1 2 3 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 4 #include <petsc/private/vecimpl.h> 5 #include <petsc/private/isimpl.h> 6 #include <petscblaslapack.h> 7 #include <petscsf.h> 8 9 /*MC 10 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 11 12 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 13 and MATMPIAIJ otherwise. As a result, for single process communicators, 14 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 15 for communicators controlling multiple processes. It is recommended that you call both of 16 the above preallocation routines for simplicity. 17 18 Options Database Keys: 19 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 20 21 Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when 22 enough exist. 23 24 Level: beginner 25 26 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ, MATMPIAIJ 27 M*/ 28 29 /*MC 30 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 31 32 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 33 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 34 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 35 for communicators controlling multiple processes. It is recommended that you call both of 36 the above preallocation routines for simplicity. 37 38 Options Database Keys: 39 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 40 41 Level: beginner 42 43 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 44 M*/ 45 46 PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 50 51 PetscFunctionBegin; 52 if (mat->A) { 53 ierr = MatSetBlockSizes(mat->A,rbs,cbs);CHKERRQ(ierr); 54 ierr = MatSetBlockSizes(mat->B,rbs,1);CHKERRQ(ierr); 55 } 56 PetscFunctionReturn(0); 57 } 58 59 PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows) 60 { 61 PetscErrorCode ierr; 62 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 63 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data; 64 Mat_SeqAIJ *b = (Mat_SeqAIJ*)mat->B->data; 65 const PetscInt *ia,*ib; 66 const MatScalar *aa,*bb; 67 PetscInt na,nb,i,j,*rows,cnt=0,n0rows; 68 PetscInt m = M->rmap->n,rstart = M->rmap->rstart; 69 70 PetscFunctionBegin; 71 *keptrows = 0; 72 ia = a->i; 73 ib = b->i; 74 for (i=0; i<m; i++) { 75 na = ia[i+1] - ia[i]; 76 nb = ib[i+1] - ib[i]; 77 if (!na && !nb) { 78 cnt++; 79 goto ok1; 80 } 81 aa = a->a + ia[i]; 82 for (j=0; j<na; j++) { 83 if (aa[j] != 0.0) goto ok1; 84 } 85 bb = b->a + ib[i]; 86 for (j=0; j <nb; j++) { 87 if (bb[j] != 0.0) goto ok1; 88 } 89 cnt++; 90 ok1:; 91 } 92 ierr = MPIU_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr); 93 if (!n0rows) PetscFunctionReturn(0); 94 ierr = PetscMalloc1(M->rmap->n-cnt,&rows);CHKERRQ(ierr); 95 cnt = 0; 96 for (i=0; i<m; i++) { 97 na = ia[i+1] - ia[i]; 98 nb = ib[i+1] - ib[i]; 99 if (!na && !nb) continue; 100 aa = a->a + ia[i]; 101 for (j=0; j<na;j++) { 102 if (aa[j] != 0.0) { 103 rows[cnt++] = rstart + i; 104 goto ok2; 105 } 106 } 107 bb = b->a + ib[i]; 108 for (j=0; j<nb; j++) { 109 if (bb[j] != 0.0) { 110 rows[cnt++] = rstart + i; 111 goto ok2; 112 } 113 } 114 ok2:; 115 } 116 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 117 PetscFunctionReturn(0); 118 } 119 120 PetscErrorCode MatDiagonalSet_MPIAIJ(Mat Y,Vec D,InsertMode is) 121 { 122 PetscErrorCode ierr; 123 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) Y->data; 124 125 PetscFunctionBegin; 126 if (Y->assembled && Y->rmap->rstart == Y->cmap->rstart && Y->rmap->rend == Y->cmap->rend) { 127 ierr = MatDiagonalSet(aij->A,D,is);CHKERRQ(ierr); 128 } else { 129 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 130 } 131 PetscFunctionReturn(0); 132 } 133 134 PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows) 135 { 136 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)M->data; 137 PetscErrorCode ierr; 138 PetscInt i,rstart,nrows,*rows; 139 140 PetscFunctionBegin; 141 *zrows = NULL; 142 ierr = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr); 143 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 144 for (i=0; i<nrows; i++) rows[i] += rstart; 145 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 146 PetscFunctionReturn(0); 147 } 148 149 PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms) 150 { 151 PetscErrorCode ierr; 152 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 153 PetscInt i,n,*garray = aij->garray; 154 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ*) aij->A->data; 155 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ*) aij->B->data; 156 PetscReal *work; 157 158 PetscFunctionBegin; 159 ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr); 160 ierr = PetscCalloc1(n,&work);CHKERRQ(ierr); 161 if (type == NORM_2) { 162 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 163 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]); 164 } 165 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 166 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]); 167 } 168 } else if (type == NORM_1) { 169 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 170 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 171 } 172 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 173 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 174 } 175 } else if (type == NORM_INFINITY) { 176 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 177 work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 178 } 179 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 180 work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]); 181 } 182 183 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 184 if (type == NORM_INFINITY) { 185 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 186 } else { 187 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 188 } 189 ierr = PetscFree(work);CHKERRQ(ierr); 190 if (type == NORM_2) { 191 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 192 } 193 PetscFunctionReturn(0); 194 } 195 196 PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A,IS *is) 197 { 198 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 199 IS sis,gis; 200 PetscErrorCode ierr; 201 const PetscInt *isis,*igis; 202 PetscInt n,*iis,nsis,ngis,rstart,i; 203 204 PetscFunctionBegin; 205 ierr = MatFindOffBlockDiagonalEntries(a->A,&sis);CHKERRQ(ierr); 206 ierr = MatFindNonzeroRows(a->B,&gis);CHKERRQ(ierr); 207 ierr = ISGetSize(gis,&ngis);CHKERRQ(ierr); 208 ierr = ISGetSize(sis,&nsis);CHKERRQ(ierr); 209 ierr = ISGetIndices(sis,&isis);CHKERRQ(ierr); 210 ierr = ISGetIndices(gis,&igis);CHKERRQ(ierr); 211 212 ierr = PetscMalloc1(ngis+nsis,&iis);CHKERRQ(ierr); 213 ierr = PetscMemcpy(iis,igis,ngis*sizeof(PetscInt));CHKERRQ(ierr); 214 ierr = PetscMemcpy(iis+ngis,isis,nsis*sizeof(PetscInt));CHKERRQ(ierr); 215 n = ngis + nsis; 216 ierr = PetscSortRemoveDupsInt(&n,iis);CHKERRQ(ierr); 217 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 218 for (i=0; i<n; i++) iis[i] += rstart; 219 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),n,iis,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 220 221 ierr = ISRestoreIndices(sis,&isis);CHKERRQ(ierr); 222 ierr = ISRestoreIndices(gis,&igis);CHKERRQ(ierr); 223 ierr = ISDestroy(&sis);CHKERRQ(ierr); 224 ierr = ISDestroy(&gis);CHKERRQ(ierr); 225 PetscFunctionReturn(0); 226 } 227 228 /* 229 Distributes a SeqAIJ matrix across a set of processes. Code stolen from 230 MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type. 231 232 Only for square matrices 233 234 Used by a preconditioner, hence PETSC_EXTERN 235 */ 236 PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat) 237 { 238 PetscMPIInt rank,size; 239 PetscInt *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz = 0,*gmataj,cnt,row,*ld,bses[2]; 240 PetscErrorCode ierr; 241 Mat mat; 242 Mat_SeqAIJ *gmata; 243 PetscMPIInt tag; 244 MPI_Status status; 245 PetscBool aij; 246 MatScalar *gmataa,*ao,*ad,*gmataarestore=0; 247 248 PetscFunctionBegin; 249 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 250 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 251 if (!rank) { 252 ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr); 253 if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name); 254 } 255 if (reuse == MAT_INITIAL_MATRIX) { 256 ierr = MatCreate(comm,&mat);CHKERRQ(ierr); 257 ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 258 ierr = MatGetBlockSizes(gmat,&bses[0],&bses[1]);CHKERRQ(ierr); 259 ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr); 260 ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr); 261 ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr); 262 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 263 ierr = PetscMalloc2(m,&dlens,m,&olens);CHKERRQ(ierr); 264 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 265 266 rowners[0] = 0; 267 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 268 rstart = rowners[rank]; 269 rend = rowners[rank+1]; 270 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 271 if (!rank) { 272 gmata = (Mat_SeqAIJ*) gmat->data; 273 /* send row lengths to all processors */ 274 for (i=0; i<m; i++) dlens[i] = gmata->ilen[i]; 275 for (i=1; i<size; i++) { 276 ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 277 } 278 /* determine number diagonal and off-diagonal counts */ 279 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 280 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 281 jj = 0; 282 for (i=0; i<m; i++) { 283 for (j=0; j<dlens[i]; j++) { 284 if (gmata->j[jj] < rstart) ld[i]++; 285 if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++; 286 jj++; 287 } 288 } 289 /* send column indices to other processes */ 290 for (i=1; i<size; i++) { 291 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 292 ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 293 ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 294 } 295 296 /* send numerical values to other processes */ 297 for (i=1; i<size; i++) { 298 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 299 ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 300 } 301 gmataa = gmata->a; 302 gmataj = gmata->j; 303 304 } else { 305 /* receive row lengths */ 306 ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 307 /* receive column indices */ 308 ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 309 ierr = PetscMalloc2(nz,&gmataa,nz,&gmataj);CHKERRQ(ierr); 310 ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 311 /* determine number diagonal and off-diagonal counts */ 312 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 313 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 314 jj = 0; 315 for (i=0; i<m; i++) { 316 for (j=0; j<dlens[i]; j++) { 317 if (gmataj[jj] < rstart) ld[i]++; 318 if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++; 319 jj++; 320 } 321 } 322 /* receive numerical values */ 323 ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 324 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 325 } 326 /* set preallocation */ 327 for (i=0; i<m; i++) { 328 dlens[i] -= olens[i]; 329 } 330 ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr); 331 ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr); 332 333 for (i=0; i<m; i++) { 334 dlens[i] += olens[i]; 335 } 336 cnt = 0; 337 for (i=0; i<m; i++) { 338 row = rstart + i; 339 ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr); 340 cnt += dlens[i]; 341 } 342 if (rank) { 343 ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr); 344 } 345 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 346 ierr = PetscFree(rowners);CHKERRQ(ierr); 347 348 ((Mat_MPIAIJ*)(mat->data))->ld = ld; 349 350 *inmat = mat; 351 } else { /* column indices are already set; only need to move over numerical values from process 0 */ 352 Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data; 353 Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data; 354 mat = *inmat; 355 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 356 if (!rank) { 357 /* send numerical values to other processes */ 358 gmata = (Mat_SeqAIJ*) gmat->data; 359 ierr = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr); 360 gmataa = gmata->a; 361 for (i=1; i<size; i++) { 362 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 363 ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 364 } 365 nz = gmata->i[rowners[1]]-gmata->i[rowners[0]]; 366 } else { 367 /* receive numerical values from process 0*/ 368 nz = Ad->nz + Ao->nz; 369 ierr = PetscMalloc1(nz,&gmataa);CHKERRQ(ierr); gmataarestore = gmataa; 370 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 371 } 372 /* transfer numerical values into the diagonal A and off diagonal B parts of mat */ 373 ld = ((Mat_MPIAIJ*)(mat->data))->ld; 374 ad = Ad->a; 375 ao = Ao->a; 376 if (mat->rmap->n) { 377 i = 0; 378 nz = ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 379 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 380 } 381 for (i=1; i<mat->rmap->n; i++) { 382 nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 383 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 384 } 385 i--; 386 if (mat->rmap->n) { 387 nz = Ao->i[i+1] - Ao->i[i] - ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 388 } 389 if (rank) { 390 ierr = PetscFree(gmataarestore);CHKERRQ(ierr); 391 } 392 } 393 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 394 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 395 PetscFunctionReturn(0); 396 } 397 398 /* 399 Local utility routine that creates a mapping from the global column 400 number to the local number in the off-diagonal part of the local 401 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 402 a slightly higher hash table cost; without it it is not scalable (each processor 403 has an order N integer array but is fast to acess. 404 */ 405 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 406 { 407 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 408 PetscErrorCode ierr; 409 PetscInt n = aij->B->cmap->n,i; 410 411 PetscFunctionBegin; 412 if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray"); 413 #if defined(PETSC_USE_CTABLE) 414 ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 415 for (i=0; i<n; i++) { 416 ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr); 417 } 418 #else 419 ierr = PetscCalloc1(mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 420 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N+1)*sizeof(PetscInt));CHKERRQ(ierr); 421 for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1; 422 #endif 423 PetscFunctionReturn(0); 424 } 425 426 #define MatSetValues_SeqAIJ_A_Private(row,col,value,addv,orow,ocol) \ 427 { \ 428 if (col <= lastcol1) low1 = 0; \ 429 else high1 = nrow1; \ 430 lastcol1 = col;\ 431 while (high1-low1 > 5) { \ 432 t = (low1+high1)/2; \ 433 if (rp1[t] > col) high1 = t; \ 434 else low1 = t; \ 435 } \ 436 for (_i=low1; _i<high1; _i++) { \ 437 if (rp1[_i] > col) break; \ 438 if (rp1[_i] == col) { \ 439 if (addv == ADD_VALUES) ap1[_i] += value; \ 440 else ap1[_i] = value; \ 441 goto a_noinsert; \ 442 } \ 443 } \ 444 if (value == 0.0 && ignorezeroentries && row != col) {low1 = 0; high1 = nrow1;goto a_noinsert;} \ 445 if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;} \ 446 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 447 MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \ 448 N = nrow1++ - 1; a->nz++; high1++; \ 449 /* shift up all the later entries in this row */ \ 450 for (ii=N; ii>=_i; ii--) { \ 451 rp1[ii+1] = rp1[ii]; \ 452 ap1[ii+1] = ap1[ii]; \ 453 } \ 454 rp1[_i] = col; \ 455 ap1[_i] = value; \ 456 A->nonzerostate++;\ 457 a_noinsert: ; \ 458 ailen[row] = nrow1; \ 459 } 460 461 #define MatSetValues_SeqAIJ_B_Private(row,col,value,addv,orow,ocol) \ 462 { \ 463 if (col <= lastcol2) low2 = 0; \ 464 else high2 = nrow2; \ 465 lastcol2 = col; \ 466 while (high2-low2 > 5) { \ 467 t = (low2+high2)/2; \ 468 if (rp2[t] > col) high2 = t; \ 469 else low2 = t; \ 470 } \ 471 for (_i=low2; _i<high2; _i++) { \ 472 if (rp2[_i] > col) break; \ 473 if (rp2[_i] == col) { \ 474 if (addv == ADD_VALUES) ap2[_i] += value; \ 475 else ap2[_i] = value; \ 476 goto b_noinsert; \ 477 } \ 478 } \ 479 if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 480 if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 481 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 482 MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \ 483 N = nrow2++ - 1; b->nz++; high2++; \ 484 /* shift up all the later entries in this row */ \ 485 for (ii=N; ii>=_i; ii--) { \ 486 rp2[ii+1] = rp2[ii]; \ 487 ap2[ii+1] = ap2[ii]; \ 488 } \ 489 rp2[_i] = col; \ 490 ap2[_i] = value; \ 491 B->nonzerostate++; \ 492 b_noinsert: ; \ 493 bilen[row] = nrow2; \ 494 } 495 496 PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[]) 497 { 498 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)A->data; 499 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data; 500 PetscErrorCode ierr; 501 PetscInt l,*garray = mat->garray,diag; 502 503 PetscFunctionBegin; 504 /* code only works for square matrices A */ 505 506 /* find size of row to the left of the diagonal part */ 507 ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr); 508 row = row - diag; 509 for (l=0; l<b->i[row+1]-b->i[row]; l++) { 510 if (garray[b->j[b->i[row]+l]] > diag) break; 511 } 512 ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr); 513 514 /* diagonal part */ 515 ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr); 516 517 /* right of diagonal part */ 518 ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr); 519 PetscFunctionReturn(0); 520 } 521 522 PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 523 { 524 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 525 PetscScalar value; 526 PetscErrorCode ierr; 527 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 528 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 529 PetscBool roworiented = aij->roworiented; 530 531 /* Some Variables required in the macro */ 532 Mat A = aij->A; 533 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 534 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 535 MatScalar *aa = a->a; 536 PetscBool ignorezeroentries = a->ignorezeroentries; 537 Mat B = aij->B; 538 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 539 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 540 MatScalar *ba = b->a; 541 542 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 543 PetscInt nonew; 544 MatScalar *ap1,*ap2; 545 546 PetscFunctionBegin; 547 for (i=0; i<m; i++) { 548 if (im[i] < 0) continue; 549 #if defined(PETSC_USE_DEBUG) 550 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 551 #endif 552 if (im[i] >= rstart && im[i] < rend) { 553 row = im[i] - rstart; 554 lastcol1 = -1; 555 rp1 = aj + ai[row]; 556 ap1 = aa + ai[row]; 557 rmax1 = aimax[row]; 558 nrow1 = ailen[row]; 559 low1 = 0; 560 high1 = nrow1; 561 lastcol2 = -1; 562 rp2 = bj + bi[row]; 563 ap2 = ba + bi[row]; 564 rmax2 = bimax[row]; 565 nrow2 = bilen[row]; 566 low2 = 0; 567 high2 = nrow2; 568 569 for (j=0; j<n; j++) { 570 if (roworiented) value = v[i*n+j]; 571 else value = v[i+j*m]; 572 if (in[j] >= cstart && in[j] < cend) { 573 col = in[j] - cstart; 574 nonew = a->nonew; 575 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 576 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 577 } else if (in[j] < 0) continue; 578 #if defined(PETSC_USE_DEBUG) 579 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 580 #endif 581 else { 582 if (mat->was_assembled) { 583 if (!aij->colmap) { 584 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 585 } 586 #if defined(PETSC_USE_CTABLE) 587 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 588 col--; 589 #else 590 col = aij->colmap[in[j]] - 1; 591 #endif 592 if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) { 593 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 594 col = in[j]; 595 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 596 B = aij->B; 597 b = (Mat_SeqAIJ*)B->data; 598 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a; 599 rp2 = bj + bi[row]; 600 ap2 = ba + bi[row]; 601 rmax2 = bimax[row]; 602 nrow2 = bilen[row]; 603 low2 = 0; 604 high2 = nrow2; 605 bm = aij->B->rmap->n; 606 ba = b->a; 607 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", im[i], in[j]); 608 } else col = in[j]; 609 nonew = b->nonew; 610 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 611 } 612 } 613 } else { 614 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 615 if (!aij->donotstash) { 616 mat->assembled = PETSC_FALSE; 617 if (roworiented) { 618 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 619 } else { 620 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 621 } 622 } 623 } 624 } 625 PetscFunctionReturn(0); 626 } 627 628 PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 629 { 630 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 631 PetscErrorCode ierr; 632 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 633 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 634 635 PetscFunctionBegin; 636 for (i=0; i<m; i++) { 637 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 638 if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1); 639 if (idxm[i] >= rstart && idxm[i] < rend) { 640 row = idxm[i] - rstart; 641 for (j=0; j<n; j++) { 642 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 643 if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1); 644 if (idxn[j] >= cstart && idxn[j] < cend) { 645 col = idxn[j] - cstart; 646 ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 647 } else { 648 if (!aij->colmap) { 649 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 650 } 651 #if defined(PETSC_USE_CTABLE) 652 ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr); 653 col--; 654 #else 655 col = aij->colmap[idxn[j]] - 1; 656 #endif 657 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0; 658 else { 659 ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 660 } 661 } 662 } 663 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 664 } 665 PetscFunctionReturn(0); 666 } 667 668 extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec); 669 670 PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode) 671 { 672 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 673 PetscErrorCode ierr; 674 PetscInt nstash,reallocs; 675 676 PetscFunctionBegin; 677 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 678 679 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 680 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 681 ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 682 PetscFunctionReturn(0); 683 } 684 685 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode) 686 { 687 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 688 Mat_SeqAIJ *a = (Mat_SeqAIJ*)aij->A->data; 689 PetscErrorCode ierr; 690 PetscMPIInt n; 691 PetscInt i,j,rstart,ncols,flg; 692 PetscInt *row,*col; 693 PetscBool other_disassembled; 694 PetscScalar *val; 695 696 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 697 698 PetscFunctionBegin; 699 if (!aij->donotstash && !mat->nooffprocentries) { 700 while (1) { 701 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 702 if (!flg) break; 703 704 for (i=0; i<n; ) { 705 /* Now identify the consecutive vals belonging to the same row */ 706 for (j=i,rstart=row[j]; j<n; j++) { 707 if (row[j] != rstart) break; 708 } 709 if (j < n) ncols = j-i; 710 else ncols = n-i; 711 /* Now assemble all these values with a single function call */ 712 ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr); 713 714 i = j; 715 } 716 } 717 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 718 } 719 ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr); 720 ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr); 721 722 /* determine if any processor has disassembled, if so we must 723 also disassemble ourselfs, in order that we may reassemble. */ 724 /* 725 if nonzero structure of submatrix B cannot change then we know that 726 no processor disassembled thus we can skip this stuff 727 */ 728 if (!