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 for avoiding ISAllGather() and global size of iscol_local (see MatCreateSubMatrix_MPIAIJ_nonscalable) 2978 2979 Input Parameters: 2980 mat - matrix 2981 iscol - parallel column index set; its local indices are a subset of local columns of mat, 2982 i.e., mat->cstart <= iscol[i] < mat->cend 2983 Output Parameter: 2984 iscol_sub - sequential column index set, a subset of iscol 2985 iscmap - column map; iscmap[i] indicates global location of iscol_sub[i] in iscol 2986 */ 2987 PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat,IS isrow,IS iscol,IS *isrow_d,IS *iscol_d,IS *iscol_o,IS *isgarray) 2988 { 2989 PetscErrorCode ierr; 2990 Vec x,cmap; 2991 const PetscInt *is_idx; 2992 PetscScalar *xarray,*cmaparray; 2993 PetscInt ncols,isstart,*idx,*camp,count,m,rstart; 2994 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 2995 Mat B=a->B; 2996 Vec lvec=a->lvec,lcmap; 2997 PetscInt i,cstart,cend,Bn=B->cmap->N; 2998 MPI_Comm comm; 2999 3000 PetscFunctionBegin; 3001 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3002 PetscMPIInt rank; 3003 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3004 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 3005 3006 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3007 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3008 ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3009 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3010 3011 /* get start indices */ 3012 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3013 isstart -= ncols; 3014 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3015 3016 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3017 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3018 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3019 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3020 for (i=0; i<ncols; i++) { 3021 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3022 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3023 3024 idx[i] = is_idx[i]-cstart; 3025 } 3026 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3027 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3028 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3029 3030 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_COPY_VALUES,iscol_d);CHKERRQ(ierr); 3031 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3032 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3033 ierr = PetscFree(idx);CHKERRQ(ierr); 3034 3035 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3036 rstart = mat->rmap->rstart; 3037 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3038 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3039 for (i=0; i<m; i++) { 3040 idx[i] = is_idx[i]-rstart; 3041 } 3042 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3043 3044 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_COPY_VALUES,isrow_d);CHKERRQ(ierr); 3045 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3046 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3047 ierr = PetscFree(idx);CHKERRQ(ierr); 3048 3049 /* (2) scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3050 ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3051 3052 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3053 3054 ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3055 ierr = VecScatterBegin(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3056 3057 count = ncols + Bn; 3058 ierr = PetscMalloc2(count,&idx,count,&camp);CHKERRQ(ierr); 3059 3060 ierr = VecScatterEnd(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3061 3062 /* (3) create scalable iscol_sub (a subset of iscol) and iscmap */ 3063 /* local column indices */ 3064 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3065 for (i=0; i<ncols; i++) { 3066 idx[i] = is_idx[i]; 3067 camp[i] = i + isstart; /* global index of iscol = column index in submat */ 3068 } 3069 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3070 count = ncols; 3071 3072 /* off-process column indices */ 3073 PetscInt *idx1,*cmap1,count1=0; 3074 ierr = PetscMalloc2(Bn,&idx1,Bn,&cmap1);CHKERRQ(ierr); 3075 3076 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3077 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3078 for (i=0; i<Bn; i++) { 3079 if (PetscRealPart(xarray[i]) > -1.0) { 3080 idx1[count1] = i; /* local column index in off-diagonal part B */ 3081 cmap1[count1++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3082 3083 idx[count] = (PetscInt)PetscRealPart(xarray[i]); 3084 camp[count++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3085 } 3086 } 3087 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3088 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3089 3090 ierr = PetscSortIntWithArray(count,camp,idx);CHKERRQ(ierr); 3091 3092 ierr = ISCreateGeneral(PETSC_COMM_SELF,count1,idx1,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr); 3093 ierr = ISCreateGeneral(PETSC_COMM_SELF,count1,cmap1,PETSC_COPY_VALUES,isgarray);CHKERRQ(ierr); 3094 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3095 ierr = ISSetBlockSize(*iscol_o,i);CHKERRQ(ierr); 3096 ierr = PetscFree2(idx1,cmap1);CHKERRQ(ierr); 3097 3098 ierr = PetscFree2(idx,camp);CHKERRQ(ierr); 3099 ierr = VecDestroy(&x);CHKERRQ(ierr); 3100 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3101 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3102 PetscFunctionReturn(0); 3103 } 3104 3105 /* Both isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */ 3106 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *submat) 3107 { 3108 PetscErrorCode ierr; 3109 PetscInt i,m,n,rstart,row,rend,nz,j,rbs,cbs; 3110 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3111 Mat M=NULL,B=a->B; 3112 PetscInt *garray = a->garray,*colsub,Ncols; 3113 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3114 IS iscol_sub,iscmap; 3115 const PetscInt *is_idx,*cmap; 3116 PetscBool allcolumns=PETSC_FALSE; 3117 IS iscol_local=NULL; 3118 MPI_Comm comm; 3119 IS iscol_d,isrow_d,iscol_o,isgarray; 3120 Mat Asub=NULL,Bsub=NULL; 3121 3122 PetscFunctionBegin; 3123 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3124 PetscMPIInt rank; 3125 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3126 3127 if (call == MAT_REUSE_MATRIX) { 3128 Mat_MPIAIJ *matsub=(Mat_MPIAIJ*)(*submat)->data; 3129 3130 ierr = PetscObjectQuery((PetscObject)*submat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3131 if (!isrow_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow_d passed in was not used before, cannot reuse"); 3132 3133 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_d",(PetscObject*)&iscol_d);CHKERRQ(ierr); 3134 if (!iscol_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_d passed in was not used before, cannot reuse"); 3135 3136 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_o",(PetscObject*)&iscol_o);CHKERRQ(ierr); 3137 if (!iscol_o) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_o passed in was not used before, cannot reuse"); 3138 3139 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,call,&matsub->A);CHKERRQ(ierr); 3140 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,call,&matsub->B);CHKERRQ(ierr); 3141 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3142 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3143 3144 } else { /* call == MAT_INITIAL_MATRIX) */ 3145 const PetscInt *garray1; 3146 3147 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&isrow_d,&iscol_d,&iscol_o,&isgarray);CHKERRQ(ierr); 3148 3149 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,call,&Asub);CHKERRQ(ierr); 3150 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,call,&Bsub);CHKERRQ(ierr); 3151 3152 PetscInt BsubN = Bsub->cmap->N; 3153 ierr = ISGetIndices(isgarray,&garray1);CHKERRQ(ierr); 3154 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray1,&M);CHKERRQ(ierr); 3155 ierr = ISRestoreIndices(isgarray,&garray1);CHKERRQ(ierr); 3156 3157 /* Check is Bsub == M->B? If not, compress iscol_o accordingly */ 3158 3159 a = (Mat_MPIAIJ*)M->data; 3160 #if 1 3161 if (BsubN != a->B->cmap->N) { 3162 printf("[%d] Bsub->cmap->N %d != a->B->cmap->N %d\n",rank,BsubN,a->B->cmap->N); 3163 } 3164 #endif 3165 3166 ierr = ISDestroy(&isgarray);CHKERRQ(ierr); 3167 3168 /* Save isrow_d, iscol_d and iscol_o used in processor for next request */ 3169 ierr = PetscObjectCompose((PetscObject)M,"isrow_d",(PetscObject)isrow_d);CHKERRQ(ierr); 3170 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3171 3172 ierr = PetscObjectCompose((PetscObject)M,"iscol_d",(PetscObject)iscol_d);CHKERRQ(ierr); 3173 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3174 3175 ierr = PetscObjectCompose((PetscObject)M,"iscol_o",(PetscObject)iscol_o);CHKERRQ(ierr); 3176 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3177 3178 *submat = M; 3179 } 3180 PetscFunctionReturn(0); 3181 } 3182 3183 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3184 { 3185 PetscErrorCode ierr; 3186 IS iscol_local,isrow_d; 3187 PetscInt csize; 3188 PetscInt n,i,j,start,end; 3189 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3190 MPI_Comm comm; 3191 3192 PetscFunctionBegin; 3193 /* If isrow has same processor distribution as mat, 3194 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3195 if (call == MAT_REUSE_MATRIX) { 3196 ierr = PetscObjectQuery((PetscObject)*newmat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3197 if (isrow_d) { 3198 sameRowDist = PETSC_TRUE; 3199 tsameDist[1] = PETSC_TRUE; /* sameColDist */ 3200 } else { 3201 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3202 if (iscol_local) { 3203 sameRowDist = PETSC_TRUE; 3204 tsameDist[1] = PETSC_FALSE; /* !sameColDist */ 3205 } 3206 } 3207 } else { 3208 /* Check if isrow has same processor distribution as mat */ 3209 sameDist[0] = PETSC_FALSE; 3210 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3211 if (!n) { 3212 sameDist[0] = PETSC_TRUE; 3213 } else { 3214 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3215 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3216 if (i >= start && j < end) { 3217 sameDist[0] = PETSC_TRUE; 3218 } 3219 } 3220 3221 /* Check if iscol has same processor distribution as mat */ 3222 sameDist[1] = PETSC_FALSE; 3223 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3224 if (!n) { 3225 sameDist[1] = PETSC_TRUE; 3226 } else { 3227 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3228 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3229 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3230 } 3231 3232 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3233 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3234 sameRowDist = tsameDist[0]; 3235 } 3236 3237 if (sameRowDist) { 3238 if (tsameDist[1]) { 3239 /* isrow and iscol have same processor distribution as mat */ 3240 ierr = MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3241 } else { 3242 /* isrow has same processor distribution as mat */ 3243 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3244 } 3245 PetscFunctionReturn(0); 3246 } 3247 3248 /* General case: iscol -> iscol_local which has global size of iscol */ 3249 if (call == MAT_REUSE_MATRIX) { 3250 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3251 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3252 } else { 3253 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3254 } 3255 3256 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3257 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3258 3259 if (call == MAT_INITIAL_MATRIX) { 3260 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3261 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3262 } 3263 PetscFunctionReturn(0); 3264 } 3265 3266 /*@C 3267 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3268 and "off-diagonal" part of the matrix in CSR format. 3269 3270 Collective on MPI_Comm 3271 3272 Input Parameters: 3273 + comm - MPI communicator 3274 . A - "diagonal" portion of matrix 3275 . B - "off-diagonal" portion of matrix, destroyed by this routine 3276 - garray - global index of B columns 3277 3278 Output Parameter: 3279 . mat - the matrix, with input A as its local diagonal matrix 3280 Level: advanced 3281 3282 Notes: 3283 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3284 A becomes part of output mat, B is destroyed by this routine. The user cannot use A and B anymore. 