 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3228 3229 ierr = PetscObjectCompose((PetscObject)M,"iscol_o",(PetscObject)iscol_o);CHKERRQ(ierr); 3230 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3231 } 3232 PetscFunctionReturn(0); 3233 } 3234 3235 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3236 { 3237 PetscErrorCode ierr; 3238 IS iscol_local=NULL,isrow_d; 3239 PetscInt csize; 3240 PetscInt n,i,j,start,end; 3241 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3242 MPI_Comm comm; 3243 3244 PetscFunctionBegin; 3245 /* If isrow has same processor distribution as mat, 3246 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3247 if (call == MAT_REUSE_MATRIX) { 3248 ierr = PetscObjectQuery((PetscObject)*newmat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3249 if (isrow_d) { 3250 sameRowDist = PETSC_TRUE; 3251 tsameDist[1] = PETSC_TRUE; /* sameColDist */ 3252 } else { 3253 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3254 if (iscol_local) { 3255 sameRowDist = PETSC_TRUE; 3256 tsameDist[1] = PETSC_FALSE; /* !sameColDist */ 3257 } 3258 } 3259 } else { 3260 /* Check if isrow has same processor distribution as mat */ 3261 sameDist[0] = PETSC_FALSE; 3262 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3263 if (!n) { 3264 sameDist[0] = PETSC_TRUE; 3265 } else { 3266 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3267 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3268 if (i >= start && j < end) { 3269 sameDist[0] = PETSC_TRUE; 3270 } 3271 } 3272 3273 /* Check if iscol has same processor distribution as mat */ 3274 sameDist[1] = PETSC_FALSE; 3275 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3276 if (!n) { 3277 sameDist[1] = PETSC_TRUE; 3278 } else { 3279 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3280 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3281 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3282 } 3283 3284 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3285 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3286 sameRowDist = tsameDist[0]; 3287 } 3288 3289 if (sameRowDist) { 3290 if (tsameDist[1]) { /* sameRowDist & sameColDist */ 3291 /* isrow and iscol have same processor distribution as mat */ 3292 ierr = MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3293 PetscFunctionReturn(0); 3294 } else { /* sameRowDist */ 3295 /* isrow has same processor distribution as mat */ 3296 if (call == MAT_INITIAL_MATRIX) { 3297 PetscBool sorted; 3298 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3299 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3300 ierr = ISGetSize(iscol,&i);CHKERRQ(ierr); 3301 if (n != i) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != size of iscol %d",n,i); 3302 3303 ierr = ISSorted(iscol_local,&sorted);CHKERRQ(ierr); 3304 if (sorted) { 3305 /* MatCreateSubMatrix_MPIAIJ_SameRowDist() requires iscol_local be sorted; it can have duplicate indices */ 3306 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,iscol_local,MAT_INITIAL_MATRIX,newmat);CHKERRQ(ierr); 3307 PetscFunctionReturn(0); 3308 } 3309 } else { /* call == MAT_REUSE_MATRIX */ 3310 IS iscol_sub; 3311 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3312 if (iscol_sub) { 3313 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,NULL,call,newmat);CHKERRQ(ierr); 3314 PetscFunctionReturn(0); 3315 } 3316 } 3317 } 3318 } 3319 3320 /* General case: iscol -> iscol_local which has global size of iscol */ 3321 if (call == MAT_REUSE_MATRIX) { 3322 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3323 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3324 } else { 3325 if (!iscol_local) { 3326 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3327 } 3328 } 3329 3330 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3331 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3332 3333 if (call == MAT_INITIAL_MATRIX) { 3334 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3335 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3336 } 3337 PetscFunctionReturn(0); 3338 } 3339 3340 /*@C 3341 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3342 and "off-diagonal" part of the matrix in CSR format. 3343 3344 Collective on MPI_Comm 3345 3346 Input Parameters: 3347 + comm - MPI communicator 3348 . A - "diagonal" portion of matrix 3349 . B - "off-diagonal" portion of matrix, may have empty columns, will be destroyed by this routine 3350 - garray - global index of B columns 3351 3352 Output Parameter: 3353 . mat - the matrix, with input A as its local diagonal matrix 3354 Level: advanced 3355 3356 Notes: 3357 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3358 A becomes part of output mat, B is destroyed by this routine. The user cannot use A and B anymore. 3359 3360 .seealso: MatCreateMPIAIJWithSplitArrays() 3361 @*/ 3362 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3363 { 3364 PetscErrorCode ierr; 3365 Mat_MPIAIJ *maij; 3366 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data,*bnew; 3367 PetscInt *oi=b->i,*oj=b->j,i,nz,col; 3368 PetscScalar *oa=b->a; 3369 Mat Bnew; 3370 PetscInt m,n,N; 3371 3372 PetscFunctionBegin; 3373 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3374 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3375 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %D != Bm %D",m,B->rmap->N); 3376 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); 3377 /* remove check below; When B is created using iscol_o from ISGetSeqIS_SameColDist_Private(), its bs may not be same as A */ 3378 /* 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); */ 3379 3380 /* Get global columns of mat */ 3381 ierr = MPIU_Allreduce(&n,&N,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3382 3383 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3384 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3385 ierr = MatSetBlockSizes(*mat,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 3386 maij = (Mat_MPIAIJ*)(*mat)->data; 3387 3388 (*mat)->preallocated = PETSC_TRUE; 3389 3390 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3391 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3392 3393 /* Set A as diagonal portion of *mat */ 3394 maij->A = A; 3395 3396 nz = oi[m]; 3397 for (i=0; i<nz; i++) { 3398 col = oj[i]; 3399 oj[i] = garray[col]; 3400 } 3401 3402 /* Set Bnew as off-diagonal portion of *mat */ 3403 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Bnew);CHKERRQ(ierr); 3404 bnew = (Mat_SeqAIJ*)Bnew->data; 3405 bnew->maxnz = b->maxnz; /* allocated nonzeros of B */ 3406 maij->B = Bnew; 3407 3408 if (B->rmap->N != Bnew->rmap->N) SETERRQ2(PETSC_COMM_SELF,0,"BN %d != BnewN %d",B->rmap->N,Bnew->rmap->N); 3409 3410 b->singlemalloc = PETSC_FALSE; /* B arrays are shared by Bnew */ 3411 b->free_a = PETSC_FALSE; 3412 b->free_ij = PETSC_FALSE; 3413 ierr = MatDestroy(&B);CHKERRQ(ierr); 3414 3415 bnew->singlemalloc = PETSC_TRUE; /* arrays will be freed by MatDestroy(&Bnew) */ 3416 bnew->free_a = PETSC_TRUE; 3417 bnew->free_ij = PETSC_TRUE; 3418 3419 /* condense columns of maij->B */ 3420 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3421 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3422 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3423 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3424 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3425 PetscFunctionReturn(0); 3426 } 3427 3428 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3429 3430 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,IS iscol_local,MatReuse call,Mat *newmat) 3431 { 3432 PetscErrorCode ierr; 3433 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3434 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3435 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3436 Mat M,Msub,B=a->B; 3437 MatScalar *aa; 3438 Mat_SeqAIJ *aij; 3439 PetscInt *garray = a->garray,*colsub,Ncols; 3440 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3441 IS iscol_sub,iscmap; 3442 const PetscInt *is_idx,*cmap; 3443 PetscBool allcolumns=PETSC_FALSE; 3444 MPI_Comm comm; 3445 3446 PetscFunctionBegin; 3447 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3448 3449 if (call == MAT_REUSE_MATRIX) { 3450 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3451 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3452 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3453 3454 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3455 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3456 3457 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3458 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3459 3460 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3461 3462 } else { /* call == MAT_INITIAL_MATRIX) */ 3463 PetscBool flg; 3464 3465 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3466 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3467 3468 /* (1) iscol -> nonscalable iscol_local */ 3469 /* Check for special case: each processor gets entire matrix columns */ 3470 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3471 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3472 if (allcolumns) { 3473 iscol_sub = iscol_local; 3474 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3475 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3476 3477 } else { 3478 /* (2) iscol_local -> iscol_sub and iscmap. Implementation below requires iscol_local be sorted, it can have duplicate indices */ 3479 PetscInt *idx,*cmap1,k; 3480 ierr = PetscMalloc1(Ncols,&idx);CHKERRQ(ierr); 3481 ierr = PetscMalloc1(Ncols,&cmap1);CHKERRQ(ierr); 3482 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3483 count = 0; 3484 k = 0; 3485 for (i=0; i<Ncols; i++) { 3486 j = is_idx[i]; 3487 if (j >= cstart && j < cend) { 3488 /* diagonal part of mat */ 3489 idx[count] = j; 3490 cmap1[count++] = i; /* column index in submat */ 3491 } else if (Bn) { 3492 /* off-diagonal part of mat */ 3493 if (j == garray[k]) { 3494 idx[count] = j; 3495 cmap1[count++] = i; /* column index in submat */ 3496 } else if (j > garray[k]) { 3497 while (j > garray[k] && k < Bn-1) k++; 3498 if (j == garray[k]) { 3499 idx[count] = j; 3500 cmap1[count++] = i; /* column index in submat */ 3501 } 3502 } 3503 } 3504 } 3505 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3506 3507 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_OWN_POINTER,&iscol_sub);CHKERRQ(ierr); 3508 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3509 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3510 3511 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_OWN_POINTER,&iscmap);CHKERRQ(ierr); 3512 } 3513 3514 /* (3) Create sequential Msub */ 3515 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3516 } 3517 3518 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3519 aij = (Mat_SeqAIJ*)(Msub)->data; 3520 ii = aij->i; 3521 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3522 3523 /* 3524 m - number of local rows 3525 Ncols - number of columns (same on all processors) 3526 rstart - first row in new global matrix generated 3527 */ 3528 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3529 3530 if (call == MAT_INITIAL_MATRIX) { 3531 /* (4) Create parallel newmat */ 3532 PetscMPIInt rank,size; 3533 PetscInt csize; 3534 3535 