((Mat_SeqAIJ*)aij->B->data)->nonew) { 729 ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 730 if (mat->was_assembled && !other_disassembled) { 731 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 732 } 733 } 734 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 735 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 736 } 737 ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr); 738 ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr); 739 ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr); 740 741 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 742 743 aij->rowvalues = 0; 744 745 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 746 if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ; 747 748 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 749 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 750 PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate; 751 ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 752 } 753 PetscFunctionReturn(0); 754 } 755 756 PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 757 { 758 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 759 PetscErrorCode ierr; 760 761 PetscFunctionBegin; 762 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 763 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 764 PetscFunctionReturn(0); 765 } 766 767 PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 768 { 769 Mat_MPIAIJ *mat = (Mat_MPIAIJ *) A->data; 770 PetscInt *lrows; 771 PetscInt r, len; 772 PetscErrorCode ierr; 773 774 PetscFunctionBegin; 775 /* get locally owned rows */ 776 ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr); 777 /* fix right hand side if needed */ 778 if (x && b) { 779 const PetscScalar *xx; 780 PetscScalar *bb; 781 782 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 783 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 784 for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]]; 785 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 786 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 787 } 788 /* Must zero l->B before l->A because the (diag) case below may put values into l->B*/ 789 ierr = MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 790 if (A->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 791 PetscBool cong; 792 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 793 if (cong) A->congruentlayouts = 1; 794 else A->congruentlayouts = 0; 795 } 796 if ((diag != 0.0) && A->congruentlayouts) { 797 ierr = MatZeroRows(mat->A, len, lrows, diag, NULL, NULL);CHKERRQ(ierr); 798 } else if (diag != 0.0) { 799 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 800 if (((Mat_SeqAIJ *) mat->A->data)->nonew) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 801 for (r = 0; r < len; ++r) { 802 const PetscInt row = lrows[r] + A->rmap->rstart; 803 ierr = MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES);CHKERRQ(ierr); 804 } 805 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 806 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 807 } else { 808 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 809 } 810 ierr = PetscFree(lrows);CHKERRQ(ierr); 811 812 /* only change matrix nonzero state if pattern was allowed to be changed */ 813 if (!((Mat_SeqAIJ*)(mat->A->data))->keepnonzeropattern) { 814 PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate; 815 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 816 } 817 PetscFunctionReturn(0); 818 } 819 820 PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 821 { 822 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 823 PetscErrorCode ierr; 824 PetscMPIInt n = A->rmap->n; 825 PetscInt i,j,r,m,p = 0,len = 0; 826 PetscInt *lrows,*owners = A->rmap->range; 827 PetscSFNode *rrows; 828 PetscSF sf; 829 const PetscScalar *xx; 830 PetscScalar *bb,*mask; 831 Vec xmask,lmask; 832 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)l->B->data; 833 const PetscInt *aj, *ii,*ridx; 834 PetscScalar *aa; 835 836 PetscFunctionBegin; 837 /* Create SF where leaves are input rows and roots are owned rows */ 838 ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr); 839 for (r = 0; r < n; ++r) lrows[r] = -1; 840 ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr); 841 for (r = 0; r < N; ++r) { 842 const PetscInt idx = rows[r]; 843 if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N); 844 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */ 845 ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr); 846 } 847 rrows[r].rank = p; 848 rrows[r].index = rows[r] - owners[p]; 849 } 850 ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr); 851 ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr); 852 /* Collect flags for rows to be zeroed */ 853 ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 854 ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 855 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 856 /* Compress and put in row numbers */ 857 for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r; 858 /* zero diagonal part of matrix */ 859 ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr); 860 /* handle off diagonal part of matrix */ 861 ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr); 862 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 863 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 864 for (i=0; i<len; i++) bb[lrows[i]] = 1; 865 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 866 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 867 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 868 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 869 if (x) { 870 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 871 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 872 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 873 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 874 } 875 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 876 /* remove zeroed rows of off diagonal matrix */ 877 ii = aij->i; 878 for (i=0; i<len; i++) { 879 ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr); 880 } 881 /* loop over all elements of off process part of matrix zeroing removed columns*/ 882 if (aij->compressedrow.use) { 883 m = aij->compressedrow.nrows; 884 ii = aij->compressedrow.i; 885 ridx = aij->compressedrow.rindex; 886 for (i=0; i<m; i++) { 887 n = ii[i+1] - ii[i]; 888 aj = aij->j + ii[i]; 889 aa = aij->a + ii[i]; 890 891 for (j=0; j<n; j++) { 892 if (PetscAbsScalar(mask[*aj])) { 893 if (b) bb[*ridx] -= *aa*xx[*aj]; 894 *aa = 0.0; 895 } 896 aa++; 897 aj++; 898 } 899 ridx++; 900 } 901 } else { /* do not use compressed row format */ 902 m = l->B->rmap->n; 903 for (i=0; i<m; i++) { 904 n = ii[i+1] - ii[i]; 905 aj = aij->j + ii[i]; 906 aa = aij->a + ii[i]; 907 for (j=0; j<n; j++) { 908 if (PetscAbsScalar(mask[*aj])) { 909 if (b) bb[i] -= *aa*xx[*aj]; 910 *aa = 0.0; 911 } 912 aa++; 913 aj++; 914 } 915 } 916 } 917 if (x) { 918 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 919 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 920 } 921 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 922 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 923 ierr = PetscFree(lrows);CHKERRQ(ierr); 924 925 /* only change matrix nonzero state if pattern was allowed to be changed */ 926 if (!((Mat_SeqAIJ*)(l->A->data))->keepnonzeropattern) { 927 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 928 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 929 } 930 PetscFunctionReturn(0); 931 } 932 933 PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy) 934 { 935 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 936 PetscErrorCode ierr; 937 PetscInt nt; 938 939 PetscFunctionBegin; 940 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 941 if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt); 942 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 943 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 944 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 945 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 946 PetscFunctionReturn(0); 947 } 948 949 PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx) 950 { 951 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 952 PetscErrorCode ierr; 953 954 PetscFunctionBegin; 955 ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr); 956 PetscFunctionReturn(0); 957 } 958 959 PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 960 { 961 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 962 PetscErrorCode ierr; 963 964 PetscFunctionBegin; 965 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 966 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 967 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 968 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 969 PetscFunctionReturn(0); 970 } 971 972 PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy) 973 { 974 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 975 PetscErrorCode ierr; 976 PetscBool merged; 977 978 PetscFunctionBegin; 979 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 980 /* do nondiagonal part */ 981 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 982 if (!merged) { 983 /* send it on its way */ 984 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 985 /* do local part */ 986 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 987 /* receive remote parts: note this assumes the values are not actually */ 988 /* added in yy until the next line, */ 989 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 990 } else { 991 /* do local part */ 992 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 993 /* send it on its way */ 994 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 995 /* values actually were received in the Begin() but we need to call this nop */ 996 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 997 } 998 PetscFunctionReturn(0); 999 } 1000 1001 PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool *f) 1002 { 1003 MPI_Comm comm; 1004 Mat_MPIAIJ *Aij = (Mat_MPIAIJ*) Amat->data, *Bij; 1005 Mat Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs; 1006 IS Me,Notme; 1007 PetscErrorCode ierr; 1008 PetscInt M,N,first,last,*notme,i; 1009 PetscMPIInt size; 1010 1011 PetscFunctionBegin; 1012 /* Easy test: symmetric diagonal block */ 1013 Bij = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A; 1014 ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr); 1015 if (!*f) PetscFunctionReturn(0); 1016 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1017 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1018 if (size == 1) PetscFunctionReturn(0); 1019 1020 /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */ 1021 ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr); 1022 ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr); 1023 ierr = PetscMalloc1(N-last+first,¬me);CHKERRQ(ierr); 1024 for (i=0; i<first; i++) notme[i] = i; 1025 for (i=last; i<M; i++) notme[i-last+first] = i; 1026 ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr); 1027 ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr); 1028 ierr = MatCreateSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr); 1029 Aoff = Aoffs[0]; 1030 ierr = MatCreateSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr); 1031 Boff = Boffs[0]; 1032 ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr); 1033 ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr); 1034 ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr); 1035 ierr = ISDestroy(&Me);CHKERRQ(ierr); 1036 ierr = ISDestroy(&Notme);CHKERRQ(ierr); 1037 ierr = PetscFree(notme);CHKERRQ(ierr); 1038 PetscFunctionReturn(0); 1039 } 1040 1041 PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1042 { 1043 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1044 PetscErrorCode ierr; 1045 1046 PetscFunctionBegin; 1047 /* do nondiagonal part */ 1048 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1049 /* send it on its way */ 1050 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1051 /* do local part */ 1052 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1053 /* receive remote parts */ 1054 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1055 PetscFunctionReturn(0); 1056 } 1057 1058 /* 1059 This only works correctly for square matrices where the subblock A->A is the 1060 diagonal block 1061 */ 1062 PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v) 1063 { 1064 PetscErrorCode ierr; 1065 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1066 1067 PetscFunctionBegin; 1068 if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1069 if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition"); 1070 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1071 PetscFunctionReturn(0); 1072 } 1073 1074 PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa) 1075 { 1076 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1077 PetscErrorCode ierr; 1078 1079 PetscFunctionBegin; 1080 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1081 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1082 PetscFunctionReturn(0); 1083 } 1084 1085 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 1086 { 1087 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1088 PetscErrorCode ierr; 1089 1090 PetscFunctionBegin; 1091 #if defined(PETSC_USE_LOG) 1092 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N); 1093 #endif 1094 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1095 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 1096 ierr = MatDestroy(&aij->A);CHKERRQ(ierr); 1097 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 1098 #if defined(PETSC_USE_CTABLE) 1099 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 1100 #else 1101 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 1102 #endif 1103 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 1104 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 1105 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 1106 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 1107 ierr = PetscFree(aij->ld);CHKERRQ(ierr); 1108 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1109 1110 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1111 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1112 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1113 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1114 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1115 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1116 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1117 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1118 #if defined(PETSC_HAVE_ELEMENTAL) 1119 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_elemental_C",NULL);CHKERRQ(ierr); 1120 #endif 1121 #if defined(PETSC_HAVE_HYPRE) 1122 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_hypre_C",NULL);CHKERRQ(ierr); 1123 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMatMatMult_transpose_mpiaij_mpiaij_C",NULL);CHKERRQ(ierr); 1124 #endif 1125 PetscFunctionReturn(0); 1126 } 1127 1128 PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer) 1129 { 1130 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1131 Mat_SeqAIJ *A = (Mat_SeqAIJ*)aij->A->data; 1132 Mat_SeqAIJ *B = (Mat_SeqAIJ*)aij->B->data; 1133 PetscErrorCode ierr; 1134 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1135 int fd; 1136 PetscInt nz,header[4],*row_lengths,*range=0,rlen,i; 1137 PetscInt nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz = 0; 1138 PetscScalar *column_values; 1139 PetscInt message_count,flowcontrolcount; 1140 FILE *file; 1141 1142 PetscFunctionBegin; 1143 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1144 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1145 nz = A->nz + B->nz; 1146 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1147 if (!rank) { 1148 header[0] = MAT_FILE_CLASSID; 1149 header[1] = mat->rmap->N; 1150 header[2] = mat->cmap->N; 1151 1152 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1153 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1154 /* get largest number of rows any processor has */ 1155 rlen = mat->rmap->n; 1156 range = mat->rmap->range; 1157 for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]); 1158 } else { 1159 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1160 rlen = mat->rmap->n; 1161 } 1162 1163 /* load up the local row counts */ 1164 ierr = PetscMalloc1(rlen+1,&row_lengths);CHKERRQ(ierr); 1165 for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1166 1167 /* store the row lengths to the file */ 1168 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1169 if (!rank) { 1170 ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1171 for (i=1; i<size; i++) { 1172 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1173 rlen = range[i+1] - range[i]; 1174 ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1175 ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1176 } 1177 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1178 } else { 1179 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1180 ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1181 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1182 } 1183 ierr = PetscFree(row_lengths);CHKERRQ(ierr); 1184 1185 /* load up the local column indices */ 1186 nzmax = nz; /* th processor needs space a largest processor needs */ 1187 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1188 ierr = PetscMalloc1(nzmax+1,&column_indices);CHKERRQ(ierr); 1189 cnt = 0; 1190 for (i=0; i<mat->rmap->n; i++) { 1191 for (j=B->i[i]; j<B->i[i+1]; j++) { 1192 if ((col = garray[B->j[j]]) > cstart) break; 1193 column_indices[cnt++] = col; 1194 } 1195 for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart; 1196 for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]]; 1197 } 1198 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1199 1200 /* store the column indices to the file */ 1201 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1202 if (!rank) { 1203 MPI_Status status; 1204 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1205 for (i=1; i<size; i++) { 1206 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1207 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1208 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1209 ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1210 ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1211 } 1212 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1213 } else { 1214 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1215 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1216 ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1217 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1218 } 1219 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1220 1221 /* load up the local column values */ 1222 ierr = PetscMalloc1(nzmax+1,&column_values);CHKERRQ(ierr); 1223 cnt = 0; 1224 for (i=0; i<mat->rmap->n; i++) { 1225 for (j=B->i[i]; j<B->i[i+1]; j++) { 1226 if (garray[B->j[j]] > cstart) break; 1227 column_values[cnt++] = B->a[j]; 1228 } 1229 for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k]; 1230 for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j]; 1231 } 1232 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1233 1234 /* store the column values to the file */ 1235 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1236 if (!rank) { 1237 MPI_Status status; 1238 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1239 for (i=1; i<size; i++) { 1240 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1241 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1242 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1243 ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1244 ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1245 } 1246 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1247 } else { 1248 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1249 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1250 ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1251 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1252 } 1253 ierr = PetscFree(column_values);CHKERRQ(ierr); 1254 1255 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1256 if (file) fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(mat->rmap->bs)); 1257 PetscFunctionReturn(0); 1258 } 1259 1260 #include <petscdraw.h> 1261 PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 1262 { 1263 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1264 PetscErrorCode ierr; 1265 PetscMPIInt rank = aij->rank,size = aij->size; 1266 PetscBool isdraw,iascii,isbinary; 1267 PetscViewer sviewer; 1268 PetscViewerFormat format; 1269 1270 PetscFunctionBegin; 1271 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1272 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1273 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1274 if (iascii) { 1275 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1276 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1277 MatInfo info; 1278 PetscBool inodes; 1279 1280 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1281 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 1282 ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr); 1283 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 1284 if (!inodes) { 1285 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n", 1286 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1287 } else { 1288 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n", 1289 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1290 } 1291 ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1292 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1293 ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1294 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1295 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1296 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 1297 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1298 ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr); 1299 PetscFunctionReturn(0); 1300 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1301 PetscInt inodecount,inodelimit,*inodes; 1302 ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr); 1303 if (inodes) { 1304 ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr); 1305 } else { 1306 ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr); 1307 } 1308 PetscFunctionReturn(0); 1309 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1310 PetscFunctionReturn(0); 1311 } 1312 } else if (isbinary) { 1313 if (size == 1) { 1314 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1315 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1316 } else { 1317 ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1318 } 1319 PetscFunctionReturn(0); 1320 } else if (isdraw) { 1321 PetscDraw draw; 1322 PetscBool isnull; 1323 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1324 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 1325 if (isnull) PetscFunctionReturn(0); 1326 } 1327 1328 { 1329 /* assemble the entire matrix onto first processor. */ 1330 Mat A; 1331 Mat_SeqAIJ *Aloc; 1332 PetscInt M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct; 1333 MatScalar *a; 1334 1335 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1336 if (!rank) { 1337 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1338 } else { 1339 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1340 } 1341 /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */ 1342 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 1343 ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr); 1344 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1345 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1346 1347 /* copy over the A part */ 1348 Aloc = (Mat_SeqAIJ*)aij->A->data; 1349 m = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1350 row = mat->rmap->rstart; 1351 for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart; 1352 for (i=0; i<m; i++) { 1353 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr); 1354 row++; 1355 a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i]; 1356 } 1357 aj = Aloc->j; 1358 for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart; 1359 1360 /* copy over the B part */ 1361 Aloc = (Mat_SeqAIJ*)aij->B->data; 1362 m = aij->B->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1363 row = mat->rmap->rstart; 1364 ierr = PetscMalloc1(ai[m]+1,&cols);CHKERRQ(ierr); 1365 ct = cols; 1366 for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]]; 1367 for (i=0; i<m; i++) { 1368 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr); 1369 row++; 1370 a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i]; 1371 } 1372 ierr = PetscFree(ct);CHKERRQ(ierr); 1373 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1374 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1375 /* 1376 Everyone has to call to draw the matrix since the graphics waits are 1377 synchronized across all processors that share the PetscDraw object 1378 */ 1379 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1380 if (!rank) { 1381 ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1382 ierr = MatView_SeqAIJ(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1383 } 1384 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1385 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1386 ierr = MatDestroy(&A);CHKERRQ(ierr); 1387 } 1388 PetscFunctionReturn(0); 1389 } 1390 1391 PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer) 1392 { 1393 PetscErrorCode ierr; 1394 PetscBool iascii,isdraw,issocket,isbinary; 1395 1396 PetscFunctionBegin; 1397 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1398 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1399 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1400 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1401 if (iascii || isdraw || isbinary || issocket) { 1402 ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1403 } 1404 PetscFunctionReturn(0); 1405 } 1406 1407 PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1408 { 1409 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1410 PetscErrorCode ierr; 1411 Vec bb1 = 0; 1412 PetscBool hasop; 1413 1414 PetscFunctionBegin; 1415 if (flag == SOR_APPLY_UPPER) { 1416 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1417 PetscFunctionReturn(0); 1418 } 1419 1420 