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 static PetscErrorCode MatSetValuesLocal_IS(Mat,PetscInt,const PetscInt*,PetscInt,const PetscInt*,const PetscScalar*,InsertMode); 16 static PetscErrorCode MatSetValuesBlockedLocal_IS(Mat,PetscInt,const PetscInt*,PetscInt,const PetscInt*,const PetscScalar*,InsertMode); 17 18 static PetscErrorCode MatISContainerDestroyFields_Private(void *ptr) 19 { 20 MatISLocalFields lf = (MatISLocalFields)ptr; 21 PetscInt i; 22 PetscErrorCode ierr; 23 24 PetscFunctionBegin; 25 for (i=0;i<lf->nr;i++) { 26 ierr = ISDestroy(&lf->rf[i]);CHKERRQ(ierr); 27 } 28 for (i=0;i<lf->nc;i++) { 29 ierr = ISDestroy(&lf->cf[i]);CHKERRQ(ierr); 30 } 31 ierr = PetscFree2(lf->rf,lf->cf);CHKERRQ(ierr); 32 ierr = PetscFree(lf);CHKERRQ(ierr); 33 PetscFunctionReturn(0); 34 } 35 36 static PetscErrorCode MatISContainerDestroyArray_Private(void *ptr) 37 { 38 PetscErrorCode ierr; 39 40 PetscFunctionBeginUser; 41 ierr = PetscFree(ptr);CHKERRQ(ierr); 42 PetscFunctionReturn(0); 43 } 44 45 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat A,MatType type,MatReuse reuse,Mat *newmat) 46 { 47 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 48 Mat_SeqAIJ *diag = (Mat_SeqAIJ*)(aij->A->data); 49 Mat_SeqAIJ *offd = (Mat_SeqAIJ*)(aij->B->data); 50 Mat lA; 51 ISLocalToGlobalMapping rl2g,cl2g; 52 IS is; 53 MPI_Comm comm; 54 void *ptrs[2]; 55 const char *names[2] = {"_convert_csr_aux","_convert_csr_data"}; 56 PetscScalar *dd,*od,*aa,*data; 57 PetscInt *di,*dj,*oi,*oj; 58 PetscInt *aux,*ii,*jj; 59 PetscInt lc,dr,dc,oc,str,stc,nnz,i,jd,jo,cum; 60 PetscErrorCode ierr; 61 62 PetscFunctionBegin; 63 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 64 if (!aij->garray) SETERRQ(comm,PETSC_ERR_SUP,"garray not present"); 65 66 /* access relevant information from MPIAIJ */ 67 ierr = MatGetOwnershipRange(A,&str,NULL);CHKERRQ(ierr); 68 ierr = MatGetOwnershipRangeColumn(A,&stc,NULL);CHKERRQ(ierr); 69 ierr = MatGetLocalSize(A,&dr,&dc);CHKERRQ(ierr); 70 di = diag->i; 71 dj = diag->j; 72 dd = diag->a; 73 oc = aij->B->cmap->n; 74 oi = offd->i; 75 oj = offd->j; 76 od = offd->a; 77 nnz = diag->i[dr] + offd->i[dr]; 78 79 /* generate l2g maps for rows and cols */ 80 ierr = ISCreateStride(comm,dr,str,1,&is);CHKERRQ(ierr); 81 ierr = ISLocalToGlobalMappingCreateIS(is,&rl2g);CHKERRQ(ierr); 82 ierr = ISDestroy(&is);CHKERRQ(ierr); 83 if (dr) { 84 ierr = PetscMalloc1(dc+oc,&aux);CHKERRQ(ierr); 85 for (i=0; i<dc; i++) aux[i] = i+stc; 86 for (i=0; i<oc; i++) aux[i+dc] = aij->garray[i]; 87 ierr = ISCreateGeneral(comm,dc+oc,aux,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 88 lc = dc+oc; 89 } else { 90 ierr = ISCreateGeneral(comm,0,NULL,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 91 lc = 0; 92 } 93 ierr = ISLocalToGlobalMappingCreateIS(is,&cl2g);CHKERRQ(ierr); 94 ierr = ISDestroy(&is);CHKERRQ(ierr); 95 96 /* create MATIS object */ 97 ierr = MatCreate(comm,newmat);CHKERRQ(ierr); 98 ierr = MatSetSizes(*newmat,dr,dc,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); 99 ierr = MatSetType(*newmat,MATIS);CHKERRQ(ierr); 100 ierr = MatSetLocalToGlobalMapping(*newmat,rl2g,cl2g);CHKERRQ(ierr); 101 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 102 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 103 104 /* merge local matrices */ 105 ierr = PetscMalloc1(nnz+dr+1,&aux);CHKERRQ(ierr); 106 ierr = PetscMalloc1(nnz,&data);CHKERRQ(ierr); 107 ii = aux; 108 jj = aux+dr+1; 109 aa = data; 110 *ii = *(di++) + *(oi++); 111 for (jd=0,jo=0,cum=0;*ii<nnz;cum++) 112 { 113 for (;jd<*di;jd++) { *jj++ = *dj++; *aa++ = *dd++; } 114 for (;jo<*oi;jo++) { *jj++ = *oj++ + dc; *aa++ = *od++; } 115 *(++ii) = *(di++) + *(oi++); 116 } 117 for (;cum<dr;cum++) *(++ii) = nnz; 118 ii = aux; 119 jj = aux+dr+1; 120 aa = data; 121 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,dr,lc,ii,jj,aa,&lA);CHKERRQ(ierr); 122 123 /* create containers to destroy the data */ 124 ptrs[0] = aux; 125 ptrs[1] = data; 126 for (i=0; i<2; i++) { 127 PetscContainer c; 128 129 ierr = PetscContainerCreate(PETSC_COMM_SELF,&c);CHKERRQ(ierr); 130 ierr = PetscContainerSetPointer(c,ptrs[i]);CHKERRQ(ierr); 131 ierr = PetscContainerSetUserDestroy(c,MatISContainerDestroyArray_Private);CHKERRQ(ierr); 132 ierr = PetscObjectCompose((PetscObject)lA,names[i],(PetscObject)c);CHKERRQ(ierr); 133 ierr = PetscContainerDestroy(&c);CHKERRQ(ierr); 134 } 135 136 /* finalize matrix */ 137 ierr = MatISSetLocalMat(*newmat,lA);CHKERRQ(ierr); 138 ierr = MatDestroy(&lA);CHKERRQ(ierr); 139 ierr = MatAssemblyBegin(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 140 ierr = MatAssemblyEnd(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 141 PetscFunctionReturn(0); 142 } 143 144 /*@ 145 MatISSetUpSF - Setup star forest objects used by MatIS. 146 147 Collective on MPI_Comm 148 149 Input Parameters: 150 + A - the matrix 151 152 Level: advanced 153 154 Notes: This function does not need to be called by the user. 155 156 .keywords: matrix 157 158 .seealso: MatCreate(), MatCreateIS(), MatISSetPreallocation(), MatISGetLocalMat() 159 @*/ 160 PetscErrorCode MatISSetUpSF(Mat A) 161 { 162 PetscErrorCode ierr; 163 164 PetscFunctionBegin; 165 PetscValidHeaderSpecific(A,MAT_CLASSID,1); 166 PetscValidType(A,1); 167 ierr = PetscTryMethod(A,"MatISSetUpSF_C",(Mat),(A));CHKERRQ(ierr); 168 PetscFunctionReturn(0); 169 } 170 171 PETSC_INTERN PetscErrorCode MatConvert_Nest_IS(Mat A,MatType type,MatReuse reuse,Mat *newmat) 172 { 173 Mat **nest,*snest,**rnest,lA,B; 174 IS *iscol,*isrow,*islrow,*islcol; 175 ISLocalToGlobalMapping rl2g,cl2g; 176 MPI_Comm comm; 177 PetscInt *lr,*lc,*l2gidxs; 178 PetscInt i,j,nr,nc,rbs,cbs; 179 PetscBool convert,lreuse,*istrans; 180 PetscErrorCode ierr; 181 182 PetscFunctionBegin; 183 ierr = MatNestGetSubMats(A,&nr,&nc,&nest);CHKERRQ(ierr); 184 lreuse = PETSC_FALSE; 185 rnest = NULL; 186 if (reuse == MAT_REUSE_MATRIX) { 187 PetscBool ismatis,isnest; 188 189 ierr = PetscObjectTypeCompare((PetscObject)*newmat,MATIS,&ismatis);CHKERRQ(ierr); 190 if (!ismatis) SETERRQ1(PetscObjectComm((PetscObject)*newmat),PETSC_ERR_USER,"Cannot reuse matrix of type %s",((PetscObject)(*newmat))->type); 191 ierr = MatISGetLocalMat(*newmat,&lA);CHKERRQ(ierr); 192 ierr = PetscObjectTypeCompare((PetscObject)lA,MATNEST,&isnest);CHKERRQ(ierr); 193 if (isnest) { 194 ierr = MatNestGetSubMats(lA,&i,&j,&rnest);CHKERRQ(ierr); 195 lreuse = (PetscBool)(i == nr && j == nc); 196 if (!lreuse) rnest = NULL; 197 } 198 } 199 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 200 ierr = PetscCalloc2(nr,&lr,nc,&lc);CHKERRQ(ierr); 201 ierr = PetscCalloc6(nr,&isrow,nc,&iscol, 202 nr,&islrow,nc,&islcol, 203 nr*nc,&snest,nr*nc,&istrans);CHKERRQ(ierr); 204 ierr = MatNestGetISs(A,isrow,iscol);CHKERRQ(ierr); 205 for (i=0;i<nr;i++) { 206 for (j=0;j<nc;j++) { 207 PetscBool ismatis; 208 PetscInt l1,l2,lb1,lb2,ij=i*nc+j; 209 210 /* Null matrix pointers are allowed in MATNEST */ 211 if (!nest[i][j]) continue; 212 213 /* Nested matrices should be of type MATIS */ 214 ierr = PetscObjectTypeCompare((PetscObject)nest[i][j],MATTRANSPOSEMAT,&istrans[ij]);CHKERRQ(ierr); 215 if (istrans[ij]) { 216 Mat T,lT; 217 ierr = MatTransposeGetMat(nest[i][j],&T);CHKERRQ(ierr); 218 ierr = PetscObjectTypeCompare((PetscObject)T,MATIS,&ismatis);CHKERRQ(ierr); 219 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); 220 ierr = MatISGetLocalMat(T,&lT);CHKERRQ(ierr); 221 ierr = MatCreateTranspose(lT,&snest[ij]);CHKERRQ(ierr); 222 } else { 223 ierr = PetscObjectTypeCompare((PetscObject)nest[i][j],MATIS,&ismatis);CHKERRQ(ierr); 224 if (!ismatis) SETERRQ2(comm,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) is not of type MATIS",i,j); 225 ierr = MatISGetLocalMat(nest[i][j],&snest[ij]);CHKERRQ(ierr); 226 } 227 228 /* Check compatibility of local sizes */ 229 ierr = MatGetSize(snest[ij],&l1,&l2);CHKERRQ(ierr); 230 ierr = MatGetBlockSizes(snest[ij],&lb1,&lb2);CHKERRQ(ierr); 231 if (!l1 || !l2) continue; 232 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); 233 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); 234 lr[i] = l1; 235 lc[j] = l2; 236 237 /* check compatibilty for local matrix reusage */ 238 if (rnest && !rnest[i][j] != !snest[ij]) lreuse = PETSC_FALSE; 239 } 240 } 241 242 #if defined (PETSC_USE_DEBUG) 243 /* Check compatibility of l2g maps for rows */ 244 for (i=0;i<nr;i++) { 245 rl2g = NULL; 246 for (j=0;j<nc;j++) { 247 PetscInt n1,n2; 248 249 if (!nest[i][j]) continue; 250 if (istrans[i*nc+j]) { 251 Mat T; 252 253 ierr = MatTransposeGetMat(nest[i][j],&T);CHKERRQ(ierr); 254 ierr = MatGetLocalToGlobalMapping(T,NULL,&cl2g);CHKERRQ(ierr); 255 } else { 256 ierr = MatGetLocalToGlobalMapping(nest[i][j],&cl2g,NULL);CHKERRQ(ierr); 257 } 258 ierr = ISLocalToGlobalMappingGetSize(cl2g,&n1);CHKERRQ(ierr); 259 if (!n1) continue; 260 if (!rl2g) { 261 rl2g = cl2g; 262 } else { 263 const PetscInt *idxs1,*idxs2; 264 PetscBool same; 265 266 ierr = ISLocalToGlobalMappingGetSize(rl2g,&n2);CHKERRQ(ierr); 267 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); 268 ierr = ISLocalToGlobalMappingGetIndices(cl2g,&idxs1);CHKERRQ(ierr); 269 ierr = ISLocalToGlobalMappingGetIndices(rl2g,&idxs2);CHKERRQ(ierr); 270 ierr = PetscMemcmp(idxs1,idxs2,n1*sizeof(PetscInt),&same);CHKERRQ(ierr); 271 ierr = ISLocalToGlobalMappingRestoreIndices(cl2g,&idxs1);CHKERRQ(ierr); 272 ierr = ISLocalToGlobalMappingRestoreIndices(rl2g,&idxs2);CHKERRQ(ierr); 273 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); 274 } 275 } 276 } 277 /* Check compatibility of l2g maps for columns */ 278 for (i=0;i<nc;i++) { 279 rl2g = NULL; 280 for (j=0;j<nr;j++) { 281 PetscInt n1,n2; 282 283 if (!nest[j][i]) continue; 284 if (istrans[j*nc+i]) { 285 Mat T; 286 287 ierr = MatTransposeGetMat(nest[j][i],&T);CHKERRQ(ierr); 288 ierr = MatGetLocalToGlobalMapping(T,&cl2g,NULL);CHKERRQ(ierr); 289 } else { 290 ierr = MatGetLocalToGlobalMapping(nest[j][i],NULL,&cl2g);CHKERRQ(ierr); 291 } 292 ierr = ISLocalToGlobalMappingGetSize(cl2g,&n1);CHKERRQ(ierr); 293 if (!n1) continue; 294 if (!rl2g) { 295 rl2g = cl2g; 296 } else { 297 const PetscInt *idxs1,*idxs2; 298 PetscBool same; 299 300 ierr = ISLocalToGlobalMappingGetSize(rl2g,&n2);CHKERRQ(ierr); 301 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); 302 ierr = ISLocalToGlobalMappingGetIndices(cl2g,&idxs1);CHKERRQ(ierr); 303 ierr = ISLocalToGlobalMappingGetIndices(rl2g,&idxs2);CHKERRQ(ierr); 304 ierr = PetscMemcmp(idxs1,idxs2,n1*sizeof(PetscInt),&same);CHKERRQ(ierr); 305 ierr = ISLocalToGlobalMappingRestoreIndices(cl2g,&idxs1);CHKERRQ(ierr); 306 ierr = ISLocalToGlobalMappingRestoreIndices(rl2g,&idxs2);CHKERRQ(ierr); 307 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); 308 } 309 } 310 } 311 #endif 312 313 B = NULL; 314 if (reuse != MAT_REUSE_MATRIX) { 315 PetscInt stl; 316 317 /* Create l2g map for the rows of the new matrix and index sets for the local MATNEST */ 318 for (i=0,stl=0;i<nr;i++) stl += lr[i]; 319 ierr = PetscMalloc1(stl,&l2gidxs);CHKERRQ(ierr); 320 for (i=0,stl=0;i<nr;i++) { 321 Mat usedmat; 322 Mat_IS *matis; 323 const PetscInt *idxs; 324 325 /* local IS for local NEST */ 326 ierr = ISCreateStride(PETSC_COMM_SELF,lr[i],stl,1,&islrow[i]);CHKERRQ(ierr); 327 328 /* l2gmap */ 329 j = 0; 330 usedmat = nest[i][j]; 331 while (!usedmat && j < nc-1) usedmat = nest[i][++j]; 332 if (!usedmat) SETERRQ(comm,PETSC_ERR_SUP,"Cannot find valid row mat"); 333 334 if (istrans[i*nc+j]) { 335 Mat T; 336 ierr = MatTransposeGetMat(usedmat,&T);CHKERRQ(ierr); 337 usedmat = T; 338 } 339 ierr = MatISSetUpSF(usedmat);CHKERRQ(ierr); 340 matis = (Mat_IS*)(usedmat->data); 341 ierr = ISGetIndices(isrow[i],&idxs);CHKERRQ(ierr); 342 if (istrans[i*nc+j]) { 343 ierr = PetscSFBcastBegin(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 344 ierr = PetscSFBcastEnd(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 345 } else { 346 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 347 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 348 } 349 ierr = ISRestoreIndices(isrow[i],&idxs);CHKERRQ(ierr); 350 stl += lr[i]; 351 } 352 ierr = ISLocalToGlobalMappingCreate(comm,1,stl,l2gidxs,PETSC_OWN_POINTER,&rl2g);CHKERRQ(ierr); 353 354 /* Create l2g map for columns of the new matrix and index sets for the local MATNEST */ 355 for (i=0,stl=0;i<nc;i++) stl += lc[i]; 356 ierr = PetscMalloc1(stl,&l2gidxs);CHKERRQ(ierr); 357 for (i=0,stl=0;i<nc;i++) { 358 Mat usedmat; 359 Mat_IS *matis; 360 const PetscInt *idxs; 361 362 /* local IS for local NEST */ 363 ierr = ISCreateStride(PETSC_COMM_SELF,lc[i],stl,1,&islcol[i]);CHKERRQ(ierr); 364 365 /* l2gmap */ 366 j = 0; 367 usedmat = nest[j][i]; 368 while (!usedmat && j < nr-1) usedmat = nest[++j][i]; 369 if (!usedmat) SETERRQ(comm,PETSC_ERR_SUP,"Cannot find valid column mat"); 370 if (istrans[j*nc+i]) { 371 Mat T; 372 ierr = MatTransposeGetMat(usedmat,&T);CHKERRQ(ierr); 373 usedmat = T; 374 } 375 ierr = MatISSetUpSF(usedmat);CHKERRQ(ierr); 376 matis = (Mat_IS*)(usedmat->data); 377 ierr = ISGetIndices(iscol[i],&idxs);CHKERRQ(ierr); 378 if (istrans[j*nc+i]) { 379 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 380 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 381 } else { 382 ierr = PetscSFBcastBegin(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 383 ierr = PetscSFBcastEnd(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 384 } 385 ierr = ISRestoreIndices(iscol[i],&idxs);CHKERRQ(ierr); 386 stl += lc[i]; 387 } 388 ierr = ISLocalToGlobalMappingCreate(comm,1,stl,l2gidxs,PETSC_OWN_POINTER,&cl2g);CHKERRQ(ierr); 389 390 /* Create MATIS */ 391 ierr = MatCreate(comm,&B);CHKERRQ(ierr); 392 ierr = MatSetSizes(B,A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N);CHKERRQ(ierr); 393 ierr = MatGetBlockSizes(A,&rbs,&cbs);CHKERRQ(ierr); 394 ierr = MatSetBlockSizes(B,rbs,cbs);CHKERRQ(ierr); 395 ierr = MatSetType(B,MATIS);CHKERRQ(ierr); 396 ierr = MatSetLocalToGlobalMapping(B,rl2g,cl2g);CHKERRQ(ierr); 397 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 398 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 399 ierr = MatCreateNest(PETSC_COMM_SELF,nr,islrow,nc,islcol,snest,&lA);CHKERRQ(ierr); 400 for (i=0;i<nr*nc;i++) { 401 if (istrans[i]) { 402 ierr = MatDestroy(&snest[i]);CHKERRQ(ierr); 403 } 404 } 405 ierr = MatISSetLocalMat(B,lA);CHKERRQ(ierr); 406 ierr = MatDestroy(&lA);CHKERRQ(ierr); 407 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 408 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 409 if (reuse == MAT_INPLACE_MATRIX) { 410 ierr = MatHeaderReplace(A,&B);CHKERRQ(ierr); 411 } else { 412 *newmat = B; 413 } 414 } else { 415 if (lreuse) { 416 ierr = MatISGetLocalMat(*newmat,&lA);CHKERRQ(ierr); 417 for (i=0;i<nr;i++) { 418 for (j=0;j<nc;j++) { 419 if (snest[i*nc+j]) { 420 ierr = MatNestSetSubMat(lA,i,j,snest[i*nc+j]);CHKERRQ(ierr); 421 if (istrans[i*nc+j]) { 422 ierr = MatDestroy(&snest[i*nc+j]);CHKERRQ(ierr); 423 } 424 } 425 } 426 } 427 } else { 428 PetscInt stl; 429 for (i=0,stl=0;i<nr;i++) { 430 ierr = ISCreateStride(PETSC_COMM_SELF,lr[i],stl,1,&islrow[i]);CHKERRQ(ierr); 431 stl += lr[i]; 432 } 433 for (i=0,stl=0;i<nc;i++) { 434 ierr = ISCreateStride(PETSC_COMM_SELF,lc[i],stl,1,&islcol[i]);CHKERRQ(ierr); 435 stl += lc[i]; 436 } 437 ierr = MatCreateNest(PETSC_COMM_SELF,nr,islrow,nc,islcol,snest,&lA);CHKERRQ(ierr); 438 for (i=0;i<nr*nc;i++) { 439 if (istrans[i]) { 440 ierr = MatDestroy(&snest[i]);CHKERRQ(ierr); 441 } 442 } 443 ierr = MatISSetLocalMat(*newmat,lA);CHKERRQ(ierr); 444 ierr = MatDestroy(&lA);CHKERRQ(ierr); 445 } 446 ierr = MatAssemblyBegin(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 447 ierr = MatAssemblyEnd(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 448 } 449 450 /* Create local matrix in MATNEST format */ 451 convert = PETSC_FALSE; 452 ierr = PetscOptionsGetBool(NULL,((PetscObject)A)->prefix,"-matis_convert_local_nest",&convert,NULL);CHKERRQ(ierr); 453 if (convert) { 454 Mat M; 455 MatISLocalFields lf; 456 PetscContainer c; 457 458 ierr = MatISGetLocalMat(*newmat,&lA);CHKERRQ(ierr); 459 ierr = MatConvert(lA,MATAIJ,MAT_INITIAL_MATRIX,&M);CHKERRQ(ierr); 460 ierr = MatISSetLocalMat(*newmat,M);CHKERRQ(ierr); 461 ierr = MatDestroy(&M);CHKERRQ(ierr); 462 463 /* attach local fields to the matrix */ 464 ierr = PetscNew(&lf);CHKERRQ(ierr); 465 ierr = PetscCalloc2(nr,&lf->rf,nc,&lf->cf);CHKERRQ(ierr); 466 for (i=0;i<nr;i++) { 467 PetscInt n,st; 468 469 ierr = ISGetLocalSize(islrow[i],&n);CHKERRQ(ierr); 470 ierr = ISStrideGetInfo(islrow[i],&st,NULL);CHKERRQ(ierr); 471 ierr = ISCreateStride(comm,n,st,1,&lf->rf[i]);CHKERRQ(ierr); 472 } 473 for (i=0;i<nc;i++) { 474 PetscInt n,st; 475 476 ierr = ISGetLocalSize(islcol[i],&n);CHKERRQ(ierr); 477 ierr = ISStrideGetInfo(islcol[i],&st,NULL);CHKERRQ(ierr); 478 ierr = ISCreateStride(comm,n,st,1,&lf->cf[i]);CHKERRQ(ierr); 479 } 480 lf->nr = nr; 481 lf->nc = nc; 482 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)(*newmat)),&c);CHKERRQ(ierr); 483 ierr = PetscContainerSetPointer(c,lf);CHKERRQ(ierr); 484 ierr = PetscContainerSetUserDestroy(c,MatISContainerDestroyFields_Private);CHKERRQ(ierr); 485 ierr = PetscObjectCompose((PetscObject)(*newmat),"_convert_nest_lfields",(PetscObject)c);CHKERRQ(ierr); 486 ierr = PetscContainerDestroy(&c);CHKERRQ(ierr); 487 } 488 489 /* Free workspace */ 490 for (i=0;i<nr;i++) { 491 ierr = ISDestroy(&islrow[i]);CHKERRQ(ierr); 492 } 493 for (i=0;i<nc;i++) { 494 ierr = ISDestroy(&islcol[i]);CHKERRQ(ierr); 495 } 496 ierr = PetscFree6(isrow,iscol,islrow,islcol,snest,istrans);CHKERRQ(ierr); 497 ierr = PetscFree2(lr,lc);CHKERRQ(ierr); 498 PetscFunctionReturn(0); 499 } 500 501 static PetscErrorCode MatDiagonalScale_IS(Mat A, Vec l, Vec r) 502 { 503 Mat_IS *matis = (Mat_IS*)A->data; 504 Vec ll,rr; 505 const PetscScalar *Y,*X; 506 PetscScalar *x,*y; 507 PetscErrorCode ierr; 508 509 PetscFunctionBegin; 510 ierr = MatISSetUpSF(A);CHKERRQ(ierr); 511 if (l) { 512 ll = matis->y; 513 ierr = VecGetArrayRead(l,&Y);CHKERRQ(ierr); 514 ierr = VecGetArray(ll,&y);CHKERRQ(ierr); 515 ierr = PetscSFBcastBegin(matis->sf,MPIU_SCALAR,Y,y);CHKERRQ(ierr); 516 } else { 517 ll = NULL; 518 } 519 if (r) { 520 rr = matis->x; 521 ierr = VecGetArrayRead(r,&X);CHKERRQ(ierr); 522 ierr = VecGetArray(rr,&x);CHKERRQ(ierr); 523 ierr = PetscSFBcastBegin(matis->csf,MPIU_SCALAR,X,x);CHKERRQ(ierr); 524 } else { 525 rr = NULL; 526 } 527 if (ll) { 528 ierr = PetscSFBcastEnd(matis->sf,MPIU_SCALAR,Y,y);CHKERRQ(ierr); 529 ierr = VecRestoreArrayRead(l,&Y);CHKERRQ(ierr); 530 ierr = VecRestoreArray(ll,&y);CHKERRQ(ierr); 531 } 532 if (rr) { 533 ierr = PetscSFBcastEnd(matis->csf,MPIU_SCALAR,X,x);CHKERRQ(ierr); 534 ierr = VecRestoreArrayRead(r,&X);CHKERRQ(ierr); 535 ierr = VecRestoreArray(rr,&x);CHKERRQ(ierr); 536 } 537 ierr = MatDiagonalScale(matis->A,ll,rr);CHKERRQ(ierr); 538 PetscFunctionReturn(0); 539 } 540 541 static PetscErrorCode MatGetInfo_IS(Mat A,MatInfoType flag,MatInfo *ginfo) 542 { 543 Mat_IS *matis = (Mat_IS*)A->data; 544 MatInfo info; 545 PetscReal isend[6],irecv[6]; 546 PetscInt bs; 547 PetscErrorCode ierr; 548 549 PetscFunctionBegin; 550 ierr = MatGetBlockSize(A,&bs);CHKERRQ(ierr); 551 if (matis->A->ops->getinfo) { 552 ierr = MatGetInfo(matis->A,MAT_LOCAL,&info);CHKERRQ(ierr); 553 isend[0] = info.nz_used; 554 isend[1] = info.nz_allocated; 555 isend[2] = info.nz_unneeded; 556 isend[3] = info.memory; 557 isend[4] = info.mallocs; 558 } else { 559 isend[0] = 0.; 560 isend[1] = 0.; 561 isend[2] = 0.; 562 isend[3] = 0.; 563 isend[4] = 0.; 564 } 565 isend[5] = matis->A->num_ass; 566 if (flag == MAT_LOCAL) { 567 ginfo->nz_used = isend[0]; 568 ginfo->nz_allocated = isend[1]; 569 ginfo->nz_unneeded = isend[2]; 570 ginfo->memory = isend[3]; 571 ginfo->mallocs = isend[4]; 572 ginfo->assemblies = isend[5]; 573 } else if (flag == MAT_GLOBAL_MAX) { 574 ierr = MPIU_Allreduce(isend,irecv,6,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 575 576 ginfo->nz_used = irecv[0]; 577 ginfo->nz_allocated = irecv[1]; 578 ginfo->nz_unneeded = irecv[2]; 579 ginfo->memory = irecv[3]; 580 ginfo->mallocs = irecv[4]; 581 ginfo->assemblies = irecv[5]; 582 } else if (flag == MAT_GLOBAL_SUM) { 583 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 584 585 ginfo->nz_used = irecv[0]; 586 ginfo->nz_allocated = irecv[1]; 587 ginfo->nz_unneeded = irecv[2]; 588 ginfo->memory = irecv[3]; 589 ginfo->mallocs = irecv[4]; 590 ginfo->assemblies = A->num_ass; 591 } 592 ginfo->block_size = bs; 593 ginfo->fill_ratio_given = 0; 594 ginfo->fill_ratio_needed = 0; 595 ginfo->factor_mallocs = 0; 596 PetscFunctionReturn(0); 597 } 598 599 PetscErrorCode MatTranspose_IS(Mat A,MatReuse reuse,Mat *B) 600 { 601 Mat C,lC,lA; 602 PetscErrorCode ierr; 603 604 PetscFunctionBegin; 605 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_INPLACE_MATRIX) { 606 ISLocalToGlobalMapping rl2g,cl2g; 607 ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr); 608 ierr = MatSetSizes(C,A->cmap->n,A->rmap->n,A->cmap->N,A->rmap->N);CHKERRQ(ierr); 609 ierr = MatSetBlockSizes(C,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 610 ierr = MatSetType(C,MATIS);CHKERRQ(ierr); 611 ierr = MatGetLocalToGlobalMapping(A,&rl2g,&cl2g);CHKERRQ(ierr); 612 ierr = MatSetLocalToGlobalMapping(C,cl2g,rl2g);CHKERRQ(ierr); 613 } else { 614 C = *B; 615 } 616 617 /* perform local transposition */ 618 ierr = MatISGetLocalMat(A,&lA);CHKERRQ(ierr); 619 ierr = MatTranspose(lA,MAT_INITIAL_MATRIX,&lC);CHKERRQ(ierr); 620 ierr = MatISSetLocalMat(C,lC);CHKERRQ(ierr); 621 ierr = MatDestroy(&lC);CHKERRQ(ierr); 622 623 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 624 *B = C; 625 } else { 626 ierr = MatHeaderMerge(A,&C);CHKERRQ(ierr); 627 } 628 ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 629 ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 630 PetscFunctionReturn(0); 631 } 632 633 PetscErrorCode MatDiagonalSet_IS(Mat A,Vec D,InsertMode insmode) 634 { 635 Mat_IS *is = (Mat_IS*)A->data; 636 PetscErrorCode ierr; 637 638 PetscFunctionBegin; 639 if (D) { /* MatShift_IS pass D = NULL */ 640 ierr = VecScatterBegin(is->rctx,D,is->y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 641 ierr = VecScatterEnd(is->rctx,D,is->y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 642 } 643 ierr = VecPointwiseDivide(is->y,is->y,is->counter);CHKERRQ(ierr); 644 ierr = MatDiagonalSet(is->A,is->y,insmode);CHKERRQ(ierr); 645 PetscFunctionReturn(0); 646 } 647 648 PetscErrorCode MatShift_IS(Mat A,PetscScalar a) 649 { 650 Mat_IS *is = (Mat_IS*)A->data; 651 PetscErrorCode ierr; 652 653 PetscFunctionBegin; 654 ierr = VecSet(is->y,a);CHKERRQ(ierr); 655 ierr = MatDiagonalSet_IS(A,NULL,ADD_VALUES);CHKERRQ(ierr); 656 PetscFunctionReturn(0); 657 } 658 659 static PetscErrorCode MatSetValuesLocal_SubMat_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 660 { 661 PetscErrorCode ierr; 662 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 663 664 PetscFunctionBegin; 665 #if defined(PETSC_USE_DEBUG) 666 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); 667 #endif 668 ierr = ISLocalToGlobalMappingApply(A->rmap->mapping,m,rows,rows_l);CHKERRQ(ierr); 669 ierr = ISLocalToGlobalMappingApply(A->cmap->mapping,n,cols,cols_l);CHKERRQ(ierr); 