1 2 3 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 4 #include <petsc/private/vecimpl.h> 5 #include <petsc/private/isimpl.h> 6 #include <petscblaslapack.h> 7 #include <petscsf.h> 8 9 /*MC 10 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 11 12 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 13 and MATMPIAIJ otherwise. As a result, for single process communicators, 14 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 15 for communicators controlling multiple processes. It is recommended that you call both of 16 the above preallocation routines for simplicity. 17 18 Options Database Keys: 19 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 20 21 Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when 22 enough exist. 23 24 Level: beginner 25 26 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ, MATMPIAIJ 27 M*/ 28 29 /*MC 30 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 31 32 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 33 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 34 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 35 for communicators controlling multiple processes. It is recommended that you call both of 36 the above preallocation routines for simplicity. 37 38 Options Database Keys: 39 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 40 41 Level: beginner 42 43 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 44 M*/ 45 46 PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 50 51 PetscFunctionBegin; 52 if (mat->A) { 53 ierr = MatSetBlockSizes(mat->A,rbs,cbs);CHKERRQ(ierr); 54 ierr = MatSetBlockSizes(mat->B,rbs,1);CHKERRQ(ierr); 55 } 56 PetscFunctionReturn(0); 57 } 58 59 PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows) 60 { 61 PetscErrorCode ierr; 62 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 63 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data; 64 Mat_SeqAIJ *b = (Mat_SeqAIJ*)mat->B->data; 65 const PetscInt *ia,*ib; 66 const MatScalar *aa,*bb; 67 PetscInt na,nb,i,j,*rows,cnt=0,n0rows; 68 PetscInt m = M->rmap->n,rstart = M->rmap->rstart; 69 70 PetscFunctionBegin; 71 *keptrows = 0; 72 ia = a->i; 73 ib = b->i; 74 for (i=0; i<m; i++) { 75 na = ia[i+1] - ia[i]; 76 nb = ib[i+1] - ib[i]; 77 if (!na && !nb) { 78 cnt++; 79 goto ok1; 80 } 81 aa = a->a + ia[i]; 82 for (j=0; j<na; j++) { 83 if (aa[j] != 0.0) goto ok1; 84 } 85 bb = b->a + ib[i]; 86 for (j=0; j <nb; j++) { 87 if (bb[j] != 0.0) goto ok1; 88 } 89 cnt++; 90 ok1:; 91 } 92 ierr = MPIU_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr); 93 if (!n0rows) PetscFunctionReturn(0); 94 ierr = PetscMalloc1(M->rmap->n-cnt,&rows);CHKERRQ(ierr); 95 cnt = 0; 96 for (i=0; i<m; i++) { 97 na = ia[i+1] - ia[i]; 98 nb = ib[i+1] - ib[i]; 99 if (!na && !nb) continue; 100 aa = a->a + ia[i]; 101 for (j=0; j<na;j++) { 102 if (aa[j] != 0.0) { 103 rows[cnt++] = rstart + i; 104 goto ok2; 105 } 106 } 107 bb = b->a + ib[i]; 108 for (j=0; j<nb; j++) { 109 if (bb[j] != 0.0) { 110 rows[cnt++] = rstart + i; 111 goto ok2; 112 } 113 } 114 ok2:; 115 } 116 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 117 PetscFunctionReturn(0); 118 } 119 120 PetscErrorCode MatDiagonalSet_MPIAIJ(Mat Y,Vec D,InsertMode is) 121 { 122 PetscErrorCode ierr; 123 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) Y->data; 124 125 PetscFunctionBegin; 126 if (Y->assembled && Y->rmap->rstart == Y->cmap->rstart && Y->rmap->rend == Y->cmap->rend) { 127 ierr = MatDiagonalSet(aij->A,D,is);CHKERRQ(ierr); 128 } else { 129 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 130 } 131 PetscFunctionReturn(0); 132 } 133 134 PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows) 135 { 136 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)M->data; 137 PetscErrorCode ierr; 138 PetscInt i,rstart,nrows,*rows; 139 140 PetscFunctionBegin; 141 *zrows = NULL; 142 ierr = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr); 143 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 144 for (i=0; i<nrows; i++) rows[i] += rstart; 145 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 146 PetscFunctionReturn(0); 147 } 148 149 PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms) 150 { 151 PetscErrorCode ierr; 152 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 153 PetscInt i,n,*garray = aij->garray; 154 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ*) aij->A->data; 155 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ*) aij->B->data; 156 PetscReal *work; 157 158 PetscFunctionBegin; 159 ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr); 160 ierr = PetscCalloc1(n,&work);CHKERRQ(ierr); 161 if (type == NORM_2) { 162 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 163 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]); 164 } 165 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 166 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]); 167 } 168 } else if (type == NORM_1) { 169 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 170 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 171 } 172 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 173 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 174 } 175 } else if (type == NORM_INFINITY) { 176 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 177 work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 178 } 179 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 180 work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]); 181 } 182 183 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 184 if (type == NORM_INFINITY) { 185 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 186 } else { 187 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 188 } 189 ierr = PetscFree(work);CHKERRQ(ierr); 190 if (type == NORM_2) { 191 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 192 } 193 PetscFunctionReturn(0); 194 } 195 196 PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A,IS *is) 197 { 198 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 199 IS sis,gis; 200 PetscErrorCode ierr; 201 const PetscInt *isis,*igis; 202 PetscInt n,*iis,nsis,ngis,rstart,i; 203 204 PetscFunctionBegin; 205 ierr = MatFindOffBlockDiagonalEntries(a->A,&sis);CHKERRQ(ierr); 206 ierr = MatFindNonzeroRows(a->B,&gis);CHKERRQ(ierr); 207 ierr = ISGetSize(gis,&ngis);CHKERRQ(ierr); 208 ierr = ISGetSize(sis,&nsis);CHKERRQ(ierr); 209 ierr = ISGetIndices(sis,&isis);CHKERRQ(ierr); 210 ierr = ISGetIndices(gis,&igis);CHKERRQ(ierr); 211 212 ierr = PetscMalloc1(ngis+nsis,&iis);CHKERRQ(ierr); 213 ierr = PetscMemcpy(iis,igis,ngis*sizeof(PetscInt));CHKERRQ(ierr); 214 ierr = PetscMemcpy(iis+ngis,isis,nsis*sizeof(PetscInt));CHKERRQ(ierr); 215 n = ngis + nsis; 216 ierr = PetscSortRemoveDupsInt(&n,iis);CHKERRQ(ierr); 217 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 218 for (i=0; i<n; i++) iis[i] += rstart; 219 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),n,iis,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 220 221 ierr = ISRestoreIndices(sis,&isis);CHKERRQ(ierr); 222 ierr = ISRestoreIndices(gis,&igis);CHKERRQ(ierr); 223 ierr = ISDestroy(&sis);CHKERRQ(ierr); 224 ierr = ISDestroy(&gis);CHKERRQ(ierr); 225 PetscFunctionReturn(0); 226 } 227 228 /* 229 Distributes a SeqAIJ matrix across a set of processes. Code stolen from 230 MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type. 231 232 Only for square matrices 233 234 Used by a preconditioner, hence PETSC_EXTERN 235 */ 236 PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat) 237 { 238 PetscMPIInt rank,size; 239 PetscInt *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz = 0,*gmataj,cnt,row,*ld,bses[2]; 240 PetscErrorCode ierr; 241 Mat mat; 242 Mat_SeqAIJ *gmata; 243 PetscMPIInt tag; 244 MPI_Status status; 245 PetscBool aij; 246 MatScalar *gmataa,*ao,*ad,*gmataarestore=0; 247 248 PetscFunctionBegin; 249 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 250 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 251 if (!rank) { 252 ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr); 253 if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name); 254 } 255 if (reuse == MAT_INITIAL_MATRIX) { 256 ierr = MatCreate(comm,&mat);CHKERRQ(ierr); 257 ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 258 ierr = MatGetBlockSizes(gmat,&bses[0],&bses[1]);CHKERRQ(ierr); 259 ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr); 260 ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr); 261 ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr); 262 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 263 ierr = PetscMalloc2(m,&dlens,m,&olens);CHKERRQ(ierr); 264 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 265 266 rowners[0] = 0; 267 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 268 rstart = rowners[rank]; 269 rend = rowners[rank+1]; 270 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 271 if (!rank) { 272 gmata = (Mat_SeqAIJ*) gmat->data; 273 /* send row lengths to all processors */ 274 for (i=0; i<m; i++) dlens[i] = gmata->ilen[i]; 275 for (i=1; i<size; i++) { 276 ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 277 } 278 /* determine number diagonal and off-diagonal counts */ 279 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 280 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 281 jj = 0; 282 for (i=0; i<m; i++) { 283 for (j=0; j<dlens[i]; j++) { 284 if (gmata->j[jj] < rstart) ld[i]++; 285 if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++; 286 jj++; 287 } 288 } 289 /* send column indices to other processes */ 290 for (i=1; i<size; i++) { 291 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 292 ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 293 ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 294 } 295 296 /* send numerical values to other processes */ 297 for (i=1; i<size; i++) { 298 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 299 ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 300 } 301 gmataa = gmata->a; 302 gmataj = gmata->j; 303 304 } else { 305 /* receive row lengths */ 306 ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 307 /* receive column indices */ 308 ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 309 ierr = PetscMalloc2(nz,&gmataa,nz,&gmataj);CHKERRQ(ierr); 310 ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 311 /* determine number diagonal and off-diagonal counts */ 312 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 313 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 314 jj = 0; 315 for (i=0; i<m; i++) { 316 for (j=0; j<dlens[i]; j++) { 317 if (gmataj[jj] < rstart) ld[i]++; 318 if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++; 319 jj++; 320 } 321 } 322 /* receive numerical values */ 323 ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 324 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 325 } 326 /* set preallocation */ 327 for (i=0; i<m; i++) { 328 dlens[i] -= olens[i]; 329 } 330 ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr); 331 ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr); 332 333 for (i=0; i<m; i++) { 334 dlens[i] += olens[i]; 335 } 336 cnt = 0; 337 for (i=0; i<m; i++) { 338 row = rstart + i; 339 ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr); 340 cnt += dlens[i]; 341 } 342 if (rank) { 343 ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr); 344 } 345 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 346 ierr = PetscFree(rowners);CHKERRQ(ierr); 347 348 ((Mat_MPIAIJ*)(mat->data))->ld = ld; 349 350 *inmat = mat; 351 } else { /* column indices are already set; only need to move over numerical values from process 0 */ 352 Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data; 353 Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data; 354 mat = *inmat; 355 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 356 if (!rank) { 357 /* send numerical values to other processes */ 358 gmata = (Mat_SeqAIJ*) gmat->data; 359 ierr = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr); 360 gmataa = gmata->a; 361 for (i=1; i<size; i++) { 362 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 363 ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 364 } 365 nz = gmata->i[rowners[1]]-gmata->i[rowners[0]]; 366 } else { 367 /* receive numerical values from process 0*/ 368 nz = Ad->nz + Ao->nz; 369 ierr = PetscMalloc1(nz,&gmataa);CHKERRQ(ierr); gmataarestore = gmataa; 370 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 371 } 372 /* transfer numerical values into the diagonal A and off diagonal B parts of mat */ 373 ld = ((Mat_MPIAIJ*)(mat->data))->ld; 374 ad = Ad->a; 375 ao = Ao->a; 376 if (mat->rmap->n) { 377 i = 0; 378 nz = ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 379 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 380 } 381 for (i=1; i<mat->rmap->n; i++) { 382 nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 383 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 384 } 385 i--; 386 if (mat->rmap->n) { 387 nz = Ao->i[i+1] - Ao->i[i] - ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 388 } 389 if (rank) { 390 ierr = PetscFree(gmataarestore);CHKERRQ(ierr); 391 } 392 } 393 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 394 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 395 PetscFunctionReturn(0); 396 } 397 398 /* 399 Local utility routine that creates a mapping from the global column 400 number to the local number in the off-diagonal part of the local 401 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 402 a slightly higher hash table cost; without it it is not scalable (each processor 403 has an order N integer array but is fast to acess. 404 */ 405 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 406 { 407 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 408 PetscErrorCode ierr; 409 PetscInt n = aij->B->cmap->n,i; 410 411 PetscFunctionBegin; 412 if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray"); 413 #if defined(PETSC_USE_CTABLE) 414 ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 415 for (i=0; i<n; i++) { 416 ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr); 417 } 418 #else 419 ierr = PetscCalloc1(mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 420 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N+1)*sizeof(PetscInt));CHKERRQ(ierr); 421 for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1; 422 #endif 423 PetscFunctionReturn(0); 424 } 425 426 #define MatSetValues_SeqAIJ_A_Private(row,col,value,addv,orow,ocol) \ 427 { \ 428 if (col <= lastcol1) low1 = 0; \ 429 else high1 = nrow1; \ 430 lastcol1 = col;\ 431 while (high1-low1 > 5) { \ 432 t = (low1+high1)/2; \ 433 if (rp1[t] > col) high1 = t; \ 434 else low1 = t; \ 435 } \ 436 for (_i=low1; _i<high1; _i++) { \ 437 if (rp1[_i] > col) break; \ 438 if (rp1[_i] == col) { \ 439 if (addv == ADD_VALUES) ap1[_i] += value; \ 440 else ap1[_i] = value; \ 441 goto a_noinsert; \ 442 } \ 443 } \ 444 if (value == 0.0 && ignorezeroentries && row != col) {low1 = 0; high1 = nrow1;goto a_noinsert;} \ 445 if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;} \ 446 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 447 MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \ 448 N = nrow1++ - 1; a->nz++; high1++; \ 449 /* shift up all the later entries in this row */ \ 450 for (ii=N; ii>=_i; ii--) { \ 451 rp1[ii+1] = rp1[ii]; \ 452 ap1[ii+1] = ap1[ii]; \ 453 } \ 454 rp1[_i] = col; \ 455 ap1[_i] = value; \ 456 A->nonzerostate++;\ 457 a_noinsert: ; \ 458 ailen[row] = nrow1; \ 459 } 460 461 #define MatSetValues_SeqAIJ_B_Private(row,col,value,addv,orow,ocol) \ 462 { \ 463 if (col <= lastcol2) low2 = 0; \ 464 else high2 = nrow2; \ 465 lastcol2 = col; \ 466 while (high2-low2 > 5) { \ 467 t = (low2+high2)/2; \ 468 if (rp2[t] > col) high2 = t; \ 469 else low2 = t; \ 470 } \ 471 for (_i=low2; _i<high2; _i++) { \ 472 if (rp2[_i] > col) break; \ 473 if (rp2[_i] == col) { \ 474 if (addv == ADD_VALUES) ap2[_i] += value; \ 475 else ap2[_i] = value; \ 476 goto b_noinsert; \ 477 } \ 478 } \ 479 if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 480 if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 481 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 482 MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \ 483 N = nrow2++ - 1; b->nz++; high2++; \ 484 /* shift up all the later entries in this row */ \ 485 for (ii=N; ii>=_i; ii--) { \ 486 rp2[ii+1] = rp2[ii]; \ 487 ap2[ii+1] = ap2[ii]; \ 488 } \ 489 rp2[_i] = col; \ 490 ap2[_i] = value; \ 491 B->nonzerostate++; \ 492 b_noinsert: ; \ 493 bilen[row] = nrow2; \ 494 } 495 496 PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[]) 497 { 498 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)A->data; 499 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data; 500 PetscErrorCode ierr; 501 PetscInt l,*garray = mat->garray,diag; 502 503 PetscFunctionBegin; 504 /* code only works for square matrices A */ 505 506 /* find size of row to the left of the diagonal part */ 507 ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr); 508 row = row - diag; 509 for (l=0; l<b->i[row+1]-b->i[row]; l++) { 510 if (garray[b->j[b->i[row]+l]] > diag) break; 511 } 512 ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr); 513 514 /* diagonal part */ 515 ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr); 516 517 /* right of diagonal part */ 518 ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr); 519 PetscFunctionReturn(0); 520 } 521 522 PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 523 { 524 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 525 PetscScalar value; 526 PetscErrorCode ierr; 527 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 528 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 529 PetscBool roworiented = aij->roworiented; 530 531 /* Some Variables required in the macro */ 532 Mat A = aij->A; 533 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 534 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 535 MatScalar *aa = a->a; 536 PetscBool ignorezeroentries = a->ignorezeroentries; 537 Mat B = aij->B; 538 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 539 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 540 MatScalar *ba = b->a; 541 542 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 543 PetscInt nonew; 544 MatScalar *ap1,*ap2; 545 546 PetscFunctionBegin; 547 for (i=0; i<m; i++) { 548 if (im[i] < 0) continue; 549 #if defined(PETSC_USE_DEBUG) 550 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 551 #endif 552 if (im[i] >= rstart && im[i] < rend) { 553 row = im[i] - rstart; 554 lastcol1 = -1; 555 rp1 = aj + ai[row]; 556 ap1 = aa + ai[row]; 557 rmax1 = aimax[row]; 558 nrow1 = ailen[row]; 559 low1 = 0; 560 high1 = nrow1; 561 lastcol2 = -1; 562 rp2 = bj + bi[row]; 563 ap2 = ba + bi[row]; 564 rmax2 = bimax[row]; 565 nrow2 = bilen[row]; 566 low2 = 0; 567 high2 = nrow2; 568 569 for (j=0; j<n; j++) { 570 if (roworiented) value = v[i*n+j]; 571 else value = v[i+j*m]; 572 if (in[j] >= cstart && in[j] < cend) { 573 col = in[j] - cstart; 574 nonew = a->nonew; 575 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 576 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 577 } else if (in[j] < 0) continue; 578 #if defined(PETSC_USE_DEBUG) 579 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 580 #endif 581 else { 582 if (mat->was_assembled) { 583 if (!aij->colmap) { 584 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 585 } 586 #if defined(PETSC_USE_CTABLE) 587 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 588 col--; 589 #else 590 col = aij->colmap[in[j]] - 1; 591 #endif 592 if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) { 593 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 594 col = in[j]; 595 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 596 B = aij->B; 597 b = (Mat_SeqAIJ*)B->data; 598 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a; 599 rp2 = bj + bi[row]; 600 ap2 = ba + bi[row]; 601 rmax2 = bimax[row]; 602 nrow2 = bilen[row]; 603 low2 = 0; 604 high2 = nrow2; 605 bm = aij->B->rmap->n; 606 ba = b->a; 607 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", im[i], in[j]); 608 } else col = in[j]; 609 nonew = b->nonew; 610 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 611 } 612 } 613 } else { 614 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 615 if (!aij->donotstash) { 616 mat->assembled = PETSC_FALSE; 617 if (roworiented) { 618 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 619 } else { 620 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 621 } 622 } 623 } 624 } 625 PetscFunctionReturn(0); 626 } 627 628 PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 629 { 630 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 631 PetscErrorCode ierr; 632 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 633 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 634 635 PetscFunctionBegin; 636 for (i=0; i<m; i++) { 637 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 638 if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1); 639 if (idxm[i] >= rstart && idxm[i] < rend) { 640 row = idxm[i] - rstart; 641 for (j=0; j<n; j++) { 642 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 643 if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1); 644 if (idxn[j] >= cstart && idxn[j] < cend) { 645 col = idxn[j] - cstart; 646 ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 647 } else { 648 if (!aij->colmap) { 649 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 650 } 651 #if defined(PETSC_USE_CTABLE) 652 ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr); 653 col--; 654 #else 655 col = aij->colmap[idxn[j]] - 1; 656 #endif 657 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0; 658 else { 659 ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 660 } 661 } 662 } 663 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 664 } 665 PetscFunctionReturn(0); 666 } 667 668 extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec); 669 670 PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode) 671 { 672 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 673 PetscErrorCode ierr; 674 PetscInt nstash,reallocs; 675 676 PetscFunctionBegin; 677 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 678 679 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 680 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 681 ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 682 PetscFunctionReturn(0); 683 } 684 685 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode) 686 { 687 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 688 Mat_SeqAIJ *a = (Mat_SeqAIJ*)aij->A->data; 689 PetscErrorCode ierr; 690 PetscMPIInt n; 691 PetscInt i,j,rstart,ncols,flg; 692 PetscInt *row,*col; 693 PetscBool other_disassembled; 694 PetscScalar *val; 695 696 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 697 698 PetscFunctionBegin; 699 if (!aij->donotstash && !mat->nooffprocentries) { 700 while (1) { 701 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 702 if (!flg) break; 703 704 for (i=0; i<n; ) { 705 /* Now identify the consecutive vals belonging to the same row */ 706 for (j=i,rstart=row[j]; j<n; j++) { 707 if (row[j] != rstart) break; 708 } 709 if (j < n) ncols = j-i; 710 else ncols = n-i; 711 /* Now assemble all these values with a single function call */ 712 ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr); 713 714 i = j; 715 } 716 } 717 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 718 } 719 ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr); 720 ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr); 721 722 /* determine if any processor has disassembled, if so we must 723 also disassemble ourselfs, in order that we may reassemble. */ 724 /* 725 if nonzero structure of submatrix B cannot change then we know that 726 no processor disassembled thus we can skip this stuff 727 */ 728 if (!