1 2 3 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 4 #include <petsc/private/vecimpl.h> 5 #include <petsc/private/isimpl.h> 6 #include <petscblaslapack.h> 7 #include <petscsf.h> 8 9 /*MC 10 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 11 12 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 13 and MATMPIAIJ otherwise. As a result, for single process communicators, 14 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 15 for communicators controlling multiple processes. It is recommended that you call both of 16 the above preallocation routines for simplicity. 17 18 Options Database Keys: 19 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 20 21 Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when 22 enough exist. 23 24 Level: beginner 25 26 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ, MATMPIAIJ 27 M*/ 28 29 /*MC 30 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 31 32 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 33 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 34 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 35 for communicators controlling multiple processes. It is recommended that you call both of 36 the above preallocation routines for simplicity. 37 38 Options Database Keys: 39 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 40 41 Level: beginner 42 43 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 44 M*/ 45 46 PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 50 51 PetscFunctionBegin; 52 if (mat->A) { 53 ierr = MatSetBlockSizes(mat->A,rbs,cbs);CHKERRQ(ierr); 54 ierr = MatSetBlockSizes(mat->B,rbs,1);CHKERRQ(ierr); 55 } 56 PetscFunctionReturn(0); 57 } 58 59 PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows) 60 { 61 PetscErrorCode ierr; 62 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 63 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data; 64 Mat_SeqAIJ *b = (Mat_SeqAIJ*)mat->B->data; 65 const PetscInt *ia,*ib; 66 const MatScalar *aa,*bb; 67 PetscInt na,nb,i,j,*rows,cnt=0,n0rows; 68 PetscInt m = M->rmap->n,rstart = M->rmap->rstart; 69 70 PetscFunctionBegin; 71 *keptrows = 0; 72 ia = a->i; 73 ib = b->i; 74 for (i=0; i<m; i++) { 75 na = ia[i+1] - ia[i]; 76 nb = ib[i+1] - ib[i]; 77 if (!na && !nb) { 78 cnt++; 79 goto ok1; 80 } 81 aa = a->a + ia[i]; 82 for (j=0; j<na; j++) { 83 if (aa[j] != 0.0) goto ok1; 84 } 85 bb = b->a + ib[i]; 86 for (j=0; j <nb; j++) { 87 if (bb[j] != 0.0) goto ok1; 88 } 89 cnt++; 90 ok1:; 91 } 92 ierr = MPIU_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr); 93 if (!n0rows) PetscFunctionReturn(0); 94 ierr = PetscMalloc1(M->rmap->n-cnt,&rows);CHKERRQ(ierr); 95 cnt = 0; 96 for (i=0; i<m; i++) { 97 na = ia[i+1] - ia[i]; 98 nb = ib[i+1] - ib[i]; 99 if (!na && !nb) continue; 100 aa = a->a + ia[i]; 101 for (j=0; j<na;j++) { 102 if (aa[j] != 0.0) { 103 rows[cnt++] = rstart + i; 104 goto ok2; 105 } 106 } 107 bb = b->a + ib[i]; 108 for (j=0; j<nb; j++) { 109 if (bb[j] != 0.0) { 110 rows[cnt++] = rstart + i; 111 goto ok2; 112 } 113 } 114 ok2:; 115 } 116 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 117 PetscFunctionReturn(0); 118 } 119 120 PetscErrorCode MatDiagonalSet_MPIAIJ(Mat Y,Vec D,InsertMode is) 121 { 122 PetscErrorCode ierr; 123 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) Y->data; 124 125 PetscFunctionBegin; 126 if (Y->assembled && Y->rmap->rstart == Y->cmap->rstart && Y->rmap->rend == Y->cmap->rend) { 127 ierr = MatDiagonalSet(aij->A,D,is);CHKERRQ(ierr); 128 } else { 129 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 130 } 131 PetscFunctionReturn(0); 132 } 133 134 135 PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows) 136 { 137 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)M->data; 138 PetscErrorCode ierr; 139 PetscInt i,rstart,nrows,*rows; 140 141 PetscFunctionBegin; 142 *zrows = NULL; 143 ierr = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr); 144 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 145 for (i=0; i<nrows; i++) rows[i] += rstart; 146 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 147 PetscFunctionReturn(0); 148 } 149 150 PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms) 151 { 152 PetscErrorCode ierr; 153 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 154 PetscInt i,n,*garray = aij->garray; 155 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ*) aij->A->data; 156 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ*) aij->B->data; 157 PetscReal *work; 158 159 PetscFunctionBegin; 160 ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr); 161 ierr = PetscCalloc1(n,&work);CHKERRQ(ierr); 162 if (type == NORM_2) { 163 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 164 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]); 165 } 166 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 167 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]); 168 } 169 } else if (type == NORM_1) { 170 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 171 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 172 } 173 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 174 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 175 } 176 } else if (type == NORM_INFINITY) { 177 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 178 work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 179 } 180 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 181 work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]); 182 } 183 184 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 185 if (type == NORM_INFINITY) { 186 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 187 } else { 188 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 189 } 190 ierr = PetscFree(work);CHKERRQ(ierr); 191 if (type == NORM_2) { 192 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 193 } 194 PetscFunctionReturn(0); 195 } 196 197 PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A,IS *is) 198 { 199 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 200 IS sis,gis; 201 PetscErrorCode ierr; 202 const PetscInt *isis,*igis; 203 PetscInt n,*iis,nsis,ngis,rstart,i; 204 205 PetscFunctionBegin; 206 ierr = MatFindOffBlockDiagonalEntries(a->A,&sis);CHKERRQ(ierr); 207 ierr = MatFindNonzeroRows(a->B,&gis);CHKERRQ(ierr); 208 ierr = ISGetSize(gis,&ngis);CHKERRQ(ierr); 209 ierr = ISGetSize(sis,&nsis);CHKERRQ(ierr); 210 ierr = ISGetIndices(sis,&isis);CHKERRQ(ierr); 211 ierr = ISGetIndices(gis,&igis);CHKERRQ(ierr); 212 213 ierr = PetscMalloc1(ngis+nsis,&iis);CHKERRQ(ierr); 214 ierr = PetscMemcpy(iis,igis,ngis*sizeof(PetscInt));CHKERRQ(ierr); 215 ierr = PetscMemcpy(iis+ngis,isis,nsis*sizeof(PetscInt));CHKERRQ(ierr); 216 n = ngis + nsis; 217 ierr = PetscSortRemoveDupsInt(&n,iis);CHKERRQ(ierr); 218 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 219 for (i=0; i<n; i++) iis[i] += rstart; 220 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),n,iis,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 221 222 ierr = ISRestoreIndices(sis,&isis);CHKERRQ(ierr); 223 ierr = ISRestoreIndices(gis,&igis);CHKERRQ(ierr); 224 ierr = ISDestroy(&sis);CHKERRQ(ierr); 225 ierr = ISDestroy(&gis);CHKERRQ(ierr); 226 PetscFunctionReturn(0); 227 } 228 229 /* 230 Distributes a SeqAIJ matrix across a set of processes. Code stolen from 231 MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type. 232 233 Only for square matrices 234 235 Used by a preconditioner, hence PETSC_EXTERN 236 */ 237 PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat) 238 { 239 PetscMPIInt rank,size; 240 PetscInt *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz = 0,*gmataj,cnt,row,*ld,bses[2]; 241 PetscErrorCode ierr; 242 Mat mat; 243 Mat_SeqAIJ *gmata; 244 PetscMPIInt tag; 245 MPI_Status status; 246 PetscBool aij; 247 MatScalar *gmataa,*ao,*ad,*gmataarestore=0; 248 249 PetscFunctionBegin; 250 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 251 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 252 if (!rank) { 253 ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr); 254 if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name); 255 } 256 if (reuse == MAT_INITIAL_MATRIX) { 257 ierr = MatCreate(comm,&mat);CHKERRQ(ierr); 258 ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 259 ierr = MatGetBlockSizes(gmat,&bses[0],&bses[1]);CHKERRQ(ierr); 260 ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr); 261 ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr); 262 ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr); 263 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 264 ierr = PetscMalloc2(m,&dlens,m,&olens);CHKERRQ(ierr); 265 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 266 267 rowners[0] = 0; 268 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 269 rstart = rowners[rank]; 270 rend = rowners[rank+1]; 271 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 272 if (!rank) { 273 gmata = (Mat_SeqAIJ*) gmat->data; 274 /* send row lengths to all processors */ 275 for (i=0; i<m; i++) dlens[i] = gmata->ilen[i]; 276 for (i=1; i<size; i++) { 277 ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 278 } 279 /* determine number diagonal and off-diagonal counts */ 280 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 281 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 282 jj = 0; 283 for (i=0; i<m; i++) { 284 for (j=0; j<dlens[i]; j++) { 285 if (gmata->j[jj] < rstart) ld[i]++; 286 if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++; 287 jj++; 288 } 289 } 290 /* send column indices to other processes */ 291 for (i=1; i<size; i++) { 292 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 293 ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 294 ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 295 } 296 297 /* send numerical values to other processes */ 298 for (i=1; i<size; i++) { 299 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 300 ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 301 } 302 gmataa = gmata->a; 303 gmataj = gmata->j; 304 305 } else { 306 /* receive row lengths */ 307 ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 308 /* receive column indices */ 309 ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 310 ierr = PetscMalloc2(nz,&gmataa,nz,&gmataj);CHKERRQ(ierr); 311 ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 312 /* determine number diagonal and off-diagonal counts */ 313 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 314 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 315 jj = 0; 316 for (i=0; i<m; i++) { 317 for (j=0; j<dlens[i]; j++) { 318 if (gmataj[jj] < rstart) ld[i]++; 319 if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++; 320 jj++; 321 } 322 } 323 /* receive numerical values */ 324 ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 325 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 326 } 327 /* set preallocation */ 328 for (i=0; i<m; i++) { 329 dlens[i] -= olens[i]; 330 } 331 ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr); 332 ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr); 333 334 for (i=0; i<m; i++) { 335 dlens[i] += olens[i]; 336 } 337 cnt = 0; 338 for (i=0; i<m; i++) { 339 row = rstart + i; 340 ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr); 341 cnt += dlens[i]; 342 } 343 if (rank) { 344 ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr); 345 } 346 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 347 ierr = PetscFree(rowners);CHKERRQ(ierr); 348 349 ((Mat_MPIAIJ*)(mat->data))->ld = ld; 350 351 *inmat = mat; 352 } else { /* column indices are already set; only need to move over numerical values from process 0 */ 353 Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data; 354 Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data; 355 mat = *inmat; 356 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 357 if (!rank) { 358 /* send numerical values to other processes */ 359 gmata = (Mat_SeqAIJ*) gmat->data; 360 ierr = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr); 361 gmataa = gmata->a; 362 for (i=1; i<size; i++) { 363 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 364 ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 365 } 366 nz = gmata->i[rowners[1]]-gmata->i[rowners[0]]; 367 } else { 368 /* receive numerical values from process 0*/ 369 nz = Ad->nz + Ao->nz; 370 ierr = PetscMalloc1(nz,&gmataa);CHKERRQ(ierr); gmataarestore = gmataa; 371 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 372 } 373 /* transfer numerical values into the diagonal A and off diagonal B parts of mat */ 374 ld = ((Mat_MPIAIJ*)(mat->data))->ld; 375 ad = Ad->a; 376 ao = Ao->a; 377 if (mat->rmap->n) { 378 i = 0; 379 nz = ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 380 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 381 } 382 for (i=1; i<mat->rmap->n; i++) { 383 nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 384 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 385 } 386 i--; 387 if (mat->rmap->n) { 388 nz = Ao->i[i+1] - Ao->i[i] - ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 389 } 390 if (rank) { 391 ierr = PetscFree(gmataarestore);CHKERRQ(ierr); 392 } 393 } 394 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 395 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 396 PetscFunctionReturn(0); 397 } 398 399 /* 400 Local utility routine that creates a mapping from the global column 401 number to the local number in the off-diagonal part of the local 402 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 403 a slightly higher hash table cost; without it it is not scalable (each processor 404 has an order N integer array but is fast to acess. 405 */ 406 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 407 { 408 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 409 PetscErrorCode ierr; 410 PetscInt n = aij->B->cmap->n,i; 411 412 PetscFunctionBegin; 413 if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray"); 414 #if defined(PETSC_USE_CTABLE) 415 ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 416 for (i=0; i<n; i++) { 417 ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr); 418 } 419 #else 420 ierr = PetscCalloc1(mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 421 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N+1)*sizeof(PetscInt));CHKERRQ(ierr); 422 for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1; 423 #endif 424 PetscFunctionReturn(0); 425 } 426 427 #define MatSetValues_SeqAIJ_A_Private(row,col,value,addv,orow,ocol) \ 428 { \ 429 if (col <= lastcol1) low1 = 0; \ 430 else high1 = nrow1; \ 431 lastcol1 = col;\ 432 while (high1-low1 > 5) { \ 433 t = (low1+high1)/2; \ 434 if (rp1[t] > col) high1 = t; \ 435 else low1 = t; \ 436 } \ 437 for (_i=low1; _i<high1; _i++) { \ 438 if (rp1[_i] > col) break; \ 439 if (rp1[_i] == col) { \ 440 if (addv == ADD_VALUES) ap1[_i] += value; \ 441 else ap1[_i] = value; \ 442 goto a_noinsert; \ 443 } \ 444 } \ 445 if (value == 0.0 && ignorezeroentries && row != col) {low1 = 0; high1 = nrow1;goto a_noinsert;} \ 446 if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;} \ 447 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 448 MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \ 449 N = nrow1++ - 1; a->nz++; high1++; \ 450 /* shift up all the later entries in this row */ \ 451 for (ii=N; ii>=_i; ii--) { \ 452 rp1[ii+1] = rp1[ii]; \ 453 ap1[ii+1] = ap1[ii]; \ 454 } \ 455 rp1[_i] = col; \ 456 ap1[_i] = value; \ 457 A->nonzerostate++;\ 458 a_noinsert: ; \ 459 ailen[row] = nrow1; \ 460 } 461 462 463 #define MatSetValues_SeqAIJ_B_Private(row,col,value,addv,orow,ocol) \ 464 { \ 465 if (col <= lastcol2) low2 = 0; \ 466 else high2 = nrow2; \ 467 lastcol2 = col; \ 468 while (high2-low2 > 5) { \ 469 t = (low2+high2)/2; \ 470 if (rp2[t] > col) high2 = t; \ 471 else low2 = t; \ 472 } \ 473 for (_i=low2; _i<high2; _i++) { \ 474 if (rp2[_i] > col) break; \ 475 if (rp2[_i] == col) { \ 476 if (addv == ADD_VALUES) ap2[_i] += value; \ 477 else ap2[_i] = value; \ 478 goto b_noinsert; \ 479 } \ 480 } \ 481 if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 482 if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 483 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 484 MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \ 485 N = nrow2++ - 1; b->nz++; high2++; \ 486 /* shift up all the later entries in this row */ \ 487 for (ii=N; ii>=_i; ii--) { \ 488 rp2[ii+1] = rp2[ii]; \ 489 ap2[ii+1] = ap2[ii]; \ 490 } \ 491 rp2[_i] = col; \ 492 ap2[_i] = value; \ 493 B->nonzerostate++; \ 494 b_noinsert: ; \ 495 bilen[row] = nrow2; \ 496 } 497 498 PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[]) 499 { 500 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)A->data; 501 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data; 502 PetscErrorCode ierr; 503 PetscInt l,*garray = mat->garray,diag; 504 505 PetscFunctionBegin; 506 /* code only works for square matrices A */ 507 508 /* find size of row to the left of the diagonal part */ 509 ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr); 510 row = row - diag; 511 for (l=0; l<b->i[row+1]-b->i[row]; l++) { 512 if (garray[b->j[b->i[row]+l]] > diag) break; 513 } 514 ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr); 515 516 /* diagonal part */ 517 ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr); 518 519 /* right of diagonal part */ 520 ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr); 521 PetscFunctionReturn(0); 522 } 523 524 PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 525 { 526 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 527 PetscScalar value; 528 PetscErrorCode ierr; 529 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 530 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 531 PetscBool roworiented = aij->roworiented; 532 533 /* Some Variables required in the macro */ 534 Mat A = aij->A; 535 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 536 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 537 MatScalar *aa = a->a; 538 PetscBool ignorezeroentries = a->ignorezeroentries; 539 Mat B = aij->B; 540 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 541 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 542 MatScalar *ba = b->a; 543 544 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 545 PetscInt nonew; 546 MatScalar *ap1,*ap2; 547 548 PetscFunctionBegin; 549 for (i=0; i<m; i++) { 550 if (im[i] < 0) continue; 551 #if defined(PETSC_USE_DEBUG) 552 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 553 #endif 554 if (im[i] >= rstart && im[i] < rend) { 555 row = im[i] - rstart; 556 lastcol1 = -1; 557 rp1 = aj + ai[row]; 558 ap1 = aa + ai[row]; 559 rmax1 = aimax[row]; 560 nrow1 = ailen[row]; 561 low1 = 0; 562 high1 = nrow1; 563 lastcol2 = -1; 564 rp2 = bj + bi[row]; 565 ap2 = ba + bi[row]; 566 rmax2 = bimax[row]; 567 nrow2 = bilen[row]; 568 low2 = 0; 569 high2 = nrow2; 570 571 for (j=0; j<n; j++) { 572 if (roworiented) value = v[i*n+j]; 573 else value = v[i+j*m]; 574 if (in[j] >= cstart && in[j] < cend) { 575 col = in[j] - cstart; 576 nonew = a->nonew; 577 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 578 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 579 } else if (in[j] < 0) continue; 580 #if defined(PETSC_USE_DEBUG) 581 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 582 #endif 583 else { 584 if (mat->was_assembled) { 585 if (!aij->colmap) { 586 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 587 } 588 #if defined(PETSC_USE_CTABLE) 589 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 590 col--; 591 #else 592 col = aij->colmap[in[j]] - 1; 593 #endif 594 if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) { 595 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 596 col = in[j]; 597 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 598 B = aij->B; 599 b = (Mat_SeqAIJ*)B->data; 600 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a; 601 rp2 = bj + bi[row]; 602 ap2 = ba + bi[row]; 603 rmax2 = bimax[row]; 604 nrow2 = bilen[row]; 605 low2 = 0; 606 high2 = nrow2; 607 bm = aij->B->rmap->n; 608 ba = b->a; 609 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", im[i], in[j]); 610 } else col = in[j]; 611 nonew = b->nonew; 612 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 613 } 614 } 615 } else { 616 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 617 if (!aij->donotstash) { 618 mat->assembled = PETSC_FALSE; 619 if (roworiented) { 620 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 621 } else { 622 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 623 } 624 } 625 } 626 } 627 PetscFunctionReturn(0); 628 } 629 630 PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 631 { 632 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 633 PetscErrorCode ierr; 634 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 635 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 636 637 PetscFunctionBegin; 638 for (i=0; i<m; i++) { 639 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 640 if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1); 641 if (idxm[i] >= rstart && idxm[i] < rend) { 642 row = idxm[i] - rstart; 643 for (j=0; j<n; j++) { 644 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 645 if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1); 646 if (idxn[j] >= cstart && idxn[j] < cend) { 647 col = idxn[j] - cstart; 648 ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 649 } else { 650 if (!aij->colmap) { 651 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 652 } 653 #if defined(PETSC_USE_CTABLE) 654 ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr); 655 col--; 656 #else 657 col = aij->colmap[idxn[j]] - 1; 658 #endif 659 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0; 660 else { 661 ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 662 } 663 } 664 } 665 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 666 } 667 PetscFunctionReturn(0); 668 } 669 670 extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec); 671 672 PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode) 673 { 674 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 675 PetscErrorCode ierr; 676 PetscInt nstash,reallocs; 677 678 PetscFunctionBegin; 679 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 680 681 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 682 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 683 ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 684 PetscFunctionReturn(0); 685 } 686 687 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode) 688 { 689 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 690 Mat_SeqAIJ *a = (Mat_SeqAIJ*)aij->A->data; 691 PetscErrorCode ierr; 692 PetscMPIInt n; 693 PetscInt i,j,rstart,ncols,flg; 694 PetscInt *row,*col; 695 PetscBool other_disassembled; 696 PetscScalar *val; 697 698 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 699 700 PetscFunctionBegin; 701 if (!aij->donotstash && !mat->nooffprocentries) { 702 while (1) { 703 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 704 if (!flg) break; 705 706 for (i=0; i<n; ) { 707 /* Now identify the consecutive vals belonging to the same row */ 708 for (j=i,rstart=row[j]; j<n; j++) { 709 if (row[j] != rstart) break; 710 } 711 if (j < n) ncols = j-i; 712 else ncols = n-i; 713 /* Now assemble all these values with a single function call */ 714 ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr); 715 716 i = j; 717 } 718 } 719 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 720 } 721 ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr); 722 ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr); 723 724 /* determine if any processor has disassembled, if so we must 725 also disassemble ourselfs, in order that we may reassemble. */ 726 /* 727 if nonzero structure of submatrix B cannot change then we know that 728 no processor disassembled thus we can skip this stuff 729 */ 730 if (!