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 //printf("[%d] n %d, isstart %d\n",rank,n,isstart); 3004 3005 /* (1) iscol is a sub-vector of mat, pad it with '-1.' to form a full vector x */ 3006 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3007 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3008 3009 ierr = MatCreateVecs(mat,&cmap,NULL);CHKERRQ(ierr); 3010 ierr = VecSet(cmap,-1.0);CHKERRQ(ierr); 3011 3012 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3013 3014 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3015 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3016 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3017 for (i=0; i<n; i++) { 3018 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3019 cmaparray[is_idx[i]-cstart] = i + isstart; 3020 } 3021 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3022 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3023 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3024 3025 /* (2) scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3026 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3027 3028 ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3029 ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3030 3031 ierr = VecScatterBegin(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3032 ierr = VecScatterEnd(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3033 3034 if (lvec->map->n != Bn) SETERRQ2(PETSC_COMM_SELF,0,"n(lvec) %d != Bn %d",lvec->map->n,Bn); 3035 if (rank == -1) { 3036 printf("[%d] lvec:\n",rank); 3037 ierr = VecView(lvec,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3038 } 3039 3040 /* (3) create scalable iscol_sub (a subset of iscol) and iscmap */ 3041 ierr = PetscMalloc2(n+Bn,&idx,n+Bn,&cmap1);CHKERRQ(ierr); 3042 count = 0; 3043 3044 /* A part */ 3045 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3046 j = cstart; 3047 for (i=0; i<n; i++) { 3048 if (j >= cend) break; 3049 if (is_idx[i] == j) { 3050 idx[count] = j; 3051 cmap1[count] = i + isstart; /* column index in submat */ 3052 count++; j++; 3053 } else if (is_idx[i] > j) { 3054 while (is_idx[i] > j && j < cend-1) j++; 3055 if (is_idx[i] == j) { 3056 idx[count] = j; 3057 cmap1[count] = i + isstart; /* column index in submat */ 3058 count++; j++; 3059 } 3060 } 3061 } 3062 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3063 3064 /* B part */ 3065 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3066 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3067 j = 0; 3068 for (i=0; i<Bn; i++) { 3069 if (j >= Bn) break; 3070 if ((PetscInt)xarray[i] == garray[j]) { 3071 idx[count] = garray[j]; 3072 cmap1[count] = cmaparray[i]; /* column index in submat */ 3073 count++; j++; 3074 } else if ((PetscInt)xarray[i] > garray[j]) { 3075 while ((PetscInt)xarray[i] > garray[j] && j < Bn-1) j++; 3076 if ((PetscInt)xarray[i] == garray[j]) { 3077 idx[count] = garray[j]; 3078 cmap1[count] = cmaparray[i]; /* column index in submat */ 3079 count++; j++; 3080 } 3081 } 3082 } 3083 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3084 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3085 //printf("[%d] n %d + Bn %d = %d; count %d, isN %d, matN %d\n",rank,n,Bn,n+Bn,count,N,mat->cmap->N); 3086 3087 ierr = PetscSortInt(count,idx);CHKERRQ(ierr); //should idx be sorted with cmap1??? 3088 ierr = PetscSortInt(count,cmap1);CHKERRQ(ierr); 3089 3090 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,iscol_sub);CHKERRQ(ierr); 3091 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,cmap1,PETSC_COPY_VALUES,iscmap);CHKERRQ(ierr); 3092 3093 if (rank == -1) { 3094 printf("[%d] iscmap:\n",rank); 3095 ierr = ISView(*iscmap,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3096 } 3097 3098 ierr = PetscFree2(idx,cmap1);CHKERRQ(ierr); 3099 ierr = VecDestroy(&x);CHKERRQ(ierr); 3100 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3101 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3102 PetscFunctionReturn(0); 3103 } 3104 3105 extern PetscErrorCode MatCreateSubMatrix_MPIAIJ_Private_SameDist(Mat,IS,IS,IS,PetscInt,MatReuse,Mat*); 3106 3107 /* isrow has same processor distribution as mat, avoid iscol_local which uses O(mat->cmap->N) ctable */ 3108 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3109 { 3110 PetscErrorCode ierr; 3111 IS iscol_local; 3112 PetscInt csize; 3113 MPI_Comm comm; 3114 PetscMPIInt rank; 3115 PetscBool sorted,sameColDist = PETSC_FALSE,tsameColDist; 3116 PetscInt n,i,j,cstart,cend,N; 3117 3118 PetscFunctionBegin; 3119 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3120 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3121 //ierr = ISView(iscol,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3122 3123 /* If iscol has same processor distribution as mat, then use a scalable routine */ 3124 ierr = ISSorted(iscol,&sorted);CHKERRQ(ierr); //must be locally sorted??? 3125 if (!sorted) printf("[%d] iscol !sorted\n",rank); 3126 3127 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3128 ierr = ISGetSize(iscol,&N);CHKERRQ(ierr); 3129 if (!n) { 3130 sameColDist = PETSC_TRUE; 3131 } else { 3132 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3133 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3134 if (i >= cstart && j < cend) sameColDist = PETSC_TRUE; 3135 } 3136 ierr = MPIU_Allreduce(&sameColDist,&tsameColDist,1,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3137 if (!rank) printf("[%d]..SubMatrix_MPIAIJ_SameDist ...reuse %d, sameColDist for column %d \n",rank,call,tsameColDist); 3138 3139 if (tsameColDist) { /* get iscol_sub without calling ISAllGather() */ 3140 IS iscol_sub,iscmap; 3141 ierr = ISGetSeqIS_SameDist_Private(mat,iscol,&iscol_sub,&iscmap);CHKERRQ(ierr); 3142 3143 if (rank == -1) { 3144 printf("[%d] iscol_sub:\n",rank); 3145 ierr = ISView(iscol_sub,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3146 3147 //printf("[%d] iscmap:\n",rank); 3148 //ierr = ISView(iscmap,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3149 } 3150 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3151 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3152 } 3153 //----------------------------------------------- 3154 3155 /* Get nonscalable iscol_local -- will replace it with iscol_sub! */ 3156 if (call == MAT_REUSE_MATRIX) { 3157 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3158 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3159 } else { 3160 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3161 PetscBool sorted; 3162 ierr = ISSorted(iscol_local,&sorted);CHKERRQ(ierr); 3163 if (!sorted) printf("[%d] iscol_local !sorted\n",rank); 3164 } 3165 3166 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3167 ierr = MatCreateSubMatrix_MPIAIJ_Private_SameDist(mat,isrow,iscol,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3168 3169 if (call == MAT_INITIAL_MATRIX) { 3170 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3171 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3172 } 3173 PetscFunctionReturn(0); 3174 } 3175 3176 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3177 { 3178 PetscErrorCode ierr; 3179 IS iscol_local; 3180 PetscInt csize; 3181 PetscInt n,i,j,rstart,rend; 3182 PetscBool sameRowDist=PETSC_FALSE,tsameRowDist; 3183 MPI_Comm comm; 3184 3185 PetscFunctionBegin; 3186 /* If isrow has same processor distribution as mat, then use a scalable routine */ 3187 if (call == MAT_REUSE_MATRIX) { 3188 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3189 if (iscol_local) tsameRowDist = PETSC_TRUE; 3190 } else { 3191 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3192 if (!n) { 3193 sameRowDist = PETSC_TRUE; 3194 } else { 3195 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3196 ierr = MatGetOwnershipRange(mat,&rstart,&rend);CHKERRQ(ierr); 3197 if (i >= rstart && j < rend) sameRowDist = PETSC_TRUE; 3198 } 3199 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3200 ierr = MPIU_Allreduce(&sameRowDist,&tsameRowDist,1,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3201 } 3202 3203 if (tsameRowDist) { 3204 ierr = MatCreateSubMatrix_MPIAIJ_SameDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3205 PetscFunctionReturn(0); 3206 } 3207 3208 /* General case */ 3209 /* --------------------------------------- */ 3210 if (call == MAT_REUSE_MATRIX) { 3211 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3212 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3213 } else { 3214 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3215 } 3216 3217 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3218 ierr = MatCreateSubMatrix_MPIAIJ_Private(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3219 3220 if (call == MAT_INITIAL_MATRIX) { 3221 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3222 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3223 } 3224 PetscFunctionReturn(0); 3225 } 3226 3227 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat*); 3228 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3229 3230 PetscErrorCode MatCreateSubMatrix_MPIAIJ_Private_SameDist(Mat mat,IS isrow,IS iscolmpi,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3231 { 3232 PetscErrorCode ierr; 3233 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3234 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3235 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3236 Mat M,Msub,B=a->B; 3237 MatScalar *aa; 3238 Mat_SeqAIJ *aij; 3239 PetscInt *garray = a->garray,*colsub; 3240 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3241 IS iscol_sub,iscmap; 3242 const PetscInt *is_idx,*cmap; 3243 3244 PetscFunctionBegin; 3245 MPI_Comm comm; 3246 PetscMPIInt rank; 3247 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3248 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3249 //printf("SubMatrix_MPIAIJ_Private_SameDist ...