1 2 3 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 4 #include <petsc/private/vecimpl.h> 5 #include <petsc/private/isimpl.h> 6 #include <petscblaslapack.h> 7 #include <petscsf.h> 8 9 /*MC 10 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 11 12 This matrix type is identical to MATSEQAIJ when constructed with a single process communicator, 13 and MATMPIAIJ otherwise. As a result, for single process communicators, 14 MatSeqAIJSetPreallocation is supported, and similarly MatMPIAIJSetPreallocation is supported 15 for communicators controlling multiple processes. It is recommended that you call both of 16 the above preallocation routines for simplicity. 17 18 Options Database Keys: 19 . -mat_type aij - sets the matrix type to "aij" during a call to MatSetFromOptions() 20 21 Developer Notes: Subclasses include MATAIJCUSP, MATAIJCUSPARSE, MATAIJPERM, MATAIJCRL, and also automatically switches over to use inodes when 22 enough exist. 23 24 Level: beginner 25 26 .seealso: MatCreateAIJ(), MatCreateSeqAIJ(), MATSEQAIJ, MATMPIAIJ 27 M*/ 28 29 /*MC 30 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 31 32 This matrix type is identical to MATSEQAIJCRL when constructed with a single process communicator, 33 and MATMPIAIJCRL otherwise. As a result, for single process communicators, 34 MatSeqAIJSetPreallocation() is supported, and similarly MatMPIAIJSetPreallocation() is supported 35 for communicators controlling multiple processes. It is recommended that you call both of 36 the above preallocation routines for simplicity. 37 38 Options Database Keys: 39 . -mat_type aijcrl - sets the matrix type to "aijcrl" during a call to MatSetFromOptions() 40 41 Level: beginner 42 43 .seealso: MatCreateMPIAIJCRL,MATSEQAIJCRL,MATMPIAIJCRL, MATSEQAIJCRL, MATMPIAIJCRL 44 M*/ 45 46 PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs) 47 { 48 PetscErrorCode ierr; 49 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 50 51 PetscFunctionBegin; 52 if (mat->A) { 53 ierr = MatSetBlockSizes(mat->A,rbs,cbs);CHKERRQ(ierr); 54 ierr = MatSetBlockSizes(mat->B,rbs,1);CHKERRQ(ierr); 55 } 56 PetscFunctionReturn(0); 57 } 58 59 PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M,IS *keptrows) 60 { 61 PetscErrorCode ierr; 62 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)M->data; 63 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data; 64 Mat_SeqAIJ *b = (Mat_SeqAIJ*)mat->B->data; 65 const PetscInt *ia,*ib; 66 const MatScalar *aa,*bb; 67 PetscInt na,nb,i,j,*rows,cnt=0,n0rows; 68 PetscInt m = M->rmap->n,rstart = M->rmap->rstart; 69 70 PetscFunctionBegin; 71 *keptrows = 0; 72 ia = a->i; 73 ib = b->i; 74 for (i=0; i<m; i++) { 75 na = ia[i+1] - ia[i]; 76 nb = ib[i+1] - ib[i]; 77 if (!na && !nb) { 78 cnt++; 79 goto ok1; 80 } 81 aa = a->a + ia[i]; 82 for (j=0; j<na; j++) { 83 if (aa[j] != 0.0) goto ok1; 84 } 85 bb = b->a + ib[i]; 86 for (j=0; j <nb; j++) { 87 if (bb[j] != 0.0) goto ok1; 88 } 89 cnt++; 90 ok1:; 91 } 92 ierr = MPIU_Allreduce(&cnt,&n0rows,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)M));CHKERRQ(ierr); 93 if (!n0rows) PetscFunctionReturn(0); 94 ierr = PetscMalloc1(M->rmap->n-cnt,&rows);CHKERRQ(ierr); 95 cnt = 0; 96 for (i=0; i<m; i++) { 97 na = ia[i+1] - ia[i]; 98 nb = ib[i+1] - ib[i]; 99 if (!na && !nb) continue; 100 aa = a->a + ia[i]; 101 for (j=0; j<na;j++) { 102 if (aa[j] != 0.0) { 103 rows[cnt++] = rstart + i; 104 goto ok2; 105 } 106 } 107 bb = b->a + ib[i]; 108 for (j=0; j<nb; j++) { 109 if (bb[j] != 0.0) { 110 rows[cnt++] = rstart + i; 111 goto ok2; 112 } 113 } 114 ok2:; 115 } 116 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),cnt,rows,PETSC_OWN_POINTER,keptrows);CHKERRQ(ierr); 117 PetscFunctionReturn(0); 118 } 119 120 PetscErrorCode MatDiagonalSet_MPIAIJ(Mat Y,Vec D,InsertMode is) 121 { 122 PetscErrorCode ierr; 123 Mat_MPIAIJ *aij = (Mat_MPIAIJ*) Y->data; 124 125 PetscFunctionBegin; 126 if (Y->assembled && Y->rmap->rstart == Y->cmap->rstart && Y->rmap->rend == Y->cmap->rend) { 127 ierr = MatDiagonalSet(aij->A,D,is);CHKERRQ(ierr); 128 } else { 129 ierr = MatDiagonalSet_Default(Y,D,is);CHKERRQ(ierr); 130 } 131 PetscFunctionReturn(0); 132 } 133 134 PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M,IS *zrows) 135 { 136 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)M->data; 137 PetscErrorCode ierr; 138 PetscInt i,rstart,nrows,*rows; 139 140 PetscFunctionBegin; 141 *zrows = NULL; 142 ierr = MatFindZeroDiagonals_SeqAIJ_Private(aij->A,&nrows,&rows);CHKERRQ(ierr); 143 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 144 for (i=0; i<nrows; i++) rows[i] += rstart; 145 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)M),nrows,rows,PETSC_OWN_POINTER,zrows);CHKERRQ(ierr); 146 PetscFunctionReturn(0); 147 } 148 149 PetscErrorCode MatGetColumnNorms_MPIAIJ(Mat A,NormType type,PetscReal *norms) 150 { 151 PetscErrorCode ierr; 152 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 153 PetscInt i,n,*garray = aij->garray; 154 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ*) aij->A->data; 155 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ*) aij->B->data; 156 PetscReal *work; 157 158 PetscFunctionBegin; 159 ierr = MatGetSize(A,NULL,&n);CHKERRQ(ierr); 160 ierr = PetscCalloc1(n,&work);CHKERRQ(ierr); 161 if (type == NORM_2) { 162 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 163 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]*a_aij->a[i]); 164 } 165 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 166 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]*b_aij->a[i]); 167 } 168 } else if (type == NORM_1) { 169 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 170 work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 171 } 172 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 173 work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 174 } 175 } else if (type == NORM_INFINITY) { 176 for (i=0; i<a_aij->i[aij->A->rmap->n]; i++) { 177 work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 178 } 179 for (i=0; i<b_aij->i[aij->B->rmap->n]; i++) { 180 work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]),work[garray[b_aij->j[i]]]); 181 } 182 183 } else SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Unknown NormType"); 184 if (type == NORM_INFINITY) { 185 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 186 } else { 187 ierr = MPIU_Allreduce(work,norms,n,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 188 } 189 ierr = PetscFree(work);CHKERRQ(ierr); 190 if (type == NORM_2) { 191 for (i=0; i<n; i++) norms[i] = PetscSqrtReal(norms[i]); 192 } 193 PetscFunctionReturn(0); 194 } 195 196 PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A,IS *is) 197 { 198 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 199 IS sis,gis; 200 PetscErrorCode ierr; 201 const PetscInt *isis,*igis; 202 PetscInt n,*iis,nsis,ngis,rstart,i; 203 204 PetscFunctionBegin; 205 ierr = MatFindOffBlockDiagonalEntries(a->A,&sis);CHKERRQ(ierr); 206 ierr = MatFindNonzeroRows(a->B,&gis);CHKERRQ(ierr); 207 ierr = ISGetSize(gis,&ngis);CHKERRQ(ierr); 208 ierr = ISGetSize(sis,&nsis);CHKERRQ(ierr); 209 ierr = ISGetIndices(sis,&isis);CHKERRQ(ierr); 210 ierr = ISGetIndices(gis,&igis);CHKERRQ(ierr); 211 212 ierr = PetscMalloc1(ngis+nsis,&iis);CHKERRQ(ierr); 213 ierr = PetscMemcpy(iis,igis,ngis*sizeof(PetscInt));CHKERRQ(ierr); 214 ierr = PetscMemcpy(iis+ngis,isis,nsis*sizeof(PetscInt));CHKERRQ(ierr); 215 n = ngis + nsis; 216 ierr = PetscSortRemoveDupsInt(&n,iis);CHKERRQ(ierr); 217 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 218 for (i=0; i<n; i++) iis[i] += rstart; 219 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),n,iis,PETSC_OWN_POINTER,is);CHKERRQ(ierr); 220 221 ierr = ISRestoreIndices(sis,&isis);CHKERRQ(ierr); 222 ierr = ISRestoreIndices(gis,&igis);CHKERRQ(ierr); 223 ierr = ISDestroy(&sis);CHKERRQ(ierr); 224 ierr = ISDestroy(&gis);CHKERRQ(ierr); 225 PetscFunctionReturn(0); 226 } 227 228 /* 229 Distributes a SeqAIJ matrix across a set of processes. Code stolen from 230 MatLoad_MPIAIJ(). Horrible lack of reuse. Should be a routine for each matrix type. 231 232 Only for square matrices 233 234 Used by a preconditioner, hence PETSC_EXTERN 235 */ 236 PETSC_EXTERN PetscErrorCode MatDistribute_MPIAIJ(MPI_Comm comm,Mat gmat,PetscInt m,MatReuse reuse,Mat *inmat) 237 { 238 PetscMPIInt rank,size; 239 PetscInt *rowners,*dlens,*olens,i,rstart,rend,j,jj,nz = 0,*gmataj,cnt,row,*ld,bses[2]; 240 PetscErrorCode ierr; 241 Mat mat; 242 Mat_SeqAIJ *gmata; 243 PetscMPIInt tag; 244 MPI_Status status; 245 PetscBool aij; 246 MatScalar *gmataa,*ao,*ad,*gmataarestore=0; 247 248 PetscFunctionBegin; 249 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 250 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 251 if (!rank) { 252 ierr = PetscObjectTypeCompare((PetscObject)gmat,MATSEQAIJ,&aij);CHKERRQ(ierr); 253 if (!aij) SETERRQ1(PetscObjectComm((PetscObject)gmat),PETSC_ERR_SUP,"Currently no support for input matrix of type %s\n",((PetscObject)gmat)->type_name); 254 } 255 if (reuse == MAT_INITIAL_MATRIX) { 256 ierr = MatCreate(comm,&mat);CHKERRQ(ierr); 257 ierr = MatSetSizes(mat,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 258 ierr = MatGetBlockSizes(gmat,&bses[0],&bses[1]);CHKERRQ(ierr); 259 ierr = MPI_Bcast(bses,2,MPIU_INT,0,comm);CHKERRQ(ierr); 260 ierr = MatSetBlockSizes(mat,bses[0],bses[1]);CHKERRQ(ierr); 261 ierr = MatSetType(mat,MATAIJ);CHKERRQ(ierr); 262 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 263 ierr = PetscMalloc2(m,&dlens,m,&olens);CHKERRQ(ierr); 264 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 265 266 rowners[0] = 0; 267 for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; 268 rstart = rowners[rank]; 269 rend = rowners[rank+1]; 270 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 271 if (!rank) { 272 gmata = (Mat_SeqAIJ*) gmat->data; 273 /* send row lengths to all processors */ 274 for (i=0; i<m; i++) dlens[i] = gmata->ilen[i]; 275 for (i=1; i<size; i++) { 276 ierr = MPI_Send(gmata->ilen + rowners[i],rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 277 } 278 /* determine number diagonal and off-diagonal counts */ 279 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 280 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 281 jj = 0; 282 for (i=0; i<m; i++) { 283 for (j=0; j<dlens[i]; j++) { 284 if (gmata->j[jj] < rstart) ld[i]++; 285 if (gmata->j[jj] < rstart || gmata->j[jj] >= rend) olens[i]++; 286 jj++; 287 } 288 } 289 /* send column indices to other processes */ 290 for (i=1; i<size; i++) { 291 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 292 ierr = MPI_Send(&nz,1,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 293 ierr = MPI_Send(gmata->j + gmata->i[rowners[i]],nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 294 } 295 296 /* send numerical values to other processes */ 297 for (i=1; i<size; i++) { 298 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 299 ierr = MPI_Send(gmata->a + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 300 } 301 gmataa = gmata->a; 302 gmataj = gmata->j; 303 304 } else { 305 /* receive row lengths */ 306 ierr = MPI_Recv(dlens,m,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 307 /* receive column indices */ 308 ierr = MPI_Recv(&nz,1,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 309 ierr = PetscMalloc2(nz,&gmataa,nz,&gmataj);CHKERRQ(ierr); 310 ierr = MPI_Recv(gmataj,nz,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 311 /* determine number diagonal and off-diagonal counts */ 312 ierr = PetscMemzero(olens,m*sizeof(PetscInt));CHKERRQ(ierr); 313 ierr = PetscCalloc1(m,&ld);CHKERRQ(ierr); 314 jj = 0; 315 for (i=0; i<m; i++) { 316 for (j=0; j<dlens[i]; j++) { 317 if (gmataj[jj] < rstart) ld[i]++; 318 if (gmataj[jj] < rstart || gmataj[jj] >= rend) olens[i]++; 319 jj++; 320 } 321 } 322 /* receive numerical values */ 323 ierr = PetscMemzero(gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 324 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 325 } 326 /* set preallocation */ 327 for (i=0; i<m; i++) { 328 dlens[i] -= olens[i]; 329 } 330 ierr = MatSeqAIJSetPreallocation(mat,0,dlens);CHKERRQ(ierr); 331 ierr = MatMPIAIJSetPreallocation(mat,0,dlens,0,olens);CHKERRQ(ierr); 332 333 for (i=0; i<m; i++) { 334 dlens[i] += olens[i]; 335 } 336 cnt = 0; 337 for (i=0; i<m; i++) { 338 row = rstart + i; 339 ierr = MatSetValues(mat,1,&row,dlens[i],gmataj+cnt,gmataa+cnt,INSERT_VALUES);CHKERRQ(ierr); 340 cnt += dlens[i]; 341 } 342 if (rank) { 343 ierr = PetscFree2(gmataa,gmataj);CHKERRQ(ierr); 344 } 345 ierr = PetscFree2(dlens,olens);CHKERRQ(ierr); 346 ierr = PetscFree(rowners);CHKERRQ(ierr); 347 348 ((Mat_MPIAIJ*)(mat->data))->ld = ld; 349 350 *inmat = mat; 351 } else { /* column indices are already set; only need to move over numerical values from process 0 */ 352 Mat_SeqAIJ *Ad = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->A->data; 353 Mat_SeqAIJ *Ao = (Mat_SeqAIJ*)((Mat_MPIAIJ*)((*inmat)->data))->B->data; 354 mat = *inmat; 355 ierr = PetscObjectGetNewTag((PetscObject)mat,&tag);CHKERRQ(ierr); 356 if (!rank) { 357 /* send numerical values to other processes */ 358 gmata = (Mat_SeqAIJ*) gmat->data; 359 ierr = MatGetOwnershipRanges(mat,(const PetscInt**)&rowners);CHKERRQ(ierr); 360 gmataa = gmata->a; 361 for (i=1; i<size; i++) { 362 nz = gmata->i[rowners[i+1]]-gmata->i[rowners[i]]; 363 ierr = MPI_Send(gmataa + gmata->i[rowners[i]],nz,MPIU_SCALAR,i,tag,comm);CHKERRQ(ierr); 364 } 365 nz = gmata->i[rowners[1]]-gmata->i[rowners[0]]; 366 } else { 367 /* receive numerical values from process 0*/ 368 nz = Ad->nz + Ao->nz; 369 ierr = PetscMalloc1(nz,&gmataa);CHKERRQ(ierr); gmataarestore = gmataa; 370 ierr = MPI_Recv(gmataa,nz,MPIU_SCALAR,0,tag,comm,&status);CHKERRQ(ierr); 371 } 372 /* transfer numerical values into the diagonal A and off diagonal B parts of mat */ 373 ld = ((Mat_MPIAIJ*)(mat->data))->ld; 374 ad = Ad->a; 375 ao = Ao->a; 376 if (mat->rmap->n) { 377 i = 0; 378 nz = ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 379 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 380 } 381 for (i=1; i<mat->rmap->n; i++) { 382 nz = Ao->i[i] - Ao->i[i-1] - ld[i-1] + ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ao += nz; gmataa += nz; 383 nz = Ad->i[i+1] - Ad->i[i]; ierr = PetscMemcpy(ad,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); ad += nz; gmataa += nz; 384 } 385 i--; 386 if (mat->rmap->n) { 387 nz = Ao->i[i+1] - Ao->i[i] - ld[i]; ierr = PetscMemcpy(ao,gmataa,nz*sizeof(PetscScalar));CHKERRQ(ierr); 388 } 389 if (rank) { 390 ierr = PetscFree(gmataarestore);CHKERRQ(ierr); 391 } 392 } 393 ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 394 ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 395 PetscFunctionReturn(0); 396 } 397 398 /* 399 Local utility routine that creates a mapping from the global column 400 number to the local number in the off-diagonal part of the local 401 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 402 a slightly higher hash table cost; without it it is not scalable (each processor 403 has an order N integer array but is fast to acess. 404 */ 405 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 406 { 407 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 408 PetscErrorCode ierr; 409 PetscInt n = aij->B->cmap->n,i; 410 411 PetscFunctionBegin; 412 if (!aij->garray) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPIAIJ Matrix was assembled but is missing garray"); 413 #if defined(PETSC_USE_CTABLE) 414 ierr = PetscTableCreate(n,mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 415 for (i=0; i<n; i++) { 416 ierr = PetscTableAdd(aij->colmap,aij->garray[i]+1,i+1,INSERT_VALUES);CHKERRQ(ierr); 417 } 418 #else 419 ierr = PetscCalloc1(mat->cmap->N+1,&aij->colmap);CHKERRQ(ierr); 420 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N+1)*sizeof(PetscInt));CHKERRQ(ierr); 421 for (i=0; i<n; i++) aij->colmap[aij->garray[i]] = i+1; 422 #endif 423 PetscFunctionReturn(0); 424 } 425 426 #define MatSetValues_SeqAIJ_A_Private(row,col,value,addv,orow,ocol) \ 427 { \ 428 if (col <= lastcol1) low1 = 0; \ 429 else high1 = nrow1; \ 430 lastcol1 = col;\ 431 while (high1-low1 > 5) { \ 432 t = (low1+high1)/2; \ 433 if (rp1[t] > col) high1 = t; \ 434 else low1 = t; \ 435 } \ 436 for (_i=low1; _i<high1; _i++) { \ 437 if (rp1[_i] > col) break; \ 438 if (rp1[_i] == col) { \ 439 if (addv == ADD_VALUES) ap1[_i] += value; \ 440 else ap1[_i] = value; \ 441 goto a_noinsert; \ 442 } \ 443 } \ 444 if (value == 0.0 && ignorezeroentries && row != col) {low1 = 0; high1 = nrow1;goto a_noinsert;} \ 445 if (nonew == 1) {low1 = 0; high1 = nrow1; goto a_noinsert;} \ 446 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 447 MatSeqXAIJReallocateAIJ(A,am,1,nrow1,row,col,rmax1,aa,ai,aj,rp1,ap1,aimax,nonew,MatScalar); \ 448 N = nrow1++ - 1; a->nz++; high1++; \ 449 /* shift up all the later entries in this row */ \ 450 for (ii=N; ii>=_i; ii--) { \ 451 rp1[ii+1] = rp1[ii]; \ 452 ap1[ii+1] = ap1[ii]; \ 453 } \ 454 rp1[_i] = col; \ 455 ap1[_i] = value; \ 456 A->nonzerostate++;\ 457 a_noinsert: ; \ 458 ailen[row] = nrow1; \ 459 } 460 461 #define MatSetValues_SeqAIJ_B_Private(row,col,value,addv,orow,ocol) \ 462 { \ 463 if (col <= lastcol2) low2 = 0; \ 464 else high2 = nrow2; \ 465 lastcol2 = col; \ 466 while (high2-low2 > 5) { \ 467 t = (low2+high2)/2; \ 468 if (rp2[t] > col) high2 = t; \ 469 else low2 = t; \ 470 } \ 471 for (_i=low2; _i<high2; _i++) { \ 472 if (rp2[_i] > col) break; \ 473 if (rp2[_i] == col) { \ 474 if (addv == ADD_VALUES) ap2[_i] += value; \ 475 else ap2[_i] = value; \ 476 goto b_noinsert; \ 477 } \ 478 } \ 479 if (value == 0.0 && ignorezeroentries) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 480 if (nonew == 1) {low2 = 0; high2 = nrow2; goto b_noinsert;} \ 481 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", orow, ocol); \ 482 MatSeqXAIJReallocateAIJ(B,bm,1,nrow2,row,col,rmax2,ba,bi,bj,rp2,ap2,bimax,nonew,MatScalar); \ 483 N = nrow2++ - 1; b->nz++; high2++; \ 484 /* shift up all the later entries in this row */ \ 485 for (ii=N; ii>=_i; ii--) { \ 486 rp2[ii+1] = rp2[ii]; \ 487 ap2[ii+1] = ap2[ii]; \ 488 } \ 489 rp2[_i] = col; \ 490 ap2[_i] = value; \ 491 B->nonzerostate++; \ 492 b_noinsert: ; \ 493 bilen[row] = nrow2; \ 494 } 495 496 PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A,PetscInt row,const PetscScalar v[]) 497 { 498 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)A->data; 499 Mat_SeqAIJ *a = (Mat_SeqAIJ*)mat->A->data,*b = (Mat_SeqAIJ*)mat->B->data; 500 PetscErrorCode ierr; 501 PetscInt l,*garray = mat->garray,diag; 502 503 PetscFunctionBegin; 504 /* code only works for square matrices A */ 505 506 /* find size of row to the left of the diagonal part */ 507 ierr = MatGetOwnershipRange(A,&diag,0);CHKERRQ(ierr); 508 row = row - diag; 509 for (l=0; l<b->i[row+1]-b->i[row]; l++) { 510 if (garray[b->j[b->i[row]+l]] > diag) break; 511 } 512 ierr = PetscMemcpy(b->a+b->i[row],v,l*sizeof(PetscScalar));CHKERRQ(ierr); 513 514 /* diagonal part */ 515 ierr = PetscMemcpy(a->a+a->i[row],v+l,(a->i[row+1]-a->i[row])*sizeof(PetscScalar));CHKERRQ(ierr); 516 517 /* right of diagonal part */ 518 ierr = PetscMemcpy(b->a+b->i[row]+l,v+l+a->i[row+1]-a->i[row],(b->i[row+1]-b->i[row]-l)*sizeof(PetscScalar));CHKERRQ(ierr); 519 PetscFunctionReturn(0); 520 } 521 522 PetscErrorCode MatSetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode addv) 523 { 524 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 525 PetscScalar value; 526 PetscErrorCode ierr; 527 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 528 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 529 PetscBool roworiented = aij->roworiented; 530 531 /* Some Variables required in the macro */ 532 Mat A = aij->A; 533 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 534 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 535 MatScalar *aa = a->a; 536 PetscBool ignorezeroentries = a->ignorezeroentries; 537 Mat B = aij->B; 538 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 539 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 540 MatScalar *ba = b->a; 541 542 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 543 PetscInt nonew; 544 MatScalar *ap1,*ap2; 545 546 PetscFunctionBegin; 547 for (i=0; i<m; i++) { 548 if (im[i] < 0) continue; 549 #if defined(PETSC_USE_DEBUG) 550 if (im[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",im[i],mat->rmap->N-1); 551 #endif 552 if (im[i] >= rstart && im[i] < rend) { 553 row = im[i] - rstart; 554 lastcol1 = -1; 555 rp1 = aj + ai[row]; 556 ap1 = aa + ai[row]; 557 rmax1 = aimax[row]; 558 nrow1 = ailen[row]; 559 low1 = 0; 560 high1 = nrow1; 561 lastcol2 = -1; 562 rp2 = bj + bi[row]; 563 ap2 = ba + bi[row]; 564 rmax2 = bimax[row]; 565 nrow2 = bilen[row]; 566 low2 = 0; 567 high2 = nrow2; 568 569 for (j=0; j<n; j++) { 570 if (roworiented) value = v[i*n+j]; 571 else value = v[i+j*m]; 572 if (in[j] >= cstart && in[j] < cend) { 573 col = in[j] - cstart; 574 nonew = a->nonew; 575 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 576 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 577 } else if (in[j] < 0) continue; 578 #if defined(PETSC_USE_DEBUG) 579 else if (in[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[j],mat->cmap->N-1); 580 #endif 581 else { 582 if (mat->was_assembled) { 583 if (!aij->colmap) { 584 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 585 } 586 #if defined(PETSC_USE_CTABLE) 587 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 588 col--; 589 #else 590 col = aij->colmap[in[j]] - 1; 591 #endif 592 if (col < 0 && !((Mat_SeqAIJ*)(aij->B->data))->nonew) { 593 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 594 col = in[j]; 595 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 596 B = aij->B; 597 b = (Mat_SeqAIJ*)B->data; 598 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; ba = b->a; 599 rp2 = bj + bi[row]; 600 ap2 = ba + bi[row]; 601 rmax2 = bimax[row]; 602 nrow2 = bilen[row]; 603 low2 = 0; 604 high2 = nrow2; 605 bm = aij->B->rmap->n; 606 ba = b->a; 607 } else if (col < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero at global row/column (%D, %D) into matrix", im[i], in[j]); 608 } else col = in[j]; 609 nonew = b->nonew; 610 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 611 } 612 } 613 } else { 614 if (mat->nooffprocentries) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Setting off process row %D even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set",im[i]); 615 if (!aij->donotstash) { 616 mat->assembled = PETSC_FALSE; 617 if (roworiented) { 618 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 619 } else { 620 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 621 } 622 } 623 } 624 } 625 PetscFunctionReturn(0); 626 } 627 628 PetscErrorCode MatGetValues_MPIAIJ(Mat mat,PetscInt m,const PetscInt idxm[],PetscInt n,const PetscInt idxn[],PetscScalar v[]) 629 { 630 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 631 PetscErrorCode ierr; 632 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 633 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 634 635 PetscFunctionBegin; 636 for (i=0; i<m; i++) { 637 if (idxm[i] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",idxm[i]);*/ 638 if (idxm[i] >= mat->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",idxm[i],mat->rmap->N-1); 639 if (idxm[i] >= rstart && idxm[i] < rend) { 640 row = idxm[i] - rstart; 641 for (j=0; j<n; j++) { 642 if (idxn[j] < 0) continue; /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",idxn[j]); */ 643 if (idxn[j] >= mat->cmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",idxn[j],mat->cmap->N-1); 644 if (idxn[j] >= cstart && idxn[j] < cend) { 645 col = idxn[j] - cstart; 646 ierr = MatGetValues(aij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 647 } else { 648 if (!aij->colmap) { 649 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 650 } 651 #if defined(PETSC_USE_CTABLE) 652 ierr = PetscTableFind(aij->colmap,idxn[j]+1,&col);CHKERRQ(ierr); 653 col--; 654 #else 655 col = aij->colmap[idxn[j]] - 1; 656 #endif 657 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v+i*n+j) = 0.0; 658 else { 659 ierr = MatGetValues(aij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); 660 } 661 } 662 } 663 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only local values currently supported"); 664 } 665 PetscFunctionReturn(0); 666 } 667 668 extern PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat,Vec,Vec); 669 670 PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat,MatAssemblyType mode) 671 { 672 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 673 PetscErrorCode ierr; 674 PetscInt nstash,reallocs; 675 676 PetscFunctionBegin; 677 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(0); 678 679 ierr = MatStashScatterBegin_Private(mat,&mat->stash,mat->rmap->range);CHKERRQ(ierr); 680 ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); 681 ierr = PetscInfo2(aij->A,"Stash has %D entries, uses %D mallocs.\n",nstash,reallocs);CHKERRQ(ierr); 682 PetscFunctionReturn(0); 683 } 684 685 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat,MatAssemblyType mode) 686 { 687 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 688 Mat_SeqAIJ *a = (Mat_SeqAIJ*)aij->A->data; 689 PetscErrorCode ierr; 690 PetscMPIInt n; 691 PetscInt i,j,rstart,ncols,flg; 692 PetscInt *row,*col; 693 PetscBool other_disassembled; 694 PetscScalar *val; 695 696 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 697 698 PetscFunctionBegin; 699 if (!aij->donotstash && !mat->nooffprocentries) { 700 while (1) { 701 ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); 702 if (!flg) break; 703 704 for (i=0; i<n; ) { 705 /* Now identify the consecutive vals belonging to the same row */ 706 for (j=i,rstart=row[j]; j<n; j++) { 707 if (row[j] != rstart) break; 708 } 709 if (j < n) ncols = j-i; 710 else ncols = n-i; 711 /* Now assemble all these values with a single function call */ 712 ierr = MatSetValues_MPIAIJ(mat,1,row+i,ncols,col+i,val+i,mat->insertmode);CHKERRQ(ierr); 713 714 i = j; 715 } 716 } 717 ierr = MatStashScatterEnd_Private(&mat->stash);CHKERRQ(ierr); 718 } 719 ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr); 720 ierr = MatAssemblyEnd(aij->A,mode);CHKERRQ(ierr); 721 722 /* determine if any processor has disassembled, if so we must 723 also disassemble ourselfs, in order that we may reassemble. */ 724 /* 725 if nonzero structure of submatrix B cannot change then we know that 726 no processor disassembled thus we can skip this stuff 727 */ 728 if (!