((Mat_SeqAIJ*)aij->B->data)->nonew) { 729 ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 730 if (mat->was_assembled && !other_disassembled) { 731 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 732 } 733 } 734 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 735 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 736 } 737 ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr); 738 ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr); 739 ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr); 740 741 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 742 743 aij->rowvalues = 0; 744 745 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 746 if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ; 747 748 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 749 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 750 PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate; 751 ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 752 } 753 PetscFunctionReturn(0); 754 } 755 756 PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 757 { 758 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 759 PetscErrorCode ierr; 760 761 PetscFunctionBegin; 762 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 763 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 764 PetscFunctionReturn(0); 765 } 766 767 PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 768 { 769 Mat_MPIAIJ *mat = (Mat_MPIAIJ *) A->data; 770 PetscInt *lrows; 771 PetscInt r, len; 772 PetscErrorCode ierr; 773 774 PetscFunctionBegin; 775 /* get locally owned rows */ 776 ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr); 777 /* fix right hand side if needed */ 778 if (x && b) { 779 const PetscScalar *xx; 780 PetscScalar *bb; 781 782 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 783 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 784 for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]]; 785 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 786 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 787 } 788 /* Must zero l->B before l->A because the (diag) case below may put values into l->B*/ 789 ierr = MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 790 if (A->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 791 PetscBool cong; 792 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 793 if (cong) A->congruentlayouts = 1; 794 else A->congruentlayouts = 0; 795 } 796 if ((diag != 0.0) && A->congruentlayouts) { 797 ierr = MatZeroRows(mat->A, len, lrows, diag, NULL, NULL);CHKERRQ(ierr); 798 } else if (diag != 0.0) { 799 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 800 if (((Mat_SeqAIJ *) mat->A->data)->nonew) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 801 for (r = 0; r < len; ++r) { 802 const PetscInt row = lrows[r] + A->rmap->rstart; 803 ierr = MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES);CHKERRQ(ierr); 804 } 805 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 806 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 807 } else { 808 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 809 } 810 ierr = PetscFree(lrows);CHKERRQ(ierr); 811 812 /* only change matrix nonzero state if pattern was allowed to be changed */ 813 if (!((Mat_SeqAIJ*)(mat->A->data))->keepnonzeropattern) { 814 PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate; 815 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 816 } 817 PetscFunctionReturn(0); 818 } 819 820 PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 821 { 822 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 823 PetscErrorCode ierr; 824 PetscMPIInt n = A->rmap->n; 825 PetscInt i,j,r,m,p = 0,len = 0; 826 PetscInt *lrows,*owners = A->rmap->range; 827 PetscSFNode *rrows; 828 PetscSF sf; 829 const PetscScalar *xx; 830 PetscScalar *bb,*mask; 831 Vec xmask,lmask; 832 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)l->B->data; 833 const PetscInt *aj, *ii,*ridx; 834 PetscScalar *aa; 835 836 PetscFunctionBegin; 837 /* Create SF where leaves are input rows and roots are owned rows */ 838 ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr); 839 for (r = 0; r < n; ++r) lrows[r] = -1; 840 ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr); 841 for (r = 0; r < N; ++r) { 842 const PetscInt idx = rows[r]; 843 if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N); 844 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */ 845 ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr); 846 } 847 rrows[r].rank = p; 848 rrows[r].index = rows[r] - owners[p]; 849 } 850 ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr); 851 ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr); 852 /* Collect flags for rows to be zeroed */ 853 ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 854 ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 855 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 856 /* Compress and put in row numbers */ 857 for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r; 858 /* zero diagonal part of matrix */ 859 ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr); 860 /* handle off diagonal part of matrix */ 861 ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr); 862 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 863 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 864 for (i=0; i<len; i++) bb[lrows[i]] = 1; 865 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 866 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 867 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 868 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 869 if (x) { 870 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 871 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 872 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 873 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 874 } 875 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 876 /* remove zeroed rows of off diagonal matrix */ 877 ii = aij->i; 878 for (i=0; i<len; i++) { 879 ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr); 880 } 881 /* loop over all elements of off process part of matrix zeroing removed columns*/ 882 if (aij->compressedrow.use) { 883 m = aij->compressedrow.nrows; 884 ii = aij->compressedrow.i; 885 ridx = aij->compressedrow.rindex; 886 for (i=0; i<m; i++) { 887 n = ii[i+1] - ii[i]; 888 aj = aij->j + ii[i]; 889 aa = aij->a + ii[i]; 890 891 for (j=0; j<n; j++) { 892 if (PetscAbsScalar(mask[*aj])) { 893 if (b) bb[*ridx] -= *aa*xx[*aj]; 894 *aa = 0.0; 895 } 896 aa++; 897 aj++; 898 } 899 ridx++; 900 } 901 } else { /* do not use compressed row format */ 902 m = l->B->rmap->n; 903 for (i=0; i<m; i++) { 904 n = ii[i+1] - ii[i]; 905 aj = aij->j + ii[i]; 906 aa = aij->a + ii[i]; 907 for (j=0; j<n; j++) { 908 if (PetscAbsScalar(mask[*aj])) { 909 if (b) bb[i] -= *aa*xx[*aj]; 910 *aa = 0.0; 911 } 912 aa++; 913 aj++; 914 } 915 } 916 } 917 if (x) { 918 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 919 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 920 } 921 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 922 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 923 ierr = PetscFree(lrows);CHKERRQ(ierr); 924 925 /* only change matrix nonzero state if pattern was allowed to be changed */ 926 if (!((Mat_SeqAIJ*)(l->A->data))->keepnonzeropattern) { 927 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 928 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 929 } 930 PetscFunctionReturn(0); 931 } 932 933 PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy) 934 { 935 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 936 PetscErrorCode ierr; 937 PetscInt nt; 938 939 PetscFunctionBegin; 940 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 941 if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt); 942 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 943 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 944 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 945 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 946 PetscFunctionReturn(0); 947 } 948 949 PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx) 950 { 951 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 952 PetscErrorCode ierr; 953 954 PetscFunctionBegin; 955 ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr); 956 PetscFunctionReturn(0); 957 } 958 959 PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 960 { 961 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 962 PetscErrorCode ierr; 963 964 PetscFunctionBegin; 965 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 966 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 967 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 968 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 969 PetscFunctionReturn(0); 970 } 971 972 PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy) 973 { 974 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 975 PetscErrorCode ierr; 976 PetscBool merged; 977 978 PetscFunctionBegin; 979 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 980 /* do nondiagonal part */ 981 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 982 if (!merged) { 983 /* send it on its way */ 984 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 985 /* do local part */ 986 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 987 /* receive remote parts: note this assumes the values are not actually */ 988 /* added in yy until the next line, */ 989 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 990 } else { 991 /* do local part */ 992 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 993 /* send it on its way */ 994 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 995 /* values actually were received in the Begin() but we need to call this nop */ 996 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 997 } 998 PetscFunctionReturn(0); 999 } 1000 1001 PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool *f) 1002 { 1003 MPI_Comm comm; 1004 Mat_MPIAIJ *Aij = (Mat_MPIAIJ*) Amat->data, *Bij; 1005 Mat Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs; 1006 IS Me,Notme; 1007 PetscErrorCode ierr; 1008 PetscInt M,N,first,last,*notme,i; 1009 PetscMPIInt size; 1010 1011 PetscFunctionBegin; 1012 /* Easy test: symmetric diagonal block */ 1013 Bij = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A; 1014 ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr); 1015 if (!*f) PetscFunctionReturn(0); 1016 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1017 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1018 if (size == 1) PetscFunctionReturn(0); 1019 1020 /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */ 1021 ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr); 1022 ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr); 1023 ierr = PetscMalloc1(N-last+first,¬me);CHKERRQ(ierr); 1024 for (i=0; i<first; i++) notme[i] = i; 1025 for (i=last; i<M; i++) notme[i-last+first] = i; 1026 ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr); 1027 ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr); 1028 ierr = MatCreateSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr); 1029 Aoff = Aoffs[0]; 1030 ierr = MatCreateSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr); 1031 Boff = Boffs[0]; 1032 ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr); 1033 ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr); 1034 ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr); 1035 ierr = ISDestroy(&Me);CHKERRQ(ierr); 1036 ierr = ISDestroy(&Notme);CHKERRQ(ierr); 1037 ierr = PetscFree(notme);CHKERRQ(ierr); 1038 PetscFunctionReturn(0); 1039 } 1040 1041 PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1042 { 1043 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1044 PetscErrorCode ierr; 1045 1046 PetscFunctionBegin; 1047 /* do nondiagonal part */ 1048 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1049 /* send it on its way */ 1050 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1051 /* do local part */ 1052 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1053 /* receive remote parts */ 1054 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1055 PetscFunctionReturn(0); 1056 } 1057 1058 /* 1059 This only works correctly for square matrices where the subblock A->A is the 1060 diagonal block 1061 */ 1062 PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v) 1063 { 1064 PetscErrorCode ierr; 1065 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1066 1067 PetscFunctionBegin; 1068 if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1069 if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition"); 1070 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1071 PetscFunctionReturn(0); 1072 } 1073 1074 PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa) 1075 { 1076 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1077 PetscErrorCode ierr; 1078 1079 PetscFunctionBegin; 1080 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1081 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1082 PetscFunctionReturn(0); 1083 } 1084 1085 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 1086 { 1087 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1088 PetscErrorCode ierr; 1089 1090 PetscFunctionBegin; 1091 #if defined(PETSC_USE_LOG) 1092 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N); 1093 #endif 1094 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1095 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 1096 ierr = MatDestroy(&aij->A);CHKERRQ(ierr); 1097 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 1098 #if defined(PETSC_USE_CTABLE) 1099 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 1100 #else 1101 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 1102 #endif 1103 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 1104 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 1105 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 1106 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 1107 ierr = PetscFree(aij->ld);CHKERRQ(ierr); 1108 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1109 1110 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1111 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1112 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1113 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1114 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1115 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1116 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1117 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1118 #if defined(PETSC_HAVE_ELEMENTAL) 1119 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_elemental_C",NULL);CHKERRQ(ierr); 1120 #endif 1121 #if defined(PETSC_HAVE_HYPRE) 1122 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_hypre_C",NULL);CHKERRQ(ierr); 1123 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMatMatMult_transpose_mpiaij_mpiaij_C",NULL);CHKERRQ(ierr); 1124 #endif 1125 PetscFunctionReturn(0); 1126 } 1127 1128 PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer) 1129 { 1130 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1131 Mat_SeqAIJ *A = (Mat_SeqAIJ*)aij->A->data; 1132 Mat_SeqAIJ *B = (Mat_SeqAIJ*)aij->B->data; 1133 PetscErrorCode ierr; 1134 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1135 int fd; 1136 PetscInt nz,header[4],*row_lengths,*range=0,rlen,i; 1137 PetscInt nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz = 0; 1138 PetscScalar *column_values; 1139 PetscInt message_count,flowcontrolcount; 1140 FILE *file; 1141 1142 PetscFunctionBegin; 1143 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1144 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1145 nz = A->nz + B->nz; 1146 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1147 if (!rank) { 1148 header[0] = MAT_FILE_CLASSID; 1149 header[1] = mat->rmap->N; 1150 header[2] = mat->cmap->N; 1151 1152 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1153 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1154 /* get largest number of rows any processor has */ 1155 rlen = mat->rmap->n; 1156 range = mat->rmap->range; 1157 for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]); 1158 } else { 1159 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1160 rlen = mat->rmap->n; 1161 } 1162 1163 /* load up the local row counts */ 1164 ierr = PetscMalloc1(rlen+1,&row_lengths);CHKERRQ(ierr); 1165 for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1166 1167 /* store the row lengths to the file */ 1168 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1169 if (!rank) { 1170 ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1171 for (i=1; i<size; i++) { 1172 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1173 rlen = range[i+1] - range[i]; 1174 ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1175 ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1176 } 1177 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1178 } else { 1179 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1180 ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1181 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1182 } 1183 ierr = PetscFree(row_lengths);CHKERRQ(ierr); 1184 1185 /* load up the local column indices */ 1186 nzmax = nz; /* th processor needs space a largest processor needs */ 1187 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1188 ierr = PetscMalloc1(nzmax+1,&column_indices);CHKERRQ(ierr); 1189 cnt = 0; 1190 for (i=0; i<mat->rmap->n; i++) { 1191 for (j=B->i[i]; j<B->i[i+1]; j++) { 1192 if ((col = garray[B->j[j]]) > cstart) break; 1193 column_indices[cnt++] = col; 1194 } 1195 for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart; 1196 for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]]; 1197 } 1198 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1199 1200 /* store the column indices to the file */ 1201 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1202 if (!rank) { 1203 MPI_Status status; 1204 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1205 for (i=1; i<size; i++) { 1206 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1207 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1208 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1209 ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1210 ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1211 } 1212 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1213 } else { 1214 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1215 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1216 ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1217 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1218 } 1219 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1220 1221 /* load up the local column values */ 1222 ierr = PetscMalloc1(nzmax+1,&column_values);CHKERRQ(ierr); 1223 cnt = 0; 1224 for (i=0; i<mat->rmap->n; i++) { 1225 for (j=B->i[i]; j<B->i[i+1]; j++) { 1226 if (garray[B->j[j]] > cstart) break; 1227 column_values[cnt++] = B->a[j]; 1228 } 1229 for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k]; 1230 for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j]; 1231 } 1232 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1233 1234 /* store the column values to the file */ 1235 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1236 if (!rank) { 1237 MPI_Status status; 1238 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1239 for (i=1; i<size; i++) { 1240 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1241 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1242 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1243 ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1244 ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1245 } 1246 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1247 } else { 1248 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1249 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1250 ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1251 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1252 } 1253 ierr = PetscFree(column_values);CHKERRQ(ierr); 1254 1255 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1256 if (file) fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(mat->rmap->bs)); 1257 PetscFunctionReturn(0); 1258 } 1259 1260 #include <petscdraw.h> 1261 PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 1262 { 1263 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1264 PetscErrorCode ierr; 1265 PetscMPIInt rank = aij->rank,size = aij->size; 1266 PetscBool isdraw,iascii,isbinary; 1267 PetscViewer sviewer; 1268 PetscViewerFormat format; 1269 1270 PetscFunctionBegin; 1271 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1272 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1273 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1274 if (iascii) { 1275 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1276 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1277 MatInfo info; 1278 PetscBool inodes; 1279 1280 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1281 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 1282 ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr); 1283 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 1284 if (!inodes) { 1285 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n", 1286 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1287 } else { 1288 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n", 1289 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1290 } 1291 ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1292 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1293 ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1294 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1295 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1296 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 1297 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1298 ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr); 1299 PetscFunctionReturn(0); 1300 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1301 PetscInt inodecount,inodelimit,*inodes; 1302 ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr); 1303 if (inodes) { 1304 ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr); 1305 } else { 1306 ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr); 1307 } 1308 PetscFunctionReturn(0); 1309 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1310 PetscFunctionReturn(0); 1311 } 1312 } else if (isbinary) { 1313 if (size == 1) { 1314 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1315 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1316 } else { 1317 ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1318 } 1319 PetscFunctionReturn(0); 1320 } else if (isdraw) { 1321 PetscDraw draw; 1322 PetscBool isnull; 1323 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1324 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 1325 if (isnull) PetscFunctionReturn(0); 1326 } 1327 1328 { 1329 /* assemble the entire matrix onto first processor. */ 1330 Mat A; 1331 Mat_SeqAIJ *Aloc; 1332 PetscInt M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct; 1333 MatScalar *a; 1334 1335 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1336 if (!rank) { 1337 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1338 } else { 1339 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1340 } 1341 /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */ 1342 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 1343 ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr); 1344 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1345 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1346 1347 /* copy over the A part */ 1348 Aloc = (Mat_SeqAIJ*)aij->A->data; 1349 m = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1350 row = mat->rmap->rstart; 1351 for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart; 1352 for (i=0; i<m; i++) { 1353 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr); 1354 row++; 1355 a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i]; 1356 } 1357 aj = Aloc->j; 1358 for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart; 1359 1360 /* copy over the B part */ 1361 Aloc = (Mat_SeqAIJ*)aij->B->data; 1362 m = aij->B->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1363 row = mat->rmap->rstart; 1364 ierr = PetscMalloc1(ai[m]+1,&cols);CHKERRQ(ierr); 1365 ct = cols; 1366 for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]]; 1367 for (i=0; i<m; i++) { 1368 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr); 1369 row++; 1370 a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i]; 1371 } 1372 ierr = PetscFree(ct);CHKERRQ(ierr); 1373 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1374 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1375 /* 1376 Everyone has to call to draw the matrix since the graphics waits are 1377 synchronized across all processors that share the PetscDraw object 1378 */ 1379 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1380 if (!rank) { 1381 ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1382 ierr = MatView_SeqAIJ(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1383 } 1384 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1385 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1386 ierr = MatDestroy(&A);CHKERRQ(ierr); 1387 } 1388 PetscFunctionReturn(0); 1389 } 1390 1391 PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer) 1392 { 1393 PetscErrorCode ierr; 1394 PetscBool iascii,isdraw,issocket,isbinary; 1395 1396 PetscFunctionBegin; 1397 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1398 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1399 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1400 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1401 if (iascii || isdraw || isbinary || issocket) { 1402 ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1403 } 1404 PetscFunctionReturn(0); 1405 } 1406 1407 PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1408 { 1409 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1410 PetscErrorCode ierr; 1411 Vec bb1 = 0; 1412 PetscBool hasop; 1413 1414 PetscFunctionBegin; 1415 if (flag == SOR_APPLY_UPPER) { 1416 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1417 PetscFunctionReturn(0); 1418 } 1419 1420 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) { 