\n"); 3250 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); /* iscol should be sequential */ 3251 3252 if (call == MAT_INITIAL_MATRIX) { 3253 /* create scalable iscol_sub (a subset of iscol) */ 3254 PetscInt *idx,*cmap1; 3255 3256 PetscBool sorted; 3257 ierr = ISSorted(iscol,&sorted);CHKERRQ(ierr); 3258 if (!sorted) printf("iscol_local !sorted\n"); 3259 3260 ierr = PetscMalloc2(n,&idx,n,&cmap1);CHKERRQ(ierr); 3261 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3262 count = 0; 3263 3264 /* A part */ 3265 j = cstart; 3266 for (i=0; i<n; i++) { 3267 if (j >= cend) break; 3268 if (is_idx[i] == j) { 3269 idx[count] = j; 3270 cmap1[count] = i; /* column index in submat */ 3271 count++; j++; 3272 } else if (is_idx[i] > j) { 3273 while (is_idx[i] > j && j < cend-1) j++; 3274 if (is_idx[i] == j) { 3275 idx[count] = j; 3276 cmap1[count] = i; /* column index in submat */ 3277 count++; j++; 3278 } 3279 } 3280 } 3281 3282 /* B part */ 3283 j = 0; 3284 for (i=0; i<n; i++) { 3285 if (j >= Bn) break; 3286 if (is_idx[i] == garray[j]) { 3287 idx[count] = garray[j]; 3288 cmap1[count] = i; /* column index in submat */ 3289 count++; j++; 3290 } else if (is_idx[i] > garray[j]) { 3291 while (is_idx[i] > garray[j] && j < Bn-1) j++; 3292 if (is_idx[i] == garray[j]) { 3293 idx[count] = garray[j]; 3294 cmap1[count] = i; /* column index in submat */ 3295 count++; j++; 3296 } 3297 } 3298 } 3299 ierr = PetscSortInt(count,cmap1);CHKERRQ(ierr); 3300 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3301 3302 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol),count,idx,PETSC_COPY_VALUES,&iscol_sub);CHKERRQ(ierr); 3303 ierr = ISSort(iscol_sub);CHKERRQ(ierr); 3304 3305 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol),count,cmap1,PETSC_COPY_VALUES,&iscmap);CHKERRQ(ierr); 3306 ierr = PetscFree2(idx,cmap1);CHKERRQ(ierr); 3307 3308 //printf("\n[%d] old count %d, isN %d, matN %d\n",rank,count,n,mat->cmap->N); 3309 if (rank == -1) { 3310 printf("\n[%d] old iscol_sub:\n",rank); 3311 ierr = ISView(iscol_sub,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3312 3313 //printf("\n[%d] old iscmap:\n",rank); 3314 //ierr = ISView(iscmap,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3315 } 3316 3317 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3318 3319 } else { /* call == MAT_REUSE_MATRIX */ 3320 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3321 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3322 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3323 3324 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3325 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3326 3327 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3328 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3329 3330 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3331 } 3332 3333 aij = (Mat_SeqAIJ*)(Msub)->data; 3334 ii = aij->i; 3335 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3336 3337 /* 3338 m - number of local rows 3339 n - number of columns (same on all processors) 3340 rstart - first row in new global matrix generated 3341 */ 3342 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3343 3344 if (call == MAT_INITIAL_MATRIX) { 3345 MPI_Comm comm; 3346 PetscMPIInt rank,size; 3347 3348 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3349 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3350 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3351 3352 /* 3353 Determine the number of non-zeros in the diagonal and off-diagonal 3354 portions of the matrix in order to do correct preallocation 3355 */ 3356 3357 /* first get start and end of "diagonal" columns */ 3358 if (csize == PETSC_DECIDE) { 3359 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3360 if (mglobal == n) { /* square matrix */ 3361 nlocal = m; 3362 } else { 3363 nlocal = n/size + ((n % size) > rank); 3364 } 3365 } else { 3366 nlocal = csize; 3367 } 3368 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3369 rstart = rend - nlocal; 3370 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); 3371 3372 /* next, compute all the lengths */ 3373 jj = aij->j; 3374 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3375 olens = dlens + m; 3376 for (i=0; i<m; i++) { 3377 jend = ii[i+1] - ii[i]; 3378 olen = 0; 3379 dlen = 0; 3380 for (j=0; j<jend; j++) { 3381 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3382 else dlen++; 3383 jj++; 3384 } 3385 olens[i] = olen; 3386 dlens[i] = dlen; 3387 } 3388 ierr = MatGetBlockSizes(Msub,&bs,&cbs);CHKERRQ(ierr); 3389 3390 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3391 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3392 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3393 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3394 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3395 ierr = PetscFree(dlens);CHKERRQ(ierr); 3396 } else { 3397 M = *newmat; 3398 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3399 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3400 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3401 /* 3402 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3403 rather than the slower MatSetValues(). 3404 */ 3405 M->was_assembled = PETSC_TRUE; 3406 M->assembled = PETSC_FALSE; 3407 } 3408 3409 /* set values of Msub to *newmat */ 3410 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3411 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3412 3413 jj = aij->j; 3414 aa = aij->a; 3415 for (i=0; i<m; i++) { 3416 row = rstart + i; 3417 nz = ii[i+1] - ii[i]; 3418 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3419 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3420 jj += nz; aa += nz; 3421 } 3422 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3423 3424 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3425 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3426 *newmat = M; 3427 3428 ierr = PetscFree(colsub);CHKERRQ(ierr); 3429 3430 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3431 if (call == MAT_INITIAL_MATRIX) { 3432 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3433 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3434 3435 ierr = PetscObjectCompose((PetscObject)M,"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3436 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3437 3438 ierr = PetscObjectCompose((PetscObject)M,"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3439 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3440 } 3441 PetscFunctionReturn(0); 3442 } 3443 3444 /* 3445 Not great since it makes two copies of the submatrix, first an SeqAIJ 3446 in local and then by concatenating the local matrices the end result. 3447 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3448 3449 Note: This requires a sequential iscol with all indices. 3450 */ 3451 PetscErrorCode MatCreateSubMatrix_MPIAIJ_Private(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3452 { 3453 PetscErrorCode ierr; 3454 PetscMPIInt rank,size; 3455 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3456 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3457 Mat M,Mreuse; 3458 MatScalar *aa,*vwork; 3459 MPI_Comm comm; 3460 Mat_SeqAIJ *aij; 3461 3462 PetscFunctionBegin; 3463 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3464 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3465 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3466 3467 if (call == MAT_REUSE_MATRIX) { 3468 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3469 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3470 ierr = MatCreateSubMatrices_MPIAIJ_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,&Mreuse);CHKERRQ(ierr); 3471 } else { 3472 ierr = MatCreateSubMatrices_MPIAIJ_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,&Mreuse);CHKERRQ(ierr); 3473 } 3474 3475 /* 3476 m - number of local rows 3477 n - number of columns (same on all processors) 3478 rstart - first row in new global matrix generated 3479 */ 3480 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3481 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3482 if (call == MAT_INITIAL_MATRIX) { 3483 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3484 ii = aij->i; 3485 jj = aij->j; 3486 3487 /* 3488 Determine the number of non-zeros in the diagonal and off-diagonal 3489 portions of the matrix in order to do correct preallocation 3490 */ 3491 3492 /* first get start and end of "diagonal" columns */ 3493 if (csize == PETSC_DECIDE) { 3494 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3495 if (mglobal == n) { /* square matrix */ 3496 nlocal = m; 3497 } else { 3498 nlocal = n/size + ((n % size) > rank); 3499 } 3500 } else { 3501 nlocal = csize; 3502 } 3503 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3504 rstart = rend - nlocal; 3505 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); 3506 3507 /* next, compute all the lengths */ 3508 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3509 olens = dlens + m; 3510 for (i=0; i<m; i++) { 3511 jend = ii[i+1] - ii[i]; 3512 olen = 0; 3513 dlen = 0; 3514 for (j=0; j<jend; j++) { 3515 if (*jj < rstart || *jj >= rend) olen++; 3516 else dlen++; 3517 jj++; 3518 } 3519 olens[i] = olen; 3520 dlens[i] = dlen; 3521 } 3522 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3523 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3524 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3525 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3526 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3527 ierr = PetscFree(dlens);CHKERRQ(ierr); 3528 } else { 3529 PetscInt ml,nl; 3530 3531 M = *newmat; 3532 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3533 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3534 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3535 /* 3536 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3537 rather than the slower MatSetValues(). 3538 */ 3539 M->was_assembled = PETSC_TRUE; 3540 M->assembled = PETSC_FALSE; 3541 } 3542 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3543 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3544 ii = aij->i; 3545 jj = aij->j; 3546 aa = aij->a; 3547 for (i=0; i<m; i++) { 3548 row = rstart + i; 3549 nz = ii[i+1] - ii[i]; 3550 cwork = jj; jj += nz; 3551 vwork = aa; aa += nz; 3552 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3553 } 3554 3555 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3556 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3557 *newmat = M; 3558 3559 /* save submatrix used in processor for next request */ 3560 if (call == MAT_INITIAL_MATRIX) { 3561 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3562 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3563 } 3564 PetscFunctionReturn(0); 3565 } 3566 3567 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3568 { 3569 PetscInt m,cstart, cend,j,nnz,i,d; 3570 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3571 const PetscInt *JJ; 3572 PetscScalar *values; 3573 PetscErrorCode ierr; 3574 PetscBool nooffprocentries; 3575 3576 PetscFunctionBegin; 3577 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3578 3579 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3580 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3581 m = B->rmap->n; 3582 cstart = B->cmap->rstart; 3583 cend = B->cmap->rend; 3584 rstart = B->rmap->rstart; 3585 3586 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3587 3588 #if defined(PETSC_USE_DEBUGGING) 3589 for (i=0; i<m; i++) { 3590 nnz = Ii[i+1]- Ii[i]; 3591 JJ = J + Ii[i]; 3592 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3593 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3594 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); 3595 } 3596 #endif 3597 3598 for (i=0; i<m; i++) { 3599 nnz = Ii[i+1]- Ii[i]; 3600 JJ = J + Ii[i]; 3601 nnz_max = PetscMax(nnz_max,nnz); 3602 d = 0; 3603 for (j=0; j<nnz; j++) { 3604 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3605 } 3606 d_nnz[i] = d; 3607 o_nnz[i] = nnz - d; 3608 } 3609 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3610 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3611 3612 if (v) values = (PetscScalar*)v; 3613 else { 3614 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3615 } 3616 3617 for (i=0; i<m; i++) { 3618 ii = i + rstart; 3619 nnz = Ii[i+1]- Ii[i]; 3620 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3621 } 3622 nooffprocentries = B->nooffprocentries; 3623 B->nooffprocentries = PETSC_TRUE; 3624 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3625 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3626 B->nooffprocentries = nooffprocentries; 3627 3628 if (!v) { 3629 ierr = PetscFree(values);CHKERRQ(ierr); 3630 } 3631 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3632 PetscFunctionReturn(0); 3633 } 3634 3635 /*@ 3636 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3637 (the default parallel PETSc format). 