((Mat_SeqAIJ*)aij->B->data)->nonew) { 731 ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 732 if (mat->was_assembled && !other_disassembled) { 733 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 734 } 735 } 736 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 737 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 738 } 739 ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr); 740 ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr); 741 ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr); 742 743 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 744 745 aij->rowvalues = 0; 746 747 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 748 if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ; 749 750 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 751 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 752 PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate; 753 ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 754 } 755 PetscFunctionReturn(0); 756 } 757 758 PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 759 { 760 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 761 PetscErrorCode ierr; 762 763 PetscFunctionBegin; 764 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 765 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 766 PetscFunctionReturn(0); 767 } 768 769 PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 770 { 771 Mat_MPIAIJ *mat = (Mat_MPIAIJ *) A->data; 772 PetscInt *lrows; 773 PetscInt r, len; 774 PetscErrorCode ierr; 775 776 PetscFunctionBegin; 777 /* get locally owned rows */ 778 ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr); 779 /* fix right hand side if needed */ 780 if (x && b) { 781 const PetscScalar *xx; 782 PetscScalar *bb; 783 784 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 785 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 786 for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]]; 787 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 788 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 789 } 790 /* Must zero l->B before l->A because the (diag) case below may put values into l->B*/ 791 ierr = MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 792 if (A->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 793 PetscBool cong; 794 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 795 if (cong) A->congruentlayouts = 1; 796 else A->congruentlayouts = 0; 797 } 798 if ((diag != 0.0) && A->congruentlayouts) { 799 ierr = MatZeroRows(mat->A, len, lrows, diag, NULL, NULL);CHKERRQ(ierr); 800 } else if (diag != 0.0) { 801 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 802 if (((Mat_SeqAIJ *) mat->A->data)->nonew) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 803 for (r = 0; r < len; ++r) { 804 const PetscInt row = lrows[r] + A->rmap->rstart; 805 ierr = MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES);CHKERRQ(ierr); 806 } 807 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 808 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 809 } else { 810 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 811 } 812 ierr = PetscFree(lrows);CHKERRQ(ierr); 813 814 /* only change matrix nonzero state if pattern was allowed to be changed */ 815 if (!((Mat_SeqAIJ*)(mat->A->data))->keepnonzeropattern) { 816 PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate; 817 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 818 } 819 PetscFunctionReturn(0); 820 } 821 822 PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 823 { 824 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 825 PetscErrorCode ierr; 826 PetscMPIInt n = A->rmap->n; 827 PetscInt i,j,r,m,p = 0,len = 0; 828 PetscInt *lrows,*owners = A->rmap->range; 829 PetscSFNode *rrows; 830 PetscSF sf; 831 const PetscScalar *xx; 832 PetscScalar *bb,*mask; 833 Vec xmask,lmask; 834 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)l->B->data; 835 const PetscInt *aj, *ii,*ridx; 836 PetscScalar *aa; 837 838 PetscFunctionBegin; 839 /* Create SF where leaves are input rows and roots are owned rows */ 840 ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr); 841 for (r = 0; r < n; ++r) lrows[r] = -1; 842 ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr); 843 for (r = 0; r < N; ++r) { 844 const PetscInt idx = rows[r]; 845 if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N); 846 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */ 847 ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr); 848 } 849 rrows[r].rank = p; 850 rrows[r].index = rows[r] - owners[p]; 851 } 852 ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr); 853 ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr); 854 /* Collect flags for rows to be zeroed */ 855 ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 856 ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 857 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 858 /* Compress and put in row numbers */ 859 for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r; 860 /* zero diagonal part of matrix */ 861 ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr); 862 /* handle off diagonal part of matrix */ 863 ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr); 864 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 865 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 866 for (i=0; i<len; i++) bb[lrows[i]] = 1; 867 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 868 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 869 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 870 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 871 if (x) { 872 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 873 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 874 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 875 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 876 } 877 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 878 /* remove zeroed rows of off diagonal matrix */ 879 ii = aij->i; 880 for (i=0; i<len; i++) { 881 ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr); 882 } 883 /* loop over all elements of off process part of matrix zeroing removed columns*/ 884 if (aij->compressedrow.use) { 885 m = aij->compressedrow.nrows; 886 ii = aij->compressedrow.i; 887 ridx = aij->compressedrow.rindex; 888 for (i=0; i<m; i++) { 889 n = ii[i+1] - ii[i]; 890 aj = aij->j + ii[i]; 891 aa = aij->a + ii[i]; 892 893 for (j=0; j<n; j++) { 894 if (PetscAbsScalar(mask[*aj])) { 895 if (b) bb[*ridx] -= *aa*xx[*aj]; 896 *aa = 0.0; 897 } 898 aa++; 899 aj++; 900 } 901 ridx++; 902 } 903 } else { /* do not use compressed row format */ 904 m = l->B->rmap->n; 905 for (i=0; i<m; i++) { 906 n = ii[i+1] - ii[i]; 907 aj = aij->j + ii[i]; 908 aa = aij->a + ii[i]; 909 for (j=0; j<n; j++) { 910 if (PetscAbsScalar(mask[*aj])) { 911 if (b) bb[i] -= *aa*xx[*aj]; 912 *aa = 0.0; 913 } 914 aa++; 915 aj++; 916 } 917 } 918 } 919 if (x) { 920 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 921 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 922 } 923 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 924 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 925 ierr = PetscFree(lrows);CHKERRQ(ierr); 926 927 /* only change matrix nonzero state if pattern was allowed to be changed */ 928 if (!((Mat_SeqAIJ*)(l->A->data))->keepnonzeropattern) { 929 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 930 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 931 } 932 PetscFunctionReturn(0); 933 } 934 935 PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy) 936 { 937 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 938 PetscErrorCode ierr; 939 PetscInt nt; 940 941 PetscFunctionBegin; 942 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 943 if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt); 944 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 945 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 946 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 947 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 948 PetscFunctionReturn(0); 949 } 950 951 PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx) 952 { 953 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 954 PetscErrorCode ierr; 955 956 PetscFunctionBegin; 957 ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr); 958 PetscFunctionReturn(0); 959 } 960 961 PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 962 { 963 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 964 PetscErrorCode ierr; 965 966 PetscFunctionBegin; 967 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 968 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 969 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 970 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 971 PetscFunctionReturn(0); 972 } 973 974 PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy) 975 { 976 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 977 PetscErrorCode ierr; 978 PetscBool merged; 979 980 PetscFunctionBegin; 981 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 982 /* do nondiagonal part */ 983 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 984 if (!merged) { 985 /* send it on its way */ 986 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 987 /* do local part */ 988 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 989 /* receive remote parts: note this assumes the values are not actually */ 990 /* added in yy until the next line, */ 991 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 992 } else { 993 /* do local part */ 994 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 995 /* send it on its way */ 996 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 997 /* values actually were received in the Begin() but we need to call this nop */ 998 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 999 } 1000 PetscFunctionReturn(0); 1001 } 1002 1003 PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool *f) 1004 { 1005 MPI_Comm comm; 1006 Mat_MPIAIJ *Aij = (Mat_MPIAIJ*) Amat->data, *Bij; 1007 Mat Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs; 1008 IS Me,Notme; 1009 PetscErrorCode ierr; 1010 PetscInt M,N,first,last,*notme,i; 1011 PetscMPIInt size; 1012 1013 PetscFunctionBegin; 1014 /* Easy test: symmetric diagonal block */ 1015 Bij = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A; 1016 ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr); 1017 if (!*f) PetscFunctionReturn(0); 1018 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1019 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1020 if (size == 1) PetscFunctionReturn(0); 1021 1022 /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */ 1023 ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr); 1024 ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr); 1025 ierr = PetscMalloc1(N-last+first,¬me);CHKERRQ(ierr); 1026 for (i=0; i<first; i++) notme[i] = i; 1027 for (i=last; i<M; i++) notme[i-last+first] = i; 1028 ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr); 1029 ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr); 1030 ierr = MatCreateSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr); 1031 Aoff = Aoffs[0]; 1032 ierr = MatCreateSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr); 1033 Boff = Boffs[0]; 1034 ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr); 1035 ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr); 1036 ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr); 1037 ierr = ISDestroy(&Me);CHKERRQ(ierr); 1038 ierr = ISDestroy(&Notme);CHKERRQ(ierr); 1039 ierr = PetscFree(notme);CHKERRQ(ierr); 1040 PetscFunctionReturn(0); 1041 } 1042 1043 PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1044 { 1045 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1046 PetscErrorCode ierr; 1047 1048 PetscFunctionBegin; 1049 /* do nondiagonal part */ 1050 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1051 /* send it on its way */ 1052 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1053 /* do local part */ 1054 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1055 /* receive remote parts */ 1056 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1057 PetscFunctionReturn(0); 1058 } 1059 1060 /* 1061 This only works correctly for square matrices where the subblock A->A is the 1062 diagonal block 1063 */ 1064 PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v) 1065 { 1066 PetscErrorCode ierr; 1067 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1068 1069 PetscFunctionBegin; 1070 if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1071 if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition"); 1072 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1073 PetscFunctionReturn(0); 1074 } 1075 1076 PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa) 1077 { 1078 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1079 PetscErrorCode ierr; 1080 1081 PetscFunctionBegin; 1082 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1083 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1084 PetscFunctionReturn(0); 1085 } 1086 1087 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 1088 { 1089 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1090 PetscErrorCode ierr; 1091 1092 PetscFunctionBegin; 1093 #if defined(PETSC_USE_LOG) 1094 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N); 1095 #endif 1096 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1097 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 1098 ierr = MatDestroy(&aij->A);CHKERRQ(ierr); 1099 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 1100 #if defined(PETSC_USE_CTABLE) 1101 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 1102 #else 1103 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 1104 #endif 1105 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 1106 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 1107 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 1108 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 1109 ierr = PetscFree(aij->ld);CHKERRQ(ierr); 1110 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1111 1112 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1113 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1114 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1115 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1116 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1117 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1118 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1119 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1120 #if defined(PETSC_HAVE_ELEMENTAL) 1121 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_elemental_C",NULL);CHKERRQ(ierr); 1122 #endif 1123 #if defined(PETSC_HAVE_HYPRE) 1124 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_hypre_C",NULL);CHKERRQ(ierr); 1125 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMatMatMult_transpose_mpiaij_mpiaij_C",NULL);CHKERRQ(ierr); 1126 #endif 1127 PetscFunctionReturn(0); 1128 } 1129 1130 PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer) 1131 { 1132 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1133 Mat_SeqAIJ *A = (Mat_SeqAIJ*)aij->A->data; 1134 Mat_SeqAIJ *B = (Mat_SeqAIJ*)aij->B->data; 1135 PetscErrorCode ierr; 1136 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1137 int fd; 1138 PetscInt nz,header[4],*row_lengths,*range=0,rlen,i; 1139 PetscInt nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz = 0; 1140 PetscScalar *column_values; 1141 PetscInt message_count,flowcontrolcount; 1142 FILE *file; 1143 1144 PetscFunctionBegin; 1145 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1146 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1147 nz = A->nz + B->nz; 1148 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1149 if (!rank) { 1150 header[0] = MAT_FILE_CLASSID; 1151 header[1] = mat->rmap->N; 1152 header[2] = mat->cmap->N; 1153 1154 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1155 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1156 /* get largest number of rows any processor has */ 1157 rlen = mat->rmap->n; 1158 range = mat->rmap->range; 1159 for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]); 1160 } else { 1161 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1162 rlen = mat->rmap->n; 1163 } 1164 1165 /* load up the local row counts */ 1166 ierr = PetscMalloc1(rlen+1,&row_lengths);CHKERRQ(ierr); 1167 for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1168 1169 /* store the row lengths to the file */ 1170 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1171 if (!rank) { 1172 ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1173 for (i=1; i<size; i++) { 1174 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1175 rlen = range[i+1] - range[i]; 1176 ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1177 ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1178 } 1179 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1180 } else { 1181 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1182 ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1183 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1184 } 1185 ierr = PetscFree(row_lengths);CHKERRQ(ierr); 1186 1187 /* load up the local column indices */ 1188 nzmax = nz; /* th processor needs space a largest processor needs */ 1189 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1190 ierr = PetscMalloc1(nzmax+1,&column_indices);CHKERRQ(ierr); 1191 cnt = 0; 1192 for (i=0; i<mat->rmap->n; i++) { 1193 for (j=B->i[i]; j<B->i[i+1]; j++) { 1194 if ((col = garray[B->j[j]]) > cstart) break; 1195 column_indices[cnt++] = col; 1196 } 1197 for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart; 1198 for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]]; 1199 } 1200 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1201 1202 /* store the column indices to the file */ 1203 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1204 if (!rank) { 1205 MPI_Status status; 1206 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1207 for (i=1; i<size; i++) { 1208 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1209 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1210 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1211 ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1212 ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1213 } 1214 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1215 } else { 1216 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1217 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1218 ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1219 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1220 } 1221 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1222 1223 /* load up the local column values */ 1224 ierr = PetscMalloc1(nzmax+1,&column_values);CHKERRQ(ierr); 1225 cnt = 0; 1226 for (i=0; i<mat->rmap->n; i++) { 1227 for (j=B->i[i]; j<B->i[i+1]; j++) { 1228 if (garray[B->j[j]] > cstart) break; 1229 column_values[cnt++] = B->a[j]; 1230 } 1231 for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k]; 1232 for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j]; 1233 } 1234 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1235 1236 /* store the column values to the file */ 1237 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1238 if (!rank) { 1239 MPI_Status status; 1240 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1241 for (i=1; i<size; i++) { 1242 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1243 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1244 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1245 ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1246 ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1247 } 1248 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1249 } else { 1250 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1251 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1252 ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1253 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1254 } 1255 ierr = PetscFree(column_values);CHKERRQ(ierr); 1256 1257 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1258 if (file) fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(mat->rmap->bs)); 1259 PetscFunctionReturn(0); 1260 } 1261 1262 #include <petscdraw.h> 1263 PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 1264 { 1265 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1266 PetscErrorCode ierr; 1267 PetscMPIInt rank = aij->rank,size = aij->size; 1268 PetscBool isdraw,iascii,isbinary; 1269 PetscViewer sviewer; 1270 PetscViewerFormat format; 1271 1272 PetscFunctionBegin; 1273 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1274 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1275 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1276 if (iascii) { 1277 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1278 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1279 MatInfo info; 1280 PetscBool inodes; 1281 1282 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1283 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 1284 ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr); 1285 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 1286 if (!inodes) { 1287 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n", 1288 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1289 } else { 1290 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n", 1291 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1292 } 1293 ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1294 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1295 ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1296 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1297 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1298 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 1299 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1300 ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr); 1301 PetscFunctionReturn(0); 1302 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1303 PetscInt inodecount,inodelimit,*inodes; 1304 ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr); 1305 if (inodes) { 1306 ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr); 1307 } else { 1308 ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr); 1309 } 1310 PetscFunctionReturn(0); 1311 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1312 PetscFunctionReturn(0); 1313 } 1314 } else if (isbinary) { 1315 if (size == 1) { 1316 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1317 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1318 } else { 1319 ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1320 } 1321 PetscFunctionReturn(0); 1322 } else if (isdraw) { 1323 PetscDraw draw; 1324 PetscBool isnull; 1325 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1326 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 1327 if (isnull) PetscFunctionReturn(0); 1328 } 1329 1330 { 1331 /* assemble the entire matrix onto first processor. */ 1332 Mat A; 1333 Mat_SeqAIJ *Aloc; 1334 PetscInt M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct; 1335 MatScalar *a; 1336 1337 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1338 if (!rank) { 1339 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1340 } else { 1341 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1342 } 1343 /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */ 1344 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 1345 ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr); 1346 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1347 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1348 1349 /* copy over the A part */ 1350 Aloc = (Mat_SeqAIJ*)aij->A->data; 1351 m = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1352 row = mat->rmap->rstart; 1353 for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart; 1354 for (i=0; i<m; i++) { 1355 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr); 1356 row++; 1357 a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i]; 1358 } 1359 aj = Aloc->j; 1360 for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart; 1361 1362 /* copy over the B part */ 1363 Aloc = (Mat_SeqAIJ*)aij->B->data; 1364 m = aij->B->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1365 row = mat->rmap->rstart; 1366 ierr = PetscMalloc1(ai[m]+1,&cols);CHKERRQ(ierr); 1367 ct = cols; 1368 for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]]; 1369 for (i=0; i<m; i++) { 1370 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr); 