1 2 3 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 4 #include <petsc/private/vecimpl.h> 5 #include <petsc/private/isimpl.h> 6 #include <petscblaslapack.h> 7 #include <petscsf.h> 8 9 /*MC 10 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 11 12 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 13 and MATMPIAIJ otherwise. As a result, for single process communicators, 14 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 15 for communicators controlling multiple processes. It is recommended that you call both of 16 the above preallocation routines for simplicity. 17 18 Options Database Keys: 19 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 20 21 Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when 22 enough exist. 23 24 Level: beginner 25 26 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ, MATMPIAIJ 27 M*/ 28 29 /*MC 30 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 31 32 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 33 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 34 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 35 for communicators controlling multiple processes. It is recommended that you call both of 36 the above preallocation routines for simplicity. 37 38 Options Database Keys: 39 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 40 41 Level: beginner 42 43 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 44 M*/ 45 46 PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 50 51 PetscFunctionBegin; 52 if (mat->A) { 53 ierr = MatSetBlockSizes(mat->A,rbs,cbs);CHKERRQ(ierr); 54 ierr = MatSetBlockSizes(mat->B,rbs,1);CHKERRQ(ierr); 55 } 56 PetscFunctionReturn(0); 57 } 58 59 PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows) 60 { 61 PetscErrorCode ierr; 62 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 63 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data; 64 Mat_SeqAIJ *b = (Mat_SeqAIJ*)mat->B->data; 65 const PetscInt *ia,*ib; 66 const MatScalar *aa,*bb; 67 PetscInt na,nb,i,j,*rows,cnt=0,n0rows; 68 PetscInt m = M->rmap->n,rstart = M->rmap->rstart; 69 70 PetscFunctionBegin; 71 *keptrows = 0; 72 ia = a->i; 73 ib = b->i; 74 for (i=0; i<m; i++) { 75 na = ia[i+1] - ia[i]; 76 nb = ib[i+1] - ib[i]; 77 if (!na && !nb) { 78 cnt++; 79 goto ok1; 80 } 81 aa = a->a + ia[i]; 82 for (j=0; j<na; j++) { 83 if (aa[j] != 0.0) goto ok1; 84 } 85 bb = b->a + ib[i]; 86 for (j=0; j <nb; j++) { 87 if (bb[j] != 0.0) goto ok1; 88 } 89 cnt++; 90 ok1:; 91 } 92 ierr = MPIU_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr); 93 if (!n0rows) PetscFunctionReturn(0); 94 ierr = PetscMalloc1(M->rmap->n-cnt,&rows);CHKERRQ(ierr); 95 cnt = 0; 96 for (i=0; i<m; i++) { 97 na = ia[i+1] - ia[i]; 98 nb = ib[i+1] - ib[i]; 99 if (!na && !nb) continue; 100 aa = a->a + ia[i]; 101 for (j=0; j<na;j++) { 102 if (aa[j] != 0.0) { 103 rows[cnt++] = rstart + i; 104 goto ok2; 105 } 106 } 107 bb = b->a + ib[i]; 108 for (j=0; j<nb; j++) { 109 if (bb[j] != 0.0) { 110 rows[cnt++] = rstart + i; 111 goto ok2; 112 } 113 } 114 ok2:; 115 } 116 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 117 PetscFunctionReturn(0); 118 } 119 120 PetscErrorCode MatDiagonalSet_MPIAIJ(Mat Y,Vec D,InsertMode is) 121 { 122 PetscErrorCode ierr; 123 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) Y->data; 124 125 PetscFunctionBegin; 126 if (Y->assembled && Y->rmap->rstart == Y->cmap->rstart && Y->rmap->rend == Y->cmap->rend) { 127 ierr = MatDiagonalSet(aij->A,D,is);CHKERRQ(ierr); 128 } else { 129 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 130 } 131 PetscFunctionReturn(0); 132 } 133 134 PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows) 135 { 136 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)M->data; 137 PetscErrorCode ierr; 138 PetscInt i,rstart,nrows,*rows; 139 140 PetscFunctionBegin; 141 *zrows = NULL; 142 ierr = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr); 143 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 144 for (i=0; i<nrows; i++) rows[i] += rstart; 145 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 146 PetscFunctionReturn(0); 147 } 148 149 PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms) 150 { 151 PetscErrorCode ierr; 152 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 153 PetscInt i,n,*garray = aij->garray; 154 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ*) aij->A->data; 155 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ*) aij->B->data; 156 PetscReal *work; 157 158 PetscFunctionBegin; 159 ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr); 160 ierr = PetscCalloc1(n,&work);CHKERRQ(ierr); 161 if (type == NORM_2) { 162 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 163 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]); 164 } 165 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 166 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]); 167 } 168 } else if (type == NORM_1) { 169 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 170 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 171 } 172 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 173 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 174 } 175 } else if (type == NORM_INFINITY) { 176 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 177 work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 178 } 179 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 180 work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]); 181 } 182 183 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 184 if (type == NORM_INFINITY) { 185 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 186 } else { 187 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 188 } 189 ierr = PetscFree(work);CHKERRQ(ierr); 190 if (type == NORM_2) { 191 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 192 } 193 PetscFunctionReturn(0); 194 } 195 196 PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A,IS *is) 197 { 198 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 199 IS sis,gis; 200 PetscErrorCode ierr; 201 const PetscInt *isis,*igis; 202 PetscInt n,*iis,nsis,ngis,rstart,i; 203 204 PetscFunctionBegin; 205 ierr = MatFindOffBlockDiagonalEntries(a->A,&sis);CHKERRQ(ierr); 206 ierr = MatFindNonzeroRows(a->B,&gis);CHKERRQ(ierr); 207 ierr = ISGetSize(gis,&ngis);CHKERRQ(ierr); 208 ierr = ISGetSize(sis,&nsis);CHKERRQ(ierr); 209 ierr = ISGetIndices(sis,&isis);CHKERRQ(ierr); 210 ierr = ISGetIndices(gis,&igis);CHKERRQ(ierr); 211 212 ierr = PetscMalloc1(ngis+nsis,&iis);CHKERRQ(ierr); 213 ierr = PetscMemcpy(iis,igis,ngis*sizeof(PetscInt));CHKERRQ(ierr); 214 ierr = PetscMemcpy(iis+ngis,isis,nsis*sizeof(PetscInt));CHKERRQ(ierr); 215 n = ngis + nsis; 216 ierr = PetscSortRemoveDupsInt(&n,iis);CHKERRQ(ierr); 217 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 218 for (i=0; i<n; i++) iis[i] += rstart; 219 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),n,iis,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 220 221 ierr = ISRestoreIndices(sis,&isis);CHKERRQ(ierr); 222 ierr = ISRestoreIndices(gis,&igis);CHKERRQ(ierr); 223 ierr = ISDestroy(&sis);CHKERRQ(ierr); 224 ierr = ISDestroy(&gis);CHKERRQ(ierr); 225 PetscFunctionReturn(0); 226 } 227 228 /* 229 Distributes a SeqAIJ matrix across a set of processes. Code stolen from 230 MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type. 231 232 Only for square matrices 233 234 Used by a preconditioner, hence PETSC_EXTERN 235 */ 236 PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat) 237 { 238 PetscMPIInt rank,size; 239 PetscInt *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz = 0,*gmataj,cnt,row,*ld,bses[2]; 240 PetscErrorCode ierr; 241 Mat mat; 242 Mat_SeqAIJ *gmata; 243 PetscMPIInt tag; 244 MPI_Status status; 245 PetscBool aij; 246 MatScalar *gmataa,*ao,*ad,*gmataarestore=0; 247 248 PetscFunctionBegin; 249 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 250 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 251 if (!rank) { 252 ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr); 253 if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name); 254 } 255 if (reuse == MAT_INITIAL_MATRIX) { 256 ierr = MatCreate(comm,&mat);CHKERRQ(ierr); 257 ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 258 ierr = MatGetBlockSizes(gmat,&bses[0],&bses[1]);CHKERRQ(ierr); 259 ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr); 260 ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr); 261 ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr); 262 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 263 ierr = PetscMalloc2(m,&dlens,m,&olens);CHKERRQ(ierr); 264 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 265 266 rowners[0] = 0; 267 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 268 rstart = rowners[rank]; 269 rend = rowners[rank+1]; 270 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 271 if (!rank) { 272 gmata = (Mat_SeqAIJ*) gmat->data; 273 /* send row lengths to all processors */ 274 for (i=0; i<m; i++) dlens[i] = gmata->ilen[i]; 275 for (i=1; i<size; i++) { 276 ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 277 } 278 /* determine number diagonal and off-diagonal counts */ 279 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 280 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 281 jj = 0; 282 for (i=0; i<m; i++) { 283 for (j=0; j<dlens[i]; j++) { 284 if (gmata->j[jj] < rstart) ld[i]++; 285 if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++; 286 jj++; 287 } 288 } 289 /* send column indices to other processes */ 290 for (i=1; i<size; i++) { 291 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 292 ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 293 ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 294 } 295 296 /* send numerical values to other processes */ 297 for (i=1; i<size; i++) { 298 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 299 ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 300 } 301 gmataa = gmata->a; 302 gmataj = gmata->j; 303 304 } else { 305 /* receive row lengths */ 306 ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 307 /* receive column indices */ 308 ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 309 ierr = PetscMalloc2(nz,&gmataa,nz,&gmataj);CHKERRQ(ierr); 310 ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 311 /* determine number diagonal and off-diagonal counts */ 312 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 313 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 314 jj = 0; 315 for (i=0; i<m; i++) { 316 for (j=0; j<dlens[i]; j++) { 317 if (gmataj[jj] < rstart) ld[i]++; 318 if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++; 319 jj++; 320 } 321 } 322 /* receive numerical values */ 323 ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 324 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 325 } 326 /* set preallocation */ 327 for (i=0; i<m; i++) { 328 dlens[i] -= olens[i]; 329 } 330 ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr); 331 ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr); 332 333 for (i=0; i<m; i++) { 334 dlens[i] += olens[i]; 335 } 336 cnt = 0; 337 for (i=0; i<m; i++) { 338 row = rstart + i; 339 ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr); 340 cnt += dlens[i]; 341 } 342 if (rank) { 343 ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr); 344 } 345 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 346 ierr = PetscFree(rowners);CHKERRQ(ierr); 347 348 ((Mat_MPIAIJ*)(mat->data))->ld = ld; 349 350 *inmat = mat; 351 } else { /* column indices are already set; only need to move over numerical values from process 0 */ 352 Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data; 353 Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data; 354 mat = *inmat; 355 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 356 if (!rank) { 357 /* send numerical values to other processes */ 358 gmata = (Mat_SeqAIJ*) gmat->data; 359 ierr = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr); 360 gmataa = gmata->a; 361 for (i=1; i<size; i++) { 362 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 363 ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 364 } 365 nz = gmata->i[rowners[1]]-gmata->i[rowners[0]]; 366 } else { 367 /* receive numerical values from process 0*/ 368 nz = Ad->nz + Ao->nz; 369 ierr = PetscMalloc1(nz,&gmataa);CHKERRQ(ierr); gmataarestore = gmataa; 370 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 371 } 372 /* transfer numerical values into the diagonal A and off diagonal B parts of mat */ 373 ld = ((Mat_MPIAIJ*)(mat->data))->ld; 374 ad = Ad->a; 375 ao = Ao->a; 376 if (mat->rmap->n) { 377 i = 0; 378 nz = ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 379 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 380 } 381 for (i=1; i<mat->rmap->n; i++) { 382 nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 383 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 384 } 385 i--; 386 if (mat->rmap->n) { 387 nz = Ao->i[i+1] - Ao->i[i] - ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 388 } 389 if (rank) { 390 ierr = PetscFree(gmataarestore);CHKERRQ(ierr); 391 } 392 } 393 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 394 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 395 PetscFunctionReturn(0); 396 } 397 398 /* 399 Local utility routine that creates a mapping from the global column 400 number to the local number in the off-diagonal part of the local 401 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 402 a slightly higher hash table cost; without it it is not scalable (each processor 403 has an order N integer array but is fast to acess. 404 */ 405 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 406 { 407 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 408 PetscErrorCode ierr; 409 PetscInt n = aij->B->cmap->n,i; 410 411 PetscFunctionBegin; 412 if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray"); 413 #if defined(PETSC_USE_CTABLE) 414 ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 415 for (i=0; i<n; i++) { 416 ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr); 417 } 418 #else 419 ierr = PetscCalloc1(mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 420 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N+1)*sizeof(PetscInt));CHKERRQ(ierr); 421 for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1; 422 #endif 423 PetscFunctionReturn(0); 424 } 425 426 #define MatSetValues_SeqAIJ_A_Private(row,col,value,addv,orow,ocol) \ 427 { \ 428 if (col <= lastcol1) low1 = 0; \ 429 else high1 = nrow1; \ 430 lastcol1 = col;\ 431 while (high1-low1 > 5) { \ 432 t = (low1+high1)/2; \ 433 if (rp1[t] > col) high1 = t; \ 434 else low1 = t; \ 435 } \ 436 for (_i=low1; _i<high1; _i++) { \ 437 if (rp1[_i] > col) break; \ 438 if (rp1[_i] == col) { \ 439 if (addv == ADD_VALUES) ap1[_i] += value; \ 440 else ap1[_i] = value; \ 441 goto a_noinsert; \ 442 } \ 443 } \ 444 if (value == 0.0 && ignorezeroentries && row != col) {low1 = 0; high1 = nrow1;goto a_noinsert;} \ 445 if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;} \ 446 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 447 MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \ 448 N = nrow1++ - 1; a->nz++; high1++; \ 449 /* shift up all the later entries in this row */ \ 450 for (ii=N; ii>=_i; ii--) { \ 451 rp1[ii+1] = rp1[ii]; \ 452 ap1[ii+1] = ap1[ii]; \ 453 } \ 454 rp1[_i] = col; \ 455 ap1[_i] = value; \ 456 A->nonzerostate++;\ 457 a_noinsert: ; \ 458 ailen[row] = nrow1; \ 459 } 460 461 #define MatSetValues_SeqAIJ_B_Private(row,col,value,addv,orow,ocol) \ 462 { \ 463 if (col <= lastcol2) low2 = 0; \ 464 else high2 = nrow2; \ 465 lastcol2 = col; \ 466 while (high2-low2 > 5) { \ 467 t = (low2+high2)/2; \ 468 if (rp2[t] > col) high2 = t; \ 469 else low2 = t; \ 470 } \ 471 for (_i=low2; _i<high2; _i++) { \ 472 if (rp2[_i] > col) break; \ 473 if (rp2[_i] == col) { \ 474 if (addv == ADD_VALUES) ap2[_i] += value; \ 475 else ap2[_i] = value; \ 476 goto b_noinsert; \ 477 } \ 478 } \ 479 if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 480 if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 481 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 482 MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \ 483 N = nrow2++ - 1; b->nz++; high2++; \ 484 /* shift up all the later entries in this row */ \ 485 for (ii=N; ii>=_i; ii--) { \ 486 rp2[ii+1] = rp2[ii]; \ 487 ap2[ii+1] = ap2[ii]; \ 488 } \ 489 rp2[_i] = col; \ 490 ap2[_i] = value; \ 491 B->nonzerostate++; \ 492 b_noinsert: ; \ 493 bilen[row] = nrow2; \ 494 } 495 496 PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[]) 497 { 498 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)A->data; 499 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data; 500 PetscErrorCode ierr; 501 PetscInt l,*garray = mat->garray,diag; 502 503 PetscFunctionBegin; 504 /* code only works for square matrices A */ 505 506 /* find size of row to the left of the diagonal part */ 507 ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr); 508 row = row - diag; 509 for (l=0; l<b->i[row+1]-b->i[row]; l++) { 510 if (garray[b->j[b->i[row]+l]] > diag) break; 511 } 512 ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr); 513 514 /* diagonal part */ 515 ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr); 516 517 /* right of diagonal part */ 518 ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr); 519 PetscFunctionReturn(0); 520 } 521 522 PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 523 { 524 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 525 PetscScalar value; 526 PetscErrorCode ierr; 527 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 528 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 529 PetscBool roworiented = aij->roworiented; 530 531 /* Some Variables required in the macro */ 532 Mat A = aij->A; 533 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 534 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 535 MatScalar *aa = a->a; 536 PetscBool ignorezeroentries = a->ignorezeroentries; 537 Mat B = aij->B; 538 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 539 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 540 MatScalar *ba = b->a; 541 542 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 543 PetscInt nonew; 544 MatScalar *ap1,*ap2; 545 546 PetscFunctionBegin; 547 for (i=0; i<m; i++) { 548 if (im[i] < 0) continue; 549 #if defined(PETSC_USE_DEBUG) 550 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 551 #endif 552 if (im[i] >= rstart && im[i] < rend) { 553 row = im[i] - rstart; 554 lastcol1 = -1; 555 rp1 = aj + ai[row]; 556 ap1 = aa + ai[row]; 557 rmax1 = aimax[row]; 558 nrow1 = ailen[row]; 559 low1 = 0; 560 high1 = nrow1; 561 lastcol2 = -1; 562 rp2 = bj + bi[row]; 563 ap2 = ba + bi[row]; 564 rmax2 = bimax[row]; 565 nrow2 = bilen[row]; 566 low2 = 0; 567 high2 = nrow2; 568 569 for (j=0; j<n; j++) { 570 if (roworiented) value = v[i*n+j]; 571 else value = v[i+j*m]; 572 if (in[j] >= cstart && in[j] < cend) { 573 col = in[j] - cstart; 574 nonew = a->nonew; 575 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 576 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 577 } else if (in[j] < 0) continue; 578 #if defined(PETSC_USE_DEBUG) 579 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 580 #endif 581 else { 582 if (mat->was_assembled) { 583 if (!aij->colmap) { 584 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 585 } 586 #if defined(PETSC_USE_CTABLE) 587 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 588 col--; 589 #else 590 col = aij->colmap[in[j]] - 1; 591 #endif 592 if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) { 593 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 594 col = in[j]; 595 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 596 B = aij->B; 597 b = (Mat_SeqAIJ*)B->data; 598 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a; 599 rp2 = bj + bi[row]; 600 ap2 = ba + bi[row]; 601 rmax2 = bimax[row]; 602 nrow2 = bilen[row]; 603 low2 = 0; 604 high2 = nrow2; 605 bm = aij->B->rmap->n; 606 ba = b->a; 607 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", im[i], in[j]); 608 } else col = in[j]; 609 nonew = b->nonew; 610 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 611 } 612 } 613 } else { 614 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 615 if (!aij->donotstash) { 616 mat->assembled = PETSC_FALSE; 617 if (roworiented) { 618 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 619 } else { 620 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 621 } 622 } 623 } 624 } 625 PetscFunctionReturn(0); 626 } 627 628 PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 629 { 630 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 631 PetscErrorCode ierr; 632 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 633 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 634 635 PetscFunctionBegin; 636 for (i=0; i<m; i++) { 637 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 638 if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1); 639 if (idxm[i] >= rstart && idxm[i] < rend) { 640 row = idxm[i] - rstart; 641 for (j=0; j<n; j++) { 642 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 643 if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1); 644 if (idxn[j] >= cstart && idxn[j] < cend) { 645 col = idxn[j] - cstart; 646 ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 647 } else { 648 if (!aij->colmap) { 649 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 650 } 651 #if defined(PETSC_USE_CTABLE) 652 ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr); 653 col--; 654 #else 655 col = aij->colmap[idxn[j]] - 1; 656 #endif 657 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0; 658 else { 659 ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 660 } 661 } 662 } 663 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 664 } 665 PetscFunctionReturn(0); 666 } 667 668 extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec); 669 670 PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode) 671 { 672 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 673 PetscErrorCode ierr; 674 PetscInt nstash,reallocs; 675 676 PetscFunctionBegin; 677 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 678 679 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 680 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 681 ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 682 PetscFunctionReturn(0); 683 } 684 685 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode) 686 { 687 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 688 Mat_SeqAIJ *a = (Mat_SeqAIJ*)aij->A->data; 689 PetscErrorCode ierr; 690 PetscMPIInt n; 691 PetscInt i,j,rstart,ncols,flg; 692 PetscInt *row,*col; 693 PetscBool other_disassembled; 694 PetscScalar *val; 695 696 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 697 698 PetscFunctionBegin; 699 if (!aij->donotstash && !mat->nooffprocentries) { 700 while (1) { 701 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 702 if (!flg) break; 703 704 for (i=0; i<n; ) { 705 /* Now identify the consecutive vals belonging to the same row */ 706 for (j=i,rstart=row[j]; j<n; j++) { 707 if (row[j] != rstart) break; 708 } 709 if (j < n) ncols = j-i; 710 else ncols = n-i; 711 /* Now assemble all these values with a single function call */ 712 ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr); 713 714 i = j; 715 } 716 } 717 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 718 } 719 ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr); 720 ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr); 721 722 /* determine if any processor has disassembled, if so we must 723 also disassemble ourselfs, in order that we may reassemble. */ 724 /* 725 if nonzero structure of submatrix B cannot change then we know that 726 no processor disassembled thus we can skip this stuff 727 */ 728 if (!