1 2 3 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 4 #include <petsc/private/vecimpl.h> 5 #include <petsc/private/isimpl.h> 6 #include <petscblaslapack.h> 7 #include <petscsf.h> 8 9 /*MC 10 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 11 12 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 13 and MATMPIAIJ otherwise. As a result, for single process communicators, 14 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 15 for communicators controlling multiple processes. It is recommended that you call both of 16 the above preallocation routines for simplicity. 17 18 Options Database Keys: 19 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 20 21 Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when 22 enough exist. 23 24 Level: beginner 25 26 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ, MATMPIAIJ 27 M*/ 28 29 /*MC 30 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 31 32 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 33 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 34 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 35 for communicators controlling multiple processes. It is recommended that you call both of 36 the above preallocation routines for simplicity. 37 38 Options Database Keys: 39 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 40 41 Level: beginner 42 43 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 44 M*/ 45 46 PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 50 51 PetscFunctionBegin; 52 if (mat->A) { 53 ierr = MatSetBlockSizes(mat->A,rbs,cbs);CHKERRQ(ierr); 54 ierr = MatSetBlockSizes(mat->B,rbs,1);CHKERRQ(ierr); 55 } 56 PetscFunctionReturn(0); 57 } 58 59 PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows) 60 { 61 PetscErrorCode ierr; 62 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 63 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data; 64 Mat_SeqAIJ *b = (Mat_SeqAIJ*)mat->B->data; 65 const PetscInt *ia,*ib; 66 const MatScalar *aa,*bb; 67 PetscInt na,nb,i,j,*rows,cnt=0,n0rows; 68 PetscInt m = M->rmap->n,rstart = M->rmap->rstart; 69 70 PetscFunctionBegin; 71 *keptrows = 0; 72 ia = a->i; 73 ib = b->i; 74 for (i=0; i<m; i++) { 75 na = ia[i+1] - ia[i]; 76 nb = ib[i+1] - ib[i]; 77 if (!na && !nb) { 78 cnt++; 79 goto ok1; 80 } 81 aa = a->a + ia[i]; 82 for (j=0; j<na; j++) { 83 if (aa[j] != 0.0) goto ok1; 84 } 85 bb = b->a + ib[i]; 86 for (j=0; j <nb; j++) { 87 if (bb[j] != 0.0) goto ok1; 88 } 89 cnt++; 90 ok1:; 91 } 92 ierr = MPIU_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr); 93 if (!n0rows) PetscFunctionReturn(0); 94 ierr = PetscMalloc1(M->rmap->n-cnt,&rows);CHKERRQ(ierr); 95 cnt = 0; 96 for (i=0; i<m; i++) { 97 na = ia[i+1] - ia[i]; 98 nb = ib[i+1] - ib[i]; 99 if (!na && !nb) continue; 100 aa = a->a + ia[i]; 101 for (j=0; j<na;j++) { 102 if (aa[j] != 0.0) { 103 rows[cnt++] = rstart + i; 104 goto ok2; 105 } 106 } 107 bb = b->a + ib[i]; 108 for (j=0; j<nb; j++) { 109 if (bb[j] != 0.0) { 110 rows[cnt++] = rstart + i; 111 goto ok2; 112 } 113 } 114 ok2:; 115 } 116 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 117 PetscFunctionReturn(0); 118 } 119 120 PetscErrorCode MatDiagonalSet_MPIAIJ(Mat Y,Vec D,InsertMode is) 121 { 122 PetscErrorCode ierr; 123 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) Y->data; 124 125 PetscFunctionBegin; 126 if (Y->assembled && Y->rmap->rstart == Y->cmap->rstart && Y->rmap->rend == Y->cmap->rend) { 127 ierr = MatDiagonalSet(aij->A,D,is);CHKERRQ(ierr); 128 } else { 129 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 130 } 131 PetscFunctionReturn(0); 132 } 133 134 PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows) 135 { 136 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)M->data; 137 PetscErrorCode ierr; 138 PetscInt i,rstart,nrows,*rows; 139 140 PetscFunctionBegin; 141 *zrows = NULL; 142 ierr = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr); 143 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 144 for (i=0; i<nrows; i++) rows[i] += rstart; 145 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 146 PetscFunctionReturn(0); 147 } 148 149 PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms) 150 { 151 PetscErrorCode ierr; 152 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 153 PetscInt i,n,*garray = aij->garray; 154 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ*) aij->A->data; 155 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ*) aij->B->data; 156 PetscReal *work; 157 158 PetscFunctionBegin; 159 ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr); 160 ierr = PetscCalloc1(n,&work);CHKERRQ(ierr); 161 if (type == NORM_2) { 162 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 163 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]); 164 } 165 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 166 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]); 167 } 168 } else if (type == NORM_1) { 169 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 170 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 171 } 172 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 173 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 174 } 175 } else if (type == NORM_INFINITY) { 176 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 177 work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 178 } 179 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 180 work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]); 181 } 182 183 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 184 if (type == NORM_INFINITY) { 185 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 186 } else { 187 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 188 } 189 ierr = PetscFree(work);CHKERRQ(ierr); 190 if (type == NORM_2) { 191 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 192 } 193 PetscFunctionReturn(0); 194 } 195 196 PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A,IS *is) 197 { 198 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 199 IS sis,gis; 200 PetscErrorCode ierr; 201 const PetscInt *isis,*igis; 202 PetscInt n,*iis,nsis,ngis,rstart,i; 203 204 PetscFunctionBegin; 205 ierr = MatFindOffBlockDiagonalEntries(a->A,&sis);CHKERRQ(ierr); 206 ierr = MatFindNonzeroRows(a->B,&gis);CHKERRQ(ierr); 207 ierr = ISGetSize(gis,&ngis);CHKERRQ(ierr); 208 ierr = ISGetSize(sis,&nsis);CHKERRQ(ierr); 209 ierr = ISGetIndices(sis,&isis);CHKERRQ(ierr); 210 ierr = ISGetIndices(gis,&igis);CHKERRQ(ierr); 211 212 ierr = PetscMalloc1(ngis+nsis,&iis);CHKERRQ(ierr); 213 ierr = PetscMemcpy(iis,igis,ngis*sizeof(PetscInt));CHKERRQ(ierr); 214 ierr = PetscMemcpy(iis+ngis,isis,nsis*sizeof(PetscInt));CHKERRQ(ierr); 215 n = ngis + nsis; 216 ierr = PetscSortRemoveDupsInt(&n,iis);CHKERRQ(ierr); 217 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 218 for (i=0; i<n; i++) iis[i] += rstart; 219 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),n,iis,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 220 221 ierr = ISRestoreIndices(sis,&isis);CHKERRQ(ierr); 222 ierr = ISRestoreIndices(gis,&igis);CHKERRQ(ierr); 223 ierr = ISDestroy(&sis);CHKERRQ(ierr); 224 ierr = ISDestroy(&gis);CHKERRQ(ierr); 225 PetscFunctionReturn(0); 226 } 227 228 /* 229 Distributes a SeqAIJ matrix across a set of processes. Code stolen from 230 MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type. 231 232 Only for square matrices 233 234 Used by a preconditioner, hence PETSC_EXTERN 235 */ 236 PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat) 237 { 238 PetscMPIInt rank,size; 239 PetscInt *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz = 0,*gmataj,cnt,row,*ld,bses[2]; 240 PetscErrorCode ierr; 241 Mat mat; 242 Mat_SeqAIJ *gmata; 243 PetscMPIInt tag; 244 MPI_Status status; 245 PetscBool aij; 246 MatScalar *gmataa,*ao,*ad,*gmataarestore=0; 247 248 PetscFunctionBegin; 249 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 250 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 251 if (!rank) { 252 ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr); 253 if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name); 254 } 255 if (reuse == MAT_INITIAL_MATRIX) { 256 ierr = MatCreate(comm,&mat);CHKERRQ(ierr); 257 ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 258 ierr = MatGetBlockSizes(gmat,&bses[0],&bses[1]);CHKERRQ(ierr); 259 ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr); 260 ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr); 261 ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr); 262 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 263 ierr = PetscMalloc2(m,&dlens,m,&olens);CHKERRQ(ierr); 264 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 265 266 rowners[0] = 0; 267 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 268 rstart = rowners[rank]; 269 rend = rowners[rank+1]; 270 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 271 if (!rank) { 272 gmata = (Mat_SeqAIJ*) gmat->data; 273 /* send row lengths to all processors */ 274 for (i=0; i<m; i++) dlens[i] = gmata->ilen[i]; 275 for (i=1; i<size; i++) { 276 ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 277 } 278 /* determine number diagonal and off-diagonal counts */ 279 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 280 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 281 jj = 0; 282 for (i=0; i<m; i++) { 283 for (j=0; j<dlens[i]; j++) { 284 if (gmata->j[jj] < rstart) ld[i]++; 285 if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++; 286 jj++; 287 } 288 } 289 /* send column indices to other processes */ 290 for (i=1; i<size; i++) { 291 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 292 ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 293 ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 294 } 295 296 /* send numerical values to other processes */ 297 for (i=1; i<size; i++) { 298 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 299 ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 300 } 301 gmataa = gmata->a; 302 gmataj = gmata->j; 303 304 } else { 305 /* receive row lengths */ 306 ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 307 /* receive column indices */ 308 ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 309 ierr = PetscMalloc2(nz,&gmataa,nz,&gmataj);CHKERRQ(ierr); 310 ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 311 /* determine number diagonal and off-diagonal counts */ 312 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 313 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 314 jj = 0; 315 for (i=0; i<m; i++) { 316 for (j=0; j<dlens[i]; j++) { 317 if (gmataj[jj] < rstart) ld[i]++; 318 if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++; 319 jj++; 320 } 321 } 322 /* receive numerical values */ 323 ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 324 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 325 } 326 /* set preallocation */ 327 for (i=0; i<m; i++) { 328 dlens[i] -= olens[i]; 329 } 330 ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr); 331 ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr); 332 333 for (i=0; i<m; i++) { 334 dlens[i] += olens[i]; 335 } 336 cnt = 0; 337 for (i=0; i<m; i++) { 338 row = rstart + i; 339 ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr); 340 cnt += dlens[i]; 341 } 342 if (rank) { 343 ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr); 344 } 345 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 346 ierr = PetscFree(rowners);CHKERRQ(ierr); 347 348 ((Mat_MPIAIJ*)(mat->data))->ld = ld; 349 350 *inmat = mat; 351 } else { /* column indices are already set; only need to move over numerical values from process 0 */ 352 Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data; 353 Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data; 354 mat = *inmat; 355 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 356 if (!rank) { 357 /* send numerical values to other processes */ 358 gmata = (Mat_SeqAIJ*) gmat->data; 359 ierr = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr); 360 gmataa = gmata->a; 361 for (i=1; i<size; i++) { 362 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 363 ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 364 } 365 nz = gmata->i[rowners[1]]-gmata->i[rowners[0]]; 366 } else { 367 /* receive numerical values from process 0*/ 368 nz = Ad->nz + Ao->nz; 369 ierr = PetscMalloc1(nz,&gmataa);CHKERRQ(ierr); gmataarestore = gmataa; 370 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 371 } 372 /* transfer numerical values into the diagonal A and off diagonal B parts of mat */ 373 ld = ((Mat_MPIAIJ*)(mat->data))->ld; 374 ad = Ad->a; 375 ao = Ao->a; 376 if (mat->rmap->n) { 377 i = 0; 378 nz = ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 379 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 380 } 381 for (i=1; i<mat->rmap->n; i++) { 382 nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 383 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 384 } 385 i--; 386 if (mat->rmap->n) { 387 nz = Ao->i[i+1] - Ao->i[i] - ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 388 } 389 if (rank) { 390 ierr = PetscFree(gmataarestore);CHKERRQ(ierr); 391 } 392 } 393 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 394 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 395 PetscFunctionReturn(0); 396 } 397 398 /* 399 Local utility routine that creates a mapping from the global column 400 number to the local number in the off-diagonal part of the local 401 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 402 a slightly higher hash table cost; without it it is not scalable (each processor 403 has an order N integer array but is fast to acess. 404 */ 405 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 406 { 407 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 408 PetscErrorCode ierr; 409 PetscInt n = aij->B->cmap->n,i; 410 411 PetscFunctionBegin; 412 if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray"); 413 #if defined(PETSC_USE_CTABLE) 414 ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 415 for (i=0; i<n; i++) { 416 ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr); 417 } 418 #else 419 ierr = PetscCalloc1(mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 420 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N+1)*sizeof(PetscInt));CHKERRQ(ierr); 421 for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1; 422 #endif 423 PetscFunctionReturn(0); 424 } 425 426 #define MatSetValues_SeqAIJ_A_Private(row,col,value,addv,orow,ocol) \ 427 { \ 428 if (col <= lastcol1) low1 = 0; \ 429 else high1 = nrow1; \ 430 lastcol1 = col;\ 431 while (high1-low1 > 5) { \ 432 t = (low1+high1)/2; \ 433 if (rp1[t] > col) high1 = t; \ 434 else low1 = t; \ 435 } \ 436 for (_i=low1; _i<high1; _i++) { \ 437 if (rp1[_i] > col) break; \ 438 if (rp1[_i] == col) { \ 439 if (addv == ADD_VALUES) ap1[_i] += value; \ 440 else ap1[_i] = value; \ 441 goto a_noinsert; \ 442 } \ 443 } \ 444 if (value == 0.0 && ignorezeroentries && row != col) {low1 = 0; high1 = nrow1;goto a_noinsert;} \ 445 if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;} \ 446 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 447 MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \ 448 N = nrow1++ - 1; a->nz++; high1++; \ 449 /* shift up all the later entries in this row */ \ 450 for (ii=N; ii>=_i; ii--) { \ 451 rp1[ii+1] = rp1[ii]; \ 452 ap1[ii+1] = ap1[ii]; \ 453 } \ 454 rp1[_i] = col; \ 455 ap1[_i] = value; \ 456 A->nonzerostate++;\ 457 a_noinsert: ; \ 458 ailen[row] = nrow1; \ 459 } 460 461 #define MatSetValues_SeqAIJ_B_Private(row,col,value,addv,orow,ocol) \ 462 { \ 463 if (col <= lastcol2) low2 = 0; \ 464 else high2 = nrow2; \ 465 lastcol2 = col; \ 466 while (high2-low2 > 5) { \ 467 t = (low2+high2)/2; \ 468 if (rp2[t] > col) high2 = t; \ 469 else low2 = t; \ 470 } \ 471 for (_i=low2; _i<high2; _i++) { \ 472 if (rp2[_i] > col) break; \ 473 if (rp2[_i] == col) { \ 474 if (addv == ADD_VALUES) ap2[_i] += value; \ 475 else ap2[_i] = value; \ 476 goto b_noinsert; \ 477 } \ 478 } \ 479 if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 480 if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 481 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 482 MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \ 483 N = nrow2++ - 1; b->nz++; high2++; \ 484 /* shift up all the later entries in this row */ \ 485 for (ii=N; ii>=_i; ii--) { \ 486 rp2[ii+1] = rp2[ii]; \ 487 ap2[ii+1] = ap2[ii]; \ 488 } \ 489 rp2[_i] = col; \ 490 ap2[_i] = value; \ 491 B->nonzerostate++; \ 492 b_noinsert: ; \ 493 bilen[row] = nrow2; \ 494 } 495 496 PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[]) 497 { 498 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)A->data; 499 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data; 500 PetscErrorCode ierr; 501 PetscInt l,*garray = mat->garray,diag; 502 503 PetscFunctionBegin; 504 /* code only works for square matrices A */ 505 506 /* find size of row to the left of the diagonal part */ 507 ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr); 508 row = row - diag; 509 for (l=0; l<b->i[row+1]-b->i[row]; l++) { 510 if (garray[b->j[b->i[row]+l]] > diag) break; 511 } 512 ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr); 513 514 /* diagonal part */ 515 ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr); 516 517 /* right of diagonal part */ 518 ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr); 519 PetscFunctionReturn(0); 520 } 521 522 PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 523 { 524 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 525 PetscScalar value; 526 PetscErrorCode ierr; 527 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 528 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 529 PetscBool roworiented = aij->roworiented; 530 531 /* Some Variables required in the macro */ 532 Mat A = aij->A; 533 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 534 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 535 MatScalar *aa = a->a; 536 PetscBool ignorezeroentries = a->ignorezeroentries; 537 Mat B = aij->B; 538 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 539 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 540 MatScalar *ba = b->a; 541 542 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 543 PetscInt nonew; 544 MatScalar *ap1,*ap2; 545 546 PetscFunctionBegin; 547 for (i=0; i<m; i++) { 548 if (im[i] < 0) continue; 549 #if defined(PETSC_USE_DEBUG) 550 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 551 #endif 552 if (im[i] >= rstart && im[i] < rend) { 553 row = im[i] - rstart; 554 lastcol1 = -1; 555 rp1 = aj + ai[row]; 556 ap1 = aa + ai[row]; 557 rmax1 = aimax[row]; 558 nrow1 = ailen[row]; 559 low1 = 0; 560 high1 = nrow1; 561 lastcol2 = -1; 562 rp2 = bj + bi[row]; 563 ap2 = ba + bi[row]; 564 rmax2 = bimax[row]; 565 nrow2 = bilen[row]; 566 low2 = 0; 567 high2 = nrow2; 568 569 for (j=0; j<n; j++) { 570 if (roworiented) value = v[i*n+j]; 571 else value = v[i+j*m]; 572 if (in[j] >= cstart && in[j] < cend) { 573 col = in[j] - cstart; 574 nonew = a->nonew; 575 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 576 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 577 } else if (in[j] < 0) continue; 578 #if defined(PETSC_USE_DEBUG) 579 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 580 #endif 581 else { 582 if (mat->was_assembled) { 583 if (!aij->colmap) { 584 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 585 } 586 #if defined(PETSC_USE_CTABLE) 587 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 588 col--; 589 #else 590 col = aij->colmap[in[j]] - 1; 591 #endif 592 if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) { 593 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 594 col = in[j]; 595 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 596 B = aij->B; 597 b = (Mat_SeqAIJ*)B->data; 598 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a; 599 rp2 = bj + bi[row]; 600 ap2 = ba + bi[row]; 601 rmax2 = bimax[row]; 602 nrow2 = bilen[row]; 603 low2 = 0; 604 high2 = nrow2; 605 bm = aij->B->rmap->n; 606 ba = b->a; 607 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", im[i], in[j]); 608 } else col = in[j]; 609 nonew = b->nonew; 610 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 611 } 612 } 613 } else { 614 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 615 if (!aij->donotstash) { 616 mat->assembled = PETSC_FALSE; 617 if (roworiented) { 618 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 619 } else { 620 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 621 } 622 } 623 } 624 } 625 PetscFunctionReturn(0); 626 } 627 628 PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 629 { 630 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 631 PetscErrorCode ierr; 632 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 633 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 634 635 PetscFunctionBegin; 636 for (i=0; i<m; i++) { 637 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 638 if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1); 639 if (idxm[i] >= rstart && idxm[i] < rend) { 640 row = idxm[i] - rstart; 641 for (j=0; j<n; j++) { 642 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 643 if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1); 644 if (idxn[j] >= cstart && idxn[j] < cend) { 645 col = idxn[j] - cstart; 646 ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 647 } else { 648 if (!aij->colmap) { 649 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 650 } 651 #if defined(PETSC_USE_CTABLE) 652 ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr); 653 col--; 654 #else 655 col = aij->colmap[idxn[j]] - 1; 656 #endif 657 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0; 658 else { 659 ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 660 } 661 } 662 } 663 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 664 } 665 PetscFunctionReturn(0); 666 } 667 668 extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec); 669 670 PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode) 671 { 672 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 673 PetscErrorCode ierr; 674 PetscInt nstash,reallocs; 675 676 PetscFunctionBegin; 677 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 678 679 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 680 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 681 ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 682 PetscFunctionReturn(0); 683 } 684 685 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode) 686 { 687 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 688 Mat_SeqAIJ *a = (Mat_SeqAIJ*)aij->A->data; 689 PetscErrorCode ierr; 690 PetscMPIInt n; 691 PetscInt i,j,rstart,ncols,flg; 692 PetscInt *row,*col; 693 PetscBool other_disassembled; 694 PetscScalar *val; 695 696 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 697 698 PetscFunctionBegin; 699 if (!aij->donotstash && !mat->nooffprocentries) { 700 while (1) { 701 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 702 if (!flg) break; 703 704 for (i=0; i<n; ) { 705 /* Now identify the consecutive vals belonging to the same row */ 706 for (j=i,rstart=row[j]; j<n; j++) { 707 if (row[j] != rstart) break; 708 } 709 if (j < n) ncols = j-i; 710 else ncols = n-i; 711 /* Now assemble all these values with a single function call */ 712 ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr); 713 714 i = j; 715 } 716 } 717 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 718 } 719 ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr); 720 ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr); 721 722 /* determine if any processor has disassembled, if so we must 723 also disassemble ourselfs, in order that we may reassemble. */ 724 /* 725 if nonzero structure of submatrix B cannot change then we know that 726 no processor disassembled thus we can skip this stuff 727 */ 728 if (!