670 ierr = MatSetValuesLocal_IS(A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 671 PetscFunctionReturn(0); 672 } 673 674 static PetscErrorCode MatSetValuesBlockedLocal_SubMat_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 675 { 676 PetscErrorCode ierr; 677 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 678 679 PetscFunctionBegin; 680 #if defined(PETSC_USE_DEBUG) 681 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); 682 #endif 683 ierr = ISLocalToGlobalMappingApplyBlock(A->rmap->mapping,m,rows,rows_l);CHKERRQ(ierr); 684 ierr = ISLocalToGlobalMappingApplyBlock(A->cmap->mapping,n,cols,cols_l);CHKERRQ(ierr); 685 ierr = MatSetValuesBlockedLocal_IS(A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 686 PetscFunctionReturn(0); 687 } 688 689 static PetscErrorCode PetscLayoutMapLocal_Private(PetscLayout map,PetscInt N,const PetscInt idxs[], PetscInt *on,PetscInt **oidxs,PetscInt **ogidxs) 690 { 691 PetscInt *owners = map->range; 692 PetscInt n = map->n; 693 PetscSF sf; 694 PetscInt *lidxs,*work = NULL; 695 PetscSFNode *ridxs; 696 PetscMPIInt rank; 697 PetscInt r, p = 0, len = 0; 698 PetscErrorCode ierr; 699 700 PetscFunctionBegin; 701 if (on) *on = 0; /* squelch -Wmaybe-uninitialized */ 702 /* Create SF where leaves are input idxs and roots are owned idxs (code adapted from MatZeroRowsMapLocal_Private) */ 703 ierr = MPI_Comm_rank(map->comm,&rank);CHKERRQ(ierr); 704 ierr = PetscMalloc1(n,&lidxs);CHKERRQ(ierr); 705 for (r = 0; r < n; ++r) lidxs[r] = -1; 706 ierr = PetscMalloc1(N,&ridxs);CHKERRQ(ierr); 707 for (r = 0; r < N; ++r) { 708 const PetscInt idx = idxs[r]; 709 if (idx < 0 || map->N <= idx) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index %D out of range [0,%D)",idx,map->N); 710 if (idx < owners[p] || owners[p+1] <= idx) { /* short-circuit the search if the last p owns this idx too */ 711 ierr = PetscLayoutFindOwner(map,idx,&p);CHKERRQ(ierr); 712 } 713 ridxs[r].rank = p; 714 ridxs[r].index = idxs[r] - owners[p]; 715 } 716 ierr = PetscSFCreate(map->comm,&sf);CHKERRQ(ierr); 717 ierr = PetscSFSetGraph(sf,n,N,NULL,PETSC_OWN_POINTER,ridxs,PETSC_OWN_POINTER);CHKERRQ(ierr); 718 ierr = PetscSFReduceBegin(sf,MPIU_INT,(PetscInt*)idxs,lidxs,MPI_LOR);CHKERRQ(ierr); 719 ierr = PetscSFReduceEnd(sf,MPIU_INT,(PetscInt*)idxs,lidxs,MPI_LOR);CHKERRQ(ierr); 720 if (ogidxs) { /* communicate global idxs */ 721 PetscInt cum = 0,start,*work2; 722 723 ierr = PetscMalloc1(n,&work);CHKERRQ(ierr); 724 ierr = PetscCalloc1(N,&work2);CHKERRQ(ierr); 725 for (r = 0; r < N; ++r) if (idxs[r] >=0) cum++; 726 ierr = MPI_Scan(&cum,&start,1,MPIU_INT,MPI_SUM,map->comm);CHKERRQ(ierr); 727 start -= cum; 728 cum = 0; 729 for (r = 0; r < N; ++r) if (idxs[r] >=0) work2[r] = start+cum++; 730 ierr = PetscSFReduceBegin(sf,MPIU_INT,work2,work,MPIU_REPLACE);CHKERRQ(ierr); 731 ierr = PetscSFReduceEnd(sf,MPIU_INT,work2,work,MPIU_REPLACE);CHKERRQ(ierr); 732 ierr = PetscFree(work2);CHKERRQ(ierr); 733 } 734 ierr = PetscSFDestroy(&sf);CHKERRQ(ierr); 735 /* Compress and put in indices */ 736 for (r = 0; r < n; ++r) 737 if (lidxs[r] >= 0) { 738 if (work) work[len] = work[r]; 739 lidxs[len++] = r; 740 } 741 if (on) *on = len; 742 if (oidxs) *oidxs = lidxs; 743 if (ogidxs) *ogidxs = work; 744 PetscFunctionReturn(0); 745 } 746 747 static PetscErrorCode MatCreateSubMatrix_IS(Mat mat,IS irow,IS icol,MatReuse scall,Mat *newmat) 748 { 749 Mat locmat,newlocmat; 750 Mat_IS *newmatis; 751 #if defined(PETSC_USE_DEBUG) 752 Vec rtest,ltest; 753 const PetscScalar *array; 754 #endif 755 const PetscInt *idxs; 756 PetscInt i,m,n; 757 PetscErrorCode ierr; 758 759 PetscFunctionBegin; 760 if (scall == MAT_REUSE_MATRIX) { 761 PetscBool ismatis; 762 763 ierr = PetscObjectTypeCompare((PetscObject)*newmat,MATIS,&ismatis);CHKERRQ(ierr); 764 if (!ismatis) SETERRQ(PetscObjectComm((PetscObject)*newmat),PETSC_ERR_ARG_WRONG,"Cannot reuse matrix! Not of MATIS type"); 765 newmatis = (Mat_IS*)(*newmat)->data; 766 if (!newmatis->getsub_ris) SETERRQ(PetscObjectComm((PetscObject)*newmat),PETSC_ERR_ARG_WRONG,"Cannot reuse matrix! Misses local row IS"); 767 if (!newmatis->getsub_cis) SETERRQ(PetscObjectComm((PetscObject)*newmat),PETSC_ERR_ARG_WRONG,"Cannot reuse matrix! Misses local col IS"); 768 } 769 /* irow and icol may not have duplicate entries */ 770 #if defined(PETSC_USE_DEBUG) 771 ierr = MatCreateVecs(mat,<est,&rtest);CHKERRQ(ierr); 772 ierr = ISGetLocalSize(irow,&n);CHKERRQ(ierr); 773 ierr = ISGetIndices(irow,&idxs);CHKERRQ(ierr); 774 for (i=0;i<n;i++) { 775 ierr = VecSetValue(rtest,idxs[i],1.0,ADD_VALUES);CHKERRQ(ierr); 776 } 777 ierr = VecAssemblyBegin(rtest);CHKERRQ(ierr); 778 ierr = VecAssemblyEnd(rtest);CHKERRQ(ierr); 779 ierr = VecGetLocalSize(rtest,&n);CHKERRQ(ierr); 780 ierr = VecGetOwnershipRange(rtest,&m,NULL);CHKERRQ(ierr); 781 ierr = VecGetArrayRead(rtest,&array);CHKERRQ(ierr); 782 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])); 783 ierr = VecRestoreArrayRead(rtest,&array);CHKERRQ(ierr); 784 ierr = ISRestoreIndices(irow,&idxs);CHKERRQ(ierr); 785 ierr = ISGetLocalSize(icol,&n);CHKERRQ(ierr); 786 ierr = ISGetIndices(icol,&idxs);CHKERRQ(ierr); 787 for (i=0;i<n;i++) { 788 ierr = VecSetValue(ltest,idxs[i],1.0,ADD_VALUES);CHKERRQ(ierr); 789 } 790 ierr = VecAssemblyBegin(ltest);CHKERRQ(ierr); 791 ierr = VecAssemblyEnd(ltest);CHKERRQ(ierr); 792 ierr = VecGetLocalSize(ltest,&n);CHKERRQ(ierr); 793 ierr = VecGetOwnershipRange(ltest,&m,NULL);CHKERRQ(ierr); 794 ierr = VecGetArrayRead(ltest,&array);CHKERRQ(ierr); 795 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])); 796 ierr = VecRestoreArrayRead(ltest,&array);CHKERRQ(ierr); 797 ierr = ISRestoreIndices(icol,&idxs);CHKERRQ(ierr); 798 ierr = VecDestroy(&rtest);CHKERRQ(ierr); 799 ierr = VecDestroy(<est);CHKERRQ(ierr); 800 #endif 801 if (scall == MAT_INITIAL_MATRIX) { 802 Mat_IS *matis = (Mat_IS*)mat->data; 803 ISLocalToGlobalMapping rl2g; 804 IS is; 805 PetscInt *lidxs,*lgidxs,*newgidxs; 806 PetscInt ll,newloc,irbs,icbs,arbs,acbs,rbs,cbs; 807 MPI_Comm comm; 808 809 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 810 ierr = MatGetBlockSizes(mat,&arbs,&acbs);CHKERRQ(ierr); 811 ierr = ISGetBlockSize(irow,&irbs);CHKERRQ(ierr); 812 ierr = ISGetBlockSize(icol,&icbs);CHKERRQ(ierr); 813 rbs = arbs == irbs ? irbs : 1; 814 cbs = acbs == icbs ? icbs : 1; 815 ierr = ISGetLocalSize(irow,&m);CHKERRQ(ierr); 816 ierr = ISGetLocalSize(icol,&n);CHKERRQ(ierr); 817 ierr = MatCreate(comm,newmat);CHKERRQ(ierr); 818 ierr = MatSetType(*newmat,MATIS);CHKERRQ(ierr); 819 ierr = MatSetSizes(*newmat,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); 820 ierr = MatSetBlockSizes(*newmat,rbs,cbs);CHKERRQ(ierr); 821 /* communicate irow to their owners in the layout */ 822 ierr = ISGetIndices(irow,&idxs);CHKERRQ(ierr); 823 ierr = PetscLayoutMapLocal_Private(mat->rmap,m,idxs,&ll,&lidxs,&lgidxs);CHKERRQ(ierr); 824 ierr = ISRestoreIndices(irow,&idxs);CHKERRQ(ierr); 825 ierr = MatISSetUpSF(mat);CHKERRQ(ierr); 826 ierr = PetscMemzero(matis->sf_rootdata,matis->sf->nroots*sizeof(PetscInt));CHKERRQ(ierr); 827 for (i=0;i<ll;i++) matis->sf_rootdata[lidxs[i]] = lgidxs[i]+1; 828 ierr = PetscFree(lidxs);CHKERRQ(ierr); 829 ierr = PetscFree(lgidxs);CHKERRQ(ierr); 830 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 831 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 832 for (i=0,newloc=0;i<matis->sf->nleaves;i++) if (matis->sf_leafdata[i]) newloc++; 833 ierr = PetscMalloc1(newloc,&newgidxs);CHKERRQ(ierr); 834 ierr = PetscMalloc1(newloc,&lidxs);CHKERRQ(ierr); 835 for (i=0,newloc=0;i<matis->sf->nleaves;i++) 836 if (matis->sf_leafdata[i]) { 837 lidxs[newloc] = i; 838 newgidxs[newloc++] = matis->sf_leafdata[i]-1; 839 } 840 ierr = ISCreateGeneral(comm,newloc,newgidxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 841 ierr = ISLocalToGlobalMappingCreateIS(is,&rl2g);CHKERRQ(ierr); 842 ierr = ISLocalToGlobalMappingSetBlockSize(rl2g,rbs);CHKERRQ(ierr); 843 ierr = ISDestroy(&is);CHKERRQ(ierr); 844 /* local is to extract local submatrix */ 845 newmatis = (Mat_IS*)(*newmat)->data; 846 ierr = ISCreateGeneral(comm,newloc,lidxs,PETSC_OWN_POINTER,&newmatis->getsub_ris);CHKERRQ(ierr); 847 if (mat->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 848 PetscBool cong; 849 850 ierr = PetscLayoutCompare(mat->rmap,mat->cmap,&cong);CHKERRQ(ierr); 851 if (cong) mat->congruentlayouts = 1; 852 else mat->congruentlayouts = 0; 853 } 854 if (mat->congruentlayouts && irow == icol && matis->csf == matis->sf) { 855 ierr = MatSetLocalToGlobalMapping(*newmat,rl2g,rl2g);CHKERRQ(ierr); 856 ierr = PetscObjectReference((PetscObject)newmatis->getsub_ris);CHKERRQ(ierr); 857 newmatis->getsub_cis = newmatis->getsub_ris; 858 } else { 859 ISLocalToGlobalMapping cl2g; 860 861 /* communicate icol to their owners in the layout */ 862 ierr = ISGetIndices(icol,&idxs);CHKERRQ(ierr); 863 ierr = PetscLayoutMapLocal_Private(mat->cmap,n,idxs,&ll,&lidxs,&lgidxs);CHKERRQ(ierr); 864 ierr = ISRestoreIndices(icol,&idxs);CHKERRQ(ierr); 865 ierr = PetscMemzero(matis->csf_rootdata,matis->csf->nroots*sizeof(PetscInt));CHKERRQ(ierr); 866 for (i=0;i<ll;i++) matis->csf_rootdata[lidxs[i]] = lgidxs[i]+1; 867 ierr = PetscFree(lidxs);CHKERRQ(ierr); 868 ierr = PetscFree(lgidxs);CHKERRQ(ierr); 869 ierr = PetscSFBcastBegin(matis->csf,MPIU_INT,matis->csf_rootdata,matis->csf_leafdata);CHKERRQ(ierr); 870 ierr = PetscSFBcastEnd(matis->csf,MPIU_INT,matis->csf_rootdata,matis->csf_leafdata);CHKERRQ(ierr); 871 for (i=0,newloc=0;i<matis->csf->nleaves;i++) if (matis->csf_leafdata[i]) newloc++; 872 ierr = PetscMalloc1(newloc,&newgidxs);CHKERRQ(ierr); 873 ierr = PetscMalloc1(newloc,&lidxs);CHKERRQ(ierr); 874 for (i=0,newloc=0;i<matis->csf->nleaves;i++) 875 if (matis->csf_leafdata[i]) { 876 lidxs[newloc] = i; 877 newgidxs[newloc++] = matis->csf_leafdata[i]-1; 878 } 879 ierr = ISCreateGeneral(comm,newloc,newgidxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 880 ierr = ISLocalToGlobalMappingCreateIS(is,&cl2g);CHKERRQ(ierr); 881 ierr = ISLocalToGlobalMappingSetBlockSize(cl2g,cbs);CHKERRQ(ierr); 882 ierr = ISDestroy(&is);CHKERRQ(ierr); 883 /* local is to extract local submatrix */ 884 ierr = ISCreateGeneral(comm,newloc,lidxs,PETSC_OWN_POINTER,&newmatis->getsub_cis);CHKERRQ(ierr); 885 ierr = MatSetLocalToGlobalMapping(*newmat,rl2g,cl2g);CHKERRQ(ierr); 886 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 887 } 888 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 889 } else { 890 ierr = MatISGetLocalMat(*newmat,&newlocmat);CHKERRQ(ierr); 891 } 892 ierr = MatISGetLocalMat(mat,&locmat);CHKERRQ(ierr); 893 newmatis = (Mat_IS*)(*newmat)->data; 894 ierr = MatCreateSubMatrix(locmat,newmatis->getsub_ris,newmatis->getsub_cis,scall,&newlocmat);CHKERRQ(ierr); 895 if (scall == MAT_INITIAL_MATRIX) { 896 ierr = MatISSetLocalMat(*newmat,newlocmat);CHKERRQ(ierr); 897 ierr = MatDestroy(&newlocmat);CHKERRQ(ierr); 898 } 899 ierr = MatAssemblyBegin(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 900 ierr = MatAssemblyEnd(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 901 PetscFunctionReturn(0); 902 } 903 904 static PetscErrorCode MatCopy_IS(Mat A,Mat B,MatStructure str) 905 { 906 Mat_IS *a = (Mat_IS*)A->data,*b; 907 PetscBool ismatis; 908 PetscErrorCode ierr; 909 910 PetscFunctionBegin; 911 ierr = PetscObjectTypeCompare((PetscObject)B,MATIS,&ismatis);CHKERRQ(ierr); 912 if (!ismatis) SETERRQ(PetscObjectComm((PetscObject)B),PETSC_ERR_SUP,"Need to be implemented"); 913 b = (Mat_IS*)B->data; 914 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 915 ierr = PetscObjectStateIncrease((PetscObject)B);CHKERRQ(ierr); 916 PetscFunctionReturn(0); 917 } 918 919 static PetscErrorCode MatMissingDiagonal_IS(Mat A,PetscBool *missing,PetscInt *d) 920 { 921 Vec v; 922 const PetscScalar *array; 923 PetscInt i,n; 924 PetscErrorCode ierr; 925 926 PetscFunctionBegin; 927 *missing = PETSC_FALSE; 928 ierr = MatCreateVecs(A,NULL,&v);CHKERRQ(ierr); 929 ierr = MatGetDiagonal(A,v);CHKERRQ(ierr); 930 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 931 ierr = VecGetArrayRead(v,&array);CHKERRQ(ierr); 932 for (i=0;i<n;i++) if (array[i] == 0.) break; 933 ierr = VecRestoreArrayRead(v,&array);CHKERRQ(ierr); 934 ierr = VecDestroy(&v);CHKERRQ(ierr); 935 if (i != n) *missing = PETSC_TRUE; 936 if (d) { 937 *d = -1; 938 if (*missing) { 939 PetscInt rstart; 940 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 941 *d = i+rstart; 942 } 943 } 944 PetscFunctionReturn(0); 945 } 946 947 static PetscErrorCode MatISSetUpSF_IS(Mat B) 948 { 949 Mat_IS *matis = (Mat_IS*)(B->data); 950 const PetscInt *gidxs; 951 PetscInt nleaves; 952 PetscErrorCode ierr; 953 954 PetscFunctionBegin; 955 if (matis->sf) PetscFunctionReturn(0); 956 ierr = PetscSFCreate(PetscObjectComm((PetscObject)B),&matis->sf);CHKERRQ(ierr); 957 ierr = ISLocalToGlobalMappingGetIndices(B->rmap->mapping,&gidxs);CHKERRQ(ierr); 958 ierr = ISLocalToGlobalMappingGetSize(B->rmap->mapping,&nleaves);CHKERRQ(ierr); 959 ierr = PetscSFSetGraphLayout(matis->sf,B->rmap,nleaves,NULL,PETSC_OWN_POINTER,gidxs);CHKERRQ(ierr); 960 ierr = ISLocalToGlobalMappingRestoreIndices(B->rmap->mapping,&gidxs);CHKERRQ(ierr); 961 ierr = PetscMalloc2(matis->sf->nroots,&matis->sf_rootdata,matis->sf->nleaves,&matis->sf_leafdata);CHKERRQ(ierr); 962 if (B->rmap->mapping != B->cmap->mapping) { /* setup SF for columns */ 963 ierr = ISLocalToGlobalMappingGetSize(B->cmap->mapping,&nleaves);CHKERRQ(ierr); 964 ierr = PetscSFCreate(PetscObjectComm((PetscObject)B),&matis->csf);CHKERRQ(ierr); 965 ierr = ISLocalToGlobalMappingGetIndices(B->cmap->mapping,&gidxs);CHKERRQ(ierr); 966 ierr = PetscSFSetGraphLayout(matis->csf,B->cmap,nleaves,NULL,PETSC_OWN_POINTER,gidxs);CHKERRQ(ierr); 967 ierr = ISLocalToGlobalMappingRestoreIndices(B->cmap->mapping,&gidxs);CHKERRQ(ierr); 968 ierr = PetscMalloc2(matis->csf->nroots,&matis->csf_rootdata,matis->csf->nleaves,&matis->csf_leafdata);CHKERRQ(ierr); 969 } else { 970 matis->csf = matis->sf; 971 matis->csf_leafdata = matis->sf_leafdata; 972 matis->csf_rootdata = matis->sf_rootdata; 973 } 974 PetscFunctionReturn(0); 975 } 976 977 /*@ 978 MatISSetPreallocation - Preallocates memory for a MATIS parallel matrix. 979 980 Collective on MPI_Comm 981 982 Input Parameters: 983 + B - the matrix 984 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 985 (same value is used for all local rows) 986 . d_nnz - array containing the number of nonzeros in the various rows of the 987 DIAGONAL portion of the local submatrix (possibly different for each row) 988 or NULL, if d_nz is used to specify the nonzero structure. 989 The size of this array is equal to the number of local rows, i.e 'm'. 990 For matrices that will be factored, you must leave room for (and set) 991 the diagonal entry even if it is zero. 992 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 993 submatrix (same value is used for all local rows). 994 - o_nnz - array containing the number of nonzeros in the various rows of the 995 OFF-DIAGONAL portion of the local submatrix (possibly different for 996 each row) or NULL, if o_nz is used to specify the nonzero 997 structure. The size of this array is equal to the number 998 of local rows, i.e 'm'. 999 1000 If the *_nnz parameter is given then the *_nz parameter is ignored 1001 1002 Level: intermediate 1003 1004 Notes: This function has the same interface as the MPIAIJ preallocation routine in order to simplify the transition 1005 from the asssembled format to the unassembled one. It overestimates the preallocation of MATIS local 1006 matrices; for exact preallocation, the user should set the preallocation directly on local matrix objects. 1007 1008 .keywords: matrix 1009 1010 .seealso: MatCreate(), MatCreateIS(), MatMPIAIJSetPreallocation(), MatISGetLocalMat(), MATIS 1011 @*/ 1012 PetscErrorCode MatISSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 1013 { 1014 PetscErrorCode ierr; 1015 1016 PetscFunctionBegin; 1017 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 1018 PetscValidType(B,1); 1019 ierr = PetscTryMethod(B,"MatISSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 1020 PetscFunctionReturn(0); 1021 } 1022 1023 static PetscErrorCode MatISSetPreallocation_IS(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 1024 { 1025 Mat_IS *matis = (Mat_IS*)(B->data); 1026 PetscInt bs,i,nlocalcols; 1027 PetscErrorCode ierr; 1028 1029 PetscFunctionBegin; 1030 if (!matis->A) SETERRQ(PetscObjectComm((PetscObject)B),PETSC_ERR_SUP,"You should first call MatSetLocalToGlobalMapping"); 1031 ierr = MatISSetUpSF(B);CHKERRQ(ierr); 1032 1033 if (!d_nnz) for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] = d_nz; 1034 else for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] = d_nnz[i]; 1035 1036 if (!o_nnz) for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] += o_nz; 1037 else for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] += o_nnz[i]; 1038 1039 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1040 ierr = MatGetSize(matis->A,NULL,&nlocalcols);CHKERRQ(ierr); 1041 ierr = MatGetBlockSize(matis->A,&bs);CHKERRQ(ierr); 1042 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1043 1044 for (i=0;i<matis->sf->nleaves;i++) matis->sf_leafdata[i] = PetscMin(matis->sf_leafdata[i],nlocalcols); 1045 ierr = MatSeqAIJSetPreallocation(matis->A,0,matis->sf_leafdata);CHKERRQ(ierr); 1046 #if defined(PETSC_HAVE_HYPRE) 1047 ierr = MatHYPRESetPreallocation(matis->A,0,matis->sf_leafdata,0,NULL);CHKERRQ(ierr); 1048 #endif 1049 1050 for (i=0;i<matis->sf->nleaves/bs;i++) matis->sf_leafdata[i] = matis->sf_leafdata[i*bs]/bs; 1051 ierr = MatSeqBAIJSetPreallocation(matis->A,bs,0,matis->sf_leafdata);CHKERRQ(ierr); 1052 1053 for (i=0;i<matis->sf->nleaves/bs;i++) matis->sf_leafdata[i] = matis->sf_leafdata[i]-i; 1054 ierr = MatSeqSBAIJSetPreallocation(matis->A,bs,0,matis->sf_leafdata);CHKERRQ(ierr); 1055 1056 /* for other matrix types */ 1057 ierr = MatSetUp(matis->A);CHKERRQ(ierr); 1058 PetscFunctionReturn(0); 1059 } 1060 1061 PETSC_EXTERN PetscErrorCode MatISSetMPIXAIJPreallocation_Private(Mat A, Mat B, PetscBool maxreduce) 1062 { 1063 Mat_IS *matis = (Mat_IS*)(A->data); 1064 PetscInt *my_dnz,*my_onz,*dnz,*onz,*mat_ranges,*row_ownership; 1065 const PetscInt *global_indices_r,*global_indices_c; 1066 PetscInt i,j,bs,rows,cols; 1067 PetscInt lrows,lcols; 1068 PetscInt local_rows,local_cols; 1069 PetscMPIInt nsubdomains; 1070 PetscBool isdense,issbaij; 1071 PetscErrorCode ierr; 1072 1073 PetscFunctionBegin; 1074 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)A),&nsubdomains);CHKERRQ(ierr); 1075 ierr = MatGetSize(A,&rows,&cols);CHKERRQ(ierr); 1076 ierr = MatGetBlockSize(A,&bs);CHKERRQ(ierr); 1077 ierr = MatGetSize(matis->A,&local_rows,&local_cols);CHKERRQ(ierr); 1078 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQDENSE,&isdense);CHKERRQ(ierr); 1079 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQSBAIJ,&issbaij);CHKERRQ(ierr); 1080 ierr = ISLocalToGlobalMappingGetIndices(A->rmap->mapping,&global_indices_r);CHKERRQ(ierr); 1081 if (A->rmap->mapping != A->cmap->mapping) { 1082 ierr = ISLocalToGlobalMappingGetIndices(A->cmap->mapping,&global_indices_c);CHKERRQ(ierr); 1083 } else { 1084 global_indices_c = global_indices_r; 1085 } 1086 1087 if (issbaij) { 1088 ierr = MatGetRowUpperTriangular(matis->A);CHKERRQ(ierr); 1089 } 1090 /* 1091 An SF reduce is needed to sum up properly on shared rows. 1092 Note that generally preallocation is not exact, since it overestimates nonzeros 1093 */ 1094 ierr = MatISSetUpSF(A);CHKERRQ(ierr); 1095 ierr = MatGetLocalSize(A,&lrows,&lcols);CHKERRQ(ierr); 1096 ierr = MatPreallocateInitialize(PetscObjectComm((PetscObject)A),lrows,lcols,dnz,onz);CHKERRQ(ierr); 1097 /* All processes need to compute entire row ownership */ 1098 ierr = PetscMalloc1(rows,&row_ownership);CHKERRQ(ierr); 1099 ierr = MatGetOwnershipRanges(A,(const PetscInt**)&mat_ranges);CHKERRQ(ierr); 1100 for (i=0;i<nsubdomains;i++) { 1101 for (j=mat_ranges[i];j<mat_ranges[i+1];j++) { 1102 row_ownership[j] = i; 1103 } 1104 } 1105 ierr = MatGetOwnershipRangesColumn(A,(const PetscInt**)&mat_ranges);CHKERRQ(ierr); 1106 1107 /* 1108 my_dnz and my_onz contains exact contribution to preallocation from each local mat 1109 then, they will be summed up properly. This way, preallocation is always sufficient 1110 */ 1111 ierr = PetscCalloc2(local_rows,&my_dnz,local_rows,&my_onz);CHKERRQ(ierr); 1112 /* preallocation as a MATAIJ */ 1113 if (isdense) { /* special case for dense local matrices */ 1114 for (i=0;i<local_rows;i++) { 1115 PetscInt owner = row_ownership[global_indices_r[i]]; 1116 for (j=0;j<local_cols;j++) { 1117 PetscInt index_col = global_indices_c[j]; 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 } 1124 } 1125 } else if (matis->A->ops->getrowij) { 1126 const PetscInt *ii,*jj,*jptr; 1127 PetscBool done; 1128 ierr = MatGetRowIJ(matis->A,0,PETSC_FALSE,PETSC_FALSE,&local_rows,&ii,&jj,&done);CHKERRQ(ierr); 1129 if (!done) SETERRQ(PetscObjectComm((PetscObject)(matis->A)),PETSC_ERR_PLIB,"Error in MatGetRowIJ"); 1130 jptr = jj; 1131 for (i=0;i<local_rows;i++) { 1132 PetscInt index_row = global_indices_r[i]; 1133 for (j=0;j<ii[i+1]-ii[i];j++,jptr++) { 1134 PetscInt owner = row_ownership[index_row]; 1135 PetscInt index_col = global_indices_c[*jptr]; 1136 if (index_col > mat_ranges[owner]-1 && index_col < mat_ranges[owner+1] ) { /* diag block */ 1137 my_dnz[i] += 1; 1138 } else { /* offdiag block */ 1139 my_onz[i] += 1; 1140 } 1141 /* same as before, interchanging rows and cols */ 1142 if (issbaij && index_col != index_row) { 1143 owner = row_ownership[index_col]; 1144 if (index_row > mat_ranges[owner]-1 && index_row < mat_ranges[owner+1] ) { 1145 my_dnz[*jptr] += 1; 1146 } else { 1147 my_onz[*jptr] += 1; 1148 } 1149 } 1150 } 1151 } 1152 ierr = MatRestoreRowIJ(matis->A,0,PETSC_FALSE,PETSC_FALSE,&local_rows,&ii,&jj,&done);CHKERRQ(ierr); 1153 if (!done) SETERRQ(PetscObjectComm((PetscObject)(matis->A)),PETSC_ERR_PLIB,"Error in MatRestoreRowIJ"); 1154 } else { /* loop over rows and use MatGetRow */ 1155 for (i=0;i<local_rows;i++) { 1156 const PetscInt *cols; 1157 PetscInt ncols,index_row = global_indices_r[i]; 1158 ierr = MatGetRow(matis->A,i,&ncols,&cols,NULL);CHKERRQ(ierr); 1159 for (j=0;j<ncols;j++) { 1160 PetscInt owner = row_ownership[index_row]; 1161 PetscInt index_col = global_indices_c[cols[j]]; 1162 if (index_col > mat_ranges[owner]-1 && index_col < mat_ranges[owner+1] ) { /* diag block */ 1163 my_dnz[i] += 1; 1164 } else { /* offdiag block */ 1165 my_onz[i] += 1; 1166 } 1167 /* same as before, interchanging rows and cols */ 1168 if (issbaij && index_col != index_row) { 1169 owner = row_ownership[index_col]; 1170 if (index_row > mat_ranges[owner]-1 && index_row < mat_ranges[owner+1] ) { 1171 my_dnz[cols[j]] += 1; 1172 } else { 1173 my_onz[cols[j]] += 1; 1174 } 1175 } 1176 } 1177 ierr = MatRestoreRow(matis->A,i,&ncols,&cols,NULL);CHKERRQ(ierr); 1178 } 1179 } 1180 if (global_indices_c != global_indices_r) { 1181 ierr = ISLocalToGlobalMappingRestoreIndices(A->cmap->mapping,&global_indices_c);CHKERRQ(ierr); 1182 } 1183 ierr = ISLocalToGlobalMappingRestoreIndices(A->rmap->mapping,&global_indices_r);CHKERRQ(ierr); 