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 #if 1 3093 //==================== new ==================== 3094 Mat_MPIAIJ *a = (Mat_MPIAIJ*)mat->data; 3095 Mat A = a->A,B = a->B; 3096 PetscInt *garray = a->garray; 3097 PetscInt count = 0,An=A->cmap->N,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3098 const PetscInt *is_idx; 3099 IS iscol_local = iscol; 3100 3101 if (rank==-1) { 3102 ierr = ISView(iscol_local,0);CHKERRQ(ierr); 3103 } 3104 3105 //ierr = ISGetLocalSize(iscol_local,&nlocal);CHKERRQ(ierr); 3106 //printf("[%d] cstart/end: %d - %d; nlocal %d\n",rank,cstart,cend,nlocal); 3107 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3108 3109 /* (1) create a reduced scalable iscol_loc */ 3110 IS iscol_loc; 3111 PetscInt idx[nlocal],cmap[nlocal]; 3112 count = 0; 3113 3114 /* A part */ 3115 j = cstart; 3116 for (i=0; i<nlocal; i++) { 3117 if (j >= cend) break; 3118 if (is_idx[i] == j) { 3119 idx[count] = j; 3120 cmap[count] = i; /* column index in submat */ 3121 count++; j++; 3122 } else if (is_idx[i] > j) { 3123 while (is_idx[i] > j && j < cend-1) j++; 3124 if (is_idx[i] == j) { 3125 idx[count] = j; 3126 cmap[count] = i; /* column index in submat */ 3127 count++; j++; 3128 } 3129 } 3130 } 3131 3132 /* B part */ 3133 j = 0; 3134 for (i=0; i<nlocal; i++) { 3135 if (j >= Bn) break; 3136 if (is_idx[i] == garray[j]) { 3137 idx[count] = garray[j]; 3138 cmap[count] = i; /* column index in submat */ 3139 count++; j++; 3140 } else if (is_idx[i] > garray[j]) { 3141 while (is_idx[i] > garray[j] && j < Bn-1) j++; 3142 if (is_idx[i] == garray[j]) { 3143 idx[count] = garray[j]; 3144 cmap[count] = i; /* column index in submat */ 3145 count++; j++; 3146 } 3147 } 3148 } 3149 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3150 printf("[%d] nlocal %d, N %d, Bn %d + An %d = %d, count %d\n",rank,nlocal,mat->cmap->N,Bn,An,Bn+An,count); 3151 3152 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,idx,PETSC_COPY_VALUES,&iscol_loc);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==0) { 3161 printf("[%d] Msub: %d %d \n",rank,Msub->rmap->N,Msub->cmap->N); 3162 ierr = MatView(Msub,0);CHKERRQ(ierr); 3163 } 3164 3165 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3166 ierr = ISDestroy(&iscol_loc);CHKERRQ(ierr); 3167 //========================================================== 3168 3169 #endif 3170 3171 if (call == MAT_REUSE_MATRIX) { 3172 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3173 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3174 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3175 } else { 3176 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3177 } 3178 3179 /* 3180 m - number of local rows 3181 n - number of columns (same on all processors) 3182 rstart - first row in new global matrix generated 3183 */ 3184 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3185 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3186 if (call == MAT_INITIAL_MATRIX) { 3187 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3188 ii = aij->i; 3189 jj = aij->j; 3190 3191 /* 3192 Determine the number of non-zeros in the diagonal and off-diagonal 3193 portions of the matrix in order to do correct preallocation 3194 */ 3195 3196 /* first get start and end of "diagonal" columns */ 3197 if (csize == PETSC_DECIDE) { 3198 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3199 if (mglobal == n) { /* square matrix */ 3200 nlocal = m; 3201 } else { 3202 nlocal = n/size + ((n % size) > rank); 3203 } 3204 } else { 3205 nlocal = csize; 3206 } 3207 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3208 rstart = rend - nlocal; 3209 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); 3210 3211 /* next, compute all the lengths */ 3212 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3213 olens = dlens + m; 3214 for (i=0; i<m; i++) { 3215 jend = ii[i+1] - ii[i]; 3216 olen = 0; 3217 dlen = 0; 3218 for (j=0; j<jend; j++) { 3219 if (*jj < rstart || *jj >= rend) olen++; 3220 else dlen++; 3221 jj++; 3222 } 3223 olens[i] = olen; 3224 dlens[i] = dlen; 3225 } 3226 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3227 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3228 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3229 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3230 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3231 ierr = PetscFree(dlens);CHKERRQ(ierr); 3232 } else { 3233 PetscInt ml,nl; 3234 3235 M = *newmat; 3236 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3237 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3238 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3239 /* 3240 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3241 rather than the slower MatSetValues(). 3242 */ 3243 M->was_assembled = PETSC_TRUE; 3244 M->assembled = PETSC_FALSE; 3245 } 3246 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3247 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3248 ii = aij->i; 3249 jj = aij->j; 3250 aa = aij->a; 3251 for (i=0; i<m; i++) { 3252 row = rstart + i; 3253 nz = ii[i+1] - ii[i]; 3254 cwork = jj; jj += nz; 3255 vwork = aa; aa += nz; 3256 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3257 } 3258 3259 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3260 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3261 *newmat = M; 3262 ierr = MatView(M,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3263 3264 /* save submatrix used in processor for next request */ 3265 if (call == MAT_INITIAL_MATRIX) { 3266 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3267 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3268 } 3269 PetscFunctionReturn(0); 3270 } 3271 3272 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3273 { 3274 PetscInt m,cstart, cend,j,nnz,i,d; 3275 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3276 const PetscInt *JJ; 3277 PetscScalar *values; 3278 PetscErrorCode ierr; 3279 PetscBool nooffprocentries; 3280 3281 PetscFunctionBegin; 3282 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3283 3284 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3285 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3286 m = B->rmap->n; 3287 cstart = B->cmap->rstart; 3288 cend = B->cmap->rend; 3289 rstart = B->rmap->rstart; 3290 3291 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3292 3293 #if defined(PETSC_USE_DEBUGGING) 3294 for (i=0; i<m; i++) { 3295 nnz = Ii[i+1]- Ii[i]; 3296 JJ = J + Ii[i]; 3297 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3298 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3299 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); 3300 } 3301 #endif 3302 3303 for (i=0; i<m; i++) { 3304 nnz = Ii[i+1]- Ii[i]; 3305 JJ = J + Ii[i]; 3306 nnz_max = PetscMax(nnz_max,nnz); 3307 d = 0; 3308 for (j=0; j<nnz; j++) { 3309 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3310 } 3311 d_nnz[i] = d; 3312 o_nnz[i] = nnz - d; 3313 } 3314 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3315 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3316 3317 if (v) values = (PetscScalar*)v; 3318 else { 3319 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3320 } 3321 3322 for (i=0; i<m; i++) { 3323 ii = i + rstart; 3324 nnz = Ii[i+1]- Ii[i]; 3325 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3326 } 3327 nooffprocentries = B->nooffprocentries; 3328 B->nooffprocentries = PETSC_TRUE; 3329 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3330 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3331 B->nooffprocentries = nooffprocentries; 3332 3333 if (!v) { 3334 ierr = PetscFree(values);CHKERRQ(ierr); 3335 } 3336 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3337 PetscFunctionReturn(0); 3338 } 3339 3340 /*@ 3341 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3342 (the default parallel PETSc format). 3343 3344 Collective on MPI_Comm 3345 3346 Input Parameters: 3347 + B - the matrix 3348 . i - the indices into j for the start of each local row (starts with zero) 3349 . j - the column indices for each local row (starts with zero) 3350 - v - optional values in the matrix 3351 3352 Level: developer 3353 3354 Notes: 3355 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3356 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3357 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3358 3359 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3360 3361 The format which is used for the sparse matrix input, is equivalent to a 3362 row-major ordering.. i.e for the following matrix, the input data expected is 3363 as shown 3364 3365 $ 1 0 0 3366 $ 2 0 3 P0 3367 $ ------- 3368 $ 4 5 6 P1 3369 $ 3370 $ Process0 [P0]: rows_owned=[0,1] 3371 $ i = {0,1,3} [size = nrow+1 = 2+1] 3372 $ j = {0,0,2} [size = 3] 3373 $ v = {1,2,3} [size = 3] 3374 $ 3375 $ Process1 [P1]: rows_owned=[2] 3376 $ i = {0,3} [size = nrow+1 = 1+1] 3377 $ j = {0,1,2} [size = 3] 3378 $ v = {4,5,6} [size = 3] 3379 3380 .keywords: matrix, aij, compressed row, sparse, parallel 3381 3382 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3383 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3384 @*/ 3385 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3386 { 3387 PetscErrorCode ierr; 3388 3389 PetscFunctionBegin; 3390 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3391 PetscFunctionReturn(0); 3392 } 3393 3394 /*@C 3395 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3396 (the default parallel PETSc format). For good matrix assembly performance 3397 the user should preallocate the matrix storage by setting the parameters 3398 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3399 performance can be increased by more than a factor of 50. 