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3536 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3537 3538 /* 3539 Determine the number of non-zeros in the diagonal and off-diagonal 3540 portions of the matrix in order to do correct preallocation 3541 */ 3542 3543 /* first get start and end of "diagonal" columns */ 3544 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3545 if (csize == PETSC_DECIDE) { 3546 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3547 if (mglobal == Ncols) { /* square matrix */ 3548 nlocal = m; 3549 } else { 3550 nlocal = Ncols/size + ((Ncols % size) > rank); 3551 } 3552 } else { 3553 nlocal = csize; 3554 } 3555 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3556 rstart = rend - nlocal; 3557 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); 3558 3559 /* next, compute all the lengths */ 3560 jj = aij->j; 3561 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3562 olens = dlens + m; 3563 for (i=0; i<m; i++) { 3564 jend = ii[i+1] - ii[i]; 3565 olen = 0; 3566 dlen = 0; 3567 for (j=0; j<jend; j++) { 3568 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3569 else dlen++; 3570 jj++; 3571 } 3572 olens[i] = olen; 3573 dlens[i] = dlen; 3574 } 3575 3576 ierr = ISGetBlockSize(isrow,&bs);CHKERRQ(ierr); 3577 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3578 3579 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3580 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr); 3581 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3582 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3583 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3584 ierr = PetscFree(dlens);CHKERRQ(ierr); 3585 3586 } else { /* call == MAT_REUSE_MATRIX */ 3587 M = *newmat; 3588 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3589 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3590 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3591 /* 3592 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3593 rather than the slower MatSetValues(). 3594 */ 3595 M->was_assembled = PETSC_TRUE; 3596 M->assembled = PETSC_FALSE; 3597 } 3598 3599 /* (5) Set values of Msub to *newmat */ 3600 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3601 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3602 3603 jj = aij->j; 3604 aa = aij->a; 3605 for (i=0; i<m; i++) { 3606 row = rstart + i; 3607 nz = ii[i+1] - ii[i]; 3608 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3609 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3610 jj += nz; aa += nz; 3611 } 3612 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3613 3614 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3615 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3616 3617 ierr = PetscFree(colsub);CHKERRQ(ierr); 3618 3619 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3620 if (call == MAT_INITIAL_MATRIX) { 3621 *newmat = M; 3622 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3623 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3624 3625 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3626 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3627 3628 ierr = PetscObjectCompose((PetscObject)(*newmat),"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3629 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3630 3631 if (iscol_local) { 3632 ierr = PetscObjectCompose((PetscObject)(*newmat),"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3633 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3634 } 3635 } 3636 PetscFunctionReturn(0); 3637 } 3638 3639 /* 3640 Not great since it makes two copies of the submatrix, first an SeqAIJ 3641 in local and then by concatenating the local matrices the end result. 3642 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3643 3644 Note: This requires a sequential iscol with all indices. 3645 */ 3646 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3647 { 3648 PetscErrorCode ierr; 3649 PetscMPIInt rank,size; 3650 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3651 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3652 Mat M,Mreuse; 3653 MatScalar *aa,*vwork; 3654 MPI_Comm comm; 3655 Mat_SeqAIJ *aij; 3656 PetscBool colflag,allcolumns=PETSC_FALSE; 3657 3658 PetscFunctionBegin; 3659 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3660 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3661 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3662 3663 /* Check for special case: each processor gets entire matrix columns */ 3664 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3665 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3666 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3667 3668 if (call == MAT_REUSE_MATRIX) { 3669 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3670 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3671 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3672 } else { 3673 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3674 } 3675 3676 /* 3677 m - number of local rows 3678 n - number of columns (same on all processors) 3679 rstart - first row in new global matrix generated 3680 */ 3681 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3682 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3683 if (call == MAT_INITIAL_MATRIX) { 3684 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3685 ii = aij->i; 3686 jj = aij->j; 3687 3688 /* 3689 Determine the number of non-zeros in the diagonal and off-diagonal 3690 portions of the matrix in order to do correct preallocation 3691 */ 3692 3693 /* first get start and end of "diagonal" columns */ 3694 if (csize == PETSC_DECIDE) { 3695 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3696 if (mglobal == n) { /* square matrix */ 3697 nlocal = m; 3698 } else { 3699 nlocal = n/size + ((n % size) > rank); 3700 } 3701 } else { 3702 nlocal = csize; 3703 } 3704 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3705 rstart = rend - nlocal; 3706 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); 3707 3708 /* next, compute all the lengths */ 3709 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3710 olens = dlens + m; 3711 for (i=0; i<m; i++) { 3712 jend = ii[i+1] - ii[i]; 3713 olen = 0; 3714 dlen = 0; 3715 for (j=0; j<jend; j++) { 3716 if (*jj < rstart || *jj >= rend) olen++; 3717 else dlen++; 3718 jj++; 3719 } 3720 olens[i] = olen; 3721 dlens[i] = dlen; 3722 } 3723 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3724 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3725 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3726 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3727 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3728 ierr = PetscFree(dlens);CHKERRQ(ierr); 3729 } else { 3730 PetscInt ml,nl; 3731 3732 M = *newmat; 3733 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3734 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3735 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3736 /* 3737 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3738 rather than the slower MatSetValues(). 3739 */ 3740 M->was_assembled = PETSC_TRUE; 3741 M->assembled = PETSC_FALSE; 3742 } 3743 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3744 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3745 ii = aij->i; 3746 jj = aij->j; 3747 aa = aij->a; 3748 for (i=0; i<m; i++) { 3749 row = rstart + i; 3750 nz = ii[i+1] - ii[i]; 3751 cwork = jj; jj += nz; 3752 vwork = aa; aa += nz; 3753 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3754 } 3755 3756 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3757 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3758 *newmat = M; 3759 3760 /* save submatrix used in processor for next request */ 3761 if (call == MAT_INITIAL_MATRIX) { 3762 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3763 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3764 } 3765 PetscFunctionReturn(0); 3766 } 3767 3768 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3769 { 3770 PetscInt m,cstart, cend,j,nnz,i,d; 3771 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3772 const PetscInt *JJ; 3773 PetscScalar *values; 3774 PetscErrorCode ierr; 3775 PetscBool nooffprocentries; 3776 3777 PetscFunctionBegin; 3778 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3779 3780 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3781 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3782 m = B->rmap->n; 3783 cstart = B->cmap->rstart; 3784 cend = B->cmap->rend; 3785 rstart = B->rmap->rstart; 3786 3787 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3788 3789 #if defined(PETSC_USE_DEBUGGING) 3790 for (i=0; i<m; i++) { 3791 nnz = Ii[i+1]- Ii[i]; 3792 JJ = J + Ii[i]; 3793 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3794 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3795 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); 3796 } 3797 #endif 3798 3799 for (i=0; i<m; i++) { 3800 nnz = Ii[i+1]- Ii[i]; 3801 JJ = J + Ii[i]; 3802 nnz_max = PetscMax(nnz_max,nnz); 3803 d = 0; 3804 for (j=0; j<nnz; j++) { 3805 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3806 } 3807 d_nnz[i] = d; 3808 o_nnz[i] = nnz - d; 3809 } 3810 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3811 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3812 3813 if (v) values = (PetscScalar*)v; 3814 else { 3815 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3816 } 3817 3818 for (i=0; i<m; i++) { 3819 ii = i + rstart; 3820 nnz = Ii[i+1]- Ii[i]; 3821 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3822 } 3823 nooffprocentries = B->nooffprocentries; 3824 B->nooffprocentries = PETSC_TRUE; 3825 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3826 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3827 B->nooffprocentries = nooffprocentries; 3828 3829 if (!v) { 3830 ierr = PetscFree(values);CHKERRQ(ierr); 3831 } 3832 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3833 PetscFunctionReturn(0); 3834 } 3835 3836 /*@ 3837 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3838 (the default parallel PETSc format). 3839 3840 Collective on MPI_Comm 3841 3842 Input Parameters: 3843 + B - the matrix 3844 . i - the indices into j for the start of each local row (starts with zero) 3845 . j - the column indices for each local row (starts with zero) 3846 - v - optional values in the matrix 3847 3848 Level: developer 3849 3850 Notes: 3851 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3852 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3853 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3854 3855 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3856 3857 The format which is used for the sparse matrix input, is equivalent to a 3858 row-major ordering.. i.e for the following matrix, the input data expected is 3859 as shown 3860 3861 $ 1 0 0 3862 $ 2 0 3 P0 3863 $ ------- 3864 $ 4 5 6 P1 3865 $ 3866 $ Process0 [P0]: rows_owned=[0,1] 3867 $ i = {0,1,3} [size = nrow+1 = 2+1] 3868 $ j = {0,0,2} [size = 3] 3869 $ v = {1,2,3} [size = 3] 3870 $ 3871 $ Process1 [P1]: rows_owned=[2] 3872 $ i = {0,3} [size = nrow+1 = 1+1] 3873 $ j = {0,1,2} [size = 3] 3874 $ v = {4,5,6} [size = 3] 3875 3876 .keywords: matrix, aij, compressed row, sparse, parallel 3877 3878 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3879 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3880 @*/ 3881 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3882 { 3883 PetscErrorCode ierr; 3884 3885 PetscFunctionBegin; 3886 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3887 PetscFunctionReturn(0); 3888 } 3889 3890 /*@C 3891 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3892 (the default parallel PETSc format). For good matrix assembly performance 3893 the user should preallocate the matrix storage by setting the parameters 3894 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3895 performance can be increased by more than a factor of 50. 