1 2 3 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 4 #include <petsc/private/vecimpl.h> 5 #include <petsc/private/isimpl.h> 6 #include <petscblaslapack.h> 7 #include <petscsf.h> 8 9 /*MC 10 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 11 12 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 13 and MATMPIAIJ otherwise. As a result, for single process communicators, 14 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 15 for communicators controlling multiple processes. It is recommended that you call both of 16 the above preallocation routines for simplicity. 17 18 Options Database Keys: 19 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 20 21 Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when 22 enough exist. 23 24 Level: beginner 25 26 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ, MATMPIAIJ 27 M*/ 28 29 /*MC 30 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 31 32 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 33 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 34 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 35 for communicators controlling multiple processes. It is recommended that you call both of 36 the above preallocation routines for simplicity. 37 38 Options Database Keys: 39 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 40 41 Level: beginner 42 43 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 44 M*/ 45 46 PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 50 51 PetscFunctionBegin; 52 if (mat->A) { 53 ierr = MatSetBlockSizes(mat->A,rbs,cbs);CHKERRQ(ierr); 54 ierr = MatSetBlockSizes(mat->B,rbs,1);CHKERRQ(ierr); 55 } 56 PetscFunctionReturn(0); 57 } 58 59 PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows) 60 { 61 PetscErrorCode ierr; 62 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 63 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data; 64 Mat_SeqAIJ *b = (Mat_SeqAIJ*)mat->B->data; 65 const PetscInt *ia,*ib; 66 const MatScalar *aa,*bb; 67 PetscInt na,nb,i,j,*rows,cnt=0,n0rows; 68 PetscInt m = M->rmap->n,rstart = M->rmap->rstart; 69 70 PetscFunctionBegin; 71 *keptrows = 0; 72 ia = a->i; 73 ib = b->i; 74 for (i=0; i<m; i++) { 75 na = ia[i+1] - ia[i]; 76 nb = ib[i+1] - ib[i]; 77 if (!na && !nb) { 78 cnt++; 79 goto ok1; 80 } 81 aa = a->a + ia[i]; 82 for (j=0; j<na; j++) { 83 if (aa[j] != 0.0) goto ok1; 84 } 85 bb = b->a + ib[i]; 86 for (j=0; j <nb; j++) { 87 if (bb[j] != 0.0) goto ok1; 88 } 89 cnt++; 90 ok1:; 91 } 92 ierr = MPIU_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr); 93 if (!n0rows) PetscFunctionReturn(0); 94 ierr = PetscMalloc1(M->rmap->n-cnt,&rows);CHKERRQ(ierr); 95 cnt = 0; 96 for (i=0; i<m; i++) { 97 na = ia[i+1] - ia[i]; 98 nb = ib[i+1] - ib[i]; 99 if (!na && !nb) continue; 100 aa = a->a + ia[i]; 101 for (j=0; j<na;j++) { 102 if (aa[j] != 0.0) { 103 rows[cnt++] = rstart + i; 104 goto ok2; 105 } 106 } 107 bb = b->a + ib[i]; 108 for (j=0; j<nb; j++) { 109 if (bb[j] != 0.0) { 110 rows[cnt++] = rstart + i; 111 goto ok2; 112 } 113 } 114 ok2:; 115 } 116 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 117 PetscFunctionReturn(0); 118 } 119 120 PetscErrorCode MatDiagonalSet_MPIAIJ(Mat Y,Vec D,InsertMode is) 121 { 122 PetscErrorCode ierr; 123 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) Y->data; 124 125 PetscFunctionBegin; 126 if (Y->assembled && Y->rmap->rstart == Y->cmap->rstart && Y->rmap->rend == Y->cmap->rend) { 127 ierr = MatDiagonalSet(aij->A,D,is);CHKERRQ(ierr); 128 } else { 129 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 130 } 131 PetscFunctionReturn(0); 132 } 133 134 PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows) 135 { 136 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)M->data; 137 PetscErrorCode ierr; 138 PetscInt i,rstart,nrows,*rows; 139 140 PetscFunctionBegin; 141 *zrows = NULL; 142 ierr = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr); 143 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 144 for (i=0; i<nrows; i++) rows[i] += rstart; 145 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 146 PetscFunctionReturn(0); 147 } 148 149 PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms) 150 { 151 PetscErrorCode ierr; 152 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 153 PetscInt i,n,*garray = aij->garray; 154 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ*) aij->A->data; 155 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ*) aij->B->data; 156 PetscReal *work; 157 158 PetscFunctionBegin; 159 ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr); 160 ierr = PetscCalloc1(n,&work);CHKERRQ(ierr); 161 if (type == NORM_2) { 162 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 163 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]); 164 } 165 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 166 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]); 167 } 168 } else if (type == NORM_1) { 169 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 170 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 171 } 172 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 173 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 174 } 175 } else if (type == NORM_INFINITY) { 176 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 177 work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 178 } 179 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 180 work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]); 181 } 182 183 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 184 if (type == NORM_INFINITY) { 185 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 186 } else { 187 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 188 } 189 ierr = PetscFree(work);CHKERRQ(ierr); 190 if (type == NORM_2) { 191 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 192 } 193 PetscFunctionReturn(0); 194 } 195 196 PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A,IS *is) 197 { 198 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 199 IS sis,gis; 200 PetscErrorCode ierr; 201 const PetscInt *isis,*igis; 202 PetscInt n,*iis,nsis,ngis,rstart,i; 203 204 PetscFunctionBegin; 205 ierr = MatFindOffBlockDiagonalEntries(a->A,&sis);CHKERRQ(ierr); 206 ierr = MatFindNonzeroRows(a->B,&gis);CHKERRQ(ierr); 207 ierr = ISGetSize(gis,&ngis);CHKERRQ(ierr); 208 ierr = ISGetSize(sis,&nsis);CHKERRQ(ierr); 209 ierr = ISGetIndices(sis,&isis);CHKERRQ(ierr); 210 ierr = ISGetIndices(gis,&igis);CHKERRQ(ierr); 211 212 ierr = PetscMalloc1(ngis+nsis,&iis);CHKERRQ(ierr); 213 ierr = PetscMemcpy(iis,igis,ngis*sizeof(PetscInt));CHKERRQ(ierr); 214 ierr = PetscMemcpy(iis+ngis,isis,nsis*sizeof(PetscInt));CHKERRQ(ierr); 215 n = ngis + nsis; 216 ierr = PetscSortRemoveDupsInt(&n,iis);CHKERRQ(ierr); 217 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 218 for (i=0; i<n; i++) iis[i] += rstart; 219 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),n,iis,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 220 221 ierr = ISRestoreIndices(sis,&isis);CHKERRQ(ierr); 222 ierr = ISRestoreIndices(gis,&igis);CHKERRQ(ierr); 223 ierr = ISDestroy(&sis);CHKERRQ(ierr); 224 ierr = ISDestroy(&gis);CHKERRQ(ierr); 225 PetscFunctionReturn(0); 226 } 227 228 /* 229 Distributes a SeqAIJ matrix across a set of processes. Code stolen from 230 MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type. 231 232 Only for square matrices 233 234 Used by a preconditioner, hence PETSC_EXTERN 235 */ 236 PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat) 237 { 238 PetscMPIInt rank,size; 239 PetscInt *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz = 0,*gmataj,cnt,row,*ld,bses[2]; 240 PetscErrorCode ierr; 241 Mat mat; 242 Mat_SeqAIJ *gmata; 243 PetscMPIInt tag; 244 MPI_Status status; 245 PetscBool aij; 246 MatScalar *gmataa,*ao,*ad,*gmataarestore=0; 247 248 PetscFunctionBegin; 249 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 250 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 251 if (!rank) { 252 ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr); 253 if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name); 254 } 255 if (reuse == MAT_INITIAL_MATRIX) { 256 ierr = MatCreate(comm,&mat);CHKERRQ(ierr); 257 ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 258 ierr = MatGetBlockSizes(gmat,&bses[0],&bses[1]);CHKERRQ(ierr); 259 ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr); 260 ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr); 261 ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr); 262 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 263 ierr = PetscMalloc2(m,&dlens,m,&olens);CHKERRQ(ierr); 264 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 265 266 rowners[0] = 0; 267 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 268 rstart = rowners[rank]; 269 rend = rowners[rank+1]; 270 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 271 if (!rank) { 272 gmata = (Mat_SeqAIJ*) gmat->data; 273 /* send row lengths to all processors */ 274 for (i=0; i<m; i++) dlens[i] = gmata->ilen[i]; 275 for (i=1; i<size; i++) { 276 ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 277 } 278 /* determine number diagonal and off-diagonal counts */ 279 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 280 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 281 jj = 0; 282 for (i=0; i<m; i++) { 283 for (j=0; j<dlens[i]; j++) { 284 if (gmata->j[jj] < rstart) ld[i]++; 285 if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++; 286 jj++; 287 } 288 } 289 /* send column indices to other processes */ 290 for (i=1; i<size; i++) { 291 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 292 ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 293 ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 294 } 295 296 /* send numerical values to other processes */ 297 for (i=1; i<size; i++) { 298 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 299 ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 300 } 301 gmataa = gmata->a; 302 gmataj = gmata->j; 303 304 } else { 305 /* receive row lengths */ 306 ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 307 /* receive column indices */ 308 ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 309 ierr = PetscMalloc2(nz,&gmataa,nz,&gmataj);CHKERRQ(ierr); 310 ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 311 /* determine number diagonal and off-diagonal counts */ 312 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 313 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 314 jj = 0; 315 for (i=0; i<m; i++) { 316 for (j=0; j<dlens[i]; j++) { 317 if (gmataj[jj] < rstart) ld[i]++; 318 if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++; 319 jj++; 320 } 321 } 322 /* receive numerical values */ 323 ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 324 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 325 } 326 /* set preallocation */ 327 for (i=0; i<m; i++) { 328 dlens[i] -= olens[i]; 329 } 330 ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr); 331 ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr); 332 333 for (i=0; i<m; i++) { 334 dlens[i] += olens[i]; 335 } 336 cnt = 0; 337 for (i=0; i<m; i++) { 338 row = rstart + i; 339 ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr); 340 cnt += dlens[i]; 341 } 342 if (rank) { 343 ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr); 344 } 345 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 346 ierr = PetscFree(rowners);CHKERRQ(ierr); 347 348 ((Mat_MPIAIJ*)(mat->data))->ld = ld; 349 350 *inmat = mat; 351 } else { /* column indices are already set; only need to move over numerical values from process 0 */ 352 Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data; 353 Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data; 354 mat = *inmat; 355 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 356 if (!rank) { 357 /* send numerical values to other processes */ 358 gmata = (Mat_SeqAIJ*) gmat->data; 359 ierr = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr); 360 gmataa = gmata->a; 361 for (i=1; i<size; i++) { 362 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 363 ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 364 } 365 nz = gmata->i[rowners[1]]-gmata->i[rowners[0]]; 366 } else { 367 /* receive numerical values from process 0*/ 368 nz = Ad->nz + Ao->nz; 369 ierr = PetscMalloc1(nz,&gmataa);CHKERRQ(ierr); gmataarestore = gmataa; 370 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 371 } 372 /* transfer numerical values into the diagonal A and off diagonal B parts of mat */ 373 ld = ((Mat_MPIAIJ*)(mat->data))->ld; 374 ad = Ad->a; 375 ao = Ao->a; 376 if (mat->rmap->n) { 377 i = 0; 378 nz = ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 379 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 380 } 381 for (i=1; i<mat->rmap->n; i++) { 382 nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 383 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 384 } 385 i--; 386 if (mat->rmap->n) { 387 nz = Ao->i[i+1] - Ao->i[i] - ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 388 } 389 if (rank) { 390 ierr = PetscFree(gmataarestore);CHKERRQ(ierr); 391 } 392 } 393 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 394 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 395 PetscFunctionReturn(0); 396 } 397 398 /* 399 Local utility routine that creates a mapping from the global column 400 number to the local number in the off-diagonal part of the local 401 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 402 a slightly higher hash table cost; without it it is not scalable (each processor 403 has an order N integer array but is fast to acess. 