3400 3401 Collective on MPI_Comm 3402 3403 Input Parameters: 3404 + B - the matrix 3405 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3406 (same value is used for all local rows) 3407 . d_nnz - array containing the number of nonzeros in the various rows of the 3408 DIAGONAL portion of the local submatrix (possibly different for each row) 3409 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3410 The size of this array is equal to the number of local rows, i.e 'm'. 3411 For matrices that will be factored, you must leave room for (and set) 3412 the diagonal entry even if it is zero. 3413 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3414 submatrix (same value is used for all local rows). 3415 - o_nnz - array containing the number of nonzeros in the various rows of the 3416 OFF-DIAGONAL portion of the local submatrix (possibly different for 3417 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3418 structure. The size of this array is equal to the number 3419 of local rows, i.e 'm'. 3420 3421 If the *_nnz parameter is given then the *_nz parameter is ignored 3422 3423 The AIJ format (also called the Yale sparse matrix format or 3424 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3425 storage. The stored row and column indices begin with zero. 3426 See Users-Manual: ch_mat for details. 3427 3428 The parallel matrix is partitioned such that the first m0 rows belong to 3429 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3430 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3431 3432 The DIAGONAL portion of the local submatrix of a processor can be defined 3433 as the submatrix which is obtained by extraction the part corresponding to 3434 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3435 first row that belongs to the processor, r2 is the last row belonging to 3436 the this processor, and c1-c2 is range of indices of the local part of a 3437 vector suitable for applying the matrix to. This is an mxn matrix. In the 3438 common case of a square matrix, the row and column ranges are the same and 3439 the DIAGONAL part is also square. The remaining portion of the local 3440 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3441 3442 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3443 3444 You can call MatGetInfo() to get information on how effective the preallocation was; 3445 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3446 You can also run with the option -info and look for messages with the string 3447 malloc in them to see if additional memory allocation was needed. 3448 3449 Example usage: 3450 3451 Consider the following 8x8 matrix with 34 non-zero values, that is 3452 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3453 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3454 as follows: 3455 3456 .vb 3457 1 2 0 | 0 3 0 | 0 4 3458 Proc0 0 5 6 | 7 0 0 | 8 0 3459 9 0 10 | 11 0 0 | 12 0 3460 ------------------------------------- 3461 13 0 14 | 15 16 17 | 0 0 3462 Proc1 0 18 0 | 19 20 21 | 0 0 3463 0 0 0 | 22 23 0 | 24 0 3464 ------------------------------------- 3465 Proc2 25 26 27 | 0 0 28 | 29 0 3466 30 0 0 | 31 32 33 | 0 34 3467 .ve 3468 3469 This can be represented as a collection of submatrices as: 3470 3471 .vb 3472 A B C 3473 D E F 3474 G H I 3475 .ve 3476 3477 Where the submatrices A,B,C are owned by proc0, D,E,F are 3478 owned by proc1, G,H,I are owned by proc2. 3479 3480 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3481 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3482 The 'M','N' parameters are 8,8, and have the same values on all procs. 3483 3484 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3485 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3486 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3487 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3488 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3489 matrix, ans [DF] as another SeqAIJ matrix. 3490 3491 When d_nz, o_nz parameters are specified, d_nz storage elements are 3492 allocated for every row of the local diagonal submatrix, and o_nz 3493 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3494 One way to choose d_nz and o_nz is to use the max nonzerors per local 3495 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3496 In this case, the values of d_nz,o_nz are: 3497 .vb 3498 proc0 : dnz = 2, o_nz = 2 3499 proc1 : dnz = 3, o_nz = 2 3500 proc2 : dnz = 1, o_nz = 4 3501 .ve 3502 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3503 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3504 for proc3. i.e we are using 12+15+10=37 storage locations to store 3505 34 values. 3506 3507 When d_nnz, o_nnz parameters are specified, the storage is specified 3508 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3509 In the above case the values for d_nnz,o_nnz are: 3510 .vb 3511 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3512 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3513 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3514 .ve 3515 Here the space allocated is sum of all the above values i.e 34, and 3516 hence pre-allocation is perfect. 3517 3518 Level: intermediate 3519 3520 .keywords: matrix, aij, compressed row, sparse, parallel 3521 3522 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 3523 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 3524 @*/ 3525 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3526 { 3527 PetscErrorCode ierr; 3528 3529 PetscFunctionBegin; 3530 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3531 PetscValidType(B,1); 3532 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 3533 PetscFunctionReturn(0); 3534 } 3535 3536 /*@ 3537 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 3538 CSR format the local rows. 3539 3540 Collective on MPI_Comm 3541 3542 Input Parameters: 3543 + comm - MPI communicator 3544 . m - number of local rows (Cannot be PETSC_DECIDE) 3545 . n - This value should be the same as the local size used in creating the 3546 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3547 calculated if N is given) For square matrices n is almost always m. 3548 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3549 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3550 . i - row indices 3551 . j - column indices 3552 - a - matrix values 3553 3554 Output Parameter: 3555 . mat - the matrix 3556 3557 Level: intermediate 3558 3559 Notes: 3560 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3561 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3562 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3563 3564 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3565 3566 The format which is used for the sparse matrix input, is equivalent to a 3567 row-major ordering.. i.e for the following matrix, the input data expected is 3568 as shown 3569 3570 $ 1 0 0 3571 $ 2 0 3 P0 3572 $ ------- 3573 $ 4 5 6 P1 3574 $ 3575 $ Process0 [P0]: rows_owned=[0,1] 3576 $ i = {0,1,3} [size = nrow+1 = 2+1] 3577 $ j = {0,0,2} [size = 3] 3578 $ v = {1,2,3} [size = 3] 3579 $ 3580 $ Process1 [P1]: rows_owned=[2] 3581 $ i = {0,3} [size = nrow+1 = 1+1] 3582 $ j = {0,1,2} [size = 3] 3583 $ v = {4,5,6} [size = 3] 3584 3585 .keywords: matrix, aij, compressed row, sparse, parallel 3586 3587 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 3588 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 3589 @*/ 3590 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 3591 { 3592 PetscErrorCode ierr; 3593 3594 PetscFunctionBegin; 3595 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 3596 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 3597 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3598 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 3599 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 3600 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3601 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 3602 PetscFunctionReturn(0); 3603 } 3604 3605 /*@C 3606 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 3607 (the default parallel PETSc format). For good matrix assembly performance 3608 the user should preallocate the matrix storage by setting the parameters 3609 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3610 performance can be increased by more than a factor of 50. 3611 3612 Collective on MPI_Comm 3613 3614 Input Parameters: 3615 + comm - MPI communicator 3616 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 3617 This value should be the same as the local size used in creating the 3618 y vector for the matrix-vector product y = Ax. 3619 . n - This value should be the same as the local size used in creating the 3620 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3621 calculated if N is given) For square matrices n is almost always m. 3622 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3623 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3624 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3625 (same value is used for all local rows) 3626 . d_nnz - array containing the number of nonzeros in the various rows of the 3627 DIAGONAL portion of the local submatrix (possibly different for each row) 3628 or NULL, if d_nz is used to specify the nonzero structure. 