3896 3897 Collective on MPI_Comm 3898 3899 Input Parameters: 3900 + B - the matrix 3901 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3902 (same value is used for all local rows) 3903 . d_nnz - array containing the number of nonzeros in the various rows of the 3904 DIAGONAL portion of the local submatrix (possibly different for each row) 3905 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3906 The size of this array is equal to the number of local rows, i.e 'm'. 3907 For matrices that will be factored, you must leave room for (and set) 3908 the diagonal entry even if it is zero. 3909 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3910 submatrix (same value is used for all local rows). 3911 - o_nnz - array containing the number of nonzeros in the various rows of the 3912 OFF-DIAGONAL portion of the local submatrix (possibly different for 3913 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3914 structure. The size of this array is equal to the number 3915 of local rows, i.e 'm'. 3916 3917 If the *_nnz parameter is given then the *_nz parameter is ignored 3918 3919 The AIJ format (also called the Yale sparse matrix format or 3920 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3921 storage. The stored row and column indices begin with zero. 3922 See Users-Manual: ch_mat for details. 3923 3924 The parallel matrix is partitioned such that the first m0 rows belong to 3925 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3926 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3927 3928 The DIAGONAL portion of the local submatrix of a processor can be defined 3929 as the submatrix which is obtained by extraction the part corresponding to 3930 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3931 first row that belongs to the processor, r2 is the last row belonging to 3932 the this processor, and c1-c2 is range of indices of the local part of a 3933 vector suitable for applying the matrix to. This is an mxn matrix. In the 3934 common case of a square matrix, the row and column ranges are the same and 3935 the DIAGONAL part is also square. The remaining portion of the local 3936 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3937 3938 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3939 3940 You can call MatGetInfo() to get information on how effective the preallocation was; 3941 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3942 You can also run with the option -info and look for messages with the string 3943 malloc in them to see if additional memory allocation was needed. 3944 3945 Example usage: 3946 3947 Consider the following 8x8 matrix with 34 non-zero values, that is 3948 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3949 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3950 as follows: 3951 3952 .vb 3953 1 2 0 | 0 3 0 | 0 4 3954 Proc0 0 5 6 | 7 0 0 | 8 0 3955 9 0 10 | 11 0 0 | 12 0 3956 ------------------------------------- 3957 13 0 14 | 15 16 17 | 0 0 3958 Proc1 0 18 0 | 19 20 21 | 0 0 3959 0 0 0 | 22 23 0 | 24 0 3960 ------------------------------------- 3961 Proc2 25 26 27 | 0 0 28 | 29 0 3962 30 0 0 | 31 32 33 | 0 34 3963 .ve 3964 3965 This can be represented as a collection of submatrices as: 3966 3967 .vb 3968 A B C 3969 D E F 3970 G H I 3971 .ve 3972 3973 Where the submatrices A,B,C are owned by proc0, D,E,F are 3974 owned by proc1, G,H,I are owned by proc2. 3975 3976 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3977 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3978 The 'M','N' parameters are 8,8, and have the same values on all procs. 3979 3980 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3981 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3982 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3983 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3984 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3985 matrix, ans [DF] as another SeqAIJ matrix. 3986 3987 When d_nz, o_nz parameters are specified, d_nz storage elements are 3988 allocated for every row of the local diagonal submatrix, and o_nz 3989 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3990 One way to choose d_nz and o_nz is to use the max nonzerors per local 3991 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3992 In this case, the values of d_nz,o_nz are: 3993 .vb 3994 proc0 : dnz = 2, o_nz = 2 3995 proc1 : dnz = 3, o_nz = 2 3996 proc2 : dnz = 1, o_nz = 4 3997 .ve 3998 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3999 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4000 for proc3. i.e we are using 12+15+10=37 storage locations to store 4001 34 values. 4002 4003 When d_nnz, o_nnz parameters are specified, the storage is specified 4004 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4005 In the above case the values for d_nnz,o_nnz are: 4006 .vb 4007 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4008 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4009 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4010 .ve 4011 Here the space allocated is sum of all the above values i.e 34, and 4012 hence pre-allocation is perfect. 4013 4014 Level: intermediate 4015 4016 .keywords: matrix, aij, compressed row, sparse, parallel 4017 4018 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 4019 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 4020 @*/ 4021 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 4022 { 4023 PetscErrorCode ierr; 4024 4025 PetscFunctionBegin; 4026 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 4027 PetscValidType(B,1); 4028 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 4029 PetscFunctionReturn(0); 4030 } 4031 4032 /*@ 4033 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 4034 CSR format the local rows. 4035 4036 Collective on MPI_Comm 4037 4038 Input Parameters: 4039 + comm - MPI communicator 4040 . m - number of local rows (Cannot be PETSC_DECIDE) 4041 . n - This value should be the same as the local size used in creating the 4042 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4043 calculated if N is given) For square matrices n is almost always m. 4044 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4045 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4046 . i - row indices 4047 . j - column indices 4048 - a - matrix values 4049 4050 Output Parameter: 4051 . mat - the matrix 4052 4053 Level: intermediate 4054 4055 Notes: 4056 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 4057 thus you CANNOT change the matrix entries by changing the values of a[] after you have 4058 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 4059 4060 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4061 4062 The format which is used for the sparse matrix input, is equivalent to a 4063 row-major ordering.. i.e for the following matrix, the input data expected is 4064 as shown 4065 4066 $ 1 0 0 4067 $ 2 0 3 P0 4068 $ ------- 4069 $ 4 5 6 P1 4070 $ 4071 $ Process0 [P0]: rows_owned=[0,1] 4072 $ i = {0,1,3} [size = nrow+1 = 2+1] 4073 $ j = {0,0,2} [size = 3] 4074 $ v = {1,2,3} [size = 3] 4075 $ 4076 $ Process1 [P1]: rows_owned=[2] 4077 $ i = {0,3} [size = nrow+1 = 1+1] 4078 $ j = {0,1,2} [size = 3] 4079 $ v = {4,5,6} [size = 3] 4080 4081 .keywords: matrix, aij, compressed row, sparse, parallel 4082 4083 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4084 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4085 @*/ 4086 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 4087 { 4088 PetscErrorCode ierr; 4089 4090 PetscFunctionBegin; 4091 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4092 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4093 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4094 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4095 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 4096 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 4097 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 4098 PetscFunctionReturn(0); 4099 } 4100 4101 /*@C 4102 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 4103 (the default parallel PETSc format). For good matrix assembly performance 4104 the user should preallocate the matrix storage by setting the parameters 4105 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4106 performance can be increased by more than a factor of 50. 4107 4108 Collective on MPI_Comm 4109 4110 Input Parameters: 4111 + comm - MPI communicator 4112 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 4113 This value should be the same as the local size used in creating the 4114 y vector for the matrix-vector product y = Ax. 4115 . n - This value should be the same as the local size used in creating the 4116 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4117 calculated if N is given) For square matrices n is almost always m. 4118 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4119 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4120 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4121 (same value is used for all local rows) 4122 . d_nnz - array containing the number of nonzeros in the various rows of the 4123 DIAGONAL portion of the local submatrix (possibly different for each row) 4124 or NULL, if d_nz is used to specify the nonzero structure. 4125 The size of this array is equal to the number of local rows, i.e 'm'. 4126 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4127 submatrix (same value is used for all local rows). 4128 - o_nnz - array containing the number of nonzeros in the various rows of the 4129 OFF-DIAGONAL portion of the local submatrix (possibly different for 4130 each row) or NULL, if o_nz is used to specify the nonzero 4131 structure. The size of this array is equal to the number 4132 of local rows, i.e 'm'. 4133 4134 Output Parameter: 4135 . A - the matrix 4136 4137 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4138 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4139 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4140 4141 Notes: 4142 If the *_nnz parameter is given then the *_nz parameter is ignored 4143 4144 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4145 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4146 storage requirements for this matrix. 4147 4148 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4149 processor than it must be used on all processors that share the object for 4150 that argument. 4151 4152 The user MUST specify either the local or global matrix dimensions 4153 (possibly both). 