1421 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 1422 } 1423 1424 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1425 if (flag & SOR_ZERO_INITIAL_GUESS) { 1426 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1427 its--; 1428 } 1429 1430 while (its--) { 1431 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1432 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1433 1434 /* update rhs: bb1 = bb - B*x */ 1435 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1436 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1437 1438 /* local sweep */ 1439 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1440 } 1441 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1442 if (flag & SOR_ZERO_INITIAL_GUESS) { 1443 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1444 its--; 1445 } 1446 while (its--) { 1447 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1448 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1449 1450 /* update rhs: bb1 = bb - B*x */ 1451 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1452 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1453 1454 /* local sweep */ 1455 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1456 } 1457 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1458 if (flag & SOR_ZERO_INITIAL_GUESS) { 1459 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1460 its--; 1461 } 1462 while (its--) { 1463 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1464 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1465 1466 /* update rhs: bb1 = bb - B*x */ 1467 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1468 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1469 1470 /* local sweep */ 1471 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1472 } 1473 } else if (flag & SOR_EISENSTAT) { 1474 Vec xx1; 1475 1476 ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr); 1477 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr); 1478 1479 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1480 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1481 if (!mat->diag) { 1482 ierr = MatCreateVecs(matin,&mat->diag,NULL);CHKERRQ(ierr); 1483 ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr); 1484 } 1485 ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr); 1486 if (hasop) { 1487 ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr); 1488 } else { 1489 ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr); 1490 } 1491 ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr); 1492 1493 ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr); 1494 1495 /* local sweep */ 1496 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr); 1497 ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr); 1498 ierr = VecDestroy(&xx1);CHKERRQ(ierr); 1499 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported"); 1500 1501 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 1502 1503 matin->factorerrortype = mat->A->factorerrortype; 1504 PetscFunctionReturn(0); 1505 } 1506 1507 PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B) 1508 { 1509 Mat aA,aB,Aperm; 1510 const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj; 1511 PetscScalar *aa,*ba; 1512 PetscInt i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest; 1513 PetscSF rowsf,sf; 1514 IS parcolp = NULL; 1515 PetscBool done; 1516 PetscErrorCode ierr; 1517 1518 PetscFunctionBegin; 1519 ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); 1520 ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr); 1521 ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr); 1522 ierr = PetscMalloc3(PetscMax(m,n),&work,m,&rdest,n,&cdest);CHKERRQ(ierr); 1523 1524 /* Invert row permutation to find out where my rows should go */ 1525 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr); 1526 ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr); 1527 ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr); 1528 for (i=0; i<m; i++) work[i] = A->rmap->rstart + i; 1529 ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1530 ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1531 1532 /* Invert column permutation to find out where my columns should go */ 1533 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1534 ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr); 1535 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1536 for (i=0; i<n; i++) work[i] = A->cmap->rstart + i; 1537 ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1538 ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1539 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1540 1541 ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr); 1542 ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr); 1543 ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr); 1544 1545 /* Find out where my gcols should go */ 1546 ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr); 1547 ierr = PetscMalloc1(ng,&gcdest);CHKERRQ(ierr); 1548 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1549 ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr); 1550 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1551 ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1552 ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1553 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1554 1555 ierr = PetscCalloc4(m,&dnnz,m,&onnz,m,&tdnnz,m,&tonnz);CHKERRQ(ierr); 1556 ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1557 ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1558 for (i=0; i<m; i++) { 1559 PetscInt row = rdest[i],rowner; 1560 ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr); 1561 for (j=ai[i]; j<ai[i+1]; j++) { 1562 PetscInt cowner,col = cdest[aj[j]]; 1563 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */ 1564 if (rowner == cowner) dnnz[i]++; 1565 else onnz[i]++; 1566 } 1567 for (j=bi[i]; j<bi[i+1]; j++) { 1568 PetscInt cowner,col = gcdest[bj[j]]; 1569 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); 1570 if (rowner == cowner) dnnz[i]++; 1571 else onnz[i]++; 1572 } 1573 } 1574 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1575 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1576 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1577 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1578 ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr); 1579 1580 ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr); 1581 ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr); 1582 ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr); 1583 for (i=0; i<m; i++) { 1584 PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */ 1585 PetscInt j0,rowlen; 1586 rowlen = ai[i+1] - ai[i]; 1587 for (j0=j=0; j<rowlen; j0=j) { /* rowlen could be larger than number of rows m, so sum in batches */ 1588 for ( ; j<PetscMin(rowlen,j0+m); j++) acols[j-j0] = cdest[aj[ai[i]+j]]; 1589 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,acols,aa+ai[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1590 } 1591 rowlen = bi[i+1] - bi[i]; 1592 for (j0=j=0; j<rowlen; j0=j) { 1593 for ( ; j<PetscMin(rowlen,j0+m); j++) bcols[j-j0] = gcdest[bj[bi[i]+j]]; 1594 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,bcols,ba+bi[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1595 } 1596 } 1597 ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1598 ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1599 ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1600 ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1601 ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr); 1602 ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr); 1603 ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr); 1604 ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr); 1605 ierr = PetscFree(gcdest);CHKERRQ(ierr); 1606 if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);} 1607 *B = Aperm; 1608 PetscFunctionReturn(0); 1609 } 1610 1611 PetscErrorCode MatGetGhosts_MPIAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 1612 { 1613 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1614 PetscErrorCode ierr; 1615 1616 PetscFunctionBegin; 1617 ierr = MatGetSize(aij->B,NULL,nghosts);CHKERRQ(ierr); 1618 if (ghosts) *ghosts = aij->garray; 1619 PetscFunctionReturn(0); 1620 } 1621 1622 PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1623 { 1624 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1625 Mat A = mat->A,B = mat->B; 1626 PetscErrorCode ierr; 1627 PetscReal isend[5],irecv[5]; 1628 1629 PetscFunctionBegin; 1630 info->block_size = 1.0; 1631 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1632 1633 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1634 isend[3] = info->memory; isend[4] = info->mallocs; 1635 1636 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1637 1638 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1639 isend[3] += info->memory; isend[4] += info->mallocs; 1640 if (flag == MAT_LOCAL) { 1641 info->nz_used = isend[0]; 1642 info->nz_allocated = isend[1]; 1643 info->nz_unneeded = isend[2]; 1644 info->memory = isend[3]; 1645 info->mallocs = isend[4]; 1646 } else if (flag == MAT_GLOBAL_MAX) { 1647 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1648 1649 info->nz_used = irecv[0]; 1650 info->nz_allocated = irecv[1]; 1651 info->nz_unneeded = irecv[2]; 1652 info->memory = irecv[3]; 1653 info->mallocs = irecv[4]; 1654 } else if (flag == MAT_GLOBAL_SUM) { 1655 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1656 1657 info->nz_used = irecv[0]; 1658 info->nz_allocated = irecv[1]; 1659 info->nz_unneeded = irecv[2]; 1660 info->memory = irecv[3]; 1661 info->mallocs = irecv[4]; 1662 } 1663 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1664 info->fill_ratio_needed = 0; 1665 info->factor_mallocs = 0; 1666 PetscFunctionReturn(0); 1667 } 1668 1669 PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg) 1670 { 1671 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1672 PetscErrorCode ierr; 1673 1674 PetscFunctionBegin; 1675 switch (op) { 1676 case MAT_NEW_NONZERO_LOCATIONS: 1677 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1678 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1679 case MAT_KEEP_NONZERO_PATTERN: 1680 case MAT_NEW_NONZERO_LOCATION_ERR: 1681 case MAT_USE_INODES: 1682 case MAT_IGNORE_ZERO_ENTRIES: 1683 MatCheckPreallocated(A,1); 1684 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1685 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1686 break; 1687 case MAT_ROW_ORIENTED: 1688 MatCheckPreallocated(A,1); 1689 a->roworiented = flg; 1690 1691 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1692 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1693 break; 1694 case MAT_NEW_DIAGONALS: 1695 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1696 break; 1697 case MAT_IGNORE_OFF_PROC_ENTRIES: 1698 a->donotstash = flg; 1699 break; 1700 case MAT_SPD: 1701 A->spd_set = PETSC_TRUE; 1702 A->spd = flg; 1703 if (flg) { 1704 A->symmetric = PETSC_TRUE; 1705 A->structurally_symmetric = PETSC_TRUE; 1706 A->symmetric_set = PETSC_TRUE; 1707 A->structurally_symmetric_set = PETSC_TRUE; 1708 } 1709 break; 1710 case MAT_SYMMETRIC: 1711 MatCheckPreallocated(A,1); 1712 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1713 break; 1714 case MAT_STRUCTURALLY_SYMMETRIC: 1715 MatCheckPreallocated(A,1); 1716 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1717 break; 1718 case MAT_HERMITIAN: 1719 MatCheckPreallocated(A,1); 1720 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1721 break; 1722 case MAT_SYMMETRY_ETERNAL: 1723 MatCheckPreallocated(A,1); 1724 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1725 break; 1726 case MAT_SUBMAT_SINGLEIS: 1727 A->submat_singleis = flg; 1728 break; 1729 case MAT_STRUCTURE_ONLY: 1730 /* The option is handled directly by MatSetOption() */ 1731 break; 1732 default: 1733 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1734 } 1735 PetscFunctionReturn(0); 1736 } 1737 1738 PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1739 { 1740 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1741 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1742 PetscErrorCode ierr; 1743 PetscInt i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart; 1744 PetscInt nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend; 1745 PetscInt *cmap,*idx_p; 1746 1747 PetscFunctionBegin; 1748 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1749 mat->getrowactive = PETSC_TRUE; 1750 1751 if (!mat->rowvalues && (idx || v)) { 1752 /* 1753 allocate enough space to hold information from the longest row. 1754 */ 1755 Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data; 1756 PetscInt max = 1,tmp; 1757 for (i=0; i<matin->rmap->n; i++) { 1758 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1759 if (max < tmp) max = tmp; 1760 } 1761 ierr = PetscMalloc2(max,&mat->rowvalues,max,&mat->rowindices);CHKERRQ(ierr); 1762 } 1763 1764 if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows"); 1765 lrow = row - rstart; 1766 1767 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1768 if (!v) {pvA = 0; pvB = 0;} 1769 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1770 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1771 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1772 nztot = nzA + nzB; 1773 1774 cmap = mat->garray; 1775 if (v || idx) { 1776 if (nztot) { 1777 /* Sort by increasing column numbers, assuming A and B already sorted */ 1778 PetscInt imark = -1; 1779 if (v) { 1780 *v = v_p = mat->rowvalues; 1781 for (i=0; i<nzB; i++) { 1782 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1783 else break; 1784 } 1785 imark = i; 1786 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1787 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1788 } 1789 if (idx) { 1790 *idx = idx_p = mat->rowindices; 1791 if (imark > -1) { 1792 for (i=0; i<imark; i++) { 1793 idx_p[i] = cmap[cworkB[i]]; 1794 } 1795 } else { 1796 for (i=0; i<nzB; i++) { 1797 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1798 else break; 1799 } 1800 imark = i; 1801 } 1802 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart + cworkA[i]; 1803 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]]; 1804 } 1805 } else { 1806 if (idx) *idx = 0; 1807 if (v) *v = 0; 1808 } 1809 } 1810 *nz = nztot; 1811 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1812 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1813 PetscFunctionReturn(0); 1814 } 1815 1816 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1817 { 1818 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1819 1820 PetscFunctionBegin; 1821 if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first"); 1822 aij->getrowactive = PETSC_FALSE; 1823 PetscFunctionReturn(0); 1824 } 1825 1826 PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm) 1827 { 1828 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1829 Mat_SeqAIJ *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data; 1830 PetscErrorCode ierr; 1831 PetscInt i,j,cstart = mat->cmap->rstart; 1832 PetscReal sum = 0.0; 1833 MatScalar *v; 1834 1835 PetscFunctionBegin; 1836 if (aij->size == 1) { 1837 ierr = MatNorm(aij->A,type,norm);CHKERRQ(ierr); 1838 } else { 1839 if (type == NORM_FROBENIUS) { 1840 v = amat->a; 1841 for (i=0; i<amat->nz; i++) { 1842 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1843 } 1844 v = bmat->a; 1845 for (i=0; i<bmat->nz; i++) { 1846 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1847 } 1848 ierr = MPIU_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1849 *norm = PetscSqrtReal(*norm); 1850 ierr = PetscLogFlops(2*amat->nz+2*bmat->nz);CHKERRQ(ierr); 1851 } else if (type == NORM_1) { /* max column norm */ 1852 PetscReal *tmp,*tmp2; 1853 PetscInt *jj,*garray = aij->garray; 1854 ierr = PetscCalloc1(mat->cmap->N+1,&tmp);CHKERRQ(ierr); 1855 ierr = PetscMalloc1(mat->cmap->N+1,&tmp2);CHKERRQ(ierr); 1856 *norm = 0.0; 1857 v = amat->a; jj = amat->j; 1858 for (j=0; j<amat->nz; j++) { 1859 tmp[cstart + *jj++] += PetscAbsScalar(*v); v++; 1860 } 1861 v = bmat->a; jj = bmat->j; 1862 for (j=0; j<bmat->nz; j++) { 1863 tmp[garray[*jj++]] += PetscAbsScalar(*v); v++; 1864 } 1865 ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1866 for (j=0; j<mat->cmap->N; j++) { 1867 if (tmp2[j] > *norm) *norm = tmp2[j]; 1868 } 1869 ierr = PetscFree(tmp);CHKERRQ(ierr); 1870 ierr = PetscFree(tmp2);CHKERRQ(ierr); 1871 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1872 } else if (type == NORM_INFINITY) { /* max row norm */ 1873 PetscReal ntemp = 0.0; 1874 for (j=0; j<aij->A->rmap->n; j++) { 1875 v = amat->a + amat->i[j]; 1876 sum = 0.0; 1877 for (i=0; i<amat->i[j+1]-amat->i[j]; i++) { 1878 sum += PetscAbsScalar(*v); v++; 1879 } 1880 v = bmat->a + bmat->i[j]; 1881 for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) { 1882 sum += PetscAbsScalar(*v); v++; 1883 } 1884 if (sum > ntemp) ntemp = sum; 1885 } 1886 ierr = MPIU_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1887 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1888 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm"); 1889 } 1890 PetscFunctionReturn(0); 1891 } 1892 1893 PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout) 1894 { 1895 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1896 Mat_SeqAIJ *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data; 1897 PetscErrorCode ierr; 1898 PetscInt M = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i; 1899 PetscInt cstart = A->cmap->rstart,ncol; 1900 Mat B; 1901 MatScalar *array; 1902 1903 PetscFunctionBegin; 1904 if (reuse == MAT_INPLACE_MATRIX && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1905 1906 ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n; 1907 ai = Aloc->i; aj = Aloc->j; 1908 bi = Bloc->i; bj = Bloc->j; 1909 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1910 PetscInt *d_nnz,*g_nnz,*o_nnz; 1911 PetscSFNode *oloc; 1912 PETSC_UNUSED PetscSF sf; 1913 1914 ierr = PetscMalloc4(na,&d_nnz,na,&o_nnz,nb,&g_nnz,nb,&oloc);CHKERRQ(ierr); 1915 /* compute d_nnz for preallocation */ 1916 ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1917 for (i=0; i<ai[ma]; i++) { 1918 d_nnz[aj[i]]++; 1919 aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1920 } 1921 /* compute local off-diagonal contributions */ 1922 ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr); 1923 for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++; 1924 /* map those to global */ 1925 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1926 ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr); 1927 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1928 ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1929 ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1930 ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1931 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1932 1933 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1934 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1935 ierr = MatSetBlockSizes(B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 1936 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1937 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 1938 ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr); 1939 } else { 1940 B = *matout; 1941 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1942 for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1943 } 1944 1945 /* copy over the A part */ 1946 array = Aloc->a; 1947 row = A->rmap->rstart; 1948 for (i=0; i<ma; i++) { 1949 ncol = ai[i+1]-ai[i]; 1950 ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1951 row++; 1952 array += ncol; aj += ncol; 1953 } 1954 aj = Aloc->j; 1955 for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */ 1956 1957 /* copy over the B part */ 1958 ierr = PetscCalloc1(bi[mb],&cols);CHKERRQ(ierr); 1959 array = Bloc->a; 1960 row = A->rmap->rstart; 1961 for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]]; 1962 cols_tmp = cols; 1963 for (i=0; i<mb; i++) { 1964 ncol = bi[i+1]-bi[i]; 1965 ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1966 row++; 1967 array += ncol; cols_tmp += ncol; 1968 } 1969 ierr = PetscFree(cols);CHKERRQ(ierr); 1970 1971 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1972 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1973 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 1974 *matout = B; 1975 } else { 1976 ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr); 1977 } 1978 PetscFunctionReturn(0); 1979 } 1980 1981 PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr) 1982 { 1983 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1984 Mat a = aij->A,b = aij->B; 1985 PetscErrorCode ierr; 1986 PetscInt s1,s2,s3; 1987 1988 PetscFunctionBegin; 1989 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1990 if (rr) { 1991 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1992 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1993 /* Overlap communication with computation. */ 1994 ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1995 } 1996 if (ll) { 1997 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1998 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1999 ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr); 2000 } 2001 /* scale the diagonal block */ 2002 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 2003 2004 if (rr) { 2005 /* Do a scatter end and then right scale the off-diagonal block */ 2006 ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2007 ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr); 2008 } 2009 PetscFunctionReturn(0); 2010 } 2011 2012 PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2013 { 2014 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2015 PetscErrorCode ierr; 2016 2017 PetscFunctionBegin; 2018 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 2019 PetscFunctionReturn(0); 2020 } 2021 2022 PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool *flag) 2023 { 2024 Mat_MPIAIJ *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data; 2025 Mat a,b,c,d; 2026 PetscBool flg; 2027 PetscErrorCode ierr; 2028 2029 PetscFunctionBegin; 2030 a = matA->A; b = matA->B; 2031 c = matB->A; d = matB->B; 2032 2033 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 2034 if (flg) { 2035 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 2036 } 2037 ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2038 PetscFunctionReturn(0); 2039 } 2040 2041 PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str) 2042 { 2043 PetscErrorCode ierr; 2044 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2045 Mat_MPIAIJ *b = (Mat_MPIAIJ*)B->data; 2046 2047 PetscFunctionBegin; 2048 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2049 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2050 /* because of the column compression in the off-processor part of the matrix a->B, 2051 the number of columns in a->B and b->B may be different, hence we cannot call 2052 the MatCopy() directly on the two parts. If need be, we can provide a more 2053 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2054 then copying the submatrices */ 2055 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2056 } else { 2057 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 2058 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 2059 } 2060 ierr = PetscObjectStateIncrease((PetscObject)B);CHKERRQ(ierr); 2061 PetscFunctionReturn(0); 2062 } 2063 2064 PetscErrorCode MatSetUp_MPIAIJ(Mat A) 2065 { 2066 PetscErrorCode ierr; 2067 2068 PetscFunctionBegin; 2069 ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 2070 PetscFunctionReturn(0); 2071 } 2072 2073 /* 2074 Computes the number of nonzeros per row needed for preallocation when X and Y 2075 have different nonzero structure. 