((Mat_SeqAIJ*)aij->B->data)->nonew) { 729 ierr = MPIU_Allreduce(&mat->was_assembled,&other_disassembled,1,MPIU_BOOL,MPI_PROD,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 730 if (mat->was_assembled && !other_disassembled) { 731 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 732 } 733 } 734 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { 735 ierr = MatSetUpMultiply_MPIAIJ(mat);CHKERRQ(ierr); 736 } 737 ierr = MatSetOption(aij->B,MAT_USE_INODES,PETSC_FALSE);CHKERRQ(ierr); 738 ierr = MatAssemblyBegin(aij->B,mode);CHKERRQ(ierr); 739 ierr = MatAssemblyEnd(aij->B,mode);CHKERRQ(ierr); 740 741 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 742 743 aij->rowvalues = 0; 744 745 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 746 if (a->inode.size) mat->ops->multdiagonalblock = MatMultDiagonalBlock_MPIAIJ; 747 748 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 749 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 750 PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate; 751 ierr = MPIU_Allreduce(&state,&mat->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 752 } 753 PetscFunctionReturn(0); 754 } 755 756 PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 757 { 758 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 759 PetscErrorCode ierr; 760 761 PetscFunctionBegin; 762 ierr = MatZeroEntries(l->A);CHKERRQ(ierr); 763 ierr = MatZeroEntries(l->B);CHKERRQ(ierr); 764 PetscFunctionReturn(0); 765 } 766 767 PetscErrorCode MatZeroRows_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 768 { 769 Mat_MPIAIJ *mat = (Mat_MPIAIJ *) A->data; 770 PetscInt *lrows; 771 PetscInt r, len; 772 PetscErrorCode ierr; 773 774 PetscFunctionBegin; 775 /* get locally owned rows */ 776 ierr = MatZeroRowsMapLocal_Private(A,N,rows,&len,&lrows);CHKERRQ(ierr); 777 /* fix right hand side if needed */ 778 if (x && b) { 779 const PetscScalar *xx; 780 PetscScalar *bb; 781 782 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 783 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 784 for (r = 0; r < len; ++r) bb[lrows[r]] = diag*xx[lrows[r]]; 785 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 786 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 787 } 788 /* Must zero l->B before l->A because the (diag) case below may put values into l->B*/ 789 ierr = MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 790 if (A->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 791 PetscBool cong; 792 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 793 if (cong) A->congruentlayouts = 1; 794 else A->congruentlayouts = 0; 795 } 796 if ((diag != 0.0) && A->congruentlayouts) { 797 ierr = MatZeroRows(mat->A, len, lrows, diag, NULL, NULL);CHKERRQ(ierr); 798 } else if (diag != 0.0) { 799 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 800 if (((Mat_SeqAIJ *) mat->A->data)->nonew) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "MatZeroRows() on rectangular matrices cannot be used with the Mat options\nMAT_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); 801 for (r = 0; r < len; ++r) { 802 const PetscInt row = lrows[r] + A->rmap->rstart; 803 ierr = MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES);CHKERRQ(ierr); 804 } 805 ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 806 ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 807 } else { 808 ierr = MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL);CHKERRQ(ierr); 809 } 810 ierr = PetscFree(lrows);CHKERRQ(ierr); 811 812 /* only change matrix nonzero state if pattern was allowed to be changed */ 813 if (!((Mat_SeqAIJ*)(mat->A->data))->keepnonzeropattern) { 814 PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate; 815 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 816 } 817 PetscFunctionReturn(0); 818 } 819 820 PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A,PetscInt N,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 821 { 822 Mat_MPIAIJ *l = (Mat_MPIAIJ*)A->data; 823 PetscErrorCode ierr; 824 PetscMPIInt n = A->rmap->n; 825 PetscInt i,j,r,m,p = 0,len = 0; 826 PetscInt *lrows,*owners = A->rmap->range; 827 PetscSFNode *rrows; 828 PetscSF sf; 829 const PetscScalar *xx; 830 PetscScalar *bb,*mask; 831 Vec xmask,lmask; 832 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)l->B->data; 833 const PetscInt *aj, *ii,*ridx; 834 PetscScalar *aa; 835 836 PetscFunctionBegin; 837 /* Create SF where leaves are input rows and roots are owned rows */ 838 ierr = PetscMalloc1(n, &lrows);CHKERRQ(ierr); 839 for (r = 0; r < n; ++r) lrows[r] = -1; 840 ierr = PetscMalloc1(N, &rrows);CHKERRQ(ierr); 841 for (r = 0; r < N; ++r) { 842 const PetscInt idx = rows[r]; 843 if (idx < 0 || A->rmap->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D out of range [0,%D)",idx,A->rmap->N); 844 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this row too */ 845 ierr = PetscLayoutFindOwner(A->rmap,idx,&p);CHKERRQ(ierr); 846 } 847 rrows[r].rank = p; 848 rrows[r].index = rows[r] - owners[p]; 849 } 850 ierr = PetscSFCreate(PetscObjectComm((PetscObject) A), &sf);CHKERRQ(ierr); 851 ierr = PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER);CHKERRQ(ierr); 852 /* Collect flags for rows to be zeroed */ 853 ierr = PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 854 ierr = PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *) rows, lrows, MPI_LOR);CHKERRQ(ierr); 855 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 856 /* Compress and put in row numbers */ 857 for (r = 0; r < n; ++r) if (lrows[r] >= 0) lrows[len++] = r; 858 /* zero diagonal part of matrix */ 859 ierr = MatZeroRowsColumns(l->A,len,lrows,diag,x,b);CHKERRQ(ierr); 860 /* handle off diagonal part of matrix */ 861 ierr = MatCreateVecs(A,&xmask,NULL);CHKERRQ(ierr); 862 ierr = VecDuplicate(l->lvec,&lmask);CHKERRQ(ierr); 863 ierr = VecGetArray(xmask,&bb);CHKERRQ(ierr); 864 for (i=0; i<len; i++) bb[lrows[i]] = 1; 865 ierr = VecRestoreArray(xmask,&bb);CHKERRQ(ierr); 866 ierr = VecScatterBegin(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 867 ierr = VecScatterEnd(l->Mvctx,xmask,lmask,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 868 ierr = VecDestroy(&xmask);CHKERRQ(ierr); 869 if (x) { 870 ierr = VecScatterBegin(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 871 ierr = VecScatterEnd(l->Mvctx,x,l->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 872 ierr = VecGetArrayRead(l->lvec,&xx);CHKERRQ(ierr); 873 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 874 } 875 ierr = VecGetArray(lmask,&mask);CHKERRQ(ierr); 876 /* remove zeroed rows of off diagonal matrix */ 877 ii = aij->i; 878 for (i=0; i<len; i++) { 879 ierr = PetscMemzero(aij->a + ii[lrows[i]],(ii[lrows[i]+1] - ii[lrows[i]])*sizeof(PetscScalar));CHKERRQ(ierr); 880 } 881 /* loop over all elements of off process part of matrix zeroing removed columns*/ 882 if (aij->compressedrow.use) { 883 m = aij->compressedrow.nrows; 884 ii = aij->compressedrow.i; 885 ridx = aij->compressedrow.rindex; 886 for (i=0; i<m; i++) { 887 n = ii[i+1] - ii[i]; 888 aj = aij->j + ii[i]; 889 aa = aij->a + ii[i]; 890 891 for (j=0; j<n; j++) { 892 if (PetscAbsScalar(mask[*aj])) { 893 if (b) bb[*ridx] -= *aa*xx[*aj]; 894 *aa = 0.0; 895 } 896 aa++; 897 aj++; 898 } 899 ridx++; 900 } 901 } else { /* do not use compressed row format */ 902 m = l->B->rmap->n; 903 for (i=0; i<m; i++) { 904 n = ii[i+1] - ii[i]; 905 aj = aij->j + ii[i]; 906 aa = aij->a + ii[i]; 907 for (j=0; j<n; j++) { 908 if (PetscAbsScalar(mask[*aj])) { 909 if (b) bb[i] -= *aa*xx[*aj]; 910 *aa = 0.0; 911 } 912 aa++; 913 aj++; 914 } 915 } 916 } 917 if (x) { 918 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 919 ierr = VecRestoreArrayRead(l->lvec,&xx);CHKERRQ(ierr); 920 } 921 ierr = VecRestoreArray(lmask,&mask);CHKERRQ(ierr); 922 ierr = VecDestroy(&lmask);CHKERRQ(ierr); 923 ierr = PetscFree(lrows);CHKERRQ(ierr); 924 925 /* only change matrix nonzero state if pattern was allowed to be changed */ 926 if (!((Mat_SeqAIJ*)(l->A->data))->keepnonzeropattern) { 927 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 928 ierr = MPIU_Allreduce(&state,&A->nonzerostate,1,MPIU_INT64,MPI_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 929 } 930 PetscFunctionReturn(0); 931 } 932 933 PetscErrorCode MatMult_MPIAIJ(Mat A,Vec xx,Vec yy) 934 { 935 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 936 PetscErrorCode ierr; 937 PetscInt nt; 938 939 PetscFunctionBegin; 940 ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); 941 if (nt != A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Incompatible partition of A (%D) and xx (%D)",A->cmap->n,nt); 942 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 943 ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); 944 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 945 ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); 946 PetscFunctionReturn(0); 947 } 948 949 PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A,Vec bb,Vec xx) 950 { 951 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 952 PetscErrorCode ierr; 953 954 PetscFunctionBegin; 955 ierr = MatMultDiagonalBlock(a->A,bb,xx);CHKERRQ(ierr); 956 PetscFunctionReturn(0); 957 } 958 959 PetscErrorCode MatMultAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 960 { 961 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 962 PetscErrorCode ierr; 963 964 PetscFunctionBegin; 965 ierr = VecScatterBegin(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 966 ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 967 ierr = VecScatterEnd(a->Mvctx,xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 968 ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); 969 PetscFunctionReturn(0); 970 } 971 972 PetscErrorCode MatMultTranspose_MPIAIJ(Mat A,Vec xx,Vec yy) 973 { 974 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 975 PetscErrorCode ierr; 976 PetscBool merged; 977 978 PetscFunctionBegin; 979 ierr = VecScatterGetMerged(a->Mvctx,&merged);CHKERRQ(ierr); 980 /* do nondiagonal part */ 981 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 982 if (!merged) { 983 /* send it on its way */ 984 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 985 /* do local part */ 986 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 987 /* receive remote parts: note this assumes the values are not actually */ 988 /* added in yy until the next line, */ 989 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 990 } else { 991 /* do local part */ 992 ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); 993 /* send it on its way */ 994 ierr = VecScatterBegin(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 995 /* values actually were received in the Begin() but we need to call this nop */ 996 ierr = VecScatterEnd(a->Mvctx,a->lvec,yy,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 997 } 998 PetscFunctionReturn(0); 999 } 1000 1001 PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat,Mat Bmat,PetscReal tol,PetscBool *f) 1002 { 1003 MPI_Comm comm; 1004 Mat_MPIAIJ *Aij = (Mat_MPIAIJ*) Amat->data, *Bij; 1005 Mat Adia = Aij->A, Bdia, Aoff,Boff,*Aoffs,*Boffs; 1006 IS Me,Notme; 1007 PetscErrorCode ierr; 1008 PetscInt M,N,first,last,*notme,i; 1009 PetscMPIInt size; 1010 1011 PetscFunctionBegin; 1012 /* Easy test: symmetric diagonal block */ 1013 Bij = (Mat_MPIAIJ*) Bmat->data; Bdia = Bij->A; 1014 ierr = MatIsTranspose(Adia,Bdia,tol,f);CHKERRQ(ierr); 1015 if (!*f) PetscFunctionReturn(0); 1016 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1017 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1018 if (size == 1) PetscFunctionReturn(0); 1019 1020 /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */ 1021 ierr = MatGetSize(Amat,&M,&N);CHKERRQ(ierr); 1022 ierr = MatGetOwnershipRange(Amat,&first,&last);CHKERRQ(ierr); 1023 ierr = PetscMalloc1(N-last+first,¬me);CHKERRQ(ierr); 1024 for (i=0; i<first; i++) notme[i] = i; 1025 for (i=last; i<M; i++) notme[i-last+first] = i; 1026 ierr = ISCreateGeneral(MPI_COMM_SELF,N-last+first,notme,PETSC_COPY_VALUES,&Notme);CHKERRQ(ierr); 1027 ierr = ISCreateStride(MPI_COMM_SELF,last-first,first,1,&Me);CHKERRQ(ierr); 1028 ierr = MatCreateSubMatrices(Amat,1,&Me,&Notme,MAT_INITIAL_MATRIX,&Aoffs);CHKERRQ(ierr); 1029 Aoff = Aoffs[0]; 1030 ierr = MatCreateSubMatrices(Bmat,1,&Notme,&Me,MAT_INITIAL_MATRIX,&Boffs);CHKERRQ(ierr); 1031 Boff = Boffs[0]; 1032 ierr = MatIsTranspose(Aoff,Boff,tol,f);CHKERRQ(ierr); 1033 ierr = MatDestroyMatrices(1,&Aoffs);CHKERRQ(ierr); 1034 ierr = MatDestroyMatrices(1,&Boffs);CHKERRQ(ierr); 1035 ierr = ISDestroy(&Me);CHKERRQ(ierr); 1036 ierr = ISDestroy(&Notme);CHKERRQ(ierr); 1037 ierr = PetscFree(notme);CHKERRQ(ierr); 1038 PetscFunctionReturn(0); 1039 } 1040 1041 PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A,Vec xx,Vec yy,Vec zz) 1042 { 1043 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1044 PetscErrorCode ierr; 1045 1046 PetscFunctionBegin; 1047 /* do nondiagonal part */ 1048 ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); 1049 /* send it on its way */ 1050 ierr = VecScatterBegin(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1051 /* do local part */ 1052 ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); 1053 /* receive remote parts */ 1054 ierr = VecScatterEnd(a->Mvctx,a->lvec,zz,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1055 PetscFunctionReturn(0); 1056 } 1057 1058 /* 1059 This only works correctly for square matrices where the subblock A->A is the 1060 diagonal block 1061 */ 1062 PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A,Vec v) 1063 { 1064 PetscErrorCode ierr; 1065 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1066 1067 PetscFunctionBegin; 1068 if (A->rmap->N != A->cmap->N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); 1069 if (A->rmap->rstart != A->cmap->rstart || A->rmap->rend != A->cmap->rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"row partition must equal col partition"); 1070 ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); 1071 PetscFunctionReturn(0); 1072 } 1073 1074 PetscErrorCode MatScale_MPIAIJ(Mat A,PetscScalar aa) 1075 { 1076 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1077 PetscErrorCode ierr; 1078 1079 PetscFunctionBegin; 1080 ierr = MatScale(a->A,aa);CHKERRQ(ierr); 1081 ierr = MatScale(a->B,aa);CHKERRQ(ierr); 1082 PetscFunctionReturn(0); 1083 } 1084 1085 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 1086 { 1087 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1088 PetscErrorCode ierr; 1089 1090 PetscFunctionBegin; 1091 #if defined(PETSC_USE_LOG) 1092 PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D",mat->rmap->N,mat->cmap->N); 1093 #endif 1094 ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); 1095 ierr = VecDestroy(&aij->diag);CHKERRQ(ierr); 1096 ierr = MatDestroy(&aij->A);CHKERRQ(ierr); 1097 ierr = MatDestroy(&aij->B);CHKERRQ(ierr); 1098 #if defined(PETSC_USE_CTABLE) 1099 ierr = PetscTableDestroy(&aij->colmap);CHKERRQ(ierr); 1100 #else 1101 ierr = PetscFree(aij->colmap);CHKERRQ(ierr); 1102 #endif 1103 ierr = PetscFree(aij->garray);CHKERRQ(ierr); 1104 ierr = VecDestroy(&aij->lvec);CHKERRQ(ierr); 1105 ierr = VecScatterDestroy(&aij->Mvctx);CHKERRQ(ierr); 1106 ierr = PetscFree2(aij->rowvalues,aij->rowindices);CHKERRQ(ierr); 1107 ierr = PetscFree(aij->ld);CHKERRQ(ierr); 1108 ierr = PetscFree(mat->data);CHKERRQ(ierr); 1109 1110 ierr = PetscObjectChangeTypeName((PetscObject)mat,0);CHKERRQ(ierr); 1111 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatStoreValues_C",NULL);CHKERRQ(ierr); 1112 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 1113 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatIsTranspose_C",NULL);CHKERRQ(ierr); 1114 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 1115 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMPIAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 1116 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatDiagonalScaleLocal_C",NULL);CHKERRQ(ierr); 1117 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_mpisbaij_C",NULL);CHKERRQ(ierr); 1118 #if defined(PETSC_HAVE_ELEMENTAL) 1119 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_elemental_C",NULL);CHKERRQ(ierr); 1120 #endif 1121 #if defined(PETSC_HAVE_HYPRE) 1122 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatConvert_mpiaij_hypre_C",NULL);CHKERRQ(ierr); 1123 ierr = PetscObjectComposeFunction((PetscObject)mat,"MatMatMatMult_transpose_mpiaij_mpiaij_C",NULL);CHKERRQ(ierr); 1124 #endif 1125 PetscFunctionReturn(0); 1126 } 1127 1128 PetscErrorCode MatView_MPIAIJ_Binary(Mat mat,PetscViewer viewer) 1129 { 1130 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1131 Mat_SeqAIJ *A = (Mat_SeqAIJ*)aij->A->data; 1132 Mat_SeqAIJ *B = (Mat_SeqAIJ*)aij->B->data; 1133 PetscErrorCode ierr; 1134 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 1135 int fd; 1136 PetscInt nz,header[4],*row_lengths,*range=0,rlen,i; 1137 PetscInt nzmax,*column_indices,j,k,col,*garray = aij->garray,cnt,cstart = mat->cmap->rstart,rnz = 0; 1138 PetscScalar *column_values; 1139 PetscInt message_count,flowcontrolcount; 1140 FILE *file; 1141 1142 PetscFunctionBegin; 1143 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1144 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&size);CHKERRQ(ierr); 1145 nz = A->nz + B->nz; 1146 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 1147 if (!rank) { 1148 header[0] = MAT_FILE_CLASSID; 1149 header[1] = mat->rmap->N; 1150 header[2] = mat->cmap->N; 1151 1152 ierr = MPI_Reduce(&nz,&header[3],1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1153 ierr = PetscBinaryWrite(fd,header,4,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1154 /* get largest number of rows any processor has */ 1155 rlen = mat->rmap->n; 1156 range = mat->rmap->range; 1157 for (i=1; i<size; i++) rlen = PetscMax(rlen,range[i+1] - range[i]); 1158 } else { 1159 ierr = MPI_Reduce(&nz,0,1,MPIU_INT,MPI_SUM,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1160 rlen = mat->rmap->n; 1161 } 1162 1163 /* load up the local row counts */ 1164 ierr = PetscMalloc1(rlen+1,&row_lengths);CHKERRQ(ierr); 1165 for (i=0; i<mat->rmap->n; i++) row_lengths[i] = A->i[i+1] - A->i[i] + B->i[i+1] - B->i[i]; 1166 1167 /* store the row lengths to the file */ 1168 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1169 if (!rank) { 1170 ierr = PetscBinaryWrite(fd,row_lengths,mat->rmap->n,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1171 for (i=1; i<size; i++) { 1172 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1173 rlen = range[i+1] - range[i]; 1174 ierr = MPIULong_Recv(row_lengths,rlen,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1175 ierr = PetscBinaryWrite(fd,row_lengths,rlen,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1176 } 1177 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1178 } else { 1179 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1180 ierr = MPIULong_Send(row_lengths,mat->rmap->n,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1181 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1182 } 1183 ierr = PetscFree(row_lengths);CHKERRQ(ierr); 1184 1185 /* load up the local column indices */ 1186 nzmax = nz; /* th processor needs space a largest processor needs */ 1187 ierr = MPI_Reduce(&nz,&nzmax,1,MPIU_INT,MPI_MAX,0,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1188 ierr = PetscMalloc1(nzmax+1,&column_indices);CHKERRQ(ierr); 1189 cnt = 0; 1190 for (i=0; i<mat->rmap->n; i++) { 1191 for (j=B->i[i]; j<B->i[i+1]; j++) { 1192 if ((col = garray[B->j[j]]) > cstart) break; 1193 column_indices[cnt++] = col; 1194 } 1195 for (k=A->i[i]; k<A->i[i+1]; k++) column_indices[cnt++] = A->j[k] + cstart; 1196 for (; j<B->i[i+1]; j++) column_indices[cnt++] = garray[B->j[j]]; 1197 } 1198 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1199 1200 /* store the column indices to the file */ 1201 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1202 if (!rank) { 1203 MPI_Status status; 1204 ierr = PetscBinaryWrite(fd,column_indices,nz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1205 for (i=1; i<size; i++) { 1206 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1207 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1208 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1209 ierr = MPIULong_Recv(column_indices,rnz,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1210 ierr = PetscBinaryWrite(fd,column_indices,rnz,PETSC_INT,PETSC_TRUE);CHKERRQ(ierr); 1211 } 1212 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1213 } else { 1214 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1215 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1216 ierr = MPIULong_Send(column_indices,nz,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1217 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1218 } 1219 ierr = PetscFree(column_indices);CHKERRQ(ierr); 1220 1221 /* load up the local column values */ 1222 ierr = PetscMalloc1(nzmax+1,&column_values);CHKERRQ(ierr); 1223 cnt = 0; 1224 for (i=0; i<mat->rmap->n; i++) { 1225 for (j=B->i[i]; j<B->i[i+1]; j++) { 1226 if (garray[B->j[j]] > cstart) break; 1227 column_values[cnt++] = B->a[j]; 1228 } 1229 for (k=A->i[i]; k<A->i[i+1]; k++) column_values[cnt++] = A->a[k]; 1230 for (; j<B->i[i+1]; j++) column_values[cnt++] = B->a[j]; 1231 } 1232 if (cnt != A->nz + B->nz) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Internal PETSc error: cnt = %D nz = %D",cnt,A->nz+B->nz); 1233 1234 /* store the column values to the file */ 1235 ierr = PetscViewerFlowControlStart(viewer,&message_count,&flowcontrolcount);CHKERRQ(ierr); 1236 if (!rank) { 1237 MPI_Status status; 1238 ierr = PetscBinaryWrite(fd,column_values,nz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1239 for (i=1; i<size; i++) { 1240 ierr = PetscViewerFlowControlStepMaster(viewer,i,&message_count,flowcontrolcount);CHKERRQ(ierr); 1241 ierr = MPI_Recv(&rnz,1,MPIU_INT,i,tag,PetscObjectComm((PetscObject)mat),&status);CHKERRQ(ierr); 1242 if (rnz > nzmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_LIB,"Internal PETSc error: nz = %D nzmax = %D",nz,nzmax); 1243 ierr = MPIULong_Recv(column_values,rnz,MPIU_SCALAR,i,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1244 ierr = PetscBinaryWrite(fd,column_values,rnz,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr); 1245 } 1246 ierr = PetscViewerFlowControlEndMaster(viewer,&message_count);CHKERRQ(ierr); 1247 } else { 1248 ierr = PetscViewerFlowControlStepWorker(viewer,rank,&message_count);CHKERRQ(ierr); 1249 ierr = MPI_Send(&nz,1,MPIU_INT,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1250 ierr = MPIULong_Send(column_values,nz,MPIU_SCALAR,0,tag,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1251 ierr = PetscViewerFlowControlEndWorker(viewer,&message_count);CHKERRQ(ierr); 1252 } 1253 ierr = PetscFree(column_values);CHKERRQ(ierr); 1254 1255 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 1256 if (file) fprintf(file,"-matload_block_size %d\n",(int)PetscAbs(mat->rmap->bs)); 1257 PetscFunctionReturn(0); 1258 } 1259 1260 #include <petscdraw.h> 1261 PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) 1262 { 1263 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1264 PetscErrorCode ierr; 1265 PetscMPIInt rank = aij->rank,size = aij->size; 1266 PetscBool isdraw,iascii,isbinary; 1267 PetscViewer sviewer; 1268 PetscViewerFormat format; 1269 1270 PetscFunctionBegin; 1271 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1272 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1273 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1274 if (iascii) { 1275 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1276 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1277 MatInfo info; 1278 PetscBool inodes; 1279 1280 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)mat),&rank);CHKERRQ(ierr); 1281 ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); 1282 ierr = MatInodeGetInodeSizes(aij->A,NULL,(PetscInt**)&inodes,NULL);CHKERRQ(ierr); 1283 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 1284 if (!inodes) { 1285 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, not using I-node routines\n", 1286 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1287 } else { 1288 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %D nz %D nz alloced %D mem %D, using I-node routines\n", 1289 rank,mat->rmap->n,(PetscInt)info.nz_used,(PetscInt)info.nz_allocated,(PetscInt)info.memory);CHKERRQ(ierr); 1290 } 1291 ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); 1292 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1293 ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); 1294 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %D \n",rank,(PetscInt)info.nz_used);CHKERRQ(ierr); 1295 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1296 ierr = PetscViewerASCIIPopSynchronized(viewer);CHKERRQ(ierr); 1297 ierr = PetscViewerASCIIPrintf(viewer,"Information on VecScatter used in matrix-vector product: \n");CHKERRQ(ierr); 1298 ierr = VecScatterView(aij->Mvctx,viewer);CHKERRQ(ierr); 1299 PetscFunctionReturn(0); 1300 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1301 PetscInt inodecount,inodelimit,*inodes; 1302 ierr = MatInodeGetInodeSizes(aij->A,&inodecount,&inodes,&inodelimit);CHKERRQ(ierr); 1303 if (inodes) { 1304 ierr = PetscViewerASCIIPrintf(viewer,"using I-node (on process 0) routines: found %D nodes, limit used is %D\n",inodecount,inodelimit);CHKERRQ(ierr); 1305 } else { 1306 ierr = PetscViewerASCIIPrintf(viewer,"not using I-node (on process 0) routines\n");CHKERRQ(ierr); 1307 } 1308 PetscFunctionReturn(0); 1309 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1310 PetscFunctionReturn(0); 1311 } 1312 } else if (isbinary) { 1313 if (size == 1) { 1314 ierr = PetscObjectSetName((PetscObject)aij->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1315 ierr = MatView(aij->A,viewer);CHKERRQ(ierr); 1316 } else { 1317 ierr = MatView_MPIAIJ_Binary(mat,viewer);CHKERRQ(ierr); 1318 } 1319 PetscFunctionReturn(0); 1320 } else if (isdraw) { 1321 PetscDraw draw; 1322 PetscBool isnull; 1323 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 1324 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); 1325 if (isnull) PetscFunctionReturn(0); 1326 } 1327 1328 { 1329 /* assemble the entire matrix onto first processor. */ 1330 Mat A; 1331 Mat_SeqAIJ *Aloc; 1332 PetscInt M = mat->rmap->N,N = mat->cmap->N,m,*ai,*aj,row,*cols,i,*ct; 1333 MatScalar *a; 1334 1335 ierr = MatCreate(PetscObjectComm((PetscObject)mat),&A);CHKERRQ(ierr); 1336 if (!rank) { 1337 ierr = MatSetSizes(A,M,N,M,N);CHKERRQ(ierr); 1338 } else { 1339 ierr = MatSetSizes(A,0,0,M,N);CHKERRQ(ierr); 1340 } 1341 /* This is just a temporary matrix, so explicitly using MATMPIAIJ is probably best */ 1342 ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); 1343 ierr = MatMPIAIJSetPreallocation(A,0,NULL,0,NULL);CHKERRQ(ierr); 1344 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 1345 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)A);CHKERRQ(ierr); 1346 1347 /* copy over the A part */ 1348 Aloc = (Mat_SeqAIJ*)aij->A->data; 1349 m = aij->A->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1350 row = mat->rmap->rstart; 1351 for (i=0; i<ai[m]; i++) aj[i] += mat->cmap->rstart; 1352 for (i=0; i<m; i++) { 1353 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],aj,a,INSERT_VALUES);CHKERRQ(ierr); 1354 row++; 1355 a += ai[i+1]-ai[i]; aj += ai[i+1]-ai[i]; 1356 } 1357 aj = Aloc->j; 1358 for (i=0; i<ai[m]; i++) aj[i] -= mat->cmap->rstart; 1359 1360 /* copy over the B part */ 1361 Aloc = (Mat_SeqAIJ*)aij->B->data; 1362 m = aij->B->rmap->n; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; 1363 row = mat->rmap->rstart; 1364 ierr = PetscMalloc1(ai[m]+1,&cols);CHKERRQ(ierr); 1365 ct = cols; 1366 for (i=0; i<ai[m]; i++) cols[i] = aij->garray[aj[i]]; 1367 for (i=0; i<m; i++) { 1368 ierr = MatSetValues(A,1,&row,ai[i+1]-ai[i],cols,a,INSERT_VALUES);CHKERRQ(ierr); 1369 row++; 1370 a += ai[i+1]-ai[i]; cols += ai[i+1]-ai[i]; 1371 } 1372 ierr = PetscFree(ct);CHKERRQ(ierr); 1373 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1374 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1375 /* 1376 Everyone has to call to draw the matrix since the graphics waits are 1377 synchronized across all processors that share the PetscDraw object 1378 */ 1379 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1380 if (!rank) { 1381 ierr = PetscObjectSetName((PetscObject)((Mat_MPIAIJ*)(A->data))->A,((PetscObject)mat)->name);CHKERRQ(ierr); 1382 ierr = MatView_SeqAIJ(((Mat_MPIAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); 1383 } 1384 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1385 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1386 ierr = MatDestroy(&A);CHKERRQ(ierr); 1387 } 1388 PetscFunctionReturn(0); 