4154 4155 The parallel matrix is partitioned across processors such that the 4156 first m0 rows belong to process 0, the next m1 rows belong to 4157 process 1, the next m2 rows belong to process 2 etc.. where 4158 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4159 values corresponding to [m x N] submatrix. 4160 4161 The columns are logically partitioned with the n0 columns belonging 4162 to 0th partition, the next n1 columns belonging to the next 4163 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4164 4165 The DIAGONAL portion of the local submatrix on any given processor 4166 is the submatrix corresponding to the rows and columns m,n 4167 corresponding to the given processor. i.e diagonal matrix on 4168 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4169 etc. The remaining portion of the local submatrix [m x (N-n)] 4170 constitute the OFF-DIAGONAL portion. The example below better 4171 illustrates this concept. 4172 4173 For a square global matrix we define each processor's diagonal portion 4174 to be its local rows and the corresponding columns (a square submatrix); 4175 each processor's off-diagonal portion encompasses the remainder of the 4176 local matrix (a rectangular submatrix). 4177 4178 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4179 4180 When calling this routine with a single process communicator, a matrix of 4181 type SEQAIJ is returned. If a matrix of type MPIAIJ is desired for this 4182 type of communicator, use the construction mechanism 4183 .vb 4184 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4185 .ve 4186 4187 $ MatCreate(...,&A); 4188 $ MatSetType(A,MATMPIAIJ); 4189 $ MatSetSizes(A, m,n,M,N); 4190 $ MatMPIAIJSetPreallocation(A,...); 4191 4192 By default, this format uses inodes (identical nodes) when possible. 4193 We search for consecutive rows with the same nonzero structure, thereby 4194 reusing matrix information to achieve increased efficiency. 4195 4196 Options Database Keys: 4197 + -mat_no_inode - Do not use inodes 4198 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4199 - -mat_aij_oneindex - Internally use indexing starting at 1 4200 rather than 0. Note that when calling MatSetValues(), 4201 the user still MUST index entries starting at 0! 4202 4203 4204 Example usage: 4205 4206 Consider the following 8x8 matrix with 34 non-zero values, that is 4207 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4208 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4209 as follows 4210 4211 .vb 4212 1 2 0 | 0 3 0 | 0 4 4213 Proc0 0 5 6 | 7 0 0 | 8 0 4214 9 0 10 | 11 0 0 | 12 0 4215 ------------------------------------- 4216 13 0 14 | 15 16 17 | 0 0 4217 Proc1 0 18 0 | 19 20 21 | 0 0 4218 0 0 0 | 22 23 0 | 24 0 4219 ------------------------------------- 4220 Proc2 25 26 27 | 0 0 28 | 29 0 4221 30 0 0 | 31 32 33 | 0 34 4222 .ve 4223 4224 This can be represented as a collection of submatrices as 4225 4226 .vb 4227 A B C 4228 D E F 4229 G H I 4230 .ve 4231 4232 Where the submatrices A,B,C are owned by proc0, D,E,F are 4233 owned by proc1, G,H,I are owned by proc2. 4234 4235 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4236 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4237 The 'M','N' parameters are 8,8, and have the same values on all procs. 4238 4239 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4240 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4241 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4242 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4243 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4244 matrix, ans [DF] as another SeqAIJ matrix. 4245 4246 When d_nz, o_nz parameters are specified, d_nz storage elements are 4247 allocated for every row of the local diagonal submatrix, and o_nz 4248 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4249 One way to choose d_nz and o_nz is to use the max nonzerors per local 4250 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4251 In this case, the values of d_nz,o_nz are 4252 .vb 4253 proc0 : dnz = 2, o_nz = 2 4254 proc1 : dnz = 3, o_nz = 2 4255 proc2 : dnz = 1, o_nz = 4 4256 .ve 4257 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4258 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4259 for proc3. i.e we are using 12+15+10=37 storage locations to store 4260 34 values. 4261 4262 When d_nnz, o_nnz parameters are specified, the storage is specified 4263 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4264 In the above case the values for d_nnz,o_nnz are 4265 .vb 4266 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4267 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4268 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4269 .ve 4270 Here the space allocated is sum of all the above values i.e 34, and 4271 hence pre-allocation is perfect. 4272 4273 Level: intermediate 4274 4275 .keywords: matrix, aij, compressed row, sparse, parallel 4276 4277 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4278 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4279 @*/ 4280 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) 4281 { 4282 PetscErrorCode ierr; 4283 PetscMPIInt size; 4284 4285 PetscFunctionBegin; 4286 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4287 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4288 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4289 if (size > 1) { 4290 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4291 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4292 } else { 4293 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4294 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4295 } 4296 PetscFunctionReturn(0); 4297 } 4298 4299 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4300 { 4301 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4302 PetscBool flg; 4303 PetscErrorCode ierr; 4304 4305 PetscFunctionBegin; 4306 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4307 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4308 if (Ad) *Ad = a->A; 4309 if (Ao) *Ao = a->B; 4310 if (colmap) *colmap = a->garray; 4311 PetscFunctionReturn(0); 4312 } 4313 4314 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4315 { 4316 PetscErrorCode ierr; 4317 PetscInt m,N,i,rstart,nnz,Ii; 4318 PetscInt *indx; 4319 PetscScalar *values; 4320 4321 PetscFunctionBegin; 4322 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4323 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4324 PetscInt *dnz,*onz,sum,bs,cbs; 4325 4326 if (n == PETSC_DECIDE) { 4327 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4328 } 4329 /* Check sum(n) = N */ 4330 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4331 if (sum != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns %D != global columns %D",sum,N); 4332 4333 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4334 rstart -= m; 4335 4336 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4337 for (i=0; i<m; i++) { 4338 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4339 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4340 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4341 } 4342 4343 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4344 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4345 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4346 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4347 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4348 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4349 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4350 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4351 } 4352 4353 /* numeric phase */ 4354 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4355 for (i=0; i<m; i++) { 4356 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4357 Ii = i + rstart; 4358 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4359 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4360 } 4361 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4362 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4363 PetscFunctionReturn(0); 4364 } 4365 4366 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4367 { 4368 PetscErrorCode ierr; 4369 PetscMPIInt rank; 4370 PetscInt m,N,i,rstart,nnz; 4371 size_t len; 4372 const PetscInt *indx; 4373 PetscViewer out; 4374 char *name; 4375 Mat B; 4376 const PetscScalar *values; 4377 4378 PetscFunctionBegin; 4379 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4380 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4381 /* Should this be the type of the diagonal block of A? */ 4382 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4383 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4384 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4385 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4386 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4387 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4388 for (i=0; i<m; i++) { 4389 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4390 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4391 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4392 } 4393 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4394 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4395 4396 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4397 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4398 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4399 sprintf(name,"%s.%d",outfile,rank); 4400 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4401 ierr = PetscFree(name);CHKERRQ(ierr); 4402 ierr = MatView(B,out);CHKERRQ(ierr); 4403 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4404 ierr = MatDestroy(&B);CHKERRQ(ierr); 4405 PetscFunctionReturn(0); 4406 } 4407 4408 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4409 { 4410 PetscErrorCode ierr; 4411 Mat_Merge_SeqsToMPI *merge; 4412 PetscContainer container; 4413 4414 PetscFunctionBegin; 4415 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4416 if (container) { 4417 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4418 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4419 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4420 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4421 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4422 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4423 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4424 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4425 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4426 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4427 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4428 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4429 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4430 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4431 ierr = PetscFree(merge);CHKERRQ(ierr); 4432 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4433 } 4434 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4435 PetscFunctionReturn(0); 4436 } 4437 4438 #include <../src/mat/utils/freespace.h> 4439 #include <petscbt.h> 4440 4441 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4442 { 4443 PetscErrorCode ierr; 4444 MPI_Comm comm; 4445 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4446 PetscMPIInt