3638 3639 Collective on MPI_Comm 3640 3641 Input Parameters: 3642 + B - the matrix 3643 . i - the indices into j for the start of each local row (starts with zero) 3644 . j - the column indices for each local row (starts with zero) 3645 - v - optional values in the matrix 3646 3647 Level: developer 3648 3649 Notes: 3650 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3651 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3652 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3653 3654 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3655 3656 The format which is used for the sparse matrix input, is equivalent to a 3657 row-major ordering.. i.e for the following matrix, the input data expected is 3658 as shown 3659 3660 $ 1 0 0 3661 $ 2 0 3 P0 3662 $ ------- 3663 $ 4 5 6 P1 3664 $ 3665 $ Process0 [P0]: rows_owned=[0,1] 3666 $ i = {0,1,3} [size = nrow+1 = 2+1] 3667 $ j = {0,0,2} [size = 3] 3668 $ v = {1,2,3} [size = 3] 3669 $ 3670 $ Process1 [P1]: rows_owned=[2] 3671 $ i = {0,3} [size = nrow+1 = 1+1] 3672 $ j = {0,1,2} [size = 3] 3673 $ v = {4,5,6} [size = 3] 3674 3675 .keywords: matrix, aij, compressed row, sparse, parallel 3676 3677 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3678 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3679 @*/ 3680 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3681 { 3682 PetscErrorCode ierr; 3683 3684 PetscFunctionBegin; 3685 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3686 PetscFunctionReturn(0); 3687 } 3688 3689 /*@C 3690 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3691 (the default parallel PETSc format). For good matrix assembly performance 3692 the user should preallocate the matrix storage by setting the parameters 3693 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3694 performance can be increased by more than a factor of 50. 3695 3696 Collective on MPI_Comm 3697 3698 Input Parameters: 3699 + B - the matrix 3700 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3701 (same value is used for all local rows) 3702 . d_nnz - array containing the number of nonzeros in the various rows of the 3703 DIAGONAL portion of the local submatrix (possibly different for each row) 3704 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3705 The size of this array is equal to the number of local rows, i.e 'm'. 3706 For matrices that will be factored, you must leave room for (and set) 3707 the diagonal entry even if it is zero. 3708 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3709 submatrix (same value is used for all local rows). 3710 - o_nnz - array containing the number of nonzeros in the various rows of the 3711 OFF-DIAGONAL portion of the local submatrix (possibly different for 3712 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3713 structure. The size of this array is equal to the number 3714 of local rows, i.e 'm'. 3715 3716 If the *_nnz parameter is given then the *_nz parameter is ignored 3717 3718 The AIJ format (also called the Yale sparse matrix format or 3719 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3720 storage. The stored row and column indices begin with zero. 3721 See Users-Manual: ch_mat for details. 3722 3723 The parallel matrix is partitioned such that the first m0 rows belong to 3724 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3725 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3726 3727 The DIAGONAL portion of the local submatrix of a processor can be defined 3728 as the submatrix which is obtained by extraction the part corresponding to 3729 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3730 first row that belongs to the processor, r2 is the last row belonging to 3731 the this processor, and c1-c2 is range of indices of the local part of a 3732 vector suitable for applying the matrix to. This is an mxn matrix. In the 3733 common case of a square matrix, the row and column ranges are the same and 3734 the DIAGONAL part is also square. The remaining portion of the local 3735 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3736 3737 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3738 3739 You can call MatGetInfo() to get information on how effective the preallocation was; 3740 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3741 You can also run with the option -info and look for messages with the string 3742 malloc in them to see if additional memory allocation was needed. 3743 3744 Example usage: 3745 3746 Consider the following 8x8 matrix with 34 non-zero values, that is 3747 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3748 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3749 as follows: 3750 3751 .vb 3752 1 2 0 | 0 3 0 | 0 4 3753 Proc0 0 5 6 | 7 0 0 | 8 0 3754 9 0 10 | 11 0 0 | 12 0 3755 ------------------------------------- 3756 13 0 14 | 15 16 17 | 0 0 3757 Proc1 0 18 0 | 19 20 21 | 0 0 3758 0 0 0 | 22 23 0 | 24 0 3759 ------------------------------------- 3760 Proc2 25 26 27 | 0 0 28 | 29 0 3761 30 0 0 | 31 32 33 | 0 34 3762 .ve 3763 3764 This can be represented as a collection of submatrices as: 3765 3766 .vb 3767 A B C 3768 D E F 3769 G H I 3770 .ve 3771 3772 Where the submatrices A,B,C are owned by proc0, D,E,F are 3773 owned by proc1, G,H,I are owned by proc2. 3774 3775 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3776 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3777 The 'M','N' parameters are 8,8, and have the same values on all procs. 3778 3779 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3780 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3781 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3782 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3783 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3784 matrix, ans [DF] as another SeqAIJ matrix. 3785 3786 When d_nz, o_nz parameters are specified, d_nz storage elements are 3787 allocated for every row of the local diagonal submatrix, and o_nz 3788 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3789 One way to choose d_nz and o_nz is to use the max nonzerors per local 3790 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3791 In this case, the values of d_nz,o_nz are: 3792 .vb 3793 proc0 : dnz = 2, o_nz = 2 3794 proc1 : dnz = 3, o_nz = 2 3795 proc2 : dnz = 1, o_nz = 4 3796 .ve 3797 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3798 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3799 for proc3. i.e we are using 12+15+10=37 storage locations to store 3800 34 values. 3801 3802 When d_nnz, o_nnz parameters are specified, the storage is specified 3803 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3804 In the above case the values for d_nnz,o_nnz are: 3805 .vb 3806 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3807 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3808 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3809 .ve 3810 Here the space allocated is sum of all the above values i.e 34, and 3811 hence pre-allocation is perfect. 3812 3813 Level: intermediate 3814 3815 .keywords: matrix, aij, compressed row, sparse, parallel 3816 3817 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 3818 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 3819 @*/ 3820 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3821 { 3822 PetscErrorCode ierr; 3823 3824 PetscFunctionBegin; 3825 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3826 PetscValidType(B,1); 3827 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 3828 PetscFunctionReturn(0); 3829 } 3830 3831 /*@ 3832 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 3833 CSR format the local rows. 3834 3835 Collective on MPI_Comm 3836 3837 Input Parameters: 3838 + comm - MPI communicator 3839 . m - number of local rows (Cannot be PETSC_DECIDE) 3840 . n - This value should be the same as the local size used in creating the 3841 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3842 calculated if N is given) For square matrices n is almost always m. 3843 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3844 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3845 . i - row indices 3846 . j - column indices 3847 - a - matrix values 3848 3849 Output Parameter: 3850 . mat - the matrix 3851 3852 Level: intermediate 3853 3854 Notes: 3855 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3856 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3857 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3858 3859 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3860 3861 The format which is used for the sparse matrix input, is equivalent to a 3862 row-major ordering.. i.e for the following matrix, the input data expected is 3863 as shown 3864 3865 $ 1 0 0 3866 $ 2 0 3 P0 3867 $ ------- 3868 $ 4 5 6 P1 3869 $ 3870 $ Process0 [P0]: rows_owned=[0,1] 3871 $ i = {0,1,3} [size = nrow+1 = 2+1] 3872 $ j = {0,0,2} [size = 3] 3873 $ v = {1,2,3} [size = 3] 3874 $ 3875 $ Process1 [P1]: rows_owned=[2] 3876 $ i = {0,3} [size = nrow+1 = 1+1] 3877 $ j = {0,1,2} [size = 3] 3878 $ v = {4,5,6} [size = 3] 3879 3880 .keywords: matrix, aij, compressed row, sparse, parallel 3881 3882 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 3883 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 3884 @*/ 3885 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 3886 { 3887 PetscErrorCode ierr; 3888 3889 PetscFunctionBegin; 3890 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 3891 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 3892 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3893 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 3894 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 3895 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3896 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 3897 PetscFunctionReturn(0); 3898 } 3899 3900 /*@C 3901 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 3902 (the default parallel PETSc format). For good matrix assembly performance 3903 the user should preallocate the matrix storage by setting the parameters 3904 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3905 performance can be increased by more than a factor of 50. 3906 3907 Collective on MPI_Comm 3908 3909 Input Parameters: 3910 + comm - MPI communicator 3911 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 3912 This value should be the same as the local size used in creating the 3913 y vector for the matrix-vector product y = Ax. 3914 . n - This value should be the same as the local size used in creating the 3915 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3916 calculated if N is given) For square matrices n is almost always m. 3917 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3918 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3919 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3920 (same value is used for all local rows) 3921 . d_nnz - array containing the number of nonzeros in the various rows of the 3922 DIAGONAL portion of the local submatrix (possibly different for each row) 3923 or NULL, if d_nz is used to specify the nonzero structure. 3924 The size of this array is equal to the number of local rows, i.e 'm'. 