3285 3286 .seealso: MatCreateMPIAIJWithSplitArrays() 3287 @*/ 3288 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3289 { 3290 PetscErrorCode ierr; 3291 Mat_MPIAIJ *maij; 3292 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data,*bnew; 3293 PetscInt *oi=b->i,*oj=b->j,i,nz,col; 3294 PetscScalar *oa=b->a; 3295 Mat Bnew; 3296 PetscInt m,n,N; 3297 3298 PetscFunctionBegin; 3299 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3300 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3301 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %D != Bm %D",m,B->rmap->N); 3302 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); 3303 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); 3304 3305 /* Get global columns of mat */ 3306 ierr = MPIU_Allreduce(&n,&N,1,MPI_INT,MPI_SUM,comm);CHKERRQ(ierr); 3307 3308 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3309 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3310 ierr = MatSetBlockSizes(*mat,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 3311 maij = (Mat_MPIAIJ*)(*mat)->data; 3312 3313 (*mat)->preallocated = PETSC_TRUE; 3314 3315 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3316 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3317 3318 /* Set A as diagonal portion of *mat */ 3319 maij->A = A; 3320 3321 nz = oi[m]; 3322 for (i=0; i<nz; i++) { 3323 col = oj[i]; 3324 oj[i] = garray[col]; 3325 } 3326 3327 /* Set Bnew as off-diagonal portion of *mat */ 3328 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Bnew);CHKERRQ(ierr); 3329 bnew = (Mat_SeqAIJ*)Bnew->data; 3330 bnew->maxnz = b->maxnz; /* allocated nonzeros of B */ 3331 maij->B = Bnew; 3332 3333 PetscMPIInt rank; 3334 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3335 if (rank == -1) { 3336 printf("[%d] Bnew:\n",rank); 3337 ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_SELF, PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr); 3338 ierr = MatView(Bnew,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3339 ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3340 if (!rank) printf("--------------------\n"); 3341 } 3342 3343 // Check B == Bnew??? see src/ksp/ksp/examples/tests/runex21_2,3 3344 3345 if (B->rmap->N != Bnew->rmap->N) SETERRQ2(PETSC_COMM_SELF,0,"BN %d != BnewN %d",B->rmap->N,Bnew->rmap->N); 3346 3347 b->singlemalloc = PETSC_FALSE; /* B arrays are shared by Bnew */ 3348 b->free_a = PETSC_FALSE; 3349 b->free_ij = PETSC_FALSE; 3350 ierr = MatDestroy(&B);CHKERRQ(ierr); 3351 3352 bnew->singlemalloc = PETSC_TRUE; /* arrays will be freed by MatDestroy(&Bnew) */ 3353 bnew->free_a = PETSC_TRUE; 3354 bnew->free_ij = PETSC_TRUE; 3355 3356 /* condense columns of maij->B */ 3357 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3358 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3359 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3360 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3361 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3362 PetscFunctionReturn(0); 3363 } 3364 3365 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3366 3367 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3368 { 3369 PetscErrorCode ierr; 3370 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3371 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3372 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3373 Mat M,Msub,B=a->B,Mnew=NULL; 3374 MatScalar *aa; 3375 Mat_SeqAIJ *aij; 3376 PetscInt *garray = a->garray,*colsub,Ncols; 3377 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3378 IS iscol_sub,iscmap; 3379 const PetscInt *is_idx,*cmap; 3380 PetscBool allcolumns=PETSC_FALSE; 3381 IS iscol_local=NULL; 3382 MPI_Comm comm; 3383 IS iscol_d,isrow_d,iscol_o,isgarray; 3384 Mat Asub=NULL,Bsub=NULL; 3385 3386 PetscFunctionBegin; 3387 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3388 PetscMPIInt rank; 3389 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3390 3391 if (call == MAT_REUSE_MATRIX) { 3392 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3393 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3394 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3395 3396 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3397 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3398 3399 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3400 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3401 3402 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3403 3404 } else { /* call == MAT_INITIAL_MATRIX) */ 3405 PetscBool flg; 3406 3407 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3408 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3409 3410 /* (1) iscol -> nonscalable iscol_local */ 3411 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3412 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3413 if (n != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != Ncols %d",n,Ncols); 3414 3415 /* Check for special case: each processor gets entire matrix columns */ 3416 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3417 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3418 if (allcolumns) { 3419 iscol_sub = iscol_local; 3420 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3421 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3422 3423 } else { 3424 /* (2) iscol_local -> iscol_sub and iscmap */ 3425 PetscInt *idx,*cmap1,k,cbs; 3426 3427 /* implementation below requires iscol_local be sorted, it can have duplicate indices */ 3428 ierr = ISSorted(iscol_local,&flg);CHKERRQ(ierr); 3429 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsorted iscol_local is not implemented yet"); 3430 3431 ierr = PetscMalloc2(Ncols,&idx,Ncols,&cmap1);CHKERRQ(ierr); 3432 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3433 count = 0; 3434 k = 0; 3435 for (i=0; i<Ncols; i++) { 3436 j = is_idx[i]; 3437 if (j >= cstart && j < cend) { 3438 /* diagonal part of mat */ 3439 idx[count] = j; 3440 cmap1[count++] = i; /* column index in submat */ 3441 } else if (Bn) { 3442 /* off-diagonal part of mat */ 3443 if (j == garray[k]) { 3444 idx[count] = j; 3445 cmap1[count++] = i; /* column index in submat */ 3446 } else if (j > garray[k]) { 3447 while (j > garray[k] && k < Bn-1) k++; 3448 if (j == garray[k]) { 3449 idx[count] = j; 3450 cmap1[count++] = i; /* column index in submat */ 3451 } 3452 } 3453 } 3454 } 3455 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3456 3457 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,&iscol_sub);CHKERRQ(ierr); 3458 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3459 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3460 3461 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_COPY_VALUES,&iscmap);CHKERRQ(ierr); 3462 ierr = PetscFree2(idx,cmap1);CHKERRQ(ierr); 3463 } 3464 3465 /* (3) Create sequential Msub */ 3466 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3467 } 3468 3469 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3470 aij = (Mat_SeqAIJ*)(Msub)->data; 3471 ii = aij->i; 3472 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3473 3474 /* 3475 m - number of local rows 3476 Ncols - number of columns (same on all processors) 3477 rstart - first row in new global matrix generated 3478 */ 3479 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3480 3481 if (call == MAT_INITIAL_MATRIX) { 3482 /* (4) Create parallel newmat */ 3483 PetscMPIInt rank,size; 3484 PetscInt csize; 3485 3486 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3487 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3488 3489 /* 3490 Determine the number of non-zeros in the diagonal and off-diagonal 3491 portions of the matrix in order to do correct preallocation 3492 */ 3493 3494 /* first get start and end of "diagonal" columns */ 3495 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3496 if (csize == PETSC_DECIDE) { 3497 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3498 if (mglobal == Ncols) { /* square matrix */ 3499 nlocal = m; 3500 } else { 3501 nlocal = Ncols/size + ((Ncols % size) > rank); 3502 } 3503 } else { 3504 nlocal = csize; 3505 } 3506 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3507 rstart = rend - nlocal; 3508 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); 3509 3510 /* next, compute all the lengths */ 3511 jj = aij->j; 3512 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3513 olens = dlens + m; 3514 for (i=0; i<m; i++) { 3515 jend = ii[i+1] - ii[i]; 3516 olen = 0; 3517 dlen = 0; 3518 for (j=0; j<jend; j++) { 3519 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3520 else dlen++; 3521 jj++; 3522 } 3523 olens[i] = olen; 3524 dlens[i] = dlen; 3525 } 3526 ierr = MatGetBlockSizes(Msub,&bs,&cbs);CHKERRQ(ierr); 3527 3528 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3529 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr); 3530 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3531 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3532 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3533 ierr = PetscFree(dlens);CHKERRQ(ierr); 3534 3535 } else { /* call == MAT_REUSE_MATRIX */ 3536 M = *newmat; 3537 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3538 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3539 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3540 /* 3541 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3542 rather than the slower MatSetValues(). 3543 */ 3544 M->was_assembled = PETSC_TRUE; 3545 M->assembled = PETSC_FALSE; 3546 } 3547 3548 /* (5) Set values of Msub to *newmat */ 3549 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3550 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3551 3552 jj = aij->j; 3553 aa = aij->a; 3554 for (i=0; i<m; i++) { 3555 row = rstart + i; 3556 nz = ii[i+1] - ii[i]; 3557 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3558 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3559 jj += nz; aa += nz; 3560 } 3561 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3562 3563 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3564 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3565 3566 ierr = PetscFree(colsub);CHKERRQ(ierr); 3567 3568 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3569 if (call == MAT_INITIAL_MATRIX) { 3570 *newmat = M; 3571 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3572 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3573 3574 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3575 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3576 3577 ierr = PetscObjectCompose((PetscObject)(*newmat),"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3578 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3579 3580 if (iscol_local) { 3581 ierr = PetscObjectCompose((PetscObject)(*newmat),"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3582 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3583 } 3584 } 3585 PetscFunctionReturn(0); 3586 } 3587 3588 /* 3589 Not great since it makes two copies of the submatrix, first an SeqAIJ 3590 in local and then by concatenating the local matrices the end result. 3591 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3592 3593 Note: This requires a sequential iscol with all indices. 