404 */ 405 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 406 { 407 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 408 PetscErrorCode ierr; 409 PetscInt n = aij->B->cmap->n,i; 410 411 PetscFunctionBegin; 412 if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray"); 413 #if defined(PETSC_USE_CTABLE) 414 ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 415 for (i=0; i<n; i++) { 416 ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr); 417 } 418 #else 419 ierr = PetscCalloc1(mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 420 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N+1)*sizeof(PetscInt));CHKERRQ(ierr); 421 for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1; 422 #endif 423 PetscFunctionReturn(0); 424 } 425 426 #define MatSetValues_SeqAIJ_A_Private(row,col,value,addv,orow,ocol) \ 427 { \ 428 if (col <= lastcol1) low1 = 0; \ 429 else high1 = nrow1; \ 430 lastcol1 = col;\ 431 while (high1-low1 > 5) { \ 432 t = (low1+high1)/2; \ 433 if (rp1[t] > col) high1 = t; \ 434 else low1 = t; \ 435 } \ 436 for (_i=low1; _i<high1; _i++) { \ 437 if (rp1[_i] > col) break; \ 438 if (rp1[_i] == col) { \ 439 if (addv == ADD_VALUES) ap1[_i] += value; \ 440 else ap1[_i] = value; \ 441 goto a_noinsert; \ 442 } \ 443 } \ 444 if (value == 0.0 && ignorezeroentries && row != col) {low1 = 0; high1 = nrow1;goto a_noinsert;} \ 445 if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;} \ 446 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 447 MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \ 448 N = nrow1++ - 1; a->nz++; high1++; \ 449 /* shift up all the later entries in this row */ \ 450 for (ii=N; ii>=_i; ii--) { \ 451 rp1[ii+1] = rp1[ii]; \ 452 ap1[ii+1] = ap1[ii]; \ 453 } \ 454 rp1[_i] = col; \ 455 ap1[_i] = value; \ 456 A->nonzerostate++;\ 457 a_noinsert: ; \ 458 ailen[row] = nrow1; \ 459 } 460 461 #define MatSetValues_SeqAIJ_B_Private(row,col,value,addv,orow,ocol) \ 462 { \ 463 if (col <= lastcol2) low2 = 0; \ 464 else high2 = nrow2; \ 465 lastcol2 = col; \ 466 while (high2-low2 > 5) { \ 467 t = (low2+high2)/2; \ 468 if (rp2[t] > col) high2 = t; \ 469 else low2 = t; \ 470 } \ 471 for (_i=low2; _i<high2; _i++) { \ 472 if (rp2[_i] > col) break; \ 473 if (rp2[_i] == col) { \ 474 if (addv == ADD_VALUES) ap2[_i] += value; \ 475 else ap2[_i] = value; \ 476 goto b_noinsert; \ 477 } \ 478 } \ 479 if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 480 if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 481 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 482 MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \ 483 N = nrow2++ - 1; b->nz++; high2++; \ 484 /* shift up all the later entries in this row */ \ 485 for (ii=N; ii>=_i; ii--) { \ 486 rp2[ii+1] = rp2[ii]; \ 487 ap2[ii+1] = ap2[ii]; \ 488 } \ 489 rp2[_i] = col; \ 490 ap2[_i] = value; \ 491 B->nonzerostate++; \ 492 b_noinsert: ; \ 493 bilen[row] = nrow2; \ 494 } 495 496 PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[]) 497 { 498 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)A->data; 499 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data; 500 PetscErrorCode ierr; 501 PetscInt l,*garray = mat->garray,diag; 502 503 PetscFunctionBegin; 504 /* code only works for square matrices A */ 505 506 /* find size of row to the left of the diagonal part */ 507 ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr); 508 row = row - diag; 509 for (l=0; l<b->i[row+1]-b->i[row]; l++) { 510 if (garray[b->j[b->i[row]+l]] > diag) break; 511 } 512 ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr); 513 514 /* diagonal part */ 515 ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr); 516 517 /* right of diagonal part */ 518 ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr); 519 PetscFunctionReturn(0); 520 } 521 522 PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 523 { 524 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 525 PetscScalar value; 526 PetscErrorCode ierr; 527 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 528 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 529 PetscBool roworiented = aij->roworiented; 530 531 /* Some Variables required in the macro */ 532 Mat A = aij->A; 533 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 534 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 535 MatScalar *aa = a->a; 536 PetscBool ignorezeroentries = a->ignorezeroentries; 537 Mat B = aij->B; 538 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 539 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 540 MatScalar *ba = b->a; 541 542 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 543 PetscInt nonew; 544 MatScalar *ap1,*ap2; 545 546 PetscFunctionBegin; 547 for (i=0; i<m; i++) { 548 if (im[i] < 0) continue; 549 #if defined(PETSC_USE_DEBUG) 550 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 551 #endif 552 if (im[i] >= rstart && im[i] < rend) { 553 row = im[i] - rstart; 554 lastcol1 = -1; 555 rp1 = aj + ai[row]; 556 ap1 = aa + ai[row]; 557 rmax1 = aimax[row]; 558 nrow1 = ailen[row]; 559 low1 = 0; 560 high1 = nrow1; 561 lastcol2 = -1; 562 rp2 = bj + bi[row]; 563 ap2 = ba + bi[row]; 564 rmax2 = bimax[row]; 565 nrow2 = bilen[row]; 566 low2 = 0; 567 high2 = nrow2; 568 569 for (j=0; j<n; j++) { 570 if (roworiented) value = v[i*n+j]; 571 else value = v[i+j*m]; 572 if (in[j] >= cstart && in[j] < cend) { 573 col = in[j] - cstart; 574 nonew = a->nonew; 575 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 576 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 577 } else if (in[j] < 0) continue; 578 #if defined(PETSC_USE_DEBUG) 579 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 580 #endif 581 else { 582 if (mat->was_assembled) { 583 if (!aij->colmap) { 584 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 585 } 586 #if defined(PETSC_USE_CTABLE) 587 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 588 col--; 589 #else 590 col = aij->colmap[in[j]] - 1; 591 #endif 592 if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) { 593 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 594 col = in[j]; 595 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 596 B = aij->B; 597 b = (Mat_SeqAIJ*)B->data; 598 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a; 599 rp2 = bj + bi[row]; 600 ap2 = ba + bi[row]; 601 rmax2 = bimax[row]; 602 nrow2 = bilen[row]; 603 low2 = 0; 604 high2 = nrow2; 605 bm = aij->B->rmap->n; 606 ba = b->a; 607 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", im[i], in[j]); 608 } else col = in[j]; 609 nonew = b->nonew; 610 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 611 } 612 } 613 } else { 614 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 615 if (!aij->donotstash) { 616 mat->assembled = PETSC_FALSE; 617 if (roworiented) { 618 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 619 } else { 620 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 621 } 622 } 623 } 624 } 625 PetscFunctionReturn(0); 626 } 627 628 PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 629 { 630 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 631 PetscErrorCode ierr; 632 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 633 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 634 635 PetscFunctionBegin; 636 for (i=0; i<m; i++) { 637 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 638 if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1); 639 if (idxm[i] >= rstart && idxm[i] < rend) { 640 row = idxm[i] - rstart; 641 for (j=0; j<n; j++) { 642 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 643 if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1); 644 if (idxn[j] >= cstart && idxn[j] < cend) { 645 col = idxn[j] - cstart; 646 ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 647 } else { 648 if (!aij->colmap) { 649 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 650 } 651 #if defined(PETSC_USE_CTABLE) 652 ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr); 653 col--; 654 #else 655 col = aij->colmap[idxn[j]] - 1; 656 #endif 657 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0; 658 else { 659 ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 660 } 661 } 662 } 663 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 664 } 665 PetscFunctionReturn(0); 666 } 667 668 extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec); 669 670 PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode) 671 { 672 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 673 PetscErrorCode ierr; 674 PetscInt nstash,reallocs; 675 676 PetscFunctionBegin; 677 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 678 679 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 680 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 681 ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 682 PetscFunctionReturn(0); 683 } 684 685 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode) 686 { 687 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 688 Mat_SeqAIJ *a = (Mat_SeqAIJ*)aij->A->data; 689 PetscErrorCode ierr; 690 PetscMPIInt n; 691 PetscInt i,j,rstart,ncols,flg; 692 PetscInt *row,*col; 693 PetscBool other_disassembled; 694 PetscScalar *val; 695 696 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 697 698 PetscFunctionBegin; 699 if (!aij->donotstash && !mat->nooffprocentries) { 700 while (1) { 701 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 702 if (!flg) break; 703 704 for (i=0; i<n; ) { 705 /* Now identify the consecutive vals belonging to the same row */ 706 for (j=i,rstart=row[j]; j<n; j++) { 707 if (row[j] != rstart) break; 708 } 709 if (j < n) ncols = j-i; 710 else ncols = n-i; 711 /* Now assemble all these values with a single function call */ 712 ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr); 713 714 i = j; 715 } 716 } 717 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 718 } 719 ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr); 720 ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr); 721 722 /* determine if any processor has disassembled, if so we must 723 also disassemble ourselfs, in order that we may reassemble. */ 724 /* 725 if nonzero structure of submatrix B cannot change then we know that 726 no processor disassembled thus we can skip this stuff 727 */ 728 if (!((Mat_SeqAIJ*)aij->B->data)->nonew) { 729 ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 730 if (mat->was_assembled && !other_disassembled) { 731 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 732 } 733 } 734 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 735 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 736 } 737 ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr); 738 ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr); 739 ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr); 740 741 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 742 743 aij->rowvalues = 0; 744 745 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 746 if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ; 747 748 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 749 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 750 PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate; 751 ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 752 } 753 PetscFunctionReturn(0); 754 } 755 756 PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 757 { 758 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 759 PetscErrorCode ierr; 760 761 PetscFunctionBegin; 762 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 763 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 764 PetscFunctionReturn(0); 765 } 766 767 PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 768 { 769 Mat_MPIAIJ *mat = (Mat_MPIAIJ *) A->data; 770 PetscInt *lrows; 771 PetscInt r, len; 772 PetscErrorCode ierr; 773 774 PetscFunctionBegin; 775 /* get locally owned rows */ 776 ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr); 777 /* fix right hand side if needed */ 778 if (x && b) { 779 const PetscScalar *xx; 780 PetscScalar *bb; 781 782 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 783 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 784 for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]]; 785 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 786 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 787 } 788 /* Must zero l->B before l->A because the (diag) case below may put values into l->B*/ 789 ierr = MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 790 if (A->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 791 PetscBool cong; 792 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 793 if (cong) A->congruentlayouts = 1; 794 else A->congruentlayouts = 0; 795 } 796 if ((diag != 0.0) && A->congruentlayouts) { 797 ierr = MatZeroRows(mat->A, len, lrows, diag, NULL, NULL);CHKERRQ(ierr); 798 } else if (diag != 0.0) { 799 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 800 if (((Mat_SeqAIJ *) mat->A->data)->nonew) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 801 for (r = 0; r < len; ++r) { 802 const PetscInt row = lrows[r] + A->rmap->rstart; 803 ierr = MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES);CHKERRQ(ierr); 804 } 805 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 806 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 807 } else { 808 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 809 } 810 ierr = PetscFree(lrows);CHKERRQ(ierr); 811 812 /* only change matrix nonzero state if pattern was allowed to be changed */ 813 if (!((Mat_SeqAIJ*)(mat->A->data))->keepnonzeropattern) { 814 PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate; 815 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 816 } 817 PetscFunctionReturn(0); 818 } 819 820 PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 821 { 822 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 823 PetscErrorCode ierr; 824 PetscMPIInt n = A->rmap->n; 825 PetscInt i,j,r,m,p = 0,len = 0; 826 PetscInt *lrows,*owners = A->rmap->range; 827 PetscSFNode *rrows; 828 PetscSF sf; 829 const PetscScalar *xx; 830 PetscScalar *bb,*mask; 831 Vec xmask,lmask; 832 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)l->B->data; 833 const PetscInt *aj, *ii,*ridx; 834 PetscScalar *aa; 835 836 PetscFunctionBegin; 837 /* Create SF where leaves are input rows and roots are owned rows */ 838 ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr); 839 for (r = 0; r < n; ++r) lrows[r] = -1; 840 ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr); 841 for (r = 0; r < N; ++r) { 842 const PetscInt idx = rows[r]; 843 if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N); 844 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */ 845 ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr); 846 } 847 rrows[r].rank = p; 848 rrows[r].index = rows[r] - owners[p]; 849 } 850 ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr); 851 ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr); 852 /* Collect flags for rows to be zeroed */ 853 ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 854 ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 855 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 856 /* Compress and put in row numbers */ 857 for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r; 858 /* zero diagonal part of matrix */ 859 ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr); 860 /* handle off diagonal part of matrix */ 861 ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr); 862 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 863 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 864 for (i=0; i<len; i++) bb[lrows[i]] = 1; 865 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 866 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 867 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 868 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 869 if (x) { 870 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 871 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 872 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 873 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 874 } 875 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 876 /* remove zeroed rows of off diagonal matrix */ 877 ii = aij->i; 878 for (i=0; i<len; i++) { 879 ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr); 880 } 881 /* loop over all elements of off process part of matrix zeroing removed columns*/ 882 if (aij->compressedrow.use) { 883 m = aij->compressedrow.nrows; 884 ii = aij->compressedrow.i; 885 ridx = aij->compressedrow.rindex; 886 for (i=0; i<m; i++) { 887 n = ii[i+1] - ii[i]; 888 aj = aij->j + ii[i]; 889 aa = aij->a + ii[i]; 890 891 for (j=0; j<n; j++) { 892 if (PetscAbsScalar(mask[*aj])) { 893 if (b) bb[*ridx] -= *aa*xx[*aj]; 894 *aa = 0.0; 895 } 896 aa++; 897 aj++; 898 } 899 ridx++; 900 } 901 } else { /* do not use compressed row format */ 902 m = l->B->rmap->n; 903 for (i=0; i<m; i++) { 904 n = ii[i+1] - ii[i]; 905 aj = aij->j + ii[i]; 906 aa = aij->a + ii[i]; 907 for (j=0; j<n; j++) { 908 if (PetscAbsScalar(mask[*aj])) { 909 if (b) bb[i] -= *aa*xx[*aj]; 910 *aa = 0.0; 911 } 912 aa++; 913 aj++; 914 } 915 } 916 } 917 if (x) { 918 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 919 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 920 } 921 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 922 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 923 ierr = PetscFree(lrows);CHKERRQ(ierr); 924 925 /* only change matrix nonzero state if pattern was allowed to be changed */ 926 if (!