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) { 1421 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 1422 } 1423 1424 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1425 if (flag & SOR_ZERO_INITIAL_GUESS) { 1426 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1427 its--; 1428 } 1429 1430 while (its--) { 1431 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1432 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1433 1434 /* update rhs: bb1 = bb - B*x */ 1435 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1436 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1437 1438 /* local sweep */ 1439 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1440 } 1441 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1442 if (flag & SOR_ZERO_INITIAL_GUESS) { 1443 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1444 its--; 1445 } 1446 while (its--) { 1447 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1448 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1449 1450 /* update rhs: bb1 = bb - B*x */ 1451 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1452 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1453 1454 /* local sweep */ 1455 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1456 } 1457 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1458 if (flag & SOR_ZERO_INITIAL_GUESS) { 1459 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1460 its--; 1461 } 1462 while (its--) { 1463 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1464 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1465 1466 /* update rhs: bb1 = bb - B*x */ 1467 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1468 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1469 1470 /* local sweep */ 1471 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1472 } 1473 } else if (flag & SOR_EISENSTAT) { 1474 Vec xx1; 1475 1476 ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr); 1477 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr); 1478 1479 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1480 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1481 if (!mat->diag) { 1482 ierr = MatCreateVecs(matin,&mat->diag,NULL);CHKERRQ(ierr); 1483 ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr); 1484 } 1485 ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr); 1486 if (hasop) { 1487 ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr); 1488 } else { 1489 ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr); 1490 } 1491 ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr); 1492 1493 ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr); 1494 1495 /* local sweep */ 1496 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr); 1497 ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr); 1498 ierr = VecDestroy(&xx1);CHKERRQ(ierr); 1499 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported"); 1500 1501 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 1502 1503 matin->factorerrortype = mat->A->factorerrortype; 1504 PetscFunctionReturn(0); 1505 } 1506 1507 PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B) 1508 { 1509 Mat aA,aB,Aperm; 1510 const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj; 1511 PetscScalar *aa,*ba; 1512 PetscInt i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest; 1513 PetscSF rowsf,sf; 1514 IS parcolp = NULL; 1515 PetscBool done; 1516 PetscErrorCode ierr; 1517 1518 PetscFunctionBegin; 1519 ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); 1520 ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr); 1521 ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr); 1522 ierr = PetscMalloc3(PetscMax(m,n),&work,m,&rdest,n,&cdest);CHKERRQ(ierr); 1523 1524 /* Invert row permutation to find out where my rows should go */ 1525 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr); 1526 ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr); 1527 ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr); 1528 for (i=0; i<m; i++) work[i] = A->rmap->rstart + i; 1529 ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1530 ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1531 1532 /* Invert column permutation to find out where my columns should go */ 1533 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1534 ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr); 1535 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1536 for (i=0; i<n; i++) work[i] = A->cmap->rstart + i; 1537 ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1538 ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1539 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1540 1541 ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr); 1542 ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr); 1543 ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr); 1544 1545 /* Find out where my gcols should go */ 1546 ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr); 1547 ierr = PetscMalloc1(ng,&gcdest);CHKERRQ(ierr); 1548 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1549 ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr); 1550 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1551 ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1552 ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1553 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1554 1555 ierr = PetscCalloc4(m,&dnnz,m,&onnz,m,&tdnnz,m,&tonnz);CHKERRQ(ierr); 1556 ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1557 ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1558 for (i=0; i<m; i++) { 1559 PetscInt row = rdest[i],rowner; 1560 ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr); 1561 for (j=ai[i]; j<ai[i+1]; j++) { 1562 PetscInt cowner,col = cdest[aj[j]]; 1563 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */ 1564 if (rowner == cowner) dnnz[i]++; 1565 else onnz[i]++; 1566 } 1567 for (j=bi[i]; j<bi[i+1]; j++) { 1568 PetscInt cowner,col = gcdest[bj[j]]; 1569 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); 1570 if (rowner == cowner) dnnz[i]++; 1571 else onnz[i]++; 1572 } 1573 } 1574 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1575 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1576 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1577 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1578 ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr); 1579 1580 ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr); 1581 ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr); 1582 ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr); 1583 for (i=0; i<m; i++) { 1584 PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */ 1585 PetscInt j0,rowlen; 1586 rowlen = ai[i+1] - ai[i]; 1587 for (j0=j=0; j<rowlen; j0=j) { /* rowlen could be larger than number of rows m, so sum in batches */ 1588 for ( ; j<PetscMin(rowlen,j0+m); j++) acols[j-j0] = cdest[aj[ai[i]+j]]; 1589 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,acols,aa+ai[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1590 } 1591 rowlen = bi[i+1] - bi[i]; 1592 for (j0=j=0; j<rowlen; j0=j) { 1593 for ( ; j<PetscMin(rowlen,j0+m); j++) bcols[j-j0] = gcdest[bj[bi[i]+j]]; 1594 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,bcols,ba+bi[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1595 } 1596 } 1597 ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1598 ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1599 ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1600 ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1601 ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr); 1602 ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr); 1603 ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr); 1604 ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr); 1605 ierr = PetscFree(gcdest);CHKERRQ(ierr); 1606 if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);} 1607 *B = Aperm; 1608 PetscFunctionReturn(0); 1609 } 1610 1611 PetscErrorCode MatGetGhosts_MPIAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 1612 { 1613 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1614 PetscErrorCode ierr; 1615 1616 PetscFunctionBegin; 1617 ierr = MatGetSize(aij->B,NULL,nghosts);CHKERRQ(ierr); 1618 if (ghosts) *ghosts = aij->garray; 1619 PetscFunctionReturn(0); 1620 } 1621 1622 PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1623 { 1624 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1625 Mat A = mat->A,B = mat->B; 1626 PetscErrorCode ierr; 1627 PetscReal isend[5],irecv[5]; 1628 1629 PetscFunctionBegin; 1630 info->block_size = 1.0; 1631 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1632 1633 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1634 isend[3] = info->memory; isend[4] = info->mallocs; 1635 1636 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1637 1638 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1639 isend[3] += info->memory; isend[4] += info->mallocs; 1640 if (flag == MAT_LOCAL) { 1641 info->nz_used = isend[0]; 1642 info->nz_allocated = isend[1]; 1643 info->nz_unneeded = isend[2]; 1644 info->memory = isend[3]; 1645 info->mallocs = isend[4]; 1646 } else if (flag == MAT_GLOBAL_MAX) { 1647 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1648 1649 info->nz_used = irecv[0]; 1650 info->nz_allocated = irecv[1]; 1651 info->nz_unneeded = irecv[2]; 1652 info->memory = irecv[3]; 1653 info->mallocs = irecv[4]; 1654 } else if (flag == MAT_GLOBAL_SUM) { 1655 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1656 1657 info->nz_used = irecv[0]; 1658 info->nz_allocated = irecv[1]; 1659 info->nz_unneeded = irecv[2]; 1660 info->memory = irecv[3]; 1661 info->mallocs = irecv[4]; 1662 } 1663 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1664 info->fill_ratio_needed = 0; 1665 info->factor_mallocs = 0; 1666 PetscFunctionReturn(0); 1667 } 1668 1669 PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg) 1670 { 1671 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1672 PetscErrorCode ierr; 1673 1674 PetscFunctionBegin; 1675 switch (op) { 1676 case MAT_NEW_NONZERO_LOCATIONS: 1677 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1678 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1679 case MAT_KEEP_NONZERO_PATTERN: 1680 case MAT_NEW_NONZERO_LOCATION_ERR: 1681 case MAT_USE_INODES: 1682 case MAT_IGNORE_ZERO_ENTRIES: 1683 MatCheckPreallocated(A,1); 1684 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1685 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1686 break; 1687 case MAT_ROW_ORIENTED: 1688 MatCheckPreallocated(A,1); 1689 a->roworiented = flg; 1690 1691 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1692 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1693 break; 1694 case MAT_NEW_DIAGONALS: 1695 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1696 break; 1697 case MAT_IGNORE_OFF_PROC_ENTRIES: 1698 a->donotstash = flg; 1699 break; 1700 case MAT_SPD: 1701 A->spd_set = PETSC_TRUE; 1702 A->spd = flg; 1703 if (flg) { 1704 A->symmetric = PETSC_TRUE; 1705 A->structurally_symmetric = PETSC_TRUE; 1706 A->symmetric_set = PETSC_TRUE; 1707 A->structurally_symmetric_set = PETSC_TRUE; 1708 } 1709 break; 1710 case MAT_SYMMETRIC: 1711 MatCheckPreallocated(A,1); 1712 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1713 break; 1714 case MAT_STRUCTURALLY_SYMMETRIC: 1715 MatCheckPreallocated(A,1); 1716 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1717 break; 1718 case MAT_HERMITIAN: 1719 MatCheckPreallocated(A,1); 1720 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1721 break; 1722 case MAT_SYMMETRY_ETERNAL: 1723 MatCheckPreallocated(A,1); 1724 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1725 break; 1726 case MAT_SUBMAT_SINGLEIS: 1727 A->submat_singleis = flg; 1728 break; 1729 case MAT_STRUCTURE_ONLY: 1730 /* The option is handled directly by MatSetOption() */ 1731 break; 1732 default: 1733 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1734 } 1735 PetscFunctionReturn(0); 1736 } 1737 1738 PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1739 { 1740 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1741 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1742 PetscErrorCode ierr; 1743 PetscInt i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart; 1744 PetscInt nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend; 1745 PetscInt *cmap,*idx_p; 1746 1747 PetscFunctionBegin; 1748 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1749 mat->getrowactive = PETSC_TRUE; 1750 1751 if (!mat->rowvalues && (idx || v)) { 1752 /* 1753 allocate enough space to hold information from the longest row. 1754 */ 1755 Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data; 1756 PetscInt max = 1,tmp; 1757 for (i=0; i<matin->rmap->n; i++) { 1758 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1759 if (max < tmp) max = tmp; 1760 } 1761 ierr = PetscMalloc2(max,&mat->rowvalues,max,&mat->rowindices);CHKERRQ(ierr); 1762 } 1763 1764 if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows"); 1765 lrow = row - rstart; 1766 1767 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1768 if (!v) {pvA = 0; pvB = 0;} 1769 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1770 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1771 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1772 nztot = nzA + nzB; 1773 1774 cmap = mat->garray; 1775 if (v || idx) { 1776 if (nztot) { 1777 /* Sort by increasing column numbers, assuming A and B already sorted */ 1778 PetscInt imark = -1; 1779 if (v) { 1780 *v = v_p = mat->rowvalues; 1781 for (i=0; i<nzB; i++) { 1782 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1783 else break; 1784 } 1785 imark = i; 1786 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1787 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1788 } 1789 if (idx) { 1790 *idx = idx_p = mat->rowindices; 1791 if (imark > -1) { 1792 for (i=0; i<imark; i++) { 1793 idx_p[i] = cmap[cworkB[i]]; 1794 } 1795 } else { 1796 for (i=0; i<nzB; i++) { 1797 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1798 else break; 1799 } 1800 imark = i; 1801 } 1802 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart + cworkA[i]; 1803 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]]; 1804 } 1805 } else { 1806 if (idx) *idx = 0; 1807 if (v) *v = 0; 1808 } 1809 } 1810 *nz = nztot; 1811 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1812 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1813 PetscFunctionReturn(0); 1814 } 1815 1816 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1817 { 1818 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1819 1820 PetscFunctionBegin; 1821 if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first"); 1822 aij->getrowactive = PETSC_FALSE; 1823 PetscFunctionReturn(0); 1824 } 1825 1826 PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm) 1827 { 1828 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1829 Mat_SeqAIJ *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data; 1830 PetscErrorCode ierr; 1831 PetscInt i,j,cstart = mat->cmap->rstart; 1832 PetscReal sum = 0.0; 1833 MatScalar *v; 1834 1835 PetscFunctionBegin; 1836 if (aij->size == 1) { 1837 ierr = MatNorm(aij->A,type,norm);CHKERRQ(ierr); 1838 } else { 1839 if (type == NORM_FROBENIUS) { 1840 v = amat->a; 1841 for (i=0; i<amat->nz; i++) { 1842 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1843 } 1844 v = bmat->a; 1845 for (i=0; i<bmat->nz; i++) { 1846 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1847 } 1848 ierr = MPIU_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1849 *norm = PetscSqrtReal(*norm); 1850 ierr = PetscLogFlops(2*amat->nz+2*bmat->nz);CHKERRQ(ierr); 1851 } else if (type == NORM_1) { /* max column norm */ 1852 PetscReal *tmp,*tmp2; 1853 PetscInt *jj,*garray = aij->garray; 1854 ierr = PetscCalloc1(mat->cmap->N+1,&tmp);CHKERRQ(ierr); 1855 ierr = PetscMalloc1(mat->cmap->N+1,&tmp2);CHKERRQ(ierr); 1856 *norm = 0.0; 1857 v = amat->a; jj = amat->j; 1858 for (j=0; j<amat->nz; j++) { 1859 tmp[cstart + *jj++] += PetscAbsScalar(*v); v++; 1860 } 1861 v = bmat->a; jj = bmat->j; 1862 for (j=0; j<bmat->nz; j++) { 1863 tmp[garray[*jj++]] += PetscAbsScalar(*v); v++; 1864 } 1865 ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1866 for (j=0; j<mat->cmap->N; j++) { 1867 if (tmp2[j] > *norm) *norm = tmp2[j]; 1868 } 1869 ierr = PetscFree(tmp);CHKERRQ(ierr); 1870 ierr = PetscFree(tmp2);CHKERRQ(ierr); 1871 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1872 } else if (type == NORM_INFINITY) { /* max row norm */ 1873 PetscReal ntemp = 0.0; 1874 for (j=0; j<aij->A->rmap->n; j++) { 1875 v = amat->a + amat->i[j]; 1876 sum = 0.0; 1877 for (i=0; i<amat->i[j+1]-amat->i[j]; i++) { 1878 sum += PetscAbsScalar(*v); v++; 1879 } 1880 v = bmat->a + bmat->i[j]; 1881 for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) { 1882 sum += PetscAbsScalar(*v); v++; 1883 } 1884 if (sum > ntemp) ntemp = sum; 1885 } 1886 ierr = MPIU_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1887 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1888 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm"); 1889 } 1890 PetscFunctionReturn(0); 1891 } 1892 1893 PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout) 1894 { 1895 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1896 Mat_SeqAIJ *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data; 1897 PetscErrorCode ierr; 1898 PetscInt M = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i; 1899 PetscInt cstart = A->cmap->rstart,ncol; 1900 Mat B; 1901 MatScalar *array; 1902 1903 PetscFunctionBegin; 1904 if (reuse == MAT_INPLACE_MATRIX && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1905 1906 ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n; 1907 ai = Aloc->i; aj = Aloc->j; 1908 bi = Bloc->i; bj = Bloc->j; 1909 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1910 PetscInt *d_nnz,*g_nnz,*o_nnz; 1911 PetscSFNode *oloc; 1912 PETSC_UNUSED PetscSF sf; 1913 1914 ierr = PetscMalloc4(na,&d_nnz,na,&o_nnz,nb,&g_nnz,nb,&oloc);CHKERRQ(ierr); 1915 /* compute d_nnz for preallocation */ 1916 ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1917 for (i=0; i<ai[ma]; i++) { 1918 d_nnz[aj[i]]++; 1919 aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1920 } 1921 /* compute local off-diagonal contributions */ 1922 ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr); 1923 for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++; 1924 /* map those to global */ 1925 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1926 ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr); 1927 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1928 ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1929 ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1930 ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1931 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1932 1933 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1934 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1935 ierr = MatSetBlockSizes(B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 1936 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1937 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 1938 ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr); 1939 } else { 1940 B = *matout; 1941 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1942 for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1943 } 1944 1945 /* copy over the A part */ 1946 array = Aloc->a; 1947 row = A->rmap->rstart; 1948 for (i=0; i<ma; i++) { 1949 ncol = ai[i+1]-ai[i]; 1950 ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1951 row++; 1952 array += ncol; aj += ncol; 1953 } 1954 aj = Aloc->j; 1955 for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */ 1956 1957 /* copy over the B part */ 1958 ierr = PetscCalloc1(bi[mb],&cols);CHKERRQ(ierr); 1959 array = Bloc->a; 1960 row = A->rmap->rstart; 1961 for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]]; 1962 cols_tmp = cols; 1963 for (i=0; i<mb; i++) { 1964 ncol = bi[i+1]-bi[i]; 1965 ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1966 row++; 1967 array += ncol; cols_tmp += ncol; 1968 } 1969 ierr = PetscFree(cols);CHKERRQ(ierr); 1970 1971 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1972 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1973 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 1974 *matout = B; 1975 } else { 1976 ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr); 1977 } 1978 PetscFunctionReturn(0); 1979 } 1980 1981 PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr) 1982 { 1983 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1984 Mat a = aij->A,b = aij->B; 1985 PetscErrorCode ierr; 1986 PetscInt s1,s2,s3; 1987 1988 PetscFunctionBegin; 1989 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1990 if (rr) { 1991 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1992 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1993 /* Overlap communication with computation. */ 1994 ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1995 } 1996 if (ll) { 1997 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1998 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1999 ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr); 2000 } 2001 /* scale the diagonal block */ 2002 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 2003 2004 if (rr) { 2005 /* Do a scatter end and then right scale the off-diagonal block */ 2006 ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2007 ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr); 2008 } 2009 PetscFunctionReturn(0); 2010 } 2011 2012 PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2013 { 2014 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2015 PetscErrorCode ierr; 2016 2017 PetscFunctionBegin; 2018 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 2019 PetscFunctionReturn(0); 2020 } 2021 2022 PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool *flag) 2023 { 2024 Mat_MPIAIJ *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data; 2025 Mat a,b,c,d; 2026 PetscBool flg; 2027 PetscErrorCode ierr; 2028 2029 PetscFunctionBegin; 2030 a = matA->A; b = matA->B; 2031 c = matB->A; d = matB->B; 2032 2033 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 2034 if (flg) { 2035 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 2036 } 2037 ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2038 PetscFunctionReturn(0); 2039 } 2040 2041 PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str) 2042 { 2043 PetscErrorCode ierr; 2044 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2045 Mat_MPIAIJ *b = (Mat_MPIAIJ*)B->data; 2046 2047 PetscFunctionBegin; 2048 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2049 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2050 /* because of the column compression in the off-processor part of the matrix a->B, 2051 the number of columns in a->B and b->B may be different, hence we cannot call 2052 the MatCopy() directly on the two parts. If need be, we can provide a more 2053 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2054 then copying the submatrices */ 2055 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2056 } else { 2057 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 2058 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 2059 } 2060 PetscFunctionReturn(0); 2061 } 2062 2063 PetscErrorCode MatSetUp_MPIAIJ(Mat A) 2064 { 2065 PetscErrorCode ierr; 2066 2067 PetscFunctionBegin; 2068 ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 2069 PetscFunctionReturn(0); 2070 } 2071 2072 /* 2073 Computes the number of nonzeros per row needed for preallocation when X and Y 2074 have different nonzero structure. 