((Mat_SeqAIJ*)aij->B->data)->nonew) { 729 ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 730 if (mat->was_assembled && !other_disassembled) { 731 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 732 } 733 } 734 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 735 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 736 } 737 ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr); 738 ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr); 739 ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr); 740 741 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 742 743 aij->rowvalues = 0; 744 745 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 746 if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ; 747 748 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 749 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 750 PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate; 751 ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 752 } 753 PetscFunctionReturn(0); 754 } 755 756 PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 757 { 758 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 759 PetscErrorCode ierr; 760 761 PetscFunctionBegin; 762 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 763 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 764 PetscFunctionReturn(0); 765 } 766 767 PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 768 { 769 Mat_MPIAIJ *mat = (Mat_MPIAIJ *) A->data; 770 PetscInt *lrows; 771 PetscInt r, len; 772 PetscErrorCode ierr; 773 774 PetscFunctionBegin; 775 /* get locally owned rows */ 776 ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr); 777 /* fix right hand side if needed */ 778 if (x && b) { 779 const PetscScalar *xx; 780 PetscScalar *bb; 781 782 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 783 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 784 for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]]; 785 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 786 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 787 } 788 /* Must zero l->B before l->A because the (diag) case below may put values into l->B*/ 789 ierr = MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 790 if (A->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 791 PetscBool cong; 792 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 793 if (cong) A->congruentlayouts = 1; 794 else A->congruentlayouts = 0; 795 } 796 if ((diag != 0.0) && A->congruentlayouts) { 797 ierr = MatZeroRows(mat->A, len, lrows, diag, NULL, NULL);CHKERRQ(ierr); 798 } else if (diag != 0.0) { 799 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 800 if (((Mat_SeqAIJ *) mat->A->data)->nonew) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 801 for (r = 0; r < len; ++r) { 802 const PetscInt row = lrows[r] + A->rmap->rstart; 803 ierr = MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES);CHKERRQ(ierr); 804 } 805 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 806 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 807 } else { 808 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 809 } 810 ierr = PetscFree(lrows);CHKERRQ(ierr); 811 812 /* only change matrix nonzero state if pattern was allowed to be changed */ 813 if (!((Mat_SeqAIJ*)(mat->A->data))->keepnonzeropattern) { 814 PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate; 815 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 816 } 817 PetscFunctionReturn(0); 818 } 819 820 PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 821 { 822 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 823 PetscErrorCode ierr; 824 PetscMPIInt n = A->rmap->n; 825 PetscInt i,j,r,m,p = 0,len = 0; 826 PetscInt *lrows,*owners = A->rmap->range; 827 PetscSFNode *rrows; 828 PetscSF sf; 829 const PetscScalar *xx; 830 PetscScalar *bb,*mask; 831 Vec xmask,lmask; 832 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)l->B->data; 833 const PetscInt *aj, *ii,*ridx; 834 PetscScalar *aa; 835 836 PetscFunctionBegin; 837 /* Create SF where leaves are input rows and roots are owned rows */ 838 ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr); 839 for (r = 0; r < n; ++r) lrows[r] = -1; 840 ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr); 841 for (r = 0; r < N; ++r) { 842 const PetscInt idx = rows[r]; 843 if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N); 844 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */ 845 ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr); 846 } 847 rrows[r].rank = p; 848 rrows[r].index = rows[r] - owners[p]; 849 } 850 ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr); 851 ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr); 852 /* Collect flags for rows to be zeroed */ 853 ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 854 ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 855 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 856 /* Compress and put in row numbers */ 857 for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r; 858 /* zero diagonal part of matrix */ 859 ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr); 860 /* handle off diagonal part of matrix */ 861 ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr); 862 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 863 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 864 for (i=0; i<len; i++) bb[lrows[i]] = 1; 865 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 866 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 867 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 868 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 869 if (x) { 870 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 871 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 872 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 873 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 874 } 875 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 876 /* remove zeroed rows of off diagonal matrix */ 877 ii = aij->i; 878 for (i=0; i<len; i++) { 879 ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr); 880 } 881 /* loop over all elements of off process part of matrix zeroing removed columns*/ 882 if (aij->compressedrow.use) { 883 m = aij->compressedrow.nrows; 884 ii = aij->compressedrow.i; 885 ridx = aij->compressedrow.rindex; 886 for (i=0; i<m; i++) { 887 n = ii[i+1] - ii[i]; 888 aj = aij->j + ii[i]; 889 aa = aij->a + ii[i]; 890 891 for (j=0; j<n; j++) { 892 if (PetscAbsScalar(mask[*aj])) { 893 if (b) bb[*ridx] -= *aa*xx[*aj]; 894 *aa = 0.0; 895 } 896 aa++; 897 aj++; 898 } 899 ridx++; 900 } 901 } else { /* do not use compressed row format */ 902 m = l->B->rmap->n; 903 for (i=0; i<m; i++) { 904 n = ii[i+1] - ii[i]; 905 aj = aij->j + ii[i]; 906 aa = aij->a + ii[i]; 907 for (j=0; j<n; j++) { 908 if (PetscAbsScalar(mask[*aj])) { 909 if (b) bb[i] -= *aa*xx[*aj]; 910 *aa = 0.0; 911 } 912 aa++; 913 aj++; 914 } 915 } 916 } 917 if (x) { 918 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 919 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 920 } 921 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 922 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 923 ierr = PetscFree(lrows);CHKERRQ(ierr); 924 925 /* only change matrix nonzero state if pattern was allowed to be changed */ 926 if (!((Mat_SeqAIJ*)(l->A->data))->keepnonzeropattern) { 927 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 928 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 929 } 930 PetscFunctionReturn(0); 931 } 932 933 PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy) 934 { 935 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 936 PetscErrorCode ierr; 937 PetscInt nt; 938 939 PetscFunctionBegin; 940 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 941 if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt); 942 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 943 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 944 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 945 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 946 PetscFunctionReturn(0); 947 } 948 949 PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx) 950 { 951 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 952 PetscErrorCode ierr; 953 954 PetscFunctionBegin; 955 ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr); 956 PetscFunctionReturn(0); 957 } 958 959 PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 960 { 961 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 962 PetscErrorCode ierr; 963 964 PetscFunctionBegin; 965 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 966 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 967 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 968 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 969 PetscFunctionReturn(0); 970 } 971 972 PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy) 973 { 974 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 975 PetscErrorCode ierr; 976 PetscBool merged; 977 978 PetscFunctionBegin; 979 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 980 /* do nondiagonal part */ 981 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 982 if (!merged) { 983 /* send it on its way */ 984 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 985 /* do local part */ 986 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 987 /* receive remote parts: note this assumes the values are not actually */ 988 /* added in yy until the next line, */ 989 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 990 } else { 991 /* do local part */ 992 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 993 /* send it on its way */ 994 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 995 /* values actually were received in the Begin() but we need to call this nop */ 996 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 997 } 998 PetscFunctionReturn(0); 999 } 1000 1001 PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool *f) 1002 { 1003 MPI_Comm comm; 1004 Mat_MPIAIJ *Aij = (Mat_MPIAIJ*) Amat->data, *Bij; 1005 Mat Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs; 1006 IS Me,Notme; 1007 PetscErrorCode ierr; 1008 PetscInt M,N,first,last,*notme,i; 1009 PetscMPIInt size; 1010 1011 PetscFunctionBegin; 1012 /* Easy test: symmetric diagonal block */ 1013 Bij = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A; 1014 ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr); 1015 if (!*f) PetscFunctionReturn(0); 1016 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1017 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1018 if (size == 1) PetscFunctionReturn(0); 1019 1020 /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */ 1021 ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr); 1022 ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr); 1023 ierr = PetscMalloc1(N-last+first,¬me);CHKERRQ(ierr); 1024 for (i=0; i<first; i++) notme[i] = i; 1025 for (i=last; i<M; i++) notme[i-last+first] = i; 1026 ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr); 1027 ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr); 1028 ierr = MatCreateSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr); 1029 Aoff = Aoffs[0]; 1030 ierr = MatCreateSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr); 1031 Boff = Boffs[0]; 1032 ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr); 1033 ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr); 1034 ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr); 1035 ierr = ISDestroy(&Me);CHKERRQ(ierr); 1036 ierr = ISDestroy(&Notme);CHKERRQ(ierr); 1037 ierr = PetscFree(notme);CHKERRQ(ierr); 1038 PetscFunctionReturn(0); 1039 } 1040 1041 PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1042 { 1043 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1044 PetscErrorCode ierr; 1045 1046 PetscFunctionBegin; 1047 /* do nondiagonal part */ 1048 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1049 /* send it on its way */ 1050 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1051 /* do local part */ 1052 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1053 /* receive remote parts */ 1054 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1055 PetscFunctionReturn(0); 1056 } 1057 1058 /* 1059 This only works correctly for square matrices where the subblock A->A is the 1060 diagonal block 1061 */ 1062 PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v) 1063 { 1064 PetscErrorCode ierr; 1065 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1066 1067 PetscFunctionBegin; 1068 if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1069 if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition"); 1070 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1071 PetscFunctionReturn(0); 1072 } 1073 1074 PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa) 1075 { 1076 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1077 PetscErrorCode ierr; 1078 1079 PetscFunctionBegin; 1080 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1081 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1082 PetscFunctionReturn(0); 1083 } 1084 1085 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 1086 { 1087 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1088 PetscErrorCode ierr; 1089 1090 PetscFunctionBegin; 1091 #if defined(PETSC_USE_LOG) 1092 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N); 1093 #endif 1094 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1095 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 1096 ierr = MatDestroy(&aij->A);CHKERRQ(ierr); 1097 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 1098 #if defined(PETSC_USE_CTABLE) 1099 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 1100 #else 1101 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 1102 #endif 1103 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 1104 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 1105 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 1106 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 1107 ierr = PetscFree(aij->ld);CHKERRQ(ierr); 1108 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1109 1110 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1111 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1112 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1113 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1114 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1115 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1116 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1117 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1118 #if defined(PETSC_HAVE_ELEMENTAL) 1119 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_elemental_C",NULL);CHKERRQ(ierr); 1120 #endif 1121 #if defined(PETSC_HAVE_HYPRE) 1122 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_hypre_C",NULL);CHKERRQ(ierr); 1123 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMatMatMult_transpose_mpiaij_mpiaij_C",NULL);CHKERRQ(ierr); 1124 #endif 1125 PetscFunctionReturn(0); 1126 } 1127 1128 PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer) 1129 { 1130 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1131 Mat_SeqAIJ *A = (Mat_SeqAIJ*)aij->A->data; 1132 Mat_SeqAIJ *B = (Mat_SeqAIJ*)aij->B->data; 1133 PetscErrorCode ierr; 1134 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1135 int fd; 1136 PetscInt nz,header[4],*row_lengths,*range=0,rlen,i; 1137 PetscInt nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz = 0; 1138 PetscScalar *column_values; 1139 PetscInt message_count,flowcontrolcount; 1140 FILE *file; 1141 1142 PetscFunctionBegin; 1143 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1144 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1145 nz = A->nz + B->nz; 1146 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1147 if (!rank) { 1148 header[0] = MAT_FILE_CLASSID; 1149 header[1] = mat->rmap->N; 1150 header[2] = mat->cmap->N; 1151 1152 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1153 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1154 /* get largest number of rows any processor has */ 1155 rlen = mat->rmap->n; 1156 range = mat->rmap->range; 1157 for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]); 1158 } else { 1159 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1160 rlen = mat->rmap->n; 1161 } 1162 1163 /* load up the local row counts */ 1164 ierr = PetscMalloc1(rlen+1,&row_lengths);CHKERRQ(ierr); 1165 for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1166 1167 /* store the row lengths to the file */ 1168 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1169 if (!rank) { 1170 ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1171 for (i=1; i<size; i++) { 1172 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1173 rlen = range[i+1] - range[i]; 1174 ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1175 ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1176 } 1177 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1178 } else { 1179 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1180 ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1181 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1182 } 1183 ierr = PetscFree(row_lengths);CHKERRQ(ierr); 1184 1185 /* load up the local column indices */ 1186 nzmax = nz; /* th processor needs space a largest processor needs */ 1187 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1188 ierr = PetscMalloc1(nzmax+1,&column_indices);CHKERRQ(ierr); 1189 cnt = 0; 1190 for (i=0; i<mat->rmap->n; i++) { 1191 for (j=B->i[i]; j<B->i[i+1]; j++) { 1192 if ((col = garray[B->j[j]]) > cstart) break; 1193 column_indices[cnt++] = col; 1194 } 1195 for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart; 1196 for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]]; 1197 } 1198 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1199 1200 /* store the column indices to the file */ 1201 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1202 if (!rank) { 1203 MPI_Status status; 1204 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1205 for (i=1; i<size; i++) { 1206 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1207 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1208 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1209 ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1210 ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1211 } 1212 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1213 } else { 1214 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1215 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1216 ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1217 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1218 } 1219 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1220 1221 /* load up the local column values */ 1222 ierr = PetscMalloc1(nzmax+1,&column_values);CHKERRQ(ierr); 1223 cnt = 0; 1224 for (i=0; i<mat->rmap->n; i++) { 1225 for (j=B->i[i]; j<B->i[i+1]; j++) { 1226 if (garray[B->j[j]] > cstart) break; 1227 column_values[cnt++] = B->a[j]; 1228 } 1229 for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k]; 1230 for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j]; 1231 } 1232 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1233 1234 /* store the column values to the file */ 1235 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1236 if (!rank) { 1237 MPI_Status status; 1238 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1239 for (i=1; i<size; i++) { 1240 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1241 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1242 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1243 ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1244 ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1245 } 1246 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1247 } else { 1248 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1249 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1250 ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1251 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1252 } 1253 ierr = PetscFree(column_values);CHKERRQ(ierr); 1254 1255 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1256 if (file) fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(mat->rmap->bs)); 1257 PetscFunctionReturn(0); 1258 } 1259 1260 #include <petscdraw.h> 1261 PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 1262 { 1263 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1264 PetscErrorCode ierr; 1265 PetscMPIInt rank = aij->rank,size = aij->size; 1266 PetscBool isdraw,iascii,isbinary; 1267 PetscViewer sviewer; 1268 PetscViewerFormat format; 1269 1270 PetscFunctionBegin; 1271 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1272 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1273 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1274 if (iascii) { 1275 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1276 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1277 MatInfo info; 1278 PetscBool inodes; 1279 1280 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1281 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 1282 ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr); 1283 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 1284 if (!inodes) { 1285 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n", 1286 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1287 } else { 1288 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n", 1289 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1290 } 1291 ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1292 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1293 ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1294 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1295 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1296 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 1297 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1298 ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr); 1299 PetscFunctionReturn(0); 1300 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1301 PetscInt inodecount,inodelimit,*inodes; 1302 ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr); 1303 if (inodes) { 1304 ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr); 1305 } else { 1306 ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr); 1307 } 1308 PetscFunctionReturn(0); 1309 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1310 PetscFunctionReturn(0); 1311 } 1312 } else if (isbinary) { 1313 if (size == 1) { 1314 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1315 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1316 } else { 1317 ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1318 } 1319 PetscFunctionReturn(0); 1320 } else if (isdraw) { 1321 PetscDraw draw; 1322 PetscBool isnull; 1323 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1324 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 1325 if (isnull) PetscFunctionReturn(0); 1326 } 1327 1328 { 1329 /* assemble the entire matrix onto first processor. */ 1330 Mat A; 1331 Mat_SeqAIJ *Aloc; 1332 PetscInt M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct; 1333 MatScalar *a; 1334 1335 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1336 if (!rank) { 1337 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1338 } else { 1339 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1340 } 1341 /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */ 1342 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 1343 ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr); 1344 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1345 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1346 1347 /* copy over the A part */ 1348 Aloc = (Mat_SeqAIJ*)aij->A->data; 1349 m = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1350 row = mat->rmap->rstart; 1351 for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart; 1352 for (i=0; i<m; i++) { 1353 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr); 1354 row++; 1355 a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i]; 1356 } 1357 aj = Aloc->j; 1358 for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart; 1359 1360 /* copy over the B part */ 1361 Aloc = (Mat_SeqAIJ*)aij->B->data; 1362 m = aij->B->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1363 row = mat->rmap->rstart; 1364 ierr = PetscMalloc1(ai[m]+1,&cols);CHKERRQ(ierr); 1365 ct = cols; 1366 for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]]; 1367 for (i=0; i<m; i++) { 1368 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr); 1369 row++; 1370 a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i]; 1371 } 1372 ierr = PetscFree(ct);CHKERRQ(ierr); 1373 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1374 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1375 /* 1376 Everyone has to call to draw the matrix since the graphics waits are 1377 synchronized across all processors that share the PetscDraw object 1378 */ 1379 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1380 if (!rank) { 1381 ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1382 ierr = MatView_SeqAIJ(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1383 } 1384 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1385 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1386 ierr = MatDestroy(&A);CHKERRQ(ierr); 1387 } 1388 PetscFunctionReturn(0); 1389 } 1390 1391 PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer) 1392 { 1393 PetscErrorCode ierr; 1394 PetscBool iascii,isdraw,issocket,isbinary; 1395 1396 PetscFunctionBegin; 1397 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1398 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1399 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1400 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1401 if (iascii || isdraw || isbinary || issocket) { 1402 ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1403 } 1404 PetscFunctionReturn(0); 1405 } 1406 1407 PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1408 { 1409 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1410 PetscErrorCode ierr; 1411 Vec bb1 = 0; 1412 PetscBool hasop; 1413 1414 PetscFunctionBegin; 1415 if (flag == SOR_APPLY_UPPER) { 1416 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1417 PetscFunctionReturn(0); 1418 } 1419 1420 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) { 1421 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 1422 } 1423 1424 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1425 if (flag & SOR_ZERO_INITIAL_GUESS) { 1426 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1427 its--; 1428 } 1429 1430 while (its--) { 1431 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1432 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1433 1434 /* update rhs: bb1 = bb - B*x */ 1435 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1436 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1437 1438 /* local sweep */ 1439 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1440 } 1441 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1442 if (flag & SOR_ZERO_INITIAL_GUESS) { 1443 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1444 its--; 1445 } 1446 while (its--) { 1447 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1448 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1449 1450 /* update rhs: bb1 = bb - B*x */ 1451 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1452 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1453 1454 /* local sweep */ 1455 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1456 } 1457 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1458 if (flag & SOR_ZERO_INITIAL_GUESS) { 1459 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1460 its--; 1461 } 1462 while (its--) { 1463 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1464 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1465 1466 /* update rhs: bb1 = bb - B*x */ 1467 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1468 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1469 1470 /* local sweep */ 1471 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1472 } 1473 } else if (flag & SOR_EISENSTAT) { 1474 Vec xx1; 1475 1476 ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr); 1477 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr); 1478 1479 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1480 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1481 if (!mat->diag) { 1482 ierr = MatCreateVecs(matin,&mat->diag,NULL);CHKERRQ(ierr); 1483 ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr); 1484 } 1485 ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr); 1486 if (hasop) { 1487 ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr); 1488 } else { 1489 ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr); 1490 } 1491 ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr); 1492 1493 ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr); 1494 1495 /* local sweep */ 1496 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr); 1497 ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr); 1498 ierr = VecDestroy(&xx1);CHKERRQ(ierr); 1499 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported"); 1500 1501 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 1502 1503 matin->factorerrortype = mat->A->factorerrortype; 1504 PetscFunctionReturn(0); 1505 } 1506 1507 PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B) 1508 { 1509 Mat aA,aB,Aperm; 1510 const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj; 1511 PetscScalar *aa,*ba; 1512 PetscInt i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest; 1513 PetscSF rowsf,sf; 1514 IS parcolp = NULL; 1515 PetscBool done; 1516 PetscErrorCode ierr; 1517 1518 PetscFunctionBegin; 1519 ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); 1520 ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr); 1521 ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr); 1522 ierr = PetscMalloc3(PetscMax(m,n),&work,m,&rdest,n,&cdest);CHKERRQ(ierr); 1523 1524 /* Invert row permutation to find out where my rows should go */ 1525 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr); 1526 ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr); 1527 ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr); 1528 for (i=0; i<m; i++) work[i] = A->rmap->rstart + i; 1529 ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1530 ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1531 1532 /* Invert column permutation to find out where my columns should go */ 1533 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1534 ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr); 1535 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1536 for (i=0; i<n; i++) work[i] = A->cmap->rstart + i; 1537 ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1538 ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1539 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1540 1541 ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr); 1542 ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr); 1543 ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr); 1544 1545 /* Find out where my gcols should go */ 1546 ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr); 1547 ierr = PetscMalloc1(ng,&gcdest);CHKERRQ(ierr); 1548 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1549 ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr); 1550 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1551 ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1552 ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1553 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1554 1555 ierr = PetscCalloc4(m,&dnnz,m,&onnz,m,&tdnnz,m,&tonnz);CHKERRQ(ierr); 1556 ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1557 ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1558 for (i=0; i<m; i++) { 1559 PetscInt row = rdest[i],rowner; 1560 ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr); 1561 for (j=ai[i]; j<ai[i+1]; j++) { 1562 PetscInt cowner,col = cdest[aj[j]]; 1563 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */ 1564 if (rowner == cowner) dnnz[i]++; 1565 else onnz[i]++; 1566 } 1567 for (j=bi[i]; j<bi[i+1]; j++) { 1568 PetscInt cowner,col = gcdest[bj[j]]; 1569 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); 1570 if (rowner == cowner) dnnz[i]++; 1571 else onnz[i]++; 1572 } 1573 } 1574 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1575 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1576 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1577 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1578 ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr); 1579 1580 ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr); 1581 ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr); 1582 ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr); 1583 for (i=0; i<m; i++) { 1584 PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */ 1585 PetscInt j0,rowlen; 1586 rowlen = ai[i+1] - ai[i]; 1587 for (j0=j=0; j<rowlen; j0=j) { /* rowlen could be larger than number of rows m, so sum in batches */ 1588 for ( ; j<PetscMin(rowlen,j0+m); j++) acols[j-j0] = cdest[aj[ai[i]+j]]; 1589 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,acols,aa+ai[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1590 } 1591 rowlen = bi[i+1] - bi[i]; 1592 for (j0=j=0; j<rowlen; j0=j) { 1593 for ( ; j<PetscMin(rowlen,j0+m); j++) bcols[j-j0] = gcdest[bj[bi[i]+j]]; 1594 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,bcols,ba+bi[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1595 } 1596 } 1597 ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1598 ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1599 ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1600 ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1601 ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr); 1602 ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr); 1603 ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr); 1604 ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr); 1605 ierr = PetscFree(gcdest);CHKERRQ(ierr); 1606 if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);} 1607 *B = Aperm; 1608 PetscFunctionReturn(0); 1609 } 1610 1611 PetscErrorCode MatGetGhosts_MPIAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 1612 { 1613 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1614 PetscErrorCode ierr; 1615 1616 PetscFunctionBegin; 1617 ierr = MatGetSize(aij->B,NULL,nghosts);CHKERRQ(ierr); 1618 if (ghosts) *ghosts = aij->garray; 1619 PetscFunctionReturn(0); 1620 } 1621 1622 PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1623 { 1624 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1625 Mat A = mat->A,B = mat->B; 1626 PetscErrorCode ierr; 1627 PetscReal isend[5],irecv[5]; 1628 1629 PetscFunctionBegin; 1630 info->block_size = 1.0; 1631 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1632 1633 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1634 isend[3] = info->memory; isend[4] = info->mallocs; 1635 1636 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1637 1638 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1639 isend[3] += info->memory; isend[4] += info->mallocs; 1640 if (flag == MAT_LOCAL) { 1641 info->nz_used = isend[0]; 1642 info->nz_allocated = isend[1]; 1643 info->nz_unneeded = isend[2]; 1644 info->memory = isend[3]; 1645 info->mallocs = isend[4]; 1646 } else if (flag == MAT_GLOBAL_MAX) { 1647 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1648 1649 info->nz_used = irecv[0]; 1650 info->nz_allocated = irecv[1]; 1651 info->nz_unneeded = irecv[2]; 1652 info->memory = irecv[3]; 1653 info->mallocs = irecv[4]; 1654 } else if (flag == MAT_GLOBAL_SUM) { 1655 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1656 1657 info->nz_used = irecv[0]; 1658 info->nz_allocated = irecv[1]; 1659 info->nz_unneeded = irecv[2]; 1660 info->memory = irecv[3]; 1661 info->mallocs = irecv[4]; 1662 } 1663 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1664 info->fill_ratio_needed = 0; 1665 info->factor_mallocs = 0; 1666 PetscFunctionReturn(0); 1667 } 1668 1669 PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg) 1670 { 1671 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1672 PetscErrorCode ierr; 1673 1674 PetscFunctionBegin; 1675 switch (op) { 1676 case MAT_NEW_NONZERO_LOCATIONS: 1677 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1678 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1679 case MAT_KEEP_NONZERO_PATTERN: 1680 case MAT_NEW_NONZERO_LOCATION_ERR: 1681 case MAT_USE_INODES: 1682 case MAT_IGNORE_ZERO_ENTRIES: 1683 MatCheckPreallocated(A,1); 1684 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1685 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1686 break; 1687 case MAT_ROW_ORIENTED: 1688 MatCheckPreallocated(A,1); 1689 a->roworiented = flg; 1690 1691 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1692 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1693 break; 1694 case MAT_NEW_DIAGONALS: 1695 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1696 break; 1697 case MAT_IGNORE_OFF_PROC_ENTRIES: 1698 a->donotstash = flg; 1699 break; 1700 case MAT_SPD: 1701 A->spd_set = PETSC_TRUE; 1702 A->spd = flg; 1703 if (flg) { 1704 A->symmetric = PETSC_TRUE; 1705 A->structurally_symmetric = PETSC_TRUE; 1706 A->symmetric_set = PETSC_TRUE; 1707 A->structurally_symmetric_set = PETSC_TRUE; 1708 } 1709 break; 1710 case MAT_SYMMETRIC: 1711 MatCheckPreallocated(A,1); 1712 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1713 break; 1714 case MAT_STRUCTURALLY_SYMMETRIC: 1715 MatCheckPreallocated(A,1); 1716 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1717 break; 1718 case MAT_HERMITIAN: 1719 MatCheckPreallocated(A,1); 1720 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1721 break; 1722 case MAT_SYMMETRY_ETERNAL: 1723 MatCheckPreallocated(A,1); 1724 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1725 break; 1726 case MAT_SUBMAT_SINGLEIS: 1727 A->submat_singleis = flg; 1728 break; 1729 default: 1730 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1731 } 1732 PetscFunctionReturn(0); 1733 } 1734 1735 PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1736 { 1737 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1738 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1739 PetscErrorCode ierr; 1740 PetscInt i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart; 1741 PetscInt nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend; 1742 PetscInt *cmap,*idx_p; 1743 1744 PetscFunctionBegin; 1745 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1746 mat->getrowactive = PETSC_TRUE; 1747 1748 if (!mat->rowvalues && (idx || v)) { 1749 /* 1750 allocate enough space to hold information from the longest row. 1751 */ 1752 Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data; 1753 PetscInt max = 1,tmp; 1754 for (i=0; i<matin->rmap->n; i++) { 1755 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1756 if (max < tmp) max = tmp; 1757 } 1758 ierr = PetscMalloc2(max,&mat->rowvalues,max,&mat->rowindices);CHKERRQ(ierr); 1759 } 1760 1761 if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows"); 1762 lrow = row - rstart; 1763 1764 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1765 if (!v) {pvA = 0; pvB = 0;} 1766 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1767 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1768 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1769 nztot = nzA + nzB; 1770 1771 cmap = mat->garray; 1772 if (v || idx) { 1773 if (nztot) { 1774 /* Sort by increasing column numbers, assuming A and B already sorted */ 1775 PetscInt imark = -1; 1776 if (v) { 1777 *v = v_p = mat->rowvalues; 1778 for (i=0; i<nzB; i++) { 1779 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1780 else break; 1781 } 1782 imark = i; 1783 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1784 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1785 } 1786 if (idx) { 1787 *idx = idx_p = mat->rowindices; 1788 if (imark > -1) { 1789 for (i=0; i<imark; i++) { 1790 idx_p[i] = cmap[cworkB[i]]; 1791 } 1792 } else { 1793 for (i=0; i<nzB; i++) { 1794 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1795 else break; 1796 } 1797 imark = i; 1798 } 1799 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart + cworkA[i]; 1800 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]]; 1801 } 1802 } else { 1803 if (idx) *idx = 0; 1804 if (v) *v = 0; 1805 } 1806 } 1807 *nz = nztot; 1808 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1809 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1810 PetscFunctionReturn(0); 1811 } 1812 1813 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1814 { 1815 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1816 1817 PetscFunctionBegin; 1818 if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first"); 1819 aij->getrowactive = PETSC_FALSE; 1820 PetscFunctionReturn(0); 1821 } 1822 1823 PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm) 1824 { 1825 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1826 Mat_SeqAIJ *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data; 1827 PetscErrorCode ierr; 1828 PetscInt i,j,cstart = mat->cmap->rstart; 1829 PetscReal sum = 0.0; 1830 MatScalar *v; 1831 1832 PetscFunctionBegin; 1833 if (aij->size == 1) { 1834 ierr = MatNorm(aij->A,type,norm);CHKERRQ(ierr); 1835 } else { 1836 if (type == NORM_FROBENIUS) { 1837 v = amat->a; 1838 for (i=0; i<amat->nz; i++) { 1839 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1840 } 1841 v = bmat->a; 1842 for (i=0; i<bmat->nz; i++) { 1843 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1844 } 1845 ierr = MPIU_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1846 *norm = PetscSqrtReal(*norm); 1847 ierr = PetscLogFlops(2*amat->nz+2*bmat->nz);CHKERRQ(ierr); 1848 } else if (type == NORM_1) { /* max column norm */ 1849 PetscReal *tmp,*tmp2; 1850 PetscInt *jj,*garray = aij->garray; 1851 ierr = PetscCalloc1(mat->cmap->N+1,&tmp);CHKERRQ(ierr); 1852 ierr = PetscMalloc1(mat->cmap->N+1,&tmp2);CHKERRQ(ierr); 1853 *norm = 0.0; 1854 v = amat->a; jj = amat->j; 1855 for (j=0; j<amat->nz; j++) { 1856 tmp[cstart + *jj++] += PetscAbsScalar(*v); v++; 1857 } 1858 v = bmat->a; jj = bmat->j; 1859 for (j=0; j<bmat->nz; j++) { 1860 tmp[garray[*jj++]] += PetscAbsScalar(*v); v++; 1861 } 1862 ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1863 for (j=0; j<mat->cmap->N; j++) { 1864 if (tmp2[j] > *norm) *norm = tmp2[j]; 1865 } 1866 ierr = PetscFree(tmp);CHKERRQ(ierr); 1867 ierr = PetscFree(tmp2);CHKERRQ(ierr); 1868 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1869 } else if (type == NORM_INFINITY) { /* max row norm */ 1870 PetscReal ntemp = 0.0; 1871 for (j=0; j<aij->A->rmap->n; j++) { 1872 v = amat->a + amat->i[j]; 1873 sum = 0.0; 1874 for (i=0; i<amat->i[j+1]-amat->i[j]; i++) { 1875 sum += PetscAbsScalar(*v); v++; 1876 } 1877 v = bmat->a + bmat->i[j]; 1878 for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) { 1879 sum += PetscAbsScalar(*v); v++; 1880 } 1881 if (sum > ntemp) ntemp = sum; 1882 } 1883 ierr = MPIU_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1884 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1885 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm"); 1886 } 1887 PetscFunctionReturn(0); 1888 } 1889 1890 PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout) 1891 { 1892 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1893 Mat_SeqAIJ *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data; 1894 PetscErrorCode ierr; 1895 PetscInt M = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i; 1896 PetscInt cstart = A->cmap->rstart,ncol; 1897 Mat B; 1898 MatScalar *array; 1899 1900 PetscFunctionBegin; 1901 if (reuse == MAT_INPLACE_MATRIX && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1902 1903 ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n; 1904 ai = Aloc->i; aj = Aloc->j; 1905 bi = Bloc->i; bj = Bloc->j; 1906 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1907 PetscInt *d_nnz,*g_nnz,*o_nnz; 1908 PetscSFNode *oloc; 1909 PETSC_UNUSED PetscSF sf; 1910 1911 ierr = PetscMalloc4(na,&d_nnz,na,&o_nnz,nb,&g_nnz,nb,&oloc);CHKERRQ(ierr); 1912 /* compute d_nnz for preallocation */ 1913 ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1914 for (i=0; i<ai[ma]; i++) { 1915 d_nnz[aj[i]]++; 1916 aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1917 } 1918 /* compute local off-diagonal contributions */ 1919 ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr); 1920 for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++; 1921 /* map those to global */ 1922 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1923 ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr); 1924 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1925 ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1926 ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1927 ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1928 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1929 1930 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1931 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1932 ierr = MatSetBlockSizes(B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 1933 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1934 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 1935 ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr); 1936 } else { 1937 B = *matout; 1938 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1939 for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1940 } 1941 1942 /* copy over the A part */ 1943 array = Aloc->a; 1944 row = A->rmap->rstart; 1945 for (i=0; i<ma; i++) { 1946 ncol = ai[i+1]-ai[i]; 1947 ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1948 row++; 1949 array += ncol; aj += ncol; 1950 } 1951 aj = Aloc->j; 1952 for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */ 1953 1954 /* copy over the B part */ 1955 ierr = PetscCalloc1(bi[mb],&cols);CHKERRQ(ierr); 1956 array = Bloc->a; 1957 row = A->rmap->rstart; 1958 for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]]; 1959 cols_tmp = cols; 1960 for (i=0; i<mb; i++) { 1961 ncol = bi[i+1]-bi[i]; 1962 ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1963 row++; 1964 array += ncol; cols_tmp += ncol; 1965 } 1966 ierr = PetscFree(cols);CHKERRQ(ierr); 1967 1968 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1969 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1970 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 1971 *matout = B; 1972 } else { 1973 ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr); 1974 } 1975 PetscFunctionReturn(0); 1976 } 1977 1978 PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr) 1979 { 1980 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1981 Mat a = aij->A,b = aij->B; 1982 PetscErrorCode ierr; 1983 PetscInt s1,s2,s3; 1984 1985 PetscFunctionBegin; 1986 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1987 if (rr) { 1988 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1989 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1990 /* Overlap communication with computation. */ 1991 ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1992 } 1993 if (ll) { 1994 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1995 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1996 ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr); 1997 } 1998 /* scale the diagonal block */ 1999 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 2000 2001 if (rr) { 2002 /* Do a scatter end and then right scale the off-diagonal block */ 2003 ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2004 ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr); 2005 } 2006 PetscFunctionReturn(0); 2007 } 2008 2009 PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2010 { 2011 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2012 PetscErrorCode ierr; 2013 2014 PetscFunctionBegin; 2015 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 2016 PetscFunctionReturn(0); 2017 } 2018 2019 PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool *flag) 2020 { 2021 Mat_MPIAIJ *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data; 2022 Mat a,b,c,d; 2023 PetscBool flg; 2024 PetscErrorCode ierr; 2025 2026 PetscFunctionBegin; 2027 a = matA->A; b = matA->B; 2028 c = matB->A; d = matB->B; 2029 2030 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 2031 if (flg) { 2032 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 2033 } 2034 ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2035 PetscFunctionReturn(0); 2036 } 2037 2038 PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str) 2039 { 2040 PetscErrorCode ierr; 2041 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2042 Mat_MPIAIJ *b = (Mat_MPIAIJ*)B->data; 2043 2044 PetscFunctionBegin; 2045 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2046 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2047 /* because of the column compression in the off-processor part of the matrix a->B, 2048 the number of columns in a->B and b->B may be different, hence we cannot call 2049 the MatCopy() directly on the two parts. If need be, we can provide a more 2050 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2051 then copying the submatrices */ 2052 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2053 } else { 2054 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 2055 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 2056 } 2057 PetscFunctionReturn(0); 2058 } 2059 2060 PetscErrorCode MatSetUp_MPIAIJ(Mat A) 2061 { 2062 PetscErrorCode ierr; 2063 2064 PetscFunctionBegin; 2065 ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 2066 PetscFunctionReturn(0); 2067 } 2068 2069 /* 2070 Computes the number of nonzeros per row needed for preallocation when X and Y 2071 have different nonzero structure. 