1389 } 1390 1391 PetscErrorCode MatView_MPIAIJ(Mat mat,PetscViewer viewer) 1392 { 1393 PetscErrorCode ierr; 1394 PetscBool iascii,isdraw,issocket,isbinary; 1395 1396 PetscFunctionBegin; 1397 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 1398 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 1399 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 1400 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSOCKET,&issocket);CHKERRQ(ierr); 1401 if (iascii || isdraw || isbinary || issocket) { 1402 ierr = MatView_MPIAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); 1403 } 1404 PetscFunctionReturn(0); 1405 } 1406 1407 PetscErrorCode MatSOR_MPIAIJ(Mat matin,Vec bb,PetscReal omega,MatSORType flag,PetscReal fshift,PetscInt its,PetscInt lits,Vec xx) 1408 { 1409 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1410 PetscErrorCode ierr; 1411 Vec bb1 = 0; 1412 PetscBool hasop; 1413 1414 PetscFunctionBegin; 1415 if (flag == SOR_APPLY_UPPER) { 1416 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1417 PetscFunctionReturn(0); 1418 } 1419 1420 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) { 1421 ierr = VecDuplicate(bb,&bb1);CHKERRQ(ierr); 1422 } 1423 1424 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1425 if (flag & SOR_ZERO_INITIAL_GUESS) { 1426 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1427 its--; 1428 } 1429 1430 while (its--) { 1431 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1432 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1433 1434 /* update rhs: bb1 = bb - B*x */ 1435 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1436 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1437 1438 /* local sweep */ 1439 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_SYMMETRIC_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1440 } 1441 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1442 if (flag & SOR_ZERO_INITIAL_GUESS) { 1443 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1444 its--; 1445 } 1446 while (its--) { 1447 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1448 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1449 1450 /* update rhs: bb1 = bb - B*x */ 1451 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1452 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1453 1454 /* local sweep */ 1455 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_FORWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1456 } 1457 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1458 if (flag & SOR_ZERO_INITIAL_GUESS) { 1459 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,flag,fshift,lits,1,xx);CHKERRQ(ierr); 1460 its--; 1461 } 1462 while (its--) { 1463 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1464 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1465 1466 /* update rhs: bb1 = bb - B*x */ 1467 ierr = VecScale(mat->lvec,-1.0);CHKERRQ(ierr); 1468 ierr = (*mat->B->ops->multadd)(mat->B,mat->lvec,bb,bb1);CHKERRQ(ierr); 1469 1470 /* local sweep */ 1471 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,SOR_BACKWARD_SWEEP,fshift,lits,1,xx);CHKERRQ(ierr); 1472 } 1473 } else if (flag & SOR_EISENSTAT) { 1474 Vec xx1; 1475 1476 ierr = VecDuplicate(bb,&xx1);CHKERRQ(ierr); 1477 ierr = (*mat->A->ops->sor)(mat->A,bb,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP),fshift,lits,1,xx);CHKERRQ(ierr); 1478 1479 ierr = VecScatterBegin(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1480 ierr = VecScatterEnd(mat->Mvctx,xx,mat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1481 if (!mat->diag) { 1482 ierr = MatCreateVecs(matin,&mat->diag,NULL);CHKERRQ(ierr); 1483 ierr = MatGetDiagonal(matin,mat->diag);CHKERRQ(ierr); 1484 } 1485 ierr = MatHasOperation(matin,MATOP_MULT_DIAGONAL_BLOCK,&hasop);CHKERRQ(ierr); 1486 if (hasop) { 1487 ierr = MatMultDiagonalBlock(matin,xx,bb1);CHKERRQ(ierr); 1488 } else { 1489 ierr = VecPointwiseMult(bb1,mat->diag,xx);CHKERRQ(ierr); 1490 } 1491 ierr = VecAYPX(bb1,(omega-2.0)/omega,bb);CHKERRQ(ierr); 1492 1493 ierr = MatMultAdd(mat->B,mat->lvec,bb1,bb1);CHKERRQ(ierr); 1494 1495 /* local sweep */ 1496 ierr = (*mat->A->ops->sor)(mat->A,bb1,omega,(MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP),fshift,lits,1,xx1);CHKERRQ(ierr); 1497 ierr = VecAXPY(xx,1.0,xx1);CHKERRQ(ierr); 1498 ierr = VecDestroy(&xx1);CHKERRQ(ierr); 1499 } else SETERRQ(PetscObjectComm((PetscObject)matin),PETSC_ERR_SUP,"Parallel SOR not supported"); 1500 1501 ierr = VecDestroy(&bb1);CHKERRQ(ierr); 1502 1503 matin->factorerrortype = mat->A->factorerrortype; 1504 PetscFunctionReturn(0); 1505 } 1506 1507 PetscErrorCode MatPermute_MPIAIJ(Mat A,IS rowp,IS colp,Mat *B) 1508 { 1509 Mat aA,aB,Aperm; 1510 const PetscInt *rwant,*cwant,*gcols,*ai,*bi,*aj,*bj; 1511 PetscScalar *aa,*ba; 1512 PetscInt i,j,m,n,ng,anz,bnz,*dnnz,*onnz,*tdnnz,*tonnz,*rdest,*cdest,*work,*gcdest; 1513 PetscSF rowsf,sf; 1514 IS parcolp = NULL; 1515 PetscBool done; 1516 PetscErrorCode ierr; 1517 1518 PetscFunctionBegin; 1519 ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); 1520 ierr = ISGetIndices(rowp,&rwant);CHKERRQ(ierr); 1521 ierr = ISGetIndices(colp,&cwant);CHKERRQ(ierr); 1522 ierr = PetscMalloc3(PetscMax(m,n),&work,m,&rdest,n,&cdest);CHKERRQ(ierr); 1523 1524 /* Invert row permutation to find out where my rows should go */ 1525 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&rowsf);CHKERRQ(ierr); 1526 ierr = PetscSFSetGraphLayout(rowsf,A->rmap,A->rmap->n,NULL,PETSC_OWN_POINTER,rwant);CHKERRQ(ierr); 1527 ierr = PetscSFSetFromOptions(rowsf);CHKERRQ(ierr); 1528 for (i=0; i<m; i++) work[i] = A->rmap->rstart + i; 1529 ierr = PetscSFReduceBegin(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1530 ierr = PetscSFReduceEnd(rowsf,MPIU_INT,work,rdest,MPIU_REPLACE);CHKERRQ(ierr); 1531 1532 /* Invert column permutation to find out where my columns should go */ 1533 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1534 ierr = PetscSFSetGraphLayout(sf,A->cmap,A->cmap->n,NULL,PETSC_OWN_POINTER,cwant);CHKERRQ(ierr); 1535 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1536 for (i=0; i<n; i++) work[i] = A->cmap->rstart + i; 1537 ierr = PetscSFReduceBegin(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1538 ierr = PetscSFReduceEnd(sf,MPIU_INT,work,cdest,MPIU_REPLACE);CHKERRQ(ierr); 1539 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1540 1541 ierr = ISRestoreIndices(rowp,&rwant);CHKERRQ(ierr); 1542 ierr = ISRestoreIndices(colp,&cwant);CHKERRQ(ierr); 1543 ierr = MatMPIAIJGetSeqAIJ(A,&aA,&aB,&gcols);CHKERRQ(ierr); 1544 1545 /* Find out where my gcols should go */ 1546 ierr = MatGetSize(aB,NULL,&ng);CHKERRQ(ierr); 1547 ierr = PetscMalloc1(ng,&gcdest);CHKERRQ(ierr); 1548 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1549 ierr = PetscSFSetGraphLayout(sf,A->cmap,ng,NULL,PETSC_OWN_POINTER,gcols);CHKERRQ(ierr); 1550 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1551 ierr = PetscSFBcastBegin(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1552 ierr = PetscSFBcastEnd(sf,MPIU_INT,cdest,gcdest);CHKERRQ(ierr); 1553 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1554 1555 ierr = PetscCalloc4(m,&dnnz,m,&onnz,m,&tdnnz,m,&tonnz);CHKERRQ(ierr); 1556 ierr = MatGetRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1557 ierr = MatGetRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1558 for (i=0; i<m; i++) { 1559 PetscInt row = rdest[i],rowner; 1560 ierr = PetscLayoutFindOwner(A->rmap,row,&rowner);CHKERRQ(ierr); 1561 for (j=ai[i]; j<ai[i+1]; j++) { 1562 PetscInt cowner,col = cdest[aj[j]]; 1563 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); /* Could build an index for the columns to eliminate this search */ 1564 if (rowner == cowner) dnnz[i]++; 1565 else onnz[i]++; 1566 } 1567 for (j=bi[i]; j<bi[i+1]; j++) { 1568 PetscInt cowner,col = gcdest[bj[j]]; 1569 ierr = PetscLayoutFindOwner(A->cmap,col,&cowner);CHKERRQ(ierr); 1570 if (rowner == cowner) dnnz[i]++; 1571 else onnz[i]++; 1572 } 1573 } 1574 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1575 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,dnnz,tdnnz);CHKERRQ(ierr); 1576 ierr = PetscSFBcastBegin(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1577 ierr = PetscSFBcastEnd(rowsf,MPIU_INT,onnz,tonnz);CHKERRQ(ierr); 1578 ierr = PetscSFDestroy(&rowsf);CHKERRQ(ierr); 1579 1580 ierr = MatCreateAIJ(PetscObjectComm((PetscObject)A),A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N,0,tdnnz,0,tonnz,&Aperm);CHKERRQ(ierr); 1581 ierr = MatSeqAIJGetArray(aA,&aa);CHKERRQ(ierr); 1582 ierr = MatSeqAIJGetArray(aB,&ba);CHKERRQ(ierr); 1583 for (i=0; i<m; i++) { 1584 PetscInt *acols = dnnz,*bcols = onnz; /* Repurpose now-unneeded arrays */ 1585 PetscInt j0,rowlen; 1586 rowlen = ai[i+1] - ai[i]; 1587 for (j0=j=0; j<rowlen; j0=j) { /* rowlen could be larger than number of rows m, so sum in batches */ 1588 for ( ; j<PetscMin(rowlen,j0+m); j++) acols[j-j0] = cdest[aj[ai[i]+j]]; 1589 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,acols,aa+ai[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1590 } 1591 rowlen = bi[i+1] - bi[i]; 1592 for (j0=j=0; j<rowlen; j0=j) { 1593 for ( ; j<PetscMin(rowlen,j0+m); j++) bcols[j-j0] = gcdest[bj[bi[i]+j]]; 1594 ierr = MatSetValues(Aperm,1,&rdest[i],j-j0,bcols,ba+bi[i]+j0,INSERT_VALUES);CHKERRQ(ierr); 1595 } 1596 } 1597 ierr = MatAssemblyBegin(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1598 ierr = MatAssemblyEnd(Aperm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1599 ierr = MatRestoreRowIJ(aA,0,PETSC_FALSE,PETSC_FALSE,&anz,&ai,&aj,&done);CHKERRQ(ierr); 1600 ierr = MatRestoreRowIJ(aB,0,PETSC_FALSE,PETSC_FALSE,&bnz,&bi,&bj,&done);CHKERRQ(ierr); 1601 ierr = MatSeqAIJRestoreArray(aA,&aa);CHKERRQ(ierr); 1602 ierr = MatSeqAIJRestoreArray(aB,&ba);CHKERRQ(ierr); 1603 ierr = PetscFree4(dnnz,onnz,tdnnz,tonnz);CHKERRQ(ierr); 1604 ierr = PetscFree3(work,rdest,cdest);CHKERRQ(ierr); 1605 ierr = PetscFree(gcdest);CHKERRQ(ierr); 1606 if (parcolp) {ierr = ISDestroy(&colp);CHKERRQ(ierr);} 1607 *B = Aperm; 1608 PetscFunctionReturn(0); 1609 } 1610 1611 PetscErrorCode MatGetGhosts_MPIAIJ(Mat mat,PetscInt *nghosts,const PetscInt *ghosts[]) 1612 { 1613 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1614 PetscErrorCode ierr; 1615 1616 PetscFunctionBegin; 1617 ierr = MatGetSize(aij->B,NULL,nghosts);CHKERRQ(ierr); 1618 if (ghosts) *ghosts = aij->garray; 1619 PetscFunctionReturn(0); 1620 } 1621 1622 PetscErrorCode MatGetInfo_MPIAIJ(Mat matin,MatInfoType flag,MatInfo *info) 1623 { 1624 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1625 Mat A = mat->A,B = mat->B; 1626 PetscErrorCode ierr; 1627 PetscReal isend[5],irecv[5]; 1628 1629 PetscFunctionBegin; 1630 info->block_size = 1.0; 1631 ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); 1632 1633 isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; 1634 isend[3] = info->memory; isend[4] = info->mallocs; 1635 1636 ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); 1637 1638 isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; 1639 isend[3] += info->memory; isend[4] += info->mallocs; 1640 if (flag == MAT_LOCAL) { 1641 info->nz_used = isend[0]; 1642 info->nz_allocated = isend[1]; 1643 info->nz_unneeded = isend[2]; 1644 info->memory = isend[3]; 1645 info->mallocs = isend[4]; 1646 } else if (flag == MAT_GLOBAL_MAX) { 1647 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1648 1649 info->nz_used = irecv[0]; 1650 info->nz_allocated = irecv[1]; 1651 info->nz_unneeded = irecv[2]; 1652 info->memory = irecv[3]; 1653 info->mallocs = irecv[4]; 1654 } else if (flag == MAT_GLOBAL_SUM) { 1655 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)matin));CHKERRQ(ierr); 1656 1657 info->nz_used = irecv[0]; 1658 info->nz_allocated = irecv[1]; 1659 info->nz_unneeded = irecv[2]; 1660 info->memory = irecv[3]; 1661 info->mallocs = irecv[4]; 1662 } 1663 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1664 info->fill_ratio_needed = 0; 1665 info->factor_mallocs = 0; 1666 PetscFunctionReturn(0); 1667 } 1668 1669 PetscErrorCode MatSetOption_MPIAIJ(Mat A,MatOption op,PetscBool flg) 1670 { 1671 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1672 PetscErrorCode ierr; 1673 1674 PetscFunctionBegin; 1675 switch (op) { 1676 case MAT_NEW_NONZERO_LOCATIONS: 1677 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1678 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1679 case MAT_KEEP_NONZERO_PATTERN: 1680 case MAT_NEW_NONZERO_LOCATION_ERR: 1681 case MAT_USE_INODES: 1682 case MAT_IGNORE_ZERO_ENTRIES: 1683 MatCheckPreallocated(A,1); 1684 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1685 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1686 break; 1687 case MAT_ROW_ORIENTED: 1688 MatCheckPreallocated(A,1); 1689 a->roworiented = flg; 1690 1691 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1692 ierr = MatSetOption(a->B,op,flg);CHKERRQ(ierr); 1693 break; 1694 case MAT_NEW_DIAGONALS: 1695 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 1696 break; 1697 case MAT_IGNORE_OFF_PROC_ENTRIES: 1698 a->donotstash = flg; 1699 break; 1700 case MAT_SPD: 1701 A->spd_set = PETSC_TRUE; 1702 A->spd = flg; 1703 if (flg) { 1704 A->symmetric = PETSC_TRUE; 1705 A->structurally_symmetric = PETSC_TRUE; 1706 A->symmetric_set = PETSC_TRUE; 1707 A->structurally_symmetric_set = PETSC_TRUE; 1708 } 1709 break; 1710 case MAT_SYMMETRIC: 1711 MatCheckPreallocated(A,1); 1712 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1713 break; 1714 case MAT_STRUCTURALLY_SYMMETRIC: 1715 MatCheckPreallocated(A,1); 1716 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1717 break; 1718 case MAT_HERMITIAN: 1719 MatCheckPreallocated(A,1); 1720 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1721 break; 1722 case MAT_SYMMETRY_ETERNAL: 1723 MatCheckPreallocated(A,1); 1724 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 1725 break; 1726 case MAT_SUBMAT_SINGLEIS: 1727 A->submat_singleis = flg; 1728 break; 1729 default: 1730 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 1731 } 1732 PetscFunctionReturn(0); 1733 } 1734 1735 PetscErrorCode MatGetRow_MPIAIJ(Mat matin,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1736 { 1737 Mat_MPIAIJ *mat = (Mat_MPIAIJ*)matin->data; 1738 PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; 1739 PetscErrorCode ierr; 1740 PetscInt i,*cworkA,*cworkB,**pcA,**pcB,cstart = matin->cmap->rstart; 1741 PetscInt nztot,nzA,nzB,lrow,rstart = matin->rmap->rstart,rend = matin->rmap->rend; 1742 PetscInt *cmap,*idx_p; 1743 1744 PetscFunctionBegin; 1745 if (mat->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Already active"); 1746 mat->getrowactive = PETSC_TRUE; 1747 1748 if (!mat->rowvalues && (idx || v)) { 1749 /* 1750 allocate enough space to hold information from the longest row. 1751 */ 1752 Mat_SeqAIJ *Aa = (Mat_SeqAIJ*)mat->A->data,*Ba = (Mat_SeqAIJ*)mat->B->data; 1753 PetscInt max = 1,tmp; 1754 for (i=0; i<matin->rmap->n; i++) { 1755 tmp = Aa->i[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; 1756 if (max < tmp) max = tmp; 1757 } 1758 ierr = PetscMalloc2(max,&mat->rowvalues,max,&mat->rowindices);CHKERRQ(ierr); 1759 } 1760 1761 if (row < rstart || row >= rend) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Only local rows"); 1762 lrow = row - rstart; 1763 1764 pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; 1765 if (!v) {pvA = 0; pvB = 0;} 1766 if (!idx) {pcA = 0; if (!v) pcB = 0;} 1767 ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1768 ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1769 nztot = nzA + nzB; 1770 1771 cmap = mat->garray; 1772 if (v || idx) { 1773 if (nztot) { 1774 /* Sort by increasing column numbers, assuming A and B already sorted */ 1775 PetscInt imark = -1; 1776 if (v) { 1777 *v = v_p = mat->rowvalues; 1778 for (i=0; i<nzB; i++) { 1779 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1780 else break; 1781 } 1782 imark = i; 1783 for (i=0; i<nzA; i++) v_p[imark+i] = vworkA[i]; 1784 for (i=imark; i<nzB; i++) v_p[nzA+i] = vworkB[i]; 1785 } 1786 if (idx) { 1787 *idx = idx_p = mat->rowindices; 1788 if (imark > -1) { 1789 for (i=0; i<imark; i++) { 1790 idx_p[i] = cmap[cworkB[i]]; 1791 } 1792 } else { 1793 for (i=0; i<nzB; i++) { 1794 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1795 else break; 1796 } 1797 imark = i; 1798 } 1799 for (i=0; i<nzA; i++) idx_p[imark+i] = cstart + cworkA[i]; 1800 for (i=imark; i<nzB; i++) idx_p[nzA+i] = cmap[cworkB[i]]; 1801 } 1802 } else { 1803 if (idx) *idx = 0; 1804 if (v) *v = 0; 1805 } 1806 } 1807 *nz = nztot; 1808 ierr = (*mat->A->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); 1809 ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); 1810 PetscFunctionReturn(0); 1811 } 1812 1813 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 1814 { 1815 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1816 1817 PetscFunctionBegin; 1818 if (!aij->getrowactive) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatGetRow() must be called first"); 1819 aij->getrowactive = PETSC_FALSE; 1820 PetscFunctionReturn(0); 1821 } 1822 1823 PetscErrorCode MatNorm_MPIAIJ(Mat mat,NormType type,PetscReal *norm) 1824 { 1825 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1826 Mat_SeqAIJ *amat = (Mat_SeqAIJ*)aij->A->data,*bmat = (Mat_SeqAIJ*)aij->B->data; 1827 PetscErrorCode ierr; 1828 PetscInt i,j,cstart = mat->cmap->rstart; 1829 PetscReal sum = 0.0; 1830 MatScalar *v; 1831 1832 PetscFunctionBegin; 1833 if (aij->size == 1) { 1834 ierr = MatNorm(aij->A,type,norm);CHKERRQ(ierr); 1835 } else { 1836 if (type == NORM_FROBENIUS) { 1837 v = amat->a; 1838 for (i=0; i<amat->nz; i++) { 1839 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1840 } 1841 v = bmat->a; 1842 for (i=0; i<bmat->nz; i++) { 1843 sum += PetscRealPart(PetscConj(*v)*(*v)); v++; 1844 } 1845 ierr = MPIU_Allreduce(&sum,norm,1,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1846 *norm = PetscSqrtReal(*norm); 1847 ierr = PetscLogFlops(2*amat->nz+2*bmat->nz);CHKERRQ(ierr); 1848 } else if (type == NORM_1) { /* max column norm */ 1849 PetscReal *tmp,*tmp2; 1850 PetscInt *jj,*garray = aij->garray; 1851 ierr = PetscCalloc1(mat->cmap->N+1,&tmp);CHKERRQ(ierr); 1852 ierr = PetscMalloc1(mat->cmap->N+1,&tmp2);CHKERRQ(ierr); 1853 *norm = 0.0; 1854 v = amat->a; jj = amat->j; 1855 for (j=0; j<amat->nz; j++) { 1856 tmp[cstart + *jj++] += PetscAbsScalar(*v); v++; 1857 } 1858 v = bmat->a; jj = bmat->j; 1859 for (j=0; j<bmat->nz; j++) { 1860 tmp[garray[*jj++]] += PetscAbsScalar(*v); v++; 1861 } 1862 ierr = MPIU_Allreduce(tmp,tmp2,mat->cmap->N,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1863 for (j=0; j<mat->cmap->N; j++) { 1864 if (tmp2[j] > *norm) *norm = tmp2[j]; 1865 } 1866 ierr = PetscFree(tmp);CHKERRQ(ierr); 1867 ierr = PetscFree(tmp2);CHKERRQ(ierr); 1868 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1869 } else if (type == NORM_INFINITY) { /* max row norm */ 1870 PetscReal ntemp = 0.0; 1871 for (j=0; j<aij->A->rmap->n; j++) { 1872 v = amat->a + amat->i[j]; 1873 sum = 0.0; 1874 for (i=0; i<amat->i[j+1]-amat->i[j]; i++) { 1875 sum += PetscAbsScalar(*v); v++; 1876 } 1877 v = bmat->a + bmat->i[j]; 1878 for (i=0; i<bmat->i[j+1]-bmat->i[j]; i++) { 1879 sum += PetscAbsScalar(*v); v++; 1880 } 1881 if (sum > ntemp) ntemp = sum; 1882 } 1883 ierr = MPIU_Allreduce(&ntemp,norm,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1884 ierr = PetscLogFlops(PetscMax(amat->nz+bmat->nz-1,0));CHKERRQ(ierr); 1885 } else SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"No support for two norm"); 1886 } 1887 PetscFunctionReturn(0); 1888 } 1889 1890 PetscErrorCode MatTranspose_MPIAIJ(Mat A,MatReuse reuse,Mat *matout) 1891 { 1892 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 1893 Mat_SeqAIJ *Aloc=(Mat_SeqAIJ*)a->A->data,*Bloc=(Mat_SeqAIJ*)a->B->data; 1894 PetscErrorCode ierr; 1895 PetscInt M = A->rmap->N,N = A->cmap->N,ma,na,mb,nb,*ai,*aj,*bi,*bj,row,*cols,*cols_tmp,i; 1896 PetscInt cstart = A->cmap->rstart,ncol; 1897 Mat B; 1898 MatScalar *array; 1899 1900 PetscFunctionBegin; 1901 if (reuse == MAT_INPLACE_MATRIX && M != N) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); 1902 1903 ma = A->rmap->n; na = A->cmap->n; mb = a->B->rmap->n; nb = a->B->cmap->n; 1904 ai = Aloc->i; aj = Aloc->j; 1905 bi = Bloc->i; bj = Bloc->j; 1906 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1907 PetscInt *d_nnz,*g_nnz,*o_nnz; 1908 PetscSFNode *oloc; 1909 PETSC_UNUSED PetscSF sf; 1910 1911 ierr = PetscMalloc4(na,&d_nnz,na,&o_nnz,nb,&g_nnz,nb,&oloc);CHKERRQ(ierr); 1912 /* compute d_nnz for preallocation */ 1913 ierr = PetscMemzero(d_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1914 for (i=0; i<ai[ma]; i++) { 1915 d_nnz[aj[i]]++; 1916 aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1917 } 1918 /* compute local off-diagonal contributions */ 1919 ierr = PetscMemzero(g_nnz,nb*sizeof(PetscInt));CHKERRQ(ierr); 1920 for (i=0; i<bi[ma]; i++) g_nnz[bj[i]]++; 1921 /* map those to global */ 1922 ierr = PetscSFCreate(PetscObjectComm((PetscObject)A),&sf);CHKERRQ(ierr); 1923 ierr = PetscSFSetGraphLayout(sf,A->cmap,nb,NULL,PETSC_USE_POINTER,a->garray);CHKERRQ(ierr); 1924 ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr); 1925 ierr = PetscMemzero(o_nnz,na*sizeof(PetscInt));CHKERRQ(ierr); 1926 ierr = PetscSFReduceBegin(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1927 ierr = PetscSFReduceEnd(sf,MPIU_INT,g_nnz,o_nnz,MPIU_SUM);CHKERRQ(ierr); 1928 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 1929 1930 ierr = MatCreate(PetscObjectComm((PetscObject)A),&B);CHKERRQ(ierr); 1931 ierr = MatSetSizes(B,A->cmap->n,A->rmap->n,N,M);CHKERRQ(ierr); 1932 ierr = MatSetBlockSizes(B,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 1933 ierr = MatSetType(B,((PetscObject)A)->type_name);CHKERRQ(ierr); 1934 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 1935 ierr = PetscFree4(d_nnz,o_nnz,g_nnz,oloc);CHKERRQ(ierr); 1936 } else { 1937 B = *matout; 1938 ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1939 for (i=0; i<ai[ma]; i++) aj[i] += cstart; /* global col index to be used by MatSetValues() */ 1940 } 1941 1942 /* copy over the A part */ 1943 array = Aloc->a; 1944 row = A->rmap->rstart; 1945 for (i=0; i<ma; i++) { 1946 ncol = ai[i+1]-ai[i]; 1947 ierr = MatSetValues(B,ncol,aj,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1948 row++; 1949 array += ncol; aj += ncol; 1950 } 1951 aj = Aloc->j; 1952 for (i=0; i<ai[ma]; i++) aj[i] -= cstart; /* resume local col index */ 1953 1954 /* copy over the B part */ 1955 ierr = PetscCalloc1(bi[mb],&cols);CHKERRQ(ierr); 1956 array = Bloc->a; 1957 row = A->rmap->rstart; 1958 for (i=0; i<bi[mb]; i++) cols[i] = a->garray[bj[i]]; 1959 cols_tmp = cols; 1960 for (i=0; i<mb; i++) { 1961 ncol = bi[i+1]-bi[i]; 1962 ierr = MatSetValues(B,ncol,cols_tmp,1,&row,array,INSERT_VALUES);CHKERRQ(ierr); 1963 row++; 1964 array += ncol; cols_tmp += ncol; 1965 } 1966 ierr = PetscFree(cols);CHKERRQ(ierr); 1967 1968 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1969 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1970 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 1971 *matout = B; 1972 } else { 1973 ierr = MatHeaderMerge(A,&B);CHKERRQ(ierr); 1974 } 1975 PetscFunctionReturn(0); 1976 } 1977 1978 PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat,Vec ll,Vec rr) 1979 { 1980 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 1981 Mat a = aij->A,b = aij->B; 1982 PetscErrorCode ierr; 1983 PetscInt s1,s2,s3; 1984 1985 PetscFunctionBegin; 1986 ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); 1987 if (rr) { 1988 ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); 1989 if (s1!=s3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); 1990 /* Overlap communication with computation. */ 1991 ierr = VecScatterBegin(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1992 } 1993 if (ll) { 1994 ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); 1995 if (s1!=s2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); 1996 ierr = (*b->ops->diagonalscale)(b,ll,0);CHKERRQ(ierr); 1997 } 1998 /* scale the diagonal block */ 1999 ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); 2000 2001 if (rr) { 2002 /* Do a scatter end and then right scale the off-diagonal block */ 2003 ierr = VecScatterEnd(aij->Mvctx,rr,aij->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 2004 ierr = (*b->ops->diagonalscale)(b,0,aij->lvec);CHKERRQ(ierr); 2005 } 2006 PetscFunctionReturn(0); 2007 } 2008 2009 PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2010 { 2011 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2012 PetscErrorCode ierr; 2013 2014 PetscFunctionBegin; 2015 ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); 2016 PetscFunctionReturn(0); 2017 } 2018 2019 PetscErrorCode MatEqual_MPIAIJ(Mat A,Mat B,PetscBool *flag) 2020 { 2021 Mat_MPIAIJ *matB = (Mat_MPIAIJ*)B->data,*matA = (Mat_MPIAIJ*)A->data; 2022 Mat a,b,c,d; 2023 PetscBool flg; 2024 PetscErrorCode ierr; 2025 2026 PetscFunctionBegin; 2027 a = matA->A; b = matA->B; 2028 c = matB->A; d = matB->B; 2029 2030 ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); 2031 if (flg) { 2032 ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); 2033 } 2034 ierr = MPIU_Allreduce(&flg,flag,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 2035 PetscFunctionReturn(0); 2036 } 2037 2038 PetscErrorCode MatCopy_MPIAIJ(Mat A,Mat B,MatStructure str) 2039 { 2040 PetscErrorCode ierr; 2041 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2042 Mat_MPIAIJ *b = (Mat_MPIAIJ*)B->data; 2043 2044 PetscFunctionBegin; 2045 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2046 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2047 /* because of the column compression in the off-processor part of the matrix a->B, 2048 the number of columns in a->B and b->B may be different, hence we cannot call 2049 the MatCopy() directly on the two parts. If need be, we can provide a more 2050 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2051 then copying the submatrices */ 2052 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 2053 } else { 2054 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 2055 ierr = MatCopy(a->B,b->B,str);CHKERRQ(ierr); 2056 } 2057 PetscFunctionReturn(0); 2058 } 2059 2060 PetscErrorCode MatSetUp_MPIAIJ(Mat A) 2061 { 2062 PetscErrorCode ierr; 2063 2064 PetscFunctionBegin; 2065 ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); 2066 PetscFunctionReturn(0); 2067 } 2068 2069 /* 2070 Computes the number of nonzeros per row needed for preallocation when X and Y 2071 have different nonzero structure. 