3925 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3926 submatrix (same value is used for all local rows). 3927 - o_nnz - array containing the number of nonzeros in the various rows of the 3928 OFF-DIAGONAL portion of the local submatrix (possibly different for 3929 each row) or NULL, if o_nz is used to specify the nonzero 3930 structure. The size of this array is equal to the number 3931 of local rows, i.e 'm'. 3932 3933 Output Parameter: 3934 . A - the matrix 3935 3936 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 3937 MatXXXXSetPreallocation() paradgm instead of this routine directly. 3938 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 3939 3940 Notes: 3941 If the *_nnz parameter is given then the *_nz parameter is ignored 3942 3943 m,n,M,N parameters specify the size of the matrix, and its partitioning across 3944 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 3945 storage requirements for this matrix. 3946 3947 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 3948 processor than it must be used on all processors that share the object for 3949 that argument. 3950 3951 The user MUST specify either the local or global matrix dimensions 3952 (possibly both). 3953 3954 The parallel matrix is partitioned across processors such that the 3955 first m0 rows belong to process 0, the next m1 rows belong to 3956 process 1, the next m2 rows belong to process 2 etc.. where 3957 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 3958 values corresponding to [m x N] submatrix. 3959 3960 The columns are logically partitioned with the n0 columns belonging 3961 to 0th partition, the next n1 columns belonging to the next 3962 partition etc.. where n0,n1,n2... are the input parameter 'n'. 3963 3964 The DIAGONAL portion of the local submatrix on any given processor 3965 is the submatrix corresponding to the rows and columns m,n 3966 corresponding to the given processor. i.e diagonal matrix on 3967 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 3968 etc. The remaining portion of the local submatrix [m x (N-n)] 3969 constitute the OFF-DIAGONAL portion. The example below better 3970 illustrates this concept. 3971 3972 For a square global matrix we define each processor's diagonal portion 3973 to be its local rows and the corresponding columns (a square submatrix); 3974 each processor's off-diagonal portion encompasses the remainder of the 3975 local matrix (a rectangular submatrix). 3976 3977 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3978 3979 When calling this routine with a single process communicator, a matrix of 3980 type SEQAIJ is returned. If a matrix of type MATMPIAIJ is desired for this 3981 type of communicator, use the construction mechanism: 3982 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 3983 3984 By default, this format uses inodes (identical nodes) when possible. 3985 We search for consecutive rows with the same nonzero structure, thereby 3986 reusing matrix information to achieve increased efficiency. 3987 3988 Options Database Keys: 3989 + -mat_no_inode - Do not use inodes 3990 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 3991 - -mat_aij_oneindex - Internally use indexing starting at 1 3992 rather than 0. Note that when calling MatSetValues(), 3993 the user still MUST index entries starting at 0! 3994 3995 3996 Example usage: 3997 3998 Consider the following 8x8 matrix with 34 non-zero values, that is 3999 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4000 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4001 as follows: 4002 4003 .vb 4004 1 2 0 | 0 3 0 | 0 4 4005 Proc0 0 5 6 | 7 0 0 | 8 0 4006 9 0 10 | 11 0 0 | 12 0 4007 ------------------------------------- 4008 13 0 14 | 15 16 17 | 0 0 4009 Proc1 0 18 0 | 19 20 21 | 0 0 4010 0 0 0 | 22 23 0 | 24 0 4011 ------------------------------------- 4012 Proc2 25 26 27 | 0 0 28 | 29 0 4013 30 0 0 | 31 32 33 | 0 34 4014 .ve 4015 4016 This can be represented as a collection of submatrices as: 4017 4018 .vb 4019 A B C 4020 D E F 4021 G H I 4022 .ve 4023 4024 Where the submatrices A,B,C are owned by proc0, D,E,F are 4025 owned by proc1, G,H,I are owned by proc2. 4026 4027 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4028 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4029 The 'M','N' parameters are 8,8, and have the same values on all procs. 4030 4031 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4032 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4033 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4034 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4035 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4036 matrix, ans [DF] as another SeqAIJ matrix. 4037 4038 When d_nz, o_nz parameters are specified, d_nz storage elements are 4039 allocated for every row of the local diagonal submatrix, and o_nz 4040 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4041 One way to choose d_nz and o_nz is to use the max nonzerors per local 4042 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4043 In this case, the values of d_nz,o_nz are: 4044 .vb 4045 proc0 : dnz = 2, o_nz = 2 4046 proc1 : dnz = 3, o_nz = 2 4047 proc2 : dnz = 1, o_nz = 4 4048 .ve 4049 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4050 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4051 for proc3. i.e we are using 12+15+10=37 storage locations to store 4052 34 values. 4053 4054 When d_nnz, o_nnz parameters are specified, the storage is specified 4055 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4056 In the above case the values for d_nnz,o_nnz are: 4057 .vb 4058 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4059 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4060 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4061 .ve 4062 Here the space allocated is sum of all the above values i.e 34, and 4063 hence pre-allocation is perfect. 4064 4065 Level: intermediate 4066 4067 .keywords: matrix, aij, compressed row, sparse, parallel 4068 4069 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4070 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4071 @*/ 4072 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) 4073 { 4074 PetscErrorCode ierr; 4075 PetscMPIInt size; 4076 4077 PetscFunctionBegin; 4078 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4079 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4080 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4081 if (size > 1) { 4082 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4083 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4084 } else { 4085 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4086 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4087 } 4088 PetscFunctionReturn(0); 4089 } 4090 4091 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4092 { 4093 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4094 PetscBool flg; 4095 PetscErrorCode ierr; 4096 4097 PetscFunctionBegin; 4098 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4099 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4100 if (Ad) *Ad = a->A; 4101 if (Ao) *Ao = a->B; 4102 if (colmap) *colmap = a->garray; 4103 PetscFunctionReturn(0); 4104 } 4105 4106 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4107 { 4108 PetscErrorCode ierr; 4109 PetscInt m,N,i,rstart,nnz,Ii; 4110 PetscInt *indx; 4111 PetscScalar *values; 4112 4113 PetscFunctionBegin; 4114 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4115 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4116 PetscInt *dnz,*onz,sum,bs,cbs; 4117 4118 if (n == PETSC_DECIDE) { 4119 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4120 } 4121 /* Check sum(n) = N */ 4122 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4123 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 4124 4125 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4126 rstart -= m; 4127 4128 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4129 for (i=0; i<m; i++) { 4130 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4131 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4132 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4133 } 4134 4135 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4136 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4137 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4138 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4139 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4140 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4141 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4142 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4143 } 4144 4145 /* numeric phase */ 4146 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4147 for (i=0; i<m; i++) { 4148 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4149 Ii = i + rstart; 4150 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4151 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4152 } 4153 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4154 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4155 PetscFunctionReturn(0); 4156 } 4157 4158 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4159 { 4160 PetscErrorCode ierr; 4161 PetscMPIInt rank; 4162 PetscInt m,N,i,rstart,nnz; 4163 size_t len; 4164 const PetscInt *indx; 4165 PetscViewer out; 4166 char *name; 4167 Mat B; 4168 const PetscScalar *values; 4169 4170 PetscFunctionBegin; 4171 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4172 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4173 /* Should this be the type of the diagonal block of A? */ 4174 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4175 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4176 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4177 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4178 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4179 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4180 for (i=0; i<m; i++) { 4181 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4182 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4183 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4184 } 4185 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4186 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4187 4188 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4189 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4190 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4191 sprintf(name,"%s.