1184 ierr = PetscFree(row_ownership);CHKERRQ(ierr); 1185 1186 /* Reduce my_dnz and my_onz */ 1187 if (maxreduce) { 1188 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_dnz,dnz,MPI_MAX);CHKERRQ(ierr); 1189 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_onz,onz,MPI_MAX);CHKERRQ(ierr); 1190 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_dnz,dnz,MPI_MAX);CHKERRQ(ierr); 1191 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_onz,onz,MPI_MAX);CHKERRQ(ierr); 1192 } else { 1193 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_dnz,dnz,MPI_SUM);CHKERRQ(ierr); 1194 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_onz,onz,MPI_SUM);CHKERRQ(ierr); 1195 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_dnz,dnz,MPI_SUM);CHKERRQ(ierr); 1196 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_onz,onz,MPI_SUM);CHKERRQ(ierr); 1197 } 1198 ierr = PetscFree2(my_dnz,my_onz);CHKERRQ(ierr); 1199 1200 /* Resize preallocation if overestimated */ 1201 for (i=0;i<lrows;i++) { 1202 dnz[i] = PetscMin(dnz[i],lcols); 1203 onz[i] = PetscMin(onz[i],cols-lcols); 1204 } 1205 1206 /* Set preallocation */ 1207 ierr = MatSeqAIJSetPreallocation(B,0,dnz);CHKERRQ(ierr); 1208 ierr = MatMPIAIJSetPreallocation(B,0,dnz,0,onz);CHKERRQ(ierr); 1209 for (i=0;i<lrows/bs;i++) { 1210 dnz[i] = dnz[i*bs]/bs; 1211 onz[i] = onz[i*bs]/bs; 1212 } 1213 ierr = MatSeqBAIJSetPreallocation(B,bs,0,dnz);CHKERRQ(ierr); 1214 ierr = MatMPIBAIJSetPreallocation(B,bs,0,dnz,0,onz);CHKERRQ(ierr); 1215 ierr = MatMPISBAIJSetPreallocation(B,bs,0,dnz,0,onz);CHKERRQ(ierr); 1216 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1217 if (issbaij) { 1218 ierr = MatRestoreRowUpperTriangular(matis->A);CHKERRQ(ierr); 1219 } 1220 PetscFunctionReturn(0); 1221 } 1222 1223 static PetscErrorCode MatISGetMPIXAIJ_IS(Mat mat, MatReuse reuse, Mat *M) 1224 { 1225 Mat_IS *matis = (Mat_IS*)(mat->data); 1226 Mat local_mat; 1227 /* info on mat */ 1228 PetscInt bs,rows,cols,lrows,lcols; 1229 PetscInt local_rows,local_cols; 1230 PetscBool isseqdense,isseqsbaij,isseqaij,isseqbaij; 1231 #if defined (PETSC_USE_DEBUG) 1232 PetscBool lb[4],bb[4]; 1233 #endif 1234 PetscMPIInt nsubdomains; 1235 /* values insertion */ 1236 PetscScalar *array; 1237 /* work */ 1238 PetscErrorCode ierr; 1239 1240 PetscFunctionBegin; 1241 /* get info from mat */ 1242 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&nsubdomains);CHKERRQ(ierr); 1243 if (nsubdomains == 1) { 1244 Mat B; 1245 IS rows,cols; 1246 IS irows,icols; 1247 const PetscInt *ridxs,*cidxs; 1248 1249 ierr = ISLocalToGlobalMappingGetIndices(mat->rmap->mapping,&ridxs);CHKERRQ(ierr); 1250 ierr = ISLocalToGlobalMappingGetIndices(mat->cmap->mapping,&cidxs);CHKERRQ(ierr); 1251 ierr = ISCreateGeneral(PETSC_COMM_SELF,mat->rmap->n,ridxs,PETSC_USE_POINTER,&rows);CHKERRQ(ierr); 1252 ierr = ISCreateGeneral(PETSC_COMM_SELF,mat->cmap->n,cidxs,PETSC_USE_POINTER,&cols);CHKERRQ(ierr); 1253 ierr = ISSetPermutation(rows);CHKERRQ(ierr); 1254 ierr = ISSetPermutation(cols);CHKERRQ(ierr); 1255 ierr = ISInvertPermutation(rows,mat->rmap->n,&irows);CHKERRQ(ierr); 1256 ierr = ISInvertPermutation(cols,mat->cmap->n,&icols);CHKERRQ(ierr); 1257 ierr = ISLocalToGlobalMappingRestoreIndices(mat->rmap->mapping,&ridxs);CHKERRQ(ierr); 1258 ierr = ISLocalToGlobalMappingRestoreIndices(mat->cmap->mapping,&cidxs);CHKERRQ(ierr); 1259 ierr = ISDestroy(&cols);CHKERRQ(ierr); 1260 ierr = ISDestroy(&rows);CHKERRQ(ierr); 1261 ierr = MatConvert(matis->A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 1262 ierr = MatCreateSubMatrix(B,irows,icols,reuse,M);CHKERRQ(ierr); 1263 ierr = MatDestroy(&B);CHKERRQ(ierr); 1264 ierr = ISDestroy(&icols);CHKERRQ(ierr); 1265 ierr = ISDestroy(&irows);CHKERRQ(ierr); 1266 PetscFunctionReturn(0); 1267 } 1268 ierr = MatGetSize(mat,&rows,&cols);CHKERRQ(ierr); 1269 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 1270 ierr = MatGetLocalSize(mat,&lrows,&lcols);CHKERRQ(ierr); 1271 ierr = MatGetSize(matis->A,&local_rows,&local_cols);CHKERRQ(ierr); 1272 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQDENSE,&isseqdense);CHKERRQ(ierr); 1273 ierr = PetscObjectBaseTypeCompare((PetscObject)matis->A,MATSEQAIJ,&isseqaij);CHKERRQ(ierr); 1274 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQBAIJ,&isseqbaij);CHKERRQ(ierr); 1275 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQSBAIJ,&isseqsbaij);CHKERRQ(ierr); 1276 if (!isseqdense && !isseqaij && !isseqbaij && !isseqsbaij) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not for matrix type %s",((PetscObject)(matis->A))->type_name); 1277 #if defined (PETSC_USE_DEBUG) 1278 lb[0] = isseqdense; 1279 lb[1] = isseqaij; 1280 lb[2] = isseqbaij; 1281 lb[3] = isseqsbaij; 1282 ierr = MPIU_Allreduce(lb,bb,4,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1283 if (!bb[0] && !bb[1] && !bb[2] && !bb[3]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Local matrices must have the same type"); 1284 #endif 1285 1286 if (reuse == MAT_INITIAL_MATRIX) { 1287 ierr = MatCreate(PetscObjectComm((PetscObject)mat),M);CHKERRQ(ierr); 1288 ierr = MatSetSizes(*M,lrows,lcols,rows,cols);CHKERRQ(ierr); 1289 if (!isseqsbaij) { 1290 ierr = MatSetType(*M,MATAIJ);CHKERRQ(ierr); 1291 } else { 1292 ierr = MatSetType(*M,MATSBAIJ);CHKERRQ(ierr); 1293 } 1294 ierr = MatSetBlockSize(*M,bs);CHKERRQ(ierr); 1295 ierr = MatISSetMPIXAIJPreallocation_Private(mat,*M,PETSC_FALSE);CHKERRQ(ierr); 1296 } else { 1297 PetscInt mbs,mrows,mcols,mlrows,mlcols; 1298 /* some checks */ 1299 ierr = MatGetBlockSize(*M,&mbs);CHKERRQ(ierr); 1300 ierr = MatGetSize(*M,&mrows,&mcols);CHKERRQ(ierr); 1301 ierr = MatGetLocalSize(*M,&mlrows,&mlcols);CHKERRQ(ierr); 1302 if (mrows != rows) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of rows (%d != %d)",rows,mrows); 1303 if (mcols != cols) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of cols (%d != %d)",cols,mcols); 1304 if (mlrows != lrows) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of local rows (%d != %d)",lrows,mlrows); 1305 if (mlcols != lcols) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of local cols (%d != %d)",lcols,mlcols); 1306 if (mbs != bs) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong block size (%d != %d)",bs,mbs); 1307 ierr = MatZeroEntries(*M);CHKERRQ(ierr); 1308 } 1309 1310 if (isseqsbaij) { 1311 ierr = MatConvert(matis->A,MATSEQBAIJ,MAT_INITIAL_MATRIX,&local_mat);CHKERRQ(ierr); 1312 } else { 1313 ierr = PetscObjectReference((PetscObject)matis->A);CHKERRQ(ierr); 1314 local_mat = matis->A; 1315 } 1316 1317 /* Set values */ 1318 ierr = MatSetLocalToGlobalMapping(*M,mat->rmap->mapping,mat->cmap->mapping);CHKERRQ(ierr); 1319 if (isseqdense) { /* special case for dense local matrices */ 1320 PetscInt i,*dummy; 1321 1322 ierr = PetscMalloc1(PetscMax(local_rows,local_cols),&dummy);CHKERRQ(ierr); 1323 for (i=0;i<PetscMax(local_rows,local_cols);i++) dummy[i] = i; 1324 ierr = MatSetOption(*M,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr); 1325 ierr = MatDenseGetArray(local_mat,&array);CHKERRQ(ierr); 1326 ierr = MatSetValuesLocal(*M,local_rows,dummy,local_cols,dummy,array,ADD_VALUES);CHKERRQ(ierr); 1327 ierr = MatDenseRestoreArray(local_mat,&array);CHKERRQ(ierr); 1328 ierr = PetscFree(dummy);CHKERRQ(ierr); 1329 } else if (isseqaij) { 1330 PetscInt i,nvtxs,*xadj,*adjncy; 1331 PetscBool done; 1332 1333 ierr = MatGetRowIJ(local_mat,0,PETSC_FALSE,PETSC_FALSE,&nvtxs,(const PetscInt**)&xadj,(const PetscInt**)&adjncy,&done);CHKERRQ(ierr); 1334 if (!done) SETERRQ(PetscObjectComm((PetscObject)local_mat),PETSC_ERR_PLIB,"Error in MatGetRowIJ"); 1335 ierr = MatSeqAIJGetArray(local_mat,&array);CHKERRQ(ierr); 1336 for (i=0;i<nvtxs;i++) { 1337 ierr = MatSetValuesLocal(*M,1,&i,xadj[i+1]-xadj[i],adjncy+xadj[i],array+xadj[i],ADD_VALUES);CHKERRQ(ierr); 1338 } 1339 ierr = MatRestoreRowIJ(local_mat,0,PETSC_FALSE,PETSC_FALSE,&nvtxs,(const PetscInt**)&xadj,(const PetscInt**)&adjncy,&done);CHKERRQ(ierr); 1340 if (!done) SETERRQ(PetscObjectComm((PetscObject)local_mat),PETSC_ERR_PLIB,"Error in MatRestoreRowIJ"); 1341 ierr = MatSeqAIJRestoreArray(local_mat,&array);CHKERRQ(ierr); 1342 } else { /* very basic values insertion for all other matrix types */ 1343 PetscInt i; 1344 1345 for (i=0;i<local_rows;i++) { 1346 PetscInt j; 1347 const PetscInt *local_indices_cols; 1348 1349 ierr = MatGetRow(local_mat,i,&j,&local_indices_cols,(const PetscScalar**)&array);CHKERRQ(ierr); 1350 ierr = MatSetValuesLocal(*M,1,&i,j,local_indices_cols,array,ADD_VALUES);CHKERRQ(ierr); 1351 ierr = MatRestoreRow(local_mat,i,&j,&local_indices_cols,(const PetscScalar**)&array);CHKERRQ(ierr); 1352 } 1353 } 1354 ierr = MatAssemblyBegin(*M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1355 ierr = MatDestroy(&local_mat);CHKERRQ(ierr); 1356 ierr = MatAssemblyEnd(*M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1357 if (isseqdense) { 1358 ierr = MatSetOption(*M,MAT_ROW_ORIENTED,PETSC_TRUE);CHKERRQ(ierr); 1359 } 1360 PetscFunctionReturn(0); 1361 } 1362 1363 /*@ 1364 MatISGetMPIXAIJ - Converts MATIS matrix into a parallel AIJ format 1365 1366 Input Parameter: 1367 . mat - the matrix (should be of type MATIS) 1368 . reuse - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 1369 1370 Output Parameter: 1371 . newmat - the matrix in AIJ format 1372 1373 Level: developer 1374 1375 Notes: mat and *newmat cannot be the same object when MAT_REUSE_MATRIX is requested. 1376 1377 .seealso: MATIS 1378 @*/ 1379 PetscErrorCode MatISGetMPIXAIJ(Mat mat, MatReuse reuse, Mat *newmat) 1380 { 1381 PetscErrorCode ierr; 1382 1383 PetscFunctionBegin; 1384 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1385 PetscValidLogicalCollectiveEnum(mat,reuse,2); 1386 PetscValidPointer(newmat,3); 1387 if (reuse != MAT_INITIAL_MATRIX) { 1388 PetscValidHeaderSpecific(*newmat,MAT_CLASSID,3); 1389 PetscCheckSameComm(mat,1,*newmat,3); 1390 if (mat == *newmat) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse the same matrix"); 1391 } 1392 ierr = PetscUseMethod(mat,"MatISGetMPIXAIJ_C",(Mat,MatReuse,Mat*),(mat,reuse,newmat));CHKERRQ(ierr); 1393 PetscFunctionReturn(0); 1394 } 1395 1396 PetscErrorCode MatDuplicate_IS(Mat mat,MatDuplicateOption op,Mat *newmat) 1397 { 1398 PetscErrorCode ierr; 1399 Mat_IS *matis = (Mat_IS*)(mat->data); 1400 PetscInt bs,m,n,M,N; 1401 Mat B,localmat; 1402 1403 PetscFunctionBegin; 1404 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 1405 ierr = MatGetSize(mat,&M,&N);CHKERRQ(ierr); 1406 ierr = MatGetLocalSize(mat,&m,&n);CHKERRQ(ierr); 1407 ierr = MatCreateIS(PetscObjectComm((PetscObject)mat),bs,m,n,M,N,mat->rmap->mapping,mat->cmap->mapping,&B);CHKERRQ(ierr); 1408 ierr = MatDuplicate(matis->A,op,&localmat);CHKERRQ(ierr); 1409 ierr = MatISSetLocalMat(B,localmat);CHKERRQ(ierr); 1410 ierr = MatDestroy(&localmat);CHKERRQ(ierr); 1411 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1412 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1413 *newmat = B; 1414 PetscFunctionReturn(0); 1415 } 1416 1417 static PetscErrorCode MatIsHermitian_IS(Mat A,PetscReal tol,PetscBool *flg) 1418 { 1419 PetscErrorCode ierr; 1420 Mat_IS *matis = (Mat_IS*)A->data; 1421 PetscBool local_sym; 1422 1423 PetscFunctionBegin; 1424 ierr = MatIsHermitian(matis->A,tol,&local_sym);CHKERRQ(ierr); 1425 ierr = MPIU_Allreduce(&local_sym,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1426 PetscFunctionReturn(0); 1427 } 1428 1429 static PetscErrorCode MatIsSymmetric_IS(Mat A,PetscReal tol,PetscBool *flg) 1430 { 1431 PetscErrorCode ierr; 1432 Mat_IS *matis = (Mat_IS*)A->data; 1433 