1371 row++; 1372 a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i]; 1373 } 1374 ierr = PetscFree(ct);CHKERRQ(ierr); 1375 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1376 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1377 /* 1378 Everyone has to call to draw the matrix since the graphics waits are 1379 synchronized across all processors that share the PetscDraw object 1380 */ 1381 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1382 if (!rank) { 1383 ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1384 ierr = MatView_SeqAIJ(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1385 } 1386 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1387 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1388 ierr = MatDestroy(&A);CHKERRQ(ierr); 1389 } 1390 PetscFunctionReturn(0); 1391 } 1392 1393 PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer) 1394 { 1395 PetscErrorCode ierr; 1396 PetscBool iascii,isdraw,issocket,isbinary; 1397 1398 PetscFunctionBegin; 1399 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1400 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1401 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1402 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1403 if (iascii || isdraw || isbinary || issocket) { 1404 ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1405 } 1406 PetscFunctionReturn(0); 1407 } 1408 1409 PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1410 { 1411 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1412 PetscErrorCode ierr; 1413 Vec bb1 = 0; 1414 PetscBool hasop; 1415 1416 PetscFunctionBegin; 1417 if (flag == SOR_APPLY_UPPER) { 1418 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1419 PetscFunctionReturn(0); 1420 } 1421 1422 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) { 1423 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 1424 } 1425 1426 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1427 if (flag & SOR_ZERO_INITIAL_GUESS) { 1428 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1429 its--; 1430 } 1431 1432 while (its--) { 1433 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1434 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1435 1436 /* update rhs: bb1 = bb - B*x */ 1437 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1438 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1439 1440 /* local sweep */ 1441 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1442 } 1443 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1444 if (flag & SOR_ZERO_INITIAL_GUESS) { 1445 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1446 its--; 1447 } 1448 while (its--) { 1449 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1450 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1451 1452 /* update rhs: bb1 = bb - B*x */ 1453 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1454 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1455 1456 /* local sweep */ 1457 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1458 } 1459 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1460 if (flag & SOR_ZERO_INITIAL_GUESS) { 1461 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1462 its--; 1463 } 1464 while (its--) { 1465 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1466 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1467 1468 /* update rhs: bb1 = bb - B*x */ 1469 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1470 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1471 1472 /* local sweep */ 1473 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1474 } 1475 } else if (flag & SOR_EISENSTAT) { 1476 Vec xx1; 1477 1478 ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr); 1479 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr); 1480 1481 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1482 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1483 if (!mat->diag) { 1484 ierr = MatCreateVecs(matin,&mat->diag,NULL);CHKERRQ(ierr); 1485 ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr); 1486 } 1487 ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr); 1488 if (hasop) { 1489 ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr); 1490 } else { 1491 ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr); 1492 } 1493 ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr); 1494 1495 ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr); 1496 1497 /* local sweep */ 1498 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr); 1499 ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr); 1500 ierr = VecDestroy(&xx1);CHKERRQ(ierr); 1501 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported"); 1502 1503 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 1504 1505 matin->factorerrortype = mat->A->factorerrortype; 1506 PetscFunctionReturn(0); 1507 } 1508 1509 PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B) 1510 { 1511 Mat aA,aB,Aperm; 1512 const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj; 1513 PetscScalar *aa,*ba; 1514 PetscInt i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest; 1515 PetscSF rowsf,sf; 1516 IS parcolp = NULL; 1517 PetscBool done; 1518 PetscErrorCode ierr; 1519 1520 PetscFunctionBegin; 1521 ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); 1522 ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr); 1523 ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr); 1524 ierr = PetscMalloc3(PetscMax(m,n),&work,m,&rdest,n,&cdest);CHKERRQ(ierr); 1525 1526 /* Invert row permutation to find out where my rows should go */ 1527 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr); 1528 ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr); 1529 ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr); 1530 for (i=0; i<m; i++) work[i] = A->rmap->rstart + i; 1531 ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1532 ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1533 1534 /* Invert column permutation to find out where my columns should go */ 1535 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1536 ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr); 1537 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1538 for (i=0; i<n; i++) work[i] = A->cmap->rstart + i; 1539 ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1540 ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1541 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1542 1543 ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr); 1544 ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr); 1545 ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr); 1546 1547 /* Find out where my gcols should go */ 1548 ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr); 1549 ierr = PetscMalloc1(ng,&gcdest);CHKERRQ(ierr); 1550 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1551 ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr); 1552 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1553 ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1554 ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1555 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1556 1557 ierr = PetscCalloc4(m,&dnnz,m,&onnz,m,&tdnnz,m,&tonnz);CHKERRQ(ierr); 1558 ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1559 ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1560 for (i=0; i<m; i++) { 1561 PetscInt row = rdest[i],rowner; 1562 ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr); 1563 for (j=ai[i]; j<ai[i+1]; j++) { 1564 PetscInt cowner,col = cdest[aj[j]]; 1565 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */ 1566 if (rowner == cowner) dnnz[i]++; 1567 else onnz[i]++; 1568 } 1569 for (j=bi[i]; j<bi[i+1]; j++) { 1570 PetscInt cowner,col = gcdest[bj[j]]; 1571 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); 1572 if (rowner == cowner) dnnz[i]++; 1573 else onnz[i]++; 1574 } 1575 } 1576 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1577 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1578 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1579 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1580 ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr); 1581 1582 ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr); 1583 ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr); 1584 ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr); 1585 for (i=0; i<m; i++) { 1586 PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */ 1587 PetscInt j0,rowlen; 1588 rowlen = ai[i+1] - ai[i]; 1589 for (j0=j=0; j<rowlen; j0=j) { /* rowlen could be larger than number of rows m, so sum in batches */ 1590 for ( ; j<PetscMin(rowlen,j0+m); j++) acols[j-j0] = cdest[aj[ai[i]+j]]; 1591 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,acols,aa+ai[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1592 } 1593 rowlen = bi[i+1] - bi[i]; 1594 for (j0=j=0; j<rowlen; j0=j) { 1595 for ( ; j<PetscMin(rowlen,j0+m); j++) bcols[j-j0] = gcdest[bj[bi[i]+j]]; 1596 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,bcols,ba+bi[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1597 } 1598 } 1599 ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1600 ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1601 ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1602 ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1603 ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr); 1604 ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr); 1605 ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr); 1606 ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr); 1607 ierr = PetscFree(gcdest);CHKERRQ(ierr); 1608 if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);} 1609 *B = Aperm; 1610 PetscFunctionReturn(0); 1611 } 1612 1613 PetscErrorCode MatGetGhosts_MPIAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 1614 { 1615 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1616 PetscErrorCode ierr; 1617 1618 PetscFunctionBegin; 1619 ierr = MatGetSize(aij->B,NULL,nghosts);CHKERRQ(ierr); 1620 if (ghosts) *ghosts = aij->garray; 1621 PetscFunctionReturn(0); 1622 } 1623 1624 PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1625 { 1626 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1627 Mat A = mat->A,B = mat->B; 1628 PetscErrorCode ierr; 1629 PetscReal isend[5],irecv[5]; 1630 1631 PetscFunctionBegin; 1632 info->block_size = 1.0; 1633 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1634 1635 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1636 isend[3] = info->memory; isend[4] = info->mallocs; 1637 1638 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1639 1640 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1641 isend[3] += info->memory; isend[4] += info->mallocs; 1642 if (flag == MAT_LOCAL) { 1643 info->nz_used = isend[0]; 1644 info->nz_allocated = isend[1]; 1645 info->nz_unneeded = isend[2]; 1646 info->memory = isend[3]; 1647 info->mallocs = isend[4]; 1648 } else if (flag == MAT_GLOBAL_MAX) { 1649 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1650 1651 info->nz_used = irecv[0]; 1652 info->nz_allocated = irecv[1]; 1653 info->nz_unneeded = irecv[2]; 1654 info->memory = irecv[3]; 1655 info->mallocs = irecv[4]; 1656 } else if (flag == MAT_GLOBAL_SUM) { 1657 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1658 1659 info->nz_used = irecv[0]; 1660 info->nz_allocated = irecv[1]; 1661 info->nz_unneeded = irecv[2]; 1662 info->memory = irecv[3]; 1663 info->mallocs = irecv[4]; 1664 } 1665 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1666 info->fill_ratio_needed = 0; 1667 info->factor_mallocs = 0; 1668 PetscFunctionReturn(0); 1669 } 1670 1671 PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg) 1672 { 1673 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1674 PetscErrorCode ierr; 1675 1676 PetscFunctionBegin; 1677 switch (op) { 1678 case MAT_NEW_NONZERO_LOCATIONS: 1679 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1680 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1681 case MAT_KEEP_NONZERO_PATTERN: 1682 case MAT_NEW_NONZERO_LOCATION_ERR: 1683 case MAT_USE_INODES: 1684 case MAT_IGNORE_ZERO_ENTRIES: 1685 MatCheckPreallocated(A,1); 1686 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1687 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1688 break; 1689 case MAT_ROW_ORIENTED: 1690 MatCheckPreallocated(A,1); 1691 a->roworiented = flg; 1692 1693 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1694 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1695 break; 1696 case MAT_NEW_DIAGONALS: 1697 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1698 break; 1699 case MAT_IGNORE_OFF_PROC_ENTRIES: 1700 a->donotstash = flg; 1701 break; 1702 case MAT_SPD: 1703 A->spd_set = PETSC_TRUE; 1704 A->spd = flg; 1705 if (flg) { 1706 A->symmetric = PETSC_TRUE; 1707 A->structurally_symmetric = PETSC_TRUE; 1708 A->symmetric_set = PETSC_TRUE; 1709 A->structurally_symmetric_set = PETSC_TRUE; 1710 } 1711 break; 1712 case MAT_SYMMETRIC: 1713 MatCheckPreallocated(A,1); 1714 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1715 break; 1716 case MAT_STRUCTURALLY_SYMMETRIC: 1717 MatCheckPreallocated(A,1); 1718 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1719 break; 1720 case MAT_HERMITIAN: 1721 MatCheckPreallocated(A,1); 1722 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1723 break; 1724 case MAT_SYMMETRY_ETERNAL: 1725 MatCheckPreallocated(A,1); 1726 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1727 break; 1728 case MAT_SUBMAT_SINGLEIS: 1729 A->submat_singleis = flg; 1730 break; 1731 default: 1732 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1733 } 1734 PetscFunctionReturn(0); 1735 } 1736 1737 PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1738 { 1739 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1740 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1741 PetscErrorCode ierr; 1742 PetscInt i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart; 1743 PetscInt nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend; 1744 PetscInt *cmap,*idx_p; 1745 1746 PetscFunctionBegin; 1747 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1748 mat->getrowactive = PETSC_TRUE; 1749 1750 if (!mat->rowvalues && (idx || v)) { 1751 /* 1752 allocate enough space to hold information from the longest row. 1753 */ 1754 Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data; 1755 PetscInt max = 1,tmp; 1756 for (i=0; i<matin->rmap->n; i++) { 1757 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1758 if (max < tmp) max = tmp; 1759 } 1760 ierr = PetscMalloc2(max,&mat->rowvalues,max,&mat->rowindices);CHKERRQ(ierr); 1761 } 1762 1763 if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows"); 1764 lrow = row - rstart; 1765 1766 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1767 if (!v) {pvA = 0; pvB = 0;} 1768 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1769 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1770 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1771 nztot = nzA + nzB; 1772 1773 cmap = mat->garray; 1774 if (v || idx) { 1775 if (nztot) { 1776 /* Sort by increasing column numbers, assuming A and B already sorted */ 1777 PetscInt imark = -1; 1778 if (v) { 1779 *v = v_p = mat->rowvalues; 1780 for (i=0; i<nzB; i++) { 1781 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1782 else break; 1783 } 1784 imark = i; 1785 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1786 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1787 } 1788 if (idx) { 1789 *idx = idx_p = mat->rowindices; 1790 if (imark > -1) { 1791 for (i=0; i<imark; i++) { 1792 idx_p[i] = cmap[cworkB[i]]; 1793 } 1794 } else { 1795 for (i=0; i<nzB; i++) { 1796 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1797 else break; 1798 } 1799 imark = i; 1800 } 1801 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart + cworkA[i]; 1802 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]]; 1803 } 1804 } else { 1805 if (idx) *idx = 0; 1806 if (v) *v = 0; 1807 } 1808 } 1809 *nz = nztot; 1810 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1811 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1812 PetscFunctionReturn(0); 1813 } 1814 1815 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1816 { 1817 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1818 1819 PetscFunctionBegin; 1820 if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first"); 1821 aij->getrowactive = PETSC_FALSE; 1822 PetscFunctionReturn(0); 1823 } 1824 1825 PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm) 1826 { 1827 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1828 Mat_SeqAIJ *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data; 1829 PetscErrorCode ierr; 1830 PetscInt i,j,cstart = mat->cmap->rstart; 1831 PetscReal sum = 0.0; 1832 MatScalar *v; 1833 1834 PetscFunctionBegin; 1835 if (aij->size == 1) { 1836 ierr = MatNorm(aij->A,type,norm);CHKERRQ(ierr); 1837 } else { 1838 if (type == NORM_FROBENIUS) { 1839 v = amat->a; 1840 for (i=0; i<amat->nz; i++) { 1841 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1842 } 1843 v = bmat->a; 1844 for (i=0; i<bmat->nz; i++) { 1845 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1846 } 1847 ierr = MPIU_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1848 *norm = PetscSqrtReal(*norm); 1849 ierr = PetscLogFlops(2*amat->nz+2*bmat->nz);CHKERRQ(ierr); 1850 } else if (type == NORM_1) { /* max column norm */ 1851 PetscReal *tmp,*tmp2; 1852 PetscInt *jj,*garray = aij->garray; 1853 ierr = PetscCalloc1(mat->cmap->N+1,&tmp);CHKERRQ(ierr); 1854 ierr = PetscMalloc1(mat->cmap->N+1,&tmp2);CHKERRQ(ierr); 1855 *norm = 0.0; 1856 v = amat->a; jj = amat->j; 1857 for (j=0; j<amat->nz; j++) { 1858 tmp[cstart + *jj++] += PetscAbsScalar(*v); v++; 1859 } 1860 v = bmat->a; jj = bmat->j; 1861 for (j=0; j<bmat->nz; j++) { 1862 tmp[garray[*jj++]] += PetscAbsScalar(*v); v++; 1863 } 1864 ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1865 for (j=0; j<mat->cmap->N; j++) { 1866 if (tmp2[j] > *norm) *norm = tmp2[j]; 1867 } 1868 ierr = PetscFree(tmp);CHKERRQ(ierr); 1869 ierr = PetscFree(tmp2);CHKERRQ(ierr); 1870 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1871 } else if (type == NORM_INFINITY) { /* max row norm */ 1872 PetscReal ntemp = 0.0; 1873 for (j=0; j<aij->A->rmap->n; j++) { 1874 v = amat->a + amat->i[j]; 1875 sum = 0.0; 1876 for (i=0; i<amat->i[j+1]-amat->i[j]; i++) { 1877 sum += PetscAbsScalar(*v); v++; 1878 } 1879 v = bmat->a + bmat->i[j]; 1880 for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) { 1881 sum += PetscAbsScalar(*v); v++; 1882 } 1883 if (sum > ntemp) ntemp = sum; 1884 } 1885 ierr = MPIU_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1886 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1887 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm"); 1888 } 1889 PetscFunctionReturn(0); 1890 } 1891 1892 PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout) 1893 { 1894 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1895 Mat_SeqAIJ *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data; 1896 PetscErrorCode ierr; 1897 PetscInt M = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i; 1898 PetscInt cstart = A->cmap->rstart,ncol; 1899 Mat B; 1900 MatScalar *array; 1901 1902 PetscFunctionBegin; 1903 if (reuse == MAT_INPLACE_MATRIX && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1904 1905 ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n; 1906 ai = Aloc->i; aj = Aloc->j; 1907 bi = Bloc->i; bj = Bloc->j; 1908 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1909 PetscInt *d_nnz,*g_nnz,*o_nnz; 1910 PetscSFNode *oloc; 1911 PETSC_UNUSED PetscSF sf; 1912 1913 ierr = PetscMalloc4(na,&d_nnz,na,&o_nnz,nb,&g_nnz,nb,&oloc);CHKERRQ(ierr); 1914 /* compute d_nnz for preallocation */ 1915 ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1916 for (i=0; i<ai[ma]; i++) { 1917 d_nnz[aj[i]]++; 1918 aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1919 } 1920 /* compute local off-diagonal contributions */ 1921 ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr); 1922 for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++; 1923 /* map those to global */ 1924 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1925 ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr); 1926 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1927 ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1928 ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1929 ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1930 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1931 1932 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1933 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1934 ierr = MatSetBlockSizes(B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 1935 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1936 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 1937 ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr); 1938 } else { 1939 B = *matout; 1940 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1941 for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1942 } 1943 1944 /* copy over the A part */ 1945 array = Aloc->a; 1946 row = A->rmap->rstart; 1947 for (i=0; i<ma; i++) { 1948 ncol = ai[i+1]-ai[i]; 1949 ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1950 row++; 1951 array += ncol; aj += ncol; 1952 } 1953 aj = Aloc->j; 1954 for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */ 1955 1956 /* copy over the B part */ 1957 ierr = PetscCalloc1(bi[mb],&cols);CHKERRQ(ierr); 1958 array = Bloc->a; 1959 row = A->rmap->rstart; 1960 for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]]; 1961 cols_tmp = cols; 1962 for (i=0; i<mb; i++) { 1963 ncol = bi[i+1]-bi[i]; 1964 ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1965 row++; 1966 array += ncol; cols_tmp += ncol; 1967 } 1968 ierr = PetscFree(cols);CHKERRQ(ierr); 1969 1970 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1971 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1972 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 1973 *matout = B; 1974 } else { 1975 ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr); 1976 } 1977 PetscFunctionReturn(0); 1978 } 1979 1980 PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr) 1981 { 1982 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1983 Mat a = aij->A,b = aij->B; 1984 PetscErrorCode ierr; 1985 PetscInt s1,s2,s3; 1986 1987 PetscFunctionBegin; 1988 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1989 if (rr) { 1990 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1991 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1992 /* Overlap communication with computation. */ 1993 ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1994 } 1995 if (ll) { 1996 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1997 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1998 ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr); 1999 } 2000 /* scale the diagonal block */ 2001 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 2002 2003 if (rr) { 2004 /* Do a scatter end and then right scale the off-diagonal block */ 2005 ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2006 ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr); 2007 } 2008 PetscFunctionReturn(0); 2009 } 2010 2011 PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2012 { 2013 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2014 PetscErrorCode ierr; 2015 2016 PetscFunctionBegin; 2017 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 2018 PetscFunctionReturn(0); 2019 } 2020 2021 PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool *flag) 2022 { 2023 Mat_MPIAIJ *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data; 2024 Mat a,b,c,d; 2025 PetscBool flg; 2026 PetscErrorCode ierr; 2027 2028 PetscFunctionBegin; 2029 a = matA->A; b = matA->B; 2030 c = matB->A; d = matB->B; 2031 2032 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 2033 if (flg) { 2034 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 2035 } 2036 ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2037 PetscFunctionReturn(0); 2038 } 2039 2040 PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str) 2041 { 2042 PetscErrorCode ierr; 2043 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2044 Mat_MPIAIJ *b = (Mat_MPIAIJ*)B->data; 2045 2046 PetscFunctionBegin; 2047 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2048 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2049 /* because of the column compression in the off-processor part of the matrix a->B, 2050 the number of columns in a->B and b->B may be different, hence we cannot call 2051 the MatCopy() directly on the two parts. If need be, we can provide a more 2052 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2053 then copying the submatrices */ 2054 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2055 } else { 2056 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 2057 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 2058 } 2059 PetscFunctionReturn(0); 2060 } 2061 2062 PetscErrorCode MatSetUp_MPIAIJ(Mat A) 2063 { 2064 PetscErrorCode ierr; 2065 2066 PetscFunctionBegin; 2067 ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 2068 PetscFunctionReturn(0); 2069 } 2070 2071 /* 2072 Computes the number of nonzeros per row needed for preallocation when X and Y 2073 have different nonzero structure. 