2076 */ 2077 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) 2078 { 2079 PetscInt i,j,k,nzx,nzy; 2080 2081 PetscFunctionBegin; 2082 /* Set the number of nonzeros in the new matrix */ 2083 for (i=0; i<m; i++) { 2084 const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i]; 2085 nzx = xi[i+1] - xi[i]; 2086 nzy = yi[i+1] - yi[i]; 2087 nnz[i] = 0; 2088 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2089 for (; k<nzy && yltog[yjj[k]]<xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */ 2090 if (k<nzy && yltog[yjj[k]]==xltog[xjj[j]]) k++; /* Skip duplicate */ 2091 nnz[i]++; 2092 } 2093 for (; k<nzy; k++) nnz[i]++; 2094 } 2095 PetscFunctionReturn(0); 2096 } 2097 2098 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2099 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 2100 { 2101 PetscErrorCode ierr; 2102 PetscInt m = Y->rmap->N; 2103 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2104 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2105 2106 PetscFunctionBegin; 2107 ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr); 2108 PetscFunctionReturn(0); 2109 } 2110 2111 PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2112 { 2113 PetscErrorCode ierr; 2114 Mat_MPIAIJ *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data; 2115 PetscBLASInt bnz,one=1; 2116 Mat_SeqAIJ *x,*y; 2117 2118 PetscFunctionBegin; 2119 if (str == SAME_NONZERO_PATTERN) { 2120 PetscScalar alpha = a; 2121 x = (Mat_SeqAIJ*)xx->A->data; 2122 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2123 y = (Mat_SeqAIJ*)yy->A->data; 2124 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2125 x = (Mat_SeqAIJ*)xx->B->data; 2126 y = (Mat_SeqAIJ*)yy->B->data; 2127 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2128 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2129 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 2130 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2131 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 2132 } else { 2133 Mat B; 2134 PetscInt *nnz_d,*nnz_o; 2135 ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr); 2136 ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr); 2137 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2138 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2139 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2140 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 2141 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2142 ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 2143 ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 2144 ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 2145 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2146 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 2147 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 2148 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 2149 } 2150 PetscFunctionReturn(0); 2151 } 2152 2153 extern PetscErrorCode MatConjugate_SeqAIJ(Mat); 2154 2155 PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2156 { 2157 #if defined(PETSC_USE_COMPLEX) 2158 PetscErrorCode ierr; 2159 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2160 2161 PetscFunctionBegin; 2162 ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr); 2163 ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr); 2164 #else 2165 PetscFunctionBegin; 2166 #endif 2167 PetscFunctionReturn(0); 2168 } 2169 2170 PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2171 { 2172 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2173 PetscErrorCode ierr; 2174 2175 PetscFunctionBegin; 2176 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2177 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2178 PetscFunctionReturn(0); 2179 } 2180 2181 PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2182 { 2183 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2184 PetscErrorCode ierr; 2185 2186 PetscFunctionBegin; 2187 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2188 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2189 PetscFunctionReturn(0); 2190 } 2191 2192 PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2193 { 2194 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2195 PetscErrorCode ierr; 2196 PetscInt i,*idxb = 0; 2197 PetscScalar *va,*vb; 2198 Vec vtmp; 2199 2200 PetscFunctionBegin; 2201 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 2202 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2203 if (idx) { 2204 for (i=0; i<A->rmap->n; i++) { 2205 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2206 } 2207 } 2208 2209 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2210 if (idx) { 2211 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2212 } 2213 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2214 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2215 2216 for (i=0; i<A->rmap->n; i++) { 2217 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 2218 va[i] = vb[i]; 2219 if (idx) idx[i] = a->garray[idxb[i]]; 2220 } 2221 } 2222 2223 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2224 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2225 ierr = PetscFree(idxb);CHKERRQ(ierr); 2226 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2227 PetscFunctionReturn(0); 2228 } 2229 2230 PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2231 { 2232 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2233 PetscErrorCode ierr; 2234 PetscInt i,*idxb = 0; 2235 PetscScalar *va,*vb; 2236 Vec vtmp; 2237 2238 PetscFunctionBegin; 2239 ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr); 2240 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2241 if (idx) { 2242 for (i=0; i<A->cmap->n; i++) { 2243 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2244 } 2245 } 2246 2247 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2248 if (idx) { 2249 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2250 } 2251 ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2252 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2253 2254 for (i=0; i<A->rmap->n; i++) { 2255 if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) { 2256 va[i] = vb[i]; 2257 if (idx) idx[i] = a->garray[idxb[i]]; 2258 } 2259 } 2260 2261 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2262 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2263 ierr = PetscFree(idxb);CHKERRQ(ierr); 2264 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2265 PetscFunctionReturn(0); 2266 } 2267 2268 PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2269 { 2270 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2271 PetscInt n = A->rmap->n; 2272 PetscInt cstart = A->cmap->rstart; 2273 PetscInt *cmap = mat->garray; 2274 PetscInt *diagIdx, *offdiagIdx; 2275 Vec diagV, offdiagV; 2276 PetscScalar *a, *diagA, *offdiagA; 2277 PetscInt r; 2278 PetscErrorCode ierr; 2279 2280 PetscFunctionBegin; 2281 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2282 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr); 2283 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr); 2284 ierr = MatGetRowMin(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2285 ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2286 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2287 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2288 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2289 for (r = 0; r < n; ++r) { 2290 if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) { 2291 a[r] = diagA[r]; 2292 idx[r] = cstart + diagIdx[r]; 2293 } else { 2294 a[r] = offdiagA[r]; 2295 idx[r] = cmap[offdiagIdx[r]]; 2296 } 2297 } 2298 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2299 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2300 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2301 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2302 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2303 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2304 PetscFunctionReturn(0); 2305 } 2306 2307 PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2308 { 2309 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2310 PetscInt n = A->rmap->n; 2311 PetscInt cstart = A->cmap->rstart; 2312 PetscInt *cmap = mat->garray; 2313 PetscInt *diagIdx, *offdiagIdx; 2314 Vec diagV, offdiagV; 2315 PetscScalar *a, *diagA, *offdiagA; 2316 PetscInt r; 2317 PetscErrorCode ierr; 2318 2319 PetscFunctionBegin; 2320 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2321 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr); 2322 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr); 2323 ierr = MatGetRowMax(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2324 ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2325 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2326 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2327 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2328 for (r = 0; r < n; ++r) { 2329 if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) { 2330 a[r] = diagA[r]; 2331 idx[r] = cstart + diagIdx[r]; 2332 } else { 2333 a[r] = offdiagA[r]; 2334 idx[r] = cmap[offdiagIdx[r]]; 2335 } 2336 } 2337 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2338 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2339 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2340 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2341 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2342 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2343 PetscFunctionReturn(0); 2344 } 2345 2346 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat) 2347 { 2348 PetscErrorCode ierr; 2349 Mat *dummy; 2350 2351 PetscFunctionBegin; 2352 ierr = MatCreateSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr); 2353 *newmat = *dummy; 2354 ierr = PetscFree(dummy);CHKERRQ(ierr); 2355 PetscFunctionReturn(0); 2356 } 2357 2358 PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values) 2359 { 2360 Mat_MPIAIJ *a = (Mat_MPIAIJ*) A->data; 2361 PetscErrorCode ierr; 2362 2363 PetscFunctionBegin; 2364 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2365 A->factorerrortype = a->A->factorerrortype; 2366 PetscFunctionReturn(0); 2367 } 2368 2369 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx) 2370 { 2371 PetscErrorCode ierr; 2372 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)x->data; 2373 2374 PetscFunctionBegin; 2375 ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr); 2376 ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr); 2377 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2378 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2379 PetscFunctionReturn(0); 2380 } 2381 2382 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A,PetscBool sc) 2383 { 2384 PetscFunctionBegin; 2385 if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable; 2386 else A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ; 2387 PetscFunctionReturn(0); 2388 } 2389 2390 /*@ 2391 MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap 2392 2393 Collective on Mat 2394 2395 Input Parameters: 2396 + A - the matrix 2397 - sc - PETSC_TRUE indicates use the scalable algorithm (default is not to use the scalable algorithm) 2398 2399 Level: advanced 2400 2401 @*/ 2402 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A,PetscBool sc) 2403 { 2404 PetscErrorCode ierr; 2405 2406 PetscFunctionBegin; 2407 ierr = PetscTryMethod(A,"MatMPIAIJSetUseScalableIncreaseOverlap_C",(Mat,PetscBool),(A,sc));CHKERRQ(ierr); 2408 PetscFunctionReturn(0); 2409 } 2410 2411 PetscErrorCode MatSetFromOptions_MPIAIJ(PetscOptionItems *PetscOptionsObject,Mat A) 2412 { 2413 PetscErrorCode ierr; 2414 PetscBool sc = PETSC_FALSE,flg; 2415 Mat_MPIAIJ *maij = (Mat_MPIAIJ*)A->data; 2416 2417 PetscFunctionBegin; 2418 ierr = PetscOptionsHead(PetscOptionsObject,"MPIAIJ options");CHKERRQ(ierr); 2419 ierr = PetscObjectOptionsBegin((PetscObject)A); 2420 if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE; 2421 ierr = PetscOptionsBool("-mat_increase_overlap_scalable","Use a scalable algorithm to compute the overlap","MatIncreaseOverlap",sc,&sc,&flg);CHKERRQ(ierr); 2422 if (flg) { 2423 ierr = MatMPIAIJSetUseScalableIncreaseOverlap(A,sc);CHKERRQ(ierr); 2424 } 2425 if (maij->A) {ierr = MatSetFromOptions(maij->A);CHKERRQ(ierr);} 2426 if (maij->A) {ierr = MatSetFromOptions(maij->B);CHKERRQ(ierr);} 2427 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2428 PetscFunctionReturn(0); 2429 } 2430 2431 PetscErrorCode MatShift_MPIAIJ(Mat Y,PetscScalar a) 2432 { 2433 PetscErrorCode ierr; 2434 Mat_MPIAIJ *maij = (Mat_MPIAIJ*)Y->data; 2435 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)maij->A->data; 2436 2437 PetscFunctionBegin; 2438 if (!Y->preallocated) { 2439 ierr = MatMPIAIJSetPreallocation(Y,1,NULL,0,NULL);CHKERRQ(ierr); 2440 } else if (!aij->nz) { 2441 PetscInt nonew = aij->nonew; 2442 ierr = MatSeqAIJSetPreallocation(maij->A,1,NULL);CHKERRQ(ierr); 2443 aij->nonew = nonew; 2444 } 2445 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2446 PetscFunctionReturn(0); 2447 } 2448 2449 PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A,PetscBool *missing,PetscInt *d) 2450 { 2451 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2452 PetscErrorCode ierr; 2453 2454 PetscFunctionBegin; 2455 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2456 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2457 if (d) { 2458 PetscInt rstart; 2459 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2460 *d += rstart; 2461 2462 } 2463 PetscFunctionReturn(0); 2464 } 2465 2466 2467 /* -------------------------------------------------------------------*/ 2468 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 2469 MatGetRow_MPIAIJ, 2470 MatRestoreRow_MPIAIJ, 2471 MatMult_MPIAIJ, 2472 /* 4*/ MatMultAdd_MPIAIJ, 2473 MatMultTranspose_MPIAIJ, 2474 MatMultTransposeAdd_MPIAIJ, 2475 0, 2476 0, 2477 0, 2478 /*10*/ 0, 2479 0, 2480 0, 2481 MatSOR_MPIAIJ, 2482 MatTranspose_MPIAIJ, 2483 /*15*/ MatGetInfo_MPIAIJ, 2484 MatEqual_MPIAIJ, 2485 MatGetDiagonal_MPIAIJ, 2486 MatDiagonalScale_MPIAIJ, 2487 MatNorm_MPIAIJ, 2488 /*20*/ MatAssemblyBegin_MPIAIJ, 2489 MatAssemblyEnd_MPIAIJ, 2490 MatSetOption_MPIAIJ, 2491 MatZeroEntries_MPIAIJ, 2492 /*24*/ MatZeroRows_MPIAIJ, 2493 0, 2494 0, 2495 0, 2496 0, 2497 /*29*/ MatSetUp_MPIAIJ, 2498 0, 2499 0, 2500 MatGetDiagonalBlock_MPIAIJ, 2501 0, 2502 /*34*/ MatDuplicate_MPIAIJ, 2503 0, 2504 0, 2505 0, 2506 0, 2507 /*39*/ MatAXPY_MPIAIJ, 2508 MatCreateSubMatrices_MPIAIJ, 2509 MatIncreaseOverlap_MPIAIJ, 2510 MatGetValues_MPIAIJ, 2511 MatCopy_MPIAIJ, 2512 /*44*/ MatGetRowMax_MPIAIJ, 2513 MatScale_MPIAIJ, 2514 MatShift_MPIAIJ, 2515 MatDiagonalSet_MPIAIJ, 2516 MatZeroRowsColumns_MPIAIJ, 2517 /*49*/ MatSetRandom_MPIAIJ, 2518 0, 2519 0, 2520 0, 2521 0, 2522 /*54*/ MatFDColoringCreate_MPIXAIJ, 2523 0, 2524 MatSetUnfactored_MPIAIJ, 2525 MatPermute_MPIAIJ, 2526 0, 2527 /*59*/ MatCreateSubMatrix_MPIAIJ, 2528 MatDestroy_MPIAIJ, 2529 MatView_MPIAIJ, 2530 0, 2531 MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ, 2532 /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ, 2533 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 2534 0, 2535 0, 2536 0, 2537 /*69*/ MatGetRowMaxAbs_MPIAIJ, 2538 MatGetRowMinAbs_MPIAIJ, 2539 0, 2540 0, 2541 0, 2542 0, 2543 /*75*/ MatFDColoringApply_AIJ, 2544 MatSetFromOptions_MPIAIJ, 2545 0, 2546 0, 2547 MatFindZeroDiagonals_MPIAIJ, 2548 /*80*/ 0, 2549 0, 2550 0, 2551 /*83*/ MatLoad_MPIAIJ, 2552 0, 2553 0, 2554 0, 2555 0, 2556 0, 2557 /*89*/ MatMatMult_MPIAIJ_MPIAIJ, 2558 MatMatMultSymbolic_MPIAIJ_MPIAIJ, 2559 MatMatMultNumeric_MPIAIJ_MPIAIJ, 2560 MatPtAP_MPIAIJ_MPIAIJ, 2561 MatPtAPSymbolic_MPIAIJ_MPIAIJ, 2562 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 2563 0, 2564 0, 2565 0, 2566 0, 2567 /*99*/ 0, 2568 0, 2569 0, 2570 MatConjugate_MPIAIJ, 2571 0, 2572 /*104*/MatSetValuesRow_MPIAIJ, 2573 MatRealPart_MPIAIJ, 2574 MatImaginaryPart_MPIAIJ, 2575 0, 2576 0, 2577 /*109*/0, 2578 0, 2579 MatGetRowMin_MPIAIJ, 2580 0, 2581 MatMissingDiagonal_MPIAIJ, 2582 /*114*/MatGetSeqNonzeroStructure_MPIAIJ, 2583 0, 2584 MatGetGhosts_MPIAIJ, 2585 0, 2586 0, 2587 /*119*/0, 2588 0, 2589 0, 2590 0, 2591 MatGetMultiProcBlock_MPIAIJ, 2592 /*124*/MatFindNonzeroRows_MPIAIJ, 2593 MatGetColumnNorms_MPIAIJ, 2594 MatInvertBlockDiagonal_MPIAIJ, 2595 0, 2596 MatCreateSubMatricesMPI_MPIAIJ, 2597 /*129*/0, 2598 MatTransposeMatMult_MPIAIJ_MPIAIJ, 2599 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ, 2600 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 2601 0, 2602 /*134*/0, 2603 0, 2604 MatRARt_MPIAIJ_MPIAIJ, 2605 0, 2606 0, 2607 /*139*/MatSetBlockSizes_MPIAIJ, 2608 0, 2609 0, 2610 MatFDColoringSetUp_MPIXAIJ, 2611 MatFindOffBlockDiagonalEntries_MPIAIJ, 2612 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIAIJ 2613 }; 2614 2615 /* ----------------------------------------------------------------------------------------*/ 2616 2617 PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 2618 { 2619 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2620 PetscErrorCode ierr; 2621 2622 PetscFunctionBegin; 2623 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 2624 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 2625 PetscFunctionReturn(0); 2626 } 2627 2628 PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 2629 { 2630 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2631 PetscErrorCode ierr; 2632 2633 PetscFunctionBegin; 2634 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 2635 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 2636 PetscFunctionReturn(0); 2637 } 2638 2639 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 2640 { 2641 Mat_MPIAIJ *b; 2642 PetscErrorCode ierr; 2643 2644 PetscFunctionBegin; 2645 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2646 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2647 b = (Mat_MPIAIJ*)B->data; 2648 2649 #if defined(PETSC_USE_CTABLE) 2650 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2651 #else 2652 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2653 #endif 2654 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2655 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2656 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2657 2658 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2659 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2660 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2661 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 2662 ierr = MatSetBlockSizesFromMats(b->B,B,B);CHKERRQ(ierr); 2663 ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr); 2664 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2665 2666 if (!B->preallocated) { 2667 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2668 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2669 ierr = MatSetBlockSizesFromMats(b->A,B,B);CHKERRQ(ierr); 2670 ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr); 2671 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2672 } 2673 2674 ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr); 2675 ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr); 2676 B->preallocated = PETSC_TRUE; 2677 B->was_assembled = PETSC_FALSE; 2678 B->assembled = PETSC_FALSE;; 2679 PetscFunctionReturn(0); 2680 } 2681 2682 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 2683 { 2684 Mat mat; 2685 Mat_MPIAIJ *a,*oldmat = (Mat_MPIAIJ*)matin->data; 2686 PetscErrorCode ierr; 2687 2688 PetscFunctionBegin; 2689 *newmat = 0; 2690 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 2691 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 2692 ierr = MatSetBlockSizesFromMats(mat,matin,matin);CHKERRQ(ierr); 2693 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 2694 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2695 a = (Mat_MPIAIJ*)mat->data; 2696 2697 mat->factortype = matin->factortype; 2698 mat->assembled = PETSC_TRUE; 2699 mat->insertmode = NOT_SET_VALUES; 2700 mat->preallocated = PETSC_TRUE; 2701 2702 a->size = oldmat->size; 2703 a->rank = oldmat->rank; 2704 a->donotstash = oldmat->donotstash; 2705 a->roworiented = oldmat->roworiented; 2706 a->rowindices = 0; 2707 a->rowvalues = 0; 2708 a->getrowactive = PETSC_FALSE; 2709 2710 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 2711 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 2712 2713 if (oldmat->colmap) { 2714 #if defined(PETSC_USE_CTABLE) 2715 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 2716 #else 2717 ierr = PetscMalloc1(mat->cmap->N,&a->colmap);CHKERRQ(ierr); 2718 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2719 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2720 #endif 2721 } else a->colmap = 0; 2722 if (oldmat->garray) { 2723 PetscInt len; 2724 len = oldmat->B->cmap->n; 2725 ierr = PetscMalloc1(len+1,&a->garray);CHKERRQ(ierr); 2726 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 2727 if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); } 2728 } else a->garray = 0; 2729 2730 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 2731 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 2732 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 2733 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 2734 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 2735 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 2736 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 2737 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 2738 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 2739 *newmat = mat; 2740 PetscFunctionReturn(0); 2741 } 2742 2743 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 2744 { 2745 PetscScalar *vals,*svals; 2746 MPI_Comm comm; 2747 PetscErrorCode ierr; 2748 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 2749 PetscInt i,nz,j,rstart,rend,mmax,maxnz = 0; 2750 PetscInt header[4],*rowlengths = 0,M,N,m,*cols; 2751 PetscInt *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols; 2752 PetscInt cend,cstart,n,*rowners; 2753 int fd; 2754 PetscInt bs = newMat->rmap->bs; 2755 2756 PetscFunctionBegin; 2757 /* force binary viewer to load .info file if it has not yet done so */ 2758 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 2759 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2760 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2761 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2762 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2763 if (!rank) { 2764 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 2765 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 2766 if (header[3] < 0) SETERRQ(PetscObjectComm((PetscObject)newMat),PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as MATMPIAIJ"); 2767 } 2768 2769 ierr = PetscOptionsBegin(comm,NULL,"Options for loading MATMPIAIJ matrix","Mat");CHKERRQ(ierr); 2770 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 2771 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2772 if (bs < 0) bs = 1; 2773 2774 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 2775 M = header[1]; N = header[2]; 2776 2777 /* If global sizes are set, check if they are consistent with that given in the file */ 2778 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); 2779 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); 2780 2781 /* determine ownership of all (block) rows */ 2782 if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs); 2783 if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank)); /* PETSC_DECIDE */ 2784 else m = newMat->rmap->n; /* Set by user */ 2785 2786 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 2787 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 2788 2789 /* First process needs enough room for process with most rows */ 2790 if (!rank) { 2791 mmax = rowners[1]; 2792 for (i=2; i<=size; i++) { 2793 mmax = PetscMax(mmax, rowners[i]); 2794 } 2795 } else mmax = -1; /* unused, but compilers complain */ 2796 2797 rowners[0] = 0; 2798 for (i=2; i<=size; i++) { 2799 rowners[i] += rowners[i-1]; 2800 } 2801 rstart = rowners[rank]; 2802 rend = rowners[rank+1]; 2803 2804 /* distribute row lengths to all processors */ 2805 ierr = PetscMalloc2(m,&ourlens,m,&offlens);CHKERRQ(ierr); 2806 if (!rank) { 2807 ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr); 2808 ierr = PetscMalloc1(mmax,&rowlengths);CHKERRQ(ierr); 2809 ierr = PetscCalloc1(size,&procsnz);CHKERRQ(ierr); 2810 for (j=0; j<m; j++) { 2811 procsnz[0] += ourlens[j]; 2812 } 2813 for (i=1; i<size; i++) { 2814 ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr); 2815 /* calculate the number of nonzeros on each processor */ 2816 for (j=0; j<rowners[i+1]-rowners[i]; j++) { 2817 procsnz[i] += rowlengths[j]; 2818 } 2819 ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2820 } 2821 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2822 } else { 2823 ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2824 } 2825 2826 if (!rank) { 2827 /* determine max buffer needed and allocate it */ 2828 maxnz = 0; 2829 for (i=0; i<size; i++) { 2830 maxnz = PetscMax(maxnz,procsnz[i]); 2831 } 2832 ierr = PetscMalloc1(maxnz,&cols);CHKERRQ(ierr); 2833 2834 /* read in my part of the matrix column indices */ 2835 nz = procsnz[0]; 2836 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2837 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 2838 2839 /* read in every one elses and ship off */ 2840 for (i=1; i<size; i++) { 2841 nz = procsnz[i]; 2842 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 2843 ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2844 } 2845 ierr = PetscFree(cols);CHKERRQ(ierr); 2846 } else { 2847 /* determine buffer space needed for message */ 2848 nz = 0; 2849 for (i=0; i<m; i++) { 2850 nz += ourlens[i]; 2851 } 2852 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2853 2854 /* receive message of column indices*/ 2855 ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2856 } 2857 2858 /* determine column ownership if matrix is not square */ 2859 if (N != M) { 2860 if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank); 2861 else n = newMat->cmap->n; 2862 ierr = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2863 cstart = cend - n; 2864 } else { 2865 cstart = rstart; 2866 cend = rend; 2867 n = cend - cstart; 2868 } 2869 2870 /* loop over local rows, determining number of off diagonal entries */ 2871 ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr); 2872 jj = 0; 2873 for (i=0; i<m; i++) { 2874 for (j=0; j<ourlens[i]; j++) { 2875 if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++; 2876 jj++; 2877 } 2878 } 2879 2880 for (i=0; i<m; i++) { 2881 ourlens[i] -= offlens[i]; 2882 } 2883 ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr); 2884 2885 if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);} 2886 2887 ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr); 2888 2889 for (i=0; i<m; i++) { 2890 ourlens[i] += offlens[i]; 2891 } 2892 2893 if (!rank) { 2894 ierr = PetscMalloc1(maxnz+1,&vals);CHKERRQ(ierr); 2895 2896 /* read in my part of the matrix numerical values */ 2897 nz = procsnz[0]; 2898 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2899 2900 /* insert into matrix */ 2901 jj = rstart; 2902 smycols = mycols; 2903 svals = vals; 2904 for (i=0; i<m; i++) { 2905 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2906 smycols += ourlens[i]; 2907 svals += ourlens[i]; 2908 jj++; 2909 } 2910 2911 /* read in other processors and ship out */ 2912 for (i=1; i<size; i++) { 2913 nz = procsnz[i]; 2914 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2915 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2916 } 2917 ierr = PetscFree(procsnz);CHKERRQ(ierr); 2918 } else { 2919 /* receive numeric values */ 2920 ierr = PetscMalloc1(nz+1,&vals);CHKERRQ(ierr); 2921 2922 /* receive message of values*/ 2923 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2924 2925 /* insert into matrix */ 2926 jj = rstart; 2927 smycols = mycols; 2928 svals = vals; 2929 for (i=0; i<m; i++) { 2930 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2931 smycols += ourlens[i]; 2932 svals += ourlens[i]; 2933 jj++; 2934 } 2935 } 2936 ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr); 2937 ierr = PetscFree(vals);CHKERRQ(ierr); 2938 ierr = PetscFree(mycols);CHKERRQ(ierr); 2939 ierr = PetscFree(rowners);CHKERRQ(ierr); 2940 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2941 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2942 PetscFunctionReturn(0); 2943 } 2944 2945 /* Not scalable because of ISAllGather() unless getting all columns. */ 2946 PetscErrorCode ISGetSeqIS_Private(Mat mat,IS iscol,IS *isseq) 2947 { 2948 PetscErrorCode ierr; 2949 IS iscol_local; 2950 PetscBool isstride; 2951 PetscMPIInt lisstride=0,gisstride; 2952 2953 PetscFunctionBegin; 2954 /* check if we are grabbing all columns*/ 2955 ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&isstride);CHKERRQ(ierr); 2956 2957 if (isstride) { 2958 PetscInt start,len,mstart,mlen; 2959 ierr = ISStrideGetInfo(iscol,&start,NULL);CHKERRQ(ierr); 2960 ierr = ISGetLocalSize(iscol,&len);CHKERRQ(ierr); 2961 ierr = MatGetOwnershipRangeColumn(mat,&mstart,&mlen);CHKERRQ(ierr); 2962 if (mstart == start && mlen-mstart == len) lisstride = 1; 2963 } 2964 2965 ierr = MPIU_Allreduce(&lisstride,&gisstride,1,MPI_INT,MPI_MIN,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2966 if (gisstride) { 2967 PetscInt N; 2968 ierr = MatGetSize(mat,NULL,&N);CHKERRQ(ierr); 2969 ierr = ISCreateStride(PetscObjectComm((PetscObject)mat),N,0,1,&iscol_local);CHKERRQ(ierr); 2970 ierr = ISSetIdentity(iscol_local);CHKERRQ(ierr); 2971 ierr = PetscInfo(mat,"Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n");CHKERRQ(ierr); 2972 } else { 2973 PetscInt cbs; 2974 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 2975 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 2976 ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr); 2977 } 2978 2979 *isseq = iscol_local; 2980 PetscFunctionReturn(0); 2981 } 2982 2983 /* 2984 Used by MatCreateSubMatrix_MPIAIJ_SameRowColDist() to avoid ISAllGather() and global size of iscol_local 2985 (see MatCreateSubMatrix_MPIAIJ_nonscalable) 2986 2987 Input Parameters: 2988 mat - matrix 2989 isrow - parallel row index set; its local indices are a subset of local columns of mat, 2990 i.e., mat->rstart <= isrow[i] < mat->rend 2991 iscol - parallel column index set; its local indices are a subset of local columns of mat, 2992 i.e., mat->cstart <= iscol[i] < mat->cend 2993 Output Parameter: 2994 isrow_d,iscol_d - sequential row and column index sets for retrieving mat->A 2995 iscol_o - sequential column index set for retrieving mat->B 2996 garray - column map; garray[i] indicates global location of iscol_o[i] in iscol 2997 */ 2998 PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat,IS isrow,IS iscol,IS *isrow_d,IS *iscol_d,IS *iscol_o,const PetscInt *garray[]) 2999 { 3000 PetscErrorCode ierr; 3001 Vec x,cmap; 3002 const PetscInt *is_idx; 3003 PetscScalar *xarray,*cmaparray; 3004 PetscInt ncols,isstart,*idx,m,rstart,*cmap1,count; 3005 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3006 Mat B=a->B; 3007 Vec lvec=a->lvec,lcmap; 3008 PetscInt i,cstart,cend,Bn=B->cmap->N; 3009 MPI_Comm comm; 3010 3011 PetscFunctionBegin; 3012 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3013 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 3014 3015 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3016 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3017 ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3018 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3019 3020 /* Get start indices */ 3021 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3022 isstart -= ncols; 3023 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3024 3025 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3026 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3027 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3028 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3029 for (i=0; i<ncols; i++) { 3030 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3031 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3032 idx[i] = is_idx[i]-cstart; /* local index of iscol[i] */ 3033 } 3034 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3035 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3036 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3037 3038 /* Get iscol_d */ 3039 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,iscol_d);CHKERRQ(ierr); 3040 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3041 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3042 3043 /* Get isrow_d */ 3044 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3045 rstart = mat->rmap->rstart; 3046 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3047 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3048 for (i=0; i<m; i++) idx[i] = is_idx[i]-rstart; 3049 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3050 3051 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_OWN_POINTER,isrow_d);CHKERRQ(ierr); 3052 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3053 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3054 3055 /* (2) Scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3056 ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3057 3058 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3059 3060 ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3061 ierr = VecScatterBegin(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3062 ierr = VecScatterEnd(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3063 3064 /* (3) create sequential iscol_o (a subset of iscol) and isgarray */ 3065 /* off-process column indices */ 3066 count = 0; 3067 ierr = PetscMalloc1(Bn,&idx);CHKERRQ(ierr); 3068 ierr = PetscMalloc1(Bn,&cmap1);CHKERRQ(ierr); 3069 3070 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3071 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3072 for (i=0; i<Bn; i++) { 3073 if (PetscRealPart(xarray[i]) > -1.0) { 3074 idx[count] = i; /* local column index in off-diagonal part B */ 3075 cmap1[count++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3076 } 3077 } 3078 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3079 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3080 3081 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr); 3082 /* cannot ensure iscol_o has same blocksize as iscol! */ 3083 3084 ierr = PetscFree(idx);CHKERRQ(ierr); 3085 3086 *garray = cmap1; 3087 3088 ierr = VecDestroy(&x);CHKERRQ(ierr); 3089 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3090 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3091 PetscFunctionReturn(0); 3092 } 3093 3094 /* isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */ 3095 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *submat) 3096 { 3097 PetscErrorCode ierr; 3098 Mat_MPIAIJ *a = (Mat_MPIAIJ*)mat->data,*asub; 3099 Mat M = NULL; 3100 MPI_Comm comm; 3101 IS iscol_d,isrow_d,iscol_o; 3102 Mat Asub = NULL,Bsub = NULL; 3103 PetscInt n; 3104 3105 PetscFunctionBegin; 3106 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3107 3108 if (call == MAT_REUSE_MATRIX) { 3109 /* Retrieve isrow_d, iscol_d and iscol_o from submat */ 3110 ierr = PetscObjectQuery((PetscObject)*submat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3111 if (!isrow_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow_d passed in was not used before, cannot reuse"); 3112 3113 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_d",(PetscObject*)&iscol_d);CHKERRQ(ierr); 3114 if (!iscol_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_d passed in was not used before, cannot reuse"); 3115 3116 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_o",(PetscObject*)&iscol_o);CHKERRQ(ierr); 3117 if (!iscol_o) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_o passed in was not used before, cannot reuse"); 3118 3119 /* Update diagonal and off-diagonal portions of submat */ 3120 asub = (Mat_MPIAIJ*)(*submat)->data; 3121 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->A);CHKERRQ(ierr); 3122 ierr = ISGetLocalSize(iscol_o,&n);CHKERRQ(ierr); 3123 if (n) { 3124 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_REUSE_MATRIX,&asub->B);CHKERRQ(ierr); 3125 } 3126 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3127 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3128 3129 } else { /* call == MAT_INITIAL_MATRIX) */ 3130 const PetscInt *garray; 3131 PetscInt BsubN; 3132 3133 /* Create isrow_d, iscol_d, iscol_o and isgarray (replace isgarray with array?) */ 3134 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&isrow_d,&iscol_d,&iscol_o,&garray);CHKERRQ(ierr); 3135 3136 /* Create local submatrices Asub and Bsub */ 3137 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Asub);CHKERRQ(ierr); 3138 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,MAT_INITIAL_MATRIX,&Bsub);CHKERRQ(ierr); 3139 3140 /* Create submatrix M */ 3141 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray,&M);CHKERRQ(ierr); 3142 3143 /* If Bsub has empty columns, compress iscol_o such that it will retrieve condensed Bsub from a->B during reuse */ 3144 asub = (Mat_MPIAIJ*)M->data; 3145 3146 ierr = ISGetLocalSize(iscol_o,&BsubN);CHKERRQ(ierr); 3147 n = asub->B->cmap->N; 3148 if (BsubN > n) { 3149 /* This case can be tested using ~petsc/src/tao/bound/examples/tutorials/runplate2_3 */ 3150 const PetscInt *idx; 3151 PetscInt i,j,*idx_new,*subgarray = asub->garray; 3152 ierr = PetscInfo2(M,"submatrix Bn %D != BsubN %D, update iscol_o\n",n,BsubN);CHKERRQ(ierr); 3153 3154 ierr = PetscMalloc1(n,&idx_new);CHKERRQ(ierr); 3155 j = 0; 3156 ierr = ISGetIndices(iscol_o,&idx);CHKERRQ(ierr); 3157 for (i=0; i<n; i++) { 3158 if (j >= BsubN) break; 3159 while (subgarray[i] > garray[j]) j++; 3160 3161 if (subgarray[i] == garray[j]) { 3162 idx_new[i] = idx[j++]; 3163 } else SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"subgarray[%D]=%D cannot < garray[%D]=%D",i,subgarray[i],j,garray[j]); 3164 } 3165 ierr = ISRestoreIndices(iscol_o,&idx);CHKERRQ(ierr); 3166 3167 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3168 ierr = ISCreateGeneral(PETSC_COMM_SELF,n,idx_new,PETSC_OWN_POINTER,&iscol_o);CHKERRQ(ierr); 3169 3170 } else if (BsubN < n) { 3171 SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Columns of Bsub cannot be smaller than B's",BsubN,asub->B->cmap->N); 3172 } 3173 3174 ierr = PetscFree(garray);CHKERRQ(ierr); 3175 *submat = M; 3176 3177 /* Save isrow_d, iscol_d and iscol_o used in processor for next request */ 3178 ierr = PetscObjectCompose((PetscObject)M,"isrow_d",(PetscObject)isrow_d);CHKERRQ(ierr); 3179 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3180 3181 ierr = PetscObjectCompose((PetscObject)M,"iscol_d",(PetscObject)iscol_d);CHKERRQ(ierr); 3182 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3183 3184 ierr = PetscObjectCompose((PetscObject)M,"iscol_o",(PetscObject)iscol_o);CHKERRQ(ierr); 3185 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3186 } 3187 PetscFunctionReturn(0); 3188 } 3189 3190 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3191 { 3192 PetscErrorCode ierr; 3193 IS iscol_local,isrow_d; 3194 PetscInt csize; 3195 PetscInt n,i,j,start,end; 3196 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3197 MPI_Comm comm; 3198 3199 PetscFunctionBegin; 3200 /* If isrow has same processor distribution as mat, 3201 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3202 if (call == MAT_REUSE_MATRIX) { 3203 ierr = PetscObjectQuery((PetscObject)*newmat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3204 if (isrow_d) { 3205 sameRowDist = PETSC_TRUE; 3206 tsameDist[1] = PETSC_TRUE; /* sameColDist */ 3207 } else { 3208 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3209 if (iscol_local) { 3210 sameRowDist = PETSC_TRUE; 3211 tsameDist[1] = PETSC_FALSE; /* !sameColDist */ 3212 } 3213 } 3214 } else { 3215 /* Check if isrow has same processor distribution as mat */ 3216 sameDist[0] = PETSC_FALSE; 3217 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3218 if (!n) { 3219 sameDist[0] = PETSC_TRUE; 3220 } else { 3221 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3222 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3223 if (i >= start && j < end) { 3224 sameDist[0] = PETSC_TRUE; 3225 } 3226 } 3227 3228 /* Check if iscol has same processor distribution as mat */ 3229 sameDist[1] = PETSC_FALSE; 3230 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3231 if (!n) { 3232 sameDist[1] = PETSC_TRUE; 3233 } else { 3234 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3235 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3236 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3237 } 3238 3239 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3240 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3241 sameRowDist = tsameDist[0]; 3242 } 3243 3244 if (sameRowDist) { 3245 if (tsameDist[1]) { /* sameRowDist & sameColDist */ 3246 /* isrow and iscol have same processor distribution as mat */ 3247 ierr = MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3248 } else { /* sameRowDist */ 3249 /* isrow has same processor distribution as mat */ 3250 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3251 } 3252 PetscFunctionReturn(0); 3253 } 3254 3255 /* General case: iscol -> iscol_local which has global size of iscol */ 3256 if (call == MAT_REUSE_MATRIX) { 3257 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3258 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3259 } else { 3260 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3261 } 3262 3263 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3264 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3265 3266 if (call == MAT_INITIAL_MATRIX) { 3267 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3268 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3269 } 3270 PetscFunctionReturn(0); 3271 } 3272 3273 /*@C 3274 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3275 and "off-diagonal" part of the matrix in CSR format. 3276 3277 Collective on MPI_Comm 3278 3279 Input Parameters: 3280 + comm - MPI communicator 3281 . A - "diagonal" portion of matrix 3282 . B - "off-diagonal" portion of matrix, may have empty columns, will be destroyed by this routine 3283 - garray - global index of B columns 3284 3285 Output Parameter: 3286 . mat - the matrix, with input A as its local diagonal matrix 3287 Level: advanced 3288 3289 Notes: 3290 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3291 A becomes part of output mat, B is destroyed by this routine. The user cannot use A and B anymore. 3292 3293 .seealso: MatCreateMPIAIJWithSplitArrays() 3294 @*/ 3295 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3296 { 3297 PetscErrorCode ierr; 3298 Mat_MPIAIJ *maij; 3299 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data,*bnew; 3300 PetscInt *oi=b->i,*oj=b->j,i,nz,col; 3301 PetscScalar *oa=b->a; 3302 Mat Bnew; 3303 PetscInt m,n,N; 3304 3305 PetscFunctionBegin; 3306 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3307 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3308 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %D != Bm %D",m,B->rmap->N); 3309 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); 3310 /* remove check below; When B is created using iscol_o from ISGetSeqIS_SameColDist_Private(), its bs may not be same as A */ 3311 /* 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); */ 3312 3313 /* Get global columns of mat */ 3314 ierr = MPIU_Allreduce(&n,&N,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3315 3316 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3317 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3318 ierr = MatSetBlockSizes(*mat,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 3319 maij = (Mat_MPIAIJ*)(*mat)->data; 3320 3321 (*mat)->preallocated = PETSC_TRUE; 3322 3323 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3324 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3325 3326 /* Set A as diagonal portion of *mat */ 3327 maij->A = A; 3328 3329 nz = oi[m]; 3330 for (i=0; i<nz; i++) { 3331 col = oj[i]; 3332 oj[i] = garray[col]; 3333 } 3334 3335 /* Set Bnew as off-diagonal portion of *mat */ 3336 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Bnew);CHKERRQ(ierr); 3337 bnew = (Mat_SeqAIJ*)Bnew->data; 3338 bnew->maxnz = b->maxnz; /* allocated nonzeros of B */ 3339 maij->B = Bnew; 3340 3341 if (B->rmap->N != Bnew->rmap->N) SETERRQ2(PETSC_COMM_SELF,0,"BN %d != BnewN %d",B->rmap->N,Bnew->rmap->N); 3342 3343 b->singlemalloc = PETSC_FALSE; /* B arrays are shared by Bnew */ 3344 b->free_a = PETSC_FALSE; 3345 b->free_ij = PETSC_FALSE; 3346 ierr = MatDestroy(&B);CHKERRQ(ierr); 3347 3348 bnew->singlemalloc = PETSC_TRUE; /* arrays will be freed by MatDestroy(&Bnew) */ 3349 bnew->free_a = PETSC_TRUE; 3350 bnew->free_ij = PETSC_TRUE; 3351 3352 /* condense columns of maij->B */ 3353 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3354 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3355 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3356 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3357 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3358 PetscFunctionReturn(0); 3359 } 3360 3361 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3362 3363 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3364 { 3365 PetscErrorCode ierr; 3366 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3367 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3368 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3369 Mat M,Msub,B=a->B; 3370 MatScalar *aa; 3371 Mat_SeqAIJ *aij; 3372 PetscInt *garray = a->garray,*colsub,Ncols; 3373 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3374 IS iscol_sub,iscmap; 3375 const PetscInt *is_idx,*cmap; 3376 PetscBool allcolumns=PETSC_FALSE; 3377 IS iscol_local=NULL; 3378 MPI_Comm comm; 3379 3380 PetscFunctionBegin; 3381 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3382 3383 if (call == MAT_REUSE_MATRIX) { 3384 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3385 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3386 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3387 3388 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3389 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3390 3391 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3392 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3393 3394 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3395 3396 } else { /* call == MAT_INITIAL_MATRIX) */ 3397 PetscBool flg; 3398 3399 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3400 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3401 3402 /* (1) iscol -> nonscalable iscol_local */ 3403 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3404 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3405 if (n != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != Ncols %d",n,Ncols); 3406 3407 /* Check for special case: each processor gets entire matrix columns */ 3408 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3409 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3410 if (allcolumns) { 3411 iscol_sub = iscol_local; 3412 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3413 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3414 3415 } else { 3416 /* (2) iscol_local -> iscol_sub and iscmap */ 3417 PetscInt *idx,*cmap1,k; 3418 3419 /* implementation below requires iscol_local be sorted, it can have duplicate indices */ 3420 ierr = ISSorted(iscol_local,&flg);CHKERRQ(ierr); 3421 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsorted iscol_local is not implemented yet"); 3422 3423 ierr = PetscMalloc1(Ncols,&idx);CHKERRQ(ierr); 3424 ierr = PetscMalloc1(Ncols,&cmap1);CHKERRQ(ierr); 3425 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3426 count = 0; 3427 k = 0; 3428 for (i=0; i<Ncols; i++) { 3429 j = is_idx[i]; 3430 if (j >= cstart && j < cend) { 3431 /* diagonal part of mat */ 3432 idx[count] = j; 3433 cmap1[count++] = i; /* column index in submat */ 3434 } else if (Bn) { 3435 /* off-diagonal part of mat */ 3436 if (j == garray[k]) { 3437 idx[count] = j; 3438 cmap1[count++] = i; /* column index in submat */ 3439 } else if (j > garray[k]) { 3440 while (j > garray[k] && k < Bn-1) k++; 3441 if (j == garray[k]) { 3442 idx[count] = j; 3443 cmap1[count++] = i; /* column index in submat */ 3444 } 3445 } 3446 } 3447 } 3448 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3449 3450 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_OWN_POINTER,&iscol_sub);CHKERRQ(ierr); 3451 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3452 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3453 3454 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_OWN_POINTER,&iscmap);CHKERRQ(ierr); 3455 } 3456 3457 /* (3) Create sequential Msub */ 3458 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3459 } 3460 3461 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3462 aij = (Mat_SeqAIJ*)(Msub)->data; 3463 ii = aij->i; 3464 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3465 3466 /* 3467 m - number of local rows 3468 Ncols - number of columns (same on all processors) 3469 rstart - first row in new global matrix generated 3470 */ 3471 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3472 3473 if (call == MAT_INITIAL_MATRIX) { 3474 /* (4) Create parallel newmat */ 3475 PetscMPIInt rank,size; 3476 PetscInt csize; 3477 3478 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3479 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3480 3481 /* 3482 Determine the number of non-zeros in the diagonal and off-diagonal 3483 portions of the matrix in order to do correct preallocation 3484 */ 3485 3486 /* first get start and end of "diagonal" columns */ 3487 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3488 if (csize == PETSC_DECIDE) { 3489 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3490 if (mglobal == Ncols) { /* square matrix */ 3491 nlocal = m; 3492 } else { 3493 nlocal = Ncols/size + ((Ncols % size) > rank); 3494 } 3495 } else { 3496 nlocal = csize; 3497 } 3498 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3499 rstart = rend - nlocal; 3500 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); 3501 3502 /* next, compute all the lengths */ 3503 jj = aij->j; 3504 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3505 olens = dlens + m; 3506 for (i=0; i<m; i++) { 3507 jend = ii[i+1] - ii[i]; 3508 olen = 0; 3509 dlen = 0; 3510 for (j=0; j<jend; j++) { 3511 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3512 else dlen++; 3513 jj++; 3514 } 3515 olens[i] = olen; 3516 dlens[i] = dlen; 3517 } 3518 3519 ierr = ISGetBlockSize(isrow,&bs);CHKERRQ(ierr); 3520 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3521 3522 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3523 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr); 3524 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3525 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3526 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3527 ierr = PetscFree(dlens);CHKERRQ(ierr); 3528 3529 } else { /* call == MAT_REUSE_MATRIX */ 3530 M = *newmat; 3531 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3532 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3533 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3534 /* 3535 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3536 rather than the slower MatSetValues(). 