1 /* 2 Creates a matrix class for using the Neumann-Neumann type preconditioners. 3 This stores the matrices in globally unassembled form. Each processor 4 assembles only its local Neumann problem and the parallel matrix vector 5 product is handled "implicitly". 6 7 Currently this allows for only one subdomain per processor. 8 */ 9 10 #include <../src/mat/impls/is/matis.h> /*I "petscmat.h" I*/ 11 #include <../src/mat/impls/aij/mpi/mpiaij.h> 12 #include <petsc/private/sfimpl.h> 13 14 #define MATIS_MAX_ENTRIES_INSERTION 2048 15 16 static PetscErrorCode MatISContainerDestroyFields_Private(void *ptr) 17 { 18 MatISLocalFields lf = (MatISLocalFields)ptr; 19 PetscInt i; 20 PetscErrorCode ierr; 21 22 PetscFunctionBeginUser; 23 for (i=0;i<lf->nr;i++) { 24 ierr = ISDestroy(&lf->rf[i]);CHKERRQ(ierr); 25 } 26 for (i=0;i<lf->nc;i++) { 27 ierr = ISDestroy(&lf->cf[i]);CHKERRQ(ierr); 28 } 29 ierr = PetscFree2(lf->rf,lf->cf);CHKERRQ(ierr); 30 ierr = PetscFree(lf);CHKERRQ(ierr); 31 PetscFunctionReturn(0); 32 } 33 34 static PetscErrorCode MatISContainerDestroyArray_Private(void *ptr) 35 { 36 PetscErrorCode ierr; 37 38 PetscFunctionBeginUser; 39 ierr = PetscFree(ptr);CHKERRQ(ierr); 40 PetscFunctionReturn(0); 41 } 42 43 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat A,MatType type,MatReuse reuse,Mat *newmat) 44 { 45 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 46 Mat_SeqAIJ *diag = (Mat_SeqAIJ*)(aij->A->data); 47 Mat_SeqAIJ *offd = (Mat_SeqAIJ*)(aij->B->data); 48 Mat lA; 49 ISLocalToGlobalMapping rl2g,cl2g; 50 IS is; 51 MPI_Comm comm; 52 void *ptrs[2]; 53 const char *names[2] = {"_convert_csr_aux","_convert_csr_data"}; 54 PetscScalar *dd,*od,*aa,*data; 55 PetscInt *di,*dj,*oi,*oj; 56 PetscInt *aux,*ii,*jj; 57 PetscInt lc,dr,dc,oc,str,stc,nnz,i,jd,jo,cum; 58 PetscErrorCode ierr; 59 60 PetscFunctionBeginUser; 61 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 62 if (!aij->garray) SETERRQ(comm,PETSC_ERR_SUP,"garray not present"); 63 64 /* access relevant information from MPIAIJ */ 65 ierr = MatGetOwnershipRange(A,&str,NULL);CHKERRQ(ierr); 66 ierr = MatGetOwnershipRangeColumn(A,&stc,NULL);CHKERRQ(ierr); 67 ierr = MatGetLocalSize(A,&dr,&dc);CHKERRQ(ierr); 68 di = diag->i; 69 dj = diag->j; 70 dd = diag->a; 71 oc = aij->B->cmap->n; 72 oi = offd->i; 73 oj = offd->j; 74 od = offd->a; 75 nnz = diag->i[dr] + offd->i[dr]; 76 77 /* generate l2g maps for rows and cols */ 78 ierr = ISCreateStride(comm,dr,str,1,&is);CHKERRQ(ierr); 79 ierr = ISLocalToGlobalMappingCreateIS(is,&rl2g);CHKERRQ(ierr); 80 ierr = ISDestroy(&is);CHKERRQ(ierr); 81 if (dr) { 82 ierr = PetscMalloc1(dc+oc,&aux);CHKERRQ(ierr); 83 for (i=0; i<dc; i++) aux[i] = i+stc; 84 for (i=0; i<oc; i++) aux[i+dc] = aij->garray[i]; 85 ierr = ISCreateGeneral(comm,dc+oc,aux,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 86 lc = dc+oc; 87 } else { 88 ierr = ISCreateGeneral(comm,0,NULL,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 89 lc = 0; 90 } 91 ierr = ISLocalToGlobalMappingCreateIS(is,&cl2g);CHKERRQ(ierr); 92 ierr = ISDestroy(&is);CHKERRQ(ierr); 93 94 /* create MATIS object */ 95 ierr = MatCreate(comm,newmat);CHKERRQ(ierr); 96 ierr = MatSetSizes(*newmat,dr,dc,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); 97 ierr = MatSetType(*newmat,MATIS);CHKERRQ(ierr); 98 ierr = MatSetLocalToGlobalMapping(*newmat,rl2g,cl2g);CHKERRQ(ierr); 99 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 100 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 101 102 /* merge local matrices */ 103 ierr = PetscMalloc1(nnz+dr+1,&aux);CHKERRQ(ierr); 104 ierr = PetscMalloc1(nnz,&data);CHKERRQ(ierr); 105 ii = aux; 106 jj = aux+dr+1; 107 aa = data; 108 *ii = *(di++) + *(oi++); 109 for (jd=0,jo=0,cum=0;*ii<nnz;cum++) 110 { 111 for (;jd<*di;jd++) { *jj++ = *dj++; *aa++ = *dd++; } 112 for (;jo<*oi;jo++) { *jj++ = *oj++ + dc; *aa++ = *od++; } 113 *(++ii) = *(di++) + *(oi++); 114 } 115 for (;cum<dr;cum++) *(++ii) = nnz; 116 ii = aux; 117 jj = aux+dr+1; 118 aa = data; 119 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,dr,lc,ii,jj,aa,&lA);CHKERRQ(ierr); 120 121 /* create containers to destroy the data */ 122 ptrs[0] = aux; 123 ptrs[1] = data; 124 for (i=0; i<2; i++) { 125 PetscContainer c; 126 127 ierr = PetscContainerCreate(PETSC_COMM_SELF,&c);CHKERRQ(ierr); 128 ierr = PetscContainerSetPointer(c,ptrs[i]);CHKERRQ(ierr); 129 ierr = PetscContainerSetUserDestroy(c,MatISContainerDestroyArray_Private);CHKERRQ(ierr); 130 ierr = PetscObjectCompose((PetscObject)lA,names[i],(PetscObject)c);CHKERRQ(ierr); 131 ierr = PetscContainerDestroy(&c);CHKERRQ(ierr); 132 } 133 134 /* finalize matrix */ 135 ierr = MatISSetLocalMat(*newmat,lA);CHKERRQ(ierr); 136 ierr = MatDestroy(&lA);CHKERRQ(ierr); 137 ierr = MatAssemblyBegin(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 138 ierr = MatAssemblyEnd(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 139 PetscFunctionReturn(0); 140 } 141 142 /*@ 143 MatISSetUpSF - Setup star forest objects used by MatIS. 144 145 Collective on MPI_Comm 146 147 Input Parameters: 148 + A - the matrix 149 150 Level: advanced 151 152 Notes: This function does not need to be called by the user. 153 154 .keywords: matrix 155 156 .seealso: MatCreate(), MatCreateIS(), MatISSetPreallocation(), MatISGetLocalMat() 157 @*/ 158 PetscErrorCode MatISSetUpSF(Mat A) 159 { 160 PetscErrorCode ierr; 161 162 PetscFunctionBegin; 163 PetscValidHeaderSpecific(A,MAT_CLASSID,1); 164 PetscValidType(A,1); 165 ierr = PetscTryMethod(A,"MatISSetUpSF_C",(Mat),(A));CHKERRQ(ierr); 166 PetscFunctionReturn(0); 167 } 168 169 PETSC_INTERN PetscErrorCode MatConvert_Nest_IS(Mat A,MatType type,MatReuse reuse,Mat *newmat) 170 { 171 Mat **nest,*snest,**rnest,lA,B; 172 IS *iscol,*isrow,*islrow,*islcol; 173 ISLocalToGlobalMapping rl2g,cl2g; 174 MPI_Comm comm; 175 PetscInt *lr,*lc,*l2gidxs; 176 PetscInt i,j,nr,nc,rbs,cbs; 177 PetscBool convert,lreuse,*istrans; 178 PetscErrorCode ierr; 179 180 PetscFunctionBeginUser; 181 ierr = MatNestGetSubMats(A,&nr,&nc,&nest);CHKERRQ(ierr); 182 lreuse = PETSC_FALSE; 183 rnest = NULL; 184 if (reuse == MAT_REUSE_MATRIX) { 185 PetscBool ismatis,isnest; 186 187 ierr = PetscObjectTypeCompare((PetscObject)*newmat,MATIS,&ismatis);CHKERRQ(ierr); 188 if (!ismatis) SETERRQ1(PetscObjectComm((PetscObject)*newmat),PETSC_ERR_USER,"Cannot reuse matrix of type %s",((PetscObject)(*newmat))->type); 189 ierr = MatISGetLocalMat(*newmat,&lA);CHKERRQ(ierr); 190 ierr = PetscObjectTypeCompare((PetscObject)lA,MATNEST,&isnest);CHKERRQ(ierr); 191 if (isnest) { 192 ierr = MatNestGetSubMats(lA,&i,&j,&rnest);CHKERRQ(ierr); 193 lreuse = (PetscBool)(i == nr && j == nc); 194 if (!lreuse) rnest = NULL; 195 } 196 } 197 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 198 ierr = PetscCalloc2(nr,&lr,nc,&lc);CHKERRQ(ierr); 199 ierr = PetscCalloc6(nr,&isrow,nc,&iscol, 200 nr,&islrow,nc,&islcol, 201 nr*nc,&snest,nr*nc,&istrans);CHKERRQ(ierr); 202 ierr = MatNestGetISs(A,isrow,iscol);CHKERRQ(ierr); 203 for (i=0;i<nr;i++) { 204 for (j=0;j<nc;j++) { 205 PetscBool ismatis; 206 PetscInt l1,l2,lb1,lb2,ij=i*nc+j; 207 208 /* Null matrix pointers are allowed in MATNEST */ 209 if (!nest[i][j]) continue; 210 211 /* Nested matrices should be of type MATIS */ 212 ierr = PetscObjectTypeCompare((PetscObject)nest[i][j],MATTRANSPOSEMAT,&istrans[ij]);CHKERRQ(ierr); 213 if (istrans[ij]) { 214 Mat T,lT; 215 ierr = MatTransposeGetMat(nest[i][j],&T);CHKERRQ(ierr); 216 ierr = PetscObjectTypeCompare((PetscObject)T,MATIS,&ismatis);CHKERRQ(ierr); 217 if (!ismatis) SETERRQ2(comm,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) (transposed) is not of type MATIS",i,j); 218 ierr = MatISGetLocalMat(T,&lT);CHKERRQ(ierr); 219 ierr = MatCreateTranspose(lT,&snest[ij]);CHKERRQ(ierr); 220 } else { 221 ierr = PetscObjectTypeCompare((PetscObject)nest[i][j],MATIS,&ismatis);CHKERRQ(ierr); 222 if (!ismatis) SETERRQ2(comm,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) is not of type MATIS",i,j); 223 ierr = MatISGetLocalMat(nest[i][j],&snest[ij]);CHKERRQ(ierr); 224 } 225 226 /* Check compatibility of local sizes */ 227 ierr = MatGetSize(snest[ij],&l1,&l2);CHKERRQ(ierr); 228 ierr = MatGetBlockSizes(snest[ij],&lb1,&lb2);CHKERRQ(ierr); 229 if (!l1 || !l2) continue; 230 if (lr[i] && l1 != lr[i]) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid local size %D != %D",i,j,lr[i],l1); 231 if (lc[j] && l2 != lc[j]) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid local size %D != %D",i,j,lc[j],l2); 232 lr[i] = l1; 233 lc[j] = l2; 234 235 /* check compatibilty for local matrix reusage */ 236 if (rnest && !rnest[i][j] != !snest[ij]) lreuse = PETSC_FALSE; 237 } 238 } 239 240 #if defined (PETSC_USE_DEBUG) 241 /* Check compatibility of l2g maps for rows */ 242 for (i=0;i<nr;i++) { 243 rl2g = NULL; 244 for (j=0;j<nc;j++) { 245 PetscInt n1,n2; 246 247 if (!nest[i][j]) continue; 248 if (istrans[i*nc+j]) { 249 Mat T; 250 251 ierr = MatTransposeGetMat(nest[i][j],&T);CHKERRQ(ierr); 252 ierr = MatGetLocalToGlobalMapping(T,NULL,&cl2g);CHKERRQ(ierr); 253 } else { 254 ierr = MatGetLocalToGlobalMapping(nest[i][j],&cl2g,NULL);CHKERRQ(ierr); 255 } 256 ierr = ISLocalToGlobalMappingGetSize(cl2g,&n1);CHKERRQ(ierr); 257 if (!n1) continue; 258 if (!rl2g) { 259 rl2g = cl2g; 260 } else { 261 const PetscInt *idxs1,*idxs2; 262 PetscBool same; 263 264 ierr = ISLocalToGlobalMappingGetSize(rl2g,&n2);CHKERRQ(ierr); 265 if (n1 != n2) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid row l2gmap size %D != %D",i,j,n1,n2); 266 ierr = ISLocalToGlobalMappingGetIndices(cl2g,&idxs1);CHKERRQ(ierr); 267 ierr = ISLocalToGlobalMappingGetIndices(rl2g,&idxs2);CHKERRQ(ierr); 268 ierr = PetscMemcmp(idxs1,idxs2,n1*sizeof(PetscInt),&same);CHKERRQ(ierr); 269 ierr = ISLocalToGlobalMappingRestoreIndices(cl2g,&idxs1);CHKERRQ(ierr); 270 ierr = ISLocalToGlobalMappingRestoreIndices(rl2g,&idxs2);CHKERRQ(ierr); 271 if (!same) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid row l2gmap",i,j); 272 } 273 } 274 } 275 /* Check compatibility of l2g maps for columns */ 276 for (i=0;i<nc;i++) { 277 rl2g = NULL; 278 for (j=0;j<nr;j++) { 279 PetscInt n1,n2; 280 281 if (!nest[j][i]) continue; 282 if (istrans[j*nc+i]) { 283 Mat T; 284 285 ierr = MatTransposeGetMat(nest[j][i],&T);CHKERRQ(ierr); 286 ierr = MatGetLocalToGlobalMapping(T,&cl2g,NULL);CHKERRQ(ierr); 287 } else { 288 ierr = MatGetLocalToGlobalMapping(nest[j][i],NULL,&cl2g);CHKERRQ(ierr); 289 } 290 ierr = ISLocalToGlobalMappingGetSize(cl2g,&n1);CHKERRQ(ierr); 291 if (!n1) continue; 292 if (!rl2g) { 293 rl2g = cl2g; 294 } else { 295 const PetscInt *idxs1,*idxs2; 296 PetscBool same; 297 298 ierr = ISLocalToGlobalMappingGetSize(rl2g,&n2);CHKERRQ(ierr); 299 if (n1 != n2) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid column l2gmap size %D != %D",j,i,n1,n2); 300 ierr = ISLocalToGlobalMappingGetIndices(cl2g,&idxs1);CHKERRQ(ierr); 301 ierr = ISLocalToGlobalMappingGetIndices(rl2g,&idxs2);CHKERRQ(ierr); 302 ierr = PetscMemcmp(idxs1,idxs2,n1*sizeof(PetscInt),&same);CHKERRQ(ierr); 303 ierr = ISLocalToGlobalMappingRestoreIndices(cl2g,&idxs1);CHKERRQ(ierr); 304 ierr = ISLocalToGlobalMappingRestoreIndices(rl2g,&idxs2);CHKERRQ(ierr); 305 if (!same) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid column l2gmap",j,i); 306 } 307 } 308 } 309 #endif 310 311 B = NULL; 312 if (reuse != MAT_REUSE_MATRIX) { 313 PetscInt stl; 314 315 /* Create l2g map for the rows of the new matrix and index sets for the local MATNEST */ 316 for (i=0,stl=0;i<nr;i++) stl += lr[i]; 317 ierr = PetscMalloc1(stl,&l2gidxs);CHKERRQ(ierr); 318 for (i=0,stl=0;i<nr;i++) { 319 Mat usedmat; 320 Mat_IS *matis; 321 const PetscInt *idxs; 322 323 /* local IS for local NEST */ 324 ierr = ISCreateStride(PETSC_COMM_SELF,lr[i],stl,1,&islrow[i]);CHKERRQ(ierr); 325 326 /* l2gmap */ 327 j = 0; 328 usedmat = nest[i][j]; 329 while (!usedmat && j < nc-1) usedmat = nest[i][++j]; 330 if (!usedmat) SETERRQ(comm,PETSC_ERR_SUP,"Cannot find valid row mat"); 331 332 if (istrans[i*nc+j]) { 333 Mat T; 334 ierr = MatTransposeGetMat(usedmat,&T);CHKERRQ(ierr); 335 usedmat = T; 336 } 337 ierr = MatISSetUpSF(usedmat);CHKERRQ(ierr); 338 matis = (Mat_IS*)(usedmat->data); 339 ierr = ISGetIndices(isrow[i],&idxs);CHKERRQ(ierr); 340 if (istrans[i*nc+j]) { 341 ierr = PetscSFBcastBegin(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 342 ierr = PetscSFBcastEnd(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 343 } else { 344 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 345 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 346 } 347 ierr = ISRestoreIndices(isrow[i],&idxs);CHKERRQ(ierr); 348 stl += lr[i]; 349 } 350 ierr = ISLocalToGlobalMappingCreate(comm,1,stl,l2gidxs,PETSC_OWN_POINTER,&rl2g);CHKERRQ(ierr); 351 352 /* Create l2g map for columns of the new matrix and index sets for the local MATNEST */ 353 for (i=0,stl=0;i<nc;i++) stl += lc[i]; 354 ierr = PetscMalloc1(stl,&l2gidxs);CHKERRQ(ierr); 355 for (i=0,stl=0;i<nc;i++) { 356 Mat usedmat; 357 Mat_IS *matis; 358 const PetscInt *idxs; 359 360 /* local IS for local NEST */ 361 ierr = ISCreateStride(PETSC_COMM_SELF,lc[i],stl,1,&islcol[i]);CHKERRQ(ierr); 362 363 /* l2gmap */ 364 j = 0; 365 usedmat = nest[j][i]; 366 while (!usedmat && j < nr-1) usedmat = nest[++j][i]; 367 if (!usedmat) SETERRQ(comm,PETSC_ERR_SUP,"Cannot find valid column mat"); 368 if (istrans[j*nc+i]) { 369 Mat T; 370 ierr = MatTransposeGetMat(usedmat,&T);CHKERRQ(ierr); 371 usedmat = T; 372 } 373 ierr = MatISSetUpSF(usedmat);CHKERRQ(ierr); 374 matis = (Mat_IS*)(usedmat->data); 375 ierr = ISGetIndices(iscol[i],&idxs);CHKERRQ(ierr); 376 if (istrans[j*nc+i]) { 377 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 378 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 379 } else { 380 ierr = PetscSFBcastBegin(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 381 ierr = PetscSFBcastEnd(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 382 } 383 ierr = ISRestoreIndices(iscol[i],&idxs);CHKERRQ(ierr); 384 stl += lc[i]; 385 } 386 ierr = ISLocalToGlobalMappingCreate(comm,1,stl,l2gidxs,PETSC_OWN_POINTER,&cl2g);CHKERRQ(ierr); 387 388 /* Create MATIS */ 389 ierr = MatCreate(comm,&B);CHKERRQ(ierr); 390 ierr = MatSetSizes(B,A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N);CHKERRQ(ierr); 391 ierr = MatGetBlockSizes(A,&rbs,&cbs);CHKERRQ(ierr); 392 ierr = MatSetBlockSizes(B,rbs,cbs);CHKERRQ(ierr); 393 ierr = MatSetType(B,MATIS);CHKERRQ(ierr); 394 ierr = MatSetLocalToGlobalMapping(B,rl2g,cl2g);CHKERRQ(ierr); 395 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 396 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 397 ierr = MatCreateNest(PETSC_COMM_SELF,nr,islrow,nc,islcol,snest,&lA);CHKERRQ(ierr); 398 for (i=0;i<nr*nc;i++) { 399 if (istrans[i]) { 400 ierr = MatDestroy(&snest[i]);CHKERRQ(ierr); 401 } 402 } 403 ierr = MatISSetLocalMat(B,lA);CHKERRQ(ierr); 404 ierr = MatDestroy(&lA);CHKERRQ(ierr); 405 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 406 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 407 if (reuse == MAT_INPLACE_MATRIX) { 408 ierr = MatHeaderReplace(A,&B);CHKERRQ(ierr); 409 } else { 410 *newmat = B; 411 } 412 } else { 413 if (lreuse) { 414 ierr = MatISGetLocalMat(*newmat,&lA);CHKERRQ(ierr); 415 for (i=0;i<nr;i++) { 416 for (j=0;j<nc;j++) { 417 if (snest[i*nc+j]) { 418 ierr = MatNestSetSubMat(lA,i,j,snest[i*nc+j]);CHKERRQ(ierr); 419 if (istrans[i*nc+j]) { 420 ierr = MatDestroy(&snest[i*nc+j]);CHKERRQ(ierr); 421 } 422 } 423 } 424 } 425 } else { 426 PetscInt stl; 427 for (i=0,stl=0;i<nr;i++) { 428 ierr = ISCreateStride(PETSC_COMM_SELF,lr[i],stl,1,&islrow[i]);CHKERRQ(ierr); 429 stl += lr[i]; 430 } 431 for (i=0,stl=0;i<nc;i++) { 432 ierr = ISCreateStride(PETSC_COMM_SELF,lc[i],stl,1,&islcol[i]);CHKERRQ(ierr); 433 stl += lc[i]; 434 } 435 ierr = MatCreateNest(PETSC_COMM_SELF,nr,islrow,nc,islcol,snest,&lA);CHKERRQ(ierr); 436 if (istrans[i]) { 437 ierr = MatDestroy(&snest[i]);CHKERRQ(ierr); 438 } 439 ierr = MatISSetLocalMat(*newmat,lA);CHKERRQ(ierr); 440 ierr = MatDestroy(&lA);CHKERRQ(ierr); 441 } 442 ierr = MatAssemblyBegin(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 443 ierr = MatAssemblyEnd(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 444 } 445 446 /* Create local matrix in MATNEST format */ 447 convert = PETSC_FALSE; 448 ierr = PetscOptionsGetBool(NULL,((PetscObject)A)->prefix,"-matis_convert_local_nest",&convert,NULL);CHKERRQ(ierr); 449 if (convert) { 450 Mat M; 451 MatISLocalFields lf; 452 PetscContainer c; 453 454 ierr = MatISGetLocalMat(*newmat,&lA);CHKERRQ(ierr); 455 ierr = MatConvert(lA,MATAIJ,MAT_INITIAL_MATRIX,&M);CHKERRQ(ierr); 456 ierr = MatISSetLocalMat(*newmat,M);CHKERRQ(ierr); 457 ierr = MatDestroy(&M);CHKERRQ(ierr); 458 459 /* attach local fields to the matrix */ 460 ierr = PetscNew(&lf);CHKERRQ(ierr); 461 ierr = PetscCalloc2(nr,&lf->rf,nc,&lf->cf);CHKERRQ(ierr); 462 for (i=0;i<nr;i++) { 463 PetscInt n,st; 464 465 ierr = ISGetLocalSize(islrow[i],&n);CHKERRQ(ierr); 466 ierr = ISStrideGetInfo(islrow[i],&st,NULL);CHKERRQ(ierr); 467 ierr = ISCreateStride(comm,n,st,1,&lf->rf[i]);CHKERRQ(ierr); 468 } 469 for (i=0;i<nc;i++) { 470 PetscInt n,st; 471 472 ierr = ISGetLocalSize(islcol[i],&n);CHKERRQ(ierr); 473 ierr = ISStrideGetInfo(islcol[i],&st,NULL);CHKERRQ(ierr); 474 ierr = ISCreateStride(comm,n,st,1,&lf->cf[i]);CHKERRQ(ierr); 475 } 476 lf->nr = nr; 477 lf->nc = nc; 478 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)(*newmat)),&c);CHKERRQ(ierr); 479 ierr = PetscContainerSetPointer(c,lf);CHKERRQ(ierr); 480 ierr = PetscContainerSetUserDestroy(c,MatISContainerDestroyFields_Private);CHKERRQ(ierr); 481 ierr = PetscObjectCompose((PetscObject)(*newmat),"_convert_nest_lfields",(PetscObject)c);CHKERRQ(ierr); 482 ierr = PetscContainerDestroy(&c);CHKERRQ(ierr); 483 } 484 485 /* Free workspace */ 486 for (i=0;i<nr;i++) { 487 ierr = ISDestroy(&islrow[i]);CHKERRQ(ierr); 488 } 489 for (i=0;i<nc;i++) { 490 ierr = ISDestroy(&islcol[i]);CHKERRQ(ierr); 491 } 492 ierr = PetscFree6(isrow,iscol,islrow,islcol,snest,istrans);CHKERRQ(ierr); 493 ierr = PetscFree2(lr,lc);CHKERRQ(ierr); 494 PetscFunctionReturn(0); 495 } 496 497 static PetscErrorCode MatDiagonalScale_IS(Mat A, Vec l, Vec r) 498 { 499 Mat_IS *matis = (Mat_IS*)A->data; 500 Vec ll,rr; 501 const PetscScalar *Y,*X; 502 PetscScalar *x,*y; 503 PetscErrorCode ierr; 504 505 PetscFunctionBegin; 506 ierr = MatISSetUpSF(A);CHKERRQ(ierr); 507 if (l) { 508 ll = matis->y; 509 ierr = VecGetArrayRead(l,&Y);CHKERRQ(ierr); 510 ierr = VecGetArray(ll,&y);CHKERRQ(ierr); 511 ierr = PetscSFBcastBegin(matis->sf,MPIU_SCALAR,Y,y);CHKERRQ(ierr); 512 } else { 513 ll = NULL; 514 } 515 if (r) { 516 rr = matis->x; 517 ierr = VecGetArrayRead(r,&X);CHKERRQ(ierr); 518 ierr = VecGetArray(rr,&x);CHKERRQ(ierr); 519 ierr = PetscSFBcastBegin(matis->csf,MPIU_SCALAR,X,x);CHKERRQ(ierr); 520 } else { 521 rr = NULL; 522 } 523 if (ll) { 524 ierr = PetscSFBcastEnd(matis->sf,MPIU_SCALAR,Y,y);CHKERRQ(ierr); 525 ierr = VecRestoreArrayRead(l,&Y);CHKERRQ(ierr); 526 ierr = VecRestoreArray(ll,&y);CHKERRQ(ierr); 527 } 528 if (rr) { 529 ierr = PetscSFBcastEnd(matis->csf,MPIU_SCALAR,X,x);CHKERRQ(ierr); 530 ierr = VecRestoreArrayRead(r,&X);CHKERRQ(ierr); 531 ierr = VecRestoreArray(rr,&x);CHKERRQ(ierr); 532 } 533 ierr = MatDiagonalScale(matis->A,ll,rr);CHKERRQ(ierr); 534 PetscFunctionReturn(0); 535 } 536 537 static PetscErrorCode MatGetInfo_IS(Mat A,MatInfoType flag,MatInfo *ginfo) 538 { 539 Mat_IS *matis = (Mat_IS*)A->data; 540 MatInfo info; 541 PetscReal isend[6],irecv[6]; 542 PetscInt bs; 543 PetscErrorCode ierr; 544 545 PetscFunctionBegin; 546 ierr = MatGetBlockSize(A,&bs);CHKERRQ(ierr); 547 if (matis->A->ops->getinfo) { 548 ierr = MatGetInfo(matis->A,MAT_LOCAL,&info);CHKERRQ(ierr); 549 isend[0] = info.nz_used; 550 isend[1] = info.nz_allocated; 551 isend[2] = info.nz_unneeded; 552 isend[3] = info.memory; 553 isend[4] = info.mallocs; 554 } else { 555 isend[0] = 0.; 556 isend[1] = 0.; 557 isend[2] = 0.; 558 isend[3] = 0.; 559 isend[4] = 0.; 560 } 561 isend[5] = matis->A->num_ass; 562 if (flag == MAT_LOCAL) { 563 ginfo->nz_used = isend[0]; 564 ginfo->nz_allocated = isend[1]; 565 ginfo->nz_unneeded = isend[2]; 566 ginfo->memory = isend[3]; 567 ginfo->mallocs = isend[4]; 568 ginfo->assemblies = isend[5]; 569 } else if (flag == MAT_GLOBAL_MAX) { 570 ierr = MPIU_Allreduce(isend,irecv,6,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 571 572 ginfo->nz_used = irecv[0]; 573 ginfo->nz_allocated = irecv[1]; 574 ginfo->nz_unneeded = irecv[2]; 575 ginfo->memory = irecv[3]; 576 ginfo->mallocs = irecv[4]; 577 ginfo->assemblies = irecv[5]; 578 } else if (flag == MAT_GLOBAL_SUM) { 579 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 580 581 ginfo->nz_used = irecv[0]; 582 ginfo->nz_allocated = irecv[1]; 583 ginfo->nz_unneeded = irecv[2]; 584 ginfo->memory = irecv[3]; 585 ginfo->mallocs = irecv[4]; 586 ginfo->assemblies = A->num_ass; 587 } 588 ginfo->block_size = bs; 589 ginfo->fill_ratio_given = 0; 590 ginfo->fill_ratio_needed = 0; 591 ginfo->factor_mallocs = 0; 592 PetscFunctionReturn(0); 593 } 594 595 PetscErrorCode MatTranspose_IS(Mat A,MatReuse reuse,Mat *B) 596 { 597 Mat C,lC,lA; 598 PetscErrorCode ierr; 599 600 PetscFunctionBegin; 601 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_INPLACE_MATRIX) { 602 ISLocalToGlobalMapping rl2g,cl2g; 603 ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr); 604 ierr = MatSetSizes(C,A->cmap->n,A->rmap->n,A->cmap->N,A->rmap->N);CHKERRQ(ierr); 605 ierr = MatSetBlockSizes(C,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 606 ierr = MatSetType(C,MATIS);CHKERRQ(ierr); 607 ierr = MatGetLocalToGlobalMapping(A,&rl2g,&cl2g);CHKERRQ(ierr); 608 ierr = MatSetLocalToGlobalMapping(C,cl2g,rl2g);CHKERRQ(ierr); 609 } else { 610 C = *B; 611 } 612 613 /* perform local transposition */ 614 ierr = MatISGetLocalMat(A,&lA);CHKERRQ(ierr); 615 ierr = MatTranspose(lA,MAT_INITIAL_MATRIX,&lC);CHKERRQ(ierr); 616 ierr = MatISSetLocalMat(C,lC);CHKERRQ(ierr); 617 ierr = MatDestroy(&lC);CHKERRQ(ierr); 618 619 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 620 *B = C; 621 } else { 622 ierr = MatHeaderMerge(A,&C);CHKERRQ(ierr); 623 } 624 ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 625 ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 626 PetscFunctionReturn(0); 627 } 628 629 PetscErrorCode MatDiagonalSet_IS(Mat A,Vec D,InsertMode insmode) 630 { 631 Mat_IS *is = (Mat_IS*)A->data; 632 PetscErrorCode ierr; 633 634 PetscFunctionBegin; 635 if (!D) { /* this code branch is used by MatShift_IS */ 636 ierr = VecSet(is->y,1.);CHKERRQ(ierr); 637 } else { 638 ierr = VecScatterBegin(is->rctx,D,is->y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 639 ierr = VecScatterEnd(is->rctx,D,is->y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 640 } 641 ierr = VecPointwiseDivide(is->y,is->y,is->counter);CHKERRQ(ierr); 642 ierr = MatDiagonalSet(is->A,is->y,insmode);CHKERRQ(ierr); 643 PetscFunctionReturn(0); 644 } 645 646 PetscErrorCode MatShift_IS(Mat A,PetscScalar a) 647 { 648 PetscErrorCode ierr; 649 650 PetscFunctionBegin; 651 ierr = MatDiagonalSet_IS(A,NULL,ADD_VALUES);CHKERRQ(ierr); 652 PetscFunctionReturn(0); 653 } 654 655 static PetscErrorCode MatSetValuesLocal_SubMat_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 656 { 657 PetscErrorCode ierr; 658 Mat_IS *is = (Mat_IS*)A->data; 659 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 660 661 PetscFunctionBegin; 662 #if defined(PETSC_USE_DEBUG) 663 if (m > MATIS_MAX_ENTRIES_INSERTION || n > MATIS_MAX_ENTRIES_INSERTION) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_SUP,"Number of row/column indices must be <= %D: they are %D %D",MATIS_MAX_ENTRIES_INSERTION,m,n); 664 #endif 665 ierr = ISLocalToGlobalMappingApply(A->rmap->mapping,m,rows,rows_l);CHKERRQ(ierr); 666 ierr = ISLocalToGlobalMappingApply(A->cmap->mapping,n,cols,cols_l);CHKERRQ(ierr); 667 ierr = MatSetValues(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 668 PetscFunctionReturn(0); 669 } 670 671 static PetscErrorCode MatSetValuesBlockedLocal_SubMat_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 672 { 673 PetscErrorCode ierr; 674 Mat_IS *is = (Mat_IS*)A->data; 675 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 676 677 PetscFunctionBegin; 678 #if defined(PETSC_USE_DEBUG) 679 if (m > MATIS_MAX_ENTRIES_INSERTION || n > MATIS_MAX_ENTRIES_INSERTION) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_SUP,"Number of row/column block indices must be <= %D: they are %D %D",MATIS_MAX_ENTRIES_INSERTION,m,n); 680 #endif 681 ierr = ISLocalToGlobalMappingApplyBlock(A->rmap->mapping,m,rows,rows_l);CHKERRQ(ierr); 682 ierr = ISLocalToGlobalMappingApplyBlock(A->cmap->mapping,n,cols,cols_l);CHKERRQ(ierr); 683 ierr = MatSetValuesBlocked(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 684 PetscFunctionReturn(0); 685 } 686 687 static PetscErrorCode PetscLayoutMapLocal_Private(PetscLayout map,PetscInt N,const PetscInt idxs[], PetscInt *on,PetscInt **oidxs,PetscInt **ogidxs) 688 { 689 PetscInt *owners = map->range; 690 PetscInt n = map->n; 691 PetscSF sf; 692 PetscInt *lidxs,*work = NULL; 693 PetscSFNode *ridxs; 694 PetscMPIInt rank; 695 PetscInt r, p = 0, len = 0; 696 PetscErrorCode ierr; 697 698 PetscFunctionBegin; 699 if (on) *on = 0; /* squelch -Wmaybe-uninitialized */ 700 /* Create SF where leaves are input idxs and roots are owned idxs (code adapted from MatZeroRowsMapLocal_Private) */ 701 ierr = MPI_Comm_rank(map->comm,&rank);CHKERRQ(ierr); 702 ierr = PetscMalloc1(n,&lidxs);CHKERRQ(ierr); 703 for (r = 0; r < n; ++r) lidxs[r] = -1; 704 ierr = PetscMalloc1(N,&ridxs);CHKERRQ(ierr); 705 for (r = 0; r < N; ++r) { 706 const PetscInt idx = idxs[r]; 707 if (idx < 0 || map->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index %D out of range [0,%D)",idx,map->N); 708 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this idx too */ 709 ierr = PetscLayoutFindOwner(map,idx,&p);CHKERRQ(ierr); 710 } 711 ridxs[r].rank = p; 712 ridxs[r].index = idxs[r] - owners[p]; 713 } 714 ierr = PetscSFCreate(map->comm,&sf);CHKERRQ(ierr); 715 ierr = PetscSFSetGraph(sf,n,N,NULL,PETSC_OWN_POINTER,ridxs,PETSC_OWN_POINTER);CHKERRQ(ierr); 716 ierr = PetscSFReduceBegin(sf,MPIU_INT,(PetscInt*)idxs,lidxs,MPI_LOR);CHKERRQ(ierr); 717 ierr = PetscSFReduceEnd(sf,MPIU_INT,(PetscInt*)idxs,lidxs,MPI_LOR);CHKERRQ(ierr); 718 if (ogidxs) { /* communicate global idxs */ 719 PetscInt cum = 0,start,*work2; 720 721 ierr = PetscMalloc1(n,&work);CHKERRQ(ierr); 722 ierr = PetscCalloc1(N,&work2);CHKERRQ(ierr); 723 for (r = 0; r < N; ++r) if (idxs[r] >=0) cum++; 724 ierr = MPI_Scan(&cum,&start,1,MPIU_INT,MPI_SUM,map->comm);CHKERRQ(ierr); 725 start -= cum; 726 cum = 0; 727 for (r = 0; r < N; ++r) if (idxs[r] >=0) work2[r] = start+cum++; 728 ierr = PetscSFReduceBegin(sf,MPIU_INT,work2,work,MPIU_REPLACE);CHKERRQ(ierr); 729 ierr = PetscSFReduceEnd(sf,MPIU_INT,work2,work,MPIU_REPLACE);CHKERRQ(ierr); 730 ierr = PetscFree(work2);CHKERRQ(ierr); 731 } 732 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 733 /* Compress and put in indices */ 734 for (r = 0; r < n; ++r) 735 if (lidxs[r] >= 0) { 736 if (work) work[len] = work[r]; 737 lidxs[len++] = r; 738 } 739 if (on) *on = len; 740 if (oidxs) *oidxs = lidxs; 741 if (ogidxs) *ogidxs = work; 742 PetscFunctionReturn(0); 743 } 744 745 static PetscErrorCode MatCreateSubMatrix_IS(Mat mat,IS irow,IS icol,MatReuse scall,Mat *newmat) 746 { 747 Mat locmat,newlocmat; 748 Mat_IS *newmatis; 749 #if defined(PETSC_USE_DEBUG) 750 Vec rtest,ltest; 751 const PetscScalar *array; 752 #endif 753 const PetscInt *idxs; 754 PetscInt i,m,n; 755 PetscErrorCode ierr; 756 757 PetscFunctionBegin; 758 if (scall == MAT_REUSE_MATRIX) { 759 PetscBool ismatis; 760 761 ierr = PetscObjectTypeCompare((PetscObject)*newmat,MATIS,&ismatis);CHKERRQ(ierr); 762 if (!ismatis) SETERRQ(PetscObjectComm((PetscObject)*newmat),PETSC_ERR_ARG_WRONG,"Cannot reuse matrix! Not of MATIS type"); 763 newmatis = (Mat_IS*)(*newmat)->data; 764 if (!newmatis->getsub_ris) SETERRQ(PetscObjectComm((PetscObject)*newmat),PETSC_ERR_ARG_WRONG,"Cannot reuse matrix! Misses local row IS"); 765 if (!newmatis->getsub_cis) SETERRQ(PetscObjectComm((PetscObject)*newmat),PETSC_ERR_ARG_WRONG,"Cannot reuse matrix! Misses local col IS"); 766 } 767 /* irow and icol may not have duplicate entries */ 768 #if defined(PETSC_USE_DEBUG) 769 ierr = MatCreateVecs(mat,<est,&rtest);CHKERRQ(ierr); 770 ierr = ISGetLocalSize(irow,&n);CHKERRQ(ierr); 771 ierr = ISGetIndices(irow,&idxs);CHKERRQ(ierr); 772 for (i=0;i<n;i++) { 773 ierr = VecSetValue(rtest,idxs[i],1.0,ADD_VALUES);CHKERRQ(ierr); 774 } 775 ierr = VecAssemblyBegin(rtest);CHKERRQ(ierr); 776 ierr = VecAssemblyEnd(rtest);CHKERRQ(ierr); 777 ierr = VecGetLocalSize(rtest,&n);CHKERRQ(ierr); 778 ierr = VecGetOwnershipRange(rtest,&m,NULL);CHKERRQ(ierr); 779 ierr = VecGetArrayRead(rtest,&array);CHKERRQ(ierr); 780 for (i=0;i<n;i++) if (array[i] != 0. && array[i] != 1.) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Index %D counted %D times! Irow may not have duplicate entries",i+m,(PetscInt)PetscRealPart(array[i])); 781 ierr = VecRestoreArrayRead(rtest,&array);CHKERRQ(ierr); 782 ierr = ISRestoreIndices(irow,&idxs);CHKERRQ(ierr); 783 ierr = ISGetLocalSize(icol,&n);CHKERRQ(ierr); 784 ierr = ISGetIndices(icol,&idxs);CHKERRQ(ierr); 785 for (i=0;i<n;i++) { 786 ierr = VecSetValue(ltest,idxs[i],1.0,ADD_VALUES);CHKERRQ(ierr); 787 } 788 ierr = VecAssemblyBegin(ltest);CHKERRQ(ierr); 789 ierr = VecAssemblyEnd(ltest);CHKERRQ(ierr); 790 ierr = VecGetLocalSize(ltest,&n);CHKERRQ(ierr); 791 ierr = VecGetOwnershipRange(ltest,&m,NULL);CHKERRQ(ierr); 792 ierr = VecGetArrayRead(ltest,&array);CHKERRQ(ierr); 793 for (i=0;i<n;i++) if (array[i] != 0. && array[i] != 1.) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Index %D counted %D times! Icol may not have duplicate entries",i+m,(PetscInt)PetscRealPart(array[i])); 794 ierr = VecRestoreArrayRead(ltest,&array);CHKERRQ(ierr); 795 ierr = ISRestoreIndices(icol,&idxs);CHKERRQ(ierr); 796 ierr = VecDestroy(&rtest);CHKERRQ(ierr); 797 ierr = VecDestroy(<est);CHKERRQ(ierr); 798 #endif 799 if (scall == MAT_INITIAL_MATRIX) { 800 Mat_IS *matis = (Mat_IS*)mat->data; 801 ISLocalToGlobalMapping rl2g; 802 IS is; 803 PetscInt *lidxs,*lgidxs,*newgidxs; 804 PetscInt ll,newloc; 805 MPI_Comm comm; 806 807 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 808 ierr = ISGetLocalSize(irow,&m);CHKERRQ(ierr); 809 ierr = ISGetLocalSize(icol,&n);CHKERRQ(ierr); 810 ierr = MatCreate(comm,newmat);CHKERRQ(ierr); 811 ierr = MatSetType(*newmat,MATIS);CHKERRQ(ierr); 812 ierr = MatSetSizes(*newmat,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); 813 /* communicate irow to their owners in the layout */ 814 ierr = ISGetIndices(irow,&idxs);CHKERRQ(ierr); 815 ierr = PetscLayoutMapLocal_Private(mat->rmap,m,idxs,&ll,&lidxs,&lgidxs);CHKERRQ(ierr); 816 ierr = ISRestoreIndices(irow,&idxs);CHKERRQ(ierr); 817 ierr = MatISSetUpSF(mat);CHKERRQ(ierr); 818 ierr = PetscMemzero(matis->sf_rootdata,matis->sf->nroots*sizeof(PetscInt));CHKERRQ(ierr); 819 for (i=0;i<ll;i++) matis->sf_rootdata[lidxs[i]] = lgidxs[i]+1; 820 ierr = PetscFree(lidxs);CHKERRQ(ierr); 821 ierr = PetscFree(lgidxs);CHKERRQ(ierr); 822 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 823 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 824 for (i=0,newloc=0;i<matis->sf->nleaves;i++) if (matis->sf_leafdata[i]) newloc++; 825 ierr = PetscMalloc1(newloc,&newgidxs);CHKERRQ(ierr); 826 ierr = PetscMalloc1(newloc,&lidxs);CHKERRQ(ierr); 827 for (i=0,newloc=0;i<matis->sf->nleaves;i++) 828 if (matis->sf_leafdata[i]) { 829 lidxs[newloc] = i; 830 newgidxs[newloc++] = matis->sf_leafdata[i]-1; 831 } 832 ierr = ISCreateGeneral(comm,newloc,newgidxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 833 ierr = ISLocalToGlobalMappingCreateIS(is,&rl2g);CHKERRQ(ierr); 834 ierr = ISDestroy(&is);CHKERRQ(ierr); 835 /* local is to extract local submatrix */ 836 newmatis = (Mat_IS*)(*newmat)->data; 837 ierr = ISCreateGeneral(comm,newloc,lidxs,PETSC_OWN_POINTER,&newmatis->getsub_ris);CHKERRQ(ierr); 838 if (mat->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 839 PetscBool cong; 840 ierr = PetscLayoutCompare(mat->rmap,mat->cmap,&cong);CHKERRQ(ierr); 841 if (cong) mat->congruentlayouts = 1; 842 else mat->congruentlayouts = 0; 843 } 844 if (mat->congruentlayouts && irow == icol) { 845 ierr = MatSetLocalToGlobalMapping(*newmat,rl2g,rl2g);CHKERRQ(ierr); 846 ierr = PetscObjectReference((PetscObject)newmatis->getsub_ris);CHKERRQ(ierr); 847 newmatis->getsub_cis = newmatis->getsub_ris; 848 } else { 849 ISLocalToGlobalMapping cl2g; 850 851 /* communicate icol to their owners in the layout */ 852 ierr = ISGetIndices(icol,&idxs);CHKERRQ(ierr); 853 ierr = PetscLayoutMapLocal_Private(mat->cmap,n,idxs,&ll,&lidxs,&lgidxs);CHKERRQ(ierr); 854 ierr = ISRestoreIndices(icol,&idxs);CHKERRQ(ierr); 855 ierr = PetscMemzero(matis->csf_rootdata,matis->csf->nroots*sizeof(PetscInt));CHKERRQ(ierr); 856 for (i=0;i<ll;i++) matis->csf_rootdata[lidxs[i]] = lgidxs[i]+1; 857 ierr = PetscFree(lidxs);CHKERRQ(ierr); 858 ierr = PetscFree(lgidxs);CHKERRQ(ierr); 859 ierr = PetscSFBcastBegin(matis->csf,MPIU_INT,matis->csf_rootdata,matis->csf_leafdata);CHKERRQ(ierr); 860 ierr = PetscSFBcastEnd(matis->csf,MPIU_INT,matis->csf_rootdata,matis->csf_leafdata);CHKERRQ(ierr); 861 for (i=0,newloc=0;i<matis->csf->nleaves;i++) if (matis->csf_leafdata[i]) newloc++; 862 ierr = PetscMalloc1(newloc,&newgidxs);CHKERRQ(ierr); 863 ierr = PetscMalloc1(newloc,&lidxs);CHKERRQ(ierr); 864 for (i=0,newloc=0;i<matis->csf->nleaves;i++) 865 if (matis->csf_leafdata[i]) { 866 lidxs[newloc] = i; 867 newgidxs[newloc++] = matis->csf_leafdata[i]-1; 868 } 869 ierr = ISCreateGeneral(comm,newloc,newgidxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 870 ierr = ISLocalToGlobalMappingCreateIS(is,&cl2g);CHKERRQ(ierr); 871 ierr = ISDestroy(&is);CHKERRQ(ierr); 872 /* local is to extract local submatrix */ 873 ierr = ISCreateGeneral(comm,newloc,lidxs,PETSC_OWN_POINTER,&newmatis->getsub_cis);CHKERRQ(ierr); 874 ierr = MatSetLocalToGlobalMapping(*newmat,rl2g,cl2g);CHKERRQ(ierr); 875 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 876 } 877 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 878 } else { 879 ierr = MatISGetLocalMat(*newmat,&newlocmat);CHKERRQ(ierr); 880 } 881 ierr = MatISGetLocalMat(mat,&locmat);CHKERRQ(ierr); 882 newmatis = (Mat_IS*)(*newmat)->data; 883 ierr = MatCreateSubMatrix(locmat,newmatis->getsub_ris,newmatis->getsub_cis,scall,&newlocmat);CHKERRQ(ierr); 884 if (scall == MAT_INITIAL_MATRIX) { 885 ierr = MatISSetLocalMat(*newmat,newlocmat);CHKERRQ(ierr); 886 ierr = MatDestroy(&newlocmat);CHKERRQ(ierr); 887 } 888 ierr = MatAssemblyBegin(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 889 ierr = MatAssemblyEnd(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 890 PetscFunctionReturn(0); 891 } 892 893 static PetscErrorCode MatCopy_IS(Mat A,Mat B,MatStructure str) 894 { 895 Mat_IS *a = (Mat_IS*)A->data,*b; 896 PetscBool ismatis; 897 PetscErrorCode ierr; 898 899 PetscFunctionBegin; 900 ierr = PetscObjectTypeCompare((PetscObject)B,MATIS,&ismatis);CHKERRQ(ierr); 901 if (!ismatis) SETERRQ(PetscObjectComm((PetscObject)B),PETSC_ERR_SUP,"Need to be implemented"); 902 b = (Mat_IS*)B->data; 903 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 904 PetscFunctionReturn(0); 905 } 906 907 static PetscErrorCode MatMissingDiagonal_IS(Mat A,PetscBool *missing,PetscInt *d) 908 { 909 Vec v; 910 const PetscScalar *array; 911 PetscInt i,n; 912 PetscErrorCode ierr; 913 914 PetscFunctionBegin; 915 *missing = PETSC_FALSE; 916 ierr = MatCreateVecs(A,NULL,&v);CHKERRQ(ierr); 917 ierr = MatGetDiagonal(A,v);CHKERRQ(ierr); 918 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 919 ierr = VecGetArrayRead(v,&array);CHKERRQ(ierr); 920 for (i=0;i<n;i++) if (array[i] == 0.) break; 921 ierr = VecRestoreArrayRead(v,&array);CHKERRQ(ierr); 922 ierr = VecDestroy(&v);CHKERRQ(ierr); 923 if (i != n) *missing = PETSC_TRUE; 924 if (d) { 925 *d = -1; 926 if (*missing) { 927 PetscInt rstart; 928 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 929 *d = i+rstart; 930 } 931 } 932 PetscFunctionReturn(0); 933 } 934 935 static PetscErrorCode MatISSetUpSF_IS(Mat B) 936 { 937 Mat_IS *matis = (Mat_IS*)(B->data); 938 const PetscInt *gidxs; 939 PetscInt nleaves; 940 PetscErrorCode ierr; 941 942 PetscFunctionBegin; 943 if (matis->sf) PetscFunctionReturn(0); 944 ierr = PetscSFCreate(PetscObjectComm((PetscObject)B),&matis->sf);CHKERRQ(ierr); 945 ierr = ISLocalToGlobalMappingGetIndices(B->rmap->mapping,&gidxs);CHKERRQ(ierr); 946 ierr = ISLocalToGlobalMappingGetSize(B->rmap->mapping,&nleaves);CHKERRQ(ierr); 947 ierr = PetscSFSetGraphLayout(matis->sf,B->rmap,nleaves,NULL,PETSC_OWN_POINTER,gidxs);CHKERRQ(ierr); 948 ierr = ISLocalToGlobalMappingRestoreIndices(B->rmap->mapping,&gidxs);CHKERRQ(ierr); 949 ierr = PetscMalloc2(matis->sf->nroots,&matis->sf_rootdata,matis->sf->nleaves,&matis->sf_leafdata);CHKERRQ(ierr); 950 if (B->rmap->mapping != B->cmap->mapping) { /* setup SF for columns */ 951 ierr = ISLocalToGlobalMappingGetSize(B->cmap->mapping,&nleaves);CHKERRQ(ierr); 952 ierr = PetscSFCreate(PetscObjectComm((PetscObject)B),&matis->csf);CHKERRQ(ierr); 953 ierr = ISLocalToGlobalMappingGetIndices(B->cmap->mapping,&gidxs);CHKERRQ(ierr); 954 ierr = PetscSFSetGraphLayout(matis->csf,B->cmap,nleaves,NULL,PETSC_OWN_POINTER,gidxs);CHKERRQ(ierr); 955 ierr = ISLocalToGlobalMappingRestoreIndices(B->cmap->mapping,&gidxs);CHKERRQ(ierr); 956 ierr = PetscMalloc2(matis->csf->nroots,&matis->csf_rootdata,matis->csf->nleaves,&matis->csf_leafdata);CHKERRQ(ierr); 957 } else { 958 matis->csf = matis->sf; 959 matis->csf_leafdata = matis->sf_leafdata; 960 matis->csf_rootdata = matis->sf_rootdata; 961 } 962 PetscFunctionReturn(0); 963 } 964 965 /*@ 966 MatISSetPreallocation - Preallocates memory for a MATIS parallel matrix. 967 968 Collective on MPI_Comm 969 970 Input Parameters: 971 + B - the matrix 972 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 973 (same value is used for all local rows) 974 . d_nnz - array containing the number of nonzeros in the various rows of the 975 DIAGONAL portion of the local submatrix (possibly different for each row) 976 or NULL, if d_nz is used to specify the nonzero structure. 977 The size of this array is equal to the number of local rows, i.e 'm'. 978 For matrices that will be factored, you must leave room for (and set) 979 the diagonal entry even if it is zero. 980 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 981 submatrix (same value is used for all local rows). 982 - o_nnz - array containing the number of nonzeros in the various rows of the 983 OFF-DIAGONAL portion of the local submatrix (possibly different for 984 each row) or NULL, if o_nz is used to specify the nonzero 985 structure. The size of this array is equal to the number 986 of local rows, i.e 'm'. 987 988 If the *_nnz parameter is given then the *_nz parameter is ignored 989 990 Level: intermediate 991 992 Notes: This function has the same interface as the MPIAIJ preallocation routine in order to simplify the transition 993 from the asssembled format to the unassembled one. It overestimates the preallocation of MATIS local 994 matrices; for exact preallocation, the user should set the preallocation directly on local matrix objects. 995 996 .keywords: matrix 997 998 .seealso: MatCreate(), MatCreateIS(), MatMPIAIJSetPreallocation(), MatISGetLocalMat(), MATIS 999 @*/ 1000 PetscErrorCode MatISSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 1001 { 1002 PetscErrorCode ierr; 1003 1004 PetscFunctionBegin; 1005 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 1006 PetscValidType(B,1); 1007 ierr = PetscTryMethod(B,"MatISSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 1008 PetscFunctionReturn(0); 1009 } 1010 1011 static PetscErrorCode MatISSetPreallocation_IS(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 1012 { 1013 Mat_IS *matis = (Mat_IS*)(B->data); 1014 PetscInt bs,i,nlocalcols; 1015 PetscErrorCode ierr; 1016 1017 PetscFunctionBegin; 1018 if (!matis->A) SETERRQ(PetscObjectComm((PetscObject)B),PETSC_ERR_SUP,"You should first call MatSetLocalToGlobalMapping"); 1019 ierr = MatISSetUpSF(B);CHKERRQ(ierr); 1020 1021 if (!d_nnz) for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] = d_nz; 1022 else for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] = d_nnz[i]; 1023 1024 if (!o_nnz) for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] += o_nz; 1025 else for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] += o_nnz[i]; 1026 1027 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1028 ierr = MatGetSize(matis->A,NULL,&nlocalcols);CHKERRQ(ierr); 1029 ierr = MatGetBlockSize(matis->A,&bs);CHKERRQ(ierr); 1030 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1031 1032 for (i=0;i<matis->sf->nleaves;i++) matis->sf_leafdata[i] = PetscMin(matis->sf_leafdata[i],nlocalcols); 1033 ierr = MatSeqAIJSetPreallocation(matis->A,0,matis->sf_leafdata);CHKERRQ(ierr); 1034 1035 for (i=0;i<matis->sf->nleaves/bs;i++) matis->sf_leafdata[i] = matis->sf_leafdata[i*bs]/bs; 1036 ierr = MatSeqBAIJSetPreallocation(matis->A,bs,0,matis->sf_leafdata);CHKERRQ(ierr); 1037 1038 for (i=0;i<matis->sf->nleaves/bs;i++) matis->sf_leafdata[i] = matis->sf_leafdata[i]-i; 1039 ierr = MatSeqSBAIJSetPreallocation(matis->A,bs,0,matis->sf_leafdata);CHKERRQ(ierr); 1040 PetscFunctionReturn(0); 1041 } 1042 1043 PETSC_EXTERN PetscErrorCode MatISSetMPIXAIJPreallocation_Private(Mat A, Mat B, PetscBool maxreduce) 1044 { 1045 Mat_IS *matis = (Mat_IS*)(A->data); 1046 PetscInt *my_dnz,*my_onz,*dnz,*onz,*mat_ranges,*row_ownership; 1047 const PetscInt *global_indices_r,*global_indices_c; 1048 PetscInt i,j,bs,rows,cols; 1049 PetscInt lrows,lcols; 1050 PetscInt local_rows,local_cols; 1051 PetscMPIInt nsubdomains; 1052 PetscBool isdense,issbaij; 1053 PetscErrorCode ierr; 1054 1055 PetscFunctionBegin; 1056 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)A),&nsubdomains);CHKERRQ(ierr); 1057 ierr = MatGetSize(A,&rows,&cols);CHKERRQ(ierr); 1058 ierr = MatGetBlockSize(A,&bs);CHKERRQ(ierr); 1059 ierr = MatGetSize(matis->A,&local_rows,&local_cols);CHKERRQ(ierr); 1060 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQDENSE,&isdense);CHKERRQ(ierr); 1061 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQSBAIJ,&issbaij);CHKERRQ(ierr); 1062 ierr = ISLocalToGlobalMappingGetIndices(A->rmap->mapping,&global_indices_r);CHKERRQ(ierr); 1063 if (A->rmap->mapping != A->cmap->mapping) { 1064 ierr = ISLocalToGlobalMappingGetIndices(A->cmap->mapping,&global_indices_c);CHKERRQ(ierr); 1065 } else { 1066 global_indices_c = global_indices_r; 1067 } 1068 1069 if (issbaij) { 1070 ierr = MatGetRowUpperTriangular(matis->A);CHKERRQ(ierr); 1071 } 1072 /* 1073 An SF reduce is needed to sum up properly on shared rows. 1074 Note that generally preallocation is not exact, since it overestimates nonzeros 1075 */ 1076 ierr = MatISSetUpSF(A);CHKERRQ(ierr); 1077 ierr = MatGetLocalSize(A,&lrows,&lcols);CHKERRQ(ierr); 1078 ierr = MatPreallocateInitialize(PetscObjectComm((PetscObject)A),lrows,lcols,dnz,onz);CHKERRQ(ierr); 1079 /* All processes need to compute entire row ownership */ 1080 ierr = PetscMalloc1(rows,&row_ownership);CHKERRQ(ierr); 1081 ierr = MatGetOwnershipRanges(A,(const PetscInt**)&mat_ranges);CHKERRQ(ierr); 1082 for (i=0;i<nsubdomains;i++) { 1083 for (j=mat_ranges[i];j<mat_ranges[i+1];j++) { 1084 row_ownership[j] = i; 1085 } 1086 } 1087 ierr = MatGetOwnershipRangesColumn(A,(const PetscInt**)&mat_ranges);CHKERRQ(ierr); 1088 1089 /* 1090 my_dnz and my_onz contains exact contribution to preallocation from each local mat 1091 then, they will be summed up properly. This way, preallocation is always sufficient 1092 */ 1093 ierr = PetscCalloc2(local_rows,&my_dnz,local_rows,&my_onz);CHKERRQ(ierr); 1094 /* preallocation as a MATAIJ */ 1095 if (isdense) { /* special case for dense local matrices */ 1096 for (i=0;i<local_rows;i++) { 1097 PetscInt owner = row_ownership[global_indices_r[i]]; 1098 for (j=0;j<local_cols;j++) { 1099 PetscInt index_col = global_indices_c[j]; 1100 if (index_col > mat_ranges[owner]-1 && index_col < mat_ranges[owner+1] ) { /* diag block */ 1101 my_dnz[i] += 1; 1102 } else { /* offdiag block */ 1103 my_onz[i] += 1; 1104 } 1105 } 1106 } 1107 } else if (matis->A->ops->getrowij) { 1108 const PetscInt *ii,*jj,*jptr; 1109 PetscBool done; 1110 ierr = MatGetRowIJ(matis->A,0,PETSC_FALSE,PETSC_FALSE,&local_rows,&ii,&jj,&done);CHKERRQ(ierr); 1111 if (!done) SETERRQ(PetscObjectComm((PetscObject)(matis->A)),PETSC_ERR_PLIB,"Error in MatGetRowIJ"); 1112 jptr = jj; 1113 for (i=0;i<local_rows;i++) { 1114 PetscInt index_row = global_indices_r[i]; 1115 for (j=0;j<ii[i+1]-ii[i];j++,jptr++) { 1116 PetscInt owner = row_ownership[index_row]; 1117 PetscInt index_col = global_indices_c[*jptr]; 1118 if (index_col > mat_ranges[owner]-1 && index_col < mat_ranges[owner+1] ) { /* diag block */ 1119 my_dnz[i] += 1; 1120 } else { /* offdiag block */ 1121 my_onz[i] += 1; 1122 } 1123 /* same as before, interchanging rows and cols */ 1124 if (issbaij && index_col != index_row) { 1125 owner = row_ownership[index_col]; 1126 if (index_row > mat_ranges[owner]-1 && index_row < mat_ranges[owner+1] ) { 1127 my_dnz[*jptr] += 1; 1128 } else { 1129 my_onz[*jptr] += 1; 1130 } 1131 } 1132 } 1133 } 1134 ierr = MatRestoreRowIJ(matis->A,0,PETSC_FALSE,PETSC_FALSE,&local_rows,&ii,&jj,&done);CHKERRQ(ierr); 1135 if (!done) SETERRQ(PetscObjectComm((PetscObject)(matis->A)),PETSC_ERR_PLIB,"Error in MatRestoreRowIJ"); 1136 } else { /* loop over rows and use MatGetRow */ 1137 for (i=0;i<local_rows;i++) { 1138 const PetscInt *cols; 1139 PetscInt ncols,index_row = global_indices_r[i]; 1140 ierr = MatGetRow(matis->A,i,&ncols,&cols,NULL);CHKERRQ(ierr); 1141 for (j=0;j<ncols;j++) { 1142 PetscInt owner = row_ownership[index_row]; 1143 PetscInt index_col = global_indices_c[cols[j]]; 1144 if (index_col > mat_ranges[owner]-1 && index_col < mat_ranges[owner+1] ) { /* diag block */ 1145 my_dnz[i] += 1; 1146 } else { /* offdiag block */ 1147 my_onz[i] += 1; 1148 } 1149 /* same as before, interchanging rows and cols */ 1150 if (issbaij && index_col != index_row) { 1151 owner = row_ownership[index_col]; 1152 if (index_row > mat_ranges[owner]-1 && index_row < mat_ranges[owner+1] ) { 1153 my_dnz[cols[j]] += 1; 1154 } else { 1155 my_onz[cols[j]] += 1; 1156 } 1157 } 1158 } 1159 ierr = MatRestoreRow(matis->A,i,&ncols,&cols,NULL);CHKERRQ(ierr); 1160 } 1161 } 1162 if (global_indices_c != global_indices_r) { 1163 ierr = ISLocalToGlobalMappingRestoreIndices(A->cmap->mapping,&global_indices_c);CHKERRQ(ierr); 1164 } 1165 ierr = ISLocalToGlobalMappingRestoreIndices(A->rmap->mapping,&global_indices_r);CHKERRQ(ierr); 1166 ierr = PetscFree(row_ownership);CHKERRQ(ierr); 1167 1168 /* Reduce my_dnz and my_onz */ 1169 if (maxreduce) { 1170 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_dnz,dnz,MPI_MAX);CHKERRQ(ierr); 1171 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_onz,onz,MPI_MAX);CHKERRQ(ierr); 1172 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_dnz,dnz,MPI_MAX);CHKERRQ(ierr); 1173 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_onz,onz,MPI_MAX);CHKERRQ(ierr); 1174 } else { 1175 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_dnz,dnz,MPI_SUM);CHKERRQ(ierr); 1176 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_onz,onz,MPI_SUM);CHKERRQ(ierr); 1177 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_dnz,dnz,MPI_SUM);CHKERRQ(ierr); 1178 