2072 */ 2073 PetscErrorCode MatAXPYGetPreallocation_MPIX_private(PetscInt m,const PetscInt *xi,const PetscInt *xj,const PetscInt *xltog,const PetscInt *yi,const PetscInt *yj,const PetscInt *yltog,PetscInt *nnz) 2074 { 2075 PetscInt i,j,k,nzx,nzy; 2076 2077 PetscFunctionBegin; 2078 /* Set the number of nonzeros in the new matrix */ 2079 for (i=0; i<m; i++) { 2080 const PetscInt *xjj = xj+xi[i],*yjj = yj+yi[i]; 2081 nzx = xi[i+1] - xi[i]; 2082 nzy = yi[i+1] - yi[i]; 2083 nnz[i] = 0; 2084 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 2085 for (; k<nzy && yltog[yjj[k]]<xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */ 2086 if (k<nzy && yltog[yjj[k]]==xltog[xjj[j]]) k++; /* Skip duplicate */ 2087 nnz[i]++; 2088 } 2089 for (; k<nzy; k++) nnz[i]++; 2090 } 2091 PetscFunctionReturn(0); 2092 } 2093 2094 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2095 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y,const PetscInt *yltog,Mat X,const PetscInt *xltog,PetscInt *nnz) 2096 { 2097 PetscErrorCode ierr; 2098 PetscInt m = Y->rmap->N; 2099 Mat_SeqAIJ *x = (Mat_SeqAIJ*)X->data; 2100 Mat_SeqAIJ *y = (Mat_SeqAIJ*)Y->data; 2101 2102 PetscFunctionBegin; 2103 ierr = MatAXPYGetPreallocation_MPIX_private(m,x->i,x->j,xltog,y->i,y->j,yltog,nnz);CHKERRQ(ierr); 2104 PetscFunctionReturn(0); 2105 } 2106 2107 PetscErrorCode MatAXPY_MPIAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 2108 { 2109 PetscErrorCode ierr; 2110 Mat_MPIAIJ *xx = (Mat_MPIAIJ*)X->data,*yy = (Mat_MPIAIJ*)Y->data; 2111 PetscBLASInt bnz,one=1; 2112 Mat_SeqAIJ *x,*y; 2113 2114 PetscFunctionBegin; 2115 if (str == SAME_NONZERO_PATTERN) { 2116 PetscScalar alpha = a; 2117 x = (Mat_SeqAIJ*)xx->A->data; 2118 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2119 y = (Mat_SeqAIJ*)yy->A->data; 2120 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2121 x = (Mat_SeqAIJ*)xx->B->data; 2122 y = (Mat_SeqAIJ*)yy->B->data; 2123 ierr = PetscBLASIntCast(x->nz,&bnz);CHKERRQ(ierr); 2124 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 2125 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 2126 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2127 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 2128 } else { 2129 Mat B; 2130 PetscInt *nnz_d,*nnz_o; 2131 ierr = PetscMalloc1(yy->A->rmap->N,&nnz_d);CHKERRQ(ierr); 2132 ierr = PetscMalloc1(yy->B->rmap->N,&nnz_o);CHKERRQ(ierr); 2133 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 2134 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 2135 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 2136 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 2137 ierr = MatSetType(B,MATMPIAIJ);CHKERRQ(ierr); 2138 ierr = MatAXPYGetPreallocation_SeqAIJ(yy->A,xx->A,nnz_d);CHKERRQ(ierr); 2139 ierr = MatAXPYGetPreallocation_MPIAIJ(yy->B,yy->garray,xx->B,xx->garray,nnz_o);CHKERRQ(ierr); 2140 ierr = MatMPIAIJSetPreallocation(B,0,nnz_d,0,nnz_o);CHKERRQ(ierr); 2141 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 2142 ierr = MatHeaderReplace(Y,&B);CHKERRQ(ierr); 2143 ierr = PetscFree(nnz_d);CHKERRQ(ierr); 2144 ierr = PetscFree(nnz_o);CHKERRQ(ierr); 2145 } 2146 PetscFunctionReturn(0); 2147 } 2148 2149 extern PetscErrorCode MatConjugate_SeqAIJ(Mat); 2150 2151 PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2152 { 2153 #if defined(PETSC_USE_COMPLEX) 2154 PetscErrorCode ierr; 2155 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2156 2157 PetscFunctionBegin; 2158 ierr = MatConjugate_SeqAIJ(aij->A);CHKERRQ(ierr); 2159 ierr = MatConjugate_SeqAIJ(aij->B);CHKERRQ(ierr); 2160 #else 2161 PetscFunctionBegin; 2162 #endif 2163 PetscFunctionReturn(0); 2164 } 2165 2166 PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2167 { 2168 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2169 PetscErrorCode ierr; 2170 2171 PetscFunctionBegin; 2172 ierr = MatRealPart(a->A);CHKERRQ(ierr); 2173 ierr = MatRealPart(a->B);CHKERRQ(ierr); 2174 PetscFunctionReturn(0); 2175 } 2176 2177 PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2178 { 2179 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2180 PetscErrorCode ierr; 2181 2182 PetscFunctionBegin; 2183 ierr = MatImaginaryPart(a->A);CHKERRQ(ierr); 2184 ierr = MatImaginaryPart(a->B);CHKERRQ(ierr); 2185 PetscFunctionReturn(0); 2186 } 2187 2188 PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2189 { 2190 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2191 PetscErrorCode ierr; 2192 PetscInt i,*idxb = 0; 2193 PetscScalar *va,*vb; 2194 Vec vtmp; 2195 2196 PetscFunctionBegin; 2197 ierr = MatGetRowMaxAbs(a->A,v,idx);CHKERRQ(ierr); 2198 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2199 if (idx) { 2200 for (i=0; i<A->rmap->n; i++) { 2201 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2202 } 2203 } 2204 2205 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2206 if (idx) { 2207 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2208 } 2209 ierr = MatGetRowMaxAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2210 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2211 2212 for (i=0; i<A->rmap->n; i++) { 2213 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 2214 va[i] = vb[i]; 2215 if (idx) idx[i] = a->garray[idxb[i]]; 2216 } 2217 } 2218 2219 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2220 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2221 ierr = PetscFree(idxb);CHKERRQ(ierr); 2222 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2223 PetscFunctionReturn(0); 2224 } 2225 2226 PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2227 { 2228 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2229 PetscErrorCode ierr; 2230 PetscInt i,*idxb = 0; 2231 PetscScalar *va,*vb; 2232 Vec vtmp; 2233 2234 PetscFunctionBegin; 2235 ierr = MatGetRowMinAbs(a->A,v,idx);CHKERRQ(ierr); 2236 ierr = VecGetArray(v,&va);CHKERRQ(ierr); 2237 if (idx) { 2238 for (i=0; i<A->cmap->n; i++) { 2239 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2240 } 2241 } 2242 2243 ierr = VecCreateSeq(PETSC_COMM_SELF,A->rmap->n,&vtmp);CHKERRQ(ierr); 2244 if (idx) { 2245 ierr = PetscMalloc1(A->rmap->n,&idxb);CHKERRQ(ierr); 2246 } 2247 ierr = MatGetRowMinAbs(a->B,vtmp,idxb);CHKERRQ(ierr); 2248 ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); 2249 2250 for (i=0; i<A->rmap->n; i++) { 2251 if (PetscAbsScalar(va[i]) > PetscAbsScalar(vb[i])) { 2252 va[i] = vb[i]; 2253 if (idx) idx[i] = a->garray[idxb[i]]; 2254 } 2255 } 2256 2257 ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); 2258 ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); 2259 ierr = PetscFree(idxb);CHKERRQ(ierr); 2260 ierr = VecDestroy(&vtmp);CHKERRQ(ierr); 2261 PetscFunctionReturn(0); 2262 } 2263 2264 PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2265 { 2266 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2267 PetscInt n = A->rmap->n; 2268 PetscInt cstart = A->cmap->rstart; 2269 PetscInt *cmap = mat->garray; 2270 PetscInt *diagIdx, *offdiagIdx; 2271 Vec diagV, offdiagV; 2272 PetscScalar *a, *diagA, *offdiagA; 2273 PetscInt r; 2274 PetscErrorCode ierr; 2275 2276 PetscFunctionBegin; 2277 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2278 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &diagV);CHKERRQ(ierr); 2279 ierr = VecCreateSeq(PetscObjectComm((PetscObject)A), n, &offdiagV);CHKERRQ(ierr); 2280 ierr = MatGetRowMin(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2281 ierr = MatGetRowMin(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2282 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2283 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2284 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2285 for (r = 0; r < n; ++r) { 2286 if (PetscAbsScalar(diagA[r]) <= PetscAbsScalar(offdiagA[r])) { 2287 a[r] = diagA[r]; 2288 idx[r] = cstart + diagIdx[r]; 2289 } else { 2290 a[r] = offdiagA[r]; 2291 idx[r] = cmap[offdiagIdx[r]]; 2292 } 2293 } 2294 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2295 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2296 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2297 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2298 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2299 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2300 PetscFunctionReturn(0); 2301 } 2302 2303 PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2304 { 2305 Mat_MPIAIJ *mat = (Mat_MPIAIJ*) A->data; 2306 PetscInt n = A->rmap->n; 2307 PetscInt cstart = A->cmap->rstart; 2308 PetscInt *cmap = mat->garray; 2309 PetscInt *diagIdx, *offdiagIdx; 2310 Vec diagV, offdiagV; 2311 PetscScalar *a, *diagA, *offdiagA; 2312 PetscInt r; 2313 PetscErrorCode ierr; 2314 2315 PetscFunctionBegin; 2316 ierr = PetscMalloc2(n,&diagIdx,n,&offdiagIdx);CHKERRQ(ierr); 2317 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &diagV);CHKERRQ(ierr); 2318 ierr = VecCreateSeq(PETSC_COMM_SELF, n, &offdiagV);CHKERRQ(ierr); 2319 ierr = MatGetRowMax(mat->A, diagV, diagIdx);CHKERRQ(ierr); 2320 ierr = MatGetRowMax(mat->B, offdiagV, offdiagIdx);CHKERRQ(ierr); 2321 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 2322 ierr = VecGetArray(diagV, &diagA);CHKERRQ(ierr); 2323 ierr = VecGetArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2324 for (r = 0; r < n; ++r) { 2325 if (PetscAbsScalar(diagA[r]) >= PetscAbsScalar(offdiagA[r])) { 2326 a[r] = diagA[r]; 2327 idx[r] = cstart + diagIdx[r]; 2328 } else { 2329 a[r] = offdiagA[r]; 2330 idx[r] = cmap[offdiagIdx[r]]; 2331 } 2332 } 2333 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 2334 ierr = VecRestoreArray(diagV, &diagA);CHKERRQ(ierr); 2335 ierr = VecRestoreArray(offdiagV, &offdiagA);CHKERRQ(ierr); 2336 ierr = VecDestroy(&diagV);CHKERRQ(ierr); 2337 ierr = VecDestroy(&offdiagV);CHKERRQ(ierr); 2338 ierr = PetscFree2(diagIdx, offdiagIdx);CHKERRQ(ierr); 2339 PetscFunctionReturn(0); 2340 } 2341 2342 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat,Mat *newmat) 2343 { 2344 PetscErrorCode ierr; 2345 Mat *dummy; 2346 2347 PetscFunctionBegin; 2348 ierr = MatCreateSubMatrix_MPIAIJ_All(mat,MAT_DO_NOT_GET_VALUES,MAT_INITIAL_MATRIX,&dummy);CHKERRQ(ierr); 2349 *newmat = *dummy; 2350 ierr = PetscFree(dummy);CHKERRQ(ierr); 2351 PetscFunctionReturn(0); 2352 } 2353 2354 PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A,const PetscScalar **values) 2355 { 2356 Mat_MPIAIJ *a = (Mat_MPIAIJ*) A->data; 2357 PetscErrorCode ierr; 2358 2359 PetscFunctionBegin; 2360 ierr = MatInvertBlockDiagonal(a->A,values);CHKERRQ(ierr); 2361 A->factorerrortype = a->A->factorerrortype; 2362 PetscFunctionReturn(0); 2363 } 2364 2365 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x,PetscRandom rctx) 2366 { 2367 PetscErrorCode ierr; 2368 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)x->data; 2369 2370 PetscFunctionBegin; 2371 ierr = MatSetRandom(aij->A,rctx);CHKERRQ(ierr); 2372 ierr = MatSetRandom(aij->B,rctx);CHKERRQ(ierr); 2373 ierr = MatAssemblyBegin(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2374 ierr = MatAssemblyEnd(x,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2375 PetscFunctionReturn(0); 2376 } 2377 2378 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A,PetscBool sc) 2379 { 2380 PetscFunctionBegin; 2381 if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable; 2382 else A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ; 2383 PetscFunctionReturn(0); 2384 } 2385 2386 /*@ 2387 MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap 2388 2389 Collective on Mat 2390 2391 Input Parameters: 2392 + A - the matrix 2393 - sc - PETSC_TRUE indicates use the scalable algorithm (default is not to use the scalable algorithm) 2394 2395 Level: advanced 2396 2397 @*/ 2398 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A,PetscBool sc) 2399 { 2400 PetscErrorCode ierr; 2401 2402 PetscFunctionBegin; 2403 ierr = PetscTryMethod(A,"MatMPIAIJSetUseScalableIncreaseOverlap_C",(Mat,PetscBool),(A,sc));CHKERRQ(ierr); 2404 PetscFunctionReturn(0); 2405 } 2406 2407 PetscErrorCode MatSetFromOptions_MPIAIJ(PetscOptionItems *PetscOptionsObject,Mat A) 2408 { 2409 PetscErrorCode ierr; 2410 PetscBool sc = PETSC_FALSE,flg; 2411 2412 PetscFunctionBegin; 2413 ierr = PetscOptionsHead(PetscOptionsObject,"MPIAIJ options");CHKERRQ(ierr); 2414 ierr = PetscObjectOptionsBegin((PetscObject)A); 2415 if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE; 2416 ierr = PetscOptionsBool("-mat_increase_overlap_scalable","Use a scalable algorithm to compute the overlap","MatIncreaseOverlap",sc,&sc,&flg);CHKERRQ(ierr); 2417 if (flg) { 2418 ierr = MatMPIAIJSetUseScalableIncreaseOverlap(A,sc);CHKERRQ(ierr); 2419 } 2420 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2421 PetscFunctionReturn(0); 2422 } 2423 2424 PetscErrorCode MatShift_MPIAIJ(Mat Y,PetscScalar a) 2425 { 2426 PetscErrorCode ierr; 2427 Mat_MPIAIJ *maij = (Mat_MPIAIJ*)Y->data; 2428 Mat_SeqAIJ *aij = (Mat_SeqAIJ*)maij->A->data; 2429 2430 PetscFunctionBegin; 2431 if (!Y->preallocated) { 2432 ierr = MatMPIAIJSetPreallocation(Y,1,NULL,0,NULL);CHKERRQ(ierr); 2433 } else if (!aij->nz) { 2434 PetscInt nonew = aij->nonew; 2435 ierr = MatSeqAIJSetPreallocation(maij->A,1,NULL);CHKERRQ(ierr); 2436 aij->nonew = nonew; 2437 } 2438 ierr = MatShift_Basic(Y,a);CHKERRQ(ierr); 2439 PetscFunctionReturn(0); 2440 } 2441 2442 PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A,PetscBool *missing,PetscInt *d) 2443 { 2444 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 2445 PetscErrorCode ierr; 2446 2447 PetscFunctionBegin; 2448 if (A->rmap->n != A->cmap->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only works for square matrices"); 2449 ierr = MatMissingDiagonal(a->A,missing,d);CHKERRQ(ierr); 2450 if (d) { 2451 PetscInt rstart; 2452 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 2453 *d += rstart; 2454 2455 } 2456 PetscFunctionReturn(0); 2457 } 2458 2459 2460 /* -------------------------------------------------------------------*/ 2461 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 2462 MatGetRow_MPIAIJ, 2463 MatRestoreRow_MPIAIJ, 2464 MatMult_MPIAIJ, 2465 /* 4*/ MatMultAdd_MPIAIJ, 2466 MatMultTranspose_MPIAIJ, 2467 MatMultTransposeAdd_MPIAIJ, 2468 0, 2469 0, 2470 0, 2471 /*10*/ 0, 2472 0, 2473 0, 2474 MatSOR_MPIAIJ, 2475 MatTranspose_MPIAIJ, 2476 /*15*/ MatGetInfo_MPIAIJ, 2477 MatEqual_MPIAIJ, 2478 MatGetDiagonal_MPIAIJ, 2479 MatDiagonalScale_MPIAIJ, 2480 MatNorm_MPIAIJ, 2481 /*20*/ MatAssemblyBegin_MPIAIJ, 2482 MatAssemblyEnd_MPIAIJ, 2483 MatSetOption_MPIAIJ, 2484 MatZeroEntries_MPIAIJ, 2485 /*24*/ MatZeroRows_MPIAIJ, 2486 0, 2487 0, 2488 0, 2489 0, 2490 /*29*/ MatSetUp_MPIAIJ, 2491 0, 2492 0, 2493 MatGetDiagonalBlock_MPIAIJ, 2494 0, 2495 /*34*/ MatDuplicate_MPIAIJ, 2496 0, 2497 0, 2498 0, 2499 0, 2500 /*39*/ MatAXPY_MPIAIJ, 2501 MatCreateSubMatrices_MPIAIJ, 2502 MatIncreaseOverlap_MPIAIJ, 2503 MatGetValues_MPIAIJ, 2504 MatCopy_MPIAIJ, 2505 /*44*/ MatGetRowMax_MPIAIJ, 2506 MatScale_MPIAIJ, 2507 MatShift_MPIAIJ, 2508 MatDiagonalSet_MPIAIJ, 2509 MatZeroRowsColumns_MPIAIJ, 2510 /*49*/ MatSetRandom_MPIAIJ, 2511 0, 2512 0, 2513 0, 2514 0, 2515 /*54*/ MatFDColoringCreate_MPIXAIJ, 2516 0, 2517 MatSetUnfactored_MPIAIJ, 2518 MatPermute_MPIAIJ, 2519 0, 2520 /*59*/ MatCreateSubMatrix_MPIAIJ, 2521 MatDestroy_MPIAIJ, 2522 MatView_MPIAIJ, 2523 0, 2524 MatMatMatMult_MPIAIJ_MPIAIJ_MPIAIJ, 2525 /*64*/ MatMatMatMultSymbolic_MPIAIJ_MPIAIJ_MPIAIJ, 2526 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 2527 0, 2528 0, 2529 0, 2530 /*69*/ MatGetRowMaxAbs_MPIAIJ, 2531 MatGetRowMinAbs_MPIAIJ, 2532 0, 2533 0, 2534 0, 2535 0, 2536 /*75*/ MatFDColoringApply_AIJ, 2537 MatSetFromOptions_MPIAIJ, 2538 0, 2539 0, 2540 MatFindZeroDiagonals_MPIAIJ, 2541 /*80*/ 0, 2542 0, 2543 0, 2544 /*83*/ MatLoad_MPIAIJ, 2545 0, 2546 0, 2547 0, 2548 0, 2549 0, 2550 /*89*/ MatMatMult_MPIAIJ_MPIAIJ, 2551 MatMatMultSymbolic_MPIAIJ_MPIAIJ, 2552 MatMatMultNumeric_MPIAIJ_MPIAIJ, 2553 MatPtAP_MPIAIJ_MPIAIJ, 2554 MatPtAPSymbolic_MPIAIJ_MPIAIJ, 2555 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 2556 0, 2557 0, 2558 0, 2559 0, 2560 /*99*/ 0, 2561 0, 2562 0, 2563 MatConjugate_MPIAIJ, 2564 0, 2565 /*104*/MatSetValuesRow_MPIAIJ, 2566 MatRealPart_MPIAIJ, 2567 MatImaginaryPart_MPIAIJ, 2568 0, 2569 0, 2570 /*109*/0, 2571 0, 2572 MatGetRowMin_MPIAIJ, 2573 0, 2574 MatMissingDiagonal_MPIAIJ, 2575 /*114*/MatGetSeqNonzeroStructure_MPIAIJ, 2576 0, 2577 MatGetGhosts_MPIAIJ, 2578 0, 2579 0, 2580 /*119*/0, 2581 0, 2582 0, 2583 0, 2584 MatGetMultiProcBlock_MPIAIJ, 2585 /*124*/MatFindNonzeroRows_MPIAIJ, 2586 MatGetColumnNorms_MPIAIJ, 2587 MatInvertBlockDiagonal_MPIAIJ, 2588 0, 2589 MatCreateSubMatricesMPI_MPIAIJ, 2590 /*129*/0, 2591 MatTransposeMatMult_MPIAIJ_MPIAIJ, 2592 MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ, 2593 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 2594 0, 2595 /*134*/0, 2596 0, 2597 0, 2598 0, 2599 0, 2600 /*139*/MatSetBlockSizes_MPIAIJ, 2601 0, 2602 0, 2603 MatFDColoringSetUp_MPIXAIJ, 2604 MatFindOffBlockDiagonalEntries_MPIAIJ, 2605 /*144*/MatCreateMPIMatConcatenateSeqMat_MPIAIJ 2606 }; 2607 2608 /* ----------------------------------------------------------------------------------------*/ 2609 2610 PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 2611 { 2612 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2613 PetscErrorCode ierr; 2614 2615 PetscFunctionBegin; 2616 ierr = MatStoreValues(aij->A);CHKERRQ(ierr); 2617 ierr = MatStoreValues(aij->B);CHKERRQ(ierr); 2618 PetscFunctionReturn(0); 2619 } 2620 2621 PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 2622 { 2623 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 2624 PetscErrorCode ierr; 2625 2626 PetscFunctionBegin; 2627 ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); 2628 ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); 2629 PetscFunctionReturn(0); 2630 } 2631 2632 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 2633 { 2634 Mat_MPIAIJ *b; 2635 PetscErrorCode ierr; 2636 2637 PetscFunctionBegin; 2638 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 2639 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 2640 b = (Mat_MPIAIJ*)B->data; 2641 2642 #if defined(PETSC_USE_CTABLE) 2643 ierr = PetscTableDestroy(&b->colmap);CHKERRQ(ierr); 2644 #else 2645 ierr = PetscFree(b->colmap);CHKERRQ(ierr); 2646 #endif 2647 ierr = PetscFree(b->garray);CHKERRQ(ierr); 2648 ierr = VecDestroy(&b->lvec);CHKERRQ(ierr); 2649 ierr = VecScatterDestroy(&b->Mvctx);CHKERRQ(ierr); 2650 2651 /* Because the B will have been resized we simply destroy it and create a new one each time */ 2652 ierr = MatDestroy(&b->B);CHKERRQ(ierr); 2653 ierr = MatCreate(PETSC_COMM_SELF,&b->B);CHKERRQ(ierr); 2654 ierr = MatSetSizes(b->B,B->rmap->n,B->cmap->N,B->rmap->n,B->cmap->N);CHKERRQ(ierr); 2655 ierr = MatSetBlockSizesFromMats(b->B,B,B);CHKERRQ(ierr); 2656 ierr = MatSetType(b->B,MATSEQAIJ);CHKERRQ(ierr); 2657 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->B);CHKERRQ(ierr); 2658 2659 if (!B->preallocated) { 2660 ierr = MatCreate(PETSC_COMM_SELF,&b->A);CHKERRQ(ierr); 2661 ierr = MatSetSizes(b->A,B->rmap->n,B->cmap->n,B->rmap->n,B->cmap->n);CHKERRQ(ierr); 2662 ierr = MatSetBlockSizesFromMats(b->A,B,B);CHKERRQ(ierr); 2663 ierr = MatSetType(b->A,MATSEQAIJ);CHKERRQ(ierr); 2664 ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)b->A);CHKERRQ(ierr); 2665 } 2666 2667 ierr = MatSeqAIJSetPreallocation(b->A,d_nz,d_nnz);CHKERRQ(ierr); 2668 ierr = MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz);CHKERRQ(ierr); 2669 B->preallocated = PETSC_TRUE; 2670 B->was_assembled = PETSC_FALSE; 2671 B->assembled = PETSC_FALSE;; 2672 PetscFunctionReturn(0); 2673 } 2674 2675 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) 2676 { 2677 Mat mat; 2678 Mat_MPIAIJ *a,*oldmat = (Mat_MPIAIJ*)matin->data; 2679 PetscErrorCode ierr; 2680 2681 PetscFunctionBegin; 2682 *newmat = 0; 2683 ierr = MatCreate(PetscObjectComm((PetscObject)matin),&mat);CHKERRQ(ierr); 2684 ierr = MatSetSizes(mat,matin->rmap->n,matin->cmap->n,matin->rmap->N,matin->cmap->N);CHKERRQ(ierr); 2685 ierr = MatSetBlockSizesFromMats(mat,matin,matin);CHKERRQ(ierr); 2686 ierr = MatSetType(mat,((PetscObject)matin)->type_name);CHKERRQ(ierr); 2687 ierr = PetscMemcpy(mat->ops,matin->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2688 a = (Mat_MPIAIJ*)mat->data; 2689 2690 mat->factortype = matin->factortype; 2691 mat->assembled = PETSC_TRUE; 2692 mat->insertmode = NOT_SET_VALUES; 2693 mat->preallocated = PETSC_TRUE; 2694 2695 a->size = oldmat->size; 2696 a->rank = oldmat->rank; 2697 a->donotstash = oldmat->donotstash; 2698 a->roworiented = oldmat->roworiented; 2699 a->rowindices = 0; 2700 a->rowvalues = 0; 2701 a->getrowactive = PETSC_FALSE; 2702 2703 ierr = PetscLayoutReference(matin->rmap,&mat->rmap);CHKERRQ(ierr); 2704 ierr = PetscLayoutReference(matin->cmap,&mat->cmap);CHKERRQ(ierr); 2705 2706 if (oldmat->colmap) { 2707 #if defined(PETSC_USE_CTABLE) 2708 ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); 2709 #else 2710 ierr = PetscMalloc1(mat->cmap->N,&a->colmap);CHKERRQ(ierr); 2711 ierr = PetscLogObjectMemory((PetscObject)mat,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2712 ierr = PetscMemcpy(a->colmap,oldmat->colmap,(mat->cmap->N)*sizeof(PetscInt));CHKERRQ(ierr); 2713 #endif 2714 } else a->colmap = 0; 2715 if (oldmat->garray) { 2716 PetscInt len; 2717 len = oldmat->B->cmap->n; 2718 ierr = PetscMalloc1(len+1,&a->garray);CHKERRQ(ierr); 2719 ierr = PetscLogObjectMemory((PetscObject)mat,len*sizeof(PetscInt));CHKERRQ(ierr); 2720 if (len) { ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(PetscInt));CHKERRQ(ierr); } 2721 } else a->garray = 0; 2722 2723 ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); 2724 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->lvec);CHKERRQ(ierr); 2725 ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); 2726 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->Mvctx);CHKERRQ(ierr); 2727 ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); 2728 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->A);CHKERRQ(ierr); 2729 ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); 2730 ierr = PetscLogObjectParent((PetscObject)mat,(PetscObject)a->B);CHKERRQ(ierr); 2731 ierr = PetscFunctionListDuplicate(((PetscObject)matin)->qlist,&((PetscObject)mat)->qlist);CHKERRQ(ierr); 2732 *newmat = mat; 2733 PetscFunctionReturn(0); 2734 } 2735 2736 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 2737 { 2738 PetscScalar *vals,*svals; 2739 MPI_Comm comm; 2740 PetscErrorCode ierr; 2741 PetscMPIInt rank,size,tag = ((PetscObject)viewer)->tag; 2742 PetscInt i,nz,j,rstart,rend,mmax,maxnz = 0; 2743 PetscInt header[4],*rowlengths = 0,M,N,m,*cols; 2744 PetscInt *ourlens = NULL,*procsnz = NULL,*offlens = NULL,jj,*mycols,*smycols; 2745 PetscInt cend,cstart,n,*rowners; 2746 int fd; 2747 PetscInt bs = newMat->rmap->bs; 2748 2749 PetscFunctionBegin; 2750 /* force binary viewer to load .info file if it has not yet done so */ 2751 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 2752 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2753 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2754 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 2755 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2756 if (!rank) { 2757 ierr = PetscBinaryRead(fd,(char*)header,4,PETSC_INT);CHKERRQ(ierr); 2758 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); 2759 if (header[3] < 0) SETERRQ(PetscObjectComm((PetscObject)newMat),PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format on disk,cannot load as MATMPIAIJ"); 2760 } 2761 2762 ierr = PetscOptionsBegin(comm,NULL,"Options for loading MATMPIAIJ matrix","Mat");CHKERRQ(ierr); 2763 ierr = PetscOptionsInt("-matload_block_size","Set the blocksize used to store the matrix","MatLoad",bs,&bs,NULL);CHKERRQ(ierr); 2764 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2765 if (bs < 0) bs = 1; 2766 2767 ierr = MPI_Bcast(header+1,3,MPIU_INT,0,comm);CHKERRQ(ierr); 2768 M = header[1]; N = header[2]; 2769 2770 /* If global sizes are set, check if they are consistent with that given in the file */ 2771 if (newMat->rmap->N >= 0 && newMat->rmap->N != M) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of rows:Matrix in file has (%D) and input matrix has (%D)",newMat->rmap->N,M); 2772 if (newMat->cmap->N >=0 && newMat->cmap->N != N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Inconsistent # of cols:Matrix in file has (%D) and input matrix has (%D)",newMat->cmap->N,N); 2773 2774 /* determine ownership of all (block) rows */ 2775 if (M%bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Inconsistent # of rows (%d) and block size (%d)",M,bs); 2776 if (newMat->rmap->n < 0) m = bs*((M/bs)/size + (((M/bs) % size) > rank)); /* PETSC_DECIDE */ 2777 else m = newMat->rmap->n; /* Set by user */ 2778 2779 ierr = PetscMalloc1(size+1,&rowners);CHKERRQ(ierr); 2780 ierr = MPI_Allgather(&m,1,MPIU_INT,rowners+1,1,MPIU_INT,comm);CHKERRQ(ierr); 2781 2782 /* First process needs enough room for process with most rows */ 2783 if (!rank) { 2784 mmax = rowners[1]; 2785 for (i=2; i<=size; i++) { 2786 mmax = PetscMax(mmax, rowners[i]); 2787 } 2788 } else mmax = -1; /* unused, but compilers complain */ 2789 2790 rowners[0] = 0; 2791 for (i=2; i<=size; i++) { 2792 rowners[i] += rowners[i-1]; 2793 } 2794 rstart = rowners[rank]; 2795 rend = rowners[rank+1]; 2796 2797 /* distribute row lengths to all processors */ 2798 ierr = PetscMalloc2(m,&ourlens,m,&offlens);CHKERRQ(ierr); 2799 if (!rank) { 2800 ierr = PetscBinaryRead(fd,ourlens,m,PETSC_INT);CHKERRQ(ierr); 2801 ierr = PetscMalloc1(mmax,&rowlengths);CHKERRQ(ierr); 2802 ierr = PetscCalloc1(size,&procsnz);CHKERRQ(ierr); 2803 for (j=0; j<m; j++) { 2804 procsnz[0] += ourlens[j]; 2805 } 2806 for (i=1; i<size; i++) { 2807 ierr = PetscBinaryRead(fd,rowlengths,rowners[i+1]-rowners[i],PETSC_INT);CHKERRQ(ierr); 2808 /* calculate the number of nonzeros on each processor */ 2809 for (j=0; j<rowners[i+1]-rowners[i]; j++) { 2810 procsnz[i] += rowlengths[j]; 2811 } 2812 ierr = MPIULong_Send(rowlengths,rowners[i+1]-rowners[i],MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2813 } 2814 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2815 } else { 2816 ierr = MPIULong_Recv(ourlens,m,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2817 } 2818 2819 if (!rank) { 2820 /* determine max buffer needed and allocate it */ 2821 maxnz = 0; 2822 for (i=0; i<size; i++) { 2823 maxnz = PetscMax(maxnz,procsnz[i]); 2824 } 2825 ierr = PetscMalloc1(maxnz,&cols);CHKERRQ(ierr); 2826 2827 /* read in my part of the matrix column indices */ 2828 nz = procsnz[0]; 2829 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2830 ierr = PetscBinaryRead(fd,mycols,nz,PETSC_INT);CHKERRQ(ierr); 2831 2832 /* read in every one elses and ship off */ 2833 for (i=1; i<size; i++) { 2834 nz = procsnz[i]; 2835 ierr = PetscBinaryRead(fd,cols,nz,PETSC_INT);CHKERRQ(ierr); 2836 ierr = MPIULong_Send(cols,nz,MPIU_INT,i,tag,comm);CHKERRQ(ierr); 2837 } 2838 ierr = PetscFree(cols);CHKERRQ(ierr); 2839 } else { 2840 /* determine buffer space needed for message */ 2841 nz = 0; 2842 for (i=0; i<m; i++) { 2843 nz += ourlens[i]; 2844 } 2845 ierr = PetscMalloc1(nz,&mycols);CHKERRQ(ierr); 2846 2847 /* receive message of column indices*/ 2848 ierr = MPIULong_Recv(mycols,nz,MPIU_INT,0,tag,comm);CHKERRQ(ierr); 2849 } 2850 2851 /* determine column ownership if matrix is not square */ 2852 if (N != M) { 2853 if (newMat->cmap->n < 0) n = N/size + ((N % size) > rank); 2854 else n = newMat->cmap->n; 2855 ierr = MPI_Scan(&n,&cend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 2856 cstart = cend - n; 2857 } else { 2858 cstart = rstart; 2859 cend = rend; 2860 n = cend - cstart; 2861 } 2862 2863 /* loop over local rows, determining number of off diagonal entries */ 2864 ierr = PetscMemzero(offlens,m*sizeof(PetscInt));CHKERRQ(ierr); 2865 jj = 0; 2866 for (i=0; i<m; i++) { 2867 for (j=0; j<ourlens[i]; j++) { 2868 if (mycols[jj] < cstart || mycols[jj] >= cend) offlens[i]++; 2869 jj++; 2870 } 2871 } 2872 2873 for (i=0; i<m; i++) { 2874 ourlens[i] -= offlens[i]; 2875 } 2876 ierr = MatSetSizes(newMat,m,n,M,N);CHKERRQ(ierr); 2877 2878 if (bs > 1) {ierr = MatSetBlockSize(newMat,bs);CHKERRQ(ierr);} 2879 2880 ierr = MatMPIAIJSetPreallocation(newMat,0,ourlens,0,offlens);CHKERRQ(ierr); 2881 2882 for (i=0; i<m; i++) { 2883 ourlens[i] += offlens[i]; 2884 } 2885 2886 if (!rank) { 2887 ierr = PetscMalloc1(maxnz+1,&vals);CHKERRQ(ierr); 2888 2889 /* read in my part of the matrix numerical values */ 2890 nz = procsnz[0]; 2891 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2892 2893 /* insert into matrix */ 2894 jj = rstart; 2895 smycols = mycols; 2896 svals = vals; 2897 for (i=0; i<m; i++) { 2898 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2899 smycols += ourlens[i]; 