3594 */ 3595 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3596 { 3597 PetscErrorCode ierr; 3598 PetscMPIInt rank,size; 3599 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3600 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3601 Mat M,Mreuse; 3602 MatScalar *aa,*vwork; 3603 MPI_Comm comm; 3604 Mat_SeqAIJ *aij; 3605 PetscBool colflag,allcolumns=PETSC_FALSE; 3606 3607 PetscFunctionBegin; 3608 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3609 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3610 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3611 3612 /* Check for special case: each processor gets entire matrix columns */ 3613 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3614 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3615 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3616 3617 if (call == MAT_REUSE_MATRIX) { 3618 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3619 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3620 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3621 } else { 3622 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3623 } 3624 3625 /* 3626 m - number of local rows 3627 n - number of columns (same on all processors) 3628 rstart - first row in new global matrix generated 3629 */ 3630 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3631 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3632 if (call == MAT_INITIAL_MATRIX) { 3633 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3634 ii = aij->i; 3635 jj = aij->j; 3636 3637 /* 3638 Determine the number of non-zeros in the diagonal and off-diagonal 3639 portions of the matrix in order to do correct preallocation 3640 */ 3641 3642 /* first get start and end of "diagonal" columns */ 3643 if (csize == PETSC_DECIDE) { 3644 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3645 if (mglobal == n) { /* square matrix */ 3646 nlocal = m; 3647 } else { 3648 nlocal = n/size + ((n % size) > rank); 3649 } 3650 } else { 3651 nlocal = csize; 3652 } 3653 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3654 rstart = rend - nlocal; 3655 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); 3656 3657 /* next, compute all the lengths */ 3658 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3659 olens = dlens + m; 3660 for (i=0; i<m; i++) { 3661 jend = ii[i+1] - ii[i]; 3662 olen = 0; 3663 dlen = 0; 3664 for (j=0; j<jend; j++) { 3665 if (*jj < rstart || *jj >= rend) olen++; 3666 else dlen++; 3667 jj++; 3668 } 3669 olens[i] = olen; 3670 dlens[i] = dlen; 3671 } 3672 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3673 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3674 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3675 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3676 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3677 ierr = PetscFree(dlens);CHKERRQ(ierr); 3678 } else { 3679 PetscInt ml,nl; 3680 3681 M = *newmat; 3682 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3683 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3684 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3685 /* 3686 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3687 rather than the slower MatSetValues(). 3688 */ 3689 M->was_assembled = PETSC_TRUE; 3690 M->assembled = PETSC_FALSE; 3691 } 3692 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3693 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3694 ii = aij->i; 3695 jj = aij->j; 3696 aa = aij->a; 3697 for (i=0; i<m; i++) { 3698 row = rstart + i; 3699 nz = ii[i+1] - ii[i]; 3700 cwork = jj; jj += nz; 3701 vwork = aa; aa += nz; 3702 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3703 } 3704 3705 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3706 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3707 *newmat = M; 3708 3709 /* save submatrix used in processor for next request */ 3710 if (call == MAT_INITIAL_MATRIX) { 3711 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3712 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3713 } 3714 PetscFunctionReturn(0); 3715 } 3716 3717 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3718 { 3719 PetscInt m,cstart, cend,j,nnz,i,d; 3720 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3721 const PetscInt *JJ; 3722 PetscScalar *values; 3723 PetscErrorCode ierr; 3724 PetscBool nooffprocentries; 3725 3726 PetscFunctionBegin; 3727 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3728 3729 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3730 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3731 m = B->rmap->n; 3732 cstart = B->cmap->rstart; 3733 cend = B->cmap->rend; 3734 rstart = B->rmap->rstart; 3735 3736 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3737 3738 #if defined(PETSC_USE_DEBUGGING) 3739 for (i=0; i<m; i++) { 3740 nnz = Ii[i+1]- Ii[i]; 3741 JJ = J + Ii[i]; 3742 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3743 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3744 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); 3745 } 3746 #endif 3747 3748 for (i=0; i<m; i++) { 3749 nnz = Ii[i+1]- Ii[i]; 3750 JJ = J + Ii[i]; 3751 nnz_max = PetscMax(nnz_max,nnz); 3752 d = 0; 3753 for (j=0; j<nnz; j++) { 3754 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3755 } 3756 d_nnz[i] = d; 3757 o_nnz[i] = nnz - d; 3758 } 3759 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3760 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3761 3762 if (v) values = (PetscScalar*)v; 3763 else { 3764 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3765 } 3766 3767 for (i=0; i<m; i++) { 3768 ii = i + rstart; 3769 nnz = Ii[i+1]- Ii[i]; 3770 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3771 } 3772 nooffprocentries = B->nooffprocentries; 3773 B->nooffprocentries = PETSC_TRUE; 3774 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3775 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3776 B->nooffprocentries = nooffprocentries; 3777 3778 if (!v) { 3779 ierr = PetscFree(values);CHKERRQ(ierr); 3780 } 3781 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3782 PetscFunctionReturn(0); 3783 } 3784 3785 /*@ 3786 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3787 (the default parallel PETSc format). 3788 3789 Collective on MPI_Comm 3790 3791 Input Parameters: 3792 + B - the matrix 3793 . i - the indices into j for the start of each local row (starts with zero) 3794 . j - the column indices for each local row (starts with zero) 3795 - v - optional values in the matrix 3796 3797 Level: developer 3798 3799 Notes: 3800 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3801 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3802 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3803 3804 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3805 3806 The format which is used for the sparse matrix input, is equivalent to a 3807 row-major ordering.. i.e for the following matrix, the input data expected is 3808 as shown 3809 3810 $ 1 0 0 3811 $ 2 0 3 P0 3812 $ ------- 3813 $ 4 5 6 P1 3814 $ 3815 $ Process0 [P0]: rows_owned=[0,1] 3816 $ i = {0,1,3} [size = nrow+1 = 2+1] 3817 $ j = {0,0,2} [size = 3] 3818 $ v = {1,2,3} [size = 3] 3819 $ 3820 $ Process1 [P1]: rows_owned=[2] 3821 $ i = {0,3} [size = nrow+1 = 1+1] 3822 $ j = {0,1,2} [size = 3] 3823 $ v = {4,5,6} [size = 3] 3824 3825 .keywords: matrix, aij, compressed row, sparse, parallel 3826 3827 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3828 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3829 @*/ 3830 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3831 { 3832 PetscErrorCode ierr; 3833 3834 PetscFunctionBegin; 3835 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3836 PetscFunctionReturn(0); 3837 } 3838 3839 /*@C 3840 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3841 (the default parallel PETSc format). For good matrix assembly performance 3842 the user should preallocate the matrix storage by setting the parameters 3843 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3844 performance can be increased by more than a factor of 50. 3845 3846 Collective on MPI_Comm 3847 3848 Input Parameters: 3849 + B - the matrix 3850 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3851 (same value is used for all local rows) 3852 . d_nnz - array containing the number of nonzeros in the various rows of the 3853 DIAGONAL portion of the local submatrix (possibly different for each row) 3854 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3855 The size of this array is equal to the number of local rows, i.e 'm'. 3856 For matrices that will be factored, you must leave room for (and set) 3857 the diagonal entry even if it is zero. 3858 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3859 submatrix (same value is used for all local rows). 3860 - o_nnz - array containing the number of nonzeros in the various rows of the 3861 OFF-DIAGONAL portion of the local submatrix (possibly different for 3862 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3863 structure. The size of this array is equal to the number 3864 of local rows, i.e 'm'. 3865 3866 If the *_nnz parameter is given then the *_nz parameter is ignored 3867 3868 The AIJ format (also called the Yale sparse matrix format or 3869 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3870 storage. The stored row and column indices begin with zero. 3871 See Users-Manual: ch_mat for details. 3872 3873 The parallel matrix is partitioned such that the first m0 rows belong to 3874 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3875 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3876 3877 The DIAGONAL portion of the local submatrix of a processor can be defined 3878 as the submatrix which is obtained by extraction the part corresponding to 3879 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3880 first row that belongs to the processor, r2 is the last row belonging to 3881 the this processor, and c1-c2 is range of indices of the local part of a 3882 vector suitable for applying the matrix to. This is an mxn matrix. In the 3883 common case of a square matrix, the row and column ranges are the same and 3884 the DIAGONAL part is also square. The remaining portion of the local 3885 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3886 3887 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3888 3889 You can call MatGetInfo() to get information on how effective the preallocation was; 3890 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3891 You can also run with the option -info and look for messages with the string 3892 malloc in them to see if additional memory allocation was needed. 3893 3894 Example usage: 3895 3896 Consider the following 8x8 matrix with 34 non-zero values, that is 3897 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3898 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3899 as follows: 3900 3901 .vb 3902 1 2 0 | 0 3 0 | 0 4 3903 Proc0 0 5 6 | 7 0 0 | 8 0 3904 9 0 10 | 11 0 0 | 12 0 3905 ------------------------------------- 3906 13 0 14 | 15 16 17 | 0 0 3907 Proc1 0 18 0 | 19 20 21 | 0 0 3908 0 0 0 | 22 23 0 | 24 0 3909 ------------------------------------- 3910 Proc2 25 26 27 | 0 0 28 | 29 0 3911 30 0 0 | 31 32 33 | 0 34 3912 .ve 3913 3914 This can be represented as a collection of submatrices as: 3915 3916 .vb 3917 A B C 3918 D E F 3919 G H I 3920 .ve 3921 3922 Where the submatrices A,B,C are owned by proc0, D,E,F are 3923 owned by proc1, G,H,I are owned by proc2. 3924 3925 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3926 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3927 The 'M','N' parameters are 8,8, and have the same values on all procs. 3928 3929 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3930 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3931 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3932 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3933 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3934 matrix, ans [DF] as another SeqAIJ matrix. 3935 3936 When d_nz, o_nz parameters are specified, d_nz storage elements are 3937 allocated for every row of the local diagonal submatrix, and o_nz 3938 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3939 One way to choose d_nz and o_nz is to use the max nonzerors per local 3940 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3941 In this case, the values of d_nz,o_nz are: 3942 .vb 3943 proc0 : dnz = 2, o_nz = 2 3944 proc1 : dnz = 3, o_nz = 2 3945 proc2 : dnz = 1, o_nz = 4 3946 .ve 3947 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3948 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3949 for proc3. i.e we are using 12+15+10=37 storage locations to store 3950 34 values. 