1 2 3 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 4 #include <petsc/private/vecimpl.h> 5 #include <petsc/private/isimpl.h> 6 #include <petscblaslapack.h> 7 #include <petscsf.h> 8 9 /*MC 10 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 11 12 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 13 and MATMPIAIJ otherwise. As a result, for single process communicators, 14 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 15 for communicators controlling multiple processes. It is recommended that you call both of 16 the above preallocation routines for simplicity. 17 18 Options Database Keys: 19 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 20 21 Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when 22 enough exist. 23 24 Level: beginner 25 26 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ, MATMPIAIJ 27 M*/ 28 29 /*MC 30 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 31 32 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 33 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 34 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 35 for communicators controlling multiple processes. It is recommended that you call both of 36 the above preallocation routines for simplicity. 37 38 Options Database Keys: 39 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 40 41 Level: beginner 42 43 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 44 M*/ 45 46 PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 50 51 PetscFunctionBegin; 52 if (mat->A) { 53 ierr = MatSetBlockSizes(mat->A,rbs,cbs);CHKERRQ(ierr); 54 ierr = MatSetBlockSizes(mat->B,rbs,1);CHKERRQ(ierr); 55 } 56 PetscFunctionReturn(0); 57 } 58 59 PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows) 60 { 61 PetscErrorCode ierr; 62 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 63 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data; 64 Mat_SeqAIJ *b = (Mat_SeqAIJ*)mat->B->data; 65 const PetscInt *ia,*ib; 66 const MatScalar *aa,*bb; 67 PetscInt na,nb,i,j,*rows,cnt=0,n0rows; 68 PetscInt m = M->rmap->n,rstart = M->rmap->rstart; 69 70 PetscFunctionBegin; 71 *keptrows = 0; 72 ia = a->i; 73 ib = b->i; 74 for (i=0; i<m; i++) { 75 na = ia[i+1] - ia[i]; 76 nb = ib[i+1] - ib[i]; 77 if (!na && !nb) { 78 cnt++; 79 goto ok1; 80 } 81 aa = a->a + ia[i]; 82 for (j=0; j<na; j++) { 83 if (aa[j] != 0.0) goto ok1; 84 } 85 bb = b->a + ib[i]; 86 for (j=0; j <nb; j++) { 87 if (bb[j] != 0.0) goto ok1; 88 } 89 cnt++; 90 ok1:; 91 } 92 ierr = MPIU_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr); 93 if (!n0rows) PetscFunctionReturn(0); 94 ierr = PetscMalloc1(M->rmap->n-cnt,&rows);CHKERRQ(ierr); 95 cnt = 0; 96 for (i=0; i<m; i++) { 97 na = ia[i+1] - ia[i]; 98 nb = ib[i+1] - ib[i]; 99 if (!na && !nb) continue; 100 aa = a->a + ia[i]; 101 for (j=0; j<na;j++) { 102 if (aa[j] != 0.0) { 103 rows[cnt++] = rstart + i; 104 goto ok2; 105 } 106 } 107 bb = b->a + ib[i]; 108 for (j=0; j<nb; j++) { 109 if (bb[j] != 0.0) { 110 rows[cnt++] = rstart + i; 111 goto ok2; 112 } 113 } 114 ok2:; 115 } 116 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 117 PetscFunctionReturn(0); 118 } 119 120 PetscErrorCode MatDiagonalSet_MPIAIJ(Mat Y,Vec D,InsertMode is) 121 { 122 PetscErrorCode ierr; 123 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) Y->data; 124 125 PetscFunctionBegin; 126 if (Y->assembled && Y->rmap->rstart == Y->cmap->rstart && Y->rmap->rend == Y->cmap->rend) { 127 ierr = MatDiagonalSet(aij->A,D,is);CHKERRQ(ierr); 128 } else { 129 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 130 } 131 PetscFunctionReturn(0); 132 } 133 134 PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows) 135 { 136 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)M->data; 137 PetscErrorCode ierr; 138 PetscInt i,rstart,nrows,*rows; 139 140 PetscFunctionBegin; 141 *zrows = NULL; 142 ierr = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr); 143 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 144 for (i=0; i<nrows; i++) rows[i] += rstart; 145 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 146 PetscFunctionReturn(0); 147 } 148 149 PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms) 150 { 151 PetscErrorCode ierr; 152 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 153 PetscInt i,n,*garray = aij->garray; 154 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ*) aij->A->data; 155 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ*) aij->B->data; 156 PetscReal *work; 157 158 PetscFunctionBegin; 159 ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr); 160 ierr = PetscCalloc1(n,&work);CHKERRQ(ierr); 161 if (type == NORM_2) { 162 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 163 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]); 164 } 165 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 166 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]); 167 } 168 } else if (type == NORM_1) { 169 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 170 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 171 } 172 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 173 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 174 } 175 } else if (type == NORM_INFINITY) { 176 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 177 work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 178 } 179 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 180 work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]); 181 } 182 183 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 184 if (type == NORM_INFINITY) { 185 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 186 } else { 187 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 188 } 189 ierr = PetscFree(work);CHKERRQ(ierr); 190 if (type == NORM_2) { 191 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 192 } 193 PetscFunctionReturn(0); 194 } 195 196 PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A,IS *is) 197 { 198 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 199 IS sis,gis; 200 PetscErrorCode ierr; 201 const PetscInt *isis,*igis; 202 PetscInt n,*iis,nsis,ngis,rstart,i; 203 204 PetscFunctionBegin; 205 ierr = MatFindOffBlockDiagonalEntries(a->A,&sis);CHKERRQ(ierr); 206 ierr = MatFindNonzeroRows(a->B,&gis);CHKERRQ(ierr); 207 ierr = ISGetSize(gis,&ngis);CHKERRQ(ierr); 208 ierr = ISGetSize(sis,&nsis);CHKERRQ(ierr); 209 ierr = ISGetIndices(sis,&isis);CHKERRQ(ierr); 210 ierr = ISGetIndices(gis,&igis);CHKERRQ(ierr); 211 212 ierr = PetscMalloc1(ngis+nsis,&iis);CHKERRQ(ierr); 213 ierr = PetscMemcpy(iis,igis,ngis*sizeof(PetscInt));CHKERRQ(ierr); 214 ierr = PetscMemcpy(iis+ngis,isis,nsis*sizeof(PetscInt));CHKERRQ(ierr); 215 n = ngis + nsis; 216 ierr = PetscSortRemoveDupsInt(&n,iis);CHKERRQ(ierr); 217 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 218 for (i=0; i<n; i++) iis[i] += rstart; 219 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),n,iis,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 220 221 ierr = ISRestoreIndices(sis,&isis);CHKERRQ(ierr); 222 ierr = ISRestoreIndices(gis,&igis);CHKERRQ(ierr); 223 ierr = ISDestroy(&sis);CHKERRQ(ierr); 224 ierr = ISDestroy(&gis);CHKERRQ(ierr); 225 PetscFunctionReturn(0); 226 } 227 228 /* 229 Distributes a SeqAIJ matrix across a set of processes. Code stolen from 230 MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type. 231 232 Only for square matrices 233 234 Used by a preconditioner, hence PETSC_EXTERN 235 */ 236 PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat) 237 { 238 PetscMPIInt rank,size; 239 PetscInt *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz = 0,*gmataj,cnt,row,*ld,bses[2]; 240 PetscErrorCode ierr; 241 Mat mat; 242 Mat_SeqAIJ *gmata; 243 PetscMPIInt tag; 244 MPI_Status status; 245 PetscBool aij; 246 MatScalar *gmataa,*ao,*ad,*gmataarestore=0; 247 248 PetscFunctionBegin; 249 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 250 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 251 if (!rank) { 252 ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr); 253 if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name); 254 } 255 if (reuse == MAT_INITIAL_MATRIX) { 256 ierr = MatCreate(comm,&mat);CHKERRQ(ierr); 257 ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 258 ierr = MatGetBlockSizes(gmat,&bses[0],&bses[1]);CHKERRQ(ierr); 259 ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr); 260 ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr); 261 ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr); 262 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 263 ierr = PetscMalloc2(m,&dlens,m,&olens);CHKERRQ(ierr); 264 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 265 266 rowners[0] = 0; 267 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 268 rstart = rowners[rank]; 269 rend = rowners[rank+1]; 270 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 271 if (!rank) { 272 gmata = (Mat_SeqAIJ*) gmat->data; 273 /* send row lengths to all processors */ 274 for (i=0; i<m; i++) dlens[i] = gmata->ilen[i]; 275 for (i=1; i<size; i++) { 276 ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 277 } 278 /* determine number diagonal and off-diagonal counts */ 279 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 280 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 281 jj = 0; 282 for (i=0; i<m; i++) { 283 for (j=0; j<dlens[i]; j++) { 284 if (gmata->j[jj] < rstart) ld[i]++; 285 if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++; 286 jj++; 287 } 288 } 289 /* send column indices to other processes */ 290 for (i=1; i<size; i++) { 291 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 292 ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 293 ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 294 } 295 296 /* send numerical values to other processes */ 297 for (i=1; i<size; i++) { 298 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 299 ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 300 } 301 gmataa = gmata->a; 302 gmataj = gmata->j; 303 304 } else { 305 /* receive row lengths */ 306 ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 307 /* receive column indices */ 308 ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 309 ierr = PetscMalloc2(nz,&gmataa,nz,&gmataj);CHKERRQ(ierr); 310 ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 311 /* determine number diagonal and off-diagonal counts */ 312 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 313 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 314 jj = 0; 315 for (i=0; i<m; i++) { 316 for (j=0; j<dlens[i]; j++) { 317 if (gmataj[jj] < rstart) ld[i]++; 318 if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++; 319 jj++; 320 } 321 } 322 /* receive numerical values */ 323 ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 324 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 325 } 326 /* set preallocation */ 327 for (i=0; i<m; i++) { 328 dlens[i] -= olens[i]; 329 } 330 ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr); 331 ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr); 332 333 for (i=0; i<m; i++) { 334 dlens[i] += olens[i]; 335 } 336 cnt = 0; 337 for (i=0; i<m; i++) { 338 row = rstart + i; 339 ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr); 340 cnt += dlens[i]; 341 } 342 if (rank) { 343 ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr); 344 } 345 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 346 ierr = PetscFree(rowners);CHKERRQ(ierr); 347 348 ((Mat_MPIAIJ*)(mat->data))->ld = ld; 349 350 *inmat = mat; 351 } else { /* column indices are already set; only need to move over numerical values from process 0 */ 352 Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data; 353 Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data; 354 mat = *inmat; 355 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 356 if (!rank) { 357 /* send numerical values to other processes */ 358 gmata = (Mat_SeqAIJ*) gmat->data; 359 ierr = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr); 360 gmataa = gmata->a; 361 for (i=1; i<size; i++) { 362 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 363 ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 364 } 365 nz = gmata->i[rowners[1]]-gmata->i[rowners[0]]; 366 } else { 367 /* receive numerical values from process 0*/ 368 nz = Ad->nz + Ao->nz; 369 ierr = PetscMalloc1(nz,&gmataa);CHKERRQ(ierr); gmataarestore = gmataa; 370 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 371 } 372 /* transfer numerical values into the diagonal A and off diagonal B parts of mat */ 373 ld = ((Mat_MPIAIJ*)(mat->data))->ld; 374 ad = Ad->a; 375 ao = Ao->a; 376 if (mat->rmap->n) { 377 i = 0; 378 nz = ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 379 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 380 } 381 for (i=1; i<mat->rmap->n; i++) { 382 nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 383 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 384 } 385 i--; 386 if (mat->rmap->n) { 387 nz = Ao->i[i+1] - Ao->i[i] - ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 388 } 389 if (rank) { 390 ierr = PetscFree(gmataarestore);CHKERRQ(ierr); 391 } 392 } 393 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 394 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 395 PetscFunctionReturn(0); 396 } 397 398 /* 399 Local utility routine that creates a mapping from the global column 400 number to the local number in the off-diagonal part of the local 401 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 402 a slightly higher hash table cost; without it it is not scalable (each processor 403 has an order N integer array but is fast to acess. 404 */ 405 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 406 { 407 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 408 PetscErrorCode ierr; 409 PetscInt n = aij->B->cmap->n,i; 410 411 PetscFunctionBegin; 412 if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray"); 413 #if defined(PETSC_USE_CTABLE) 414 ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 415 for (i=0; i<n; i++) { 416 ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr); 417 } 418 #else 419 ierr = PetscCalloc1(mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 420 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N+1)*sizeof(PetscInt));CHKERRQ(ierr); 421 for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1; 422 #endif 423 PetscFunctionReturn(0); 424 } 425 426 #define MatSetValues_SeqAIJ_A_Private(row,col,value,addv,orow,ocol) \ 427 { \ 428 if (col <= lastcol1) low1 = 0; \ 429 else high1 = nrow1; \ 430 lastcol1 = col;\ 431 while (high1-low1 > 5) { \ 432 t = (low1+high1)/2; \ 433 if (rp1[t] > col) high1 = t; \ 434 else low1 = t; \ 435 } \ 436 for (_i=low1; _i<high1; _i++) { \ 437 if (rp1[_i] > col) break; \ 438 if (rp1[_i] == col) { \ 439 if (addv == ADD_VALUES) ap1[_i] += value; \ 440 else ap1[_i] = value; \ 441 goto a_noinsert; \ 442 } \ 443 } \ 444 if (value == 0.0 && ignorezeroentries && row != col) {low1 = 0; high1 = nrow1;goto a_noinsert;} \ 445 if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;} \ 446 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 447 MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \ 448 N = nrow1++ - 1; a->nz++; high1++; \ 449 /* shift up all the later entries in this row */ \ 450 for (ii=N; ii>=_i; ii--) { \ 451 rp1[ii+1] = rp1[ii]; \ 452 ap1[ii+1] = ap1[ii]; \ 453 } \ 454 rp1[_i] = col; \ 455 ap1[_i] = value; \ 456 A->nonzerostate++;\ 457 a_noinsert: ; \ 458 ailen[row] = nrow1; \ 459 } 460 461 #define MatSetValues_SeqAIJ_B_Private(row,col,value,addv,orow,ocol) \ 462 { \ 463 if (col <= lastcol2) low2 = 0; \ 464 else high2 = nrow2; \ 465 lastcol2 = col; \ 466 while (high2-low2 > 5) { \ 467 t = (low2+high2)/2; \ 468 if (rp2[t] > col) high2 = t; \ 469 else low2 = t; \ 470 } \ 471 for (_i=low2; _i<high2; _i++) { \ 472 if (rp2[_i] > col) break; \ 473 if (rp2[_i] == col) { \ 474 if (addv == ADD_VALUES) ap2[_i] += value; \ 475 else ap2[_i] = value; \ 476 goto b_noinsert; \ 477 } \ 478 } \ 479 if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 480 if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 481 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 482 MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \ 483 N = nrow2++ - 1; b->nz++; high2++; \ 484 /* shift up all the later entries in this row */ \ 485 for (ii=N; ii>=_i; ii--) { \ 486 rp2[ii+1] = rp2[ii]; \ 487 ap2[ii+1] = ap2[ii]; \ 488 } \ 489 rp2[_i] = col; \ 490 ap2[_i] = value; \ 491 B->nonzerostate++; \ 492 b_noinsert: ; \ 493 bilen[row] = nrow2; \ 494 } 495 496 PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[]) 497 { 498 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)A->data; 499 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data; 500 PetscErrorCode ierr; 501 PetscInt l,*garray = mat->garray,diag; 502 503 PetscFunctionBegin; 504 /* code only works for square matrices A */ 505 506 /* find size of row to the left of the diagonal part */ 507 ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr); 508 row = row - diag; 509 for (l=0; l<b->i[row+1]-b->i[row]; l++) { 510 if (garray[b->j[b->i[row]+l]] > diag) break; 511 } 512 ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr); 513 514 /* diagonal part */ 515 ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr); 516 517 /* right of diagonal part */ 518 ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr); 519 PetscFunctionReturn(0); 520 } 521 522 PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 523 { 524 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 525 PetscScalar value; 526 PetscErrorCode ierr; 527 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 528 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 529 PetscBool roworiented = aij->roworiented; 530 531 /* Some Variables required in the macro */ 532 Mat A = aij->A; 533 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 534 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 535 MatScalar *aa = a->a; 536 PetscBool ignorezeroentries = a->ignorezeroentries; 537 Mat B = aij->B; 538 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 539 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 540 MatScalar *ba = b->a; 541 542 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 543 PetscInt nonew; 544 MatScalar *ap1,*ap2; 545 546 PetscFunctionBegin; 547 for (i=0; i<m; i++) { 548 if (im[i] < 0) continue; 549 #if defined(PETSC_USE_DEBUG) 550 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 551 #endif 552 if (im[i] >= rstart && im[i] < rend) { 553 row = im[i] - rstart; 554 lastcol1 = -1; 555 rp1 = aj + ai[row]; 556 ap1 = aa + ai[row]; 557 rmax1 = aimax[row]; 558 nrow1 = ailen[row]; 559 low1 = 0; 560 high1 = nrow1; 561 lastcol2 = -1; 562 rp2 = bj + bi[row]; 563 ap2 = ba + bi[row]; 564 rmax2 = bimax[row]; 565 nrow2 = bilen[row]; 566 low2 = 0; 567 high2 = nrow2; 568 569 for (j=0; j<n; j++) { 570 if (roworiented) value = v[i*n+j]; 571 else value = v[i+j*m]; 572 if (in[j] >= cstart && in[j] < cend) { 573 col = in[j] - cstart; 574 nonew = a->nonew; 575 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 576 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 577 } else if (in[j] < 0) continue; 578 #if defined(PETSC_USE_DEBUG) 579 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 580 #endif 581 else { 582 if (mat->was_assembled) { 583 if (!aij->colmap) { 584 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 585 } 586 #if defined(PETSC_USE_CTABLE) 587 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 588 col--; 589 #else 590 col = aij->colmap[in[j]] - 1; 591 #endif 592 if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) { 593 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 594 col = in[j]; 595 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 596 B = aij->B; 597 b = (Mat_SeqAIJ*)B->data; 598 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a; 599 rp2 = bj + bi[row]; 600 ap2 = ba + bi[row]; 601 rmax2 = bimax[row]; 602 nrow2 = bilen[row]; 603 low2 = 0; 604 high2 = nrow2; 605 bm = aij->B->rmap->n; 606 ba = b->a; 607 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", im[i], in[j]); 608 } else col = in[j]; 609 nonew = b->nonew; 610 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 611 } 612 } 613 } else { 614 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 615 if (!aij->donotstash) { 616 mat->assembled = PETSC_FALSE; 617 if (roworiented) { 618 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 619 } else { 620 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 621 } 622 } 623 } 624 } 625 PetscFunctionReturn(0); 626 } 627 628 PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 629 { 630 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 631 PetscErrorCode ierr; 632 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 633 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 634 635 PetscFunctionBegin; 636 for (i=0; i<m; i++) { 637 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 638 if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1); 639 if (idxm[i] >= rstart && idxm[i] < rend) { 640 row = idxm[i] - rstart; 641 for (j=0; j<n; j++) { 642 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 643 if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1); 644 if (idxn[j] >= cstart && idxn[j] < cend) { 645 col = idxn[j] - cstart; 646 ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 647 } else { 648 if (!aij->colmap) { 649 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 650 } 651 #if defined(PETSC_USE_CTABLE) 652 ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr); 653 col--; 654 #else 655 col = aij->colmap[idxn[j]] - 1; 656 #endif 657 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0; 658 else { 659 ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 660 } 661 } 662 } 663 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 664 } 665 PetscFunctionReturn(0); 666 } 667 668 extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec); 669 670 PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode) 671 { 672 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 673 PetscErrorCode ierr; 674 PetscInt nstash,reallocs; 675 676 PetscFunctionBegin; 677 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 678 679 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 680 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 681 ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 682 PetscFunctionReturn(0); 683 } 684 685 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode) 686 { 687 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 688 Mat_SeqAIJ *a = (Mat_SeqAIJ*)aij->A->data; 689 PetscErrorCode ierr; 690 PetscMPIInt n; 691 PetscInt i,j,rstart,ncols,flg; 692 PetscInt *row,*col; 693 PetscBool other_disassembled; 694 PetscScalar *val; 695 696 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 697 698 PetscFunctionBegin; 699 if (!aij->donotstash && !mat->nooffprocentries) { 700 while (1) { 701 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 702 if (!flg) break; 703 704 for (i=0; i<n; ) { 705 /* Now identify the consecutive vals belonging to the same row */ 706 for (j=i,rstart=row[j]; j<n; j++) { 707 if (row[j] != rstart) break; 708 } 709 if (j < n) ncols = j-i; 710 else ncols = n-i; 711 /* Now assemble all these values with a single function call */ 712 ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr); 713 714 i = j; 715 } 716 } 717 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 718 } 719 ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr); 720 ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr); 721 722 /* determine if any processor has disassembled, if so we must 723 also disassemble ourselfs, in order that we may reassemble. */ 724 /* 725 if nonzero structure of submatrix B cannot change then we know that 726 no processor disassembled thus we can skip this stuff 727 */ 728 if (!