2075 */ 2076 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) 2077 { 2078 PetscInt i,j,k,nzx,nzy; 2079 2080 PetscFunctionBegin; 2081 /* Set the number of nonzeros in the new matrix */ 2082 for (i=0; i<m; i++) { 2083 const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i]; 2084 nzx = xi[i+1] - xi[i]; 2085 nzy = yi[i+1] - yi[i]; 2086 nnz[i] = 0; 2087 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2088 for (; k<nzy && yltog[yjj[k]]<xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */ 2089 if (k<nzy && yltog[yjj[k]]==xltog[xjj[j]]) k++; /* Skip duplicate */ 2090 nnz[i]++; 2091 } 2092 for (; k<nzy; k++) nnz[i]++; 2093 } 2094 PetscFunctionReturn(0); 2095 } 2096 2097 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2098 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 2099 { 2100 PetscErrorCode ierr; 2101 PetscInt m = Y->rmap->N; 2102 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2103 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2104 2105 PetscFunctionBegin; 2106 ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr); 2107 PetscFunctionReturn(0); 2108 } 2109 2110 PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2111 { 2112 PetscErrorCode ierr; 2113 Mat_MPIAIJ *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data; 2114 PetscBLASInt bnz,one=1; 2115 Mat_SeqAIJ *x,*y; 2116 2117 PetscFunctionBegin; 2118 if (str == SAME_NONZERO_PATTERN) { 2119 PetscScalar alpha = a; 2120 x = (Mat_SeqAIJ*)xx->A->data; 2121 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2122 y = (Mat_SeqAIJ*)yy->A->data; 2123 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2124 x = (Mat_SeqAIJ*)xx->B->data; 2125 y = (Mat_SeqAIJ*)yy->B->data; 2126 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2127 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2128 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 2129 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2130 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 2131 } else { 2132 Mat B; 2133 PetscInt *nnz_d,*nnz_o; 2134 ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr); 2135 ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr); 2136 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2137 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2138 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2139 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 2140 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2141 ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 2142 ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 2143 ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 2144 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2145 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 2146 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 2147 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 2148 } 2149 PetscFunctionReturn(0); 2150 } 2151 2152 extern PetscErrorCode MatConjugate_SeqAIJ(Mat); 2153 2154 PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2155 { 2156 #if defined(PETSC_USE_COMPLEX) 2157 PetscErrorCode ierr; 2158 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2159 2160 PetscFunctionBegin; 2161 ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr); 2162 ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr); 2163 #else 2164 PetscFunctionBegin; 2165 #endif 2166 PetscFunctionReturn(0); 2167 } 2168 2169 PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2170 { 2171 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2172 PetscErrorCode ierr; 2173 2174 PetscFunctionBegin; 2175 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2176 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2177 PetscFunctionReturn(0); 2178 } 2179 2180 PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2181 { 2182 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2183 PetscErrorCode ierr; 2184 2185 PetscFunctionBegin; 2186 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2187 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2188 PetscFunctionReturn(0); 2189 } 2190 2191 PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2192 { 2193 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2194 PetscErrorCode ierr; 2195 PetscInt i,*idxb = 0; 2196 PetscScalar *va,*vb; 2197 Vec vtmp; 2198 2199 PetscFunctionBegin; 2200 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 2201 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2202 if (idx) { 2203 for (i=0; i<A->rmap->n; i++) { 2204 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2205 } 2206 } 2207 2208 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2209 if (idx) { 2210 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2211 } 2212 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2213 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2214 2215 for (i=0; i<A->rmap->n; i++) { 2216 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 2217 va[i] = vb[i]; 2218 if (idx) idx[i] = a->garray[idxb[i]]; 2219 } 2220 } 2221 2222 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2223 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2224 ierr = PetscFree(idxb);CHKERRQ(ierr); 2225 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2226 PetscFunctionReturn(0); 2227 } 2228 2229 PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2230 { 2231 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2232 PetscErrorCode ierr; 2233 PetscInt i,*idxb = 0; 2234 PetscScalar *va,*vb; 2235 Vec vtmp; 2236 2237 PetscFunctionBegin; 2238 ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr); 2239 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2240 if (idx) { 2241 for (i=0; i<A->cmap->n; i++) { 2242 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2243 } 2244 } 2245 2246 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2247 if (idx) { 2248 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2249 } 2250 ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2251 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2252 2253 for (i=0; i<A->rmap->n; i++) { 2254 if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) { 2255 va[i] = vb[i]; 2256 if (idx) idx[i] = a->garray[idxb[i]]; 2257 } 2258 } 2259 2260 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2261 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2262 ierr = PetscFree(idxb);CHKERRQ(ierr); 2263 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2264 PetscFunctionReturn(0); 2265 } 2266 2267 PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2268 { 2269 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2270 PetscInt n = A->rmap->n; 2271 PetscInt cstart = A->cmap->rstart; 2272 PetscInt *cmap = mat->garray; 2273 PetscInt *diagIdx, *offdiagIdx; 2274 Vec diagV, offdiagV; 2275 PetscScalar *a, *diagA, *offdiagA; 2276 PetscInt r; 2277 PetscErrorCode ierr; 2278 2279 PetscFunctionBegin; 2280 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2281 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr); 2282 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr); 2283 ierr = MatGetRowMin(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2284 ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2285 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2286 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2287 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2288 for (r = 0; r < n; ++r) { 2289 if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) { 2290 a[r] = diagA[r]; 2291 idx[r] = cstart + diagIdx[r]; 2292 } else { 2293 a[r] = offdiagA[r]; 2294 idx[r] = cmap[offdiagIdx[r]]; 2295 } 2296 } 2297 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2298 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2299 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2300 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2301 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2302 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2303 PetscFunctionReturn(0); 2304 } 2305 2306 PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2307 { 2308 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2309 PetscInt n = A->rmap->n; 2310 PetscInt cstart = A->cmap->rstart; 2311 PetscInt *cmap = mat->garray; 2312 PetscInt *diagIdx, *offdiagIdx; 2313 Vec diagV, offdiagV; 2314 PetscScalar *a, *diagA, *offdiagA; 2315 PetscInt r; 2316 PetscErrorCode ierr; 2317 2318 PetscFunctionBegin; 2319 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2320 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr); 2321 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr); 2322 ierr = MatGetRowMax(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2323 ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2324 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2325 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2326 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2327 for (r = 0; r < n; ++r) { 2328 if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) { 2329 a[r] = diagA[r]; 2330 idx[r] = cstart + diagIdx[r]; 2331 } else { 2332 a[r] = offdiagA[r]; 2333 idx[r] = cmap[offdiagIdx[r]]; 2334 } 2335 } 2336 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2337 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2338 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2339 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2340 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2341 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2342 PetscFunctionReturn(0); 2343 } 2344 2345 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat) 2346 { 2347 PetscErrorCode ierr; 2348 Mat *dummy; 2349 2350 PetscFunctionBegin; 2351 ierr = MatCreateSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr); 2352 *newmat = *dummy; 2353 ierr = PetscFree(dummy);CHKERRQ(ierr); 2354 PetscFunctionReturn(0); 2355 } 2356 2357 PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values) 2358 { 2359 Mat_MPIAIJ *a = (Mat_MPIAIJ*) A->data; 2360 PetscErrorCode ierr; 2361 2362 PetscFunctionBegin; 2363 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2364 A->factorerrortype = a->A->factorerrortype; 2365 PetscFunctionReturn(0); 2366 } 2367 2368 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx) 2369 { 2370 PetscErrorCode ierr; 2371 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)x->data; 2372 2373 PetscFunctionBegin; 2374 ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr); 2375 ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr); 2376 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2377 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2378 PetscFunctionReturn(0); 2379 } 2380 2381 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A,PetscBool sc) 2382 { 2383 PetscFunctionBegin; 2384 if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable; 2385 else A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ; 2386 PetscFunctionReturn(0); 2387 } 2388 2389 /*@ 2390 MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap 2391 2392 Collective on Mat 2393 2394 Input Parameters: 2395 + A - the matrix 2396 - sc - PETSC_TRUE indicates use the scalable algorithm (default is not to use the scalable algorithm) 2397 2398 Level: advanced 2399 2400 @*/ 2401 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A,PetscBool sc) 2402 { 2403 PetscErrorCode ierr; 2404 2405 PetscFunctionBegin; 2406 ierr = PetscTryMethod(A,"MatMPIAIJSetUseScalableIncreaseOverlap_C",(Mat,PetscBool),(A,sc));CHKERRQ(ierr); 2407 PetscFunctionReturn(0); 2408 } 2409 2410 PetscErrorCode MatSetFromOptions_MPIAIJ(PetscOptionItems *PetscOptionsObject,Mat A) 2411 { 2412 PetscErrorCode ierr; 2413 PetscBool sc = PETSC_FALSE,flg; 2414 2415 PetscFunctionBegin; 2416 ierr = PetscOptionsHead(PetscOptionsObject,"MPIAIJ options");CHKERRQ(ierr); 2417 ierr = PetscObjectOptionsBegin((PetscObject)A); 2418 if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE; 2419 ierr = PetscOptionsBool("-mat_increase_overlap_scalable","Use a scalable algorithm to compute the overlap","MatIncreaseOverlap",sc,&sc,&flg);CHKERRQ(ierr); 2420 if (flg) { 2421 ierr = MatMPIAIJSetUseScalableIncreaseOverlap(A,sc);CHKERRQ(ierr); 2422 } 2423 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2424 PetscFunctionReturn(0); 2425 } 2426 2427 PetscErrorCode MatShift_MPIAIJ(Mat Y,PetscScalar a) 2428 { 2429 PetscErrorCode ierr; 2430 Mat_MPIAIJ *maij = (Mat_MPIAIJ*)Y->data; 2431 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)maij->A->data; 2432 2433 PetscFunctionBegin; 2434 if (!Y->preallocated) { 2435 ierr = MatMPIAIJSetPreallocation(Y,1,NULL,0,NULL);CHKERRQ(ierr); 2436 } else if (!aij->nz) { 2437 PetscInt nonew = aij->nonew; 2438 ierr = MatSeqAIJSetPreallocation(maij->A,1,NULL);CHKERRQ(ierr); 2439 aij->nonew = nonew; 2440 } 2441 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2442 PetscFunctionReturn(0); 2443 } 2444 2445 PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A,PetscBool *missing,PetscInt *d) 2446 { 2447 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2448 PetscErrorCode ierr; 2449 2450 PetscFunctionBegin; 2451 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2452 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2453 if (d) { 2454 PetscInt rstart; 2455 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2456 *d += rstart; 2457 2458 } 2459 PetscFunctionReturn(0); 2460 } 2461 2462 2463 /* -------------------------------------------------------------------*/ 2464 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 2465 MatGetRow_MPIAIJ, 2466 MatRestoreRow_MPIAIJ, 2467 MatMult_MPIAIJ, 2468 /* 4*/ MatMultAdd_MPIAIJ, 2469 MatMultTranspose_MPIAIJ, 2470 MatMultTransposeAdd_MPIAIJ, 2471 0, 2472 0, 2473 0, 2474 /*10*/ 0, 2475 0, 2476 0, 2477 MatSOR_MPIAIJ, 2478 MatTranspose_MPIAIJ, 2479 /*15*/ MatGetInfo_MPIAIJ, 2480 MatEqual_MPIAIJ, 2481 MatGetDiagonal_MPIAIJ, 2482 MatDiagonalScale_MPIAIJ, 2483 MatNorm_MPIAIJ, 2484 /*20*/ MatAssemblyBegin_MPIAIJ, 2485 MatAssemblyEnd_MPIAIJ, 2486 MatSetOption_MPIAIJ, 2487 MatZeroEntries_MPIAIJ, 2488 /*24*/ MatZeroRows_MPIAIJ, 2489 0, 2490 0, 2491 0, 2492 0, 2493 /*29*/ MatSetUp_MPIAIJ, 2494 0, 2495 0, 2496 MatGetDiagonalBlock_MPIAIJ, 2497 0, 2498 /*34*/ MatDuplicate_MPIAIJ, 2499 0, 2500 0, 2501 0, 2502 0, 2503 /*39*/ MatAXPY_MPIAIJ, 2504 MatCreateSubMatrices_MPIAIJ, 2505 MatIncreaseOverlap_MPIAIJ, 2506 MatGetValues_MPIAIJ, 2507 MatCopy_MPIAIJ, 2508 /*44*/ MatGetRowMax_MPIAIJ, 2509 MatScale_MPIAIJ, 2510 MatShift_MPIAIJ, 2511 MatDiagonalSet_MPIAIJ, 2512 MatZeroRowsColumns_MPIAIJ, 2513 /*49*/ MatSetRandom_MPIAIJ, 2514 0, 2515 0, 2516 0, 2517 0, 2518 /*54*/ MatFDColoringCreate_MPIXAIJ, 2519 0, 2520 MatSetUnfactored_MPIAIJ, 2521 MatPermute_MPIAIJ, 2522 0, 2523 /*59*/ MatCreateSubMatrix_MPIAIJ, 2524 MatDestroy_MPIAIJ, 2525 MatView_MPIAIJ, 2526 0, 2527 MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ, 2528 /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ, 2529 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 2530 0, 2531 0, 2532 0, 2533 /*69*/ MatGetRowMaxAbs_MPIAIJ, 2534 MatGetRowMinAbs_MPIAIJ, 2535 0, 2536 0, 2537 0, 2538 0, 2539 /*75*/ MatFDColoringApply_AIJ, 2540 MatSetFromOptions_MPIAIJ, 2541 0, 2542 0, 2543 MatFindZeroDiagonals_MPIAIJ, 2544 /*80*/ 0, 2545 0, 2546 0, 2547 /*83*/ MatLoad_MPIAIJ, 2548 0, 2549 0, 2550 0, 2551 0, 2552 0, 2553 /*89*/ MatMatMult_MPIAIJ_MPIAIJ, 2554 MatMatMultSymbolic_MPIAIJ_MPIAIJ, 2555 MatMatMultNumeric_MPIAIJ_MPIAIJ, 2556 MatPtAP_MPIAIJ_MPIAIJ, 2557 MatPtAPSymbolic_MPIAIJ_MPIAIJ, 2558 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 2559 0, 2560 0, 2561 0, 2562 0, 2563 /*99*/ 0, 2564 0, 2565 0, 2566 MatConjugate_MPIAIJ, 2567 0, 2568 /*104*/MatSetValuesRow_MPIAIJ, 2569 MatRealPart_MPIAIJ, 2570 MatImaginaryPart_MPIAIJ, 2571 0, 2572 0, 2573 /*109*/0, 2574 0, 2575 MatGetRowMin_MPIAIJ, 2576 0, 2577 MatMissingDiagonal_MPIAIJ, 2578 /*114*/MatGetSeqNonzeroStructure_MPIAIJ, 2579 0, 2580 MatGetGhosts_MPIAIJ, 2581 0, 2582 0, 2583 /*119*/0, 2584 0, 2585 0, 2586 0, 2587 MatGetMultiProcBlock_MPIAIJ, 2588 /*124*/MatFindNonzeroRows_MPIAIJ, 2589 MatGetColumnNorms_MPIAIJ, 2590 MatInvertBlockDiagonal_MPIAIJ, 2591 0, 2592 MatCreateSubMatricesMPI_MPIAIJ, 2593 /*129*/0, 2594 MatTransposeMatMult_MPIAIJ_MPIAIJ, 2595 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ, 2596 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 2597 0, 2598 /*134*/0, 2599 0, 2600 MatRARt_MPIAIJ_MPIAIJ, 2601 0, 2602 0, 2603 /*139*/MatSetBlockSizes_MPIAIJ, 2604 0, 2605 0, 2606 MatFDColoringSetUp_MPIXAIJ, 2607 MatFindOffBlockDiagonalEntries_MPIAIJ, 2608 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIAIJ 2609 }; 2610 2611 /* ----------------------------------------------------------------------------------------*/ 2612 2613 PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 2614 { 2615 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2616 PetscErrorCode ierr; 2617 2618 PetscFunctionBegin; 2619 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 2620 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 2621 PetscFunctionReturn(0); 2622 } 2623 2624 PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 2625 { 2626 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2627 PetscErrorCode ierr; 2628 2629 PetscFunctionBegin; 2630 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 2631 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 2632 PetscFunctionReturn(0); 2633 } 2634 2635 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 2636 { 2637 Mat_MPIAIJ *b; 2638 PetscErrorCode ierr; 2639 2640 PetscFunctionBegin; 2641 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2642 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2643 b = (Mat_MPIAIJ*)B->data; 2644 2645 #if defined(PETSC_USE_CTABLE) 2646 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2647 #else 2648 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2649 #endif 2650 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2651 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2652 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2653 2654 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2655 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2656 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2657 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 2658 ierr = MatSetBlockSizesFromMats(b->B,B,B);CHKERRQ(ierr); 2659 ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr); 2660 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2661 2662 if (!B->preallocated) { 2663 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2664 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2665 ierr = MatSetBlockSizesFromMats(b->A,B,B);CHKERRQ(ierr); 2666 ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr); 2667 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2668 } 2669 2670 ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr); 2671 ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr); 2672 B->preallocated = PETSC_TRUE; 2673 B->was_assembled = PETSC_FALSE; 2674 B->assembled = PETSC_FALSE;; 2675 PetscFunctionReturn(0); 2676 } 2677 2678 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 2679 { 2680 Mat mat; 2681 Mat_MPIAIJ *a,*oldmat = (Mat_MPIAIJ*)matin->data; 2682 PetscErrorCode ierr; 2683 2684 PetscFunctionBegin; 2685 *newmat = 0; 2686 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 2687 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 2688 ierr = MatSetBlockSizesFromMats(mat,matin,matin);CHKERRQ(ierr); 2689 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 2690 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2691 a = (Mat_MPIAIJ*)mat->data; 2692 2693 mat->factortype = matin->factortype; 2694 mat->assembled = PETSC_TRUE; 2695 mat->insertmode = NOT_SET_VALUES; 2696 mat->preallocated = PETSC_TRUE; 2697 2698 a->size = oldmat->size; 2699 a->rank = oldmat->rank; 2700 a->donotstash = oldmat->donotstash; 2701 a->roworiented = oldmat->roworiented; 2702 a->rowindices = 0; 2703 a->rowvalues = 0; 2704 a->getrowactive = PETSC_FALSE; 2705 2706 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 2707 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 2708 2709 if (oldmat->colmap) { 2710 #if defined(PETSC_USE_CTABLE) 2711 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 2712 #else 2713 ierr = PetscMalloc1(mat->cmap->N,&a->colmap);CHKERRQ(ierr); 2714 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2715 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2716 #endif 2717 } else a->colmap = 0; 2718 if (oldmat->garray) { 2719 PetscInt len; 2720 len = oldmat->B->cmap->n; 2721 ierr = PetscMalloc1(len+1,&a->garray);CHKERRQ(ierr); 2722 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 2723 if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); } 2724 } else a->garray = 0; 2725 2726 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 2727 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 2728 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 2729 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 2730 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 2731 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 2732 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 2733 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 2734 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 2735 *newmat = mat; 2736 PetscFunctionReturn(0); 2737 } 2738 2739 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 2740 { 2741 PetscScalar *vals,*svals; 2742 MPI_Comm comm; 2743 PetscErrorCode ierr; 2744 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 2745 PetscInt i,nz,j,rstart,rend,mmax,maxnz = 0; 2746 PetscInt header[4],*rowlengths = 0,M,N,m,*cols; 2747 PetscInt *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols; 2748 PetscInt cend,cstart,n,*rowners; 2749 int fd; 2750 PetscInt bs = newMat->rmap->bs; 2751 2752 PetscFunctionBegin; 2753 /* force binary viewer to load .info file if it has not yet done so */ 2754 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 2755 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2756 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2757 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2758 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2759 if (!rank) { 2760 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 2761 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 2762 if (header[3] < 0) SETERRQ(PetscObjectComm((PetscObject)newMat),PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as MATMPIAIJ"); 2763 } 2764 2765 ierr = PetscOptionsBegin(comm,NULL,"Options for loading MATMPIAIJ matrix","Mat");CHKERRQ(ierr); 2766 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 2767 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2768 if (bs < 0) bs = 1; 2769 2770 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 2771 M = header[1]; N = header[2]; 2772 2773 /* If global sizes are set, check if they are consistent with that given in the file */ 2774 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); 2775 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); 2776 2777 /* determine ownership of all (block) rows */ 2778 if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs); 2779 if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank)); /* PETSC_DECIDE */ 2780 else m = newMat->rmap->n; /* Set by user */ 2781 2782 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 2783 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 2784 2785 /* First process needs enough room for process with most rows */ 2786 if (!rank) { 2787 mmax = rowners[1]; 2788 for (i=2; i<=size; i++) { 2789 mmax = PetscMax(mmax, rowners[i]); 2790 } 2791 } else mmax = -1; /* unused, but compilers complain */ 2792 2793 rowners[0] = 0; 2794 for (i=2; i<=size; i++) { 2795 rowners[i] += rowners[i-1]; 2796 } 2797 rstart = rowners[rank]; 2798 rend = rowners[rank+1]; 2799 2800 /* distribute row lengths to all processors */ 2801 ierr = PetscMalloc2(m,&ourlens,m,&offlens);CHKERRQ(ierr); 2802 if (!rank) { 2803 ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr); 2804 ierr = PetscMalloc1(mmax,&rowlengths);CHKERRQ(ierr); 2805 ierr = PetscCalloc1(size,&procsnz);CHKERRQ(ierr); 2806 for (j=0; j<m; j++) { 2807 procsnz[0] += ourlens[j]; 2808 } 2809 for (i=1; i<size; i++) { 2810 ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr); 2811 /* calculate the number of nonzeros on each processor */ 2812 for (j=0; j<rowners[i+1]-rowners[i]; j++) { 2813 procsnz[i] += rowlengths[j]; 2814 } 2815 ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2816 } 2817 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2818 } else { 2819 ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2820 } 2821 2822 if (!rank) { 2823 /* determine max buffer needed and allocate it */ 2824 maxnz = 0; 2825 for (i=0; i<size; i++) { 2826 maxnz = PetscMax(maxnz,procsnz[i]); 2827 } 2828 ierr = PetscMalloc1(maxnz,&cols);CHKERRQ(ierr); 2829 2830 /* read in my part of the matrix column indices */ 2831 nz = procsnz[0]; 2832 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2833 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 2834 2835 /* read in every one elses and ship off */ 2836 for (i=1; i<size; i++) { 2837 nz = procsnz[i]; 2838 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 2839 ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2840 } 2841 ierr = PetscFree(cols);CHKERRQ(ierr); 2842 } else { 2843 /* determine buffer space needed for message */ 2844 nz = 0; 2845 for (i=0; i<m; i++) { 2846 nz += ourlens[i]; 2847 } 2848 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2849 2850 /* receive message of column indices*/ 2851 ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2852 } 2853 2854 /* determine column ownership if matrix is not square */ 2855 if (N != M) { 2856 if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank); 2857 else n = newMat->cmap->n; 2858 ierr = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2859 cstart = cend - n; 2860 } else { 2861 cstart = rstart; 2862 cend = rend; 2863 n = cend - cstart; 2864 } 2865 2866 /* loop over local rows, determining number of off diagonal entries */ 2867 ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr); 2868 jj = 0; 2869 for (i=0; i<m; i++) { 2870 for (j=0; j<ourlens[i]; j++) { 2871 if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++; 2872 jj++; 2873 } 2874 } 2875 2876 for (i=0; i<m; i++) { 2877 ourlens[i] -= offlens[i]; 2878 } 2879 ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr); 2880 2881 if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);} 2882 2883 ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr); 2884 2885 for (i=0; i<m; i++) { 2886 ourlens[i] += offlens[i]; 2887 } 2888 2889 if (!rank) { 2890 ierr = PetscMalloc1(maxnz+1,&vals);CHKERRQ(ierr); 2891 2892 /* read in my part of the matrix numerical values */ 2893 nz = procsnz[0]; 2894 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2895 2896 /* insert into matrix */ 2897 jj = rstart; 2898 smycols = mycols; 2899 svals = vals; 2900 for (i=0; i<m; i++) { 2901 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2902 smycols += ourlens[i]; 2903 svals += ourlens[i]; 2904 jj++; 2905 } 2906 2907 /* read in other processors and ship out */ 2908 for (i=1; i<size; i++) { 2909 nz = procsnz[i]; 2910 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2911 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2912 } 2913 ierr = PetscFree(procsnz);CHKERRQ(ierr); 2914 } else { 2915 /* receive numeric values */ 2916 ierr = PetscMalloc1(nz+1,&vals);CHKERRQ(ierr); 2917 2918 /* receive message of values*/ 2919 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2920 2921 /* insert into matrix */ 2922 jj = rstart; 2923 smycols = mycols; 2924 svals = vals; 2925 for (i=0; i<m; i++) { 2926 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2927 smycols += ourlens[i]; 2928 svals += ourlens[i]; 2929 jj++; 2930 } 2931 } 2932 ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr); 2933 ierr = PetscFree(vals);CHKERRQ(ierr); 2934 ierr = PetscFree(mycols);CHKERRQ(ierr); 2935 ierr = PetscFree(rowners);CHKERRQ(ierr); 2936 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2937 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2938 PetscFunctionReturn(0); 2939 } 2940 2941 /* Not scalable because of ISAllGather() unless getting all columns. */ 2942 PetscErrorCode ISGetSeqIS_Private(Mat mat,IS iscol,IS *isseq) 2943 { 2944 PetscErrorCode ierr; 2945 IS iscol_local; 2946 PetscBool isstride; 2947 PetscMPIInt lisstride=0,gisstride; 2948 2949 PetscFunctionBegin; 2950 /* check if we are grabbing all columns*/ 2951 ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&isstride);CHKERRQ(ierr); 2952 2953 if (isstride) { 2954 PetscInt start,len,mstart,mlen; 2955 ierr = ISStrideGetInfo(iscol,&start,NULL);CHKERRQ(ierr); 2956 ierr = ISGetLocalSize(iscol,&len);CHKERRQ(ierr); 2957 ierr = MatGetOwnershipRangeColumn(mat,&mstart,&mlen);CHKERRQ(ierr); 2958 if (mstart == start && mlen-mstart == len) lisstride = 1; 2959 } 2960 2961 ierr = MPIU_Allreduce(&lisstride,&gisstride,1,MPI_INT,MPI_MIN,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2962 if (gisstride) { 2963 PetscInt N; 2964 ierr = MatGetSize(mat,NULL,&N);CHKERRQ(ierr); 2965 ierr = ISCreateStride(PetscObjectComm((PetscObject)mat),N,0,1,&iscol_local);CHKERRQ(ierr); 2966 ierr = ISSetIdentity(iscol_local);CHKERRQ(ierr); 2967 ierr = PetscInfo(mat,"Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n");CHKERRQ(ierr); 2968 } else { 2969 PetscInt cbs; 2970 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 2971 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 2972 ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr); 2973 } 2974 2975 *isseq = iscol_local; 2976 PetscFunctionReturn(0); 2977 } 2978 2979 /* 2980 Used by MatCreateSubMatrix_MPIAIJ_SameRowColDist() to avoid ISAllGather() and global size of iscol_local 2981 (see MatCreateSubMatrix_MPIAIJ_nonscalable) 2982 2983 Input Parameters: 2984 mat - matrix 2985 isrow - parallel row index set; its local indices are a subset of local columns of mat, 2986 i.e., mat->rstart <= isrow[i] < mat->rend 2987 iscol - parallel column index set; its local indices are a subset of local columns of mat, 2988 i.e., mat->cstart <= iscol[i] < mat->cend 2989 Output Parameter: 2990 isrow_d,iscol_d - sequential row and column index sets for retrieving mat->A 2991 iscol_o - sequential column index set for retrieving mat->B 2992 garray - column map; garray[i] indicates global location of iscol_o[i] in iscol 2993 */ 2994 PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat,IS isrow,IS iscol,IS *isrow_d,IS *iscol_d,IS *iscol_o,const PetscInt *garray[]) 2995 { 2996 PetscErrorCode ierr; 2997 Vec x,cmap; 2998 const PetscInt *is_idx; 2999 PetscScalar *xarray,*cmaparray; 3000 PetscInt ncols,isstart,*idx,m,rstart,*cmap1,count; 3001 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3002 Mat B=a->B; 3003 Vec lvec=a->lvec,lcmap; 3004 PetscInt i,cstart,cend,Bn=B->cmap->N; 3005 MPI_Comm comm; 3006 3007 PetscFunctionBegin; 3008 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3009 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 3010 3011 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3012 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3013 ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3014 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3015 3016 /* Get start indices */ 3017 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3018 isstart -= ncols; 3019 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3020 3021 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3022 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3023 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3024 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3025 for (i=0; i<ncols; i++) { 3026 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3027 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3028 idx[i] = is_idx[i]-cstart; /* local index of iscol[i] */ 3029 } 3030 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3031 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3032 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3033 3034 /* Get iscol_d */ 3035 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,iscol_d);CHKERRQ(ierr); 3036 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3037 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3038 3039 /* Get isrow_d */ 3040 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3041 rstart = mat->rmap->rstart; 3042 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3043 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3044 for (i=0; i<m; i++) idx[i] = is_idx[i]-rstart; 3045 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3046 3047 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_OWN_POINTER,isrow_d);CHKERRQ(ierr); 3048 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3049 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3050 3051 /* (2) Scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3052 ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3053 3054 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3055 3056 ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3057 ierr = VecScatterBegin(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3058 ierr = VecScatterEnd(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3059 3060 /* (3) create sequential iscol_o (a subset of iscol) and isgarray */ 3061 /* off-process column indices */ 3062 count = 0; 3063 ierr = PetscMalloc1(Bn,&idx);CHKERRQ(ierr); 3064 ierr = PetscMalloc1(Bn,&cmap1);CHKERRQ(ierr); 3065 3066 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3067 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3068 for (i=0; i<Bn; i++) { 3069 if (PetscRealPart(xarray[i]) > -1.0) { 3070 idx[count] = i; /* local column index in off-diagonal part B */ 3071 cmap1[count++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3072 } 3073 } 3074 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3075 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3076 3077 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr); 3078 /* cannot ensure iscol_o has same blocksize as iscol! */ 3079 3080 ierr = PetscFree(idx);CHKERRQ(ierr); 3081 3082 *garray = cmap1; 3083 3084 ierr = VecDestroy(&x);CHKERRQ(ierr); 3085 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3086 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3087 PetscFunctionReturn(0); 3088 } 3089 3090 /* isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */ 3091 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *submat) 3092 { 3093 PetscErrorCode ierr; 3094 Mat_MPIAIJ *a = (Mat_MPIAIJ*)mat->data,*asub; 3095 Mat M = NULL; 3096 MPI_Comm comm; 3097 IS iscol_d,isrow_d,iscol_o; 3098 Mat Asub = NULL,Bsub = NULL; 3099 PetscInt n; 3100 3101 PetscFunctionBegin; 3102 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3103 3104 if (call == MAT_REUSE_MATRIX) { 3105 /* Retrieve isrow_d, iscol_d and iscol_o from submat */ 3106 ierr = PetscObjectQuery((PetscObject)*submat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3107 if (!isrow_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow_d passed in was not used before, cannot reuse"); 3108 3109 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_d",(PetscObject*)&iscol_d);CHKERRQ(ierr); 3110 if (!iscol_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_d passed in was not used before, cannot reuse"); 3111 3112 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_o",(PetscObject*)&iscol_o);CHKERRQ(ierr); 3113 if (!iscol_o) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_o passed in was not used before, cannot reuse"); 3114 3115 /* Update diagonal and off-diagonal portions of submat */ 3116 asub = (Mat_MPIAIJ*)(*submat)->data; 3117 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->A);CHKERRQ(ierr); 3118 ierr = ISGetLocalSize(iscol_o,&n);CHKERRQ(ierr); 3119 if (n) { 3120 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->B);CHKERRQ(ierr); 3121 } 3122 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3123 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3124 3125 } else { /* call == MAT_INITIAL_MATRIX) */ 3126 const PetscInt *garray; 3127 PetscInt BsubN; 3128 3129 /* Create isrow_d, iscol_d, iscol_o and isgarray (replace isgarray with array?) */ 3130 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&isrow_d,&iscol_d,&iscol_o,&garray);CHKERRQ(ierr); 3131 3132 /* Create local submatrices Asub and Bsub */ 3133 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Asub);CHKERRQ(ierr); 3134 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Bsub);CHKERRQ(ierr); 3135 3136 /* Create submatrix M */ 3137 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray,&M);CHKERRQ(ierr); 3138 3139 /* If Bsub has empty columns, compress iscol_o such that it will retrieve condensed Bsub from a->B during reuse */ 3140 asub = (Mat_MPIAIJ*)M->data; 3141 3142 ierr = ISGetLocalSize(iscol_o,&BsubN);CHKERRQ(ierr); 3143 n = asub->B->cmap->N; 3144 if (BsubN > n) { 3145 /* This case can be tested using ~petsc/src/tao/bound/examples/tutorials/runplate2_3 */ 3146 const PetscInt *idx; 3147 PetscInt i,j,*idx_new,*subgarray = asub->garray; 3148 ierr = PetscInfo2(M,"submatrix Bn %D != BsubN %D, update iscol_o\n",n,BsubN);CHKERRQ(ierr); 3149 3150 ierr = PetscMalloc1(n,&idx_new);CHKERRQ(ierr); 3151 j = 0; 3152 ierr = ISGetIndices(iscol_o,&idx);CHKERRQ(ierr); 3153 for (i=0; i<n; i++) { 3154 if (j >= BsubN) break; 3155 while (subgarray[i] > garray[j]) j++; 3156 3157 if (subgarray[i] == garray[j]) { 3158 idx_new[i] = idx[j++]; 3159 } else SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"subgarray[%D]=%D cannot < garray[%D]=%D",i,subgarray[i],j,garray[j]); 3160 } 3161 ierr = ISRestoreIndices(iscol_o,&idx);CHKERRQ(ierr); 3162 3163 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3164 ierr = ISCreateGeneral(PETSC_COMM_SELF,n,idx_new,PETSC_OWN_POINTER,&iscol_o);CHKERRQ(ierr); 3165 3166 } else if (BsubN < n) { 3167 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Columns of Bsub cannot be smaller than B's",BsubN,asub->B->cmap->N); 3168 } 3169 3170 ierr = PetscFree(garray);CHKERRQ(ierr); 3171 *submat = M; 3172 3173 /* Save isrow_d, iscol_d and iscol_o used in processor for next request */ 3174 ierr = PetscObjectCompose((PetscObject)M,"isrow_d",(PetscObject)isrow_d);CHKERRQ(ierr); 3175 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3176 3177 ierr = PetscObjectCompose((PetscObject)M,"iscol_d",(PetscObject)iscol_d);CHKERRQ(ierr); 3178 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3179 3180 ierr = PetscObjectCompose((PetscObject)M,"iscol_o",(PetscObject)iscol_o);CHKERRQ(ierr); 3181 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3182 } 3183 PetscFunctionReturn(0); 3184 } 3185 3186 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3187 { 3188 PetscErrorCode ierr; 3189 IS iscol_local,isrow_d; 3190 PetscInt csize; 3191 PetscInt n,i,j,start,end; 3192 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3193 MPI_Comm comm; 3194 3195 PetscFunctionBegin; 3196 /* If isrow has same processor distribution as mat, 3197 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3198 if (call == MAT_REUSE_MATRIX) { 3199 ierr = PetscObjectQuery((PetscObject)*newmat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3200 if (isrow_d) { 3201 sameRowDist = PETSC_TRUE; 3202 tsameDist[1] = PETSC_TRUE; /* sameColDist */ 3203 } else { 3204 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3205 if (iscol_local) { 3206 sameRowDist = PETSC_TRUE; 3207 tsameDist[1] = PETSC_FALSE; /* !sameColDist */ 3208 } 3209 } 3210 } else { 3211 /* Check if isrow has same processor distribution as mat */ 3212 sameDist[0] = PETSC_FALSE; 3213 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3214 if (!n) { 3215 sameDist[0] = PETSC_TRUE; 3216 } else { 3217 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3218 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3219 if (i >= start && j < end) { 3220 sameDist[0] = PETSC_TRUE; 3221 } 3222 } 3223 3224 /* Check if iscol has same processor distribution as mat */ 3225 sameDist[1] = PETSC_FALSE; 3226 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3227 if (!n) { 3228 sameDist[1] = PETSC_TRUE; 3229 } else { 3230 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3231 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3232 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3233 } 3234 3235 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3236 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3237 sameRowDist = tsameDist[0]; 3238 } 3239 3240 if (sameRowDist) { 3241 if (tsameDist[1]) { /* sameRowDist & sameColDist */ 3242 /* isrow and iscol have same processor distribution as mat */ 3243 ierr = MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3244 } else { /* sameRowDist */ 3245 /* isrow has same processor distribution as mat */ 3246 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3247 } 3248 PetscFunctionReturn(0); 3249 } 3250 3251 /* General case: iscol -> iscol_local which has global size of iscol */ 3252 if (call == MAT_REUSE_MATRIX) { 3253 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3254 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3255 } else { 3256 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3257 } 3258 3259 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3260 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3261 3262 if (call == MAT_INITIAL_MATRIX) { 3263 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3264 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3265 } 3266 PetscFunctionReturn(0); 3267 } 3268 3269 /*@C 3270 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3271 and "off-diagonal" part of the matrix in CSR format. 3272 3273 Collective on MPI_Comm 3274 3275 Input Parameters: 3276 + comm - MPI communicator 3277 . A - "diagonal" portion of matrix 3278 . B - "off-diagonal" portion of matrix, may have empty columns, will be destroyed by this routine 3279 - garray - global index of B columns 3280 3281 Output Parameter: 3282 . mat - the matrix, with input A as its local diagonal matrix 3283 Level: advanced 3284 3285 Notes: 3286 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3287 A becomes part of output mat, B is destroyed by this routine. The user cannot use A and B anymore. 3288 3289 .seealso: MatCreateMPIAIJWithSplitArrays() 3290 @*/ 3291 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3292 { 3293 PetscErrorCode ierr; 3294 Mat_MPIAIJ *maij; 3295 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data,*bnew; 3296 PetscInt *oi=b->i,*oj=b->j,i,nz,col; 3297 PetscScalar *oa=b->a; 3298 Mat Bnew; 3299 PetscInt m,n,N; 3300 3301 PetscFunctionBegin; 3302 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3303 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3304 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %D != Bm %D",m,B->rmap->N); 3305 if (A->rmap->bs != B->rmap->bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"A row bs %D != B row bs %D",A->rmap->bs,B->rmap->bs); 3306 /* remove check below; When B is created using iscol_o from ISGetSeqIS_SameColDist_Private(), its bs may not be same as A */ 3307 /* if (A->cmap->bs != B->cmap->bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"A column bs %D != B column bs %D",A->cmap->bs,B->cmap->bs); */ 3308 3309 /* Get global columns of mat */ 3310 ierr = MPIU_Allreduce(&n,&N,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3311 3312 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3313 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3314 ierr = MatSetBlockSizes(*mat,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 3315 maij = (Mat_MPIAIJ*)(*mat)->data; 3316 3317 (*mat)->preallocated = PETSC_TRUE; 3318 3319 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3320 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3321 3322 /* Set A as diagonal portion of *mat */ 3323 maij->A = A; 3324 3325 nz = oi[m]; 3326 for (i=0; i<nz; i++) { 3327 col = oj[i]; 3328 oj[i] = garray[col]; 3329 } 3330 3331 /* Set Bnew as off-diagonal portion of *mat */ 3332 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Bnew);CHKERRQ(ierr); 3333 bnew = (Mat_SeqAIJ*)Bnew->data; 3334 bnew->maxnz = b->maxnz; /* allocated nonzeros of B */ 3335 maij->B = Bnew; 3336 3337 if (B->rmap->N != Bnew->rmap->N) SETERRQ2(PETSC_COMM_SELF,0,"BN %d != BnewN %d",B->rmap->N,Bnew->rmap->N); 3338 3339 b->singlemalloc = PETSC_FALSE; /* B arrays are shared by Bnew */ 3340 b->free_a = PETSC_FALSE; 3341 b->free_ij = PETSC_FALSE; 3342 ierr = MatDestroy(&B);CHKERRQ(ierr); 3343 3344 bnew->singlemalloc = PETSC_TRUE; /* arrays will be freed by MatDestroy(&Bnew) */ 3345 bnew->free_a = PETSC_TRUE; 3346 bnew->free_ij = PETSC_TRUE; 3347 3348 /* condense columns of maij->B */ 3349 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3350 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3351 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3352 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3353 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3354 PetscFunctionReturn(0); 3355 } 3356 3357 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3358 3359 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3360 { 3361 PetscErrorCode ierr; 3362 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3363 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3364 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3365 Mat M,Msub,B=a->B; 3366 MatScalar *aa; 3367 Mat_SeqAIJ *aij; 3368 PetscInt *garray = a->garray,*colsub,Ncols; 3369 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3370 IS iscol_sub,iscmap; 3371 const PetscInt *is_idx,*cmap; 3372 PetscBool allcolumns=PETSC_FALSE; 3373 IS iscol_local=NULL; 3374 MPI_Comm comm; 3375 3376 PetscFunctionBegin; 3377 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3378 3379 if (call == MAT_REUSE_MATRIX) { 3380 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3381 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3382 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3383 3384 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3385 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3386 3387 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3388 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3389 3390 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3391 3392 } else { /* call == MAT_INITIAL_MATRIX) */ 3393 PetscBool flg; 3394 3395 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3396 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3397 3398 /* (1) iscol -> nonscalable iscol_local */ 3399 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3400 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3401 if (n != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != Ncols %d",n,Ncols); 3402 3403 /* Check for special case: each processor gets entire matrix columns */ 3404 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3405 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3406 if (allcolumns) { 3407 iscol_sub = iscol_local; 3408 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3409 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3410 3411 } else { 3412 /* (2) iscol_local -> iscol_sub and iscmap */ 3413 PetscInt *idx,*cmap1,k; 3414 3415 /* implementation below requires iscol_local be sorted, it can have duplicate indices */ 3416 ierr = ISSorted(iscol_local,&flg);CHKERRQ(ierr); 3417 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsorted iscol_local is not implemented yet"); 3418 3419 ierr = PetscMalloc1(Ncols,&idx);CHKERRQ(ierr); 3420 ierr = PetscMalloc1(Ncols,&cmap1);CHKERRQ(ierr); 3421 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3422 count = 0; 3423 k = 0; 3424 for (i=0; i<Ncols; i++) { 3425 j = is_idx[i]; 3426 if (j >= cstart && j < cend) { 3427 /* diagonal part of mat */ 3428 idx[count] = j; 3429 cmap1[count++] = i; /* column index in submat */ 3430 } else if (Bn) { 3431 /* off-diagonal part of mat */ 3432 if (j == garray[k]) { 3433 idx[count] = j; 3434 cmap1[count++] = i; /* column index in submat */ 3435 } else if (j > garray[k]) { 3436 while (j > garray[k] && k < Bn-1) k++; 3437 if (j == garray[k]) { 3438 idx[count] = j; 3439 cmap1[count++] = i; /* column index in submat */ 3440 } 3441 } 3442 } 3443 } 3444 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3445 3446 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_OWN_POINTER,&iscol_sub);CHKERRQ(ierr); 3447 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3448 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3449 3450 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_OWN_POINTER,&iscmap);CHKERRQ(ierr); 3451 } 3452 3453 /* (3) Create sequential Msub */ 3454 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3455 } 3456 3457 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3458 aij = (Mat_SeqAIJ*)(Msub)->data; 3459 ii = aij->i; 3460 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3461 3462 /* 3463 m - number of local rows 3464 Ncols - number of columns (same on all processors) 3465 rstart - first row in new global matrix generated 3466 */ 3467 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3468 3469 if (call == MAT_INITIAL_MATRIX) { 3470 /* (4) Create parallel newmat */ 3471 PetscMPIInt rank,size; 3472 PetscInt csize; 3473 3474 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3475 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3476 3477 /* 3478 Determine the number of non-zeros in the diagonal and off-diagonal 3479 portions of the matrix in order to do correct preallocation 3480 */ 3481 3482 /* first get start and end of "diagonal" columns */ 3483 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3484 if (csize == PETSC_DECIDE) { 3485 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3486 if (mglobal == Ncols) { /* square matrix */ 3487 nlocal = m; 3488 } else { 3489 nlocal = Ncols/size + ((Ncols % size) > rank); 3490 } 3491 } else { 3492 nlocal = csize; 3493 } 3494 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3495 rstart = rend - nlocal; 3496 if (rank == size - 1 && rend != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local column sizes %D do not add up to total number of columns %D",rend,Ncols); 3497 3498 /* next, compute all the lengths */ 3499 jj = aij->j; 3500 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3501 olens = dlens + m; 3502 for (i=0; i<m; i++) { 3503 jend = ii[i+1] - ii[i]; 3504 olen = 0; 3505 dlen = 0; 3506 for (j=0; j<jend; j++) { 3507 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3508 else dlen++; 3509 jj++; 3510 } 3511 olens[i] = olen; 3512 dlens[i] = dlen; 3513 } 3514 3515 ierr = ISGetBlockSize(isrow,&bs);CHKERRQ(ierr); 3516 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3517 3518 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3519 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr); 3520 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3521 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3522 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3523 ierr = PetscFree(dlens);CHKERRQ(ierr); 3524 3525 } else { /* call == MAT_REUSE_MATRIX */ 3526 M = *newmat; 3527 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3528 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3529 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3530 /* 3531 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3532 rather than the slower MatSetValues(). 