%d",outfile,rank); 4192 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4193 ierr = PetscFree(name);CHKERRQ(ierr); 4194 ierr = MatView(B,out);CHKERRQ(ierr); 4195 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4196 ierr = MatDestroy(&B);CHKERRQ(ierr); 4197 PetscFunctionReturn(0); 4198 } 4199 4200 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4201 { 4202 PetscErrorCode ierr; 4203 Mat_Merge_SeqsToMPI *merge; 4204 PetscContainer container; 4205 4206 PetscFunctionBegin; 4207 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4208 if (container) { 4209 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4210 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4211 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4212 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4213 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4214 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4215 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4216 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4217 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4218 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4219 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4220 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4221 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4222 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4223 ierr = PetscFree(merge);CHKERRQ(ierr); 4224 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4225 } 4226 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4227 PetscFunctionReturn(0); 4228 } 4229 4230 #include <../src/mat/utils/freespace.h> 4231 #include <petscbt.h> 4232 4233 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4234 { 4235 PetscErrorCode ierr; 4236 MPI_Comm comm; 4237 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4238 PetscMPIInt size,rank,taga,*len_s; 4239 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4240 PetscInt proc,m; 4241 PetscInt **buf_ri,**buf_rj; 4242 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4243 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4244 MPI_Request *s_waits,*r_waits; 4245 MPI_Status *status; 4246 MatScalar *aa=a->a; 4247 MatScalar **abuf_r,*ba_i; 4248 Mat_Merge_SeqsToMPI *merge; 4249 PetscContainer container; 4250 4251 PetscFunctionBegin; 4252 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4253 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4254 4255 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4256 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4257 4258 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4259 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4260 4261 bi = merge->bi; 4262 bj = merge->bj; 4263 buf_ri = merge->buf_ri; 4264 buf_rj = merge->buf_rj; 4265 4266 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4267 owners = merge->rowmap->range; 4268 len_s = merge->len_s; 4269 4270 /* send and recv matrix values */ 4271 /*-----------------------------*/ 4272 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4273 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4274 4275 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4276 for (proc=0,k=0; proc<size; proc++) { 4277 if (!len_s[proc]) continue; 4278 i = owners[proc]; 4279 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4280 k++; 4281 } 4282 4283 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4284 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4285 ierr = PetscFree(status);CHKERRQ(ierr); 4286 4287 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4288 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4289 4290 /* insert mat values of mpimat */ 4291 /*----------------------------*/ 4292 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4293 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4294 4295 for (k=0; k<merge->nrecv; k++) { 4296 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4297 nrows = *(buf_ri_k[k]); 4298 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4299 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4300 } 4301 4302 /* set values of ba */ 4303 m = merge->rowmap->n; 4304 for (i=0; i<m; i++) { 4305 arow = owners[rank] + i; 4306 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4307 bnzi = bi[i+1] - bi[i]; 4308 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4309 4310 /* add local non-zero vals of this proc's seqmat into ba */ 4311 anzi = ai[arow+1] - ai[arow]; 4312 aj = a->j + ai[arow]; 4313 aa = a->a + ai[arow]; 4314 nextaj = 0; 4315 for (j=0; nextaj<anzi; j++) { 4316 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4317 ba_i[j] += aa[nextaj++]; 4318 } 4319 } 4320 4321 /* add received vals into ba */ 4322 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4323 /* i-th row */ 4324 if (i == *nextrow[k]) { 4325 anzi = *(nextai[k]+1) - *nextai[k]; 4326 aj = buf_rj[k] + *(nextai[k]); 4327 aa = abuf_r[k] + *(nextai[k]); 4328 nextaj = 0; 4329 for (j=0; nextaj<anzi; j++) { 4330 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4331 ba_i[j] += aa[nextaj++]; 4332 } 4333 } 4334 nextrow[k]++; nextai[k]++; 4335 } 4336 } 4337 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4338 } 4339 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4340 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4341 4342 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4343 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4344 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4345 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4346 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4347 PetscFunctionReturn(0); 4348 } 4349 4350 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4351 { 4352 PetscErrorCode ierr; 4353 Mat B_mpi; 4354 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4355 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4356 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4357 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4358 PetscInt len,proc,*dnz,*onz,bs,cbs; 4359 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4360 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4361 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4362 MPI_Status *status; 4363 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4364 PetscBT lnkbt; 4365 Mat_Merge_SeqsToMPI *merge; 4366 PetscContainer container; 4367 4368 PetscFunctionBegin; 4369 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4370 4371 /* make sure it is a PETSc comm */ 4372 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4373 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4374 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4375 4376 ierr = PetscNew(&merge);CHKERRQ(ierr); 4377 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4378 4379 /* determine row ownership */ 4380 /*---------------------------------------------------------*/ 4381 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4382 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4383 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4384 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4385 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4386 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4387 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4388 4389 m = merge->rowmap->n; 4390 owners = merge->rowmap->range; 4391 4392 /* determine the number of messages to send, their lengths */ 4393 /*---------------------------------------------------------*/ 4394 len_s = merge->len_s; 4395 4396 len = 0; /* length of buf_si[] */ 4397 merge->nsend = 0; 4398 for (proc=0; proc<size; proc++) { 4399 len_si[proc] = 0; 4400 if (proc == rank) { 4401 len_s[proc] = 0; 4402 } else { 4403 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4404 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4405 } 4406 if (len_s[proc]) { 4407 merge->nsend++; 4408 nrows = 0; 4409 for (i=owners[proc]; i<owners[proc+1]; i++) { 4410 if (ai[i+1] > ai[i]) nrows++; 4411 } 4412 len_si[proc] = 2*(nrows+1); 4413 len += len_si[proc]; 4414 } 4415 } 4416 4417 /* determine the number and length of messages to receive for ij-structure */ 4418 /*-------------------------------------------------------------------------*/ 4419 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4420 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4421 4422 /* post the Irecv of j-structure */ 4423 /*-------------------------------*/ 4424 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4425 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4426 4427 /* post the Isend of j-structure */ 4428 /*--------------------------------*/ 4429 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4430 4431 for (proc=0, k=0; proc<size; proc++) { 4432 if (!len_s[proc]) continue; 4433 i = owners[proc]; 4434 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4435 k++; 4436 } 4437 4438 /* receives and sends of j-structure are complete */ 4439 /*------------------------------------------------*/ 4440 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4441 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4442 4443 /* send and recv i-structure */ 4444 /*---------------------------*/ 4445 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4446 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4447 4448 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4449 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4450 for (proc=0,k=0; proc<size; proc++) { 4451 if (!len_s[proc]) continue; 4452 /* form outgoing message for i-structure: 4453 buf_si[0]: nrows to be sent 4454 [1:nrows]: row index (global) 4455 [nrows+1:2*nrows+1]: i-structure index 4456 */ 4457 /*-------------------------------------------*/ 4458 nrows = len_si[proc]/2 - 1; 4459 buf_si_i = buf_si + nrows+1; 4460 buf_si[0] = nrows; 4461 buf_si_i[0] = 0; 4462 nrows = 0; 4463 for (i=owners[proc]; i<owners[proc+1]; i++) { 4464 anzi = ai[i+1] - ai[i]; 4465 if (anzi) { 4466 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4467 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4468 nrows++; 4469 } 4470 } 4471 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4472 k++; 4473 buf_si += len_si[proc]; 4474 } 4475 4476 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4477 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4478 4479 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4480 for (i=0; i<merge->nrecv; i++) { 4481 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); 4482 } 4483 4484 ierr = PetscFree(len_si);CHKERRQ(ierr); 4485 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4486 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4487 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4488 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4489 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4490 ierr = PetscFree(status);CHKERRQ(ierr); 4491 4492 /* compute a local seq matrix in each processor */ 4493 /*----------------------------------------------*/ 4494 /* allocate bi array and free space for accumulating nonzero column info */ 4495 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4496 bi[0] = 0; 4497 4498 /* create and initialize a linked list */ 4499 nlnk = N+1; 4500 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4501 4502 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4503 len = ai[owners[rank+1]] - ai[owners[rank]]; 4504 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4505 4506 current_space = free_space; 4507 4508 /* determine symbolic info for each local row */ 4509 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4510 4511 for (k=0; k<merge->nrecv; k++) { 4512 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4513 nrows = *buf_ri_k[k]; 4514 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4515 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4516 } 4517 4518 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4519 len = 0; 4520 for (i=0; i<m; i++) { 4521 bnzi = 0; 4522 /* add local non-zero cols of this proc's seqmat into lnk */ 4523 arow = owners[rank] + i; 4524 anzi = ai[arow+1] - ai[arow]; 