2900 svals += ourlens[i]; 2901 jj++; 2902 } 2903 2904 /* read in other processors and ship out */ 2905 for (i=1; i<size; i++) { 2906 nz = procsnz[i]; 2907 ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); 2908 ierr = MPIULong_Send(vals,nz,MPIU_SCALAR,i,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2909 } 2910 ierr = PetscFree(procsnz);CHKERRQ(ierr); 2911 } else { 2912 /* receive numeric values */ 2913 ierr = PetscMalloc1(nz+1,&vals);CHKERRQ(ierr); 2914 2915 /* receive message of values*/ 2916 ierr = MPIULong_Recv(vals,nz,MPIU_SCALAR,0,((PetscObject)newMat)->tag,comm);CHKERRQ(ierr); 2917 2918 /* insert into matrix */ 2919 jj = rstart; 2920 smycols = mycols; 2921 svals = vals; 2922 for (i=0; i<m; i++) { 2923 ierr = MatSetValues_MPIAIJ(newMat,1,&jj,ourlens[i],smycols,svals,INSERT_VALUES);CHKERRQ(ierr); 2924 smycols += ourlens[i]; 2925 svals += ourlens[i]; 2926 jj++; 2927 } 2928 } 2929 ierr = PetscFree2(ourlens,offlens);CHKERRQ(ierr); 2930 ierr = PetscFree(vals);CHKERRQ(ierr); 2931 ierr = PetscFree(mycols);CHKERRQ(ierr); 2932 ierr = PetscFree(rowners);CHKERRQ(ierr); 2933 ierr = MatAssemblyBegin(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2934 ierr = MatAssemblyEnd(newMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2935 PetscFunctionReturn(0); 2936 } 2937 2938 /* Not scalable because of ISAllGather() unless getting all columns. */ 2939 PetscErrorCode ISGetSeqIS_Private(Mat mat,IS iscol,IS *isseq) 2940 { 2941 PetscErrorCode ierr; 2942 IS iscol_local; 2943 PetscBool isstride; 2944 PetscMPIInt lisstride=0,gisstride; 2945 2946 PetscFunctionBegin; 2947 /* check if we are grabbing all columns*/ 2948 ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&isstride);CHKERRQ(ierr); 2949 2950 if (isstride) { 2951 PetscInt start,len,mstart,mlen; 2952 ierr = ISStrideGetInfo(iscol,&start,NULL);CHKERRQ(ierr); 2953 ierr = ISGetLocalSize(iscol,&len);CHKERRQ(ierr); 2954 ierr = MatGetOwnershipRangeColumn(mat,&mstart,&mlen);CHKERRQ(ierr); 2955 if (mstart == start && mlen-mstart == len) lisstride = 1; 2956 } 2957 2958 ierr = MPIU_Allreduce(&lisstride,&gisstride,1,MPI_INT,MPI_MIN,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 2959 if (gisstride) { 2960 PetscInt N; 2961 ierr = MatGetSize(mat,NULL,&N);CHKERRQ(ierr); 2962 ierr = ISCreateStride(PetscObjectComm((PetscObject)mat),N,0,1,&iscol_local);CHKERRQ(ierr); 2963 ierr = ISSetIdentity(iscol_local);CHKERRQ(ierr); 2964 ierr = PetscInfo(mat,"Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n");CHKERRQ(ierr); 2965 } else { 2966 PetscInt cbs; 2967 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 2968 ierr = ISAllGather(iscol,&iscol_local);CHKERRQ(ierr); 2969 ierr = ISSetBlockSize(iscol_local,cbs);CHKERRQ(ierr); 2970 } 2971 2972 *isseq = iscol_local; 2973 PetscFunctionReturn(0); 2974 } 2975 2976 /* 2977 Used for avoiding ISAllGather() and global size of iscol_local (see MatCreateSubMatrix_MPIAIJ_nonscalable) 2978 2979 Input Parameters: 2980 mat - matrix 2981 iscol - parallel column index set; its local indices are a subset of local columns of mat, 2982 i.e., mat->cstart <= iscol[i] < mat->cend 2983 Output Parameter: 2984 iscol_sub - sequential column index set, a subset of iscol 2985 iscmap - column map; iscmap[i] indicates global location of iscol_sub[i] in iscol 2986 */ 2987 PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat,IS isrow,IS iscol,IS *isrow_d,IS *iscol_d,IS *iscol_o,IS *isgarray) 2988 { 2989 PetscErrorCode ierr; 2990 Vec x,cmap; 2991 const PetscInt *is_idx; 2992 PetscScalar *xarray,*cmaparray; 2993 PetscInt ncols,isstart,*idx,*camp,count,m,rstart; 2994 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 2995 Mat B=a->B; 2996 Vec lvec=a->lvec,lcmap; 2997 PetscInt i,cstart,cend,Bn=B->cmap->N; 2998 MPI_Comm comm; 2999 3000 PetscFunctionBegin; 3001 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3002 PetscMPIInt rank; 3003 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3004 ierr = ISGetLocalSize(iscol,&ncols);CHKERRQ(ierr); 3005 3006 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3007 ierr = MatCreateVecs(mat,&x,NULL);CHKERRQ(ierr); 3008 ierr = VecDuplicate(x,&cmap);CHKERRQ(ierr); 3009 ierr = VecSet(x,-1.0);CHKERRQ(ierr); 3010 3011 /* get start indices */ 3012 ierr = MPI_Scan(&ncols,&isstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3013 isstart -= ncols; 3014 ierr = MatGetOwnershipRangeColumn(mat,&cstart,&cend);CHKERRQ(ierr); 3015 3016 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3017 ierr = VecGetArray(x,&xarray);CHKERRQ(ierr); 3018 ierr = VecGetArray(cmap,&cmaparray);CHKERRQ(ierr); 3019 ierr = PetscMalloc1(ncols,&idx);CHKERRQ(ierr); 3020 for (i=0; i<ncols; i++) { 3021 xarray[is_idx[i]-cstart] = (PetscScalar)is_idx[i]; 3022 cmaparray[is_idx[i]-cstart] = i + isstart; /* global index of iscol[i] */ 3023 3024 idx[i] = is_idx[i]-cstart; 3025 } 3026 ierr = VecRestoreArray(x,&xarray);CHKERRQ(ierr); 3027 ierr = VecRestoreArray(cmap,&cmaparray);CHKERRQ(ierr); 3028 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3029 3030 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_COPY_VALUES,iscol_d);CHKERRQ(ierr); 3031 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3032 ierr = ISSetBlockSize(*iscol_d,i);CHKERRQ(ierr); 3033 ierr = PetscFree(idx);CHKERRQ(ierr); 3034 3035 ierr = ISGetLocalSize(isrow,&m);CHKERRQ(ierr); 3036 rstart = mat->rmap->rstart; 3037 ierr = PetscMalloc1(m,&idx);CHKERRQ(ierr); 3038 ierr = ISGetIndices(isrow,&is_idx);CHKERRQ(ierr); 3039 for (i=0; i<m; i++) { 3040 idx[i] = is_idx[i]-rstart; 3041 } 3042 ierr = ISRestoreIndices(isrow,&is_idx);CHKERRQ(ierr); 3043 3044 ierr = ISCreateGeneral(PETSC_COMM_SELF,m,idx,PETSC_COPY_VALUES,isrow_d);CHKERRQ(ierr); 3045 ierr = ISGetBlockSize(isrow,&i);CHKERRQ(ierr); 3046 ierr = ISSetBlockSize(*isrow_d,i);CHKERRQ(ierr); 3047 ierr = PetscFree(idx);CHKERRQ(ierr); 3048 3049 /* (2) scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3050 ierr = VecScatterBegin(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3051 3052 ierr = VecDuplicate(lvec,&lcmap);CHKERRQ(ierr); 3053 3054 ierr = VecScatterEnd(a->Mvctx,x,lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3055 ierr = VecScatterBegin(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3056 3057 count = ncols + Bn; 3058 ierr = PetscMalloc2(count,&idx,count,&camp);CHKERRQ(ierr); 3059 3060 ierr = VecScatterEnd(a->Mvctx,cmap,lcmap,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 3061 3062 /* (3) create scalable iscol_sub (a subset of iscol) and iscmap */ 3063 /* local column indices */ 3064 ierr = ISGetIndices(iscol,&is_idx);CHKERRQ(ierr); 3065 for (i=0; i<ncols; i++) { 3066 idx[i] = is_idx[i]; 3067 camp[i] = i + isstart; /* global index of iscol = column index in submat */ 3068 } 3069 ierr = ISRestoreIndices(iscol,&is_idx);CHKERRQ(ierr); 3070 count = ncols; 3071 3072 /* off-process column indices */ 3073 PetscInt *idx1,*cmap1,count1=0; 3074 ierr = PetscMalloc2(Bn,&idx1,Bn,&cmap1);CHKERRQ(ierr); 3075 3076 ierr = VecGetArray(lvec,&xarray);CHKERRQ(ierr); 3077 ierr = VecGetArray(lcmap,&cmaparray);CHKERRQ(ierr); 3078 for (i=0; i<Bn; i++) { 3079 if (PetscRealPart(xarray[i]) > -1.0) { 3080 idx1[count1] = i; /* local column index in off-diagonal part B */ 3081 cmap1[count1++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3082 3083 idx[count] = (PetscInt)PetscRealPart(xarray[i]); 3084 camp[count++] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3085 } 3086 } 3087 ierr = VecRestoreArray(lvec,&xarray);CHKERRQ(ierr); 3088 ierr = VecRestoreArray(lcmap,&cmaparray);CHKERRQ(ierr); 3089 3090 ierr = PetscSortIntWithArray(count,camp,idx);CHKERRQ(ierr); 3091 3092 ierr = ISCreateGeneral(PETSC_COMM_SELF,count1,idx1,PETSC_COPY_VALUES,iscol_o);CHKERRQ(ierr); 3093 ierr = ISCreateGeneral(PETSC_COMM_SELF,count1,cmap1,PETSC_COPY_VALUES,isgarray);CHKERRQ(ierr); 3094 ierr = ISGetBlockSize(iscol,&i);CHKERRQ(ierr); 3095 ierr = ISSetBlockSize(*iscol_o,i);CHKERRQ(ierr); 3096 ierr = PetscFree2(idx1,cmap1);CHKERRQ(ierr); 3097 3098 ierr = PetscFree2(idx,camp);CHKERRQ(ierr); 3099 ierr = VecDestroy(&x);CHKERRQ(ierr); 3100 ierr = VecDestroy(&cmap);CHKERRQ(ierr); 3101 ierr = VecDestroy(&lcmap);CHKERRQ(ierr); 3102 PetscFunctionReturn(0); 3103 } 3104 3105 /* Both isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */ 3106 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *submat) 3107 { 3108 PetscErrorCode ierr; 3109 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3110 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3111 Mat M=NULL,B=a->B; 3112 PetscInt *garray = a->garray,*colsub,Ncols; 3113 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3114 IS iscol_sub,iscmap; 3115 const PetscInt *is_idx,*cmap; 3116 PetscBool allcolumns=PETSC_FALSE; 3117 IS iscol_local=NULL; 3118 MPI_Comm comm; 3119 IS iscol_d,isrow_d,iscol_o,isgarray; 3120 Mat Asub=NULL,Bsub=NULL; 3121 3122 PetscFunctionBegin; 3123 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3124 PetscMPIInt rank; 3125 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3126 3127 if (call == MAT_REUSE_MATRIX) { 3128 Mat_MPIAIJ *matsub=(Mat_MPIAIJ*)(*submat)->data; 3129 3130 ierr = PetscObjectQuery((PetscObject)*submat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3131 if (!isrow_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"isrow_d passed in was not used before, cannot reuse"); 3132 3133 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_d",(PetscObject*)&iscol_d);CHKERRQ(ierr); 3134 if (!iscol_d) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_d passed in was not used before, cannot reuse"); 3135 3136 ierr = PetscObjectQuery((PetscObject)*submat,"iscol_o",(PetscObject*)&iscol_o);CHKERRQ(ierr); 3137 if (!iscol_o) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"iscol_o passed in was not used before, cannot reuse"); 3138 3139 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,call,&matsub->A);CHKERRQ(ierr); 3140 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,call,&matsub->B);CHKERRQ(ierr); 3141 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3142 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3143 3144 } else { /* call == MAT_INITIAL_MATRIX) */ 3145 const PetscInt *garray1; 3146 3147 ierr = ISGetSeqIS_SameColDist_Private(mat,isrow,iscol,&isrow_d,&iscol_d,&iscol_o,&isgarray);CHKERRQ(ierr); 3148 3149 ierr = MatCreateSubMatrix_SeqAIJ(a->A,isrow_d,iscol_d,PETSC_DECIDE,call,&Asub);CHKERRQ(ierr); 3150 ierr = MatCreateSubMatrix_SeqAIJ(a->B,isrow_d,iscol_o,PETSC_DECIDE,call,&Bsub);CHKERRQ(ierr); 3151 3152 PetscInt BsubN = Bsub->cmap->N; 3153 #if 0 3154 ierr = ISGetBlockSize(isrow,&bs);CHKERRQ(ierr); 3155 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3156 ierr = MatSetBlockSizes(Asub,bs,cbs);CHKERRQ(ierr); 3157 printf("[%d] bs %d cbs %d Asub rbs %d, cbs %d\n",rank,bs,cbs,Asub->rmap->bs,Asub->cmap->bs); 3158 #endif 3159 3160 if (rank == -1) { 3161 printf("[%d] Asub:\n",rank); 3162 ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_SELF, PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr); 3163 ierr = MatView(Asub,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3164 ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3165 if (!rank) printf("--------------------\n"); 3166 3167 Mat_SeqAIJ *b = (Mat_SeqAIJ*)Bsub->data; 3168 printf("[%d] Bsub: allocated nz %d\n",rank,b->maxnz); 3169 ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_SELF, PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr); 3170 ierr = MatView(Bsub,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3171 ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3172 if (!rank) printf("--------------------\n"); 3173 } 3174 3175 ierr = ISGetIndices(isgarray,&garray1);CHKERRQ(ierr); 3176 ierr = MatCreateMPIAIJWithSeqAIJ(comm,Asub,Bsub,garray1,&M);CHKERRQ(ierr); 3177 ierr = ISRestoreIndices(isgarray,&garray1);CHKERRQ(ierr); 3178 3179 if (rank == -1) { 3180 printf("matrix M:\n"); 3181 ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr); 3182 ierr = MatView(M,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3183 ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 3184 if (!rank) printf("--------------------\n"); 3185 ierr = MPI_Barrier(comm);CHKERRQ(ierr); 3186 } 3187 3188 /* Check is Bsub == M->B? If not, compress iscol_o accordingly */ 3189 3190 a = (Mat_MPIAIJ*)M->data; 3191 #if 1 3192 if (BsubN != a->B->cmap->N) { 3193 printf("[%d] Bsub->cmap->N %d != a->B->cmap->N %d\n",rank,BsubN,a->B->cmap->N); 3194 } 3195 #endif 3196 3197 ierr = ISDestroy(&isgarray);CHKERRQ(ierr); 3198 3199 /* save isrow_d, iscol_d and iscol_o used in processor for next request */ 3200 ierr = PetscObjectCompose((PetscObject)M,"isrow_d",(PetscObject)isrow_d);CHKERRQ(ierr); 3201 ierr = ISDestroy(&isrow_d);CHKERRQ(ierr); 3202 3203 ierr = PetscObjectCompose((PetscObject)M,"iscol_d",(PetscObject)iscol_d);CHKERRQ(ierr); 3204 ierr = ISDestroy(&iscol_d);CHKERRQ(ierr); 3205 3206 ierr = PetscObjectCompose((PetscObject)M,"iscol_o",(PetscObject)iscol_o);CHKERRQ(ierr); 3207 ierr = ISDestroy(&iscol_o);CHKERRQ(ierr); 3208 3209 *submat = M; 3210 } 3211 PetscFunctionReturn(0); 3212 } 3213 3214 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3215 { 3216 PetscErrorCode ierr; 3217 IS iscol_local,isrow_d; 3218 PetscInt csize; 3219 PetscInt n,i,j,start,end; 3220 PetscBool sameRowDist=PETSC_FALSE,sameDist[2],tsameDist[2]; 3221 MPI_Comm comm; 3222 3223 PetscFunctionBegin; 3224 /* If isrow has same processor distribution as mat, 3225 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3226 if (call == MAT_REUSE_MATRIX) { 3227 ierr = PetscObjectQuery((PetscObject)*newmat,"isrow_d",(PetscObject*)&isrow_d);CHKERRQ(ierr); 3228 if (isrow_d) { 3229 sameRowDist = PETSC_TRUE; 3230 tsameDist[1] = PETSC_TRUE; /* sameColDist */ 3231 } else { 3232 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3233 if (iscol_local) { 3234 sameRowDist = PETSC_TRUE; 3235 tsameDist[1] = PETSC_FALSE; /* !sameColDist */ 3236 } 3237 } 3238 } else { 3239 /* check if isrow has same processor distribution as mat */ 3240 sameDist[0] = PETSC_FALSE; 3241 ierr = ISGetLocalSize(isrow,&n);CHKERRQ(ierr); 3242 if (!n) { 3243 sameDist[0] = PETSC_TRUE; 3244 } else { 3245 ierr = ISGetMinMax(isrow,&i,&j);CHKERRQ(ierr); 3246 ierr = MatGetOwnershipRange(mat,&start,&end);CHKERRQ(ierr); 3247 if (i >= start && j < end) { 3248 sameDist[0] = PETSC_TRUE; 3249 } 3250 } 3251 3252 /* check if iscol has same processor distribution as mat */ 3253 sameDist[1] = PETSC_FALSE; 3254 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3255 if (!n) { 3256 sameDist[1] = PETSC_TRUE; 3257 } else { 3258 ierr = ISGetMinMax(iscol,&i,&j);CHKERRQ(ierr); 3259 ierr = MatGetOwnershipRangeColumn(mat,&start,&end);CHKERRQ(ierr); 3260 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3261 } 3262 3263 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3264 ierr = MPIU_Allreduce(&sameDist,&tsameDist,2,MPIU_BOOL,MPI_LAND,comm);CHKERRQ(ierr); 3265 sameRowDist = tsameDist[0]; 3266 } 3267 3268 if (sameRowDist) { 3269 if (tsameDist[1]) { 3270 /* isrow and iscol have same processor distribution as mat */ 3271 ierr = MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3272 } else { 3273 /* isrow has same processor distribution as mat */ 3274 ierr = MatCreateSubMatrix_MPIAIJ_SameRowDist(mat,isrow,iscol,call,newmat);CHKERRQ(ierr); 3275 } 3276 PetscFunctionReturn(0); 3277 } 3278 3279 /* General case: iscol -> iscol_local which has global size of iscol */ 3280 if (call == MAT_REUSE_MATRIX) { 3281 ierr = PetscObjectQuery((PetscObject)*newmat,"ISAllGather",(PetscObject*)&iscol_local);CHKERRQ(ierr); 3282 if (!iscol_local) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3283 } else { 3284 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3285 } 3286 3287 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3288 ierr = MatCreateSubMatrix_MPIAIJ_nonscalable(mat,isrow,iscol_local,csize,call,newmat);CHKERRQ(ierr); 3289 3290 if (call == MAT_INITIAL_MATRIX) { 3291 ierr = PetscObjectCompose((PetscObject)*newmat,"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3292 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3293 } 3294 PetscFunctionReturn(0); 3295 } 3296 3297 /*@C 3298 MatCreateMPIAIJWithSeqAIJ - creates a MPIAIJ matrix using SeqAIJ matrices that contain the "diagonal" 3299 and "off-diagonal" part of the matrix in CSR format. 3300 3301 Collective on MPI_Comm 3302 3303 Input Parameters: 3304 + comm - MPI communicator 3305 . A - "diagonal" portion of matrix 3306 . B - "off-diagonal" portion of matrix, destroyed by this routine 3307 - garray - global index of B columns 3308 3309 Output Parameter: 3310 . mat - the matrix, with input A as its local diagonal matrix 3311 Level: advanced 3312 3313 Notes: 3314 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3315 A becomes part of output mat, B is destroyed by this routine. The user cannot use A and B anymore. 3316 3317 .seealso: MatCreateMPIAIJWithSplitArrays() 3318 @*/ 3319 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm,Mat A,Mat B,const PetscInt garray[],Mat *mat) 3320 { 3321 PetscErrorCode ierr; 3322 Mat_MPIAIJ *maij; 3323 Mat_SeqAIJ *b=(Mat_SeqAIJ*)B->data; 3324 PetscInt *oi=b->i,*oj=b->j,i,nz,col; 3325 PetscScalar *oa=b->a; 3326 Mat Btmp; 3327 PetscInt m,n,N; 3328 3329 PetscFunctionBegin; 3330 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 3331 ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); 3332 if (m != B->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Am %d != Bm %d",m,B->rmap->N); 3333 3334 /* get global columns of mat */ 3335 ierr = MPIU_Allreduce(&n,&N,1,MPI_INT,MPI_SUM,comm);CHKERRQ(ierr); 3336 3337 ierr = MatSetSizes(*mat,m,n,PETSC_DECIDE,N);CHKERRQ(ierr); 3338 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 3339 maij = (Mat_MPIAIJ*)(*mat)->data; 3340 3341 (*mat)->preallocated = PETSC_TRUE; 3342 3343 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 3344 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 3345 3346 maij->A = A; 3347 3348 nz = oi[m]; 3349 for (i=0; i<nz; i++) { 3350 col = oj[i]; 3351 oj[i] = garray[col]; 3352 } 3353 3354 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,N,oi,oj,oa,&Btmp);CHKERRQ(ierr); 3355 Mat_SeqAIJ *btmp = (Mat_SeqAIJ*)Btmp->data; 3356 btmp->maxnz = b->maxnz; /* allocated nonzeros of B */ 3357 maij->B = Btmp; 3358 3359 PetscMPIInt rank; 3360 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3361 if (rank == -1) { 3362 printf("[%d] Btmp:\n",rank); 3363 ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_SELF, PETSC_VIEWER_ASCII_INFO);CHKERRQ(ierr); 3364 ierr = MatView(Btmp,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3365 ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 3366 if (!rank) printf("--------------------\n"); 3367 } 3368 3369 // Check B == Btmp??? see src/ksp/ksp/examples/tests/runex21_2,3 3370 3371 if (B->rmap->N != Btmp->rmap->N) SETERRQ2(PETSC_COMM_SELF,0,"BN %d != BtmpN %d",B->rmap->N,Btmp->rmap->N); 3372 3373 b->singlemalloc = PETSC_FALSE; /* these arrays are shared by Btmp */ 3374 b->free_a = PETSC_FALSE; 3375 b->free_ij = PETSC_FALSE; 3376 ierr = MatDestroy(&B);CHKERRQ(ierr); 3377 3378 b = (Mat_SeqAIJ*)Btmp->data; 3379 b->singlemalloc = PETSC_TRUE; /* arrays will be freed by MatDestroy(&Btmp) */ 3380 b->free_a = PETSC_TRUE; 3381 b->free_ij = PETSC_TRUE; 3382 3383 /* condense columns of maij->B */ 3384 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 3385 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3386 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3387 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 3388 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3389 PetscFunctionReturn(0); 3390 } 3391 3392 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,PetscBool,Mat*); 3393 3394 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat,IS isrow,IS iscol,MatReuse call,Mat *newmat) 3395 { 3396 PetscErrorCode ierr; 3397 PetscInt i,m,n,rstart,row,rend,nz,j,bs,cbs; 3398 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3399 Mat_MPIAIJ *a=(Mat_MPIAIJ*)mat->data; 3400 Mat M,Msub,B=a->B,Mnew=NULL; 3401 MatScalar *aa; 3402 Mat_SeqAIJ *aij; 3403 PetscInt *garray = a->garray,*colsub,Ncols; 3404 PetscInt count,Bn=B->cmap->N,cstart=mat->cmap->rstart,cend=mat->cmap->rend; 3405 IS iscol_sub,iscmap; 3406 const PetscInt *is_idx,*cmap; 3407 PetscBool allcolumns=PETSC_FALSE; 3408 IS iscol_local=NULL; 3409 MPI_Comm comm; 3410 IS iscol_d,isrow_d,iscol_o,isgarray; 3411 Mat Asub=NULL,Bsub=NULL; 3412 3413 PetscFunctionBegin; 3414 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3415 PetscMPIInt rank; 3416 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3417 3418 if (call == MAT_REUSE_MATRIX) { 3419 ierr = PetscObjectQuery((PetscObject)*newmat,"SubIScol",(PetscObject*)&iscol_sub);CHKERRQ(ierr); 3420 if (!iscol_sub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"SubIScol passed in was not used before, cannot reuse"); 3421 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3422 3423 ierr = PetscObjectQuery((PetscObject)*newmat,"Subcmap",(PetscObject*)&iscmap);CHKERRQ(ierr); 3424 if (!iscmap) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Subcmap passed in was not used before, cannot reuse"); 3425 3426 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Msub);CHKERRQ(ierr); 3427 if (!Msub) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3428 3429 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_REUSE_MATRIX,PETSC_FALSE,&Msub);CHKERRQ(ierr); 3430 3431 } else { /* call == MAT_INITIAL_MATRIX) */ 3432 PetscBool flg; 3433 3434 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3435 ierr = ISGetSize(iscol,&Ncols);CHKERRQ(ierr); 3436 3437 /* (1) iscol -> nonscalable iscol_local */ 3438 ierr = ISGetSeqIS_Private(mat,iscol,&iscol_local);CHKERRQ(ierr); 3439 ierr = ISGetLocalSize(iscol_local,&n);CHKERRQ(ierr); /* local size of iscol_local = global columns of newmat */ 3440 if (n != Ncols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n %d != Ncols %d",n,Ncols); 3441 3442 /* Check for special case: each processor gets entire matrix columns */ 3443 ierr = ISIdentity(iscol_local,&flg);CHKERRQ(ierr); 3444 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3445 if (allcolumns) { 3446 iscol_sub = iscol_local; 3447 ierr = PetscObjectReference((PetscObject)iscol_local);CHKERRQ(ierr); 3448 ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&iscmap);CHKERRQ(ierr); 3449 3450 } else { 3451 /* (2) iscol_local -> iscol_sub and iscmap */ 3452 PetscInt *idx,*cmap1,k,cbs; 3453 3454 /* implementation below requires iscol_local be sorted, it can have duplicate indices */ 3455 ierr = ISSorted(iscol_local,&flg);CHKERRQ(ierr); 3456 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"unsorted iscol_local is not implemented yet"); 3457 3458 ierr = PetscMalloc2(Ncols,&idx,Ncols,&cmap1);CHKERRQ(ierr); 3459 ierr = ISGetIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3460 count = 0; 3461 k = 0; 3462 for (i=0; i<Ncols; i++) { 3463 j = is_idx[i]; 3464 if (j >= cstart && j < cend) { 3465 /* diagonal part of mat */ 3466 idx[count] = j; 3467 cmap1[count++] = i; /* column index in submat */ 3468 } else if (Bn) { 3469 /* off-diagonal part of mat */ 3470 if (j == garray[k]) { 3471 idx[count] = j; 3472 cmap1[count++] = i; /* column index in submat */ 3473 } else if (j > garray[k]) { 3474 while (j > garray[k] && k < Bn-1) k++; 3475 if (j == garray[k]) { 3476 idx[count] = j; 3477 cmap1[count++] = i; /* column index in submat */ 3478 } 3479 } 3480 } 3481 } 3482 ierr = ISRestoreIndices(iscol_local,&is_idx);CHKERRQ(ierr); 3483 3484 ierr = ISCreateGeneral(PETSC_COMM_SELF,count,idx,PETSC_COPY_VALUES,&iscol_sub);CHKERRQ(ierr); 3485 ierr = ISGetBlockSize(iscol,&cbs);CHKERRQ(ierr); 3486 ierr = ISSetBlockSize(iscol_sub,cbs);CHKERRQ(ierr); 3487 3488 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local),count,cmap1,PETSC_COPY_VALUES,&iscmap);CHKERRQ(ierr); 3489 ierr = PetscFree2(idx,cmap1);CHKERRQ(ierr); 3490 } 3491 3492 /* (3) Create sequential Msub */ 3493 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol_sub,MAT_INITIAL_MATRIX,allcolumns,&Msub);CHKERRQ(ierr); 3494 } 3495 3496 ierr = ISGetLocalSize(iscol_sub,&count);CHKERRQ(ierr); 3497 aij = (Mat_SeqAIJ*)(Msub)->data; 3498 ii = aij->i; 3499 ierr = ISGetIndices(iscmap,&cmap);CHKERRQ(ierr); 3500 3501 /* 3502 m - number of local rows 3503 Ncols - number of columns (same on all processors) 3504 rstart - first row in new global matrix generated 3505 */ 3506 ierr = MatGetSize(Msub,&m,NULL);CHKERRQ(ierr); 3507 3508 if (call == MAT_INITIAL_MATRIX) { 3509 /* (4) Create parallel newmat */ 3510 PetscMPIInt rank,size; 3511 PetscInt csize; 3512 3513 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3514 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3515 3516 /* 3517 Determine the number of non-zeros in the diagonal and off-diagonal 3518 portions of the matrix in order to do correct preallocation 3519 */ 3520 3521 /* first get start and end of "diagonal" columns */ 3522 ierr = ISGetLocalSize(iscol,&csize);CHKERRQ(ierr); 3523 if (csize == PETSC_DECIDE) { 3524 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3525 if (mglobal == Ncols) { /* square matrix */ 3526 nlocal = m; 3527 } else { 3528 nlocal = Ncols/size + ((Ncols % size) > rank); 3529 } 3530 } else { 3531 nlocal = csize; 3532 } 3533 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3534 rstart = rend - nlocal; 3535 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); 3536 3537 /* next, compute all the lengths */ 3538 jj = aij->j; 3539 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3540 olens = dlens + m; 3541 for (i=0; i<m; i++) { 3542 jend = ii[i+1] - ii[i]; 3543 olen = 0; 3544 dlen = 0; 3545 for (j=0; j<jend; j++) { 3546 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3547 else dlen++; 3548 jj++; 3549 } 3550 olens[i] = olen; 3551 dlens[i] = dlen; 3552 } 3553 ierr = MatGetBlockSizes(Msub,&bs,&cbs);CHKERRQ(ierr); 3554 3555 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3556 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,Ncols);CHKERRQ(ierr); 3557 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3558 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3559 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3560 ierr = PetscFree(dlens);CHKERRQ(ierr); 3561 3562 } else { /* call == MAT_REUSE_MATRIX */ 3563 M = *newmat; 3564 ierr = MatGetLocalSize(M,&i,NULL);CHKERRQ(ierr); 3565 if (i != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3566 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3567 /* 3568 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3569 rather than the slower MatSetValues(). 3570 */ 3571 M->was_assembled = PETSC_TRUE; 3572 M->assembled = PETSC_FALSE; 3573 } 3574 3575 /* (5) Set values of Msub to *newmat */ 3576 ierr = PetscMalloc1(count,&colsub);CHKERRQ(ierr); 3577 ierr = MatGetOwnershipRange(M,&rstart,NULL);CHKERRQ(ierr); 3578 3579 jj = aij->j; 3580 aa = aij->a; 3581 for (i=0; i<m; i++) { 3582 row = rstart + i; 3583 nz = ii[i+1] - ii[i]; 3584 for (j=0; j<nz; j++) colsub[j] = cmap[jj[j]]; 3585 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,colsub,aa,INSERT_VALUES);CHKERRQ(ierr); 3586 jj += nz; aa += nz; 3587 } 3588 ierr = ISRestoreIndices(iscmap,&cmap);CHKERRQ(ierr); 3589 3590 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3591 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3592 3593 ierr = PetscFree(colsub);CHKERRQ(ierr); 3594 3595 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3596 if (call == MAT_INITIAL_MATRIX) { 3597 *newmat = M; 3598 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubMatrix",(PetscObject)Msub);CHKERRQ(ierr); 3599 ierr = MatDestroy(&Msub);CHKERRQ(ierr); 3600 3601 ierr = PetscObjectCompose((PetscObject)(*newmat),"SubIScol",(PetscObject)iscol_sub);CHKERRQ(ierr); 3602 ierr = ISDestroy(&iscol_sub);CHKERRQ(ierr); 3603 3604 ierr = PetscObjectCompose((PetscObject)(*newmat),"Subcmap",(PetscObject)iscmap);CHKERRQ(ierr); 3605 ierr = ISDestroy(&iscmap);CHKERRQ(ierr); 3606 3607 if (iscol_local) { 3608 ierr = PetscObjectCompose((PetscObject)(*newmat),"ISAllGather",(PetscObject)iscol_local);CHKERRQ(ierr); 3609 ierr = ISDestroy(&iscol_local);CHKERRQ(ierr); 3610 } 3611 } 3612 PetscFunctionReturn(0); 3613 } 3614 3615 /* 3616 Not great since it makes two copies of the submatrix, first an SeqAIJ 3617 in local and then by concatenating the local matrices the end result. 