2074 */ 2075 PetscErrorCode MatAXPYGetPreallocation_MPIX_private(PetscInt m,const PetscInt *xi,const PetscInt *xj,const PetscInt *xltog,const PetscInt *yi,const PetscInt *yj,const PetscInt *yltog,PetscInt *nnz) 2076 { 2077 PetscInt i,j,k,nzx,nzy; 2078 2079 PetscFunctionBegin; 2080 /* Set the number of nonzeros in the new matrix */ 2081 for (i=0; i<m; i++) { 2082 const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i]; 2083 nzx = xi[i+1] - xi[i]; 2084 nzy = yi[i+1] - yi[i]; 2085 nnz[i] = 0; 2086 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2087 for (; k<nzy && yltog[yjj[k]]<xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */ 2088 if (k<nzy && yltog[yjj[k]]==xltog[xjj[j]]) k++; /* Skip duplicate */ 2089 nnz[i]++; 2090 } 2091 for (; k<nzy; k++) nnz[i]++; 2092 } 2093 PetscFunctionReturn(0); 2094 } 2095 2096 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2097 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 2098 { 2099 PetscErrorCode ierr; 2100 PetscInt m = Y->rmap->N; 2101 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2102 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2103 2104 PetscFunctionBegin; 2105 ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr); 2106 PetscFunctionReturn(0); 2107 } 2108 2109 PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2110 { 2111 PetscErrorCode ierr; 2112 Mat_MPIAIJ *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data; 2113 PetscBLASInt bnz,one=1; 2114 Mat_SeqAIJ *x,*y; 2115 2116 PetscFunctionBegin; 2117 if (str == SAME_NONZERO_PATTERN) { 2118 PetscScalar alpha = a; 2119 x = (Mat_SeqAIJ*)xx->A->data; 2120 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2121 y = (Mat_SeqAIJ*)yy->A->data; 2122 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2123 x = (Mat_SeqAIJ*)xx->B->data; 2124 y = (Mat_SeqAIJ*)yy->B->data; 2125 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2126 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2127 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 2128 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2129 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 2130 } else { 2131 Mat B; 2132 PetscInt *nnz_d,*nnz_o; 2133 ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr); 2134 ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr); 2135 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2136 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2137 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2138 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 2139 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2140 ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 2141 ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 2142 ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 2143 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2144 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 2145 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 2146 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 2147 } 2148 PetscFunctionReturn(0); 2149 } 2150 2151 extern PetscErrorCode MatConjugate_SeqAIJ(Mat); 2152 2153 PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2154 { 2155 #if defined(PETSC_USE_COMPLEX) 2156 PetscErrorCode ierr; 2157 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2158 2159 PetscFunctionBegin; 2160 ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr); 2161 ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr); 2162 #else 2163 PetscFunctionBegin; 2164 #endif 2165 PetscFunctionReturn(0); 2166 } 2167 2168 PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2169 { 2170 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2171 PetscErrorCode ierr; 2172 2173 PetscFunctionBegin; 2174 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2175 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2176 PetscFunctionReturn(0); 2177 } 2178 2179 PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2180 { 2181 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2182 PetscErrorCode ierr; 2183 2184 PetscFunctionBegin; 2185 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2186 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2187 PetscFunctionReturn(0); 2188 } 2189 2190 PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2191 { 2192 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2193 PetscErrorCode ierr; 2194 PetscInt i,*idxb = 0; 2195 PetscScalar *va,*vb; 2196 Vec vtmp; 2197 2198 PetscFunctionBegin; 2199 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 2200 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2201 if (idx) { 2202 for (i=0; i<A->rmap->n; i++) { 2203 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2204 } 2205 } 2206 2207 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2208 if (idx) { 2209 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2210 } 2211 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2212 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2213 2214 for (i=0; i<A->rmap->n; i++) { 2215 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 2216 va[i] = vb[i]; 2217 if (idx) idx[i] = a->garray[idxb[i]]; 2218 } 2219 } 2220 2221 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2222 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2223 ierr = PetscFree(idxb);CHKERRQ(ierr); 2224 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2225 PetscFunctionReturn(0); 2226 } 2227 2228 PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2229 { 2230 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2231 PetscErrorCode ierr; 2232 PetscInt i,*idxb = 0; 2233 PetscScalar *va,*vb; 2234 Vec vtmp; 2235 2236 PetscFunctionBegin; 2237 ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr); 2238 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2239 if (idx) { 2240 for (i=0; i<A->cmap->n; i++) { 2241 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2242 } 2243 } 2244 2245 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2246 if (idx) { 2247 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2248 } 2249 ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2250 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2251 2252 for (i=0; i<A->rmap->n; i++) { 2253 if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) { 2254 va[i] = vb[i]; 2255 if (idx) idx[i] = a->garray[idxb[i]]; 2256 } 2257 } 2258 2259 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2260 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2261 ierr = PetscFree(idxb);CHKERRQ(ierr); 2262 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2263 PetscFunctionReturn(0); 2264 } 2265 2266 PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2267 { 2268 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2269 PetscInt n = A->rmap->n; 2270 PetscInt cstart = A->cmap->rstart; 2271 PetscInt *cmap = mat->garray; 2272 PetscInt *diagIdx, *offdiagIdx; 2273 Vec diagV, offdiagV; 2274 PetscScalar *a, *diagA, *offdiagA; 2275 PetscInt r; 2276 PetscErrorCode ierr; 2277 2278 PetscFunctionBegin; 2279 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2280 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr); 2281 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr); 2282 ierr = MatGetRowMin(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2283 ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2284 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2285 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2286 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2287 for (r = 0; r < n; ++r) { 2288 if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) { 2289 a[r] = diagA[r]; 2290 idx[r] = cstart + diagIdx[r]; 2291 } else { 2292 a[r] = offdiagA[r]; 2293 idx[r] = cmap[offdiagIdx[r]]; 2294 } 2295 } 2296 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2297 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2298 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2299 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2300 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2301 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2302 PetscFunctionReturn(0); 2303 } 2304 2305 PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2306 { 2307 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2308 PetscInt n = A->rmap->n; 2309 PetscInt cstart = A->cmap->rstart; 2310 PetscInt *cmap = mat->garray; 2311 PetscInt *diagIdx, *offdiagIdx; 2312 Vec diagV, offdiagV; 2313 PetscScalar *a, *diagA, *offdiagA; 2314 PetscInt r; 2315 PetscErrorCode ierr; 2316 2317 PetscFunctionBegin; 2318 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2319 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr); 2320 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr); 2321 ierr = MatGetRowMax(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2322 ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2323 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2324 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2325 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2326 for (r = 0; r < n; ++r) { 2327 if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) { 2328 a[r] = diagA[r]; 2329 idx[r] = cstart + diagIdx[r]; 2330 } else { 2331 a[r] = offdiagA[r]; 2332 idx[r] = cmap[offdiagIdx[r]]; 2333 } 2334 } 2335 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2336 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2337 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2338 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2339 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2340 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2341 PetscFunctionReturn(0); 2342 } 2343 2344 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat) 2345 { 2346 PetscErrorCode ierr; 2347 Mat *dummy; 2348 2349 PetscFunctionBegin; 2350 ierr = MatCreateSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr); 2351 *newmat = *dummy; 2352 ierr = PetscFree(dummy);CHKERRQ(ierr); 2353 PetscFunctionReturn(0); 2354 } 2355 2356 PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values) 2357 { 2358 Mat_MPIAIJ *a = (Mat_MPIAIJ*) A->data; 2359 PetscErrorCode ierr; 2360 2361 PetscFunctionBegin; 2362 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2363 A->factorerrortype = a->A->factorerrortype; 2364 PetscFunctionReturn(0); 2365 } 2366 2367 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx) 2368 { 2369 PetscErrorCode ierr; 2370 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)x->data; 2371 2372 PetscFunctionBegin; 2373 ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr); 2374 ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr); 2375 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2376 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2377 PetscFunctionReturn(0); 2378 } 2379 2380 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A,PetscBool sc) 2381 { 2382 PetscFunctionBegin; 2383 if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable; 2384 else A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ; 2385 PetscFunctionReturn(0); 2386 } 2387 2388 /*@ 2389 MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap 2390 2391 Collective on Mat 2392 2393 Input Parameters: 2394 + A - the matrix 2395 - sc - PETSC_TRUE indicates use the scalable algorithm (default is not to use the scalable algorithm) 2396 2397 Level: advanced 2398 2399 @*/ 2400 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A,PetscBool sc) 2401 { 2402 PetscErrorCode ierr; 2403 2404 PetscFunctionBegin; 2405 ierr = PetscTryMethod(A,"MatMPIAIJSetUseScalableIncreaseOverlap_C",(Mat,PetscBool),(A,sc));CHKERRQ(ierr); 2406 PetscFunctionReturn(0); 2407 } 2408 2409 PetscErrorCode MatSetFromOptions_MPIAIJ(PetscOptionItems *PetscOptionsObject,Mat A) 2410 { 2411 PetscErrorCode ierr; 2412 PetscBool sc = PETSC_FALSE,flg; 2413 2414 PetscFunctionBegin; 2415 ierr = PetscOptionsHead(PetscOptionsObject,"MPIAIJ options");CHKERRQ(ierr); 2416 ierr = PetscObjectOptionsBegin((PetscObject)A); 2417 if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE; 2418 ierr = PetscOptionsBool("-mat_increase_overlap_scalable","Use a scalable algorithm to compute the overlap","MatIncreaseOverlap",sc,&sc,&flg);CHKERRQ(ierr); 2419 if (flg) { 2420 ierr = MatMPIAIJSetUseScalableIncreaseOverlap(A,sc);CHKERRQ(ierr); 2421 } 2422 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2423 PetscFunctionReturn(0); 2424 } 2425 2426 PetscErrorCode MatShift_MPIAIJ(Mat Y,PetscScalar a) 2427 { 2428 PetscErrorCode ierr; 2429 Mat_MPIAIJ *maij = (Mat_MPIAIJ*)Y->data; 2430 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)maij->A->data; 2431 2432 PetscFunctionBegin; 2433 if (!Y->preallocated) { 2434 ierr = MatMPIAIJSetPreallocation(Y,1,NULL,0,NULL);CHKERRQ(ierr); 2435 } else if (!aij->nz) { 2436 PetscInt nonew = aij->nonew; 2437 ierr = MatSeqAIJSetPreallocation(maij->A,1,NULL);CHKERRQ(ierr); 2438 aij->nonew = nonew; 2439 } 2440 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2441 PetscFunctionReturn(0); 2442 } 2443 2444 PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A,PetscBool *missing,PetscInt *d) 2445 { 2446 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2447 PetscErrorCode ierr; 2448 2449 PetscFunctionBegin; 2450 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2451 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2452 if (d) { 2453 PetscInt rstart; 2454 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2455 *d += rstart; 2456 2457 } 2458 PetscFunctionReturn(0); 2459 } 2460 2461 2462 /* -------------------------------------------------------------------*/ 2463 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 2464 MatGetRow_MPIAIJ, 2465 MatRestoreRow_MPIAIJ, 2466 MatMult_MPIAIJ, 2467 /* 4*/ MatMultAdd_MPIAIJ, 2468 MatMultTranspose_MPIAIJ, 2469 MatMultTransposeAdd_MPIAIJ, 2470 0, 2471 0, 2472 0, 2473 /*10*/ 0, 2474 0, 2475 0, 2476 MatSOR_MPIAIJ, 2477 MatTranspose_MPIAIJ, 2478 /*15*/ MatGetInfo_MPIAIJ, 2479 MatEqual_MPIAIJ, 2480 MatGetDiagonal_MPIAIJ, 2481 MatDiagonalScale_MPIAIJ, 2482 MatNorm_MPIAIJ, 2483 /*20*/ MatAssemblyBegin_MPIAIJ, 2484 MatAssemblyEnd_MPIAIJ, 2485 MatSetOption_MPIAIJ, 2486 MatZeroEntries_MPIAIJ, 2487 /*24*/ MatZeroRows_MPIAIJ, 2488 0, 2489 0, 2490 0, 2491 0, 2492 /*29*/ MatSetUp_MPIAIJ, 2493 0, 2494 0, 2495 MatGetDiagonalBlock_MPIAIJ, 2496 0, 2497 /*34*/ MatDuplicate_MPIAIJ, 2498 0, 2499 0, 2500 0, 2501 0, 2502 /*39*/ MatAXPY_MPIAIJ, 2503 MatCreateSubMatrices_MPIAIJ, 2504 MatIncreaseOverlap_MPIAIJ, 2505 MatGetValues_MPIAIJ, 2506 MatCopy_MPIAIJ, 2507 /*44*/ MatGetRowMax_MPIAIJ, 2508 MatScale_MPIAIJ, 2509 MatShift_MPIAIJ, 2510 MatDiagonalSet_MPIAIJ, 2511 MatZeroRowsColumns_MPIAIJ, 2512 /*49*/ MatSetRandom_MPIAIJ, 2513 0, 2514 0, 2515 0, 2516 0, 2517 /*54*/ MatFDColoringCreate_MPIXAIJ, 2518 0, 2519 MatSetUnfactored_MPIAIJ, 2520 MatPermute_MPIAIJ, 2521 0, 2522 /*59*/ MatCreateSubMatrix_MPIAIJ, 2523 MatDestroy_MPIAIJ, 2524 MatView_MPIAIJ, 2525 0, 2526 MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ, 2527 /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ, 2528 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 2529 0, 2530 0, 2531 0, 2532 /*69*/ MatGetRowMaxAbs_MPIAIJ, 2533 MatGetRowMinAbs_MPIAIJ, 2534 0, 2535 0, 2536 0, 2537 0, 2538 /*75*/ MatFDColoringApply_AIJ, 2539 MatSetFromOptions_MPIAIJ, 2540 0, 2541 0, 2542 MatFindZeroDiagonals_MPIAIJ, 2543 /*80*/ 0, 2544 0, 2545 0, 2546 /*83*/ MatLoad_MPIAIJ, 2547 0, 2548 0, 2549 0, 2550 0, 2551 0, 2552 /*89*/ MatMatMult_MPIAIJ_MPIAIJ, 2553 MatMatMultSymbolic_MPIAIJ_MPIAIJ, 2554 MatMatMultNumeric_MPIAIJ_MPIAIJ, 2555 MatPtAP_MPIAIJ_MPIAIJ, 2556 MatPtAPSymbolic_MPIAIJ_MPIAIJ, 2557 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 2558 0, 2559 0, 2560 0, 2561 0, 2562 /*99*/ 0, 2563 0, 2564 0, 2565 MatConjugate_MPIAIJ, 2566 0, 2567 /*104*/MatSetValuesRow_MPIAIJ, 2568 MatRealPart_MPIAIJ, 2569 MatImaginaryPart_MPIAIJ, 2570 0, 2571 0, 2572 /*109*/0, 2573 0, 2574 MatGetRowMin_MPIAIJ, 2575 0, 2576 MatMissingDiagonal_MPIAIJ, 2577 /*114*/MatGetSeqNonzeroStructure_MPIAIJ, 2578 0, 2579 MatGetGhosts_MPIAIJ, 2580 0, 2581 0, 2582 /*119*/0, 2583 0, 2584 0, 2585 0, 2586 MatGetMultiProcBlock_MPIAIJ, 2587 /*124*/MatFindNonzeroRows_MPIAIJ, 2588 MatGetColumnNorms_MPIAIJ, 2589 MatInvertBlockDiagonal_MPIAIJ, 2590 0, 2591 MatCreateSubMatricesMPI_MPIAIJ, 2592 /*129*/0, 2593 MatTransposeMatMult_MPIAIJ_MPIAIJ, 2594 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ, 2595 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 2596 0, 2597 /*134*/0, 2598 0, 2599 0, 2600 0, 2601 0, 2602 /*139*/MatSetBlockSizes_MPIAIJ, 2603 0, 2604 0, 2605 MatFDColoringSetUp_MPIXAIJ, 2606 MatFindOffBlockDiagonalEntries_MPIAIJ, 2607 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIAIJ 2608 }; 2609 2610 /* ----------------------------------------------------------------------------------------*/ 2611 2612 PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 2613 { 2614 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2615 PetscErrorCode ierr; 2616 2617 PetscFunctionBegin; 2618 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 2619 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 2620 PetscFunctionReturn(0); 2621 } 2622 2623 PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 2624 { 2625 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2626 PetscErrorCode ierr; 2627 2628 PetscFunctionBegin; 2629 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 2630 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 2631 PetscFunctionReturn(0); 2632 } 2633 2634 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 2635 { 2636 Mat_MPIAIJ *b; 2637 PetscErrorCode ierr; 2638 2639 PetscFunctionBegin; 2640 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2641 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2642 b = (Mat_MPIAIJ*)B->data; 2643 2644 #if defined(PETSC_USE_CTABLE) 2645 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2646 #else 2647 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2648 #endif 2649 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2650 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2651 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2652 2653 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2654 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2655 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2656 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 2657 ierr = MatSetBlockSizesFromMats(b->B,B,B);CHKERRQ(ierr); 2658 ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr); 2659 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2660 2661 if (!B->preallocated) { 2662 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2663 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2664 ierr = MatSetBlockSizesFromMats(b->A,B,B);CHKERRQ(ierr); 2665 ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr); 2666 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2667 } 2668 2669 ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr); 2670 ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr); 2671 B->preallocated = PETSC_TRUE; 2672 B->was_assembled = PETSC_FALSE; 2673 B->assembled = PETSC_FALSE;; 2674 PetscFunctionReturn(0); 2675 } 2676 2677 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 2678 { 2679 Mat mat; 2680 Mat_MPIAIJ *a,*oldmat = (Mat_MPIAIJ*)matin->data; 2681 PetscErrorCode ierr; 2682 2683 PetscFunctionBegin; 2684 *newmat = 0; 2685 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 2686 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 2687 ierr = MatSetBlockSizesFromMats(mat,matin,matin);CHKERRQ(ierr); 2688 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 2689 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2690 a = (Mat_MPIAIJ*)mat->data; 2691 2692 mat->factortype = matin->factortype; 2693 mat->assembled = PETSC_TRUE; 2694 mat->insertmode = NOT_SET_VALUES; 2695 mat->preallocated = PETSC_TRUE; 2696 2697 a->size = oldmat->size; 2698 a->rank = oldmat->rank; 2699 a->donotstash = oldmat->donotstash; 2700 a->roworiented = oldmat->roworiented; 2701 a->rowindices = 0; 2702 a->rowvalues = 0; 2703 a->getrowactive = PETSC_FALSE; 2704 2705 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 2706 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 2707 2708 if (oldmat->colmap) { 2709 #if defined(PETSC_USE_CTABLE) 2710 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 2711 #else 2712 ierr = PetscMalloc1(mat->cmap->N,&a->colmap);CHKERRQ(ierr); 2713 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2714 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2715 #endif 2716 } else a->colmap = 0; 2717 if (oldmat->garray) { 2718 PetscInt len; 2719 len = oldmat->B->cmap->n; 2720 ierr = PetscMalloc1(len+1,&a->garray);CHKERRQ(ierr); 2721 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 2722 if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); } 2723 } else a->garray = 0; 2724 2725 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 2726 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 2727 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 2728 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 2729 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 2730 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 2731 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 2732 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 2733 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 2734 *newmat = mat; 2735 PetscFunctionReturn(0); 2736 } 2737 2738 2739 2740 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 2741 { 2742 PetscScalar *vals,*svals; 2743 MPI_Comm comm; 2744 PetscErrorCode ierr; 2745 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 2746 PetscInt i,nz,j,rstart,rend,mmax,maxnz = 0; 2747 PetscInt header[4],*rowlengths = 0,M,N,m,*cols; 2748 PetscInt *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols; 2749 PetscInt cend,cstart,n,*rowners; 2750 int fd; 2751 PetscInt bs = newMat->rmap->bs; 2752 2753 PetscFunctionBegin; 2754 /* force binary viewer to load .info file if it has not yet done so */ 2755 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 2756 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2757 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2758 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2759 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2760 if (!rank) { 2761 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 2762 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 2763 if (header[3] < 0) SETERRQ(PetscObjectComm((PetscObject)newMat),PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as MATMPIAIJ"); 2764 } 2765 2766 ierr = PetscOptionsBegin(comm,NULL,"Options for loading MATMPIAIJ matrix","Mat");CHKERRQ(ierr); 2767 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 2768 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2769 if (bs < 0) bs = 1; 2770 2771 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 2772 M = header[1]; N = header[2]; 2773 2774 /* If global sizes are set, check if they are consistent with that given in the file */ 2775 if (newMat->rmap->N >= 0 && newMat->rmap->N != M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of rows:Matrix in file has (%D) and input matrix has (%D)",newMat->rmap->N,M); 2776 if (newMat->cmap->N >=0 && newMat->cmap->N != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of cols:Matrix in file has (%D) and input matrix has (%D)",newMat->cmap->N,N); 2777 2778 /* determine ownership of all (block) rows */ 2779 if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs); 2780 if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank)); /* PETSC_DECIDE */ 2781 else m = newMat->rmap->n; /* Set by user */ 2782 2783 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 2784 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 2785 2786 /* First process needs enough room for process with most rows */ 2787 if (!rank) { 2788 mmax = rowners[1]; 2789 for (i=2; i<=size; i++) { 2790 mmax = PetscMax(mmax, rowners[i]); 2791 } 2792 } else mmax = -1; /* unused, but compilers complain */ 2793 2794 rowners[0] = 0; 2795 for (i=2; i<=size; i++) { 2796 rowners[i] += rowners[i-1]; 2797 } 2798 rstart = rowners[rank]; 2799 rend = rowners[rank+1]; 2800 2801 /* distribute row lengths to all processors */ 2802 ierr = PetscMalloc2(m,&ourlens,m,&offlens);CHKERRQ(ierr); 2803 if (!rank) { 2804 ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr); 2805 ierr = PetscMalloc1(mmax,&rowlengths);CHKERRQ(ierr); 2806 ierr = PetscCalloc1(size,&procsnz);CHKERRQ(ierr); 2807 for (j=0; j<m; j++) { 2808 procsnz[0] += ourlens[j]; 2809 } 2810 for (i=1; i<size; i++) { 2811 ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr); 2812 /* calculate the number of nonzeros on each processor */ 2813 for (j=0; j<rowners[i+1]-rowners[i]; j++) { 2814 procsnz[i] += rowlengths[j]; 2815 } 2816 ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2817 } 2818 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2819 } else { 2820 ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2821 } 2822 2823 if (!rank) { 2824 /* determine max buffer needed and allocate it */ 2825 maxnz = 0; 2826 for (i=0; i<size; i++) { 2827 maxnz = PetscMax(maxnz,procsnz[i]); 2828 } 2829 ierr = PetscMalloc1(maxnz,&cols);CHKERRQ(ierr); 2830 2831 /* read in my part of the matrix column indices */ 2832 nz = procsnz[0]; 2833 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2834 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 2835 2836 /* read in every one elses and ship off */ 2837 for (i=1; i<size; i++) { 2838 nz = procsnz[i]; 2839 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 2840 ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2841 } 2842 ierr = PetscFree(cols);CHKERRQ(ierr); 2843 } else { 2844 /* determine buffer space needed for message */ 2845 nz = 0; 2846 for (i=0; i<m; i++) { 2847 nz += ourlens[i]; 2848 } 2849 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2850 2851 /* receive message of column indices*/ 2852 ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2853 } 2854 2855 /* determine column ownership if matrix is not square */ 2856 if (N != M) { 2857 if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank); 2858 else n = newMat->cmap->n; 2859 ierr = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2860 cstart = cend - n; 2861 } else { 2862 cstart = rstart; 2863 cend = rend; 2864 n = cend - cstart; 2865 } 2866 2867 /* loop over local rows, determining number of off diagonal entries */ 2868 ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr); 2869 jj = 0; 2870 for (i=0; i<m; i++) { 2871 for (j=0; j<ourlens[i]; j++) { 2872 if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++; 2873 jj++; 2874 } 2875 } 2876 2877 for (i=0; i<m; i++) { 2878 ourlens[i] -= offlens[i]; 2879 } 2880 ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr); 2881 2882 if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);} 2883 2884 ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr); 2885 2886 for (i=0; i<m; i++) { 2887 ourlens[i] += offlens[i]; 2888 } 2889 2890 if (!rank) { 2891 ierr = PetscMalloc1(maxnz+1,&vals);CHKERRQ(ierr); 2892 2893 /* read in my part of the matrix numerical values */ 2894 nz = procsnz[0]; 2895 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2896 2897 /* insert into matrix */ 2898 jj = rstart; 2899 smycols = mycols; 2900 svals = vals; 2901 for (i=0; i<m; i++) { 2902 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2903 smycols += ourlens[i]; 2904 svals += ourlens[i]; 2905 jj++; 2906 } 2907 2908 /* read in other processors and ship out */ 2909 for (i=1; i<size; i++) { 2910 nz = procsnz[i]; 2911 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2912 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2913 } 2914 ierr = PetscFree(procsnz);CHKERRQ(ierr); 2915 } else { 2916 /* receive numeric values */ 2917 ierr = PetscMalloc1(nz+1,&vals);CHKERRQ(ierr); 2918 2919 /* receive message of values*/ 2920 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2921 2922 /* insert into matrix */ 2923 jj = rstart; 2924 smycols = mycols; 2925 svals = vals; 2926 for (i=0; i<m; i++) { 2927 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2928 smycols += ourlens[i]; 2929 svals += ourlens[i]; 2930 jj++; 2931 } 2932 } 2933 ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr); 2934 ierr = PetscFree(vals);CHKERRQ(ierr); 2935 ierr = PetscFree(mycols);CHKERRQ(ierr); 2936 ierr = PetscFree(rowners);CHKERRQ(ierr); 2937 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2938 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2939 PetscFunctionReturn(0); 2940 } 2941 2942 /* Not scalable because of ISAllGather() unless getting all columns. */ 2943 PetscErrorCode ISGetSeqIS_Private(Mat mat,IS iscol,IS *isseq) 2944 { 2945 PetscErrorCode ierr; 2946 IS iscol_local; 2947 PetscBool isstride; 2948 PetscMPIInt lisstride=0,gisstride; 2949 2950 PetscFunctionBegin; 2951 /* check if we are grabbing all columns*/ 2952 ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&isstride);CHKERRQ(ierr); 2953 2954 if (isstride) { 2955 PetscInt start,len,mstart,mlen; 2956 ierr = ISStrideGetInfo(iscol,&start,NULL);CHKERRQ(ierr); 2957 ierr = ISGetLocalSize(iscol,&len);CHKERRQ(ierr); 2958 ierr = MatGetOwnershipRangeColumn(mat,&mstart,&mlen);CHKERRQ(ierr); 2959 if (mstart == start && mlen-mstart == len) lisstride = 1; 2960 } 2961 2962 ierr = MPIU_Allreduce(&lisstride,&gisstride,1,MPI_INT,MPI_MIN,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2963 if (gisstride) { 2964 PetscInt N; 2965 ierr = MatGetSize(mat,NULL,&N);CHKERRQ(ierr); 2966 ierr = ISCreateStride(PetscObjectComm((PetscObject)mat),N,0,1,&iscol_local);CHKERRQ(ierr); 2967 ierr = ISSetIdentity(iscol_local);CHKERRQ(ierr); 2968 ierr = PetscInfo(mat,"Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n");CHKERRQ(ierr); 2969 } else { 2970 PetscInt cbs; 2971 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 2972 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 2973 ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr); 2974 } 2975 2976 *isseq = iscol_local; 2977 PetscFunctionReturn(0); 2978 } 2979 2980 extern PetscErrorCode MatCreateSubMatrix_MPIAIJ_Private_SameDist(Mat,IS,IS,PetscInt,MatReuse,Mat*); 2981 2982 /* isrow has same processor distribution as mat, avoid iscol_local which uses O(mat->cmap->N) ctable */ 2983 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 2984 { 2985 PetscErrorCode ierr; 2986 IS iscol_local; 2987 PetscInt csize; 2988 MPI_Comm comm; 2989 PetscMPIInt rank; 2990 PetscBool sorted,sameDist = PETSC_FALSE,tsameDist; 2991 PetscInt n,i,j,cstart,cend,N; 2992 2993 PetscFunctionBegin; 2994 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 2995 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2996 //ierr = ISView(iscol,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2997 2998 /* If iscol has same processor distribution as mat, then use a scalable routine */ 2999 ierr = ISSorted(iscol,&sorted);CHKERRQ(ierr); //must be locally sorted??? 3000 if (!sorted) printf("[%d] iscol !sorted\n",rank); 3001 3002 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3003 ierr = ISGetSize(iscol,&N);CHKERRQ(ierr); 3004 if (!n) { 3005 sameDist = PETSC_TRUE; 3006 } else { 3007 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3008 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3009 if (i >= cstart && j < cend) sameDist = PETSC_TRUE; 3010 } 3011 ierr = MPIU_Allreduce(&sameDist,&tsameDist,1,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3012 if (!rank) printf("..SubMatrix_MPIAIJ_SameDist ...reuse %d, sameDist for column %d \n",call,tsameDist); 3013 3014 if (sameDist) { /* get iscol_sub without calling ISAllGather() */ 3015 Vec x; 3016 const PetscInt *is_idx; 3017 PetscScalar *xarray; 3018 3019 /* (1) iscol is a sub-vector of mat, pad it with '-1.' to form a full vector x */ 3020 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3021 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3022 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3023 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3024 for (i=0; i<n; i++) { 3025 //ierr = VecSetValues(x,1,&is_idx[i],&is_idx[i],); 3026 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3027 } 3028 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3029 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3030 //ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3031 3032 /* (2) scatter x using aij->Mvctx to get off-process portion of x (see MatMult_MPIAIJ) */ 3033 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3034 Mat B=a->B; 3035 Vec lvec = a->lvec; 3036 PetscInt Bn=B->cmap->N; 3037 PetscInt *garray = a->garray; 3038 3039 ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3040 ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3041 3042 //printf("[%d] n(lvec) %d, Bn %d\n",rank,a->lvec->map->n,Bn); 3043 if (lvec->map->n != Bn) SETERRQ2(PETSC_COMM_SELF,0,"n(lvec) %d != Bn %d",lvec->map->n,Bn); 3044 if (rank == -1) { 3045 printf("[%d] lvec:\n",rank); 3046 ierr = VecView(lvec,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3047 } 3048 3049 /* create scalable iscol_sub (a subset of iscol) */ 3050 PetscInt *idx,*cmap1,count; 3051 3052 ierr = PetscMalloc2(n+Bn,&idx,n+Bn,&cmap1);CHKERRQ(ierr); 3053 //ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3054 count = 0; 3055 3056 /* A part */ 3057 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3058 j = cstart; 3059 for (i=0; i<n; i++) { 3060 if (j >= cend) break; 3061 if (is_idx[i] == j) { 3062 idx[count] = j; 3063 cmap1[count] = i; /* column index in submat */ 3064 count++; j++; 3065 } else if (is_idx[i] > j) { 3066 while (is_idx[i] > j && j < cend-1) j++; 3067 if (is_idx[i] == j) { 3068 idx[count] = j; 3069 cmap1[count] = i; /* column index in submat */ 3070 count++; j++; 3071 } 3072 } 3073 } 3074 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3075 3076 /* B part */ 3077 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3078 j = 0; 3079 for (i=0; i<Bn; i++) { 3080 if (j >= Bn) break; 3081 if ((PetscInt)xarray[i] == garray[j]) { 3082 idx[count] = garray[j]; 3083 cmap1[count] = i; /* column index in submat */ 3084 count++; j++; 3085 } else if ((PetscInt)xarray[i] > garray[j]) { 3086 while ((PetscInt)xarray[i] > garray[j] && j < Bn-1) j++; 3087 if ((PetscInt)xarray[i] == garray[j]) { 3088 idx[count] = garray[j]; 3089 cmap1[count] = i; /* column index in submat */ 3090 count++; j++; 3091 } 3092 } 3093 } 3094 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3095 printf("[%d] n %d + Bn %d = %d; count %d, isN %d, matN %d\n",rank,n,Bn,n+Bn,count,N,mat->cmap->N); 3096 3097 IS iscol_sub,iscmap; 3098 ierr = PetscSortInt(count,idx);CHKERRQ(ierr); 3099 ierr = PetscSortInt(count,cmap1);CHKERRQ(ierr); 3100 3101 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,&iscol_sub);CHKERRQ(ierr); 3102 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,cmap1,PETSC_COPY_VALUES,&iscmap);CHKERRQ(ierr); 3103 3104 if (rank == -1) { 3105 printf("[%d] iscmap:\n",rank); 3106 ierr = ISView(iscmap,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3107 } 3108 3109 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3110 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3111 ierr = PetscFree2(idx,cmap1);CHKERRQ(ierr); 3112 ierr = VecDestroy(&x);CHKERRQ(ierr); 3113 } 3114 3115 //----------------------------------------------- 3116 3117 /* Get nonscalable iscol_local -- will replace it with iscol_sub! */ 3118 if (call == MAT_REUSE_MATRIX) { 3119 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3120 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3121 } else { 3122 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3123 PetscBool sorted; 3124 ierr = ISSorted(iscol_local,&sorted);CHKERRQ(ierr); 3125 if (!sorted) printf("[%d] iscol_local !sorted\n",rank); 3126 } 3127 3128 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3129 ierr = MatCreateSubMatrix_MPIAIJ_Private_SameDist(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3130 3131 if (call == MAT_INITIAL_MATRIX) { 3132 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3133 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3134 } 3135 PetscFunctionReturn(0); 3136 } 3137 3138 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3139 { 3140 PetscErrorCode ierr; 3141 IS iscol_local; 3142 PetscInt csize; 3143 PetscInt n,i,j,rstart,rend; 3144 PetscBool sameDist=PETSC_FALSE,tsameDist; 3145 MPI_Comm comm; 3146 3147 PetscFunctionBegin; 3148 /* If isrow has same processor distribution as mat, then use a scalable routine */ 3149 if (call == MAT_REUSE_MATRIX) { 3150 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3151 if (iscol_local) tsameDist = PETSC_TRUE; 3152 } else { 3153 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3154 if (!n) { 3155 sameDist = PETSC_TRUE; 3156 } else { 3157 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3158 ierr = MatGetOwnershipRange(mat,&rstart,&rend);CHKERRQ(ierr); 3159 if (i >= rstart && j < rend) sameDist = PETSC_TRUE; 3160 } 3161 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3162 ierr = MPIU_Allreduce(&sameDist,&tsameDist,1,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3163 } 3164 3165 if (tsameDist) { 3166 ierr = MatCreateSubMatrix_MPIAIJ_SameDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3167 PetscFunctionReturn(0); 3168 } 3169 3170 /* General case */ 3171 /* --------------------------------------- */ 3172 if (call == MAT_REUSE_MATRIX) { 3173 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3174 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3175 } else { 3176 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3177 } 3178 3179 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3180 ierr = MatCreateSubMatrix_MPIAIJ_Private(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3181 3182 if (call == MAT_INITIAL_MATRIX) { 3183 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3184 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3185 } 3186 PetscFunctionReturn(0); 3187 } 3188 3189 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat*); 3190 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3191 3192 PetscErrorCode MatCreateSubMatrix_MPIAIJ_Private_SameDist(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3193 { 3194 PetscErrorCode ierr; 3195 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3196 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3197 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3198 Mat M,Msub,B=a->B; 3199 MatScalar *aa; 3200 Mat_SeqAIJ *aij; 3201 PetscInt *garray = a->garray,*colsub; 3202 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3203 IS iscol_sub,iscmap; 3204 const PetscInt *is_idx,*cmap; 3205 3206 PetscFunctionBegin; 3207 MPI_Comm comm; 3208 PetscMPIInt rank; 3209 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3210 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3211 //printf("SubMatrix_MPIAIJ_Private_SameDist ...\n"); 3212 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); /* iscol should be sequential */ 3213 3214 if (call == MAT_INITIAL_MATRIX) { 3215 /* create scalable iscol_sub (a subset of iscol) */ 3216 PetscInt *idx,*cmap1; 3217 3218 PetscBool sorted; 3219 ierr = ISSorted(iscol,&sorted);CHKERRQ(ierr); 3220 if (!sorted) printf("iscol_local !sorted\n"); 3221 3222 ierr = PetscMalloc2(n,&idx,n,&cmap1);CHKERRQ(ierr); 3223 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3224 count = 0; 3225 3226 /* A part */ 3227 j = cstart; 3228 for (i=0; i<n; i++) { 3229 if (j >= cend) break; 3230 if (is_idx[i] == j) { 3231 idx[count] = j; 3232 cmap1[count] = i; /* column index in submat */ 3233 count++; j++; 3234 } else if (is_idx[i] > j) { 3235 while (is_idx[i] > j && j < cend-1) j++; 3236 if (is_idx[i] == j) { 3237 idx[count] = j; 3238 cmap1[count] = i; /* column index in submat */ 3239 count++; j++; 3240 } 3241 } 3242 } 3243 3244 /* B part */ 3245 j = 0; 3246 for (i=0; i<n; i++) { 3247 if (j >= Bn) break; 3248 if (is_idx[i] == garray[j]) { 3249 idx[count] = garray[j]; 3250 cmap1[count] = i; /* column index in submat */ 3251 count++; j++; 3252 } else if (is_idx[i] > garray[j]) { 3253 while (is_idx[i] > garray[j] && j < Bn-1) j++; 3254 if (is_idx[i] == garray[j]) { 3255 idx[count] = garray[j]; 3256 cmap1[count] = i; /* column index in submat */ 3257 count++; j++; 3258 } 3259 } 3260 } 3261 ierr = PetscSortInt(count,cmap1);CHKERRQ(ierr); 3262 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3263 3264 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol),count,idx,PETSC_COPY_VALUES,&iscol_sub);CHKERRQ(ierr); 3265 ierr = ISSort(iscol_sub);CHKERRQ(ierr); 3266 3267 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol),count,cmap1,PETSC_COPY_VALUES,&iscmap);CHKERRQ(ierr); 3268 ierr = PetscFree2(idx,cmap1);CHKERRQ(ierr); 3269 3270 printf("[%d] old count %d, isN %d, matN %d\n",rank,count,n,mat->cmap->N); 3271 if (rank == -1) { 3272 printf("[%d] old iscmap:\n",rank); 3273 ierr = ISView(iscmap,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3274 } 3275 3276 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3277 3278 } else { /* call == MAT_REUSE_MATRIX */ 3279 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3280 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3281 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3282 3283 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3284 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3285 3286 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3287 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3288 3289 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3290 } 3291 3292 aij = (Mat_SeqAIJ*)(Msub)->data; 3293 ii = aij->i; 3294 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3295 3296 /* 3297 m - number of local rows 3298 n - number of columns (same on all processors) 3299 rstart - first row in new global matrix generated 3300 */ 3301 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3302 3303 if (call == MAT_INITIAL_MATRIX) { 3304 MPI_Comm comm; 3305 PetscMPIInt rank,size; 3306 3307 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3308 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3309 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3310 3311 /* 3312 Determine the number of non-zeros in the diagonal and off-diagonal 3313 portions of the matrix in order to do correct preallocation 3314 */ 3315 3316 /* first get start and end of "diagonal" columns */ 3317 if (csize == PETSC_DECIDE) { 3318 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3319 if (mglobal == n) { /* square matrix */ 3320 nlocal = m; 3321 } else { 3322 nlocal = n/size + ((n % size) > rank); 3323 } 3324 } else { 3325 nlocal = csize; 3326 } 3327 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3328 rstart = rend - nlocal; 3329 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); 3330 3331 /* next, compute all the lengths */ 3332 jj = aij->j; 3333 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3334 olens = dlens + m; 3335 for (i=0; i<m; i++) { 3336 jend = ii[i+1] - ii[i]; 3337 olen = 0; 3338 dlen = 0; 3339 for (j=0; j<jend; j++) { 3340 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3341 else dlen++; 3342 jj++; 3343 } 3344 olens[i] = olen; 3345 dlens[i] = dlen; 3346 } 3347 ierr = MatGetBlockSizes(Msub,&bs,&cbs);CHKERRQ(ierr); 3348 3349 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3350 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3351 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3352 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3353 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3354 ierr = PetscFree(dlens);CHKERRQ(ierr); 3355 } else { 3356 M = *newmat; 3357 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3358 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3359 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3360 /* 3361 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3362 rather than the slower MatSetValues(). 3363 */ 3364 M->was_assembled = PETSC_TRUE; 3365 M->assembled = PETSC_FALSE; 3366 } 3367 3368 /* set values of Msub to *newmat */ 3369 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3370 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3371 3372 jj = aij->j; 3373 aa = aij->a; 3374 for (i=0; i<m; i++) { 3375 row = rstart + i; 3376 nz = ii[i+1] - ii[i]; 3377 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3378 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3379 jj += nz; aa += nz; 3380 } 3381 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3382 3383 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3384 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3385 *newmat = M; 3386 3387 ierr = PetscFree(colsub);CHKERRQ(ierr); 3388 3389 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3390 if (call == MAT_INITIAL_MATRIX) { 3391 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3392 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3393 3394 ierr = PetscObjectCompose((PetscObject)M,"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3395 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3396 3397 ierr = PetscObjectCompose((PetscObject)M,"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3398 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3399 } 3400 PetscFunctionReturn(0); 3401 } 3402 3403 /* 3404 Not great since it makes two copies of the submatrix, first an SeqAIJ 3405 in local and then by concatenating the local matrices the end result. 3406 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3407 3408 Note: This requires a sequential iscol with all indices. 