size,rank,taga,*len_s; 4447 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4448 PetscInt proc,m; 4449 PetscInt **buf_ri,**buf_rj; 4450 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4451 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4452 MPI_Request *s_waits,*r_waits; 4453 MPI_Status *status; 4454 MatScalar *aa=a->a; 4455 MatScalar **abuf_r,*ba_i; 4456 Mat_Merge_SeqsToMPI *merge; 4457 PetscContainer container; 4458 4459 PetscFunctionBegin; 4460 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4461 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4462 4463 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4464 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4465 4466 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4467 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4468 4469 bi = merge->bi; 4470 bj = merge->bj; 4471 buf_ri = merge->buf_ri; 4472 buf_rj = merge->buf_rj; 4473 4474 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4475 owners = merge->rowmap->range; 4476 len_s = merge->len_s; 4477 4478 /* send and recv matrix values */ 4479 /*-----------------------------*/ 4480 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4481 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4482 4483 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4484 for (proc=0,k=0; proc<size; proc++) { 4485 if (!len_s[proc]) continue; 4486 i = owners[proc]; 4487 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4488 k++; 4489 } 4490 4491 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4492 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4493 ierr = PetscFree(status);CHKERRQ(ierr); 4494 4495 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4496 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4497 4498 /* insert mat values of mpimat */ 4499 /*----------------------------*/ 4500 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4501 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4502 4503 for (k=0; k<merge->nrecv; k++) { 4504 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4505 nrows = *(buf_ri_k[k]); 4506 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4507 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4508 } 4509 4510 /* set values of ba */ 4511 m = merge->rowmap->n; 4512 for (i=0; i<m; i++) { 4513 arow = owners[rank] + i; 4514 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4515 bnzi = bi[i+1] - bi[i]; 4516 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4517 4518 /* add local non-zero vals of this proc's seqmat into ba */ 4519 anzi = ai[arow+1] - ai[arow]; 4520 aj = a->j + ai[arow]; 4521 aa = a->a + ai[arow]; 4522 nextaj = 0; 4523 for (j=0; nextaj<anzi; j++) { 4524 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4525 ba_i[j] += aa[nextaj++]; 4526 } 4527 } 4528 4529 /* add received vals into ba */ 4530 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4531 /* i-th row */ 4532 if (i == *nextrow[k]) { 4533 anzi = *(nextai[k]+1) - *nextai[k]; 4534 aj = buf_rj[k] + *(nextai[k]); 4535 aa = abuf_r[k] + *(nextai[k]); 4536 nextaj = 0; 4537 for (j=0; nextaj<anzi; j++) { 4538 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4539 ba_i[j] += aa[nextaj++]; 4540 } 4541 } 4542 nextrow[k]++; nextai[k]++; 4543 } 4544 } 4545 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4546 } 4547 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4548 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4549 4550 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4551 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4552 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4553 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4554 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4555 PetscFunctionReturn(0); 4556 } 4557 4558 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4559 { 4560 PetscErrorCode ierr; 4561 Mat B_mpi; 4562 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4563 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4564 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4565 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4566 PetscInt len,proc,*dnz,*onz,bs,cbs; 4567 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4568 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4569 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4570 MPI_Status *status; 4571 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4572 PetscBT lnkbt; 4573 Mat_Merge_SeqsToMPI *merge; 4574 PetscContainer container; 4575 4576 PetscFunctionBegin; 4577 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4578 4579 /* make sure it is a PETSc comm */ 4580 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4581 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4582 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4583 4584 ierr = PetscNew(&merge);CHKERRQ(ierr); 4585 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4586 4587 /* determine row ownership */ 4588 /*---------------------------------------------------------*/ 4589 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4590 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4591 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4592 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4593 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4594 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4595 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4596 4597 m = merge->rowmap->n; 4598 owners = merge->rowmap->range; 4599 4600 /* determine the number of messages to send, their lengths */ 4601 /*---------------------------------------------------------*/ 4602 len_s = merge->len_s; 4603 4604 len = 0; /* length of buf_si[] */ 4605 merge->nsend = 0; 4606 for (proc=0; proc<size; proc++) { 4607 len_si[proc] = 0; 4608 if (proc == rank) { 4609 len_s[proc] = 0; 4610 } else { 4611 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4612 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4613 } 4614 if (len_s[proc]) { 4615 merge->nsend++; 4616 nrows = 0; 4617 for (i=owners[proc]; i<owners[proc+1]; i++) { 4618 if (ai[i+1] > ai[i]) nrows++; 4619 } 4620 len_si[proc] = 2*(nrows+1); 4621 len += len_si[proc]; 4622 } 4623 } 4624 4625 /* determine the number and length of messages to receive for ij-structure */ 4626 /*-------------------------------------------------------------------------*/ 4627 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4628 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4629 4630 /* post the Irecv of j-structure */ 4631 /*-------------------------------*/ 4632 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4633 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4634 4635 /* post the Isend of j-structure */ 4636 /*--------------------------------*/ 4637 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4638 4639 for (proc=0, k=0; proc<size; proc++) { 4640 if (!len_s[proc]) continue; 4641 i = owners[proc]; 4642 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4643 k++; 4644 } 4645 4646 /* receives and sends of j-structure are complete */ 4647 /*------------------------------------------------*/ 4648 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4649 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4650 4651 /* send and recv i-structure */ 4652 /*---------------------------*/ 4653 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4654 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4655 4656 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4657 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4658 for (proc=0,k=0; proc<size; proc++) { 4659 if (!len_s[proc]) continue; 4660 /* form outgoing message for i-structure: 4661 buf_si[0]: nrows to be sent 4662 [1:nrows]: row index (global) 4663 [nrows+1:2*nrows+1]: i-structure index 4664 */ 4665 /*-------------------------------------------*/ 4666 nrows = len_si[proc]/2 - 1; 4667 buf_si_i = buf_si + nrows+1; 4668 buf_si[0] = nrows; 4669 buf_si_i[0] = 0; 4670 nrows = 0; 4671 for (i=owners[proc]; i<owners[proc+1]; i++) { 4672 anzi = ai[i+1] - ai[i]; 4673 if (anzi) { 4674 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4675 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4676 nrows++; 4677 } 4678 } 4679 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4680 k++; 4681 buf_si += len_si[proc]; 4682 } 4683 4684 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4685 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4686 4687 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4688 for (i=0; i<merge->nrecv; i++) { 4689 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); 4690 } 4691 4692 ierr = PetscFree(len_si);CHKERRQ(ierr); 4693 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4694 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4695 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4696 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4697 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4698 ierr = PetscFree(status);CHKERRQ(ierr); 4699 4700 /* compute a local seq matrix in each processor */ 4701 /*----------------------------------------------*/ 4702 /* allocate bi array and free space for accumulating nonzero column info */ 4703 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4704 bi[0] = 0; 4705 4706 /* create and initialize a linked list */ 4707 nlnk = N+1; 4708 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4709 4710 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4711 len = ai[owners[rank+1]] - ai[owners[rank]]; 4712 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4713 4714 current_space = free_space; 4715 4716 /* determine symbolic info for each local row */ 4717 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4718 4719 for (k=0; k<merge->nrecv; k++) { 4720 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4721 nrows = *buf_ri_k[k]; 4722 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4723 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4724 } 4725 4726 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4727 len = 0; 4728 for (i=0; i<m; i++) { 4729 bnzi = 0; 4730 /* add local non-zero cols of this proc's seqmat into lnk */ 4731 arow = owners[rank] + i; 4732 anzi = ai[arow+1] - ai[arow]; 4733 aj = a->j + ai[arow]; 4734 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4735 bnzi += nlnk; 4736 /* add received col data into lnk */ 4737 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4738 if (i == *nextrow[k]) { /* i-th row */ 4739 anzi = *(nextai[k]+1) - *nextai[k]; 4740 aj = buf_rj[k] + *nextai[k]; 4741 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4742 bnzi += nlnk; 4743 nextrow[k]++; nextai[k]++; 4744 } 4745 } 4746 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4747 4748 /* if free space is not available, make more free space */ 4749 if (current_space->local_remaining<bnzi) { 4750 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4751 nspacedouble++; 4752 } 4753 /* copy data into free space, then initialize lnk */ 4754 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4755 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4756 4757 current_space->array += bnzi; 4758 current_space->local_used += bnzi; 4759 current_space->local_remaining -= bnzi; 4760 4761 bi[i+1] = bi[i] + bnzi; 4762 } 4763 4764 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4765 4766 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4767 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4768 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4769 4770 /* create symbolic parallel matrix B_mpi */ 4771 /*---------------------------------------*/ 4772 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4773 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4774 if (n==PETSC_DECIDE) { 4775 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4776 } else { 4777 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4778 } 4779 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4780 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4781 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4782 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4783 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4784 4785 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4786 B_mpi->assembled = PETSC_FALSE; 4787 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4788 merge->bi = bi; 4789 merge->bj = bj; 4790 merge->buf_ri = buf_ri; 4791 merge->buf_rj = buf_rj; 4792 merge->coi = NULL; 4793 merge->coj = NULL; 4794 merge->owners_co = NULL; 4795 4796 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4797 4798 /* attach the supporting struct to B_mpi for reuse */ 4799 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4800 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4801 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4802 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4803 *mpimat = B_mpi; 4804 4805 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4806 PetscFunctionReturn(0); 4807 } 4808 4809 /*@C 4810 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4811 matrices from each processor 4812 4813 Collective on MPI_Comm 4814 4815 Input Parameters: 4816 + comm - the communicators the parallel matrix will live on 4817 . seqmat - the input sequential matrices 4818 . m - number of local rows (or PETSC_DECIDE) 4819 . n - number of local columns (or PETSC_DECIDE) 4820 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4821 4822 Output Parameter: 4823 . mpimat - the parallel matrix generated 4824 4825 Level: advanced 4826 4827 Notes: 4828 The dimensions of the sequential matrix in each processor MUST be the same. 4829 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4830 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4831 @*/ 4832 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4833 { 4834 PetscErrorCode ierr; 4835 PetscMPIInt size; 4836 4837 PetscFunctionBegin; 4838 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4839 if (size == 1) { 4840 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4841 if (scall == MAT_INITIAL_MATRIX) { 4842 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4843 } else { 4844 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4845 } 4846 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4847 PetscFunctionReturn(0); 4848 } 4849 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4850 if (scall == MAT_INITIAL_MATRIX) { 4851 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4852 } 4853 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4854 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4855 PetscFunctionReturn(0); 4856 } 4857 4858 /*@ 4859 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential matrix with 4860 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4861 with MatGetSize() 4862 4863 Not Collective 4864 4865 Input Parameters: 4866 + A - the matrix 4867 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4868 4869 Output Parameter: 4870 . A_loc - the local sequential matrix generated 4871 4872 Level: developer 4873 4874 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4875 4876 @*/ 4877 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4878 { 4879 PetscErrorCode ierr; 4880 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4881 Mat_SeqAIJ *mat,*a,*b; 4882 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4883 MatScalar *aa,*ba,*cam; 4884 PetscScalar *ca; 4885 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4886 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4887 PetscBool match; 4888 MPI_Comm comm; 4889 PetscMPIInt size; 4890 4891 PetscFunctionBegin; 4892 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4893 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4894 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4895 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4896 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4897 4898 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4899 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4900 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4901 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4902 aa = a->a; ba = b->a; 4903 if (scall == MAT_INITIAL_MATRIX) { 4904 if (size == 1) { 4905 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4906 PetscFunctionReturn(0); 4907 } 4908 4909 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4910 ci[0] = 0; 4911 for (i=0; i<am; i++) { 4912 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4913 } 4914 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4915 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4916 k = 0; 4917 for (i=0; i<am; i++) { 4918 ncols_o = bi[i+1] - bi[i]; 4919 ncols_d = ai[i+1] - ai[i]; 4920 /* off-diagonal portion of A */ 4921 for (jo=0; jo<ncols_o; jo++) { 4922 col = cmap[*bj]; 4923 if (col >= cstart) break; 4924 cj[k] = col; bj++; 4925 ca[k++] = *ba++; 4926 } 4927 /* diagonal portion of A */ 4928 for (j=0; j<ncols_d; j++) { 4929 cj[k] = cstart + *aj++; 4930 ca[k++] = *aa++; 4931 } 4932 /* off-diagonal portion of A */ 4933 for (j=jo; j<ncols_o; j++) { 4934 cj[k] = cmap[*bj++]; 4935 ca[k++] = *ba++; 4936 } 4937 } 4938 /* put together the new matrix */ 4939 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4940 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4941 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4942 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4943 mat->free_a = PETSC_TRUE; 4944 mat->free_ij = PETSC_TRUE; 4945 mat->nonew = 0; 4946 } else if (scall == MAT_REUSE_MATRIX) { 4947 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4948 ci = mat->i; cj = mat->j; cam = mat->a; 4949 for (i=0; i<am; i++) { 4950 /* off-diagonal portion of A */ 4951 ncols_o = bi[i+1] - bi[i]; 4952 for (jo=0; jo<ncols_o; jo++) { 4953 col = cmap[*bj]; 4954 if (col >= cstart) break; 4955 *cam++ = *ba++; bj++; 4956 } 4957 /* diagonal portion of A */ 4958 ncols_d = ai[i+1] - ai[i]; 4959 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4960 /* off-diagonal portion of A */ 4961 for (j=jo; j<ncols_o; j++) { 4962 *cam++ = *ba++; bj++; 4963 } 4964 } 4965 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4966 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4967 PetscFunctionReturn(0); 4968 } 4969 4970 /*@C 4971 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4972 4973 Not Collective 4974 4975 Input Parameters: 4976 + A - the matrix 4977 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4978 - row, col - index sets of rows and columns to extract (or NULL) 4979 4980 Output Parameter: 4981 . A_loc - the local sequential matrix generated 4982 4983 Level: developer 4984 4985 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4986 4987 @*/ 4988 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4989 { 4990 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4991 PetscErrorCode ierr; 4992 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4993 IS isrowa,iscola; 4994 Mat *aloc; 4995 PetscBool match; 4996 4997 PetscFunctionBegin; 4998 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4999 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 5000 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 5001 if (!row) { 5002 start = A->rmap->rstart; end = A->rmap->rend; 5003 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 5004 } else { 5005 isrowa = *row; 5006 } 5007 if (!col) { 5008 start = A->cmap->rstart; 5009 cmap = a->garray; 5010 nzA = a->A->cmap->n; 5011 nzB = a->B->cmap->n; 5012 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5013 ncols = 0; 5014 for (i=0; i<nzB; i++) { 5015 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5016 else break; 5017 } 5018 imark = i; 5019 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 5020 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 5021 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 5022 } else { 5023 iscola = *col; 5024 } 5025 if (scall != MAT_INITIAL_MATRIX) { 5026 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 5027 aloc[0] = *A_loc; 5028 } 5029 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 5030 *A_loc = aloc[0]; 5031 ierr = PetscFree(aloc);CHKERRQ(ierr); 5032 if (!row) { 5033 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 5034 } 5035 if (!col) { 5036 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 5037 } 5038 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 5039 PetscFunctionReturn(0); 5040 } 5041 5042 /*@C 5043 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 5044 5045 Collective on Mat 5046 5047 Input Parameters: 5048 + A,B - the matrices in mpiaij format 5049 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5050 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 5051 5052 Output Parameter: 5053 + rowb, colb - index sets of rows and columns of B to extract 5054 - B_seq - the sequential matrix generated 5055 5056 Level: developer 5057 5058 @*/ 5059 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 5060 { 5061 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5062 PetscErrorCode ierr; 5063 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 5064 IS isrowb,iscolb; 5065 Mat *bseq=NULL; 5066 5067 PetscFunctionBegin; 5068 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5069 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); 5070 } 5071 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5072 5073 if (scall == MAT_INITIAL_MATRIX) { 5074 start = A->cmap->rstart; 5075 cmap = a->garray; 5076 nzA = a->A->cmap->n; 5077 nzB = a->B->cmap->n; 5078 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5079 ncols = 0; 5080 for (i=0; i<nzB; i++) { /* row < local row index */ 5081 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5082 else break; 5083 } 5084 imark = i; 5085 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 5086 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5087 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 5088 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 5089 } else { 5090 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5091 isrowb = *rowb; iscolb = *colb; 5092 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 5093 bseq[0] = *B_seq; 5094 } 5095 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 5096 *B_seq = bseq[0]; 5097 ierr = PetscFree(bseq);CHKERRQ(ierr); 5098 if (!rowb) { 5099 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 5100 } else { 5101 *rowb = isrowb; 5102 } 5103 if (!colb) { 5104 