2072 */ 2073 PetscErrorCode MatAXPYGetPreallocation_MPIX_private(PetscInt m,const PetscInt *xi,const PetscInt *xj,const PetscInt *xltog,const PetscInt *yi,const PetscInt *yj,const PetscInt *yltog,PetscInt *nnz) 2074 { 2075 PetscInt i,j,k,nzx,nzy; 2076 2077 PetscFunctionBegin; 2078 /* Set the number of nonzeros in the new matrix */ 2079 for (i=0; i<m; i++) { 2080 const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i]; 2081 nzx = xi[i+1] - xi[i]; 2082 nzy = yi[i+1] - yi[i]; 2083 nnz[i] = 0; 2084 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2085 for (; k<nzy && yltog[yjj[k]]<xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */ 2086 if (k<nzy && yltog[yjj[k]]==xltog[xjj[j]]) k++; /* Skip duplicate */ 2087 nnz[i]++; 2088 } 2089 for (; k<nzy; k++) nnz[i]++; 2090 } 2091 PetscFunctionReturn(0); 2092 } 2093 2094 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2095 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 2096 { 2097 PetscErrorCode ierr; 2098 PetscInt m = Y->rmap->N; 2099 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2100 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2101 2102 PetscFunctionBegin; 2103 ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr); 2104 PetscFunctionReturn(0); 2105 } 2106 2107 PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2108 { 2109 PetscErrorCode ierr; 2110 Mat_MPIAIJ *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data; 2111 PetscBLASInt bnz,one=1; 2112 Mat_SeqAIJ *x,*y; 2113 2114 PetscFunctionBegin; 2115 if (str == SAME_NONZERO_PATTERN) { 2116 PetscScalar alpha = a; 2117 x = (Mat_SeqAIJ*)xx->A->data; 2118 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2119 y = (Mat_SeqAIJ*)yy->A->data; 2120 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2121 x = (Mat_SeqAIJ*)xx->B->data; 2122 y = (Mat_SeqAIJ*)yy->B->data; 2123 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2124 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2125 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 2126 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2127 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 2128 } else { 2129 Mat B; 2130 PetscInt *nnz_d,*nnz_o; 2131 ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr); 2132 ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr); 2133 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2134 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2135 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2136 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 2137 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2138 ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 2139 ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 2140 ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 2141 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2142 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 2143 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 2144 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 2145 } 2146 PetscFunctionReturn(0); 2147 } 2148 2149 extern PetscErrorCode MatConjugate_SeqAIJ(Mat); 2150 2151 PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2152 { 2153 #if defined(PETSC_USE_COMPLEX) 2154 PetscErrorCode ierr; 2155 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2156 2157 PetscFunctionBegin; 2158 ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr); 2159 ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr); 2160 #else 2161 PetscFunctionBegin; 2162 #endif 2163 PetscFunctionReturn(0); 2164 } 2165 2166 PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2167 { 2168 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2169 PetscErrorCode ierr; 2170 2171 PetscFunctionBegin; 2172 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2173 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2174 PetscFunctionReturn(0); 2175 } 2176 2177 PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2178 { 2179 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2180 PetscErrorCode ierr; 2181 2182 PetscFunctionBegin; 2183 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2184 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2185 PetscFunctionReturn(0); 2186 } 2187 2188 PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2189 { 2190 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2191 PetscErrorCode ierr; 2192 PetscInt i,*idxb = 0; 2193 PetscScalar *va,*vb; 2194 Vec vtmp; 2195 2196 PetscFunctionBegin; 2197 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 2198 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2199 if (idx) { 2200 for (i=0; i<A->rmap->n; i++) { 2201 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2202 } 2203 } 2204 2205 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2206 if (idx) { 2207 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2208 } 2209 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2210 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2211 2212 for (i=0; i<A->rmap->n; i++) { 2213 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 2214 va[i] = vb[i]; 2215 if (idx) idx[i] = a->garray[idxb[i]]; 2216 } 2217 } 2218 2219 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2220 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2221 ierr = PetscFree(idxb);CHKERRQ(ierr); 2222 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2223 PetscFunctionReturn(0); 2224 } 2225 2226 PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2227 { 2228 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2229 PetscErrorCode ierr; 2230 PetscInt i,*idxb = 0; 2231 PetscScalar *va,*vb; 2232 Vec vtmp; 2233 2234 PetscFunctionBegin; 2235 ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr); 2236 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2237 if (idx) { 2238 for (i=0; i<A->cmap->n; i++) { 2239 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2240 } 2241 } 2242 2243 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2244 if (idx) { 2245 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2246 } 2247 ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2248 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2249 2250 for (i=0; i<A->rmap->n; i++) { 2251 if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) { 2252 va[i] = vb[i]; 2253 if (idx) idx[i] = a->garray[idxb[i]]; 2254 } 2255 } 2256 2257 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2258 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2259 ierr = PetscFree(idxb);CHKERRQ(ierr); 2260 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2261 PetscFunctionReturn(0); 2262 } 2263 2264 PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2265 { 2266 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2267 PetscInt n = A->rmap->n; 2268 PetscInt cstart = A->cmap->rstart; 2269 PetscInt *cmap = mat->garray; 2270 PetscInt *diagIdx, *offdiagIdx; 2271 Vec diagV, offdiagV; 2272 PetscScalar *a, *diagA, *offdiagA; 2273 PetscInt r; 2274 PetscErrorCode ierr; 2275 2276 PetscFunctionBegin; 2277 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2278 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr); 2279 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr); 2280 ierr = MatGetRowMin(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2281 ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2282 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2283 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2284 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2285 for (r = 0; r < n; ++r) { 2286 if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) { 2287 a[r] = diagA[r]; 2288 idx[r] = cstart + diagIdx[r]; 2289 } else { 2290 a[r] = offdiagA[r]; 2291 idx[r] = cmap[offdiagIdx[r]]; 2292 } 2293 } 2294 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2295 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2296 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2297 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2298 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2299 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2300 PetscFunctionReturn(0); 2301 } 2302 2303 PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2304 { 2305 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2306 PetscInt n = A->rmap->n; 2307 PetscInt cstart = A->cmap->rstart; 2308 PetscInt *cmap = mat->garray; 2309 PetscInt *diagIdx, *offdiagIdx; 2310 Vec diagV, offdiagV; 2311 PetscScalar *a, *diagA, *offdiagA; 2312 PetscInt r; 2313 PetscErrorCode ierr; 2314 2315 PetscFunctionBegin; 2316 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2317 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr); 2318 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr); 2319 ierr = MatGetRowMax(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2320 ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2321 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2322 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2323 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2324 for (r = 0; r < n; ++r) { 2325 if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) { 2326 a[r] = diagA[r]; 2327 idx[r] = cstart + diagIdx[r]; 2328 } else { 2329 a[r] = offdiagA[r]; 2330 idx[r] = cmap[offdiagIdx[r]]; 2331 } 2332 } 2333 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2334 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2335 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2336 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2337 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2338 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2339 PetscFunctionReturn(0); 2340 } 2341 2342 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat) 2343 { 2344 PetscErrorCode ierr; 2345 Mat *dummy; 2346 2347 PetscFunctionBegin; 2348 ierr = MatCreateSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr); 2349 *newmat = *dummy; 2350 ierr = PetscFree(dummy);CHKERRQ(ierr); 2351 PetscFunctionReturn(0); 2352 } 2353 2354 PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values) 2355 { 2356 Mat_MPIAIJ *a = (Mat_MPIAIJ*) A->data; 2357 PetscErrorCode ierr; 2358 2359 PetscFunctionBegin; 2360 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2361 A->factorerrortype = a->A->factorerrortype; 2362 PetscFunctionReturn(0); 2363 } 2364 2365 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx) 2366 { 2367 PetscErrorCode ierr; 2368 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)x->data; 2369 2370 PetscFunctionBegin; 2371 ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr); 2372 ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr); 2373 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2374 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2375 PetscFunctionReturn(0); 2376 } 2377 2378 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A,PetscBool sc) 2379 { 2380 PetscFunctionBegin; 2381 if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable; 2382 else A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ; 2383 PetscFunctionReturn(0); 2384 } 2385 2386 /*@ 2387 MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap 2388 2389 Collective on Mat 2390 2391 Input Parameters: 2392 + A - the matrix 2393 - sc - PETSC_TRUE indicates use the scalable algorithm (default is not to use the scalable algorithm) 2394 2395 Level: advanced 2396 2397 @*/ 2398 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A,PetscBool sc) 2399 { 2400 PetscErrorCode ierr; 2401 2402 PetscFunctionBegin; 2403 ierr = PetscTryMethod(A,"MatMPIAIJSetUseScalableIncreaseOverlap_C",(Mat,PetscBool),(A,sc));CHKERRQ(ierr); 2404 PetscFunctionReturn(0); 2405 } 2406 2407 PetscErrorCode MatSetFromOptions_MPIAIJ(PetscOptionItems *PetscOptionsObject,Mat A) 2408 { 2409 PetscErrorCode ierr; 2410 PetscBool sc = PETSC_FALSE,flg; 2411 2412 PetscFunctionBegin; 2413 ierr = PetscOptionsHead(PetscOptionsObject,"MPIAIJ options");CHKERRQ(ierr); 2414 ierr = PetscObjectOptionsBegin((PetscObject)A); 2415 if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE; 2416 ierr = PetscOptionsBool("-mat_increase_overlap_scalable","Use a scalable algorithm to compute the overlap","MatIncreaseOverlap",sc,&sc,&flg);CHKERRQ(ierr); 2417 if (flg) { 2418 ierr = MatMPIAIJSetUseScalableIncreaseOverlap(A,sc);CHKERRQ(ierr); 2419 } 2420 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2421 PetscFunctionReturn(0); 2422 } 2423 2424 PetscErrorCode MatShift_MPIAIJ(Mat Y,PetscScalar a) 2425 { 2426 PetscErrorCode ierr; 2427 Mat_MPIAIJ *maij = (Mat_MPIAIJ*)Y->data; 2428 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)maij->A->data; 2429 2430 PetscFunctionBegin; 2431 if (!Y->preallocated) { 2432 ierr = MatMPIAIJSetPreallocation(Y,1,NULL,0,NULL);CHKERRQ(ierr); 2433 } else if (!aij->nz) { 2434 PetscInt nonew = aij->nonew; 2435 ierr = MatSeqAIJSetPreallocation(maij->A,1,NULL);CHKERRQ(ierr); 2436 aij->nonew = nonew; 2437 } 2438 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2439 PetscFunctionReturn(0); 2440 } 2441 2442 PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A,PetscBool *missing,PetscInt *d) 2443 { 2444 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2445 PetscErrorCode ierr; 2446 2447 PetscFunctionBegin; 2448 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2449 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2450 if (d) { 2451 PetscInt rstart; 2452 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2453 *d += rstart; 2454 2455 } 2456 PetscFunctionReturn(0); 2457 } 2458 2459 2460 /* -------------------------------------------------------------------*/ 2461 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 2462 MatGetRow_MPIAIJ, 2463 MatRestoreRow_MPIAIJ, 2464 MatMult_MPIAIJ, 2465 /* 4*/ MatMultAdd_MPIAIJ, 2466 MatMultTranspose_MPIAIJ, 2467 MatMultTransposeAdd_MPIAIJ, 2468 0, 2469 0, 2470 0, 2471 /*10*/ 0, 2472 0, 2473 0, 2474 MatSOR_MPIAIJ, 2475 MatTranspose_MPIAIJ, 2476 /*15*/ MatGetInfo_MPIAIJ, 2477 MatEqual_MPIAIJ, 2478 MatGetDiagonal_MPIAIJ, 2479 MatDiagonalScale_MPIAIJ, 2480 MatNorm_MPIAIJ, 2481 /*20*/ MatAssemblyBegin_MPIAIJ, 2482 MatAssemblyEnd_MPIAIJ, 2483 MatSetOption_MPIAIJ, 2484 MatZeroEntries_MPIAIJ, 2485 /*24*/ MatZeroRows_MPIAIJ, 2486 0, 2487 0, 2488 0, 2489 0, 2490 /*29*/ MatSetUp_MPIAIJ, 2491 0, 2492 0, 2493 MatGetDiagonalBlock_MPIAIJ, 2494 0, 2495 /*34*/ MatDuplicate_MPIAIJ, 2496 0, 2497 0, 2498 0, 2499 0, 2500 /*39*/ MatAXPY_MPIAIJ, 2501 MatCreateSubMatrices_MPIAIJ, 2502 MatIncreaseOverlap_MPIAIJ, 2503 MatGetValues_MPIAIJ, 2504 MatCopy_MPIAIJ, 2505 /*44*/ MatGetRowMax_MPIAIJ, 2506 MatScale_MPIAIJ, 2507 MatShift_MPIAIJ, 2508 MatDiagonalSet_MPIAIJ, 2509 MatZeroRowsColumns_MPIAIJ, 2510 /*49*/ MatSetRandom_MPIAIJ, 2511 0, 2512 0, 2513 0, 2514 0, 2515 /*54*/ MatFDColoringCreate_MPIXAIJ, 2516 0, 2517 MatSetUnfactored_MPIAIJ, 2518 MatPermute_MPIAIJ, 2519 0, 2520 /*59*/ MatCreateSubMatrix_MPIAIJ, 2521 MatDestroy_MPIAIJ, 2522 MatView_MPIAIJ, 2523 0, 2524 MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ, 2525 /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ, 2526 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 2527 0, 2528 0, 2529 0, 2530 /*69*/ MatGetRowMaxAbs_MPIAIJ, 2531 MatGetRowMinAbs_MPIAIJ, 2532 0, 2533 0, 2534 0, 2535 0, 2536 /*75*/ MatFDColoringApply_AIJ, 2537 MatSetFromOptions_MPIAIJ, 2538 0, 2539 0, 2540 MatFindZeroDiagonals_MPIAIJ, 2541 /*80*/ 0, 2542 0, 2543 0, 2544 /*83*/ MatLoad_MPIAIJ, 2545 0, 2546 0, 2547 0, 2548 0, 2549 0, 2550 /*89*/ MatMatMult_MPIAIJ_MPIAIJ, 2551 MatMatMultSymbolic_MPIAIJ_MPIAIJ, 2552 MatMatMultNumeric_MPIAIJ_MPIAIJ, 2553 MatPtAP_MPIAIJ_MPIAIJ, 2554 MatPtAPSymbolic_MPIAIJ_MPIAIJ, 2555 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 2556 0, 2557 0, 2558 0, 2559 0, 2560 /*99*/ 0, 2561 0, 2562 0, 2563 MatConjugate_MPIAIJ, 2564 0, 2565 /*104*/MatSetValuesRow_MPIAIJ, 2566 MatRealPart_MPIAIJ, 2567 MatImaginaryPart_MPIAIJ, 2568 0, 2569 0, 2570 /*109*/0, 2571 0, 2572 MatGetRowMin_MPIAIJ, 2573 0, 2574 MatMissingDiagonal_MPIAIJ, 2575 /*114*/MatGetSeqNonzeroStructure_MPIAIJ, 2576 0, 2577 MatGetGhosts_MPIAIJ, 2578 0, 2579 0, 2580 /*119*/0, 2581 0, 2582 0, 2583 0, 2584 MatGetMultiProcBlock_MPIAIJ, 2585 /*124*/MatFindNonzeroRows_MPIAIJ, 2586 MatGetColumnNorms_MPIAIJ, 2587 MatInvertBlockDiagonal_MPIAIJ, 2588 0, 2589 MatCreateSubMatricesMPI_MPIAIJ, 2590 /*129*/0, 2591 MatTransposeMatMult_MPIAIJ_MPIAIJ, 2592 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ, 2593 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 2594 0, 2595 /*134*/0, 2596 0, 2597 0, 2598 0, 2599 0, 2600 /*139*/MatSetBlockSizes_MPIAIJ, 2601 0, 2602 0, 2603 MatFDColoringSetUp_MPIXAIJ, 2604 MatFindOffBlockDiagonalEntries_MPIAIJ, 2605 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIAIJ 2606 }; 2607 2608 /* ----------------------------------------------------------------------------------------*/ 2609 2610 PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 2611 { 2612 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2613 PetscErrorCode ierr; 2614 2615 PetscFunctionBegin; 2616 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 2617 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 2618 PetscFunctionReturn(0); 2619 } 2620 2621 PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 2622 { 2623 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2624 PetscErrorCode ierr; 2625 2626 PetscFunctionBegin; 2627 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 2628 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 2629 PetscFunctionReturn(0); 2630 } 2631 2632 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 2633 { 2634 Mat_MPIAIJ *b; 2635 PetscErrorCode ierr; 2636 2637 PetscFunctionBegin; 2638 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2639 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2640 b = (Mat_MPIAIJ*)B->data; 2641 2642 #if defined(PETSC_USE_CTABLE) 2643 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2644 #else 2645 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2646 #endif 2647 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2648 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2649 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2650 2651 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2652 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2653 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2654 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 2655 ierr = MatSetBlockSizesFromMats(b->B,B,B);CHKERRQ(ierr); 2656 ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr); 2657 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2658 2659 if (!B->preallocated) { 2660 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2661 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2662 ierr = MatSetBlockSizesFromMats(b->A,B,B);CHKERRQ(ierr); 2663 ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr); 2664 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2665 } 2666 2667 ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr); 2668 ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr); 2669 B->preallocated = PETSC_TRUE; 2670 B->was_assembled = PETSC_FALSE; 2671 B->assembled = PETSC_FALSE;; 2672 PetscFunctionReturn(0); 2673 } 2674 2675 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 2676 { 2677 Mat mat; 2678 Mat_MPIAIJ *a,*oldmat = (Mat_MPIAIJ*)matin->data; 2679 PetscErrorCode ierr; 2680 2681 PetscFunctionBegin; 2682 *newmat = 0; 2683 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 2684 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 2685 ierr = MatSetBlockSizesFromMats(mat,matin,matin);CHKERRQ(ierr); 2686 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 2687 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2688 a = (Mat_MPIAIJ*)mat->data; 2689 2690 mat->factortype = matin->factortype; 2691 mat->assembled = PETSC_TRUE; 2692 mat->insertmode = NOT_SET_VALUES; 2693 mat->preallocated = PETSC_TRUE; 2694 2695 a->size = oldmat->size; 2696 a->rank = oldmat->rank; 2697 a->donotstash = oldmat->donotstash; 2698 a->roworiented = oldmat->roworiented; 2699 a->rowindices = 0; 2700 a->rowvalues = 0; 2701 a->getrowactive = PETSC_FALSE; 2702 2703 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 2704 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 2705 2706 if (oldmat->colmap) { 2707 #if defined(PETSC_USE_CTABLE) 2708 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 2709 #else 2710 ierr = PetscMalloc1(mat->cmap->N,&a->colmap);CHKERRQ(ierr); 2711 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2712 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2713 #endif 2714 } else a->colmap = 0; 2715 if (oldmat->garray) { 2716 PetscInt len; 2717 len = oldmat->B->cmap->n; 2718 ierr = PetscMalloc1(len+1,&a->garray);CHKERRQ(ierr); 2719 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 2720 if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); } 2721 } else a->garray = 0; 2722 2723 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 2724 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 2725 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 2726 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 2727 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 2728 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 2729 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 2730 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 2731 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 2732 *newmat = mat; 2733 PetscFunctionReturn(0); 2734 } 2735 2736 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 2737 { 2738 PetscScalar *vals,*svals; 2739 MPI_Comm comm; 2740 PetscErrorCode ierr; 2741 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 2742 PetscInt i,nz,j,rstart,rend,mmax,maxnz = 0; 2743 PetscInt header[4],*rowlengths = 0,M,N,m,*cols; 2744 PetscInt *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols; 2745 PetscInt cend,cstart,n,*rowners; 2746 int fd; 2747 PetscInt bs = newMat->rmap->bs; 2748 2749 PetscFunctionBegin; 2750 /* force binary viewer to load .info file if it has not yet done so */ 2751 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 2752 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2753 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2754 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2755 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2756 if (!rank) { 2757 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 2758 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 2759 if (header[3] < 0) SETERRQ(PetscObjectComm((PetscObject)newMat),PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as MATMPIAIJ"); 2760 } 2761 2762 ierr = PetscOptionsBegin(comm,NULL,"Options for loading MATMPIAIJ matrix","Mat");CHKERRQ(ierr); 2763 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 2764 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2765 if (bs < 0) bs = 1; 2766 2767 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 2768 M = header[1]; N = header[2]; 2769 2770 /* If global sizes are set, check if they are consistent with that given in the file */ 2771 if (newMat->rmap->N >= 0 && newMat->rmap->N != M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of rows:Matrix in file has (%D) and input matrix has (%D)",newMat->rmap->N,M); 2772 if (newMat->cmap->N >=0 && newMat->cmap->N != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of cols:Matrix in file has (%D) and input matrix has (%D)",newMat->cmap->N,N); 2773 2774 /* determine ownership of all (block) rows */ 2775 if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs); 2776 if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank)); /* PETSC_DECIDE */ 2777 else m = newMat->rmap->n; /* Set by user */ 2778 2779 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 2780 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 2781 2782 /* First process needs enough room for process with most rows */ 2783 if (!rank) { 2784 mmax = rowners[1]; 2785 for (i=2; i<=size; i++) { 2786 mmax = PetscMax(mmax, rowners[i]); 2787 } 2788 } else mmax = -1; /* unused, but compilers complain */ 2789 2790 rowners[0] = 0; 2791 for (i=2; i<=size; i++) { 2792 rowners[i] += rowners[i-1]; 2793 } 2794 rstart = rowners[rank]; 2795 rend = rowners[rank+1]; 2796 2797 /* distribute row lengths to all processors */ 2798 ierr = PetscMalloc2(m,&ourlens,m,&offlens);CHKERRQ(ierr); 2799 if (!rank) { 2800 ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr); 2801 ierr = PetscMalloc1(mmax,&rowlengths);CHKERRQ(ierr); 2802 ierr = PetscCalloc1(size,&procsnz);CHKERRQ(ierr); 2803 for (j=0; j<m; j++) { 2804 procsnz[0] += ourlens[j]; 2805 } 2806 for (i=1; i<size; i++) { 2807 ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr); 2808 /* calculate the number of nonzeros on each processor */ 2809 for (j=0; j<rowners[i+1]-rowners[i]; j++) { 2810 procsnz[i] += rowlengths[j]; 2811 } 2812 ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2813 } 2814 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2815 } else { 2816 ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2817 } 2818 2819 if (!rank) { 2820 /* determine max buffer needed and allocate it */ 2821 maxnz = 0; 2822 for (i=0; i<size; i++) { 2823 maxnz = PetscMax(maxnz,procsnz[i]); 2824 } 2825 ierr = PetscMalloc1(maxnz,&cols);CHKERRQ(ierr); 2826 2827 /* read in my part of the matrix column indices */ 2828 nz = procsnz[0]; 2829 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2830 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 2831 2832 /* read in every one elses and ship off */ 2833 for (i=1; i<size; i++) { 2834 nz = procsnz[i]; 2835 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 2836 ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2837 } 2838 ierr = PetscFree(cols);CHKERRQ(ierr); 2839 } else { 2840 /* determine buffer space needed for message */ 2841 nz = 0; 2842 for (i=0; i<m; i++) { 2843 nz += ourlens[i]; 2844 } 2845 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2846 2847 /* receive message of column indices*/ 2848 ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2849 } 2850 2851 /* determine column ownership if matrix is not square */ 2852 if (N != M) { 2853 if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank); 2854 else n = newMat->cmap->n; 2855 ierr = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2856 cstart = cend - n; 2857 } else { 2858 cstart = rstart; 2859 cend = rend; 2860 n = cend - cstart; 2861 } 2862 2863 /* loop over local rows, determining number of off diagonal entries */ 2864 ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr); 2865 jj = 0; 2866 for (i=0; i<m; i++) { 2867 for (j=0; j<ourlens[i]; j++) { 2868 if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++; 2869 jj++; 2870 } 2871 } 2872 2873 for (i=0; i<m; i++) { 2874 ourlens[i] -= offlens[i]; 2875 } 2876 ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr); 2877 2878 if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);} 2879 2880 ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr); 2881 2882 for (i=0; i<m; i++) { 2883 ourlens[i] += offlens[i]; 2884 } 2885 2886 if (!rank) { 2887 ierr = PetscMalloc1(maxnz+1,&vals);CHKERRQ(ierr); 2888 2889 /* read in my part of the matrix numerical values */ 2890 nz = procsnz[0]; 2891 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2892 2893 /* insert into matrix */ 2894 jj = rstart; 2895 smycols = mycols; 2896 svals = vals; 2897 for (i=0; i<m; i++) { 2898 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2899 smycols += ourlens[i]; 2900 svals += ourlens[i]; 2901 jj++; 2902 } 2903 2904 /* read in other processors and ship out */ 2905 for (i=1; i<size; i++) { 2906 nz = procsnz[i]; 2907 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2908 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2909 } 2910 ierr = PetscFree(procsnz);CHKERRQ(ierr); 2911 } else { 2912 /* receive numeric values */ 2913 ierr = PetscMalloc1(nz+1,&vals);CHKERRQ(ierr); 2914 2915 /* receive message of values*/ 2916 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2917 2918 /* insert into matrix */ 2919 jj = rstart; 2920 smycols = mycols; 2921 svals = vals; 2922 for (i=0; i<m; i++) { 2923 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2924 smycols += ourlens[i]; 2925 svals += ourlens[i]; 2926 jj++; 2927 } 2928 } 2929 ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr); 2930 ierr = PetscFree(vals);CHKERRQ(ierr); 2931 ierr = PetscFree(mycols);CHKERRQ(ierr); 2932 ierr = PetscFree(rowners);CHKERRQ(ierr); 2933 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2934 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2935 PetscFunctionReturn(0); 2936 } 2937 2938 /* Not scalable because of ISAllGather() unless getting all columns. */ 2939 PetscErrorCode ISGetSeqIS_Private(Mat mat,IS iscol,IS *isseq) 2940 { 2941 PetscErrorCode ierr; 2942 IS iscol_local; 2943 PetscBool isstride; 2944 PetscMPIInt lisstride=0,gisstride; 2945 2946 PetscFunctionBegin; 2947 /* check if we are grabbing all columns*/ 2948 ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&isstride);CHKERRQ(ierr); 2949 2950 if (isstride) { 2951 PetscInt start,len,mstart,mlen; 2952 ierr = ISStrideGetInfo(iscol,&start,NULL);CHKERRQ(ierr); 2953 ierr = ISGetLocalSize(iscol,&len);CHKERRQ(ierr); 2954 ierr = MatGetOwnershipRangeColumn(mat,&mstart,&mlen);CHKERRQ(ierr); 2955 if (mstart == start && mlen-mstart == len) lisstride = 1; 2956 } 2957 2958 ierr = MPIU_Allreduce(&lisstride,&gisstride,1,MPI_INT,MPI_MIN,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2959 if (gisstride) { 2960 PetscInt N; 2961 ierr = MatGetSize(mat,NULL,&N);CHKERRQ(ierr); 2962 ierr = ISCreateStride(PetscObjectComm((PetscObject)mat),N,0,1,&iscol_local);CHKERRQ(ierr); 2963 ierr = ISSetIdentity(iscol_local);CHKERRQ(ierr); 2964 ierr = PetscInfo(mat,"Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n");CHKERRQ(ierr); 2965 } else { 2966 PetscInt cbs; 2967 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 2968 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 2969 ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr); 2970 } 2971 2972 *isseq = iscol_local; 2973 PetscFunctionReturn(0); 2974 } 2975 2976 /* 2977 Used for avoiding ISAllGather() and global size of iscol_local (see MatCreateSubMatrix_MPIAIJ_nonscalable) 2978 2979 Input Parameters: 2980 mat - matrix 2981 iscol - parallel column index set; its local indices are a subset of local columns of mat, 2982 i.e., mat->cstart <= iscol[i] < mat->cend 2983 Output Parameter: 2984 iscol_sub - sequential column index set, a subset of iscol 2985 iscmap - column map; iscmap[i] indicates global location of iscol_sub[i] in iscol 2986 */ 2987 PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat,IS isrow,IS iscol,IS *iscol_sub,IS *iscmap,IS *isrow_d,IS *iscol_d,IS *iscol_o,IS *isgarray) 2988 { 2989 PetscErrorCode ierr; 2990 Vec x,cmap; 2991 const PetscInt *is_idx; 2992 PetscScalar *xarray,*cmaparray; 2993 PetscInt ncols,isstart,*idx,*camp,count,m,rstart; 2994 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 2995 Mat B=a->B; 2996 Vec lvec=a->lvec,lcmap; 2997 PetscInt i,cstart,cend,Bn=B->cmap->N; 2998 MPI_Comm comm; 2999 3000 PetscFunctionBegin; 3001 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3002 PetscMPIInt rank; 3003 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3004 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 3005 3006 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3007 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3008 ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3009 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3010 3011 /* get start indices */ 3012 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3013 isstart -= ncols; 3014 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3015 3016 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3017 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3018 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3019 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3020 for (i=0; i<ncols; i++) { 3021 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3022 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3023 3024 idx[i] = is_idx[i]-cstart; 3025 } 3026 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3027 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3028 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3029 3030 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_COPY_VALUES,iscol_d);CHKERRQ(ierr); 3031 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3032 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3033 ierr = PetscFree(idx);CHKERRQ(ierr); 3034 3035 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3036 rstart = mat->rmap->rstart; 3037 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3038 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3039 for (i=0; i<m; i++) { 3040 idx[i] = is_idx[i]-rstart; 3041 } 3042 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3043 3044 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_COPY_VALUES,isrow_d);CHKERRQ(ierr); 3045 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3046 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3047 ierr = PetscFree(idx);CHKERRQ(ierr); 3048 3049 /* (2) scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3050 ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3051 3052 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3053 3054 ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3055 ierr = VecScatterBegin(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3056 3057 count = ncols + Bn; 3058 ierr = PetscMalloc2(count,&idx,count,&camp);CHKERRQ(ierr); 3059 3060 ierr = VecScatterEnd(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3061 3062 /* (3) create scalable iscol_sub (a subset of iscol) and iscmap */ 3063 /* local column indices */ 3064 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3065 for (i=0; i<ncols; i++) { 3066 idx[i] = is_idx[i]; 3067 camp[i] = i + isstart; /* global index of iscol = column index in submat */ 3068 } 3069 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3070 count = ncols; 3071 3072 /* off-process column indices */ 3073 PetscInt *idx1,*cmap1,count1=0; 3074 ierr = PetscMalloc2(Bn,&idx1,Bn,&cmap1);CHKERRQ(ierr); 3075 3076 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3077 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3078 for (i=0; i<Bn; i++) { 3079 if (PetscRealPart(xarray[i]) > -1.0) { 3080 //if (rank == 1) printf("[%d] xarray[%d] = %g; cstart %d\n",rank,i,xarray[i],cstart); 3081 idx1[count1] = i; /* local column index in off-diagonal part B */ 3082 cmap1[count1++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3083 3084 idx[count] = (PetscInt)PetscRealPart(xarray[i]); 3085 camp[count++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3086 } 3087 } 3088 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3089 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3090 3091 ierr = PetscSortIntWithArray(count,camp,idx);CHKERRQ(ierr); 3092 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,iscol_sub);CHKERRQ(ierr); 3093 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,camp,PETSC_COPY_VALUES,iscmap);CHKERRQ(ierr); 3094 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3095 ierr = ISSetBlockSize(*iscol_sub,i);CHKERRQ(ierr); 3096 3097 ierr = ISCreateGeneral(PETSC_COMM_SELF,count1,idx1,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr); 3098 ierr = ISCreateGeneral(PETSC_COMM_SELF,count1,cmap1,PETSC_COPY_VALUES,isgarray);CHKERRQ(ierr); 3099 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3100 ierr = ISSetBlockSize(*iscol_o,i);CHKERRQ(ierr); 3101 ierr = PetscFree2(idx1,cmap1);CHKERRQ(ierr); 3102 3103 ierr = PetscFree2(idx,camp);CHKERRQ(ierr); 3104 ierr = VecDestroy(&x);CHKERRQ(ierr); 3105 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3106 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3107 PetscFunctionReturn(0); 3108 } 3109 3110 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3111 { 3112 PetscErrorCode ierr; 3113 IS iscol_local; 3114 PetscInt csize; 3115 PetscInt n,i,j,start,end; 3116 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3117 MPI_Comm comm; 3118 3119 PetscFunctionBegin; 3120 /* If isrow has same processor distribution as mat, 3121 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3122 if (call == MAT_REUSE_MATRIX) { 3123 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3124 if (iscol_local) sameRowDist = PETSC_TRUE; 3125 } else { 3126 /* check if isrow has same processor distribution as mat */ 3127 sameDist[0] = PETSC_FALSE; 3128 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3129 if (!n) { 3130 sameDist[0] = PETSC_TRUE; 3131 } else { 3132 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3133 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3134 if (i >= start && j < end) { 3135 sameDist[0] = PETSC_TRUE; 3136 } 3137 } 3138 3139 /* check if iscol has same processor distribution as mat */ 3140 sameDist[1] = PETSC_FALSE; 3141 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3142 if (!n) { 3143 sameDist[1] = PETSC_TRUE; 3144 } else { 3145 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3146 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3147 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3148 } 3149 3150 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3151 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3152 sameRowDist = tsameDist[0]; 3153 } 3154 3155 if (sameRowDist) { 3156 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,call,tsameDist[1],newmat);CHKERRQ(ierr); 3157 PetscFunctionReturn(0); 3158 } 3159 3160 /* General case: iscol -> iscol_local which has global size of iscol */ 3161 if (call == MAT_REUSE_MATRIX) { 3162 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3163 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3164 } else { 3165 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3166 } 3167 3168 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3169 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3170 3171 if (call == MAT_INITIAL_MATRIX) { 3172 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3173 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3174 } 3175 PetscFunctionReturn(0); 3176 } 3177 3178 /*@C 3179 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3180 and "off-diagonal" part of the matrix in CSR format. 3181 3182 Collective on MPI_Comm 3183 3184 Input Parameters: 3185 + comm - MPI communicator 3186 . A - "diagonal" portion of matrix 3187 . B - "off-diagonal" portion of matrix 3188 - garray - global index of B columns 3189 3190 Output Parameter: 3191 . mat - the matrix 3192 3193 Level: advanced 3194 3195 Notes: 3196 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 3197 3198 .keywords: matrix, aij, compressed row, sparse, parallel 3199 3200 .seealso: MatCreateMPIAIJWithSplitArrays() 3201 @*/ 3202 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3203 { 3204 PetscErrorCode ierr; 3205 Mat_MPIAIJ *maij; 3206 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data; 3207 PetscInt *oi=b->i,*oj=b->j,i,j,nz; 3208 PetscScalar *oa=b->a; 3209 Mat Btmp; 3210 PetscInt m,n,N; 3211 3212 PetscFunctionBegin; 3213 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3214 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3215 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %d != Bm %d",m,B->rmap->N); 3216 3217 ierr = MPIU_Allreduce(&n,&N,1,MPI_INT,MPI_SUM,comm);CHKERRQ(ierr); 3218 3219 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3220 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3221 maij = (Mat_MPIAIJ*)(*mat)->data; 3222 3223 (*mat)->preallocated = PETSC_TRUE; 3224 3225 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3226 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3227 3228 maij->A = A; 3229 3230 for (i=0; i<m; i++) { 3231 nz = oi[i+1] - oi[i]; 3232 for (j=0; j<nz; j++) { 3233 oj[oi[i] + j] = garray[oj[oi[i] + j]]; 3234 } 3235 } 3236 3237 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Btmp);CHKERRQ(ierr); 3238 maij->B = Btmp; 3239 3240 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3241 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3242 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3243 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3244 3245 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3246 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3247 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3248 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3249 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3250 PetscFunctionReturn(0); 3251 } 3252 3253 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3254 3255 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,MatReuse call,PetscBool sameColDist,Mat *newmat) 3256 { 3257 PetscErrorCode ierr; 3258 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3259 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3260 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3261 Mat M,Msub,B=a->B,Mnew=NULL; 3262 MatScalar *aa; 3263 Mat_SeqAIJ *aij; 3264 PetscInt *garray = a->garray,*colsub,Ncols; 3265 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3266 IS iscol_sub,iscmap; 3267 const PetscInt *is_idx,*cmap; 3268 PetscBool allcolumns=PETSC_FALSE; 3269 IS iscol_local=NULL; 3270 MPI_Comm comm; 3271 IS iscol_d,isrow_d,iscol_o,isgarray; 3272 Mat Asub=NULL,Bsub=NULL; 3273 3274 PetscFunctionBegin; 3275 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3276 PetscMPIInt rank; 3277 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3278 3279 if (call == MAT_INITIAL_MATRIX) { 3280 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3281 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3282 3283 /* (1) Create scalable iscol_sub and iscmap */ 3284 if (sameColDist) { 3285 /* iscol has same processor distribution as mat, use a scalable routine to generate iscol_sub and iscmap */ 3286 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&iscol_sub,&iscmap,&isrow_d,&iscol_d,&iscol_o,&isgarray);CHKERRQ(ierr); 3287 3288 //====================================== 3289 3290 if (rank == -1) { 3291 //printf("[%d] isrow_d\n",rank); 3292 //ierr = ISView(isrow_d,0);CHKERRQ(ierr); 3293 3294 //printf("[%d] iscol_diag\n",rank); 3295 //ierr = ISView(iscol_d,0);CHKERRQ(ierr); 3296 3297 printf("[%d] iscol_o\n",rank); 3298 ierr = ISView(iscol_o,0);CHKERRQ(ierr); 3299 3300 printf("[%d] a->B, %d, %d\n",rank,a->B->rmap->N,a->B->cmap->N); 3301 ierr = MatView(a->B,0);CHKERRQ(ierr); 3302 } 3303 3304 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,call,&Asub);CHKERRQ(ierr); 3305 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,call,&Bsub);CHKERRQ(ierr); 3306 if (rank == -1) { 3307 printf("[%d] Bsub\n",rank); 3308 ierr = MatView(Bsub,0);CHKERRQ(ierr); 3309 } 3310 3311 const PetscInt *garray1; 3312 ierr = ISGetIndices(isgarray,&garray1);CHKERRQ(ierr); 3313 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray1,&Mnew);CHKERRQ(ierr); 3314 ierr = ISRestoreIndices(isgarray,&garray1);CHKERRQ(ierr); 3315 //ierr = MatView(Mnew,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3316 3317 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3318 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3319 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3320 //====================================== 3321 3322 } else { /* iscol -> nonscalable iscol_local, then get scalable iscol_sub and iscmap */ 3323 PetscBool flg; 3324 3325 /* iscol -> nonscalable iscol_local */ 3326 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3327 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3328 if (n != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != Ncols %d",n,Ncols); 3329 3330 /* Check for special case: each processor gets entire matrix columns */ 3331 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3332 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3333 if (allcolumns) { 3334 iscol_sub = iscol_local; 3335 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3336 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3337 3338 } else { /* iscol_local -> iscol_sub and iscmap */ 3339 PetscInt *idx,*cmap1,k,cbs; 3340 3341 /* implementation below requires iscol_local be sorted, it can have duplicate indices */ 3342 ierr = ISSorted(iscol_local,&flg);CHKERRQ(ierr); 3343 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsorted iscol_local is not implemented yet"); 3344 3345 ierr = PetscMalloc2(Ncols,&idx,Ncols,&cmap1);CHKERRQ(ierr); 3346 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3347 count = 0; 3348 k = 0; 3349 for (i=0; i<Ncols; i++) { 3350 j = is_idx[i]; 3351 if (j >= cstart && j < cend) { 3352 /* diagonal part of mat */ 3353 idx[count] = j; 3354 cmap1[count++] = i; /* column index in submat */ 3355 } else if (Bn) { 3356 /* off-diagonal part of mat */ 3357 if (j == garray[k]) { 3358 idx[count] = j; 3359 cmap1[count++] = i; /* column index in submat */ 3360 } else if (j > garray[k]) { 3361 while (j > garray[k] && k < Bn-1) k++; 3362 if (j == garray[k]) { 3363 idx[count] = j; 3364 cmap1[count++] = i; /* column index in submat */ 3365 } 3366 } 3367 } 3368 } 3369 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3370 3371 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,&iscol_sub);CHKERRQ(ierr); 3372 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3373 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3374 3375 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_COPY_VALUES,&iscmap);CHKERRQ(ierr); 3376 ierr = PetscFree2(idx,cmap1);CHKERRQ(ierr); 3377 } 3378 } 3379 3380 /* (2) Create sequential Msub */ 3381 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3382 3383 } else { /* 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 3397 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3398 aij = (Mat_SeqAIJ*)(Msub)->data; 3399 ii = aij->i; 3400 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3401 3402 /* 3403 m - number of local rows 3404 Ncols - number of columns (same on all processors) 3405 rstart - first row in new global matrix generated 3406 */ 3407 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3408 3409 if (call == MAT_INITIAL_MATRIX) { 3410 /* (3) Create parallel newmat */ 3411 PetscMPIInt rank,size; 3412 PetscInt csize; 3413 3414 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3415 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3416 3417 /* 3418 Determine the number of non-zeros in the diagonal and off-diagonal 3419 portions of the matrix in order to do correct preallocation 3420 */ 3421 3422 /* first get start and end of "diagonal" columns */ 3423 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3424 if (csize == PETSC_DECIDE) { 3425 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3426 if (mglobal == Ncols) { /* square matrix */ 3427 nlocal = m; 3428 } else { 3429 nlocal = Ncols/size + ((Ncols % size) > rank); 3430 } 3431 } else { 3432 nlocal = csize; 3433 } 3434 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3435 rstart = rend - nlocal; 3436 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); 3437 3438 /* next, compute all the lengths */ 3439 jj = aij->j; 3440 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3441 olens = dlens + m; 3442 for (i=0; i<m; i++) { 3443 jend = ii[i+1] - ii[i]; 3444 olen = 0; 3445 dlen = 0; 3446 for (j=0; j<jend; j++) { 3447 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3448 else dlen++; 3449 jj++; 3450 } 3451 olens[i] = olen; 3452 dlens[i] = dlen; 3453 } 3454 ierr = MatGetBlockSizes(Msub,&bs,&cbs);CHKERRQ(ierr); 3455 3456 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3457 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr); 3458 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3459 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3460 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3461 ierr = PetscFree(dlens);CHKERRQ(ierr); 3462 } else { 3463 M = *newmat; 3464 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3465 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3466 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3467 /* 3468 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3469 rather than the slower MatSetValues(). 3470 */ 3471 M->was_assembled = PETSC_TRUE; 3472 M->assembled = PETSC_FALSE; 3473 } 3474 3475 /* (4) Set values of Msub to *newmat */ 3476 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3477 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3478 3479 jj = aij->j; 3480 aa = aij->a; 3481 for (i=0; i<m; i++) { 3482 row = rstart + i; 3483 nz = ii[i+1] - ii[i]; 3484 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3485 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3486 jj += nz; aa += nz; 3487 } 3488 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3489 3490 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3491 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3492 *newmat = M; 3493 3494 ierr = PetscFree(colsub);CHKERRQ(ierr); 3495 3496 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3497 if (call == MAT_INITIAL_MATRIX) { 3498 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3499 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3500 3501 ierr = PetscObjectCompose((PetscObject)M,"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3502 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3503 3504 ierr = PetscObjectCompose((PetscObject)M,"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3505 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3506 3507 if (iscol_local) { 3508 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3509 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3510 } 3511 3512 if (Mnew) { 3513 PetscBool equal; 3514 ierr = MatEqual(M,Mnew,&equal);CHKERRQ(ierr); 3515 if (!equal) SETERRQ(PETSC_COMM_SELF,0,"M != Mnew"); 3516 ierr = MatDestroy(&Mnew);CHKERRQ(ierr); 3517 ierr = MatDestroy(&Bsub);CHKERRQ(ierr); 3518 ierr = ISDestroy(&isgarray);CHKERRQ(ierr); 3519 } 3520 #if 0 3521 a=(Mat_MPIAIJ*)M->data; 3522 if (Asub) { 3523 ierr = MatEqual(Asub,a->A,&equal);CHKERRQ(ierr); 3524 if (!equal) SETERRQ(PETSC_COMM_SELF,0,"Asub != M->A"); 3525 if (rank == -1) { 3526 printf("[%d] M->A\n",rank); 3527 ierr = MatView(a->A,0);CHKERRQ(ierr); 3528 } 3529 ierr = MatDestroy(&Asub);CHKERRQ(ierr); 3530 } 3531 3532 if (Bsub && a->B->cmap->N) { 3533 ierr = MatEqual(Bsub,a->B,&equal);CHKERRQ(ierr); 3534 if (!equal) SETERRQ(PETSC_COMM_SELF,0,"Bsub != M->B"); 3535 3536 if (rank == -1) { 3537 printf("[%d] M->B\n",rank); 3538 ierr = MatView(a->B,0);CHKERRQ(ierr); 3539 } 3540 ierr = MatDestroy(&Asub);CHKERRQ(ierr); 3541 ierr = MatDestroy(&Bsub);CHKERRQ(ierr); 3542 3543 /* check isgarray */ 3544 ierr = ISGetLocalSize(isgarray,&count);CHKERRQ(ierr); 3545 if (count != a->B->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"count %d != a->B->cmap->N %d",count,a->B->cmap->N); 3546 if (count) { 3547 garray = a->garray; 3548 ierr = ISGetIndices(isgarray,&cmap);CHKERRQ(ierr); 3549 for (i=0; i<count; i++) { 3550 if (garray[i] != cmap[i]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ," garray %d != cmap %d",garray[i],cmap[i]); 3551 } 3552 ierr = ISRestoreIndices(isgarray,&cmap);CHKERRQ(ierr); 3553 } 3554 ierr = ISDestroy(&isgarray);CHKERRQ(ierr); 3555 } 3556 #endif 3557 } 3558 PetscFunctionReturn(0); 3559 } 3560 3561 /* 3562 Not great since it makes two copies of the submatrix, first an SeqAIJ 3563 in local and then by concatenating the local matrices the end result. 