((Mat_SeqAIJ*)aij->B->data)->nonew) { 729 ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 730 if (mat->was_assembled && !other_disassembled) { 731 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 732 } 733 } 734 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 735 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 736 } 737 ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr); 738 ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr); 739 ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr); 740 741 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 742 743 aij->rowvalues = 0; 744 745 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 746 if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ; 747 748 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 749 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 750 PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate; 751 ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 752 } 753 PetscFunctionReturn(0); 754 } 755 756 PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 757 { 758 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 759 PetscErrorCode ierr; 760 761 PetscFunctionBegin; 762 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 763 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 764 PetscFunctionReturn(0); 765 } 766 767 PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 768 { 769 Mat_MPIAIJ *mat = (Mat_MPIAIJ *) A->data; 770 PetscInt *lrows; 771 PetscInt r, len; 772 PetscErrorCode ierr; 773 774 PetscFunctionBegin; 775 /* get locally owned rows */ 776 ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr); 777 /* fix right hand side if needed */ 778 if (x && b) { 779 const PetscScalar *xx; 780 PetscScalar *bb; 781 782 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 783 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 784 for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]]; 785 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 786 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 787 } 788 /* Must zero l->B before l->A because the (diag) case below may put values into l->B*/ 789 ierr = MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 790 if (A->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 791 PetscBool cong; 792 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 793 if (cong) A->congruentlayouts = 1; 794 else A->congruentlayouts = 0; 795 } 796 if ((diag != 0.0) && A->congruentlayouts) { 797 ierr = MatZeroRows(mat->A, len, lrows, diag, NULL, NULL);CHKERRQ(ierr); 798 } else if (diag != 0.0) { 799 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 800 if (((Mat_SeqAIJ *) mat->A->data)->nonew) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 801 for (r = 0; r < len; ++r) { 802 const PetscInt row = lrows[r] + A->rmap->rstart; 803 ierr = MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES);CHKERRQ(ierr); 804 } 805 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 806 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 807 } else { 808 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 809 } 810 ierr = PetscFree(lrows);CHKERRQ(ierr); 811 812 /* only change matrix nonzero state if pattern was allowed to be changed */ 813 if (!((Mat_SeqAIJ*)(mat->A->data))->keepnonzeropattern) { 814 PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate; 815 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 816 } 817 PetscFunctionReturn(0); 818 } 819 820 PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 821 { 822 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 823 PetscErrorCode ierr; 824 PetscMPIInt n = A->rmap->n; 825 PetscInt i,j,r,m,p = 0,len = 0; 826 PetscInt *lrows,*owners = A->rmap->range; 827 PetscSFNode *rrows; 828 PetscSF sf; 829 const PetscScalar *xx; 830 PetscScalar *bb,*mask; 831 Vec xmask,lmask; 832 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)l->B->data; 833 const PetscInt *aj, *ii,*ridx; 834 PetscScalar *aa; 835 836 PetscFunctionBegin; 837 /* Create SF where leaves are input rows and roots are owned rows */ 838 ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr); 839 for (r = 0; r < n; ++r) lrows[r] = -1; 840 ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr); 841 for (r = 0; r < N; ++r) { 842 const PetscInt idx = rows[r]; 843 if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N); 844 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */ 845 ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr); 846 } 847 rrows[r].rank = p; 848 rrows[r].index = rows[r] - owners[p]; 849 } 850 ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr); 851 ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr); 852 /* Collect flags for rows to be zeroed */ 853 ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 854 ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 855 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 856 /* Compress and put in row numbers */ 857 for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r; 858 /* zero diagonal part of matrix */ 859 ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr); 860 /* handle off diagonal part of matrix */ 861 ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr); 862 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 863 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 864 for (i=0; i<len; i++) bb[lrows[i]] = 1; 865 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 866 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 867 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 868 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 869 if (x) { 870 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 871 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 872 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 873 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 874 } 875 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 876 /* remove zeroed rows of off diagonal matrix */ 877 ii = aij->i; 878 for (i=0; i<len; i++) { 879 ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr); 880 } 881 /* loop over all elements of off process part of matrix zeroing removed columns*/ 882 if (aij->compressedrow.use) { 883 m = aij->compressedrow.nrows; 884 ii = aij->compressedrow.i; 885 ridx = aij->compressedrow.rindex; 886 for (i=0; i<m; i++) { 887 n = ii[i+1] - ii[i]; 888 aj = aij->j + ii[i]; 889 aa = aij->a + ii[i]; 890 891 for (j=0; j<n; j++) { 892 if (PetscAbsScalar(mask[*aj])) { 893 if (b) bb[*ridx] -= *aa*xx[*aj]; 894 *aa = 0.0; 895 } 896 aa++; 897 aj++; 898 } 899 ridx++; 900 } 901 } else { /* do not use compressed row format */ 902 m = l->B->rmap->n; 903 for (i=0; i<m; i++) { 904 n = ii[i+1] - ii[i]; 905 aj = aij->j + ii[i]; 906 aa = aij->a + ii[i]; 907 for (j=0; j<n; j++) { 908 if (PetscAbsScalar(mask[*aj])) { 909 if (b) bb[i] -= *aa*xx[*aj]; 910 *aa = 0.0; 911 } 912 aa++; 913 aj++; 914 } 915 } 916 } 917 if (x) { 918 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 919 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 920 } 921 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 922 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 923 ierr = PetscFree(lrows);CHKERRQ(ierr); 924 925 /* only change matrix nonzero state if pattern was allowed to be changed */ 926 if (!((Mat_SeqAIJ*)(l->A->data))->keepnonzeropattern) { 927 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 928 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 929 } 930 PetscFunctionReturn(0); 931 } 932 933 PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy) 934 { 935 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 936 PetscErrorCode ierr; 937 PetscInt nt; 938 939 PetscFunctionBegin; 940 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 941 if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt); 942 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 943 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 944 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 945 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 946 PetscFunctionReturn(0); 947 } 948 949 PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx) 950 { 951 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 952 PetscErrorCode ierr; 953 954 PetscFunctionBegin; 955 ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr); 956 PetscFunctionReturn(0); 957 } 958 959 PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 960 { 961 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 962 PetscErrorCode ierr; 963 964 PetscFunctionBegin; 965 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 966 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 967 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 968 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 969 PetscFunctionReturn(0); 970 } 971 972 PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy) 973 { 974 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 975 PetscErrorCode ierr; 976 PetscBool merged; 977 978 PetscFunctionBegin; 979 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 980 /* do nondiagonal part */ 981 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 982 if (!merged) { 983 /* send it on its way */ 984 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 985 /* do local part */ 986 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 987 /* receive remote parts: note this assumes the values are not actually */ 988 /* added in yy until the next line, */ 989 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 990 } else { 991 /* do local part */ 992 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 993 /* send it on its way */ 994 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 995 /* values actually were received in the Begin() but we need to call this nop */ 996 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 997 } 998 PetscFunctionReturn(0); 999 } 1000 1001 PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool *f) 1002 { 1003 MPI_Comm comm; 1004 Mat_MPIAIJ *Aij = (Mat_MPIAIJ*) Amat->data, *Bij; 1005 Mat Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs; 1006 IS Me,Notme; 1007 PetscErrorCode ierr; 1008 PetscInt M,N,first,last,*notme,i; 1009 PetscMPIInt size; 1010 1011 PetscFunctionBegin; 1012 /* Easy test: symmetric diagonal block */ 1013 Bij = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A; 1014 ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr); 1015 if (!*f) PetscFunctionReturn(0); 1016 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1017 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1018 if (size == 1) PetscFunctionReturn(0); 1019 1020 /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */ 1021 ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr); 1022 ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr); 1023 ierr = PetscMalloc1(N-last+first,¬me);CHKERRQ(ierr); 1024 for (i=0; i<first; i++) notme[i] = i; 1025 for (i=last; i<M; i++) notme[i-last+first] = i; 1026 ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr); 1027 ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr); 1028 ierr = MatCreateSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr); 1029 Aoff = Aoffs[0]; 1030 ierr = MatCreateSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr); 1031 Boff = Boffs[0]; 1032 ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr); 1033 ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr); 1034 ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr); 1035 ierr = ISDestroy(&Me);CHKERRQ(ierr); 1036 ierr = ISDestroy(&Notme);CHKERRQ(ierr); 1037 ierr = PetscFree(notme);CHKERRQ(ierr); 1038 PetscFunctionReturn(0); 1039 } 1040 1041 PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1042 { 1043 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1044 PetscErrorCode ierr; 1045 1046 PetscFunctionBegin; 1047 /* do nondiagonal part */ 1048 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1049 /* send it on its way */ 1050 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1051 /* do local part */ 1052 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1053 /* receive remote parts */ 1054 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1055 PetscFunctionReturn(0); 1056 } 1057 1058 /* 1059 This only works correctly for square matrices where the subblock A->A is the 1060 diagonal block 1061 */ 1062 PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v) 1063 { 1064 PetscErrorCode ierr; 1065 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1066 1067 PetscFunctionBegin; 1068 if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1069 if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition"); 1070 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1071 PetscFunctionReturn(0); 1072 } 1073 1074 PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa) 1075 { 1076 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1077 PetscErrorCode ierr; 1078 1079 PetscFunctionBegin; 1080 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1081 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1082 PetscFunctionReturn(0); 1083 } 1084 1085 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 1086 { 1087 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1088 PetscErrorCode ierr; 1089 1090 PetscFunctionBegin; 1091 #if defined(PETSC_USE_LOG) 1092 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N); 1093 #endif 1094 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1095 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 1096 ierr = MatDestroy(&aij->A);CHKERRQ(ierr); 1097 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 1098 #if defined(PETSC_USE_CTABLE) 1099 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 1100 #else 1101 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 1102 #endif 1103 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 1104 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 1105 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 1106 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 1107 ierr = PetscFree(aij->ld);CHKERRQ(ierr); 1108 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1109 1110 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1111 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1112 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1113 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1114 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1115 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1116 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1117 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1118 #if defined(PETSC_HAVE_ELEMENTAL) 1119 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_elemental_C",NULL);CHKERRQ(ierr); 1120 #endif 1121 #if defined(PETSC_HAVE_HYPRE) 1122 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_hypre_C",NULL);CHKERRQ(ierr); 1123 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMatMatMult_transpose_mpiaij_mpiaij_C",NULL);CHKERRQ(ierr); 1124 #endif 1125 PetscFunctionReturn(0); 1126 } 1127 1128 PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer) 1129 { 1130 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1131 Mat_SeqAIJ *A = (Mat_SeqAIJ*)aij->A->data; 1132 Mat_SeqAIJ *B = (Mat_SeqAIJ*)aij->B->data; 1133 PetscErrorCode ierr; 1134 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1135 int fd; 1136 PetscInt nz,header[4],*row_lengths,*range=0,rlen,i; 1137 PetscInt nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz = 0; 1138 PetscScalar *column_values; 1139 PetscInt message_count,flowcontrolcount; 1140 FILE *file; 1141 1142 PetscFunctionBegin; 1143 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1144 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1145 nz = A->nz + B->nz; 1146 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1147 if (!rank) { 1148 header[0] = MAT_FILE_CLASSID; 1149 header[1] = mat->rmap->N; 1150 header[2] = mat->cmap->N; 1151 1152 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1153 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1154 /* get largest number of rows any processor has */ 1155 rlen = mat->rmap->n; 1156 range = mat->rmap->range; 1157 for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]); 1158 } else { 1159 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1160 rlen = mat->rmap->n; 1161 } 1162 1163 /* load up the local row counts */ 1164 ierr = PetscMalloc1(rlen+1,&row_lengths);CHKERRQ(ierr); 1165 for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1166 1167 /* store the row lengths to the file */ 1168 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1169 if (!rank) { 1170 ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1171 for (i=1; i<size; i++) { 1172 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1173 rlen = range[i+1] - range[i]; 1174 ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1175 ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1176 } 1177 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1178 } else { 1179 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1180 ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1181 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1182 } 1183 ierr = PetscFree(row_lengths);CHKERRQ(ierr); 1184 1185 /* load up the local column indices */ 1186 nzmax = nz; /* th processor needs space a largest processor needs */ 1187 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1188 ierr = PetscMalloc1(nzmax+1,&column_indices);CHKERRQ(ierr); 1189 cnt = 0; 1190 for (i=0; i<mat->rmap->n; i++) { 1191 for (j=B->i[i]; j<B->i[i+1]; j++) { 1192 if ((col = garray[B->j[j]]) > cstart) break; 1193 column_indices[cnt++] = col; 1194 } 1195 for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart; 1196 for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]]; 1197 } 1198 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1199 1200 /* store the column indices to the file */ 1201 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1202 if (!rank) { 1203 MPI_Status status; 1204 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1205 for (i=1; i<size; i++) { 1206 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1207 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1208 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1209 ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1210 ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1211 } 1212 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1213 } else { 1214 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1215 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1216 ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1217 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1218 } 1219 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1220 1221 /* load up the local column values */ 1222 ierr = PetscMalloc1(nzmax+1,&column_values);CHKERRQ(ierr); 1223 cnt = 0; 1224 for (i=0; i<mat->rmap->n; i++) { 1225 for (j=B->i[i]; j<B->i[i+1]; j++) { 1226 if (garray[B->j[j]] > cstart) break; 1227 column_values[cnt++] = B->a[j]; 1228 } 1229 for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k]; 1230 for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j]; 1231 } 1232 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1233 1234 /* store the column values to the file */ 1235 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1236 if (!rank) { 1237 MPI_Status status; 1238 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1239 for (i=1; i<size; i++) { 1240 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1241 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1242 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1243 ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1244 ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1245 } 1246 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1247 } else { 1248 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1249 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1250 ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1251 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1252 } 1253 ierr = PetscFree(column_values);CHKERRQ(ierr); 1254 1255 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1256 if (file) fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(mat->rmap->bs)); 1257 PetscFunctionReturn(0); 1258 } 1259 1260 #include <petscdraw.h> 1261 PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 1262 { 1263 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1264 PetscErrorCode ierr; 1265 PetscMPIInt rank = aij->rank,size = aij->size; 1266 PetscBool isdraw,iascii,isbinary; 1267 PetscViewer sviewer; 1268 PetscViewerFormat format; 1269 1270 PetscFunctionBegin; 1271 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1272 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1273 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1274 if (iascii) { 1275 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1276 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1277 MatInfo info; 1278 PetscBool inodes; 1279 1280 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1281 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 1282 ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr); 1283 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 1284 if (!inodes) { 1285 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n", 1286 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1287 } else { 1288 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n", 1289 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1290 } 1291 ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1292 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1293 ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1294 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1295 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1296 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 1297 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1298 ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr); 1299 PetscFunctionReturn(0); 1300 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1301 PetscInt inodecount,inodelimit,*inodes; 1302 ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr); 1303 if (inodes) { 1304 ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr); 1305 } else { 1306 ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr); 1307 } 1308 PetscFunctionReturn(0); 1309 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1310 PetscFunctionReturn(0); 1311 } 1312 } else if (isbinary) { 1313 if (size == 1) { 1314 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1315 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1316 } else { 1317 ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1318 } 1319 PetscFunctionReturn(0); 1320 } else if (isdraw) { 1321 PetscDraw draw; 1322 PetscBool isnull; 1323 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1324 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 1325 if (isnull) PetscFunctionReturn(0); 1326 } 1327 1328 { 1329 /* assemble the entire matrix onto first processor. */ 1330 Mat A; 1331 Mat_SeqAIJ *Aloc; 1332 PetscInt M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct; 1333 MatScalar *a; 1334 1335 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1336 if (!rank) { 1337 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1338 } else { 1339 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1340 } 1341 /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */ 1342 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 1343 ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr); 1344 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1345 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1346 1347 /* copy over the A part */ 1348 Aloc = (Mat_SeqAIJ*)aij->A->data; 1349 m = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1350 row = mat->rmap->rstart; 1351 for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart; 1352 for (i=0; i<m; i++) { 1353 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr); 1354 row++; 1355 a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i]; 1356 } 1357 aj = Aloc->j; 1358 for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart; 1359 1360 /* copy over the B part */ 1361 Aloc = (Mat_SeqAIJ*)aij->B->data; 1362 m = aij->B->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1363 row = mat->rmap->rstart; 1364 ierr = PetscMalloc1(ai[m]+1,&cols);CHKERRQ(ierr); 1365 ct = cols; 1366 for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]]; 1367 for (i=0; i<m; i++) { 1368 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr); 1369 row++; 1370 a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i]; 1371 } 1372 ierr = PetscFree(ct);CHKERRQ(ierr); 1373 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1374 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1375 /* 1376 Everyone has to call to draw the matrix since the graphics waits are 1377 synchronized across all processors that share the PetscDraw object 1378 */ 1379 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1380 if (!rank) { 1381 ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1382 ierr = MatView_SeqAIJ(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1383 } 1384 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1385 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1386 ierr = MatDestroy(&A);CHKERRQ(ierr); 1387 } 1388 PetscFunctionReturn(0); 1389 } 1390 1391 PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer) 1392 { 1393 PetscErrorCode ierr; 1394 PetscBool iascii,isdraw,issocket,isbinary; 1395 1396 PetscFunctionBegin; 1397 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1398 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1399 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1400 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1401 if (iascii || isdraw || isbinary || issocket) { 1402 ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1403 } 1404 PetscFunctionReturn(0); 1405 } 1406 1407 PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1408 { 1409 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1410 PetscErrorCode ierr; 1411 Vec bb1 = 0; 1412 PetscBool hasop; 1413 1414 PetscFunctionBegin; 1415 if (flag == SOR_APPLY_UPPER) { 1416 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1417 PetscFunctionReturn(0); 1418 } 1419 1420 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) { 1421 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 