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 5105 } else { 5106 *colb = iscolb; 5107 } 5108 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5109 PetscFunctionReturn(0); 5110 } 5111 5112 /* 5113 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 5114 of the OFF-DIAGONAL portion of local A 5115 5116 Collective on Mat 5117 5118 Input Parameters: 5119 + A,B - the matrices in mpiaij format 5120 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5121 5122 Output Parameter: 5123 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5124 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5125 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5126 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5127 5128 Level: developer 5129 5130 */ 5131 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5132 { 5133 VecScatter_MPI_General *gen_to,*gen_from; 5134 PetscErrorCode ierr; 5135 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5136 Mat_SeqAIJ *b_oth; 5137 VecScatter ctx; 5138 MPI_Comm comm; 5139 PetscMPIInt *rprocs,*sprocs,tag,rank; 5140 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5141 PetscInt *rvalues,*svalues; 5142 MatScalar *b_otha,*bufa,*bufA; 5143 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5144 MPI_Request *rwaits = NULL,*swaits = NULL; 5145 MPI_Status *sstatus,rstatus; 5146 PetscMPIInt jj,size; 5147 PetscInt *cols,sbs,rbs; 5148 PetscScalar *vals; 5149 5150 PetscFunctionBegin; 5151 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5152 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5153 5154 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5155 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); 5156 } 5157 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5158 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5159 5160 if (size == 1) { 5161 startsj_s = NULL; 5162 bufa_ptr = NULL; 5163 *B_oth = NULL; 5164 PetscFunctionReturn(0); 5165 } 5166 5167 if (!a->Mvctx_mpi1) { /* create a->Mvctx_mpi1 to be used for Mat-Mat ops */ 5168 a->Mvctx_mpi1_flg = PETSC_TRUE; 5169 ierr = MatSetUpMultiply_MPIAIJ(A);CHKERRQ(ierr); 5170 } 5171 ctx = a->Mvctx_mpi1; 5172 tag = ((PetscObject)ctx)->tag; 5173 5174 gen_to = (VecScatter_MPI_General*)ctx->todata; 5175 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5176 nrecvs = gen_from->n; 5177 nsends = gen_to->n; 5178 5179 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 5180 srow = gen_to->indices; /* local row index to be sent */ 5181 sstarts = gen_to->starts; 5182 sprocs = gen_to->procs; 5183 sstatus = gen_to->sstatus; 5184 sbs = gen_to->bs; 5185 rstarts = gen_from->starts; 5186 rprocs = gen_from->procs; 5187 rbs = gen_from->bs; 5188 5189 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5190 if (scall == MAT_INITIAL_MATRIX) { 5191 /* i-array */ 5192 /*---------*/ 5193 /* post receives */ 5194 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 5195 for (i=0; i<nrecvs; i++) { 5196 rowlen = rvalues + rstarts[i]*rbs; 5197 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5198 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5199 } 5200 5201 /* pack the outgoing message */ 5202 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 5203 5204 sstartsj[0] = 0; 5205 rstartsj[0] = 0; 5206 len = 0; /* total length of j or a array to be sent */ 5207 k = 0; 5208 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 5209 for (i=0; i<nsends; i++) { 5210 rowlen = svalues + sstarts[i]*sbs; 5211 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5212 for (j=0; j<nrows; j++) { 5213 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5214 for (l=0; l<sbs; l++) { 5215 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5216 5217 rowlen[j*sbs+l] = ncols; 5218 5219 len += ncols; 5220 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5221 } 5222 k++; 5223 } 5224 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5225 5226 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5227 } 5228 /* recvs and sends of i-array are completed */ 5229 i = nrecvs; 5230 while (i--) { 5231 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5232 } 5233 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5234 ierr = PetscFree(svalues);CHKERRQ(ierr); 5235 5236 /* allocate buffers for sending j and a arrays */ 5237 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5238 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5239 5240 /* create i-array of B_oth */ 5241 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5242 5243 b_othi[0] = 0; 5244 len = 0; /* total length of j or a array to be received */ 5245 k = 0; 5246 for (i=0; i<nrecvs; i++) { 5247 rowlen = rvalues + rstarts[i]*rbs; 5248 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5249 for (j=0; j<nrows; j++) { 5250 b_othi[k+1] = b_othi[k] + rowlen[j]; 5251 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5252 k++; 5253 } 5254 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5255 } 5256 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5257 5258 /* allocate space for j and a arrrays of B_oth */ 5259 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5260 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5261 5262 /* j-array */ 5263 /*---------*/ 5264 /* post receives of j-array */ 5265 for (i=0; i<nrecvs; i++) { 5266 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5267 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5268 } 5269 5270 /* pack the outgoing message j-array */ 5271 k = 0; 5272 for (i=0; i<nsends; i++) { 5273 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5274 bufJ = bufj+sstartsj[i]; 5275 for (j=0; j<nrows; j++) { 5276 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5277 for (ll=0; ll<sbs; ll++) { 5278 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5279 for (l=0; l<ncols; l++) { 5280 *bufJ++ = cols[l]; 5281 } 5282 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5283 } 5284 } 5285 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5286 } 5287 5288 /* recvs and sends of j-array are completed */ 5289 i = nrecvs; 5290 while (i--) { 5291 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5292 } 5293 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5294 } else if (scall == MAT_REUSE_MATRIX) { 5295 sstartsj = *startsj_s; 5296 rstartsj = *startsj_r; 5297 bufa = *bufa_ptr; 5298 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5299 b_otha = b_oth->a; 5300 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5301 5302 /* a-array */ 5303 /*---------*/ 5304 /* post receives of a-array */ 5305 for (i=0; i<nrecvs; i++) { 5306 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5307 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5308 } 5309 5310 /* pack the outgoing message a-array */ 5311 k = 0; 5312 for (i=0; i<nsends; i++) { 5313 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5314 bufA = bufa+sstartsj[i]; 5315 for (j=0; j<nrows; j++) { 5316 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5317 for (ll=0; ll<sbs; ll++) { 5318 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5319 for (l=0; l<ncols; l++) { 5320 *bufA++ = vals[l]; 5321 } 5322 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5323 } 5324 } 5325 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5326 } 5327 /* recvs and sends of a-array are completed */ 5328 i = nrecvs; 5329 while (i--) { 5330 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5331 } 5332 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5333 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5334 5335 if (scall == MAT_INITIAL_MATRIX) { 5336 /* put together the new matrix */ 5337 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5338 5339 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5340 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5341 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5342 b_oth->free_a = PETSC_TRUE; 5343 b_oth->free_ij = PETSC_TRUE; 5344 b_oth->nonew = 0; 5345 5346 ierr = PetscFree(bufj);CHKERRQ(ierr); 5347 if (!startsj_s || !bufa_ptr) { 5348 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5349 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5350 } else { 5351 *startsj_s = sstartsj; 5352 *startsj_r = rstartsj; 5353 *bufa_ptr = bufa; 5354 } 5355 } 5356 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5357 PetscFunctionReturn(0); 5358 } 5359 5360 /*@C 5361 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5362 5363 Not Collective 5364 5365 Input Parameters: 5366 . A - The matrix in mpiaij format 5367 5368 Output Parameter: 5369 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5370 . colmap - A map from global column index to local index into lvec 5371 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5372 5373 Level: developer 5374 5375 @*/ 5376 #if defined(PETSC_USE_CTABLE) 5377 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5378 #else 5379 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5380 #endif 5381 { 5382 Mat_MPIAIJ *a; 5383 5384 PetscFunctionBegin; 5385 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5386 PetscValidPointer(lvec, 2); 5387 PetscValidPointer(colmap, 3); 5388 PetscValidPointer(multScatter, 4); 5389 a = (Mat_MPIAIJ*) A->data; 5390 if (lvec) *lvec = a->lvec; 5391 if (colmap) *colmap = a->colmap; 5392 if (multScatter) *multScatter = a->Mvctx; 5393 PetscFunctionReturn(0); 5394 } 5395 5396 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5397 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5398 #if defined(PETSC_HAVE_MKL_SPARSE) 5399 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJMKL(Mat,MatType,MatReuse,Mat*); 5400 #endif 5401 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5402 #if defined(PETSC_HAVE_ELEMENTAL) 5403 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5404 #endif 5405 #if defined(PETSC_HAVE_HYPRE) 5406 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5407 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5408 #endif 5409 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5410 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISELL(Mat,MatType,MatReuse,Mat*); 5411 5412 /* 5413 Computes (B'*A')' since computing B*A directly is untenable 5414 5415 n p p 5416 ( ) ( ) ( ) 5417 m ( A ) * n ( B ) = m ( C ) 5418 ( ) ( ) ( ) 5419 5420 */ 5421 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5422 { 5423 PetscErrorCode ierr; 5424 Mat At,Bt,Ct; 5425 5426 PetscFunctionBegin; 5427 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5428 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5429 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5430 ierr = MatDestroy(&At);CHKERRQ(ierr); 5431 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5432 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5433 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5434 PetscFunctionReturn(0); 5435 } 5436 5437 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5438 { 5439 PetscErrorCode ierr; 5440 PetscInt m=A->rmap->n,n=B->cmap->n; 5441 Mat Cmat; 5442 5443 PetscFunctionBegin; 5444 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); 5445 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5446 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5447 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5448 