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