3564 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3565 3566 Note: This requires a sequential iscol with all indices. 3567 */ 3568 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3569 { 3570 PetscErrorCode ierr; 3571 PetscMPIInt rank,size; 3572 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3573 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3574 Mat M,Mreuse; 3575 MatScalar *aa,*vwork; 3576 MPI_Comm comm; 3577 Mat_SeqAIJ *aij; 3578 PetscBool colflag,allcolumns=PETSC_FALSE; 3579 3580 PetscFunctionBegin; 3581 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3582 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3583 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3584 3585 /* Check for special case: each processor gets entire matrix columns */ 3586 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3587 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3588 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3589 3590 if (call == MAT_REUSE_MATRIX) { 3591 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3592 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3593 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3594 } else { 3595 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3596 } 3597 3598 /* 3599 m - number of local rows 3600 n - number of columns (same on all processors) 3601 rstart - first row in new global matrix generated 3602 */ 3603 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3604 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3605 if (call == MAT_INITIAL_MATRIX) { 3606 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3607 ii = aij->i; 3608 jj = aij->j; 3609 3610 /* 3611 Determine the number of non-zeros in the diagonal and off-diagonal 3612 portions of the matrix in order to do correct preallocation 3613 */ 3614 3615 /* first get start and end of "diagonal" columns */ 3616 if (csize == PETSC_DECIDE) { 3617 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3618 if (mglobal == n) { /* square matrix */ 3619 nlocal = m; 3620 } else { 3621 nlocal = n/size + ((n % size) > rank); 3622 } 3623 } else { 3624 nlocal = csize; 3625 } 3626 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3627 rstart = rend - nlocal; 3628 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); 3629 3630 /* next, compute all the lengths */ 3631 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3632 olens = dlens + m; 3633 for (i=0; i<m; i++) { 3634 jend = ii[i+1] - ii[i]; 3635 olen = 0; 3636 dlen = 0; 3637 for (j=0; j<jend; j++) { 3638 if (*jj < rstart || *jj >= rend) olen++; 3639 else dlen++; 3640 jj++; 3641 } 3642 olens[i] = olen; 3643 dlens[i] = dlen; 3644 } 3645 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3646 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3647 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3648 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3649 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3650 ierr = PetscFree(dlens);CHKERRQ(ierr); 3651 } else { 3652 PetscInt ml,nl; 3653 3654 M = *newmat; 3655 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3656 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3657 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3658 /* 3659 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3660 rather than the slower MatSetValues(). 3661 */ 3662 M->was_assembled = PETSC_TRUE; 3663 M->assembled = PETSC_FALSE; 3664 } 3665 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3666 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3667 ii = aij->i; 3668 jj = aij->j; 3669 aa = aij->a; 3670 for (i=0; i<m; i++) { 3671 row = rstart + i; 3672 nz = ii[i+1] - ii[i]; 3673 cwork = jj; jj += nz; 3674 vwork = aa; aa += nz; 3675 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3676 } 3677 3678 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3679 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3680 *newmat = M; 3681 3682 /* save submatrix used in processor for next request */ 3683 if (call == MAT_INITIAL_MATRIX) { 3684 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3685 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3686 } 3687 PetscFunctionReturn(0); 3688 } 3689 3690 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3691 { 3692 PetscInt m,cstart, cend,j,nnz,i,d; 3693 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3694 const PetscInt *JJ; 3695 PetscScalar *values; 3696 PetscErrorCode ierr; 3697 PetscBool nooffprocentries; 3698 3699 PetscFunctionBegin; 3700 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3701 3702 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3703 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3704 m = B->rmap->n; 3705 cstart = B->cmap->rstart; 3706 cend = B->cmap->rend; 3707 rstart = B->rmap->rstart; 3708 3709 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3710 3711 #if defined(PETSC_USE_DEBUGGING) 3712 for (i=0; i<m; i++) { 3713 nnz = Ii[i+1]- Ii[i]; 3714 JJ = J + Ii[i]; 3715 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3716 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3717 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); 3718 } 3719 #endif 3720 3721 for (i=0; i<m; i++) { 3722 nnz = Ii[i+1]- Ii[i]; 3723 JJ = J + Ii[i]; 3724 nnz_max = PetscMax(nnz_max,nnz); 3725 d = 0; 3726 for (j=0; j<nnz; j++) { 3727 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3728 } 3729 d_nnz[i] = d; 3730 o_nnz[i] = nnz - d; 3731 } 3732 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3733 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3734 3735 if (v) values = (PetscScalar*)v; 3736 else { 3737 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3738 } 3739 3740 for (i=0; i<m; i++) { 3741 ii = i + rstart; 3742 nnz = Ii[i+1]- Ii[i]; 3743 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3744 } 3745 nooffprocentries = B->nooffprocentries; 3746 B->nooffprocentries = PETSC_TRUE; 3747 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3748 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3749 B->nooffprocentries = nooffprocentries; 3750 3751 if (!v) { 3752 ierr = PetscFree(values);CHKERRQ(ierr); 3753 } 3754 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3755 PetscFunctionReturn(0); 3756 } 3757 3758 /*@ 3759 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3760 (the default parallel PETSc format). 3761 3762 Collective on MPI_Comm 3763 3764 Input Parameters: 3765 + B - the matrix 3766 . i - the indices into j for the start of each local row (starts with zero) 3767 . j - the column indices for each local row (starts with zero) 3768 - v - optional values in the matrix 3769 3770 Level: developer 3771 3772 Notes: 3773 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3774 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3775 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3776 3777 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3778 3779 The format which is used for the sparse matrix input, is equivalent to a 3780 row-major ordering.. i.e for the following matrix, the input data expected is 3781 as shown 3782 3783 $ 1 0 0 3784 $ 2 0 3 P0 3785 $ ------- 3786 $ 4 5 6 P1 3787 $ 3788 $ Process0 [P0]: rows_owned=[0,1] 3789 $ i = {0,1,3} [size = nrow+1 = 2+1] 3790 $ j = {0,0,2} [size = 3] 3791 $ v = {1,2,3} [size = 3] 3792 $ 3793 $ Process1 [P1]: rows_owned=[2] 3794 $ i = {0,3} [size = nrow+1 = 1+1] 3795 $ j = {0,1,2} [size = 3] 3796 $ v = {4,5,6} [size = 3] 3797 3798 .keywords: matrix, aij, compressed row, sparse, parallel 3799 3800 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3801 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3802 @*/ 3803 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3804 { 3805 PetscErrorCode ierr; 3806 3807 PetscFunctionBegin; 3808 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3809 PetscFunctionReturn(0); 3810 } 3811 3812 /*@C 3813 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3814 (the default parallel PETSc format). For good matrix assembly performance 3815 the user should preallocate the matrix storage by setting the parameters 3816 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3817 performance can be increased by more than a factor of 50. 3818 3819 Collective on MPI_Comm 3820 3821 Input Parameters: 3822 + B - the matrix 3823 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3824 (same value is used for all local rows) 3825 . d_nnz - array containing the number of nonzeros in the various rows of the 3826 DIAGONAL portion of the local submatrix (possibly different for each row) 3827 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3828 The size of this array is equal to the number of local rows, i.e 'm'. 3829 For matrices that will be factored, you must leave room for (and set) 3830 the diagonal entry even if it is zero. 3831 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3832 submatrix (same value is used for all local rows). 3833 - o_nnz - array containing the number of nonzeros in the various rows of the 3834 OFF-DIAGONAL portion of the local submatrix (possibly different for 3835 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3836 structure. The size of this array is equal to the number 3837 of local rows, i.e 'm'. 3838 3839 If the *_nnz parameter is given then the *_nz parameter is ignored 3840 3841 The AIJ format (also called the Yale sparse matrix format or 3842 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3843 storage. The stored row and column indices begin with zero. 3844 See Users-Manual: ch_mat for details. 3845 3846 The parallel matrix is partitioned such that the first m0 rows belong to 3847 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3848 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3849 3850 The DIAGONAL portion of the local submatrix of a processor can be defined 3851 as the submatrix which is obtained by extraction the part corresponding to 3852 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3853 first row that belongs to the processor, r2 is the last row belonging to 3854 the this processor, and c1-c2 is range of indices of the local part of a 3855 vector suitable for applying the matrix to. This is an mxn matrix. In the 3856 common case of a square matrix, the row and column ranges are the same and 3857 the DIAGONAL part is also square. The remaining portion of the local 3858 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3859 3860 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3861 3862 You can call MatGetInfo() to get information on how effective the preallocation was; 3863 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3864 You can also run with the option -info and look for messages with the string 3865 malloc in them to see if additional memory allocation was needed. 3866 3867 Example usage: 3868 3869 Consider the following 8x8 matrix with 34 non-zero values, that is 3870 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3871 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3872 as follows: 3873 3874 .vb 3875 1 2 0 | 0 3 0 | 0 4 3876 Proc0 0 5 6 | 7 0 0 | 8 0 3877 9 0 10 | 11 0 0 | 12 0 3878 ------------------------------------- 3879 13 0 14 | 15 16 17 | 0 0 3880 Proc1 0 18 0 | 19 20 21 | 0 0 3881 0 0 0 | 22 23 0 | 24 0 3882 ------------------------------------- 3883 Proc2 25 26 27 | 0 0 28 | 29 0 3884 30 0 0 | 31 32 33 | 0 34 3885 .ve 3886 3887 This can be represented as a collection of submatrices as: 3888 3889 .vb 3890 A B C 3891 D E F 3892 G H I 3893 .ve 3894 3895 Where the submatrices A,B,C are owned by proc0, D,E,F are 3896 owned by proc1, G,H,I are owned by proc2. 3897 3898 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3899 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3900 The 'M','N' parameters are 8,8, and have the same values on all procs. 3901 3902 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3903 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3904 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3905 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3906 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3907 matrix, ans [DF] as another SeqAIJ matrix. 3908 3909 When d_nz, o_nz parameters are specified, d_nz storage elements are 3910 allocated for every row of the local diagonal submatrix, and o_nz 3911 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3912 One way to choose d_nz and o_nz is to use the max nonzerors per local 3913 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3914 In this case, the values of d_nz,o_nz are: 3915 .vb 3916 proc0 : dnz = 2, o_nz = 2 3917 proc1 : dnz = 3, o_nz = 2 3918 proc2 : dnz = 1, o_nz = 4 3919 .ve 3920 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3921 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3922 for proc3. i.e we are using 12+15+10=37 storage locations to store 3923 34 values. 3924 3925 When d_nnz, o_nnz parameters are specified, the storage is specified 3926 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3927 In the above case the values for d_nnz,o_nnz are: 3928 .vb 3929 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3930 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3931 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3932 .ve 3933 Here the space allocated is sum of all the above values i.e 34, and 3934 hence pre-allocation is perfect. 3935 3936 Level: intermediate 3937 3938 .keywords: matrix, aij, compressed row, sparse, parallel 3939 3940 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 3941 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 3942 @*/ 3943 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3944 { 3945 PetscErrorCode ierr; 3946 3947 PetscFunctionBegin; 3948 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3949 PetscValidType(B,1); 3950 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 3951 PetscFunctionReturn(0); 3952 } 3953 3954 /*@ 3955 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 3956 CSR format the local rows. 3957 3958 Collective on MPI_Comm 3959 3960 Input Parameters: 3961 + comm - MPI communicator 3962 . m - number of local rows (Cannot be PETSC_DECIDE) 3963 . n - This value should be the same as the local size used in creating the 3964 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3965 calculated if N is given) For square matrices n is almost always m. 3966 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3967 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3968 . i - row indices 3969 . j - column indices 3970 - a - matrix values 3971 3972 Output Parameter: 3973 . mat - the matrix 3974 3975 Level: intermediate 3976 3977 Notes: 3978 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3979 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3980 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3981 3982 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3983 3984 The format which is used for the sparse matrix input, is equivalent to a 3985 row-major ordering.. i.e for the following matrix, the input data expected is 3986 as shown 3987 3988 $ 1 0 0 3989 $ 2 0 3 P0 3990 $ ------- 3991 $ 4 5 6 P1 3992 $ 3993 $ Process0 [P0]: rows_owned=[0,1] 3994 $ i = {0,1,3} [size = nrow+1 = 2+1] 3995 $ j = {0,0,2} [size = 3] 3996 $ v = {1,2,3} [size = 3] 3997 $ 3998 $ Process1 [P1]: rows_owned=[2] 3999 $ i = {0,3} [size = nrow+1 = 1+1] 4000 $ j = {0,1,2} [size = 3] 4001 $ v = {4,5,6} [size = 3] 4002 4003 .keywords: matrix, aij, compressed row, sparse, parallel 4004 4005 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4006 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4007 @*/ 4008 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 4009 { 4010 PetscErrorCode ierr; 4011 4012 PetscFunctionBegin; 4013 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4014 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4015 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4016 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4017 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 4018 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 4019 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 4020 PetscFunctionReturn(0); 4021 } 4022 4023 /*@C 4024 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 4025 (the default parallel PETSc format). For good matrix assembly performance 4026 the user should preallocate the matrix storage by setting the parameters 4027 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4028 performance can be increased by more than a factor of 50. 4029 4030 Collective on MPI_Comm 4031 4032 Input Parameters: 4033 + comm - MPI communicator 4034 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 4035 This value should be the same as the local size used in creating the 4036 y vector for the matrix-vector product y = Ax. 4037 . n - This value should be the same as the local size used in creating the 4038 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4039 calculated if N is given) For square matrices n is almost always m. 4040 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4041 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4042 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4043 (same value is used for all local rows) 4044 . d_nnz - array containing the number of nonzeros in the various rows of the 4045 DIAGONAL portion of the local submatrix (possibly different for each row) 4046 or NULL, if d_nz is used to specify the nonzero structure. 4047 The size of this array is equal to the number of local rows, i.e 'm'. 4048 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4049 submatrix (same value is used for all local rows). 4050 - o_nnz - array containing the number of nonzeros in the various rows of the 4051 OFF-DIAGONAL portion of the local submatrix (possibly different for 4052 each row) or NULL, if o_nz is used to specify the nonzero 4053 structure. The size of this array is equal to the number 4054 of local rows, i.e 'm'. 4055 4056 Output Parameter: 4057 . A - the matrix 4058 4059 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4060 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4061 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4062 4063 Notes: 4064 If the *_nnz parameter is given then the *_nz parameter is ignored 4065 4066 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4067 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4068 storage requirements for this matrix. 4069 4070 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4071 processor than it must be used on all processors that share the object for 4072 that argument. 4073 4074 The user MUST specify either the local or global matrix dimensions 4075 (possibly both). 4076 4077 The parallel matrix is partitioned across processors such that the 4078 first m0 rows belong to process 0, the next m1 rows belong to 4079 process 1, the next m2 rows belong to process 2 etc.. where 4080 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4081 values corresponding to [m x N] submatrix. 4082 4083 The columns are logically partitioned with the n0 columns belonging 4084 to 0th partition, the next n1 columns belonging to the next 4085 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4086 4087 The DIAGONAL portion of the local submatrix on any given processor 4088 is the submatrix corresponding to the rows and columns m,n 4089 corresponding to the given processor. i.e diagonal matrix on 4090 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4091 etc. The remaining portion of the local submatrix [m x (N-n)] 4092 constitute the OFF-DIAGONAL portion. The example below better 4093 illustrates this concept. 4094 4095 For a square global matrix we define each processor's diagonal portion 4096 to be its local rows and the corresponding columns (a square submatrix); 4097 each processor's off-diagonal portion encompasses the remainder of the 4098 local matrix (a rectangular submatrix). 4099 4100 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4101 4102 When calling this routine with a single process communicator, a matrix of 4103 type SEQAIJ is returned. If a matrix of type MATMPIAIJ is desired for this 4104 type of communicator, use the construction mechanism: 4105 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4106 4107 By default, this format uses inodes (identical nodes) when possible. 4108 We search for consecutive rows with the same nonzero structure, thereby 4109 reusing matrix information to achieve increased efficiency. 4110 4111 Options Database Keys: 4112 + -mat_no_inode - Do not use inodes 4113 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4114 - -mat_aij_oneindex - Internally use indexing starting at 1 4115 rather than 0. Note that when calling MatSetValues(), 4116 the user still MUST index entries starting at 0! 4117 4118 4119 Example usage: 4120 4121 Consider the following 8x8 matrix with 34 non-zero values, that is 4122 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4123 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4124 as follows: 4125 4126 .vb 4127 1 2 0 | 0 3 0 | 0 4 4128 Proc0 0 5 6 | 7 0 0 | 8 0 4129 9 0 10 | 11 0 0 | 12 0 4130 ------------------------------------- 4131 13 0 14 | 15 16 17 | 0 0 4132 Proc1 0 18 0 | 19 20 21 | 0 0 4133 0 0 0 | 22 23 0 | 24 0 4134 ------------------------------------- 4135 Proc2 25 26 27 | 0 0 28 | 29 0 4136 30 0 0 | 31 32 33 | 0 34 4137 .ve 4138 4139 This can be represented as a collection of submatrices as: 4140 4141 .vb 4142 A B C 4143 D E F 4144 G H I 4145 .ve 4146 4147 Where the submatrices A,B,C are owned by proc0, D,E,F are 4148 owned by proc1, G,H,I are owned by proc2. 4149 4150 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4151 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4152 The 'M','N' parameters are 8,8, and have the same values on all procs. 4153 4154 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4155 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4156 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4157 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4158 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4159 matrix, ans [DF] as another SeqAIJ matrix. 4160 4161 When d_nz, o_nz parameters are specified, d_nz storage elements are 4162 allocated for every row of the local diagonal submatrix, and o_nz 4163 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4164 One way to choose d_nz and o_nz is to use the max nonzerors per local 4165 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4166 In this case, the values of d_nz,o_nz are: 4167 .vb 4168 proc0 : dnz = 2, o_nz = 2 4169 proc1 : dnz = 3, o_nz = 2 4170 proc2 : dnz = 1, o_nz = 4 4171 .ve 4172 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4173 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4174 for proc3. i.e we are using 12+15+10=37 storage locations to store 4175 34 values. 4176 4177 When d_nnz, o_nnz parameters are specified, the storage is specified 4178 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4179 In the above case the values for d_nnz,o_nnz are: 4180 .vb 4181 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4182 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4183 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4184 .ve 4185 Here the space allocated is sum of all the above values i.e 34, and 4186 hence pre-allocation is perfect. 