3629 The size of this array is equal to the number of local rows, i.e 'm'. 3630 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3631 submatrix (same value is used for all local rows). 3632 - o_nnz - array containing the number of nonzeros in the various rows of the 3633 OFF-DIAGONAL portion of the local submatrix (possibly different for 3634 each row) or NULL, if o_nz is used to specify the nonzero 3635 structure. The size of this array is equal to the number 3636 of local rows, i.e 'm'. 3637 3638 Output Parameter: 3639 . A - the matrix 3640 3641 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 3642 MatXXXXSetPreallocation() paradgm instead of this routine directly. 3643 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 3644 3645 Notes: 3646 If the *_nnz parameter is given then the *_nz parameter is ignored 3647 3648 m,n,M,N parameters specify the size of the matrix, and its partitioning across 3649 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 3650 storage requirements for this matrix. 3651 3652 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 3653 processor than it must be used on all processors that share the object for 3654 that argument. 3655 3656 The user MUST specify either the local or global matrix dimensions 3657 (possibly both). 3658 3659 The parallel matrix is partitioned across processors such that the 3660 first m0 rows belong to process 0, the next m1 rows belong to 3661 process 1, the next m2 rows belong to process 2 etc.. where 3662 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 3663 values corresponding to [m x N] submatrix. 3664 3665 The columns are logically partitioned with the n0 columns belonging 3666 to 0th partition, the next n1 columns belonging to the next 3667 partition etc.. where n0,n1,n2... are the input parameter 'n'. 3668 3669 The DIAGONAL portion of the local submatrix on any given processor 3670 is the submatrix corresponding to the rows and columns m,n 3671 corresponding to the given processor. i.e diagonal matrix on 3672 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 3673 etc. The remaining portion of the local submatrix [m x (N-n)] 3674 constitute the OFF-DIAGONAL portion. The example below better 3675 illustrates this concept. 3676 3677 For a square global matrix we define each processor's diagonal portion 3678 to be its local rows and the corresponding columns (a square submatrix); 3679 each processor's off-diagonal portion encompasses the remainder of the 3680 local matrix (a rectangular submatrix). 3681 3682 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3683 3684 When calling this routine with a single process communicator, a matrix of 3685 type SEQAIJ is returned. If a matrix of type MATMPIAIJ is desired for this 3686 type of communicator, use the construction mechanism: 3687 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 3688 3689 By default, this format uses inodes (identical nodes) when possible. 3690 We search for consecutive rows with the same nonzero structure, thereby 3691 reusing matrix information to achieve increased efficiency. 3692 3693 Options Database Keys: 3694 + -mat_no_inode - Do not use inodes 3695 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 3696 - -mat_aij_oneindex - Internally use indexing starting at 1 3697 rather than 0. Note that when calling MatSetValues(), 3698 the user still MUST index entries starting at 0! 3699 3700 3701 Example usage: 3702 3703 Consider the following 8x8 matrix with 34 non-zero values, that is 3704 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3705 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3706 as follows: 3707 3708 .vb 3709 1 2 0 | 0 3 0 | 0 4 3710 Proc0 0 5 6 | 7 0 0 | 8 0 3711 9 0 10 | 11 0 0 | 12 0 3712 ------------------------------------- 3713 13 0 14 | 15 16 17 | 0 0 3714 Proc1 0 18 0 | 19 20 21 | 0 0 3715 0 0 0 | 22 23 0 | 24 0 3716 ------------------------------------- 3717 Proc2 25 26 27 | 0 0 28 | 29 0 3718 30 0 0 | 31 32 33 | 0 34 3719 .ve 3720 3721 This can be represented as a collection of submatrices as: 3722 3723 .vb 3724 A B C 3725 D E F 3726 G H I 3727 .ve 3728 3729 Where the submatrices A,B,C are owned by proc0, D,E,F are 3730 owned by proc1, G,H,I are owned by proc2. 3731 3732 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3733 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3734 The 'M','N' parameters are 8,8, and have the same values on all procs. 3735 3736 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3737 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3738 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3739 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3740 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3741 matrix, ans [DF] as another SeqAIJ matrix. 3742 3743 When d_nz, o_nz parameters are specified, d_nz storage elements are 3744 allocated for every row of the local diagonal submatrix, and o_nz 3745 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3746 One way to choose d_nz and o_nz is to use the max nonzerors per local 3747 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3748 In this case, the values of d_nz,o_nz are: 3749 .vb 3750 proc0 : dnz = 2, o_nz = 2 3751 proc1 : dnz = 3, o_nz = 2 3752 proc2 : dnz = 1, o_nz = 4 3753 .ve 3754 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3755 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3756 for proc3. i.e we are using 12+15+10=37 storage locations to store 3757 34 values. 3758 3759 When d_nnz, o_nnz parameters are specified, the storage is specified 3760 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3761 In the above case the values for d_nnz,o_nnz are: 3762 .vb 3763 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3764 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3765 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3766 .ve 3767 Here the space allocated is sum of all the above values i.e 34, and 3768 hence pre-allocation is perfect. 3769 3770 Level: intermediate 3771 3772 .keywords: matrix, aij, compressed row, sparse, parallel 3773 3774 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 3775 MATMPIAIJ, MatCreateMPIAIJWithArrays() 3776 @*/ 3777 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) 3778 { 3779 PetscErrorCode ierr; 3780 PetscMPIInt size; 3781 3782 PetscFunctionBegin; 3783 ierr = MatCreate(comm,A);CHKERRQ(ierr); 3784 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 3785 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3786 if (size > 1) { 3787 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 3788 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 3789 } else { 3790 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 3791 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 3792 } 3793 PetscFunctionReturn(0); 3794 } 3795 3796 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 3797 { 3798 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 3799 PetscBool flg; 3800 PetscErrorCode ierr; 3801 3802 PetscFunctionBegin; 3803 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 3804 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 3805 if (Ad) *Ad = a->A; 3806 if (Ao) *Ao = a->B; 3807 if (colmap) *colmap = a->garray; 3808 PetscFunctionReturn(0); 3809 } 3810 3811 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 3812 { 3813 PetscErrorCode ierr; 3814 PetscInt m,N,i,rstart,nnz,Ii; 3815 PetscInt *indx; 3816 PetscScalar *values; 3817 3818 PetscFunctionBegin; 3819 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 3820 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 3821 PetscInt *dnz,*onz,sum,bs,cbs; 3822 3823 if (n == PETSC_DECIDE) { 3824 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 3825 } 3826 /* Check sum(n) = N */ 3827 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3828 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 3829 3830 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3831 rstart -= m; 3832 3833 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 3834 for (i=0; i<m; i++) { 3835 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 3836 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 3837 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 3838 } 3839 3840 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 3841 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 3842 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 3843 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 3844 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 3845 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 3846 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 3847 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 3848 } 3849 3850 /* numeric phase */ 3851 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 3852 for (i=0; i<m; i++) { 3853 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 3854 Ii = i + rstart; 3855 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 3856 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 3857 } 3858 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3859 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3860 PetscFunctionReturn(0); 3861 } 3862 3863 PetscErrorCode MatFileSplit(Mat A,char *outfile) 3864 { 3865 PetscErrorCode ierr; 3866 PetscMPIInt rank; 3867 PetscInt m,N,i,rstart,nnz; 3868 size_t len; 3869 const PetscInt *indx; 3870 PetscViewer out; 3871 char *name; 3872 Mat B; 3873 const PetscScalar *values; 3874 3875 PetscFunctionBegin; 3876 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 3877 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 3878 /* Should this be the type of the diagonal block of A? */ 3879 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 3880 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 3881 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 3882 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 3883 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 3884 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 3885 for (i=0; i<m; i++) { 3886 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 3887 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 3888 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 3889 } 3890 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3891 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3892 3893 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 3894 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 3895 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 3896 sprintf(name,"%s.