4525 aj = a->j + ai[arow]; 4526 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4527 bnzi += nlnk; 4528 /* add received col data into lnk */ 4529 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4530 if (i == *nextrow[k]) { /* i-th row */ 4531 anzi = *(nextai[k]+1) - *nextai[k]; 4532 aj = buf_rj[k] + *nextai[k]; 4533 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4534 bnzi += nlnk; 4535 nextrow[k]++; nextai[k]++; 4536 } 4537 } 4538 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4539 4540 /* if free space is not available, make more free space */ 4541 if (current_space->local_remaining<bnzi) { 4542 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4543 nspacedouble++; 4544 } 4545 /* copy data into free space, then initialize lnk */ 4546 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4547 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4548 4549 current_space->array += bnzi; 4550 current_space->local_used += bnzi; 4551 current_space->local_remaining -= bnzi; 4552 4553 bi[i+1] = bi[i] + bnzi; 4554 } 4555 4556 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4557 4558 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4559 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4560 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4561 4562 /* create symbolic parallel matrix B_mpi */ 4563 /*---------------------------------------*/ 4564 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4565 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4566 if (n==PETSC_DECIDE) { 4567 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4568 } else { 4569 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4570 } 4571 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4572 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4573 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4574 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4575 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4576 4577 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4578 B_mpi->assembled = PETSC_FALSE; 4579 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4580 merge->bi = bi; 4581 merge->bj = bj; 4582 merge->buf_ri = buf_ri; 4583 merge->buf_rj = buf_rj; 4584 merge->coi = NULL; 4585 merge->coj = NULL; 4586 merge->owners_co = NULL; 4587 4588 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4589 4590 /* attach the supporting struct to B_mpi for reuse */ 4591 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4592 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4593 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4594 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4595 *mpimat = B_mpi; 4596 4597 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4598 PetscFunctionReturn(0); 4599 } 4600 4601 /*@C 4602 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4603 matrices from each processor 4604 4605 Collective on MPI_Comm 4606 4607 Input Parameters: 4608 + comm - the communicators the parallel matrix will live on 4609 . seqmat - the input sequential matrices 4610 . m - number of local rows (or PETSC_DECIDE) 4611 . n - number of local columns (or PETSC_DECIDE) 4612 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4613 4614 Output Parameter: 4615 . mpimat - the parallel matrix generated 4616 4617 Level: advanced 4618 4619 Notes: 4620 The dimensions of the sequential matrix in each processor MUST be the same. 4621 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4622 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4623 @*/ 4624 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4625 { 4626 PetscErrorCode ierr; 4627 PetscMPIInt size; 4628 4629 PetscFunctionBegin; 4630 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4631 if (size == 1) { 4632 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4633 if (scall == MAT_INITIAL_MATRIX) { 4634 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4635 } else { 4636 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4637 } 4638 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4639 PetscFunctionReturn(0); 4640 } 4641 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4642 if (scall == MAT_INITIAL_MATRIX) { 4643 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4644 } 4645 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4646 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4647 PetscFunctionReturn(0); 4648 } 4649 4650 /*@ 4651 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 4652 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4653 with MatGetSize() 4654 4655 Not Collective 4656 4657 Input Parameters: 4658 + A - the matrix 4659 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4660 4661 Output Parameter: 4662 . A_loc - the local sequential matrix generated 4663 4664 Level: developer 4665 4666 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4667 4668 @*/ 4669 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4670 { 4671 PetscErrorCode ierr; 4672 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4673 Mat_SeqAIJ *mat,*a,*b; 4674 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4675 MatScalar *aa,*ba,*cam; 4676 PetscScalar *ca; 4677 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4678 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4679 PetscBool match; 4680 MPI_Comm comm; 4681 PetscMPIInt size; 4682 4683 PetscFunctionBegin; 4684 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4685 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4686 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4687 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4688 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4689 4690 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4691 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4692 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4693 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4694 aa = a->a; ba = b->a; 4695 if (scall == MAT_INITIAL_MATRIX) { 4696 if (size == 1) { 4697 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4698 PetscFunctionReturn(0); 4699 } 4700 4701 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4702 ci[0] = 0; 4703 for (i=0; i<am; i++) { 4704 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4705 } 4706 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4707 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4708 k = 0; 4709 for (i=0; i<am; i++) { 4710 ncols_o = bi[i+1] - bi[i]; 4711 ncols_d = ai[i+1] - ai[i]; 4712 /* off-diagonal portion of A */ 4713 for (jo=0; jo<ncols_o; jo++) { 4714 col = cmap[*bj]; 4715 if (col >= cstart) break; 4716 cj[k] = col; bj++; 4717 ca[k++] = *ba++; 4718 } 4719 /* diagonal portion of A */ 4720 for (j=0; j<ncols_d; j++) { 4721 cj[k] = cstart + *aj++; 4722 ca[k++] = *aa++; 4723 } 4724 /* off-diagonal portion of A */ 4725 for (j=jo; j<ncols_o; j++) { 4726 cj[k] = cmap[*bj++]; 4727 ca[k++] = *ba++; 4728 } 4729 } 4730 /* put together the new matrix */ 4731 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4732 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4733 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4734 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4735 mat->free_a = PETSC_TRUE; 4736 mat->free_ij = PETSC_TRUE; 4737 mat->nonew = 0; 4738 } else if (scall == MAT_REUSE_MATRIX) { 4739 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4740 ci = mat->i; cj = mat->j; cam = mat->a; 4741 for (i=0; i<am; i++) { 4742 /* off-diagonal portion of A */ 4743 ncols_o = bi[i+1] - bi[i]; 4744 for (jo=0; jo<ncols_o; jo++) { 4745 col = cmap[*bj]; 4746 if (col >= cstart) break; 4747 *cam++ = *ba++; bj++; 4748 } 4749 /* diagonal portion of A */ 4750 ncols_d = ai[i+1] - ai[i]; 4751 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4752 /* off-diagonal portion of A */ 4753 for (j=jo; j<ncols_o; j++) { 4754 *cam++ = *ba++; bj++; 4755 } 4756 } 4757 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4758 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4759 PetscFunctionReturn(0); 4760 } 4761 4762 /*@C 4763 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4764 4765 Not Collective 4766 4767 Input Parameters: 4768 + A - the matrix 4769 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4770 - row, col - index sets of rows and columns to extract (or NULL) 4771 4772 Output Parameter: 4773 . A_loc - the local sequential matrix generated 4774 4775 Level: developer 4776 4777 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4778 4779 @*/ 4780 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4781 { 4782 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4783 PetscErrorCode ierr; 4784 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4785 IS isrowa,iscola; 4786 Mat *aloc; 4787 PetscBool match; 4788 4789 PetscFunctionBegin; 4790 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4791 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4792 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4793 if (!row) { 4794 start = A->rmap->rstart; end = A->rmap->rend; 4795 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 4796 } else { 4797 isrowa = *row; 4798 } 4799 if (!col) { 4800 start = A->cmap->rstart; 4801 cmap = a->garray; 4802 nzA = a->A->cmap->n; 4803 nzB = a->B->cmap->n; 4804 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4805 ncols = 0; 4806 for (i=0; i<nzB; i++) { 4807 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4808 else break; 4809 } 4810 imark = i; 4811 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 4812 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 4813 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 4814 } else { 4815 iscola = *col; 4816 } 4817 if (scall != MAT_INITIAL_MATRIX) { 4818 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 4819 aloc[0] = *A_loc; 4820 } 4821 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 4822 *A_loc = aloc[0]; 4823 ierr = PetscFree(aloc);CHKERRQ(ierr); 4824 if (!row) { 4825 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 4826 } 4827 if (!col) { 4828 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 4829 } 4830 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4831 PetscFunctionReturn(0); 4832 } 4833 4834 /*@C 4835 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 4836 4837 Collective on Mat 4838 4839 Input Parameters: 4840 + A,B - the matrices in mpiaij format 4841 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4842 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 4843 4844 Output Parameter: 4845 + rowb, colb - index sets of rows and columns of B to extract 4846 - B_seq - the sequential matrix generated 4847 4848 Level: developer 4849 4850 @*/ 4851 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 4852 { 4853 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4854 PetscErrorCode ierr; 4855 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 4856 IS isrowb,iscolb; 4857 Mat *bseq=NULL; 4858 4859 PetscFunctionBegin; 4860 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 4861 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); 4862 } 4863 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 4864 4865 if (scall == MAT_INITIAL_MATRIX) { 4866 start = A->cmap->rstart; 4867 cmap = a->garray; 4868 nzA = a->A->cmap->n; 4869 nzB = a->B->cmap->n; 