3409 */ 3410 PetscErrorCode MatCreateSubMatrix_MPIAIJ_Private(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3411 { 3412 PetscErrorCode ierr; 3413 PetscMPIInt rank,size; 3414 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3415 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3416 Mat M,Mreuse; 3417 MatScalar *aa,*vwork; 3418 MPI_Comm comm; 3419 Mat_SeqAIJ *aij; 3420 //PetscBool sameDist=PETSC_FALSE,tsameDist; 3421 3422 PetscFunctionBegin; 3423 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3424 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3425 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3426 #if 0 3427 /* If isrow has same processor distribution as mat, then use a scalable routine */ 3428 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3429 if (!n) { 3430 sameDist=PETSC_TRUE; 3431 } else { 3432 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3433 ierr = MatGetOwnershipRange(mat,&rstart,&rend);CHKERRQ(ierr); 3434 if (i >= rstart && j < rend) sameDist=PETSC_TRUE; 3435 } 3436 ierr = MPIU_Allreduce(&sameDist,&tsameDist,1,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3437 if (tsameDist) { 3438 ierr = MatCreateSubMatrix_MPIAIJ_Private_SameDist(mat,isrow,iscol,csize,call,newmat);CHKERRQ(ierr); 3439 PetscFunctionReturn(0); 3440 } 3441 #endif 3442 3443 if (call == MAT_REUSE_MATRIX) { 3444 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3445 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3446 ierr = MatCreateSubMatrices_MPIAIJ_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,&Mreuse);CHKERRQ(ierr); 3447 } else { 3448 ierr = MatCreateSubMatrices_MPIAIJ_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,&Mreuse);CHKERRQ(ierr); 3449 } 3450 3451 /* 3452 m - number of local rows 3453 n - number of columns (same on all processors) 3454 rstart - first row in new global matrix generated 3455 */ 3456 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3457 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3458 if (call == MAT_INITIAL_MATRIX) { 3459 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3460 ii = aij->i; 3461 jj = aij->j; 3462 3463 /* 3464 Determine the number of non-zeros in the diagonal and off-diagonal 3465 portions of the matrix in order to do correct preallocation 3466 */ 3467 3468 /* first get start and end of "diagonal" columns */ 3469 if (csize == PETSC_DECIDE) { 3470 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3471 if (mglobal == n) { /* square matrix */ 3472 nlocal = m; 3473 } else { 3474 nlocal = n/size + ((n % size) > rank); 3475 } 3476 } else { 3477 nlocal = csize; 3478 } 3479 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3480 rstart = rend - nlocal; 3481 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); 3482 3483 /* next, compute all the lengths */ 3484 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3485 olens = dlens + m; 3486 for (i=0; i<m; i++) { 3487 jend = ii[i+1] - ii[i]; 3488 olen = 0; 3489 dlen = 0; 3490 for (j=0; j<jend; j++) { 3491 if (*jj < rstart || *jj >= rend) olen++; 3492 else dlen++; 3493 jj++; 3494 } 3495 olens[i] = olen; 3496 dlens[i] = dlen; 3497 } 3498 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3499 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3500 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3501 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3502 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3503 ierr = PetscFree(dlens);CHKERRQ(ierr); 3504 } else { 3505 PetscInt ml,nl; 3506 3507 M = *newmat; 3508 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3509 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3510 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3511 /* 3512 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3513 rather than the slower MatSetValues(). 3514 */ 3515 M->was_assembled = PETSC_TRUE; 3516 M->assembled = PETSC_FALSE; 3517 } 3518 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3519 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3520 ii = aij->i; 3521 jj = aij->j; 3522 aa = aij->a; 3523 for (i=0; i<m; i++) { 3524 row = rstart + i; 3525 nz = ii[i+1] - ii[i]; 3526 cwork = jj; jj += nz; 3527 vwork = aa; aa += nz; 3528 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3529 } 3530 3531 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3532 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3533 *newmat = M; 3534 3535 /* save submatrix used in processor for next request */ 3536 if (call == MAT_INITIAL_MATRIX) { 3537 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3538 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3539 } 3540 PetscFunctionReturn(0); 3541 } 3542 3543 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3544 { 3545 PetscInt m,cstart, cend,j,nnz,i,d; 3546 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3547 const PetscInt *JJ; 3548 PetscScalar *values; 3549 PetscErrorCode ierr; 3550 PetscBool nooffprocentries; 3551 3552 PetscFunctionBegin; 3553 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3554 3555 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3556 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3557 m = B->rmap->n; 3558 cstart = B->cmap->rstart; 3559 cend = B->cmap->rend; 3560 rstart = B->rmap->rstart; 3561 3562 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3563 3564 #if defined(PETSC_USE_DEBUGGING) 3565 for (i=0; i<m; i++) { 3566 nnz = Ii[i+1]- Ii[i]; 3567 JJ = J + Ii[i]; 3568 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3569 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3570 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); 3571 } 3572 #endif 3573 3574 for (i=0; i<m; i++) { 3575 nnz = Ii[i+1]- Ii[i]; 3576 JJ = J + Ii[i]; 3577 nnz_max = PetscMax(nnz_max,nnz); 3578 d = 0; 3579 for (j=0; j<nnz; j++) { 3580 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3581 } 3582 d_nnz[i] = d; 3583 o_nnz[i] = nnz - d; 3584 } 3585 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3586 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3587 3588 if (v) values = (PetscScalar*)v; 3589 else { 3590 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3591 } 3592 3593 for (i=0; i<m; i++) { 3594 ii = i + rstart; 3595 nnz = Ii[i+1]- Ii[i]; 3596 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3597 } 3598 nooffprocentries = B->nooffprocentries; 3599 B->nooffprocentries = PETSC_TRUE; 3600 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3601 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3602 B->nooffprocentries = nooffprocentries; 3603 3604 if (!v) { 3605 ierr = PetscFree(values);CHKERRQ(ierr); 3606 } 3607 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3608 PetscFunctionReturn(0); 3609 } 3610 3611 /*@ 3612 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3613 (the default parallel PETSc format). 3614 3615 Collective on MPI_Comm 3616 3617 Input Parameters: 3618 + B - the matrix 3619 . i - the indices into j for the start of each local row (starts with zero) 3620 . j - the column indices for each local row (starts with zero) 3621 - v - optional values in the matrix 3622 3623 Level: developer 3624 3625 Notes: 3626 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3627 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3628 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3629 3630 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3631 3632 The format which is used for the sparse matrix input, is equivalent to a 3633 row-major ordering.. i.e for the following matrix, the input data expected is 3634 as shown 3635 3636 $ 1 0 0 3637 $ 2 0 3 P0 3638 $ ------- 3639 $ 4 5 6 P1 3640 $ 3641 $ Process0 [P0]: rows_owned=[0,1] 3642 $ i = {0,1,3} [size = nrow+1 = 2+1] 3643 $ j = {0,0,2} [size = 3] 3644 $ v = {1,2,3} [size = 3] 3645 $ 3646 $ Process1 [P1]: rows_owned=[2] 3647 $ i = {0,3} [size = nrow+1 = 1+1] 3648 $ j = {0,1,2} [size = 3] 3649 $ v = {4,5,6} [size = 3] 3650 3651 .keywords: matrix, aij, compressed row, sparse, parallel 3652 3653 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3654 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3655 @*/ 3656 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3657 { 3658 PetscErrorCode ierr; 3659 3660 PetscFunctionBegin; 3661 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3662 PetscFunctionReturn(0); 3663 } 3664 3665 /*@C 3666 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3667 (the default parallel PETSc format). For good matrix assembly performance 3668 the user should preallocate the matrix storage by setting the parameters 3669 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3670 performance can be increased by more than a factor of 50. 3671 3672 Collective on MPI_Comm 3673 3674 Input Parameters: 3675 + B - the matrix 3676 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3677 (same value is used for all local rows) 3678 . d_nnz - array containing the number of nonzeros in the various rows of the 3679 DIAGONAL portion of the local submatrix (possibly different for each row) 3680 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3681 The size of this array is equal to the number of local rows, i.e 'm'. 3682 For matrices that will be factored, you must leave room for (and set) 3683 the diagonal entry even if it is zero. 3684 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3685 submatrix (same value is used for all local rows). 3686 - o_nnz - array containing the number of nonzeros in the various rows of the 3687 OFF-DIAGONAL portion of the local submatrix (possibly different for 3688 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3689 structure. The size of this array is equal to the number 3690 of local rows, i.e 'm'. 3691 3692 If the *_nnz parameter is given then the *_nz parameter is ignored 3693 3694 The AIJ format (also called the Yale sparse matrix format or 3695 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3696 storage. The stored row and column indices begin with zero. 3697 See Users-Manual: ch_mat for details. 3698 3699 The parallel matrix is partitioned such that the first m0 rows belong to 3700 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3701 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3702 3703 The DIAGONAL portion of the local submatrix of a processor can be defined 3704 as the submatrix which is obtained by extraction the part corresponding to 3705 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3706 first row that belongs to the processor, r2 is the last row belonging to 3707 the this processor, and c1-c2 is range of indices of the local part of a 3708 vector suitable for applying the matrix to. This is an mxn matrix. In the 3709 common case of a square matrix, the row and column ranges are the same and 3710 the DIAGONAL part is also square. The remaining portion of the local 3711 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3712 3713 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3714 3715 You can call MatGetInfo() to get information on how effective the preallocation was; 3716 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3717 You can also run with the option -info and look for messages with the string 3718 malloc in them to see if additional memory allocation was needed. 3719 3720 Example usage: 3721 3722 Consider the following 8x8 matrix with 34 non-zero values, that is 3723 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3724 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3725 as follows: 3726 3727 .vb 3728 1 2 0 | 0 3 0 | 0 4 3729 Proc0 0 5 6 | 7 0 0 | 8 0 3730 9 0 10 | 11 0 0 | 12 0 3731 ------------------------------------- 3732 13 0 14 | 15 16 17 | 0 0 3733 Proc1 0 18 0 | 19 20 21 | 0 0 3734 0 0 0 | 22 23 0 | 24 0 3735 ------------------------------------- 3736 Proc2 25 26 27 | 0 0 28 | 29 0 3737 30 0 0 | 31 32 33 | 0 34 3738 .ve 3739 3740 This can be represented as a collection of submatrices as: 3741 3742 .vb 3743 A B C 3744 D E F 3745 G H I 3746 .ve 3747 3748 Where the submatrices A,B,C are owned by proc0, D,E,F are 3749 owned by proc1, G,H,I are owned by proc2. 3750 3751 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3752 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3753 The 'M','N' parameters are 8,8, and have the same values on all procs. 3754 3755 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3756 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3757 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3758 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3759 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3760 matrix, ans [DF] as another SeqAIJ matrix. 3761 3762 When d_nz, o_nz parameters are specified, d_nz storage elements are 3763 allocated for every row of the local diagonal submatrix, and o_nz 3764 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3765 One way to choose d_nz and o_nz is to use the max nonzerors per local 3766 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3767 In this case, the values of d_nz,o_nz are: 3768 .vb 3769 proc0 : dnz = 2, o_nz = 2 3770 proc1 : dnz = 3, o_nz = 2 3771 proc2 : dnz = 1, o_nz = 4 3772 .ve 3773 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3774 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3775 for proc3. i.e we are using 12+15+10=37 storage locations to store 3776 34 values. 3777 3778 When d_nnz, o_nnz parameters are specified, the storage is specified 3779 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3780 In the above case the values for d_nnz,o_nnz are: 3781 .vb 3782 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3783 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3784 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3785 .ve 3786 Here the space allocated is sum of all the above values i.e 34, and 3787 hence pre-allocation is perfect. 3788 3789 Level: intermediate 3790 3791 .keywords: matrix, aij, compressed row, sparse, parallel 3792 3793 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 3794 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 3795 @*/ 3796 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3797 { 3798 PetscErrorCode ierr; 3799 3800 PetscFunctionBegin; 3801 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3802 PetscValidType(B,1); 3803 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 3804 PetscFunctionReturn(0); 3805 } 3806 3807 /*@ 3808 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 3809 CSR format the local rows. 3810 3811 Collective on MPI_Comm 3812 3813 Input Parameters: 3814 + comm - MPI communicator 3815 . m - number of local rows (Cannot be PETSC_DECIDE) 3816 . n - This value should be the same as the local size used in creating the 3817 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3818 calculated if N is given) For square matrices n is almost always m. 3819 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3820 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3821 . i - row indices 3822 . j - column indices 3823 - a - matrix values 3824 3825 Output Parameter: 3826 . mat - the matrix 3827 3828 Level: intermediate 3829 3830 Notes: 3831 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3832 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3833 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3834 3835 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3836 3837 The format which is used for the sparse matrix input, is equivalent to a 3838 row-major ordering.. i.e for the following matrix, the input data expected is 3839 as shown 3840 3841 $ 1 0 0 3842 $ 2 0 3 P0 3843 $ ------- 3844 $ 4 5 6 P1 3845 $ 3846 $ Process0 [P0]: rows_owned=[0,1] 3847 $ i = {0,1,3} [size = nrow+1 = 2+1] 3848 $ j = {0,0,2} [size = 3] 3849 $ v = {1,2,3} [size = 3] 3850 $ 3851 $ Process1 [P1]: rows_owned=[2] 3852 $ i = {0,3} [size = nrow+1 = 1+1] 3853 $ j = {0,1,2} [size = 3] 3854 $ v = {4,5,6} [size = 3] 3855 3856 .keywords: matrix, aij, compressed row, sparse, parallel 3857 3858 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 3859 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 3860 @*/ 3861 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 3862 { 3863 PetscErrorCode ierr; 3864 3865 PetscFunctionBegin; 3866 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 3867 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 3868 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3869 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 3870 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 3871 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3872 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 3873 PetscFunctionReturn(0); 3874 } 3875 3876 /*@C 3877 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 3878 (the default parallel PETSc format). For good matrix assembly performance 3879 the user should preallocate the matrix storage by setting the parameters 3880 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3881 performance can be increased by more than a factor of 50. 3882 3883 Collective on MPI_Comm 3884 3885 Input Parameters: 3886 + comm - MPI communicator 3887 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 3888 This value should be the same as the local size used in creating the 3889 y vector for the matrix-vector product y = Ax. 3890 . n - This value should be the same as the local size used in creating the 3891 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3892 calculated if N is given) For square matrices n is almost always m. 3893 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3894 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3895 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3896 (same value is used for all local rows) 3897 . d_nnz - array containing the number of nonzeros in the various rows of the 3898 DIAGONAL portion of the local submatrix (possibly different for each row) 3899 or NULL, if d_nz is used to specify the nonzero structure. 3900 The size of this array is equal to the number of local rows, i.e 'm'. 3901 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3902 submatrix (same value is used for all local rows). 3903 - o_nnz - array containing the number of nonzeros in the various rows of the 3904 OFF-DIAGONAL portion of the local submatrix (possibly different for 3905 each row) or NULL, if o_nz is used to specify the nonzero 3906 structure. The size of this array is equal to the number 3907 of local rows, i.e 'm'. 3908 3909 Output Parameter: 3910 . A - the matrix 3911 3912 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 3913 MatXXXXSetPreallocation() paradgm instead of this routine directly. 3914 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 3915 3916 Notes: 3917 If the *_nnz parameter is given then the *_nz parameter is ignored 3918 3919 m,n,M,N parameters specify the size of the matrix, and its partitioning across 3920 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 3921 storage requirements for this matrix. 3922 3923 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 3924 processor than it must be used on all processors that share the object for 3925 that argument. 3926 3927 The user MUST specify either the local or global matrix dimensions 3928 (possibly both). 3929 3930 The parallel matrix is partitioned across processors such that the 3931 first m0 rows belong to process 0, the next m1 rows belong to 3932 process 1, the next m2 rows belong to process 2 etc.. where 3933 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 3934 values corresponding to [m x N] submatrix. 3935 3936 The columns are logically partitioned with the n0 columns belonging 3937 to 0th partition, the next n1 columns belonging to the next 3938 partition etc.. where n0,n1,n2... are the input parameter 'n'. 3939 3940 The DIAGONAL portion of the local submatrix on any given processor 3941 is the submatrix corresponding to the rows and columns m,n 3942 corresponding to the given processor. i.e diagonal matrix on 3943 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 3944 etc. The remaining portion of the local submatrix [m x (N-n)] 3945 constitute the OFF-DIAGONAL portion. The example below better 3946 illustrates this concept. 3947 3948 For a square global matrix we define each processor's diagonal portion 3949 to be its local rows and the corresponding columns (a square submatrix); 3950 each processor's off-diagonal portion encompasses the remainder of the 3951 local matrix (a rectangular submatrix). 3952 3953 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3954 3955 When calling this routine with a single process communicator, a matrix of 3956 type SEQAIJ is returned. If a matrix of type MATMPIAIJ is desired for this 3957 type of communicator, use the construction mechanism: 3958 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 3959 3960 By default, this format uses inodes (identical nodes) when possible. 3961 We search for consecutive rows with the same nonzero structure, thereby 3962 reusing matrix information to achieve increased efficiency. 3963 3964 Options Database Keys: 3965 + -mat_no_inode - Do not use inodes 3966 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 3967 - -mat_aij_oneindex - Internally use indexing starting at 1 3968 rather than 0. Note that when calling MatSetValues(), 3969 the user still MUST index entries starting at 0! 3970 3971 3972 Example usage: 3973 3974 Consider the following 8x8 matrix with 34 non-zero values, that is 3975 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3976 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3977 as follows: 3978 3979 .vb 3980 1 2 0 | 0 3 0 | 0 4 3981 Proc0 0 5 6 | 7 0 0 | 8 0 3982 9 0 10 | 11 0 0 | 12 0 3983 ------------------------------------- 3984 13 0 14 | 15 16 17 | 0 0 3985 Proc1 0 18 0 | 19 20 21 | 0 0 3986 0 0 0 | 22 23 0 | 24 0 3987 ------------------------------------- 3988 Proc2 25 26 27 | 0 0 28 | 29 0 3989 30 0 0 | 31 32 33 | 0 34 3990 .ve 3991 3992 This can be represented as a collection of submatrices as: 3993 3994 .vb 3995 A B C 3996 D E F 3997 G H I 3998 .ve 3999 4000 Where the submatrices A,B,C are owned by proc0, D,E,F are 4001 owned by proc1, G,H,I are owned by proc2. 4002 4003 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4004 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4005 The 'M','N' parameters are 8,8, and have the same values on all procs. 4006 4007 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4008 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4009 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4010 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4011 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4012 matrix, ans [DF] as another SeqAIJ matrix. 4013 4014 When d_nz, o_nz parameters are specified, d_nz storage elements are 4015 allocated for every row of the local diagonal submatrix, and o_nz 4016 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4017 One way to choose d_nz and o_nz is to use the max nonzerors per local 4018 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4019 In this case, the values of d_nz,o_nz are: 4020 .vb 4021 proc0 : dnz = 2, o_nz = 2 4022 proc1 : dnz = 3, o_nz = 2 4023 proc2 : dnz = 1, o_nz = 4 4024 .ve 4025 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4026 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4027 for proc3. i.e we are using 12+15+10=37 storage locations to store 4028 34 values. 4029 4030 When d_nnz, o_nnz parameters are specified, the storage is specified 4031 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4032 In the above case the values for d_nnz,o_nnz are: 4033 .vb 4034 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4035 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4036 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4037 .ve 4038 Here the space allocated is sum of all the above values i.e 34, and 4039 hence pre-allocation is perfect. 