3537 */ 3538 M->was_assembled = PETSC_TRUE; 3539 M->assembled = PETSC_FALSE; 3540 } 3541 3542 /* (5) Set values of Msub to *newmat */ 3543 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3544 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3545 3546 jj = aij->j; 3547 aa = aij->a; 3548 for (i=0; i<m; i++) { 3549 row = rstart + i; 3550 nz = ii[i+1] - ii[i]; 3551 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3552 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3553 jj += nz; aa += nz; 3554 } 3555 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3556 3557 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3558 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3559 3560 ierr = PetscFree(colsub);CHKERRQ(ierr); 3561 3562 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3563 if (call == MAT_INITIAL_MATRIX) { 3564 *newmat = M; 3565 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3566 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3567 3568 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3569 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3570 3571 ierr = PetscObjectCompose((PetscObject)(*newmat),"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3572 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3573 3574 if (iscol_local) { 3575 ierr = PetscObjectCompose((PetscObject)(*newmat),"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3576 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3577 } 3578 } 3579 PetscFunctionReturn(0); 3580 } 3581 3582 /* 3583 Not great since it makes two copies of the submatrix, first an SeqAIJ 3584 in local and then by concatenating the local matrices the end result. 3585 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3586 3587 Note: This requires a sequential iscol with all indices. 3588 */ 3589 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3590 { 3591 PetscErrorCode ierr; 3592 PetscMPIInt rank,size; 3593 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3594 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3595 Mat M,Mreuse; 3596 MatScalar *aa,*vwork; 3597 MPI_Comm comm; 3598 Mat_SeqAIJ *aij; 3599 PetscBool colflag,allcolumns=PETSC_FALSE; 3600 3601 PetscFunctionBegin; 3602 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3603 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3604 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3605 3606 /* Check for special case: each processor gets entire matrix columns */ 3607 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3608 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3609 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3610 3611 if (call == MAT_REUSE_MATRIX) { 3612 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3613 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3614 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3615 } else { 3616 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3617 } 3618 3619 /* 3620 m - number of local rows 3621 n - number of columns (same on all processors) 3622 rstart - first row in new global matrix generated 3623 */ 3624 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3625 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3626 if (call == MAT_INITIAL_MATRIX) { 3627 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3628 ii = aij->i; 3629 jj = aij->j; 3630 3631 /* 3632 Determine the number of non-zeros in the diagonal and off-diagonal 3633 portions of the matrix in order to do correct preallocation 3634 */ 3635 3636 /* first get start and end of "diagonal" columns */ 3637 if (csize == PETSC_DECIDE) { 3638 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3639 if (mglobal == n) { /* square matrix */ 3640 nlocal = m; 3641 } else { 3642 nlocal = n/size + ((n % size) > rank); 3643 } 3644 } else { 3645 nlocal = csize; 3646 } 3647 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3648 rstart = rend - nlocal; 3649 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); 3650 3651 /* next, compute all the lengths */ 3652 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3653 olens = dlens + m; 3654 for (i=0; i<m; i++) { 3655 jend = ii[i+1] - ii[i]; 3656 olen = 0; 3657 dlen = 0; 3658 for (j=0; j<jend; j++) { 3659 if (*jj < rstart || *jj >= rend) olen++; 3660 else dlen++; 3661 jj++; 3662 } 3663 olens[i] = olen; 3664 dlens[i] = dlen; 3665 } 3666 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3667 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3668 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3669 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3670 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3671 ierr = PetscFree(dlens);CHKERRQ(ierr); 3672 } else { 3673 PetscInt ml,nl; 3674 3675 M = *newmat; 3676 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3677 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3678 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3679 /* 3680 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3681 rather than the slower MatSetValues(). 3682 */ 3683 M->was_assembled = PETSC_TRUE; 3684 M->assembled = PETSC_FALSE; 3685 } 3686 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3687 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3688 ii = aij->i; 3689 jj = aij->j; 3690 aa = aij->a; 3691 for (i=0; i<m; i++) { 3692 row = rstart + i; 3693 nz = ii[i+1] - ii[i]; 3694 cwork = jj; jj += nz; 3695 vwork = aa; aa += nz; 3696 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3697 } 3698 3699 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3700 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3701 *newmat = M; 3702 3703 /* save submatrix used in processor for next request */ 3704 if (call == MAT_INITIAL_MATRIX) { 3705 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3706 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3707 } 3708 PetscFunctionReturn(0); 3709 } 3710 3711 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3712 { 3713 PetscInt m,cstart, cend,j,nnz,i,d; 3714 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3715 const PetscInt *JJ; 3716 PetscScalar *values; 3717 PetscErrorCode ierr; 3718 PetscBool nooffprocentries; 3719 3720 PetscFunctionBegin; 3721 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3722 3723 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3724 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3725 m = B->rmap->n; 3726 cstart = B->cmap->rstart; 3727 cend = B->cmap->rend; 3728 rstart = B->rmap->rstart; 3729 3730 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3731 3732 #if defined(PETSC_USE_DEBUGGING) 3733 for (i=0; i<m; i++) { 3734 nnz = Ii[i+1]- Ii[i]; 3735 JJ = J + Ii[i]; 3736 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3737 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3738 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); 3739 } 3740 #endif 3741 3742 for (i=0; i<m; i++) { 3743 nnz = Ii[i+1]- Ii[i]; 3744 JJ = J + Ii[i]; 3745 nnz_max = PetscMax(nnz_max,nnz); 3746 d = 0; 3747 for (j=0; j<nnz; j++) { 3748 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3749 } 3750 d_nnz[i] = d; 3751 o_nnz[i] = nnz - d; 3752 } 3753 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3754 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3755 3756 if (v) values = (PetscScalar*)v; 3757 else { 3758 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3759 } 3760 3761 for (i=0; i<m; i++) { 3762 ii = i + rstart; 3763 nnz = Ii[i+1]- Ii[i]; 3764 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3765 } 3766 nooffprocentries = B->nooffprocentries; 3767 B->nooffprocentries = PETSC_TRUE; 3768 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3769 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3770 B->nooffprocentries = nooffprocentries; 3771 3772 if (!v) { 3773 ierr = PetscFree(values);CHKERRQ(ierr); 3774 } 3775 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3776 PetscFunctionReturn(0); 3777 } 3778 3779 /*@ 3780 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3781 (the default parallel PETSc format). 3782 3783 Collective on MPI_Comm 3784 3785 Input Parameters: 3786 + B - the matrix 3787 . i - the indices into j for the start of each local row (starts with zero) 3788 . j - the column indices for each local row (starts with zero) 3789 - v - optional values in the matrix 3790 3791 Level: developer 3792 3793 Notes: 3794 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3795 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3796 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3797 3798 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3799 3800 The format which is used for the sparse matrix input, is equivalent to a 3801 row-major ordering.. i.e for the following matrix, the input data expected is 3802 as shown 3803 3804 $ 1 0 0 3805 $ 2 0 3 P0 3806 $ ------- 3807 $ 4 5 6 P1 3808 $ 3809 $ Process0 [P0]: rows_owned=[0,1] 3810 $ i = {0,1,3} [size = nrow+1 = 2+1] 3811 $ j = {0,0,2} [size = 3] 3812 $ v = {1,2,3} [size = 3] 3813 $ 3814 $ Process1 [P1]: rows_owned=[2] 3815 $ i = {0,3} [size = nrow+1 = 1+1] 3816 $ j = {0,1,2} [size = 3] 3817 $ v = {4,5,6} [size = 3] 3818 3819 .keywords: matrix, aij, compressed row, sparse, parallel 3820 3821 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3822 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3823 @*/ 3824 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3825 { 3826 PetscErrorCode ierr; 3827 3828 PetscFunctionBegin; 3829 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3830 PetscFunctionReturn(0); 3831 } 3832 3833 /*@C 3834 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3835 (the default parallel PETSc format). For good matrix assembly performance 3836 the user should preallocate the matrix storage by setting the parameters 3837 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3838 performance can be increased by more than a factor of 50. 3839 3840 Collective on MPI_Comm 3841 3842 Input Parameters: 3843 + B - the matrix 3844 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3845 (same value is used for all local rows) 3846 . d_nnz - array containing the number of nonzeros in the various rows of the 3847 DIAGONAL portion of the local submatrix (possibly different for each row) 3848 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3849 The size of this array is equal to the number of local rows, i.e 'm'. 3850 For matrices that will be factored, you must leave room for (and set) 3851 the diagonal entry even if it is zero. 3852 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3853 submatrix (same value is used for all local rows). 3854 - o_nnz - array containing the number of nonzeros in the various rows of the 3855 OFF-DIAGONAL portion of the local submatrix (possibly different for 3856 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3857 structure. The size of this array is equal to the number 3858 of local rows, i.e 'm'. 3859 3860 If the *_nnz parameter is given then the *_nz parameter is ignored 3861 3862 The AIJ format (also called the Yale sparse matrix format or 3863 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3864 storage. The stored row and column indices begin with zero. 3865 See Users-Manual: ch_mat for details. 3866 3867 The parallel matrix is partitioned such that the first m0 rows belong to 3868 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3869 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3870 3871 The DIAGONAL portion of the local submatrix of a processor can be defined 3872 as the submatrix which is obtained by extraction the part corresponding to 3873 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3874 first row that belongs to the processor, r2 is the last row belonging to 3875 the this processor, and c1-c2 is range of indices of the local part of a 3876 vector suitable for applying the matrix to. This is an mxn matrix. In the 3877 common case of a square matrix, the row and column ranges are the same and 3878 the DIAGONAL part is also square. The remaining portion of the local 3879 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3880 3881 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3882 3883 You can call MatGetInfo() to get information on how effective the preallocation was; 3884 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3885 You can also run with the option -info and look for messages with the string 3886 malloc in them to see if additional memory allocation was needed. 3887 3888 Example usage: 3889 3890 Consider the following 8x8 matrix with 34 non-zero values, that is 3891 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3892 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3893 as follows: 3894 3895 .vb 3896 1 2 0 | 0 3 0 | 0 4 3897 Proc0 0 5 6 | 7 0 0 | 8 0 3898 9 0 10 | 11 0 0 | 12 0 3899 ------------------------------------- 3900 13 0 14 | 15 16 17 | 0 0 3901 Proc1 0 18 0 | 19 20 21 | 0 0 3902 0 0 0 | 22 23 0 | 24 0 3903 ------------------------------------- 3904 Proc2 25 26 27 | 0 0 28 | 29 0 3905 30 0 0 | 31 32 33 | 0 34 3906 .ve 3907 3908 This can be represented as a collection of submatrices as: 3909 3910 .vb 3911 A B C 3912 D E F 3913 G H I 3914 .ve 3915 3916 Where the submatrices A,B,C are owned by proc0, D,E,F are 3917 owned by proc1, G,H,I are owned by proc2. 3918 3919 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3920 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3921 The 'M','N' parameters are 8,8, and have the same values on all procs. 3922 3923 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3924 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3925 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3926 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3927 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3928 matrix, ans [DF] as another SeqAIJ matrix. 3929 3930 When d_nz, o_nz parameters are specified, d_nz storage elements are 3931 allocated for every row of the local diagonal submatrix, and o_nz 3932 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3933 One way to choose d_nz and o_nz is to use the max nonzerors per local 3934 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3935 In this case, the values of d_nz,o_nz are: 3936 .vb 3937 proc0 : dnz = 2, o_nz = 2 3938 proc1 : dnz = 3, o_nz = 2 3939 proc2 : dnz = 1, o_nz = 4 3940 .ve 3941 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3942 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3943 for proc3. i.e we are using 12+15+10=37 storage locations to store 3944 34 values. 3945 3946 When d_nnz, o_nnz parameters are specified, the storage is specified 3947 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3948 In the above case the values for d_nnz,o_nnz are: 3949 .vb 3950 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3951 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3952 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3953 .ve 3954 Here the space allocated is sum of all the above values i.e 34, and 3955 hence pre-allocation is perfect. 3956 3957 Level: intermediate 3958 3959 .keywords: matrix, aij, compressed row, sparse, parallel 3960 3961 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 3962 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 3963 @*/ 3964 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3965 { 3966 PetscErrorCode ierr; 3967 3968 PetscFunctionBegin; 3969 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3970 PetscValidType(B,1); 3971 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 3972 PetscFunctionReturn(0); 3973 } 3974 3975 /*@ 3976 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 3977 CSR format the local rows. 3978 3979 Collective on MPI_Comm 3980 3981 Input Parameters: 3982 + comm - MPI communicator 3983 . m - number of local rows (Cannot be PETSC_DECIDE) 3984 . n - This value should be the same as the local size used in creating the 3985 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3986 calculated if N is given) For square matrices n is almost always m. 3987 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3988 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3989 . i - row indices 3990 . j - column indices 3991 - a - matrix values 3992 3993 Output Parameter: 3994 . mat - the matrix 3995 3996 Level: intermediate 3997 3998 Notes: 3999 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 4000 thus you CANNOT change the matrix entries by changing the values of a[] after you have 4001 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 4002 4003 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4004 4005 The format which is used for the sparse matrix input, is equivalent to a 4006 row-major ordering.. i.e for the following matrix, the input data expected is 4007 as shown 4008 4009 $ 1 0 0 4010 $ 2 0 3 P0 4011 $ ------- 4012 $ 4 5 6 P1 4013 $ 4014 $ Process0 [P0]: rows_owned=[0,1] 4015 $ i = {0,1,3} [size = nrow+1 = 2+1] 4016 $ j = {0,0,2} [size = 3] 4017 $ v = {1,2,3} [size = 3] 4018 $ 4019 $ Process1 [P1]: rows_owned=[2] 4020 $ i = {0,3} [size = nrow+1 = 1+1] 4021 $ j = {0,1,2} [size = 3] 4022 $ v = {4,5,6} [size = 3] 4023 4024 .keywords: matrix, aij, compressed row, sparse, parallel 4025 4026 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4027 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4028 @*/ 4029 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 4030 { 4031 PetscErrorCode ierr; 4032 4033 PetscFunctionBegin; 4034 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4035 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4036 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4037 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4038 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 4039 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 4040 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 4041 PetscFunctionReturn(0); 4042 } 4043 4044 /*@C 4045 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 4046 (the default parallel PETSc format). For good matrix assembly performance 4047 the user should preallocate the matrix storage by setting the parameters 4048 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4049 performance can be increased by more than a factor of 50. 4050 4051 Collective on MPI_Comm 4052 4053 Input Parameters: 4054 + comm - MPI communicator 4055 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 4056 This value should be the same as the local size used in creating the 4057 y vector for the matrix-vector product y = Ax. 4058 . n - This value should be the same as the local size used in creating the 4059 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4060 calculated if N is given) For square matrices n is almost always m. 4061 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4062 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4063 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4064 (same value is used for all local rows) 4065 . d_nnz - array containing the number of nonzeros in the various rows of the 4066 DIAGONAL portion of the local submatrix (possibly different for each row) 4067 or NULL, if d_nz is used to specify the nonzero structure. 4068 The size of this array is equal to the number of local rows, i.e 'm'. 4069 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4070 submatrix (same value is used for all local rows). 4071 - o_nnz - array containing the number of nonzeros in the various rows of the 4072 OFF-DIAGONAL portion of the local submatrix (possibly different for 4073 each row) or NULL, if o_nz is used to specify the nonzero 4074 structure. The size of this array is equal to the number 4075 of local rows, i.e 'm'. 4076 4077 Output Parameter: 4078 . A - the matrix 4079 4080 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4081 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4082 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4083 4084 Notes: 4085 If the *_nnz parameter is given then the *_nz parameter is ignored 4086 4087 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4088 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4089 storage requirements for this matrix. 4090 4091 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4092 processor than it must be used on all processors that share the object for 4093 that argument. 4094 4095 The user MUST specify either the local or global matrix dimensions 4096 (possibly both). 4097 4098 The parallel matrix is partitioned across processors such that the 4099 first m0 rows belong to process 0, the next m1 rows belong to 4100 process 1, the next m2 rows belong to process 2 etc.. where 4101 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4102 values corresponding to [m x N] submatrix. 4103 4104 The columns are logically partitioned with the n0 columns belonging 4105 to 0th partition, the next n1 columns belonging to the next 4106 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4107 4108 The DIAGONAL portion of the local submatrix on any given processor 4109 is the submatrix corresponding to the rows and columns m,n 4110 corresponding to the given processor. i.e diagonal matrix on 4111 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4112 etc. The remaining portion of the local submatrix [m x (N-n)] 4113 constitute the OFF-DIAGONAL portion. The example below better 4114 illustrates this concept. 4115 4116 For a square global matrix we define each processor's diagonal portion 4117 to be its local rows and the corresponding columns (a square submatrix); 4118 each processor's off-diagonal portion encompasses the remainder of the 4119 local matrix (a rectangular submatrix). 4120 4121 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4122 4123 When calling this routine with a single process communicator, a matrix of 4124 type SEQAIJ is returned. If a matrix of type MPIAIJ is desired for this 4125 type of communicator, use the construction mechanism 4126 .vb 4127 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4128 .ve 4129 4130 By default, this format uses inodes (identical nodes) when possible. 4131 We search for consecutive rows with the same nonzero structure, thereby 4132 reusing matrix information to achieve increased efficiency. 4133 4134 Options Database Keys: 4135 + -mat_no_inode - Do not use inodes 4136 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4137 - -mat_aij_oneindex - Internally use indexing starting at 1 4138 rather than 0. Note that when calling MatSetValues(), 4139 the user still MUST index entries starting at 0! 4140 4141 4142 Example usage: 4143 4144 Consider the following 8x8 matrix with 34 non-zero values, that is 4145 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4146 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4147 as follows 4148 4149 .vb 4150 1 2 0 | 0 3 0 | 0 4 4151 Proc0 0 5 6 | 7 0 0 | 8 0 4152 9 0 10 | 11 0 0 | 12 0 4153 ------------------------------------- 4154 13 0 14 | 15 16 17 | 0 0 4155 Proc1 0 18 0 | 19 20 21 | 0 0 4156 0 0 0 | 22 23 0 | 24 0 4157 ------------------------------------- 4158 Proc2 25 26 27 | 0 0 28 | 29 0 4159 30 0 0 | 31 32 33 | 0 34 4160 .ve 4161 4162 This can be represented as a collection of submatrices as 4163 4164 .vb 4165 A B C 4166 D E F 4167 G H I 4168 .ve 4169 4170 Where the submatrices A,B,C are owned by proc0, D,E,F are 4171 owned by proc1, G,H,I are owned by proc2. 4172 4173 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4174 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4175 The 'M','N' parameters are 8,8, and have the same values on all procs. 4176 4177 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4178 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4179 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4180 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4181 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4182 matrix, ans [DF] as another SeqAIJ matrix. 4183 4184 When d_nz, o_nz parameters are specified, d_nz storage elements are 4185 allocated for every row of the local diagonal submatrix, and o_nz 4186 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4187 One way to choose d_nz and o_nz is to use the max nonzerors per local 4188 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4189 In this case, the values of d_nz,o_nz are 4190 .vb 4191 proc0 : dnz = 2, o_nz = 2 4192 proc1 : dnz = 3, o_nz = 2 4193 proc2 : dnz = 1, o_nz = 4 4194 .ve 4195 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4196 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4197 for proc3. i.e we are using 12+15+10=37 storage locations to store 4198 34 values. 4199 4200 When d_nnz, o_nnz parameters are specified, the storage is specified 4201 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4202 In the above case the values for d_nnz,o_nnz are 4203 .vb 4204 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4205 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4206 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4207 .ve 4208 Here the space allocated is sum of all the above values i.e 34, and 4209 hence pre-allocation is perfect. 