PetscBool local_sym; 1434 1435 PetscFunctionBegin; 1436 ierr = MatIsSymmetric(matis->A,tol,&local_sym);CHKERRQ(ierr); 1437 ierr = MPIU_Allreduce(&local_sym,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1438 PetscFunctionReturn(0); 1439 } 1440 1441 static PetscErrorCode MatIsStructurallySymmetric_IS(Mat A,PetscBool *flg) 1442 { 1443 PetscErrorCode ierr; 1444 Mat_IS *matis = (Mat_IS*)A->data; 1445 PetscBool local_sym; 1446 1447 PetscFunctionBegin; 1448 if (A->rmap->mapping != A->cmap->mapping) { 1449 *flg = PETSC_FALSE; 1450 PetscFunctionReturn(0); 1451 } 1452 ierr = MatIsStructurallySymmetric(matis->A,&local_sym);CHKERRQ(ierr); 1453 ierr = MPIU_Allreduce(&local_sym,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1454 PetscFunctionReturn(0); 1455 } 1456 1457 static PetscErrorCode MatDestroy_IS(Mat A) 1458 { 1459 PetscErrorCode ierr; 1460 Mat_IS *b = (Mat_IS*)A->data; 1461 1462 PetscFunctionBegin; 1463 ierr = MatDestroy(&b->A);CHKERRQ(ierr); 1464 ierr = VecScatterDestroy(&b->cctx);CHKERRQ(ierr); 1465 ierr = VecScatterDestroy(&b->rctx);CHKERRQ(ierr); 1466 ierr = VecDestroy(&b->x);CHKERRQ(ierr); 1467 ierr = VecDestroy(&b->y);CHKERRQ(ierr); 1468 ierr = VecDestroy(&b->counter);CHKERRQ(ierr); 1469 ierr = ISDestroy(&b->getsub_ris);CHKERRQ(ierr); 1470 ierr = ISDestroy(&b->getsub_cis);CHKERRQ(ierr); 1471 if (b->sf != b->csf) { 1472 ierr = PetscSFDestroy(&b->csf);CHKERRQ(ierr); 1473 ierr = PetscFree2(b->csf_rootdata,b->csf_leafdata);CHKERRQ(ierr); 1474 } 1475 ierr = PetscSFDestroy(&b->sf);CHKERRQ(ierr); 1476 ierr = PetscFree2(b->sf_rootdata,b->sf_leafdata);CHKERRQ(ierr); 1477 ierr = PetscFree(A->data);CHKERRQ(ierr); 1478 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 1479 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetLocalMat_C",NULL);CHKERRQ(ierr); 1480 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetLocalMat_C",NULL);CHKERRQ(ierr); 1481 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetMPIXAIJ_C",NULL);CHKERRQ(ierr); 1482 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetPreallocation_C",NULL);CHKERRQ(ierr); 1483 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetUpSF_C",NULL);CHKERRQ(ierr); 1484 PetscFunctionReturn(0); 1485 } 1486 1487 static PetscErrorCode MatMult_IS(Mat A,Vec x,Vec y) 1488 { 1489 PetscErrorCode ierr; 1490 Mat_IS *is = (Mat_IS*)A->data; 1491 PetscScalar zero = 0.0; 1492 1493 PetscFunctionBegin; 1494 /* scatter the global vector x into the local work vector */ 1495 ierr = VecScatterBegin(is->cctx,x,is->x,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1496 ierr = VecScatterEnd(is->cctx,x,is->x,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1497 1498 /* multiply the local matrix */ 1499 ierr = MatMult(is->A,is->x,is->y);CHKERRQ(ierr); 1500 1501 /* scatter product back into global memory */ 1502 ierr = VecSet(y,zero);CHKERRQ(ierr); 1503 ierr = VecScatterBegin(is->rctx,is->y,y,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1504 ierr = VecScatterEnd(is->rctx,is->y,y,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1505 PetscFunctionReturn(0); 1506 } 1507 1508 static PetscErrorCode MatMultAdd_IS(Mat A,Vec v1,Vec v2,Vec v3) 1509 { 1510 Vec temp_vec; 1511 PetscErrorCode ierr; 1512 1513 PetscFunctionBegin; /* v3 = v2 + A * v1.*/ 1514 if (v3 != v2) { 1515 ierr = MatMult(A,v1,v3);CHKERRQ(ierr); 1516 ierr = VecAXPY(v3,1.0,v2);CHKERRQ(ierr); 1517 } else { 1518 ierr = VecDuplicate(v2,&temp_vec);CHKERRQ(ierr); 1519 ierr = MatMult(A,v1,temp_vec);CHKERRQ(ierr); 1520 ierr = VecAXPY(temp_vec,1.0,v2);CHKERRQ(ierr); 1521 ierr = VecCopy(temp_vec,v3);CHKERRQ(ierr); 1522 ierr = VecDestroy(&temp_vec);CHKERRQ(ierr); 1523 } 1524 PetscFunctionReturn(0); 1525 } 1526 1527 static PetscErrorCode MatMultTranspose_IS(Mat A,Vec y,Vec x) 1528 { 1529 Mat_IS *is = (Mat_IS*)A->data; 1530 PetscErrorCode ierr; 1531 1532 PetscFunctionBegin; 1533 /* scatter the global vector x into the local work vector */ 1534 ierr = VecScatterBegin(is->rctx,y,is->y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1535 ierr = VecScatterEnd(is->rctx,y,is->y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1536 1537 /* multiply the local matrix */ 1538 ierr = MatMultTranspose(is->A,is->y,is->x);CHKERRQ(ierr); 1539 1540 /* scatter product back into global vector */ 1541 ierr = VecSet(x,0);CHKERRQ(ierr); 1542 ierr = VecScatterBegin(is->cctx,is->x,x,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1543 ierr = VecScatterEnd(is->cctx,is->x,x,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1544 PetscFunctionReturn(0); 1545 } 1546 1547 static PetscErrorCode MatMultTransposeAdd_IS(Mat A,Vec v1,Vec v2,Vec v3) 1548 { 1549 Vec temp_vec; 1550 PetscErrorCode ierr; 1551 1552 PetscFunctionBegin; /* v3 = v2 + A' * v1.*/ 1553 if (v3 != v2) { 1554 ierr = MatMultTranspose(A,v1,v3);CHKERRQ(ierr); 1555 ierr = VecAXPY(v3,1.0,v2);CHKERRQ(ierr); 1556 } else { 1557 ierr = VecDuplicate(v2,&temp_vec);CHKERRQ(ierr); 1558 ierr = MatMultTranspose(A,v1,temp_vec);CHKERRQ(ierr); 1559 ierr = VecAXPY(temp_vec,1.0,v2);CHKERRQ(ierr); 1560 ierr = VecCopy(temp_vec,v3);CHKERRQ(ierr); 1561 ierr = VecDestroy(&temp_vec);CHKERRQ(ierr); 1562 } 1563 PetscFunctionReturn(0); 1564 } 1565 1566 static PetscErrorCode MatView_IS(Mat A,PetscViewer viewer) 1567 { 1568 Mat_IS *a = (Mat_IS*)A->data; 1569 PetscErrorCode ierr; 1570 PetscViewer sviewer; 1571 PetscBool isascii,view = PETSC_TRUE; 1572 1573 PetscFunctionBegin; 1574 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&isascii);CHKERRQ(ierr); 1575 if (isascii) { 1576 PetscViewerFormat format; 1577 1578 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1579 if (format == PETSC_VIEWER_ASCII_INFO) view = PETSC_FALSE; 1580 } 1581 if (!view) PetscFunctionReturn(0); 1582 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1583 ierr = MatView(a->A,sviewer);CHKERRQ(ierr); 1584 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1585 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1586 PetscFunctionReturn(0); 1587 } 1588 1589 static PetscErrorCode MatSetLocalToGlobalMapping_IS(Mat A,ISLocalToGlobalMapping rmapping,ISLocalToGlobalMapping cmapping) 1590 { 1591 PetscErrorCode ierr; 1592 PetscInt nr,rbs,nc,cbs; 1593 Mat_IS *is = (Mat_IS*)A->data; 1594 IS from,to; 1595 Vec cglobal,rglobal; 1596 1597 PetscFunctionBegin; 1598 PetscCheckSameComm(A,1,rmapping,2); 1599 PetscCheckSameComm(A,1,cmapping,3); 1600 /* Destroy any previous data */ 1601 ierr = VecDestroy(&is->x);CHKERRQ(ierr); 1602 ierr = VecDestroy(&is->y);CHKERRQ(ierr); 1603 ierr = VecDestroy(&is->counter);CHKERRQ(ierr); 1604 ierr = VecScatterDestroy(&is->rctx);CHKERRQ(ierr); 1605 ierr = VecScatterDestroy(&is->cctx);CHKERRQ(ierr); 1606 ierr = MatDestroy(&is->A);CHKERRQ(ierr); 1607 if (is->csf != is->sf) { 1608 ierr = PetscSFDestroy(&is->csf);CHKERRQ(ierr); 1609 ierr = PetscFree2(is->csf_rootdata,is->csf_leafdata);CHKERRQ(ierr); 1610 } 1611 ierr = PetscSFDestroy(&is->sf);CHKERRQ(ierr); 1612 ierr = PetscFree2(is->sf_rootdata,is->sf_leafdata);CHKERRQ(ierr); 1613 1614 /* Setup Layout and set local to global maps */ 1615 ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr); 1616 ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr); 1617 ierr = PetscLayoutSetISLocalToGlobalMapping(A->rmap,rmapping);CHKERRQ(ierr); 1618 ierr = PetscLayoutSetISLocalToGlobalMapping(A->cmap,cmapping);CHKERRQ(ierr); 1619 1620 /* Create the local matrix A */ 1621 ierr = ISLocalToGlobalMappingGetSize(rmapping,&nr);CHKERRQ(ierr); 1622 ierr = ISLocalToGlobalMappingGetBlockSize(rmapping,&rbs);CHKERRQ(ierr); 1623 ierr = ISLocalToGlobalMappingGetSize(cmapping,&nc);CHKERRQ(ierr); 1624 ierr = ISLocalToGlobalMappingGetBlockSize(cmapping,&cbs);CHKERRQ(ierr); 1625 ierr = MatCreate(PETSC_COMM_SELF,&is->A);CHKERRQ(ierr); 1626 ierr = MatSetType(is->A,MATAIJ);CHKERRQ(ierr); 1627 ierr = MatSetSizes(is->A,nr,nc,nr,nc);CHKERRQ(ierr); 1628 ierr = MatSetBlockSizes(is->A,rbs,cbs);CHKERRQ(ierr); 1629 ierr = MatSetOptionsPrefix(is->A,((PetscObject)A)->prefix);CHKERRQ(ierr); 1630 ierr = MatAppendOptionsPrefix(is->A,"is_");CHKERRQ(ierr); 1631 ierr = MatSetFromOptions(is->A);CHKERRQ(ierr); 1632 ierr = PetscLayoutSetUp(is->A->rmap);CHKERRQ(ierr); 1633 ierr = PetscLayoutSetUp(is->A->cmap);CHKERRQ(ierr); 1634 1635 if (!is->islocalref) { /* setup scatters and local vectors for MatMult */ 1636 /* Create the local work vectors */ 1637 ierr = MatCreateVecs(is->A,&is->x,&is->y);CHKERRQ(ierr); 1638 1639 /* setup the global to local scatters */ 1640 ierr = MatCreateVecs(A,&cglobal,&rglobal);CHKERRQ(ierr); 1641 ierr = ISCreateStride(PETSC_COMM_SELF,nr,0,1,&to);CHKERRQ(ierr); 1642 ierr = ISLocalToGlobalMappingApplyIS(rmapping,to,&from);CHKERRQ(ierr); 1643 ierr = VecScatterCreate(rglobal,from,is->y,to,&is->rctx);CHKERRQ(ierr); 1644 if (rmapping != cmapping) { 1645 ierr = ISDestroy(&to);CHKERRQ(ierr); 1646 ierr = ISDestroy(&from);CHKERRQ(ierr); 1647 ierr = ISCreateStride(PETSC_COMM_SELF,nc,0,1,&to);CHKERRQ(ierr); 1648 ierr = ISLocalToGlobalMappingApplyIS(cmapping,to,&from);CHKERRQ(ierr); 1649 ierr = VecScatterCreate(cglobal,from,is->x,to,&is->cctx);CHKERRQ(ierr); 1650 } else { 1651 ierr = PetscObjectReference((PetscObject)is->rctx);CHKERRQ(ierr); 1652 is->cctx = is->rctx; 1653 } 1654 1655 /* interface counter vector (local) */ 1656 ierr = VecDuplicate(is->y,&is->counter);CHKERRQ(ierr); 1657 ierr = VecSet(is->y,1.);CHKERRQ(ierr); 1658 ierr = VecScatterBegin(is->rctx,is->y,rglobal,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1659 ierr = VecScatterEnd(is->rctx,is->y,rglobal,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1660 ierr = VecScatterBegin(is->rctx,rglobal,is->counter,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1661 ierr = VecScatterEnd(is->rctx,rglobal,is->counter,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1662 1663 /* free workspace */ 1664 ierr = VecDestroy(&rglobal);CHKERRQ(ierr); 1665 ierr = VecDestroy(&cglobal);CHKERRQ(ierr); 1666 ierr = ISDestroy(&to);CHKERRQ(ierr); 1667 ierr = ISDestroy(&from);CHKERRQ(ierr); 1668 } 1669 ierr = MatSetUp(A);CHKERRQ(ierr); 1670 PetscFunctionReturn(0); 1671 } 1672 1673 static PetscErrorCode MatSetValues_IS(Mat mat, PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols, const PetscScalar *values, InsertMode addv) 1674 { 1675 Mat_IS *is = (Mat_IS*)mat->data; 1676 PetscErrorCode ierr; 1677 #if defined(PETSC_USE_DEBUG) 1678 PetscInt i,zm,zn; 1679 #endif 1680 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 1681 1682 PetscFunctionBegin; 1683 #if defined(PETSC_USE_DEBUG) 1684 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); 1685 /* count negative indices */ 1686 for (i=0,zm=0;i<m;i++) if (rows[i] < 0) zm++; 1687 for (i=0,zn=0;i<n;i++) if (cols[i] < 0) zn++; 1688 #endif 1689 ierr = ISGlobalToLocalMappingApply(mat->rmap->mapping,IS_GTOLM_MASK,m,rows,&m,rows_l);CHKERRQ(ierr); 1690 ierr = ISGlobalToLocalMappingApply(mat->cmap->mapping,IS_GTOLM_MASK,n,cols,&n,cols_l);CHKERRQ(ierr); 1691 #if defined(PETSC_USE_DEBUG) 1692 /* count negative indices (should be the same as before) */ 1693 for (i=0;i<m;i++) if (rows_l[i] < 0) zm--; 1694 for (i=0;i<n;i++) if (cols_l[i] < 0) zn--; 1695 if (!is->A->rmap->mapping && zm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the row indices can not be mapped! Maybe you should not use MATIS"); 1696 if (!is->A->cmap->mapping && zn) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the column indices can not be mapped! Maybe you should not use MATIS"); 1697 #endif 1698 ierr = MatSetValues(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 1699 PetscFunctionReturn(0); 