3951 3952 When d_nnz, o_nnz parameters are specified, the storage is specified 3953 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3954 In the above case the values for d_nnz,o_nnz are: 3955 .vb 3956 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3957 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3958 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3959 .ve 3960 Here the space allocated is sum of all the above values i.e 34, and 3961 hence pre-allocation is perfect. 3962 3963 Level: intermediate 3964 3965 .keywords: matrix, aij, compressed row, sparse, parallel 3966 3967 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 3968 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 3969 @*/ 3970 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3971 { 3972 PetscErrorCode ierr; 3973 3974 PetscFunctionBegin; 3975 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3976 PetscValidType(B,1); 3977 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 3978 PetscFunctionReturn(0); 3979 } 3980 3981 /*@ 3982 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 3983 CSR format the local rows. 3984 3985 Collective on MPI_Comm 3986 3987 Input Parameters: 3988 + comm - MPI communicator 3989 . m - number of local rows (Cannot be PETSC_DECIDE) 3990 . n - This value should be the same as the local size used in creating the 3991 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3992 calculated if N is given) For square matrices n is almost always m. 3993 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3994 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3995 . i - row indices 3996 . j - column indices 3997 - a - matrix values 3998 3999 Output Parameter: 4000 . mat - the matrix 4001 4002 Level: intermediate 4003 4004 Notes: 4005 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 4006 thus you CANNOT change the matrix entries by changing the values of a[] after you have 4007 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 4008 4009 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4010 4011 The format which is used for the sparse matrix input, is equivalent to a 4012 row-major ordering.. i.e for the following matrix, the input data expected is 4013 as shown 4014 4015 $ 1 0 0 4016 $ 2 0 3 P0 4017 $ ------- 4018 $ 4 5 6 P1 4019 $ 4020 $ Process0 [P0]: rows_owned=[0,1] 4021 $ i = {0,1,3} [size = nrow+1 = 2+1] 4022 $ j = {0,0,2} [size = 3] 4023 $ v = {1,2,3} [size = 3] 4024 $ 4025 $ Process1 [P1]: rows_owned=[2] 4026 $ i = {0,3} [size = nrow+1 = 1+1] 4027 $ j = {0,1,2} [size = 3] 4028 $ v = {4,5,6} [size = 3] 4029 4030 .keywords: matrix, aij, compressed row, sparse, parallel 4031 4032 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4033 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4034 @*/ 4035 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 4036 { 4037 PetscErrorCode ierr; 4038 4039 PetscFunctionBegin; 4040 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4041 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4042 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4043 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4044 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 4045 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 4046 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 4047 PetscFunctionReturn(0); 4048 } 4049 4050 /*@C 4051 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 4052 (the default parallel PETSc format). For good matrix assembly performance 4053 the user should preallocate the matrix storage by setting the parameters 4054 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4055 performance can be increased by more than a factor of 50. 4056 4057 Collective on MPI_Comm 4058 4059 Input Parameters: 4060 + comm - MPI communicator 4061 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 4062 This value should be the same as the local size used in creating the 4063 y vector for the matrix-vector product y = Ax. 4064 . n - This value should be the same as the local size used in creating the 4065 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4066 calculated if N is given) For square matrices n is almost always m. 4067 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4068 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4069 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4070 (same value is used for all local rows) 4071 . d_nnz - array containing the number of nonzeros in the various rows of the 4072 DIAGONAL portion of the local submatrix (possibly different for each row) 4073 or NULL, if d_nz is used to specify the nonzero structure. 4074 The size of this array is equal to the number of local rows, i.e 'm'. 4075 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4076 submatrix (same value is used for all local rows). 4077 - o_nnz - array containing the number of nonzeros in the various rows of the 4078 OFF-DIAGONAL portion of the local submatrix (possibly different for 4079 each row) or NULL, if o_nz is used to specify the nonzero 4080 structure. The size of this array is equal to the number 4081 of local rows, i.e 'm'. 4082 4083 Output Parameter: 4084 . A - the matrix 4085 4086 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4087 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4088 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4089 4090 Notes: 4091 If the *_nnz parameter is given then the *_nz parameter is ignored 4092 4093 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4094 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4095 storage requirements for this matrix. 4096 4097 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4098 processor than it must be used on all processors that share the object for 4099 that argument. 4100 4101 The user MUST specify either the local or global matrix dimensions 4102 (possibly both). 4103 4104 The parallel matrix is partitioned across processors such that the 4105 first m0 rows belong to process 0, the next m1 rows belong to 4106 process 1, the next m2 rows belong to process 2 etc.. where 4107 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4108 values corresponding to [m x N] submatrix. 4109 4110 The columns are logically partitioned with the n0 columns belonging 4111 to 0th partition, the next n1 columns belonging to the next 4112 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4113 4114 The DIAGONAL portion of the local submatrix on any given processor 4115 is the submatrix corresponding to the rows and columns m,n 4116 corresponding to the given processor. i.e diagonal matrix on 4117 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4118 etc. The remaining portion of the local submatrix [m x (N-n)] 4119 constitute the OFF-DIAGONAL portion. The example below better 4120 illustrates this concept. 4121 4122 For a square global matrix we define each processor's diagonal portion 4123 to be its local rows and the corresponding columns (a square submatrix); 4124 each processor's off-diagonal portion encompasses the remainder of the 4125 local matrix (a rectangular submatrix). 4126 4127 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4128 4129 When calling this routine with a single process communicator, a matrix of 4130 type SEQAIJ is returned. If a matrix of type MATMPIAIJ is desired for this 4131 type of communicator, use the construction mechanism: 4132 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4133 4134 By default, this format uses inodes (identical nodes) when possible. 4135 We search for consecutive rows with the same nonzero structure, thereby 4136 reusing matrix information to achieve increased efficiency. 4137 4138 Options Database Keys: 4139 + -mat_no_inode - Do not use inodes 4140 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4141 - -mat_aij_oneindex - Internally use indexing starting at 1 4142 rather than 0. Note that when calling MatSetValues(), 4143 the user still MUST index entries starting at 0! 4144 4145 4146 Example usage: 4147 4148 Consider the following 8x8 matrix with 34 non-zero values, that is 4149 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4150 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4151 as follows: 4152 4153 .vb 4154 1 2 0 | 0 3 0 | 0 4 4155 Proc0 0 5 6 | 7 0 0 | 8 0 4156 9 0 10 | 11 0 0 | 12 0 4157 ------------------------------------- 4158 13 0 14 | 15 16 17 | 0 0 4159 Proc1 0 18 0 | 19 20 21 | 0 0 4160 0 0 0 | 22 23 0 | 24 0 4161 ------------------------------------- 4162 Proc2 25 26 27 | 0 0 28 | 29 0 4163 30 0 0 | 31 32 33 | 0 34 4164 .ve 4165 4166 This can be represented as a collection of submatrices as: 4167 4168 .vb 4169 A B C 4170 D E F 4171 G H I 4172 .ve 4173 4174 Where the submatrices A,B,C are owned by proc0, D,E,F are 4175 owned by proc1, G,H,I are owned by proc2. 4176 4177 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4178 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4179 The 'M','N' parameters are 8,8, and have the same values on all procs. 4180 4181 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4182 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4183 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4184 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4185 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4186 matrix, ans [DF] as another SeqAIJ matrix. 4187 4188 When d_nz, o_nz parameters are specified, d_nz storage elements are 4189 allocated for every row of the local diagonal submatrix, and o_nz 4190 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4191 One way to choose d_nz and o_nz is to use the max nonzerors per local 4192 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4193 In this case, the values of d_nz,o_nz are: 4194 .vb 4195 proc0 : dnz = 2, o_nz = 2 4196 proc1 : dnz = 3, o_nz = 2 4197 proc2 : dnz = 1, o_nz = 4 4198 .ve 4199 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4200 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4201 for proc3. i.e we are using 12+15+10=37 storage locations to store 4202 34 values. 4203 4204 When d_nnz, o_nnz parameters are specified, the storage is specified 4205 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4206 In the above case the values for d_nnz,o_nnz are: 4207 .vb 4208 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4209 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4210 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4211 .ve 4212 Here the space allocated is sum of all the above values i.e 34, and 4213 hence pre-allocation is perfect. 4214 4215 Level: intermediate 4216 4217 .keywords: matrix, aij, compressed row, sparse, parallel 4218 4219 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4220 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4221 @*/ 4222 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) 4223 { 4224 PetscErrorCode ierr; 4225 PetscMPIInt size; 4226 4227 PetscFunctionBegin; 4228 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4229 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4230 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4231 if (size > 1) { 4232 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4233 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4234 } else { 4235 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4236 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4237 } 4238 PetscFunctionReturn(0); 4239 } 4240 4241 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4242 { 4243 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4244 PetscBool flg; 4245 PetscErrorCode ierr; 4246 4247 PetscFunctionBegin; 4248 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4249 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4250 if (Ad) *Ad = a->A; 4251 if (Ao) *Ao = a->B; 4252 if (colmap) *colmap = a->garray; 4253 PetscFunctionReturn(0); 4254 } 4255 4256 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4257 { 4258 PetscErrorCode ierr; 4259 PetscInt m,N,i,rstart,nnz,Ii; 4260 PetscInt *indx; 4261 PetscScalar *values; 4262 4263 PetscFunctionBegin; 4264 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4265 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4266 PetscInt *dnz,*onz,sum,bs,cbs; 4267 4268 if (n == PETSC_DECIDE) { 4269 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4270 } 4271 /* Check sum(n) = N */ 4272 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4273 