((Mat_SeqAIJ*)(l->A->data))->keepnonzeropattern) { 927 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 928 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 929 } 930 PetscFunctionReturn(0); 931 } 932 933 PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy) 934 { 935 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 936 PetscErrorCode ierr; 937 PetscInt nt; 938 939 PetscFunctionBegin; 940 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 941 if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt); 942 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 943 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 944 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 945 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 946 PetscFunctionReturn(0); 947 } 948 949 PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx) 950 { 951 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 952 PetscErrorCode ierr; 953 954 PetscFunctionBegin; 955 ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr); 956 PetscFunctionReturn(0); 957 } 958 959 PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 960 { 961 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 962 PetscErrorCode ierr; 963 964 PetscFunctionBegin; 965 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 966 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 967 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 968 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 969 PetscFunctionReturn(0); 970 } 971 972 PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy) 973 { 974 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 975 PetscErrorCode ierr; 976 PetscBool merged; 977 978 PetscFunctionBegin; 979 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 980 /* do nondiagonal part */ 981 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 982 if (!merged) { 983 /* send it on its way */ 984 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 985 /* do local part */ 986 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 987 /* receive remote parts: note this assumes the values are not actually */ 988 /* added in yy until the next line, */ 989 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 990 } else { 991 /* do local part */ 992 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 993 /* send it on its way */ 994 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 995 /* values actually were received in the Begin() but we need to call this nop */ 996 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 997 } 998 PetscFunctionReturn(0); 999 } 1000 1001 PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool *f) 1002 { 1003 MPI_Comm comm; 1004 Mat_MPIAIJ *Aij = (Mat_MPIAIJ*) Amat->data, *Bij; 1005 Mat Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs; 1006 IS Me,Notme; 1007 PetscErrorCode ierr; 1008 PetscInt M,N,first,last,*notme,i; 1009 PetscMPIInt size; 1010 1011 PetscFunctionBegin; 1012 /* Easy test: symmetric diagonal block */ 1013 Bij = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A; 1014 ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr); 1015 if (!*f) PetscFunctionReturn(0); 1016 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1017 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1018 if (size == 1) PetscFunctionReturn(0); 1019 1020 /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */ 1021 ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr); 1022 ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr); 1023 ierr = PetscMalloc1(N-last+first,¬me);CHKERRQ(ierr); 1024 for (i=0; i<first; i++) notme[i] = i; 1025 for (i=last; i<M; i++) notme[i-last+first] = i; 1026 ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr); 1027 ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr); 1028 ierr = MatCreateSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr); 1029 Aoff = Aoffs[0]; 1030 ierr = MatCreateSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr); 1031 Boff = Boffs[0]; 1032 ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr); 1033 ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr); 1034 ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr); 1035 ierr = ISDestroy(&Me);CHKERRQ(ierr); 1036 ierr = ISDestroy(&Notme);CHKERRQ(ierr); 1037 ierr = PetscFree(notme);CHKERRQ(ierr); 1038 PetscFunctionReturn(0); 1039 } 1040 1041 PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1042 { 1043 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1044 PetscErrorCode ierr; 1045 1046 PetscFunctionBegin; 1047 /* do nondiagonal part */ 1048 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1049 /* send it on its way */ 1050 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1051 /* do local part */ 1052 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1053 /* receive remote parts */ 1054 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1055 PetscFunctionReturn(0); 1056 } 1057 1058 /* 1059 This only works correctly for square matrices where the subblock A->A is the 1060 diagonal block 1061 */ 1062 PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v) 1063 { 1064 PetscErrorCode ierr; 1065 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1066 1067 PetscFunctionBegin; 1068 if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1069 if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition"); 1070 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1071 PetscFunctionReturn(0); 1072 } 1073 1074 PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa) 1075 { 1076 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1077 PetscErrorCode ierr; 1078 1079 PetscFunctionBegin; 1080 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1081 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1082 PetscFunctionReturn(0); 1083 } 1084 1085 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 1086 { 1087 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1088 PetscErrorCode ierr; 1089 1090 PetscFunctionBegin; 1091 #if defined(PETSC_USE_LOG) 1092 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N); 1093 #endif 1094 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1095 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 1096 ierr = MatDestroy(&aij->A);CHKERRQ(ierr); 1097 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 1098 #if defined(PETSC_USE_CTABLE) 1099 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 1100 #else 1101 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 1102 #endif 1103 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 1104 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 1105 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 1106 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 1107 ierr = PetscFree(aij->ld);CHKERRQ(ierr); 1108 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1109 1110 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1111 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1112 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1113 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1114 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1115 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1116 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1117 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1118 #if defined(PETSC_HAVE_ELEMENTAL) 1119 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_elemental_C",NULL);CHKERRQ(ierr); 1120 #endif 1121 #if defined(PETSC_HAVE_HYPRE) 1122 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_hypre_C",NULL);CHKERRQ(ierr); 1123 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMatMatMult_transpose_mpiaij_mpiaij_C",NULL);CHKERRQ(ierr); 1124 #endif 1125 PetscFunctionReturn(0); 1126 } 1127 1128 PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer) 1129 { 1130 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1131 Mat_SeqAIJ *A = (Mat_SeqAIJ*)aij->A->data; 1132 Mat_SeqAIJ *B = (Mat_SeqAIJ*)aij->B->data; 1133 PetscErrorCode ierr; 1134 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1135 int fd; 1136 PetscInt nz,header[4],*row_lengths,*range=0,rlen,i; 1137 PetscInt nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz = 0; 1138 PetscScalar *column_values; 1139 PetscInt message_count,flowcontrolcount; 1140 FILE *file; 1141 1142 PetscFunctionBegin; 1143 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1144 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1145 nz = A->nz + B->nz; 1146 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1147 if (!rank) { 1148 header[0] = MAT_FILE_CLASSID; 1149 header[1] = mat->rmap->N; 1150 header[2] = mat->cmap->N; 1151 1152 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1153 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1154 /* get largest number of rows any processor has */ 1155 rlen = mat->rmap->n; 1156 range = mat->rmap->range; 1157 for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]); 1158 } else { 1159 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1160 rlen = mat->rmap->n; 1161 } 1162 1163 /* load up the local row counts */ 1164 ierr = PetscMalloc1(rlen+1,&row_lengths);CHKERRQ(ierr); 1165 for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1166 1167 /* store the row lengths to the file */ 1168 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1169 if (!rank) { 1170 ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1171 for (i=1; i<size; i++) { 1172 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1173 rlen = range[i+1] - range[i]; 1174 ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1175 ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1176 } 1177 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1178 } else { 1179 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1180 ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1181 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1182 } 1183 ierr = PetscFree(row_lengths);CHKERRQ(ierr); 1184 1185 /* load up the local column indices */ 1186 nzmax = nz; /* th processor needs space a largest processor needs */ 1187 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1188 ierr = PetscMalloc1(nzmax+1,&column_indices);CHKERRQ(ierr); 1189 cnt = 0; 1190 for (i=0; i<mat->rmap->n; i++) { 1191 for (j=B->i[i]; j<B->i[i+1]; j++) { 1192 if ((col = garray[B->j[j]]) > cstart) break; 1193 column_indices[cnt++] = col; 1194 } 1195 for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart; 1196 for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]]; 1197 } 1198 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1199 1200 /* store the column indices to the file */ 1201 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1202 if (!rank) { 1203 MPI_Status status; 1204 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1205 for (i=1; i<size; i++) { 1206 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1207 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1208 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1209 ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1210 ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1211 } 1212 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1213 } else { 1214 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1215 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1216 ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1217 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1218 } 1219 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1220 1221 /* load up the local column values */ 1222 ierr = PetscMalloc1(nzmax+1,&column_values);CHKERRQ(ierr); 1223 cnt = 0; 1224 for (i=0; i<mat->rmap->n; i++) { 1225 for (j=B->i[i]; j<B->i[i+1]; j++) { 1226 if (garray[B->j[j]] > cstart) break; 1227 column_values[cnt++] = B->a[j]; 1228 } 1229 for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k]; 1230 for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j]; 1231 } 1232 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1233 1234 /* store the column values to the file */ 1235 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1236 if (!rank) { 1237 MPI_Status status; 1238 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1239 for (i=1; i<size; i++) { 1240 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1241 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1242 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1243 ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1244 ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1245 } 1246 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1247 } else { 1248 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1249 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1250 ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1251 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1252 } 1253 ierr = PetscFree(column_values);CHKERRQ(ierr); 1254 1255 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1256 if (file) fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(mat->rmap->bs)); 1257 PetscFunctionReturn(0); 1258 } 1259 1260 #include <petscdraw.h> 1261 PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 1262 { 1263 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1264 PetscErrorCode ierr; 1265 PetscMPIInt rank = aij->rank,size = aij->size; 1266 PetscBool isdraw,iascii,isbinary; 1267 PetscViewer sviewer; 1268 PetscViewerFormat format; 1269 1270 PetscFunctionBegin; 1271 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1272 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1273 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1274 if (iascii) { 1275 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1276 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1277 MatInfo info; 1278 PetscBool inodes; 1279 1280 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1281 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 1282 ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr); 1283 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 1284 if (!inodes) { 1285 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n", 1286 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1287 } else { 1288 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n", 1289 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1290 } 1291 ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1292 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1293 ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1294 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1295 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1296 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 1297 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1298 ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr); 1299 PetscFunctionReturn(0); 1300 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1301 PetscInt inodecount,inodelimit,*inodes; 1302 ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr); 1303 if (inodes) { 1304 ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr); 1305 } else { 1306 ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr); 1307 } 1308 PetscFunctionReturn(0); 1309 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1310 PetscFunctionReturn(0); 1311 } 1312 } else if (isbinary) { 1313 if (size == 1) { 1314 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1315 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1316 } else { 1317 ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1318 } 1319 PetscFunctionReturn(0); 1320 } else if (isdraw) { 1321 PetscDraw draw; 1322 PetscBool isnull; 1323 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1324 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 