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