1700 } 1701 1702 static PetscErrorCode MatSetValuesBlocked_IS(Mat mat, PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols, const PetscScalar *values, InsertMode addv) 1703 { 1704 Mat_IS *is = (Mat_IS*)mat->data; 1705 PetscErrorCode ierr; 1706 #if defined(PETSC_USE_DEBUG) 1707 PetscInt i,zm,zn; 1708 #endif 1709 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 1710 1711 PetscFunctionBegin; 1712 #if defined(PETSC_USE_DEBUG) 1713 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); 1714 /* count negative indices */ 1715 for (i=0,zm=0;i<m;i++) if (rows[i] < 0) zm++; 1716 for (i=0,zn=0;i<n;i++) if (cols[i] < 0) zn++; 1717 #endif 1718 ierr = ISGlobalToLocalMappingApplyBlock(mat->rmap->mapping,IS_GTOLM_MASK,m,rows,&m,rows_l);CHKERRQ(ierr); 1719 ierr = ISGlobalToLocalMappingApplyBlock(mat->cmap->mapping,IS_GTOLM_MASK,n,cols,&n,cols_l);CHKERRQ(ierr); 1720 #if defined(PETSC_USE_DEBUG) 1721 /* count negative indices (should be the same as before) */ 1722 for (i=0;i<m;i++) if (rows_l[i] < 0) zm--; 1723 for (i=0;i<n;i++) if (cols_l[i] < 0) zn--; 1724 if (!is->A->rmap->mapping && zm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the row indices can not be mapped! Maybe you should not use MATIS"); 1725 if (!is->A->cmap->mapping && zn) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the column indices can not be mapped! Maybe you should not use MATIS"); 1726 #endif 1727 ierr = MatSetValuesBlocked(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 1728 PetscFunctionReturn(0); 1729 } 1730 1731 static PetscErrorCode MatSetValuesLocal_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 1732 { 1733 PetscErrorCode ierr; 1734 Mat_IS *is = (Mat_IS*)A->data; 1735 1736 PetscFunctionBegin; 1737 if (is->A->rmap->mapping) { 1738 ierr = MatSetValuesLocal(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr); 1739 } else { 1740 ierr = MatSetValues(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr); 1741 } 1742 PetscFunctionReturn(0); 1743 } 1744 1745 static PetscErrorCode MatSetValuesBlockedLocal_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 1746 { 1747 PetscErrorCode ierr; 1748 Mat_IS *is = (Mat_IS*)A->data; 1749 1750 PetscFunctionBegin; 1751 if (is->A->rmap->mapping) { 1752 #if defined(PETSC_USE_DEBUG) 1753 PetscInt ibs,bs; 1754 1755 ierr = ISLocalToGlobalMappingGetBlockSize(is->A->rmap->mapping,&ibs);CHKERRQ(ierr); 1756 ierr = MatGetBlockSize(is->A,&bs);CHKERRQ(ierr); 1757 if (ibs != bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Different block sizes! local mat %D, local l2g map %D",bs,ibs); 1758 #endif 1759 ierr = MatSetValuesBlockedLocal(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr); 1760 } else { 1761 ierr = MatSetValuesBlocked(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr); 1762 } 1763 PetscFunctionReturn(0); 1764 } 1765 1766 static PetscErrorCode MatISZeroRowsColumnsLocal_Private(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,PetscBool columns) 1767 { 1768 Mat_IS *is = (Mat_IS*)A->data; 1769 PetscErrorCode ierr; 1770 1771 PetscFunctionBegin; 1772 if (!n) { 1773 is->pure_neumann = PETSC_TRUE; 1774 } else { 1775 PetscInt i; 1776 is->pure_neumann = PETSC_FALSE; 1777 1778 if (columns) { 1779 ierr = MatZeroRowsColumns(is->A,n,rows,diag,0,0);CHKERRQ(ierr); 1780 } else { 1781 ierr = MatZeroRows(is->A,n,rows,diag,0,0);CHKERRQ(ierr); 1782 } 1783 if (diag != 0.) { 1784 const PetscScalar *array; 1785 ierr = VecGetArrayRead(is->counter,&array);CHKERRQ(ierr); 1786 for (i=0; i<n; i++) { 1787 ierr = MatSetValue(is->A,rows[i],rows[i],diag/(array[rows[i]]),INSERT_VALUES);CHKERRQ(ierr); 1788 } 1789 ierr = VecRestoreArrayRead(is->counter,&array);CHKERRQ(ierr); 1790 } 1791 ierr = MatAssemblyBegin(is->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1792 ierr = MatAssemblyEnd(is->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1793 } 1794 PetscFunctionReturn(0); 1795 } 1796 1797 static PetscErrorCode MatZeroRowsColumns_Private_IS(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,Vec x,Vec b,PetscBool columns) 1798 { 1799 Mat_IS *matis = (Mat_IS*)A->data; 1800 PetscInt nr,nl,len,i; 1801 PetscInt *lrows; 1802 PetscErrorCode ierr; 1803 1804 PetscFunctionBegin; 1805 #if defined(PETSC_USE_DEBUG) 1806 if (columns || diag != 0. || (x && b)) { 1807 PetscBool cong; 1808 1809 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 1810 cong = (PetscBool)(cong && matis->sf == matis->csf); 1811 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 and the l2g maps are the same for MATIS"); 1812 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 and the l2g maps are the same for MATIS"); 1813 if (!cong && x && b) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"A->rmap and A->cmap need to be congruent, and the l2g maps be the same"); 1814 } 1815 #endif 1816 /* get locally owned rows */ 1817 ierr = PetscLayoutMapLocal_Private(A->rmap,n,rows,&len,&lrows,NULL);CHKERRQ(ierr); 1818 /* fix right hand side if needed */ 1819 if (x && b) { 1820 const PetscScalar *xx; 1821 PetscScalar *bb; 1822 1823 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 1824 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 1825 for (i=0;i<len;++i) bb[lrows[i]] = diag*xx[lrows[i]]; 1826 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 1827 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 1828 } 1829 /* get rows associated to the local matrices */ 1830 ierr = MatISSetUpSF(A);CHKERRQ(ierr); 1831 ierr = MatGetSize(matis->A,&nl,NULL);CHKERRQ(ierr); 1832 ierr = PetscMemzero(matis->sf_leafdata,nl*sizeof(PetscInt));CHKERRQ(ierr); 1833 ierr = PetscMemzero(matis->sf_rootdata,A->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 1834 for (i=0;i<len;i++) matis->sf_rootdata[lrows[i]] = 1; 1835 ierr = PetscFree(lrows);CHKERRQ(ierr); 1836 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1837 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1838 ierr = PetscMalloc1(nl,&lrows);CHKERRQ(ierr); 1839 for (i=0,nr=0;i<nl;i++) if (matis->sf_leafdata[i]) lrows[nr++] = i; 1840 ierr = MatISZeroRowsColumnsLocal_Private(A,nr,lrows,diag,columns);CHKERRQ(ierr); 1841 ierr = PetscFree(lrows);CHKERRQ(ierr); 1842 PetscFunctionReturn(0); 1843 } 1844 1845 static PetscErrorCode MatZeroRows_IS(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1846 { 1847 PetscErrorCode ierr; 1848 1849 PetscFunctionBegin; 1850 ierr = MatZeroRowsColumns_Private_IS(A,n,rows,diag,x,b,PETSC_FALSE);CHKERRQ(ierr); 1851 PetscFunctionReturn(0); 1852 } 1853 1854 static PetscErrorCode MatZeroRowsColumns_IS(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1855 { 1856 PetscErrorCode ierr; 1857 1858 PetscFunctionBegin; 1859 ierr = MatZeroRowsColumns_Private_IS(A,n,rows,diag,x,b,PETSC_TRUE);CHKERRQ(ierr); 1860 PetscFunctionReturn(0); 1861 } 1862 1863 static PetscErrorCode MatAssemblyBegin_IS(Mat A,MatAssemblyType type) 1864 { 1865 Mat_IS *is = (Mat_IS*)A->data; 1866 PetscErrorCode ierr; 1867 1868 PetscFunctionBegin; 1869 ierr = MatAssemblyBegin(is->A,type);CHKERRQ(ierr); 1870 PetscFunctionReturn(0); 1871 } 1872 1873 static PetscErrorCode MatAssemblyEnd_IS(Mat A,MatAssemblyType type) 1874 { 1875 Mat_IS *is = (Mat_IS*)A->data; 1876 PetscErrorCode ierr; 1877 1878 PetscFunctionBegin; 1879 ierr = MatAssemblyEnd(is->A,type);CHKERRQ(ierr); 1880 /* fix for local empty rows/cols */ 1881 if (is->locempty && type == MAT_FINAL_ASSEMBLY) { 1882 Mat newlA; 1883 ISLocalToGlobalMapping l2g; 1884 IS tis; 1885 const PetscScalar *v; 1886 PetscInt i,n,cf,*loce,*locf; 1887 PetscBool sym; 1888 1889 ierr = MatGetRowMaxAbs(is->A,is->y,NULL);CHKERRQ(ierr); 1890 ierr = MatIsSymmetric(is->A,PETSC_SMALL,&sym);CHKERRQ(ierr); 1891 if (!sym) SETERRQ(PetscObjectComm((PetscObject)is->A),PETSC_ERR_SUP,"Not yet implemented for unsymmetric case"); 1892 ierr = VecGetLocalSize(is->y,&n);CHKERRQ(ierr); 1893 ierr = PetscMalloc1(n,&loce);CHKERRQ(ierr); 1894 ierr = PetscMalloc1(n,&locf);CHKERRQ(ierr); 1895 ierr = VecGetArrayRead(is->y,&v);CHKERRQ(ierr); 1896 for (i=0,cf=0;i<n;i++) { 1897 if (v[i] == 0.0) { 1898 loce[i] = -1; 1899 } else { 1900 loce[i] = cf; 1901 locf[cf++] = i; 1902 } 1903 } 1904 ierr = VecRestoreArrayRead(is->y,&v);CHKERRQ(ierr); 1905 /* extract valid submatrix */ 1906 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)is->A),cf,locf,PETSC_USE_POINTER,&tis);CHKERRQ(ierr); 1907 ierr = MatCreateSubMatrix(is->A,tis,tis,MAT_INITIAL_MATRIX,&newlA);CHKERRQ(ierr); 1908 ierr = ISDestroy(&tis);CHKERRQ(ierr); 1909 /* attach local l2g map for successive calls of MatSetValues */ 1910 ierr = ISLocalToGlobalMappingCreate(PetscObjectComm((PetscObject)is->A),1,n,loce,PETSC_OWN_POINTER,&l2g);CHKERRQ(ierr); 1911 ierr = MatSetLocalToGlobalMapping(newlA,l2g,l2g);CHKERRQ(ierr); 1912 ierr = ISLocalToGlobalMappingDestroy(&l2g);CHKERRQ(ierr); 1913 /* attach new global l2g map */ 1914 ierr = ISLocalToGlobalMappingApply(A->rmap->mapping,cf,locf,locf);CHKERRQ(ierr); 1915 ierr = ISLocalToGlobalMappingCreate(PetscObjectComm((PetscObject)A),1,cf,locf,PETSC_OWN_POINTER,&l2g);CHKERRQ(ierr); 1916 ierr = MatSetLocalToGlobalMapping(A,l2g,l2g);CHKERRQ(ierr); 1917 ierr = MatISSetLocalMat(A,newlA);CHKERRQ(ierr); 1918 ierr = MatDestroy(&newlA);CHKERRQ(ierr); 1919 ierr = ISLocalToGlobalMappingDestroy(&l2g);CHKERRQ(ierr); 1920 } 1921 is->locempty = PETSC_FALSE; 1922 PetscFunctionReturn(0); 1923 } 1924 1925 static PetscErrorCode MatISGetLocalMat_IS(Mat mat,Mat *local) 1926 { 1927 Mat_IS *is = (Mat_IS*)mat->data; 1928 1929 PetscFunctionBegin; 1930 *local = is->A; 1931 PetscFunctionReturn(0); 1932 } 1933 1934 static PetscErrorCode MatISRestoreLocalMat_IS(Mat mat,Mat *local) 1935 { 1936 PetscFunctionBegin; 1937 *local = NULL; 1938 PetscFunctionReturn(0); 1939 } 1940 1941 /*@ 1942 MatISGetLocalMat - Gets the local matrix stored inside a MATIS matrix. 1943 1944 Input Parameter: 1945 . mat - the matrix 1946 1947 Output Parameter: 1948 . local - the local matrix 1949 1950 Level: advanced 1951 1952 Notes: 1953 This can be called if you have precomputed the nonzero structure of the 1954 matrix and want to provide it to the inner matrix object to improve the performance 1955 of the MatSetValues() operation. 1956 1957 Call MatISRestoreLocalMat() when finished with the local matrix. 1958 1959 .seealso: MATIS 1960 @*/ 1961 PetscErrorCode MatISGetLocalMat(Mat mat,Mat *local) 1962 { 1963 PetscErrorCode ierr; 1964 1965 PetscFunctionBegin; 1966 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1967 PetscValidPointer(local,2); 1968 ierr = PetscUseMethod(mat,"MatISGetLocalMat_C",(Mat,Mat*),(mat,local));CHKERRQ(ierr); 1969 PetscFunctionReturn(0); 1970 } 1971 1972 /*@ 1973 MatISRestoreLocalMat - Restores the local matrix obtained with MatISGetLocalMat() 1974 1975 Input Parameter: 1976 . mat - the matrix 1977 1978 Output Parameter: 1979 . local - the local matrix 1980 1981 Level: advanced 1982 1983 .seealso: MATIS 1984 @*/ 1985 PetscErrorCode MatISRestoreLocalMat(Mat mat,Mat *local) 1986 { 1987 PetscErrorCode ierr; 1988 1989 PetscFunctionBegin; 1990 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1991 PetscValidPointer(local,2); 1992 ierr = PetscUseMethod(mat,"MatISRestoreLocalMat_C",(Mat,Mat*),(mat,local));CHKERRQ(ierr); 1993 PetscFunctionReturn(0); 1994 } 1995 1996 static PetscErrorCode MatISSetLocalMat_IS(Mat mat,Mat local) 1997 { 1998 Mat_IS *is = (Mat_IS*)mat->data; 1999 PetscInt nrows,ncols,orows,ocols; 2000 PetscErrorCode ierr; 2001 2002 PetscFunctionBegin; 2003 if (is->A) { 2004 ierr = MatGetSize(is->A,&orows,&ocols);CHKERRQ(ierr); 2005 ierr = MatGetSize(local,&nrows,&ncols);CHKERRQ(ierr); 2006 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); 2007 } 2008 ierr = PetscObjectReference((PetscObject)local);CHKERRQ(ierr); 2009 ierr = MatDestroy(&is->A);CHKERRQ(ierr); 2010 is->A = local; 2011 PetscFunctionReturn(0); 2012 } 2013 2014 /*@ 2015 MatISSetLocalMat - Replace the local matrix stored inside a MATIS object. 