3618 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3619 3620 Note: This requires a sequential iscol with all indices. 3621 */ 3622 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat,IS isrow,IS iscol,PetscInt csize,MatReuse call,Mat *newmat) 3623 { 3624 PetscErrorCode ierr; 3625 PetscMPIInt rank,size; 3626 PetscInt i,m,n,rstart,row,rend,nz,*cwork,j,bs,cbs; 3627 PetscInt *ii,*jj,nlocal,*dlens,*olens,dlen,olen,jend,mglobal; 3628 Mat M,Mreuse; 3629 MatScalar *aa,*vwork; 3630 MPI_Comm comm; 3631 Mat_SeqAIJ *aij; 3632 PetscBool colflag,allcolumns=PETSC_FALSE; 3633 3634 PetscFunctionBegin; 3635 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 3636 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 3637 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 3638 3639 /* Check for special case: each processor gets entire matrix columns */ 3640 ierr = ISIdentity(iscol,&colflag);CHKERRQ(ierr); 3641 ierr = ISGetLocalSize(iscol,&n);CHKERRQ(ierr); 3642 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3643 3644 if (call == MAT_REUSE_MATRIX) { 3645 ierr = PetscObjectQuery((PetscObject)*newmat,"SubMatrix",(PetscObject*)&Mreuse);CHKERRQ(ierr); 3646 if (!Mreuse) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Submatrix passed in was not used before, cannot reuse"); 3647 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_REUSE_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3648 } else { 3649 ierr = MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,allcolumns,&Mreuse);CHKERRQ(ierr); 3650 } 3651 3652 /* 3653 m - number of local rows 3654 n - number of columns (same on all processors) 3655 rstart - first row in new global matrix generated 3656 */ 3657 ierr = MatGetSize(Mreuse,&m,&n);CHKERRQ(ierr); 3658 ierr = MatGetBlockSizes(Mreuse,&bs,&cbs);CHKERRQ(ierr); 3659 if (call == MAT_INITIAL_MATRIX) { 3660 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3661 ii = aij->i; 3662 jj = aij->j; 3663 3664 /* 3665 Determine the number of non-zeros in the diagonal and off-diagonal 3666 portions of the matrix in order to do correct preallocation 3667 */ 3668 3669 /* first get start and end of "diagonal" columns */ 3670 if (csize == PETSC_DECIDE) { 3671 ierr = ISGetSize(isrow,&mglobal);CHKERRQ(ierr); 3672 if (mglobal == n) { /* square matrix */ 3673 nlocal = m; 3674 } else { 3675 nlocal = n/size + ((n % size) > rank); 3676 } 3677 } else { 3678 nlocal = csize; 3679 } 3680 ierr = MPI_Scan(&nlocal,&rend,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 3681 rstart = rend - nlocal; 3682 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); 3683 3684 /* next, compute all the lengths */ 3685 ierr = PetscMalloc1(2*m+1,&dlens);CHKERRQ(ierr); 3686 olens = dlens + m; 3687 for (i=0; i<m; i++) { 3688 jend = ii[i+1] - ii[i]; 3689 olen = 0; 3690 dlen = 0; 3691 for (j=0; j<jend; j++) { 3692 if (*jj < rstart || *jj >= rend) olen++; 3693 else dlen++; 3694 jj++; 3695 } 3696 olens[i] = olen; 3697 dlens[i] = dlen; 3698 } 3699 ierr = MatCreate(comm,&M);CHKERRQ(ierr); 3700 ierr = MatSetSizes(M,m,nlocal,PETSC_DECIDE,n);CHKERRQ(ierr); 3701 ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); 3702 ierr = MatSetType(M,((PetscObject)mat)->type_name);CHKERRQ(ierr); 3703 ierr = MatMPIAIJSetPreallocation(M,0,dlens,0,olens);CHKERRQ(ierr); 3704 ierr = PetscFree(dlens);CHKERRQ(ierr); 3705 } else { 3706 PetscInt ml,nl; 3707 3708 M = *newmat; 3709 ierr = MatGetLocalSize(M,&ml,&nl);CHKERRQ(ierr); 3710 if (ml != m) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Previous matrix must be same size/layout as request"); 3711 ierr = MatZeroEntries(M);CHKERRQ(ierr); 3712 /* 3713 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3714 rather than the slower MatSetValues(). 3715 */ 3716 M->was_assembled = PETSC_TRUE; 3717 M->assembled = PETSC_FALSE; 3718 } 3719 ierr = MatGetOwnershipRange(M,&rstart,&rend);CHKERRQ(ierr); 3720 aij = (Mat_SeqAIJ*)(Mreuse)->data; 3721 ii = aij->i; 3722 jj = aij->j; 3723 aa = aij->a; 3724 for (i=0; i<m; i++) { 3725 row = rstart + i; 3726 nz = ii[i+1] - ii[i]; 3727 cwork = jj; jj += nz; 3728 vwork = aa; aa += nz; 3729 ierr = MatSetValues_MPIAIJ(M,1,&row,nz,cwork,vwork,INSERT_VALUES);CHKERRQ(ierr); 3730 } 3731 3732 ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3733 ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3734 *newmat = M; 3735 3736 /* save submatrix used in processor for next request */ 3737 if (call == MAT_INITIAL_MATRIX) { 3738 ierr = PetscObjectCompose((PetscObject)M,"SubMatrix",(PetscObject)Mreuse);CHKERRQ(ierr); 3739 ierr = MatDestroy(&Mreuse);CHKERRQ(ierr); 3740 } 3741 PetscFunctionReturn(0); 3742 } 3743 3744 PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B,const PetscInt Ii[],const PetscInt J[],const PetscScalar v[]) 3745 { 3746 PetscInt m,cstart, cend,j,nnz,i,d; 3747 PetscInt *d_nnz,*o_nnz,nnz_max = 0,rstart,ii; 3748 const PetscInt *JJ; 3749 PetscScalar *values; 3750 PetscErrorCode ierr; 3751 PetscBool nooffprocentries; 3752 3753 PetscFunctionBegin; 3754 if (Ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Ii[0] must be 0 it is %D",Ii[0]); 3755 3756 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 3757 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 3758 m = B->rmap->n; 3759 cstart = B->cmap->rstart; 3760 cend = B->cmap->rend; 3761 rstart = B->rmap->rstart; 3762 3763 ierr = PetscMalloc2(m,&d_nnz,m,&o_nnz);CHKERRQ(ierr); 3764 3765 #if defined(PETSC_USE_DEBUGGING) 3766 for (i=0; i<m; i++) { 3767 nnz = Ii[i+1]- Ii[i]; 3768 JJ = J + Ii[i]; 3769 if (nnz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Local row %D has a negative %D number of columns",i,nnz); 3770 if (nnz && (JJ[0] < 0)) SETERRRQ1(PETSC_ERR_ARG_WRONGSTATE,"Row %D starts with negative column index",i,j); 3771 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); 3772 } 3773 #endif 3774 3775 for (i=0; i<m; i++) { 3776 nnz = Ii[i+1]- Ii[i]; 3777 JJ = J + Ii[i]; 3778 nnz_max = PetscMax(nnz_max,nnz); 3779 d = 0; 3780 for (j=0; j<nnz; j++) { 3781 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3782 } 3783 d_nnz[i] = d; 3784 o_nnz[i] = nnz - d; 3785 } 3786 ierr = MatMPIAIJSetPreallocation(B,0,d_nnz,0,o_nnz);CHKERRQ(ierr); 3787 ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); 3788 3789 if (v) values = (PetscScalar*)v; 3790 else { 3791 ierr = PetscCalloc1(nnz_max+1,&values);CHKERRQ(ierr); 3792 } 3793 3794 for (i=0; i<m; i++) { 3795 ii = i + rstart; 3796 nnz = Ii[i+1]- Ii[i]; 3797 ierr = MatSetValues_MPIAIJ(B,1,&ii,nnz,J+Ii[i],values+(v ? Ii[i] : 0),INSERT_VALUES);CHKERRQ(ierr); 3798 } 3799 nooffprocentries = B->nooffprocentries; 3800 B->nooffprocentries = PETSC_TRUE; 3801 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3802 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 3803 B->nooffprocentries = nooffprocentries; 3804 3805 if (!v) { 3806 ierr = PetscFree(values);CHKERRQ(ierr); 3807 } 3808 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 3809 PetscFunctionReturn(0); 3810 } 3811 3812 /*@ 3813 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in AIJ format 3814 (the default parallel PETSc format). 3815 3816 Collective on MPI_Comm 3817 3818 Input Parameters: 3819 + B - the matrix 3820 . i - the indices into j for the start of each local row (starts with zero) 3821 . j - the column indices for each local row (starts with zero) 3822 - v - optional values in the matrix 3823 3824 Level: developer 3825 3826 Notes: 3827 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 3828 thus you CANNOT change the matrix entries by changing the values of a[] after you have 3829 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 3830 3831 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 3832 3833 The format which is used for the sparse matrix input, is equivalent to a 3834 row-major ordering.. i.e for the following matrix, the input data expected is 3835 as shown 3836 3837 $ 1 0 0 3838 $ 2 0 3 P0 3839 $ ------- 3840 $ 4 5 6 P1 3841 $ 3842 $ Process0 [P0]: rows_owned=[0,1] 3843 $ i = {0,1,3} [size = nrow+1 = 2+1] 3844 $ j = {0,0,2} [size = 3] 3845 $ v = {1,2,3} [size = 3] 3846 $ 3847 $ Process1 [P1]: rows_owned=[2] 3848 $ i = {0,3} [size = nrow+1 = 1+1] 3849 $ j = {0,1,2} [size = 3] 3850 $ v = {4,5,6} [size = 3] 3851 3852 .keywords: matrix, aij, compressed row, sparse, parallel 3853 3854 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatCreateAIJ(), MATMPIAIJ, 3855 MatCreateSeqAIJWithArrays(), MatCreateMPIAIJWithSplitArrays() 3856 @*/ 3857 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 3858 { 3859 PetscErrorCode ierr; 3860 3861 PetscFunctionBegin; 3862 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocationCSR_C",(Mat,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,i,j,v));CHKERRQ(ierr); 3863 PetscFunctionReturn(0); 3864 } 3865 3866 /*@C 3867 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in AIJ format 3868 (the default parallel PETSc format). For good matrix assembly performance 3869 the user should preallocate the matrix storage by setting the parameters 3870 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 3871 performance can be increased by more than a factor of 50. 3872 3873 Collective on MPI_Comm 3874 3875 Input Parameters: 3876 + B - the matrix 3877 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 3878 (same value is used for all local rows) 3879 . d_nnz - array containing the number of nonzeros in the various rows of the 3880 DIAGONAL portion of the local submatrix (possibly different for each row) 3881 or NULL (PETSC_NULL_INTEGER in Fortran), if d_nz is used to specify the nonzero structure. 3882 The size of this array is equal to the number of local rows, i.e 'm'. 3883 For matrices that will be factored, you must leave room for (and set) 3884 the diagonal entry even if it is zero. 3885 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 3886 submatrix (same value is used for all local rows). 3887 - o_nnz - array containing the number of nonzeros in the various rows of the 3888 OFF-DIAGONAL portion of the local submatrix (possibly different for 3889 each row) or NULL (PETSC_NULL_INTEGER in Fortran), if o_nz is used to specify the nonzero 3890 structure. The size of this array is equal to the number 3891 of local rows, i.e 'm'. 3892 3893 If the *_nnz parameter is given then the *_nz parameter is ignored 3894 3895 The AIJ format (also called the Yale sparse matrix format or 3896 compressed row storage (CSR)), is fully compatible with standard Fortran 77 3897 storage. The stored row and column indices begin with zero. 3898 See Users-Manual: ch_mat for details. 3899 3900 The parallel matrix is partitioned such that the first m0 rows belong to 3901 process 0, the next m1 rows belong to process 1, the next m2 rows belong 3902 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 3903 3904 The DIAGONAL portion of the local submatrix of a processor can be defined 3905 as the submatrix which is obtained by extraction the part corresponding to 3906 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 3907 first row that belongs to the processor, r2 is the last row belonging to 3908 the this processor, and c1-c2 is range of indices of the local part of a 3909 vector suitable for applying the matrix to. This is an mxn matrix. In the 3910 common case of a square matrix, the row and column ranges are the same and 3911 the DIAGONAL part is also square. The remaining portion of the local 3912 submatrix (mxN) constitute the OFF-DIAGONAL portion. 3913 3914 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 3915 3916 You can call MatGetInfo() to get information on how effective the preallocation was; 3917 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 3918 You can also run with the option -info and look for messages with the string 3919 malloc in them to see if additional memory allocation was needed. 3920 3921 Example usage: 3922 3923 Consider the following 8x8 matrix with 34 non-zero values, that is 3924 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 3925 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 3926 as follows: 3927 3928 .vb 3929 1 2 0 | 0 3 0 | 0 4 3930 Proc0 0 5 6 | 7 0 0 | 8 0 3931 9 0 10 | 11 0 0 | 12 0 3932 ------------------------------------- 3933 13 0 14 | 15 16 17 | 0 0 3934 Proc1 0 18 0 | 19 20 21 | 0 0 3935 0 0 0 | 22 23 0 | 24 0 3936 ------------------------------------- 3937 Proc2 25 26 27 | 0 0 28 | 29 0 3938 30 0 0 | 31 32 33 | 0 34 3939 .ve 3940 3941 This can be represented as a collection of submatrices as: 3942 3943 .vb 3944 A B C 3945 D E F 3946 G H I 3947 .ve 3948 3949 Where the submatrices A,B,C are owned by proc0, D,E,F are 3950 owned by proc1, G,H,I are owned by proc2. 3951 3952 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3953 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 3954 The 'M','N' parameters are 8,8, and have the same values on all procs. 3955 3956 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 3957 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 3958 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 3959 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 3960 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 3961 matrix, ans [DF] as another SeqAIJ matrix. 3962 3963 When d_nz, o_nz parameters are specified, d_nz storage elements are 3964 allocated for every row of the local diagonal submatrix, and o_nz 3965 storage locations are allocated for every row of the OFF-DIAGONAL submat. 3966 One way to choose d_nz and o_nz is to use the max nonzerors per local 3967 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 3968 In this case, the values of d_nz,o_nz are: 3969 .vb 3970 proc0 : dnz = 2, o_nz = 2 3971 proc1 : dnz = 3, o_nz = 2 3972 proc2 : dnz = 1, o_nz = 4 3973 .ve 3974 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 3975 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 3976 for proc3. i.e we are using 12+15+10=37 storage locations to store 3977 34 values. 3978 3979 When d_nnz, o_nnz parameters are specified, the storage is specified 3980 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 3981 In the above case the values for d_nnz,o_nnz are: 3982 .vb 3983 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 3984 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 3985 proc2: d_nnz = [1,1] and o_nnz = [4,4] 3986 .ve 3987 Here the space allocated is sum of all the above values i.e 34, and 3988 hence pre-allocation is perfect. 3989 3990 Level: intermediate 3991 3992 .keywords: matrix, aij, compressed row, sparse, parallel 3993 3994 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateAIJ(), MatMPIAIJSetPreallocationCSR(), 3995 MATMPIAIJ, MatGetInfo(), PetscSplitOwnership() 3996 @*/ 3997 PetscErrorCode MatMPIAIJSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 3998 { 3999 PetscErrorCode ierr; 4000 4001 PetscFunctionBegin; 4002 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 4003 PetscValidType(B,1); 4004 ierr = PetscTryMethod(B,"MatMPIAIJSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 4005 PetscFunctionReturn(0); 4006 } 4007 4008 /*@ 4009 MatCreateMPIAIJWithArrays - creates a MPI AIJ matrix using arrays that contain in standard 4010 CSR format the local rows. 4011 4012 Collective on MPI_Comm 4013 4014 Input Parameters: 4015 + comm - MPI communicator 4016 . m - number of local rows (Cannot be PETSC_DECIDE) 4017 . n - This value should be the same as the local size used in creating the 4018 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4019 calculated if N is given) For square matrices n is almost always m. 4020 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4021 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4022 . i - row indices 4023 . j - column indices 4024 - a - matrix values 4025 4026 Output Parameter: 4027 . mat - the matrix 4028 4029 Level: intermediate 4030 4031 Notes: 4032 The i, j, and a arrays ARE copied by this routine into the internal format used by PETSc; 4033 thus you CANNOT change the matrix entries by changing the values of a[] after you have 4034 called this routine. Use MatCreateMPIAIJWithSplitArrays() to avoid needing to copy the arrays. 4035 4036 The i and j indices are 0 based, and i indices are indices corresponding to the local j array. 4037 4038 The format which is used for the sparse matrix input, is equivalent to a 4039 row-major ordering.. i.e for the following matrix, the input data expected is 4040 as shown 4041 4042 $ 1 0 0 4043 $ 2 0 3 P0 4044 $ ------- 4045 $ 4 5 6 P1 4046 $ 4047 $ Process0 [P0]: rows_owned=[0,1] 4048 $ i = {0,1,3} [size = nrow+1 = 2+1] 4049 $ j = {0,0,2} [size = 3] 4050 $ v = {1,2,3} [size = 3] 4051 $ 4052 $ Process1 [P1]: rows_owned=[2] 4053 $ i = {0,3} [size = nrow+1 = 1+1] 4054 $ j = {0,1,2} [size = 3] 4055 $ v = {4,5,6} [size = 3] 4056 4057 .keywords: matrix, aij, compressed row, sparse, parallel 4058 4059 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4060 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithSplitArrays() 4061 @*/ 4062 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm,PetscInt m,PetscInt n,PetscInt M,PetscInt N,const PetscInt i[],const PetscInt j[],const PetscScalar a[],Mat *mat) 4063 { 4064 PetscErrorCode ierr; 4065 4066 PetscFunctionBegin; 4067 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 4068 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4069 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 4070 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 4071 /* ierr = MatSetBlockSizes(M,bs,cbs);CHKERRQ(ierr); */ 4072 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 4073 ierr = MatMPIAIJSetPreallocationCSR(*mat,i,j,a);CHKERRQ(ierr); 4074 PetscFunctionReturn(0); 4075 } 4076 4077 /*@C 4078 MatCreateAIJ - Creates a sparse parallel matrix in AIJ format 4079 (the default parallel PETSc format). For good matrix assembly performance 4080 the user should preallocate the matrix storage by setting the parameters 4081 d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, 4082 performance can be increased by more than a factor of 50. 4083 4084 Collective on MPI_Comm 4085 4086 Input Parameters: 4087 + comm - MPI communicator 4088 . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) 4089 This value should be the same as the local size used in creating the 4090 y vector for the matrix-vector product y = Ax. 4091 . n - This value should be the same as the local size used in creating the 4092 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 4093 calculated if N is given) For square matrices n is almost always m. 4094 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 4095 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 4096 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4097 (same value is used for all local rows) 4098 . d_nnz - array containing the number of nonzeros in the various rows of the 4099 DIAGONAL portion of the local submatrix (possibly different for each row) 4100 or NULL, if d_nz is used to specify the nonzero structure. 4101 The size of this array is equal to the number of local rows, i.e 'm'. 4102 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4103 submatrix (same value is used for all local rows). 4104 - o_nnz - array containing the number of nonzeros in the various rows of the 4105 OFF-DIAGONAL portion of the local submatrix (possibly different for 4106 each row) or NULL, if o_nz is used to specify the nonzero 4107 structure. The size of this array is equal to the number 4108 of local rows, i.e 'm'. 4109 4110 Output Parameter: 4111 . A - the matrix 4112 4113 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 4114 MatXXXXSetPreallocation() paradgm instead of this routine directly. 4115 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 4116 4117 Notes: 4118 If the *_nnz parameter is given then the *_nz parameter is ignored 4119 4120 m,n,M,N parameters specify the size of the matrix, and its partitioning across 4121 processors, while d_nz,d_nnz,o_nz,o_nnz parameters specify the approximate 4122 storage requirements for this matrix. 4123 4124 If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one 4125 processor than it must be used on all processors that share the object for 4126 that argument. 4127 4128 The user MUST specify either the local or global matrix dimensions 4129 (possibly both). 4130 4131 The parallel matrix is partitioned across processors such that the 4132 first m0 rows belong to process 0, the next m1 rows belong to 4133 process 1, the next m2 rows belong to process 2 etc.. where 4134 m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores 4135 values corresponding to [m x N] submatrix. 4136 4137 The columns are logically partitioned with the n0 columns belonging 4138 to 0th partition, the next n1 columns belonging to the next 4139 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4140 4141 The DIAGONAL portion of the local submatrix on any given processor 4142 is the submatrix corresponding to the rows and columns m,n 4143 corresponding to the given processor. i.e diagonal matrix on 4144 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4145 etc. The remaining portion of the local submatrix [m x (N-n)] 4146 constitute the OFF-DIAGONAL portion. The example below better 4147 illustrates this concept. 4148 4149 For a square global matrix we define each processor's diagonal portion 4150 to be its local rows and the corresponding columns (a square submatrix); 4151 each processor's off-diagonal portion encompasses the remainder of the 4152 local matrix (a rectangular submatrix). 4153 4154 If o_nnz, d_nnz are specified, then o_nz, and d_nz are ignored. 4155 4156 When calling this routine with a single process communicator, a matrix of 4157 type SEQAIJ is returned. If a matrix of type MATMPIAIJ is desired for this 4158 type of communicator, use the construction mechanism: 4159 MatCreate(...,&A); MatSetType(A,MATMPIAIJ); MatSetSizes(A, m,n,M,N); MatMPIAIJSetPreallocation(A,...); 4160 4161 By default, this format uses inodes (identical nodes) when possible. 4162 We search for consecutive rows with the same nonzero structure, thereby 4163 reusing matrix information to achieve increased efficiency. 4164 4165 Options Database Keys: 4166 + -mat_no_inode - Do not use inodes 4167 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4168 - -mat_aij_oneindex - Internally use indexing starting at 1 4169 rather than 0. Note that when calling MatSetValues(), 4170 the user still MUST index entries starting at 0! 4171 4172 4173 Example usage: 4174 4175 Consider the following 8x8 matrix with 34 non-zero values, that is 4176 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4177 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4178 as follows: 4179 4180 .vb 4181 1 2 0 | 0 3 0 | 0 4 4182 Proc0 0 5 6 | 7 0 0 | 8 0 4183 9 0 10 | 11 0 0 | 12 0 4184 ------------------------------------- 4185 13 0 14 | 15 16 17 | 0 0 4186 Proc1 0 18 0 | 19 20 21 | 0 0 4187 0 0 0 | 22 23 0 | 24 0 4188 ------------------------------------- 4189 Proc2 25 26 27 | 0 0 28 | 29 0 4190 30 0 0 | 31 32 33 | 0 34 4191 .ve 4192 4193 This can be represented as a collection of submatrices as: 4194 4195 .vb 4196 A B C 4197 D E F 4198 G H I 4199 .ve 4200 4201 Where the submatrices A,B,C are owned by proc0, D,E,F are 4202 owned by proc1, G,H,I are owned by proc2. 4203 4204 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4205 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4206 The 'M','N' parameters are 8,8, and have the same values on all procs. 4207 4208 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4209 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4210 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4211 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4212 part as SeqAIJ matrices. for eg: proc1 will store [E] as a SeqAIJ 4213 matrix, ans [DF] as another SeqAIJ matrix. 4214 4215 When d_nz, o_nz parameters are specified, d_nz storage elements are 4216 allocated for every row of the local diagonal submatrix, and o_nz 4217 storage locations are allocated for every row of the OFF-DIAGONAL submat. 4218 One way to choose d_nz and o_nz is to use the max nonzerors per local 4219 rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4220 In this case, the values of d_nz,o_nz are: 4221 .vb 4222 proc0 : dnz = 2, o_nz = 2 4223 proc1 : dnz = 3, o_nz = 2 4224 proc2 : dnz = 1, o_nz = 4 4225 .ve 4226 We are allocating m*(d_nz+o_nz) storage locations for every proc. This 4227 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4228 for proc3. i.e we are using 12+15+10=37 storage locations to store 4229 34 values. 4230 4231 When d_nnz, o_nnz parameters are specified, the storage is specified 4232 for every row, coresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4233 In the above case the values for d_nnz,o_nnz are: 4234 .vb 4235 proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2] 4236 proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1] 4237 proc2: d_nnz = [1,1] and o_nnz = [4,4] 4238 .ve 4239 Here the space allocated is sum of all the above values i.e 34, and 4240 hence pre-allocation is perfect. 