1422 } 1423 1424 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1425 if (flag & SOR_ZERO_INITIAL_GUESS) { 1426 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1427 its--; 1428 } 1429 1430 while (its--) { 1431 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1432 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1433 1434 /* update rhs: bb1 = bb - B*x */ 1435 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1436 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1437 1438 /* local sweep */ 1439 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1440 } 1441 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1442 if (flag & SOR_ZERO_INITIAL_GUESS) { 1443 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1444 its--; 1445 } 1446 while (its--) { 1447 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1448 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1449 1450 /* update rhs: bb1 = bb - B*x */ 1451 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1452 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1453 1454 /* local sweep */ 1455 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1456 } 1457 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1458 if (flag & SOR_ZERO_INITIAL_GUESS) { 1459 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1460 its--; 1461 } 1462 while (its--) { 1463 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1464 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1465 1466 /* update rhs: bb1 = bb - B*x */ 1467 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1468 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1469 1470 /* local sweep */ 1471 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1472 } 1473 } else if (flag & SOR_EISENSTAT) { 1474 Vec xx1; 1475 1476 ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr); 1477 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr); 1478 1479 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1480 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1481 if (!mat->diag) { 1482 ierr = MatCreateVecs(matin,&mat->diag,NULL);CHKERRQ(ierr); 1483 ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr); 1484 } 1485 ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr); 1486 if (hasop) { 1487 ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr); 1488 } else { 1489 ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr); 1490 } 1491 ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr); 1492 1493 ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr); 1494 1495 /* local sweep */ 1496 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr); 1497 ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr); 1498 ierr = VecDestroy(&xx1);CHKERRQ(ierr); 1499 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported"); 1500 1501 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 1502 1503 matin->factorerrortype = mat->A->factorerrortype; 1504 PetscFunctionReturn(0); 1505 } 1506 1507 PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B) 1508 { 1509 Mat aA,aB,Aperm; 1510 const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj; 1511 PetscScalar *aa,*ba; 1512 PetscInt i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest; 1513 PetscSF rowsf,sf; 1514 IS parcolp = NULL; 1515 PetscBool done; 1516 PetscErrorCode ierr; 1517 1518 PetscFunctionBegin; 1519 ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); 1520 ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr); 1521 ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr); 1522 ierr = PetscMalloc3(PetscMax(m,n),&work,m,&rdest,n,&cdest);CHKERRQ(ierr); 1523 1524 /* Invert row permutation to find out where my rows should go */ 1525 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr); 1526 ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr); 1527 ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr); 1528 for (i=0; i<m; i++) work[i] = A->rmap->rstart + i; 1529 ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1530 ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1531 1532 /* Invert column permutation to find out where my columns should go */ 1533 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1534 ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr); 1535 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1536 for (i=0; i<n; i++) work[i] = A->cmap->rstart + i; 1537 ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1538 ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1539 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1540 1541 ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr); 1542 ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr); 1543 ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr); 1544 1545 /* Find out where my gcols should go */ 1546 ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr); 1547 ierr = PetscMalloc1(ng,&gcdest);CHKERRQ(ierr); 1548 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1549 ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr); 1550 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1551 ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1552 ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1553 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1554 1555 ierr = PetscCalloc4(m,&dnnz,m,&onnz,m,&tdnnz,m,&tonnz);CHKERRQ(ierr); 1556 ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1557 ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1558 for (i=0; i<m; i++) { 1559 PetscInt row = rdest[i],rowner; 1560 ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr); 1561 for (j=ai[i]; j<ai[i+1]; j++) { 1562 PetscInt cowner,col = cdest[aj[j]]; 1563 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */ 1564 if (rowner == cowner) dnnz[i]++; 1565 else onnz[i]++; 1566 } 1567 for (j=bi[i]; j<bi[i+1]; j++) { 1568 PetscInt cowner,col = gcdest[bj[j]]; 1569 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); 1570 if (rowner == cowner) dnnz[i]++; 1571 else onnz[i]++; 1572 } 1573 } 1574 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1575 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1576 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1577 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1578 ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr); 1579 1580 ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr); 1581 ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr); 1582 ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr); 1583 for (i=0; i<m; i++) { 1584 PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */ 1585 PetscInt j0,rowlen; 1586 rowlen = ai[i+1] - ai[i]; 1587 for (j0=j=0; j<rowlen; j0=j) { /* rowlen could be larger than number of rows m, so sum in batches */ 1588 for ( ; j<PetscMin(rowlen,j0+m); j++) acols[j-j0] = cdest[aj[ai[i]+j]]; 1589 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,acols,aa+ai[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1590 } 1591 rowlen = bi[i+1] - bi[i]; 1592 for (j0=j=0; j<rowlen; j0=j) { 1593 for ( ; j<PetscMin(rowlen,j0+m); j++) bcols[j-j0] = gcdest[bj[bi[i]+j]]; 1594 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,bcols,ba+bi[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1595 } 1596 } 1597 ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1598 ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1599 ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1600 ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1601 ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr); 1602 ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr); 1603 ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr); 1604 ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr); 1605 ierr = PetscFree(gcdest);CHKERRQ(ierr); 1606 if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);} 1607 *B = Aperm; 1608 PetscFunctionReturn(0); 1609 } 1610 1611 PetscErrorCode MatGetGhosts_MPIAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 1612 { 1613 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1614 PetscErrorCode ierr; 1615 1616 PetscFunctionBegin; 1617 ierr = MatGetSize(aij->B,NULL,nghosts);CHKERRQ(ierr); 1618 if (ghosts) *ghosts = aij->garray; 1619 PetscFunctionReturn(0); 1620 } 1621 1622 PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1623 { 1624 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1625 Mat A = mat->A,B = mat->B; 1626 PetscErrorCode ierr; 1627 PetscReal isend[5],irecv[5]; 1628 1629 PetscFunctionBegin; 1630 info->block_size = 1.0; 1631 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1632 1633 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1634 isend[3] = info->memory; isend[4] = info->mallocs; 1635 1636 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1637 1638 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1639 isend[3] += info->memory; isend[4] += info->mallocs; 1640 if (flag == MAT_LOCAL) { 1641 info->nz_used = isend[0]; 1642 info->nz_allocated = isend[1]; 1643 info->nz_unneeded = isend[2]; 1644 info->memory = isend[3]; 1645 info->mallocs = isend[4]; 1646 } else if (flag == MAT_GLOBAL_MAX) { 1647 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1648 1649 info->nz_used = irecv[0]; 1650 info->nz_allocated = irecv[1]; 1651 info->nz_unneeded = irecv[2]; 1652 info->memory = irecv[3]; 1653 info->mallocs = irecv[4]; 1654 } else if (flag == MAT_GLOBAL_SUM) { 1655 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1656 1657 info->nz_used = irecv[0]; 1658 info->nz_allocated = irecv[1]; 1659 info->nz_unneeded = irecv[2]; 1660 info->memory = irecv[3]; 1661 info->mallocs = irecv[4]; 1662 } 1663 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1664 info->fill_ratio_needed = 0; 1665 info->factor_mallocs = 0; 1666 PetscFunctionReturn(0); 1667 } 1668 1669 PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg) 1670 { 1671 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1672 PetscErrorCode ierr; 1673 1674 PetscFunctionBegin; 1675 switch (op) { 1676 case MAT_NEW_NONZERO_LOCATIONS: 1677 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1678 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1679 case MAT_KEEP_NONZERO_PATTERN: 1680 case MAT_NEW_NONZERO_LOCATION_ERR: 1681 case MAT_USE_INODES: 1682 case MAT_IGNORE_ZERO_ENTRIES: 1683 MatCheckPreallocated(A,1); 1684 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1685 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1686 break; 1687 case MAT_ROW_ORIENTED: 1688 MatCheckPreallocated(A,1); 1689 a->roworiented = flg; 1690 1691 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1692 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1693 break; 1694 case MAT_NEW_DIAGONALS: 1695 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1696 break; 1697 case MAT_IGNORE_OFF_PROC_ENTRIES: 1698 a->donotstash = flg; 1699 break; 1700 case MAT_SPD: 1701 A->spd_set = PETSC_TRUE; 1702 A->spd = flg; 1703 if (flg) { 1704 A->symmetric = PETSC_TRUE; 1705 A->structurally_symmetric = PETSC_TRUE; 1706 A->symmetric_set = PETSC_TRUE; 1707 A->structurally_symmetric_set = PETSC_TRUE; 1708 } 1709 break; 1710 case MAT_SYMMETRIC: 1711 MatCheckPreallocated(A,1); 1712 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1713 break; 1714 case MAT_STRUCTURALLY_SYMMETRIC: 1715 MatCheckPreallocated(A,1); 1716 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1717 break; 1718 case MAT_HERMITIAN: 1719 MatCheckPreallocated(A,1); 1720 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1721 break; 1722 case MAT_SYMMETRY_ETERNAL: 1723 MatCheckPreallocated(A,1); 1724 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1725 break; 1726 case MAT_SUBMAT_SINGLEIS: 1727 A->submat_singleis = flg; 1728 break; 1729 default: 1730 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1731 } 1732 PetscFunctionReturn(0); 1733 } 1734 1735 PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1736 { 1737 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1738 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1739 PetscErrorCode ierr; 1740 PetscInt i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart; 1741 PetscInt nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend; 1742 PetscInt *cmap,*idx_p; 1743 1744 PetscFunctionBegin; 1745 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1746 mat->getrowactive = PETSC_TRUE; 1747 1748 if (!mat->rowvalues && (idx || v)) { 1749 /* 1750 allocate enough space to hold information from the longest row. 1751 */ 1752 Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data; 1753 PetscInt max = 1,tmp; 1754 for (i=0; i<matin->rmap->n; i++) { 1755 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1756 if (max < tmp) max = tmp; 1757 } 1758 ierr = PetscMalloc2(max,&mat->rowvalues,max,&mat->rowindices);CHKERRQ(ierr); 1759 } 1760 1761 if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows"); 1762 lrow = row - rstart; 1763 1764 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1765 if (!v) {pvA = 0; pvB = 0;} 1766 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1767 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1768 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1769 nztot = nzA + nzB; 1770 1771 cmap = mat->garray; 1772 if (v || idx) { 1773 if (nztot) { 1774 /* Sort by increasing column numbers, assuming A and B already sorted */ 1775 PetscInt imark = -1; 1776 if (v) { 1777 *v = v_p = mat->rowvalues; 1778 for (i=0; i<nzB; i++) { 1779 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1780 else break; 1781 } 1782 imark = i; 1783 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1784 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1785 } 1786 if (idx) { 1787 *idx = idx_p = mat->rowindices; 1788 if (imark > -1) { 1789 for (i=0; i<imark; i++) { 1790 idx_p[i] = cmap[cworkB[i]]; 1791 } 1792 } else { 1793 for (i=0; i<nzB; i++) { 1794 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1795 else break; 1796 } 1797 imark = i; 1798 } 1799 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart + cworkA[i]; 1800 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]]; 1801 } 1802 } else { 1803 if (idx) *idx = 0; 1804 if (v) *v = 0; 1805 } 1806 } 1807 *nz = nztot; 1808 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1809 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1810 PetscFunctionReturn(0); 1811 } 1812 1813 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1814 { 1815 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1816 1817 PetscFunctionBegin; 1818 if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first"); 1819 aij->getrowactive = PETSC_FALSE; 1820 PetscFunctionReturn(0); 1821 } 1822 1823 PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm) 1824 { 1825 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1826 Mat_SeqAIJ *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data; 1827 PetscErrorCode ierr; 1828 PetscInt i,j,cstart = mat->cmap->rstart; 1829 PetscReal sum = 0.0; 1830 MatScalar *v; 1831 1832 PetscFunctionBegin; 1833 if (aij->size == 1) { 1834 ierr = MatNorm(aij->A,type,norm);CHKERRQ(ierr); 1835 } else { 1836 if (type == NORM_FROBENIUS) { 1837 v = amat->a; 1838 for (i=0; i<amat->nz; i++) { 1839 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1840 } 1841 v = bmat->a; 1842 for (i=0; i<bmat->nz; i++) { 1843 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1844 } 1845 ierr = MPIU_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1846 *norm = PetscSqrtReal(*norm); 1847 ierr = PetscLogFlops(2*amat->nz+2*bmat->nz);CHKERRQ(ierr); 1848 } else if (type == NORM_1) { /* max column norm */ 1849 PetscReal *tmp,*tmp2; 1850 PetscInt *jj,*garray = aij->garray; 1851 ierr = PetscCalloc1(mat->cmap->N+1,&tmp);CHKERRQ(ierr); 1852 ierr = PetscMalloc1(mat->cmap->N+1,&tmp2);CHKERRQ(ierr); 1853 *norm = 0.0; 1854 v = amat->a; jj = amat->j; 1855 for (j=0; j<amat->nz; j++) { 1856 tmp[cstart + *jj++] += PetscAbsScalar(*v); v++; 1857 } 1858 v = bmat->a; jj = bmat->j; 1859 for (j=0; j<bmat->nz; j++) { 1860 tmp[garray[*jj++]] += PetscAbsScalar(*v); v++; 1861 } 1862 ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1863 for (j=0; j<mat->cmap->N; j++) { 1864 if (tmp2[j] > *norm) *norm = tmp2[j]; 1865 } 1866 ierr = PetscFree(tmp);CHKERRQ(ierr); 1867 ierr = PetscFree(tmp2);CHKERRQ(ierr); 1868 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1869 } else if (type == NORM_INFINITY) { /* max row norm */ 1870 PetscReal ntemp = 0.0; 1871 for (j=0; j<aij->A->rmap->n; j++) { 1872 v = amat->a + amat->i[j]; 1873 sum = 0.0; 1874 for (i=0; i<amat->i[j+1]-amat->i[j]; i++) { 1875 sum += PetscAbsScalar(*v); v++; 1876 } 1877 v = bmat->a + bmat->i[j]; 1878 for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) { 1879 sum += PetscAbsScalar(*v); v++; 1880 } 1881 if (sum > ntemp) ntemp = sum; 1882 } 1883 ierr = MPIU_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1884 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1885 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm"); 1886 } 1887 PetscFunctionReturn(0); 1888 } 1889 1890 PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout) 1891 { 1892 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1893 Mat_SeqAIJ *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data; 1894 PetscErrorCode ierr; 1895 PetscInt M = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i; 1896 PetscInt cstart = A->cmap->rstart,ncol; 1897 Mat B; 1898 MatScalar *array; 1899 1900 PetscFunctionBegin; 1901 if (reuse == MAT_INPLACE_MATRIX && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1902 1903 ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n; 1904 ai = Aloc->i; aj = Aloc->j; 1905 bi = Bloc->i; bj = Bloc->j; 1906 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1907 PetscInt *d_nnz,*g_nnz,*o_nnz; 1908 PetscSFNode *oloc; 1909 PETSC_UNUSED PetscSF sf; 1910 1911 ierr = PetscMalloc4(na,&d_nnz,na,&o_nnz,nb,&g_nnz,nb,&oloc);CHKERRQ(ierr); 1912 /* compute d_nnz for preallocation */ 1913 ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1914 for (i=0; i<ai[ma]; i++) { 1915 d_nnz[aj[i]]++; 1916 aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1917 } 1918 /* compute local off-diagonal contributions */ 1919 ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr); 1920 for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++; 1921 /* map those to global */ 1922 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1923 ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr); 1924 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1925 ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1926 ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1927 ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1928 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1929 1930 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1931 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1932 ierr = MatSetBlockSizes(B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 1933 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1934 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 1935 ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr); 1936 } else { 1937 B = *matout; 1938 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1939 for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1940 } 1941 1942 /* copy over the A part */ 1943 array = Aloc->a; 1944 row = A->rmap->rstart; 1945 for (i=0; i<ma; i++) { 1946 ncol = ai[i+1]-ai[i]; 1947 ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1948 row++; 1949 array += ncol; aj += ncol; 1950 } 1951 aj = Aloc->j; 1952 for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */ 1953 1954 /* copy over the B part */ 1955 ierr = PetscCalloc1(bi[mb],&cols);CHKERRQ(ierr); 1956 array = Bloc->a; 1957 row = A->rmap->rstart; 1958 for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]]; 1959 cols_tmp = cols; 1960 for (i=0; i<mb; i++) { 1961 ncol = bi[i+1]-bi[i]; 1962 ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1963 row++; 1964 array += ncol; cols_tmp += ncol; 1965 } 1966 ierr = PetscFree(cols);CHKERRQ(ierr); 1967 1968 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1969 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1970 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 1971 *matout = B; 1972 } else { 1973 ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr); 1974 } 1975 PetscFunctionReturn(0); 1976 } 1977 1978 PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr) 1979 { 1980 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1981 Mat a = aij->A,b = aij->B; 1982 PetscErrorCode ierr; 1983 PetscInt s1,s2,s3; 1984 1985 PetscFunctionBegin; 1986 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1987 if (rr) { 1988 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1989 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1990 /* Overlap communication with computation. */ 1991 ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1992 } 1993 if (ll) { 1994 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1995 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1996 ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr); 1997 } 1998 /* scale the diagonal block */ 1999 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 2000 2001 if (rr) { 2002 /* Do a scatter end and then right scale the off-diagonal block */ 2003 ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2004 ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr); 2005 } 2006 PetscFunctionReturn(0); 2007 } 2008 2009 PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2010 { 2011 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2012 PetscErrorCode ierr; 2013 2014 PetscFunctionBegin; 2015 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 2016 PetscFunctionReturn(0); 2017 } 2018 2019 PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool *flag) 2020 { 2021 Mat_MPIAIJ *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data; 2022 Mat a,b,c,d; 2023 PetscBool flg; 2024 PetscErrorCode ierr; 2025 2026 PetscFunctionBegin; 2027 a = matA->A; b = matA->B; 2028 c = matB->A; d = matB->B; 2029 2030 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 2031 if (flg) { 2032 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 2033 } 2034 ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2035 PetscFunctionReturn(0); 2036 } 2037 2038 PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str) 2039 { 2040 PetscErrorCode ierr; 2041 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2042 Mat_MPIAIJ *b = (Mat_MPIAIJ*)B->data; 2043 2044 PetscFunctionBegin; 2045 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2046 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2047 /* because of the column compression in the off-processor part of the matrix a->B, 2048 the number of columns in a->B and b->B may be different, hence we cannot call 2049 the MatCopy() directly on the two parts. If need be, we can provide a more 2050 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2051 then copying the submatrices */ 2052 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2053 } else { 2054 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 2055 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 2056 } 2057 PetscFunctionReturn(0); 2058 } 2059 2060 PetscErrorCode MatSetUp_MPIAIJ(Mat A) 2061 { 2062 PetscErrorCode ierr; 2063 2064 PetscFunctionBegin; 2065 ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 2066 PetscFunctionReturn(0); 2067 } 2068 2069 /* 2070 Computes the number of nonzeros per row needed for preallocation when X and Y 2071 have different nonzero structure. 