4187 4188 Level: intermediate 4189 4190 .keywords: matrix, aij, compressed row, sparse, parallel 4191 4192 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4193 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4194 @*/ 4195 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) 4196 { 4197 PetscErrorCode ierr; 4198 PetscMPIInt size; 4199 4200 PetscFunctionBegin; 4201 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4202 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4203 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4204 if (size > 1) { 4205 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4206 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4207 } else { 4208 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4209 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4210 } 4211 PetscFunctionReturn(0); 4212 } 4213 4214 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4215 { 4216 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4217 PetscBool flg; 4218 PetscErrorCode ierr; 4219 4220 PetscFunctionBegin; 4221 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4222 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4223 if (Ad) *Ad = a->A; 4224 if (Ao) *Ao = a->B; 4225 if (colmap) *colmap = a->garray; 4226 PetscFunctionReturn(0); 4227 } 4228 4229 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4230 { 4231 PetscErrorCode ierr; 4232 PetscInt m,N,i,rstart,nnz,Ii; 4233 PetscInt *indx; 4234 PetscScalar *values; 4235 4236 PetscFunctionBegin; 4237 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4238 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4239 PetscInt *dnz,*onz,sum,bs,cbs; 4240 4241 if (n == PETSC_DECIDE) { 4242 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4243 } 4244 /* Check sum(n) = N */ 4245 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4246 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 4247 4248 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4249 rstart -= m; 4250 4251 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4252 for (i=0; i<m; i++) { 4253 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4254 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4255 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4256 } 4257 4258 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4259 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4260 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4261 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4262 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4263 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4264 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4265 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4266 } 4267 4268 /* numeric phase */ 4269 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4270 for (i=0; i<m; i++) { 4271 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4272 Ii = i + rstart; 4273 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4274 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4275 } 4276 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4277 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4278 PetscFunctionReturn(0); 4279 } 4280 4281 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4282 { 4283 PetscErrorCode ierr; 4284 PetscMPIInt rank; 4285 PetscInt m,N,i,rstart,nnz; 4286 size_t len; 4287 const PetscInt *indx; 4288 PetscViewer out; 4289 char *name; 4290 Mat B; 4291 const PetscScalar *values; 4292 4293 PetscFunctionBegin; 4294 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4295 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4296 /* Should this be the type of the diagonal block of A? */ 4297 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4298 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4299 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4300 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4301 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4302 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4303 for (i=0; i<m; i++) { 4304 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4305 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4306 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4307 } 4308 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4309 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4310 4311 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4312 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4313 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4314 sprintf(name,"%s.%d",outfile,rank); 4315 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4316 ierr = PetscFree(name);CHKERRQ(ierr); 4317 ierr = MatView(B,out);CHKERRQ(ierr); 4318 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4319 ierr = MatDestroy(&B);CHKERRQ(ierr); 4320 PetscFunctionReturn(0); 4321 } 4322 4323 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4324 { 4325 PetscErrorCode ierr; 4326 Mat_Merge_SeqsToMPI *merge; 4327 PetscContainer container; 4328 4329 PetscFunctionBegin; 4330 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4331 if (container) { 4332 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4333 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4334 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4335 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4336 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4337 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4338 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4339 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4340 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4341 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4342 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4343 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4344 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4345 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4346 ierr = PetscFree(merge);CHKERRQ(ierr); 4347 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4348 } 4349 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4350 PetscFunctionReturn(0); 4351 } 4352 4353 #include <../src/mat/utils/freespace.h> 4354 #include <petscbt.h> 4355 4356 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4357 { 4358 PetscErrorCode ierr; 4359 MPI_Comm comm; 4360 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4361 PetscMPIInt size,rank,taga,*len_s; 4362 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4363 PetscInt proc,m; 4364 PetscInt **buf_ri,**buf_rj; 4365 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4366 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4367 MPI_Request *s_waits,*r_waits; 4368 MPI_Status *status; 4369 MatScalar *aa=a->a; 4370 MatScalar **abuf_r,*ba_i; 4371 Mat_Merge_SeqsToMPI *merge; 4372 PetscContainer container; 4373 4374 PetscFunctionBegin; 4375 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4376 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4377 4378 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4379 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4380 4381 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4382 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4383 4384 bi = merge->bi; 4385 bj = merge->bj; 4386 buf_ri = merge->buf_ri; 4387 buf_rj = merge->buf_rj; 4388 4389 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4390 owners = merge->rowmap->range; 4391 len_s = merge->len_s; 4392 4393 /* send and recv matrix values */ 4394 /*-----------------------------*/ 4395 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4396 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4397 4398 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4399 for (proc=0,k=0; proc<size; proc++) { 4400 if (!len_s[proc]) continue; 4401 i = owners[proc]; 4402 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4403 k++; 4404 } 4405 4406 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4407 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4408 ierr = PetscFree(status);CHKERRQ(ierr); 4409 4410 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4411 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4412 4413 /* insert mat values of mpimat */ 4414 /*----------------------------*/ 4415 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4416 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4417 4418 for (k=0; k<merge->nrecv; k++) { 4419 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4420 nrows = *(buf_ri_k[k]); 4421 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4422 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4423 } 4424 4425 /* set values of ba */ 4426 m = merge->rowmap->n; 4427 for (i=0; i<m; i++) { 4428 arow = owners[rank] + i; 4429 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4430 bnzi = bi[i+1] - bi[i]; 4431 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4432 4433 /* add local non-zero vals of this proc's seqmat into ba */ 4434 anzi = ai[arow+1] - ai[arow]; 4435 aj = a->j + ai[arow]; 4436 aa = a->a + ai[arow]; 4437 nextaj = 0; 4438 for (j=0; nextaj<anzi; j++) { 4439 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4440 ba_i[j] += aa[nextaj++]; 4441 } 4442 } 4443 4444 /* add received vals into ba */ 4445 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4446 /* i-th row */ 4447 if (i == *nextrow[k]) { 4448 anzi = *(nextai[k]+1) - *nextai[k]; 4449 aj = buf_rj[k] + *(nextai[k]); 4450 aa = abuf_r[k] + *(nextai[k]); 4451 nextaj = 0; 4452 for (j=0; nextaj<anzi; j++) { 4453 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4454 ba_i[j] += aa[nextaj++]; 4455 } 4456 } 4457 nextrow[k]++; nextai[k]++; 4458 } 4459 } 4460 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4461 } 4462 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4463 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4464 4465 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4466 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4467 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4468 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4469 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4470 PetscFunctionReturn(0); 4471 } 4472 4473 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4474 { 4475 PetscErrorCode ierr; 4476 Mat B_mpi; 4477 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4478 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4479 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4480 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4481 PetscInt len,proc,*dnz,*onz,bs,cbs; 4482 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4483 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4484 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4485 MPI_Status *status; 4486 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4487 PetscBT lnkbt; 4488 Mat_Merge_SeqsToMPI *merge; 4489 PetscContainer container; 4490 4491 PetscFunctionBegin; 4492 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4493 4494 /* make sure it is a PETSc comm */ 4495 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4496 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4497 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4498 4499 ierr = PetscNew(&merge);CHKERRQ(ierr); 4500 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4501 4502 /* determine row ownership */ 4503 /*---------------------------------------------------------*/ 4504 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4505 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4506 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4507 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4508 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4509 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4510 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4511 4512 m = merge->rowmap->n; 4513 owners = merge->rowmap->range; 4514 4515 /* determine the number of messages to send, their lengths */ 4516 /*---------------------------------------------------------*/ 4517 len_s = merge->len_s; 4518 4519 len = 0; /* length of buf_si[] */ 4520 merge->nsend = 0; 4521 for (proc=0; proc<size; proc++) { 4522 len_si[proc] = 0; 4523 if (proc == rank) { 4524 len_s[proc] = 0; 4525 } else { 4526 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4527 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4528 } 4529 if (len_s[proc]) { 4530 merge->nsend++; 4531 nrows = 0; 4532 for (i=owners[proc]; i<owners[proc+1]; i++) { 4533 if (ai[i+1] > ai[i]) nrows++; 4534 } 4535 len_si[proc] = 2*(nrows+1); 4536 len += len_si[proc]; 4537 } 4538 } 4539 4540 /* determine the number and length of messages to receive for ij-structure */ 4541 /*-------------------------------------------------------------------------*/ 4542 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4543 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4544 4545 /* post the Irecv of j-structure */ 4546 /*-------------------------------*/ 4547 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4548 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4549 4550 /* post the Isend of j-structure */ 4551 /*--------------------------------*/ 4552 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4553 4554 for (proc=0, k=0; proc<size; proc++) { 4555 if (!len_s[proc]) continue; 4556 i = owners[proc]; 4557 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4558 k++; 4559 } 4560 4561 /* receives and sends of j-structure are complete */ 4562 /*------------------------------------------------*/ 4563 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4564 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4565 4566 /* send and recv i-structure */ 4567 /*---------------------------*/ 4568 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4569 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4570 4571 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4572 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4573 for (proc=0,k=0; proc<size; proc++) { 4574 if (!len_s[proc]) continue; 4575 /* form outgoing message for i-structure: 4576 buf_si[0]: nrows to be sent 4577 [1:nrows]: row index (global) 4578 [nrows+1:2*nrows+1]: i-structure index 4579 */ 4580 /*-------------------------------------------*/ 4581 nrows = len_si[proc]/2 - 1; 4582 buf_si_i = buf_si + nrows+1; 4583 buf_si[0] = nrows; 4584 buf_si_i[0] = 0; 4585 nrows = 0; 4586 for (i=owners[proc]; i<owners[proc+1]; i++) { 4587 anzi = ai[i+1] - ai[i]; 4588 if (anzi) { 4589 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4590 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4591 nrows++; 4592 } 4593 } 4594 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4595 k++; 4596 buf_si += len_si[proc]; 4597 } 4598 4599 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4600 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4601 4602 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4603 for (i=0; i<merge->nrecv; i++) { 4604 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); 4605 } 4606 4607 ierr = PetscFree(len_si);CHKERRQ(ierr); 4608 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4609 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4610 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4611 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4612 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4613 ierr = PetscFree(status);CHKERRQ(ierr); 4614 4615 /* compute a local seq matrix in each processor */ 4616 /*----------------------------------------------*/ 4617 /* allocate bi array and free space for accumulating nonzero column info */ 4618 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4619 bi[0] = 0; 4620 4621 /* create and initialize a linked list */ 4622 nlnk = N+1; 4623 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4624 4625 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4626 len = ai[owners[rank+1]] - ai[owners[rank]]; 4627 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4628 4629 current_space = free_space; 4630 4631 /* determine symbolic info for each local row */ 4632 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4633 4634 for (k=0; k<merge->nrecv; k++) { 4635 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4636 nrows = *buf_ri_k[k]; 4637 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4638 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4639 } 4640 4641 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4642 len = 0; 4643 for (i=0; i<m; i++) { 4644 bnzi = 0; 4645 /* add local non-zero cols of this proc's seqmat into lnk */ 4646 arow = owners[rank] + i; 4647 anzi = ai[arow+1] - ai[arow]; 4648 aj = a->j + ai[arow]; 4649 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4650 bnzi += nlnk; 4651 /* add received col data into lnk */ 4652 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4653 if (i == *nextrow[k]) { /* i-th row */ 4654 anzi = *(nextai[k]+1) - *nextai[k]; 4655 aj = buf_rj[k] + *nextai[k]; 4656 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4657 bnzi += nlnk; 4658 nextrow[k]++; nextai[k]++; 4659 } 4660 } 4661 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4662 4663 /* if free space is not available, make more free space */ 4664 if (current_space->local_remaining<bnzi) { 4665 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4666 nspacedouble++; 4667 } 4668 /* copy data into free space, then initialize lnk */ 4669 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4670 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4671 4672 current_space->array += bnzi; 4673 current_space->local_used += bnzi; 4674 current_space->local_remaining -= bnzi; 4675 4676 bi[i+1] = bi[i] + bnzi; 4677 } 4678 4679 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4680 4681 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4682 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4683 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4684 4685 /* create symbolic parallel matrix B_mpi */ 4686 /*---------------------------------------*/ 4687 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4688 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4689 if (n==PETSC_DECIDE) { 4690 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4691 } else { 4692 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4693 } 4694 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4695 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4696 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4697 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4698 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4699 4700 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4701 B_mpi->assembled = PETSC_FALSE; 4702 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4703 merge->bi = bi; 4704 merge->bj = bj; 4705 merge->buf_ri = buf_ri; 4706 merge->buf_rj = buf_rj; 4707 merge->coi = NULL; 4708 merge->coj = NULL; 4709 merge->owners_co = NULL; 4710 4711 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4712 4713 /* attach the supporting struct to B_mpi for reuse */ 4714 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4715 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4716 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4717 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4718 *mpimat = B_mpi; 4719 4720 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4721 PetscFunctionReturn(0); 4722 } 4723 4724 /*@C 4725 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4726 matrices from each processor 4727 4728 Collective on MPI_Comm 4729 4730 Input Parameters: 4731 + comm - the communicators the parallel matrix will live on 4732 . seqmat - the input sequential matrices 4733 . m - number of local rows (or PETSC_DECIDE) 4734 . n - number of local columns (or PETSC_DECIDE) 4735 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4736 4737 Output Parameter: 4738 . mpimat - the parallel matrix generated 4739 4740 Level: advanced 4741 4742 Notes: 4743 The dimensions of the sequential matrix in each processor MUST be the same. 4744 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4745 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4746 @*/ 4747 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4748 { 4749 PetscErrorCode ierr; 4750 PetscMPIInt size; 4751 4752 PetscFunctionBegin; 4753 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4754 if (size == 1) { 4755 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4756 if (scall == MAT_INITIAL_MATRIX) { 4757 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4758 } else { 4759 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4760 } 4761 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4762 PetscFunctionReturn(0); 4763 } 4764 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4765 if (scall == MAT_INITIAL_MATRIX) { 4766 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4767 } 4768 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4769 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4770 PetscFunctionReturn(0); 4771 } 4772 4773 /*@ 4774 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 4775 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4776 with MatGetSize() 4777 4778 Not Collective 4779 4780 Input Parameters: 4781 + A - the matrix 4782 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4783 4784 Output Parameter: 4785 . A_loc - the local sequential matrix generated 4786 4787 Level: developer 4788 4789 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4790 4791 @*/ 4792 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4793 { 4794 PetscErrorCode ierr; 4795 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4796 Mat_SeqAIJ *mat,*a,*b; 4797 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4798 MatScalar *aa,*ba,*cam; 4799 PetscScalar *ca; 4800 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4801 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4802 PetscBool match; 4803 MPI_Comm comm; 4804 PetscMPIInt size; 4805 4806 PetscFunctionBegin; 4807 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4808 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4809 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4810 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4811 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4812 4813 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4814 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4815 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4816 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4817 aa = a->a; ba = b->a; 4818 if (scall == MAT_INITIAL_MATRIX) { 4819 if (size == 1) { 4820 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4821 PetscFunctionReturn(0); 4822 } 4823 4824 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4825 ci[0] = 0; 4826 for (i=0; i<am; i++) { 4827 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4828 } 4829 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4830 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4831 k = 0; 4832 for (i=0; i<am; i++) { 4833 ncols_o = bi[i+1] - bi[i]; 4834 ncols_d = ai[i+1] - ai[i]; 4835 /* off-diagonal portion of A */ 4836 for (jo=0; jo<ncols_o; jo++) { 4837 col = cmap[*bj]; 4838 if (col >= cstart) break; 4839 cj[k] = col; bj++; 4840 ca[k++] = *ba++; 4841 } 4842 /* diagonal portion of A */ 4843 for (j=0; j<ncols_d; j++) { 4844 cj[k] = cstart + *aj++; 4845 ca[k++] = *aa++; 4846 } 4847 /* off-diagonal portion of A */ 4848 for (j=jo; j<ncols_o; j++) { 4849 cj[k] = cmap[*bj++]; 4850 ca[k++] = *ba++; 4851 } 4852 } 4853 /* put together the new matrix */ 4854 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4855 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4856 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4857 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4858 mat->free_a = PETSC_TRUE; 4859 mat->free_ij = PETSC_TRUE; 4860 mat->nonew = 0; 4861 } else if (scall == MAT_REUSE_MATRIX) { 4862 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4863 ci = mat->i; cj = mat->j; cam = mat->a; 4864 for (i=0; i<am; i++) { 4865 /* off-diagonal portion of A */ 4866 ncols_o = bi[i+1] - bi[i]; 4867 for (jo=0; jo<ncols_o; jo++) { 4868 col = cmap[*bj]; 4869 if (col >= cstart) break; 4870 *cam++ = *ba++; bj++; 4871 } 4872 /* diagonal portion of A */ 4873 ncols_d = ai[i+1] - ai[i]; 4874 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4875 /* off-diagonal portion of A */ 4876 for (j=jo; j<ncols_o; j++) { 4877 *cam++ = *ba++; bj++; 4878 } 4879 } 4880 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4881 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4882 PetscFunctionReturn(0); 4883 } 4884 4885 /*@C 4886 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4887 4888 Not Collective 4889 4890 Input Parameters: 4891 + A - the matrix 4892 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4893 - row, col - index sets of rows and columns to extract (or NULL) 4894 4895 Output Parameter: 4896 . A_loc - the local sequential matrix generated 4897 4898 Level: developer 4899 4900 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4901 4902 @*/ 4903 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4904 { 4905 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4906 PetscErrorCode ierr; 4907 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4908 IS isrowa,iscola; 4909 Mat *aloc; 4910 PetscBool match; 4911 4912 PetscFunctionBegin; 4913 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4914 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4915 