%d",outfile,rank); 3897 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 3898 ierr = PetscFree(name);CHKERRQ(ierr); 3899 ierr = MatView(B,out);CHKERRQ(ierr); 3900 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 3901 ierr = MatDestroy(&B);CHKERRQ(ierr); 3902 PetscFunctionReturn(0); 3903 } 3904 3905 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 3906 { 3907 PetscErrorCode ierr; 3908 Mat_Merge_SeqsToMPI *merge; 3909 PetscContainer container; 3910 3911 PetscFunctionBegin; 3912 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 3913 if (container) { 3914 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 3915 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 3916 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 3917 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 3918 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 3919 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 3920 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 3921 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 3922 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 3923 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 3924 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 3925 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 3926 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 3927 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 3928 ierr = PetscFree(merge);CHKERRQ(ierr); 3929 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 3930 } 3931 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 3932 PetscFunctionReturn(0); 3933 } 3934 3935 #include <../src/mat/utils/freespace.h> 3936 #include <petscbt.h> 3937 3938 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 3939 { 3940 PetscErrorCode ierr; 3941 MPI_Comm comm; 3942 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 3943 PetscMPIInt size,rank,taga,*len_s; 3944 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 3945 PetscInt proc,m; 3946 PetscInt **buf_ri,**buf_rj; 3947 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 3948 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 3949 MPI_Request *s_waits,*r_waits; 3950 MPI_Status *status; 3951 MatScalar *aa=a->a; 3952 MatScalar **abuf_r,*ba_i; 3953 Mat_Merge_SeqsToMPI *merge; 3954 PetscContainer container; 3955 3956 PetscFunctionBegin; 3957 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 3958 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 3959 3960 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3961 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3962 3963 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 3964 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 3965 3966 bi = merge->bi; 3967 bj = merge->bj; 3968 buf_ri = merge->buf_ri; 3969 buf_rj = merge->buf_rj; 3970 3971 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 3972 owners = merge->rowmap->range; 3973 len_s = merge->len_s; 3974 3975 /* send and recv matrix values */ 3976 /*-----------------------------*/ 3977 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 3978 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 3979 3980 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 3981 for (proc=0,k=0; proc<size; proc++) { 3982 if (!len_s[proc]) continue; 3983 i = owners[proc]; 3984 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 3985 k++; 3986 } 3987 3988 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 3989 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 3990 ierr = PetscFree(status);CHKERRQ(ierr); 3991 3992 ierr = PetscFree(s_waits);CHKERRQ(ierr); 3993 ierr = PetscFree(r_waits);CHKERRQ(ierr); 3994 3995 /* insert mat values of mpimat */ 3996 /*----------------------------*/ 3997 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 3998 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 3999 4000 for (k=0; k<merge->nrecv; k++) { 4001 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4002 nrows = *(buf_ri_k[k]); 4003 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4004 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4005 } 4006 4007 /* set values of ba */ 4008 m = merge->rowmap->n; 4009 for (i=0; i<m; i++) { 4010 arow = owners[rank] + i; 4011 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4012 bnzi = bi[i+1] - bi[i]; 4013 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4014 4015 /* add local non-zero vals of this proc's seqmat into ba */ 4016 anzi = ai[arow+1] - ai[arow]; 4017 aj = a->j + ai[arow]; 4018 aa = a->a + ai[arow]; 4019 nextaj = 0; 4020 for (j=0; nextaj<anzi; j++) { 4021 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4022 ba_i[j] += aa[nextaj++]; 4023 } 4024 } 4025 4026 /* add received vals into ba */ 4027 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4028 /* i-th row */ 4029 if (i == *nextrow[k]) { 4030 anzi = *(nextai[k]+1) - *nextai[k]; 4031 aj = buf_rj[k] + *(nextai[k]); 4032 aa = abuf_r[k] + *(nextai[k]); 4033 nextaj = 0; 4034 for (j=0; nextaj<anzi; j++) { 4035 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4036 ba_i[j] += aa[nextaj++]; 4037 } 4038 } 4039 nextrow[k]++; nextai[k]++; 4040 } 4041 } 4042 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4043 } 4044 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4045 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4046 4047 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4048 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4049 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4050 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4051 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4052 PetscFunctionReturn(0); 4053 } 4054 4055 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4056 { 4057 PetscErrorCode ierr; 4058 Mat B_mpi; 4059 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4060 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4061 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4062 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4063 PetscInt len,proc,*dnz,*onz,bs,cbs; 4064 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4065 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4066 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4067 MPI_Status *status; 4068 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4069 PetscBT lnkbt; 4070 Mat_Merge_SeqsToMPI *merge; 4071 PetscContainer container; 4072 4073 PetscFunctionBegin; 4074 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4075 4076 /* make sure it is a PETSc comm */ 4077 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4078 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4079 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4080 4081 ierr = PetscNew(&merge);CHKERRQ(ierr); 4082 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4083 4084 /* determine row ownership */ 4085 /*---------------------------------------------------------*/ 4086 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4087 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4088 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4089 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4090 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4091 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4092 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4093 4094 m = merge->rowmap->n; 4095 owners = merge->rowmap->range; 4096 4097 /* determine the number of messages to send, their lengths */ 4098 /*---------------------------------------------------------*/ 4099 len_s = merge->len_s; 4100 4101 len = 0; /* length of buf_si[] */ 4102 merge->nsend = 0; 4103 for (proc=0; proc<size; proc++) { 4104 len_si[proc] = 0; 4105 if (proc == rank) { 4106 len_s[proc] = 0; 4107 } else { 4108 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4109 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4110 } 4111 if (len_s[proc]) { 4112 merge->nsend++; 4113 nrows = 0; 4114 for (i=owners[proc]; i<owners[proc+1]; i++) { 4115 if (ai[i+1] > ai[i]) nrows++; 4116 } 4117 len_si[proc] = 2*(nrows+1); 4118 len += len_si[proc]; 4119 } 4120 } 4121 4122 /* determine the number and length of messages to receive for ij-structure */ 4123 /*-------------------------------------------------------------------------*/ 4124 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4125 