2072 */ 2073 PetscErrorCode MatAXPYGetPreallocation_MPIX_private(PetscInt m,const PetscInt *xi,const PetscInt *xj,const PetscInt *xltog,const PetscInt *yi,const PetscInt *yj,const PetscInt *yltog,PetscInt *nnz) 2074 { 2075 PetscInt i,j,k,nzx,nzy; 2076 2077 PetscFunctionBegin; 2078 /* Set the number of nonzeros in the new matrix */ 2079 for (i=0; i<m; i++) { 2080 const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i]; 2081 nzx = xi[i+1] - xi[i]; 2082 nzy = yi[i+1] - yi[i]; 2083 nnz[i] = 0; 2084 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2085 for (; k<nzy && yltog[yjj[k]]<xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */ 2086 if (k<nzy && yltog[yjj[k]]==xltog[xjj[j]]) k++; /* Skip duplicate */ 2087 nnz[i]++; 2088 } 2089 for (; k<nzy; k++) nnz[i]++; 2090 } 2091 PetscFunctionReturn(0); 2092 } 2093 2094 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2095 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 2096 { 2097 PetscErrorCode ierr; 2098 PetscInt m = Y->rmap->N; 2099 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2100 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2101 2102 PetscFunctionBegin; 2103 ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr); 2104 PetscFunctionReturn(0); 2105 } 2106 2107 PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2108 { 2109 PetscErrorCode ierr; 2110 Mat_MPIAIJ *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data; 2111 PetscBLASInt bnz,one=1; 2112 Mat_SeqAIJ *x,*y; 2113 2114 PetscFunctionBegin; 2115 if (str == SAME_NONZERO_PATTERN) { 2116 PetscScalar alpha = a; 2117 x = (Mat_SeqAIJ*)xx->A->data; 2118 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2119 y = (Mat_SeqAIJ*)yy->A->data; 2120 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2121 x = (Mat_SeqAIJ*)xx->B->data; 2122 y = (Mat_SeqAIJ*)yy->B->data; 2123 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2124 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2125 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 2126 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2127 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 2128 } else { 2129 Mat B; 2130 PetscInt *nnz_d,*nnz_o; 2131 ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr); 2132 ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr); 2133 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2134 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2135 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2136 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 2137 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2138 ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 2139 ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 2140 ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 2141 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2142 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 2143 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 2144 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 2145 } 2146 PetscFunctionReturn(0); 2147 } 2148 2149 extern PetscErrorCode MatConjugate_SeqAIJ(Mat); 2150 2151 PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2152 { 2153 #if defined(PETSC_USE_COMPLEX) 2154 PetscErrorCode ierr; 2155 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2156 2157 PetscFunctionBegin; 2158 ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr); 2159 ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr); 2160 #else 2161 PetscFunctionBegin; 2162 #endif 2163 PetscFunctionReturn(0); 2164 } 2165 2166 PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2167 { 2168 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2169 PetscErrorCode ierr; 2170 2171 PetscFunctionBegin; 2172 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2173 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2174 PetscFunctionReturn(0); 2175 } 2176 2177 PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2178 { 2179 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2180 PetscErrorCode ierr; 2181 2182 PetscFunctionBegin; 2183 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2184 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2185 PetscFunctionReturn(0); 2186 } 2187 2188 PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2189 { 2190 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2191 PetscErrorCode ierr; 2192 PetscInt i,*idxb = 0; 2193 PetscScalar *va,*vb; 2194 Vec vtmp; 2195 2196 PetscFunctionBegin; 2197 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 2198 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2199 if (idx) { 2200 for (i=0; i<A->rmap->n; i++) { 2201 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2202 } 2203 } 2204 2205 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2206 if (idx) { 2207 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2208 } 2209 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2210 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2211 2212 for (i=0; i<A->rmap->n; i++) { 2213 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 2214 va[i] = vb[i]; 2215 if (idx) idx[i] = a->garray[idxb[i]]; 2216 } 2217 } 2218 2219 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2220 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2221 ierr = PetscFree(idxb);CHKERRQ(ierr); 2222 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2223 PetscFunctionReturn(0); 2224 } 2225 2226 PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2227 { 2228 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2229 PetscErrorCode ierr; 2230 PetscInt i,*idxb = 0; 2231 PetscScalar *va,*vb; 2232 Vec vtmp; 2233 2234 PetscFunctionBegin; 2235 ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr); 2236 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2237 if (idx) { 2238 for (i=0; i<A->cmap->n; i++) { 2239 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2240 } 2241 } 2242 2243 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2244 if (idx) { 2245 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2246 } 2247 ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2248 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2249 2250 for (i=0; i<A->rmap->n; i++) { 2251 if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) { 2252 va[i] = vb[i]; 2253 if (idx) idx[i] = a->garray[idxb[i]]; 2254 } 2255 } 2256 2257 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2258 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2259 ierr = PetscFree(idxb);CHKERRQ(ierr); 2260 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2261 PetscFunctionReturn(0); 2262 } 2263 2264 PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2265 { 2266 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2267 PetscInt n = A->rmap->n; 2268 PetscInt cstart = A->cmap->rstart; 2269 PetscInt *cmap = mat->garray; 2270 PetscInt *diagIdx, *offdiagIdx; 2271 Vec diagV, offdiagV; 2272 PetscScalar *a, *diagA, *offdiagA; 2273 PetscInt r; 2274 PetscErrorCode ierr; 2275 2276 PetscFunctionBegin; 2277 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2278 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr); 2279 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr); 2280 ierr = MatGetRowMin(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2281 ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2282 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2283 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2284 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2285 for (r = 0; r < n; ++r) { 2286 if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) { 2287 a[r] = diagA[r]; 2288 idx[r] = cstart + diagIdx[r]; 2289 } else { 2290 a[r] = offdiagA[r]; 2291 idx[r] = cmap[offdiagIdx[r]]; 2292 } 2293 } 2294 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2295 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2296 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2297 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2298 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2299 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2300 PetscFunctionReturn(0); 2301 } 2302 2303 PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2304 { 2305 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2306 PetscInt n = A->rmap->n; 2307 PetscInt cstart = A->cmap->rstart; 2308 PetscInt *cmap = mat->garray; 2309 PetscInt *diagIdx, *offdiagIdx; 2310 Vec diagV, offdiagV; 2311 PetscScalar *a, *diagA, *offdiagA; 2312 PetscInt r; 2313 PetscErrorCode ierr; 2314 2315 PetscFunctionBegin; 2316 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2317 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr); 2318 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr); 2319 ierr = MatGetRowMax(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2320 ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2321 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2322 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2323 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2324 for (r = 0; r < n; ++r) { 2325 if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) { 2326 a[r] = diagA[r]; 2327 idx[r] = cstart + diagIdx[r]; 2328 } else { 2329 a[r] = offdiagA[r]; 2330 idx[r] = cmap[offdiagIdx[r]]; 2331 } 2332 } 2333 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2334 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2335 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2336 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2337 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2338 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2339 PetscFunctionReturn(0); 2340 } 2341 2342 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat) 2343 { 2344 PetscErrorCode ierr; 2345 Mat *dummy; 2346 2347 PetscFunctionBegin; 2348 ierr = MatCreateSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr); 2349 *newmat = *dummy; 2350 ierr = PetscFree(dummy);CHKERRQ(ierr); 2351 PetscFunctionReturn(0); 2352 } 2353 2354 PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values) 2355 { 2356 Mat_MPIAIJ *a = (Mat_MPIAIJ*) A->data; 2357 PetscErrorCode ierr; 2358 2359 PetscFunctionBegin; 2360 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2361 A->factorerrortype = a->A->factorerrortype; 2362 PetscFunctionReturn(0); 2363 } 2364 2365 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx) 2366 { 2367 PetscErrorCode ierr; 2368 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)x->data; 2369 2370 PetscFunctionBegin; 2371 ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr); 2372 ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr); 2373 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2374 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2375 PetscFunctionReturn(0); 2376 } 2377 2378 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A,PetscBool sc) 2379 { 2380 PetscFunctionBegin; 2381 if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable; 2382 else A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ; 2383 PetscFunctionReturn(0); 2384 } 2385 2386 /*@ 2387 MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap 2388 2389 Collective on Mat 2390 2391 Input Parameters: 2392 + A - the matrix 2393 - sc - PETSC_TRUE indicates use the scalable algorithm (default is not to use the scalable algorithm) 2394 2395 Level: advanced 2396 2397 @*/ 2398 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A,PetscBool sc) 2399 { 2400 PetscErrorCode ierr; 2401 2402 PetscFunctionBegin; 2403 ierr = PetscTryMethod(A,"MatMPIAIJSetUseScalableIncreaseOverlap_C",(Mat,PetscBool),(A,sc));CHKERRQ(ierr); 2404 PetscFunctionReturn(0); 2405 } 2406 2407 PetscErrorCode MatSetFromOptions_MPIAIJ(PetscOptionItems *PetscOptionsObject,Mat A) 2408 { 2409 PetscErrorCode ierr; 2410 PetscBool sc = PETSC_FALSE,flg; 2411 2412 PetscFunctionBegin; 2413 ierr = PetscOptionsHead(PetscOptionsObject,"MPIAIJ options");CHKERRQ(ierr); 2414 ierr = PetscObjectOptionsBegin((PetscObject)A); 2415 if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE; 2416 ierr = PetscOptionsBool("-mat_increase_overlap_scalable","Use a scalable algorithm to compute the overlap","MatIncreaseOverlap",sc,&sc,&flg);CHKERRQ(ierr); 2417 if (flg) { 2418 ierr = MatMPIAIJSetUseScalableIncreaseOverlap(A,sc);CHKERRQ(ierr); 2419 } 2420 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2421 PetscFunctionReturn(0); 2422 } 2423 2424 PetscErrorCode MatShift_MPIAIJ(Mat Y,PetscScalar a) 2425 { 2426 PetscErrorCode ierr; 2427 Mat_MPIAIJ *maij = (Mat_MPIAIJ*)Y->data; 2428 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)maij->A->data; 2429 2430 PetscFunctionBegin; 2431 if (!Y->preallocated) { 2432 ierr = MatMPIAIJSetPreallocation(Y,1,NULL,0,NULL);CHKERRQ(ierr); 2433 } else if (!aij->nz) { 2434 PetscInt nonew = aij->nonew; 2435 ierr = MatSeqAIJSetPreallocation(maij->A,1,NULL);CHKERRQ(ierr); 2436 aij->nonew = nonew; 2437 } 2438 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2439 PetscFunctionReturn(0); 2440 } 2441 2442 PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A,PetscBool *missing,PetscInt *d) 2443 { 2444 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2445 PetscErrorCode ierr; 2446 2447 PetscFunctionBegin; 2448 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2449 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2450 if (d) { 2451 PetscInt rstart; 2452 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2453 *d += rstart; 2454 2455 } 2456 PetscFunctionReturn(0); 2457 } 2458 2459 2460 /* -------------------------------------------------------------------*/ 2461 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 2462 MatGetRow_MPIAIJ, 2463 MatRestoreRow_MPIAIJ, 2464 MatMult_MPIAIJ, 2465 /* 4*/ MatMultAdd_MPIAIJ, 2466 MatMultTranspose_MPIAIJ, 2467 MatMultTransposeAdd_MPIAIJ, 2468 0, 2469 0, 2470 0, 2471 /*10*/ 0, 2472 0, 2473 0, 2474 MatSOR_MPIAIJ, 2475 MatTranspose_MPIAIJ, 2476 /*15*/ MatGetInfo_MPIAIJ, 2477 MatEqual_MPIAIJ, 2478 MatGetDiagonal_MPIAIJ, 2479 MatDiagonalScale_MPIAIJ, 2480 MatNorm_MPIAIJ, 2481 /*20*/ MatAssemblyBegin_MPIAIJ, 2482 MatAssemblyEnd_MPIAIJ, 2483 MatSetOption_MPIAIJ, 2484 MatZeroEntries_MPIAIJ, 2485 /*24*/ MatZeroRows_MPIAIJ, 2486 0, 2487 0, 2488 0, 2489 0, 2490 /*29*/ MatSetUp_MPIAIJ, 2491 0, 2492 0, 2493 MatGetDiagonalBlock_MPIAIJ, 2494 0, 2495 /*34*/ MatDuplicate_MPIAIJ, 2496 0, 2497 0, 2498 0, 2499 0, 2500 /*39*/ MatAXPY_MPIAIJ, 2501 MatCreateSubMatrices_MPIAIJ, 2502 MatIncreaseOverlap_MPIAIJ, 2503 MatGetValues_MPIAIJ, 2504 MatCopy_MPIAIJ, 2505 /*44*/ MatGetRowMax_MPIAIJ, 2506 MatScale_MPIAIJ, 2507 MatShift_MPIAIJ, 2508 MatDiagonalSet_MPIAIJ, 2509 MatZeroRowsColumns_MPIAIJ, 2510 /*49*/ MatSetRandom_MPIAIJ, 2511 0, 2512 0, 2513 0, 2514 0, 2515 /*54*/ MatFDColoringCreate_MPIXAIJ, 2516 0, 2517 MatSetUnfactored_MPIAIJ, 2518 MatPermute_MPIAIJ, 2519 0, 2520 /*59*/ MatCreateSubMatrix_MPIAIJ, 2521 MatDestroy_MPIAIJ, 2522 MatView_MPIAIJ, 2523 0, 2524 MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ, 2525 /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ, 2526 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 2527 0, 2528 0, 2529 0, 2530 /*69*/ MatGetRowMaxAbs_MPIAIJ, 2531 MatGetRowMinAbs_MPIAIJ, 2532 0, 2533 0, 2534 0, 2535 0, 2536 /*75*/ MatFDColoringApply_AIJ, 2537 MatSetFromOptions_MPIAIJ, 2538 0, 2539 0, 2540 MatFindZeroDiagonals_MPIAIJ, 2541 /*80*/ 0, 2542 0, 2543 0, 2544 /*83*/ MatLoad_MPIAIJ, 2545 0, 2546 0, 2547 0, 2548 0, 2549 0, 2550 /*89*/ MatMatMult_MPIAIJ_MPIAIJ, 2551 MatMatMultSymbolic_MPIAIJ_MPIAIJ, 2552 MatMatMultNumeric_MPIAIJ_MPIAIJ, 2553 MatPtAP_MPIAIJ_MPIAIJ, 2554 MatPtAPSymbolic_MPIAIJ_MPIAIJ, 2555 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 2556 0, 2557 0, 2558 0, 2559 0, 2560 /*99*/ 0, 2561 0, 2562 0, 2563 MatConjugate_MPIAIJ, 2564 0, 2565 /*104*/MatSetValuesRow_MPIAIJ, 2566 MatRealPart_MPIAIJ, 2567 MatImaginaryPart_MPIAIJ, 2568 0, 2569 0, 2570 /*109*/0, 2571 0, 2572 MatGetRowMin_MPIAIJ, 2573 0, 2574 MatMissingDiagonal_MPIAIJ, 2575 /*114*/MatGetSeqNonzeroStructure_MPIAIJ, 2576 0, 2577 MatGetGhosts_MPIAIJ, 2578 0, 2579 0, 2580 /*119*/0, 2581 0, 2582 0, 2583 0, 2584 MatGetMultiProcBlock_MPIAIJ, 2585 /*124*/MatFindNonzeroRows_MPIAIJ, 2586 MatGetColumnNorms_MPIAIJ, 2587 MatInvertBlockDiagonal_MPIAIJ, 2588 0, 2589 MatCreateSubMatricesMPI_MPIAIJ, 2590 /*129*/0, 2591 MatTransposeMatMult_MPIAIJ_MPIAIJ, 2592 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ, 2593 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 2594 0, 2595 /*134*/0, 2596 0, 2597 0, 2598 0, 2599 0, 2600 /*139*/MatSetBlockSizes_MPIAIJ, 2601 0, 2602 0, 2603 MatFDColoringSetUp_MPIXAIJ, 2604 MatFindOffBlockDiagonalEntries_MPIAIJ, 2605 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIAIJ 2606 }; 2607 2608 /* ----------------------------------------------------------------------------------------*/ 2609 2610 PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 2611 { 2612 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2613 PetscErrorCode ierr; 2614 2615 PetscFunctionBegin; 2616 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 2617 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 2618 PetscFunctionReturn(0); 2619 } 2620 2621 PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 2622 { 2623 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2624 PetscErrorCode ierr; 2625 2626 PetscFunctionBegin; 2627 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 2628 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 2629 PetscFunctionReturn(0); 2630 } 2631 2632 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 2633 { 2634 Mat_MPIAIJ *b; 2635 PetscErrorCode ierr; 2636 2637 PetscFunctionBegin; 2638 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2639 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2640 b = (Mat_MPIAIJ*)B->data; 2641 2642 #if defined(PETSC_USE_CTABLE) 2643 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2644 #else 2645 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2646 #endif 2647 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2648 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2649 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2650 2651 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2652 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2653 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2654 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 2655 ierr = MatSetBlockSizesFromMats(b->B,B,B);CHKERRQ(ierr); 2656 ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr); 2657 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2658 2659 if (!B->preallocated) { 2660 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2661 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2662 ierr = MatSetBlockSizesFromMats(b->A,B,B);CHKERRQ(ierr); 2663 ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr); 2664 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2665 } 2666 2667 ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr); 2668 ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr); 2669 B->preallocated = PETSC_TRUE; 2670 B->was_assembled = PETSC_FALSE; 2671 B->assembled = PETSC_FALSE;; 2672 PetscFunctionReturn(0); 2673 } 2674 2675 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 2676 { 2677 Mat mat; 2678 Mat_MPIAIJ *a,*oldmat = (Mat_MPIAIJ*)matin->data; 2679 PetscErrorCode ierr; 2680 2681 PetscFunctionBegin; 2682 *newmat = 0; 2683 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 2684 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 2685 ierr = MatSetBlockSizesFromMats(mat,matin,matin);CHKERRQ(ierr); 2686 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 2687 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2688 a = (Mat_MPIAIJ*)mat->data; 2689 2690 mat->factortype = matin->factortype; 2691 mat->assembled = PETSC_TRUE; 2692 mat->insertmode = NOT_SET_VALUES; 2693 mat->preallocated = PETSC_TRUE; 2694 2695 a->size = oldmat->size; 2696 a->rank = oldmat->rank; 2697 a->donotstash = oldmat->donotstash; 2698 a->roworiented = oldmat->roworiented; 2699 a->rowindices = 0; 2700 a->rowvalues = 0; 2701 a->getrowactive = PETSC_FALSE; 2702 2703 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 2704 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 2705 2706 if (oldmat->colmap) { 2707 #if defined(PETSC_USE_CTABLE) 2708 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 2709 #else 2710 ierr = PetscMalloc1(mat->cmap->N,&a->colmap);CHKERRQ(ierr); 2711 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2712 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2713 #endif 2714 } else a->colmap = 0; 2715 if (oldmat->garray) { 2716 PetscInt len; 2717 len = oldmat->B->cmap->n; 2718 ierr = PetscMalloc1(len+1,&a->garray);CHKERRQ(ierr); 2719 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 2720 if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); } 2721 } else a->garray = 0; 2722 2723 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 2724 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 2725 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 2726 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 2727 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 2728 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 2729 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 2730 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 2731 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 2732 *newmat = mat; 2733 PetscFunctionReturn(0); 2734 } 2735 2736 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 2737 { 2738 PetscScalar *vals,*svals; 2739 MPI_Comm comm; 2740 PetscErrorCode ierr; 2741 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 2742 PetscInt i,nz,j,rstart,rend,mmax,maxnz = 0; 2743 PetscInt header[4],*rowlengths = 0,M,N,m,*cols; 2744 PetscInt *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols; 2745 PetscInt cend,cstart,n,*rowners; 2746 int fd; 2747 PetscInt bs = newMat->rmap->bs; 2748 2749 PetscFunctionBegin; 2750 /* force binary viewer to load .info file if it has not yet done so */ 2751 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 2752 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2753 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2754 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2755 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2756 if (!rank) { 2757 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 2758 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 2759 if (header[3] < 0) SETERRQ(PetscObjectComm((PetscObject)newMat),PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as MATMPIAIJ"); 2760 } 2761 2762 ierr = PetscOptionsBegin(comm,NULL,"Options for loading MATMPIAIJ matrix","Mat");CHKERRQ(ierr); 2763 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 2764 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2765 if (bs < 0) bs = 1; 2766 2767 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 2768 M = header[1]; N = header[2]; 2769 2770 /* If global sizes are set, check if they are consistent with that given in the file */ 2771 if (newMat->rmap->N >= 0 && newMat->rmap->N != M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of rows:Matrix in file has (%D) and input matrix has (%D)",newMat->rmap->N,M); 2772 if (newMat->cmap->N >=0 && newMat->cmap->N != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of cols:Matrix in file has (%D) and input matrix has (%D)",newMat->cmap->N,N); 2773 2774 /* determine ownership of all (block) rows */ 2775 if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs); 2776 if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank)); /* PETSC_DECIDE */ 2777 else m = newMat->rmap->n; /* Set by user */ 2778 2779 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 2780 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 2781 2782 /* First process needs enough room for process with most rows */ 2783 if (!rank) { 2784 mmax = rowners[1]; 2785 for (i=2; i<=size; i++) { 2786 mmax = PetscMax(mmax, rowners[i]); 2787 } 2788 } else mmax = -1; /* unused, but compilers complain */ 2789 2790 rowners[0] = 0; 2791 for (i=2; i<=size; i++) { 2792 rowners[i] += rowners[i-1]; 2793 } 2794 rstart = rowners[rank]; 2795 rend = rowners[rank+1]; 2796 2797 /* distribute row lengths to all processors */ 2798 ierr = PetscMalloc2(m,&ourlens,m,&offlens);CHKERRQ(ierr); 2799 if (!rank) { 2800 ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr); 2801 ierr = PetscMalloc1(mmax,&rowlengths);CHKERRQ(ierr); 2802 ierr = PetscCalloc1(size,&procsnz);CHKERRQ(ierr); 2803 for (j=0; j<m; j++) { 2804 procsnz[0] += ourlens[j]; 2805 } 2806 for (i=1; i<size; i++) { 2807 ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr); 2808 /* calculate the number of nonzeros on each processor */ 2809 for (j=0; j<rowners[i+1]-rowners[i]; j++) { 2810 procsnz[i] += rowlengths[j]; 2811 } 2812 ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2813 } 2814 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2815 } else { 2816 ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2817 } 2818 2819 if (!rank) { 2820 /* determine max buffer needed and allocate it */ 2821 maxnz = 0; 2822 for (i=0; i<size; i++) { 2823 maxnz = PetscMax(maxnz,procsnz[i]); 2824 } 2825 ierr = PetscMalloc1(maxnz,&cols);CHKERRQ(ierr); 2826 2827 /* read in my part of the matrix column indices */ 2828 nz = procsnz[0]; 2829 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2830 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 2831 2832 /* read in every one elses and ship off */ 2833 for (i=1; i<size; i++) { 2834 nz = procsnz[i]; 2835 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 2836 ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2837 } 2838 ierr = PetscFree(cols);CHKERRQ(ierr); 2839 } else { 2840 /* determine buffer space needed for message */ 2841 nz = 0; 2842 for (i=0; i<m; i++) { 2843 nz += ourlens[i]; 2844 } 2845 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2846 2847 /* receive message of column indices*/ 2848 ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2849 } 2850 2851 /* determine column ownership if matrix is not square */ 2852 if (N != M) { 2853 if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank); 2854 else n = newMat->cmap->n; 2855 ierr = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2856 cstart = cend - n; 2857 } else { 2858 cstart = rstart; 2859 cend = rend; 2860 n = cend - cstart; 2861 } 2862 2863 /* loop over local rows, determining number of off diagonal entries */ 2864 ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr); 2865 jj = 0; 2866 for (i=0; i<m; i++) { 2867 for (j=0; j<ourlens[i]; j++) { 2868 if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++; 2869 jj++; 2870 } 2871 } 2872 2873 for (i=0; i<m; i++) { 2874 ourlens[i] -= offlens[i]; 2875 } 2876 ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr); 2877 2878 if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);} 2879 2880 ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr); 2881 2882 for (i=0; i<m; i++) { 2883 ourlens[i] += offlens[i]; 2884 } 2885 2886 if (!rank) { 2887 ierr = PetscMalloc1(maxnz+1,&vals);CHKERRQ(ierr); 2888 2889 /* read in my part of the matrix numerical values */ 2890 nz = procsnz[0]; 2891 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2892 2893 /* insert into matrix */ 2894 jj = rstart; 2895 smycols = mycols; 2896 svals = vals; 2897 for (i=0; i<m; i++) { 2898 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2899 smycols += ourlens[i]; 2900 svals += ourlens[i]; 2901 jj++; 2902 } 2903 2904 /* read in other processors and ship out */ 2905 for (i=1; i<size; i++) { 2906 nz = procsnz[i]; 2907 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2908 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2909 } 2910 ierr = PetscFree(procsnz);CHKERRQ(ierr); 2911 } else { 2912 /* receive numeric values */ 2913 ierr = PetscMalloc1(nz+1,&vals);CHKERRQ(ierr); 2914 2915 /* receive message of values*/ 2916 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2917 2918 /* insert into matrix */ 2919 jj = rstart; 2920 smycols = mycols; 2921 svals = vals; 2922 for (i=0; i<m; i++) { 2923 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2924 smycols += ourlens[i]; 2925 svals += ourlens[i]; 2926 jj++; 2927 } 2928 } 2929 ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr); 2930 ierr = PetscFree(vals);CHKERRQ(ierr); 2931 ierr = PetscFree(mycols);CHKERRQ(ierr); 2932 ierr = PetscFree(rowners);CHKERRQ(ierr); 2933 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2934 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2935 PetscFunctionReturn(0); 2936 } 2937 2938 /* Not scalable because of ISAllGather() unless getting all columns. */ 2939 PetscErrorCode ISGetSeqIS_Private(Mat mat,IS iscol,IS *isseq) 2940 { 2941 PetscErrorCode ierr; 2942 IS iscol_local; 2943 PetscBool isstride; 2944 PetscMPIInt lisstride=0,gisstride; 2945 2946 PetscFunctionBegin; 2947 /* check if we are grabbing all columns*/ 2948 ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&isstride);CHKERRQ(ierr); 2949 2950 if (isstride) { 2951 PetscInt start,len,mstart,mlen; 2952 ierr = ISStrideGetInfo(iscol,&start,NULL);CHKERRQ(ierr); 2953 ierr = ISGetLocalSize(iscol,&len);CHKERRQ(ierr); 2954 ierr = MatGetOwnershipRangeColumn(mat,&mstart,&mlen);CHKERRQ(ierr); 2955 if (mstart == start && mlen-mstart == len) lisstride = 1; 2956 } 2957 2958 ierr = MPIU_Allreduce(&lisstride,&gisstride,1,MPI_INT,MPI_MIN,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2959 if (gisstride) { 2960 PetscInt N; 2961 ierr = MatGetSize(mat,NULL,&N);CHKERRQ(ierr); 2962 ierr = ISCreateStride(PetscObjectComm((PetscObject)mat),N,0,1,&iscol_local);CHKERRQ(ierr); 2963 ierr = ISSetIdentity(iscol_local);CHKERRQ(ierr); 2964 ierr = PetscInfo(mat,"Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n");CHKERRQ(ierr); 2965 } else { 2966 PetscInt cbs; 2967 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 2968 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 2969 ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr); 2970 } 2971 2972 *isseq = iscol_local; 2973 PetscFunctionReturn(0); 2974 } 2975 2976 /* 2977 Used for avoiding ISAllGather() and global size of iscol_local (see MatCreateSubMatrix_MPIAIJ_nonscalable) 2978 2979 Input Parameters: 2980 mat - matrix 2981 iscol - parallel column index set; its local indices are a subset of local columns of mat, 2982 i.e., mat->cstart <= iscol[i] < mat->cend 2983 Output Parameter: 2984 iscol_sub - sequential column index set, a subset of iscol 2985 iscmap - column map; iscmap[i] indicates global location of iscol_sub[i] in iscol 2986 */ 2987 PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat,IS isrow,IS iscol,IS *isrow_d,IS *iscol_d,IS *iscol_o,IS *isgarray) 2988 { 2989 PetscErrorCode ierr; 2990 Vec x,cmap; 2991 const PetscInt *is_idx; 2992 PetscScalar *xarray,*cmaparray; 2993 PetscInt ncols,isstart,*idx,*camp,count,m,rstart; 2994 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 2995 Mat B=a->B; 2996 Vec lvec=a->lvec,lcmap; 2997 PetscInt i,cstart,cend,Bn=B->cmap->N; 2998 MPI_Comm comm; 2999 3000 PetscFunctionBegin; 3001 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3002 PetscMPIInt rank; 3003 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3004 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 3005 3006 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3007 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3008 ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3009 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3010 3011 /* get start indices */ 3012 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3013 isstart -= ncols; 3014 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3015 3016 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3017 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3018 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3019 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3020 for (i=0; i<ncols; i++) { 3021 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3022 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3023 3024 idx[i] = is_idx[i]-cstart; 3025 } 3026 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3027 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3028 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3029 3030 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_COPY_VALUES,iscol_d);CHKERRQ(ierr); 3031 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3032 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3033 ierr = PetscFree(idx);CHKERRQ(ierr); 3034 3035 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3036 rstart = mat->rmap->rstart; 3037 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3038 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3039 for (i=0; i<m; i++) { 3040 idx[i] = is_idx[i]-rstart; 3041 } 3042 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3043 3044 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_COPY_VALUES,isrow_d);CHKERRQ(ierr); 3045 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3046 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3047 ierr = PetscFree(idx);CHKERRQ(ierr); 3048 3049 /* (2) scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3050 ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3051 3052 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3053 3054 ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3055 ierr = VecScatterBegin(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3056 3057 count = ncols + Bn; 3058 ierr = PetscMalloc2(count,&idx,count,&camp);CHKERRQ(ierr); 3059 3060 ierr = VecScatterEnd(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3061 3062 /* (3) create scalable iscol_sub (a subset of iscol) and iscmap */ 3063 /* local column indices */ 3064 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3065 for (i=0; i<ncols; i++) { 3066 idx[i] = is_idx[i]; 3067 camp[i] = i + isstart; /* global index of iscol = column index in submat */ 3068 } 3069 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3070 count = ncols; 3071 3072 /* off-process column indices */ 3073 PetscInt *idx1,*cmap1,count1=0; 3074 ierr = PetscMalloc2(Bn,&idx1,Bn,&cmap1);CHKERRQ(ierr); 3075 3076 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3077 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3078 for (i=0; i<Bn; i++) { 3079 if (PetscRealPart(xarray[i]) > -1.0) { 3080 idx1[count1] = i; /* local column index in off-diagonal part B */ 3081 cmap1[count1++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3082 3083 idx[count] = (PetscInt)PetscRealPart(xarray[i]); 3084 camp[count++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3085 } 3086 } 3087 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3088 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3089 3090 ierr = PetscSortIntWithArray(count,camp,idx);CHKERRQ(ierr); 3091 3092 ierr = ISCreateGeneral(PETSC_COMM_SELF,count1,idx1,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr); 3093 ierr = ISCreateGeneral(PETSC_COMM_SELF,count1,cmap1,PETSC_COPY_VALUES,isgarray);CHKERRQ(ierr); 3094 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3095 ierr = ISSetBlockSize(*iscol_o,i);CHKERRQ(ierr); 3096 ierr = PetscFree2(idx1,cmap1);CHKERRQ(ierr); 3097 3098 ierr = PetscFree2(idx,camp);CHKERRQ(ierr); 3099 ierr = VecDestroy(&x);CHKERRQ(ierr); 3100 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3101 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3102 PetscFunctionReturn(0); 3103 } 3104 3105 /* Both isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */ 3106 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *submat) 3107 { 3108 PetscErrorCode ierr; 3109 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3110 Mat M=NULL; 3111 MPI_Comm comm; 3112 IS iscol_d,isrow_d,iscol_o,isgarray; 3113 Mat Asub=NULL,Bsub=NULL; 3114 3115 PetscFunctionBegin; 3116 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3117 PetscMPIInt rank; 3118 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3119 3120 if (call == MAT_REUSE_MATRIX) { 3121 Mat_MPIAIJ *matsub=(Mat_MPIAIJ*)(*submat)->data; 3122 3123 ierr = PetscObjectQuery((PetscObject)*submat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3124 if (!isrow_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow_d passed in was not used before, cannot reuse"); 3125 3126 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_d",(PetscObject*)&iscol_d);CHKERRQ(ierr); 3127 if (!iscol_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_d passed in was not used before, cannot reuse"); 3128 3129 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_o",(PetscObject*)&iscol_o);CHKERRQ(ierr); 3130 if (!iscol_o) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_o passed in was not used before, cannot reuse"); 3131 3132 /* Update *submat via diagonal and off-diagonal portions of submat */ 3133 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,call,&matsub->A);CHKERRQ(ierr); 3134 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,call,&matsub->B);CHKERRQ(ierr); 3135 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3136 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3137 3138 } else { /* call == MAT_INITIAL_MATRIX) */ 3139 const PetscInt *garray1; 3140 3141 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&isrow_d,&iscol_d,&iscol_o,&isgarray);CHKERRQ(ierr); 3142 3143 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,call,&Asub);CHKERRQ(ierr); 3144 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,call,&Bsub);CHKERRQ(ierr); 3145 3146 PetscInt BsubN = Bsub->cmap->N; 3147 ierr = ISGetIndices(isgarray,&garray1);CHKERRQ(ierr); 3148 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray1,&M);CHKERRQ(ierr); 3149 ierr = ISRestoreIndices(isgarray,&garray1);CHKERRQ(ierr); 3150 3151 /* Check is Bsub == M->B? If not, compress iscol_o accordingly */ 3152 //======================== 3153 a = (Mat_MPIAIJ*)M->data; 3154 if (BsubN > a->B->cmap->N) { 3155 printf("[%d] Bsub->cmap->N %d != a->B->cmap->N %d\n",rank,BsubN,a->B->cmap->N); 3156 } else if (BsubN < a->B->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Columns of Bsub cannot be smaller than B's",BsubN,a->B->cmap->N); 3157 3158 3159 //====================== 3160 ierr = ISDestroy(&isgarray);CHKERRQ(ierr); 3161 3162 /* Save isrow_d, iscol_d and iscol_o used in processor for next request */ 3163 ierr = PetscObjectCompose((PetscObject)M,"isrow_d",(PetscObject)isrow_d);CHKERRQ(ierr); 3164 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3165 3166 ierr = PetscObjectCompose((PetscObject)M,"iscol_d",(PetscObject)iscol_d);CHKERRQ(ierr); 3167 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3168 3169 ierr = PetscObjectCompose((PetscObject)M,"iscol_o",(PetscObject)iscol_o);CHKERRQ(ierr); 3170 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3171 3172 *submat = M; 3173 } 3174 PetscFunctionReturn(0); 3175 } 3176 3177 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3178 { 3179 PetscErrorCode ierr; 3180 IS iscol_local,isrow_d; 3181 PetscInt csize; 3182 PetscInt n,i,j,start,end; 3183 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3184 MPI_Comm comm; 3185 3186 PetscFunctionBegin; 3187 /* If isrow has same processor distribution as mat, 3188 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3189 if (call == MAT_REUSE_MATRIX) { 3190 ierr = PetscObjectQuery((PetscObject)*newmat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3191 if (isrow_d) { 3192 sameRowDist = PETSC_TRUE; 3193 tsameDist[1] = PETSC_TRUE; /* sameColDist */ 3194 } else { 3195 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3196 if (iscol_local) { 3197 sameRowDist = PETSC_TRUE; 3198 tsameDist[1] = PETSC_FALSE; /* !sameColDist */ 3199 } 3200 } 3201 } else { 3202 /* Check if isrow has same processor distribution as mat */ 3203 sameDist[0] = PETSC_FALSE; 3204 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3205 if (!n) { 3206 sameDist[0] = PETSC_TRUE; 3207 } else { 3208 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3209 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3210 if (i >= start && j < end) { 3211 sameDist[0] = PETSC_TRUE; 3212 } 3213 } 3214 3215 /* Check if iscol has same processor distribution as mat */ 3216 sameDist[1] = PETSC_FALSE; 3217 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3218 if (!n) { 3219 sameDist[1] = PETSC_TRUE; 3220 } else { 3221 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3222 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3223 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3224 } 3225 3226 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3227 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3228 sameRowDist = tsameDist[0]; 3229 } 3230 3231 if (sameRowDist) { 3232 if (tsameDist[1]) { 3233 /* isrow and iscol have same processor distribution as mat */ 3234 ierr = MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3235 } else { 3236 /* isrow has same processor distribution as mat */ 3237 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3238 } 3239 PetscFunctionReturn(0); 3240 } 3241 3242 /* General case: iscol -> iscol_local which has global size of iscol */ 3243 if (call == MAT_REUSE_MATRIX) { 3244 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3245 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3246 } else { 3247 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3248 } 3249 3250 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3251 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3252 3253 if (call == MAT_INITIAL_MATRIX) { 3254 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3255 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3256 } 3257 PetscFunctionReturn(0); 3258 } 3259 3260 /*@C 3261 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3262 and "off-diagonal" part of the matrix in CSR format. 3263 3264 Collective on MPI_Comm 3265 3266 Input Parameters: 3267 + comm - MPI communicator 3268 . A - "diagonal" portion of matrix 3269 . B - "off-diagonal" portion of matrix, destroyed by this routine 3270 - garray - global index of B columns 3271 3272 Output Parameter: 3273 . mat - the matrix, with input A as its local diagonal matrix 3274 Level: advanced 3275 3276 Notes: 3277 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3278 A becomes part of output mat, B is destroyed by this routine. The user cannot use A and B anymore. 3279 3280 .seealso: MatCreateMPIAIJWithSplitArrays() 3281 @*/ 3282 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3283 { 3284 PetscErrorCode ierr; 3285 Mat_MPIAIJ *maij; 3286 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data,*bnew; 3287 PetscInt *oi=b->i,*oj=b->j,i,nz,col; 3288 PetscScalar *oa=b->a; 3289 Mat Bnew; 3290 PetscInt m,n,N; 3291 3292 PetscFunctionBegin; 3293 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3294 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3295 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %D != Bm %D",m,B->rmap->N); 3296 if (A->rmap->bs != B->rmap->bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"A row bs %D != B row bs %D",A->rmap->bs,B->rmap->bs); 3297 if (A->cmap->bs != B->cmap->bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"A column bs %D != B column bs %D",A->cmap->bs,B->cmap->bs); 3298 3299 /* Get global columns of mat */ 3300 ierr = MPIU_Allreduce(&n,&N,1,MPI_INT,MPI_SUM,comm);CHKERRQ(ierr); 3301 3302 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3303 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3304 ierr = MatSetBlockSizes(*mat,A->rmap->bs,A->cmap->bs);CHKERRQ(ierr); 3305 maij = (Mat_MPIAIJ*)(*mat)->data; 3306 3307 (*mat)->preallocated = PETSC_TRUE; 3308 3309 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3310 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3311 3312 /* Set A as diagonal portion of *mat */ 3313 maij->A = A; 3314 3315 nz = oi[m]; 3316 for (i=0; i<nz; i++) { 3317 col = oj[i]; 3318 oj[i] = garray[col]; 3319 } 3320 3321 /* Set Bnew as off-diagonal portion of *mat */ 3322 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Bnew);CHKERRQ(ierr); 3323 bnew = (Mat_SeqAIJ*)Bnew->data; 3324 bnew->maxnz = b->maxnz; /* allocated nonzeros of B */ 3325 maij->B = Bnew; 3326 3327 PetscMPIInt rank; 3328 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3329 if (rank == -1) { 3330 printf("[%d] Bnew:\n",rank); 3331 ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_SELF, PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr); 3332 ierr = MatView(Bnew,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3333 ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3334 if (!rank) printf("--------------------\n"); 3335 } 3336 3337 // Check B == Bnew??? see src/ksp/ksp/examples/tests/runex21_2,3 3338 3339 if (B->rmap->N != Bnew->rmap->N) SETERRQ2(PETSC_COMM_SELF,0,"BN %d != BnewN %d",B->rmap->N,Bnew->rmap->N); 3340 3341 b->singlemalloc = PETSC_FALSE; /* B arrays are shared by Bnew */ 3342 b->free_a = PETSC_FALSE; 3343 b->free_ij = PETSC_FALSE; 3344 ierr = MatDestroy(&B);CHKERRQ(ierr); 3345 3346 bnew->singlemalloc = PETSC_TRUE; /* arrays will be freed by MatDestroy(&Bnew) */ 3347 bnew->free_a = PETSC_TRUE; 3348 bnew->free_ij = PETSC_TRUE; 3349 3350 /* condense columns of maij->B */ 3351 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3352 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3353 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3354 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3355 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3356 PetscFunctionReturn(0); 3357 } 3358 3359 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3360 3361 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3362 { 3363 PetscErrorCode ierr; 3364 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3365 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3366 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3367 Mat M,Msub,B=a->B; 3368 MatScalar *aa; 3369 Mat_SeqAIJ *aij; 3370 PetscInt *garray = a->garray,*colsub,Ncols; 3371 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3372 IS iscol_sub,iscmap; 3373 const PetscInt *is_idx,*cmap; 3374 PetscBool allcolumns=PETSC_FALSE; 3375 IS iscol_local=NULL; 3376 MPI_Comm comm; 3377 3378 PetscFunctionBegin; 3379 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3380 PetscMPIInt rank; 3381 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3382 3383 if (call == MAT_REUSE_MATRIX) { 3384 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3385 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3386 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3387 3388 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3389 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3390 3391 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3392 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3393 3394 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3395 3396 } else { /* call == MAT_INITIAL_MATRIX) */ 3397 PetscBool flg; 3398 3399 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3400 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3401 3402 /* (1) iscol -> nonscalable iscol_local */ 3403 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3404 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3405 if (n != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != Ncols %d",n,Ncols); 3406 3407 /* Check for special case: each processor gets entire matrix columns */ 3408 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3409 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3410 if (allcolumns) { 3411 iscol_sub = iscol_local; 3412 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3413 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3414 3415 } else { 3416 /* (2) iscol_local -> iscol_sub and iscmap */ 3417 PetscInt *idx,*cmap1,k,cbs; 3418 3419 /* implementation below requires iscol_local be sorted, it can have duplicate indices */ 3420 ierr = ISSorted(iscol_local,&flg);CHKERRQ(ierr); 3421 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsorted iscol_local is not implemented yet"); 3422 3423 ierr = PetscMalloc2(Ncols,&idx,Ncols,&cmap1);CHKERRQ(ierr); 3424 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3425 count = 0; 3426 k = 0; 3427 for (i=0; i<Ncols; i++) { 3428 j = is_idx[i]; 3429 if (j >= cstart && j < cend) { 3430 /* diagonal part of mat */ 3431 idx[count] = j; 3432 cmap1[count++] = i; /* column index in submat */ 3433 } else if (Bn) { 3434 /* off-diagonal part of mat */ 3435 if (j == garray[k]) { 3436 idx[count] = j; 3437 cmap1[count++] = i; /* column index in submat */ 3438 } else if (j > garray[k]) { 3439 while (j > garray[k] && k < Bn-1) k++; 3440 if (j == garray[k]) { 3441 idx[count] = j; 3442 cmap1[count++] = i; /* column index in submat */ 3443 } 3444 } 3445 } 3446 } 3447 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3448 3449 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,&iscol_sub);CHKERRQ(ierr); 3450 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3451 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3452 3453 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_COPY_VALUES,&iscmap);CHKERRQ(ierr); 3454 ierr = PetscFree2(idx,cmap1);CHKERRQ(ierr); 3455 } 3456 3457 /* (3) Create sequential Msub */ 3458 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3459 } 3460 3461 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3462 aij = (Mat_SeqAIJ*)(Msub)->data; 3463 ii = aij->i; 3464 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3465 3466 /* 3467 m - number of local rows 3468 Ncols - number of columns (same on all processors) 3469 rstart - first row in new global matrix generated 3470 */ 3471 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3472 3473 if (call == MAT_INITIAL_MATRIX) { 3474 /* (4) Create parallel newmat */ 3475 PetscMPIInt rank,size; 3476 PetscInt csize; 3477 3478 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3479 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3480 3481 /* 3482 Determine the number of non-zeros in the diagonal and off-diagonal 3483 portions of the matrix in order to do correct preallocation 3484 */ 3485 3486 /* first get start and end of "diagonal" columns */ 3487 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3488 if (csize == PETSC_DECIDE) { 3489 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3490 if (mglobal == Ncols) { /* square matrix */ 3491 nlocal = m; 3492 } else { 3493 nlocal = Ncols/size + ((Ncols % size) > rank); 3494 } 3495 } else { 3496 nlocal = csize; 3497 } 3498 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3499 rstart = rend - nlocal; 3500 if (rank == size - 1 && rend != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local column sizes %D do not add up to total number of columns %D",rend,Ncols); 3501 3502 /* next, compute all the lengths */ 3503 jj = aij->j; 3504 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3505 olens = dlens + m; 3506 for (i=0; i<m; i++) { 3507 jend = ii[i+1] - ii[i]; 3508 olen = 0; 3509 dlen = 0; 3510 for (j=0; j<jend; j++) { 3511 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3512 else dlen++; 3513 jj++; 3514 } 3515 olens[i] = olen; 3516 dlens[i] = dlen; 3517 } 3518 ierr = MatGetBlockSizes(Msub,&bs,&cbs);CHKERRQ(ierr); 3519 3520 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3521 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr); 3522 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3523 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3524 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3525 ierr = PetscFree(dlens);CHKERRQ(ierr); 3526 3527 } else { /* call == MAT_REUSE_MATRIX */ 3528 M = *newmat; 3529 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3530 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3531 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3532 /* 3533 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3534 rather than the slower MatSetValues(). 