3533 */ 3534 M->was_assembled = PETSC_TRUE; 3535 M->assembled = PETSC_FALSE; 3536 } 3537 3538 /* (5) Set values of Msub to *newmat */ 3539 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3540 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3541 3542 jj = aij->j; 3543 aa = aij->a; 3544 for (i=0; i<m; i++) { 3545 row = rstart + i; 3546 nz = ii[i+1] - ii[i]; 3547 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3548 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3549 jj += nz; aa += nz; 3550 } 3551 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3552 3553 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3554 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3555 3556 ierr = PetscFree(colsub);CHKERRQ(ierr); 3557 3558 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3559 if (call == MAT_INITIAL_MATRIX) { 3560 *newmat = M; 3561 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3562 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3563 3564 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3565 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3566 3567 ierr = PetscObjectCompose((PetscObject)(*newmat),"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3568 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3569 3570 if (iscol_local) { 3571 ierr = PetscObjectCompose((PetscObject)(*newmat),"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3572 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3573 } 3574 } 3575 PetscFunctionReturn(0); 3576 } 3577 3578 /* 3579 Not great since it makes two copies of the submatrix, first an SeqAIJ 3580 in local and then by concatenating the local matrices the end result. 3581 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3582 3583 Note: This requires a sequential iscol with all indices. 3584 */ 3585 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3586 { 3587 PetscErrorCode ierr; 3588 PetscMPIInt rank,size; 3589 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3590 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3591 Mat M,Mreuse; 3592 MatScalar *aa,*vwork; 3593 MPI_Comm comm; 3594 Mat_SeqAIJ *aij; 3595 PetscBool colflag,allcolumns=PETSC_FALSE; 3596 3597 PetscFunctionBegin; 3598 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3599 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3600 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3601 3602 /* Check for special case: each processor gets entire matrix columns */ 3603 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3604 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3605 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3606 3607 if (call == MAT_REUSE_MATRIX) { 3608 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3609 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3610 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3611 } else { 3612 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3613 } 3614 3615 /* 3616 m - number of local rows 3617 n - number of columns (same on all processors) 3618 rstart - first row in new global matrix generated 3619 */ 3620 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3621 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3622 if (call == MAT_INITIAL_MATRIX) { 3623 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3624 ii = aij->i; 3625 jj = aij->j; 3626 3627 /* 3628 Determine the number of non-zeros in the diagonal and off-diagonal 3629 portions of the matrix in order to do correct preallocation 3630 */ 3631 3632 /* first get start and end of "diagonal" columns */ 3633 if (csize == PETSC_DECIDE) { 3634 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3635 if (mglobal == n) { /* square matrix */ 3636 nlocal = m; 3637 } else { 3638 nlocal = n/size + ((n % size) > rank); 3639 } 3640 } else { 3641 nlocal = csize; 3642 } 3643 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3644 rstart = rend - nlocal; 3645 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); 3646 3647 /* next, compute all the lengths */ 3648 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3649 olens = dlens + m; 3650 for (i=0; i<m; i++) { 3651 jend = ii[i+1] - ii[i]; 3652 olen = 0; 3653 dlen = 0; 3654 for (j=0; j<jend; j++) { 3655 if (*jj < rstart || *jj >= rend) olen++; 3656 else dlen++; 3657 jj++; 3658 } 3659 olens[i] = olen; 3660 dlens[i] = dlen; 3661 } 3662 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3663 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3664 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3665 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3666 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3667 ierr = PetscFree(dlens);CHKERRQ(ierr); 3668 } else { 3669 PetscInt ml,nl; 3670 3671 M = *newmat; 3672 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3673 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3674 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3675 /* 3676 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3677 rather than the slower MatSetValues(). 3678 */ 3679 M->was_assembled = PETSC_TRUE; 3680 M->assembled = PETSC_FALSE; 3681 } 3682 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3683 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3684 ii = aij->i; 3685 jj = aij->j; 3686 aa = aij->a; 3687 for (i=0; i<m; i++) { 3688 row = rstart + i; 3689 nz = ii[i+1] - ii[i]; 3690 cwork = jj; jj += nz; 3691 vwork = aa; aa += nz; 3692 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3693 } 3694 3695 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3696 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3697 *newmat = M; 3698 3699 /* save submatrix used in processor for next request */ 3700 if (call == MAT_INITIAL_MATRIX) { 3701 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3702 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3703 } 3704 PetscFunctionReturn(0); 3705 } 3706 3707 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3708 { 3709 PetscInt m,cstart, cend,j,nnz,i,d; 3710 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3711 const PetscInt *JJ; 3712 PetscScalar *values; 3713 PetscErrorCode ierr; 3714 PetscBool nooffprocentries; 3715 3716 PetscFunctionBegin; 3717 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3718 3719 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3720 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3721 m = B->rmap->n; 3722 cstart = B->cmap->rstart; 3723 cend = B->cmap->rend; 3724 rstart = B->rmap->rstart; 3725 3726 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3727 3728 #if defined(PETSC_USE_DEBUGGING) 3729 for (i=0; i<m; i++) { 3730 nnz = Ii[i+1]- Ii[i]; 3731 JJ = J + Ii[i]; 3732 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3733 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3734 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); 3735 } 3736 #endif 3737 3738 for (i=0; i<m; i++) { 3739 nnz = Ii[i+1]- Ii[i]; 3740 JJ = J + Ii[i]; 3741 nnz_max = PetscMax(nnz_max,nnz); 3742 d = 0; 3743 for (j=0; j<nnz; j++) { 3744 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3745 } 3746 d_nnz[i] = d; 3747 o_nnz[i] = nnz - d; 3748 } 3749 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3750 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3751 3752 if (v) values = (PetscScalar*)v; 3753 else { 3754 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3755 } 3756 3757 for (i=0; i<m; i++) { 3758 ii = i + rstart; 3759 nnz = Ii[i+1]- Ii[i]; 3760 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3761 } 3762 nooffprocentries = B->nooffprocentries; 3763 B->nooffprocentries = PETSC_TRUE; 3764 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3765 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3766 B->nooffprocentries = nooffprocentries; 3767 3768 if (!v) { 3769 ierr = PetscFree(values);CHKERRQ(ierr); 3770 } 3771 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3772 PetscFunctionReturn(0); 3773 } 3774 3775 /*@ 3776 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3777 (the default parallel PETSc format). 3778 3779 Collective on MPI_Comm 3780 3781 Input Parameters: 3782 + B - the matrix 3783 . i - the indices into j for the start of each local row (starts with zero) 3784 . j - the column indices for each local row (starts with zero) 3785 - v - optional values in the matrix 3786 3787 Level: developer 3788 3789 Notes: 3790 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3791 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3792 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3793 3794 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3795 3796 The format which is used for the sparse matrix input, is equivalent to a 3797 row-major ordering.. i.e for the following matrix, the input data expected is 3798 as shown 3799 3800 $ 1 0 0 3801 $ 2 0 3 P0 3802 $ ------- 3803 $ 4 5 6 P1 3804 $ 3805 $ Process0 [P0]: rows_owned=[0,1] 3806 $ i = {0,1,3} [size = nrow+1 = 2+1] 3807 $ j = {0,0,2} [size = 3] 3808 $ v = {1,2,3} [size = 3] 3809 $ 3810 $ Process1 [P1]: rows_owned=[2] 3811 $ i = {0,3} [size = nrow+1 = 1+1] 3812 $ j = {0,1,2} [size = 3] 3813 $ v = {4,5,6} [size = 3] 3814 3815 .keywords: matrix, aij, compressed row, sparse, parallel 3816 3817 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3818 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3819 @*/ 3820 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3821 { 3822 PetscErrorCode ierr; 3823 3824 PetscFunctionBegin; 3825 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3826 PetscFunctionReturn(0); 3827 } 3828 3829 /*@C 3830 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3831 (the default parallel PETSc format). For good matrix assembly performance 3832 the user should preallocate the matrix storage by setting the parameters 3833 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3834 performance can be increased by more than a factor of 50. 3835 3836 Collective on MPI_Comm 3837 3838 Input Parameters: 3839 + B - the matrix 3840 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3841 (same value is used for all local rows) 3842 . d_nnz - array containing the number of nonzeros in the various rows of the 3843 DIAGONAL portion of the local submatrix (possibly different for each row) 3844 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3845 The size of this array is equal to the number of local rows, i.e 'm'. 3846 For matrices that will be factored, you must leave room for (and set) 3847 the diagonal entry even if it is zero. 3848 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3849 submatrix (same value is used for all local rows). 3850 - o_nnz - array containing the number of nonzeros in the various rows of the 3851 OFF-DIAGONAL portion of the local submatrix (possibly different for 3852 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3853 structure. The size of this array is equal to the number 3854 of local rows, i.e 'm'. 3855 3856 If the *_nnz parameter is given then the *_nz parameter is ignored 3857 3858 The AIJ format (also called the Yale sparse matrix format or 3859 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3860 storage. The stored row and column indices begin with zero. 3861 See Users-Manual: ch_mat for details. 3862 3863 The parallel matrix is partitioned such that the first m0 rows belong to 3864 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3865 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3866 3867 The DIAGONAL portion of the local submatrix of a processor can be defined 3868 as the submatrix which is obtained by extraction the part corresponding to 3869 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3870 first row that belongs to the processor, r2 is the last row belonging to 3871 the this processor, and c1-c2 is range of indices of the local part of a 3872 vector suitable for applying the matrix to. This is an mxn matrix. In the 3873 common case of a square matrix, the row and column ranges are the same and 3874 the DIAGONAL part is also square. The remaining portion of the local 3875 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3876 3877 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3878 3879 You can call MatGetInfo() to get information on how effective the preallocation was; 3880 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3881 You can also run with the option -info and look for messages with the string 3882 malloc in them to see if additional memory allocation was needed. 3883 3884 Example usage: 3885 3886 Consider the following 8x8 matrix with 34 non-zero values, that is 3887 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3888 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3889 as follows: 3890 3891 .vb 3892 1 2 0 | 0 3 0 | 0 4 3893 Proc0 0 5 6 | 7 0 0 | 8 0 3894 9 0 10 | 11 0 0 | 12 0 3895 ------------------------------------- 3896 13 0 14 | 15 16 17 | 0 0 3897 Proc1 0 18 0 | 19 20 21 | 0 0 3898 0 0 0 | 22 23 0 | 24 0 3899 ------------------------------------- 3900 Proc2 25 26 27 | 0 0 28 | 29 0 3901 30 0 0 | 31 32 33 | 0 34 3902 .ve 3903 3904 This can be represented as a collection of submatrices as: 3905 3906 .vb 3907 A B C 3908 D E F 3909 G H I 3910 .ve 3911 3912 Where the submatrices A,B,C are owned by proc0, D,E,F are 3913 owned by proc1, G,H,I are owned by proc2. 3914 3915 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3916 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3917 The 'M','N' parameters are 8,8, and have the same values on all procs. 3918 3919 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3920 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3921 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3922 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3923 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3924 matrix, ans [DF] as another SeqAIJ matrix. 3925 3926 When d_nz, o_nz parameters are specified, d_nz storage elements are 3927 allocated for every row of the local diagonal submatrix, and o_nz 3928 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3929 One way to choose d_nz and o_nz is to use the max nonzerors per local 3930 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3931 In this case, the values of d_nz,o_nz are: 3932 .vb 3933 proc0 : dnz = 2, o_nz = 2 3934 proc1 : dnz = 3, o_nz = 2 3935 proc2 : dnz = 1, o_nz = 4 3936 .ve 3937 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3938 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3939 for proc3. i.e we are using 12+15+10=37 storage locations to store 3940 34 values. 3941 3942 When d_nnz, o_nnz parameters are specified, the storage is specified 3943 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3944 In the above case the values for d_nnz,o_nnz are: 3945 .vb 3946 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3947 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3948 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3949 .ve 3950 Here the space allocated is sum of all the above values i.e 34, and 3951 hence pre-allocation is perfect. 3952 3953 Level: intermediate 3954 3955 .keywords: matrix, aij, compressed row, sparse, parallel 3956 3957 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 3958 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 3959 @*/ 3960 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3961 { 3962 PetscErrorCode ierr; 3963 3964 PetscFunctionBegin; 3965 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3966 PetscValidType(B,1); 3967 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 3968 PetscFunctionReturn(0); 3969 } 3970 3971 /*@ 3972 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 3973 CSR format the local rows. 3974 3975 Collective on MPI_Comm 3976 3977 Input Parameters: 3978 + comm - MPI communicator 3979 . m - number of local rows (Cannot be PETSC_DECIDE) 3980 . n - This value should be the same as the local size used in creating the 3981 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3982 calculated if N is given) For square matrices n is almost always m. 3983 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3984 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3985 . i - row indices 3986 . j - column indices 3987 - a - matrix values 3988 3989 Output Parameter: 3990 . mat - the matrix 3991 3992 Level: intermediate 3993 3994 Notes: 3995 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3996 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3997 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3998 3999 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4000 4001 The format which is used for the sparse matrix input, is equivalent to a 4002 row-major ordering.. i.e for the following matrix, the input data expected is 4003 as shown 4004 4005 $ 1 0 0 4006 $ 2 0 3 P0 4007 $ ------- 4008 $ 4 5 6 P1 4009 $ 4010 $ Process0 [P0]: rows_owned=[0,1] 4011 $ i = {0,1,3} [size = nrow+1 = 2+1] 4012 $ j = {0,0,2} [size = 3] 4013 $ v = {1,2,3} [size = 3] 4014 $ 4015 $ Process1 [P1]: rows_owned=[2] 4016 $ i = {0,3} [size = nrow+1 = 1+1] 4017 $ j = {0,1,2} [size = 3] 4018 $ v = {4,5,6} [size = 3] 4019 4020 .keywords: matrix, aij, compressed row, sparse, parallel 4021 4022 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4023 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4024 @*/ 4025 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 4026 { 4027 PetscErrorCode ierr; 4028 4029 PetscFunctionBegin; 4030 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4031 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4032 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4033 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4034 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 4035 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 4036 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 4037 PetscFunctionReturn(0); 4038 } 4039 4040 /*@C 4041 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 4042 (the default parallel PETSc format). For good matrix assembly performance 4043 the user should preallocate the matrix storage by setting the parameters 4044 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4045 performance can be increased by more than a factor of 50. 4046 4047 Collective on MPI_Comm 4048 4049 Input Parameters: 4050 + comm - MPI communicator 4051 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 4052 This value should be the same as the local size used in creating the 4053 y vector for the matrix-vector product y = Ax. 4054 . n - This value should be the same as the local size used in creating the 4055 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4056 calculated if N is given) For square matrices n is almost always m. 4057 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4058 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4059 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4060 (same value is used for all local rows) 4061 . d_nnz - array containing the number of nonzeros in the various rows of the 4062 DIAGONAL portion of the local submatrix (possibly different for each row) 4063 or NULL, if d_nz is used to specify the nonzero structure. 4064 The size of this array is equal to the number of local rows, i.e 'm'. 4065 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4066 submatrix (same value is used for all local rows). 4067 - o_nnz - array containing the number of nonzeros in the various rows of the 4068 OFF-DIAGONAL portion of the local submatrix (possibly different for 4069 each row) or NULL, if o_nz is used to specify the nonzero 4070 structure. The size of this array is equal to the number 4071 of local rows, i.e 'm'. 4072 4073 Output Parameter: 4074 . A - the matrix 4075 4076 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4077 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4078 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4079 4080 Notes: 4081 If the *_nnz parameter is given then the *_nz parameter is ignored 4082 4083 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4084 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4085 storage requirements for this matrix. 4086 4087 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4088 processor than it must be used on all processors that share the object for 4089 that argument. 4090 4091 The user MUST specify either the local or global matrix dimensions 4092 (possibly both). 4093 4094 The parallel matrix is partitioned across processors such that the 4095 first m0 rows belong to process 0, the next m1 rows belong to 4096 process 1, the next m2 rows belong to process 2 etc.. where 4097 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4098 values corresponding to [m x N] submatrix. 4099 4100 The columns are logically partitioned with the n0 columns belonging 4101 to 0th partition, the next n1 columns belonging to the next 4102 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4103 4104 The DIAGONAL portion of the local submatrix on any given processor 4105 is the submatrix corresponding to the rows and columns m,n 4106 corresponding to the given processor. i.e diagonal matrix on 4107 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4108 etc. The remaining portion of the local submatrix [m x (N-n)] 4109 constitute the OFF-DIAGONAL portion. The example below better 4110 illustrates this concept. 4111 4112 For a square global matrix we define each processor's diagonal portion 4113 to be its local rows and the corresponding columns (a square submatrix); 4114 each processor's off-diagonal portion encompasses the remainder of the 4115 local matrix (a rectangular submatrix). 4116 4117 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4118 4119 When calling this routine with a single process communicator, a matrix of 4120 type SEQAIJ is returned. If a matrix of type MATMPIAIJ is desired for this 4121 type of communicator, use the construction mechanism: 4122 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4123 4124 By default, this format uses inodes (identical nodes) when possible. 4125 We search for consecutive rows with the same nonzero structure, thereby 4126 reusing matrix information to achieve increased efficiency. 4127 4128 Options Database Keys: 4129 + -mat_no_inode - Do not use inodes 4130 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4131 - -mat_aij_oneindex - Internally use indexing starting at 1 4132 rather than 0. Note that when calling MatSetValues(), 4133 the user still MUST index entries starting at 0! 4134 4135 4136 Example usage: 4137 4138 Consider the following 8x8 matrix with 34 non-zero values, that is 4139 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4140 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4141 as follows: 4142 4143 .vb 4144 1 2 0 | 0 3 0 | 0 4 4145 Proc0 0 5 6 | 7 0 0 | 8 0 4146 9 0 10 | 11 0 0 | 12 0 4147 ------------------------------------- 4148 13 0 14 | 15 16 17 | 0 0 4149 Proc1 0 18 0 | 19 20 21 | 0 0 4150 0 0 0 | 22 23 0 | 24 0 4151 ------------------------------------- 4152 Proc2 25 26 27 | 0 0 28 | 29 0 4153 30 0 0 | 31 32 33 | 0 34 4154 .ve 4155 4156 This can be represented as a collection of submatrices as: 4157 4158 .vb 4159 A B C 4160 D E F 4161 G H I 4162 .ve 4163 4164 Where the submatrices A,B,C are owned by proc0, D,E,F are 4165 owned by proc1, G,H,I are owned by proc2. 4166 4167 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4168 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4169 The 'M','N' parameters are 8,8, and have the same values on all procs. 4170 4171 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4172 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4173 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4174 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4175 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4176 matrix, ans [DF] as another SeqAIJ matrix. 4177 4178 When d_nz, o_nz parameters are specified, d_nz storage elements are 4179 allocated for every row of the local diagonal submatrix, and o_nz 4180 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4181 One way to choose d_nz and o_nz is to use the max nonzerors per local 4182 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4183 In this case, the values of d_nz,o_nz are: 4184 .vb 4185 proc0 : dnz = 2, o_nz = 2 4186 proc1 : dnz = 3, o_nz = 2 4187 proc2 : dnz = 1, o_nz = 4 4188 .ve 4189 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4190 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4191 for proc3. i.e we are using 12+15+10=37 storage locations to store 4192 34 values. 4193 4194 When d_nnz, o_nnz parameters are specified, the storage is specified 4195 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4196 In the above case the values for d_nnz,o_nnz are: 4197 .vb 4198 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4199 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4200 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4201 .ve 4202 Here the space allocated is sum of all the above values i.e 34, and 4203 hence pre-allocation is perfect. 