((Mat_SeqAIJ*)aij->B->data)->nonew) { 729 ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 730 if (mat->was_assembled && !other_disassembled) { 731 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 732 } 733 } 734 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 735 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 736 } 737 ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr); 738 ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr); 739 ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr); 740 741 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 742 743 aij->rowvalues = 0; 744 745 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 746 if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ; 747 748 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 749 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 750 PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate; 751 ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 752 } 753 PetscFunctionReturn(0); 754 } 755 756 PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 757 { 758 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 759 PetscErrorCode ierr; 760 761 PetscFunctionBegin; 762 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 763 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 764 PetscFunctionReturn(0); 765 } 766 767 PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 768 { 769 Mat_MPIAIJ *mat = (Mat_MPIAIJ *) A->data; 770 PetscInt *lrows; 771 PetscInt r, len; 772 PetscErrorCode ierr; 773 774 PetscFunctionBegin; 775 /* get locally owned rows */ 776 ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr); 777 /* fix right hand side if needed */ 778 if (x && b) { 779 const PetscScalar *xx; 780 PetscScalar *bb; 781 782 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 783 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 784 for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]]; 785 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 786 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 787 } 788 /* Must zero l->B before l->A because the (diag) case below may put values into l->B*/ 789 ierr = MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 790 if (A->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 791 PetscBool cong; 792 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 793 if (cong) A->congruentlayouts = 1; 794 else A->congruentlayouts = 0; 795 } 796 if ((diag != 0.0) && A->congruentlayouts) { 797 ierr = MatZeroRows(mat->A, len, lrows, diag, NULL, NULL);CHKERRQ(ierr); 798 } else if (diag != 0.0) { 799 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 800 if (((Mat_SeqAIJ *) mat->A->data)->nonew) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 801 for (r = 0; r < len; ++r) { 802 const PetscInt row = lrows[r] + A->rmap->rstart; 803 ierr = MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES);CHKERRQ(ierr); 804 } 805 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 806 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 807 } else { 808 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 809 } 810 ierr = PetscFree(lrows);CHKERRQ(ierr); 811 812 /* only change matrix nonzero state if pattern was allowed to be changed */ 813 if (!((Mat_SeqAIJ*)(mat->A->data))->keepnonzeropattern) { 814 PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate; 815 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 816 } 817 PetscFunctionReturn(0); 818 } 819 820 PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 821 { 822 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 823 PetscErrorCode ierr; 824 PetscMPIInt n = A->rmap->n; 825 PetscInt i,j,r,m,p = 0,len = 0; 826 PetscInt *lrows,*owners = A->rmap->range; 827 PetscSFNode *rrows; 828 PetscSF sf; 829 const PetscScalar *xx; 830 PetscScalar *bb,*mask; 831 Vec xmask,lmask; 832 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)l->B->data; 833 const PetscInt *aj, *ii,*ridx; 834 PetscScalar *aa; 835 836 PetscFunctionBegin; 837 /* Create SF where leaves are input rows and roots are owned rows */ 838 ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr); 839 for (r = 0; r < n; ++r) lrows[r] = -1; 840 ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr); 841 for (r = 0; r < N; ++r) { 842 const PetscInt idx = rows[r]; 843 if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N); 844 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */ 845 ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr); 846 } 847 rrows[r].rank = p; 848 rrows[r].index = rows[r] - owners[p]; 849 } 850 ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr); 851 ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr); 852 /* Collect flags for rows to be zeroed */ 853 ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 854 ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 855 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 856 /* Compress and put in row numbers */ 857 for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r; 858 /* zero diagonal part of matrix */ 859 ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr); 860 /* handle off diagonal part of matrix */ 861 ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr); 862 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 863 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 864 for (i=0; i<len; i++) bb[lrows[i]] = 1; 865 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 866 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 867 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 868 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 869 if (x) { 870 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 871 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 872 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 873 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 874 } 875 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 876 /* remove zeroed rows of off diagonal matrix */ 877 ii = aij->i; 878 for (i=0; i<len; i++) { 879 ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr); 880 } 881 /* loop over all elements of off process part of matrix zeroing removed columns*/ 882 if (aij->compressedrow.use) { 883 m = aij->compressedrow.nrows; 884 ii = aij->compressedrow.i; 885 ridx = aij->compressedrow.rindex; 886 for (i=0; i<m; i++) { 887 n = ii[i+1] - ii[i]; 888 aj = aij->j + ii[i]; 889 aa = aij->a + ii[i]; 890 891 for (j=0; j<n; j++) { 892 if (PetscAbsScalar(mask[*aj])) { 893 if (b) bb[*ridx] -= *aa*xx[*aj]; 894 *aa = 0.0; 895 } 896 aa++; 897 aj++; 898 } 899 ridx++; 900 } 901 } else { /* do not use compressed row format */ 902 m = l->B->rmap->n; 903 for (i=0; i<m; i++) { 904 n = ii[i+1] - ii[i]; 905 aj = aij->j + ii[i]; 906 aa = aij->a + ii[i]; 907 for (j=0; j<n; j++) { 908 if (PetscAbsScalar(mask[*aj])) { 909 if (b) bb[i] -= *aa*xx[*aj]; 910 *aa = 0.0; 911 } 912 aa++; 913 aj++; 914 } 915 } 916 } 917 if (x) { 918 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 919 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 920 } 921 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 922 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 923 ierr = PetscFree(lrows);CHKERRQ(ierr); 924 925 /* only change matrix nonzero state if pattern was allowed to be changed */ 926 if (!((Mat_SeqAIJ*)(l->A->data))->keepnonzeropattern) { 927 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 928 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 929 } 930 PetscFunctionReturn(0); 931 } 932 933 PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy) 934 { 935 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 936 PetscErrorCode ierr; 937 PetscInt nt; 938 939 PetscFunctionBegin; 940 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 941 if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt); 942 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 943 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 944 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 945 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 946 PetscFunctionReturn(0); 947 } 948 949 PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx) 950 { 951 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 952 PetscErrorCode ierr; 953 954 PetscFunctionBegin; 955 ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr); 956 PetscFunctionReturn(0); 957 } 958 959 PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 960 { 961 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 962 PetscErrorCode ierr; 963 964 PetscFunctionBegin; 965 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 966 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 967 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 968 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 969 PetscFunctionReturn(0); 970 } 971 972 PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy) 973 { 974 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 975 PetscErrorCode ierr; 976 PetscBool merged; 977 978 PetscFunctionBegin; 979 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 980 /* do nondiagonal part */ 981 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 982 if (!merged) { 983 /* send it on its way */ 984 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 985 /* do local part */ 986 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 987 /* receive remote parts: note this assumes the values are not actually */ 988 /* added in yy until the next line, */ 989 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 990 } else { 991 /* do local part */ 992 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 993 /* send it on its way */ 994 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 995 /* values actually were received in the Begin() but we need to call this nop */ 996 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 997 } 998 PetscFunctionReturn(0); 999 } 1000 1001 PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool *f) 1002 { 1003 MPI_Comm comm; 1004 Mat_MPIAIJ *Aij = (Mat_MPIAIJ*) Amat->data, *Bij; 1005 Mat Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs; 1006 IS Me,Notme; 1007 PetscErrorCode ierr; 1008 PetscInt M,N,first,last,*notme,i; 1009 PetscMPIInt size; 1010 1011 PetscFunctionBegin; 1012 /* Easy test: symmetric diagonal block */ 1013 Bij = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A; 1014 ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr); 1015 if (!*f) PetscFunctionReturn(0); 1016 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1017 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1018 if (size == 1) PetscFunctionReturn(0); 1019 1020 /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */ 1021 ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr); 1022 ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr); 1023 ierr = PetscMalloc1(N-last+first,¬me);CHKERRQ(ierr); 1024 for (i=0; i<first; i++) notme[i] = i; 1025 for (i=last; i<M; i++) notme[i-last+first] = i; 1026 ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr); 1027 ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr); 1028 ierr = MatCreateSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr); 1029 Aoff = Aoffs[0]; 1030 ierr = MatCreateSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr); 1031 Boff = Boffs[0]; 1032 ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr); 1033 ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr); 1034 ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr); 1035 ierr = ISDestroy(&Me);CHKERRQ(ierr); 1036 ierr = ISDestroy(&Notme);CHKERRQ(ierr); 1037 ierr = PetscFree(notme);CHKERRQ(ierr); 1038 PetscFunctionReturn(0); 1039 } 1040 1041 PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1042 { 1043 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1044 PetscErrorCode ierr; 1045 1046 PetscFunctionBegin; 1047 /* do nondiagonal part */ 1048 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1049 /* send it on its way */ 1050 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1051 /* do local part */ 1052 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1053 /* receive remote parts */ 1054 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1055 PetscFunctionReturn(0); 1056 } 1057 1058 /* 1059 This only works correctly for square matrices where the subblock A->A is the 1060 diagonal block 1061 */ 1062 PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v) 1063 { 1064 PetscErrorCode ierr; 1065 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1066 1067 PetscFunctionBegin; 1068 if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1069 if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition"); 1070 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1071 PetscFunctionReturn(0); 1072 } 1073 1074 PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa) 1075 { 1076 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1077 PetscErrorCode ierr; 1078 1079 PetscFunctionBegin; 1080 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1081 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1082 PetscFunctionReturn(0); 1083 } 1084 1085 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 1086 { 1087 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1088 PetscErrorCode ierr; 1089 1090 PetscFunctionBegin; 1091 #if defined(PETSC_USE_LOG) 1092 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N); 1093 #endif 1094 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1095 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 1096 ierr = MatDestroy(&aij->A);CHKERRQ(ierr); 1097 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 1098 #if defined(PETSC_USE_CTABLE) 1099 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 1100 #else 1101 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 1102 #endif 1103 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 1104 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 1105 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 1106 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 1107 ierr = PetscFree(aij->ld);CHKERRQ(ierr); 1108 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1109 1110 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1111 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1112 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1113 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1114 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1115 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1116 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1117 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1118 #if defined(PETSC_HAVE_ELEMENTAL) 1119 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_elemental_C",NULL);CHKERRQ(ierr); 1120 #endif 1121 #if defined(PETSC_HAVE_HYPRE) 1122 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_hypre_C",NULL);CHKERRQ(ierr); 1123 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMatMatMult_transpose_mpiaij_mpiaij_C",NULL);CHKERRQ(ierr); 1124 #endif 1125 PetscFunctionReturn(0); 1126 } 1127 1128 PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer) 1129 { 1130 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1131 Mat_SeqAIJ *A = (Mat_SeqAIJ*)aij->A->data; 1132 Mat_SeqAIJ *B = (Mat_SeqAIJ*)aij->B->data; 1133 PetscErrorCode ierr; 1134 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1135 int fd; 1136 PetscInt nz,header[4],*row_lengths,*range=0,rlen,i; 1137 PetscInt nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz = 0; 1138 PetscScalar *column_values; 1139 PetscInt message_count,flowcontrolcount; 1140 FILE *file; 1141 1142 PetscFunctionBegin; 1143 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1144 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1145 nz = A->nz + B->nz; 1146 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1147 if (!rank) { 1148 header[0] = MAT_FILE_CLASSID; 1149 header[1] = mat->rmap->N; 1150 header[2] = mat->cmap->N; 1151 1152 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1153 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1154 /* get largest number of rows any processor has */ 1155 rlen = mat->rmap->n; 1156 range = mat->rmap->range; 1157 for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]); 1158 } else { 1159 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1160 rlen = mat->rmap->n; 1161 } 1162 1163 /* load up the local row counts */ 1164 ierr = PetscMalloc1(rlen+1,&row_lengths);CHKERRQ(ierr); 1165 for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1166 1167 /* store the row lengths to the file */ 1168 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1169 if (!rank) { 1170 ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1171 for (i=1; i<size; i++) { 1172 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1173 rlen = range[i+1] - range[i]; 1174 ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1175 ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1176 } 1177 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1178 } else { 1179 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1180 ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1181 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1182 } 1183 ierr = PetscFree(row_lengths);CHKERRQ(ierr); 1184 1185 /* load up the local column indices */ 1186 nzmax = nz; /* th processor needs space a largest processor needs */ 1187 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1188 ierr = PetscMalloc1(nzmax+1,&column_indices);CHKERRQ(ierr); 1189 cnt = 0; 1190 for (i=0; i<mat->rmap->n; i++) { 1191 for (j=B->i[i]; j<B->i[i+1]; j++) { 1192 if ((col = garray[B->j[j]]) > cstart) break; 1193 column_indices[cnt++] = col; 1194 } 1195 for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart; 1196 for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]]; 1197 } 1198 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1199 1200 /* store the column indices to the file */ 1201 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1202 if (!rank) { 1203 MPI_Status status; 1204 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1205 for (i=1; i<size; i++) { 1206 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1207 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1208 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1209 ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1210 ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1211 } 1212 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1213 } else { 1214 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1215 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1216 ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1217 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1218 } 1219 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1220 1221 /* load up the local column values */ 1222 ierr = PetscMalloc1(nzmax+1,&column_values);CHKERRQ(ierr); 1223 cnt = 0; 1224 for (i=0; i<mat->rmap->n; i++) { 1225 for (j=B->i[i]; j<B->i[i+1]; j++) { 1226 if (garray[B->j[j]] > cstart) break; 1227 column_values[cnt++] = B->a[j]; 1228 } 1229 for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k]; 1230 for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j]; 1231 } 1232 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1233 1234 /* store the column values to the file */ 1235 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1236 if (!rank) { 1237 MPI_Status status; 1238 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1239 for (i=1; i<size; i++) { 1240 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1241 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1242 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1243 ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1244 ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1245 } 1246 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1247 } else { 1248 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1249 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1250 ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1251 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1252 } 1253 ierr = PetscFree(column_values);CHKERRQ(ierr); 1254 1255 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1256 if (file) fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(mat->rmap->bs)); 1257 PetscFunctionReturn(0); 1258 } 1259 1260 #include <petscdraw.h> 1261 PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 1262 { 1263 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1264 PetscErrorCode ierr; 1265 PetscMPIInt rank = aij->rank,size = aij->size; 1266 PetscBool isdraw,iascii,isbinary; 1267 PetscViewer sviewer; 1268 PetscViewerFormat format; 1269 1270 PetscFunctionBegin; 1271 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1272 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1273 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1274 if (iascii) { 1275 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1276 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1277 MatInfo info; 1278 PetscBool inodes; 1279 1280 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1281 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 1282 ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr); 1283 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 1284 if (!inodes) { 1285 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n", 1286 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1287 } else { 1288 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n", 1289 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1290 } 1291 ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1292 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1293 ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1294 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1295 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1296 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 1297 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1298 ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr); 1299 PetscFunctionReturn(0); 1300 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1301 PetscInt inodecount,inodelimit,*inodes; 1302 ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr); 1303 if (inodes) { 1304 ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr); 1305 } else { 1306 ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr); 1307 } 1308 PetscFunctionReturn(0); 1309 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1310 PetscFunctionReturn(0); 1311 } 1312 } else if (isbinary) { 1313 if (size == 1) { 1314 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1315 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1316 } else { 1317 ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1318 } 1319 PetscFunctionReturn(0); 1320 } else if (isdraw) { 1321 PetscDraw draw; 1322 PetscBool isnull; 1323 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1324 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 1325 if (isnull) PetscFunctionReturn(0); 1326 } 1327 1328 { 1329 /* assemble the entire matrix onto first processor. */ 1330 Mat A; 1331 Mat_SeqAIJ *Aloc; 1332 PetscInt M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct; 1333 MatScalar *a; 1334 1335 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1336 if (!rank) { 1337 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1338 } else { 1339 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1340 } 1341 /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */ 1342 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 1343 ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr); 1344 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1345 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1346 1347 /* copy over the A part */ 1348 Aloc = (Mat_SeqAIJ*)aij->A->data; 1349 m = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1350 row = mat->rmap->rstart; 1351 for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart; 1352 for (i=0; i<m; i++) { 1353 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr); 1354 row++; 1355 a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i]; 1356 } 1357 aj = Aloc->j; 1358 for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart; 1359 1360 /* copy over the B part */ 1361 Aloc = (Mat_SeqAIJ*)aij->B->data; 1362 m = aij->B->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1363 row = mat->rmap->rstart; 1364 ierr = PetscMalloc1(ai[m]+1,&cols);CHKERRQ(ierr); 1365 ct = cols; 1366 for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]]; 1367 for (i=0; i<m; i++) { 1368 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr); 1369 row++; 1370 a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i]; 1371 } 1372 ierr = PetscFree(ct);CHKERRQ(ierr); 1373 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1374 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1375 /* 1376 Everyone has to call to draw the matrix since the graphics waits are 1377 synchronized across all processors that share the PetscDraw object 1378 */ 1379 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1380 if (!rank) { 1381 ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1382 ierr = MatView_SeqAIJ(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1383 } 1384 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1385 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1386 ierr = MatDestroy(&A);CHKERRQ(ierr); 1387 } 1388 PetscFunctionReturn(0); 1389 } 1390 1391 PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer) 1392 { 1393 PetscErrorCode ierr; 1394 PetscBool iascii,isdraw,issocket,isbinary; 1395 1396 PetscFunctionBegin; 1397 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1398 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1399 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1400 