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_onz,onz,MPI_SUM);CHKERRQ(ierr); 1179 } 1180 ierr = PetscFree2(my_dnz,my_onz);CHKERRQ(ierr); 1181 1182 /* Resize preallocation if overestimated */ 1183 for (i=0;i<lrows;i++) { 1184 dnz[i] = PetscMin(dnz[i],lcols); 1185 onz[i] = PetscMin(onz[i],cols-lcols); 1186 } 1187 1188 /* Set preallocation */ 1189 ierr = MatMPIAIJSetPreallocation(B,0,dnz,0,onz);CHKERRQ(ierr); 1190 for (i=0;i<lrows/bs;i++) { 1191 dnz[i] = dnz[i*bs]/bs; 1192 onz[i] = onz[i*bs]/bs; 1193 } 1194 ierr = MatMPIBAIJSetPreallocation(B,bs,0,dnz,0,onz);CHKERRQ(ierr); 1195 ierr = MatMPISBAIJSetPreallocation(B,bs,0,dnz,0,onz);CHKERRQ(ierr); 1196 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1197 if (issbaij) { 1198 ierr = MatRestoreRowUpperTriangular(matis->A);CHKERRQ(ierr); 1199 } 1200 PetscFunctionReturn(0); 1201 } 1202 1203 static PetscErrorCode MatISGetMPIXAIJ_IS(Mat mat, MatReuse reuse, Mat *M) 1204 { 1205 Mat_IS *matis = (Mat_IS*)(mat->data); 1206 Mat local_mat; 1207 /* info on mat */ 1208 PetscInt bs,rows,cols,lrows,lcols; 1209 PetscInt local_rows,local_cols; 1210 PetscBool isseqdense,isseqsbaij,isseqaij,isseqbaij; 1211 #if defined (PETSC_USE_DEBUG) 1212 PetscBool lb[4],bb[4]; 1213 #endif 1214 PetscMPIInt nsubdomains; 1215 /* values insertion */ 1216 PetscScalar *array; 1217 /* work */ 1218 PetscErrorCode ierr; 1219 1220 PetscFunctionBegin; 1221 /* get info from mat */ 1222 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&nsubdomains);CHKERRQ(ierr); 1223 if (nsubdomains == 1) { 1224 Mat B; 1225 IS rows,cols; 1226 IS irows,icols; 1227 const PetscInt *ridxs,*cidxs; 1228 1229 ierr = ISLocalToGlobalMappingGetIndices(mat->rmap->mapping,&ridxs);CHKERRQ(ierr); 1230 ierr = ISLocalToGlobalMappingGetIndices(mat->cmap->mapping,&cidxs);CHKERRQ(ierr); 1231 ierr = ISCreateGeneral(PETSC_COMM_SELF,mat->rmap->n,ridxs,PETSC_USE_POINTER,&rows);CHKERRQ(ierr); 1232 ierr = ISCreateGeneral(PETSC_COMM_SELF,mat->cmap->n,cidxs,PETSC_USE_POINTER,&cols);CHKERRQ(ierr); 1233 ierr = ISLocalToGlobalMappingRestoreIndices(mat->rmap->mapping,&ridxs);CHKERRQ(ierr); 1234 ierr = ISLocalToGlobalMappingRestoreIndices(mat->cmap->mapping,&cidxs);CHKERRQ(ierr); 1235 ierr = ISSetPermutation(rows);CHKERRQ(ierr); 1236 ierr = ISSetPermutation(cols);CHKERRQ(ierr); 1237 ierr = ISInvertPermutation(rows,mat->rmap->n,&irows);CHKERRQ(ierr); 1238 ierr = ISInvertPermutation(cols,mat->cmap->n,&icols);CHKERRQ(ierr); 1239 ierr = ISDestroy(&cols);CHKERRQ(ierr); 1240 ierr = ISDestroy(&rows);CHKERRQ(ierr); 1241 ierr = MatConvert(matis->A,MATAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 1242 ierr = MatCreateSubMatrix(B,irows,icols,reuse,M);CHKERRQ(ierr); 1243 ierr = MatDestroy(&B);CHKERRQ(ierr); 1244 ierr = ISDestroy(&icols);CHKERRQ(ierr); 1245 ierr = ISDestroy(&irows);CHKERRQ(ierr); 1246 PetscFunctionReturn(0); 1247 } 1248 ierr = MatGetSize(mat,&rows,&cols);CHKERRQ(ierr); 1249 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 1250 ierr = MatGetLocalSize(mat,&lrows,&lcols);CHKERRQ(ierr); 1251 ierr = MatGetSize(matis->A,&local_rows,&local_cols);CHKERRQ(ierr); 1252 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQDENSE,&isseqdense);CHKERRQ(ierr); 1253 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQAIJ,&isseqaij);CHKERRQ(ierr); 1254 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQBAIJ,&isseqbaij);CHKERRQ(ierr); 1255 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQSBAIJ,&isseqsbaij);CHKERRQ(ierr); 1256 if (!isseqdense && !isseqaij && !isseqbaij && !isseqsbaij) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not for matrix type %s",((PetscObject)(matis->A))->type_name); 1257 #if defined (PETSC_USE_DEBUG) 1258 lb[0] = isseqdense; 1259 lb[1] = isseqaij; 1260 lb[2] = isseqbaij; 1261 lb[3] = isseqsbaij; 1262 ierr = MPIU_Allreduce(lb,bb,4,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1263 if (!bb[0] && !bb[1] && !bb[2] && !bb[3]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Local matrices must have the same type"); 1264 #endif 1265 1266 if (reuse == MAT_INITIAL_MATRIX) { 1267 ierr = MatCreate(PetscObjectComm((PetscObject)mat),M);CHKERRQ(ierr); 1268 ierr = MatSetSizes(*M,lrows,lcols,rows,cols);CHKERRQ(ierr); 1269 ierr = MatSetBlockSize(*M,bs);CHKERRQ(ierr); 1270 if (!isseqsbaij) { 1271 ierr = MatSetType(*M,MATAIJ);CHKERRQ(ierr); 1272 } else { 1273 ierr = MatSetType(*M,MATSBAIJ);CHKERRQ(ierr); 1274 } 1275 ierr = MatISSetMPIXAIJPreallocation_Private(mat,*M,PETSC_FALSE);CHKERRQ(ierr); 1276 } else { 1277 PetscInt mbs,mrows,mcols,mlrows,mlcols; 1278 /* some checks */ 1279 ierr = MatGetBlockSize(*M,&mbs);CHKERRQ(ierr); 1280 ierr = MatGetSize(*M,&mrows,&mcols);CHKERRQ(ierr); 1281 ierr = MatGetLocalSize(*M,&mlrows,&mlcols);CHKERRQ(ierr); 1282 if (mrows != rows) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of rows (%d != %d)",rows,mrows); 1283 if (mcols != cols) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of cols (%d != %d)",cols,mcols); 1284 if (mlrows != lrows) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of local rows (%d != %d)",lrows,mlrows); 1285 if (mlcols != lcols) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of local cols (%d != %d)",lcols,mlcols); 1286 if (mbs != bs) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong block size (%d != %d)",bs,mbs); 1287 ierr = MatZeroEntries(*M);CHKERRQ(ierr); 1288 } 1289 1290 if (isseqsbaij) { 1291 ierr = MatConvert(matis->A,MATSEQBAIJ,MAT_INITIAL_MATRIX,&local_mat);CHKERRQ(ierr); 1292 } else { 1293 ierr = PetscObjectReference((PetscObject)matis->A);CHKERRQ(ierr); 1294 local_mat = matis->A; 1295 } 1296 1297 /* Set values */ 1298 ierr = MatSetLocalToGlobalMapping(*M,mat->rmap->mapping,mat->cmap->mapping);CHKERRQ(ierr); 1299 if (isseqdense) { /* special case for dense local matrices */ 1300 PetscInt i,*dummy; 1301 1302 ierr = PetscMalloc1(PetscMax(local_rows,local_cols),&dummy);CHKERRQ(ierr); 1303 for (i=0;i<PetscMax(local_rows,local_cols);i++) dummy[i] = i; 1304 ierr = MatSetOption(*M,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr); 1305 ierr = MatDenseGetArray(local_mat,&array);CHKERRQ(ierr); 1306 ierr = MatSetValuesLocal(*M,local_rows,dummy,local_cols,dummy,array,ADD_VALUES);CHKERRQ(ierr); 1307 ierr = MatDenseRestoreArray(local_mat,&array);CHKERRQ(ierr); 1308 ierr = PetscFree(dummy);CHKERRQ(ierr); 1309 } else if (isseqaij) { 1310 PetscInt i,nvtxs,*xadj,*adjncy; 1311 PetscBool done; 1312 1313 ierr = MatGetRowIJ(local_mat,0,PETSC_FALSE,PETSC_FALSE,&nvtxs,(const PetscInt**)&xadj,(const PetscInt**)&adjncy,&done);CHKERRQ(ierr); 1314 if (!done) SETERRQ(PetscObjectComm((PetscObject)local_mat),PETSC_ERR_PLIB,"Error in MatGetRowIJ"); 1315 ierr = MatSeqAIJGetArray(local_mat,&array);CHKERRQ(ierr); 1316 for (i=0;i<nvtxs;i++) { 1317 ierr = MatSetValuesLocal(*M,1,&i,xadj[i+1]-xadj[i],adjncy+xadj[i],array+xadj[i],ADD_VALUES);CHKERRQ(ierr); 1318 } 1319 ierr = MatRestoreRowIJ(local_mat,0,PETSC_FALSE,PETSC_FALSE,&nvtxs,(const PetscInt**)&xadj,(const PetscInt**)&adjncy,&done);CHKERRQ(ierr); 1320 if (!done) SETERRQ(PetscObjectComm((PetscObject)local_mat),PETSC_ERR_PLIB,"Error in MatRestoreRowIJ"); 1321 ierr = MatSeqAIJRestoreArray(local_mat,&array);CHKERRQ(ierr); 1322 } else { /* very basic values insertion for all other matrix types */ 1323 PetscInt i; 1324 1325 for (i=0;i<local_rows;i++) { 1326 PetscInt j; 1327 const PetscInt *local_indices_cols; 1328 1329 ierr = MatGetRow(local_mat,i,&j,&local_indices_cols,(const PetscScalar**)&array);CHKERRQ(ierr); 1330 ierr = MatSetValuesLocal(*M,1,&i,j,local_indices_cols,array,ADD_VALUES);CHKERRQ(ierr); 1331 ierr = MatRestoreRow(local_mat,i,&j,&local_indices_cols,(const PetscScalar**)&array);CHKERRQ(ierr); 1332 } 1333 } 1334 ierr = MatAssemblyBegin(*M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1335 ierr = MatDestroy(&local_mat);CHKERRQ(ierr); 1336 ierr = MatAssemblyEnd(*M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1337 if (isseqdense) { 1338 ierr = MatSetOption(*M,MAT_ROW_ORIENTED,PETSC_TRUE);CHKERRQ(ierr); 1339 } 1340 PetscFunctionReturn(0); 1341 } 1342 1343 /*@ 1344 MatISGetMPIXAIJ - Converts MATIS matrix into a parallel AIJ format 1345 1346 Input Parameter: 1347 . mat - the matrix (should be of type MATIS) 1348 . reuse - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 1349 1350 Output Parameter: 1351 . newmat - the matrix in AIJ format 1352 1353 Level: developer 1354 1355 Notes: mat and *newmat cannot be the same object when MAT_REUSE_MATRIX is requested. 1356 1357 .seealso: MATIS 1358 @*/ 1359 PetscErrorCode MatISGetMPIXAIJ(Mat mat, MatReuse reuse, Mat *newmat) 1360 { 1361 PetscErrorCode ierr; 1362 1363 PetscFunctionBegin; 1364 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1365 PetscValidLogicalCollectiveEnum(mat,reuse,2); 1366 PetscValidPointer(newmat,3); 1367 if (reuse != MAT_INITIAL_MATRIX) { 1368 PetscValidHeaderSpecific(*newmat,MAT_CLASSID,3); 1369 PetscCheckSameComm(mat,1,*newmat,3); 1370 if (mat == *newmat) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse the same matrix"); 1371 } 1372 ierr = PetscUseMethod(mat,"MatISGetMPIXAIJ_C",(Mat,MatReuse,Mat*),(mat,reuse,newmat));CHKERRQ(ierr); 1373 PetscFunctionReturn(0); 1374 } 1375 1376 PetscErrorCode MatDuplicate_IS(Mat mat,MatDuplicateOption op,Mat *newmat) 1377 { 1378 PetscErrorCode ierr; 1379 Mat_IS *matis = (Mat_IS*)(mat->data); 1380 PetscInt bs,m,n,M,N; 1381 Mat B,localmat; 1382 1383 PetscFunctionBegin; 1384 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 1385 ierr = MatGetSize(mat,&M,&N);CHKERRQ(ierr); 1386 ierr = MatGetLocalSize(mat,&m,&n);CHKERRQ(ierr); 1387 ierr = MatCreateIS(PetscObjectComm((PetscObject)mat),bs,m,n,M,N,mat->rmap->mapping,mat->cmap->mapping,&B);CHKERRQ(ierr); 1388 ierr = MatDuplicate(matis->A,op,&localmat);CHKERRQ(ierr); 1389 ierr = MatISSetLocalMat(B,localmat);CHKERRQ(ierr); 1390 ierr = MatDestroy(&localmat);CHKERRQ(ierr); 1391 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1392 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1393 *newmat = B; 1394 PetscFunctionReturn(0); 1395 } 1396 1397 static PetscErrorCode MatIsHermitian_IS(Mat A,PetscReal tol,PetscBool *flg) 1398 { 1399 PetscErrorCode ierr; 1400 Mat_IS *matis = (Mat_IS*)A->data; 1401 PetscBool local_sym; 1402 1403 PetscFunctionBegin; 1404 ierr = MatIsHermitian(matis->A,tol,&local_sym);CHKERRQ(ierr); 1405 ierr = MPIU_Allreduce(&local_sym,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1406 PetscFunctionReturn(0); 1407 } 1408 1409 static PetscErrorCode MatIsSymmetric_IS(Mat A,PetscReal tol,PetscBool *flg) 1410 { 1411 PetscErrorCode ierr; 1412 Mat_IS *matis = (Mat_IS*)A->data; 1413 PetscBool local_sym; 1414 1415 PetscFunctionBegin; 1416 ierr = MatIsSymmetric(matis->A,tol,&local_sym);CHKERRQ(ierr); 1417 ierr = MPIU_Allreduce(&local_sym,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1418 PetscFunctionReturn(0); 1419 } 1420 1421 static PetscErrorCode MatIsStructurallySymmetric_IS(Mat A,PetscBool *flg) 1422 { 1423 PetscErrorCode ierr; 1424 Mat_IS *matis = (Mat_IS*)A->data; 1425 PetscBool local_sym; 1426 1427 PetscFunctionBegin; 1428 if (A->rmap->mapping != A->cmap->mapping) { 1429 *flg = PETSC_FALSE; 1430 PetscFunctionReturn(0); 1431 } 1432 ierr = MatIsStructurallySymmetric(matis->A,&local_sym);CHKERRQ(ierr); 1433 ierr = MPIU_Allreduce(&local_sym,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1434 PetscFunctionReturn(0); 1435 } 1436 1437 static PetscErrorCode MatDestroy_IS(Mat A) 1438 { 1439 PetscErrorCode ierr; 1440 Mat_IS *b = (Mat_IS*)A->data; 1441 1442 PetscFunctionBegin; 1443 ierr = MatDestroy(&b->A);CHKERRQ(ierr); 1444 ierr = VecScatterDestroy(&b->cctx);CHKERRQ(ierr); 1445 ierr = VecScatterDestroy(&b->rctx);CHKERRQ(ierr); 1446 ierr = VecDestroy(&b->x);CHKERRQ(ierr); 1447 ierr = VecDestroy(&b->y);CHKERRQ(ierr); 1448 ierr = VecDestroy(&b->counter);CHKERRQ(ierr); 1449 ierr = ISDestroy(&b->getsub_ris);CHKERRQ(ierr); 1450 ierr = ISDestroy(&b->getsub_cis);CHKERRQ(ierr); 1451 if (b->sf != b->csf) { 1452 ierr = PetscSFDestroy(&b->csf);CHKERRQ(ierr); 1453 ierr = PetscFree2(b->csf_rootdata,b->csf_leafdata);CHKERRQ(ierr); 1454 } 1455 ierr = PetscSFDestroy(&b->sf);CHKERRQ(ierr); 1456 ierr = PetscFree2(b->sf_rootdata,b->sf_leafdata);CHKERRQ(ierr); 1457 ierr = PetscFree(A->data);CHKERRQ(ierr); 1458 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 1459 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetLocalMat_C",NULL);CHKERRQ(ierr); 1460 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetLocalMat_C",NULL);CHKERRQ(ierr); 1461 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetMPIXAIJ_C",NULL);CHKERRQ(ierr); 1462 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetPreallocation_C",NULL);CHKERRQ(ierr); 1463 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetUpSF_C",NULL);CHKERRQ(ierr); 1464 PetscFunctionReturn(0); 1465 } 1466 1467 static PetscErrorCode MatMult_IS(Mat A,Vec x,Vec y) 1468 { 1469 PetscErrorCode ierr; 1470 Mat_IS *is = (Mat_IS*)A->data; 1471 PetscScalar zero = 0.0; 1472 1473 PetscFunctionBegin; 1474 /* scatter the global vector x into the local work vector */ 1475 ierr = VecScatterBegin(is->cctx,x,is->x,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1476 ierr = VecScatterEnd(is->cctx,x,is->x,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1477 1478 /* multiply the local matrix */ 1479 ierr = MatMult(is->A,is->x,is->y);CHKERRQ(ierr); 1480 1481 /* scatter product back into global memory */ 1482 ierr = VecSet(y,zero);CHKERRQ(ierr); 1483 ierr = VecScatterBegin(is->rctx,is->y,y,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1484 ierr = VecScatterEnd(is->rctx,is->y,y,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1485 PetscFunctionReturn(0); 1486 } 1487 1488 static PetscErrorCode MatMultAdd_IS(Mat A,Vec v1,Vec v2,Vec v3) 1489 { 1490 Vec temp_vec; 1491 PetscErrorCode ierr; 1492 1493 PetscFunctionBegin; /* v3 = v2 + A * v1.*/ 1494 if (v3 != v2) { 1495 ierr = MatMult(A,v1,v3);CHKERRQ(ierr); 1496 ierr = VecAXPY(v3,1.0,v2);CHKERRQ(ierr); 1497 } else { 1498 ierr = VecDuplicate(v2,&temp_vec);CHKERRQ(ierr); 1499 ierr = MatMult(A,v1,temp_vec);CHKERRQ(ierr); 1500 ierr = VecAXPY(temp_vec,1.0,v2);CHKERRQ(ierr); 1501 ierr = VecCopy(temp_vec,v3);CHKERRQ(ierr); 1502 ierr = VecDestroy(&temp_vec);CHKERRQ(ierr); 1503 } 1504 PetscFunctionReturn(0); 1505 } 1506 1507 static PetscErrorCode MatMultTranspose_IS(Mat A,Vec y,Vec x) 1508 { 1509 Mat_IS *is = (Mat_IS*)A->data; 1510 PetscErrorCode ierr; 1511 1512 PetscFunctionBegin; 1513 /* scatter the global vector x into the local work vector */ 1514 ierr = VecScatterBegin(is->rctx,y,is->y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1515 ierr = VecScatterEnd(is->rctx,y,is->y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1516 1517 /* multiply the local matrix */ 1518 ierr = MatMultTranspose(is->A,is->y,is->x);CHKERRQ(ierr); 1519 1520 /* scatter product back into global vector */ 1521 ierr = VecSet(x,0);CHKERRQ(ierr); 1522 ierr = VecScatterBegin(is->cctx,is->x,x,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1523 ierr = VecScatterEnd(is->cctx,is->x,x,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1524 PetscFunctionReturn(0); 1525 } 1526 1527 static PetscErrorCode MatMultTransposeAdd_IS(Mat A,Vec v1,Vec v2,Vec v3) 1528 { 1529 Vec temp_vec; 1530 PetscErrorCode ierr; 1531 1532 PetscFunctionBegin; /* v3 = v2 + A' * v1.*/ 1533 if (v3 != v2) { 1534 ierr = MatMultTranspose(A,v1,v3);CHKERRQ(ierr); 1535 ierr = VecAXPY(v3,1.0,v2);CHKERRQ(ierr); 1536 } else { 1537 ierr = VecDuplicate(v2,&temp_vec);CHKERRQ(ierr); 1538 ierr = MatMultTranspose(A,v1,temp_vec);CHKERRQ(ierr); 1539 ierr = VecAXPY(temp_vec,1.0,v2);CHKERRQ(ierr); 1540 ierr = VecCopy(temp_vec,v3);CHKERRQ(ierr); 1541 ierr = VecDestroy(&temp_vec);CHKERRQ(ierr); 1542 } 1543 PetscFunctionReturn(0); 1544 } 1545 1546 static PetscErrorCode MatView_IS(Mat A,PetscViewer viewer) 1547 { 1548 Mat_IS *a = (Mat_IS*)A->data; 1549 PetscErrorCode ierr; 1550 PetscViewer sviewer; 1551 PetscBool isascii,view = PETSC_TRUE; 1552 1553 PetscFunctionBegin; 1554 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&isascii);CHKERRQ(ierr); 1555 if (isascii) { 1556 PetscViewerFormat format; 1557 1558 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1559 if (format == PETSC_VIEWER_ASCII_INFO) view = PETSC_FALSE; 1560 } 1561 if (!view) PetscFunctionReturn(0); 1562 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1563 ierr = MatView(a->A,sviewer);CHKERRQ(ierr); 1564 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1565 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1566 PetscFunctionReturn(0); 1567 } 1568 1569 static PetscErrorCode MatSetLocalToGlobalMapping_IS(Mat A,ISLocalToGlobalMapping rmapping,ISLocalToGlobalMapping cmapping) 1570 { 1571 PetscErrorCode ierr; 1572 PetscInt nr,rbs,nc,cbs; 1573 Mat_IS *is = (Mat_IS*)A->data; 1574 IS from,to; 1575 Vec cglobal,rglobal; 1576 1577 PetscFunctionBegin; 1578 PetscCheckSameComm(A,1,rmapping,2); 1579 PetscCheckSameComm(A,1,cmapping,3); 1580 /* Destroy any previous data */ 1581 ierr = VecDestroy(&is->x);CHKERRQ(ierr); 1582 ierr = VecDestroy(&is->y);CHKERRQ(ierr); 1583 ierr = VecDestroy(&is->counter);CHKERRQ(ierr); 1584 ierr = VecScatterDestroy(&is->rctx);CHKERRQ(ierr); 1585 ierr = VecScatterDestroy(&is->cctx);CHKERRQ(ierr); 1586 ierr = MatDestroy(&is->A);CHKERRQ(ierr); 1587 if (is->csf != is->sf) { 1588 ierr = PetscSFDestroy(&is->csf);CHKERRQ(ierr); 1589 ierr = PetscFree2(is->csf_rootdata,is->csf_leafdata);CHKERRQ(ierr); 1590 } 1591 ierr = PetscSFDestroy(&is->sf);CHKERRQ(ierr); 1592 ierr = PetscFree2(is->sf_rootdata,is->sf_leafdata);CHKERRQ(ierr); 1593 1594 /* Setup Layout and set local to global maps */ 1595 ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr); 1596 ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr); 1597 ierr = PetscLayoutSetISLocalToGlobalMapping(A->rmap,rmapping);CHKERRQ(ierr); 1598 ierr = PetscLayoutSetISLocalToGlobalMapping(A->cmap,cmapping);CHKERRQ(ierr); 1599 1600 /* Create the local matrix A */ 1601 ierr = ISLocalToGlobalMappingGetSize(rmapping,&nr);CHKERRQ(ierr); 1602 ierr = ISLocalToGlobalMappingGetBlockSize(rmapping,&rbs);CHKERRQ(ierr); 1603 ierr = ISLocalToGlobalMappingGetSize(cmapping,&nc);CHKERRQ(ierr); 1604 ierr = ISLocalToGlobalMappingGetBlockSize(cmapping,&cbs);CHKERRQ(ierr); 1605 ierr = MatCreate(PETSC_COMM_SELF,&is->A);CHKERRQ(ierr); 1606 ierr = MatSetType(is->A,MATAIJ);CHKERRQ(ierr); 1607 ierr = MatSetSizes(is->A,nr,nc,nr,nc);CHKERRQ(ierr); 1608 ierr = MatSetBlockSizes(is->A,rbs,cbs);CHKERRQ(ierr); 1609 ierr = MatSetOptionsPrefix(is->A,((PetscObject)A)->prefix);CHKERRQ(ierr); 1610 ierr = MatAppendOptionsPrefix(is->A,"is_");CHKERRQ(ierr); 1611 ierr = MatSetFromOptions(is->A);CHKERRQ(ierr); 1612 1613 if (!is->islocalref) { /* setup scatters and local vectors for MatMult */ 1614 /* Create the local work vectors */ 1615 ierr = MatCreateVecs(is->A,&is->x,&is->y);CHKERRQ(ierr); 1616 1617 /* setup the global to local scatters */ 1618 ierr = MatCreateVecs(A,&cglobal,&rglobal);CHKERRQ(ierr); 1619 ierr = ISCreateStride(PETSC_COMM_SELF,nr,0,1,&to);CHKERRQ(ierr); 1620 ierr = ISLocalToGlobalMappingApplyIS(rmapping,to,&from);CHKERRQ(ierr); 1621 ierr = VecScatterCreate(rglobal,from,is->y,to,&is->rctx);CHKERRQ(ierr); 1622 if (rmapping != cmapping) { 1623 ierr = ISDestroy(&to);CHKERRQ(ierr); 1624 ierr = ISDestroy(&from);CHKERRQ(ierr); 1625 ierr = ISCreateStride(PETSC_COMM_SELF,nc,0,1,&to);CHKERRQ(ierr); 1626 ierr = ISLocalToGlobalMappingApplyIS(cmapping,to,&from);CHKERRQ(ierr); 1627 ierr = VecScatterCreate(cglobal,from,is->x,to,&is->cctx);CHKERRQ(ierr); 1628 } else { 1629 ierr = PetscObjectReference((PetscObject)is->rctx);CHKERRQ(ierr); 1630 is->cctx = is->rctx; 1631 } 1632 1633 /* interface counter vector (local) */ 1634 ierr = VecDuplicate(is->y,&is->counter);CHKERRQ(ierr); 1635 ierr = VecSet(is->y,1.);CHKERRQ(ierr); 1636 ierr = VecScatterBegin(is->rctx,is->y,rglobal,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1637 ierr = VecScatterEnd(is->rctx,is->y,rglobal,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1638 ierr = VecScatterBegin(is->rctx,rglobal,is->counter,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1639 ierr = VecScatterEnd(is->rctx,rglobal,is->counter,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1640 1641 /* free workspace */ 1642 ierr = VecDestroy(&rglobal);CHKERRQ(ierr); 1643 ierr = VecDestroy(&cglobal);CHKERRQ(ierr); 1644 ierr = ISDestroy(&to);CHKERRQ(ierr); 1645 ierr = ISDestroy(&from);CHKERRQ(ierr); 1646 } 1647 ierr = MatSetUp(A);CHKERRQ(ierr); 1648 PetscFunctionReturn(0); 1649 } 1650 1651 static PetscErrorCode MatSetValues_IS(Mat mat, PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols, const PetscScalar *values, InsertMode addv) 1652 { 1653 Mat_IS *is = (Mat_IS*)mat->data; 1654 PetscErrorCode ierr; 1655 #if defined(PETSC_USE_DEBUG) 1656 PetscInt i,zm,zn; 1657 #endif 1658 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 1659 1660 PetscFunctionBegin; 1661 #if defined(PETSC_USE_DEBUG) 1662 if (m > MATIS_MAX_ENTRIES_INSERTION || n > MATIS_MAX_ENTRIES_INSERTION) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_SUP,"Number of row/column indices must be <= %D: they are %D %D",MATIS_MAX_ENTRIES_INSERTION,m,n); 1663 /* count negative indices */ 1664 for (i=0,zm=0;i<m;i++) if (rows[i] < 0) zm++; 1665 for (i=0,zn=0;i<n;i++) if (cols[i] < 0) zn++; 1666 #endif 1667 ierr = ISGlobalToLocalMappingApply(mat->rmap->mapping,IS_GTOLM_MASK,m,rows,&m,rows_l);CHKERRQ(ierr); 1668 ierr = ISGlobalToLocalMappingApply(mat->cmap->mapping,IS_GTOLM_MASK,n,cols,&n,cols_l);CHKERRQ(ierr); 1669 #if defined(PETSC_USE_DEBUG) 1670 /* count negative indices (should be the same as before) */ 1671 for (i=0;i<m;i++) if (rows_l[i] < 0) zm--; 1672 for (i=0;i<n;i++) if (cols_l[i] < 0) zn--; 1673 /* disable check when usesetlocal is true */ 1674 if (!is->usesetlocal && zm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the row indices can not be mapped! Maybe you should not use MATIS"); 1675 if (!is->usesetlocal && zn) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the column indices can not be mapped! Maybe you should not use MATIS"); 1676 #endif 1677 if (is->usesetlocal) { 1678 ierr = MatSetValuesLocal(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 1679 } else { 1680 ierr = MatSetValues(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 1681 } 1682 PetscFunctionReturn(0); 1683 } 1684 1685 static PetscErrorCode MatSetValuesBlocked_IS(Mat mat, PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols, const PetscScalar *values, InsertMode addv) 1686 { 1687 Mat_IS *is = (Mat_IS*)mat->data; 1688 PetscErrorCode ierr; 1689 #if defined(PETSC_USE_DEBUG) 1690 PetscInt i,zm,zn; 1691 #endif 1692 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 1693 1694 PetscFunctionBegin; 1695 #if defined(PETSC_USE_DEBUG) 1696 if (m > MATIS_MAX_ENTRIES_INSERTION || n > MATIS_MAX_ENTRIES_INSERTION) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_SUP,"Number of row/column block indices must be <= %D: they are %D %D",MATIS_MAX_ENTRIES_INSERTION,m,n); 1697 /* count negative indices */ 1698 for (i=0,zm=0;i<m;i++) if (rows[i] < 0) zm++; 1699 for (i=0,zn=0;i<n;i++) if (cols[i] < 0) zn++; 1700 #endif 1701 ierr = ISGlobalToLocalMappingApplyBlock(mat->rmap->mapping,IS_GTOLM_MASK,m,rows,&m,rows_l);CHKERRQ(ierr); 1702 ierr = ISGlobalToLocalMappingApplyBlock(mat->cmap->mapping,IS_GTOLM_MASK,n,cols,&n,cols_l);CHKERRQ(ierr); 1703 #if defined(PETSC_USE_DEBUG) 1704 /* count negative indices (should be the same as before) */ 1705 for (i=0;i<m;i++) if (rows_l[i] < 0) zm--; 1706 for (i=0;i<n;i++) if (cols_l[i] < 0) zn--; 1707 if (zm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the row indices can not be mapped! Maybe you should not use MATIS"); 1708 if (zn) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the column indices can not be mapped! Maybe you should not use MATIS"); 1709 #endif 1710 ierr = MatSetValuesBlocked(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 1711 PetscFunctionReturn(0); 1712 } 1713 1714 static PetscErrorCode MatSetValuesLocal_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 1715 { 1716 PetscErrorCode ierr; 1717 Mat_IS *is = (Mat_IS*)A->data; 1718 1719 PetscFunctionBegin; 1720 if (is->usesetlocal) { 1721 ierr = MatSetValuesLocal(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr); 1722 } else { 1723 ierr = MatSetValues(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr); 1724 } 1725 PetscFunctionReturn(0); 1726 } 1727 1728 static PetscErrorCode MatSetValuesBlockedLocal_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 1729 { 1730 PetscErrorCode ierr; 1731 Mat_IS *is = (Mat_IS*)A->data; 1732 1733 PetscFunctionBegin; 1734 ierr = MatSetValuesBlocked(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr); 1735 PetscFunctionReturn(0); 1736 } 1737 1738 static PetscErrorCode MatISZeroRowsColumnsLocal_Private(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,PetscBool columns) 1739 { 1740 Mat_IS *is = (Mat_IS*)A->data; 1741 PetscErrorCode ierr; 1742 1743 PetscFunctionBegin; 1744 if (!n) { 1745 is->pure_neumann = PETSC_TRUE; 1746 } else { 1747 PetscInt i; 1748 is->pure_neumann = PETSC_FALSE; 1749 1750 if (columns) { 1751 ierr = MatZeroRowsColumns(is->A,n,rows,diag,0,0);CHKERRQ(ierr); 1752 } else { 1753 ierr = MatZeroRows(is->A,n,rows,diag,0,0);CHKERRQ(ierr); 1754 } 1755 if (diag != 0.) { 1756 const PetscScalar *array; 1757 ierr = VecGetArrayRead(is->counter,&array);CHKERRQ(ierr); 1758 for (i=0; i<n; i++) { 1759 ierr = MatSetValue(is->A,rows[i],rows[i],diag/(array[rows[i]]),INSERT_VALUES);CHKERRQ(ierr); 1760 } 1761 ierr = VecRestoreArrayRead(is->counter,&array);CHKERRQ(ierr); 1762 } 1763 ierr = MatAssemblyBegin(is->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1764 ierr = MatAssemblyEnd(is->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1765 } 1766 PetscFunctionReturn(0); 1767 } 1768 1769 static PetscErrorCode MatZeroRowsColumns_Private_IS(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,Vec x,Vec b,PetscBool columns) 1770 { 1771 Mat_IS *matis = (Mat_IS*)A->data; 1772 PetscInt nr,nl,len,i; 1773 PetscInt *lrows; 1774 PetscErrorCode ierr; 1775 1776 PetscFunctionBegin; 1777 #if defined(PETSC_USE_DEBUG) 1778 if (columns || diag != 0. || (x && b)) { 1779 PetscBool cong; 1780 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 1781 if (!cong && columns) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Columns can be zeroed if and only if A->rmap and A->cmap are congruent for MATIS"); 1782 if (!cong && diag != 0.) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Nonzero diagonal value supported if and only if A->rmap and A->cmap are congruent for MATIS"); 1783 if (!cong && x && b) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"A->rmap and A->cmap need to be congruent"); 1784 } 1785 #endif 1786 /* get locally owned rows */ 1787 ierr = PetscLayoutMapLocal_Private(A->rmap,n,rows,&len,&lrows,NULL);CHKERRQ(ierr); 1788 /* fix right hand side if needed */ 1789 if (x && b) { 1790 const PetscScalar *xx; 1791 PetscScalar *bb; 1792 1793 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 1794 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 1795 for (i=0;i<len;++i) bb[lrows[i]] = diag*xx[lrows[i]]; 1796 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 1797 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 1798 } 1799 /* get rows associated to the local matrices */ 1800 ierr = MatISSetUpSF(A);CHKERRQ(ierr); 1801 ierr = MatGetSize(matis->A,&nl,NULL);CHKERRQ(ierr); 1802 ierr = PetscMemzero(matis->sf_leafdata,nl*sizeof(PetscInt));CHKERRQ(ierr); 1803 ierr = PetscMemzero(matis->sf_rootdata,A->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 1804 for (i=0;i<len;i++) matis->sf_rootdata[lrows[i]] = 1; 1805 ierr = PetscFree(lrows);CHKERRQ(ierr); 1806 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1807 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1808 ierr = PetscMalloc1(nl,&lrows);CHKERRQ(ierr); 1809 for (i=0,nr=0;i<nl;i++) if (matis->sf_leafdata[i]) lrows[nr++] = i; 1810 ierr = MatISZeroRowsColumnsLocal_Private(A,nr,lrows,diag,columns);CHKERRQ(ierr); 1811 ierr = PetscFree(lrows);CHKERRQ(ierr); 1812 PetscFunctionReturn(0); 1813 } 1814 1815 static PetscErrorCode MatZeroRows_IS(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1816 { 1817 PetscErrorCode ierr; 1818 1819 PetscFunctionBegin; 1820 ierr = MatZeroRowsColumns_Private_IS(A,n,rows,diag,x,b,PETSC_FALSE);CHKERRQ(ierr); 1821 PetscFunctionReturn(0); 1822 } 1823 1824 static PetscErrorCode MatZeroRowsColumns_IS(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1825 { 1826 PetscErrorCode ierr; 1827 1828 PetscFunctionBegin; 1829 ierr = MatZeroRowsColumns_Private_IS(A,n,rows,diag,x,b,PETSC_TRUE);CHKERRQ(ierr); 1830 PetscFunctionReturn(0); 1831 } 1832 1833 static PetscErrorCode MatAssemblyBegin_IS(Mat A,MatAssemblyType type) 1834 { 1835 Mat_IS *is = (Mat_IS*)A->data; 1836 PetscErrorCode ierr; 1837 1838 PetscFunctionBegin; 1839 ierr = MatAssemblyBegin(is->A,type);CHKERRQ(ierr); 1840 PetscFunctionReturn(0); 1841 } 1842 1843 static PetscErrorCode MatAssemblyEnd_IS(Mat A,MatAssemblyType type) 1844 { 1845 Mat_IS *is = (Mat_IS*)A->data; 1846 PetscErrorCode ierr; 1847 1848 PetscFunctionBegin; 1849 ierr = MatAssemblyEnd(is->A,type);CHKERRQ(ierr); 1850 /* fix for local empty rows/cols */ 1851 if (is->locempty && type == MAT_FINAL_ASSEMBLY) { 1852 Mat newlA; 1853 ISLocalToGlobalMapping l2g; 1854 IS tis; 1855 const PetscScalar *v; 1856 PetscInt i,n,cf,*loce,*locf; 1857 PetscBool sym; 1858 1859 ierr = MatGetRowMaxAbs(is->A,is->y,NULL);CHKERRQ(ierr); 1860 ierr = MatIsSymmetric(is->A,PETSC_SMALL,&sym);CHKERRQ(ierr); 1861 if (!sym) SETERRQ(PetscObjectComm((PetscObject)is->A),PETSC_ERR_SUP,"Not yet implemented for unsymmetric case"); 1862 ierr = VecGetLocalSize(is->y,&n);CHKERRQ(ierr); 1863 ierr = PetscMalloc1(n,&loce);CHKERRQ(ierr); 1864 ierr = PetscMalloc1(n,&locf);CHKERRQ(ierr); 1865 ierr = VecGetArrayRead(is->y,&v);CHKERRQ(ierr); 1866 for (i=0,cf=0;i<n;i++) { 1867 if (v[i] == 0.0) { 1868 loce[i] = -1; 1869 } else { 1870 loce[i] = cf; 1871 locf[cf++] = i; 1872 } 1873 } 1874 ierr = VecRestoreArrayRead(is->y,&v);CHKERRQ(ierr); 1875 /* extract valid submatrix */ 1876 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)is->A),cf,locf,PETSC_USE_POINTER,&tis);CHKERRQ(ierr); 1877 ierr = MatCreateSubMatrix(is->A,tis,tis,MAT_INITIAL_MATRIX,&newlA);CHKERRQ(ierr); 1878 ierr = ISDestroy(&tis);CHKERRQ(ierr); 1879 /* attach local l2g map for successive calls of MatSetValues */ 1880 ierr = ISLocalToGlobalMappingCreate(PetscObjectComm((PetscObject)is->A),1,n,loce,PETSC_OWN_POINTER,&l2g);CHKERRQ(ierr); 1881 ierr = MatSetLocalToGlobalMapping(newlA,l2g,l2g);CHKERRQ(ierr); 1882 ierr = ISLocalToGlobalMappingDestroy(&l2g);CHKERRQ(ierr); 1883 /* flag MatSetValues */ 1884 is->usesetlocal = PETSC_TRUE; 1885 /* attach new global l2g map */ 1886 ierr = ISLocalToGlobalMappingApply(A->rmap->mapping,cf,locf,locf);CHKERRQ(ierr); 1887 ierr = ISLocalToGlobalMappingCreate(PetscObjectComm((PetscObject)A),1,cf,locf,PETSC_OWN_POINTER,&l2g);CHKERRQ(ierr); 1888 ierr = MatSetLocalToGlobalMapping(A,l2g,l2g);CHKERRQ(ierr); 1889 ierr = MatISSetLocalMat(A,newlA);CHKERRQ(ierr); 1890 ierr = MatDestroy(&newlA);CHKERRQ(ierr); 1891 ierr = ISLocalToGlobalMappingDestroy(&l2g);CHKERRQ(ierr); 1892 } 1893 is->locempty = PETSC_FALSE; 1894 PetscFunctionReturn(0); 1895 } 1896 1897 static PetscErrorCode MatISGetLocalMat_IS(Mat mat,Mat *local) 1898 { 1899 Mat_IS *is = (Mat_IS*)mat->data; 1900 1901 PetscFunctionBegin; 1902 *local = is->A; 1903 PetscFunctionReturn(0); 1904 } 1905 1906 static PetscErrorCode MatISRestoreLocalMat_IS(Mat mat,Mat *local) 1907 { 1908 PetscFunctionBegin; 1909 *local = NULL; 1910 PetscFunctionReturn(0); 1911 } 1912 1913 /*@ 1914 MatISGetLocalMat - Gets the local matrix stored inside a MATIS matrix. 1915 1916 Input Parameter: 1917 . mat - the matrix 1918 1919 Output Parameter: 1920 . local - the local matrix 1921 1922 Level: advanced 1923 1924 Notes: 1925 This can be called if you have precomputed the nonzero structure of the 1926 matrix and want to provide it to the inner matrix object to improve the performance 1927 of the MatSetValues() operation. 1928 1929 Call MatISRestoreLocalMat() when finished with the local matrix. 1930 1931 .seealso: MATIS 1932 @*/ 1933 PetscErrorCode MatISGetLocalMat(Mat mat,Mat *local) 1934 { 1935 PetscErrorCode ierr; 1936 1937 PetscFunctionBegin; 1938 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1939 PetscValidPointer(local,2); 1940 ierr = PetscUseMethod(mat,"MatISGetLocalMat_C",(Mat,Mat*),(mat,local));CHKERRQ(ierr); 1941 PetscFunctionReturn(0); 1942 } 1943 1944 /*@ 1945 MatISRestoreLocalMat - Restores the local matrix obtained with MatISGetLocalMat() 1946 1947 Input Parameter: 1948 . mat - the matrix 1949 1950 Output Parameter: 1951 . local - the local matrix 1952 1953 Level: advanced 1954 1955 .seealso: MATIS 1956 @*/ 1957 PetscErrorCode MatISRestoreLocalMat(Mat mat,Mat *local) 1958 { 1959 PetscErrorCode ierr; 1960 1961 PetscFunctionBegin; 1962 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1963 PetscValidPointer(local,2); 1964 ierr = PetscUseMethod(mat,"MatISRestoreLocalMat_C",(Mat,Mat*),(mat,local));CHKERRQ(ierr); 1965 PetscFunctionReturn(0); 1966 } 1967 1968 static PetscErrorCode MatISSetLocalMat_IS(Mat mat,Mat local) 1969 { 1970 Mat_IS *is = (Mat_IS*)mat->data; 1971 PetscInt nrows,ncols,orows,ocols; 1972 PetscErrorCode ierr; 1973 1974 PetscFunctionBegin; 1975 if (is->A) { 1976 ierr = MatGetSize(is->A,&orows,&ocols);CHKERRQ(ierr); 1977 ierr = MatGetSize(local,&nrows,&ncols);CHKERRQ(ierr); 1978 if (orows != nrows || ocols != ncols) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Local MATIS matrix should be of size %Dx%D (you passed a %Dx%D matrix)",orows,ocols,nrows,ncols); 1979 } 1980 ierr = PetscObjectReference((PetscObject)local);CHKERRQ(ierr); 1981 ierr = MatDestroy(&is->A);CHKERRQ(ierr); 1982 is->A = local; 1983 PetscFunctionReturn(0); 1984 } 1985 1986 /*@ 1987 MatISSetLocalMat - Replace the local matrix stored inside a MATIS object. 1988 1989 Input Parameter: 1990 . mat - the matrix 1991 . local - the local matrix 1992 1993 Output Parameter: 1994 1995 Level: advanced 1996 1997 Notes: 1998 This can be called if you have precomputed the local matrix and 1999 want to provide it to the matrix object MATIS. 