4204 4205 Level: intermediate 4206 4207 .keywords: matrix, aij, compressed row, sparse, parallel 4208 4209 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4210 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4211 @*/ 4212 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) 4213 { 4214 PetscErrorCode ierr; 4215 PetscMPIInt size; 4216 4217 PetscFunctionBegin; 4218 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4219 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4220 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4221 if (size > 1) { 4222 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4223 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4224 } else { 4225 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4226 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4227 } 4228 PetscFunctionReturn(0); 4229 } 4230 4231 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4232 { 4233 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4234 PetscBool flg; 4235 PetscErrorCode ierr; 4236 4237 PetscFunctionBegin; 4238 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4239 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4240 if (Ad) *Ad = a->A; 4241 if (Ao) *Ao = a->B; 4242 if (colmap) *colmap = a->garray; 4243 PetscFunctionReturn(0); 4244 } 4245 4246 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4247 { 4248 PetscErrorCode ierr; 4249 PetscInt m,N,i,rstart,nnz,Ii; 4250 PetscInt *indx; 4251 PetscScalar *values; 4252 4253 PetscFunctionBegin; 4254 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4255 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4256 PetscInt *dnz,*onz,sum,bs,cbs; 4257 4258 if (n == PETSC_DECIDE) { 4259 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4260 } 4261 /* Check sum(n) = N */ 4262 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4263 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 4264 4265 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4266 rstart -= m; 4267 4268 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4269 for (i=0; i<m; i++) { 4270 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4271 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4272 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4273 } 4274 4275 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4276 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4277 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4278 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4279 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4280 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4281 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4282 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4283 } 4284 4285 /* numeric phase */ 4286 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4287 for (i=0; i<m; i++) { 4288 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4289 Ii = i + rstart; 4290 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4291 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4292 } 4293 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4294 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4295 PetscFunctionReturn(0); 4296 } 4297 4298 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4299 { 4300 PetscErrorCode ierr; 4301 PetscMPIInt rank; 4302 PetscInt m,N,i,rstart,nnz; 4303 size_t len; 4304 const PetscInt *indx; 4305 PetscViewer out; 4306 char *name; 4307 Mat B; 4308 const PetscScalar *values; 4309 4310 PetscFunctionBegin; 4311 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4312 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4313 /* Should this be the type of the diagonal block of A? */ 4314 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4315 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4316 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4317 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4318 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4319 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4320 for (i=0; i<m; i++) { 4321 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4322 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4323 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4324 } 4325 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4326 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4327 4328 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4329 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4330 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4331 sprintf(name,"%s.%d",outfile,rank); 4332 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4333 ierr = PetscFree(name);CHKERRQ(ierr); 4334 ierr = MatView(B,out);CHKERRQ(ierr); 4335 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4336 ierr = MatDestroy(&B);CHKERRQ(ierr); 4337 PetscFunctionReturn(0); 4338 } 4339 4340 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4341 { 4342 PetscErrorCode ierr; 4343 Mat_Merge_SeqsToMPI *merge; 4344 PetscContainer container; 4345 4346 PetscFunctionBegin; 4347 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4348 if (container) { 4349 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4350 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4351 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4352 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4353 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4354 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4355 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4356 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4357 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4358 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4359 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4360 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4361 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4362 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4363 ierr = PetscFree(merge);CHKERRQ(ierr); 4364 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4365 } 4366 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4367 PetscFunctionReturn(0); 4368 } 4369 4370 #include <../src/mat/utils/freespace.h> 4371 #include <petscbt.h> 4372 4373 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4374 { 4375 PetscErrorCode ierr; 4376 MPI_Comm comm; 4377 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4378 PetscMPIInt size,rank,taga,*len_s; 4379 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4380 PetscInt proc,m; 4381 PetscInt **buf_ri,**buf_rj; 4382 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4383 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4384 MPI_Request *s_waits,*r_waits; 4385 MPI_Status *status; 4386 MatScalar *aa=a->a; 4387 MatScalar **abuf_r,*ba_i; 4388 Mat_Merge_SeqsToMPI *merge; 4389 PetscContainer container; 4390 4391 PetscFunctionBegin; 4392 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4393 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4394 4395 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4396 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4397 4398 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4399 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4400 4401 bi = merge->bi; 4402 bj = merge->bj; 4403 buf_ri = merge->buf_ri; 4404 buf_rj = merge->buf_rj; 4405 4406 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4407 owners = merge->rowmap->range; 4408 len_s = merge->len_s; 4409 4410 /* send and recv matrix values */ 4411 /*-----------------------------*/ 4412 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4413 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4414 4415 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4416 for (proc=0,k=0; proc<size; proc++) { 4417 if (!len_s[proc]) continue; 4418 i = owners[proc]; 4419 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4420 k++; 4421 } 4422 4423 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4424 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4425 ierr = PetscFree(status);CHKERRQ(ierr); 4426 4427 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4428 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4429 4430 /* insert mat values of mpimat */ 4431 /*----------------------------*/ 4432 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4433 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4434 4435 for (k=0; k<merge->nrecv; k++) { 4436 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4437 nrows = *(buf_ri_k[k]); 4438 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4439 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4440 } 4441 4442 /* set values of ba */ 4443 m = merge->rowmap->n; 4444 for (i=0; i<m; i++) { 4445 arow = owners[rank] + i; 4446 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4447 bnzi = bi[i+1] - bi[i]; 4448 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4449 4450 /* add local non-zero vals of this proc's seqmat into ba */ 4451 anzi = ai[arow+1] - ai[arow]; 4452 aj = a->j + ai[arow]; 4453 aa = a->a + ai[arow]; 4454 nextaj = 0; 4455 for (j=0; nextaj<anzi; j++) { 4456 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4457 ba_i[j] += aa[nextaj++]; 4458 } 4459 } 4460 4461 /* add received vals into ba */ 4462 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4463 /* i-th row */ 4464 if (i == *nextrow[k]) { 4465 anzi = *(nextai[k]+1) - *nextai[k]; 4466 aj = buf_rj[k] + *(nextai[k]); 4467 aa = abuf_r[k] + *(nextai[k]); 4468 nextaj = 0; 4469 for (j=0; nextaj<anzi; j++) { 4470 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4471 ba_i[j] += aa[nextaj++]; 4472 } 4473 } 4474 nextrow[k]++; nextai[k]++; 4475 } 4476 } 4477 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4478 } 4479 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4480 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4481 4482 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4483 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4484 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4485 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4486 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4487 PetscFunctionReturn(0); 4488 } 4489 4490 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4491 { 4492 PetscErrorCode ierr; 4493 Mat B_mpi; 4494 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4495 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4496 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4497 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4498 PetscInt len,proc,*dnz,*onz,bs,cbs; 4499 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4500 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4501 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4502 MPI_Status *status; 4503 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4504 PetscBT lnkbt; 4505 Mat_Merge_SeqsToMPI *merge; 4506 PetscContainer container; 4507 4508 PetscFunctionBegin; 4509 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4510 4511 /* make sure it is a PETSc comm */ 4512 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4513 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4514 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4515 4516 ierr = PetscNew(&merge);CHKERRQ(ierr); 4517 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4518 4519 /* determine row ownership */ 4520 /*---------------------------------------------------------*/ 4521 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4522 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4523 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4524 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4525 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4526 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4527 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4528 4529 m = merge->rowmap->n; 4530 owners = merge->rowmap->range; 4531 4532 /* determine the number of messages to send, their lengths */ 4533 /*---------------------------------------------------------*/ 4534 len_s = merge->len_s; 4535 4536 len = 0; /* length of buf_si[] */ 4537 merge->nsend = 0; 4538 for (proc=0; proc<size; proc++) { 4539 len_si[proc] = 0; 4540 if (proc == rank) { 4541 len_s[proc] = 0; 4542 } else { 4543 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4544 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4545 } 4546 if (len_s[proc]) { 4547 merge->nsend++; 4548 nrows = 0; 4549 for (i=owners[proc]; i<owners[proc+1]; i++) { 4550 if (ai[i+1] > ai[i]) nrows++; 4551 } 4552 len_si[proc] = 2*(nrows+1); 4553 len += len_si[proc]; 4554 } 4555 } 4556 4557 /* determine the number and length of messages to receive for ij-structure */ 4558 /*-------------------------------------------------------------------------*/ 4559 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4560 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4561 4562 /* post the Irecv of j-structure */ 4563 /*-------------------------------*/ 4564 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4565 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4566 4567 /* post the Isend of j-structure */ 4568 /*--------------------------------*/ 4569 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4570 4571 for (proc=0, k=0; proc<size; proc++) { 4572 if (!len_s[proc]) continue; 4573 i = owners[proc]; 4574 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4575 k++; 4576 } 4577 4578 /* receives and sends of j-structure are complete */ 4579 /*------------------------------------------------*/ 4580 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4581 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4582 4583 /* send and recv i-structure */ 4584 /*---------------------------*/ 4585 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4586 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4587 4588 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4589 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4590 for (proc=0,k=0; proc<size; proc++) { 4591 if (!len_s[proc]) continue; 4592 /* form outgoing message for i-structure: 4593 buf_si[0]: nrows to be sent 4594 [1:nrows]: row index (global) 4595 [nrows+1:2*nrows+1]: i-structure index 4596 */ 4597 /*-------------------------------------------*/ 4598 nrows = len_si[proc]/2 - 1; 4599 buf_si_i = buf_si + nrows+1; 4600 buf_si[0] = nrows; 4601 buf_si_i[0] = 0; 4602 nrows = 0; 4603 for (i=owners[proc]; i<owners[proc+1]; i++) { 4604 anzi = ai[i+1] - ai[i]; 4605 if (anzi) { 4606 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4607 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4608 nrows++; 4609 } 4610 } 4611 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4612 k++; 4613 buf_si += len_si[proc]; 4614 } 4615 4616 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4617 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4618 4619 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4620 for (i=0; i<merge->nrecv; i++) { 4621 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); 4622 } 4623 4624 ierr = PetscFree(len_si);CHKERRQ(ierr); 4625 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4626 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4627 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4628 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4629 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4630 ierr = PetscFree(status);CHKERRQ(ierr); 4631 4632 /* compute a local seq matrix in each processor */ 4633 /*----------------------------------------------*/ 4634 /* allocate bi array and free space for accumulating nonzero column info */ 4635 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4636 bi[0] = 0; 4637 4638 /* create and initialize a linked list */ 4639 nlnk = N+1; 4640 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4641 4642 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4643 len = ai[owners[rank+1]] - ai[owners[rank]]; 4644 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4645 4646 current_space = free_space; 4647 4648 /* determine symbolic info for each local row */ 4649 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4650 4651 for (k=0; k<merge->nrecv; k++) { 4652 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4653 nrows = *buf_ri_k[k]; 4654 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4655 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4656 } 4657 4658 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4659 len = 0; 4660 for (i=0; i<m; i++) { 4661 bnzi = 0; 4662 /* add local non-zero cols of this proc's seqmat into lnk */ 4663 arow = owners[rank] + i; 4664 anzi = ai[arow+1] - ai[arow]; 4665 aj = a->j + ai[arow]; 4666 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4667 bnzi += nlnk; 4668 /* add received col data into lnk */ 4669 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4670 if (i == *nextrow[k]) { /* i-th row */ 4671 anzi = *(nextai[k]+1) - *nextai[k]; 4672 aj = buf_rj[k] + *nextai[k]; 4673 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4674 bnzi += nlnk; 4675 nextrow[k]++; nextai[k]++; 4676 } 4677 } 4678 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4679 4680 /* if free space is not available, make more free space */ 4681 if (current_space->local_remaining<bnzi) { 4682 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4683 nspacedouble++; 4684 } 4685 /* copy data into free space, then initialize lnk */ 4686 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4687 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4688 4689 current_space->array += bnzi; 4690 current_space->local_used += bnzi; 4691 current_space->local_remaining -= bnzi; 4692 4693 bi[i+1] = bi[i] + bnzi; 4694 } 4695 4696 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4697 4698 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4699 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4700 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4701 4702 /* create symbolic parallel matrix B_mpi */ 4703 /*---------------------------------------*/ 4704 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4705 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4706 if (n==PETSC_DECIDE) { 4707 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4708 } else { 4709 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4710 } 4711 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4712 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4713 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4714 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4715 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4716 4717 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4718 B_mpi->assembled = PETSC_FALSE; 4719 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4720 merge->bi = bi; 4721 merge->bj = bj; 4722 merge->buf_ri = buf_ri; 4723 merge->buf_rj = buf_rj; 4724 merge->coi = NULL; 4725 merge->coj = NULL; 4726 merge->owners_co = NULL; 4727 4728 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4729 4730 /* attach the supporting struct to B_mpi for reuse */ 4731 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4732 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4733 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4734 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4735 *mpimat = B_mpi; 4736 4737 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4738 PetscFunctionReturn(0); 4739 } 4740 4741 /*@C 4742 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4743 matrices from each processor 4744 4745 Collective on MPI_Comm 4746 4747 Input Parameters: 4748 + comm - the communicators the parallel matrix will live on 4749 . seqmat - the input sequential matrices 4750 . m - number of local rows (or PETSC_DECIDE) 4751 . n - number of local columns (or PETSC_DECIDE) 4752 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4753 4754 Output Parameter: 4755 . mpimat - the parallel matrix generated 4756 4757 Level: advanced 4758 4759 Notes: 4760 The dimensions of the sequential matrix in each processor MUST be the same. 4761 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4762 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4763 @*/ 4764 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4765 { 4766 PetscErrorCode ierr; 4767 PetscMPIInt size; 4768 4769 PetscFunctionBegin; 4770 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4771 if (size == 1) { 4772 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4773 if (scall == MAT_INITIAL_MATRIX) { 4774 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4775 } else { 4776 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4777 } 4778 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4779 PetscFunctionReturn(0); 4780 } 4781 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4782 if (scall == MAT_INITIAL_MATRIX) { 4783 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4784 } 4785 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4786 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4787 PetscFunctionReturn(0); 4788 } 4789 4790 /*@ 4791 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 4792 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4793 with MatGetSize() 4794 4795 Not Collective 4796 4797 Input Parameters: 4798 + A - the matrix 4799 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4800 4801 Output Parameter: 4802 . A_loc - the local sequential matrix generated 4803 4804 Level: developer 4805 4806 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4807 4808 @*/ 4809 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4810 { 4811 PetscErrorCode ierr; 4812 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4813 Mat_SeqAIJ *mat,*a,*b; 4814 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4815 MatScalar *aa,*ba,*cam; 4816 PetscScalar *ca; 4817 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4818 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4819 PetscBool match; 4820 MPI_Comm comm; 4821 PetscMPIInt size; 4822 4823 PetscFunctionBegin; 4824 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4825 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4826 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4827 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4828 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4829 4830 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4831 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4832 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4833 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4834 aa = a->a; ba = b->a; 4835 if (scall == MAT_INITIAL_MATRIX) { 4836 if (size == 1) { 4837 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4838 PetscFunctionReturn(0); 4839 } 4840 4841 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4842 ci[0] = 0; 4843 for (i=0; i<am; i++) { 4844 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4845 } 4846 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4847 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4848 k = 0; 4849 for (i=0; i<am; i++) { 4850 ncols_o = bi[i+1] - bi[i]; 4851 ncols_d = ai[i+1] - ai[i]; 4852 /* off-diagonal portion of A */ 4853 for (jo=0; jo<ncols_o; jo++) { 4854 col = cmap[*bj]; 4855 if (col >= cstart) break; 4856 cj[k] = col; bj++; 4857 ca[k++] = *ba++; 4858 } 4859 /* diagonal portion of A */ 4860 for (j=0; j<ncols_d; j++) { 4861 cj[k] = cstart + *aj++; 4862 ca[k++] = *aa++; 4863 } 4864 /* off-diagonal portion of A */ 4865 for (j=jo; j<ncols_o; j++) { 4866 cj[k] = cmap[*bj++]; 4867 ca[k++] = *ba++; 4868 } 4869 } 4870 /* put together the new matrix */ 4871 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4872 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4873 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4874 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4875 mat->free_a = PETSC_TRUE; 4876 mat->free_ij = PETSC_TRUE; 4877 mat->nonew = 0; 4878 } else if (scall == MAT_REUSE_MATRIX) { 4879 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4880 ci = mat->i; cj = mat->j; cam = mat->a; 4881 for (i=0; i<am; i++) { 4882 /* off-diagonal portion of A */ 4883 ncols_o = bi[i+1] - bi[i]; 4884 for (jo=0; jo<ncols_o; jo++) { 4885 col = cmap[*bj]; 4886 if (col >= cstart) break; 4887 *cam++ = *ba++; bj++; 4888 } 4889 /* diagonal portion of A */ 4890 ncols_d = ai[i+1] - ai[i]; 4891 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4892 /* off-diagonal portion of A */ 4893 for (j=jo; j<ncols_o; j++) { 4894 *cam++ = *ba++; bj++; 4895 } 4896 } 4897 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4898 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4899 PetscFunctionReturn(0); 4900 } 4901 4902 /*@C 4903 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4904 4905 Not Collective 4906 4907 Input Parameters: 4908 + A - the matrix 4909 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4910 - row, col - index sets of rows and columns to extract (or NULL) 4911 4912 Output Parameter: 4913 . A_loc - the local sequential matrix generated 4914 4915 Level: developer 4916 4917 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4918 4919 @*/ 4920 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4921 { 4922 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4923 PetscErrorCode ierr; 4924 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4925 IS