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