2000 2001 .seealso: MATIS 2002 @*/ 2003 PetscErrorCode MatISSetLocalMat(Mat mat,Mat local) 2004 { 2005 PetscErrorCode ierr; 2006 2007 PetscFunctionBegin; 2008 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 2009 PetscValidHeaderSpecific(local,MAT_CLASSID,2); 2010 ierr = PetscUseMethod(mat,"MatISSetLocalMat_C",(Mat,Mat),(mat,local));CHKERRQ(ierr); 2011 PetscFunctionReturn(0); 2012 } 2013 2014 static PetscErrorCode MatZeroEntries_IS(Mat A) 2015 { 2016 Mat_IS *a = (Mat_IS*)A->data; 2017 PetscErrorCode ierr; 2018 2019 PetscFunctionBegin; 2020 ierr = MatZeroEntries(a->A);CHKERRQ(ierr); 2021 PetscFunctionReturn(0); 2022 } 2023 2024 static PetscErrorCode MatScale_IS(Mat A,PetscScalar a) 2025 { 2026 Mat_IS *is = (Mat_IS*)A->data; 2027 PetscErrorCode ierr; 2028 2029 PetscFunctionBegin; 2030 ierr = MatScale(is->A,a);CHKERRQ(ierr); 2031 PetscFunctionReturn(0); 2032 } 2033 2034 static PetscErrorCode MatGetDiagonal_IS(Mat A, Vec v) 2035 { 2036 Mat_IS *is = (Mat_IS*)A->data; 2037 PetscErrorCode ierr; 2038 2039 PetscFunctionBegin; 2040 /* get diagonal of the local matrix */ 2041 ierr = MatGetDiagonal(is->A,is->y);CHKERRQ(ierr); 2042 2043 /* scatter diagonal back into global vector */ 2044 ierr = VecSet(v,0);CHKERRQ(ierr); 2045 ierr = VecScatterBegin(is->rctx,is->y,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 2046 ierr = VecScatterEnd(is->rctx,is->y,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 2047 PetscFunctionReturn(0); 2048 } 2049 2050 static PetscErrorCode MatSetOption_IS(Mat A,MatOption op,PetscBool flg) 2051 { 2052 Mat_IS *a = (Mat_IS*)A->data; 2053 PetscErrorCode ierr; 2054 2055 PetscFunctionBegin; 2056 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 2057 PetscFunctionReturn(0); 2058 } 2059 2060 static PetscErrorCode MatAXPY_IS(Mat Y,PetscScalar a,Mat X,MatStructure str) 2061 { 2062 Mat_IS *y = (Mat_IS*)Y->data; 2063 Mat_IS *x; 2064 #if defined(PETSC_USE_DEBUG) 2065 PetscBool ismatis; 2066 #endif 2067 PetscErrorCode ierr; 2068 2069 PetscFunctionBegin; 2070 #if defined(PETSC_USE_DEBUG) 2071 ierr = PetscObjectTypeCompare((PetscObject)X,MATIS,&ismatis);CHKERRQ(ierr); 2072 if (!ismatis) SETERRQ(PetscObjectComm((PetscObject)Y),PETSC_ERR_SUP,"Cannot call MatAXPY(Y,a,X,str) with X not of type MATIS"); 2073 #endif 2074 x = (Mat_IS*)X->data; 2075 ierr = MatAXPY(y->A,a,x->A,str);CHKERRQ(ierr); 2076 PetscFunctionReturn(0); 2077 } 2078 2079 static PetscErrorCode MatGetLocalSubMatrix_IS(Mat A,IS row,IS col,Mat *submat) 2080 { 2081 Mat lA; 2082 Mat_IS *matis; 2083 ISLocalToGlobalMapping rl2g,cl2g; 2084 IS is; 2085 const PetscInt *rg,*rl; 2086 PetscInt nrg; 2087 PetscInt N,M,nrl,i,*idxs; 2088 PetscErrorCode ierr; 2089 2090 PetscFunctionBegin; 2091 ierr = ISLocalToGlobalMappingGetIndices(A->rmap->mapping,&rg);CHKERRQ(ierr); 2092 ierr = ISGetLocalSize(row,&nrl);CHKERRQ(ierr); 2093 ierr = ISGetIndices(row,&rl);CHKERRQ(ierr); 2094 ierr = ISLocalToGlobalMappingGetSize(A->rmap->mapping,&nrg);CHKERRQ(ierr); 2095 #if defined(PETSC_USE_DEBUG) 2096 for (i=0;i<nrl;i++) if (rl[i]>=nrg) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Local row index %D -> %D greater than maximum possible %D",i,rl[i],nrg); 2097 #endif 2098 ierr = PetscMalloc1(nrg,&idxs);CHKERRQ(ierr); 2099 /* map from [0,nrl) to row */ 2100 for (i=0;i<nrl;i++) idxs[i] = rl[i]; 2101 #if defined(PETSC_USE_DEBUG) 2102 for (i=nrl;i<nrg;i++) idxs[i] = nrg; 2103 #else 2104 for (i=nrl;i<nrg;i++) idxs[i] = -1; 2105 #endif 2106 ierr = ISRestoreIndices(row,&rl);CHKERRQ(ierr); 2107 ierr = ISLocalToGlobalMappingRestoreIndices(A->rmap->mapping,&rg);CHKERRQ(ierr); 2108 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),nrg,idxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 2109 ierr = ISLocalToGlobalMappingCreateIS(is,&rl2g);CHKERRQ(ierr); 2110 ierr = ISDestroy(&is);CHKERRQ(ierr); 2111 /* compute new l2g map for columns */ 2112 if (col != row || A->rmap->mapping != A->cmap->mapping) { 2113 const PetscInt *cg,*cl; 2114 PetscInt ncg; 2115 PetscInt ncl; 2116 2117 ierr = ISLocalToGlobalMappingGetIndices(A->cmap->mapping,&cg);CHKERRQ(ierr); 2118 ierr = ISGetLocalSize(col,&ncl);CHKERRQ(ierr); 2119 ierr = ISGetIndices(col,&cl);CHKERRQ(ierr); 2120 ierr = ISLocalToGlobalMappingGetSize(A->cmap->mapping,&ncg);CHKERRQ(ierr); 2121 #if defined(PETSC_USE_DEBUG) 2122 for (i=0;i<ncl;i++) if (cl[i]>=ncg) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Local column index %D -> %D greater than maximum possible %D",i,cl[i],ncg); 2123 #endif 2124 ierr = PetscMalloc1(ncg,&idxs);CHKERRQ(ierr); 2125 /* map from [0,ncl) to col */ 2126 for (i=0;i<ncl;i++) idxs[i] = cl[i]; 2127 #if defined(PETSC_USE_DEBUG) 2128 for (i=ncl;i<ncg;i++) idxs[i] = ncg; 2129 #else 2130 for (i=ncl;i<ncg;i++) idxs[i] = -1; 2131 #endif 2132 ierr = ISRestoreIndices(col,&cl);CHKERRQ(ierr); 2133 ierr = ISLocalToGlobalMappingRestoreIndices(A->cmap->mapping,&cg);CHKERRQ(ierr); 2134 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),ncg,idxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 2135 ierr = ISLocalToGlobalMappingCreateIS(is,&cl2g);CHKERRQ(ierr); 2136 ierr = ISDestroy(&is);CHKERRQ(ierr); 2137 } else { 2138 ierr = PetscObjectReference((PetscObject)rl2g);CHKERRQ(ierr); 2139 cl2g = rl2g; 2140 } 2141 /* create the MATIS submatrix */ 2142 ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr); 2143 ierr = MatCreate(PetscObjectComm((PetscObject)A),submat);CHKERRQ(ierr); 2144 ierr = MatSetSizes(*submat,PETSC_DECIDE,PETSC_DECIDE,M,N);CHKERRQ(ierr); 2145 ierr = MatSetType(*submat,MATIS);CHKERRQ(ierr); 2146 matis = (Mat_IS*)((*submat)->data); 2147 matis->islocalref = PETSC_TRUE; 2148 ierr = MatSetLocalToGlobalMapping(*submat,rl2g,cl2g);CHKERRQ(ierr); 2149 ierr = MatISGetLocalMat(A,&lA);CHKERRQ(ierr); 2150 ierr = MatISSetLocalMat(*submat,lA);CHKERRQ(ierr); 2151 ierr = MatSetUp(*submat);CHKERRQ(ierr); 2152 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2153 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2154 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 2155 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 2156 /* remove unsupported ops */ 2157 ierr = PetscMemzero((*submat)->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2158 (*submat)->ops->destroy = MatDestroy_IS; 2159 (*submat)->ops->setvalueslocal = MatSetValuesLocal_SubMat_IS; 2160 (*submat)->ops->setvaluesblockedlocal = MatSetValuesBlockedLocal_SubMat_IS; 2161 (*submat)->ops->assemblybegin = MatAssemblyBegin_IS; 2162 (*submat)->ops->assemblyend = MatAssemblyEnd_IS; 2163 PetscFunctionReturn(0); 2164 } 2165 2166 static PetscErrorCode MatSetFromOptions_IS(PetscOptionItems *PetscOptionsObject, Mat A) 2167 { 2168 Mat_IS *a = (Mat_IS*)A->data; 2169 PetscErrorCode ierr; 2170 2171 PetscFunctionBegin; 2172 ierr = PetscOptionsHead(PetscOptionsObject,"MATIS options");CHKERRQ(ierr); 2173 ierr = PetscObjectOptionsBegin((PetscObject)A); 2174 ierr = PetscOptionsBool("-matis_fixempty","Fix local matrices in case of empty local rows/columns",NULL,a->locempty,&a->locempty,NULL);CHKERRQ(ierr); 2175 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2176 PetscFunctionReturn(0); 2177 } 2178 2179 /*@ 2180 MatCreateIS - Creates a "process" unassembled matrix, assembled on each 2181 process but not across processes. 2182 2183 Input Parameters: 2184 + comm - MPI communicator that will share the matrix 2185 . bs - block size of the matrix 2186 . m,n,M,N - local and/or global sizes of the left and right vector used in matrix vector products 2187 . rmap - local to global map for rows 2188 - cmap - local to global map for cols 2189 2190 Output Parameter: 2191 . A - the resulting matrix 2192 2193 Level: advanced 2194 2195 Notes: See MATIS for more details. 2196 m and n are NOT related to the size of the map; they represent the size of the local parts of the vectors 2197 used in MatMult operations. The sizes of rmap and cmap define the size of the local matrices. 2198 If either rmap or cmap are NULL, then the matrix is assumed to be square. 2199 2200 .seealso: MATIS, MatSetLocalToGlobalMapping() 2201 @*/ 2202 PetscErrorCode MatCreateIS(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt M,PetscInt N,ISLocalToGlobalMapping rmap,ISLocalToGlobalMapping cmap,Mat *A) 2203 { 2204 PetscErrorCode ierr; 2205 2206 PetscFunctionBegin; 2207 if (!rmap && !cmap) SETERRQ(comm,PETSC_ERR_USER,"You need to provide at least one of the mappings"); 2208 ierr = MatCreate(comm,A);CHKERRQ(ierr); 2209 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 2210 if (bs > 0) { 2211 ierr = MatSetBlockSize(*A,bs);CHKERRQ(ierr); 2212 } 2213 ierr = MatSetType(*A,MATIS);CHKERRQ(ierr); 2214 if (rmap && cmap) { 2215 ierr = MatSetLocalToGlobalMapping(*A,rmap,cmap);CHKERRQ(ierr); 2216 } else if (!rmap) { 2217 ierr = MatSetLocalToGlobalMapping(*A,cmap,cmap);CHKERRQ(ierr); 2218 } else { 2219 ierr = MatSetLocalToGlobalMapping(*A,rmap,rmap);CHKERRQ(ierr); 2220 } 2221 PetscFunctionReturn(0); 2222 } 2223 2224 /*MC 2225 MATIS - MATIS = "is" - A matrix type to be used for using the non-overlapping domain decomposition methods (e.g. PCBDDC or KSPFETIDP). 2226 This stores the matrices in globally unassembled form. Each processor 2227 assembles only its local Neumann problem and the parallel matrix vector 2228 product is handled "implicitly". 2229 2230 Operations Provided: 2231 + MatMult() 2232 . MatMultAdd() 2233 . MatMultTranspose() 2234 . MatMultTransposeAdd() 2235 . MatZeroEntries() 2236 . MatSetOption() 2237 . MatZeroRows() 2238 . MatSetValues() 2239 . MatSetValuesBlocked() 2240 . MatSetValuesLocal() 2241 . MatSetValuesBlockedLocal() 2242 . MatScale() 2243 . MatGetDiagonal() 2244 . MatMissingDiagonal() 2245 . MatDuplicate() 2246 . MatCopy() 2247 . MatAXPY() 2248 . MatCreateSubMatrix() 2249 . MatGetLocalSubMatrix() 2250 . MatTranspose() 2251 - MatSetLocalToGlobalMapping() 2252 2253 Options Database Keys: 2254 . -mat_type is - sets the matrix type to "is" during a call to MatSetFromOptions() 2255 2256 Notes: Options prefix for the inner matrix are given by -is_mat_xxx 2257 2258 You must call MatSetLocalToGlobalMapping() before using this matrix type. 2259 2260 You can do matrix preallocation on the local matrix after you obtain it with 2261 MatISGetLocalMat(); otherwise, you could use MatISSetPreallocation() 2262 2263 Level: advanced 2264 2265 .seealso: Mat, MatISGetLocalMat(), MatSetLocalToGlobalMapping(), MatISSetPreallocation(), MatCreateIS(), PCBDDC, KSPFETIDP 2266 2267 M*/ 2268 2269 PETSC_EXTERN PetscErrorCode MatCreate_IS(Mat A) 2270 { 2271 PetscErrorCode ierr; 2272 Mat_IS *b; 2273 2274 PetscFunctionBegin; 2275 ierr = PetscNewLog(A,&b);CHKERRQ(ierr); 2276 A->data = (void*)b; 2277 2278 /* matrix ops */ 2279 ierr = PetscMemzero(A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2280 A->ops->mult = MatMult_IS; 2281 A->ops->multadd = MatMultAdd_IS; 2282 A->ops->multtranspose = MatMultTranspose_IS; 2283 A->ops->multtransposeadd = MatMultTransposeAdd_IS; 2284 A->ops->destroy = MatDestroy_IS; 2285 A->ops->setlocaltoglobalmapping = MatSetLocalToGlobalMapping_IS; 2286 A->ops->setvalues = MatSetValues_IS; 2287 A->ops->setvaluesblocked = MatSetValuesBlocked_IS; 2288 A->ops->setvalueslocal = MatSetValuesLocal_IS; 2289 A->ops->setvaluesblockedlocal = MatSetValuesBlockedLocal_IS; 2290 A->ops->zerorows = MatZeroRows_IS; 2291 A->ops->zerorowscolumns = MatZeroRowsColumns_IS; 2292 A->ops->assemblybegin = MatAssemblyBegin_IS; 2293 A->ops->assemblyend = MatAssemblyEnd_IS; 2294 A->ops->view = MatView_IS; 2295 A->ops->zeroentries = MatZeroEntries_IS; 2296 A->ops->scale = MatScale_IS; 2297 A->ops->getdiagonal = MatGetDiagonal_IS; 2298 A->ops->setoption = MatSetOption_IS; 2299 A->ops->ishermitian = MatIsHermitian_IS; 2300 A->ops->issymmetric = MatIsSymmetric_IS; 2301 A->ops->isstructurallysymmetric = MatIsStructurallySymmetric_IS; 2302 A->ops->duplicate = MatDuplicate_IS; 2303 A->ops->missingdiagonal = MatMissingDiagonal_IS; 2304 A->ops->copy = MatCopy_IS; 2305 A->ops->getlocalsubmatrix = MatGetLocalSubMatrix_IS; 2306 A->ops->createsubmatrix = MatCreateSubMatrix_IS; 2307 A->ops->axpy = MatAXPY_IS; 2308 A->ops->diagonalset = MatDiagonalSet_IS; 2309 A->ops->shift = MatShift_IS; 2310 A->ops->transpose = MatTranspose_IS; 2311 A->ops->getinfo = MatGetInfo_IS; 2312 A->ops->diagonalscale = MatDiagonalScale_IS; 2313 A->ops->setfromoptions = MatSetFromOptions_IS; 2314 2315 /* special MATIS functions */ 2316 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetLocalMat_C",MatISGetLocalMat_IS);CHKERRQ(ierr); 2317 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISRestoreLocalMat_C",MatISRestoreLocalMat_IS);CHKERRQ(ierr); 2318 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetLocalMat_C",MatISSetLocalMat_IS);CHKERRQ(ierr); 2319 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetMPIXAIJ_C",MatISGetMPIXAIJ_IS);CHKERRQ(ierr); 2320 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetPreallocation_C",MatISSetPreallocation_IS);CHKERRQ(ierr); 2321 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetUpSF_C",MatISSetUpSF_IS);CHKERRQ(ierr); 2322 ierr = PetscObjectChangeTypeName((PetscObject)A,MATIS);CHKERRQ(ierr); 2323 PetscFunctionReturn(0); 2324 } 2325