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4126 4127 /* post the Irecv of j-structure */ 4128 /*-------------------------------*/ 4129 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4130 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4131 4132 /* post the Isend of j-structure */ 4133 /*--------------------------------*/ 4134 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4135 4136 for (proc=0, k=0; proc<size; proc++) { 4137 if (!len_s[proc]) continue; 4138 i = owners[proc]; 4139 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4140 k++; 4141 } 4142 4143 /* receives and sends of j-structure are complete */ 4144 /*------------------------------------------------*/ 4145 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4146 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4147 4148 /* send and recv i-structure */ 4149 /*---------------------------*/ 4150 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4151 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4152 4153 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4154 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4155 for (proc=0,k=0; proc<size; proc++) { 4156 if (!len_s[proc]) continue; 4157 /* form outgoing message for i-structure: 4158 buf_si[0]: nrows to be sent 4159 [1:nrows]: row index (global) 4160 [nrows+1:2*nrows+1]: i-structure index 4161 */ 4162 /*-------------------------------------------*/ 4163 nrows = len_si[proc]/2 - 1; 4164 buf_si_i = buf_si + nrows+1; 4165 buf_si[0] = nrows; 4166 buf_si_i[0] = 0; 4167 nrows = 0; 4168 for (i=owners[proc]; i<owners[proc+1]; i++) { 4169 anzi = ai[i+1] - ai[i]; 4170 if (anzi) { 4171 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4172 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4173 nrows++; 4174 } 4175 } 4176 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4177 k++; 4178 buf_si += len_si[proc]; 4179 } 4180 4181 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4182 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4183 4184 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4185 for (i=0; i<merge->nrecv; i++) { 4186 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); 4187 } 4188 4189 ierr = PetscFree(len_si);CHKERRQ(ierr); 4190 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4191 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4192 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4193 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4194 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4195 ierr = PetscFree(status);CHKERRQ(ierr); 4196 4197 /* compute a local seq matrix in each processor */ 4198 /*----------------------------------------------*/ 4199 /* allocate bi array and free space for accumulating nonzero column info */ 4200 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4201 bi[0] = 0; 4202 4203 /* create and initialize a linked list */ 4204 nlnk = N+1; 4205 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4206 4207 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4208 len = ai[owners[rank+1]] - ai[owners[rank]]; 4209 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4210 4211 current_space = free_space; 4212 4213 /* determine symbolic info for each local row */ 4214 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4215 4216 for (k=0; k<merge->nrecv; k++) { 4217 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4218 nrows = *buf_ri_k[k]; 4219 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4220 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4221 } 4222 4223 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4224 len = 0; 4225 for (i=0; i<m; i++) { 4226 bnzi = 0; 4227 /* add local non-zero cols of this proc's seqmat into lnk */ 4228 arow = owners[rank] + i; 4229 anzi = ai[arow+1] - ai[arow]; 4230 aj = a->j + ai[arow]; 4231 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4232 bnzi += nlnk; 4233 /* add received col data into lnk */ 4234 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4235 if (i == *nextrow[k]) { /* i-th row */ 4236 anzi = *(nextai[k]+1) - *nextai[k]; 4237 aj = buf_rj[k] + *nextai[k]; 4238 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4239 bnzi += nlnk; 4240 nextrow[k]++; nextai[k]++; 4241 } 4242 } 4243 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4244 4245 /* if free space is not available, make more free space */ 4246 if (current_space->local_remaining<bnzi) { 4247 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4248 nspacedouble++; 4249 } 4250 /* copy data into free space, then initialize lnk */ 4251 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4252 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4253 4254 current_space->array += bnzi; 4255 current_space->local_used += bnzi; 4256 current_space->local_remaining -= bnzi; 4257 4258 bi[i+1] = bi[i] + bnzi; 4259 } 4260 4261 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4262 4263 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4264 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4265 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4266 4267 /* create symbolic parallel matrix B_mpi */ 4268 /*---------------------------------------*/ 4269 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4270 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4271 if (n==PETSC_DECIDE) { 4272 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4273 } else { 4274 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4275 } 4276 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4277 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4278 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4279 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4280 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4281 4282 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4283 B_mpi->assembled = PETSC_FALSE; 4284 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4285 merge->bi = bi; 4286 merge->bj = bj; 4287 merge->buf_ri = buf_ri; 4288 merge->buf_rj = buf_rj; 4289 merge->coi = NULL; 4290 merge->coj = NULL; 4291 merge->owners_co = NULL; 4292 4293 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4294 4295 /* attach the supporting struct to B_mpi for reuse */ 4296 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4297 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4298 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4299 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4300 *mpimat = B_mpi; 4301 4302 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4303 PetscFunctionReturn(0); 4304 } 4305 4306 /*@C 4307 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4308 matrices from each processor 4309 4310 Collective on MPI_Comm 4311 4312 Input Parameters: 4313 + comm - the communicators the parallel matrix will live on 4314 . seqmat - the input sequential matrices 4315 . m - number of local rows (or PETSC_DECIDE) 4316 . n - number of local columns (or PETSC_DECIDE) 4317 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4318 4319 Output Parameter: 4320 . mpimat - the parallel matrix generated 4321 4322 Level: advanced 4323 4324 Notes: 4325 The dimensions of the sequential matrix in each processor MUST be the same. 4326 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4327 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4328 @*/ 4329 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4330 { 4331 PetscErrorCode ierr; 4332 PetscMPIInt size; 4333 4334 PetscFunctionBegin; 4335 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4336 if (size == 1) { 4337 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4338 if (scall == MAT_INITIAL_MATRIX) { 4339 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4340 } else { 4341 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4342 } 4343 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4344 PetscFunctionReturn(0); 4345 } 4346 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4347 if (scall == MAT_INITIAL_MATRIX) { 4348 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4349 } 4350 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4351 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4352 PetscFunctionReturn(0); 4353 } 4354 4355 /*@ 4356 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 4357 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4358 with MatGetSize() 4359 4360 Not Collective 4361 4362 Input Parameters: 4363 + A - the matrix 4364 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4365 4366 Output Parameter: 4367 . A_loc - the local sequential matrix generated 4368 4369 Level: developer 4370 4371 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4372 4373 @*/ 4374 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4375 { 4376 PetscErrorCode ierr; 4377 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4378 Mat_SeqAIJ *mat,*a,*b; 4379 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4380 MatScalar *aa,*ba,*cam; 4381 PetscScalar *ca; 4382 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4383 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4384 PetscBool match; 4385 MPI_Comm comm; 4386 PetscMPIInt size; 4387 4388 PetscFunctionBegin; 4389 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4390 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4391 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4392 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4393 