3535 */ 3536 M->was_assembled = PETSC_TRUE; 3537 M->assembled = PETSC_FALSE; 3538 } 3539 3540 /* (5) Set values of Msub to *newmat */ 3541 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3542 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3543 3544 jj = aij->j; 3545 aa = aij->a; 3546 for (i=0; i<m; i++) { 3547 row = rstart + i; 3548 nz = ii[i+1] - ii[i]; 3549 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3550 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3551 jj += nz; aa += nz; 3552 } 3553 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3554 3555 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3556 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3557 3558 ierr = PetscFree(colsub);CHKERRQ(ierr); 3559 3560 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3561 if (call == MAT_INITIAL_MATRIX) { 3562 *newmat = M; 3563 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3564 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3565 3566 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3567 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3568 3569 ierr = PetscObjectCompose((PetscObject)(*newmat),"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3570 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3571 3572 if (iscol_local) { 3573 ierr = PetscObjectCompose((PetscObject)(*newmat),"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3574 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3575 } 3576 } 3577 PetscFunctionReturn(0); 3578 } 3579 3580 /* 3581 Not great since it makes two copies of the submatrix, first an SeqAIJ 3582 in local and then by concatenating the local matrices the end result. 3583 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3584 3585 Note: This requires a sequential iscol with all indices. 3586 */ 3587 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3588 { 3589 PetscErrorCode ierr; 3590 PetscMPIInt rank,size; 3591 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3592 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3593 Mat M,Mreuse; 3594 MatScalar *aa,*vwork; 3595 MPI_Comm comm; 3596 Mat_SeqAIJ *aij; 3597 PetscBool colflag,allcolumns=PETSC_FALSE; 3598 3599 PetscFunctionBegin; 3600 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3601 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3602 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3603 3604 /* Check for special case: each processor gets entire matrix columns */ 3605 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3606 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3607 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3608 3609 if (call == MAT_REUSE_MATRIX) { 3610 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3611 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3612 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3613 } else { 3614 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3615 } 3616 3617 /* 3618 m - number of local rows 3619 n - number of columns (same on all processors) 3620 rstart - first row in new global matrix generated 3621 */ 3622 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3623 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3624 if (call == MAT_INITIAL_MATRIX) { 3625 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3626 ii = aij->i; 3627 jj = aij->j; 3628 3629 /* 3630 Determine the number of non-zeros in the diagonal and off-diagonal 3631 portions of the matrix in order to do correct preallocation 3632 */ 3633 3634 /* first get start and end of "diagonal" columns */ 3635 if (csize == PETSC_DECIDE) { 3636 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3637 if (mglobal == n) { /* square matrix */ 3638 nlocal = m; 3639 } else { 3640 nlocal = n/size + ((n % size) > rank); 3641 } 3642 } else { 3643 nlocal = csize; 3644 } 3645 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3646 rstart = rend - nlocal; 3647 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); 3648 3649 /* next, compute all the lengths */ 3650 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3651 olens = dlens + m; 3652 for (i=0; i<m; i++) { 3653 jend = ii[i+1] - ii[i]; 3654 olen = 0; 3655 dlen = 0; 3656 for (j=0; j<jend; j++) { 3657 if (*jj < rstart || *jj >= rend) olen++; 3658 else dlen++; 3659 jj++; 3660 } 3661 olens[i] = olen; 3662 dlens[i] = dlen; 3663 } 3664 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3665 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3666 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3667 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3668 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3669 ierr = PetscFree(dlens);CHKERRQ(ierr); 3670 } else { 3671 PetscInt ml,nl; 3672 3673 M = *newmat; 3674 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3675 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3676 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3677 /* 3678 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3679 rather than the slower MatSetValues(). 3680 */ 3681 M->was_assembled = PETSC_TRUE; 3682 M->assembled = PETSC_FALSE; 3683 } 3684 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3685 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3686 ii = aij->i; 3687 jj = aij->j; 3688 aa = aij->a; 3689 for (i=0; i<m; i++) { 3690 row = rstart + i; 3691 nz = ii[i+1] - ii[i]; 3692 cwork = jj; jj += nz; 3693 vwork = aa; aa += nz; 3694 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3695 } 3696 3697 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3698 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3699 *newmat = M; 3700 3701 /* save submatrix used in processor for next request */ 3702 if (call == MAT_INITIAL_MATRIX) { 3703 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3704 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3705 } 3706 PetscFunctionReturn(0); 3707 } 3708 3709 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3710 { 3711 PetscInt m,cstart, cend,j,nnz,i,d; 3712 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3713 const PetscInt *JJ; 3714 PetscScalar *values; 3715 PetscErrorCode ierr; 3716 PetscBool nooffprocentries; 3717 3718 PetscFunctionBegin; 3719 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3720 3721 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3722 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3723 m = B->rmap->n; 3724 cstart = B->cmap->rstart; 3725 cend = B->cmap->rend; 3726 rstart = B->rmap->rstart; 3727 3728 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3729 3730 #if defined(PETSC_USE_DEBUGGING) 3731 for (i=0; i<m; i++) { 3732 nnz = Ii[i+1]- Ii[i]; 3733 JJ = J + Ii[i]; 3734 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3735 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3736 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); 3737 } 3738 #endif 3739 3740 for (i=0; i<m; i++) { 3741 nnz = Ii[i+1]- Ii[i]; 3742 JJ = J + Ii[i]; 3743 nnz_max = PetscMax(nnz_max,nnz); 3744 d = 0; 3745 for (j=0; j<nnz; j++) { 3746 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3747 } 3748 d_nnz[i] = d; 3749 o_nnz[i] = nnz - d; 3750 } 3751 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3752 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3753 3754 if (v) values = (PetscScalar*)v; 3755 else { 3756 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3757 } 3758 3759 for (i=0; i<m; i++) { 3760 ii = i + rstart; 3761 nnz = Ii[i+1]- Ii[i]; 3762 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3763 } 3764 nooffprocentries = B->nooffprocentries; 3765 B->nooffprocentries = PETSC_TRUE; 3766 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3767 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3768 B->nooffprocentries = nooffprocentries; 3769 3770 if (!v) { 3771 ierr = PetscFree(values);CHKERRQ(ierr); 3772 } 3773 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3774 PetscFunctionReturn(0); 3775 } 3776 3777 /*@ 3778 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3779 (the default parallel PETSc format). 3780 3781 Collective on MPI_Comm 3782 3783 Input Parameters: 3784 + B - the matrix 3785 . i - the indices into j for the start of each local row (starts with zero) 3786 . j - the column indices for each local row (starts with zero) 3787 - v - optional values in the matrix 3788 3789 Level: developer 3790 3791 Notes: 3792 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3793 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3794 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3795 3796 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3797 3798 The format which is used for the sparse matrix input, is equivalent to a 3799 row-major ordering.. i.e for the following matrix, the input data expected is 3800 as shown 3801 3802 $ 1 0 0 3803 $ 2 0 3 P0 3804 $ ------- 3805 $ 4 5 6 P1 3806 $ 3807 $ Process0 [P0]: rows_owned=[0,1] 3808 $ i = {0,1,3} [size = nrow+1 = 2+1] 3809 $ j = {0,0,2} [size = 3] 3810 $ v = {1,2,3} [size = 3] 3811 $ 3812 $ Process1 [P1]: rows_owned=[2] 3813 $ i = {0,3} [size = nrow+1 = 1+1] 3814 $ j = {0,1,2} [size = 3] 3815 $ v = {4,5,6} [size = 3] 3816 3817 .keywords: matrix, aij, compressed row, sparse, parallel 3818 3819 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3820 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3821 @*/ 3822 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3823 { 3824 PetscErrorCode ierr; 3825 3826 PetscFunctionBegin; 3827 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3828 PetscFunctionReturn(0); 3829 } 3830 3831 /*@C 3832 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3833 (the default parallel PETSc format). For good matrix assembly performance 3834 the user should preallocate the matrix storage by setting the parameters 3835 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3836 performance can be increased by more than a factor of 50. 3837 3838 Collective on MPI_Comm 3839 3840 Input Parameters: 3841 + B - the matrix 3842 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3843 (same value is used for all local rows) 3844 . d_nnz - array containing the number of nonzeros in the various rows of the 3845 DIAGONAL portion of the local submatrix (possibly different for each row) 3846 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3847 The size of this array is equal to the number of local rows, i.e 'm'. 3848 For matrices that will be factored, you must leave room for (and set) 3849 the diagonal entry even if it is zero. 3850 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3851 submatrix (same value is used for all local rows). 3852 - o_nnz - array containing the number of nonzeros in the various rows of the 3853 OFF-DIAGONAL portion of the local submatrix (possibly different for 3854 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3855 structure. The size of this array is equal to the number 3856 of local rows, i.e 'm'. 3857 3858 If the *_nnz parameter is given then the *_nz parameter is ignored 3859 3860 The AIJ format (also called the Yale sparse matrix format or 3861 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3862 storage. The stored row and column indices begin with zero. 3863 See Users-Manual: ch_mat for details. 3864 3865 The parallel matrix is partitioned such that the first m0 rows belong to 3866 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3867 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3868 3869 The DIAGONAL portion of the local submatrix of a processor can be defined 3870 as the submatrix which is obtained by extraction the part corresponding to 3871 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3872 first row that belongs to the processor, r2 is the last row belonging to 3873 the this processor, and c1-c2 is range of indices of the local part of a 3874 vector suitable for applying the matrix to. This is an mxn matrix. In the 3875 common case of a square matrix, the row and column ranges are the same and 3876 the DIAGONAL part is also square. The remaining portion of the local 3877 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3878 3879 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3880 3881 You can call MatGetInfo() to get information on how effective the preallocation was; 3882 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3883 You can also run with the option -info and look for messages with the string 3884 malloc in them to see if additional memory allocation was needed. 3885 3886 Example usage: 3887 3888 Consider the following 8x8 matrix with 34 non-zero values, that is 3889 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3890 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3891 as follows: 3892 3893 .vb 3894 1 2 0 | 0 3 0 | 0 4 3895 Proc0 0 5 6 | 7 0 0 | 8 0 3896 9 0 10 | 11 0 0 | 12 0 3897 ------------------------------------- 3898 13 0 14 | 15 16 17 | 0 0 3899 Proc1 0 18 0 | 19 20 21 | 0 0 3900 0 0 0 | 22 23 0 | 24 0 3901 ------------------------------------- 3902 Proc2 25 26 27 | 0 0 28 | 29 0 3903 30 0 0 | 31 32 33 | 0 34 3904 .ve 3905 3906 This can be represented as a collection of submatrices as: 3907 3908 .vb 3909 A B C 3910 D E F 3911 G H I 3912 .ve 3913 3914 Where the submatrices A,B,C are owned by proc0, D,E,F are 3915 owned by proc1, G,H,I are owned by proc2. 3916 3917 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3918 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3919 The 'M','N' parameters are 8,8, and have the same values on all procs. 3920 3921 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3922 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3923 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3924 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3925 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3926 matrix, ans [DF] as another SeqAIJ matrix. 3927 3928 When d_nz, o_nz parameters are specified, d_nz storage elements are 3929 allocated for every row of the local diagonal submatrix, and o_nz 3930 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3931 One way to choose d_nz and o_nz is to use the max nonzerors per local 3932 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3933 In this case, the values of d_nz,o_nz are: 3934 .vb 3935 proc0 : dnz = 2, o_nz = 2 3936 proc1 : dnz = 3, o_nz = 2 3937 proc2 : dnz = 1, o_nz = 4 3938 .ve 3939 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3940 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3941 for proc3. i.e we are using 12+15+10=37 storage locations to store 3942 34 values. 3943 3944 When d_nnz, o_nnz parameters are specified, the storage is specified 3945 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3946 In the above case the values for d_nnz,o_nnz are: 3947 .vb 3948 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3949 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3950 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3951 .ve 3952 Here the space allocated is sum of all the above values i.e 34, and 3953 hence pre-allocation is perfect. 3954 3955 Level: intermediate 3956 3957 .keywords: matrix, aij, compressed row, sparse, parallel 3958 3959 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 3960 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 3961 @*/ 3962 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3963 { 3964 PetscErrorCode ierr; 3965 3966 PetscFunctionBegin; 3967 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 3968 PetscValidType(B,1); 3969 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 3970 PetscFunctionReturn(0); 3971 } 3972 3973 /*@ 3974 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 3975 CSR format the local rows. 3976 3977 Collective on MPI_Comm 3978 3979 Input Parameters: 3980 + comm - MPI communicator 3981 . m - number of local rows (Cannot be PETSC_DECIDE) 3982 . n - This value should be the same as the local size used in creating the 3983 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 3984 calculated if N is given) For square matrices n is almost always m. 3985 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 3986 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 3987 . i - row indices 3988 . j - column indices 3989 - a - matrix values 3990 3991 Output Parameter: 3992 . mat - the matrix 3993 3994 Level: intermediate 3995 3996 Notes: 3997 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3998 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3999 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 4000 4001 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4002 4003 The format which is used for the sparse matrix input, is equivalent to a 4004 row-major ordering.. i.e for the following matrix, the input data expected is 4005 as shown 4006 4007 $ 1 0 0 4008 $ 2 0 3 P0 4009 $ ------- 4010 $ 4 5 6 P1 4011 $ 4012 $ Process0 [P0]: rows_owned=[0,1] 4013 $ i = {0,1,3} [size = nrow+1 = 2+1] 4014 $ j = {0,0,2} [size = 3] 4015 $ v = {1,2,3} [size = 3] 4016 $ 4017 $ Process1 [P1]: rows_owned=[2] 4018 $ i = {0,3} [size = nrow+1 = 1+1] 4019 $ j = {0,1,2} [size = 3] 4020 $ v = {4,5,6} [size = 3] 4021 4022 .keywords: matrix, aij, compressed row, sparse, parallel 4023 4024 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4025 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4026 @*/ 4027 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 4028 { 4029 PetscErrorCode ierr; 4030 4031 PetscFunctionBegin; 4032 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4033 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4034 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4035 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4036 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 4037 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 4038 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 4039 PetscFunctionReturn(0); 4040 } 4041 4042 /*@C 4043 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 4044 (the default parallel PETSc format). For good matrix assembly performance 4045 the user should preallocate the matrix storage by setting the parameters 4046 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4047 performance can be increased by more than a factor of 50. 4048 4049 Collective on MPI_Comm 4050 4051 Input Parameters: 4052 + comm - MPI communicator 4053 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 4054 This value should be the same as the local size used in creating the 4055 y vector for the matrix-vector product y = Ax. 4056 . n - This value should be the same as the local size used in creating the 4057 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4058 calculated if N is given) For square matrices n is almost always m. 4059 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4060 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4061 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4062 (same value is used for all local rows) 4063 . d_nnz - array containing the number of nonzeros in the various rows of the 4064 DIAGONAL portion of the local submatrix (possibly different for each row) 4065 or NULL, if d_nz is used to specify the nonzero structure. 4066 The size of this array is equal to the number of local rows, i.e 'm'. 4067 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4068 submatrix (same value is used for all local rows). 4069 - o_nnz - array containing the number of nonzeros in the various rows of the 4070 OFF-DIAGONAL portion of the local submatrix (possibly different for 4071 each row) or NULL, if o_nz is used to specify the nonzero 4072 structure. The size of this array is equal to the number 4073 of local rows, i.e 'm'. 4074 4075 Output Parameter: 4076 . A - the matrix 4077 4078 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4079 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4080 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4081 4082 Notes: 4083 If the *_nnz parameter is given then the *_nz parameter is ignored 4084 4085 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4086 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4087 storage requirements for this matrix. 4088 4089 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4090 processor than it must be used on all processors that share the object for 4091 that argument. 4092 4093 The user MUST specify either the local or global matrix dimensions 4094 (possibly both). 4095 4096 The parallel matrix is partitioned across processors such that the 4097 first m0 rows belong to process 0, the next m1 rows belong to 4098 process 1, the next m2 rows belong to process 2 etc.. where 4099 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4100 values corresponding to [m x N] submatrix. 4101 4102 The columns are logically partitioned with the n0 columns belonging 4103 to 0th partition, the next n1 columns belonging to the next 4104 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4105 4106 The DIAGONAL portion of the local submatrix on any given processor 4107 is the submatrix corresponding to the rows and columns m,n 4108 corresponding to the given processor. i.e diagonal matrix on 4109 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4110 etc. The remaining portion of the local submatrix [m x (N-n)] 4111 constitute the OFF-DIAGONAL portion. The example below better 4112 illustrates this concept. 4113 4114 For a square global matrix we define each processor's diagonal portion 4115 to be its local rows and the corresponding columns (a square submatrix); 4116 each processor's off-diagonal portion encompasses the remainder of the 4117 local matrix (a rectangular submatrix). 4118 4119 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4120 4121 When calling this routine with a single process communicator, a matrix of 4122 type SEQAIJ is returned. If a matrix of type MATMPIAIJ is desired for this 4123 type of communicator, use the construction mechanism: 4124 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4125 4126 By default, this format uses inodes (identical nodes) when possible. 4127 We search for consecutive rows with the same nonzero structure, thereby 4128 reusing matrix information to achieve increased efficiency. 4129 4130 Options Database Keys: 4131 + -mat_no_inode - Do not use inodes 4132 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4133 - -mat_aij_oneindex - Internally use indexing starting at 1 4134 rather than 0. Note that when calling MatSetValues(), 4135 the user still MUST index entries starting at 0! 4136 4137 4138 Example usage: 4139 4140 Consider the following 8x8 matrix with 34 non-zero values, that is 4141 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4142 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4143 as follows: 4144 4145 .vb 4146 1 2 0 | 0 3 0 | 0 4 4147 Proc0 0 5 6 | 7 0 0 | 8 0 4148 9 0 10 | 11 0 0 | 12 0 4149 ------------------------------------- 4150 13 0 14 | 15 16 17 | 0 0 4151 Proc1 0 18 0 | 19 20 21 | 0 0 4152 0 0 0 | 22 23 0 | 24 0 4153 ------------------------------------- 4154 Proc2 25 26 27 | 0 0 28 | 29 0 4155 30 0 0 | 31 32 33 | 0 34 4156 .ve 4157 4158 This can be represented as a collection of submatrices as: 4159 4160 .vb 4161 A B C 4162 D E F 4163 G H I 4164 .ve 4165 4166 Where the submatrices A,B,C are owned by proc0, D,E,F are 4167 owned by proc1, G,H,I are owned by proc2. 4168 4169 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4170 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4171 The 'M','N' parameters are 8,8, and have the same values on all procs. 4172 4173 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4174 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4175 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4176 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4177 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4178 matrix, ans [DF] as another SeqAIJ matrix. 4179 4180 When d_nz, o_nz parameters are specified, d_nz storage elements are 4181 allocated for every row of the local diagonal submatrix, and o_nz 4182 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4183 One way to choose d_nz and o_nz is to use the max nonzerors per local 4184 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4185 In this case, the values of d_nz,o_nz are: 4186 .vb 4187 proc0 : dnz = 2, o_nz = 2 4188 proc1 : dnz = 3, o_nz = 2 4189 proc2 : dnz = 1, o_nz = 4 4190 .ve 4191 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4192 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4193 for proc3. i.e we are using 12+15+10=37 storage locations to store 4194 34 values. 4195 4196 When d_nnz, o_nnz parameters are specified, the storage is specified 4197 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4198 In the above case the values for d_nnz,o_nnz are: 4199 .vb 4200 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4201 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4202 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4203 .ve 4204 Here the space allocated is sum of all the above values i.e 34, and 4205 hence pre-allocation is perfect. 