4870 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4871 ncols = 0; 4872 for (i=0; i<nzB; i++) { /* row < local row index */ 4873 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4874 else break; 4875 } 4876 imark = i; 4877 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 4878 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 4879 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 4880 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 4881 } else { 4882 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 4883 isrowb = *rowb; iscolb = *colb; 4884 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 4885 bseq[0] = *B_seq; 4886 } 4887 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 4888 *B_seq = bseq[0]; 4889 ierr = PetscFree(bseq);CHKERRQ(ierr); 4890 if (!rowb) { 4891 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 4892 } else { 4893 *rowb = isrowb; 4894 } 4895 if (!colb) { 4896 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 4897 } else { 4898 *colb = iscolb; 4899 } 4900 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 4901 PetscFunctionReturn(0); 4902 } 4903 4904 /* 4905 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 4906 of the OFF-DIAGONAL portion of local A 4907 4908 Collective on Mat 4909 4910 Input Parameters: 4911 + A,B - the matrices in mpiaij format 4912 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4913 4914 Output Parameter: 4915 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 4916 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 4917 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 4918 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 4919 4920 Level: developer 4921 4922 */ 4923 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 4924 { 4925 VecScatter_MPI_General *gen_to,*gen_from; 4926 PetscErrorCode ierr; 4927 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4928 Mat_SeqAIJ *b_oth; 4929 VecScatter ctx =a->Mvctx; 4930 MPI_Comm comm; 4931 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 4932 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 4933 PetscInt *rvalues,*svalues; 4934 MatScalar *b_otha,*bufa,*bufA; 4935 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 4936 MPI_Request *rwaits = NULL,*swaits = NULL; 4937 MPI_Status *sstatus,rstatus; 4938 PetscMPIInt jj,size; 4939 PetscInt *cols,sbs,rbs; 4940 PetscScalar *vals; 4941 4942 PetscFunctionBegin; 4943 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4944 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4945 4946 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 4947 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); 4948 } 4949 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 4950 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4951 4952 if (size == 1) { 4953 startsj_s = NULL; 4954 bufa_ptr = NULL; 4955 *B_oth = NULL; 4956 PetscFunctionReturn(0); 4957 } 4958 4959 gen_to = (VecScatter_MPI_General*)ctx->todata; 4960 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 4961 nrecvs = gen_from->n; 4962 nsends = gen_to->n; 4963 4964 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 4965 srow = gen_to->indices; /* local row index to be sent */ 4966 sstarts = gen_to->starts; 4967 sprocs = gen_to->procs; 4968 sstatus = gen_to->sstatus; 4969 sbs = gen_to->bs; 4970 rstarts = gen_from->starts; 4971 rprocs = gen_from->procs; 4972 rbs = gen_from->bs; 4973 4974 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 4975 if (scall == MAT_INITIAL_MATRIX) { 4976 /* i-array */ 4977 /*---------*/ 4978 /* post receives */ 4979 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 4980 for (i=0; i<nrecvs; i++) { 4981 rowlen = rvalues + rstarts[i]*rbs; 4982 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 4983 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 4984 } 4985 4986 /* pack the outgoing message */ 4987 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 4988 4989 sstartsj[0] = 0; 4990 rstartsj[0] = 0; 4991 len = 0; /* total length of j or a array to be sent */ 4992 k = 0; 4993 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 4994 for (i=0; i<nsends; i++) { 4995 rowlen = svalues + sstarts[i]*sbs; 4996 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 4997 for (j=0; j<nrows; j++) { 4998 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 4999 for (l=0; l<sbs; l++) { 5000 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5001 5002 rowlen[j*sbs+l] = ncols; 5003 5004 len += ncols; 5005 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5006 } 5007 k++; 5008 } 5009 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5010 5011 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5012 } 5013 /* recvs and sends of i-array are completed */ 5014 i = nrecvs; 5015 while (i--) { 5016 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5017 } 5018 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5019 ierr = PetscFree(svalues);CHKERRQ(ierr); 5020 5021 /* allocate buffers for sending j and a arrays */ 5022 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5023 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5024 5025 /* create i-array of B_oth */ 5026 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5027 5028 b_othi[0] = 0; 5029 len = 0; /* total length of j or a array to be received */ 5030 k = 0; 5031 for (i=0; i<nrecvs; i++) { 5032 rowlen = rvalues + rstarts[i]*rbs; 5033 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5034 for (j=0; j<nrows; j++) { 5035 b_othi[k+1] = b_othi[k] + rowlen[j]; 5036 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5037 k++; 5038 } 5039 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5040 } 5041 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5042 5043 /* allocate space for j and a arrrays of B_oth */ 5044 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5045 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5046 5047 /* j-array */ 5048 /*---------*/ 5049 /* post receives of j-array */ 5050 for (i=0; i<nrecvs; i++) { 5051 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5052 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5053 } 5054 5055 /* pack the outgoing message j-array */ 5056 k = 0; 5057 for (i=0; i<nsends; i++) { 5058 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5059 bufJ = bufj+sstartsj[i]; 5060 for (j=0; j<nrows; j++) { 5061 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5062 for (ll=0; ll<sbs; ll++) { 5063 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5064 for (l=0; l<ncols; l++) { 5065 *bufJ++ = cols[l]; 5066 } 5067 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5068 } 5069 } 5070 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5071 } 5072 5073 /* recvs and sends of j-array are completed */ 5074 i = nrecvs; 5075 while (i--) { 5076 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5077 } 5078 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5079 } else if (scall == MAT_REUSE_MATRIX) { 5080 sstartsj = *startsj_s; 5081 rstartsj = *startsj_r; 5082 bufa = *bufa_ptr; 5083 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5084 b_otha = b_oth->a; 5085 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5086 5087 /* a-array */ 5088 /*---------*/ 5089 /* post receives of a-array */ 5090 for (i=0; i<nrecvs; i++) { 5091 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5092 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5093 } 5094 5095 /* pack the outgoing message a-array */ 5096 k = 0; 5097 for (i=0; i<nsends; i++) { 5098 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5099 bufA = bufa+sstartsj[i]; 5100 for (j=0; j<nrows; j++) { 5101 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5102 for (ll=0; ll<sbs; ll++) { 5103 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5104 for (l=0; l<ncols; l++) { 5105 *bufA++ = vals[l]; 5106 } 5107 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5108 } 5109 } 5110 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5111 } 5112 /* recvs and sends of a-array are completed */ 5113 i = nrecvs; 5114 while (i--) { 5115 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5116 } 5117 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5118 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5119 5120 if (scall == MAT_INITIAL_MATRIX) { 5121 /* put together the new matrix */ 5122 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5123 5124 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5125 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5126 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5127 b_oth->free_a = PETSC_TRUE; 5128 b_oth->free_ij = PETSC_TRUE; 5129 b_oth->nonew = 0; 5130 5131 ierr = PetscFree(bufj);CHKERRQ(ierr); 5132 if (!startsj_s || !bufa_ptr) { 5133 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5134 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5135 } else { 5136 *startsj_s = sstartsj; 5137 *startsj_r = rstartsj; 5138 *bufa_ptr = bufa; 5139 } 5140 } 5141 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5142 PetscFunctionReturn(0); 5143 } 5144 5145 /*@C 5146 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5147 5148 Not Collective 5149 5150 Input Parameters: 5151 . A - The matrix in mpiaij format 5152 5153 Output Parameter: 5154 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5155 . colmap - A map from global column index to local index into lvec 5156 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5157 5158 Level: developer 5159 5160 @*/ 5161 #if defined(PETSC_USE_CTABLE) 5162 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5163 #else 5164 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5165 #endif 5166 { 5167 Mat_MPIAIJ *a; 5168 5169 PetscFunctionBegin; 5170 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5171 PetscValidPointer(lvec, 2); 5172 PetscValidPointer(colmap, 3); 5173 PetscValidPointer(multScatter, 4); 5174 a = (Mat_MPIAIJ*) A->data; 5175 if (lvec) *lvec = a->lvec; 5176 if (colmap) *colmap = a->colmap; 5177 if (multScatter) *multScatter = a->Mvctx; 5178 PetscFunctionReturn(0); 5179 } 5180 5181 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5182 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5183 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5184 #if defined(PETSC_HAVE_ELEMENTAL) 5185 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5186 #endif 5187 #if defined(PETSC_HAVE_HYPRE) 5188 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5189 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5190 #endif 5191 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5192 5193 /* 5194 Computes (B'*A')' since computing B*A directly is untenable 5195 5196 n p p 5197 ( ) ( ) ( ) 5198 m ( A ) * n ( B ) = m ( C ) 5199 ( ) ( ) ( ) 5200 5201 */ 5202 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5203 { 5204 PetscErrorCode ierr; 5205 Mat At,Bt,Ct; 5206 5207 PetscFunctionBegin; 5208 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5209 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5210 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5211 ierr = MatDestroy(&At);CHKERRQ(ierr); 5212 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5213 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5214 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5215 PetscFunctionReturn(0); 