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 4274 4275 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4276 rstart -= m; 4277 4278 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4279 for (i=0; i<m; i++) { 4280 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4281 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4282 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4283 } 4284 4285 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4286 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4287 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4288 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4289 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4290 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4291 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4292 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4293 } 4294 4295 /* numeric phase */ 4296 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4297 for (i=0; i<m; i++) { 4298 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4299 Ii = i + rstart; 4300 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4301 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4302 } 4303 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4304 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4305 PetscFunctionReturn(0); 4306 } 4307 4308 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4309 { 4310 PetscErrorCode ierr; 4311 PetscMPIInt rank; 4312 PetscInt m,N,i,rstart,nnz; 4313 size_t len; 4314 const PetscInt *indx; 4315 PetscViewer out; 4316 char *name; 4317 Mat B; 4318 const PetscScalar *values; 4319 4320 PetscFunctionBegin; 4321 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4322 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4323 /* Should this be the type of the diagonal block of A? */ 4324 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4325 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4326 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4327 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4328 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4329 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4330 for (i=0; i<m; i++) { 4331 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4332 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4333 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4334 } 4335 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4336 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4337 4338 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4339 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4340 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4341 sprintf(name,"%s.%d",outfile,rank); 4342 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4343 ierr = PetscFree(name);CHKERRQ(ierr); 4344 ierr = MatView(B,out);CHKERRQ(ierr); 4345 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4346 ierr = MatDestroy(&B);CHKERRQ(ierr); 4347 PetscFunctionReturn(0); 4348 } 4349 4350 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4351 { 4352 PetscErrorCode ierr; 4353 Mat_Merge_SeqsToMPI *merge; 4354 PetscContainer container; 4355 4356 PetscFunctionBegin; 4357 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4358 if (container) { 4359 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4360 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4361 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4362 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4363 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4364 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4365 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4366 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4367 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4368 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4369 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4370 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4371 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4372 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4373 ierr = PetscFree(merge);CHKERRQ(ierr); 4374 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4375 } 4376 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4377 PetscFunctionReturn(0); 4378 } 4379 4380 #include <../src/mat/utils/freespace.h> 4381 #include <petscbt.h> 4382 4383 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4384 { 4385 PetscErrorCode ierr; 4386 MPI_Comm comm; 4387 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4388 PetscMPIInt size,rank,taga,*len_s; 4389 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4390 PetscInt proc,m; 4391 PetscInt **buf_ri,**buf_rj; 4392 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4393 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4394 MPI_Request *s_waits,*r_waits; 4395 MPI_Status *status; 4396 MatScalar *aa=a->a; 4397 MatScalar **abuf_r,*ba_i; 4398 Mat_Merge_SeqsToMPI *merge; 4399 PetscContainer container; 4400 4401 PetscFunctionBegin; 4402 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4403 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4404 4405 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4406 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4407 4408 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4409 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4410 4411 bi = merge->bi; 4412 bj = merge->bj; 4413 buf_ri = merge->buf_ri; 4414 buf_rj = merge->buf_rj; 4415 4416 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4417 owners = merge->rowmap->range; 4418 len_s = merge->len_s; 4419 4420 /* send and recv matrix values */ 4421 /*-----------------------------*/ 4422 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4423 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4424 4425 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4426 for (proc=0,k=0; proc<size; proc++) { 4427 if (!len_s[proc]) continue; 4428 i = owners[proc]; 4429 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4430 k++; 4431 } 4432 4433 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4434 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4435 ierr = PetscFree(status);CHKERRQ(ierr); 4436 4437 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4438 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4439 4440 /* insert mat values of mpimat */ 4441 /*----------------------------*/ 4442 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4443 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4444 4445 for (k=0; k<merge->nrecv; k++) { 4446 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4447 nrows = *(buf_ri_k[k]); 4448 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4449 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4450 } 4451 4452 /* set values of ba */ 4453 m = merge->rowmap->n; 4454 for (i=0; i<m; i++) { 4455 arow = owners[rank] + i; 4456 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4457 bnzi = bi[i+1] - bi[i]; 4458 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4459 4460 /* add local non-zero vals of this proc's seqmat into ba */ 4461 anzi = ai[arow+1] - ai[arow]; 4462 aj = a->j + ai[arow]; 4463 aa = a->a + ai[arow]; 4464 nextaj = 0; 4465 for (j=0; nextaj<anzi; j++) { 4466 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4467 ba_i[j] += aa[nextaj++]; 4468 } 4469 } 4470 4471 /* add received vals into ba */ 4472 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4473 /* i-th row */ 4474 if (i == *nextrow[k]) { 4475 anzi = *(nextai[k]+1) - *nextai[k]; 4476 aj = buf_rj[k] + *(nextai[k]); 4477 aa = abuf_r[k] + *(nextai[k]); 4478 nextaj = 0; 4479 for (j=0; nextaj<anzi; j++) { 4480 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4481 ba_i[j] += aa[nextaj++]; 4482 } 4483 } 4484 nextrow[k]++; nextai[k]++; 4485 } 4486 } 4487 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4488 } 4489 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4490 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4491 4492 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4493 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4494 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4495 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4496 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4497 PetscFunctionReturn(0); 4498 } 4499 4500 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4501 { 4502 PetscErrorCode ierr; 4503 Mat B_mpi; 4504 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4505 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4506 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4507 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4508 PetscInt len,proc,*dnz,*onz,bs,cbs; 4509 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4510 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4511 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4512 MPI_Status *status; 4513 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4514 PetscBT lnkbt; 4515 Mat_Merge_SeqsToMPI *merge; 4516 PetscContainer container; 4517 4518 PetscFunctionBegin; 4519 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4520 4521 /* make sure it is a PETSc comm */ 4522 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4523 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4524 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4525 4526 ierr = PetscNew(&merge);CHKERRQ(ierr); 4527 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4528 4529 /* determine row ownership */ 4530 /*---------------------------------------------------------*/ 4531 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4532 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4533 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4534 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4535 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4536 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4537 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4538 4539 m = merge->rowmap->n; 4540 owners = merge->rowmap->range; 4541 4542 /* determine the number of messages to send, their lengths */ 4543 /*---------------------------------------------------------*/ 4544 len_s = merge->len_s; 4545 4546 len = 0; /* length of buf_si[] */ 4547 merge->nsend = 0; 4548 for (proc=0; proc<size; proc++) { 4549 len_si[proc] = 0; 4550 if (proc == rank) { 4551 len_s[proc] = 0; 4552 } else { 4553 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4554 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4555 } 4556 if (len_s[proc]) { 4557 merge->nsend++; 4558 nrows = 0; 4559 for (i=owners[proc]; i<owners[proc+1]; i++) { 4560 if (ai[i+1] > ai[i]) nrows++; 4561 } 4562 len_si[proc] = 2*(nrows+1); 4563 len += len_si[proc]; 4564 } 4565 } 4566 4567 /* determine the number and length of messages to receive for ij-structure */ 4568 /*-------------------------------------------------------------------------*/ 4569 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4570 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4571 4572 /* post the Irecv of j-structure */ 4573 /*-------------------------------*/ 4574 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4575 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4576 4577 /* post the Isend of j-structure */ 4578 /*--------------------------------*/ 4579 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4580 4581 for (proc=0, k=0; proc<size; proc++) { 4582 if (!len_s[proc]) continue; 4583 i = owners[proc]; 4584 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4585 k++; 4586 } 4587 4588 /* receives and sends of j-structure are complete */ 4589 /*------------------------------------------------*/ 4590 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4591 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4592 4593 /* send and recv i-structure */ 4594 /*---------------------------*/ 4595 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4596 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4597 4598 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4599 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4600 for (proc=0,k=0; proc<size; proc++) { 4601 if (!len_s[proc]) continue; 4602 /* form outgoing message for i-structure: 4603 buf_si[0]: nrows to be sent 4604 [1:nrows]: row index (global) 4605 [nrows+1:2*nrows+1]: i-structure index 4606 */ 4607 /*-------------------------------------------*/ 4608 nrows = len_si[proc]/2 - 1; 4609 buf_si_i = buf_si + nrows+1; 4610 buf_si[0] = nrows; 4611 buf_si_i[0] = 0; 4612 nrows = 0; 4613 for (i=owners[proc]; i<owners[proc+1]; i++) { 4614 anzi = ai[i+1] - ai[i]; 4615 if (anzi) { 4616 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4617 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4618 nrows++; 4619 } 4620 } 4621 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4622 k++; 4623 buf_si += len_si[proc]; 4624 } 4625 4626 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4627 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4628 4629 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4630 for (i=0; i<merge->nrecv; i++) { 4631 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); 4632 } 4633 4634 ierr = PetscFree(len_si);CHKERRQ(ierr); 4635 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4636 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4637 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4638 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4639 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4640 ierr = PetscFree(status);CHKERRQ(ierr); 4641 4642 /* compute a local seq matrix in each processor */ 4643 /*----------------------------------------------*/ 4644 /* allocate bi array and free space for accumulating nonzero column info */ 4645 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4646 bi[0] = 0; 4647 4648 /* create and initialize a linked list */ 4649 nlnk = N+1; 4650 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4651 4652 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4653 len = ai[owners[rank+1]] - ai[owners[rank]]; 4654 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4655 4656 current_space = free_space; 4657 4658 /* determine symbolic info for each local row */ 4659 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4660 4661 for (k=0; k<merge->nrecv; k++) { 4662 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4663 nrows = *buf_ri_k[k]; 4664 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4665 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4666 } 4667 4668 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4669 len = 0; 4670 for (i=0; i<m; i++) { 4671 bnzi = 0; 4672 /* add local non-zero cols of this proc's seqmat into lnk */ 4673 arow = owners[rank] + i; 4674 anzi = ai[arow+1] - ai[arow]; 4675 aj = a->j + ai[arow]; 4676 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4677 bnzi += nlnk; 4678 /* add received col data into lnk */ 4679 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4680 if (i == *nextrow[k]) { /* i-th row */ 4681 anzi = *(nextai[k]+1) - *nextai[k]; 4682 aj = buf_rj[k] + *nextai[k]; 4683 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4684 bnzi += nlnk; 4685 nextrow[k]++; nextai[k]++; 4686 } 4687 } 4688 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4689 4690 /* if free space is not available, make more free space */ 4691 if (current_space->local_remaining<bnzi) { 4692 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4693 nspacedouble++; 4694 } 4695 /* copy data into free space, then initialize lnk */ 4696 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4697 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4698 4699 current_space->array += bnzi; 4700 current_space->local_used += bnzi; 4701 current_space->local_remaining -= bnzi; 4702 4703 bi[i+1] = bi[i] + bnzi; 4704 } 4705 4706 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4707 4708 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4709 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4710 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4711 4712 /* create symbolic parallel matrix B_mpi */ 4713 /*---------------------------------------*/ 4714 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4715 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4716 if (n==PETSC_DECIDE) { 4717 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4718 } else { 4719 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4720 } 4721 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4722 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4723 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4724 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4725 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4726 4727 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4728 B_mpi->assembled = PETSC_FALSE; 4729 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4730 merge->bi = bi; 4731 merge->bj = bj; 4732 merge->buf_ri = buf_ri; 4733 merge->buf_rj = buf_rj; 4734 merge->coi = NULL; 4735 merge->coj = NULL; 4736 merge->owners_co = NULL; 4737 4738 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4739 4740 /* attach the supporting struct to B_mpi for reuse */ 4741 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4742 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4743 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4744 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4745 *mpimat = B_mpi; 4746 4747 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4748 PetscFunctionReturn(0); 4749 } 4750 4751 /*@C 4752 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4753 matrices from each processor 4754 4755 Collective on MPI_Comm 4756 4757 Input Parameters: 4758 + comm - the communicators the parallel matrix will live on 4759 . seqmat - the input sequential matrices 4760 . m - number of local rows (or PETSC_DECIDE) 4761 . n - number of local columns (or PETSC_DECIDE) 4762 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4763 4764 Output Parameter: 4765 . mpimat - the parallel matrix generated 4766 4767 Level: advanced 4768 4769 Notes: 4770 The dimensions of the sequential matrix in each processor MUST be the same. 4771 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4772 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4773 @*/ 4774 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4775 { 4776 PetscErrorCode ierr; 4777 PetscMPIInt size; 4778 4779 PetscFunctionBegin; 4780 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4781 if (size == 1) { 4782 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4783 if (scall == MAT_INITIAL_MATRIX) { 4784 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4785 } else { 4786 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4787 } 4788 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4789 PetscFunctionReturn(0); 4790 } 4791 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4792 if (scall == MAT_INITIAL_MATRIX) { 4793 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4794 } 4795 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4796 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4797 PetscFunctionReturn(0); 4798 } 4799 4800 /*@ 4801 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 4802 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4803 with MatGetSize() 4804 4805 Not Collective 4806 4807 Input Parameters: 4808 + A - the matrix 4809 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4810 4811 Output Parameter: 4812 . A_loc - the local sequential matrix generated 4813 4814 Level: developer 4815 4816 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4817 4818 @*/ 4819 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4820 { 4821 PetscErrorCode ierr; 4822 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4823 Mat_SeqAIJ *mat,*a,*b; 4824 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4825 MatScalar *aa,*ba,*cam; 4826 PetscScalar *ca; 4827 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4828 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4829 PetscBool match; 4830 MPI_Comm comm; 4831 PetscMPIInt size; 4832 4833 PetscFunctionBegin; 4834 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4835 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4836 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4837 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4838 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4839 4840 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4841 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4842 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4843 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4844 aa = a->a; ba = b->a; 4845 if (scall == MAT_INITIAL_MATRIX) { 4846 if (size == 1) { 4847 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4848 PetscFunctionReturn(0); 4849 } 4850 4851 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4852 ci[0] = 0; 4853 for (i=0; i<am; i++) { 4854 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4855 } 4856 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4857 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4858 k = 0; 4859 for (i=0; i<am; i++) { 4860 ncols_o = bi[i+1] - bi[i]; 4861 ncols_d = ai[i+1] - ai[i]; 4862 /* off-diagonal portion of A */ 4863 for (jo=0; jo<ncols_o; jo++) { 4864 col = cmap[*bj]; 4865 if (col >= cstart) break; 4866 cj[k] = col; bj++; 4867 ca[k++] = *ba++; 4868 } 4869 /* diagonal portion of A */ 4870 for (j=0; j<ncols_d; j++) { 4871 cj[k] = cstart + *aj++; 4872 ca[k++] = *aa++; 4873 } 4874 /* off-diagonal portion of A */ 4875 for (j=jo; j<ncols_o; j++) { 4876 cj[k] = cmap[*bj++]; 4877 ca[k++] = *ba++; 4878 } 4879 } 4880 /* put together the new matrix */ 4881 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4882 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4883 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4884 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4885 mat->free_a = PETSC_TRUE; 4886 mat->free_ij = PETSC_TRUE; 4887 mat->nonew = 0; 4888 } else if (scall == MAT_REUSE_MATRIX) { 4889 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4890 ci = mat->i; cj = mat->j; cam = mat->a; 4891 for (i=0; i<am; i++) { 4892 /* off-diagonal portion of A */ 4893 ncols_o = bi[i+1] - bi[i]; 4894 for (jo=0; jo<ncols_o; jo++) { 4895 col = cmap[*bj]; 4896 if (col >= cstart) break; 4897 *cam++ = *ba++; bj++; 4898 } 4899 /* diagonal portion of A */ 4900 ncols_d = ai[i+1] - ai[i]; 4901 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4902 /* off-diagonal portion of A */ 4903 for (j=jo; j<ncols_o; j++) { 4904 *cam++ = *ba++; bj++; 4905 } 4906 } 4907 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4908 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4909 PetscFunctionReturn(0); 4910 } 4911 4912 /*@C 4913 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4914 4915 Not Collective 4916 4917 Input Parameters: 4918 + A - the matrix 4919 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4920 - row, col - index sets of rows and columns to extract (or NULL) 4921 4922 Output Parameter: 4923 . A_loc - the local sequential matrix generated 4924 4925 Level: developer 4926 4927 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4928 4929 @*/ 4930 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4931 { 4932 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4933 PetscErrorCode ierr; 4934 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4935 IS isrowa,iscola; 4936 Mat *aloc; 4937 PetscBool match; 4938 4939 PetscFunctionBegin; 4940 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4941 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4942 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4943 if (!row) { 4944 start = A->rmap->rstart; end = A->rmap->rend; 4945 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 4946 } else { 4947 isrowa = *row; 4948 } 4949 if (!col) { 4950 start = A->cmap->rstart; 4951 cmap = a->garray; 4952 nzA = a->A->cmap->n; 4953 nzB = a->B->cmap->n; 4954 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4955 ncols = 0; 4956 for (i=0; i<nzB; i++) { 4957 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4958 else break; 4959 } 4960 imark = i; 4961 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 