4206 4207 Level: intermediate 4208 4209 .keywords: matrix, aij, compressed row, sparse, parallel 4210 4211 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4212 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4213 @*/ 4214 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) 4215 { 4216 PetscErrorCode ierr; 4217 PetscMPIInt size; 4218 4219 PetscFunctionBegin; 4220 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4221 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4222 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4223 if (size > 1) { 4224 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4225 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4226 } else { 4227 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4228 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4229 } 4230 PetscFunctionReturn(0); 4231 } 4232 4233 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4234 { 4235 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4236 PetscBool flg; 4237 PetscErrorCode ierr; 4238 4239 PetscFunctionBegin; 4240 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4241 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4242 if (Ad) *Ad = a->A; 4243 if (Ao) *Ao = a->B; 4244 if (colmap) *colmap = a->garray; 4245 PetscFunctionReturn(0); 4246 } 4247 4248 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4249 { 4250 PetscErrorCode ierr; 4251 PetscInt m,N,i,rstart,nnz,Ii; 4252 PetscInt *indx; 4253 PetscScalar *values; 4254 4255 PetscFunctionBegin; 4256 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4257 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4258 PetscInt *dnz,*onz,sum,bs,cbs; 4259 4260 if (n == PETSC_DECIDE) { 4261 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4262 } 4263 /* Check sum(n) = N */ 4264 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4265 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 4266 4267 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4268 rstart -= m; 4269 4270 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4271 for (i=0; i<m; i++) { 4272 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4273 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4274 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4275 } 4276 4277 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4278 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4279 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4280 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4281 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4282 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4283 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4284 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4285 } 4286 4287 /* numeric phase */ 4288 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4289 for (i=0; i<m; i++) { 4290 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4291 Ii = i + rstart; 4292 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4293 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4294 } 4295 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4296 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4297 PetscFunctionReturn(0); 4298 } 4299 4300 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4301 { 4302 PetscErrorCode ierr; 4303 PetscMPIInt rank; 4304 PetscInt m,N,i,rstart,nnz; 4305 size_t len; 4306 const PetscInt *indx; 4307 PetscViewer out; 4308 char *name; 4309 Mat B; 4310 const PetscScalar *values; 4311 4312 PetscFunctionBegin; 4313 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4314 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4315 /* Should this be the type of the diagonal block of A? */ 4316 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4317 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4318 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4319 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4320 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4321 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4322 for (i=0; i<m; i++) { 4323 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4324 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4325 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4326 } 4327 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4328 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4329 4330 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4331 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4332 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4333 sprintf(name,"%s.%d",outfile,rank); 4334 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4335 ierr = PetscFree(name);CHKERRQ(ierr); 4336 ierr = MatView(B,out);CHKERRQ(ierr); 4337 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4338 ierr = MatDestroy(&B);CHKERRQ(ierr); 4339 PetscFunctionReturn(0); 4340 } 4341 4342 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4343 { 4344 PetscErrorCode ierr; 4345 Mat_Merge_SeqsToMPI *merge; 4346 PetscContainer container; 4347 4348 PetscFunctionBegin; 4349 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4350 if (container) { 4351 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4352 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4353 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4354 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4355 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4356 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4357 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4358 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4359 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4360 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4361 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4362 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4363 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4364 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4365 ierr = PetscFree(merge);CHKERRQ(ierr); 4366 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4367 } 4368 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4369 PetscFunctionReturn(0); 4370 } 4371 4372 #include <../src/mat/utils/freespace.h> 4373 #include <petscbt.h> 4374 4375 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4376 { 4377 PetscErrorCode ierr; 4378 MPI_Comm comm; 4379 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4380 PetscMPIInt size,rank,taga,*len_s; 4381 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4382 PetscInt proc,m; 4383 PetscInt **buf_ri,**buf_rj; 4384 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4385 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4386 MPI_Request *s_waits,*r_waits; 4387 MPI_Status *status; 4388 MatScalar *aa=a->a; 4389 MatScalar **abuf_r,*ba_i; 4390 Mat_Merge_SeqsToMPI *merge; 4391 PetscContainer container; 4392 4393 PetscFunctionBegin; 4394 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4395 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4396 4397 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4398 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4399 4400 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4401 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4402 4403 bi = merge->bi; 4404 bj = merge->bj; 4405 buf_ri = merge->buf_ri; 4406 buf_rj = merge->buf_rj; 4407 4408 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4409 owners = merge->rowmap->range; 4410 len_s = merge->len_s; 4411 4412 /* send and recv matrix values */ 4413 /*-----------------------------*/ 4414 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4415 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4416 4417 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4418 for (proc=0,k=0; proc<size; proc++) { 4419 if (!len_s[proc]) continue; 4420 i = owners[proc]; 4421 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4422 k++; 4423 } 4424 4425 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4426 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4427 ierr = PetscFree(status);CHKERRQ(ierr); 4428 4429 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4430 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4431 4432 /* insert mat values of mpimat */ 4433 /*----------------------------*/ 4434 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4435 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4436 4437 for (k=0; k<merge->nrecv; k++) { 4438 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4439 nrows = *(buf_ri_k[k]); 4440 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4441 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4442 } 4443 4444 /* set values of ba */ 4445 m = merge->rowmap->n; 4446 for (i=0; i<m; i++) { 4447 arow = owners[rank] + i; 4448 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4449 bnzi = bi[i+1] - bi[i]; 4450 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4451 4452 /* add local non-zero vals of this proc's seqmat into ba */ 4453 anzi = ai[arow+1] - ai[arow]; 4454 aj = a->j + ai[arow]; 4455 aa = a->a + ai[arow]; 4456 nextaj = 0; 4457 for (j=0; nextaj<anzi; j++) { 4458 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4459 ba_i[j] += aa[nextaj++]; 4460 } 4461 } 4462 4463 /* add received vals into ba */ 4464 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4465 /* i-th row */ 4466 if (i == *nextrow[k]) { 4467 anzi = *(nextai[k]+1) - *nextai[k]; 4468 aj = buf_rj[k] + *(nextai[k]); 4469 aa = abuf_r[k] + *(nextai[k]); 4470 nextaj = 0; 4471 for (j=0; nextaj<anzi; j++) { 4472 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4473 ba_i[j] += aa[nextaj++]; 4474 } 4475 } 4476 nextrow[k]++; nextai[k]++; 4477 } 4478 } 4479 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4480 } 4481 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4482 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4483 4484 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4485 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4486 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4487 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4488 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4489 PetscFunctionReturn(0); 4490 } 4491 4492 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4493 { 4494 PetscErrorCode ierr; 4495 Mat B_mpi; 4496 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4497 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4498 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4499 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4500 PetscInt len,proc,*dnz,*onz,bs,cbs; 4501 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4502 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4503 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4504 MPI_Status *status; 4505 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4506 PetscBT lnkbt; 4507 Mat_Merge_SeqsToMPI *merge; 4508 PetscContainer container; 4509 4510 PetscFunctionBegin; 4511 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4512 4513 /* make sure it is a PETSc comm */ 4514 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4515 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4516 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4517 4518 ierr = PetscNew(&merge);CHKERRQ(ierr); 4519 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4520 4521 /* determine row ownership */ 4522 /*---------------------------------------------------------*/ 4523 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4524 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4525 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4526 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4527 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4528 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4529 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4530 4531 m = merge->rowmap->n; 4532 owners = merge->rowmap->range; 4533 4534 /* determine the number of messages to send, their lengths */ 4535 /*---------------------------------------------------------*/ 4536 len_s = merge->len_s; 4537 4538 len = 0; /* length of buf_si[] */ 4539 merge->nsend = 0; 4540 for (proc=0; proc<size; proc++) { 4541 len_si[proc] = 0; 4542 if (proc == rank) { 4543 len_s[proc] = 0; 4544 } else { 4545 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4546 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4547 } 4548 if (len_s[proc]) { 4549 merge->nsend++; 4550 nrows = 0; 4551 for (i=owners[proc]; i<owners[proc+1]; i++) { 4552 if (ai[i+1] > ai[i]) nrows++; 4553 } 4554 len_si[proc] = 2*(nrows+1); 4555 len += len_si[proc]; 4556 } 4557 } 4558 4559 /* determine the number and length of messages to receive for ij-structure */ 4560 /*-------------------------------------------------------------------------*/ 4561 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4562 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4563 4564 /* post the Irecv of j-structure */ 4565 /*-------------------------------*/ 4566 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4567 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4568 4569 /* post the Isend of j-structure */ 4570 /*--------------------------------*/ 4571 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4572 4573 for (proc=0, k=0; proc<size; proc++) { 4574 if (!len_s[proc]) continue; 4575 i = owners[proc]; 4576 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4577 k++; 4578 } 4579 4580 /* receives and sends of j-structure are complete */ 4581 /*------------------------------------------------*/ 4582 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4583 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4584 4585 /* send and recv i-structure */ 4586 /*---------------------------*/ 4587 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4588 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4589 4590 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4591 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4592 for (proc=0,k=0; proc<size; proc++) { 4593 if (!len_s[proc]) continue; 4594 /* form outgoing message for i-structure: 4595 buf_si[0]: nrows to be sent 4596 [1:nrows]: row index (global) 4597 [nrows+1:2*nrows+1]: i-structure index 4598 */ 4599 /*-------------------------------------------*/ 4600 nrows = len_si[proc]/2 - 1; 4601 buf_si_i = buf_si + nrows+1; 4602 buf_si[0] = nrows; 4603 buf_si_i[0] = 0; 4604 nrows = 0; 4605 for (i=owners[proc]; i<owners[proc+1]; i++) { 4606 anzi = ai[i+1] - ai[i]; 4607 if (anzi) { 4608 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4609 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4610 nrows++; 4611 } 4612 } 4613 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4614 k++; 4615 buf_si += len_si[proc]; 4616 } 4617 4618 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4619 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4620 4621 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4622 for (i=0; i<merge->nrecv; i++) { 4623 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); 4624 } 4625 4626 ierr = PetscFree(len_si);CHKERRQ(ierr); 4627 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4628 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4629 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4630 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4631 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4632 ierr = PetscFree(status);CHKERRQ(ierr); 4633 4634 /* compute a local seq matrix in each processor */ 4635 /*----------------------------------------------*/ 4636 /* allocate bi array and free space for accumulating nonzero column info */ 4637 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4638 bi[0] = 0; 4639 4640 /* create and initialize a linked list */ 4641 nlnk = N+1; 4642 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4643 4644 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4645 len = ai[owners[rank+1]] - ai[owners[rank]]; 4646 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4647 4648 current_space = free_space; 4649 4650 /* determine symbolic info for each local row */ 4651 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4652 4653 for (k=0; k<merge->nrecv; k++) { 4654 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4655 nrows = *buf_ri_k[k]; 4656 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4657 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4658 } 4659 4660 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4661 len = 0; 4662 for (i=0; i<m; i++) { 4663 bnzi = 0; 4664 /* add local non-zero cols of this proc's seqmat into lnk */ 4665 arow = owners[rank] + i; 4666 anzi = ai[arow+1] - ai[arow]; 4667 aj = a->j + ai[arow]; 4668 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4669 bnzi += nlnk; 4670 /* add received col data into lnk */ 4671 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4672 if (i == *nextrow[k]) { /* i-th row */ 4673 anzi = *(nextai[k]+1) - *nextai[k]; 4674 aj = buf_rj[k] + *nextai[k]; 4675 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4676 bnzi += nlnk; 4677 nextrow[k]++; nextai[k]++; 4678 } 4679 } 4680 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4681 4682 /* if free space is not available, make more free space */ 4683 if (current_space->local_remaining<bnzi) { 4684 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4685 nspacedouble++; 4686 } 4687 /* copy data into free space, then initialize lnk */ 4688 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4689 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4690 4691 current_space->array += bnzi; 4692 current_space->local_used += bnzi; 4693 current_space->local_remaining -= bnzi; 4694 4695 bi[i+1] = bi[i] + bnzi; 4696 } 4697 4698 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4699 4700 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4701 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4702 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4703 4704 /* create symbolic parallel matrix B_mpi */ 4705 /*---------------------------------------*/ 4706 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4707 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4708 if (n==PETSC_DECIDE) { 4709 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4710 } else { 4711 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4712 } 4713 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4714 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4715 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4716 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4717 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4718 4719 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4720 B_mpi->assembled = PETSC_FALSE; 4721 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4722 merge->bi = bi; 4723 merge->bj = bj; 4724 merge->buf_ri = buf_ri; 4725 merge->buf_rj = buf_rj; 4726 merge->coi = NULL; 4727 merge->coj = NULL; 4728 merge->owners_co = NULL; 4729 4730 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4731 4732 /* attach the supporting struct to B_mpi for reuse */ 4733 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4734 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4735 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4736 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4737 *mpimat = B_mpi; 4738 4739 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4740 PetscFunctionReturn(0); 4741 } 4742 4743 /*@C 4744 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4745 matrices from each processor 4746 4747 Collective on MPI_Comm 4748 4749 Input Parameters: 4750 + comm - the communicators the parallel matrix will live on 4751 . seqmat - the input sequential matrices 4752 . m - number of local rows (or PETSC_DECIDE) 4753 . n - number of local columns (or PETSC_DECIDE) 4754 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4755 4756 Output Parameter: 4757 . mpimat - the parallel matrix generated 4758 4759 Level: advanced 4760 4761 Notes: 4762 The dimensions of the sequential matrix in each processor MUST be the same. 4763 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4764 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4765 @*/ 4766 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4767 { 4768 PetscErrorCode ierr; 4769 PetscMPIInt size; 4770 4771 PetscFunctionBegin; 4772 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4773 if (size == 1) { 4774 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4775 if (scall == MAT_INITIAL_MATRIX) { 4776 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4777 } else { 4778 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4779 } 4780 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4781 PetscFunctionReturn(0); 4782 } 4783 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4784 if (scall == MAT_INITIAL_MATRIX) { 4785 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4786 } 4787 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4788 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4789 PetscFunctionReturn(0); 4790 } 4791 4792 /*@ 4793 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 4794 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4795 with MatGetSize() 4796 4797 Not Collective 4798 4799 Input Parameters: 4800 + A - the matrix 4801 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4802 4803 Output Parameter: 4804 . A_loc - the local sequential matrix generated 4805 4806 Level: developer 4807 4808 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4809 4810 @*/ 4811 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4812 { 4813 PetscErrorCode ierr; 4814 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4815 Mat_SeqAIJ *mat,*a,*b; 4816 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4817 MatScalar *aa,*ba,*cam; 4818 PetscScalar *ca; 4819 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4820 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4821 PetscBool match; 4822 MPI_Comm comm; 4823 PetscMPIInt size; 4824 4825 PetscFunctionBegin; 4826 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4827 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4828 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4829 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4830 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4831 4832 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4833 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4834 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4835 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4836 aa = a->a; ba = b->a; 4837 if (scall == MAT_INITIAL_MATRIX) { 4838 if (size == 1) { 4839 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4840 PetscFunctionReturn(0); 4841 } 4842 4843 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4844 ci[0] = 0; 4845 for (i=0; i<am; i++) { 4846 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4847 } 4848 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4849 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4850 k = 0; 4851 for (i=0; i<am; i++) { 4852 ncols_o = bi[i+1] - bi[i]; 4853 ncols_d = ai[i+1] - ai[i]; 4854 /* off-diagonal portion of A */ 4855 for (jo=0; jo<ncols_o; jo++) { 4856 col = cmap[*bj]; 4857 if (col >= cstart) break; 4858 cj[k] = col; bj++; 4859 ca[k++] = *ba++; 4860 } 4861 /* diagonal portion of A */ 4862 for (j=0; j<ncols_d; j++) { 4863 cj[k] = cstart + *aj++; 4864 ca[k++] = *aa++; 4865 } 4866 /* off-diagonal portion of A */ 4867 for (j=jo; j<ncols_o; j++) { 4868 cj[k] = cmap[*bj++]; 4869 ca[k++] = *ba++; 4870 } 4871 } 4872 /* put together the new matrix */ 4873 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4874 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4875 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4876 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4877 mat->free_a = PETSC_TRUE; 4878 mat->free_ij = PETSC_TRUE; 4879 mat->nonew = 0; 4880 } else if (scall == MAT_REUSE_MATRIX) { 4881 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4882 ci = mat->i; cj = mat->j; cam = mat->a; 4883 for (i=0; i<am; i++) { 4884 /* off-diagonal portion of A */ 4885 ncols_o = bi[i+1] - bi[i]; 4886 for (jo=0; jo<ncols_o; jo++) { 4887 col = cmap[*bj]; 4888 if (col >= cstart) break; 4889 *cam++ = *ba++; bj++; 4890 } 4891 /* diagonal portion of A */ 4892 ncols_d = ai[i+1] - ai[i]; 4893 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4894 /* off-diagonal portion of A */ 4895 for (j=jo; j<ncols_o; j++) { 4896 *cam++ = *ba++; bj++; 4897 } 4898 } 4899 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4900 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4901 PetscFunctionReturn(0); 4902 } 4903 4904 /*@C 4905 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4906 4907 Not Collective 4908 4909 Input Parameters: 4910 + A - the matrix 4911 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4912 - row, col - index sets of rows and columns to extract (or NULL) 4913 4914 Output Parameter: 4915 . A_loc - the local sequential matrix generated 4916 4917 Level: developer 4918 4919 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4920 4921 @*/ 4922 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4923 { 4924 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4925 PetscErrorCode ierr; 4926 