1325 if (isnull) PetscFunctionReturn(0); 1326 } 1327 1328 { 1329 /* assemble the entire matrix onto first processor. */ 1330 Mat A; 1331 Mat_SeqAIJ *Aloc; 1332 PetscInt M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct; 1333 MatScalar *a; 1334 1335 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1336 if (!rank) { 1337 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1338 } else { 1339 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1340 } 1341 /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */ 1342 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 1343 ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr); 1344 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1345 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1346 1347 /* copy over the A part */ 1348 Aloc = (Mat_SeqAIJ*)aij->A->data; 1349 m = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1350 row = mat->rmap->rstart; 1351 for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart; 1352 for (i=0; i<m; i++) { 1353 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr); 1354 row++; 1355 a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i]; 1356 } 1357 aj = Aloc->j; 1358 for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart; 1359 1360 /* copy over the B part */ 1361 Aloc = (Mat_SeqAIJ*)aij->B->data; 1362 m = aij->B->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1363 row = mat->rmap->rstart; 1364 ierr = PetscMalloc1(ai[m]+1,&cols);CHKERRQ(ierr); 1365 ct = cols; 1366 for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]]; 1367 for (i=0; i<m; i++) { 1368 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr); 1369 row++; 1370 a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i]; 1371 } 1372 ierr = PetscFree(ct);CHKERRQ(ierr); 1373 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1374 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1375 /* 1376 Everyone has to call to draw the matrix since the graphics waits are 1377 synchronized across all processors that share the PetscDraw object 1378 */ 1379 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1380 if (!rank) { 1381 ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1382 ierr = MatView_SeqAIJ(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1383 } 1384 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1385 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1386 ierr = MatDestroy(&A);CHKERRQ(ierr); 1387 } 1388 PetscFunctionReturn(0); 1389 } 1390 1391 PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer) 1392 { 1393 PetscErrorCode ierr; 1394 PetscBool iascii,isdraw,issocket,isbinary; 1395 1396 PetscFunctionBegin; 1397 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1398 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1399 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1400 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1401 if (iascii || isdraw || isbinary || issocket) { 1402 ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1403 } 1404 PetscFunctionReturn(0); 1405 } 1406 1407 PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1408 { 1409 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1410 PetscErrorCode ierr; 1411 Vec bb1 = 0; 1412 PetscBool hasop; 1413 1414 PetscFunctionBegin; 1415 if (flag == SOR_APPLY_UPPER) { 1416 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1417 PetscFunctionReturn(0); 1418 } 1419 1420 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) { 1421 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 1422 } 1423 1424 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1425 if (flag & SOR_ZERO_INITIAL_GUESS) { 1426 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1427 its--; 1428 } 1429 1430 while (its--) { 1431 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1432 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1433 1434 /* update rhs: bb1 = bb - B*x */ 1435 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1436 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1437 1438 /* local sweep */ 1439 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1440 } 1441 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1442 if (flag & SOR_ZERO_INITIAL_GUESS) { 1443 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1444 its--; 1445 } 1446 while (its--) { 1447 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1448 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1449 1450 /* update rhs: bb1 = bb - B*x */ 1451 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1452 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1453 1454 /* local sweep */ 1455 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1456 } 1457 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1458 if (flag & SOR_ZERO_INITIAL_GUESS) { 1459 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1460 its--; 1461 } 1462 while (its--) { 1463 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1464 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1465 1466 /* update rhs: bb1 = bb - B*x */ 1467 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1468 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1469 1470 /* local sweep */ 1471 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1472 } 1473 } else if (flag & SOR_EISENSTAT) { 1474 Vec xx1; 1475 1476 ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr); 1477 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr); 1478 1479 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1480 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1481 if (!mat->diag) { 1482 ierr = MatCreateVecs(matin,&mat->diag,NULL);CHKERRQ(ierr); 1483 ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr); 1484 } 1485 ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr); 1486 if (hasop) { 1487 ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr); 1488 } else { 1489 ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr); 1490 } 1491 ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr); 1492 1493 ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr); 1494 1495 /* local sweep */ 1496 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr); 1497 ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr); 1498 ierr = VecDestroy(&xx1);CHKERRQ(ierr); 1499 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported"); 1500 1501 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 1502 1503 matin->factorerrortype = mat->A->factorerrortype; 1504 PetscFunctionReturn(0); 1505 } 1506 1507 PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B) 1508 { 1509 Mat aA,aB,Aperm; 1510 const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj; 1511 PetscScalar *aa,*ba; 1512 PetscInt i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest; 1513 PetscSF rowsf,sf; 1514 IS parcolp = NULL; 1515 PetscBool done; 1516 PetscErrorCode ierr; 1517 1518 PetscFunctionBegin; 1519 ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); 1520 ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr); 1521 ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr); 1522 ierr = PetscMalloc3(PetscMax(m,n),&work,m,&rdest,n,&cdest);CHKERRQ(ierr); 1523 1524 /* Invert row permutation to find out where my rows should go */ 1525 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr); 1526 ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr); 1527 ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr); 1528 for (i=0; i<m; i++) work[i] = A->rmap->rstart + i; 1529 ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1530 ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1531 1532 /* Invert column permutation to find out where my columns should go */ 1533 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1534 ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr); 1535 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1536 for (i=0; i<n; i++) work[i] = A->cmap->rstart + i; 1537 ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1538 ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1539 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1540 1541 ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr); 1542 ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr); 1543 ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr); 1544 1545 /* Find out where my gcols should go */ 1546 ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr); 1547 ierr = PetscMalloc1(ng,&gcdest);CHKERRQ(ierr); 1548 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1549 ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr); 1550 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1551 ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1552 ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1553 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1554 1555 ierr = PetscCalloc4(m,&dnnz,m,&onnz,m,&tdnnz,m,&tonnz);CHKERRQ(ierr); 1556 ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1557 ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1558 for (i=0; i<m; i++) { 1559 PetscInt row = rdest[i],rowner; 1560 ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr); 1561 for (j=ai[i]; j<ai[i+1]; j++) { 1562 PetscInt cowner,col = cdest[aj[j]]; 1563 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */ 1564 if (rowner == cowner) dnnz[i]++; 1565 else onnz[i]++; 1566 } 1567 for (j=bi[i]; j<bi[i+1]; j++) { 1568 PetscInt cowner,col = gcdest[bj[j]]; 1569 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); 1570 if (rowner == cowner) dnnz[i]++; 1571 else onnz[i]++; 1572 } 1573 } 1574 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1575 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1576 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1577 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1578 ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr); 1579 1580 ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr); 1581 ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr); 1582 ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr); 1583 for (i=0; i<m; i++) { 1584 PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */ 1585 PetscInt j0,rowlen; 1586 rowlen = ai[i+1] - ai[i]; 1587 for (j0=j=0; j<rowlen; j0=j) { /* rowlen could be larger than number of rows m, so sum in batches */ 1588 for ( ; j<PetscMin(rowlen,j0+m); j++) acols[j-j0] = cdest[aj[ai[i]+j]]; 1589 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,acols,aa+ai[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1590 } 1591 rowlen = bi[i+1] - bi[i]; 1592 for (j0=j=0; j<rowlen; j0=j) { 1593 for ( ; j<PetscMin(rowlen,j0+m); j++) bcols[j-j0] = gcdest[bj[bi[i]+j]]; 1594 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,bcols,ba+bi[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1595 } 1596 } 1597 ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1598 ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1599 ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1600 ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1601 ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr); 1602 ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr); 1603 ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr); 1604 ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr); 1605 ierr = PetscFree(gcdest);CHKERRQ(ierr); 1606 if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);} 1607 *B = Aperm; 1608 PetscFunctionReturn(0); 1609 } 1610 1611 PetscErrorCode MatGetGhosts_MPIAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 1612 { 1613 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1614 PetscErrorCode ierr; 1615 1616 PetscFunctionBegin; 1617 ierr = MatGetSize(aij->B,NULL,nghosts);CHKERRQ(ierr); 1618 if (ghosts) *ghosts = aij->garray; 1619 PetscFunctionReturn(0); 1620 } 1621 1622 PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1623 { 1624 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1625 Mat A = mat->A,B = mat->B; 1626 PetscErrorCode ierr; 1627 PetscReal isend[5],irecv[5]; 1628 1629 PetscFunctionBegin; 1630 info->block_size = 1.0; 1631 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1632 1633 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1634 isend[3] = info->memory; isend[4] = info->mallocs; 1635 1636 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1637 1638 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1639 isend[3] += info->memory; isend[4] += info->mallocs; 1640 if (flag == MAT_LOCAL) { 1641 info->nz_used = isend[0]; 1642 info->nz_allocated = isend[1]; 1643 info->nz_unneeded = isend[2]; 1644 info->memory = isend[3]; 1645 info->mallocs = isend[4]; 1646 } else if (flag == MAT_GLOBAL_MAX) { 1647 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1648 1649 info->nz_used = irecv[0]; 1650 info->nz_allocated = irecv[1]; 1651 info->nz_unneeded = irecv[2]; 1652 info->memory = irecv[3]; 1653 info->mallocs = irecv[4]; 1654 } else if (flag == MAT_GLOBAL_SUM) { 1655 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1656 1657 info->nz_used = irecv[0]; 1658 info->nz_allocated = irecv[1]; 1659 info->nz_unneeded = irecv[2]; 1660 info->memory = irecv[3]; 1661 info->mallocs = irecv[4]; 1662 } 1663 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1664 info->fill_ratio_needed = 0; 1665 info->factor_mallocs = 0; 1666 PetscFunctionReturn(0); 1667 } 1668 1669 PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg) 1670 { 1671 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1672 PetscErrorCode ierr; 1673 1674 PetscFunctionBegin; 1675 switch (op) { 1676 case MAT_NEW_NONZERO_LOCATIONS: 1677 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1678 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1679 case MAT_KEEP_NONZERO_PATTERN: 1680 case MAT_NEW_NONZERO_LOCATION_ERR: 1681 case MAT_USE_INODES: 1682 case MAT_IGNORE_ZERO_ENTRIES: 1683 MatCheckPreallocated(A,1); 1684 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1685 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1686 break; 1687 case MAT_ROW_ORIENTED: 1688 MatCheckPreallocated(A,1); 1689 a->roworiented = flg; 1690 1691 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1692 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1693 break; 1694 case MAT_NEW_DIAGONALS: 1695 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1696 break; 1697 case MAT_IGNORE_OFF_PROC_ENTRIES: 1698 a->donotstash = flg; 1699 break; 1700 case MAT_SPD: 1701 A->spd_set = PETSC_TRUE; 1702 A->spd = flg; 1703 if (flg) { 1704 A->symmetric = PETSC_TRUE; 1705 A->structurally_symmetric = PETSC_TRUE; 1706 A->symmetric_set = PETSC_TRUE; 1707 A->structurally_symmetric_set = PETSC_TRUE; 1708 } 1709 break; 1710 case MAT_SYMMETRIC: 1711 MatCheckPreallocated(A,1); 1712 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1713 break; 1714 case MAT_STRUCTURALLY_SYMMETRIC: 1715 MatCheckPreallocated(A,1); 1716 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1717 break; 1718 case MAT_HERMITIAN: 1719 MatCheckPreallocated(A,1); 1720 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1721 break; 1722 case MAT_SYMMETRY_ETERNAL: 1723 MatCheckPreallocated(A,1); 1724 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1725 break; 1726 case MAT_SUBMAT_SINGLEIS: 1727 A->submat_singleis = flg; 1728 break; 1729 default: 1730 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1731 } 1732 PetscFunctionReturn(0); 1733 } 1734 1735 PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1736 { 1737 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1738 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1739 PetscErrorCode ierr; 1740 PetscInt i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart; 1741 PetscInt nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend; 1742 PetscInt *cmap,*idx_p; 1743 1744 PetscFunctionBegin; 1745 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1746 mat->getrowactive = PETSC_TRUE; 1747 1748 if (!mat->rowvalues && (idx || v)) { 1749 /* 1750 allocate enough space to hold information from the longest row. 1751 */ 1752 Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data; 1753 PetscInt max = 1,tmp; 1754 for (i=0; i<matin->rmap->n; i++) { 1755 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1756 if (max < tmp) max = tmp; 1757 } 1758 ierr = PetscMalloc2(max,&mat->rowvalues,max,&mat->rowindices);CHKERRQ(ierr); 1759 } 1760 1761 if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows"); 1762 lrow = row - rstart; 1763 1764 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1765 if (!v) {pvA = 0; pvB = 0;} 1766 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1767 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1768 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1769 nztot = nzA + nzB; 1770 1771 cmap = mat->garray; 1772 if (v || idx) { 1773 if (nztot) { 1774 /* Sort by increasing column numbers, assuming A and B already sorted */ 1775 PetscInt imark = -1; 1776 if (v) { 1777 *v = v_p = mat->rowvalues; 1778 for (i=0; i<nzB; i++) { 1779 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1780 else break; 1781 } 1782 imark = i; 1783 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1784 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1785 } 1786 if (idx) { 1787 *idx = idx_p = mat->rowindices; 1788 if (imark > -1) { 1789 for (i=0; i<imark; i++) { 1790 idx_p[i] = cmap[cworkB[i]]; 1791 } 1792 } else { 1793 for (i=0; i<nzB; i++) { 1794 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1795 else break; 1796 } 1797 imark = i; 1798 } 1799 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart + cworkA[i]; 1800 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]]; 1801 } 1802 } else { 1803 if (idx) *idx = 0; 1804 if (v) *v = 0; 1805 } 1806 } 1807 *nz = nztot; 1808 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1809 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1810 PetscFunctionReturn(0); 1811 } 1812 1813 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1814 { 1815 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1816 1817 PetscFunctionBegin; 1818 if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first"); 1819 aij->getrowactive = PETSC_FALSE; 1820 PetscFunctionReturn(0); 1821 } 1822 1823 PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm) 1824 { 1825 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1826 Mat_SeqAIJ *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data; 1827 PetscErrorCode ierr; 1828 PetscInt i,j,cstart = mat->cmap->rstart; 1829 PetscReal sum = 0.0; 1830 MatScalar *v; 1831 1832 PetscFunctionBegin; 1833 if (aij->size == 1) { 1834 ierr = MatNorm(aij->A,type,norm);CHKERRQ(ierr); 1835 } else { 1836 if (type == NORM_FROBENIUS) { 1837 v = amat->a; 1838 for (i=0; i<amat->nz; i++) { 1839 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1840 } 1841 v = bmat->a; 1842 for (i=0; i<bmat->nz; i++) { 1843 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1844 } 1845 ierr = MPIU_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1846 *norm = PetscSqrtReal(*norm); 1847 ierr = PetscLogFlops(2*amat->nz+2*bmat->nz);CHKERRQ(ierr); 1848 } else if (type == NORM_1) { /* max column norm */ 1849 PetscReal *tmp,*tmp2; 1850 PetscInt *jj,*garray = aij->garray; 1851 ierr = PetscCalloc1(mat->cmap->N+1,&tmp);CHKERRQ(ierr); 1852 ierr = PetscMalloc1(mat->cmap->N+1,&tmp2);CHKERRQ(ierr); 1853 *norm = 0.0; 1854 v = amat->a; jj = amat->j; 1855 for (j=0; j<amat->nz; j++) { 1856 tmp[cstart + *jj++] += PetscAbsScalar(*v); v++; 1857 } 1858 v = bmat->a; jj = bmat->j; 1859 for (j=0; j<bmat->nz; j++) { 1860 tmp[garray[*jj++]] += PetscAbsScalar(*v); v++; 1861 } 1862 ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1863 for (j=0; j<mat->cmap->N; j++) { 1864 if (tmp2[j] > *norm) *norm = tmp2[j]; 1865 } 1866 ierr = PetscFree(tmp);CHKERRQ(ierr); 1867 ierr = PetscFree(tmp2);CHKERRQ(ierr); 1868 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1869 } else if (type == NORM_INFINITY) { /* max row norm */ 1870 PetscReal ntemp = 0.0; 1871 for (j=0; j<aij->A->rmap->n; j++) { 1872 v = amat->a + amat->i[j]; 1873 sum = 0.0; 1874 for (i=0; i<amat->i[j+1]-amat->i[j]; i++) { 1875 sum += PetscAbsScalar(*v); v++; 1876 } 1877 v = bmat->a + bmat->i[j]; 1878 for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) { 1879 sum += PetscAbsScalar(*v); v++; 1880 } 1881 if (sum > ntemp) ntemp = sum; 1882 } 1883 ierr = MPIU_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1884 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1885 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm"); 1886 } 1887 PetscFunctionReturn(0); 1888 } 1889 1890 PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout) 1891 { 1892 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1893 Mat_SeqAIJ *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data; 1894 PetscErrorCode ierr; 1895 PetscInt M = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i; 1896 PetscInt cstart = A->cmap->rstart,ncol; 1897 Mat B; 1898 MatScalar *array; 1899 1900 PetscFunctionBegin; 1901 if (reuse == MAT_INPLACE_MATRIX && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1902 1903 ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n; 1904 ai = Aloc->i; aj = Aloc->j; 1905 bi = Bloc->i; bj = Bloc->j; 1906 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1907 PetscInt *d_nnz,*g_nnz,*o_nnz; 1908 PetscSFNode *oloc; 1909 PETSC_UNUSED PetscSF sf; 1910 1911 ierr = PetscMalloc4(na,&d_nnz,na,&o_nnz,nb,&g_nnz,nb,&oloc);CHKERRQ(ierr); 1912 /* compute d_nnz for preallocation */ 1913 ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1914 for (i=0; i<ai[ma]; i++) { 1915 d_nnz[aj[i]]++; 1916 aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1917 } 1918 /* compute local off-diagonal contributions */ 1919 ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr); 1920 for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++; 1921 /* map those to global */ 1922 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1923 ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr); 1924 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1925 ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1926 ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1927 ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1928 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1929 1930 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1931 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1932 ierr = MatSetBlockSizes(B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 1933 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1934 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 1935 ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr); 1936 } else { 1937 B = *matout; 1938 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1939 for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1940 } 1941 1942 /* copy over the A part */ 1943 array = Aloc->a; 1944 row = A->rmap->rstart; 1945 for (i=0; i<ma; i++) { 1946 ncol = ai[i+1]-ai[i]; 1947 ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1948 row++; 1949 array += ncol; aj += ncol; 1950 } 1951 aj = Aloc->j; 1952 for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */ 1953 1954 /* copy over the B part */ 1955 ierr = PetscCalloc1(bi[mb],&cols);CHKERRQ(ierr); 1956 array = Bloc->a; 1957 row = A->rmap->rstart; 1958 for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]]; 1959 cols_tmp = cols; 1960 for (i=0; i<mb; i++) { 1961 ncol = bi[i+1]-bi[i]; 1962 ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1963 row++; 1964 array += ncol; cols_tmp += ncol; 1965 } 1966 ierr = PetscFree(cols);CHKERRQ(ierr); 1967 1968 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1969 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1970 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 1971 *matout = B; 1972 } else { 1973 ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr); 1974 } 1975 PetscFunctionReturn(0); 1976 } 1977 1978 PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr) 1979 { 1980 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1981 Mat a = aij->A,b = aij->B; 1982 PetscErrorCode ierr; 1983 PetscInt s1,s2,s3; 1984 1985 PetscFunctionBegin; 1986 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1987 if (rr) { 1988 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1989 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1990 /* Overlap communication with computation. */ 1991 ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1992 } 1993 if (ll) { 1994 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1995 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1996 ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr); 1997 } 1998 /* scale the diagonal block */ 1999 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 2000 2001 if (rr) { 2002 /* Do a scatter end and then right scale the off-diagonal block */ 2003 ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2004 ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr); 2005 } 2006 PetscFunctionReturn(0); 2007 } 2008 2009 PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2010 { 2011 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2012 PetscErrorCode ierr; 2013 2014 PetscFunctionBegin; 2015 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 2016 PetscFunctionReturn(0); 2017 } 2018 2019 PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool *flag) 2020 { 2021 Mat_MPIAIJ *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data; 2022 Mat a,b,c,d; 2023 PetscBool flg; 2024 PetscErrorCode ierr; 2025 2026 PetscFunctionBegin; 2027 a = matA->A; b = matA->B; 2028 c = matB->A; d = matB->B; 2029 2030 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 2031 if (flg) { 2032 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 2033 } 2034 ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2035 PetscFunctionReturn(0); 2036 } 2037 2038 PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str) 2039 { 2040 PetscErrorCode ierr; 2041 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2042 Mat_MPIAIJ *b = (Mat_MPIAIJ*)B->data; 2043 2044 PetscFunctionBegin; 2045 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2046 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2047 /* because of the column compression in the off-processor part of the matrix a->B, 2048 the number of columns in a->B and b->B may be different, hence we cannot call 2049 the MatCopy() directly on the two parts. If need be, we can provide a more 2050 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2051 then copying the submatrices */ 2052 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2053 } else { 2054 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 2055 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 2056 } 2057 PetscFunctionReturn(0); 2058 } 2059 2060 PetscErrorCode MatSetUp_MPIAIJ(Mat A) 2061 { 2062 PetscErrorCode ierr; 2063 2064 PetscFunctionBegin; 2065 ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 2066 PetscFunctionReturn(0); 2067 } 2068 2069 /* 2070 Computes the number of nonzeros per row needed for preallocation when X and Y 2071 have different nonzero structure. 2072 */ 2073 PetscErrorCode MatAXPYGetPreallocation_MPIX_private(PetscInt m,const PetscInt *xi,const PetscInt *xj,const PetscInt *xltog,const PetscInt *yi,const PetscInt *yj,const PetscInt *yltog,PetscInt *nnz) 2074 { 2075 PetscInt i,j,k,nzx,nzy; 2076 2077 PetscFunctionBegin; 2078 /* Set the number of nonzeros in the new matrix */ 2079 for (i=0; i<m; i++) { 2080 const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i]; 2081 nzx = xi[i+1] - xi[i]; 2082 nzy = yi[i+1] - yi[i]; 2083 nnz[i] = 0; 2084 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2085 for (; k<nzy && yltog[yjj[k]]<xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */ 2086 if (k<nzy && yltog[yjj[k]]==xltog[xjj[j]]) k++; /* Skip duplicate */ 2087 nnz[i]++; 2088 } 2089 for (; k<nzy; k++) nnz[i]++; 2090 } 2091 PetscFunctionReturn(0); 2092 } 2093 2094 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2095 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 2096 { 2097 PetscErrorCode ierr; 2098 PetscInt m = Y->rmap->N; 2099 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2100 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2101 2102 PetscFunctionBegin; 2103 ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr); 2104 PetscFunctionReturn(0); 2105 } 2106 2107 PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2108 { 2109 PetscErrorCode ierr; 2110 Mat_MPIAIJ *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data; 2111 PetscBLASInt bnz,one=1; 2112 Mat_SeqAIJ *x,*y; 2113 2114 PetscFunctionBegin; 2115 if (str == SAME_NONZERO_PATTERN) { 2116 PetscScalar alpha = a; 2117 x = (Mat_SeqAIJ*)xx->A->data; 2118 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2119 y = (Mat_SeqAIJ*)yy->A->data; 2120 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2121 x = (Mat_SeqAIJ*)xx->B->data; 2122 y = (Mat_SeqAIJ*)yy->B->data; 2123 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2124 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2125 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 2126 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2127 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 2128 } else { 2129 Mat B; 2130 PetscInt *nnz_d,*nnz_o; 2131 ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr); 2132 ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr); 2133 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2134 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2135 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2136 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 2137 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2138 ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 2139 ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 2140 ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 2141 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2142 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 2143 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 2144 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 2145 } 2146 PetscFunctionReturn(0); 2147 } 2148 2149 extern PetscErrorCode MatConjugate_SeqAIJ(Mat); 2150 2151 PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2152 { 2153 #if defined(PETSC_USE_COMPLEX) 2154 PetscErrorCode ierr; 2155 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2156 2157 PetscFunctionBegin; 2158 ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr); 2159 ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr); 2160 #else 2161 PetscFunctionBegin; 2162 #endif 2163 PetscFunctionReturn(0); 2164 } 2165 2166 PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2167 { 2168 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2169 PetscErrorCode ierr; 2170 2171 PetscFunctionBegin; 2172 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2173 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2174 PetscFunctionReturn(0); 2175 } 2176 2177 PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2178 { 2179 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2180 PetscErrorCode ierr; 2181 2182 PetscFunctionBegin; 2183 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2184 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2185 