4962 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 4963 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 4964 } else { 4965 iscola = *col; 4966 } 4967 if (scall != MAT_INITIAL_MATRIX) { 4968 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 4969 aloc[0] = *A_loc; 4970 } 4971 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 4972 *A_loc = aloc[0]; 4973 ierr = PetscFree(aloc);CHKERRQ(ierr); 4974 if (!row) { 4975 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 4976 } 4977 if (!col) { 4978 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 4979 } 4980 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4981 PetscFunctionReturn(0); 4982 } 4983 4984 /*@C 4985 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 4986 4987 Collective on Mat 4988 4989 Input Parameters: 4990 + A,B - the matrices in mpiaij format 4991 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4992 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 4993 4994 Output Parameter: 4995 + rowb, colb - index sets of rows and columns of B to extract 4996 - B_seq - the sequential matrix generated 4997 4998 Level: developer 4999 5000 @*/ 5001 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 5002 { 5003 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5004 PetscErrorCode ierr; 5005 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 5006 IS isrowb,iscolb; 5007 Mat *bseq=NULL; 5008 5009 PetscFunctionBegin; 5010 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5011 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); 5012 } 5013 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5014 5015 if (scall == MAT_INITIAL_MATRIX) { 5016 start = A->cmap->rstart; 5017 cmap = a->garray; 5018 nzA = a->A->cmap->n; 5019 nzB = a->B->cmap->n; 5020 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5021 ncols = 0; 5022 for (i=0; i<nzB; i++) { /* row < local row index */ 5023 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5024 else break; 5025 } 5026 imark = i; 5027 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 5028 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5029 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 5030 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 5031 } else { 5032 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5033 isrowb = *rowb; iscolb = *colb; 5034 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 5035 bseq[0] = *B_seq; 5036 } 5037 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 5038 *B_seq = bseq[0]; 5039 ierr = PetscFree(bseq);CHKERRQ(ierr); 5040 if (!rowb) { 5041 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 5042 } else { 5043 *rowb = isrowb; 5044 } 5045 if (!colb) { 5046 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 5047 } else { 5048 *colb = iscolb; 5049 } 5050 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5051 PetscFunctionReturn(0); 5052 } 5053 5054 /* 5055 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 5056 of the OFF-DIAGONAL portion of local A 5057 5058 Collective on Mat 5059 5060 Input Parameters: 5061 + A,B - the matrices in mpiaij format 5062 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5063 5064 Output Parameter: 5065 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5066 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5067 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5068 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5069 5070 Level: developer 5071 5072 */ 5073 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5074 { 5075 VecScatter_MPI_General *gen_to,*gen_from; 5076 PetscErrorCode ierr; 5077 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5078 Mat_SeqAIJ *b_oth; 5079 VecScatter ctx =a->Mvctx; 5080 MPI_Comm comm; 5081 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 5082 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5083 PetscInt *rvalues,*svalues; 5084 MatScalar *b_otha,*bufa,*bufA; 5085 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5086 MPI_Request *rwaits = NULL,*swaits = NULL; 5087 MPI_Status *sstatus,rstatus; 5088 PetscMPIInt jj,size; 5089 PetscInt *cols,sbs,rbs; 5090 PetscScalar *vals; 5091 5092 PetscFunctionBegin; 5093 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5094 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5095 5096 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5097 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); 5098 } 5099 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5100 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5101 5102 if (size == 1) { 5103 startsj_s = NULL; 5104 bufa_ptr = NULL; 5105 *B_oth = NULL; 5106 PetscFunctionReturn(0); 5107 } 5108 5109 gen_to = (VecScatter_MPI_General*)ctx->todata; 5110 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5111 nrecvs = gen_from->n; 5112 nsends = gen_to->n; 5113 5114 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 5115 srow = gen_to->indices; /* local row index to be sent */ 5116 sstarts = gen_to->starts; 5117 sprocs = gen_to->procs; 5118 sstatus = gen_to->sstatus; 5119 sbs = gen_to->bs; 5120 rstarts = gen_from->starts; 5121 rprocs = gen_from->procs; 5122 rbs = gen_from->bs; 5123 5124 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5125 if (scall == MAT_INITIAL_MATRIX) { 5126 /* i-array */ 5127 /*---------*/ 5128 /* post receives */ 5129 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 5130 for (i=0; i<nrecvs; i++) { 5131 rowlen = rvalues + rstarts[i]*rbs; 5132 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5133 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5134 } 5135 5136 /* pack the outgoing message */ 5137 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 5138 5139 sstartsj[0] = 0; 5140 rstartsj[0] = 0; 5141 len = 0; /* total length of j or a array to be sent */ 5142 k = 0; 5143 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 5144 for (i=0; i<nsends; i++) { 5145 rowlen = svalues + sstarts[i]*sbs; 5146 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5147 for (j=0; j<nrows; j++) { 5148 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5149 for (l=0; l<sbs; l++) { 5150 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5151 5152 rowlen[j*sbs+l] = ncols; 5153 5154 len += ncols; 5155 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5156 } 5157 k++; 5158 } 5159 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5160 5161 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5162 } 5163 /* recvs and sends of i-array are completed */ 5164 i = nrecvs; 5165 while (i--) { 5166 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5167 } 5168 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5169 ierr = PetscFree(svalues);CHKERRQ(ierr); 5170 5171 /* allocate buffers for sending j and a arrays */ 5172 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5173 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5174 5175 /* create i-array of B_oth */ 5176 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5177 5178 b_othi[0] = 0; 5179 len = 0; /* total length of j or a array to be received */ 5180 k = 0; 5181 for (i=0; i<nrecvs; i++) { 5182 rowlen = rvalues + rstarts[i]*rbs; 5183 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5184 for (j=0; j<nrows; j++) { 5185 b_othi[k+1] = b_othi[k] + rowlen[j]; 5186 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5187 k++; 5188 } 5189 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5190 } 5191 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5192 5193 /* allocate space for j and a arrrays of B_oth */ 5194 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5195 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5196 5197 /* j-array */ 5198 /*---------*/ 5199 /* post receives of j-array */ 5200 for (i=0; i<nrecvs; i++) { 5201 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5202 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5203 } 5204 5205 /* pack the outgoing message j-array */ 5206 k = 0; 5207 for (i=0; i<nsends; i++) { 5208 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5209 bufJ = bufj+sstartsj[i]; 5210 for (j=0; j<nrows; j++) { 5211 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5212 for (ll=0; ll<sbs; ll++) { 5213 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5214 for (l=0; l<ncols; l++) { 5215 *bufJ++ = cols[l]; 5216 } 5217 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5218 } 5219 } 5220 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5221 } 5222 5223 /* recvs and sends of j-array are completed */ 5224 i = nrecvs; 5225 while (i--) { 5226 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5227 } 5228 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5229 } else if (scall == MAT_REUSE_MATRIX) { 5230 sstartsj = *startsj_s; 5231 rstartsj = *startsj_r; 5232 bufa = *bufa_ptr; 5233 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5234 b_otha = b_oth->a; 5235 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5236 5237 /* a-array */ 5238 /*---------*/ 5239 /* post receives of a-array */ 5240 for (i=0; i<nrecvs; i++) { 5241 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5242 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5243 } 5244 5245 /* pack the outgoing message a-array */ 5246 k = 0; 5247 for (i=0; i<nsends; i++) { 5248 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5249 bufA = bufa+sstartsj[i]; 5250 for (j=0; j<nrows; j++) { 5251 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5252 for (ll=0; ll<sbs; ll++) { 5253 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5254 for (l=0; l<ncols; l++) { 5255 *bufA++ = vals[l]; 5256 } 5257 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5258 } 5259 } 5260 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5261 } 5262 /* recvs and sends of a-array are completed */ 5263 i = nrecvs; 5264 while (i--) { 5265 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5266 } 5267 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5268 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5269 5270 if (scall == MAT_INITIAL_MATRIX) { 5271 /* put together the new matrix */ 5272 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5273 5274 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5275 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5276 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5277 b_oth->free_a = PETSC_TRUE; 5278 b_oth->free_ij = PETSC_TRUE; 5279 b_oth->nonew = 0; 5280 5281 ierr = PetscFree(bufj);CHKERRQ(ierr); 5282 if (!startsj_s || !bufa_ptr) { 5283 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5284 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5285 } else { 5286 *startsj_s = sstartsj; 5287 *startsj_r = rstartsj; 5288 *bufa_ptr = bufa; 5289 } 5290 } 5291 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5292 PetscFunctionReturn(0); 5293 } 5294 5295 /*@C 5296 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5297 5298 Not Collective 5299 5300 Input Parameters: 5301 . A - The matrix in mpiaij format 5302 5303 Output Parameter: 5304 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5305 . colmap - A map from global column index to local index into lvec 5306 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5307 5308 Level: developer 5309 5310 @*/ 5311 #if defined(PETSC_USE_CTABLE) 5312 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5313 #else 5314 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5315 #endif 5316 { 5317 Mat_MPIAIJ *a; 5318 5319 PetscFunctionBegin; 5320 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5321 PetscValidPointer(lvec, 2); 5322 PetscValidPointer(colmap, 3); 5323 PetscValidPointer(multScatter, 4); 5324 a = (Mat_MPIAIJ*) A->data; 5325 if (lvec) *lvec = a->lvec; 5326 if (colmap) *colmap = a->colmap; 5327 if (multScatter) *multScatter = a->Mvctx; 5328 PetscFunctionReturn(0); 5329 } 5330 5331 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5332 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5333 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5334 #if defined(PETSC_HAVE_ELEMENTAL) 5335 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5336 #endif 5337 #if defined(PETSC_HAVE_HYPRE) 5338 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5339 