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4394 4395 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4396 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4397 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4398 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4399 aa = a->a; ba = b->a; 4400 if (scall == MAT_INITIAL_MATRIX) { 4401 if (size == 1) { 4402 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4403 PetscFunctionReturn(0); 4404 } 4405 4406 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4407 ci[0] = 0; 4408 for (i=0; i<am; i++) { 4409 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4410 } 4411 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4412 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4413 k = 0; 4414 for (i=0; i<am; i++) { 4415 ncols_o = bi[i+1] - bi[i]; 4416 ncols_d = ai[i+1] - ai[i]; 4417 /* off-diagonal portion of A */ 4418 for (jo=0; jo<ncols_o; jo++) { 4419 col = cmap[*bj]; 4420 if (col >= cstart) break; 4421 cj[k] = col; bj++; 4422 ca[k++] = *ba++; 4423 } 4424 /* diagonal portion of A */ 4425 for (j=0; j<ncols_d; j++) { 4426 cj[k] = cstart + *aj++; 4427 ca[k++] = *aa++; 4428 } 4429 /* off-diagonal portion of A */ 4430 for (j=jo; j<ncols_o; j++) { 4431 cj[k] = cmap[*bj++]; 4432 ca[k++] = *ba++; 4433 } 4434 } 4435 /* put together the new matrix */ 4436 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4437 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4438 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4439 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4440 mat->free_a = PETSC_TRUE; 4441 mat->free_ij = PETSC_TRUE; 4442 mat->nonew = 0; 4443 } else if (scall == MAT_REUSE_MATRIX) { 4444 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4445 ci = mat->i; cj = mat->j; cam = mat->a; 4446 for (i=0; i<am; i++) { 4447 /* off-diagonal portion of A */ 4448 ncols_o = bi[i+1] - bi[i]; 4449 for (jo=0; jo<ncols_o; jo++) { 4450 col = cmap[*bj]; 4451 if (col >= cstart) break; 4452 *cam++ = *ba++; bj++; 4453 } 4454 /* diagonal portion of A */ 4455 ncols_d = ai[i+1] - ai[i]; 4456 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4457 /* off-diagonal portion of A */ 4458 for (j=jo; j<ncols_o; j++) { 4459 *cam++ = *ba++; bj++; 4460 } 4461 } 4462 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4463 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4464 PetscFunctionReturn(0); 4465 } 4466 4467 /*@C 4468 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4469 4470 Not Collective 4471 4472 Input Parameters: 4473 + A - the matrix 4474 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4475 - row, col - index sets of rows and columns to extract (or NULL) 4476 4477 Output Parameter: 4478 . A_loc - the local sequential matrix generated 4479 4480 Level: developer 4481 4482 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4483 4484 @*/ 4485 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4486 { 4487 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4488 PetscErrorCode ierr; 4489 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4490 IS isrowa,iscola; 4491 Mat *aloc; 4492 PetscBool match; 4493 4494 PetscFunctionBegin; 4495 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4496 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4497 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4498 if (!row) { 4499 start = A->rmap->rstart; end = A->rmap->rend; 4500 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 4501 } else { 4502 isrowa = *row; 4503 } 4504 if (!col) { 4505 start = A->cmap->rstart; 4506 cmap = a->garray; 4507 nzA = a->A->cmap->n; 4508 nzB = a->B->cmap->n; 4509 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4510 ncols = 0; 4511 for (i=0; i<nzB; i++) { 4512 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4513 else break; 4514 } 4515 imark = i; 4516 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 4517 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 4518 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 4519 } else { 4520 iscola = *col; 4521 } 4522 if (scall != MAT_INITIAL_MATRIX) { 4523 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 4524 aloc[0] = *A_loc; 4525 } 4526 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 4527 *A_loc = aloc[0]; 4528 ierr = PetscFree(aloc);CHKERRQ(ierr); 4529 if (!row) { 4530 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 4531 } 4532 if (!col) { 4533 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 4534 } 4535 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4536 PetscFunctionReturn(0); 4537 } 4538 4539 /*@C 4540 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 4541 4542 Collective on Mat 4543 4544 Input Parameters: 4545 + A,B - the matrices in mpiaij format 4546 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4547 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 4548 4549 Output Parameter: 4550 + rowb, colb - index sets of rows and columns of B to extract 4551 - B_seq - the sequential matrix generated 4552 4553 Level: developer 4554 4555 @*/ 4556 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 4557 { 4558 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4559 PetscErrorCode ierr; 4560 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 4561 IS isrowb,iscolb; 4562 Mat *bseq=NULL; 4563 4564 PetscFunctionBegin; 4565 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 4566 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); 4567 } 4568 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 4569 4570 if (scall == MAT_INITIAL_MATRIX) { 4571 start = A->cmap->rstart; 4572 cmap = a->garray; 4573 nzA = a->A->cmap->n; 4574 nzB = a->B->cmap->n; 4575 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4576 ncols = 0; 4577 for (i=0; i<nzB; i++) { /* row < local row index */ 4578 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4579 else break; 4580 } 4581 imark = i; 4582 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 4583 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 4584 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 4585 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 4586 } else { 4587 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 4588 isrowb = *rowb; iscolb = *colb; 4589 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 4590 bseq[0] = *B_seq; 4591 } 4592 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 4593 *B_seq = bseq[0]; 4594 ierr = PetscFree(bseq);CHKERRQ(ierr); 4595 if (!rowb) { 4596 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 4597 } else { 4598 *rowb = isrowb; 4599 } 4600 if (!colb) { 4601 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 4602 } else { 4603 *colb = iscolb; 4604 } 4605 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 4606 PetscFunctionReturn(0); 4607 } 4608 4609 /* 4610 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 4611 of the OFF-DIAGONAL portion of local A 4612 4613 Collective on Mat 4614 4615 Input Parameters: 4616 + A,B - the matrices in mpiaij format 4617 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4618 4619 Output Parameter: 4620 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 4621 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 4622 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 4623 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 4624 4625 Level: developer 4626 4627 */ 4628 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 4629 { 4630 VecScatter_MPI_General *gen_to,*gen_from; 4631 PetscErrorCode ierr; 4632 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4633 Mat_SeqAIJ *b_oth; 4634 VecScatter ctx =a->Mvctx; 4635 MPI_Comm comm; 4636 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 4637 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 4638 PetscInt *rvalues,*svalues; 4639 MatScalar *b_otha,*bufa,*bufA; 4640 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 4641 MPI_Request *rwaits = NULL,*swaits = NULL; 4642 MPI_Status *sstatus,rstatus; 4643 PetscMPIInt jj,size; 4644 PetscInt *cols,sbs,rbs; 4645 PetscScalar *vals; 4646 4647 PetscFunctionBegin; 4648 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4649 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4650 4651 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 4652 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); 4653 } 4654 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 4655 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4656 4657 if (size == 1) { 4658 startsj_s = NULL; 4659 bufa_ptr = NULL; 4660 *B_oth = NULL; 4661 PetscFunctionReturn(0); 4662 } 4663 4664 gen_to = (VecScatter_MPI_General*)ctx->todata; 4665 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 4666 nrecvs = gen_from->n; 4667 nsends = gen_to->n; 4668 4669 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 4670 srow = gen_to->indices; /* local row index to be sent */ 4671 sstarts = gen_to->starts; 4672 sprocs = gen_to->procs; 4673 sstatus = gen_to->sstatus; 4674 sbs = gen_to->bs; 4675 rstarts = gen_from->starts; 4676 rprocs = gen_from->procs; 4677 rbs = gen_from->bs; 4678 4679 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 4680 if (scall == MAT_INITIAL_MATRIX) { 4681 /* i-array */ 4682 /*---------*/ 4683 /* post receives */ 4684 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 4685 for (i=0; i<nrecvs; i++) { 4686 rowlen = rvalues + rstarts[i]*rbs; 4687 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 4688 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 