isrowa,iscola; 4926 Mat *aloc; 4927 PetscBool match; 4928 4929 PetscFunctionBegin; 4930 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4931 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4932 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4933 if (!row) { 4934 start = A->rmap->rstart; end = A->rmap->rend; 4935 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 4936 } else { 4937 isrowa = *row; 4938 } 4939 if (!col) { 4940 start = A->cmap->rstart; 4941 cmap = a->garray; 4942 nzA = a->A->cmap->n; 4943 nzB = a->B->cmap->n; 4944 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4945 ncols = 0; 4946 for (i=0; i<nzB; i++) { 4947 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4948 else break; 4949 } 4950 imark = i; 4951 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 4952 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 4953 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 4954 } else { 4955 iscola = *col; 4956 } 4957 if (scall != MAT_INITIAL_MATRIX) { 4958 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 4959 aloc[0] = *A_loc; 4960 } 4961 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 4962 *A_loc = aloc[0]; 4963 ierr = PetscFree(aloc);CHKERRQ(ierr); 4964 if (!row) { 4965 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 4966 } 4967 if (!col) { 4968 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 4969 } 4970 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4971 PetscFunctionReturn(0); 4972 } 4973 4974 /*@C 4975 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 4976 4977 Collective on Mat 4978 4979 Input Parameters: 4980 + A,B - the matrices in mpiaij format 4981 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4982 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 4983 4984 Output Parameter: 4985 + rowb, colb - index sets of rows and columns of B to extract 4986 - B_seq - the sequential matrix generated 4987 4988 Level: developer 4989 4990 @*/ 4991 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 4992 { 4993 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4994 PetscErrorCode ierr; 4995 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 4996 IS isrowb,iscolb; 4997 Mat *bseq=NULL; 4998 4999 PetscFunctionBegin; 5000 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5001 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); 5002 } 5003 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5004 5005 if (scall == MAT_INITIAL_MATRIX) { 5006 start = A->cmap->rstart; 5007 cmap = a->garray; 5008 nzA = a->A->cmap->n; 5009 nzB = a->B->cmap->n; 5010 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5011 ncols = 0; 5012 for (i=0; i<nzB; i++) { /* row < local row index */ 5013 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5014 else break; 5015 } 5016 imark = i; 5017 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 5018 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5019 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 5020 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 5021 } else { 5022 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5023 isrowb = *rowb; iscolb = *colb; 5024 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 5025 bseq[0] = *B_seq; 5026 } 5027 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 5028 *B_seq = bseq[0]; 5029 ierr = PetscFree(bseq);CHKERRQ(ierr); 5030 if (!rowb) { 5031 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 5032 } else { 5033 *rowb = isrowb; 5034 } 5035 if (!colb) { 5036 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 5037 } else { 5038 *colb = iscolb; 5039 } 5040 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5041 PetscFunctionReturn(0); 5042 } 5043 5044 /* 5045 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 5046 of the OFF-DIAGONAL portion of local A 5047 5048 Collective on Mat 5049 5050 Input Parameters: 5051 + A,B - the matrices in mpiaij format 5052 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5053 5054 Output Parameter: 5055 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5056 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5057 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5058 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5059 5060 Level: developer 5061 5062 */ 5063 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5064 { 5065 VecScatter_MPI_General *gen_to,*gen_from; 5066 PetscErrorCode ierr; 5067 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5068 Mat_SeqAIJ *b_oth; 5069 VecScatter ctx =a->Mvctx; 5070 MPI_Comm comm; 5071 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 5072 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5073 PetscInt *rvalues,*svalues; 5074 MatScalar *b_otha,*bufa,*bufA; 5075 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5076 MPI_Request *rwaits = NULL,*swaits = NULL; 5077 MPI_Status *sstatus,rstatus; 5078 PetscMPIInt jj,size; 5079 PetscInt *cols,sbs,rbs; 5080 PetscScalar *vals; 5081 5082 PetscFunctionBegin; 5083 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5084 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5085 5086 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5087 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); 5088 } 5089 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5090 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5091 5092 if (size == 1) { 5093 startsj_s = NULL; 5094 bufa_ptr = NULL; 5095 *B_oth = NULL; 5096 PetscFunctionReturn(0); 5097 } 5098 5099 gen_to = (VecScatter_MPI_General*)ctx->todata; 5100 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5101 nrecvs = gen_from->n; 5102 nsends = gen_to->n; 5103 5104 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 5105 srow = gen_to->indices; /* local row index to be sent */ 5106 sstarts = gen_to->starts; 5107 sprocs = gen_to->procs; 5108 sstatus = gen_to->sstatus; 5109 sbs = gen_to->bs; 5110 rstarts = gen_from->starts; 5111 rprocs = gen_from->procs; 5112 rbs = gen_from->bs; 5113 5114 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5115 if (scall == MAT_INITIAL_MATRIX) { 5116 /* i-array */ 5117 /*---------*/ 5118 /* post receives */ 5119 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 5120 for (i=0; i<nrecvs; i++) { 5121 rowlen = rvalues + rstarts[i]*rbs; 5122 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5123 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5124 } 5125 5126 /* pack the outgoing message */ 5127 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 5128 5129 sstartsj[0] = 0; 5130 rstartsj[0] = 0; 5131 len = 0; /* total length of j or a array to be sent */ 5132 k = 0; 5133 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 5134 for (i=0; i<nsends; i++) { 5135 rowlen = svalues + sstarts[i]*sbs; 5136 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5137 for (j=0; j<nrows; j++) { 5138 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5139 for (l=0; l<sbs; l++) { 5140 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5141 5142 rowlen[j*sbs+l] = ncols; 5143 5144 len += ncols; 5145 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5146 } 5147 k++; 5148 } 5149 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5150 5151 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5152 } 5153 /* recvs and sends of i-array are completed */ 5154 i = nrecvs; 5155 while (i--) { 5156 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5157 } 5158 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5159 ierr = PetscFree(svalues);CHKERRQ(ierr); 5160 5161 /* allocate buffers for sending j and a arrays */ 5162 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5163 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5164 5165 /* create i-array of B_oth */ 5166 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5167 5168 b_othi[0] = 0; 5169 len = 0; /* total length of j or a array to be received */ 5170 k = 0; 5171 for (i=0; i<nrecvs; i++) { 5172 rowlen = rvalues + rstarts[i]*rbs; 5173 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5174 for (j=0; j<nrows; j++) { 5175 b_othi[k+1] = b_othi[k] + rowlen[j]; 5176 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5177 k++; 5178 } 5179 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5180 } 5181 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5182 5183 /* allocate space for j and a arrrays of B_oth */ 5184 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5185 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5186 5187 /* j-array */ 5188 /*---------*/ 5189 /* post receives of j-array */ 5190 for (i=0; i<nrecvs; i++) { 5191 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5192 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5193 } 5194 5195 /* pack the outgoing message j-array */ 5196 k = 0; 5197 for (i=0; i<nsends; i++) { 5198 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5199 bufJ = bufj+sstartsj[i]; 5200 for (j=0; j<nrows; j++) { 5201 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5202 for (ll=0; ll<sbs; ll++) { 5203 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5204 for (l=0; l<ncols; l++) { 5205 *bufJ++ = cols[l]; 5206 } 5207 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5208 } 5209 } 5210 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5211 } 5212 5213 /* recvs and sends of j-array are completed */ 5214 i = nrecvs; 5215 while (i--) { 5216 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5217 } 5218 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5219 } else if (scall == MAT_REUSE_MATRIX) { 5220 sstartsj = *startsj_s; 5221 rstartsj = *startsj_r; 5222 bufa = *bufa_ptr; 5223 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5224 b_otha = b_oth->a; 5225 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5226 5227 /* a-array */ 5228 /*---------*/ 5229 /* post receives of a-array */ 5230 for (i=0; i<nrecvs; i++) { 5231 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5232 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5233 } 5234 5235 /* pack the outgoing message a-array */ 5236 k = 0; 5237 for (i=0; i<nsends; i++) { 5238 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5239 bufA = bufa+sstartsj[i]; 5240 for (j=0; j<nrows; j++) { 5241 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5242 for (ll=0; ll<sbs; ll++) { 5243 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5244 for (l=0; l<ncols; l++) { 5245 *bufA++ = vals[l]; 5246 } 5247 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5248 } 5249 } 5250 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5251 } 5252 /* recvs and sends of a-array are completed */ 5253 i = nrecvs; 5254 while (i--) { 5255 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5256 } 5257 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5258 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5259 5260 if (scall == MAT_INITIAL_MATRIX) { 5261 /* put together the new matrix */ 5262 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5263 5264 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5265 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5266 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5267 b_oth->free_a = PETSC_TRUE; 5268 b_oth->free_ij = PETSC_TRUE; 5269 b_oth->nonew = 0; 5270 5271 ierr = PetscFree(bufj);CHKERRQ(ierr); 5272 if (!startsj_s || !bufa_ptr) { 5273 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5274 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5275 } else { 5276 *startsj_s = sstartsj; 5277 *startsj_r = rstartsj; 5278 *bufa_ptr = bufa; 5279 } 5280 } 5281 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5282 PetscFunctionReturn(0); 5283 } 5284 5285 /*@C 5286 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5287 5288 Not Collective 5289 5290 Input Parameters: 5291 . A - The matrix in mpiaij format 5292 5293 Output Parameter: 5294 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5295 . colmap - A map from global column index to local index into lvec 5296 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5297 5298 Level: developer 5299 5300 @*/ 5301 #if defined(PETSC_USE_CTABLE) 5302 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5303 #else 5304 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5305 #endif 5306 { 5307 Mat_MPIAIJ *a; 5308 5309 PetscFunctionBegin; 5310 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5311 PetscValidPointer(lvec, 2); 5312 PetscValidPointer(colmap, 3); 5313 PetscValidPointer(multScatter, 4); 5314 a = (Mat_MPIAIJ*) A->data; 5315 if (lvec) *lvec = a->lvec; 5316 if (colmap) *colmap = a->colmap; 5317 if (multScatter) *multScatter = a->Mvctx; 5318 PetscFunctionReturn(0); 5319 } 5320 5321 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5322 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5323 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5324 #if defined(PETSC_HAVE_ELEMENTAL) 5325 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5326 #endif 5327 #if defined(PETSC_HAVE_HYPRE) 5328 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5329 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5330 #endif 5331 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5332 5333 /* 5334 Computes (B'*A')' since computing B*A directly is untenable 5335 5336 n p p 5337 ( ) ( ) ( ) 5338 m ( A ) * n ( B ) = m ( C ) 5339 ( ) ( ) ( ) 5340 5341 */ 5342 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5343 { 5344 PetscErrorCode ierr; 5345 Mat At,Bt,Ct; 5346 5347 PetscFunctionBegin; 5348 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5349 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5350 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5351 ierr = MatDestroy(&At);CHKERRQ(ierr); 5352 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5353 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5354 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5355 PetscFunctionReturn(0); 5356 } 5357 5358 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5359 { 5360 PetscErrorCode ierr; 5361 PetscInt m=A->rmap->n,n=B->cmap->n; 5362 Mat Cmat; 5363 5364 PetscFunctionBegin; 5365 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); 5366 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5367 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5368 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5369 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5370 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5371 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5372 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5373 5374 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5375 5376 *C = Cmat; 5377 PetscFunctionReturn(0); 5378 } 5379 5380 /* ----------------------------------------------------------------*/ 5381 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5382 { 5383 PetscErrorCode ierr; 5384 5385 PetscFunctionBegin; 5386 if (scall == MAT_INITIAL_MATRIX) { 5387 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5388 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5389 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5390 } 5391 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5392 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5393 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5394 PetscFunctionReturn(0); 5395 } 5396 5397 /*MC 5398 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5399 5400 Options Database Keys: 5401 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5402 5403 Level: beginner 5404 5405 .seealso: MatCreateAIJ() 5406 M*/ 5407 5408 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5409 { 5410 Mat_MPIAIJ *b; 5411 PetscErrorCode ierr; 5412 PetscMPIInt size; 5413 5414 PetscFunctionBegin; 5415 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5416 5417 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5418 B->data = (void*)b; 5419 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5420 B->assembled = PETSC_FALSE; 5421 B->insertmode = NOT_SET_VALUES; 5422 b->size = size; 5423 5424 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5425 5426 /* build cache for off array entries formed */ 5427 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5428 5429 b->donotstash = PETSC_FALSE; 5430 b->colmap = 0; 5431 b->garray = 0; 5432 b->roworiented = PETSC_TRUE; 5433 5434 /* stuff used for matrix vector multiply */ 5435 b->lvec = NULL; 5436 b->Mvctx = NULL; 5437 5438 /* stuff for MatGetRow() */ 5439 b->rowindices = 0; 5440 b->rowvalues = 0; 5441 b->getrowactive = PETSC_FALSE; 5442 5443 /* flexible pointer used in CUSP/CUSPARSE classes */ 5444 b->spptr = NULL; 5445 5446 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5447 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5448 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5449 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5450 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5451 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5452 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5453 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5454 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5455 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5456 #if defined(PETSC_HAVE_ELEMENTAL) 5457 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5458 #endif 5459 #if defined(PETSC_HAVE_HYPRE) 5460 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5461 #endif 5462 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5463 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5464 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5465 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5466 #if defined(PETSC_HAVE_HYPRE) 5467 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5468 #endif 5469 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5470 PetscFunctionReturn(0); 5471 } 5472 5473 /*@C 5474 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5475 and "off-diagonal" part of the matrix in CSR format. 5476 5477 Collective on MPI_Comm 5478 5479 Input Parameters: 5480 + comm - MPI communicator 5481 . m - number of local rows (Cannot be PETSC_DECIDE) 5482 . n - This value should be the same as the local size used in creating the 5483 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5484 calculated if N is given) For square matrices n is almost always m. 5485 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5486 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5487 . i - row indices for "diagonal" portion of matrix 5488 . j - column indices 5489 . a - matrix values 5490 . oi - row indices for "off-diagonal" portion of matrix 5491 . oj - column indices 5492 - oa - matrix values 5493 5494 Output Parameter: 5495 . mat - the matrix 5496 5497 Level: advanced 5498 5499 Notes: 5500 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5501 must free the arrays once the matrix has been destroyed and not before. 5502 5503 The i and j indices are 0 based 5504 5505 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5506 5507 This sets local rows and cannot be used to set off-processor values. 5508 5509 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5510 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5511 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5512 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5513 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5514 communication if it is known that only local entries will be set. 5515 5516 .keywords: matrix, aij, compressed row, sparse, parallel 5517 5518 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5519 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5520 @*/ 5521 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) 5522 { 5523 PetscErrorCode ierr; 5524 Mat_MPIAIJ *maij; 5525 5526 PetscFunctionBegin; 5527 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5528 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5529 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5530 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5531 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5532 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5533 maij = (Mat_MPIAIJ*) (*mat)->data; 5534 5535 (*mat)->preallocated = PETSC_TRUE; 5536 5537 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5538 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5539 5540 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5541 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5542 5543 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5544 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5545 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5546 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5547 5548 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5549 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5550 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5551 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5552 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5553 PetscFunctionReturn(0); 5554 } 5555 5556 /* 5557 Special version for direct calls from Fortran 5558 */ 5559 #include <petsc/private/fortranimpl.h> 5560 5561 /* Change these macros so can be used in void function */ 5562 #undef CHKERRQ 5563 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5564 #undef SETERRQ2 5565 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5566 #undef SETERRQ3 5567 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5568 #undef SETERRQ 5569 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5570 5571 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5572 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5573 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5574 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5575 #else 5576 #endif 5577 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) 5578 { 5579 Mat mat = *mmat; 5580 PetscInt m = *mm, n = *mn; 5581 InsertMode addv = *maddv; 5582 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5583 PetscScalar value; 5584 PetscErrorCode ierr; 5585 5586 MatCheckPreallocated(mat,1); 5587 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5588 5589 #if defined(PETSC_USE_DEBUG) 5590 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5591 #endif 5592 { 5593 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5594 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5595 PetscBool roworiented = aij->roworiented; 5596 5597 /* Some Variables required in the macro */ 5598 Mat A = aij->A; 5599 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5600 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5601 MatScalar *aa = a->a; 5602 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5603 Mat B = aij->B; 5604 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5605 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5606 MatScalar *ba = b->a; 5607 5608 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5609 PetscInt nonew = a->nonew; 5610 MatScalar *ap1,*ap2; 5611 5612 PetscFunctionBegin; 5613 for (i=0; i<m; i++) { 5614 if (im[i] < 0) continue; 5615 #if defined(PETSC_USE_DEBUG) 5616 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); 5617 #endif 5618 if (im[i] >= rstart && im[i] < rend) { 5619 row = im[i] - rstart; 5620 lastcol1 = -1; 5621 rp1 = aj + ai[row]; 5622 ap1 = aa + ai[row]; 5623 rmax1 = aimax[row]; 5624 nrow1 = ailen[row]; 5625 low1 = 0; 5626 high1 = nrow1; 5627 lastcol2 = -1; 5628 rp2 = bj + bi[row]; 5629 ap2 = ba + bi[row]; 5630 rmax2 = bimax[row]; 5631 nrow2 = bilen[row]; 5632 low2 = 0; 5633 high2 = nrow2; 5634 5635 for (j=0; j<n; j++) { 5636 if (roworiented) value = v[i*n+j]; 5637 else value = v[i+j*m]; 5638 if (in[j] >= cstart && in[j] < cend) { 5639 col = in[j] - cstart; 5640 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5641 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5642 } else if (in[j] < 0) continue; 5643 #if defined(PETSC_USE_DEBUG) 5644 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); 5645 #endif 5646 else { 5647 if (mat->was_assembled) { 5648 if (!aij->colmap) { 5649 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5650 } 5651 #if defined(PETSC_USE_CTABLE) 5652 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5653 col--; 5654 #else 5655 col = aij->colmap[in[j]] - 1; 5656 #endif 5657 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5658 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5659 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5660 col = in[j]; 5661 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5662 B = aij->B; 5663 b = (Mat_SeqAIJ*)B->data; 5664 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5665 rp2 = bj + bi[row]; 5666 ap2 = ba + bi[row]; 5667 rmax2 = bimax[row]; 5668 nrow2 = bilen[row]; 5669 low2 = 0; 5670 high2 = nrow2; 5671 bm = aij->B->rmap->n; 5672 ba = b->a; 5673 } 5674 } else col = in[j]; 5675 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5676 } 5677 } 5678 } else if (!aij->donotstash) { 5679 if (roworiented) { 5680 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5681 } else { 5682 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5683 } 5684 } 5685 } 5686 } 5687 PetscFunctionReturnVoid(); 5688 } 5689 5690