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1401 if (iascii || isdraw || isbinary || issocket) { 1402 ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1403 } 1404 PetscFunctionReturn(0); 1405 } 1406 1407 PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1408 { 1409 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1410 PetscErrorCode ierr; 1411 Vec bb1 = 0; 1412 PetscBool hasop; 1413 1414 PetscFunctionBegin; 1415 if (flag == SOR_APPLY_UPPER) { 1416 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1417 PetscFunctionReturn(0); 1418 } 1419 1420 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) { 1421 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 1422 } 1423 1424 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1425 if (flag & SOR_ZERO_INITIAL_GUESS) { 1426 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1427 its--; 1428 } 1429 1430 while (its--) { 1431 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1432 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1433 1434 /* update rhs: bb1 = bb - B*x */ 1435 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1436 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1437 1438 /* local sweep */ 1439 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1440 } 1441 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1442 if (flag & SOR_ZERO_INITIAL_GUESS) { 1443 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1444 its--; 1445 } 1446 while (its--) { 1447 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1448 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1449 1450 /* update rhs: bb1 = bb - B*x */ 1451 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1452 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1453 1454 /* local sweep */ 1455 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1456 } 1457 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1458 if (flag & SOR_ZERO_INITIAL_GUESS) { 1459 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1460 its--; 1461 } 1462 while (its--) { 1463 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1464 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1465 1466 /* update rhs: bb1 = bb - B*x */ 1467 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1468 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1469 1470 /* local sweep */ 1471 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1472 } 1473 } else if (flag & SOR_EISENSTAT) { 1474 Vec xx1; 1475 1476 ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr); 1477 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr); 1478 1479 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1480 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1481 if (!mat->diag) { 1482 ierr = MatCreateVecs(matin,&mat->diag,NULL);CHKERRQ(ierr); 1483 ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr); 1484 } 1485 ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr); 1486 if (hasop) { 1487 ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr); 1488 } else { 1489 ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr); 1490 } 1491 ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr); 1492 1493 ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr); 1494 1495 /* local sweep */ 1496 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr); 1497 ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr); 1498 ierr = VecDestroy(&xx1);CHKERRQ(ierr); 1499 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported"); 1500 1501 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 1502 1503 matin->factorerrortype = mat->A->factorerrortype; 1504 PetscFunctionReturn(0); 1505 } 1506 1507 PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B) 1508 { 1509 Mat aA,aB,Aperm; 1510 const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj; 1511 PetscScalar *aa,*ba; 1512 PetscInt i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest; 1513 PetscSF rowsf,sf; 1514 IS parcolp = NULL; 1515 PetscBool done; 1516 PetscErrorCode ierr; 1517 1518 PetscFunctionBegin; 1519 ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); 1520 ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr); 1521 ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr); 1522 ierr = PetscMalloc3(PetscMax(m,n),&work,m,&rdest,n,&cdest);CHKERRQ(ierr); 1523 1524 /* Invert row permutation to find out where my rows should go */ 1525 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr); 1526 ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr); 1527 ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr); 1528 for (i=0; i<m; i++) work[i] = A->rmap->rstart + i; 1529 ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1530 ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1531 1532 /* Invert column permutation to find out where my columns should go */ 1533 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1534 ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr); 1535 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1536 for (i=0; i<n; i++) work[i] = A->cmap->rstart + i; 1537 ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1538 ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1539 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1540 1541 ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr); 1542 ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr); 1543 ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr); 1544 1545 /* Find out where my gcols should go */ 1546 ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr); 1547 ierr = PetscMalloc1(ng,&gcdest);CHKERRQ(ierr); 1548 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1549 ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr); 1550 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1551 ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1552 ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1553 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1554 1555 ierr = PetscCalloc4(m,&dnnz,m,&onnz,m,&tdnnz,m,&tonnz);CHKERRQ(ierr); 1556 ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1557 ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1558 for (i=0; i<m; i++) { 1559 PetscInt row = rdest[i],rowner; 1560 ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr); 1561 for (j=ai[i]; j<ai[i+1]; j++) { 1562 PetscInt cowner,col = cdest[aj[j]]; 1563 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */ 1564 if (rowner == cowner) dnnz[i]++; 1565 else onnz[i]++; 1566 } 1567 for (j=bi[i]; j<bi[i+1]; j++) { 1568 PetscInt cowner,col = gcdest[bj[j]]; 1569 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); 1570 if (rowner == cowner) dnnz[i]++; 1571 else onnz[i]++; 1572 } 1573 } 1574 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1575 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1576 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1577 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1578 ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr); 1579 1580 ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr); 1581 ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr); 1582 ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr); 1583 for (i=0; i<m; i++) { 1584 PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */ 1585 PetscInt j0,rowlen; 1586 rowlen = ai[i+1] - ai[i]; 1587 for (j0=j=0; j<rowlen; j0=j) { /* rowlen could be larger than number of rows m, so sum in batches */ 1588 for ( ; j<PetscMin(rowlen,j0+m); j++) acols[j-j0] = cdest[aj[ai[i]+j]]; 1589 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,acols,aa+ai[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1590 } 1591 rowlen = bi[i+1] - bi[i]; 1592 for (j0=j=0; j<rowlen; j0=j) { 1593 for ( ; j<PetscMin(rowlen,j0+m); j++) bcols[j-j0] = gcdest[bj[bi[i]+j]]; 1594 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,bcols,ba+bi[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1595 } 1596 } 1597 ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1598 ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1599 ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1600 ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1601 ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr); 1602 ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr); 1603 ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr); 1604 ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr); 1605 ierr = PetscFree(gcdest);CHKERRQ(ierr); 1606 if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);} 1607 *B = Aperm; 1608 PetscFunctionReturn(0); 1609 } 1610 1611 PetscErrorCode MatGetGhosts_MPIAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 1612 { 1613 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1614 PetscErrorCode ierr; 1615 1616 PetscFunctionBegin; 1617 ierr = MatGetSize(aij->B,NULL,nghosts);CHKERRQ(ierr); 1618 if (ghosts) *ghosts = aij->garray; 1619 PetscFunctionReturn(0); 1620 } 1621 1622 PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1623 { 1624 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1625 Mat A = mat->A,B = mat->B; 1626 PetscErrorCode ierr; 1627 PetscReal isend[5],irecv[5]; 1628 1629 PetscFunctionBegin; 1630 info->block_size = 1.0; 1631 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1632 1633 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1634 isend[3] = info->memory; isend[4] = info->mallocs; 1635 1636 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1637 1638 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1639 isend[3] += info->memory; isend[4] += info->mallocs; 1640 if (flag == MAT_LOCAL) { 1641 info->nz_used = isend[0]; 1642 info->nz_allocated = isend[1]; 1643 info->nz_unneeded = isend[2]; 1644 info->memory = isend[3]; 1645 info->mallocs = isend[4]; 1646 } else if (flag == MAT_GLOBAL_MAX) { 1647 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1648 1649 info->nz_used = irecv[0]; 1650 info->nz_allocated = irecv[1]; 1651 info->nz_unneeded = irecv[2]; 1652 info->memory = irecv[3]; 1653 info->mallocs = irecv[4]; 1654 } else if (flag == MAT_GLOBAL_SUM) { 1655 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1656 1657 info->nz_used = irecv[0]; 1658 info->nz_allocated = irecv[1]; 1659 info->nz_unneeded = irecv[2]; 1660 info->memory = irecv[3]; 1661 info->mallocs = irecv[4]; 1662 } 1663 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1664 info->fill_ratio_needed = 0; 1665 info->factor_mallocs = 0; 1666 PetscFunctionReturn(0); 1667 } 1668 1669 PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg) 1670 { 1671 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1672 PetscErrorCode ierr; 1673 1674 PetscFunctionBegin; 1675 switch (op) { 1676 case MAT_NEW_NONZERO_LOCATIONS: 1677 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1678 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1679 case MAT_KEEP_NONZERO_PATTERN: 1680 case MAT_NEW_NONZERO_LOCATION_ERR: 1681 case MAT_USE_INODES: 1682 case MAT_IGNORE_ZERO_ENTRIES: 1683 MatCheckPreallocated(A,1); 1684 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1685 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1686 break; 1687 case MAT_ROW_ORIENTED: 1688 MatCheckPreallocated(A,1); 1689 a->roworiented = flg; 1690 1691 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1692 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1693 break; 1694 case MAT_NEW_DIAGONALS: 1695 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1696 break; 1697 case MAT_IGNORE_OFF_PROC_ENTRIES: 1698 a->donotstash = flg; 1699 break; 1700 case MAT_SPD: 1701 A->spd_set = PETSC_TRUE; 1702 A->spd = flg; 1703 if (flg) { 1704 A->symmetric = PETSC_TRUE; 1705 A->structurally_symmetric = PETSC_TRUE; 1706 A->symmetric_set = PETSC_TRUE; 1707 A->structurally_symmetric_set = PETSC_TRUE; 1708 } 1709 break; 1710 case MAT_SYMMETRIC: 1711 MatCheckPreallocated(A,1); 1712 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1713 break; 1714 case MAT_STRUCTURALLY_SYMMETRIC: 1715 MatCheckPreallocated(A,1); 1716 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1717 break; 1718 case MAT_HERMITIAN: 1719 MatCheckPreallocated(A,1); 1720 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1721 break; 1722 case MAT_SYMMETRY_ETERNAL: 1723 MatCheckPreallocated(A,1); 1724 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1725 break; 1726 case MAT_SUBMAT_SINGLEIS: 1727 A->submat_singleis = flg; 1728 break; 1729 default: 1730 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1731 } 1732 PetscFunctionReturn(0); 1733 } 1734 1735 PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1736 { 1737 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1738 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1739 PetscErrorCode ierr; 1740 PetscInt i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart; 1741 PetscInt nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend; 1742 PetscInt *cmap,*idx_p; 1743 1744 PetscFunctionBegin; 1745 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1746 mat->getrowactive = PETSC_TRUE; 1747 1748 if (!mat->rowvalues && (idx || v)) { 1749 /* 1750 allocate enough space to hold information from the longest row. 1751 */ 1752 Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data; 1753 PetscInt max = 1,tmp; 1754 for (i=0; i<matin->rmap->n; i++) { 1755 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1756 if (max < tmp) max = tmp; 1757 } 1758 ierr = PetscMalloc2(max,&mat->rowvalues,max,&mat->rowindices);CHKERRQ(ierr); 1759 } 1760 1761 if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows"); 1762 lrow = row - rstart; 1763 1764 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1765 if (!v) {pvA = 0; pvB = 0;} 1766 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1767 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1768 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1769 nztot = nzA + nzB; 1770 1771 cmap = mat->garray; 1772 if (v || idx) { 1773 if (nztot) { 1774 /* Sort by increasing column numbers, assuming A and B already sorted */ 1775 PetscInt imark = -1; 1776 if (v) { 1777 *v = v_p = mat->rowvalues; 1778 for (i=0; i<nzB; i++) { 1779 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1780 else break; 1781 } 1782 imark = i; 1783 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1784 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1785 } 1786 if (idx) { 1787 *idx = idx_p = mat->rowindices; 1788 if (imark > -1) { 1789 for (i=0; i<imark; i++) { 1790 idx_p[i] = cmap[cworkB[i]]; 1791 } 1792 } else { 1793 for (i=0; i<nzB; i++) { 1794 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1795 else break; 1796 } 1797 imark = i; 1798 } 1799 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart + cworkA[i]; 1800 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]]; 1801 } 1802 } else { 1803 if (idx) *idx = 0; 1804 if (v) *v = 0; 1805 } 1806 } 1807 *nz = nztot; 1808 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1809 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1810 PetscFunctionReturn(0); 1811 } 1812 1813 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1814 { 1815 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1816 1817 PetscFunctionBegin; 1818 if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first"); 1819 aij->getrowactive = PETSC_FALSE; 1820 PetscFunctionReturn(0); 1821 } 1822 1823 PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm) 1824 { 1825 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1826 Mat_SeqAIJ *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data; 1827 PetscErrorCode ierr; 1828 PetscInt i,j,cstart = mat->cmap->rstart; 1829 PetscReal sum = 0.0; 1830 MatScalar *v; 1831 1832 PetscFunctionBegin; 1833 if (aij->size == 1) { 1834 ierr = MatNorm(aij->A,type,norm);CHKERRQ(ierr); 1835 } else { 1836 if (type == NORM_FROBENIUS) { 1837 v = amat->a; 1838 for (i=0; i<amat->nz; i++) { 1839 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1840 } 1841 v = bmat->a; 1842 for (i=0; i<bmat->nz; i++) { 1843 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1844 } 1845 ierr = MPIU_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1846 *norm = PetscSqrtReal(*norm); 1847 ierr = PetscLogFlops(2*amat->nz+2*bmat->nz);CHKERRQ(ierr); 1848 } else if (type == NORM_1) { /* max column norm */ 1849 PetscReal *tmp,*tmp2; 1850 PetscInt *jj,*garray = aij->garray; 1851 ierr = PetscCalloc1(mat->cmap->N+1,&tmp);CHKERRQ(ierr); 1852 ierr = PetscMalloc1(mat->cmap->N+1,&tmp2);CHKERRQ(ierr); 1853 *norm = 0.0; 1854 v = amat->a; jj = amat->j; 1855 for (j=0; j<amat->nz; j++) { 1856 tmp[cstart + *jj++] += PetscAbsScalar(*v); v++; 1857 } 1858 v = bmat->a; jj = bmat->j; 1859 for (j=0; j<bmat->nz; j++) { 1860 tmp[garray[*jj++]] += PetscAbsScalar(*v); v++; 1861 } 1862 ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1863 for (j=0; j<mat->cmap->N; j++) { 1864 if (tmp2[j] > *norm) *norm = tmp2[j]; 1865 } 1866 ierr = PetscFree(tmp);CHKERRQ(ierr); 1867 ierr = PetscFree(tmp2);CHKERRQ(ierr); 1868 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1869 } else if (type == NORM_INFINITY) { /* max row norm */ 1870 PetscReal ntemp = 0.0; 1871 for (j=0; j<aij->A->rmap->n; j++) { 1872 v = amat->a + amat->i[j]; 1873 sum = 0.0; 1874 for (i=0; i<amat->i[j+1]-amat->i[j]; i++) { 1875 sum += PetscAbsScalar(*v); v++; 1876 } 1877 v = bmat->a + bmat->i[j]; 1878 for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) { 1879 sum += PetscAbsScalar(*v); v++; 1880 } 1881 if (sum > ntemp) ntemp = sum; 1882 } 1883 ierr = MPIU_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1884 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1885 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm"); 1886 } 1887 PetscFunctionReturn(0); 1888 } 1889 1890 PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout) 1891 { 1892 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1893 Mat_SeqAIJ *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data; 1894 PetscErrorCode ierr; 1895 PetscInt M = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i; 1896 PetscInt cstart = A->cmap->rstart,ncol; 1897 Mat B; 1898 MatScalar *array; 1899 1900 PetscFunctionBegin; 1901 if (reuse == MAT_INPLACE_MATRIX && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1902 1903 ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n; 1904 ai = Aloc->i; aj = Aloc->j; 1905 bi = Bloc->i; bj = Bloc->j; 1906 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1907 PetscInt *d_nnz,*g_nnz,*o_nnz; 1908 PetscSFNode *oloc; 1909 PETSC_UNUSED PetscSF sf; 1910 1911 ierr = PetscMalloc4(na,&d_nnz,na,&o_nnz,nb,&g_nnz,nb,&oloc);CHKERRQ(ierr); 1912 /* compute d_nnz for preallocation */ 1913 ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1914 for (i=0; i<ai[ma]; i++) { 1915 d_nnz[aj[i]]++; 1916 aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1917 } 1918 /* compute local off-diagonal contributions */ 1919 ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr); 1920 for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++; 1921 /* map those to global */ 1922 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1923 ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr); 1924 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1925 ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1926 ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1927 ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1928 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1929 1930 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1931 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1932 ierr = MatSetBlockSizes(B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 1933 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1934 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 1935 ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr); 1936 } else { 1937 B = *matout; 1938 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1939 for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1940 } 1941 1942 /* copy over the A part */ 1943 array = Aloc->a; 1944 row = A->rmap->rstart; 1945 for (i=0; i<ma; i++) { 1946 ncol = ai[i+1]-ai[i]; 1947 ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1948 row++; 1949 array += ncol; aj += ncol; 1950 } 1951 aj = Aloc->j; 1952 for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */ 1953 1954 /* copy over the B part */ 1955 ierr = PetscCalloc1(bi[mb],&cols);CHKERRQ(ierr); 1956 array = Bloc->a; 1957 row = A->rmap->rstart; 1958 for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]]; 1959 cols_tmp = cols; 1960 for (i=0; i<mb; i++) { 1961 ncol = bi[i+1]-bi[i]; 1962 ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1963 row++; 1964 array += ncol; cols_tmp += ncol; 1965 } 1966 ierr = PetscFree(cols);CHKERRQ(ierr); 1967 1968 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1969 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1970 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 1971 *matout = B; 1972 } else { 1973 ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr); 1974 } 1975 PetscFunctionReturn(0); 1976 } 1977 1978 PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr) 1979 { 1980 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1981 Mat a = aij->A,b = aij->B; 1982 PetscErrorCode ierr; 1983 PetscInt s1,s2,s3; 1984 1985 PetscFunctionBegin; 1986 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1987 if (rr) { 1988 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1989 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1990 /* Overlap communication with computation. */ 1991 ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1992 } 1993 if (ll) { 1994 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1995 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1996 ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr); 1997 } 1998 /* scale the diagonal block */ 1999 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 2000 2001 if (rr) { 2002 /* Do a scatter end and then right scale the off-diagonal block */ 2003 ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2004 ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr); 2005 } 2006 PetscFunctionReturn(0); 2007 } 2008 2009 PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2010 { 2011 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2012 PetscErrorCode ierr; 2013 2014 PetscFunctionBegin; 2015 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 2016 PetscFunctionReturn(0); 2017 } 2018 2019 PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool *flag) 2020 { 2021 Mat_MPIAIJ *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data; 2022 Mat a,b,c,d; 2023 PetscBool flg; 2024 PetscErrorCode ierr; 2025 2026 PetscFunctionBegin; 2027 a = matA->A; b = matA->B; 2028 c = matB->A; d = matB->B; 2029 2030 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 2031 if (flg) { 2032 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 2033 } 2034 ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2035 PetscFunctionReturn(0); 2036 } 2037 2038 PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str) 2039 { 2040 PetscErrorCode ierr; 2041 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2042 Mat_MPIAIJ *b = (Mat_MPIAIJ*)B->data; 2043 2044 PetscFunctionBegin; 2045 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2046 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2047 /* because of the column compression in the off-processor part of the matrix a->B, 2048 the number of columns in a->B and b->B may be different, hence we cannot call 2049 the MatCopy() directly on the two parts. If need be, we can provide a more 2050 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2051 then copying the submatrices */ 2052 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2053 } else { 2054 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 2055 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 2056 } 2057 PetscFunctionReturn(0); 2058 } 2059 2060 PetscErrorCode MatSetUp_MPIAIJ(Mat A) 2061 { 2062 PetscErrorCode ierr; 2063 2064 PetscFunctionBegin; 2065 ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 2066 PetscFunctionReturn(0); 2067 } 2068 2069 /* 2070 Computes the number of nonzeros per row needed for preallocation when X and Y 2071 have different nonzero structure. 