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5340 #endif 5341 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5342 5343 /* 5344 Computes (B'*A')' since computing B*A directly is untenable 5345 5346 n p p 5347 ( ) ( ) ( ) 5348 m ( A ) * n ( B ) = m ( C ) 5349 ( ) ( ) ( ) 5350 5351 */ 5352 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5353 { 5354 PetscErrorCode ierr; 5355 Mat At,Bt,Ct; 5356 5357 PetscFunctionBegin; 5358 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5359 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5360 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5361 ierr = MatDestroy(&At);CHKERRQ(ierr); 5362 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5363 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5364 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5365 PetscFunctionReturn(0); 5366 } 5367 5368 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5369 { 5370 PetscErrorCode ierr; 5371 PetscInt m=A->rmap->n,n=B->cmap->n; 5372 Mat Cmat; 5373 5374 PetscFunctionBegin; 5375 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); 5376 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5377 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5378 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5379 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5380 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5381 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5382 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5383 5384 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5385 5386 *C = Cmat; 5387 PetscFunctionReturn(0); 5388 } 5389 5390 /* ----------------------------------------------------------------*/ 5391 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5392 { 5393 PetscErrorCode ierr; 5394 5395 PetscFunctionBegin; 5396 if (scall == MAT_INITIAL_MATRIX) { 5397 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5398 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5399 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5400 } 5401 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5402 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5403 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5404 PetscFunctionReturn(0); 5405 } 5406 5407 /*MC 5408 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5409 5410 Options Database Keys: 5411 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5412 5413 Level: beginner 5414 5415 .seealso: MatCreateAIJ() 5416 M*/ 5417 5418 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5419 { 5420 Mat_MPIAIJ *b; 5421 PetscErrorCode ierr; 5422 PetscMPIInt size; 5423 5424 PetscFunctionBegin; 5425 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5426 5427 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5428 B->data = (void*)b; 5429 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5430 B->assembled = PETSC_FALSE; 5431 B->insertmode = NOT_SET_VALUES; 5432 b->size = size; 5433 5434 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5435 5436 /* build cache for off array entries formed */ 5437 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5438 5439 b->donotstash = PETSC_FALSE; 5440 b->colmap = 0; 5441 b->garray = 0; 5442 b->roworiented = PETSC_TRUE; 5443 5444 /* stuff used for matrix vector multiply */ 5445 b->lvec = NULL; 5446 b->Mvctx = NULL; 5447 5448 /* stuff for MatGetRow() */ 5449 b->rowindices = 0; 5450 b->rowvalues = 0; 5451 b->getrowactive = PETSC_FALSE; 5452 5453 /* flexible pointer used in CUSP/CUSPARSE classes */ 5454 b->spptr = NULL; 5455 5456 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5457 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5458 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5459 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5460 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5461 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5462 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5463 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5464 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5465 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5466 #if defined(PETSC_HAVE_ELEMENTAL) 5467 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5468 #endif 5469 #if defined(PETSC_HAVE_HYPRE) 5470 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5471 #endif 5472 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5473 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5474 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5475 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5476 #if defined(PETSC_HAVE_HYPRE) 5477 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5478 #endif 5479 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5480 PetscFunctionReturn(0); 5481 } 5482 5483 /*@C 5484 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5485 and "off-diagonal" part of the matrix in CSR format. 5486 5487 Collective on MPI_Comm 5488 5489 Input Parameters: 5490 + comm - MPI communicator 5491 . m - number of local rows (Cannot be PETSC_DECIDE) 5492 . n - This value should be the same as the local size used in creating the 5493 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5494 calculated if N is given) For square matrices n is almost always m. 5495 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5496 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5497 . i - row indices for "diagonal" portion of matrix 5498 . j - column indices 5499 . a - matrix values 5500 . oi - row indices for "off-diagonal" portion of matrix 5501 . oj - column indices 5502 - oa - matrix values 5503 5504 Output Parameter: 5505 . mat - the matrix 5506 5507 Level: advanced 5508 5509 Notes: 5510 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5511 must free the arrays once the matrix has been destroyed and not before. 5512 5513 The i and j indices are 0 based 5514 5515 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5516 5517 This sets local rows and cannot be used to set off-processor values. 5518 5519 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5520 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5521 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5522 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5523 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5524 communication if it is known that only local entries will be set. 5525 5526 .keywords: matrix, aij, compressed row, sparse, parallel 5527 5528 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5529 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5530 @*/ 5531 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) 5532 { 5533 PetscErrorCode ierr; 5534 Mat_MPIAIJ *maij; 5535 5536 PetscFunctionBegin; 5537 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5538 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5539 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5540 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5541 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5542 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5543 maij = (Mat_MPIAIJ*) (*mat)->data; 5544 5545 (*mat)->preallocated = PETSC_TRUE; 5546 5547 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5548 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5549 5550 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5551 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5552 5553 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5554 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5555 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5556 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5557 5558 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5559 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5560 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5561 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5562 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5563 PetscFunctionReturn(0); 5564 } 5565 5566 /* 5567 Special version for direct calls from Fortran 5568 */ 5569 #include <petsc/private/fortranimpl.h> 5570 5571 /* Change these macros so can be used in void function */ 5572 #undef CHKERRQ 5573 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5574 #undef SETERRQ2 5575 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5576 #undef SETERRQ3 5577 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5578 #undef SETERRQ 5579 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5580 5581 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5582 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5583 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5584 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5585 #else 5586 #endif 5587 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) 5588 { 5589 Mat mat = *mmat; 5590 PetscInt m = *mm, n = *mn; 5591 InsertMode addv = *maddv; 5592 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5593 PetscScalar value; 5594 PetscErrorCode ierr; 5595 5596 MatCheckPreallocated(mat,1); 5597 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5598 5599 #if defined(PETSC_USE_DEBUG) 5600 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5601 #endif 5602 { 5603 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5604 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5605 PetscBool roworiented = aij->roworiented; 5606 5607 /* Some Variables required in the macro */ 5608 Mat A = aij->A; 5609 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5610 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5611 MatScalar *aa = a->a; 5612 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5613 Mat B = aij->B; 5614 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5615 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5616 MatScalar *ba = b->a; 5617 5618 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5619 PetscInt nonew = a->nonew; 5620 MatScalar *ap1,*ap2; 5621 5622 PetscFunctionBegin; 5623 for (i=0; i<m; i++) { 5624 if (im[i] < 0) continue; 5625 #if defined(PETSC_USE_DEBUG) 5626 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); 5627 #endif 5628 if (im[i] >= rstart && im[i] < rend) { 5629 row = im[i] - rstart; 5630 lastcol1 = -1; 5631 rp1 = aj + ai[row]; 5632 ap1 = aa + ai[row]; 5633 rmax1 = aimax[row]; 5634 nrow1 = ailen[row]; 5635 low1 = 0; 5636 high1 = nrow1; 5637 lastcol2 = -1; 5638 rp2 = bj + bi[row]; 5639 ap2 = ba + bi[row]; 5640 rmax2 = bimax[row]; 5641 nrow2 = bilen[row]; 5642 low2 = 0; 5643 high2 = nrow2; 5644 5645 for (j=0; j<n; j++) { 5646 if (roworiented) value = v[i*n+j]; 5647 else value = v[i+j*m]; 5648 if (in[j] >= cstart && in[j] < cend) { 5649 col = in[j] - cstart; 5650 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5651 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5652 } else if (in[j] < 0) continue; 5653 #if defined(PETSC_USE_DEBUG) 5654 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); 5655 #endif 5656 else { 5657 if (mat->was_assembled) { 5658 if (!aij->colmap) { 5659 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5660 } 5661 #if defined(PETSC_USE_CTABLE) 5662 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5663 col--; 5664 #else 5665 col = aij->colmap[in[j]] - 1; 5666 #endif 5667 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5668 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5669 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5670 col = in[j]; 5671 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5672 B = aij->B; 5673 b = (Mat_SeqAIJ*)B->data; 5674 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5675 rp2 = bj + bi[row]; 5676 ap2 = ba + bi[row]; 5677 rmax2 = bimax[row]; 5678 nrow2 = bilen[row]; 5679 low2 = 0; 5680 high2 = nrow2; 5681 bm = aij->B->rmap->n; 5682 ba = b->a; 5683 } 5684 } else col = in[j]; 5685 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5686 } 5687 } 5688 } else if (!aij->donotstash) { 5689 if (roworiented) { 5690 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5691 } else { 5692 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5693 } 5694 } 5695 } 5696 } 5697 PetscFunctionReturnVoid(); 5698 } 5699 5700