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5449 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5450 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5451 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5452 5453 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5454 5455 *C = Cmat; 5456 PetscFunctionReturn(0); 5457 } 5458 5459 /* ----------------------------------------------------------------*/ 5460 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5461 { 5462 PetscErrorCode ierr; 5463 5464 PetscFunctionBegin; 5465 if (scall == MAT_INITIAL_MATRIX) { 5466 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5467 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5468 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5469 } 5470 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5471 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5472 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5473 PetscFunctionReturn(0); 5474 } 5475 5476 /*MC 5477 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5478 5479 Options Database Keys: 5480 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5481 5482 Level: beginner 5483 5484 .seealso: MatCreateAIJ() 5485 M*/ 5486 5487 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5488 { 5489 Mat_MPIAIJ *b; 5490 PetscErrorCode ierr; 5491 PetscMPIInt size; 5492 5493 PetscFunctionBegin; 5494 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5495 5496 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5497 B->data = (void*)b; 5498 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5499 B->assembled = PETSC_FALSE; 5500 B->insertmode = NOT_SET_VALUES; 5501 b->size = size; 5502 5503 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5504 5505 /* build cache for off array entries formed */ 5506 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5507 5508 b->donotstash = PETSC_FALSE; 5509 b->colmap = 0; 5510 b->garray = 0; 5511 b->roworiented = PETSC_TRUE; 5512 5513 /* stuff used for matrix vector multiply */ 5514 b->lvec = NULL; 5515 b->Mvctx = NULL; 5516 5517 /* stuff for MatGetRow() */ 5518 b->rowindices = 0; 5519 b->rowvalues = 0; 5520 b->getrowactive = PETSC_FALSE; 5521 5522 /* flexible pointer used in CUSP/CUSPARSE classes */ 5523 b->spptr = NULL; 5524 5525 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5526 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5527 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5528 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5529 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5530 ierr = PetscObjectComposeFunction((PetscObject)B,"MatResetPreallocation_C",MatResetPreallocation_MPIAIJ);CHKERRQ(ierr); 5531 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5532 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5533 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5534 #if defined(PETSC_HAVE_MKL_SPARSE) 5535 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijmkl_C",MatConvert_MPIAIJ_MPIAIJMKL);CHKERRQ(ierr); 5536 #endif 5537 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5538 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5539 #if defined(PETSC_HAVE_ELEMENTAL) 5540 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5541 #endif 5542 #if defined(PETSC_HAVE_HYPRE) 5543 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5544 #endif 5545 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5546 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisell_C",MatConvert_MPIAIJ_MPISELL);CHKERRQ(ierr); 5547 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5548 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5549 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5550 #if defined(PETSC_HAVE_HYPRE) 5551 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5552 #endif 5553 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5554 PetscFunctionReturn(0); 5555 } 5556 5557 /*@C 5558 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5559 and "off-diagonal" part of the matrix in CSR format. 5560 5561 Collective on MPI_Comm 5562 5563 Input Parameters: 5564 + comm - MPI communicator 5565 . m - number of local rows (Cannot be PETSC_DECIDE) 5566 . n - This value should be the same as the local size used in creating the 5567 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5568 calculated if N is given) For square matrices n is almost always m. 5569 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5570 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5571 . i - row indices for "diagonal" portion of matrix 5572 . j - column indices 5573 . a - matrix values 5574 . oi - row indices for "off-diagonal" portion of matrix 5575 . oj - column indices 5576 - oa - matrix values 5577 5578 Output Parameter: 5579 . mat - the matrix 5580 5581 Level: advanced 5582 5583 Notes: 5584 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5585 must free the arrays once the matrix has been destroyed and not before. 5586 5587 The i and j indices are 0 based 5588 5589 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5590 5591 This sets local rows and cannot be used to set off-processor values. 5592 5593 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5594 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5595 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5596 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5597 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5598 communication if it is known that only local entries will be set. 5599 5600 .keywords: matrix, aij, compressed row, sparse, parallel 5601 5602 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5603 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5604 @*/ 5605 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) 5606 { 5607 PetscErrorCode ierr; 5608 Mat_MPIAIJ *maij; 5609 5610 PetscFunctionBegin; 5611 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5612 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5613 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5614 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5615 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5616 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5617 maij = (Mat_MPIAIJ*) (*mat)->data; 5618 5619 (*mat)->preallocated = PETSC_TRUE; 5620 5621 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5622 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5623 5624 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5625 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5626 5627 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5628 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5629 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5630 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5631 5632 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5633 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5634 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5635 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5636 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5637 PetscFunctionReturn(0); 5638 } 5639 5640 /* 5641 Special version for direct calls from Fortran 5642 */ 5643 #include <petsc/private/fortranimpl.h> 5644 5645 /* Change these macros so can be used in void function */ 5646 #undef CHKERRQ 5647 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5648 #undef SETERRQ2 5649 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5650 #undef SETERRQ3 5651 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5652 #undef SETERRQ 5653 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5654 5655 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5656 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5657 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5658 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5659 #else 5660 #endif 5661 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) 5662 { 5663 Mat mat = *mmat; 5664 PetscInt m = *mm, n = *mn; 5665 InsertMode addv = *maddv; 5666 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5667 PetscScalar value; 5668 PetscErrorCode ierr; 5669 5670 MatCheckPreallocated(mat,1); 5671 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5672 5673 #if defined(PETSC_USE_DEBUG) 5674 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5675 #endif 5676 { 5677 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5678 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5679 PetscBool roworiented = aij->roworiented; 5680 5681 /* Some Variables required in the macro */ 5682 Mat A = aij->A; 5683 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5684 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5685 MatScalar *aa = a->a; 5686 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5687 Mat B = aij->B; 5688 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5689 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5690 MatScalar *ba = b->a; 5691 5692 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5693 PetscInt nonew = a->nonew; 5694 MatScalar *ap1,*ap2; 5695 5696 PetscFunctionBegin; 5697 for (i=0; i<m; i++) { 5698 if (im[i] < 0) continue; 5699 #if defined(PETSC_USE_DEBUG) 5700 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); 5701 #endif 5702 if (im[i] >= rstart && im[i] < rend) { 5703 row = im[i] - rstart; 5704 lastcol1 = -1; 5705 rp1 = aj + ai[row]; 5706 ap1 = aa + ai[row]; 5707 rmax1 = aimax[row]; 5708 nrow1 = ailen[row]; 5709 low1 = 0; 5710 high1 = nrow1; 5711 lastcol2 = -1; 5712 rp2 = bj + bi[row]; 5713 ap2 = ba + bi[row]; 5714 rmax2 = bimax[row]; 5715 nrow2 = bilen[row]; 5716 low2 = 0; 5717 high2 = nrow2; 5718 5719 for (j=0; j<n; j++) { 5720 if (roworiented) value = v[i*n+j]; 5721 else value = v[i+j*m]; 5722 if (in[j] >= cstart && in[j] < cend) { 5723 col = in[j] - cstart; 5724 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5725 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5726 } else if (in[j] < 0) continue; 5727 #if defined(PETSC_USE_DEBUG) 5728 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); 5729 #endif 5730 else { 5731 if (mat->was_assembled) { 5732 if (!aij->colmap) { 5733 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5734 } 5735 #if defined(PETSC_USE_CTABLE) 5736 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5737 col--; 5738 #else 5739 col = aij->colmap[in[j]] - 1; 5740 #endif 5741 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5742 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5743 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5744 col = in[j]; 5745 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5746 B = aij->B; 5747 b = (Mat_SeqAIJ*)B->data; 5748 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5749 rp2 = bj + bi[row]; 5750 ap2 = ba + bi[row]; 5751 rmax2 = bimax[row]; 5752 nrow2 = bilen[row]; 5753 low2 = 0; 5754 high2 = nrow2; 5755 bm = aij->B->rmap->n; 5756 ba = b->a; 5757 } 5758 } else col = in[j]; 5759 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5760 } 5761 } 5762 } else if (!aij->donotstash) { 5763 if (roworiented) { 5764 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5765 } else { 5766 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5767 } 5768 } 5769 } 5770 } 5771 PetscFunctionReturnVoid(); 5772 } 5773 5774