2072 */ 2073 PetscErrorCode MatAXPYGetPreallocation_MPIX_private(PetscInt m,const PetscInt *xi,const PetscInt *xj,const PetscInt *xltog,const PetscInt *yi,const PetscInt *yj,const PetscInt *yltog,PetscInt *nnz) 2074 { 2075 PetscInt i,j,k,nzx,nzy; 2076 2077 PetscFunctionBegin; 2078 /* Set the number of nonzeros in the new matrix */ 2079 for (i=0; i<m; i++) { 2080 const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i]; 2081 nzx = xi[i+1] - xi[i]; 2082 nzy = yi[i+1] - yi[i]; 2083 nnz[i] = 0; 2084 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2085 for (; k<nzy && yltog[yjj[k]]<xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */ 2086 if (k<nzy && yltog[yjj[k]]==xltog[xjj[j]]) k++; /* Skip duplicate */ 2087 nnz[i]++; 2088 } 2089 for (; k<nzy; k++) nnz[i]++; 2090 } 2091 PetscFunctionReturn(0); 2092 } 2093 2094 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2095 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 2096 { 2097 PetscErrorCode ierr; 2098 PetscInt m = Y->rmap->N; 2099 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2100 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2101 2102 PetscFunctionBegin; 2103 ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr); 2104 PetscFunctionReturn(0); 2105 } 2106 2107 PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2108 { 2109 PetscErrorCode ierr; 2110 Mat_MPIAIJ *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data; 2111 PetscBLASInt bnz,one=1; 2112 Mat_SeqAIJ *x,*y; 2113 2114 PetscFunctionBegin; 2115 if (str == SAME_NONZERO_PATTERN) { 2116 PetscScalar alpha = a; 2117 x = (Mat_SeqAIJ*)xx->A->data; 2118 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2119 y = (Mat_SeqAIJ*)yy->A->data; 2120 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2121 x = (Mat_SeqAIJ*)xx->B->data; 2122 y = (Mat_SeqAIJ*)yy->B->data; 2123 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2124 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2125 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 2126 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2127 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 2128 } else { 2129 Mat B; 2130 PetscInt *nnz_d,*nnz_o; 2131 ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr); 2132 ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr); 2133 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2134 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2135 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2136 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 2137 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2138 ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 2139 ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 2140 ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 2141 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2142 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 2143 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 2144 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 2145 } 2146 PetscFunctionReturn(0); 2147 } 2148 2149 extern PetscErrorCode MatConjugate_SeqAIJ(Mat); 2150 2151 PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2152 { 2153 #if defined(PETSC_USE_COMPLEX) 2154 PetscErrorCode ierr; 2155 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2156 2157 PetscFunctionBegin; 2158 ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr); 2159 ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr); 2160 #else 2161 PetscFunctionBegin; 2162 #endif 2163 PetscFunctionReturn(0); 2164 } 2165 2166 PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2167 { 2168 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2169 PetscErrorCode ierr; 2170 2171 PetscFunctionBegin; 2172 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2173 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2174 PetscFunctionReturn(0); 2175 } 2176 2177 PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2178 { 2179 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2180 PetscErrorCode ierr; 2181 2182 PetscFunctionBegin; 2183 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2184 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2185 PetscFunctionReturn(0); 2186 } 2187 2188 PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2189 { 2190 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2191 PetscErrorCode ierr; 2192 PetscInt i,*idxb = 0; 2193 PetscScalar *va,*vb; 2194 Vec vtmp; 2195 2196 PetscFunctionBegin; 2197 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 2198 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2199 if (idx) { 2200 for (i=0; i<A->rmap->n; i++) { 2201 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2202 } 2203 } 2204 2205 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2206 if (idx) { 2207 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2208 } 2209 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2210 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2211 2212 for (i=0; i<A->rmap->n; i++) { 2213 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 2214 va[i] = vb[i]; 2215 if (idx) idx[i] = a->garray[idxb[i]]; 2216 } 2217 } 2218 2219 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2220 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2221 ierr = PetscFree(idxb);CHKERRQ(ierr); 2222 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2223 PetscFunctionReturn(0); 2224 } 2225 2226 PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2227 { 2228 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2229 PetscErrorCode ierr; 2230 PetscInt i,*idxb = 0; 2231 PetscScalar *va,*vb; 2232 Vec vtmp; 2233 2234 PetscFunctionBegin; 2235 ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr); 2236 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2237 if (idx) { 2238 for (i=0; i<A->cmap->n; i++) { 2239 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2240 } 2241 } 2242 2243 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2244 if (idx) { 2245 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2246 } 2247 ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2248 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2249 2250 for (i=0; i<A->rmap->n; i++) { 2251 if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) { 2252 va[i] = vb[i]; 2253 if (idx) idx[i] = a->garray[idxb[i]]; 2254 } 2255 } 2256 2257 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2258 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2259 ierr = PetscFree(idxb);CHKERRQ(ierr); 2260 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2261 PetscFunctionReturn(0); 2262 } 2263 2264 PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2265 { 2266 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2267 PetscInt n = A->rmap->n; 2268 PetscInt cstart = A->cmap->rstart; 2269 PetscInt *cmap = mat->garray; 2270 PetscInt *diagIdx, *offdiagIdx; 2271 Vec diagV, offdiagV; 2272 PetscScalar *a, *diagA, *offdiagA; 2273 PetscInt r; 2274 PetscErrorCode ierr; 2275 2276 PetscFunctionBegin; 2277 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2278 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr); 2279 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr); 2280 ierr = MatGetRowMin(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2281 ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2282 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2283 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2284 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2285 for (r = 0; r < n; ++r) { 2286 if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) { 2287 a[r] = diagA[r]; 2288 idx[r] = cstart + diagIdx[r]; 2289 } else { 2290 a[r] = offdiagA[r]; 2291 idx[r] = cmap[offdiagIdx[r]]; 2292 } 2293 } 2294 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2295 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2296 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2297 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2298 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2299 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2300 PetscFunctionReturn(0); 2301 } 2302 2303 PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2304 { 2305 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2306 PetscInt n = A->rmap->n; 2307 PetscInt cstart = A->cmap->rstart; 2308 PetscInt *cmap = mat->garray; 2309 PetscInt *diagIdx, *offdiagIdx; 2310 Vec diagV, offdiagV; 2311 PetscScalar *a, *diagA, *offdiagA; 2312 PetscInt r; 2313 PetscErrorCode ierr; 2314 2315 PetscFunctionBegin; 2316 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2317 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr); 2318 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr); 2319 ierr = MatGetRowMax(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2320 ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2321 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2322 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2323 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2324 for (r = 0; r < n; ++r) { 2325 if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) { 2326 a[r] = diagA[r]; 2327 idx[r] = cstart + diagIdx[r]; 2328 } else { 2329 a[r] = offdiagA[r]; 2330 idx[r] = cmap[offdiagIdx[r]]; 2331 } 2332 } 2333 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2334 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2335 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2336 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2337 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2338 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2339 PetscFunctionReturn(0); 2340 } 2341 2342 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat) 2343 { 2344 PetscErrorCode ierr; 2345 Mat *dummy; 2346 2347 PetscFunctionBegin; 2348 ierr = MatCreateSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr); 2349 *newmat = *dummy; 2350 ierr = PetscFree(dummy);CHKERRQ(ierr); 2351 PetscFunctionReturn(0); 2352 } 2353 2354 PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values) 2355 { 2356 Mat_MPIAIJ *a = (Mat_MPIAIJ*) A->data; 2357 PetscErrorCode ierr; 2358 2359 PetscFunctionBegin; 2360 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2361 A->factorerrortype = a->A->factorerrortype; 2362 PetscFunctionReturn(0); 2363 } 2364 2365 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx) 2366 { 2367 PetscErrorCode ierr; 2368 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)x->data; 2369 2370 PetscFunctionBegin; 2371 ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr); 2372 ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr); 2373 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2374 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2375 PetscFunctionReturn(0); 2376 } 2377 2378 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A,PetscBool sc) 2379 { 2380 PetscFunctionBegin; 2381 if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable; 2382 else A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ; 2383 PetscFunctionReturn(0); 2384 } 2385 2386 /*@ 2387 MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap 2388 2389 Collective on Mat 2390 2391 Input Parameters: 2392 + A - the matrix 2393 - sc - PETSC_TRUE indicates use the scalable algorithm (default is not to use the scalable algorithm) 2394 2395 Level: advanced 2396 2397 @*/ 2398 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A,PetscBool sc) 2399 { 2400 PetscErrorCode ierr; 2401 2402 PetscFunctionBegin; 2403 ierr = PetscTryMethod(A,"MatMPIAIJSetUseScalableIncreaseOverlap_C",(Mat,PetscBool),(A,sc));CHKERRQ(ierr); 2404 PetscFunctionReturn(0); 2405 } 2406 2407 PetscErrorCode MatSetFromOptions_MPIAIJ(PetscOptionItems *PetscOptionsObject,Mat A) 2408 { 2409 PetscErrorCode ierr; 2410 PetscBool sc = PETSC_FALSE,flg; 2411 2412 PetscFunctionBegin; 2413 ierr = PetscOptionsHead(PetscOptionsObject,"MPIAIJ options");CHKERRQ(ierr); 2414 ierr = PetscObjectOptionsBegin((PetscObject)A); 2415 if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE; 2416 ierr = PetscOptionsBool("-mat_increase_overlap_scalable","Use a scalable algorithm to compute the overlap","MatIncreaseOverlap",sc,&sc,&flg);CHKERRQ(ierr); 2417 if (flg) { 2418 ierr = MatMPIAIJSetUseScalableIncreaseOverlap(A,sc);CHKERRQ(ierr); 2419 } 2420 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2421 PetscFunctionReturn(0); 2422 } 2423 2424 PetscErrorCode MatShift_MPIAIJ(Mat Y,PetscScalar a) 2425 { 2426 PetscErrorCode ierr; 2427 Mat_MPIAIJ *maij = (Mat_MPIAIJ*)Y->data; 2428 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)maij->A->data; 2429 2430 PetscFunctionBegin; 2431 if (!Y->preallocated) { 2432 ierr = MatMPIAIJSetPreallocation(Y,1,NULL,0,NULL);CHKERRQ(ierr); 2433 } else if (!aij->nz) { 2434 PetscInt nonew = aij->nonew; 2435 ierr = MatSeqAIJSetPreallocation(maij->A,1,NULL);CHKERRQ(ierr); 2436 aij->nonew = nonew; 2437 } 2438 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2439 PetscFunctionReturn(0); 2440 } 2441 2442 PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A,PetscBool *missing,PetscInt *d) 2443 { 2444 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2445 PetscErrorCode ierr; 2446 2447 PetscFunctionBegin; 2448 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2449 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2450 if (d) { 2451 PetscInt rstart; 2452 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2453 *d += rstart; 2454 2455 } 2456 PetscFunctionReturn(0); 2457 } 2458 2459 2460 /* -------------------------------------------------------------------*/ 2461 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 2462 MatGetRow_MPIAIJ, 2463 MatRestoreRow_MPIAIJ, 2464 MatMult_MPIAIJ, 2465 /* 4*/ MatMultAdd_MPIAIJ, 2466 MatMultTranspose_MPIAIJ, 2467 MatMultTransposeAdd_MPIAIJ, 2468 0, 2469 0, 2470 0, 2471 /*10*/ 0, 2472 0, 2473 0, 2474 MatSOR_MPIAIJ, 2475 MatTranspose_MPIAIJ, 2476 /*15*/ MatGetInfo_MPIAIJ, 2477 MatEqual_MPIAIJ, 2478 MatGetDiagonal_MPIAIJ, 2479 MatDiagonalScale_MPIAIJ, 2480 MatNorm_MPIAIJ, 2481 /*20*/ MatAssemblyBegin_MPIAIJ, 2482 MatAssemblyEnd_MPIAIJ, 2483 MatSetOption_MPIAIJ, 2484 MatZeroEntries_MPIAIJ, 2485 /*24*/ MatZeroRows_MPIAIJ, 2486 0, 2487 0, 2488 0, 2489 0, 2490 /*29*/ MatSetUp_MPIAIJ, 2491 0, 2492 0, 2493 MatGetDiagonalBlock_MPIAIJ, 2494 0, 2495 /*34*/ MatDuplicate_MPIAIJ, 2496 0, 2497 0, 2498 0, 2499 0, 2500 /*39*/ MatAXPY_MPIAIJ, 2501 MatCreateSubMatrices_MPIAIJ, 2502 MatIncreaseOverlap_MPIAIJ, 2503 MatGetValues_MPIAIJ, 2504 MatCopy_MPIAIJ, 2505 /*44*/ MatGetRowMax_MPIAIJ, 2506 MatScale_MPIAIJ, 2507 MatShift_MPIAIJ, 2508 MatDiagonalSet_MPIAIJ, 2509 MatZeroRowsColumns_MPIAIJ, 2510 /*49*/ MatSetRandom_MPIAIJ, 2511 0, 2512 0, 2513 0, 2514 0, 2515 /*54*/ MatFDColoringCreate_MPIXAIJ, 2516 0, 2517 MatSetUnfactored_MPIAIJ, 2518 MatPermute_MPIAIJ, 2519 0, 2520 /*59*/ MatCreateSubMatrix_MPIAIJ, 2521 MatDestroy_MPIAIJ, 2522 MatView_MPIAIJ, 2523 0, 2524 MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ, 2525 /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ, 2526 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 2527 0, 2528 0, 2529 0, 2530 /*69*/ MatGetRowMaxAbs_MPIAIJ, 2531 MatGetRowMinAbs_MPIAIJ, 2532 0, 2533 0, 2534 0, 2535 0, 2536 /*75*/ MatFDColoringApply_AIJ, 2537 MatSetFromOptions_MPIAIJ, 2538 0, 2539 0, 2540 MatFindZeroDiagonals_MPIAIJ, 2541 /*80*/ 0, 2542 0, 2543 0, 2544 /*83*/ MatLoad_MPIAIJ, 2545 0, 2546 0, 2547 0, 2548 0, 2549 0, 2550 /*89*/ MatMatMult_MPIAIJ_MPIAIJ, 2551 MatMatMultSymbolic_MPIAIJ_MPIAIJ, 2552 MatMatMultNumeric_MPIAIJ_MPIAIJ, 2553 MatPtAP_MPIAIJ_MPIAIJ, 2554 MatPtAPSymbolic_MPIAIJ_MPIAIJ, 2555 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 2556 0, 2557 0, 2558 0, 2559 0, 2560 /*99*/ 0, 2561 0, 2562 0, 2563 MatConjugate_MPIAIJ, 2564 0, 2565 /*104*/MatSetValuesRow_MPIAIJ, 2566 MatRealPart_MPIAIJ, 2567 MatImaginaryPart_MPIAIJ, 2568 0, 2569 0, 2570 /*109*/0, 2571 0, 2572 MatGetRowMin_MPIAIJ, 2573 0, 2574 MatMissingDiagonal_MPIAIJ, 2575 /*114*/MatGetSeqNonzeroStructure_MPIAIJ, 2576 0, 2577 MatGetGhosts_MPIAIJ, 2578 0, 2579 0, 2580 /*119*/0, 2581 0, 2582 0, 2583 0, 2584 MatGetMultiProcBlock_MPIAIJ, 2585 /*124*/MatFindNonzeroRows_MPIAIJ, 2586 MatGetColumnNorms_MPIAIJ, 2587 MatInvertBlockDiagonal_MPIAIJ, 2588 0, 2589 MatCreateSubMatricesMPI_MPIAIJ, 2590 /*129*/0, 2591 MatTransposeMatMult_MPIAIJ_MPIAIJ, 2592 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ, 2593 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 2594 0, 2595 /*134*/0, 2596 0, 2597 0, 2598 0, 2599 0, 2600 /*139*/MatSetBlockSizes_MPIAIJ, 2601 0, 2602 0, 2603 MatFDColoringSetUp_MPIXAIJ, 2604 MatFindOffBlockDiagonalEntries_MPIAIJ, 2605 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIAIJ 2606 }; 2607 2608 /* ----------------------------------------------------------------------------------------*/ 2609 2610 PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 2611 { 2612 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2613 PetscErrorCode ierr; 2614 2615 PetscFunctionBegin; 2616 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 2617 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 2618 PetscFunctionReturn(0); 2619 } 2620 2621 PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 2622 { 2623 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2624 PetscErrorCode ierr; 2625 2626 PetscFunctionBegin; 2627 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 2628 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 2629 PetscFunctionReturn(0); 2630 } 2631 2632 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 2633 { 2634 Mat_MPIAIJ *b; 2635 PetscErrorCode ierr; 2636 2637 PetscFunctionBegin; 2638 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2639 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2640 b = (Mat_MPIAIJ*)B->data; 2641 2642 #if defined(PETSC_USE_CTABLE) 2643 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2644 #else 2645 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2646 #endif 2647 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2648 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2649 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2650 2651 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2652 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2653 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2654 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 2655 ierr = MatSetBlockSizesFromMats(b->B,B,B);CHKERRQ(ierr); 2656 ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr); 2657 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2658 2659 if (!B->preallocated) { 2660 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2661 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2662 ierr = MatSetBlockSizesFromMats(b->A,B,B);CHKERRQ(ierr); 2663 ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr); 2664 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2665 } 2666 2667 ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr); 2668 ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr); 2669 B->preallocated = PETSC_TRUE; 2670 B->was_assembled = PETSC_FALSE; 2671 B->assembled = PETSC_FALSE;; 2672 PetscFunctionReturn(0); 2673 } 2674 2675 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 2676 { 2677 Mat mat; 2678 Mat_MPIAIJ *a,*oldmat = (Mat_MPIAIJ*)matin->data; 2679 PetscErrorCode ierr; 2680 2681 PetscFunctionBegin; 2682 *newmat = 0; 2683 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 2684 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 2685 ierr = MatSetBlockSizesFromMats(mat,matin,matin);CHKERRQ(ierr); 2686 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 2687 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2688 a = (Mat_MPIAIJ*)mat->data; 2689 2690 mat->factortype = matin->factortype; 2691 mat->assembled = PETSC_TRUE; 2692 mat->insertmode = NOT_SET_VALUES; 2693 mat->preallocated = PETSC_TRUE; 2694 2695 a->size = oldmat->size; 2696 a->rank = oldmat->rank; 2697 a->donotstash = oldmat->donotstash; 2698 a->roworiented = oldmat->roworiented; 2699 a->rowindices = 0; 2700 a->rowvalues = 0; 2701 a->getrowactive = PETSC_FALSE; 2702 2703 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 2704 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 2705 2706 if (oldmat->colmap) { 2707 #if defined(PETSC_USE_CTABLE) 2708 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 2709 #else 2710 ierr = PetscMalloc1(mat->cmap->N,&a->colmap);CHKERRQ(ierr); 2711 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2712 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2713 #endif 2714 } else a->colmap = 0; 2715 if (oldmat->garray) { 2716 PetscInt len; 2717 len = oldmat->B->cmap->n; 2718 ierr = PetscMalloc1(len+1,&a->garray);CHKERRQ(ierr); 2719 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 2720 if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); } 2721 } else a->garray = 0; 2722 2723 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 2724 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 2725 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 2726 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 2727 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 2728 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 2729 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 2730 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 2731 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 2732 *newmat = mat; 2733 PetscFunctionReturn(0); 2734 } 2735 2736 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 2737 { 2738 PetscScalar *vals,*svals; 2739 MPI_Comm comm; 2740 PetscErrorCode ierr; 2741 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 2742 PetscInt i,nz,j,rstart,rend,mmax,maxnz = 0; 2743 PetscInt header[4],*rowlengths = 0,M,N,m,*cols; 2744 PetscInt *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols; 2745 PetscInt cend,cstart,n,*rowners; 2746 int fd; 2747 PetscInt bs = newMat->rmap->bs; 2748 2749 PetscFunctionBegin; 2750 /* force binary viewer to load .info file if it has not yet done so */ 2751 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 2752 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2753 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2754 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2755 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2756 if (!rank) { 2757 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 2758 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 2759 if (header[3] < 0) SETERRQ(PetscObjectComm((PetscObject)newMat),PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as MATMPIAIJ"); 2760 } 2761 2762 ierr = PetscOptionsBegin(comm,NULL,"Options for loading MATMPIAIJ matrix","Mat");CHKERRQ(ierr); 2763 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 2764 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2765 if (bs < 0) bs = 1; 2766 2767 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 2768 M = header[1]; N = header[2]; 2769 2770 /* If global sizes are set, check if they are consistent with that given in the file */ 2771 if (newMat->rmap->N >= 0 && newMat->rmap->N != M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of rows:Matrix in file has (%D) and input matrix has (%D)",newMat->rmap->N,M); 2772 if (newMat->cmap->N >=0 && newMat->cmap->N != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of cols:Matrix in file has (%D) and input matrix has (%D)",newMat->cmap->N,N); 2773 2774 /* determine ownership of all (block) rows */ 2775 if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs); 2776 if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank)); /* PETSC_DECIDE */ 2777 else m = newMat->rmap->n; /* Set by user */ 2778 2779 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 2780 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 2781 2782 /* First process needs enough room for process with most rows */ 2783 if (!rank) { 2784 mmax = rowners[1]; 2785 for (i=2; i<=size; i++) { 2786 mmax = PetscMax(mmax, rowners[i]); 2787 } 2788 } else mmax = -1; /* unused, but compilers complain */ 2789 2790 rowners[0] = 0; 2791 for (i=2; i<=size; i++) { 2792 rowners[i] += rowners[i-1]; 2793 } 2794 rstart = rowners[rank]; 2795 rend = rowners[rank+1]; 2796 2797 /* distribute row lengths to all processors */ 2798 ierr = PetscMalloc2(m,&ourlens,m,&offlens);CHKERRQ(ierr); 2799 if (!rank) { 2800 ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr); 2801 ierr = PetscMalloc1(mmax,&rowlengths);CHKERRQ(ierr); 2802 ierr = PetscCalloc1(size,&procsnz);CHKERRQ(ierr); 2803 for (j=0; j<m; j++) { 2804 procsnz[0] += ourlens[j]; 2805 } 2806 for (i=1; i<size; i++) { 2807 ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr); 2808 /* calculate the number of nonzeros on each processor */ 2809 for (j=0; j<rowners[i+1]-rowners[i]; j++) { 2810 procsnz[i] += rowlengths[j]; 2811 } 2812 ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2813 } 2814 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2815 } else { 2816 ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2817 } 2818 2819 if (!rank) { 2820 /* determine max buffer needed and allocate it */ 2821 maxnz = 0; 2822 for (i=0; i<size; i++) { 2823 maxnz = PetscMax(maxnz,procsnz[i]); 2824 } 2825 ierr = PetscMalloc1(maxnz,&cols);CHKERRQ(ierr); 2826 2827 /* read in my part of the matrix column indices */ 2828 nz = procsnz[0]; 2829 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2830 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 2831 2832 /* read in every one elses and ship off */ 2833 for (i=1; i<size; i++) { 2834 nz = procsnz[i]; 2835 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 2836 ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2837 } 2838 ierr = PetscFree(cols);CHKERRQ(ierr); 2839 } else { 2840 /* determine buffer space needed for message */ 2841 nz = 0; 2842 for (i=0; i<m; i++) { 2843 nz += ourlens[i]; 2844 } 2845 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2846 2847 /* receive message of column indices*/ 2848 ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2849 } 2850 2851 /* determine column ownership if matrix is not square */ 2852 if (N != M) { 2853 if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank); 2854 else n = newMat->cmap->n; 2855 ierr = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2856 cstart = cend - n; 2857 } else { 2858 cstart = rstart; 2859 cend = rend; 2860 n = cend - cstart; 2861 } 2862 2863 /* loop over local rows, determining number of off diagonal entries */ 2864 ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr); 2865 jj = 0; 2866 for (i=0; i<m; i++) { 2867 for (j=0; j<ourlens[i]; j++) { 2868 if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++; 2869 jj++; 2870 } 2871 } 2872 2873 for (i=0; i<m; i++) { 2874 ourlens[i] -= offlens[i]; 2875 } 2876 ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr); 2877 2878 if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);} 2879 2880 ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr); 2881 2882 for (i=0; i<m; i++) { 2883 ourlens[i] += offlens[i]; 2884 } 2885 2886 if (!rank) { 2887 ierr = PetscMalloc1(maxnz+1,&vals);CHKERRQ(ierr); 2888 2889 /* read in my part of the matrix numerical values */ 2890 nz = procsnz[0]; 2891 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2892 2893 /* insert into matrix */ 2894 jj = rstart; 2895 smycols = mycols; 2896 svals = vals; 2897 for (i=0; i<m; i++) { 2898 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2899 smycols += ourlens[i]; 2900 svals += ourlens[i]; 2901 jj++; 2902 } 2903 2904 /* read in other processors and ship out */ 2905 for (i=1; i<size; i++) { 2906 nz = procsnz[i]; 2907 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2908 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2909 } 2910 ierr = PetscFree(procsnz);CHKERRQ(ierr); 2911 } else { 2912 /* receive numeric values */ 2913 ierr = PetscMalloc1(nz+1,&vals);CHKERRQ(ierr); 2914 2915 /* receive message of values*/ 2916 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2917 2918 /* insert into matrix */ 2919 jj = rstart; 2920 smycols = mycols; 2921 svals = vals; 2922 for (i=0; i<m; i++) { 2923 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2924 smycols += ourlens[i]; 2925 svals += ourlens[i]; 2926 jj++; 2927 } 2928 } 2929 ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr); 2930 ierr = PetscFree(vals);CHKERRQ(ierr); 2931 ierr = PetscFree(mycols);CHKERRQ(ierr); 2932 ierr = PetscFree(rowners);CHKERRQ(ierr); 2933 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2934 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2935 PetscFunctionReturn(0); 2936 } 2937 2938 /* Not scalable because of ISAllGather() unless getting all columns. */ 2939 PetscErrorCode ISGetSeqIS_Private(Mat mat,IS iscol,IS *isseq) 2940 { 2941 PetscErrorCode ierr; 2942 IS iscol_local; 2943 PetscBool isstride; 2944 PetscMPIInt lisstride=0,gisstride; 2945 2946 PetscFunctionBegin; 2947 /* check if we are grabbing all columns*/ 2948 ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&isstride);CHKERRQ(ierr); 2949 2950 if (isstride) { 2951 PetscInt start,len,mstart,mlen; 2952 ierr = ISStrideGetInfo(iscol,&start,NULL);CHKERRQ(ierr); 2953 ierr = ISGetLocalSize(iscol,&len);CHKERRQ(ierr); 2954 ierr = MatGetOwnershipRangeColumn(mat,&mstart,&mlen);CHKERRQ(ierr); 2955 if (mstart == start && mlen-mstart == len) lisstride = 1; 2956 } 2957 2958 ierr = MPIU_Allreduce(&lisstride,&gisstride,1,MPI_INT,MPI_MIN,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2959 if (gisstride) { 2960 PetscInt N; 2961 ierr = MatGetSize(mat,NULL,&N);CHKERRQ(ierr); 2962 ierr = ISCreateStride(PetscObjectComm((PetscObject)mat),N,0,1,&iscol_local);CHKERRQ(ierr); 2963 ierr = ISSetIdentity(iscol_local);CHKERRQ(ierr); 2964 ierr = PetscInfo(mat,"Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n");CHKERRQ(ierr); 2965 } else { 2966 PetscInt cbs; 2967 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 2968 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 2969 ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr); 2970 } 2971 2972 *isseq = iscol_local; 2973 PetscFunctionReturn(0); 2974 } 2975 2976 /* 2977 Used for avoiding ISAllGather() and global size of iscol_local (see MatCreateSubMatrix_MPIAIJ_nonscalable) 2978 2979 Input Parameters: 2980 mat - matrix 2981 iscol - parallel column index set; its local indices are a subset of local columns of mat, 2982 i.e., mat->cstart <= iscol[i] < mat->cend 2983 Output Parameter: 2984 iscol_sub - sequential column index set, a subset of iscol 2985 iscmap - column map; iscmap[i] indicates global location of iscol_sub[i] in iscol 2986 */ 2987 PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat,IS isrow,IS iscol,IS *iscol_sub,IS *iscmap,IS *isrow_d,IS *iscol_d,IS *iscol_o,IS *isgarray) 2988 { 2989 PetscErrorCode ierr; 2990 Vec x,cmap; 2991 const PetscInt *is_idx; 2992 PetscScalar *xarray,*cmaparray; 2993 PetscInt ncols,isstart,*idx,*camp,count,m,rstart; 2994 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 2995 Mat B=a->B; 2996 Vec lvec=a->lvec,lcmap; 2997 PetscInt i,cstart,cend,Bn=B->cmap->N; 2998 MPI_Comm comm; 2999 3000 PetscFunctionBegin; 3001 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3002 PetscMPIInt rank; 3003 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3004 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 3005 3006 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3007 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3008 ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3009 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3010 3011 /* get start indices */ 3012 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3013 isstart -= ncols; 3014 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3015 3016 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3017 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3018 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3019 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3020 for (i=0; i<ncols; i++) { 3021 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3022 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3023 3024 idx[i] = is_idx[i]-cstart; 3025 } 3026 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3027 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3028 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3029 3030 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_COPY_VALUES,iscol_d);CHKERRQ(ierr); 3031 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3032 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3033 ierr = PetscFree(idx);CHKERRQ(ierr); 3034 3035 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3036 rstart = mat->rmap->rstart; 3037 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3038 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3039 for (i=0; i<m; i++) { 3040 idx[i] = is_idx[i]-rstart; 3041 } 3042 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3043 3044 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_COPY_VALUES,isrow_d);CHKERRQ(ierr); 3045 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3046 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3047 ierr = PetscFree(idx);CHKERRQ(ierr); 3048 3049 /* (2) scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3050 ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3051 3052 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3053 3054 ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3055 ierr = VecScatterBegin(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3056 3057 count = ncols + Bn; 3058 ierr = PetscMalloc2(count,&idx,count,&camp);CHKERRQ(ierr); 3059 3060 ierr = VecScatterEnd(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3061 3062 /* (3) create scalable iscol_sub (a subset of iscol) and iscmap */ 3063 /* local column indices */ 3064 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3065 for (i=0; i<ncols; i++) { 3066 idx[i] = is_idx[i]; 3067 camp[i] = i + isstart; /* global index of iscol = column index in submat */ 3068 } 3069 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3070 count = ncols; 3071 3072 /* off-process column indices */ 3073 PetscInt *idx1,*cmap1,count1=0; 3074 ierr = PetscMalloc2(Bn,&idx1,Bn,&cmap1);CHKERRQ(ierr); 3075 3076 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3077 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3078 for (i=0; i<Bn; i++) { 3079 if (PetscRealPart(xarray[i]) > -1.0) { 3080 //if (rank == 1) printf("[%d] xarray[%d] = %g; cstart %d\n",rank,i,xarray[i],cstart); 3081 idx1[count1] = i; /* local column index in off-diagonal part B */ 3082 cmap1[count1++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3083 3084 idx[count] = (PetscInt)PetscRealPart(xarray[i]); 3085 camp[count++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3086 } 3087 } 3088 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3089 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3090 3091 ierr = PetscSortIntWithArray(count,camp,idx);CHKERRQ(ierr); 3092 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,iscol_sub);CHKERRQ(ierr); 3093 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,camp,PETSC_COPY_VALUES,iscmap);CHKERRQ(ierr); 3094 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3095 ierr = ISSetBlockSize(*iscol_sub,i);CHKERRQ(ierr); 3096 3097 ierr = ISCreateGeneral(PETSC_COMM_SELF,count1,idx1,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr); 3098 ierr = ISCreateGeneral(PETSC_COMM_SELF,count1,cmap1,PETSC_COPY_VALUES,isgarray);CHKERRQ(ierr); 3099 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3100 ierr = ISSetBlockSize(*iscol_o,i);CHKERRQ(ierr); 3101 ierr = PetscFree2(idx1,cmap1);CHKERRQ(ierr); 3102 3103 ierr = PetscFree2(idx,camp);CHKERRQ(ierr); 3104 ierr = VecDestroy(&x);CHKERRQ(ierr); 3105 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3106 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3107 PetscFunctionReturn(0); 3108 } 3109 3110 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3111 { 3112 PetscErrorCode ierr; 3113 IS iscol_local; 3114 PetscInt csize; 3115 PetscInt n,i,j,start,end; 3116 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3117 MPI_Comm comm; 3118 3119 PetscFunctionBegin; 3120 /* If isrow has same processor distribution as mat, 3121 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3122 if (call == MAT_REUSE_MATRIX) { 3123 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3124 if (iscol_local) sameRowDist = PETSC_TRUE; 3125 } else { 3126 /* check if isrow has same processor distribution as mat */ 3127 sameDist[0] = PETSC_FALSE; 3128 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3129 if (!n) { 3130 sameDist[0] = PETSC_TRUE; 3131 } else { 3132 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3133 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3134 if (i >= start && j < end) { 3135 sameDist[0] = PETSC_TRUE; 3136 } 3137 } 3138 3139 /* check if iscol has same processor distribution as mat */ 3140 sameDist[1] = PETSC_FALSE; 3141 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3142 if (!n) { 3143 sameDist[1] = PETSC_TRUE; 3144 } else { 3145 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3146 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3147 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3148 } 3149 3150 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3151 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3152 sameRowDist = tsameDist[0]; 3153 } 3154 3155 if (sameRowDist) { 3156 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,call,tsameDist[1],newmat);CHKERRQ(ierr); 3157 PetscFunctionReturn(0); 3158 } 3159 3160 /* General case: iscol -> iscol_local which has global size of iscol */ 3161 if (call == MAT_REUSE_MATRIX) { 3162 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3163 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3164 } else { 3165 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3166 } 3167 3168 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3169 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3170 3171 if (call == MAT_INITIAL_MATRIX) { 3172 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3173 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3174 } 3175 PetscFunctionReturn(0); 3176 } 3177 3178 /*@C 3179 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3180 and "off-diagonal" part of the matrix in CSR format. 3181 3182 Collective on MPI_Comm 3183 3184 Input Parameters: 3185 + comm - MPI communicator 3186 . A - "diagonal" portion of matrix 3187 . B - "off-diagonal" portion of matrix 3188 - garray - global index of B columns 3189 3190 Output Parameter: 3191 . mat - the matrix 3192 3193 Level: advanced 3194 3195 Notes: 3196 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 3197 3198 .keywords: matrix, aij, compressed row, sparse, parallel 3199 3200 .seealso: MatCreateMPIAIJWithSplitArrays() 3201 @*/ 3202 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3203 { 3204 PetscErrorCode ierr; 3205 Mat_MPIAIJ *maij; 3206 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data; 3207 PetscInt *oi=b->i,*oj=b->j,i,nz,col; 3208 PetscScalar *oa=b->a; 3209 Mat Btmp; 3210 PetscInt m,n,N; 3211 3212 PetscFunctionBegin; 3213 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3214 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3215 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %d != Bm %d",m,B->rmap->N); 3216 3217 /* get global columns of mat */ 3218 ierr = MPIU_Allreduce(&n,&N,1,MPI_INT,MPI_SUM,comm);CHKERRQ(ierr); 3219 3220 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3221 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3222 maij = (Mat_MPIAIJ*)(*mat)->data; 3223 3224 (*mat)->preallocated = PETSC_TRUE; 3225 3226 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3227 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3228 3229 maij->A = A; 3230 3231 nz = oi[m]; 3232 for (i=0; i<nz; i++) { 3233 col = oj[i]; 3234 oj[i] = garray[col]; 3235 } 3236 3237 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Btmp);CHKERRQ(ierr); 3238 maij->B = Btmp; /* cannot destroy B because its arrays are used by Btmp? */ 3239 //b->free_ij = PETSC_FALSE; 3240 //b->free_a = PETSC_FALSE; 3241 //ierr = MatDestroy(&B);CHKERRQ(ierr); 3242 //B = Btmp; 3243 3244 /* condense columns of maij->B */ 3245 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3246 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3247 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3248 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3249 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3250 PetscFunctionReturn(0); 3251 } 3252 3253 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3254 3255 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,MatReuse call,PetscBool sameColDist,Mat *newmat) 3256 { 3257 PetscErrorCode ierr; 3258 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3259 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3260 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3261 Mat M,Msub,B=a->B,Mnew=NULL; 3262 MatScalar *aa; 3263 Mat_SeqAIJ *aij; 3264 PetscInt *garray = a->garray,*colsub,Ncols; 3265 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3266 IS iscol_sub,iscmap; 3267 const PetscInt *is_idx,*cmap; 3268 PetscBool allcolumns=PETSC_FALSE; 3269 IS iscol_local=NULL; 3270 MPI_Comm comm; 3271 IS iscol_d,isrow_d,iscol_o,isgarray; 3272 Mat Asub=NULL,Bsub=NULL; 3273 3274 PetscFunctionBegin; 3275 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3276 PetscMPIInt rank; 3277 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3278 3279 if (call == MAT_INITIAL_MATRIX) { 3280 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3281 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3282 3283 /* (1) Create scalable iscol_sub and iscmap */ 3284 if (sameColDist) { 3285 /* iscol has same processor distribution as mat, use a scalable routine to generate iscol_sub and iscmap */ 3286 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&iscol_sub,&iscmap,&isrow_d,&iscol_d,&iscol_o,&isgarray);CHKERRQ(ierr); 3287 3288 //====================================== 3289 3290 if (rank == -1) { 3291 //printf("[%d] isrow_d\n",rank); 3292 //ierr = ISView(isrow_d,0);CHKERRQ(ierr); 3293 3294 //printf("[%d] iscol_diag\n",rank); 3295 //ierr = ISView(iscol_d,0);CHKERRQ(ierr); 3296 3297 printf("[%d] iscol_o\n",rank); 3298 ierr = ISView(iscol_o,0);CHKERRQ(ierr); 3299 3300 printf("[%d] a->B, %d, %d\n",rank,a->B->rmap->N,a->B->cmap->N); 3301 ierr = MatView(a->B,0);CHKERRQ(ierr); 3302 } 3303 3304 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,call,&Asub);CHKERRQ(ierr); 3305 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,call,&Bsub);CHKERRQ(ierr); 3306 if (rank == -1) { 3307 printf("[%d] Bsub\n",rank); 3308 ierr = MatView(Bsub,0);CHKERRQ(ierr); 3309 } 3310 3311 const PetscInt *garray1; 3312 ierr = ISGetIndices(isgarray,&garray1);CHKERRQ(ierr); 3313 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray1,&Mnew);CHKERRQ(ierr); 3314 ierr = ISRestoreIndices(isgarray,&garray1);CHKERRQ(ierr); 3315 //ierr = MatView(Mnew,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3316 3317 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3318 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3319 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3320 //====================================== 3321 3322 } else { /* iscol -> nonscalable iscol_local, then get scalable iscol_sub and iscmap */ 3323 PetscBool flg; 3324 3325 /* iscol -> nonscalable iscol_local */ 3326 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3327 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3328 if (n != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != Ncols %d",n,Ncols); 3329 3330 /* Check for special case: each processor gets entire matrix columns */ 3331 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3332 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3333 if (allcolumns) { 3334 iscol_sub = iscol_local; 3335 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3336 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3337 3338 } else { /* iscol_local -> iscol_sub and iscmap */ 3339 PetscInt *idx,*cmap1,k,cbs; 3340 3341 /* implementation below requires iscol_local be sorted, it can have duplicate indices */ 3342 ierr = ISSorted(iscol_local,&flg);CHKERRQ(ierr); 3343 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsorted iscol_local is not implemented yet"); 3344 3345 ierr = PetscMalloc2(Ncols,&idx,Ncols,&cmap1);CHKERRQ(ierr); 3346 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3347 count = 0; 3348 k = 0; 3349 for (i=0; i<Ncols; i++) { 3350 j = is_idx[i]; 3351 if (j >= cstart && j < cend) { 3352 /* diagonal part of mat */ 3353 idx[count] = j; 3354 cmap1[count++] = i; /* column index in submat */ 3355 } else if (Bn) { 3356 /* off-diagonal part of mat */ 3357 if (j == garray[k]) { 3358 idx[count] = j; 3359 cmap1[count++] = i; /* column index in submat */ 3360 } else if (j > garray[k]) { 3361 while (j > garray[k] && k < Bn-1) k++; 3362 if (j == garray[k]) { 3363 idx[count] = j; 3364 cmap1[count++] = i; /* column index in submat */ 3365 } 3366 } 3367 } 3368 } 3369 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3370 3371 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,&iscol_sub);CHKERRQ(ierr); 3372 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3373 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3374 3375 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_COPY_VALUES,&iscmap);CHKERRQ(ierr); 3376 ierr = PetscFree2(idx,cmap1);CHKERRQ(ierr); 3377 } 3378 } 3379 3380 /* (2) Create sequential Msub */ 3381 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3382 3383 } else { /* call == MAT_REUSE_MATRIX */ 3384 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3385 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3386 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3387 3388 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3389 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3390 3391 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3392 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3393 3394 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3395 } 3396 3397 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3398 aij = (Mat_SeqAIJ*)(Msub)->data; 3399 ii = aij->i; 3400 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3401 3402 /* 3403 m - number of local rows 3404 Ncols - number of columns (same on all processors) 3405 rstart - first row in new global matrix generated 3406 */ 3407 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3408 3409 if (call == MAT_INITIAL_MATRIX) { 3410 /* (3) Create parallel newmat */ 3411 PetscMPIInt rank,size; 3412 PetscInt csize; 3413 3414 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3415 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3416 3417 /* 3418 Determine the number of non-zeros in the diagonal and off-diagonal 3419 portions of the matrix in order to do correct preallocation 3420 */ 3421 3422 /* first get start and end of "diagonal" columns */ 3423 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3424 if (csize == PETSC_DECIDE) { 3425 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3426 if (mglobal == Ncols) { /* square matrix */ 3427 nlocal = m; 3428 } else { 3429 nlocal = Ncols/size + ((Ncols % size) > rank); 3430 } 3431 } else { 3432 nlocal = csize; 3433 } 3434 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3435 rstart = rend - nlocal; 3436 if (rank == size - 1 && rend != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local column sizes %D do not add up to total number of columns %D",rend,Ncols); 3437 3438 /* next, compute all the lengths */ 3439 jj = aij->j; 3440 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3441 olens = dlens + m; 3442 for (i=0; i<m; i++) { 3443 jend = ii[i+1] - ii[i]; 3444 olen = 0; 3445 dlen = 0; 3446 for (j=0; j<jend; j++) { 3447 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3448 else dlen++; 3449 jj++; 3450 } 3451 olens[i] = olen; 3452 dlens[i] = dlen; 3453 } 3454 ierr = MatGetBlockSizes(Msub,&bs,&cbs);CHKERRQ(ierr); 3455 3456 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3457 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr); 3458 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3459 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3460 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3461 ierr = PetscFree(dlens);CHKERRQ(ierr); 3462 } else { 3463 M = *newmat; 3464 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3465 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3466 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3467 /* 3468 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3469 rather than the slower MatSetValues(). 3470 */ 3471 M->was_assembled = PETSC_TRUE; 3472 M->assembled = PETSC_FALSE; 3473 } 3474 3475 /* (4) Set values of Msub to *newmat */ 3476 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3477 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3478 3479 jj = aij->j; 3480 aa = aij->a; 3481 for (i=0; i<m; i++) { 3482 row = rstart + i; 3483 nz = ii[i+1] - ii[i]; 3484 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3485 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3486 jj += nz; aa += nz; 3487 } 3488 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3489 3490 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3491 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3492 *newmat = M; 3493 3494 ierr = PetscFree(colsub);CHKERRQ(ierr); 3495 3496 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3497 if (call == MAT_INITIAL_MATRIX) { 3498 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3499 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3500 3501 ierr = PetscObjectCompose((PetscObject)M,"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3502 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3503 3504 ierr = PetscObjectCompose((PetscObject)M,"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3505 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3506 3507 if (iscol_local) { 3508 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3509 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3510 } 3511 3512 if (Mnew) { 3513 PetscBool equal; 3514 ierr = MatEqual(M,Mnew,&equal);CHKERRQ(ierr); 3515 if (!equal) SETERRQ(PETSC_COMM_SELF,0,"M != Mnew"); 3516 ierr = MatDestroy(&Mnew);CHKERRQ(ierr); 3517 ierr = MatDestroy(&Bsub);CHKERRQ(ierr); 3518 ierr = ISDestroy(&isgarray);CHKERRQ(ierr); 3519 } 3520 } 3521 PetscFunctionReturn(0); 3522 } 3523 3524 /* 3525 Not great since it makes two copies of the submatrix, first an SeqAIJ 3526 in local and then by concatenating the local matrices the end result. 