PetscFunctionReturn(0); 2186 } 2187 2188 PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2189 { 2190 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2191 PetscErrorCode ierr; 2192 PetscInt i,*idxb = 0; 2193 PetscScalar *va,*vb; 2194 Vec vtmp; 2195 2196 PetscFunctionBegin; 2197 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 2198 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2199 if (idx) { 2200 for (i=0; i<A->rmap->n; i++) { 2201 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2202 } 2203 } 2204 2205 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2206 if (idx) { 2207 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2208 } 2209 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2210 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2211 2212 for (i=0; i<A->rmap->n; i++) { 2213 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 2214 va[i] = vb[i]; 2215 if (idx) idx[i] = a->garray[idxb[i]]; 2216 } 2217 } 2218 2219 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2220 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2221 ierr = PetscFree(idxb);CHKERRQ(ierr); 2222 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2223 PetscFunctionReturn(0); 2224 } 2225 2226 PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2227 { 2228 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2229 PetscErrorCode ierr; 2230 PetscInt i,*idxb = 0; 2231 PetscScalar *va,*vb; 2232 Vec vtmp; 2233 2234 PetscFunctionBegin; 2235 ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr); 2236 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2237 if (idx) { 2238 for (i=0; i<A->cmap->n; i++) { 2239 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2240 } 2241 } 2242 2243 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2244 if (idx) { 2245 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2246 } 2247 ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2248 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2249 2250 for (i=0; i<A->rmap->n; i++) { 2251 if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) { 2252 va[i] = vb[i]; 2253 if (idx) idx[i] = a->garray[idxb[i]]; 2254 } 2255 } 2256 2257 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2258 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2259 ierr = PetscFree(idxb);CHKERRQ(ierr); 2260 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2261 PetscFunctionReturn(0); 2262 } 2263 2264 PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2265 { 2266 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2267 PetscInt n = A->rmap->n; 2268 PetscInt cstart = A->cmap->rstart; 2269 PetscInt *cmap = mat->garray; 2270 PetscInt *diagIdx, *offdiagIdx; 2271 Vec diagV, offdiagV; 2272 PetscScalar *a, *diagA, *offdiagA; 2273 PetscInt r; 2274 PetscErrorCode ierr; 2275 2276 PetscFunctionBegin; 2277 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2278 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr); 2279 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr); 2280 ierr = MatGetRowMin(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2281 ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2282 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2283 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2284 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2285 for (r = 0; r < n; ++r) { 2286 if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) { 2287 a[r] = diagA[r]; 2288 idx[r] = cstart + diagIdx[r]; 2289 } else { 2290 a[r] = offdiagA[r]; 2291 idx[r] = cmap[offdiagIdx[r]]; 2292 } 2293 } 2294 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2295 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2296 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2297 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2298 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2299 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2300 PetscFunctionReturn(0); 2301 } 2302 2303 PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2304 { 2305 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2306 PetscInt n = A->rmap->n; 2307 PetscInt cstart = A->cmap->rstart; 2308 PetscInt *cmap = mat->garray; 2309 PetscInt *diagIdx, *offdiagIdx; 2310 Vec diagV, offdiagV; 2311 PetscScalar *a, *diagA, *offdiagA; 2312 PetscInt r; 2313 PetscErrorCode ierr; 2314 2315 PetscFunctionBegin; 2316 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2317 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr); 2318 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr); 2319 ierr = MatGetRowMax(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2320 ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2321 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2322 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2323 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2324 for (r = 0; r < n; ++r) { 2325 if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) { 2326 a[r] = diagA[r]; 2327 idx[r] = cstart + diagIdx[r]; 2328 } else { 2329 a[r] = offdiagA[r]; 2330 idx[r] = cmap[offdiagIdx[r]]; 2331 } 2332 } 2333 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2334 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2335 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2336 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2337 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2338 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2339 PetscFunctionReturn(0); 2340 } 2341 2342 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat) 2343 { 2344 PetscErrorCode ierr; 2345 Mat *dummy; 2346 2347 PetscFunctionBegin; 2348 ierr = MatCreateSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr); 2349 *newmat = *dummy; 2350 ierr = PetscFree(dummy);CHKERRQ(ierr); 2351 PetscFunctionReturn(0); 2352 } 2353 2354 PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values) 2355 { 2356 Mat_MPIAIJ *a = (Mat_MPIAIJ*) A->data; 2357 PetscErrorCode ierr; 2358 2359 PetscFunctionBegin; 2360 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2361 A->factorerrortype = a->A->factorerrortype; 2362 PetscFunctionReturn(0); 2363 } 2364 2365 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx) 2366 { 2367 PetscErrorCode ierr; 2368 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)x->data; 2369 2370 PetscFunctionBegin; 2371 ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr); 2372 ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr); 2373 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2374 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2375 PetscFunctionReturn(0); 2376 } 2377 2378 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A,PetscBool sc) 2379 { 2380 PetscFunctionBegin; 2381 if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable; 2382 else A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ; 2383 PetscFunctionReturn(0); 2384 } 2385 2386 /*@ 2387 MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap 2388 2389 Collective on Mat 2390 2391 Input Parameters: 2392 + A - the matrix 2393 - sc - PETSC_TRUE indicates use the scalable algorithm (default is not to use the scalable algorithm) 2394 2395 Level: advanced 2396 2397 @*/ 2398 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A,PetscBool sc) 2399 { 2400 PetscErrorCode ierr; 2401 2402 PetscFunctionBegin; 2403 ierr = PetscTryMethod(A,"MatMPIAIJSetUseScalableIncreaseOverlap_C",(Mat,PetscBool),(A,sc));CHKERRQ(ierr); 2404 PetscFunctionReturn(0); 2405 } 2406 2407 PetscErrorCode MatSetFromOptions_MPIAIJ(PetscOptionItems *PetscOptionsObject,Mat A) 2408 { 2409 PetscErrorCode ierr; 2410 PetscBool sc = PETSC_FALSE,flg; 2411 2412 PetscFunctionBegin; 2413 ierr = PetscOptionsHead(PetscOptionsObject,"MPIAIJ options");CHKERRQ(ierr); 2414 ierr = PetscObjectOptionsBegin((PetscObject)A); 2415 if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE; 2416 ierr = PetscOptionsBool("-mat_increase_overlap_scalable","Use a scalable algorithm to compute the overlap","MatIncreaseOverlap",sc,&sc,&flg);CHKERRQ(ierr); 2417 if (flg) { 2418 ierr = MatMPIAIJSetUseScalableIncreaseOverlap(A,sc);CHKERRQ(ierr); 2419 } 2420 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2421 PetscFunctionReturn(0); 2422 } 2423 2424 PetscErrorCode MatShift_MPIAIJ(Mat Y,PetscScalar a) 2425 { 2426 PetscErrorCode ierr; 2427 Mat_MPIAIJ *maij = (Mat_MPIAIJ*)Y->data; 2428 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)maij->A->data; 2429 2430 PetscFunctionBegin; 2431 if (!Y->preallocated) { 2432 ierr = MatMPIAIJSetPreallocation(Y,1,NULL,0,NULL);CHKERRQ(ierr); 2433 } else if (!aij->nz) { 2434 PetscInt nonew = aij->nonew; 2435 ierr = MatSeqAIJSetPreallocation(maij->A,1,NULL);CHKERRQ(ierr); 2436 aij->nonew = nonew; 2437 } 2438 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2439 PetscFunctionReturn(0); 2440 } 2441 2442 PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A,PetscBool *missing,PetscInt *d) 2443 { 2444 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2445 PetscErrorCode ierr; 2446 2447 PetscFunctionBegin; 2448 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2449 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2450 if (d) { 2451 PetscInt rstart; 2452 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2453 *d += rstart; 2454 2455 } 2456 PetscFunctionReturn(0); 2457 } 2458 2459 2460 /* -------------------------------------------------------------------*/ 2461 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 2462 MatGetRow_MPIAIJ, 2463 MatRestoreRow_MPIAIJ, 2464 MatMult_MPIAIJ, 2465 /* 4*/ MatMultAdd_MPIAIJ, 2466 MatMultTranspose_MPIAIJ, 2467 MatMultTransposeAdd_MPIAIJ, 2468 0, 2469 0, 2470 0, 2471 /*10*/ 0, 2472 0, 2473 0, 2474 MatSOR_MPIAIJ, 2475 MatTranspose_MPIAIJ, 2476 /*15*/ MatGetInfo_MPIAIJ, 2477 MatEqual_MPIAIJ, 2478 MatGetDiagonal_MPIAIJ, 2479 MatDiagonalScale_MPIAIJ, 2480 MatNorm_MPIAIJ, 2481 /*20*/ MatAssemblyBegin_MPIAIJ, 2482 MatAssemblyEnd_MPIAIJ, 2483 MatSetOption_MPIAIJ, 2484 MatZeroEntries_MPIAIJ, 2485 /*24*/ MatZeroRows_MPIAIJ, 2486 0, 2487 0, 2488 0, 2489 0, 2490 /*29*/ MatSetUp_MPIAIJ, 2491 0, 2492 0, 2493 MatGetDiagonalBlock_MPIAIJ, 2494 0, 2495 /*34*/ MatDuplicate_MPIAIJ, 2496 0, 2497 0, 2498 0, 2499 0, 2500 /*39*/ MatAXPY_MPIAIJ, 2501 MatCreateSubMatrices_MPIAIJ, 2502 MatIncreaseOverlap_MPIAIJ, 2503 MatGetValues_MPIAIJ, 2504 MatCopy_MPIAIJ, 2505 /*44*/ MatGetRowMax_MPIAIJ, 2506 MatScale_MPIAIJ, 2507 MatShift_MPIAIJ, 2508 MatDiagonalSet_MPIAIJ, 2509 MatZeroRowsColumns_MPIAIJ, 2510 /*49*/ MatSetRandom_MPIAIJ, 2511 0, 2512 0, 2513 0, 2514 0, 2515 /*54*/ MatFDColoringCreate_MPIXAIJ, 2516 0, 2517 MatSetUnfactored_MPIAIJ, 2518 MatPermute_MPIAIJ, 2519 0, 2520 /*59*/ MatCreateSubMatrix_MPIAIJ, 2521 MatDestroy_MPIAIJ, 2522 MatView_MPIAIJ, 2523 0, 2524 MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ, 2525 /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ, 2526 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 2527 0, 2528 0, 2529 0, 2530 /*69*/ MatGetRowMaxAbs_MPIAIJ, 2531 MatGetRowMinAbs_MPIAIJ, 2532 0, 2533 0, 2534 0, 2535 0, 2536 /*75*/ MatFDColoringApply_AIJ, 2537 MatSetFromOptions_MPIAIJ, 2538 0, 2539 0, 2540 MatFindZeroDiagonals_MPIAIJ, 2541 /*80*/ 0, 2542 0, 2543 0, 2544 /*83*/ MatLoad_MPIAIJ, 2545 0, 2546 0, 2547 0, 2548 0, 2549 0, 2550 /*89*/ MatMatMult_MPIAIJ_MPIAIJ, 2551 MatMatMultSymbolic_MPIAIJ_MPIAIJ, 2552 MatMatMultNumeric_MPIAIJ_MPIAIJ, 2553 MatPtAP_MPIAIJ_MPIAIJ, 2554 MatPtAPSymbolic_MPIAIJ_MPIAIJ, 2555 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 2556 0, 2557 0, 2558 0, 2559 0, 2560 /*99*/ 0, 2561 0, 2562 0, 2563 MatConjugate_MPIAIJ, 2564 0, 2565 /*104*/MatSetValuesRow_MPIAIJ, 2566 MatRealPart_MPIAIJ, 2567 MatImaginaryPart_MPIAIJ, 2568 0, 2569 0, 2570 /*109*/0, 2571 0, 2572 MatGetRowMin_MPIAIJ, 2573 0, 2574 MatMissingDiagonal_MPIAIJ, 2575 /*114*/MatGetSeqNonzeroStructure_MPIAIJ, 2576 0, 2577 MatGetGhosts_MPIAIJ, 2578 0, 2579 0, 2580 /*119*/0, 2581 0, 2582 0, 2583 0, 2584 MatGetMultiProcBlock_MPIAIJ, 2585 /*124*/MatFindNonzeroRows_MPIAIJ, 2586 MatGetColumnNorms_MPIAIJ, 2587 MatInvertBlockDiagonal_MPIAIJ, 2588 0, 2589 MatCreateSubMatricesMPI_MPIAIJ, 2590 /*129*/0, 2591 MatTransposeMatMult_MPIAIJ_MPIAIJ, 2592 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ, 2593 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 2594 0, 2595 /*134*/0, 2596 0, 2597 0, 2598 0, 2599 0, 2600 /*139*/MatSetBlockSizes_MPIAIJ, 2601 0, 2602 0, 2603 MatFDColoringSetUp_MPIXAIJ, 2604 MatFindOffBlockDiagonalEntries_MPIAIJ, 2605 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIAIJ 2606 }; 2607 2608 /* ----------------------------------------------------------------------------------------*/ 2609 2610 PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 2611 { 2612 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2613 PetscErrorCode ierr; 2614 2615 PetscFunctionBegin; 2616 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 2617 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 2618 PetscFunctionReturn(0); 2619 } 2620 2621 PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 2622 { 2623 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2624 PetscErrorCode ierr; 2625 2626 PetscFunctionBegin; 2627 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 2628 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 2629 PetscFunctionReturn(0); 2630 } 2631 2632 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 2633 { 2634 Mat_MPIAIJ *b; 2635 PetscErrorCode ierr; 2636 2637 PetscFunctionBegin; 2638 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2639 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2640 b = (Mat_MPIAIJ*)B->data; 2641 2642 #if defined(PETSC_USE_CTABLE) 2643 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2644 #else 2645 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2646 #endif 2647 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2648 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2649 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2650 2651 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2652 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2653 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2654 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 2655 ierr = MatSetBlockSizesFromMats(b->B,B,B);CHKERRQ(ierr); 2656 ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr); 2657 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2658 2659 if (!B->preallocated) { 2660 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2661 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2662 ierr = MatSetBlockSizesFromMats(b->A,B,B);CHKERRQ(ierr); 2663 ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr); 2664 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2665 } 2666 2667 ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr); 2668 ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr); 2669 B->preallocated = PETSC_TRUE; 2670 B->was_assembled = PETSC_FALSE; 2671 B->assembled = PETSC_FALSE;; 2672 PetscFunctionReturn(0); 2673 } 2674 2675 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 2676 { 2677 Mat mat; 2678 Mat_MPIAIJ *a,*oldmat = (Mat_MPIAIJ*)matin->data; 2679 PetscErrorCode ierr; 2680 2681 PetscFunctionBegin; 2682 *newmat = 0; 2683 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 2684 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 2685 ierr = MatSetBlockSizesFromMats(mat,matin,matin);CHKERRQ(ierr); 2686 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 2687 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2688 a = (Mat_MPIAIJ*)mat->data; 2689 2690 mat->factortype = matin->factortype; 2691 mat->assembled = PETSC_TRUE; 