4689 } 4690 4691 /* pack the outgoing message */ 4692 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 4693 4694 sstartsj[0] = 0; 4695 rstartsj[0] = 0; 4696 len = 0; /* total length of j or a array to be sent */ 4697 k = 0; 4698 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 4699 for (i=0; i<nsends; i++) { 4700 rowlen = svalues + sstarts[i]*sbs; 4701 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 4702 for (j=0; j<nrows; j++) { 4703 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 4704 for (l=0; l<sbs; l++) { 4705 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 4706 4707 rowlen[j*sbs+l] = ncols; 4708 4709 len += ncols; 4710 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 4711 } 4712 k++; 4713 } 4714 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 4715 4716 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 4717 } 4718 /* recvs and sends of i-array are completed */ 4719 i = nrecvs; 4720 while (i--) { 4721 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 4722 } 4723 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 4724 ierr = PetscFree(svalues);CHKERRQ(ierr); 4725 4726 /* allocate buffers for sending j and a arrays */ 4727 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 4728 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 4729 4730 /* create i-array of B_oth */ 4731 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 4732 4733 b_othi[0] = 0; 4734 len = 0; /* total length of j or a array to be received */ 4735 k = 0; 4736 for (i=0; i<nrecvs; i++) { 4737 rowlen = rvalues + rstarts[i]*rbs; 4738 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 4739 for (j=0; j<nrows; j++) { 4740 b_othi[k+1] = b_othi[k] + rowlen[j]; 4741 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 4742 k++; 4743 } 4744 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 4745 } 4746 ierr = PetscFree(rvalues);CHKERRQ(ierr); 4747 4748 /* allocate space for j and a arrrays of B_oth */ 4749 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 4750 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 4751 4752 /* j-array */ 4753 /*---------*/ 4754 /* post receives of j-array */ 4755 for (i=0; i<nrecvs; i++) { 4756 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 4757 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 4758 } 4759 4760 /* pack the outgoing message j-array */ 4761 k = 0; 4762 for (i=0; i<nsends; i++) { 4763 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 4764 bufJ = bufj+sstartsj[i]; 4765 for (j=0; j<nrows; j++) { 4766 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 4767 for (ll=0; ll<sbs; ll++) { 4768 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 4769 for (l=0; l<ncols; l++) { 4770 *bufJ++ = cols[l]; 4771 } 4772 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 4773 } 4774 } 4775 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 4776 } 4777 4778 /* recvs and sends of j-array are completed */ 4779 i = nrecvs; 4780 while (i--) { 4781 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 4782 } 4783 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 4784 } else if (scall == MAT_REUSE_MATRIX) { 4785 sstartsj = *startsj_s; 4786 rstartsj = *startsj_r; 4787 bufa = *bufa_ptr; 4788 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 4789 b_otha = b_oth->a; 4790 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 4791 4792 /* a-array */ 4793 /*---------*/ 4794 /* post receives of a-array */ 4795 for (i=0; i<nrecvs; i++) { 4796 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 4797 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 4798 } 4799 4800 /* pack the outgoing message a-array */ 4801 k = 0; 4802 for (i=0; i<nsends; i++) { 4803 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 4804 bufA = bufa+sstartsj[i]; 4805 for (j=0; j<nrows; j++) { 4806 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 4807 for (ll=0; ll<sbs; ll++) { 4808 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 4809 for (l=0; l<ncols; l++) { 4810 *bufA++ = vals[l]; 4811 } 4812 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 4813 } 4814 } 4815 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 4816 } 4817 /* recvs and sends of a-array are completed */ 4818 i = nrecvs; 4819 while (i--) { 4820 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 4821 } 4822 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 4823 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 4824 4825 if (scall == MAT_INITIAL_MATRIX) { 4826 /* put together the new matrix */ 4827 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 4828 4829 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4830 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4831 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 4832 b_oth->free_a = PETSC_TRUE; 4833 b_oth->free_ij = PETSC_TRUE; 4834 b_oth->nonew = 0; 4835 4836 ierr = PetscFree(bufj);CHKERRQ(ierr); 4837 if (!startsj_s || !bufa_ptr) { 4838 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 4839 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 4840 } else { 4841 *startsj_s = sstartsj; 4842 *startsj_r = rstartsj; 4843 *bufa_ptr = bufa; 4844 } 4845 } 4846 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 4847 PetscFunctionReturn(0); 4848 } 4849 4850 /*@C 4851 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 4852 4853 Not Collective 4854 4855 Input Parameters: 4856 . A - The matrix in mpiaij format 4857 4858 Output Parameter: 4859 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 4860 . colmap - A map from global column index to local index into lvec 4861 - multScatter - A scatter from the argument of a matrix-vector product to lvec 4862 4863 Level: developer 4864 4865 @*/ 4866 #if defined(PETSC_USE_CTABLE) 4867 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 4868 #else 4869 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 4870 #endif 4871 { 4872 Mat_MPIAIJ *a; 4873 4874 PetscFunctionBegin; 4875 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 4876 PetscValidPointer(lvec, 2); 4877 PetscValidPointer(colmap, 3); 4878 PetscValidPointer(multScatter, 4); 4879 a = (Mat_MPIAIJ*) A->data; 4880 if (lvec) *lvec = a->lvec; 4881 if (colmap) *colmap = a->colmap; 4882 if (multScatter) *multScatter = a->Mvctx; 4883 PetscFunctionReturn(0); 4884 } 4885 4886 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 4887 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 4888 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 4889 #if defined(PETSC_HAVE_ELEMENTAL) 4890 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 4891 #endif 4892 #if defined(PETSC_HAVE_HYPRE) 4893 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 4894 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 4895 #endif 4896 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 4897 4898 /* 4899 Computes (B'*A')' since computing B*A directly is untenable 4900 4901 n p p 4902 ( ) ( ) ( ) 4903 m ( A ) * n ( B ) = m ( C ) 4904 ( ) ( ) ( ) 4905 4906 */ 4907 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 4908 { 4909 PetscErrorCode ierr; 4910 Mat At,Bt,Ct; 4911 4912 PetscFunctionBegin; 4913 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 4914 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 4915 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 4916 ierr = MatDestroy(&At);CHKERRQ(ierr); 4917 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 4918 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 4919 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 4920 PetscFunctionReturn(0); 4921 } 4922 4923 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 4924 { 4925 PetscErrorCode ierr; 4926 PetscInt m=A->rmap->n,n=B->cmap->n; 4927 Mat Cmat; 4928 4929 PetscFunctionBegin; 4930 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); 4931 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 4932 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4933 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 4934 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 4935 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 4936 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4937 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4938 4939 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 4940 4941 *C = Cmat; 4942 PetscFunctionReturn(0); 4943 } 4944 4945 /* ----------------------------------------------------------------*/ 4946 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 4947 { 4948 PetscErrorCode ierr; 4949 4950 PetscFunctionBegin; 4951 if (scall == MAT_INITIAL_MATRIX) { 4952 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 4953 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 4954 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 4955 } 4956 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 4957 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 4958 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 4959 PetscFunctionReturn(0); 4960 } 4961 4962 /*MC 4963 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 4964 4965 Options Database Keys: 4966 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 4967 4968 Level: beginner 4969 4970 .seealso: MatCreateAIJ() 4971 M*/ 4972 4973 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 4974 { 4975 Mat_MPIAIJ *b; 4976 PetscErrorCode ierr; 4977 PetscMPIInt size; 4978 4979 PetscFunctionBegin; 4980 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 