3527 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3528 3529 Note: This requires a sequential iscol with all indices. 3530 */ 3531 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3532 { 3533 PetscErrorCode ierr; 3534 PetscMPIInt rank,size; 3535 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3536 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3537 Mat M,Mreuse; 3538 MatScalar *aa,*vwork; 3539 MPI_Comm comm; 3540 Mat_SeqAIJ *aij; 3541 PetscBool colflag,allcolumns=PETSC_FALSE; 3542 3543 PetscFunctionBegin; 3544 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3545 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3546 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3547 3548 /* Check for special case: each processor gets entire matrix columns */ 3549 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3550 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3551 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3552 3553 if (call == MAT_REUSE_MATRIX) { 3554 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3555 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3556 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3557 } else { 3558 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3559 } 3560 3561 /* 3562 m - number of local rows 3563 n - number of columns (same on all processors) 3564 rstart - first row in new global matrix generated 3565 */ 3566 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3567 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3568 if (call == MAT_INITIAL_MATRIX) { 3569 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3570 ii = aij->i; 3571 jj = aij->j; 3572 3573 /* 3574 Determine the number of non-zeros in the diagonal and off-diagonal 3575 portions of the matrix in order to do correct preallocation 3576 */ 3577 3578 /* first get start and end of "diagonal" columns */ 3579 if (csize == PETSC_DECIDE) { 3580 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3581 if (mglobal == n) { /* square matrix */ 3582 nlocal = m; 3583 } else { 3584 nlocal = n/size + ((n % size) > rank); 3585 } 3586 } else { 3587 nlocal = csize; 3588 } 3589 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3590 rstart = rend - nlocal; 3591 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); 3592 3593 /* next, compute all the lengths */ 3594 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3595 olens = dlens + m; 3596 for (i=0; i<m; i++) { 3597 jend = ii[i+1] - ii[i]; 3598 olen = 0; 3599 dlen = 0; 3600 for (j=0; j<jend; j++) { 3601 if (*jj < rstart || *jj >= rend) olen++; 3602 else dlen++; 3603 jj++; 3604 } 3605 olens[i] = olen; 3606 dlens[i] = dlen; 3607 } 3608 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3609 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3610 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3611 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3612 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3613 ierr = PetscFree(dlens);CHKERRQ(ierr); 3614 } else { 3615 PetscInt ml,nl; 3616 3617 M = *newmat; 3618 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3619 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3620 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3621 /* 3622 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3623 rather than the slower MatSetValues(). 3624 */ 3625 M->was_assembled = PETSC_TRUE; 3626 M->assembled = PETSC_FALSE; 3627 } 3628 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3629 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3630 ii = aij->i; 3631 jj = aij->j; 3632 aa = aij->a; 3633 for (i=0; i<m; i++) { 3634 row = rstart + i; 3635 nz = ii[i+1] - ii[i]; 3636 cwork = jj; jj += nz; 3637 vwork = aa; aa += nz; 3638 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3639 } 3640 3641 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3642 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3643 *newmat = M; 3644 3645 /* save submatrix used in processor for next request */ 3646 if (call == MAT_INITIAL_MATRIX) { 3647 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3648 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3649 } 3650 PetscFunctionReturn(0); 3651 } 3652 3653 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3654 { 3655 PetscInt m,cstart, cend,j,nnz,i,d; 3656 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3657 const PetscInt *JJ; 3658 PetscScalar *values; 3659 PetscErrorCode ierr; 3660 PetscBool nooffprocentries; 3661 3662 PetscFunctionBegin; 3663 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3664 3665 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3666 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3667 m = B->rmap->n; 3668 cstart = B->cmap->rstart; 3669 cend = B->cmap->rend; 3670 rstart = B->rmap->rstart; 3671 3672 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3673 3674 #if defined(PETSC_USE_DEBUGGING) 3675 for (i=0; i<m; i++) { 3676 nnz = Ii[i+1]- Ii[i]; 3677 JJ = J + Ii[i]; 3678 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3679 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3680 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); 3681 } 3682 #endif 3683 3684 for (i=0; i<m; i++) { 3685 nnz = Ii[i+1]- Ii[i]; 3686 JJ = J + Ii[i]; 3687 nnz_max = PetscMax(nnz_max,nnz); 3688 d = 0; 3689 for (j=0; j<nnz; j++) { 3690 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3691 } 3692 d_nnz[i] = d; 3693 o_nnz[i] = nnz - d; 3694 } 3695 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3696 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3697 3698 if (v) values = (PetscScalar*)v; 3699 else { 3700 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3701 } 3702 3703 for (i=0; i<m; i++) { 3704 ii = i + rstart; 3705 nnz = Ii[i+1]- Ii[i]; 3706 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3707 } 3708 nooffprocentries = B->nooffprocentries; 3709 B->nooffprocentries = PETSC_TRUE; 3710 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3711 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3712 B->nooffprocentries = nooffprocentries; 3713 3714 if (!v) { 3715 ierr = PetscFree(values);CHKERRQ(ierr); 3716 } 3717 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3718 PetscFunctionReturn(0); 3719 } 3720 3721 /*@ 3722 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3723 (the default parallel PETSc format). 3724 3725 Collective on MPI_Comm 3726 3727 Input Parameters: 3728 + B - the matrix 3729 . i - the indices into j for the start of each local row (starts with zero) 3730 . j - the column indices for each local row (starts with zero) 3731 - v - optional values in the matrix 3732 3733 Level: developer 3734 3735 Notes: 3736 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3737 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3738 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3739 3740 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3741 3742 The format which is used for the sparse matrix input, is equivalent to a 3743 row-major ordering.. i.e for the following matrix, the input data expected is 3744 as shown 3745 3746 $ 1 0 0 3747 $ 2 0 3 P0 3748 $ ------- 3749 $ 4 5 6 P1 3750 $ 3751 $ Process0 [P0]: rows_owned=[0,1] 3752 $ i = {0,1,3} [size = nrow+1 = 2+1] 3753 $ j = {0,0,2} [size = 3] 3754 $ v = {1,2,3} [size = 3] 3755 $ 3756 $ Process1 [P1]: rows_owned=[2] 3757 $ i = {0,3} [size = nrow+1 = 1+1] 3758 $ j = {0,1,2} [size = 3] 3759 $ v = {4,5,6} [size = 3] 3760 3761 .keywords: matrix, aij, compressed row, sparse, parallel 3762 3763 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3764 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3765 @*/ 3766 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3767 { 3768 PetscErrorCode ierr; 3769 3770 PetscFunctionBegin; 3771 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3772 PetscFunctionReturn(0); 3773 } 3774 3775 /*@C 3776 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3777 (the default parallel PETSc format). For good matrix assembly performance 3778 the user should preallocate the matrix storage by setting the parameters 3779 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3780 performance can be increased by more than a factor of 50. 3781 3782 Collective on MPI_Comm 3783 3784 Input Parameters: 3785 + B - the matrix 3786 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3787 (same value is used for all local rows) 3788 . d_nnz - array containing the number of nonzeros in the various rows of the 3789 DIAGONAL portion of the local submatrix (possibly different for each row) 3790 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3791 The size of this array is equal to the number of local rows, i.e 'm'. 3792 For matrices that will be factored, you must leave room for (and set) 3793 the diagonal entry even if it is zero. 3794 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3795 submatrix (same value is used for all local rows). 3796 - o_nnz - array containing the number of nonzeros in the various rows of the 3797 OFF-DIAGONAL portion of the local submatrix (possibly different for 3798 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3799 structure. The size of this array is equal to the number 3800 of local rows, i.e 'm'. 3801 3802 If the *_nnz parameter is given then the *_nz parameter is ignored 3803 3804 The AIJ format (also called the Yale sparse matrix format or 3805 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3806 storage. The stored row and column indices begin with zero. 3807 See Users-Manual: ch_mat for details. 3808 3809 The parallel matrix is partitioned such that the first m0 rows belong to 3810 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3811 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3812 3813 The DIAGONAL portion of the local submatrix of a processor can be defined 3814 as the submatrix which is obtained by extraction the part corresponding to 3815 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3816 first row that belongs to the processor, r2 is the last row belonging to 3817 the this processor, and c1-c2 is range of indices of the local part of a 3818 vector suitable for applying the matrix to. This is an mxn matrix. In the 3819 common case of a square matrix, the row and column ranges are the same and 3820 the DIAGONAL part is also square. The remaining portion of the local 3821 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3822 3823 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3824 3825 You can call MatGetInfo() to get information on how effective the preallocation was; 3826 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3827 You can also run with the option -info and look for messages with the string 3828 malloc in them to see if additional memory allocation was needed. 3829 3830 Example usage: 3831 3832 Consider the following 8x8 matrix with 34 non-zero values, that is 3833 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3834 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3835 as follows: 3836 3837 .vb 3838 1 2 0 | 0 3 0 | 0 4 3839 Proc0 0 5 6 | 7 0 0 | 8 0 3840 9 0 10 | 11 0 0 | 12 0 3841 ------------------------------------- 3842 13 0 14 | 15 16 17 | 0 0 3843 Proc1 0 18 0 | 19 20 21 | 0 0 3844 0 0 0 | 22 23 0 | 24 0 3845 ------------------------------------- 3846 Proc2 25 26 27 | 0 0 28 | 29 0 3847 30 0 0 | 31 32 33 | 0 34 3848 .ve 3849 3850 This can be represented as a collection of submatrices as: 3851 3852 .vb 3853 A B C 3854 D E F 3855 G H I 3856 .ve 3857 3858 Where the submatrices A,B,C are owned by proc0, D,E,F are 3859 owned by proc1, G,H,I are owned by proc2. 3860 3861 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3862 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3863 The 'M','N' parameters are 8,8, and have the same values on all procs. 3864 3865 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3866 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3867 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3868 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3869 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3870 matrix, ans [DF] as another SeqAIJ matrix. 3871 3872 When d_nz, o_nz parameters are specified, d_nz storage elements are 3873 allocated for every row of the local diagonal submatrix, and o_nz 3874 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3875 One way to choose d_nz and o_nz is to use the max nonzerors per local 3876 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3877 In this case, the values of d_nz,o_nz are: 3878 .vb 3879 proc0 : dnz = 2, o_nz = 2 3880 proc1 : dnz = 3, o_nz = 2 3881 proc2 : dnz = 1, o_nz = 4 3882 .ve 3883 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3884 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3885 for proc3. i.e we are using 12+15+10=37 storage locations to store 3886 34 values. 3887 3888 When d_nnz, o_nnz parameters are specified, the storage is specified 3889 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3890 In the above case the values for d_nnz,o_nnz are: 3891 .vb 3892 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3893 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3894 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3895 .ve 3896 Here the space allocated is sum of all the above values i.e 34, and 3897 hence pre-allocation is perfect. 3898 3899 Level: intermediate 3900 3901 .keywords: matrix, aij, compressed row, sparse, parallel 3902 3903 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 3904 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 3905 @*/ 3906 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3907 { 3908 PetscErrorCode ierr; 3909 3910 PetscFunctionBegin; 3911 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3912 PetscValidType(B,1); 3913 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 3914 PetscFunctionReturn(0); 3915 } 3916 3917 /*@ 3918 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 3919 CSR format the local rows. 3920 3921 Collective on MPI_Comm 3922 3923 Input Parameters: 3924 + comm - MPI communicator 3925 . m - number of local rows (Cannot be PETSC_DECIDE) 3926 . n - This value should be the same as the local size used in creating the 3927 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3928 calculated if N is given) For square matrices n is almost always m. 3929 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3930 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3931 . i - row indices 3932 . j - column indices 3933 - a - matrix values 3934 3935 Output Parameter: 3936 . mat - the matrix 3937 3938 Level: intermediate 3939 3940 Notes: 3941 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3942 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3943 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3944 3945 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3946 3947 The format which is used for the sparse matrix input, is equivalent to a 3948 row-major ordering.. i.e for the following matrix, the input data expected is 3949 as shown 3950 3951 $ 1 0 0 3952 $ 2 0 3 P0 3953 $ ------- 3954 $ 4 5 6 P1 3955 $ 3956 $ Process0 [P0]: rows_owned=[0,1] 3957 $ i = {0,1,3} [size = nrow+1 = 2+1] 3958 $ j = {0,0,2} [size = 3] 3959 $ v = {1,2,3} [size = 3] 3960 $ 3961 $ Process1 [P1]: rows_owned=[2] 3962 $ i = {0,3} [size = nrow+1 = 1+1] 3963 $ j = {0,1,2} [size = 3] 3964 $ v = {4,5,6} [size = 3] 3965 3966 .keywords: matrix, aij, compressed row, sparse, parallel 3967 3968 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 3969 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 3970 @*/ 3971 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 3972 { 3973 PetscErrorCode ierr; 3974 3975 PetscFunctionBegin; 3976 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 3977 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 3978 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3979 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 3980 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 3981 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3982 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 3983 PetscFunctionReturn(0); 3984 } 3985 3986 /*@C 3987 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 3988 (the default parallel PETSc format). For good matrix assembly performance 3989 the user should preallocate the matrix storage by setting the parameters 3990 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3991 performance can be increased by more than a factor of 50. 3992 3993 Collective on MPI_Comm 3994 3995 Input Parameters: 3996 + comm - MPI communicator 3997 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 3998 This value should be the same as the local size used in creating the 3999 y vector for the matrix-vector product y = Ax. 4000 . n - This value should be the same as the local size used in creating the 4001 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4002 calculated if N is given) For square matrices n is almost always m. 4003 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4004 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4005 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4006 (same value is used for all local rows) 4007 . d_nnz - array containing the number of nonzeros in the various rows of the 4008 DIAGONAL portion of the local submatrix (possibly different for each row) 4009 or NULL, if d_nz is used to specify the nonzero structure. 4010 The size of this array is equal to the number of local rows, i.e 'm'. 4011 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4012 submatrix (same value is used for all local rows). 4013 - o_nnz - array containing the number of nonzeros in the various rows of the 4014 OFF-DIAGONAL portion of the local submatrix (possibly different for 4015 each row) or NULL, if o_nz is used to specify the nonzero 4016 structure. The size of this array is equal to the number 4017 of local rows, i.e 'm'. 4018 4019 Output Parameter: 4020 . A - the matrix 4021 4022 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4023 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4024 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4025 4026 Notes: 4027 If the *_nnz parameter is given then the *_nz parameter is ignored 4028 4029 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4030 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4031 storage requirements for this matrix. 4032 4033 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4034 processor than it must be used on all processors that share the object for 4035 that argument. 4036 4037 The user MUST specify either the local or global matrix dimensions 4038 (possibly both). 4039 4040 The parallel matrix is partitioned across processors such that the 4041 first m0 rows belong to process 0, the next m1 rows belong to 4042 process 1, the next m2 rows belong to process 2 etc.. where 4043 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4044 values corresponding to [m x N] submatrix. 4045 4046 The columns are logically partitioned with the n0 columns belonging 4047 to 0th partition, the next n1 columns belonging to the next 4048 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4049 4050 The DIAGONAL portion of the local submatrix on any given processor 4051 is the submatrix corresponding to the rows and columns m,n 4052 corresponding to the given processor. i.e diagonal matrix on 4053 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4054 etc. The remaining portion of the local submatrix [m x (N-n)] 4055 constitute the OFF-DIAGONAL portion. The example below better 4056 illustrates this concept. 4057 4058 For a square global matrix we define each processor's diagonal portion 4059 to be its local rows and the corresponding columns (a square submatrix); 4060 each processor's off-diagonal portion encompasses the remainder of the 4061 local matrix (a rectangular submatrix). 4062 4063 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4064 4065 When calling this routine with a single process communicator, a matrix of 4066 type SEQAIJ is returned. If a matrix of type MATMPIAIJ is desired for this 4067 type of communicator, use the construction mechanism: 4068 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4069 4070 By default, this format uses inodes (identical nodes) when possible. 4071 We search for consecutive rows with the same nonzero structure, thereby 4072 reusing matrix information to achieve increased efficiency. 4073 4074 Options Database Keys: 4075 + -mat_no_inode - Do not use inodes 4076 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4077 - -mat_aij_oneindex - Internally use indexing starting at 1 4078 rather than 0. Note that when calling MatSetValues(), 4079 the user still MUST index entries starting at 0! 4080 4081 4082 Example usage: 4083 4084 Consider the following 8x8 matrix with 34 non-zero values, that is 4085 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4086 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4087 as follows: 4088 4089 .vb 4090 1 2 0 | 0 3 0 | 0 4 4091 Proc0 0 5 6 | 7 0 0 | 8 0 4092 9 0 10 | 11 0 0 | 12 0 4093 ------------------------------------- 4094 13 0 14 | 15 16 17 | 0 0 4095 Proc1 0 18 0 | 19 20 21 | 0 0 4096 0 0 0 | 22 23 0 | 24 0 4097 ------------------------------------- 4098 Proc2 25 26 27 | 0 0 28 | 29 0 4099 30 0 0 | 31 32 33 | 0 34 4100 .ve 4101 4102 This can be represented as a collection of submatrices as: 4103 4104 .vb 4105 A B C 4106 D E F 4107 G H I 4108 .ve 4109 4110 Where the submatrices A,B,C are owned by proc0, D,E,F are 4111 owned by proc1, G,H,I are owned by proc2. 4112 4113 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4114 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4115 The 'M','N' parameters are 8,8, and have the same values on all procs. 4116 4117 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4118 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4119 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4120 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4121 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4122 matrix, ans [DF] as another SeqAIJ matrix. 4123 4124 When d_nz, o_nz parameters are specified, d_nz storage elements are 4125 allocated for every row of the local diagonal submatrix, and o_nz 4126 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4127 One way to choose d_nz and o_nz is to use the max nonzerors per local 4128 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4129 In this case, the values of d_nz,o_nz are: 4130 .vb 4131 proc0 : dnz = 2, o_nz = 2 4132 proc1 : dnz = 3, o_nz = 2 4133 proc2 : dnz = 1, o_nz = 4 4134 .ve 4135 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4136 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4137 for proc3. i.e we are using 12+15+10=37 storage locations to store 4138 34 values. 4139 4140 When d_nnz, o_nnz parameters are specified, the storage is specified 4141 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4142 In the above case the values for d_nnz,o_nnz are: 4143 .vb 4144 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4145 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4146 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4147 .ve 4148 Here the space allocated is sum of all the above values i.e 34, and 4149 hence pre-allocation is perfect. 