4040 4041 Level: intermediate 4042 4043 .keywords: matrix, aij, compressed row, sparse, parallel 4044 4045 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4046 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4047 @*/ 4048 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) 4049 { 4050 PetscErrorCode ierr; 4051 PetscMPIInt size; 4052 4053 PetscFunctionBegin; 4054 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4055 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4056 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4057 if (size > 1) { 4058 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4059 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4060 } else { 4061 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4062 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4063 } 4064 PetscFunctionReturn(0); 4065 } 4066 4067 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4068 { 4069 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4070 PetscBool flg; 4071 PetscErrorCode ierr; 4072 4073 PetscFunctionBegin; 4074 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4075 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4076 if (Ad) *Ad = a->A; 4077 if (Ao) *Ao = a->B; 4078 if (colmap) *colmap = a->garray; 4079 PetscFunctionReturn(0); 4080 } 4081 4082 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4083 { 4084 PetscErrorCode ierr; 4085 PetscInt m,N,i,rstart,nnz,Ii; 4086 PetscInt *indx; 4087 PetscScalar *values; 4088 4089 PetscFunctionBegin; 4090 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4091 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4092 PetscInt *dnz,*onz,sum,bs,cbs; 4093 4094 if (n == PETSC_DECIDE) { 4095 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4096 } 4097 /* Check sum(n) = N */ 4098 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4099 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 4100 4101 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4102 rstart -= m; 4103 4104 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4105 for (i=0; i<m; i++) { 4106 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4107 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4108 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4109 } 4110 4111 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4112 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4113 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4114 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4115 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4116 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4117 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4118 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4119 } 4120 4121 /* numeric phase */ 4122 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4123 for (i=0; i<m; i++) { 4124 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4125 Ii = i + rstart; 4126 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4127 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4128 } 4129 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4130 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4131 PetscFunctionReturn(0); 4132 } 4133 4134 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4135 { 4136 PetscErrorCode ierr; 4137 PetscMPIInt rank; 4138 PetscInt m,N,i,rstart,nnz; 4139 size_t len; 4140 const PetscInt *indx; 4141 PetscViewer out; 4142 char *name; 4143 Mat B; 4144 const PetscScalar *values; 4145 4146 PetscFunctionBegin; 4147 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4148 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4149 /* Should this be the type of the diagonal block of A? */ 4150 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4151 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4152 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4153 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4154 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4155 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4156 for (i=0; i<m; i++) { 4157 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4158 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4159 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4160 } 4161 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4162 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4163 4164 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4165 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4166 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4167 sprintf(name,"%s.%d",outfile,rank); 4168 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4169 ierr = PetscFree(name);CHKERRQ(ierr); 4170 ierr = MatView(B,out);CHKERRQ(ierr); 4171 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4172 ierr = MatDestroy(&B);CHKERRQ(ierr); 4173 PetscFunctionReturn(0); 4174 } 4175 4176 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4177 { 4178 PetscErrorCode ierr; 4179 Mat_Merge_SeqsToMPI *merge; 4180 PetscContainer container; 4181 4182 PetscFunctionBegin; 4183 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4184 if (container) { 4185 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4186 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4187 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4188 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4189 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4190 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4191 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4192 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4193 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4194 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4195 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4196 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4197 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4198 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4199 ierr = PetscFree(merge);CHKERRQ(ierr); 4200 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4201 } 4202 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4203 PetscFunctionReturn(0); 4204 } 4205 4206 #include <../src/mat/utils/freespace.h> 4207 #include <petscbt.h> 4208 4209 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4210 { 4211 PetscErrorCode ierr; 4212 MPI_Comm comm; 4213 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4214 PetscMPIInt size,rank,taga,*len_s; 4215 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4216 PetscInt proc,m; 4217 PetscInt **buf_ri,**buf_rj; 4218 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4219 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4220 MPI_Request *s_waits,*r_waits; 4221 MPI_Status *status; 4222 MatScalar *aa=a->a; 4223 MatScalar **abuf_r,*ba_i; 4224 Mat_Merge_SeqsToMPI *merge; 4225 PetscContainer container; 4226 4227 PetscFunctionBegin; 4228 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4229 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4230 4231 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4232 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4233 4234 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4235 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4236 4237 bi = merge->bi; 4238 bj = merge->bj; 4239 buf_ri = merge->buf_ri; 4240 buf_rj = merge->buf_rj; 4241 4242 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4243 owners = merge->rowmap->range; 4244 len_s = merge->len_s; 4245 4246 /* send and recv matrix values */ 4247 /*-----------------------------*/ 4248 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4249 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4250 4251 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4252 for (proc=0,k=0; proc<size; proc++) { 4253 if (!len_s[proc]) continue; 4254 i = owners[proc]; 4255 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4256 k++; 4257 } 4258 4259 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4260 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4261 ierr = PetscFree(status);CHKERRQ(ierr); 4262 4263 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4264 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4265 4266 /* insert mat values of mpimat */ 4267 /*----------------------------*/ 4268 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4269 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4270 4271 for (k=0; k<merge->nrecv; k++) { 4272 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4273 nrows = *(buf_ri_k[k]); 4274 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4275 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4276 } 4277 4278 /* set values of ba */ 4279 m = merge->rowmap->n; 4280 for (i=0; i<m; i++) { 4281 arow = owners[rank] + i; 4282 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4283 bnzi = bi[i+1] - bi[i]; 4284 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4285 4286 /* add local non-zero vals of this proc's seqmat into ba */ 4287 anzi = ai[arow+1] - ai[arow]; 4288 aj = a->j + ai[arow]; 4289 aa = a->a + ai[arow]; 4290 nextaj = 0; 4291 for (j=0; nextaj<anzi; j++) { 4292 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4293 ba_i[j] += aa[nextaj++]; 4294 } 4295 } 4296 4297 /* add received vals into ba */ 4298 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4299 /* i-th row */ 4300 if (i == *nextrow[k]) { 4301 anzi = *(nextai[k]+1) - *nextai[k]; 4302 aj = buf_rj[k] + *(nextai[k]); 4303 aa = abuf_r[k] + *(nextai[k]); 4304 nextaj = 0; 4305 for (j=0; nextaj<anzi; j++) { 4306 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4307 ba_i[j] += aa[nextaj++]; 4308 } 4309 } 4310 nextrow[k]++; nextai[k]++; 4311 } 4312 } 4313 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4314 } 4315 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4316 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4317 4318 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4319 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4320 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4321 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4322 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4323 PetscFunctionReturn(0); 4324 } 4325 4326 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4327 { 4328 PetscErrorCode ierr; 4329 Mat B_mpi; 4330 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4331 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4332 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4333 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4334 PetscInt len,proc,*dnz,*onz,bs,cbs; 4335 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4336 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4337 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4338 MPI_Status *status; 4339 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4340 PetscBT lnkbt; 4341 Mat_Merge_SeqsToMPI *merge; 4342 PetscContainer container; 4343 4344 PetscFunctionBegin; 4345 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4346 4347 /* make sure it is a PETSc comm */ 4348 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4349 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4350 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4351 4352 ierr = PetscNew(&merge);CHKERRQ(ierr); 4353 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4354 4355 /* determine row ownership */ 4356 /*---------------------------------------------------------*/ 4357 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4358 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4359 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4360 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4361 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4362 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4363 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4364 4365 m = merge->rowmap->n; 4366 owners = merge->rowmap->range; 4367 4368 /* determine the number of messages to send, their lengths */ 4369 /*---------------------------------------------------------*/ 4370 len_s = merge->len_s; 4371 4372 len = 0; /* length of buf_si[] */ 4373 merge->nsend = 0; 4374 for (proc=0; proc<size; proc++) { 4375 len_si[proc] = 0; 4376 if (proc == rank) { 4377 len_s[proc] = 0; 4378 } else { 4379 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4380 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4381 } 4382 if (len_s[proc]) { 4383 merge->nsend++; 4384 nrows = 0; 4385 for (i=owners[proc]; i<owners[proc+1]; i++) { 4386 if (ai[i+1] > ai[i]) nrows++; 4387 } 4388 len_si[proc] = 2*(nrows+1); 4389 len += len_si[proc]; 4390 } 4391 } 4392 4393 /* determine the number and length of messages to receive for ij-structure */ 4394 /*-------------------------------------------------------------------------*/ 4395 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4396 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4397 4398 /* post the Irecv of j-structure */ 4399 /*-------------------------------*/ 4400 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4401 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4402 4403 /* post the Isend of j-structure */ 4404 /*--------------------------------*/ 4405 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4406 4407 for (proc=0, k=0; proc<size; proc++) { 4408 if (!len_s[proc]) continue; 4409 i = owners[proc]; 4410 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4411 k++; 4412 } 4413 4414 /* receives and sends of j-structure are complete */ 4415 /*------------------------------------------------*/ 4416 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4417 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4418 4419 /* send and recv i-structure */ 4420 /*---------------------------*/ 4421 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4422 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4423 4424 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4425 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4426 for (proc=0,k=0; proc<size; proc++) { 4427 if (!len_s[proc]) continue; 4428 /* form outgoing message for i-structure: 4429 buf_si[0]: nrows to be sent 4430 [1:nrows]: row index (global) 4431 [nrows+1:2*nrows+1]: i-structure index 4432 */ 4433 /*-------------------------------------------*/ 4434 nrows = len_si[proc]/2 - 1; 4435 buf_si_i = buf_si + nrows+1; 4436 buf_si[0] = nrows; 4437 buf_si_i[0] = 0; 4438 nrows = 0; 4439 for (i=owners[proc]; i<owners[proc+1]; i++) { 4440 anzi = ai[i+1] - ai[i]; 4441 if (anzi) { 4442 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4443 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4444 nrows++; 4445 } 4446 } 4447 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4448 k++; 4449 buf_si += len_si[proc]; 4450 } 4451 4452 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4453 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4454 4455 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4456 for (i=0; i<merge->nrecv; i++) { 4457 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); 4458 } 4459 4460 ierr = PetscFree(len_si);CHKERRQ(ierr); 4461 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4462 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4463 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4464 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4465 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4466 ierr = PetscFree(status);CHKERRQ(ierr); 4467 4468 /* compute a local seq matrix in each processor */ 4469 /*----------------------------------------------*/ 4470 /* allocate bi array and free space for accumulating nonzero column info */ 4471 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4472 bi[0] = 0; 4473 4474 /* create and initialize a linked list */ 4475 nlnk = N+1; 4476 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4477 4478 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4479 len = ai[owners[rank+1]] - ai[owners[rank]]; 4480 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4481 4482 current_space = free_space; 4483 4484 /* determine symbolic info for each local row */ 4485 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4486 4487 for (k=0; k<merge->nrecv; k++) { 4488 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4489 nrows = *buf_ri_k[k]; 4490 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4491 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4492 } 4493 4494 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4495 len = 0; 4496 for (i=0; i<m; i++) { 4497 bnzi = 0; 4498 /* add local non-zero cols of this proc's seqmat into lnk */ 4499 arow = owners[rank] + i; 4500 anzi = ai[arow+1] - ai[arow]; 4501 aj = a->j + ai[arow]; 4502 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4503 bnzi += nlnk; 4504 /* add received col data into lnk */ 4505 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4506 if (i == *nextrow[k]) { /* i-th row */ 4507 anzi = *(nextai[k]+1) - *nextai[k]; 4508 aj = buf_rj[k] + *nextai[k]; 4509 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4510 bnzi += nlnk; 4511 nextrow[k]++; nextai[k]++; 4512 } 4513 } 4514 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4515 4516 /* if free space is not available, make more free space */ 4517 if (current_space->local_remaining<bnzi) { 4518 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4519 nspacedouble++; 4520 } 4521 /* copy data into free space, then initialize lnk */ 4522 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4523 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4524 4525 current_space->array += bnzi; 4526 current_space->local_used += bnzi; 4527 current_space->local_remaining -= bnzi; 4528 4529 bi[i+1] = bi[i] + bnzi; 4530 } 4531 4532 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4533 4534 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4535 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4536 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4537 4538 /* create symbolic parallel matrix B_mpi */ 4539 /*---------------------------------------*/ 4540 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4541 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4542 if (n==PETSC_DECIDE) { 4543 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4544 } else { 4545 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4546 } 4547 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4548 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4549 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4550 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4551 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4552 4553 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4554 B_mpi->assembled = PETSC_FALSE; 4555 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4556 merge->bi = bi; 4557 merge->bj = bj; 4558 merge->buf_ri = buf_ri; 4559 merge->buf_rj = buf_rj; 4560 merge->coi = NULL; 4561 merge->coj = NULL; 4562 merge->owners_co = NULL; 4563 4564 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4565 4566 /* attach the supporting struct to B_mpi for reuse */ 4567 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4568 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4569 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4570 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4571 *mpimat = B_mpi; 4572 4573 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4574 PetscFunctionReturn(0); 4575 } 4576 4577 /*@C 4578 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4579 matrices from each processor 4580 4581 Collective on MPI_Comm 4582 4583 Input Parameters: 4584 + comm - the communicators the parallel matrix will live on 4585 . seqmat - the input sequential matrices 4586 . m - number of local rows (or PETSC_DECIDE) 4587 . n - number of local columns (or PETSC_DECIDE) 4588 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4589 4590 Output Parameter: 4591 . mpimat - the parallel matrix generated 4592 4593 Level: advanced 4594 4595 Notes: 4596 The dimensions of the sequential matrix in each processor MUST be the same. 4597 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4598 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4599 @*/ 4600 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4601 { 4602 PetscErrorCode ierr; 4603 PetscMPIInt size; 4604 4605 PetscFunctionBegin; 4606 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4607 if (size == 1) { 4608 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4609 if (scall == MAT_INITIAL_MATRIX) { 4610 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4611 } else { 4612 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4613 } 4614 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4615 PetscFunctionReturn(0); 4616 } 4617 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4618 if (scall == MAT_INITIAL_MATRIX) { 4619 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4620 } 4621 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4622 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4623 PetscFunctionReturn(0); 4624 } 4625 4626 /*@ 4627 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 4628 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4629 with MatGetSize() 4630 4631 Not Collective 4632 4633 Input Parameters: 4634 + A - the matrix 4635 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4636 4637 Output Parameter: 4638 . A_loc - the local sequential matrix generated 4639 4640 Level: developer 4641 4642 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4643 4644 @*/ 4645 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4646 { 4647 PetscErrorCode ierr; 4648 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4649 Mat_SeqAIJ *mat,*a,*b; 4650 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4651 MatScalar *aa,*ba,*cam; 4652 PetscScalar *ca; 4653 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4654 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4655 PetscBool match; 4656 MPI_Comm comm; 4657 PetscMPIInt size; 4658 4659 PetscFunctionBegin; 4660 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4661 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4662 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4663 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4664 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4665 4666 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4667 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4668 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4669 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4670 aa = a->a; ba = b->a; 4671 if (scall == MAT_INITIAL_MATRIX) { 4672 if (size == 1) { 4673 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4674 PetscFunctionReturn(0); 4675 } 4676 4677 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4678 ci[0] = 0; 4679 for (i=0; i<am; i++) { 4680 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4681 } 4682 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4683 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4684 k = 0; 4685 for (i=0; i<am; i++) { 4686 ncols_o = bi[i+1] - bi[i]; 4687 ncols_d = ai[i+1] - ai[i]; 4688 /* off-diagonal portion of A */ 4689 for (jo=0; jo<ncols_o; jo++) { 4690 col = cmap[*bj]; 4691 if (col >= cstart) break; 4692 cj[k] = col; bj++; 4693 ca[k++] = *ba++; 4694 } 4695 /* diagonal portion of A */ 4696 for (j=0; j<ncols_d; j++) { 4697 cj[k] = cstart + *aj++; 4698 ca[k++] = *aa++; 4699 } 4700 /* off-diagonal portion of A */ 4701 for (j=jo; j<ncols_o; j++) { 4702 cj[k] = cmap[*bj++]; 4703 ca[k++] = *ba++; 4704 } 4705 } 4706 /* put together the new matrix */ 4707 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4708 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4709 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4710 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4711 mat->free_a = PETSC_TRUE; 4712 mat->free_ij = PETSC_TRUE; 4713 mat->nonew = 0; 4714 } else if (scall == MAT_REUSE_MATRIX) { 4715 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4716 ci = mat->i; cj = mat->j; cam = mat->a; 4717 for (i=0; i<am; i++) { 4718 /* off-diagonal portion of A */ 4719 ncols_o = bi[i+1] - bi[i]; 4720 for (jo=0; jo<ncols_o; jo++) { 4721 col = cmap[*bj]; 4722 if (col >= cstart) break; 4723 *cam++ = *ba++; bj++; 4724 } 4725 /* diagonal portion of A */ 4726 ncols_d = ai[i+1] - ai[i]; 4727 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4728 /* off-diagonal portion of A */ 4729 for (j=jo; j<ncols_o; j++) { 4730 *cam++ = *ba++; bj++; 4731 } 4732 } 4733 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4734 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4735 PetscFunctionReturn(0); 4736 } 4737 4738 /*@C 4739 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4740 4741 Not Collective 4742 4743 Input Parameters: 4744 + A - the matrix 4745 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4746 - row, col - index sets of rows and columns to extract (or NULL) 4747 4748 Output Parameter: 4749 . A_loc - the local sequential matrix generated 4750 4751 Level: developer 4752 4753 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4754 4755 @*/ 4756 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4757 { 4758 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4759 PetscErrorCode ierr; 4760 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4761 IS isrowa,iscola; 4762 Mat *aloc; 4763 PetscBool match; 4764 4765 PetscFunctionBegin; 4766 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4767 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4768 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4769 if (!row) { 4770 start = A->rmap->rstart; end = A->rmap->rend; 4771 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 4772 } else { 4773 isrowa = *row; 4774 } 4775 if (!col) { 4776 start = A->cmap->rstart; 4777 cmap = a->garray; 4778 nzA = a->A->cmap->n; 4779 nzB = a->B->cmap->n; 4780 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4781 ncols = 0; 4782 for (i=0; i<nzB; i++) { 4783 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4784 else break; 4785 } 4786 imark = i; 4787 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 4788 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 4789 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 