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4927 IS isrowa,iscola; 4928 Mat *aloc; 4929 PetscBool match; 4930 4931 PetscFunctionBegin; 4932 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4933 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4934 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4935 if (!row) { 4936 start = A->rmap->rstart; end = A->rmap->rend; 4937 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 4938 } else { 4939 isrowa = *row; 4940 } 4941 if (!col) { 4942 start = A->cmap->rstart; 4943 cmap = a->garray; 4944 nzA = a->A->cmap->n; 4945 nzB = a->B->cmap->n; 4946 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4947 ncols = 0; 4948 for (i=0; i<nzB; i++) { 4949 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4950 else break; 4951 } 4952 imark = i; 4953 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 4954 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 4955 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 4956 } else { 4957 iscola = *col; 4958 } 4959 if (scall != MAT_INITIAL_MATRIX) { 4960 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 4961 aloc[0] = *A_loc; 4962 } 4963 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 4964 *A_loc = aloc[0]; 4965 ierr = PetscFree(aloc);CHKERRQ(ierr); 4966 if (!row) { 4967 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 4968 } 4969 if (!col) { 4970 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 4971 } 4972 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4973 PetscFunctionReturn(0); 4974 } 4975 4976 /*@C 4977 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 4978 4979 Collective on Mat 4980 4981 Input Parameters: 4982 + A,B - the matrices in mpiaij format 4983 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4984 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 4985 4986 Output Parameter: 4987 + rowb, colb - index sets of rows and columns of B to extract 4988 - B_seq - the sequential matrix generated 4989 4990 Level: developer 4991 4992 @*/ 4993 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 4994 { 4995 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4996 PetscErrorCode ierr; 4997 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 4998 IS isrowb,iscolb; 4999 Mat *bseq=NULL; 5000 5001 PetscFunctionBegin; 5002 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5003 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); 5004 } 5005 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5006 5007 if (scall == MAT_INITIAL_MATRIX) { 5008 start = A->cmap->rstart; 5009 cmap = a->garray; 5010 nzA = a->A->cmap->n; 5011 nzB = a->B->cmap->n; 5012 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5013 ncols = 0; 5014 for (i=0; i<nzB; i++) { /* row < local row index */ 5015 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5016 else break; 5017 } 5018 imark = i; 5019 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 5020 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5021 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 5022 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 5023 } else { 5024 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5025 isrowb = *rowb; iscolb = *colb; 5026 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 5027 bseq[0] = *B_seq; 5028 } 5029 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 5030 *B_seq = bseq[0]; 5031 ierr = PetscFree(bseq);CHKERRQ(ierr); 5032 if (!rowb) { 5033 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 5034 } else { 5035 *rowb = isrowb; 5036 } 5037 if (!colb) { 5038 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 5039 } else { 5040 *colb = iscolb; 5041 } 5042 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5043 PetscFunctionReturn(0); 5044 } 5045 5046 /* 5047 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 5048 of the OFF-DIAGONAL portion of local A 5049 5050 Collective on Mat 5051 5052 Input Parameters: 5053 + A,B - the matrices in mpiaij format 5054 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5055 5056 Output Parameter: 5057 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5058 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5059 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5060 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5061 5062 Level: developer 5063 5064 */ 5065 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5066 { 5067 VecScatter_MPI_General *gen_to,*gen_from; 5068 PetscErrorCode ierr; 5069 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5070 Mat_SeqAIJ *b_oth; 5071 VecScatter ctx =a->Mvctx; 5072 MPI_Comm comm; 5073 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 5074 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5075 PetscInt *rvalues,*svalues; 5076 MatScalar *b_otha,*bufa,*bufA; 5077 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5078 MPI_Request *rwaits = NULL,*swaits = NULL; 5079 MPI_Status *sstatus,rstatus; 5080 PetscMPIInt jj,size; 5081 PetscInt *cols,sbs,rbs; 5082 PetscScalar *vals; 5083 5084 PetscFunctionBegin; 5085 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5086 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5087 5088 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5089 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); 5090 } 5091 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5092 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5093 5094 if (size == 1) { 5095 startsj_s = NULL; 5096 bufa_ptr = NULL; 5097 *B_oth = NULL; 5098 PetscFunctionReturn(0); 5099 } 5100 5101 gen_to = (VecScatter_MPI_General*)ctx->todata; 5102 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5103 nrecvs = gen_from->n; 5104 nsends = gen_to->n; 5105 5106 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 5107 srow = gen_to->indices; /* local row index to be sent */ 5108 sstarts = gen_to->starts; 5109 sprocs = gen_to->procs; 5110 sstatus = gen_to->sstatus; 5111 sbs = gen_to->bs; 5112 rstarts = gen_from->starts; 5113 rprocs = gen_from->procs; 5114 rbs = gen_from->bs; 5115 5116 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5117 if (scall == MAT_INITIAL_MATRIX) { 5118 /* i-array */ 5119 /*---------*/ 5120 /* post receives */ 5121 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 5122 for (i=0; i<nrecvs; i++) { 5123 rowlen = rvalues + rstarts[i]*rbs; 5124 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5125 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5126 } 5127 5128 /* pack the outgoing message */ 5129 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 5130 5131 sstartsj[0] = 0; 5132 rstartsj[0] = 0; 5133 len = 0; /* total length of j or a array to be sent */ 5134 k = 0; 5135 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 5136 for (i=0; i<nsends; i++) { 5137 rowlen = svalues + sstarts[i]*sbs; 5138 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5139 for (j=0; j<nrows; j++) { 5140 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5141 for (l=0; l<sbs; l++) { 5142 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5143 5144 rowlen[j*sbs+l] = ncols; 5145 5146 len += ncols; 5147 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5148 } 5149 k++; 5150 } 5151 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5152 5153 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5154 } 5155 /* recvs and sends of i-array are completed */ 5156 i = nrecvs; 5157 while (i--) { 5158 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5159 } 5160 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5161 ierr = PetscFree(svalues);CHKERRQ(ierr); 5162 5163 /* allocate buffers for sending j and a arrays */ 5164 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5165 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5166 5167 /* create i-array of B_oth */ 5168 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5169 5170 b_othi[0] = 0; 5171 len = 0; /* total length of j or a array to be received */ 5172 k = 0; 5173 for (i=0; i<nrecvs; i++) { 5174 rowlen = rvalues + rstarts[i]*rbs; 5175 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5176 for (j=0; j<nrows; j++) { 5177 b_othi[k+1] = b_othi[k] + rowlen[j]; 5178 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5179 k++; 5180 } 5181 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5182 } 5183 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5184 5185 /* allocate space for j and a arrrays of B_oth */ 5186 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5187 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5188 5189 /* j-array */ 5190 /*---------*/ 5191 /* post receives of j-array */ 5192 for (i=0; i<nrecvs; i++) { 5193 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5194 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5195 } 5196 5197 /* pack the outgoing message j-array */ 5198 k = 0; 5199 for (i=0; i<nsends; i++) { 5200 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5201 bufJ = bufj+sstartsj[i]; 5202 for (j=0; j<nrows; j++) { 5203 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5204 for (ll=0; ll<sbs; ll++) { 5205 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5206 for (l=0; l<ncols; l++) { 5207 *bufJ++ = cols[l]; 5208 } 5209 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5210 } 5211 } 5212 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5213 } 5214 5215 /* recvs and sends of j-array are completed */ 5216 i = nrecvs; 5217 while (i--) { 5218 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5219 } 5220 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5221 } else if (scall == MAT_REUSE_MATRIX) { 5222 sstartsj = *startsj_s; 5223 rstartsj = *startsj_r; 5224 bufa = *bufa_ptr; 5225 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5226 b_otha = b_oth->a; 5227 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5228 5229 /* a-array */ 5230 /*---------*/ 5231 /* post receives of a-array */ 5232 for (i=0; i<nrecvs; i++) { 5233 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5234 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5235 } 5236 5237 /* pack the outgoing message a-array */ 5238 k = 0; 5239 for (i=0; i<nsends; i++) { 5240 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5241 bufA = bufa+sstartsj[i]; 5242 for (j=0; j<nrows; j++) { 5243 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5244 for (ll=0; ll<sbs; ll++) { 5245 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5246 for (l=0; l<ncols; l++) { 5247 *bufA++ = vals[l]; 5248 } 5249 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5250 } 5251 } 5252 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5253 } 5254 /* recvs and sends of a-array are completed */ 5255 i = nrecvs; 5256 while (i--) { 5257 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5258 } 5259 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5260 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5261 5262 if (scall == MAT_INITIAL_MATRIX) { 5263 /* put together the new matrix */ 5264 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5265 5266 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5267 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5268 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5269 b_oth->free_a = PETSC_TRUE; 5270 b_oth->free_ij = PETSC_TRUE; 5271 b_oth->nonew = 0; 5272 5273 ierr = PetscFree(bufj);CHKERRQ(ierr); 5274 if (!startsj_s || !bufa_ptr) { 5275 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5276 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5277 } else { 5278 *startsj_s = sstartsj; 5279 *startsj_r = rstartsj; 5280 *bufa_ptr = bufa; 5281 } 5282 } 5283 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5284 PetscFunctionReturn(0); 5285 } 5286 5287 /*@C 5288 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5289 5290 Not Collective 5291 5292 Input Parameters: 5293 . A - The matrix in mpiaij format 5294 5295 Output Parameter: 5296 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5297 . colmap - A map from global column index to local index into lvec 5298 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5299 5300 Level: developer 5301 5302 @*/ 5303 #if defined(PETSC_USE_CTABLE) 5304 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5305 #else 5306 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5307 #endif 5308 { 5309 Mat_MPIAIJ *a; 5310 5311 PetscFunctionBegin; 5312 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5313 PetscValidPointer(lvec, 2); 5314 PetscValidPointer(colmap, 3); 5315 PetscValidPointer(multScatter, 4); 5316 a = (Mat_MPIAIJ*) A->data; 5317 if (lvec) *lvec = a->lvec; 5318 if (colmap) *colmap = a->colmap; 5319 if (multScatter) *multScatter = a->Mvctx; 5320 PetscFunctionReturn(0); 5321 } 5322 5323 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5324 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5325 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5326 #if defined(PETSC_HAVE_ELEMENTAL) 5327 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5328 #endif 5329 #if defined(PETSC_HAVE_HYPRE) 5330 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5331 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5332 #endif 5333 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5334 5335 /* 5336 Computes (B'*A')' since computing B*A directly is untenable 5337 5338 n p p 5339 ( ) ( ) ( ) 5340 m ( A ) * n ( B ) = m ( C ) 5341 ( ) ( ) ( ) 5342 5343 */ 5344 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5345 { 5346 PetscErrorCode ierr; 5347 Mat At,Bt,Ct; 5348 5349 PetscFunctionBegin; 5350 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5351 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5352 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5353 ierr = MatDestroy(&At);CHKERRQ(ierr); 5354 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5355 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5356 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5357 PetscFunctionReturn(0); 5358 } 5359 5360 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5361 { 5362 PetscErrorCode ierr; 5363 PetscInt m=A->rmap->n,n=B->cmap->n; 5364 Mat Cmat; 5365 5366 PetscFunctionBegin; 5367 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); 5368 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5369 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5370 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5371 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5372 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5373 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5374 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5375 5376 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5377 5378 *C = Cmat; 5379 PetscFunctionReturn(0); 5380 } 5381 5382 /* ----------------------------------------------------------------*/ 5383 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5384 { 5385 PetscErrorCode ierr; 5386 5387 PetscFunctionBegin; 5388 if (scall == MAT_INITIAL_MATRIX) { 5389 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5390 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5391 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5392 } 5393 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5394 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5395 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5396 PetscFunctionReturn(0); 5397 } 5398 5399 /*MC 5400 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5401 5402 Options Database Keys: 5403 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5404 5405 Level: beginner 5406 5407 .seealso: MatCreateAIJ() 5408 M*/ 5409 5410 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5411 { 5412 Mat_MPIAIJ *b; 5413 PetscErrorCode ierr; 5414 PetscMPIInt size; 5415 5416 PetscFunctionBegin; 5417 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5418 5419 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5420 B->data = (void*)b; 5421 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5422 B->assembled = PETSC_FALSE; 5423 B->insertmode = NOT_SET_VALUES; 5424 b->size = size; 5425 5426 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5427 5428 /* build cache for off array entries formed */ 5429 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5430 5431 b->donotstash = PETSC_FALSE; 5432 b->colmap = 0; 5433 b->garray = 0; 5434 b->roworiented = PETSC_TRUE; 5435 5436 /* stuff used for matrix vector multiply */ 5437 b->lvec = NULL; 5438 b->Mvctx = NULL; 5439 5440 /* stuff for MatGetRow() */ 5441 b->rowindices = 0; 5442 b->rowvalues = 0; 5443 b->getrowactive = PETSC_FALSE; 5444 5445 /* flexible pointer used in CUSP/CUSPARSE classes */ 5446 b->spptr = NULL; 5447 5448 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5449 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5450 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5451 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5452 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5453 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5454 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5455 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5456 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5457 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5458 #if defined(PETSC_HAVE_ELEMENTAL) 5459 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5460 #endif 5461 #if defined(PETSC_HAVE_HYPRE) 5462 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5463 #endif 5464 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5465 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5466 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5467 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5468 #if defined(PETSC_HAVE_HYPRE) 5469 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5470 #endif 5471 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5472 PetscFunctionReturn(0); 5473 } 5474 5475 /*@C 5476 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5477 and "off-diagonal" part of the matrix in CSR format. 5478 5479 Collective on MPI_Comm 5480 5481 Input Parameters: 5482 + comm - MPI communicator 5483 . m - number of local rows (Cannot be PETSC_DECIDE) 5484 . n - This value should be the same as the local size used in creating the 5485 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5486 calculated if N is given) For square matrices n is almost always m. 5487 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5488 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5489 . i - row indices for "diagonal" portion of matrix 5490 . j - column indices 5491 . a - matrix values 5492 . oi - row indices for "off-diagonal" portion of matrix 5493 . oj - column indices 5494 - oa - matrix values 5495 5496 Output Parameter: 5497 . mat - the matrix 5498 5499 Level: advanced 5500 5501 Notes: 5502 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5503 must free the arrays once the matrix has been destroyed and not before. 5504 5505 The i and j indices are 0 based 5506 5507 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5508 5509 This sets local rows and cannot be used to set off-processor values. 5510 5511 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5512 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5513 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5514 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5515 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5516 communication if it is known that only local entries will be set. 5517 5518 .keywords: matrix, aij, compressed row, sparse, parallel 5519 5520 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5521 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5522 @*/ 5523 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) 5524 { 5525 PetscErrorCode ierr; 5526 Mat_MPIAIJ *maij; 5527 5528 PetscFunctionBegin; 5529 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5530 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5531 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5532 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5533 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5534 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5535 maij = (Mat_MPIAIJ*) (*mat)->data; 5536 5537 (*mat)->preallocated = PETSC_TRUE; 5538 5539 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5540 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5541 5542 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5543 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5544 5545 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5546 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5547 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5548 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5549 5550 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5551 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5552 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5553 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5554 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5555 PetscFunctionReturn(0); 5556 } 5557 5558 /* 5559 Special version for direct calls from Fortran 5560 */ 5561 #include <petsc/private/fortranimpl.h> 5562 5563 /* Change these macros so can be used in void function */ 5564 #undef CHKERRQ 5565 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5566 #undef SETERRQ2 5567 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5568 #undef SETERRQ3 5569 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5570 #undef SETERRQ 5571 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5572 5573 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5574 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5575 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5576 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5577 #else 5578 #endif 5579 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) 5580 { 5581 Mat mat = *mmat; 5582 PetscInt m = *mm, n = *mn; 5583 InsertMode addv = *maddv; 5584 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5585 PetscScalar value; 5586 PetscErrorCode ierr; 5587 5588 MatCheckPreallocated(mat,1); 5589 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5590 5591 #if defined(PETSC_USE_DEBUG) 5592 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5593 #endif 5594 { 5595 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5596 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5597 PetscBool roworiented = aij->roworiented; 5598 5599 /* Some Variables required in the macro */ 5600 Mat A = aij->A; 5601 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5602 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5603 MatScalar *aa = a->a; 5604 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5605 Mat B = aij->B; 5606 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5607 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5608 MatScalar *ba = b->a; 5609 5610 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5611 PetscInt nonew = a->nonew; 5612 MatScalar *ap1,*ap2; 5613 5614 PetscFunctionBegin; 5615 for (i=0; i<m; i++) { 5616 if (im[i] < 0) continue; 5617 #if defined(PETSC_USE_DEBUG) 5618 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); 5619 #endif 5620 if (im[i] >= rstart && im[i] < rend) { 5621 row = im[i] - rstart; 5622 lastcol1 = -1; 5623 rp1 = aj + ai[row]; 5624 ap1 = aa + ai[row]; 5625 rmax1 = aimax[row]; 5626 nrow1 = ailen[row]; 5627 low1 = 0; 5628 high1 = nrow1; 5629 lastcol2 = -1; 5630 rp2 = bj + bi[row]; 5631 ap2 = ba + bi[row]; 5632 rmax2 = bimax[row]; 5633 nrow2 = bilen[row]; 5634 low2 = 0; 5635 high2 = nrow2; 5636 5637 for (j=0; j<n; j++) { 5638 if (roworiented) value = v[i*n+j]; 5639 else value = v[i+j*m]; 5640 if (in[j] >= cstart && in[j] < cend) { 5641 col = in[j] - cstart; 5642 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5643 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5644 } else if (in[j] < 0) continue; 5645 #if defined(PETSC_USE_DEBUG) 5646 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); 5647 #endif 5648 else { 5649 if (mat->was_assembled) { 5650 if (!aij->colmap) { 5651 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5652 } 5653 #if defined(PETSC_USE_CTABLE) 5654 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5655 col--; 5656 #else 5657 col = aij->colmap[in[j]] - 1; 5658 #endif 5659 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5660 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5661 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5662 col = in[j]; 5663 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5664 B = aij->B; 5665 b = (Mat_SeqAIJ*)B->data; 5666 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5667 rp2 = bj + bi[row]; 5668 ap2 = ba + bi[row]; 5669 rmax2 = bimax[row]; 5670 nrow2 = bilen[row]; 5671 low2 = 0; 5672 high2 = nrow2; 5673 bm = aij->B->rmap->n; 5674 ba = b->a; 5675 } 5676 } else col = in[j]; 5677 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5678 } 5679 } 5680 } else if (!aij->donotstash) { 5681 if (roworiented) { 5682 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5683 } else { 5684 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5685 } 5686 } 5687 } 5688 } 5689 PetscFunctionReturnVoid(); 5690 } 5691 5692