4241 4242 Level: intermediate 4243 4244 .keywords: matrix, aij, compressed row, sparse, parallel 4245 4246 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 4247 MATMPIAIJ, MatCreateMPIAIJWithArrays() 4248 @*/ 4249 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) 4250 { 4251 PetscErrorCode ierr; 4252 PetscMPIInt size; 4253 4254 PetscFunctionBegin; 4255 ierr = MatCreate(comm,A);CHKERRQ(ierr); 4256 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 4257 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4258 if (size > 1) { 4259 ierr = MatSetType(*A,MATMPIAIJ);CHKERRQ(ierr); 4260 ierr = MatMPIAIJSetPreallocation(*A,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); 4261 } else { 4262 ierr = MatSetType(*A,MATSEQAIJ);CHKERRQ(ierr); 4263 ierr = MatSeqAIJSetPreallocation(*A,d_nz,d_nnz);CHKERRQ(ierr); 4264 } 4265 PetscFunctionReturn(0); 4266 } 4267 4268 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A,Mat *Ad,Mat *Ao,const PetscInt *colmap[]) 4269 { 4270 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 4271 PetscBool flg; 4272 PetscErrorCode ierr; 4273 4274 PetscFunctionBegin; 4275 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&flg);CHKERRQ(ierr); 4276 if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"This function requires a MATMPIAIJ matrix as input"); 4277 if (Ad) *Ad = a->A; 4278 if (Ao) *Ao = a->B; 4279 if (colmap) *colmap = a->garray; 4280 PetscFunctionReturn(0); 4281 } 4282 4283 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm,Mat inmat,PetscInt n,MatReuse scall,Mat *outmat) 4284 { 4285 PetscErrorCode ierr; 4286 PetscInt m,N,i,rstart,nnz,Ii; 4287 PetscInt *indx; 4288 PetscScalar *values; 4289 4290 PetscFunctionBegin; 4291 ierr = MatGetSize(inmat,&m,&N);CHKERRQ(ierr); 4292 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4293 PetscInt *dnz,*onz,sum,bs,cbs; 4294 4295 if (n == PETSC_DECIDE) { 4296 ierr = PetscSplitOwnership(comm,&n,&N);CHKERRQ(ierr); 4297 } 4298 /* Check sum(n) = N */ 4299 ierr = MPIU_Allreduce(&n,&sum,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4300 if (sum != N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Sum of local columns != global columns %d",N); 4301 4302 ierr = MPI_Scan(&m, &rstart,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr); 4303 rstart -= m; 4304 4305 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4306 for (i=0; i<m; i++) { 4307 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4308 ierr = MatPreallocateSet(i+rstart,nnz,indx,dnz,onz);CHKERRQ(ierr); 4309 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,NULL);CHKERRQ(ierr); 4310 } 4311 4312 ierr = MatCreate(comm,outmat);CHKERRQ(ierr); 4313 ierr = MatSetSizes(*outmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4314 ierr = MatGetBlockSizes(inmat,&bs,&cbs);CHKERRQ(ierr); 4315 ierr = MatSetBlockSizes(*outmat,bs,cbs);CHKERRQ(ierr); 4316 ierr = MatSetType(*outmat,MATAIJ);CHKERRQ(ierr); 4317 ierr = MatSeqAIJSetPreallocation(*outmat,0,dnz);CHKERRQ(ierr); 4318 ierr = MatMPIAIJSetPreallocation(*outmat,0,dnz,0,onz);CHKERRQ(ierr); 4319 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4320 } 4321 4322 /* numeric phase */ 4323 ierr = MatGetOwnershipRange(*outmat,&rstart,NULL);CHKERRQ(ierr); 4324 for (i=0; i<m; i++) { 4325 ierr = MatGetRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4326 Ii = i + rstart; 4327 ierr = MatSetValues(*outmat,1,&Ii,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4328 ierr = MatRestoreRow_SeqAIJ(inmat,i,&nnz,&indx,&values);CHKERRQ(ierr); 4329 } 4330 ierr = MatAssemblyBegin(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4331 ierr = MatAssemblyEnd(*outmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4332 PetscFunctionReturn(0); 4333 } 4334 4335 PetscErrorCode MatFileSplit(Mat A,char *outfile) 4336 { 4337 PetscErrorCode ierr; 4338 PetscMPIInt rank; 4339 PetscInt m,N,i,rstart,nnz; 4340 size_t len; 4341 const PetscInt *indx; 4342 PetscViewer out; 4343 char *name; 4344 Mat B; 4345 const PetscScalar *values; 4346 4347 PetscFunctionBegin; 4348 ierr = MatGetLocalSize(A,&m,0);CHKERRQ(ierr); 4349 ierr = MatGetSize(A,0,&N);CHKERRQ(ierr); 4350 /* Should this be the type of the diagonal block of A? */ 4351 ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr); 4352 ierr = MatSetSizes(B,m,N,m,N);CHKERRQ(ierr); 4353 ierr = MatSetBlockSizesFromMats(B,A,A);CHKERRQ(ierr); 4354 ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr); 4355 ierr = MatSeqAIJSetPreallocation(B,0,NULL);CHKERRQ(ierr); 4356 ierr = MatGetOwnershipRange(A,&rstart,0);CHKERRQ(ierr); 4357 for (i=0; i<m; i++) { 4358 ierr = MatGetRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4359 ierr = MatSetValues(B,1,&i,nnz,indx,values,INSERT_VALUES);CHKERRQ(ierr); 4360 ierr = MatRestoreRow(A,i+rstart,&nnz,&indx,&values);CHKERRQ(ierr); 4361 } 4362 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4363 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4364 4365 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)A),&rank);CHKERRQ(ierr); 4366 ierr = PetscStrlen(outfile,&len);CHKERRQ(ierr); 4367 ierr = PetscMalloc1(len+5,&name);CHKERRQ(ierr); 4368 sprintf(name,"%s.%d",outfile,rank); 4369 ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,name,FILE_MODE_APPEND,&out);CHKERRQ(ierr); 4370 ierr = PetscFree(name);CHKERRQ(ierr); 4371 ierr = MatView(B,out);CHKERRQ(ierr); 4372 ierr = PetscViewerDestroy(&out);CHKERRQ(ierr); 4373 ierr = MatDestroy(&B);CHKERRQ(ierr); 4374 PetscFunctionReturn(0); 4375 } 4376 4377 PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(Mat A) 4378 { 4379 PetscErrorCode ierr; 4380 Mat_Merge_SeqsToMPI *merge; 4381 PetscContainer container; 4382 4383 PetscFunctionBegin; 4384 ierr = PetscObjectQuery((PetscObject)A,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4385 if (container) { 4386 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4387 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 4388 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 4389 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 4390 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 4391 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 4392 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 4393 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 4394 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 4395 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 4396 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 4397 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 4398 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 4399 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 4400 ierr = PetscFree(merge);CHKERRQ(ierr); 4401 ierr = PetscObjectCompose((PetscObject)A,"MatMergeSeqsToMPI",0);CHKERRQ(ierr); 4402 } 4403 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 4404 PetscFunctionReturn(0); 4405 } 4406 4407 #include <../src/mat/utils/freespace.h> 4408 #include <petscbt.h> 4409 4410 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat,Mat mpimat) 4411 { 4412 PetscErrorCode ierr; 4413 MPI_Comm comm; 4414 Mat_SeqAIJ *a =(Mat_SeqAIJ*)seqmat->data; 4415 PetscMPIInt size,rank,taga,*len_s; 4416 PetscInt N=mpimat->cmap->N,i,j,*owners,*ai=a->i,*aj; 4417 PetscInt proc,m; 4418 PetscInt **buf_ri,**buf_rj; 4419 PetscInt k,anzi,*bj_i,*bi,*bj,arow,bnzi,nextaj; 4420 PetscInt nrows,**buf_ri_k,**nextrow,**nextai; 4421 MPI_Request *s_waits,*r_waits; 4422 MPI_Status *status; 4423 MatScalar *aa=a->a; 4424 MatScalar **abuf_r,*ba_i; 4425 Mat_Merge_SeqsToMPI *merge; 4426 PetscContainer container; 4427 4428 PetscFunctionBegin; 4429 ierr = PetscObjectGetComm((PetscObject)mpimat,&comm);CHKERRQ(ierr); 4430 ierr = PetscLogEventBegin(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4431 4432 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4433 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4434 4435 ierr = PetscObjectQuery((PetscObject)mpimat,"MatMergeSeqsToMPI",(PetscObject*)&container);CHKERRQ(ierr); 4436 ierr = PetscContainerGetPointer(container,(void**)&merge);CHKERRQ(ierr); 4437 4438 bi = merge->bi; 4439 bj = merge->bj; 4440 buf_ri = merge->buf_ri; 4441 buf_rj = merge->buf_rj; 4442 4443 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4444 owners = merge->rowmap->range; 4445 len_s = merge->len_s; 4446 4447 /* send and recv matrix values */ 4448 /*-----------------------------*/ 4449 ierr = PetscObjectGetNewTag((PetscObject)mpimat,&taga);CHKERRQ(ierr); 4450 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 4451 4452 ierr = PetscMalloc1(merge->nsend+1,&s_waits);CHKERRQ(ierr); 4453 for (proc=0,k=0; proc<size; proc++) { 4454 if (!len_s[proc]) continue; 4455 i = owners[proc]; 4456 ierr = MPI_Isend(aa+ai[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 4457 k++; 4458 } 4459 4460 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 4461 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 4462 ierr = PetscFree(status);CHKERRQ(ierr); 4463 4464 ierr = PetscFree(s_waits);CHKERRQ(ierr); 4465 ierr = PetscFree(r_waits);CHKERRQ(ierr); 4466 4467 /* insert mat values of mpimat */ 4468 /*----------------------------*/ 4469 ierr = PetscMalloc1(N,&ba_i);CHKERRQ(ierr); 4470 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4471 4472 for (k=0; k<merge->nrecv; k++) { 4473 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4474 nrows = *(buf_ri_k[k]); 4475 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 4476 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4477 } 4478 4479 /* set values of ba */ 4480 m = merge->rowmap->n; 4481 for (i=0; i<m; i++) { 4482 arow = owners[rank] + i; 4483 bj_i = bj+bi[i]; /* col indices of the i-th row of mpimat */ 4484 bnzi = bi[i+1] - bi[i]; 4485 ierr = PetscMemzero(ba_i,bnzi*sizeof(PetscScalar));CHKERRQ(ierr); 4486 4487 /* add local non-zero vals of this proc's seqmat into ba */ 4488 anzi = ai[arow+1] - ai[arow]; 4489 aj = a->j + ai[arow]; 4490 aa = a->a + ai[arow]; 4491 nextaj = 0; 4492 for (j=0; nextaj<anzi; j++) { 4493 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4494 ba_i[j] += aa[nextaj++]; 4495 } 4496 } 4497 4498 /* add received vals into ba */ 4499 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4500 /* i-th row */ 4501 if (i == *nextrow[k]) { 4502 anzi = *(nextai[k]+1) - *nextai[k]; 4503 aj = buf_rj[k] + *(nextai[k]); 4504 aa = abuf_r[k] + *(nextai[k]); 4505 nextaj = 0; 4506 for (j=0; nextaj<anzi; j++) { 4507 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4508 ba_i[j] += aa[nextaj++]; 4509 } 4510 } 4511 nextrow[k]++; nextai[k]++; 4512 } 4513 } 4514 ierr = MatSetValues(mpimat,1,&arow,bnzi,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 4515 } 4516 ierr = MatAssemblyBegin(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4517 ierr = MatAssemblyEnd(mpimat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 4518 4519 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 4520 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 4521 ierr = PetscFree(ba_i);CHKERRQ(ierr); 4522 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4523 ierr = PetscLogEventEnd(MAT_Seqstompinum,seqmat,0,0,0);CHKERRQ(ierr); 4524 PetscFunctionReturn(0); 4525 } 4526 4527 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,Mat *mpimat) 4528 { 4529 PetscErrorCode ierr; 4530 Mat B_mpi; 4531 Mat_SeqAIJ *a=(Mat_SeqAIJ*)seqmat->data; 4532 PetscMPIInt size,rank,tagi,tagj,*len_s,*len_si,*len_ri; 4533 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 4534 PetscInt M=seqmat->rmap->n,N=seqmat->cmap->n,i,*owners,*ai=a->i,*aj=a->j; 4535 PetscInt len,proc,*dnz,*onz,bs,cbs; 4536 PetscInt k,anzi,*bi,*bj,*lnk,nlnk,arow,bnzi,nspacedouble=0; 4537 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextai; 4538 MPI_Request *si_waits,*sj_waits,*ri_waits,*rj_waits; 4539 MPI_Status *status; 4540 PetscFreeSpaceList free_space=NULL,current_space=NULL; 4541 PetscBT lnkbt; 4542 Mat_Merge_SeqsToMPI *merge; 4543 PetscContainer container; 4544 4545 PetscFunctionBegin; 4546 ierr = PetscLogEventBegin(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4547 4548 /* make sure it is a PETSc comm */ 4549 ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr); 4550 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4551 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 4552 4553 ierr = PetscNew(&merge);CHKERRQ(ierr); 4554 ierr = PetscMalloc1(size,&status);CHKERRQ(ierr); 4555 4556 /* determine row ownership */ 4557 /*---------------------------------------------------------*/ 4558 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 4559 ierr = PetscLayoutSetLocalSize(merge->rowmap,m);CHKERRQ(ierr); 4560 ierr = PetscLayoutSetSize(merge->rowmap,M);CHKERRQ(ierr); 4561 ierr = PetscLayoutSetBlockSize(merge->rowmap,1);CHKERRQ(ierr); 4562 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 4563 ierr = PetscMalloc1(size,&len_si);CHKERRQ(ierr); 4564 ierr = PetscMalloc1(size,&merge->len_s);CHKERRQ(ierr); 4565 4566 m = merge->rowmap->n; 4567 owners = merge->rowmap->range; 4568 4569 /* determine the number of messages to send, their lengths */ 4570 /*---------------------------------------------------------*/ 4571 len_s = merge->len_s; 4572 4573 len = 0; /* length of buf_si[] */ 4574 merge->nsend = 0; 4575 for (proc=0; proc<size; proc++) { 4576 len_si[proc] = 0; 4577 if (proc == rank) { 4578 len_s[proc] = 0; 4579 } else { 4580 len_si[proc] = owners[proc+1] - owners[proc] + 1; 4581 len_s[proc] = ai[owners[proc+1]] - ai[owners[proc]]; /* num of rows to be sent to [proc] */ 4582 } 4583 if (len_s[proc]) { 4584 merge->nsend++; 4585 nrows = 0; 4586 for (i=owners[proc]; i<owners[proc+1]; i++) { 4587 if (ai[i+1] > ai[i]) nrows++; 4588 } 4589 len_si[proc] = 2*(nrows+1); 4590 len += len_si[proc]; 4591 } 4592 } 4593 4594 /* determine the number and length of messages to receive for ij-structure */ 4595 /*-------------------------------------------------------------------------*/ 4596 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 4597 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 4598 4599 /* post the Irecv of j-structure */ 4600 /*-------------------------------*/ 4601 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 4602 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rj_waits);CHKERRQ(ierr); 4603 4604 /* post the Isend of j-structure */ 4605 /*--------------------------------*/ 4606 ierr = PetscMalloc2(merge->nsend,&si_waits,merge->nsend,&sj_waits);CHKERRQ(ierr); 4607 4608 for (proc=0, k=0; proc<size; proc++) { 4609 if (!len_s[proc]) continue; 4610 i = owners[proc]; 4611 ierr = MPI_Isend(aj+ai[i],len_s[proc],MPIU_INT,proc,tagj,comm,sj_waits+k);CHKERRQ(ierr); 4612 k++; 4613 } 4614 4615 /* receives and sends of j-structure are complete */ 4616 /*------------------------------------------------*/ 4617 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,rj_waits,status);CHKERRQ(ierr);} 4618 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,sj_waits,status);CHKERRQ(ierr);} 4619 4620 /* send and recv i-structure */ 4621 /*---------------------------*/ 4622 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 4623 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&ri_waits);CHKERRQ(ierr); 4624 4625 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 4626 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4627 for (proc=0,k=0; proc<size; proc++) { 4628 if (!len_s[proc]) continue; 4629 /* form outgoing message for i-structure: 4630 buf_si[0]: nrows to be sent 4631 [1:nrows]: row index (global) 4632 [nrows+1:2*nrows+1]: i-structure index 4633 */ 4634 /*-------------------------------------------*/ 4635 nrows = len_si[proc]/2 - 1; 4636 buf_si_i = buf_si + nrows+1; 4637 buf_si[0] = nrows; 4638 buf_si_i[0] = 0; 4639 nrows = 0; 4640 for (i=owners[proc]; i<owners[proc+1]; i++) { 4641 anzi = ai[i+1] - ai[i]; 4642 if (anzi) { 4643 buf_si_i[nrows+1] = buf_si_i[nrows] + anzi; /* i-structure */ 4644 buf_si[nrows+1] = i-owners[proc]; /* local row index */ 4645 nrows++; 4646 } 4647 } 4648 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,si_waits+k);CHKERRQ(ierr); 4649 k++; 4650 buf_si += len_si[proc]; 4651 } 4652 4653 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,ri_waits,status);CHKERRQ(ierr);} 4654 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,si_waits,status);CHKERRQ(ierr);} 4655 4656 ierr = PetscInfo2(seqmat,"nsend: %D, nrecv: %D\n",merge->nsend,merge->nrecv);CHKERRQ(ierr); 4657 for (i=0; i<merge->nrecv; i++) { 4658 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); 4659 } 4660 4661 ierr = PetscFree(len_si);CHKERRQ(ierr); 4662 ierr = PetscFree(len_ri);CHKERRQ(ierr); 4663 ierr = PetscFree(rj_waits);CHKERRQ(ierr); 4664 ierr = PetscFree2(si_waits,sj_waits);CHKERRQ(ierr); 4665 ierr = PetscFree(ri_waits);CHKERRQ(ierr); 4666 ierr = PetscFree(buf_s);CHKERRQ(ierr); 4667 ierr = PetscFree(status);CHKERRQ(ierr); 4668 4669 /* compute a local seq matrix in each processor */ 4670 /*----------------------------------------------*/ 4671 /* allocate bi array and free space for accumulating nonzero column info */ 4672 ierr = PetscMalloc1(m+1,&bi);CHKERRQ(ierr); 4673 bi[0] = 0; 4674 4675 /* create and initialize a linked list */ 4676 nlnk = N+1; 4677 ierr = PetscLLCreate(N,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4678 4679 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4680 len = ai[owners[rank+1]] - ai[owners[rank]]; 4681 ierr = PetscFreeSpaceGet(PetscIntMultTruncate(2,len)+1,&free_space);CHKERRQ(ierr); 4682 4683 current_space = free_space; 4684 4685 /* determine symbolic info for each local row */ 4686 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextai);CHKERRQ(ierr); 4687 4688 for (k=0; k<merge->nrecv; k++) { 4689 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4690 nrows = *buf_ri_k[k]; 4691 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4692 nextai[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 4693 } 4694 4695 ierr = MatPreallocateInitialize(comm,m,n,dnz,onz);CHKERRQ(ierr); 4696 len = 0; 4697 for (i=0; i<m; i++) { 4698 bnzi = 0; 4699 /* add local non-zero cols of this proc's seqmat into lnk */ 4700 arow = owners[rank] + i; 4701 anzi = ai[arow+1] - ai[arow]; 4702 aj = a->j + ai[arow]; 4703 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4704 bnzi += nlnk; 4705 /* add received col data into lnk */ 4706 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 4707 if (i == *nextrow[k]) { /* i-th row */ 4708 anzi = *(nextai[k]+1) - *nextai[k]; 4709 aj = buf_rj[k] + *nextai[k]; 4710 ierr = PetscLLAddSorted(anzi,aj,N,nlnk,lnk,lnkbt);CHKERRQ(ierr); 4711 bnzi += nlnk; 4712 nextrow[k]++; nextai[k]++; 4713 } 4714 } 4715 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 4716 4717 /* if free space is not available, make more free space */ 4718 if (current_space->local_remaining<bnzi) { 4719 ierr = PetscFreeSpaceGet(PetscIntSumTruncate(bnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); 4720 nspacedouble++; 4721 } 4722 /* copy data into free space, then initialize lnk */ 4723 ierr = PetscLLClean(N,N,bnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); 4724 ierr = MatPreallocateSet(i+owners[rank],bnzi,current_space->array,dnz,onz);CHKERRQ(ierr); 4725 4726 current_space->array += bnzi; 4727 current_space->local_used += bnzi; 4728 current_space->local_remaining -= bnzi; 4729 4730 bi[i+1] = bi[i] + bnzi; 4731 } 4732 4733 ierr = PetscFree3(buf_ri_k,nextrow,nextai);CHKERRQ(ierr); 4734 4735 ierr = PetscMalloc1(bi[m]+1,&bj);CHKERRQ(ierr); 4736 ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); 4737 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 4738 4739 /* create symbolic parallel matrix B_mpi */ 4740 /*---------------------------------------*/ 4741 ierr = MatGetBlockSizes(seqmat,&bs,&cbs);CHKERRQ(ierr); 4742 ierr = MatCreate(comm,&B_mpi);CHKERRQ(ierr); 4743 if (n==PETSC_DECIDE) { 4744 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,N);CHKERRQ(ierr); 4745 } else { 4746 ierr = MatSetSizes(B_mpi,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 4747 } 4748 ierr = MatSetBlockSizes(B_mpi,bs,cbs);CHKERRQ(ierr); 4749 ierr = MatSetType(B_mpi,MATMPIAIJ);CHKERRQ(ierr); 4750 ierr = MatMPIAIJSetPreallocation(B_mpi,0,dnz,0,onz);CHKERRQ(ierr); 4751 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 4752 ierr = MatSetOption(B_mpi,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); 4753 4754 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 4755 B_mpi->assembled = PETSC_FALSE; 4756 B_mpi->ops->destroy = MatDestroy_MPIAIJ_SeqsToMPI; 4757 merge->bi = bi; 4758 merge->bj = bj; 4759 merge->buf_ri = buf_ri; 4760 merge->buf_rj = buf_rj; 4761 merge->coi = NULL; 4762 merge->coj = NULL; 4763 merge->owners_co = NULL; 4764 4765 ierr = PetscCommDestroy(&comm);CHKERRQ(ierr); 4766 4767 /* attach the supporting struct to B_mpi for reuse */ 4768 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 4769 ierr = PetscContainerSetPointer(container,merge);CHKERRQ(ierr); 4770 ierr = PetscObjectCompose((PetscObject)B_mpi,"MatMergeSeqsToMPI",(PetscObject)container);CHKERRQ(ierr); 4771 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 4772 *mpimat = B_mpi; 4773 4774 ierr = PetscLogEventEnd(MAT_Seqstompisym,seqmat,0,0,0);CHKERRQ(ierr); 4775 PetscFunctionReturn(0); 4776 } 4777 4778 /*@C 4779 MatCreateMPIAIJSumSeqAIJ - Creates a MATMPIAIJ matrix by adding sequential 4780 matrices from each processor 4781 4782 Collective on MPI_Comm 4783 4784 Input Parameters: 4785 + comm - the communicators the parallel matrix will live on 4786 . seqmat - the input sequential matrices 4787 . m - number of local rows (or PETSC_DECIDE) 4788 . n - number of local columns (or PETSC_DECIDE) 4789 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4790 4791 Output Parameter: 4792 . mpimat - the parallel matrix generated 4793 4794 Level: advanced 4795 4796 Notes: 4797 The dimensions of the sequential matrix in each processor MUST be the same. 4798 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 4799 destroyed when mpimat is destroyed. Call PetscObjectQuery() to access seqmat. 4800 @*/ 4801 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm,Mat seqmat,PetscInt m,PetscInt n,MatReuse scall,Mat *mpimat) 4802 { 4803 PetscErrorCode ierr; 4804 PetscMPIInt size; 4805 4806 PetscFunctionBegin; 4807 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4808 if (size == 1) { 4809 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4810 if (scall == MAT_INITIAL_MATRIX) { 4811 ierr = MatDuplicate(seqmat,MAT_COPY_VALUES,mpimat);CHKERRQ(ierr); 4812 } else { 4813 ierr = MatCopy(seqmat,*mpimat,SAME_NONZERO_PATTERN);CHKERRQ(ierr); 4814 } 4815 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4816 PetscFunctionReturn(0); 4817 } 4818 ierr = PetscLogEventBegin(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4819 if (scall == MAT_INITIAL_MATRIX) { 4820 ierr = MatCreateMPIAIJSumSeqAIJSymbolic(comm,seqmat,m,n,mpimat);CHKERRQ(ierr); 4821 } 4822 ierr = MatCreateMPIAIJSumSeqAIJNumeric(seqmat,*mpimat);CHKERRQ(ierr); 4823 ierr = PetscLogEventEnd(MAT_Seqstompi,seqmat,0,0,0);CHKERRQ(ierr); 4824 PetscFunctionReturn(0); 4825 } 4826 4827 /*@ 4828 MatMPIAIJGetLocalMat - Creates a SeqAIJ from a MATMPIAIJ matrix by taking all its local rows and putting them into a sequential vector with 4829 mlocal rows and n columns. Where mlocal is the row count obtained with MatGetLocalSize() and n is the global column count obtained 4830 with MatGetSize() 4831 4832 Not Collective 4833 4834 Input Parameters: 4835 + A - the matrix 4836 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4837 4838 Output Parameter: 4839 . A_loc - the local sequential matrix generated 4840 4841 Level: developer 4842 4843 .seealso: MatGetOwnerShipRange(), MatMPIAIJGetLocalMatCondensed() 4844 4845 @*/ 4846 PetscErrorCode MatMPIAIJGetLocalMat(Mat A,MatReuse scall,Mat *A_loc) 4847 { 4848 PetscErrorCode ierr; 4849 Mat_MPIAIJ *mpimat=(Mat_MPIAIJ*)A->data; 4850 Mat_SeqAIJ *mat,*a,*b; 4851 PetscInt *ai,*aj,*bi,*bj,*cmap=mpimat->garray; 4852 MatScalar *aa,*ba,*cam; 4853 PetscScalar *ca; 4854 PetscInt am=A->rmap->n,i,j,k,cstart=A->cmap->rstart; 4855 PetscInt *ci,*cj,col,ncols_d,ncols_o,jo; 4856 PetscBool match; 4857 MPI_Comm comm; 4858 PetscMPIInt size; 4859 4860 PetscFunctionBegin; 4861 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4862 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4863 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 4864 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 4865 if (size == 1 && scall == MAT_REUSE_MATRIX) PetscFunctionReturn(0); 4866 4867 ierr = PetscLogEventBegin(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4868 a = (Mat_SeqAIJ*)(mpimat->A)->data; 4869 b = (Mat_SeqAIJ*)(mpimat->B)->data; 4870 ai = a->i; aj = a->j; bi = b->i; bj = b->j; 4871 aa = a->a; ba = b->a; 4872 if (scall == MAT_INITIAL_MATRIX) { 4873 if (size == 1) { 4874 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ai,aj,aa,A_loc);CHKERRQ(ierr); 4875 PetscFunctionReturn(0); 4876 } 4877 4878 ierr = PetscMalloc1(1+am,&ci);CHKERRQ(ierr); 4879 ci[0] = 0; 4880 for (i=0; i<am; i++) { 4881 ci[i+1] = ci[i] + (ai[i+1] - ai[i]) + (bi[i+1] - bi[i]); 4882 } 4883 ierr = PetscMalloc1(1+ci[am],&cj);CHKERRQ(ierr); 4884 ierr = PetscMalloc1(1+ci[am],&ca);CHKERRQ(ierr); 4885 k = 0; 4886 for (i=0; i<am; i++) { 4887 ncols_o = bi[i+1] - bi[i]; 4888 ncols_d = ai[i+1] - ai[i]; 4889 /* off-diagonal portion of A */ 4890 for (jo=0; jo<ncols_o; jo++) { 4891 col = cmap[*bj]; 4892 if (col >= cstart) break; 4893 cj[k] = col; bj++; 4894 ca[k++] = *ba++; 4895 } 4896 /* diagonal portion of A */ 4897 for (j=0; j<ncols_d; j++) { 4898 cj[k] = cstart + *aj++; 4899 ca[k++] = *aa++; 4900 } 4901 /* off-diagonal portion of A */ 4902 for (j=jo; j<ncols_o; j++) { 4903 cj[k] = cmap[*bj++]; 4904 ca[k++] = *ba++; 4905 } 4906 } 4907 /* put together the new matrix */ 4908 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,A->cmap->N,ci,cj,ca,A_loc);CHKERRQ(ierr); 4909 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 4910 /* Since these are PETSc arrays, change flags to free them as necessary. */ 4911 mat = (Mat_SeqAIJ*)(*A_loc)->data; 4912 mat->free_a = PETSC_TRUE; 4913 mat->free_ij = PETSC_TRUE; 4914 mat->nonew = 0; 4915 } else if (scall == MAT_REUSE_MATRIX) { 4916 mat=(Mat_SeqAIJ*)(*A_loc)->data; 4917 ci = mat->i; cj = mat->j; cam = mat->a; 4918 for (i=0; i<am; i++) { 4919 /* off-diagonal portion of A */ 4920 ncols_o = bi[i+1] - bi[i]; 4921 for (jo=0; jo<ncols_o; jo++) { 4922 col = cmap[*bj]; 4923 if (col >= cstart) break; 4924 *cam++ = *ba++; bj++; 4925 } 4926 /* diagonal portion of A */ 4927 ncols_d = ai[i+1] - ai[i]; 4928 for (j=0; j<ncols_d; j++) *cam++ = *aa++; 4929 /* off-diagonal portion of A */ 4930 for (j=jo; j<ncols_o; j++) { 4931 *cam++ = *ba++; bj++; 4932 } 4933 } 4934 } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Invalid MatReuse %d",(int)scall); 4935 ierr = PetscLogEventEnd(MAT_Getlocalmat,A,0,0,0);CHKERRQ(ierr); 4936 PetscFunctionReturn(0); 4937 } 4938 4939 /*@C 4940 MatMPIAIJGetLocalMatCondensed - Creates a SeqAIJ matrix from an MATMPIAIJ matrix by taking all its local rows and NON-ZERO columns 4941 4942 Not Collective 4943 4944 Input Parameters: 4945 + A - the matrix 4946 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 4947 - row, col - index sets of rows and columns to extract (or NULL) 4948 4949 Output Parameter: 4950 . A_loc - the local sequential matrix generated 4951 4952 Level: developer 4953 4954 .seealso: MatGetOwnershipRange(), MatMPIAIJGetLocalMat() 4955 4956 @*/ 4957 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A,MatReuse scall,IS *row,IS *col,Mat *A_loc) 4958 { 4959 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 4960 PetscErrorCode ierr; 4961 PetscInt i,start,end,ncols,nzA,nzB,*cmap,imark,*idx; 4962 IS isrowa,iscola; 4963 Mat *aloc; 4964 PetscBool match; 4965 4966 PetscFunctionBegin; 4967 ierr = PetscObjectTypeCompare((PetscObject)A,MATMPIAIJ,&match);CHKERRQ(ierr); 4968 if (!match) SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_SUP,"Requires MATMPIAIJ matrix as input"); 4969 ierr = PetscLogEventBegin(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 4970 if (!row) { 4971 start = A->rmap->rstart; end = A->rmap->rend; 4972 ierr = ISCreateStride(PETSC_COMM_SELF,end-start,start,1,&isrowa);CHKERRQ(ierr); 4973 } else { 4974 isrowa = *row; 4975 } 4976 if (!col) { 4977 start = A->cmap->rstart; 4978 cmap = a->garray; 4979 nzA = a->A->cmap->n; 4980 nzB = a->B->cmap->n; 4981 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 4982 ncols = 0; 4983 for (i=0; i<nzB; i++) { 4984 if (cmap[i] < start) idx[ncols++] = cmap[i]; 4985 else break; 4986 } 4987 imark = i; 4988 for (i=0; i<nzA; i++) idx[ncols++] = start + i; 4989 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; 4990 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&iscola);CHKERRQ(ierr); 4991 } else { 4992 iscola = *col; 4993 } 4994 if (scall != MAT_INITIAL_MATRIX) { 4995 ierr = PetscMalloc1(1,&aloc);CHKERRQ(ierr); 4996 aloc[0] = *A_loc; 4997 } 4998 ierr = MatCreateSubMatrices(A,1,&isrowa,&iscola,scall,&aloc);CHKERRQ(ierr); 4999 *A_loc = aloc[0]; 5000 ierr = PetscFree(aloc);CHKERRQ(ierr); 5001 if (!row) { 5002 ierr = ISDestroy(&isrowa);CHKERRQ(ierr); 5003 } 5004 if (!col) { 5005 ierr = ISDestroy(&iscola);CHKERRQ(ierr); 5006 } 5007 ierr = PetscLogEventEnd(MAT_Getlocalmatcondensed,A,0,0,0);CHKERRQ(ierr); 5008 PetscFunctionReturn(0); 5009 } 5010 5011 /*@C 5012 MatGetBrowsOfAcols - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 5013 5014 Collective on Mat 5015 5016 Input Parameters: 