2692 mat->insertmode = NOT_SET_VALUES; 2693 mat->preallocated = PETSC_TRUE; 2694 2695 a->size = oldmat->size; 2696 a->rank = oldmat->rank; 2697 a->donotstash = oldmat->donotstash; 2698 a->roworiented = oldmat->roworiented; 2699 a->rowindices = 0; 2700 a->rowvalues = 0; 2701 a->getrowactive = PETSC_FALSE; 2702 2703 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 2704 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 2705 2706 if (oldmat->colmap) { 2707 #if defined(PETSC_USE_CTABLE) 2708 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 2709 #else 2710 ierr = PetscMalloc1(mat->cmap->N,&a->colmap);CHKERRQ(ierr); 2711 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2712 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2713 #endif 2714 } else a->colmap = 0; 2715 if (oldmat->garray) { 2716 PetscInt len; 2717 len = oldmat->B->cmap->n; 2718 ierr = PetscMalloc1(len+1,&a->garray);CHKERRQ(ierr); 2719 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 2720 if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); } 2721 } else a->garray = 0; 2722 2723 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 2724 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 2725 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 2726 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 2727 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 2728 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 2729 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 2730 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 2731 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 2732 *newmat = mat; 2733 PetscFunctionReturn(0); 2734 } 2735 2736 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 2737 { 2738 PetscScalar *vals,*svals; 2739 MPI_Comm comm; 2740 PetscErrorCode ierr; 2741 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 2742 PetscInt i,nz,j,rstart,rend,mmax,maxnz = 0; 2743 PetscInt header[4],*rowlengths = 0,M,N,m,*cols; 2744 PetscInt *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols; 2745 PetscInt cend,cstart,n,*rowners; 2746 int fd; 2747 PetscInt bs = newMat->rmap->bs; 2748 2749 PetscFunctionBegin; 2750 /* force binary viewer to load .info file if it has not yet done so */ 2751 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 2752 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2753 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2754 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2755 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2756 if (!rank) { 2757 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 2758 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 2759 if (header[3] < 0) SETERRQ(PetscObjectComm((PetscObject)newMat),PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as MATMPIAIJ"); 2760 } 2761 2762 ierr = PetscOptionsBegin(comm,NULL,"Options for loading MATMPIAIJ matrix","Mat");CHKERRQ(ierr); 2763 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 2764 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2765 if (bs < 0) bs = 1; 2766 2767 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 2768 M = header[1]; N = header[2]; 2769 2770 /* If global sizes are set, check if they are consistent with that given in the file */ 2771 if (newMat->rmap->N >= 0 && newMat->rmap->N != M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of rows:Matrix in file has (%D) and input matrix has (%D)",newMat->rmap->N,M); 2772 if (newMat->cmap->N >=0 && newMat->cmap->N != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of cols:Matrix in file has (%D) and input matrix has (%D)",newMat->cmap->N,N); 2773 2774 /* determine ownership of all (block) rows */ 2775 if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs); 2776 if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank)); /* PETSC_DECIDE */ 2777 else m = newMat->rmap->n; /* Set by user */ 2778 2779 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 2780 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 2781 2782 /* First process needs enough room for process with most rows */ 2783 if (!rank) { 2784 mmax = rowners[1]; 2785 for (i=2; i<=size; i++) { 2786 mmax = PetscMax(mmax, rowners[i]); 2787 } 2788 } else mmax = -1; /* unused, but compilers complain */ 2789 2790 rowners[0] = 0; 2791 for (i=2; i<=size; i++) { 2792 rowners[i] += rowners[i-1]; 2793 } 2794 rstart = rowners[rank]; 2795 rend = rowners[rank+1]; 2796 2797 /* distribute row lengths to all processors */ 2798 ierr = PetscMalloc2(m,&ourlens,m,&offlens);CHKERRQ(ierr); 2799 if (!rank) { 2800 ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr); 2801 ierr = PetscMalloc1(mmax,&rowlengths);CHKERRQ(ierr); 2802 ierr = PetscCalloc1(size,&procsnz);CHKERRQ(ierr); 2803 for (j=0; j<m; j++) { 2804 procsnz[0] += ourlens[j]; 2805 } 2806 for (i=1; i<size; i++) { 2807 ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr); 2808 /* calculate the number of nonzeros on each processor */ 2809 for (j=0; j<rowners[i+1]-rowners[i]; j++) { 2810 procsnz[i] += rowlengths[j]; 2811 } 2812 ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2813 } 2814 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2815 } else { 2816 ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2817 } 2818 2819 if (!rank) { 2820 /* determine max buffer needed and allocate it */ 2821 maxnz = 0; 2822 for (i=0; i<size; i++) { 2823 maxnz = PetscMax(maxnz,procsnz[i]); 2824 } 2825 ierr = PetscMalloc1(maxnz,&cols);CHKERRQ(ierr); 2826 2827 /* read in my part of the matrix column indices */ 2828 nz = procsnz[0]; 2829 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2830 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 2831 2832 /* read in every one elses and ship off */ 2833 for (i=1; i<size; i++) { 2834 nz = procsnz[i]; 2835 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 2836 ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2837 } 2838 ierr = PetscFree(cols);CHKERRQ(ierr); 2839 } else { 2840 /* determine buffer space needed for message */ 2841 nz = 0; 2842 for (i=0; i<m; i++) { 2843 nz += ourlens[i]; 2844 } 2845 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2846 2847 /* receive message of column indices*/ 2848 ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2849 } 2850 2851 /* determine column ownership if matrix is not square */ 2852 if (N != M) { 2853 if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank); 2854 else n = newMat->cmap->n; 2855 ierr = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2856 cstart = cend - n; 2857 } else { 2858 cstart = rstart; 2859 cend = rend; 2860 n = cend - cstart; 2861 } 2862 2863 /* loop over local rows, determining number of off diagonal entries */ 2864 ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr); 2865 jj = 0; 2866 for (i=0; i<m; i++) { 2867 for (j=0; j<ourlens[i]; j++) { 2868 if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++; 2869 jj++; 2870 } 2871 } 2872 2873 for (i=0; i<m; i++) { 2874 ourlens[i] -= offlens[i]; 2875 } 2876 ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr); 2877 2878 if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);} 2879 2880 ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr); 2881 2882 for (i=0; i<m; i++) { 2883 ourlens[i] += offlens[i]; 2884 } 2885 2886 if (!rank) { 2887 ierr = PetscMalloc1(maxnz+1,&vals);CHKERRQ(ierr); 2888 2889 /* read in my part of the matrix numerical values */ 2890 nz = procsnz[0]; 2891 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2892 2893 /* insert into matrix */ 2894 jj = rstart; 2895 smycols = mycols; 2896 svals = vals; 2897 for (i=0; i<m; i++) { 2898 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2899 smycols += ourlens[i]; 2900 svals += ourlens[i]; 2901 jj++; 2902 } 2903 2904 /* read in other processors and ship out */ 2905 for (i=1; i<size; i++) { 2906 nz = procsnz[i]; 2907 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2908 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2909 } 2910 ierr = PetscFree(procsnz);CHKERRQ(ierr); 2911 } else { 2912 /* receive numeric values */ 2913 ierr = PetscMalloc1(nz+1,&vals);CHKERRQ(ierr); 2914 2915 /* receive message of values*/ 2916 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2917 2918 /* insert into matrix */ 2919 jj = rstart; 2920 smycols = mycols; 2921 svals = vals; 2922 for (i=0; i<m; i++) { 2923 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2924 smycols += ourlens[i]; 2925 svals += ourlens[i]; 2926 jj++; 2927 } 2928 } 2929 ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr); 2930 ierr = PetscFree(vals);CHKERRQ(ierr); 2931 ierr = PetscFree(mycols);CHKERRQ(ierr); 2932 ierr = PetscFree(rowners);CHKERRQ(ierr); 2933 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2934 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2935 PetscFunctionReturn(0); 2936 } 2937 2938 /* Not scalable because of ISAllGather() unless getting all columns. */ 2939 PetscErrorCode ISGetSeqIS_Private(Mat mat,IS iscol,IS *isseq) 2940 { 2941 PetscErrorCode ierr; 2942 IS iscol_local; 2943 PetscBool isstride; 2944 PetscMPIInt lisstride=0,gisstride; 2945 2946 PetscFunctionBegin; 2947 /* check if we are grabbing all columns*/ 2948 ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&isstride);CHKERRQ(ierr); 2949 2950 if (isstride) { 2951 PetscInt start,len,mstart,mlen; 2952 ierr = ISStrideGetInfo(iscol,&start,NULL);CHKERRQ(ierr); 2953 ierr = ISGetLocalSize(iscol,&len);CHKERRQ(ierr); 2954 ierr = MatGetOwnershipRangeColumn(mat,&mstart,&mlen);CHKERRQ(ierr); 2955 if (mstart == start && mlen-mstart == len) lisstride = 1; 2956 } 2957 2958 ierr = MPIU_Allreduce(&lisstride,&gisstride,1,MPI_INT,MPI_MIN,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2959 if (gisstride) { 2960 PetscInt N; 2961 ierr = MatGetSize(mat,NULL,&N);CHKERRQ(ierr); 2962 ierr = ISCreateStride(PetscObjectComm((PetscObject)mat),N,0,1,&iscol_local);CHKERRQ(ierr); 2963 ierr = ISSetIdentity(iscol_local);CHKERRQ(ierr); 2964 ierr = PetscInfo(mat,"Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n");CHKERRQ(ierr); 2965 } else { 2966 PetscInt cbs; 2967 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 2968 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 2969 ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr); 2970 } 2971 2972 *isseq = iscol_local; 2973 PetscFunctionReturn(0); 2974 } 2975 2976 /* 2977 Used by MatCreateSubMatrix_MPIAIJ_SameRowColDist() to avoid ISAllGather() and global size of iscol_local 2978 (see MatCreateSubMatrix_MPIAIJ_nonscalable) 2979 2980 Input Parameters: 2981 mat - matrix 2982 isrow - parallel row index set; its local indices are a subset of local columns of mat, 2983 i.e., mat->rstart <= isrow[i] < mat->rend 2984 iscol - parallel column index set; its local indices are a subset of local columns of mat, 2985 i.e., mat->cstart <= iscol[i] < mat->cend 2986 Output Parameter: 2987 isrow_d,iscol_d - sequential row and column index sets for retrieving mat->A 2988 iscol_o - sequential column index set for retrieving mat->B 2989 garray - column map; garray[i] indicates global location of iscol_o[i] in iscol 2990 */ 2991 PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat,IS isrow,IS iscol,IS *isrow_d,IS *iscol_d,IS *iscol_o,const PetscInt *garray[]) 2992 { 2993 PetscErrorCode ierr; 2994 Vec x,cmap; 2995 const PetscInt *is_idx; 2996 PetscScalar *xarray,*cmaparray; 2997 PetscInt ncols,isstart,*idx,m,rstart,*cmap1,count; 2998 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 2999 Mat B=a->B; 3000 Vec lvec=a->lvec,lcmap; 3001 PetscInt i,cstart,cend,Bn=B->cmap->N; 3002 MPI_Comm comm; 3003 3004 PetscFunctionBegin; 3005 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3006 PetscMPIInt rank; 3007 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3008 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 3009 3010 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3011 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3012 ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3013 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3014 3015 /* Get start indices */ 3016 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3017 isstart -= ncols; 3018 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3019 3020 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3021 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3022 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3023 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3024 for (i=0; i<ncols; i++) { 3025 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3026 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3027 idx[i] = is_idx[i]-cstart; /* local index of iscol[i] */ 3028 } 3029 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3030 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3031 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3032 3033 /* Get iscol_d */ 3034 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,iscol_d);CHKERRQ(ierr); 3035 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3036 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3037 3038 /* Get isrow_d */ 3039 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3040 rstart = mat->rmap->rstart; 3041 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3042 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3043 for (i=0; i<m; i++) idx[i] = is_idx[i]-rstart; 3044 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3045 3046 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_OWN_POINTER,isrow_d);CHKERRQ(ierr); 3047 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3048 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3049 3050 /* (2) Scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3051 ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3052 3053 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3054 3055 ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3056 ierr = VecScatterBegin(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3057 ierr = VecScatterEnd(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3058 3059 /* (3) create sequential iscol_o (a subset of iscol) and isgarray */ 3060 /* off-process column indices */ 3061 count = 0; 3062 ierr = PetscMalloc1(Bn,&idx);CHKERRQ(ierr); 3063 ierr = PetscMalloc1(Bn,&cmap1);CHKERRQ(ierr); 3064 3065 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3066 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3067 for (i=0; i<Bn; i++) { 3068 if (PetscRealPart(xarray[i]) > -1.0) { 3069 idx[count] = i; /* local column index in off-diagonal part B */ 3070 cmap1[count++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3071 } 3072 } 3073 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3074 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3075 3076 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr); 3077 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3078 ierr = ISSetBlockSize(*iscol_o,i);CHKERRQ(ierr); 3079 ierr = PetscFree(idx);CHKERRQ(ierr); 3080 3081 *garray = cmap1; 3082 3083 ierr = VecDestroy(&x);CHKERRQ(ierr); 3084 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3085 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3086 PetscFunctionReturn(0); 3087 } 3088 3089 /* isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */ 3090 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *submat) 3091 { 3092 PetscErrorCode ierr; 3093 Mat_MPIAIJ *a = (Mat_MPIAIJ*)mat->data,*asub; 3094 Mat M = NULL; 3095 MPI_Comm comm; 3096 IS iscol_d,isrow_d,iscol_o; 3097 Mat Asub = NULL,Bsub = NULL; 3098 PetscInt n; 3099 3100 PetscFunctionBegin; 3101 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3102 PetscMPIInt rank; 3103 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3104 3105 if (call == MAT_REUSE_MATRIX) { 3106 if (!rank) printf(" _SameRowColDist reuse ...