4790 } else { 4791 iscola = *col; 4792 } 4793 if (scall != MAT_INITIAL_MATRIX) { 4794 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 4795 aloc[0] = *A_loc; 4796 } 4797 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 4798 *A_loc = aloc[0]; 4799 ierr = PetscFree(aloc);CHKERRQ(ierr); 4800 if (!row) { 4801 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 4802 } 4803 if (!col) { 4804 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 4805 } 4806 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4807 PetscFunctionReturn(0); 4808 } 4809 4810 /*@C 4811 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 4812 4813 Collective on Mat 4814 4815 Input Parameters: 4816 + A,B - the matrices in mpiaij format 4817 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4818 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 4819 4820 Output Parameter: 4821 + rowb, colb - index sets of rows and columns of B to extract 4822 - B_seq - the sequential matrix generated 4823 4824 Level: developer 4825 4826 @*/ 4827 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 4828 { 4829 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4830 PetscErrorCode ierr; 4831 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 4832 IS isrowb,iscolb; 4833 Mat *bseq=NULL; 4834 4835 PetscFunctionBegin; 4836 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 4837 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); 4838 } 4839 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 4840 4841 if (scall == MAT_INITIAL_MATRIX) { 4842 start = A->cmap->rstart; 4843 cmap = a->garray; 4844 nzA = a->A->cmap->n; 4845 nzB = a->B->cmap->n; 4846 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4847 ncols = 0; 4848 for (i=0; i<nzB; i++) { /* row < local row index */ 4849 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4850 else break; 4851 } 4852 imark = i; 4853 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 4854 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 4855 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 4856 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 4857 } else { 4858 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 4859 isrowb = *rowb; iscolb = *colb; 4860 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 4861 bseq[0] = *B_seq; 4862 } 4863 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 4864 *B_seq = bseq[0]; 4865 ierr = PetscFree(bseq);CHKERRQ(ierr); 4866 if (!rowb) { 4867 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 4868 } else { 4869 *rowb = isrowb; 4870 } 4871 if (!colb) { 4872 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 4873 } else { 4874 *colb = iscolb; 4875 } 4876 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 4877 PetscFunctionReturn(0); 4878 } 4879 4880 /* 4881 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 4882 of the OFF-DIAGONAL portion of local A 4883 4884 Collective on Mat 4885 4886 Input Parameters: 4887 + A,B - the matrices in mpiaij format 4888 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4889 4890 Output Parameter: 4891 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 4892 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 4893 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 4894 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 4895 4896 Level: developer 4897 4898 */ 4899 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 4900 { 4901 VecScatter_MPI_General *gen_to,*gen_from; 4902 PetscErrorCode ierr; 4903 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4904 Mat_SeqAIJ *b_oth; 4905 VecScatter ctx =a->Mvctx; 4906 MPI_Comm comm; 4907 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 4908 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 4909 PetscInt *rvalues,*svalues; 4910 MatScalar *b_otha,*bufa,*bufA; 4911 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 4912 MPI_Request *rwaits = NULL,*swaits = NULL; 4913 MPI_Status *sstatus,rstatus; 4914 PetscMPIInt jj,size; 4915 PetscInt *cols,sbs,rbs; 4916 PetscScalar *vals; 4917 4918 PetscFunctionBegin; 4919 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4920 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4921 4922 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 4923 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); 4924 } 4925 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 4926 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4927 4928 if (size == 1) { 4929 startsj_s = NULL; 4930 bufa_ptr = NULL; 4931 *B_oth = NULL; 4932 PetscFunctionReturn(0); 4933 } 4934 4935 gen_to = (VecScatter_MPI_General*)ctx->todata; 4936 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 4937 nrecvs = gen_from->n; 4938 nsends = gen_to->n; 4939 4940 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 4941 srow = gen_to->indices; /* local row index to be sent */ 4942 sstarts = gen_to->starts; 4943 sprocs = gen_to->procs; 4944 sstatus = gen_to->sstatus; 4945 sbs = gen_to->bs; 4946 rstarts = gen_from->starts; 4947 rprocs = gen_from->procs; 4948 rbs = gen_from->bs; 4949 4950 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 4951 if (scall == MAT_INITIAL_MATRIX) { 4952 /* i-array */ 4953 /*---------*/ 4954 /* post receives */ 4955 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 4956 for (i=0; i<nrecvs; i++) { 4957 rowlen = rvalues + rstarts[i]*rbs; 4958 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 4959 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 4960 } 4961 4962 /* pack the outgoing message */ 4963 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 4964 4965 sstartsj[0] = 0; 4966 rstartsj[0] = 0; 4967 len = 0; /* total length of j or a array to be sent */ 4968 k = 0; 4969 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 4970 for (i=0; i<nsends; i++) { 4971 rowlen = svalues + sstarts[i]*sbs; 4972 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 4973 for (j=0; j<nrows; j++) { 4974 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 4975 for (l=0; l<sbs; l++) { 4976 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 4977 4978 rowlen[j*sbs+l] = ncols; 4979 4980 len += ncols; 4981 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 4982 } 4983 k++; 4984 } 4985 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 4986 4987 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 4988 } 4989 /* recvs and sends of i-array are completed */ 4990 i = nrecvs; 4991 while (i--) { 4992 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 4993 } 4994 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 4995 ierr = PetscFree(svalues);CHKERRQ(ierr); 4996 4997 /* allocate buffers for sending j and a arrays */ 4998 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 4999 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5000 5001 /* create i-array of B_oth */ 5002 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5003 5004 b_othi[0] = 0; 5005 len = 0; /* total length of j or a array to be received */ 5006 k = 0; 5007 for (i=0; i<nrecvs; i++) { 5008 rowlen = rvalues + rstarts[i]*rbs; 5009 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5010 for (j=0; j<nrows; j++) { 5011 b_othi[k+1] = b_othi[k] + rowlen[j]; 5012 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5013 k++; 5014 } 5015 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5016 } 5017 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5018 5019 /* allocate space for j and a arrrays of B_oth */ 5020 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5021 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5022 5023 /* j-array */ 5024 /*---------*/ 5025 /* post receives of j-array */ 5026 for (i=0; i<nrecvs; i++) { 5027 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5028 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5029 } 5030 5031 /* pack the outgoing message j-array */ 5032 k = 0; 5033 for (i=0; i<nsends; i++) { 5034 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5035 bufJ = bufj+sstartsj[i]; 5036 for (j=0; j<nrows; j++) { 5037 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5038 for (ll=0; ll<sbs; ll++) { 5039 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5040 for (l=0; l<ncols; l++) { 5041 *bufJ++ = cols[l]; 5042 } 5043 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5044 } 5045 } 5046 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5047 } 5048 5049 /* recvs and sends of j-array are completed */ 5050 i = nrecvs; 5051 while (i--) { 5052 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5053 } 5054 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5055 } else if (scall == MAT_REUSE_MATRIX) { 5056 sstartsj = *startsj_s; 5057 rstartsj = *startsj_r; 5058 bufa = *bufa_ptr; 5059 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5060 b_otha = b_oth->a; 5061 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5062 5063 /* a-array */ 5064 /*---------*/ 5065 /* post receives of a-array */ 5066 for (i=0; i<nrecvs; i++) { 5067 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5068 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5069 } 5070 5071 /* pack the outgoing message a-array */ 5072 k = 0; 5073 for (i=0; i<nsends; i++) { 5074 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5075 bufA = bufa+sstartsj[i]; 5076 for (j=0; j<nrows; j++) { 5077 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5078 for (ll=0; ll<sbs; ll++) { 5079 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5080 for (l=0; l<ncols; l++) { 5081 *bufA++ = vals[l]; 5082 } 5083 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5084 } 5085 } 5086 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5087 } 5088 /* recvs and sends of a-array are completed */ 5089 i = nrecvs; 5090 while (i--) { 5091 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5092 } 5093 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5094 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5095 5096 if (scall == MAT_INITIAL_MATRIX) { 5097 /* put together the new matrix */ 5098 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5099 5100 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5101 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5102 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5103 b_oth->free_a = PETSC_TRUE; 5104 b_oth->free_ij = PETSC_TRUE; 5105 b_oth->nonew = 0; 5106 5107 ierr = PetscFree(bufj);CHKERRQ(ierr); 5108 if (!startsj_s || !bufa_ptr) { 5109 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5110 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5111 } else { 5112 *startsj_s = sstartsj; 5113 *startsj_r = rstartsj; 5114 *bufa_ptr = bufa; 5115 } 5116 } 5117 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5118 PetscFunctionReturn(0); 5119 } 5120 5121 /*@C 5122 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5123 5124 Not Collective 5125 5126 Input Parameters: 5127 . A - The matrix in mpiaij format 5128 5129 Output Parameter: 5130 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5131 . colmap - A map from global column index to local index into lvec 5132 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5133 5134 Level: developer 5135 5136 @*/ 5137 #if defined(PETSC_USE_CTABLE) 5138 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5139 #else 5140 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5141 #endif 5142 { 5143 Mat_MPIAIJ *a; 5144 5145 PetscFunctionBegin; 5146 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5147 PetscValidPointer(lvec, 2); 5148 PetscValidPointer(colmap, 3); 5149 PetscValidPointer(multScatter, 4); 5150 a = (Mat_MPIAIJ*) A->data; 5151 if (lvec) *lvec = a->lvec; 5152 if (colmap) *colmap = a->colmap; 5153 if (multScatter) *multScatter = a->Mvctx; 5154 PetscFunctionReturn(0); 5155 } 5156 5157 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5158 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5159 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5160 #if defined(PETSC_HAVE_ELEMENTAL) 5161 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5162 #endif 5163 #if defined(PETSC_HAVE_HYPRE) 5164 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5165 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5166 #endif 5167 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5168 5169 /* 5170 Computes (B'*A')' since computing B*A directly is untenable 5171 5172 n p p 5173 ( ) ( ) ( ) 5174 m ( A ) * n ( B ) = m ( C ) 5175 ( ) ( ) ( ) 5176 5177 */ 5178 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5179 { 5180 PetscErrorCode ierr; 5181 Mat At,Bt,Ct; 5182 5183 PetscFunctionBegin; 5184 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5185 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5186 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5187 ierr = MatDestroy(&At);CHKERRQ(ierr); 5188 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5189 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5190 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5191 PetscFunctionReturn(0); 5192 } 5193 5194 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5195 { 5196 PetscErrorCode ierr; 5197 PetscInt m=A->rmap->n,n=B->cmap->n; 5198 Mat Cmat; 5199 5200 PetscFunctionBegin; 5201 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); 5202 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5203 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5204 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5205 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5206 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5207 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5208 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5209 5210 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5211 5212 *C = Cmat; 5213 PetscFunctionReturn(0); 5214 } 5215 5216 /* ----------------------------------------------------------------*/ 5217 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5218 { 5219 PetscErrorCode ierr; 5220 5221 PetscFunctionBegin; 5222 if (scall == MAT_INITIAL_MATRIX) { 5223 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5224 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5225 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5226 } 5227 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5228 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5229 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5230 PetscFunctionReturn(0); 5231 } 5232 5233 /*MC 5234 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5235 5236 Options Database Keys: 5237 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5238 5239 Level: beginner 5240 5241 .seealso: MatCreateAIJ() 5242 M*/ 5243 5244 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5245 { 5246 Mat_MPIAIJ *b; 5247 PetscErrorCode ierr; 5248 PetscMPIInt size; 5249 5250 PetscFunctionBegin; 5251 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5252 5253 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5254 B->data = (void*)b; 5255 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5256 B->assembled = PETSC_FALSE; 5257 B->insertmode = NOT_SET_VALUES; 5258 b->size = size; 5259 5260 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5261 5262 /* build cache for off array entries formed */ 5263 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5264 5265 b->donotstash = PETSC_FALSE; 5266 b->colmap = 0; 5267 b->garray = 0; 5268 b->roworiented = PETSC_TRUE; 5269 5270 /* stuff used for matrix vector multiply */ 5271 b->lvec = NULL; 5272 b->Mvctx = NULL; 5273 5274 /* stuff for MatGetRow() */ 5275 b->rowindices = 0; 5276 b->rowvalues = 0; 5277 b->getrowactive = PETSC_FALSE; 5278 5279 /* flexible pointer used in CUSP/CUSPARSE classes */ 5280 b->spptr = NULL; 5281 5282 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5283 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5284 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5285 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5286 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5287 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5288 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5289 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5290 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5291 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5292 #if defined(PETSC_HAVE_ELEMENTAL) 5293 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5294 #endif 5295 #if defined(PETSC_HAVE_HYPRE) 5296 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5297 #endif 5298 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5299 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5300 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5301 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5302 #if defined(PETSC_HAVE_HYPRE) 5303 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5304 #endif 5305 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5306 PetscFunctionReturn(0); 5307 } 5308 5309 /*@C 5310 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5311 and "off-diagonal" part of the matrix in CSR format. 5312 5313 Collective on MPI_Comm 5314 5315 Input Parameters: 5316 + comm - MPI communicator 5317 . m - number of local rows (Cannot be PETSC_DECIDE) 5318 . n - This value should be the same as the local size used in creating the 5319 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5320 calculated if N is given) For square matrices n is almost always m. 5321 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5322 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5323 . i - row indices for "diagonal" portion of matrix 5324 . j - column indices 5325 . a - matrix values 5326 . oi - row indices for "off-diagonal" portion of matrix 5327 . oj - column indices 5328 - oa - matrix values 5329 5330 Output Parameter: 5331 . mat - the matrix 5332 5333 Level: advanced 5334 5335 Notes: 5336 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5337 must free the arrays once the matrix has been destroyed and not before. 5338 5339 The i and j indices are 0 based 5340 5341 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5342 5343 This sets local rows and cannot be used to set off-processor values. 5344 5345 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5346 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5347 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5348 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5349 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5350 communication if it is known that only local entries will be set. 5351 5352 .keywords: matrix, aij, compressed row, sparse, parallel 5353 5354 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5355 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5356 @*/ 5357 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) 5358 { 5359 PetscErrorCode ierr; 5360 Mat_MPIAIJ *maij; 5361 5362 PetscFunctionBegin; 5363 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5364 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5365 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5366 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5367 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5368 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5369 maij = (Mat_MPIAIJ*) (*mat)->data; 5370 5371 (*mat)->preallocated = PETSC_TRUE; 5372 5373 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5374 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5375 5376 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5377 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5378 5379 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5380 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5381 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5382 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5383 5384 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5385 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5386 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5387 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5388 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5389 PetscFunctionReturn(0); 5390 } 5391 5392 /* 5393 Special version for direct calls from Fortran 5394 */ 5395 #include <petsc/private/fortranimpl.h> 5396 5397 /* Change these macros so can be used in void function */ 5398 #undef CHKERRQ 5399 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5400 #undef SETERRQ2 5401 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5402 #undef SETERRQ3 5403 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5404 #undef SETERRQ 5405 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5406 5407 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5408 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5409 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5410 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5411 #else 5412 #endif 5413 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) 5414 { 5415 Mat mat = *mmat; 5416 PetscInt m = *mm, n = *mn; 5417 InsertMode addv = *maddv; 5418 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5419 PetscScalar value; 5420 PetscErrorCode ierr; 5421 5422 MatCheckPreallocated(mat,1); 5423 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5424 5425 #if defined(PETSC_USE_DEBUG) 5426 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5427 #endif 5428 { 5429 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5430 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5431 PetscBool roworiented = aij->roworiented; 5432 5433 /* Some Variables required in the macro */ 5434 Mat A = aij->A; 5435 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5436 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5437 MatScalar *aa = a->a; 5438 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5439 Mat B = aij->B; 5440 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5441 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5442 MatScalar *ba = b->a; 5443 5444 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5445 PetscInt nonew = a->nonew; 5446 MatScalar *ap1,*ap2; 5447 5448 PetscFunctionBegin; 5449 for (i=0; i<m; i++) { 5450 if (im[i] < 0) continue; 5451 #if defined(PETSC_USE_DEBUG) 5452 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); 5453 #endif 5454 if (im[i] >= rstart && im[i] < rend) { 5455 row = im[i] - rstart; 5456 lastcol1 = -1; 5457 rp1 = aj + ai[row]; 5458 ap1 = aa + ai[row]; 5459 rmax1 = aimax[row]; 5460 nrow1 = ailen[row]; 5461 low1 = 0; 5462 high1 = nrow1; 5463 lastcol2 = -1; 5464 rp2 = bj + bi[row]; 5465 ap2 = ba + bi[row]; 5466 rmax2 = bimax[row]; 5467 nrow2 = bilen[row]; 5468 low2 = 0; 5469 high2 = nrow2; 5470 5471 for (j=0; j<n; j++) { 5472 if (roworiented) value = v[i*n+j]; 5473 else value = v[i+j*m]; 5474 if (in[j] >= cstart && in[j] < cend) { 5475 col = in[j] - cstart; 5476 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5477 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5478 } else if (in[j] < 0) continue; 5479 #if defined(PETSC_USE_DEBUG) 5480 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); 5481 #endif 5482 else { 5483 if (mat->was_assembled) { 5484 if (!aij->colmap) { 5485 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5486 } 5487 #if defined(PETSC_USE_CTABLE) 5488 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5489 col--; 5490 #else 5491 col = aij->colmap[in[j]] - 1; 5492 #endif 5493 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5494 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5495 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5496 col = in[j]; 5497 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5498 B = aij->B; 5499 b = (Mat_SeqAIJ*)B->data; 5500 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5501 rp2 = bj + bi[row]; 5502 ap2 = ba + bi[row]; 5503 rmax2 = bimax[row]; 5504 nrow2 = bilen[row]; 5505 low2 = 0; 5506 high2 = nrow2; 5507 bm = aij->B->rmap->n; 5508 ba = b->a; 5509 } 5510 } else col = in[j]; 5511 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5512 } 5513 } 5514 } else if (!aij->donotstash) { 5515 if (roworiented) { 5516 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5517 } else { 5518 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5519 } 5520 } 5521 } 5522 } 5523 PetscFunctionReturnVoid(); 5524 } 5525 5526