5017 + A,B - the matrices in mpiaij format 5018 . scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5019 - rowb, colb - index sets of rows and columns of B to extract (or NULL) 5020 5021 Output Parameter: 5022 + rowb, colb - index sets of rows and columns of B to extract 5023 - B_seq - the sequential matrix generated 5024 5025 Level: developer 5026 5027 @*/ 5028 PetscErrorCode MatGetBrowsOfAcols(Mat A,Mat B,MatReuse scall,IS *rowb,IS *colb,Mat *B_seq) 5029 { 5030 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5031 PetscErrorCode ierr; 5032 PetscInt *idx,i,start,ncols,nzA,nzB,*cmap,imark; 5033 IS isrowb,iscolb; 5034 Mat *bseq=NULL; 5035 5036 PetscFunctionBegin; 5037 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5038 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); 5039 } 5040 ierr = PetscLogEventBegin(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5041 5042 if (scall == MAT_INITIAL_MATRIX) { 5043 start = A->cmap->rstart; 5044 cmap = a->garray; 5045 nzA = a->A->cmap->n; 5046 nzB = a->B->cmap->n; 5047 ierr = PetscMalloc1(nzA+nzB, &idx);CHKERRQ(ierr); 5048 ncols = 0; 5049 for (i=0; i<nzB; i++) { /* row < local row index */ 5050 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5051 else break; 5052 } 5053 imark = i; 5054 for (i=0; i<nzA; i++) idx[ncols++] = start + i; /* local rows */ 5055 for (i=imark; i<nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5056 ierr = ISCreateGeneral(PETSC_COMM_SELF,ncols,idx,PETSC_OWN_POINTER,&isrowb);CHKERRQ(ierr); 5057 ierr = ISCreateStride(PETSC_COMM_SELF,B->cmap->N,0,1,&iscolb);CHKERRQ(ierr); 5058 } else { 5059 if (!rowb || !colb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5060 isrowb = *rowb; iscolb = *colb; 5061 ierr = PetscMalloc1(1,&bseq);CHKERRQ(ierr); 5062 bseq[0] = *B_seq; 5063 } 5064 ierr = MatCreateSubMatrices(B,1,&isrowb,&iscolb,scall,&bseq);CHKERRQ(ierr); 5065 *B_seq = bseq[0]; 5066 ierr = PetscFree(bseq);CHKERRQ(ierr); 5067 if (!rowb) { 5068 ierr = ISDestroy(&isrowb);CHKERRQ(ierr); 5069 } else { 5070 *rowb = isrowb; 5071 } 5072 if (!colb) { 5073 ierr = ISDestroy(&iscolb);CHKERRQ(ierr); 5074 } else { 5075 *colb = iscolb; 5076 } 5077 ierr = PetscLogEventEnd(MAT_GetBrowsOfAcols,A,B,0,0);CHKERRQ(ierr); 5078 PetscFunctionReturn(0); 5079 } 5080 5081 /* 5082 MatGetBrowsOfAoCols_MPIAIJ - Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns 5083 of the OFF-DIAGONAL portion of local A 5084 5085 Collective on Mat 5086 5087 Input Parameters: 5088 + A,B - the matrices in mpiaij format 5089 - scall - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 5090 5091 Output Parameter: 5092 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5093 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5094 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5095 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5096 5097 Level: developer 5098 5099 */ 5100 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscInt **startsj_s,PetscInt **startsj_r,MatScalar **bufa_ptr,Mat *B_oth) 5101 { 5102 VecScatter_MPI_General *gen_to,*gen_from; 5103 PetscErrorCode ierr; 5104 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 5105 Mat_SeqAIJ *b_oth; 5106 VecScatter ctx =a->Mvctx; 5107 MPI_Comm comm; 5108 PetscMPIInt *rprocs,*sprocs,tag=((PetscObject)ctx)->tag,rank; 5109 PetscInt *rowlen,*bufj,*bufJ,ncols,aBn=a->B->cmap->n,row,*b_othi,*b_othj; 5110 PetscInt *rvalues,*svalues; 5111 MatScalar *b_otha,*bufa,*bufA; 5112 PetscInt i,j,k,l,ll,nrecvs,nsends,nrows,*srow,*rstarts,*rstartsj = 0,*sstarts,*sstartsj,len; 5113 MPI_Request *rwaits = NULL,*swaits = NULL; 5114 MPI_Status *sstatus,rstatus; 5115 PetscMPIInt jj,size; 5116 PetscInt *cols,sbs,rbs; 5117 PetscScalar *vals; 5118 5119 PetscFunctionBegin; 5120 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 5121 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 5122 5123 if (A->cmap->rstart != B->rmap->rstart || A->cmap->rend != B->rmap->rend) { 5124 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); 5125 } 5126 ierr = PetscLogEventBegin(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5127 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 5128 5129 if (size == 1) { 5130 startsj_s = NULL; 5131 bufa_ptr = NULL; 5132 *B_oth = NULL; 5133 PetscFunctionReturn(0); 5134 } 5135 5136 gen_to = (VecScatter_MPI_General*)ctx->todata; 5137 gen_from = (VecScatter_MPI_General*)ctx->fromdata; 5138 nrecvs = gen_from->n; 5139 nsends = gen_to->n; 5140 5141 ierr = PetscMalloc2(nrecvs,&rwaits,nsends,&swaits);CHKERRQ(ierr); 5142 srow = gen_to->indices; /* local row index to be sent */ 5143 sstarts = gen_to->starts; 5144 sprocs = gen_to->procs; 5145 sstatus = gen_to->sstatus; 5146 sbs = gen_to->bs; 5147 rstarts = gen_from->starts; 5148 rprocs = gen_from->procs; 5149 rbs = gen_from->bs; 5150 5151 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5152 if (scall == MAT_INITIAL_MATRIX) { 5153 /* i-array */ 5154 /*---------*/ 5155 /* post receives */ 5156 ierr = PetscMalloc1(rbs*(rstarts[nrecvs] - rstarts[0]),&rvalues);CHKERRQ(ierr); 5157 for (i=0; i<nrecvs; i++) { 5158 rowlen = rvalues + rstarts[i]*rbs; 5159 nrows = (rstarts[i+1]-rstarts[i])*rbs; /* num of indices to be received */ 5160 ierr = MPI_Irecv(rowlen,nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5161 } 5162 5163 /* pack the outgoing message */ 5164 ierr = PetscMalloc2(nsends+1,&sstartsj,nrecvs+1,&rstartsj);CHKERRQ(ierr); 5165 5166 sstartsj[0] = 0; 5167 rstartsj[0] = 0; 5168 len = 0; /* total length of j or a array to be sent */ 5169 k = 0; 5170 ierr = PetscMalloc1(sbs*(sstarts[nsends] - sstarts[0]),&svalues);CHKERRQ(ierr); 5171 for (i=0; i<nsends; i++) { 5172 rowlen = svalues + sstarts[i]*sbs; 5173 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5174 for (j=0; j<nrows; j++) { 5175 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5176 for (l=0; l<sbs; l++) { 5177 ierr = MatGetRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); /* rowlength */ 5178 5179 rowlen[j*sbs+l] = ncols; 5180 5181 len += ncols; 5182 ierr = MatRestoreRow_MPIAIJ(B,row+l,&ncols,NULL,NULL);CHKERRQ(ierr); 5183 } 5184 k++; 5185 } 5186 ierr = MPI_Isend(rowlen,nrows*sbs,MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5187 5188 sstartsj[i+1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5189 } 5190 /* recvs and sends of i-array are completed */ 5191 i = nrecvs; 5192 while (i--) { 5193 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5194 } 5195 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5196 ierr = PetscFree(svalues);CHKERRQ(ierr); 5197 5198 /* allocate buffers for sending j and a arrays */ 5199 ierr = PetscMalloc1(len+1,&bufj);CHKERRQ(ierr); 5200 ierr = PetscMalloc1(len+1,&bufa);CHKERRQ(ierr); 5201 5202 /* create i-array of B_oth */ 5203 ierr = PetscMalloc1(aBn+2,&b_othi);CHKERRQ(ierr); 5204 5205 b_othi[0] = 0; 5206 len = 0; /* total length of j or a array to be received */ 5207 k = 0; 5208 for (i=0; i<nrecvs; i++) { 5209 rowlen = rvalues + rstarts[i]*rbs; 5210 nrows = rbs*(rstarts[i+1]-rstarts[i]); /* num of rows to be received */ 5211 for (j=0; j<nrows; j++) { 5212 b_othi[k+1] = b_othi[k] + rowlen[j]; 5213 ierr = PetscIntSumError(rowlen[j],len,&len);CHKERRQ(ierr); 5214 k++; 5215 } 5216 rstartsj[i+1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5217 } 5218 ierr = PetscFree(rvalues);CHKERRQ(ierr); 5219 5220 /* allocate space for j and a arrrays of B_oth */ 5221 ierr = PetscMalloc1(b_othi[aBn]+1,&b_othj);CHKERRQ(ierr); 5222 ierr = PetscMalloc1(b_othi[aBn]+1,&b_otha);CHKERRQ(ierr); 5223 5224 /* j-array */ 5225 /*---------*/ 5226 /* post receives of j-array */ 5227 for (i=0; i<nrecvs; i++) { 5228 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5229 ierr = MPI_Irecv(b_othj+rstartsj[i],nrows,MPIU_INT,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5230 } 5231 5232 /* pack the outgoing message j-array */ 5233 k = 0; 5234 for (i=0; i<nsends; i++) { 5235 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5236 bufJ = bufj+sstartsj[i]; 5237 for (j=0; j<nrows; j++) { 5238 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5239 for (ll=0; ll<sbs; ll++) { 5240 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5241 for (l=0; l<ncols; l++) { 5242 *bufJ++ = cols[l]; 5243 } 5244 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,&cols,NULL);CHKERRQ(ierr); 5245 } 5246 } 5247 ierr = MPI_Isend(bufj+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_INT,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5248 } 5249 5250 /* recvs and sends of j-array are completed */ 5251 i = nrecvs; 5252 while (i--) { 5253 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5254 } 5255 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5256 } else if (scall == MAT_REUSE_MATRIX) { 5257 sstartsj = *startsj_s; 5258 rstartsj = *startsj_r; 5259 bufa = *bufa_ptr; 5260 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5261 b_otha = b_oth->a; 5262 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not posses an object container"); 5263 5264 /* a-array */ 5265 /*---------*/ 5266 /* post receives of a-array */ 5267 for (i=0; i<nrecvs; i++) { 5268 nrows = rstartsj[i+1]-rstartsj[i]; /* length of the msg received */ 5269 ierr = MPI_Irecv(b_otha+rstartsj[i],nrows,MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr); 5270 } 5271 5272 /* pack the outgoing message a-array */ 5273 k = 0; 5274 for (i=0; i<nsends; i++) { 5275 nrows = sstarts[i+1]-sstarts[i]; /* num of block rows */ 5276 bufA = bufa+sstartsj[i]; 5277 for (j=0; j<nrows; j++) { 5278 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5279 for (ll=0; ll<sbs; ll++) { 5280 ierr = MatGetRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5281 for (l=0; l<ncols; l++) { 5282 *bufA++ = vals[l]; 5283 } 5284 ierr = MatRestoreRow_MPIAIJ(B,row+ll,&ncols,NULL,&vals);CHKERRQ(ierr); 5285 } 5286 } 5287 ierr = MPI_Isend(bufa+sstartsj[i],sstartsj[i+1]-sstartsj[i],MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr); 5288 } 5289 /* recvs and sends of a-array are completed */ 5290 i = nrecvs; 5291 while (i--) { 5292 ierr = MPI_Waitany(nrecvs,rwaits,&jj,&rstatus);CHKERRQ(ierr); 5293 } 5294 if (nsends) {ierr = MPI_Waitall(nsends,swaits,sstatus);CHKERRQ(ierr);} 5295 ierr = PetscFree2(rwaits,swaits);CHKERRQ(ierr); 5296 5297 if (scall == MAT_INITIAL_MATRIX) { 5298 /* put together the new matrix */ 5299 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,aBn,B->cmap->N,b_othi,b_othj,b_otha,B_oth);CHKERRQ(ierr); 5300 5301 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5302 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5303 b_oth = (Mat_SeqAIJ*)(*B_oth)->data; 5304 b_oth->free_a = PETSC_TRUE; 5305 b_oth->free_ij = PETSC_TRUE; 5306 b_oth->nonew = 0; 5307 5308 ierr = PetscFree(bufj);CHKERRQ(ierr); 5309 if (!startsj_s || !bufa_ptr) { 5310 ierr = PetscFree2(sstartsj,rstartsj);CHKERRQ(ierr); 5311 ierr = PetscFree(bufa_ptr);CHKERRQ(ierr); 5312 } else { 5313 *startsj_s = sstartsj; 5314 *startsj_r = rstartsj; 5315 *bufa_ptr = bufa; 5316 } 5317 } 5318 ierr = PetscLogEventEnd(MAT_GetBrowsOfAocols,A,B,0,0);CHKERRQ(ierr); 5319 PetscFunctionReturn(0); 5320 } 5321 5322 /*@C 5323 MatGetCommunicationStructs - Provides access to the communication structures used in matrix-vector multiplication. 5324 5325 Not Collective 5326 5327 Input Parameters: 5328 . A - The matrix in mpiaij format 5329 5330 Output Parameter: 5331 + lvec - The local vector holding off-process values from the argument to a matrix-vector product 5332 . colmap - A map from global column index to local index into lvec 5333 - multScatter - A scatter from the argument of a matrix-vector product to lvec 5334 5335 Level: developer 5336 5337 @*/ 5338 #if defined(PETSC_USE_CTABLE) 5339 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscTable *colmap, VecScatter *multScatter) 5340 #else 5341 PetscErrorCode MatGetCommunicationStructs(Mat A, Vec *lvec, PetscInt *colmap[], VecScatter *multScatter) 5342 #endif 5343 { 5344 Mat_MPIAIJ *a; 5345 5346 PetscFunctionBegin; 5347 PetscValidHeaderSpecific(A, MAT_CLASSID, 1); 5348 PetscValidPointer(lvec, 2); 5349 PetscValidPointer(colmap, 3); 5350 PetscValidPointer(multScatter, 4); 5351 a = (Mat_MPIAIJ*) A->data; 5352 if (lvec) *lvec = a->lvec; 5353 if (colmap) *colmap = a->colmap; 5354 if (multScatter) *multScatter = a->Mvctx; 5355 PetscFunctionReturn(0); 5356 } 5357 5358 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat,MatType,MatReuse,Mat*); 5359 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat,MatType,MatReuse,Mat*); 5360 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat,MatType,MatReuse,Mat*); 5361 #if defined(PETSC_HAVE_ELEMENTAL) 5362 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat,MatType,MatReuse,Mat*); 5363 #endif 5364 #if defined(PETSC_HAVE_HYPRE) 5365 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat,MatType,MatReuse,Mat*); 5366 PETSC_INTERN PetscErrorCode MatMatMatMult_Transpose_AIJ_AIJ(Mat,Mat,Mat,MatReuse,PetscReal,Mat*); 5367 #endif 5368 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat,MatType,MatReuse,Mat*); 5369 5370 /* 5371 Computes (B'*A')' since computing B*A directly is untenable 5372 5373 n p p 5374 ( ) ( ) ( ) 5375 m ( A ) * n ( B ) = m ( C ) 5376 ( ) ( ) ( ) 5377 5378 */ 5379 PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A,Mat B,Mat C) 5380 { 5381 PetscErrorCode ierr; 5382 Mat At,Bt,Ct; 5383 5384 PetscFunctionBegin; 5385 ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&At);CHKERRQ(ierr); 5386 ierr = MatTranspose(B,MAT_INITIAL_MATRIX,&Bt);CHKERRQ(ierr); 5387 ierr = MatMatMult(Bt,At,MAT_INITIAL_MATRIX,1.0,&Ct);CHKERRQ(ierr); 5388 ierr = MatDestroy(&At);CHKERRQ(ierr); 5389 ierr = MatDestroy(&Bt);CHKERRQ(ierr); 5390 ierr = MatTranspose(Ct,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 5391 ierr = MatDestroy(&Ct);CHKERRQ(ierr); 5392 PetscFunctionReturn(0); 5393 } 5394 5395 PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A,Mat B,PetscReal fill,Mat *C) 5396 { 5397 PetscErrorCode ierr; 5398 PetscInt m=A->rmap->n,n=B->cmap->n; 5399 Mat Cmat; 5400 5401 PetscFunctionBegin; 5402 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); 5403 ierr = MatCreate(PetscObjectComm((PetscObject)A),&Cmat);CHKERRQ(ierr); 5404 ierr = MatSetSizes(Cmat,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 5405 ierr = MatSetBlockSizesFromMats(Cmat,A,B);CHKERRQ(ierr); 5406 ierr = MatSetType(Cmat,MATMPIDENSE);CHKERRQ(ierr); 5407 ierr = MatMPIDenseSetPreallocation(Cmat,NULL);CHKERRQ(ierr); 5408 ierr = MatAssemblyBegin(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5409 ierr = MatAssemblyEnd(Cmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5410 5411 Cmat->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 5412 5413 *C = Cmat; 5414 PetscFunctionReturn(0); 5415 } 5416 5417 /* ----------------------------------------------------------------*/ 5418 PETSC_INTERN PetscErrorCode MatMatMult_MPIDense_MPIAIJ(Mat A,Mat B,MatReuse scall,PetscReal fill,Mat *C) 5419 { 5420 PetscErrorCode ierr; 5421 5422 PetscFunctionBegin; 5423 if (scall == MAT_INITIAL_MATRIX) { 5424 ierr = PetscLogEventBegin(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5425 ierr = MatMatMultSymbolic_MPIDense_MPIAIJ(A,B,fill,C);CHKERRQ(ierr); 5426 ierr = PetscLogEventEnd(MAT_MatMultSymbolic,A,B,0,0);CHKERRQ(ierr); 5427 } 5428 ierr = PetscLogEventBegin(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5429 ierr = MatMatMultNumeric_MPIDense_MPIAIJ(A,B,*C);CHKERRQ(ierr); 5430 ierr = PetscLogEventEnd(MAT_MatMultNumeric,A,B,0,0);CHKERRQ(ierr); 5431 PetscFunctionReturn(0); 5432 } 5433 5434 /*MC 5435 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 5436 5437 Options Database Keys: 5438 . -mat_type mpiaij - sets the matrix type to "mpiaij" during a call to MatSetFromOptions() 5439 5440 Level: beginner 5441 5442 .seealso: MatCreateAIJ() 5443 M*/ 5444 5445 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 5446 { 5447 Mat_MPIAIJ *b; 5448 PetscErrorCode ierr; 5449 PetscMPIInt size; 5450 5451 PetscFunctionBegin; 5452 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 5453 5454 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 5455 B->data = (void*)b; 5456 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 5457 B->assembled = PETSC_FALSE; 5458 B->insertmode = NOT_SET_VALUES; 5459 b->size = size; 5460 5461 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)B),&b->rank);CHKERRQ(ierr); 5462 5463 /* build cache for off array entries formed */ 5464 ierr = MatStashCreate_Private(PetscObjectComm((PetscObject)B),1,&B->stash);CHKERRQ(ierr); 5465 5466 b->donotstash = PETSC_FALSE; 5467 b->colmap = 0; 5468 b->garray = 0; 5469 b->roworiented = PETSC_TRUE; 5470 5471 /* stuff used for matrix vector multiply */ 5472 b->lvec = NULL; 5473 b->Mvctx = NULL; 5474 5475 /* stuff for MatGetRow() */ 5476 b->rowindices = 0; 5477 b->rowvalues = 0; 5478 b->getrowactive = PETSC_FALSE; 5479 5480 /* flexible pointer used in CUSP/CUSPARSE classes */ 5481 b->spptr = NULL; 5482 5483 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetUseScalableIncreaseOverlap_C",MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ);CHKERRQ(ierr); 5484 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_MPIAIJ);CHKERRQ(ierr); 5485 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_MPIAIJ);CHKERRQ(ierr); 5486 ierr = PetscObjectComposeFunction((PetscObject)B,"MatIsTranspose_C",MatIsTranspose_MPIAIJ);CHKERRQ(ierr); 5487 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocation_C",MatMPIAIJSetPreallocation_MPIAIJ);CHKERRQ(ierr); 5488 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMPIAIJSetPreallocationCSR_C",MatMPIAIJSetPreallocationCSR_MPIAIJ);CHKERRQ(ierr); 5489 ierr = PetscObjectComposeFunction((PetscObject)B,"MatDiagonalScaleLocal_C",MatDiagonalScaleLocal_MPIAIJ);CHKERRQ(ierr); 5490 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijperm_C",MatConvert_MPIAIJ_MPIAIJPERM);CHKERRQ(ierr); 5491 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpiaijcrl_C",MatConvert_MPIAIJ_MPIAIJCRL);CHKERRQ(ierr); 5492 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_mpisbaij_C",MatConvert_MPIAIJ_MPISBAIJ);CHKERRQ(ierr); 5493 #if defined(PETSC_HAVE_ELEMENTAL) 5494 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_elemental_C",MatConvert_MPIAIJ_Elemental);CHKERRQ(ierr); 5495 #endif 5496 #if defined(PETSC_HAVE_HYPRE) 5497 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_hypre_C",MatConvert_AIJ_HYPRE);CHKERRQ(ierr); 5498 #endif 5499 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_mpiaij_is_C",MatConvert_MPIAIJ_IS);CHKERRQ(ierr); 5500 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMult_mpidense_mpiaij_C",MatMatMult_MPIDense_MPIAIJ);CHKERRQ(ierr); 5501 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultSymbolic_mpidense_mpiaij_C",MatMatMultSymbolic_MPIDense_MPIAIJ);CHKERRQ(ierr); 5502 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMultNumeric_mpidense_mpiaij_C",MatMatMultNumeric_MPIDense_MPIAIJ);CHKERRQ(ierr); 5503 #if defined(PETSC_HAVE_HYPRE) 5504 ierr = PetscObjectComposeFunction((PetscObject)B,"MatMatMatMult_transpose_mpiaij_mpiaij_C",MatMatMatMult_Transpose_AIJ_AIJ);CHKERRQ(ierr); 5505 #endif 5506 ierr = PetscObjectChangeTypeName((PetscObject)B,MATMPIAIJ);CHKERRQ(ierr); 5507 PetscFunctionReturn(0); 5508 } 5509 5510 /*@C 5511 MatCreateMPIAIJWithSplitArrays - creates a MPI AIJ matrix using arrays that contain the "diagonal" 5512 and "off-diagonal" part of the matrix in CSR format. 5513 5514 Collective on MPI_Comm 5515 5516 Input Parameters: 5517 + comm - MPI communicator 5518 . m - number of local rows (Cannot be PETSC_DECIDE) 5519 . n - This value should be the same as the local size used in creating the 5520 x vector for the matrix-vector product y = Ax. (or PETSC_DECIDE to have 5521 calculated if N is given) For square matrices n is almost always m. 5522 . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) 5523 . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) 5524 . i - row indices for "diagonal" portion of matrix 5525 . j - column indices 5526 . a - matrix values 5527 . oi - row indices for "off-diagonal" portion of matrix 5528 . oj - column indices 5529 - oa - matrix values 5530 5531 Output Parameter: 5532 . mat - the matrix 5533 5534 Level: advanced 5535 5536 Notes: 5537 The i, j, and a arrays ARE NOT copied by this routine into the internal format used by PETSc. The user 5538 must free the arrays once the matrix has been destroyed and not before. 5539 5540 The i and j indices are 0 based 5541 5542 See MatCreateAIJ() for the definition of "diagonal" and "off-diagonal" portion of the matrix 5543 5544 This sets local rows and cannot be used to set off-processor values. 5545 5546 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 5547 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 5548 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 5549 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 5550 keep track of the underlying array. Use MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) to disable all 5551 communication if it is known that only local entries will be set. 5552 5553 .keywords: matrix, aij, compressed row, sparse, parallel 5554 5555 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatMPIAIJSetPreallocation(), MatMPIAIJSetPreallocationCSR(), 5556 MATMPIAIJ, MatCreateAIJ(), MatCreateMPIAIJWithArrays() 5557 @*/ 5558 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) 5559 { 5560 PetscErrorCode ierr; 5561 Mat_MPIAIJ *maij; 5562 5563 PetscFunctionBegin; 5564 if (m < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"local number of rows (m) cannot be PETSC_DECIDE, or negative"); 5565 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 5566 if (oi[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"oi (row indices) must start with 0"); 5567 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 5568 ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr); 5569 ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr); 5570 maij = (Mat_MPIAIJ*) (*mat)->data; 5571 5572 (*mat)->preallocated = PETSC_TRUE; 5573 5574 ierr = PetscLayoutSetUp((*mat)->rmap);CHKERRQ(ierr); 5575 ierr = PetscLayoutSetUp((*mat)->cmap);CHKERRQ(ierr); 5576 5577 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,n,i,j,a,&maij->A);CHKERRQ(ierr); 5578 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,m,(*mat)->cmap->N,oi,oj,oa,&maij->B);CHKERRQ(ierr); 5579 5580 ierr = MatAssemblyBegin(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5581 ierr = MatAssemblyEnd(maij->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5582 ierr = MatAssemblyBegin(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5583 ierr = MatAssemblyEnd(maij->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5584 5585 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); 5586 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5587 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 5588 ierr = MatSetOption(*mat,MAT_NO_OFF_PROC_ENTRIES,PETSC_FALSE);CHKERRQ(ierr); 5589 ierr = MatSetOption(*mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 5590 PetscFunctionReturn(0); 5591 } 5592 5593 /* 5594 Special version for direct calls from Fortran 5595 */ 5596 #include <petsc/private/fortranimpl.h> 5597 5598 /* Change these macros so can be used in void function */ 5599 #undef CHKERRQ 5600 #define CHKERRQ(ierr) CHKERRABORT(PETSC_COMM_WORLD,ierr) 5601 #undef SETERRQ2 5602 #define SETERRQ2(comm,ierr,b,c,d) CHKERRABORT(comm,ierr) 5603 #undef SETERRQ3 5604 #define SETERRQ3(comm,ierr,b,c,d,e) CHKERRABORT(comm,ierr) 5605 #undef SETERRQ 5606 #define SETERRQ(c,ierr,b) CHKERRABORT(c,ierr) 5607 5608 #if defined(PETSC_HAVE_FORTRAN_CAPS) 5609 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 5610 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 5611 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 5612 #else 5613 #endif 5614 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) 5615 { 5616 Mat mat = *mmat; 5617 PetscInt m = *mm, n = *mn; 5618 InsertMode addv = *maddv; 5619 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)mat->data; 5620 PetscScalar value; 5621 PetscErrorCode ierr; 5622 5623 MatCheckPreallocated(mat,1); 5624 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 5625 5626 #if defined(PETSC_USE_DEBUG) 5627 else if (mat->insertmode != addv) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot mix add values and insert values"); 5628 #endif 5629 { 5630 PetscInt i,j,rstart = mat->rmap->rstart,rend = mat->rmap->rend; 5631 PetscInt cstart = mat->cmap->rstart,cend = mat->cmap->rend,row,col; 5632 PetscBool roworiented = aij->roworiented; 5633 5634 /* Some Variables required in the macro */ 5635 Mat A = aij->A; 5636 Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data; 5637 PetscInt *aimax = a->imax,*ai = a->i,*ailen = a->ilen,*aj = a->j; 5638 MatScalar *aa = a->a; 5639 PetscBool ignorezeroentries = (((a->ignorezeroentries)&&(addv==ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 5640 Mat B = aij->B; 5641 Mat_SeqAIJ *b = (Mat_SeqAIJ*)B->data; 5642 PetscInt *bimax = b->imax,*bi = b->i,*bilen = b->ilen,*bj = b->j,bm = aij->B->rmap->n,am = aij->A->rmap->n; 5643 MatScalar *ba = b->a; 5644 5645 PetscInt *rp1,*rp2,ii,nrow1,nrow2,_i,rmax1,rmax2,N,low1,high1,low2,high2,t,lastcol1,lastcol2; 5646 PetscInt nonew = a->nonew; 5647 MatScalar *ap1,*ap2; 5648 5649 PetscFunctionBegin; 5650 for (i=0; i<m; i++) { 5651 if (im[i] < 0) continue; 5652 #if defined(PETSC_USE_DEBUG) 5653 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); 5654 #endif 5655 if (im[i] >= rstart && im[i] < rend) { 5656 row = im[i] - rstart; 5657 lastcol1 = -1; 5658 rp1 = aj + ai[row]; 5659 ap1 = aa + ai[row]; 5660 rmax1 = aimax[row]; 5661 nrow1 = ailen[row]; 5662 low1 = 0; 5663 high1 = nrow1; 5664 lastcol2 = -1; 5665 rp2 = bj + bi[row]; 5666 ap2 = ba + bi[row]; 5667 rmax2 = bimax[row]; 5668 nrow2 = bilen[row]; 5669 low2 = 0; 5670 high2 = nrow2; 5671 5672 for (j=0; j<n; j++) { 5673 if (roworiented) value = v[i*n+j]; 5674 else value = v[i+j*m]; 5675 if (in[j] >= cstart && in[j] < cend) { 5676 col = in[j] - cstart; 5677 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5678 MatSetValues_SeqAIJ_A_Private(row,col,value,addv,im[i],in[j]); 5679 } else if (in[j] < 0) continue; 5680 #if defined(PETSC_USE_DEBUG) 5681 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); 5682 #endif 5683 else { 5684 if (mat->was_assembled) { 5685 if (!aij->colmap) { 5686 ierr = MatCreateColmap_MPIAIJ_Private(mat);CHKERRQ(ierr); 5687 } 5688 #if defined(PETSC_USE_CTABLE) 5689 ierr = PetscTableFind(aij->colmap,in[j]+1,&col);CHKERRQ(ierr); 5690 col--; 5691 #else 5692 col = aij->colmap[in[j]] - 1; 5693 #endif 5694 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && row != col) continue; 5695 if (col < 0 && !((Mat_SeqAIJ*)(aij->A->data))->nonew) { 5696 ierr = MatDisAssemble_MPIAIJ(mat);CHKERRQ(ierr); 5697 col = in[j]; 5698 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 5699 B = aij->B; 5700 b = (Mat_SeqAIJ*)B->data; 5701 bimax = b->imax; bi = b->i; bilen = b->ilen; bj = b->j; 5702 rp2 = bj + bi[row]; 5703 ap2 = ba + bi[row]; 5704 rmax2 = bimax[row]; 5705 nrow2 = bilen[row]; 5706 low2 = 0; 5707 high2 = nrow2; 5708 bm = aij->B->rmap->n; 5709 ba = b->a; 5710 } 5711 } else col = in[j]; 5712 MatSetValues_SeqAIJ_B_Private(row,col,value,addv,im[i],in[j]); 5713 } 5714 } 5715 } else if (!aij->donotstash) { 5716 if (roworiented) { 5717 ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5718 } else { 5719 ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m,(PetscBool)(ignorezeroentries && (addv == ADD_VALUES)));CHKERRQ(ierr); 5720 } 5721 } 5722 } 5723 } 5724 PetscFunctionReturnVoid(); 5725 } 5726 5727