\n"); 3107 3108 /* Retrieve isrow_d, iscol_d and iscol_o from submat */ 3109 ierr = PetscObjectQuery((PetscObject)*submat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3110 if (!isrow_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow_d passed in was not used before, cannot reuse"); 3111 3112 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_d",(PetscObject*)&iscol_d);CHKERRQ(ierr); 3113 if (!iscol_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_d passed in was not used before, cannot reuse"); 3114 3115 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_o",(PetscObject*)&iscol_o);CHKERRQ(ierr); 3116 if (!iscol_o) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_o passed in was not used before, cannot reuse"); 3117 3118 /* Update diagonal and off-diagonal portions of submat */ 3119 asub = (Mat_MPIAIJ*)(*submat)->data; 3120 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->A);CHKERRQ(ierr); 3121 ierr = ISGetLocalSize(iscol_o,&n);CHKERRQ(ierr); 3122 if (n) { 3123 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->B);CHKERRQ(ierr); 3124 } 3125 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3126 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3127 3128 } else { /* call == MAT_INITIAL_MATRIX) */ 3129 const PetscInt *garray; 3130 PetscInt BsubN; 3131 3132 /* Create isrow_d, iscol_d, iscol_o and isgarray (replace isgarray with array?) */ 3133 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&isrow_d,&iscol_d,&iscol_o,&garray);CHKERRQ(ierr); 3134 3135 /* Create local submatrices Asub and Bsub */ 3136 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Asub);CHKERRQ(ierr); 3137 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Bsub);CHKERRQ(ierr); 3138 3139 /* Create submatrix M */ 3140 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray,&M);CHKERRQ(ierr); 3141 3142 /* If Bsub has empty columns, compress iscol_o such that it will retrieve condensed Bsub from a->B during reuse */ 3143 asub = (Mat_MPIAIJ*)M->data; 3144 3145 ierr = ISGetLocalSize(iscol_o,&BsubN);CHKERRQ(ierr); 3146 n = asub->B->cmap->N; 3147 if (BsubN > n) { 3148 /* This case can be tested using ~petsc/src/tao/bound/examples/tutorials/runplate2_3 */ 3149 const PetscInt *idx; 3150 PetscInt i,j,*idx_new,*subgarray = asub->garray; 3151 ierr = PetscInfo2(M,"submatrix Bn %D != BsubN %D, update iscol_o\n",n,BsubN);CHKERRQ(ierr); 3152 3153 ierr = PetscMalloc1(n,&idx_new);CHKERRQ(ierr); 3154 j = 0; 3155 ierr = ISGetIndices(iscol_o,&idx);CHKERRQ(ierr); 3156 for (i=0; i<n; i++) { 3157 if (j >= BsubN) break; 3158 while (subgarray[i] > garray[j]) j++; 3159 3160 if (subgarray[i] == garray[j]) { 3161 idx_new[i] = idx[j++]; 3162 } else SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"subgarray[%D]=%D cannot < garray[%D]=%D",i,subgarray[i],j,garray[j]); 3163 } 3164 ierr = ISRestoreIndices(iscol_o,&idx);CHKERRQ(ierr); 3165 3166 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3167 ierr = ISCreateGeneral(PETSC_COMM_SELF,n,idx_new,PETSC_OWN_POINTER,&iscol_o);CHKERRQ(ierr); 3168 3169 } else if (BsubN < n) { 3170 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Columns of Bsub cannot be smaller than B's",BsubN,asub->B->cmap->N); 3171 } 3172 3173 ierr = PetscFree(garray);CHKERRQ(ierr); 3174 *submat = M; 3175 3176 /* Save isrow_d, iscol_d and iscol_o used in processor for next request */ 3177 ierr = PetscObjectCompose((PetscObject)M,"isrow_d",(PetscObject)isrow_d);CHKERRQ(ierr); 3178 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3179 3180 ierr = PetscObjectCompose((PetscObject)M,"iscol_d",(PetscObject)iscol_d);CHKERRQ(ierr); 3181 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3182 3183 ierr = PetscObjectCompose((PetscObject)M,"iscol_o",(PetscObject)iscol_o);CHKERRQ(ierr); 3184 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3185 } 3186 PetscFunctionReturn(0); 3187 } 3188 3189 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3190 { 3191 PetscErrorCode ierr; 3192 IS iscol_local,isrow_d; 3193 PetscInt csize; 3194 PetscInt n,i,j,start,end; 3195 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3196 MPI_Comm comm; 3197 3198 PetscFunctionBegin; 3199 /* If isrow has same processor distribution as mat, 3200 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3201 if (call == MAT_REUSE_MATRIX) { 3202 ierr = PetscObjectQuery((PetscObject)*newmat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3203 if (isrow_d) { 3204 sameRowDist = PETSC_TRUE; 3205 tsameDist[1] = PETSC_TRUE; /* sameColDist */ 3206 } else { 3207 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3208 if (iscol_local) { 3209 sameRowDist = PETSC_TRUE; 3210 tsameDist[1] = PETSC_FALSE; /* !sameColDist */ 3211 } 3212 } 3213 } else { 3214 /* Check if isrow has same processor distribution as mat */ 3215 sameDist[0] = PETSC_FALSE; 3216 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3217 if (!n) { 3218 sameDist[0] = PETSC_TRUE; 3219 } else { 3220 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3221 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3222 if (i >= start && j < end) { 3223 sameDist[0] = PETSC_TRUE; 3224 } 3225 } 3226 3227 /* Check if iscol has same processor distribution as mat */ 3228 sameDist[1] = PETSC_FALSE; 3229 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3230 if (!n) { 3231 sameDist[1] = PETSC_TRUE; 3232 } else { 3233 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3234 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3235 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3236 } 3237 3238 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3239 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3240 sameRowDist = tsameDist[0]; 3241 } 3242 3243 if (sameRowDist) { 3244 if (tsameDist[1]) { /* sameRowDist & sameColDist */ 3245 /* isrow and iscol have same processor distribution as mat */ 3246 ierr = MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3247 } else { /* sameRowDist */ 3248 /* isrow has same processor distribution as mat */ 3249 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3250 } 3251 PetscFunctionReturn(0); 3252 } 3253 3254 /* General case: iscol -> iscol_local which has global size of iscol */ 3255 if (call == MAT_REUSE_MATRIX) { 3256 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3257 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3258 } else { 3259 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3260 } 3261 3262 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3263 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3264 3265 if (call == MAT_INITIAL_MATRIX) { 3266 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3267 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3268 } 3269 PetscFunctionReturn(0); 3270 } 3271 3272 /*@C 3273 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3274 and "off-diagonal" part of the matrix in CSR format. 3275 3276 Collective on MPI_Comm 3277 3278 Input Parameters: 3279 + comm - MPI communicator 3280 . A - "diagonal" portion of matrix 3281 . B - "off-diagonal" portion of matrix, may have empty columns, will be destroyed by this routine 3282 - garray - global index of B columns 3283 3284 Output Parameter: 3285 . mat - the matrix, with input A as its local diagonal matrix 3286 Level: advanced 3287 3288 Notes: 3289 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3290 A becomes part of output mat, B is destroyed by this routine. The user cannot use A and B anymore. 3291 3292 .seealso: MatCreateMPIAIJWithSplitArrays() 3293 @*/ 3294 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3295 { 3296 PetscErrorCode ierr; 3297 Mat_MPIAIJ *maij; 3298 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data,*bnew; 3299 PetscInt *oi=b->i,*oj=b->j,i,nz,col; 3300 PetscScalar *oa=b->a; 3301 Mat Bnew; 3302 PetscInt m,n,N; 3303 3304 PetscFunctionBegin; 3305 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3306 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3307 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %D != Bm %D",m,B->rmap->N); 3308 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); 3309 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); 3310 3311 /* Get global columns of mat */ 3312 ierr = MPIU_Allreduce(&n,&N,1,MPI_INT,MPI_SUM,comm);CHKERRQ(ierr); 3313 3314 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3315 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3316 ierr = MatSetBlockSizes(*mat,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 3317 maij = (Mat_MPIAIJ*)(*mat)->data; 3318 3319 (*mat)->preallocated = PETSC_TRUE; 3320 3321 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3322 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3323 3324 /* Set A as diagonal portion of *mat */ 3325 maij->A = A; 3326 3327 nz = oi[m]; 3328 for (i=0; i<nz; i++) { 3329 col = oj[i]; 3330 oj[i] = garray[col]; 3331 } 3332 3333 /* Set Bnew as off-diagonal portion of *mat */ 3334 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Bnew);CHKERRQ(ierr); 3335 bnew = (Mat_SeqAIJ*)Bnew->data; 3336 bnew->maxnz = b->maxnz; /* allocated nonzeros of B */ 3337 maij->B = Bnew; 3338 3339 if (B->rmap->N != Bnew->rmap->N) SETERRQ2(PETSC_COMM_SELF,0,"BN %d != BnewN %d",B->rmap->N,Bnew->rmap->N); 3340 3341 b->singlemalloc = PETSC_FALSE; /* B arrays are shared by Bnew */ 3342 b->free_a = PETSC_FALSE; 3343 b->free_ij = PETSC_FALSE; 3344 ierr = MatDestroy(&B);CHKERRQ(ierr); 3345 3346 bnew->singlemalloc = PETSC_TRUE; /* arrays will be freed by MatDestroy(&Bnew) */ 3347 bnew->free_a = PETSC_TRUE; 3348 bnew->free_ij = PETSC_TRUE; 3349 3350 /* condense columns of maij->B */ 3351 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3352 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3353 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3354 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3355 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3356 PetscFunctionReturn(0); 3357 } 3358 3359 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3360 3361 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3362 { 3363 PetscErrorCode ierr; 3364 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3365 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3366 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3367 Mat M,Msub,B=a->B; 3368 MatScalar *aa; 3369 Mat_SeqAIJ *aij; 3370 PetscInt *garray = a->garray,*colsub,Ncols; 3371 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3372 IS iscol_sub,iscmap; 3373 const PetscInt *is_idx,*cmap; 3374 PetscBool allcolumns=PETSC_FALSE; 3375 IS iscol_local=NULL; 3376 MPI_Comm comm; 3377 3378 PetscFunctionBegin; 3379 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3380 3381 if (call == MAT_REUSE_MATRIX) { 3382 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3383 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3384 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3385 3386 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3387 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3388 3389 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3390 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3391 3392 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3393 3394 } else { /* call == MAT_INITIAL_MATRIX) */ 3395 PetscBool flg; 3396 3397 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3398 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3399 3400 /* (1) iscol -> nonscalable iscol_local */ 3401 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3402 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3403 if (n != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != Ncols %d",n,Ncols); 3404 3405 /* Check for special case: each processor gets entire matrix columns */ 3406 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3407 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3408 if (allcolumns) { 3409 iscol_sub = iscol_local; 3410 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3411 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3412 3413 } else { 3414 /* (2) iscol_local -> iscol_sub and iscmap */ 3415 PetscInt *idx,*cmap1,k,cbs; 3416 3417 /* implementation below requires iscol_local be sorted, it can have duplicate indices */ 3418 ierr = ISSorted(iscol_local,&flg);CHKERRQ(ierr); 3419 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsorted iscol_local is not implemented yet"); 3420 3421 ierr = PetscMalloc1(Ncols,&idx);CHKERRQ(ierr); 3422 ierr = PetscMalloc1(Ncols,&cmap1);CHKERRQ(ierr); 3423 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3424 count = 0; 3425 k = 0; 3426 for (i=0; i<Ncols; i++) { 3427 j = is_idx[i]; 3428 if (j >= cstart && j < cend) { 3429 /* diagonal part of mat */ 3430 idx[count] = j; 3431 cmap1[count++] = i; /* column index in submat */ 3432 } else if (Bn) { 3433 /* off-diagonal part of mat */ 3434 if (j == garray[k]) { 3435 idx[count] = j; 3436 cmap1[count++] = i; /* column index in submat */ 3437 } else if (j > garray[k]) { 3438 while (j > garray[k] && k < Bn-1) k++; 3439 if (j == garray[k]) { 3440 idx[count] = j; 3441 cmap1[count++] = i; /* column index in submat */ 3442 } 3443 } 3444 } 3445 } 3446 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3447 3448 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_OWN_POINTER,&iscol_sub);CHKERRQ(ierr); 3449 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3450 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3451 3452 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_OWN_POINTER,&iscmap);CHKERRQ(ierr); 3453 } 3454 3455 /* (3) Create sequential Msub */ 3456 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3457 } 3458 3459 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3460 aij = (Mat_SeqAIJ*)(Msub)->data; 3461 ii = aij->i; 3462 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3463 3464 /* 3465 m - number of local rows 3466 Ncols - number of columns (same on all processors) 3467 rstart - first row in new global matrix generated 3468 */ 3469 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3470 3471 if (call == MAT_INITIAL_MATRIX) { 3472 /* (4) Create parallel newmat */ 3473 PetscMPIInt rank,size; 3474 PetscInt csize; 3475 3476 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3477 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3478 3479 /* 3480 Determine the number of non-zeros in the diagonal and off-diagonal 3481 portions of the matrix in order to do correct preallocation 3482 */ 3483 3484 /* first get start and end of "diagonal" columns */ 3485 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3486 if (csize == PETSC_DECIDE) { 3487 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3488 if (mglobal == Ncols) { /* square matrix */ 3489 nlocal = m; 3490 } else { 3491 nlocal = Ncols/size + ((Ncols % size) > rank); 3492 } 3493 } else { 3494 nlocal = csize; 3495 } 3496 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3497 rstart = rend - nlocal; 3498 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); 3499 3500 /* next, compute all the lengths */ 3501 jj = aij->j; 3502 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3503 olens = dlens + m; 3504 for (i=0; i<m; i++) { 3505 jend = ii[i+1] - ii[i]; 3506 olen = 0; 3507 dlen = 0; 3508 for (j=0; j<jend; j++) { 3509 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3510 else dlen++; 3511 jj++; 3512 } 3513 olens[i] = olen; 3514 dlens[i] = dlen; 3515 } 3516 ierr = MatGetBlockSizes(Msub,&bs,&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