4210 4211 Level: intermediate 4212 4213 .keywords: matrix, aij, compressed row, sparse, parallel 4214 4215 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4216 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4217 @*/ 4218 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) 4219 { 4220 PetscErrorCode ierr; 4221 PetscMPIInt size; 4222 4223 PetscFunctionBegin; 4224 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4225 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4226 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4227 if (size > 1) { 4228 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4229 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4230 } else { 4231 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4232 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4233 } 4234 PetscFunctionReturn(0); 4235 } 4236 4237 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4238 { 4239 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4240 PetscBool flg; 4241 PetscErrorCode ierr; 4242 4243 PetscFunctionBegin; 4244 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4245 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4246 if (Ad) *Ad = a->A; 4247 if (Ao) *Ao = a->B; 4248 if (colmap) *colmap = a->garray; 4249 PetscFunctionReturn(0); 4250 } 4251 4252 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4253 { 4254 PetscErrorCode ierr; 4255 PetscInt m,N,i,rstart,nnz,Ii; 4256 PetscInt *indx; 4257 PetscScalar *values; 4258 4259 PetscFunctionBegin; 4260 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4261 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4262 PetscInt *dnz,*onz,sum,bs,cbs; 4263 4264 if (n == PETSC_DECIDE) { 4265 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4266 } 4267 /* Check sum(n) = N */ 4268 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4269 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 4270 4271 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4272 rstart -= m; 4273 4274 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4275 for (i=0; i<m; i++) { 4276 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4277 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4278 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4279 } 4280 4281 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4282 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4283 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4284 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4285 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4286 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4287 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4288 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4289 } 4290 4291 /* numeric phase */ 4292 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4293 for (i=0; i<m; i++) { 4294 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4295 Ii = i + rstart; 4296 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4297 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4298 } 4299 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4300 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4301 PetscFunctionReturn(0); 4302 } 4303 4304 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4305 { 4306 PetscErrorCode ierr; 4307 PetscMPIInt rank; 4308 PetscInt m,N,i,rstart,nnz; 4309 size_t len; 4310 const PetscInt *indx; 4311 PetscViewer out; 4312 char *name; 4313 Mat B; 4314 const PetscScalar *values; 4315 4316 PetscFunctionBegin; 4317 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4318 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4319 /* Should this be the type of the diagonal block of A? */ 4320 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4321 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4322 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4323 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4324 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4325 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4326 for (i=0; i<m; i++) { 4327 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4328 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4329 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4330 } 4331 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4332 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4333 4334 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4335 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4336 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4337 sprintf(name,"%s.%d",outfile,rank); 4338 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4339 ierr = PetscFree(name);CHKERRQ(ierr); 4340 ierr = MatView(B,out);CHKERRQ(ierr); 4341 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4342 ierr = MatDestroy(&B);CHKERRQ(ierr); 4343 PetscFunctionReturn(0); 4344 } 4345 4346 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4347 { 4348 PetscErrorCode ierr; 4349 Mat_Merge_SeqsToMPI *merge; 4350 PetscContainer container; 4351 4352 PetscFunctionBegin; 4353 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4354 if (container) { 4355 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4356 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4357 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4358 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4359 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4360 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4361 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4362 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4363 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4364 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4365 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4366 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4367 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4368 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4369 ierr = PetscFree(merge);CHKERRQ(ierr); 4370 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4371 } 4372 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4373 PetscFunctionReturn(0); 4374 } 4375 4376 #include <../src/mat/utils/freespace.h> 4377 #include <petscbt.h> 4378 4379 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4380 { 4381 PetscErrorCode ierr; 4382 MPI_Comm comm; 4383 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4384 PetscMPIInt size,rank,taga,*len_s; 4385 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4386 PetscInt proc,m; 4387 PetscInt **buf_ri,**buf_rj; 4388 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4389 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4390 MPI_Request *s_waits,*r_waits; 4391 MPI_Status *status; 4392 MatScalar *aa=a->a; 4393 MatScalar **abuf_r,*ba_i; 4394 Mat_Merge_SeqsToMPI *merge; 4395 PetscContainer container; 4396 4397 PetscFunctionBegin; 4398 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4399 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4400 4401 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4402 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4403 4404 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4405 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4406 4407 bi = merge->bi; 4408 bj = merge->bj; 4409 buf_ri = merge->buf_ri; 4410 buf_rj = merge->buf_rj; 4411 4412 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4413 owners = merge->rowmap->range; 4414 len_s = merge->len_s; 4415 4416 /* send and recv matrix values */ 4417 /*-----------------------------*/ 4418 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4419 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4420 4421 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4422 for (proc=0,k=0; proc<size; proc++) { 4423 if (!len_s[proc]) continue; 4424 i = owners[proc]; 4425 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4426 k++; 4427 } 4428 4429 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4430 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4431 ierr = PetscFree(status);CHKERRQ(ierr); 4432 4433 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4434 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4435 4436 /* insert mat values of mpimat */ 4437 /*----------------------------*/ 4438 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4439 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4440 4441 for (k=0; k<merge->nrecv; k++) { 4442 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4443 nrows = *(buf_ri_k[k]); 4444 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4445 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4446 } 4447 4448 /* set values of ba */ 4449 m = merge->rowmap->n; 4450 for (i=0; i<m; i++) { 4451 arow = owners[rank] + i; 4452 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4453 bnzi = bi[i+1] - bi[i]; 4454 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4455 4456 /* add local non-zero vals of this proc's seqmat into ba */ 4457 anzi = ai[arow+1] - ai[arow]; 4458 aj = a->j + ai[arow]; 4459 aa = a->a + ai[arow]; 4460 nextaj = 0; 4461 for (j=0; nextaj<anzi; j++) { 4462 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4463 ba_i[j] += aa[nextaj++]; 4464 } 4465 } 4466 4467 /* add received vals into ba */ 4468 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4469 /* i-th row */ 4470 if (i == *nextrow[k]) { 4471 anzi = *(nextai[k]+1) - *nextai[k]; 4472 aj = buf_rj[k] + *(nextai[k]); 4473 aa = abuf_r[k] + *(nextai[k]); 4474 nextaj = 0; 4475 for (j=0; nextaj<anzi; j++) { 4476 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4477 ba_i[j] += aa[nextaj++]; 4478 } 4479 } 4480 nextrow[k]++; nextai[k]++; 4481 } 4482 } 4483 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4484 } 4485 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4486 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4487 4488 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4489 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4490 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4491 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4492 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4493 PetscFunctionReturn(0); 4494 } 4495 4496 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4497 { 4498 PetscErrorCode ierr; 4499 Mat B_mpi; 4500 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4501 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4502 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4503 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4504 PetscInt len,proc,*dnz,*onz,bs,cbs; 4505 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4506 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4507 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4508 MPI_Status *status; 4509 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4510 PetscBT lnkbt; 4511 Mat_Merge_SeqsToMPI *merge; 4512 PetscContainer container; 4513 4514 PetscFunctionBegin; 4515 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4516 4517 /* make sure it is a PETSc comm */ 4518 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4519 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4520 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4521 4522 ierr = PetscNew(&merge);CHKERRQ(ierr); 4523 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4524 4525 /* determine row ownership */ 4526 /*---------------------------------------------------------*/ 4527 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4528 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4529 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4530 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4531 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4532 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4533 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4534 4535 m = merge->rowmap->n; 4536 owners = merge->rowmap->range; 4537 4538 /* determine the number of messages to send, their lengths */ 4539 /*---------------------------------------------------------*/ 4540 len_s = merge->len_s; 4541 4542 len = 0; /* length of buf_si[] */ 4543 merge->nsend = 0; 4544 for (proc=0; proc<size; proc++) { 4545 len_si[proc] = 0; 4546 if (proc == rank) { 4547 len_s[proc] = 0; 4548 } else { 4549 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4550 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4551 } 4552 if (len_s[proc]) { 4553 merge->nsend++; 4554 nrows = 0; 4555 for (i=owners[proc]; i<owners[proc+1]; i++) { 4556 if (ai[i+1] > ai[i]) nrows++; 4557 } 4558 len_si[proc] = 2*(nrows+1); 4559 len += len_si[proc]; 4560 } 4561 } 4562 4563 /* determine the number and length of messages to receive for ij-structure */ 4564 /*-------------------------------------------------------------------------*/ 4565 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4566 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4567 4568 /* post the Irecv of j-structure */ 4569 /*-------------------------------*/ 4570 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4571 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4572 4573 /* post the Isend of j-structure */ 4574 /*--------------------------------*/ 4575 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4576 4577 for (proc=0, k=0; proc<size; proc++) { 4578 if (!len_s[proc]) continue; 4579 i = owners[proc]; 4580 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4581 k++; 4582 } 4583 4584 /* receives and sends of j-structure are complete */ 4585 /*------------------------------------------------*/ 4586 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4587 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4588 4589 /* send and recv i-structure */ 4590 /*---------------------------*/ 4591 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4592 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4593 4594 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4595 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4596 for (proc=0,k=0; proc<size; proc++) { 4597 if (!len_s[proc]) continue; 4598 /* form outgoing message for i-structure: 4599 buf_si[0]: nrows to be sent 4600 [1:nrows]: row index (global) 4601 [nrows+1:2*nrows+1]: i-structure index 4602 */ 4603 /*-------------------------------------------*/ 4604 nrows = len_si[proc]/2 - 1; 4605 buf_si_i = buf_si + nrows+1; 4606 buf_si[0] = nrows; 4607 buf_si_i[0] = 0; 4608 nrows = 0; 4609 for (i=owners[proc]; i<owners[proc+1]; i++) { 4610 anzi = ai[i+1] - ai[i]; 4611 if (anzi) { 4612 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4613 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4614 nrows++; 4615 } 4616 } 4617 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4618 k++; 4619 buf_si += len_si[proc]; 4620 } 4621 4622 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4623 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4624 4625 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4626 for (i=0; i<merge->nrecv; i++) { 4627 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); 4628 } 4629 4630 ierr = PetscFree(len_si);CHKERRQ(ierr); 4631 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4632 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4633 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4634 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4635 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4636 ierr = PetscFree(status);CHKERRQ(ierr); 4637 4638 /* compute a local seq matrix in each processor */ 4639 /*----------------------------------------------*/ 4640 /* allocate bi array and free space for accumulating nonzero column info */ 4641 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4642 bi[0] = 0; 4643 4644 /* create and initialize a linked list */ 4645 nlnk = N+1; 4646 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4647 4648 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4649 len = ai[owners[rank+1]] - ai[owners[rank]]; 4650 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4651 4652 current_space = free_space; 4653 4654 /* determine symbolic info for each local row */ 4655 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4656 4657 for (k=0; k<merge->nrecv; k++) { 4658 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4659 nrows = *buf_ri_k[k]; 4660 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4661 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4662 } 4663 4664 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4665 len = 0; 4666 for (i=0; i<m; i++) { 4667 bnzi = 0; 4668 /* add local non-zero cols of this proc's seqmat into lnk */ 4669 arow = owners[rank] + i; 4670 anzi = ai[arow+1] - ai[arow]; 4671 aj = a->j + ai[arow]; 4672 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4673 bnzi += nlnk; 4674 /* add received col data into lnk */ 4675 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4676 if (i == *nextrow[k]) { /* i-th row */ 4677 anzi = *(nextai[k]+1) - *nextai[k]; 4678 aj = buf_rj[k] + *nextai[k]; 4679 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4680 bnzi += nlnk; 4681 nextrow[k]++; nextai[k]++; 4682 } 4683 } 4684 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4685 4686 /* if free space is not available, make more free space */ 4687 if (current_space->local_remaining<bnzi) { 4688 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4689 nspacedouble++; 4690 } 4691 /* copy data into free space, then initialize lnk */ 4692 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4693 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4694 4695 current_space->array += bnzi; 4696 current_space->local_used += bnzi; 4697 current_space->local_remaining -= bnzi; 4698 4699 bi[i+1] = bi[i] + bnzi; 4700 } 4701 4702 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4703 4704 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4705 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4706 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4707 4708 /* create symbolic parallel matrix B_mpi */ 4709 /*---------------------------------------*/ 4710 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4711 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4712 if (n==PETSC_DECIDE) { 4713 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4714 } else { 4715 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4716 } 4717 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4718 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4719 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4720 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4721 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4722 4723 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4724 B_mpi->assembled = PETSC_FALSE; 4725 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4726 merge->bi = bi; 4727 merge->bj = bj; 4728 merge->buf_ri = buf_ri; 4729 merge->buf_rj = buf_rj; 4730 merge->coi = NULL; 4731 merge->coj = NULL; 4732 merge->owners_co = NULL; 4733 4734 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4735 4736 /* attach the supporting struct to B_mpi for reuse */ 4737 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4738 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4739 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4740 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4741 *mpimat = B_mpi; 4742 4743 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4744 PetscFunctionReturn(0); 4745 } 4746 4747 /*@C 4748 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4749 matrices from each processor 4750 4751 Collective on MPI_Comm 4752 4753 Input Parameters: 4754 + comm - the communicators the parallel matrix will live on 4755 . seqmat - the input sequential matrices 4756 . m - number of local rows (or PETSC_DECIDE) 4757 . n - number of local columns (or PETSC_DECIDE) 4758 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4759 4760 Output Parameter: 4761 . mpimat - the parallel matrix generated 4762 4763 Level: advanced 4764 4765 Notes: 4766 The dimensions of the sequential matrix in each processor MUST be the same. 4767 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4768 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4769 @*/ 4770 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4771 { 4772 PetscErrorCode ierr; 4773 PetscMPIInt size; 4774 4775 PetscFunctionBegin; 4776 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4777 if (size == 1) { 4778 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4779 if (scall == MAT_INITIAL_MATRIX) { 4780 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4781 } else { 4782 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4783 } 4784 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4785 PetscFunctionReturn(0); 4786 } 4787 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4788 if (scall == MAT_INITIAL_MATRIX) { 4789 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4790 } 4791 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4792 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4793 PetscFunctionReturn(0); 4794 } 4795 4796 /*@ 4797 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 4798 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4799 with MatGetSize() 4800 4801 Not Collective 4802 4803 Input Parameters: 4804 + A - the matrix 4805 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4806 4807 Output Parameter: 4808 . A_loc - the local sequential matrix generated 4809 4810 Level: developer 4811 4812 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4813 4814 @*/ 4815 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4816 { 4817 PetscErrorCode ierr; 4818 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4819 Mat_SeqAIJ *mat,*a,*b; 4820 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4821 MatScalar *aa,*ba,*cam; 4822 PetscScalar *ca; 4823 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4824 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4825 PetscBool match; 4826 MPI_Comm comm; 4827 PetscMPIInt size; 4828 4829 PetscFunctionBegin; 4830 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4831 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4832 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4833 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4834 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4835 4836 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4837 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4838 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4839 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4840 aa = a->a; ba = b->a; 4841 if (scall == MAT_INITIAL_MATRIX) { 4842 if (size == 1) { 4843 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4844 PetscFunctionReturn(0); 4845 } 4846 4847 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4848 ci[0] = 0; 4849 for (i=0; i<am; i++) { 4850 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4851 } 4852 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4853 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4854 k = 0; 4855 for (i=0; i<am; i++) { 4856 ncols_o = bi[i+1] - bi[i]; 4857 ncols_d = ai[i+1] - ai[i]; 4858 /* off-diagonal portion of A */ 4859 for (jo=0; jo<ncols_o; jo++) { 4860 col = cmap[*bj]; 4861 if (col >= cstart) break; 4862 cj[k] = col; bj++; 4863 ca[k++] = *ba++; 4864 } 4865 /* diagonal portion of A */ 4866 for (j=0; j<ncols_d; j++) { 4867 cj[k] = cstart + *aj++; 4868 ca[k++] = *aa++; 4869 } 4870 /* off-diagonal portion of A */ 4871 for (j=jo; j<ncols_o; j++) { 4872 cj[k] = cmap[*bj++]; 4873 ca[k++] = *ba++; 4874 } 4875 } 4876 /* put together the new matrix */ 4877 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4878 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4879 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4880 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4881 mat->free_a = PETSC_TRUE; 4882 mat->free_ij = PETSC_TRUE; 4883 mat->nonew = 0; 4884 } else if (scall == MAT_REUSE_MATRIX) { 4885 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4886 ci = mat->i; cj = mat->j; cam = mat->a; 4887 for (i=0; i<am; i++) { 4888 /* off-diagonal portion of A */ 4889 ncols_o = bi[i+1] - bi[i]; 4890 for (jo=0; jo<ncols_o; jo++) { 4891 col = cmap[*bj]; 4892 if (col >= cstart) break; 4893 *cam++ = *ba++; bj++; 4894 } 4895 /* diagonal portion of A */ 4896 ncols_d = ai[i+1] - ai[i]; 4897 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4898 /* off-diagonal portion of A */ 4899 for (j=jo; j<ncols_o; j++) { 4900 *cam++ = *ba++; bj++; 4901 } 4902 } 4903 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4904 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4905 PetscFunctionReturn(0); 4906 } 4907 4908 /*@C 4909 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4910 4911 Not Collective 4912 4913 Input Parameters: 4914 + A - the matrix 4915 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4916 - row, col - index sets of rows and columns to extract (or NULL) 4917 4918 Output Parameter: 4919 . A_loc - the local sequential matrix generated 4920 4921 Level: developer 4922 4923 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4924 4925 @*/ 4926 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4927 { 4928 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4929 PetscErrorCode ierr; 4930 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4931 