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4916 if (!row) { 4917 start = A->rmap->rstart; end = A->rmap->rend; 4918 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 4919 } else { 4920 isrowa = *row; 4921 } 4922 if (!col) { 4923 start = A->cmap->rstart; 4924 cmap = a->garray; 4925 nzA = a->A->cmap->n; 4926 nzB = a->B->cmap->n; 4927 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4928 ncols = 0; 4929 for (i=0; i<nzB; i++) { 4930 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4931 else break; 4932 } 4933 imark = i; 4934 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 4935 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 4936 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 4937 } else { 4938 iscola = *col; 4939 } 4940 if (scall != MAT_INITIAL_MATRIX) { 4941 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 4942 aloc[0] = *A_loc; 4943 } 4944 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 4945 *A_loc = aloc[0]; 4946 ierr = PetscFree(aloc);CHKERRQ(ierr); 4947 if (!row) { 4948 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 4949 } 4950 if (!col) { 4951 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 4952 } 4953 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4954 PetscFunctionReturn(0); 4955 } 4956 4957 /*@C 4958 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 4959 4960 Collective on Mat 4961 4962 Input Parameters: 4963 + A,B - the matrices in mpiaij format 4964 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4965 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 4966 4967 Output Parameter: 4968 + rowb, colb - index sets of rows and columns of B to extract 4969 - B_seq - the sequential matrix generated 4970 4971 Level: developer 4972 4973 @*/ 4974 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 4975 { 4976 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4977 PetscErrorCode ierr; 4978 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 4979 IS isrowb,iscolb; 4980 Mat *bseq=NULL; 4981 4982 PetscFunctionBegin; 4983 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 4984 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); 4985 } 4986 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 4987 4988 if (scall == MAT_INITIAL_MATRIX) { 4989 start = A->cmap->rstart; 4990 cmap = a->garray; 4991 nzA = a->A->cmap->n; 4992 nzB = a->B->cmap->n; 4993 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4994 ncols = 0; 4995 for (i=0; i<nzB; i++) { /* row < local row index */ 4996 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4997 else break; 4998 } 4999 imark = i; 5000 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 5001 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5002 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 5003 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 5004 } else { 5005 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5006 isrowb = *rowb; iscolb = *colb; 5007 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 5008 bseq[0] = *B_seq; 5009 } 5010 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 5011 *B_seq = bseq[0]; 5012 ierr = PetscFree(bseq);CHKERRQ(ierr); 5013 if (!rowb) { 5014 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 5015 } else { 5016 *rowb = isrowb; 5017 } 5018 if (!colb) { 5019 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 5020 } else { 5021 *colb = iscolb; 5022 } 5023 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5024 PetscFunctionReturn(0); 5025 } 5026 5027 /* 5028 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 5029 of the OFF-DIAGONAL portion of local A 5030 5031 Collective on Mat 5032 5033 Input Parameters: 5034 + A,B - the matrices in mpiaij format 5035 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5036 5037 Output Parameter: 5038 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5039 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5040 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5041 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5042 5043 Level: developer 5044 5045 */ 5046 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5047 { 5048 VecScatter_MPI_General *gen_to,*gen_from; 5049 PetscErrorCode ierr; 5050 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5051 Mat_SeqAIJ *b_oth; 5052 VecScatter ctx =a->Mvctx; 5053 MPI_Comm comm; 5054 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 5055 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5056 PetscInt *rvalues,*svalues; 5057 MatScalar *b_otha,*bufa,*bufA; 5058 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5059 MPI_Request *rwaits = NULL,*swaits = NULL; 5060 MPI_Status *sstatus,rstatus; 5061 PetscMPIInt jj,size; 5062 PetscInt *cols,sbs,rbs; 5063 PetscScalar *vals; 5064 5065 PetscFunctionBegin; 5066 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5067 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5068 5069 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5070 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); 5071 } 5072 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5073 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5074 5075 if (size == 1) { 5076 startsj_s = NULL; 5077 bufa_ptr = NULL; 5078 *B_oth = NULL; 5079 PetscFunctionReturn(0); 5080 } 5081 5082 gen_to = (VecScatter_MPI_General*)ctx->todata; 5083 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5084 nrecvs = gen_from->n; 5085 nsends = gen_to->n; 5086 5087 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 5088 srow = gen_to->indices; /* local row index to be sent */ 5089 sstarts = gen_to->starts; 5090 sprocs = gen_to->procs; 5091 sstatus = gen_to->sstatus; 5092 sbs = gen_to->bs; 5093 rstarts = gen_from->starts; 5094 rprocs = gen_from->procs; 5095 rbs = gen_from->bs; 5096 5097 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5098 if (scall == MAT_INITIAL_MATRIX) { 5099 /* i-array */ 5100 /*---------*/ 5101 /* post receives */ 5102 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 5103 for (i=0; i<nrecvs; i++) { 5104 rowlen = rvalues + rstarts[i]*rbs; 5105 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5106 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5107 } 5108 5109 /* pack the outgoing message */ 5110 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 5111 5112 sstartsj[0] = 0; 5113 rstartsj[0] = 0; 5114 len = 0; /* total length of j or a array to be sent */ 5115 k = 0; 5116 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 5117 for (i=0; i<nsends; i++) { 5118 rowlen = svalues + sstarts[i]*sbs; 5119 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5120 for (j=0; j<nrows; j++) { 5121 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5122 for (l=0; l<sbs; l++) { 5123 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5124 5125 rowlen[j*sbs+l] = ncols; 5126 5127 len += ncols; 5128 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5129 } 5130 k++; 5131 } 5132 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5133 5134 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5135 } 5136 /* recvs and sends of i-array are completed */ 5137 i = nrecvs; 5138 while (i--) { 5139 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5140 } 5141 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5142 ierr = PetscFree(svalues);CHKERRQ(ierr); 5143 5144 /* allocate buffers for sending j and a arrays */ 5145 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5146 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5147 5148 /* create i-array of B_oth */ 5149 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5150 5151 b_othi[0] = 0; 5152 len = 0; /* total length of j or a array to be received */ 5153 k = 0; 5154 for (i=0; i<nrecvs; i++) { 5155 rowlen = rvalues + rstarts[i]*rbs; 5156 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5157 for (j=0; j<nrows; j++) { 5158 b_othi[k+1] = b_othi[k] + rowlen[j]; 5159 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5160 k++; 5161 } 5162 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5163 } 5164 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5165 5166 /* allocate space for j and a arrrays of B_oth */ 5167 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5168 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5169 5170 /* j-array */ 5171 /*---------*/ 5172 /* post receives of j-array */ 5173 for (i=0; i<nrecvs; i++) { 5174 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5175 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5176 } 5177 5178 /* pack the outgoing message j-array */ 5179 k = 0; 5180 for (i=0; i<nsends; i++) { 5181 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5182 bufJ = bufj+sstartsj[i]; 5183 for (j=0; j<nrows; j++) { 5184 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5185 for (ll=0; ll<sbs; ll++) { 5186 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5187 for (l=0; l<ncols; l++) { 5188 *bufJ++ = cols[l]; 5189 } 5190 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5191 } 5192 } 5193 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5194 } 5195 5196 /* recvs and sends of j-array are completed */ 5197 i = nrecvs; 5198 while (i--) { 5199 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5200 } 5201 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5202 } else if (scall == MAT_REUSE_MATRIX) { 5203 sstartsj = *startsj_s; 5204 rstartsj = *startsj_r; 5205 bufa = *bufa_ptr; 5206 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5207 b_otha = b_oth->a; 5208 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5209 5210 /* a-array */ 5211 /*---------*/ 5212 /* post receives of a-array */ 5213 for (i=0; i<nrecvs; i++) { 5214 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5215 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5216 } 5217 5218 /* pack the outgoing message a-array */ 5219 k = 0; 5220 for (i=0; i<nsends; i++) { 5221 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5222 bufA = bufa+sstartsj[i]; 5223 for (j=0; j<nrows; j++) { 5224 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5225 for (ll=0; ll<sbs; ll++) { 5226 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5227 for (l=0; l<ncols; l++) { 5228 *bufA++ = vals[l]; 5229 } 5230 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5231 } 5232 } 5233 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5234 } 5235 /* recvs and sends of a-array are completed */ 5236 i = nrecvs; 5237 while (i--) { 5238 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5239 } 5240 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5241 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5242 5243 if (scall == MAT_INITIAL_MATRIX) { 5244 /* put together the new matrix */ 5245 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5246 5247 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5248 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5249 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5250 b_oth->free_a = PETSC_TRUE; 5251 b_oth->free_ij = PETSC_TRUE; 5252 b_oth->nonew = 0; 5253 5254 ierr = PetscFree(bufj);CHKERRQ(ierr); 5255 if (!startsj_s || !bufa_ptr) { 5256 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5257 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5258 } else { 5259 *startsj_s = sstartsj; 5260 *startsj_r = rstartsj; 5261 *bufa_ptr = bufa; 5262 } 5263 } 5264 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5265 PetscFunctionReturn(0); 5266 } 5267 5268 /*@C 5269 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5270 5271 Not Collective 5272 5273 Input Parameters: 5274 . A - The matrix in mpiaij format 5275 5276 Output Parameter: 5277 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5278 . colmap - A map from global column index to local index into lvec 5279 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5280 5281 Level: developer 5282 5283 @*/ 5284 #if defined(PETSC_USE_CTABLE) 5285 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5286 #else 5287 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5288 #endif 5289 { 5290 Mat_MPIAIJ *a; 5291 5292 PetscFunctionBegin; 5293 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5294 PetscValidPointer(lvec, 2); 5295 PetscValidPointer(colmap, 3); 5296 PetscValidPointer(multScatter, 4); 5297 a = (Mat_MPIAIJ*) A->data; 5298 if (lvec) *lvec = a->lvec; 5299 if (colmap) *colmap = a->colmap; 5300 if (multScatter) *multScatter = a->Mvctx; 5301 PetscFunctionReturn(0); 5302 } 5303 5304 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5305 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5306 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5307 #if defined(PETSC_HAVE_ELEMENTAL) 5308 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5309 #endif 5310 #if defined(PETSC_HAVE_HYPRE) 5311 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5312 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5313 #endif 5314 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5315 5316 /* 5317 Computes (B'*A')' since computing B*A directly is untenable 5318 5319 n p p 5320 ( ) ( ) ( ) 5321 m ( A ) * n ( B ) = m ( C ) 5322 ( ) ( ) ( ) 5323 5324 */ 5325 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5326 { 5327 PetscErrorCode ierr; 5328 Mat At,Bt,Ct; 5329 5330 PetscFunctionBegin; 5331 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5332 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5333 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5334 ierr = MatDestroy(&At);CHKERRQ(ierr); 5335 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5336 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5337 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5338 PetscFunctionReturn(0); 5339 } 5340 5341 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5342 { 5343 PetscErrorCode ierr; 5344 PetscInt m=A->rmap->n,n=B->cmap->n; 5345 Mat Cmat; 5346 5347 PetscFunctionBegin; 5348 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); 5349 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5350 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5351 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5352 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5353 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5354 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5355 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5356 5357 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5358 5359 *C = Cmat; 5360 PetscFunctionReturn(0); 5361 } 5362 5363 /* ----------------------------------------------------------------*/ 5364 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5365 { 5366 PetscErrorCode ierr; 5367 5368 PetscFunctionBegin; 5369 if (scall == MAT_INITIAL_MATRIX) { 5370 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5371 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5372 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5373 } 5374 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5375 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5376 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5377 PetscFunctionReturn(0); 5378 } 5379 5380 /*MC 5381 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5382 5383 Options Database Keys: 5384 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5385 5386 Level: beginner 5387 5388 .seealso: MatCreateAIJ() 5389 M*/ 5390 5391 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5392 { 5393 Mat_MPIAIJ *b; 5394 PetscErrorCode ierr; 5395 PetscMPIInt size; 5396 5397 PetscFunctionBegin; 5398 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5399 5400 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5401 B->data = (void*)b; 5402 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5403 B->assembled = PETSC_FALSE; 5404 B->insertmode = NOT_SET_VALUES; 5405 b->size = size; 5406 5407 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5408 5409 /* build cache for off array entries formed */ 5410 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5411 5412 b->donotstash = PETSC_FALSE; 5413 b->colmap = 0; 5414 b->garray = 0; 5415 b->roworiented = PETSC_TRUE; 5416 5417 /* stuff used for matrix vector multiply */ 5418 b->lvec = NULL; 5419 b->Mvctx = NULL; 5420 5421 /* stuff for MatGetRow() */ 5422 b->rowindices = 0; 5423 b->rowvalues = 0; 5424 b->getrowactive = PETSC_FALSE; 5425 5426 /* flexible pointer used in CUSP/CUSPARSE classes */ 5427 b->spptr = NULL; 5428 5429 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5430 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5431 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5432 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5433 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5434 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5435 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5436 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5437 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5438 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5439 #if defined(PETSC_HAVE_ELEMENTAL) 5440 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5441 #endif 5442 #if defined(PETSC_HAVE_HYPRE) 5443 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5444 #endif 5445 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5446 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5447 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5448 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5449 #if defined(PETSC_HAVE_HYPRE) 5450 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5451 #endif 5452 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5453 PetscFunctionReturn(0); 5454 } 5455 5456 /*@C 5457 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5458 and "off-diagonal" part of the matrix in CSR format. 5459 5460 Collective on MPI_Comm 5461 5462 Input Parameters: 5463 + comm - MPI communicator 5464 . m - number of local rows (Cannot be PETSC_DECIDE) 5465 . n - This value should be the same as the local size used in creating the 5466 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5467 calculated if N is given) For square matrices n is almost always m. 5468 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5469 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5470 . i - row indices for "diagonal" portion of matrix 5471 . j - column indices 5472 . a - matrix values 5473 . oi - row indices for "off-diagonal" portion of matrix 5474 . oj - column indices 5475 - oa - matrix values 5476 5477 Output Parameter: 5478 . mat - the matrix 5479 5480 Level: advanced 5481 5482 Notes: 5483 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5484 must free the arrays once the matrix has been destroyed and not before. 5485 5486 The i and j indices are 0 based 5487 5488 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5489 5490 This sets local rows and cannot be used to set off-processor values. 5491 5492 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5493 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5494 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5495 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5496 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5497 communication if it is known that only local entries will be set. 5498 5499 .keywords: matrix, aij, compressed row, sparse, parallel 5500 5501 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5502 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5503 @*/ 5504 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) 5505 { 5506 PetscErrorCode ierr; 5507 Mat_MPIAIJ *maij; 5508 5509 PetscFunctionBegin; 5510 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5511 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5512 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5513 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5514 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5515 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5516 maij = (Mat_MPIAIJ*) (*mat)->data; 5517 5518 (*mat)->preallocated = PETSC_TRUE; 5519 5520 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5521 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5522 5523 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5524 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5525 5526 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5527 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5528 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5529 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5530 5531 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5532 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5533 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5534 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5535 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5536 PetscFunctionReturn(0); 5537 } 5538 5539 /* 5540 Special version for direct calls from Fortran 5541 */ 5542 #include <petsc/private/fortranimpl.h> 5543 5544 /* Change these macros so can be used in void function */ 5545 #undef CHKERRQ 5546 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5547 #undef SETERRQ2 5548 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5549 #undef SETERRQ3 5550 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5551 #undef SETERRQ 5552 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5553 5554 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5555 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5556 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5557 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5558 #else 5559 #endif 5560 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) 5561 { 5562 Mat mat = *mmat; 5563 PetscInt m = *mm, n = *mn; 5564 InsertMode addv = *maddv; 5565 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5566 PetscScalar value; 5567 PetscErrorCode ierr; 5568 5569 MatCheckPreallocated(mat,1); 5570 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5571 5572 #if defined(PETSC_USE_DEBUG) 5573 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5574 #endif 5575 { 5576 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5577 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5578 PetscBool roworiented = aij->roworiented; 5579 5580 /* Some Variables required in the macro */ 5581 Mat A = aij->A; 5582 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5583 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5584 MatScalar *aa = a->a; 5585 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5586 Mat B = aij->B; 5587 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5588 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5589 MatScalar *ba = b->a; 5590 5591 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5592 PetscInt nonew = a->nonew; 5593 MatScalar *ap1,*ap2; 5594 5595 PetscFunctionBegin; 5596 for (i=0; i<m; i++) { 5597 if (im[i] < 0) continue; 5598 #if defined(PETSC_USE_DEBUG) 5599 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); 5600 #endif 5601 if (im[i] >= rstart && im[i] < rend) { 5602 row = im[i] - rstart; 5603 lastcol1 = -1; 5604 rp1 = aj + ai[row]; 5605 ap1 = aa + ai[row]; 5606 rmax1 = aimax[row]; 5607 nrow1 = ailen[row]; 5608 low1 = 0; 5609 high1 = nrow1; 5610 lastcol2 = -1; 5611 rp2 = bj + bi[row]; 5612 ap2 = ba + bi[row]; 5613 rmax2 = bimax[row]; 5614 nrow2 = bilen[row]; 5615 low2 = 0; 5616 high2 = nrow2; 5617 5618 for (j=0; j<n; j++) { 5619 if (roworiented) value = v[i*n+j]; 5620 else value = v[i+j*m]; 5621 if (in[j] >= cstart && in[j] < cend) { 5622 col = in[j] - cstart; 5623 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5624 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5625 } else if (in[j] < 0) continue; 5626 #if defined(PETSC_USE_DEBUG) 5627 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); 5628 #endif 5629 else { 5630 if (mat->was_assembled) { 5631 if (!aij->colmap) { 5632 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5633 } 5634 #if defined(PETSC_USE_CTABLE) 5635 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5636 col--; 5637 #else 5638 col = aij->colmap[in[j]] - 1; 5639 #endif 5640 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5641 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5642 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5643 col = in[j]; 5644 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5645 B = aij->B; 5646 b = (Mat_SeqAIJ*)B->data; 5647 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5648 rp2 = bj + bi[row]; 5649 ap2 = ba + bi[row]; 5650 rmax2 = bimax[row]; 5651 nrow2 = bilen[row]; 5652 low2 = 0; 5653 high2 = nrow2; 5654 bm = aij->B->rmap->n; 5655 ba = b->a; 5656 } 5657 } else col = in[j]; 5658 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5659 } 5660 } 5661 } else if (!aij->donotstash) { 5662 if (roworiented) { 5663 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5664 } else { 5665 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5666 } 5667 } 5668 } 5669 } 5670 PetscFunctionReturnVoid(); 5671 } 5672 5673