4981 4982 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 4983 B->data = (void*)b; 4984 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 4985 B->assembled = PETSC_FALSE; 4986 B->insertmode = NOT_SET_VALUES; 4987 b->size = size; 4988 4989 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 4990 4991 /* build cache for off array entries formed */ 4992 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 4993 4994 b->donotstash = PETSC_FALSE; 4995 b->colmap = 0; 4996 b->garray = 0; 4997 b->roworiented = PETSC_TRUE; 4998 4999 /* stuff used for matrix vector multiply */ 5000 b->lvec = NULL; 5001 b->Mvctx = NULL; 5002 5003 /* stuff for MatGetRow() */ 5004 b->rowindices = 0; 5005 b->rowvalues = 0; 5006 b->getrowactive = PETSC_FALSE; 5007 5008 /* flexible pointer used in CUSP/CUSPARSE classes */ 5009 b->spptr = NULL; 5010 5011 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5012 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5013 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5014 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5015 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5016 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5017 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5018 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5019 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5020 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5021 #if defined(PETSC_HAVE_ELEMENTAL) 5022 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5023 #endif 5024 #if defined(PETSC_HAVE_HYPRE) 5025 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5026 #endif 5027 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5028 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5029 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5030 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5031 #if defined(PETSC_HAVE_HYPRE) 5032 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5033 #endif 5034 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5035 PetscFunctionReturn(0); 5036 } 5037 5038 /*@C 5039 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5040 and "off-diagonal" part of the matrix in CSR format. 5041 5042 Collective on MPI_Comm 5043 5044 Input Parameters: 5045 + comm - MPI communicator 5046 . m - number of local rows (Cannot be PETSC_DECIDE) 5047 . n - This value should be the same as the local size used in creating the 5048 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5049 calculated if N is given) For square matrices n is almost always m. 5050 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5051 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5052 . i - row indices for "diagonal" portion of matrix 5053 . j - column indices 5054 . a - matrix values 5055 . oi - row indices for "off-diagonal" portion of matrix 5056 . oj - column indices 5057 - oa - matrix values 5058 5059 Output Parameter: 5060 . mat - the matrix 5061 5062 Level: advanced 5063 5064 Notes: 5065 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5066 must free the arrays once the matrix has been destroyed and not before. 5067 5068 The i and j indices are 0 based 5069 5070 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5071 5072 This sets local rows and cannot be used to set off-processor values. 5073 5074 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5075 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5076 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5077 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5078 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5079 communication if it is known that only local entries will be set. 5080 5081 .keywords: matrix, aij, compressed row, sparse, parallel 5082 5083 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5084 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5085 @*/ 5086 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) 5087 { 5088 PetscErrorCode ierr; 5089 Mat_MPIAIJ *maij; 5090 5091 PetscFunctionBegin; 5092 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5093 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5094 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5095 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5096 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5097 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5098 maij = (Mat_MPIAIJ*) (*mat)->data; 5099 5100 (*mat)->preallocated = PETSC_TRUE; 5101 5102 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5103 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5104 5105 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5106 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5107 5108 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5109 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5110 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5111 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5112 5113 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5114 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5115 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5116 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5117 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5118 PetscFunctionReturn(0); 5119 } 5120 5121 /* 5122 Special version for direct calls from Fortran 5123 */ 5124 #include <petsc/private/fortranimpl.h> 5125 5126 /* Change these macros so can be used in void function */ 5127 #undef CHKERRQ 5128 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5129 #undef SETERRQ2 5130 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5131 #undef SETERRQ3 5132 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5133 #undef SETERRQ 5134 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5135 5136 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5137 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5138 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5139 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5140 #else 5141 #endif 5142 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) 5143 { 5144 Mat mat = *mmat; 5145 PetscInt m = *mm, n = *mn; 5146 InsertMode addv = *maddv; 5147 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5148 PetscScalar value; 5149 PetscErrorCode ierr; 5150 5151 MatCheckPreallocated(mat,1); 5152 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5153 5154 #if defined(PETSC_USE_DEBUG) 5155 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5156 #endif 5157 { 5158 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5159 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5160 PetscBool roworiented = aij->roworiented; 5161 5162 /* Some Variables required in the macro */ 5163 Mat A = aij->A; 5164 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5165 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5166 MatScalar *aa = a->a; 5167 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5168 Mat B = aij->B; 5169 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5170 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5171 MatScalar *ba = b->a; 5172 5173 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5174 PetscInt nonew = a->nonew; 5175 MatScalar *ap1,*ap2; 5176 5177 PetscFunctionBegin; 5178 for (i=0; i<m; i++) { 5179 if (im[i] < 0) continue; 5180 #if defined(PETSC_USE_DEBUG) 5181 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); 5182 #endif 5183 if (im[i] >= rstart && im[i] < rend) { 5184 row = im[i] - rstart; 5185 lastcol1 = -1; 5186 rp1 = aj + ai[row]; 5187 ap1 = aa + ai[row]; 5188 rmax1 = aimax[row]; 5189 nrow1 = ailen[row]; 5190 low1 = 0; 5191 high1 = nrow1; 5192 lastcol2 = -1; 5193 rp2 = bj + bi[row]; 5194 ap2 = ba + bi[row]; 5195 rmax2 = bimax[row]; 5196 nrow2 = bilen[row]; 5197 low2 = 0; 5198 high2 = nrow2; 5199 5200 for (j=0; j<n; j++) { 5201 if (roworiented) value = v[i*n+j]; 5202 else value = v[i+j*m]; 5203 if (in[j] >= cstart && in[j] < cend) { 5204 col = in[j] - cstart; 5205 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5206 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5207 } else if (in[j] < 0) continue; 5208 #if defined(PETSC_USE_DEBUG) 5209 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); 5210 #endif 5211 else { 5212 if (mat->was_assembled) { 5213 if (!aij->colmap) { 5214 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5215 } 5216 #if defined(PETSC_USE_CTABLE) 5217 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5218 col--; 5219 #else 5220 col = aij->colmap[in[j]] - 1; 5221 #endif 5222 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5223 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5224 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5225 col = in[j]; 5226 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5227 B = aij->B; 5228 b = (Mat_SeqAIJ*)B->data; 5229 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5230 rp2 = bj + bi[row]; 5231 ap2 = ba + bi[row]; 5232 rmax2 = bimax[row]; 5233 nrow2 = bilen[row]; 5234 low2 = 0; 5235 high2 = nrow2; 5236 bm = aij->B->rmap->n; 5237 ba = b->a; 5238 } 5239 } else col = in[j]; 5240 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5241 } 5242 } 5243 } else if (!aij->donotstash) { 5244 if (roworiented) { 5245 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5246 } else { 5247 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5248 } 5249 } 5250 } 5251 } 5252 PetscFunctionReturnVoid(); 5253 } 5254 5255