4150 4151 Level: intermediate 4152 4153 .keywords: matrix, aij, compressed row, sparse, parallel 4154 4155 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4156 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4157 @*/ 4158 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) 4159 { 4160 PetscErrorCode ierr; 4161 PetscMPIInt size; 4162 4163 PetscFunctionBegin; 4164 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4165 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4166 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4167 if (size > 1) { 4168 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4169 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4170 } else { 4171 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4172 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4173 } 4174 PetscFunctionReturn(0); 4175 } 4176 4177 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4178 { 4179 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4180 PetscBool flg; 4181 PetscErrorCode ierr; 4182 4183 PetscFunctionBegin; 4184 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4185 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4186 if (Ad) *Ad = a->A; 4187 if (Ao) *Ao = a->B; 4188 if (colmap) *colmap = a->garray; 4189 PetscFunctionReturn(0); 4190 } 4191 4192 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4193 { 4194 PetscErrorCode ierr; 4195 PetscInt m,N,i,rstart,nnz,Ii; 4196 PetscInt *indx; 4197 PetscScalar *values; 4198 4199 PetscFunctionBegin; 4200 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4201 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4202 PetscInt *dnz,*onz,sum,bs,cbs; 4203 4204 if (n == PETSC_DECIDE) { 4205 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4206 } 4207 /* Check sum(n) = N */ 4208 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4209 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 4210 4211 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4212 rstart -= m; 4213 4214 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4215 for (i=0; i<m; i++) { 4216 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4217 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4218 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4219 } 4220 4221 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4222 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4223 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4224 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4225 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4226 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4227 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4228 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4229 } 4230 4231 /* numeric phase */ 4232 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4233 for (i=0; i<m; i++) { 4234 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4235 Ii = i + rstart; 4236 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4237 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4238 } 4239 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4240 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4241 PetscFunctionReturn(0); 4242 } 4243 4244 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4245 { 4246 PetscErrorCode ierr; 4247 PetscMPIInt rank; 4248 PetscInt m,N,i,rstart,nnz; 4249 size_t len; 4250 const PetscInt *indx; 4251 PetscViewer out; 4252 char *name; 4253 Mat B; 4254 const PetscScalar *values; 4255 4256 PetscFunctionBegin; 4257 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4258 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4259 /* Should this be the type of the diagonal block of A? */ 4260 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4261 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4262 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4263 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4264 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4265 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4266 for (i=0; i<m; i++) { 4267 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4268 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4269 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4270 } 4271 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4272 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4273 4274 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4275 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4276 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4277 sprintf(name,"%s.%d",outfile,rank); 4278 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4279 ierr = PetscFree(name);CHKERRQ(ierr); 4280 ierr = MatView(B,out);CHKERRQ(ierr); 4281 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4282 ierr = MatDestroy(&B);CHKERRQ(ierr); 4283 PetscFunctionReturn(0); 4284 } 4285 4286 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4287 { 4288 PetscErrorCode ierr; 4289 Mat_Merge_SeqsToMPI *merge; 4290 PetscContainer container; 4291 4292 PetscFunctionBegin; 4293 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4294 if (container) { 4295 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4296 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4297 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4298 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4299 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4300 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4301 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4302 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4303 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4304 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4305 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4306 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4307 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4308 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4309 ierr = PetscFree(merge);CHKERRQ(ierr); 4310 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4311 } 4312 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4313 PetscFunctionReturn(0); 4314 } 4315 4316 #include <../src/mat/utils/freespace.h> 4317 #include <petscbt.h> 4318 4319 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4320 { 4321 PetscErrorCode ierr; 4322 MPI_Comm comm; 4323 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4324 PetscMPIInt size,rank,taga,*len_s; 4325 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4326 PetscInt proc,m; 4327 PetscInt **buf_ri,**buf_rj; 4328 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4329 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4330 MPI_Request *s_waits,*r_waits; 4331 MPI_Status *status; 4332 MatScalar *aa=a->a; 4333 MatScalar **abuf_r,*ba_i; 4334 Mat_Merge_SeqsToMPI *merge; 4335 PetscContainer container; 4336 4337 PetscFunctionBegin; 4338 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4339 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4340 4341 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4342 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4343 4344 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4345 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4346 4347 bi = merge->bi; 4348 bj = merge->bj; 4349 buf_ri = merge->buf_ri; 4350 buf_rj = merge->buf_rj; 4351 4352 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4353 owners = merge->rowmap->range; 4354 len_s = merge->len_s; 4355 4356 /* send and recv matrix values */ 4357 /*-----------------------------*/ 4358 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4359 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4360 4361 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4362 for (proc=0,k=0; proc<size; proc++) { 4363 if (!len_s[proc]) continue; 4364 i = owners[proc]; 4365 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4366 k++; 4367 } 4368 4369 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4370 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4371 ierr = PetscFree(status);CHKERRQ(ierr); 4372 4373 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4374 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4375 4376 /* insert mat values of mpimat */ 4377 /*----------------------------*/ 4378 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4379 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4380 4381 for (k=0; k<merge->nrecv; k++) { 4382 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4383 nrows = *(buf_ri_k[k]); 4384 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4385 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4386 } 4387 4388 /* set values of ba */ 4389 m = merge->rowmap->n; 4390 for (i=0; i<m; i++) { 4391 arow = owners[rank] + i; 4392 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4393 bnzi = bi[i+1] - bi[i]; 4394 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4395 4396 /* add local non-zero vals of this proc's seqmat into ba */ 4397 anzi = ai[arow+1] - ai[arow]; 4398 aj = a->j + ai[arow]; 4399 aa = a->a + ai[arow]; 4400 nextaj = 0; 4401 for (j=0; nextaj<anzi; j++) { 4402 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4403 ba_i[j] += aa[nextaj++]; 4404 } 4405 } 4406 4407 /* add received vals into ba */ 4408 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4409 /* i-th row */ 4410 if (i == *nextrow[k]) { 4411 anzi = *(nextai[k]+1) - *nextai[k]; 4412 aj = buf_rj[k] + *(nextai[k]); 4413 aa = abuf_r[k] + *(nextai[k]); 4414 nextaj = 0; 4415 for (j=0; nextaj<anzi; j++) { 4416 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4417 ba_i[j] += aa[nextaj++]; 4418 } 4419 } 4420 nextrow[k]++; nextai[k]++; 4421 } 4422 } 4423 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4424 } 4425 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4426 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4427 4428 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4429 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4430 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4431 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4432 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4433 PetscFunctionReturn(0); 4434 } 4435 4436 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4437 { 4438 PetscErrorCode ierr; 4439 Mat B_mpi; 4440 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4441 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4442 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4443 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4444 PetscInt len,proc,*dnz,*onz,bs,cbs; 4445 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4446 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4447 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4448 MPI_Status *status; 4449 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4450 PetscBT lnkbt; 4451 Mat_Merge_SeqsToMPI *merge; 4452 PetscContainer container; 4453 4454 PetscFunctionBegin; 4455 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4456 4457 /* make sure it is a PETSc comm */ 4458 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4459 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4460 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4461 4462 ierr = PetscNew(&merge);CHKERRQ(ierr); 4463 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4464 4465 /* determine row ownership */ 4466 /*---------------------------------------------------------*/ 4467 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4468 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4469 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4470 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4471 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4472 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4473 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4474 4475 m = merge->rowmap->n; 4476 owners = merge->rowmap->range; 4477 4478 /* determine the number of messages to send, their lengths */ 4479 /*---------------------------------------------------------*/ 4480 len_s = merge->len_s; 4481 4482 len = 0; /* length of buf_si[] */ 4483 merge->nsend = 0; 4484 for (proc=0; proc<size; proc++) { 4485 len_si[proc] = 0; 4486 if (proc == rank) { 4487 len_s[proc] = 0; 4488 } else { 4489 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4490 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4491 } 4492 if (len_s[proc]) { 4493 merge->nsend++; 4494 nrows = 0; 4495 for (i=owners[proc]; i<owners[proc+1]; i++) { 4496 if (ai[i+1] > ai[i]) nrows++; 4497 } 4498 len_si[proc] = 2*(nrows+1); 4499 len += len_si[proc]; 4500 } 4501 } 4502 4503 /* determine the number and length of messages to receive for ij-structure */ 4504 /*-------------------------------------------------------------------------*/ 4505 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4506 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4507 4508 /* post the Irecv of j-structure */ 4509 /*-------------------------------*/ 4510 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4511 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4512 4513 /* post the Isend of j-structure */ 4514 /*--------------------------------*/ 4515 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4516 4517 for (proc=0, k=0; proc<size; proc++) { 4518 if (!len_s[proc]) continue; 4519 i = owners[proc]; 4520 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4521 k++; 4522 } 4523 4524 /* receives and sends of j-structure are complete */ 4525 /*------------------------------------------------*/ 4526 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4527 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4528 4529 /* send and recv i-structure */ 4530 /*---------------------------*/ 4531 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4532 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4533 4534 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4535 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4536 for (proc=0,k=0; proc<size; proc++) { 4537 if (!len_s[proc]) continue; 4538 /* form outgoing message for i-structure: 4539 buf_si[0]: nrows to be sent 4540 [1:nrows]: row index (global) 4541 [nrows+1:2*nrows+1]: i-structure index 4542 */ 4543 /*-------------------------------------------*/ 4544 nrows = len_si[proc]/2 - 1; 4545 buf_si_i = buf_si + nrows+1; 4546 buf_si[0] = nrows; 4547 buf_si_i[0] = 0; 4548 nrows = 0; 4549 for (i=owners[proc]; i<owners[proc+1]; i++) { 4550 anzi = ai[i+1] - ai[i]; 4551 if (anzi) { 4552 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4553 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4554 nrows++; 4555 } 4556 } 4557 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4558 k++; 4559 buf_si += len_si[proc]; 4560 } 4561 4562 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4563 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4564 4565 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4566 for (i=0; i<merge->nrecv; i++) { 4567 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); 4568 } 4569 4570 ierr = PetscFree(len_si);CHKERRQ(ierr); 4571 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4572 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4573 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4574 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4575 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4576 ierr = PetscFree(status);CHKERRQ(ierr); 4577 4578 /* compute a local seq matrix in each processor */ 4579 /*----------------------------------------------*/ 4580 /* allocate bi array and free space for accumulating nonzero column info */ 4581 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4582 bi[0] = 0; 4583 4584 /* create and initialize a linked list */ 4585 nlnk = N+1; 4586 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4587 4588 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4589 len = ai[owners[rank+1]] - ai[owners[rank]]; 4590 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4591 4592 current_space = free_space; 4593 4594 /* determine symbolic info for each local row */ 4595 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4596 4597 for (k=0; k<merge->nrecv; k++) { 4598 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4599 nrows = *buf_ri_k[k]; 4600 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4601 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4602 } 4603 4604 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4605 len = 0; 4606 for (i=0; i<m; i++) { 4607 bnzi = 0; 4608 /* add local non-zero cols of this proc's seqmat into lnk */ 4609 arow = owners[rank] + i; 4610 anzi = ai[arow+1] - ai[arow]; 4611 aj = a->j + ai[arow]; 4612 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4613 bnzi += nlnk; 4614 /* add received col data into lnk */ 4615 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4616 if (i == *nextrow[k]) { /* i-th row */ 4617 anzi = *(nextai[k]+1) - *nextai[k]; 4618 aj = buf_rj[k] + *nextai[k]; 4619 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4620 bnzi += nlnk; 4621 nextrow[k]++; nextai[k]++; 4622 } 4623 } 4624 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4625 4626 /* if free space is not available, make more free space */ 4627 if (current_space->local_remaining<bnzi) { 4628 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4629 nspacedouble++; 4630 } 4631 /* copy data into free space, then initialize lnk */ 4632 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4633 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4634 4635 current_space->array += bnzi; 4636 current_space->local_used += bnzi; 4637 current_space->local_remaining -= bnzi; 4638 4639 bi[i+1] = bi[i] + bnzi; 4640 } 4641 4642 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4643 4644 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4645 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4646 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4647 4648 /* create symbolic parallel matrix B_mpi */ 4649 /*---------------------------------------*/ 4650 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4651 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4652 if (n==PETSC_DECIDE) { 4653 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4654 } else { 4655 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4656 } 4657 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4658 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4659 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4660 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4661 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4662 4663 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4664 B_mpi->assembled = PETSC_FALSE; 4665 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4666 merge->bi = bi; 4667 merge->bj = bj; 4668 merge->buf_ri = buf_ri; 4669 merge->buf_rj = buf_rj; 4670 merge->coi = NULL; 4671 merge->coj = NULL; 4672 merge->owners_co = NULL; 4673 4674 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4675 4676 /* attach the supporting struct to B_mpi for reuse */ 4677 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4678 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4679 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4680 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4681 *mpimat = B_mpi; 4682 4683 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4684 PetscFunctionReturn(0); 4685 } 4686 4687 /*@C 4688 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4689 matrices from each processor 4690 4691 Collective on MPI_Comm 4692 4693 Input Parameters: 4694 + comm - the communicators the parallel matrix will live on 4695 . seqmat - the input sequential matrices 4696 . m - number of local rows (or PETSC_DECIDE) 4697 . n - number of local columns (or PETSC_DECIDE) 4698 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4699 4700 Output Parameter: 4701 . mpimat - the parallel matrix generated 4702 4703 Level: advanced 4704 4705 Notes: 4706 The dimensions of the sequential matrix in each processor MUST be the same. 4707 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4708 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4709 @*/ 4710 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4711 { 4712 PetscErrorCode ierr; 4713 PetscMPIInt size; 4714 4715 PetscFunctionBegin; 4716 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4717 if (size == 1) { 4718 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4719 if (scall == MAT_INITIAL_MATRIX) { 4720 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4721 } else { 4722 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4723 } 4724 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4725 PetscFunctionReturn(0); 4726 } 4727 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4728 if (scall == MAT_INITIAL_MATRIX) { 4729 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4730 } 4731 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4732 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4733 PetscFunctionReturn(0); 4734 } 4735 4736 /*@ 4737 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 4738 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4739 with MatGetSize() 4740 4741 Not Collective 4742 4743 Input Parameters: 4744 + A - the matrix 4745 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4746 4747 Output Parameter: 4748 . A_loc - the local sequential matrix generated 4749 4750 Level: developer 4751 4752 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4753 4754 @*/ 4755 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4756 { 4757 PetscErrorCode ierr; 4758 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4759 Mat_SeqAIJ *mat,*a,*b; 4760 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4761 MatScalar *aa,*ba,*cam; 4762 PetscScalar *ca; 4763 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4764 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4765 PetscBool match; 4766 MPI_Comm comm; 4767 PetscMPIInt size; 4768 4769 PetscFunctionBegin; 4770 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4771 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4772 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4773 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4774 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4775 4776 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4777 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4778 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4779 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4780 aa = a->a; ba = b->a; 4781 if (scall == MAT_INITIAL_MATRIX) { 4782 if (size == 1) { 4783 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4784 PetscFunctionReturn(0); 4785 } 4786 4787 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4788 ci[0] = 0; 4789 for (i=0; i<am; i++) { 4790 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4791 } 4792 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4793 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4794 k = 0; 4795 for (i=0; i<am; i++) { 4796 ncols_o = bi[i+1] - bi[i]; 4797 ncols_d = ai[i+1] - ai[i]; 4798 /* off-diagonal portion of A */ 4799 for (jo=0; jo<ncols_o; jo++) { 4800 col = cmap[*bj]; 4801 if (col >= cstart) break; 4802 cj[k] = col; bj++; 4803 ca[k++] = *ba++; 4804 } 4805 /* diagonal portion of A */ 4806 for (j=0; j<ncols_d; j++) { 4807 cj[k] = cstart + *aj++; 4808 ca[k++] = *aa++; 4809 } 4810 /* off-diagonal portion of A */ 4811 for (j=jo; j<ncols_o; j++) { 4812 cj[k] = cmap[*bj++]; 4813 ca[k++] = *ba++; 4814 } 4815 } 4816 /* put together the new matrix */ 4817 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4818 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4819 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4820 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4821 mat->free_a = PETSC_TRUE; 4822 mat->free_ij = PETSC_TRUE; 4823 mat->nonew = 0; 4824 } else if (scall == MAT_REUSE_MATRIX) { 4825 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4826 ci = mat->i; cj = mat->j; cam = mat->a; 4827 for (i=0; i<am; i++) { 4828 /* off-diagonal portion of A */ 4829 ncols_o = bi[i+1] - bi[i]; 4830 for (jo=0; jo<ncols_o; jo++) { 4831 col = cmap[*bj]; 4832 if (col >= cstart) break; 4833 *cam++ = *ba++; bj++; 4834 } 4835 /* diagonal portion of A */ 4836 ncols_d = ai[i+1] - ai[i]; 4837 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4838 /* off-diagonal portion of A */ 4839 for (j=jo; j<ncols_o; j++) { 4840 *cam++ = *ba++; bj++; 4841 } 4842 } 4843 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4844 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4845 PetscFunctionReturn(0); 4846 } 4847 4848 /*@C 4849 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4850 4851 Not Collective 4852 4853 Input Parameters: 4854 + A - the matrix 4855 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4856 - row, col - index sets of rows and columns to extract (or NULL) 4857 4858 Output Parameter: 4859 . A_loc - the local sequential matrix generated 4860 4861 Level: developer 4862 4863 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4864 4865 @*/ 4866 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4867 { 4868 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4869 PetscErrorCode ierr; 4870 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4871 IS isrowa,iscola; 4872 Mat *aloc; 4873 PetscBool match; 4874 4875 PetscFunctionBegin; 4876 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4877 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4878 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4879 if (!row) { 4880 start = A->rmap->rstart; end = A->rmap->rend; 4881 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 4882 } else { 4883 isrowa = *row; 4884 } 4885 if (!col) { 4886 start = A->cmap->rstart; 4887 cmap = a->garray; 4888 nzA = a->A->cmap->n; 4889 nzB = a->B->cmap->n; 4890 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4891 ncols = 0; 4892 for (i=0; i<nzB; i++) { 4893 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4894 else break; 4895 } 4896 imark = i; 4897 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 4898 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 4899 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 4900 } else { 4901 iscola = *col; 4902 } 4903 if (scall != MAT_INITIAL_MATRIX) { 4904 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 4905 aloc[0] = *A_loc; 4906 } 4907 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 4908 *A_loc = aloc[0]; 4909 ierr = PetscFree(aloc);CHKERRQ(ierr); 4910 if (!row) { 4911 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 4912 } 4913 if (!col) { 4914 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 4915 } 4916 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4917 PetscFunctionReturn(0); 4918 } 4919 4920 /*@C 4921 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 4922 4923 Collective on Mat 4924 4925 Input Parameters: 4926 + A,B - the matrices in mpiaij format 4927 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4928 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 4929 4930 Output Parameter: 4931 + rowb, colb - index sets of rows and columns of B to extract 4932 - B_seq - the sequential matrix generated 4933 4934 Level: developer 4935 4936 @*/ 4937 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 4938 { 4939 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4940 PetscErrorCode ierr; 4941 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 4942 IS isrowb,iscolb; 4943 Mat *bseq=NULL; 4944 4945 PetscFunctionBegin; 4946 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 4947 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, (%D, %D) != (%D,%D)",A->cmap->rstart,A->cmap->rend,B->rmap->rstart,B->rmap->rend); 4948 } 4949 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 4950 4951 if (scall == MAT_INITIAL_MATRIX) { 4952 start = A->cmap->rstart; 4953 cmap = a->garray; 4954 nzA = a->A->cmap->n; 4955 nzB = a->B->cmap->n; 4956 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4957 ncols = 0; 4958 for (i=0; i<nzB; i++) { /* row < local row index */ 4959 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4960 else break; 4961 } 4962 imark = i; 4963 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 4964 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 4965 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 4966 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 4967 } else { 4968 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 4969 isrowb = *rowb; iscolb = *colb; 4970 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 4971 bseq[0] = *B_seq; 4972 } 4973 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 4974 *B_seq = bseq[0]; 4975 ierr = PetscFree(bseq);CHKERRQ(ierr); 4976 if (!rowb) { 4977 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 4978 } else { 4979 *rowb = isrowb; 4980 } 4981 if (!colb) { 4982 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 4983 } else { 4984 *colb = iscolb; 4985 } 4986 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 4987 PetscFunctionReturn(0); 4988 } 4989 4990 /* 4991 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 4992 of the OFF-DIAGONAL portion of local A 4993 4994 Collective on Mat 4995 4996 Input Parameters: 4997 + A,B - the matrices in mpiaij format 4998 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4999 5000 Output Parameter: 5001 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5002 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5003 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5004 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5005 5006 Level: developer 5007 5008 */ 5009 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5010 { 5011 VecScatter_MPI_General *gen_to,*gen_from; 5012 PetscErrorCode ierr; 5013 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5014 Mat_SeqAIJ *b_oth; 5015 VecScatter ctx =a->Mvctx; 5016 MPI_Comm comm; 5017 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 5018 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5019 PetscInt *rvalues,*svalues; 5020 MatScalar *b_otha,*bufa,*bufA; 5021 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5022 MPI_Request *rwaits = NULL,*swaits = NULL; 5023 MPI_Status *sstatus,rstatus; 5024 PetscMPIInt jj,size; 5025 PetscInt *cols,sbs,rbs; 5026 PetscScalar *vals; 5027 5028 PetscFunctionBegin; 5029 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5030 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5031 5032 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5033 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); 5034 } 5035 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5036 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5037 5038 if (size == 1) { 5039 startsj_s = NULL; 5040 bufa_ptr = NULL; 5041 *B_oth = NULL; 5042 PetscFunctionReturn(0); 5043 } 5044 5045 gen_to = (VecScatter_MPI_General*)ctx->todata; 5046 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5047 nrecvs = gen_from->n; 5048 nsends = gen_to->n; 5049 5050 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 5051 srow = gen_to->indices; /* local row index to be sent */ 5052 sstarts = gen_to->starts; 5053 sprocs = gen_to->procs; 5054 sstatus = gen_to->sstatus; 5055 sbs = gen_to->bs; 5056 rstarts = gen_from->starts; 5057 rprocs = gen_from->procs; 5058 rbs = gen_from->bs; 5059 5060 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5061 if (scall == MAT_INITIAL_MATRIX) { 5062 /* i-array */ 5063 /*---------*/ 5064 /* post receives */ 5065 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 5066 for (i=0; i<nrecvs; i++) { 5067 rowlen = rvalues + rstarts[i]*rbs; 5068 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5069 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5070 } 5071 5072 /* pack the outgoing message */ 5073 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 5074 5075 sstartsj[0] = 0; 5076 rstartsj[0] = 0; 5077 len = 0; /* total length of j or a array to be sent */ 5078 k = 0; 5079 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 5080 for (i=0; i<nsends; i++) { 5081 rowlen = svalues + sstarts[i]*sbs; 5082 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5083 for (j=0; j<nrows; j++) { 5084 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5085 for (l=0; l<sbs; l++) { 5086 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5087 5088 rowlen[j*sbs+l] = ncols; 5089 5090 len += ncols; 5091 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5092 } 5093 k++; 5094 } 5095 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5096 5097 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5098 } 5099 /* recvs and sends of i-array are completed */ 5100 i = nrecvs; 5101 while (i--) { 5102 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5103 } 5104 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5105 ierr = PetscFree(svalues);CHKERRQ(ierr); 5106 5107 /* allocate buffers for sending j and a arrays */ 5108 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5109 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5110 5111 /* create i-array of B_oth */ 5112 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5113 5114 b_othi[0] = 0; 5115 len = 0; /* total length of j or a array to be received */ 5116 k = 0; 5117 for (i=0; i<nrecvs; i++) { 5118 rowlen = rvalues + rstarts[i]*rbs; 5119 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5120 for (j=0; j<nrows; j++) { 5121 b_othi[k+1] = b_othi[k] + rowlen[j]; 5122 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5123 k++; 5124 } 5125 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5126 } 5127 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5128 5129 /* allocate space for j and a arrrays of B_oth */ 5130 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5131 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5132 5133 /* j-array */ 5134 /*---------*/ 5135 /* post receives of j-array */ 5136 for (i=0; i<nrecvs; i++) { 5137 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5138 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5139 } 5140 5141 /* pack the outgoing message j-array */ 5142 k = 0; 5143 for (i=0; i<nsends; i++) { 5144 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5145 bufJ = bufj+sstartsj[i]; 5146 for (j=0; j<nrows; j++) { 5147 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5148 for (ll=0; ll<sbs; ll++) { 5149 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5150 for (l=0; l<ncols; l++) { 5151 *bufJ++ = cols[l]; 5152 } 5153 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5154 } 5155 } 5156 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5157 } 5158 5159 /* recvs and sends of j-array are completed */ 5160 i = nrecvs; 5161 while (i--) { 5162 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5163 } 5164 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5165 } else if (scall == MAT_REUSE_MATRIX) { 5166 sstartsj = *startsj_s; 5167 rstartsj = *startsj_r; 5168 bufa = *bufa_ptr; 5169 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5170 b_otha = b_oth->a; 5171 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5172 5173 /* a-array */ 5174 /*---------*/ 5175 /* post receives of a-array */ 5176 for (i=0; i<nrecvs; i++) { 5177 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5178 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5179 } 5180 5181 /* pack the outgoing message a-array */ 5182 k = 0; 5183 for (i=0; i<nsends; i++) { 5184 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5185 bufA = bufa+sstartsj[i]; 5186 for (j=0; j<nrows; j++) { 5187 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5188 for (ll=0; ll<sbs; ll++) { 5189 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5190 for (l=0; l<ncols; l++) { 5191 *bufA++ = vals[l]; 5192 } 5193 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5194 } 5195 } 5196 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5197 } 5198 /* recvs and sends of a-array are completed */ 5199 i = nrecvs; 5200 while (i--) { 5201 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5202 } 5203 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5204 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5205 5206 if (scall == MAT_INITIAL_MATRIX) { 5207 /* put together the new matrix */ 5208 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5209 5210 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5211 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5212 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5213 b_oth->free_a = PETSC_TRUE; 5214 b_oth->free_ij = PETSC_TRUE; 5215 b_oth->nonew = 0; 5216 5217 ierr = PetscFree(bufj);CHKERRQ(ierr); 5218 if (!startsj_s || !bufa_ptr) { 5219 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5220 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5221 } else { 5222 *startsj_s = sstartsj; 5223 *startsj_r = rstartsj; 5224 *bufa_ptr = bufa; 5225 } 5226 } 5227 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5228 PetscFunctionReturn(0); 5229 } 5230 5231 /*@C 5232 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5233 5234 Not Collective 5235 5236 Input Parameters: 5237 . A - The matrix in mpiaij format 5238 5239 Output Parameter: 5240 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5241 . colmap - A map from global column index to local index into lvec 5242 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5243 5244 Level: developer 5245 5246 @*/ 5247 #if defined(PETSC_USE_CTABLE) 5248 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5249 #else 5250 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5251 #endif 5252 { 5253 Mat_MPIAIJ *a; 5254 5255 PetscFunctionBegin; 5256 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5257 PetscValidPointer(lvec, 2); 5258 PetscValidPointer(colmap, 3); 5259 PetscValidPointer(multScatter, 4); 5260 a = (Mat_MPIAIJ*) A->data; 5261 if (lvec) *lvec = a->lvec; 5262 if (colmap) *colmap = a->colmap; 5263 if (multScatter) *multScatter = a->Mvctx; 5264 PetscFunctionReturn(0); 5265 } 5266 5267 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5268 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5269 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5270 #if defined(PETSC_HAVE_ELEMENTAL) 5271 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5272 #endif 5273 #if defined(PETSC_HAVE_HYPRE) 5274 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5275 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5276 #endif 5277 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5278 5279 /* 5280 Computes (B'*A')' since computing B*A directly is untenable 5281 5282 n p p 5283 ( ) ( ) ( ) 5284 m ( A ) * n ( B ) = m ( C ) 5285 ( ) ( ) ( ) 5286 5287 */ 5288 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5289 { 5290 PetscErrorCode ierr; 5291 Mat At,Bt,Ct; 5292 5293 PetscFunctionBegin; 5294 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5295 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5296 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5297 ierr = MatDestroy(&At);CHKERRQ(ierr); 5298 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5299 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5300 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5301 PetscFunctionReturn(0); 5302 } 5303 5304 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5305 { 5306 PetscErrorCode ierr; 5307 PetscInt m=A->rmap->n,n=B->cmap->n; 5308 Mat Cmat; 5309 5310 PetscFunctionBegin; 5311 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); 5312 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5313 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5314 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5315 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5316 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5317 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5318 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5319 5320 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5321 5322 *C = Cmat; 5323 PetscFunctionReturn(0); 5324 } 5325 5326 /* ----------------------------------------------------------------*/ 5327 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5328 { 5329 PetscErrorCode ierr; 5330 5331 PetscFunctionBegin; 5332 if (scall == MAT_INITIAL_MATRIX) { 5333 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5334 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5335 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5336 } 5337 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5338 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5339 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5340 PetscFunctionReturn(0); 5341 } 5342 5343 /*MC 5344 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5345 5346 Options Database Keys: 5347 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5348 5349 Level: beginner 5350 5351 .seealso: MatCreateAIJ() 5352 M*/ 5353 5354 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5355 { 5356 Mat_MPIAIJ *b; 5357 PetscErrorCode ierr; 5358 PetscMPIInt size; 5359 5360 PetscFunctionBegin; 5361 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5362 5363 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5364 B->data = (void*)b; 5365 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5366 B->assembled = PETSC_FALSE; 5367 B->insertmode = NOT_SET_VALUES; 5368 b->size = size; 5369 5370 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5371 5372 /* build cache for off array entries formed */ 5373 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5374 5375 b->donotstash = PETSC_FALSE; 5376 b->colmap = 0; 5377 b->garray = 0; 5378 b->roworiented = PETSC_TRUE; 5379 5380 /* stuff used for matrix vector multiply */ 5381 b->lvec = NULL; 5382 b->Mvctx = NULL; 5383 5384 /* stuff for MatGetRow() */ 5385 b->rowindices = 0; 5386 b->rowvalues = 0; 5387 b->getrowactive = PETSC_FALSE; 5388 5389 /* flexible pointer used in CUSP/CUSPARSE classes */ 5390 b->spptr = NULL; 5391 5392 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5393 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5394 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5395 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5396 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5397 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5398 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5399 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5400 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5401 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5402 #if defined(PETSC_HAVE_ELEMENTAL) 5403 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5404 #endif 5405 #if defined(PETSC_HAVE_HYPRE) 5406 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5407 #endif 5408 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5409 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5410 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5411 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5412 #if defined(PETSC_HAVE_HYPRE) 5413 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5414 #endif 5415 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5416 PetscFunctionReturn(0); 5417 } 5418 5419 /*@C 5420 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5421 and "off-diagonal" part of the matrix in CSR format. 5422 5423 Collective on MPI_Comm 5424 5425 Input Parameters: 5426 + comm - MPI communicator 5427 . m - number of local rows (Cannot be PETSC_DECIDE) 5428 . n - This value should be the same as the local size used in creating the 5429 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5430 calculated if N is given) For square matrices n is almost always m. 5431 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5432 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5433 . i - row indices for "diagonal" portion of matrix 5434 . j - column indices 5435 . a - matrix values 5436 . oi - row indices for "off-diagonal" portion of matrix 5437 . oj - column indices 5438 - oa - matrix values 5439 5440 Output Parameter: 5441 . mat - the matrix 5442 5443 Level: advanced 5444 5445 Notes: 5446 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5447 must free the arrays once the matrix has been destroyed and not before. 5448 5449 The i and j indices are 0 based 5450 5451 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5452 5453 This sets local rows and cannot be used to set off-processor values. 5454 5455 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5456 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5457 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5458 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5459 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5460 communication if it is known that only local entries will be set. 5461 5462 .keywords: matrix, aij, compressed row, sparse, parallel 5463 5464 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5465 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5466 @*/ 5467 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) 5468 { 5469 PetscErrorCode ierr; 5470 Mat_MPIAIJ *maij; 5471 5472 PetscFunctionBegin; 5473 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5474 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5475 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5476 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5477 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5478 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5479 maij = (Mat_MPIAIJ*) (*mat)->data; 5480 5481 (*mat)->preallocated = PETSC_TRUE; 5482 5483 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5484 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5485 5486 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5487 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5488 5489 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5490 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5491 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5492 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5493 5494 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5495 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5496 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5497 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5498 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5499 PetscFunctionReturn(0); 5500 } 5501 5502 /* 5503 Special version for direct calls from Fortran 5504 */ 5505 #include <petsc/private/fortranimpl.h> 5506 5507 /* Change these macros so can be used in void function */ 5508 #undef CHKERRQ 5509 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5510 #undef SETERRQ2 5511 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5512 #undef SETERRQ3 5513 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5514 #undef SETERRQ 5515 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5516 5517 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5518 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5519 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5520 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5521 #else 5522 #endif 5523 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) 5524 { 5525 Mat mat = *mmat; 5526 PetscInt m = *mm, n = *mn; 5527 InsertMode addv = *maddv; 5528 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5529 PetscScalar value; 5530 PetscErrorCode ierr; 5531 5532 MatCheckPreallocated(mat,1); 5533 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5534 5535 #if defined(PETSC_USE_DEBUG) 5536 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5537 #endif 5538 { 5539 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5540 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5541 PetscBool roworiented = aij->roworiented; 5542 5543 /* Some Variables required in the macro */ 5544 Mat A = aij->A; 5545 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5546 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5547 MatScalar *aa = a->a; 5548 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5549 Mat B = aij->B; 5550 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5551 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5552 MatScalar *ba = b->a; 5553 5554 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5555 PetscInt nonew = a->nonew; 5556 MatScalar *ap1,*ap2; 5557 5558 PetscFunctionBegin; 5559 for (i=0; i<m; i++) { 5560 if (im[i] < 0) continue; 5561 #if defined(PETSC_USE_DEBUG) 5562 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); 5563 #endif 5564 if (im[i] >= rstart && im[i] < rend) { 5565 row = im[i] - rstart; 5566 lastcol1 = -1; 5567 rp1 = aj + ai[row]; 5568 ap1 = aa + ai[row]; 5569 rmax1 = aimax[row]; 5570 nrow1 = ailen[row]; 5571 low1 = 0; 5572 high1 = nrow1; 5573 lastcol2 = -1; 5574 rp2 = bj + bi[row]; 5575 ap2 = ba + bi[row]; 5576 rmax2 = bimax[row]; 5577 nrow2 = bilen[row]; 5578 low2 = 0; 5579 high2 = nrow2; 5580 5581 for (j=0; j<n; j++) { 5582 if (roworiented) value = v[i*n+j]; 5583 else value = v[i+j*m]; 5584 if (in[j] >= cstart && in[j] < cend) { 5585 col = in[j] - cstart; 5586 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5587 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5588 } else if (in[j] < 0) continue; 5589 #if defined(PETSC_USE_DEBUG) 5590 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); 5591 #endif 5592 else { 5593 if (mat->was_assembled) { 5594 if (!aij->colmap) { 5595 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5596 } 5597 #if defined(PETSC_USE_CTABLE) 5598 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5599 col--; 5600 #else 5601 col = aij->colmap[in[j]] - 1; 5602 #endif 5603 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5604 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5605 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5606 col = in[j]; 5607 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5608 B = aij->B; 5609 b = (Mat_SeqAIJ*)B->data; 5610 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5611 rp2 = bj + bi[row]; 5612 ap2 = ba + bi[row]; 5613 rmax2 = bimax[row]; 5614 nrow2 = bilen[row]; 5615 low2 = 0; 5616 high2 = nrow2; 5617 bm = aij->B->rmap->n; 5618 ba = b->a; 5619 } 5620 } else col = in[j]; 5621 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5622 } 5623 } 5624 } else if (!aij->donotstash) { 5625 if (roworiented) { 5626 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5627 } else { 5628 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5629 } 5630 } 5631 } 5632 } 5633 PetscFunctionReturnVoid(); 5634 } 5635 5636