IS isrowa,iscola; 4932 Mat *aloc; 4933 PetscBool match; 4934 4935 PetscFunctionBegin; 4936 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4937 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4938 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4939 if (!row) { 4940 start = A->rmap->rstart; end = A->rmap->rend; 4941 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 4942 } else { 4943 isrowa = *row; 4944 } 4945 if (!col) { 4946 start = A->cmap->rstart; 4947 cmap = a->garray; 4948 nzA = a->A->cmap->n; 4949 nzB = a->B->cmap->n; 4950 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4951 ncols = 0; 4952 for (i=0; i<nzB; i++) { 4953 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4954 else break; 4955 } 4956 imark = i; 4957 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 4958 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 4959 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 4960 } else { 4961 iscola = *col; 4962 } 4963 if (scall != MAT_INITIAL_MATRIX) { 4964 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 4965 aloc[0] = *A_loc; 4966 } 4967 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 4968 *A_loc = aloc[0]; 4969 ierr = PetscFree(aloc);CHKERRQ(ierr); 4970 if (!row) { 4971 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 4972 } 4973 if (!col) { 4974 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 4975 } 4976 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4977 PetscFunctionReturn(0); 4978 } 4979 4980 /*@C 4981 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 4982 4983 Collective on Mat 4984 4985 Input Parameters: 4986 + A,B - the matrices in mpiaij format 4987 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4988 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 4989 4990 Output Parameter: 4991 + rowb, colb - index sets of rows and columns of B to extract 4992 - B_seq - the sequential matrix generated 4993 4994 Level: developer 4995 4996 @*/ 4997 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 4998 { 4999 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5000 PetscErrorCode ierr; 5001 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 5002 IS isrowb,iscolb; 5003 Mat *bseq=NULL; 5004 5005 PetscFunctionBegin; 5006 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5007 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); 5008 } 5009 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5010 5011 if (scall == MAT_INITIAL_MATRIX) { 5012 start = A->cmap->rstart; 5013 cmap = a->garray; 5014 nzA = a->A->cmap->n; 5015 nzB = a->B->cmap->n; 5016 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5017 ncols = 0; 5018 for (i=0; i<nzB; i++) { /* row < local row index */ 5019 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5020 else break; 5021 } 5022 imark = i; 5023 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 5024 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5025 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 5026 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 5027 } else { 5028 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5029 isrowb = *rowb; iscolb = *colb; 5030 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 5031 bseq[0] = *B_seq; 5032 } 5033 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 5034 *B_seq = bseq[0]; 5035 ierr = PetscFree(bseq);CHKERRQ(ierr); 5036 if (!rowb) { 5037 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 5038 } else { 5039 *rowb = isrowb; 5040 } 5041 if (!colb) { 5042 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 5043 } else { 5044 *colb = iscolb; 5045 } 5046 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5047 PetscFunctionReturn(0); 5048 } 5049 5050 /* 5051 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 5052 of the OFF-DIAGONAL portion of local A 5053 5054 Collective on Mat 5055 5056 Input Parameters: 5057 + A,B - the matrices in mpiaij format 5058 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5059 5060 Output Parameter: 5061 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5062 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5063 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5064 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5065 5066 Level: developer 5067 5068 */ 5069 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5070 { 5071 VecScatter_MPI_General *gen_to,*gen_from; 5072 PetscErrorCode ierr; 5073 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5074 Mat_SeqAIJ *b_oth; 5075 VecScatter ctx =a->Mvctx; 5076 MPI_Comm comm; 5077 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 5078 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5079 PetscInt *rvalues,*svalues; 5080 MatScalar *b_otha,*bufa,*bufA; 5081 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5082 MPI_Request *rwaits = NULL,*swaits = NULL; 5083 MPI_Status *sstatus,rstatus; 5084 PetscMPIInt jj,size; 5085 PetscInt *cols,sbs,rbs; 5086 PetscScalar *vals; 5087 5088 PetscFunctionBegin; 5089 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5090 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5091 5092 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5093 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); 5094 } 5095 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5096 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5097 5098 if (size == 1) { 5099 startsj_s = NULL; 5100 bufa_ptr = NULL; 5101 *B_oth = NULL; 5102 PetscFunctionReturn(0); 5103 } 5104 5105 gen_to = (VecScatter_MPI_General*)ctx->todata; 5106 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5107 nrecvs = gen_from->n; 5108 nsends = gen_to->n; 5109 5110 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 5111 srow = gen_to->indices; /* local row index to be sent */ 5112 sstarts = gen_to->starts; 5113 sprocs = gen_to->procs; 5114 sstatus = gen_to->sstatus; 5115 sbs = gen_to->bs; 5116 rstarts = gen_from->starts; 5117 rprocs = gen_from->procs; 5118 rbs = gen_from->bs; 5119 5120 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5121 if (scall == MAT_INITIAL_MATRIX) { 5122 /* i-array */ 5123 /*---------*/ 5124 /* post receives */ 5125 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 5126 for (i=0; i<nrecvs; i++) { 5127 rowlen = rvalues + rstarts[i]*rbs; 5128 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5129 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5130 } 5131 5132 /* pack the outgoing message */ 5133 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 5134 5135 sstartsj[0] = 0; 5136 rstartsj[0] = 0; 5137 len = 0; /* total length of j or a array to be sent */ 5138 k = 0; 5139 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 5140 for (i=0; i<nsends; i++) { 5141 rowlen = svalues + sstarts[i]*sbs; 5142 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5143 for (j=0; j<nrows; j++) { 5144 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5145 for (l=0; l<sbs; l++) { 5146 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5147 5148 rowlen[j*sbs+l] = ncols; 5149 5150 len += ncols; 5151 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5152 } 5153 k++; 5154 } 5155 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5156 5157 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5158 } 5159 /* recvs and sends of i-array are completed */ 5160 i = nrecvs; 5161 while (i--) { 5162 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5163 } 5164 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5165 ierr = PetscFree(svalues);CHKERRQ(ierr); 5166 5167 /* allocate buffers for sending j and a arrays */ 5168 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5169 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5170 5171 /* create i-array of B_oth */ 5172 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5173 5174 b_othi[0] = 0; 5175 len = 0; /* total length of j or a array to be received */ 5176 k = 0; 5177 for (i=0; i<nrecvs; i++) { 5178 rowlen = rvalues + rstarts[i]*rbs; 5179 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5180 for (j=0; j<nrows; j++) { 5181 b_othi[k+1] = b_othi[k] + rowlen[j]; 5182 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5183 k++; 5184 } 5185 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5186 } 5187 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5188 5189 /* allocate space for j and a arrrays of B_oth */ 5190 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5191 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5192 5193 /* j-array */ 5194 /*---------*/ 5195 /* post receives of j-array */ 5196 for (i=0; i<nrecvs; i++) { 5197 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5198 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5199 } 5200 5201 /* pack the outgoing message j-array */ 5202 k = 0; 5203 for (i=0; i<nsends; i++) { 5204 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5205 bufJ = bufj+sstartsj[i]; 5206 for (j=0; j<nrows; j++) { 5207 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5208 for (ll=0; ll<sbs; ll++) { 5209 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5210 for (l=0; l<ncols; l++) { 5211 *bufJ++ = cols[l]; 5212 } 5213 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5214 } 5215 } 5216 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5217 } 5218 5219 /* recvs and sends of j-array are completed */ 5220 i = nrecvs; 5221 while (i--) { 5222 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5223 } 5224 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5225 } else if (scall == MAT_REUSE_MATRIX) { 5226 sstartsj = *startsj_s; 5227 rstartsj = *startsj_r; 5228 bufa = *bufa_ptr; 5229 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5230 b_otha = b_oth->a; 5231 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5232 5233 /* a-array */ 5234 /*---------*/ 5235 /* post receives of a-array */ 5236 for (i=0; i<nrecvs; i++) { 5237 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5238 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5239 } 5240 5241 /* pack the outgoing message a-array */ 5242 k = 0; 5243 for (i=0; i<nsends; i++) { 5244 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5245 bufA = bufa+sstartsj[i]; 5246 for (j=0; j<nrows; j++) { 5247 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5248 for (ll=0; ll<sbs; ll++) { 5249 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5250 for (l=0; l<ncols; l++) { 5251 *bufA++ = vals[l]; 5252 } 5253 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5254 } 5255 } 5256 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5257 } 5258 /* recvs and sends of a-array are completed */ 5259 i = nrecvs; 5260 while (i--) { 5261 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5262 } 5263 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5264 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5265 5266 if (scall == MAT_INITIAL_MATRIX) { 5267 /* put together the new matrix */ 5268 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5269 5270 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5271 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5272 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5273 b_oth->free_a = PETSC_TRUE; 5274 b_oth->free_ij = PETSC_TRUE; 5275 b_oth->nonew = 0; 5276 5277 ierr = PetscFree(bufj);CHKERRQ(ierr); 5278 if (!startsj_s || !bufa_ptr) { 5279 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5280 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5281 } else { 5282 *startsj_s = sstartsj; 5283 *startsj_r = rstartsj; 5284 *bufa_ptr = bufa; 5285 } 5286 } 5287 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5288 PetscFunctionReturn(0); 5289 } 5290 5291 /*@C 5292 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5293 5294 Not Collective 5295 5296 Input Parameters: 5297 . A - The matrix in mpiaij format 5298 5299 Output Parameter: 5300 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5301 . colmap - A map from global column index to local index into lvec 5302 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5303 5304 Level: developer 5305 5306 @*/ 5307 #if defined(PETSC_USE_CTABLE) 5308 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5309 #else 5310 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5311 #endif 5312 { 5313 Mat_MPIAIJ *a; 5314 5315 PetscFunctionBegin; 5316 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5317 PetscValidPointer(lvec, 2); 5318 PetscValidPointer(colmap, 3); 5319 PetscValidPointer(multScatter, 4); 5320 a = (Mat_MPIAIJ*) A->data; 5321 if (lvec) *lvec = a->lvec; 5322 if (colmap) *colmap = a->colmap; 5323 if (multScatter) *multScatter = a->Mvctx; 5324 PetscFunctionReturn(0); 5325 } 5326 5327 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5328 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5329 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5330 #if defined(PETSC_HAVE_ELEMENTAL) 5331 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5332 #endif 5333 #if defined(PETSC_HAVE_HYPRE) 5334 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5335 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5336 #endif 5337 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5338 5339 /* 5340 Computes (B'*A')' since computing B*A directly is untenable 5341 5342 n p p 5343 ( ) ( ) ( ) 5344 m ( A ) * n ( B ) = m ( C ) 5345 ( ) ( ) ( ) 5346 5347 */ 5348 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5349 { 5350 PetscErrorCode ierr; 5351 Mat At,Bt,Ct; 5352 5353 PetscFunctionBegin; 5354 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5355 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5356 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5357 ierr = MatDestroy(&At);CHKERRQ(ierr); 5358 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5359 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5360 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5361 PetscFunctionReturn(0); 5362 } 5363 5364 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5365 { 5366 PetscErrorCode ierr; 5367 PetscInt m=A->rmap->n,n=B->cmap->n; 5368 Mat Cmat; 5369 5370 PetscFunctionBegin; 5371 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); 5372 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5373 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5374 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5375 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5376 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5377 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5378 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5379 5380 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5381 5382 *C = Cmat; 5383 PetscFunctionReturn(0); 5384 } 5385 5386 /* ----------------------------------------------------------------*/ 5387 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5388 { 5389 PetscErrorCode ierr; 5390 5391 PetscFunctionBegin; 5392 if (scall == MAT_INITIAL_MATRIX) { 5393 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5394 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5395 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5396 } 5397 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5398 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5399 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5400 PetscFunctionReturn(0); 5401 } 5402 5403 /*MC 5404 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5405 5406 Options Database Keys: 5407 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5408 5409 Level: beginner 5410 5411 .seealso: MatCreateAIJ() 5412 M*/ 5413 5414 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5415 { 5416 Mat_MPIAIJ *b; 5417 PetscErrorCode ierr; 5418 PetscMPIInt size; 5419 5420 PetscFunctionBegin; 5421 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5422 5423 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5424 B->data = (void*)b; 5425 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5426 B->assembled = PETSC_FALSE; 5427 B->insertmode = NOT_SET_VALUES; 5428 b->size = size; 5429 5430 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5431 5432 /* build cache for off array entries formed */ 5433 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5434 5435 b->donotstash = PETSC_FALSE; 5436 b->colmap = 0; 5437 b->garray = 0; 5438 b->roworiented = PETSC_TRUE; 5439 5440 /* stuff used for matrix vector multiply */ 5441 b->lvec = NULL; 5442 b->Mvctx = NULL; 5443 5444 /* stuff for MatGetRow() */ 5445 b->rowindices = 0; 5446 b->rowvalues = 0; 5447 b->getrowactive = PETSC_FALSE; 5448 5449 /* flexible pointer used in CUSP/CUSPARSE classes */ 5450 b->spptr = NULL; 5451 5452 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5453 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5454 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5455 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5456 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5457 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5458 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5459 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5460 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5461 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5462 #if defined(PETSC_HAVE_ELEMENTAL) 5463 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5464 #endif 5465 #if defined(PETSC_HAVE_HYPRE) 5466 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5467 #endif 5468 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5469 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5470 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5471 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5472 #if defined(PETSC_HAVE_HYPRE) 5473 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5474 #endif 5475 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5476 PetscFunctionReturn(0); 5477 } 5478 5479 /*@C 5480 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5481 and "off-diagonal" part of the matrix in CSR format. 5482 5483 Collective on MPI_Comm 5484 5485 Input Parameters: 5486 + comm - MPI communicator 5487 . m - number of local rows (Cannot be PETSC_DECIDE) 5488 . n - This value should be the same as the local size used in creating the 5489 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5490 calculated if N is given) For square matrices n is almost always m. 5491 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5492 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5493 . i - row indices for "diagonal" portion of matrix 5494 . j - column indices 5495 . a - matrix values 5496 . oi - row indices for "off-diagonal" portion of matrix 5497 . oj - column indices 5498 - oa - matrix values 5499 5500 Output Parameter: 5501 . mat - the matrix 5502 5503 Level: advanced 5504 5505 Notes: 5506 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5507 must free the arrays once the matrix has been destroyed and not before. 5508 5509 The i and j indices are 0 based 5510 5511 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5512 5513 This sets local rows and cannot be used to set off-processor values. 5514 5515 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5516 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5517 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5518 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5519 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5520 communication if it is known that only local entries will be set. 5521 5522 .keywords: matrix, aij, compressed row, sparse, parallel 5523 5524 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5525 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5526 @*/ 5527 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) 5528 { 5529 PetscErrorCode ierr; 5530 Mat_MPIAIJ *maij; 5531 5532 PetscFunctionBegin; 5533 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5534 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5535 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5536 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5537 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5538 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5539 maij = (Mat_MPIAIJ*) (*mat)->data; 5540 5541 (*mat)->preallocated = PETSC_TRUE; 5542 5543 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5544 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5545 5546 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5547 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5548 5549 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5550 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5551 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5552 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5553 5554 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5555 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5556 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5557 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5558 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5559 PetscFunctionReturn(0); 5560 } 5561 5562 /* 5563 Special version for direct calls from Fortran 5564 */ 5565 #include <petsc/private/fortranimpl.h> 5566 5567 /* Change these macros so can be used in void function */ 5568 #undef CHKERRQ 5569 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5570 #undef SETERRQ2 5571 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5572 #undef SETERRQ3 5573 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5574 #undef SETERRQ 5575 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5576 5577 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5578 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5579 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5580 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5581 #else 5582 #endif 5583 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) 5584 { 5585 Mat mat = *mmat; 5586 PetscInt m = *mm, n = *mn; 5587 InsertMode addv = *maddv; 5588 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5589 PetscScalar value; 5590 PetscErrorCode ierr; 5591 5592 MatCheckPreallocated(mat,1); 5593 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5594 5595 #if defined(PETSC_USE_DEBUG) 5596 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5597 #endif 5598 { 5599 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5600 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5601 PetscBool roworiented = aij->roworiented; 5602 5603 /* Some Variables required in the macro */ 5604 Mat A = aij->A; 5605 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5606 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5607 MatScalar *aa = a->a; 5608 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5609 Mat B = aij->B; 5610 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5611 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5612 MatScalar *ba = b->a; 5613 5614 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5615 PetscInt nonew = a->nonew; 5616 MatScalar *ap1,*ap2; 5617 5618 PetscFunctionBegin; 5619 for (i=0; i<m; i++) { 5620 if (im[i] < 0) continue; 5621 #if defined(PETSC_USE_DEBUG) 5622 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); 5623 #endif 5624 if (im[i] >= rstart && im[i] < rend) { 5625 row = im[i] - rstart; 5626 lastcol1 = -1; 5627 rp1 = aj + ai[row]; 5628 ap1 = aa + ai[row]; 5629 rmax1 = aimax[row]; 5630 nrow1 = ailen[row]; 5631 low1 = 0; 5632 high1 = nrow1; 5633 lastcol2 = -1; 5634 rp2 = bj + bi[row]; 5635 ap2 = ba + bi[row]; 5636 rmax2 = bimax[row]; 5637 nrow2 = bilen[row]; 5638 low2 = 0; 5639 high2 = nrow2; 5640 5641 for (j=0; j<n; j++) { 5642 if (roworiented) value = v[i*n+j]; 5643 else value = v[i+j*m]; 5644 if (in[j] >= cstart && in[j] < cend) { 5645 col = in[j] - cstart; 5646 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5647 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5648 } else if (in[j] < 0) continue; 5649 #if defined(PETSC_USE_DEBUG) 5650 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); 5651 #endif 5652 else { 5653 if (mat->was_assembled) { 5654 if (!aij->colmap) { 5655 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5656 } 5657 #if defined(PETSC_USE_CTABLE) 5658 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5659 col--; 5660 #else 5661 col = aij->colmap[in[j]] - 1; 5662 #endif 5663 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5664 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5665 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5666 col = in[j]; 5667 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5668 B = aij->B; 5669 b = (Mat_SeqAIJ*)B->data; 5670 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5671 rp2 = bj + bi[row]; 5672 ap2 = ba + bi[row]; 5673 rmax2 = bimax[row]; 5674 nrow2 = bilen[row]; 5675 low2 = 0; 5676 high2 = nrow2; 5677 bm = aij->B->rmap->n; 5678 ba = b->a; 5679 } 5680 } else col = in[j]; 5681 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5682 } 5683 } 5684 } else if (!aij->donotstash) { 5685 if (roworiented) { 5686 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5687 } else { 5688 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5689 } 5690 } 5691 } 5692 } 5693 PetscFunctionReturnVoid(); 5694 } 5695 5696