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