5216 } 5217 5218 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5219 { 5220 PetscErrorCode ierr; 5221 PetscInt m=A->rmap->n,n=B->cmap->n; 5222 Mat Cmat; 5223 5224 PetscFunctionBegin; 5225 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); 5226 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5227 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5228 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5229 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5230 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5231 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5232 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5233 5234 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5235 5236 *C = Cmat; 5237 PetscFunctionReturn(0); 5238 } 5239 5240 /* ----------------------------------------------------------------*/ 5241 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5242 { 5243 PetscErrorCode ierr; 5244 5245 PetscFunctionBegin; 5246 if (scall == MAT_INITIAL_MATRIX) { 5247 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5248 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5249 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5250 } 5251 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5252 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5253 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5254 PetscFunctionReturn(0); 5255 } 5256 5257 /*MC 5258 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5259 5260 Options Database Keys: 5261 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5262 5263 Level: beginner 5264 5265 .seealso: MatCreateAIJ() 5266 M*/ 5267 5268 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5269 { 5270 Mat_MPIAIJ *b; 5271 PetscErrorCode ierr; 5272 PetscMPIInt size; 5273 5274 PetscFunctionBegin; 5275 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5276 5277 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5278 B->data = (void*)b; 5279 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5280 B->assembled = PETSC_FALSE; 5281 B->insertmode = NOT_SET_VALUES; 5282 b->size = size; 5283 5284 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5285 5286 /* build cache for off array entries formed */ 5287 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5288 5289 b->donotstash = PETSC_FALSE; 5290 b->colmap = 0; 5291 b->garray = 0; 5292 b->roworiented = PETSC_TRUE; 5293 5294 /* stuff used for matrix vector multiply */ 5295 b->lvec = NULL; 5296 b->Mvctx = NULL; 5297 5298 /* stuff for MatGetRow() */ 5299 b->rowindices = 0; 5300 b->rowvalues = 0; 5301 b->getrowactive = PETSC_FALSE; 5302 5303 /* flexible pointer used in CUSP/CUSPARSE classes */ 5304 b->spptr = NULL; 5305 5306 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5307 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5308 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5309 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5310 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5311 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5312 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5313 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5314 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5315 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5316 #if defined(PETSC_HAVE_ELEMENTAL) 5317 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5318 #endif 5319 #if defined(PETSC_HAVE_HYPRE) 5320 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5321 #endif 5322 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5323 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5324 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5325 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5326 #if defined(PETSC_HAVE_HYPRE) 5327 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5328 #endif 5329 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5330 PetscFunctionReturn(0); 5331 } 5332 5333 /*@C 5334 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5335 and "off-diagonal" part of the matrix in CSR format. 5336 5337 Collective on MPI_Comm 5338 5339 Input Parameters: 5340 + comm - MPI communicator 5341 . m - number of local rows (Cannot be PETSC_DECIDE) 5342 . n - This value should be the same as the local size used in creating the 5343 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5344 calculated if N is given) For square matrices n is almost always m. 5345 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5346 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5347 . i - row indices for "diagonal" portion of matrix 5348 . j - column indices 5349 . a - matrix values 5350 . oi - row indices for "off-diagonal" portion of matrix 5351 . oj - column indices 5352 - oa - matrix values 5353 5354 Output Parameter: 5355 . mat - the matrix 5356 5357 Level: advanced 5358 5359 Notes: 5360 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5361 must free the arrays once the matrix has been destroyed and not before. 5362 5363 The i and j indices are 0 based 5364 5365 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5366 5367 This sets local rows and cannot be used to set off-processor values. 5368 5369 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5370 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5371 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5372 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5373 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5374 communication if it is known that only local entries will be set. 5375 5376 .keywords: matrix, aij, compressed row, sparse, parallel 5377 5378 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5379 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5380 @*/ 5381 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) 5382 { 5383 PetscErrorCode ierr; 5384 Mat_MPIAIJ *maij; 5385 5386 PetscFunctionBegin; 5387 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5388 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5389 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5390 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5391 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5392 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5393 maij = (Mat_MPIAIJ*) (*mat)->data; 5394 5395 (*mat)->preallocated = PETSC_TRUE; 5396 5397 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5398 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5399 5400 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5401 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5402 5403 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5404 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5405 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5406 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5407 5408 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5409 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5410 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5411 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5412 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5413 PetscFunctionReturn(0); 5414 } 5415 5416 /* 5417 Special version for direct calls from Fortran 5418 */ 5419 #include <petsc/private/fortranimpl.h> 5420 5421 /* Change these macros so can be used in void function */ 5422 #undef CHKERRQ 5423 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5424 #undef SETERRQ2 5425 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5426 #undef SETERRQ3 5427 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5428 #undef SETERRQ 5429 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5430 5431 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5432 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5433 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5434 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5435 #else 5436 #endif 5437 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) 5438 { 5439 Mat mat = *mmat; 5440 PetscInt m = *mm, n = *mn; 5441 InsertMode addv = *maddv; 5442 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5443 PetscScalar value; 5444 PetscErrorCode ierr; 5445 5446 MatCheckPreallocated(mat,1); 5447 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5448 5449 #if defined(PETSC_USE_DEBUG) 5450 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5451 #endif 5452 { 5453 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5454 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5455 PetscBool roworiented = aij->roworiented; 5456 5457 /* Some Variables required in the macro */ 5458 Mat A = aij->A; 5459 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5460 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5461 MatScalar *aa = a->a; 5462 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5463 Mat B = aij->B; 5464 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5465 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5466 MatScalar *ba = b->a; 5467 5468 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5469 PetscInt nonew = a->nonew; 5470 MatScalar *ap1,*ap2; 5471 5472 PetscFunctionBegin; 5473 for (i=0; i<m; i++) { 5474 if (im[i] < 0) continue; 5475 #if defined(PETSC_USE_DEBUG) 5476 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); 5477 #endif 5478 if (im[i] >= rstart && im[i] < rend) { 5479 row = im[i] - rstart; 5480 lastcol1 = -1; 5481 rp1 = aj + ai[row]; 5482 ap1 = aa + ai[row]; 5483 rmax1 = aimax[row]; 5484 nrow1 = ailen[row]; 5485 low1 = 0; 5486 high1 = nrow1; 5487 lastcol2 = -1; 5488 rp2 = bj + bi[row]; 5489 ap2 = ba + bi[row]; 5490 rmax2 = bimax[row]; 5491 nrow2 = bilen[row]; 5492 low2 = 0; 5493 high2 = nrow2; 5494 5495 for (j=0; j<n; j++) { 5496 if (roworiented) value = v[i*n+j]; 5497 else value = v[i+j*m]; 5498 if (in[j] >= cstart && in[j] < cend) { 5499 col = in[j] - cstart; 5500 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5501 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5502 } else if (in[j] < 0) continue; 5503 #if defined(PETSC_USE_DEBUG) 5504 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); 5505 #endif 5506 else { 5507 if (mat->was_assembled) { 5508 if (!aij->colmap) { 5509 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5510 } 5511 #if defined(PETSC_USE_CTABLE) 5512 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5513 col--; 5514 #else 5515 col = aij->colmap[in[j]] - 1; 5516 #endif 5517 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5518 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5519 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5520 col = in[j]; 5521 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5522 B = aij->B; 5523 b = (Mat_SeqAIJ*)B->data; 5524 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5525 rp2 = bj + bi[row]; 5526 ap2 = ba + bi[row]; 5527 rmax2 = bimax[row]; 5528 nrow2 = bilen[row]; 5529 low2 = 0; 5530 high2 = nrow2; 5531 bm = aij->B->rmap->n; 5532 ba = b->a; 5533 } 5534 } else col = in[j]; 5535 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5536 } 5537 } 5538 } else if (!aij->donotstash) { 5539 if (roworiented) { 5540 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5541 } else { 5542 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5543 } 5544 } 5545 } 5546 } 5547 PetscFunctionReturnVoid(); 5548 } 5549 5550