2016 2017 Input Parameter: 2018 . mat - the matrix 2019 . local - the local matrix 2020 2021 Output Parameter: 2022 2023 Level: advanced 2024 2025 Notes: 2026 This can be called if you have precomputed the local matrix and 2027 want to provide it to the matrix object MATIS. 2028 2029 .seealso: MATIS 2030 @*/ 2031 PetscErrorCode MatISSetLocalMat(Mat mat,Mat local) 2032 { 2033 PetscErrorCode ierr; 2034 2035 PetscFunctionBegin; 2036 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 2037 PetscValidHeaderSpecific(local,MAT_CLASSID,2); 2038 ierr = PetscUseMethod(mat,"MatISSetLocalMat_C",(Mat,Mat),(mat,local));CHKERRQ(ierr); 2039 PetscFunctionReturn(0); 2040 } 2041 2042 static PetscErrorCode MatZeroEntries_IS(Mat A) 2043 { 2044 Mat_IS *a = (Mat_IS*)A->data; 2045 PetscErrorCode ierr; 2046 2047 PetscFunctionBegin; 2048 ierr = MatZeroEntries(a->A);CHKERRQ(ierr); 2049 PetscFunctionReturn(0); 2050 } 2051 2052 static PetscErrorCode MatScale_IS(Mat A,PetscScalar a) 2053 { 2054 Mat_IS *is = (Mat_IS*)A->data; 2055 PetscErrorCode ierr; 2056 2057 PetscFunctionBegin; 2058 ierr = MatScale(is->A,a);CHKERRQ(ierr); 2059 PetscFunctionReturn(0); 2060 } 2061 2062 static PetscErrorCode MatGetDiagonal_IS(Mat A, Vec v) 2063 { 2064 Mat_IS *is = (Mat_IS*)A->data; 2065 PetscErrorCode ierr; 2066 2067 PetscFunctionBegin; 2068 /* get diagonal of the local matrix */ 2069 ierr = MatGetDiagonal(is->A,is->y);CHKERRQ(ierr); 2070 2071 /* scatter diagonal back into global vector */ 2072 ierr = VecSet(v,0);CHKERRQ(ierr); 2073 ierr = VecScatterBegin(is->rctx,is->y,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 2074 ierr = VecScatterEnd(is->rctx,is->y,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 2075 PetscFunctionReturn(0); 2076 } 2077 2078 static PetscErrorCode MatSetOption_IS(Mat A,MatOption op,PetscBool flg) 2079 { 2080 Mat_IS *a = (Mat_IS*)A->data; 2081 PetscErrorCode ierr; 2082 2083 PetscFunctionBegin; 2084 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 2085 PetscFunctionReturn(0); 2086 } 2087 2088 static PetscErrorCode MatAXPY_IS(Mat Y,PetscScalar a,Mat X,MatStructure str) 2089 { 2090 Mat_IS *y = (Mat_IS*)Y->data; 2091 Mat_IS *x; 2092 #if defined(PETSC_USE_DEBUG) 2093 PetscBool ismatis; 2094 #endif 2095 PetscErrorCode ierr; 2096 2097 PetscFunctionBegin; 2098 #if defined(PETSC_USE_DEBUG) 2099 ierr = PetscObjectTypeCompare((PetscObject)X,MATIS,&ismatis);CHKERRQ(ierr); 2100 if (!ismatis) SETERRQ(PetscObjectComm((PetscObject)Y),PETSC_ERR_SUP,"Cannot call MatAXPY(Y,a,X,str) with X not of type MATIS"); 2101 #endif 2102 x = (Mat_IS*)X->data; 2103 ierr = MatAXPY(y->A,a,x->A,str);CHKERRQ(ierr); 2104 PetscFunctionReturn(0); 2105 } 2106 2107 static PetscErrorCode MatGetLocalSubMatrix_IS(Mat A,IS row,IS col,Mat *submat) 2108 { 2109 Mat lA; 2110 Mat_IS *matis; 2111 ISLocalToGlobalMapping rl2g,cl2g; 2112 IS is; 2113 const PetscInt *rg,*rl; 2114 PetscInt nrg; 2115 PetscInt N,M,nrl,i,*idxs; 2116 PetscErrorCode ierr; 2117 2118 PetscFunctionBegin; 2119 ierr = ISLocalToGlobalMappingGetIndices(A->rmap->mapping,&rg);CHKERRQ(ierr); 2120 ierr = ISGetLocalSize(row,&nrl);CHKERRQ(ierr); 2121 ierr = ISGetIndices(row,&rl);CHKERRQ(ierr); 2122 ierr = ISLocalToGlobalMappingGetSize(A->rmap->mapping,&nrg);CHKERRQ(ierr); 2123 #if defined(PETSC_USE_DEBUG) 2124 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); 2125 #endif 2126 ierr = PetscMalloc1(nrg,&idxs);CHKERRQ(ierr); 2127 /* map from [0,nrl) to row */ 2128 for (i=0;i<nrl;i++) idxs[i] = rl[i]; 2129 #if defined(PETSC_USE_DEBUG) 2130 for (i=nrl;i<nrg;i++) idxs[i] = nrg; 2131 #else 2132 for (i=nrl;i<nrg;i++) idxs[i] = -1; 2133 #endif 2134 ierr = ISRestoreIndices(row,&rl);CHKERRQ(ierr); 2135 ierr = ISLocalToGlobalMappingRestoreIndices(A->rmap->mapping,&rg);CHKERRQ(ierr); 2136 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),nrg,idxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 2137 ierr = ISLocalToGlobalMappingCreateIS(is,&rl2g);CHKERRQ(ierr); 2138 ierr = ISDestroy(&is);CHKERRQ(ierr); 2139 /* compute new l2g map for columns */ 2140 if (col != row || A->rmap->mapping != A->cmap->mapping) { 2141 const PetscInt *cg,*cl; 2142 PetscInt ncg; 2143 PetscInt ncl; 2144 2145 ierr = ISLocalToGlobalMappingGetIndices(A->cmap->mapping,&cg);CHKERRQ(ierr); 2146 ierr = ISGetLocalSize(col,&ncl);CHKERRQ(ierr); 2147 ierr = ISGetIndices(col,&cl);CHKERRQ(ierr); 2148 ierr = ISLocalToGlobalMappingGetSize(A->cmap->mapping,&ncg);CHKERRQ(ierr); 2149 #if defined(PETSC_USE_DEBUG) 2150 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); 2151 #endif 2152 ierr = PetscMalloc1(ncg,&idxs);CHKERRQ(ierr); 2153 /* map from [0,ncl) to col */ 2154 for (i=0;i<ncl;i++) idxs[i] = cl[i]; 2155 #if defined(PETSC_USE_DEBUG) 2156 for (i=ncl;i<ncg;i++) idxs[i] = ncg; 2157 #else 2158 for (i=ncl;i<ncg;i++) idxs[i] = -1; 2159 #endif 2160 ierr = ISRestoreIndices(col,&cl);CHKERRQ(ierr); 2161 ierr = ISLocalToGlobalMappingRestoreIndices(A->cmap->mapping,&cg);CHKERRQ(ierr); 2162 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),ncg,idxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 2163 ierr = ISLocalToGlobalMappingCreateIS(is,&cl2g);CHKERRQ(ierr); 2164 ierr = ISDestroy(&is);CHKERRQ(ierr); 2165 } else { 2166 ierr = PetscObjectReference((PetscObject)rl2g);CHKERRQ(ierr); 2167 cl2g = rl2g; 2168 } 2169 /* create the MATIS submatrix */ 2170 ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr); 2171 ierr = MatCreate(PetscObjectComm((PetscObject)A),submat);CHKERRQ(ierr); 2172 ierr = MatSetSizes(*submat,PETSC_DECIDE,PETSC_DECIDE,M,N);CHKERRQ(ierr); 2173 ierr = MatSetType(*submat,MATIS);CHKERRQ(ierr); 2174 matis = (Mat_IS*)((*submat)->data); 2175 matis->islocalref = PETSC_TRUE; 2176 ierr = MatSetLocalToGlobalMapping(*submat,rl2g,cl2g);CHKERRQ(ierr); 2177 ierr = MatISGetLocalMat(A,&lA);CHKERRQ(ierr); 2178 ierr = MatISSetLocalMat(*submat,lA);CHKERRQ(ierr); 2179 ierr = MatSetUp(*submat);CHKERRQ(ierr); 2180 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2181 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2182 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 2183 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 2184 /* remove unsupported ops */ 2185 ierr = PetscMemzero((*submat)->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2186 (*submat)->ops->destroy = MatDestroy_IS; 2187 (*submat)->ops->setvalueslocal = MatSetValuesLocal_SubMat_IS; 2188 (*submat)->ops->setvaluesblockedlocal = MatSetValuesBlockedLocal_SubMat_IS; 2189 (*submat)->ops->assemblybegin = MatAssemblyBegin_IS; 2190 (*submat)->ops->assemblyend = MatAssemblyEnd_IS; 2191 PetscFunctionReturn(0); 2192 } 2193 2194 static PetscErrorCode MatSetFromOptions_IS(PetscOptionItems *PetscOptionsObject, Mat A) 2195 { 2196 Mat_IS *a = (Mat_IS*)A->data; 2197 PetscErrorCode ierr; 2198 2199 PetscFunctionBegin; 2200 ierr = PetscOptionsHead(PetscOptionsObject,"MATIS options");CHKERRQ(ierr); 2201 ierr = PetscObjectOptionsBegin((PetscObject)A); 2202 ierr = PetscOptionsBool("-matis_fixempty","Fix local matrices in case of empty local rows/columns",NULL,a->locempty,&a->locempty,NULL);CHKERRQ(ierr); 2203 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2204 PetscFunctionReturn(0); 2205 } 2206 2207 /*@ 2208 MatCreateIS - Creates a "process" unassembled matrix, assembled on each 2209 process but not across processes. 2210 2211 Input Parameters: 2212 + comm - MPI communicator that will share the matrix 2213 . bs - block size of the matrix 2214 . m,n,M,N - local and/or global sizes of the left and right vector used in matrix vector products 2215 . rmap - local to global map for rows 2216 - cmap - local to global map for cols 2217 2218 Output Parameter: 2219 . A - the resulting matrix 2220 2221 Level: advanced 2222 2223 Notes: See MATIS for more details. 2224 m and n are NOT related to the size of the map; they represent the size of the local parts of the vectors 2225 used in MatMult operations. The sizes of rmap and cmap define the size of the local matrices. 2226 If either rmap or cmap are NULL, then the matrix is assumed to be square. 2227 2228 .seealso: MATIS, MatSetLocalToGlobalMapping() 2229 @*/ 2230 PetscErrorCode MatCreateIS(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt M,PetscInt N,ISLocalToGlobalMapping rmap,ISLocalToGlobalMapping cmap,Mat *A) 2231 { 2232 PetscErrorCode ierr; 2233 2234 PetscFunctionBegin; 2235 if (!rmap && !cmap) SETERRQ(comm,PETSC_ERR_USER,"You need to provide at least one of the mappings"); 2236 ierr = MatCreate(comm,A);CHKERRQ(ierr); 2237 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 2238 if (bs > 0) { 2239 ierr = MatSetBlockSize(*A,bs);CHKERRQ(ierr); 2240 } 2241 ierr = MatSetType(*A,MATIS);CHKERRQ(ierr); 2242 if (rmap && cmap) { 2243 ierr = MatSetLocalToGlobalMapping(*A,rmap,cmap);CHKERRQ(ierr); 2244 } else if (!rmap) { 2245 ierr = MatSetLocalToGlobalMapping(*A,cmap,cmap);CHKERRQ(ierr); 2246 } else { 2247 ierr = MatSetLocalToGlobalMapping(*A,rmap,rmap);CHKERRQ(ierr); 2248 } 2249 PetscFunctionReturn(0); 2250 } 2251 2252 /*MC 2253 MATIS - MATIS = "is" - A matrix type to be used for using the non-overlapping domain decomposition methods (e.g. PCBDDC or KSPFETIDP). 2254 This stores the matrices in globally unassembled form. Each processor 2255 assembles only its local Neumann problem and the parallel matrix vector 2256 product is handled "implicitly". 2257 2258 Operations Provided: 2259 + MatMult() 2260 . MatMultAdd() 2261 . MatMultTranspose() 2262 . MatMultTransposeAdd() 2263 . MatZeroEntries() 2264 . MatSetOption() 2265 . MatZeroRows() 2266 . MatSetValues() 2267 . MatSetValuesBlocked() 2268 . MatSetValuesLocal() 2269 . MatSetValuesBlockedLocal() 2270 . MatScale() 2271 . MatGetDiagonal() 2272 . MatMissingDiagonal() 2273 . MatDuplicate() 2274 . MatCopy() 2275 . MatAXPY() 2276 . MatCreateSubMatrix() 2277 . MatGetLocalSubMatrix() 2278 . MatTranspose() 2279 - MatSetLocalToGlobalMapping() 2280 2281 Options Database Keys: 2282 . -mat_type is - sets the matrix type to "is" during a call to MatSetFromOptions() 2283 2284 Notes: Options prefix for the inner matrix are given by -is_mat_xxx 2285 2286 You must call MatSetLocalToGlobalMapping() before using this matrix type. 2287 2288 You can do matrix preallocation on the local matrix after you obtain it with 2289 MatISGetLocalMat(); otherwise, you could use MatISSetPreallocation() 2290 2291 Level: advanced 2292 2293 .seealso: Mat, MatISGetLocalMat(), MatSetLocalToGlobalMapping(), MatISSetPreallocation(), MatCreateIS(), PCBDDC, KSPFETIDP 2294 2295 M*/ 2296 2297 PETSC_EXTERN PetscErrorCode MatCreate_IS(Mat A) 2298 { 2299 PetscErrorCode ierr; 2300 Mat_IS *b; 2301 2302 PetscFunctionBegin; 2303 ierr = PetscNewLog(A,&b);CHKERRQ(ierr); 2304 A->data = (void*)b; 2305 2306 /* matrix ops */ 2307 ierr = PetscMemzero(A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2308 A->ops->mult = MatMult_IS; 2309 A->ops->multadd = MatMultAdd_IS; 2310 A->ops->multtranspose = MatMultTranspose_IS; 2311 A->ops->multtransposeadd = MatMultTransposeAdd_IS; 2312 A->ops->destroy = MatDestroy_IS; 2313 A->ops->setlocaltoglobalmapping = MatSetLocalToGlobalMapping_IS; 2314 A->ops->setvalues = MatSetValues_IS; 2315 A->ops->setvaluesblocked = MatSetValuesBlocked_IS; 2316 A->ops->setvalueslocal = MatSetValuesLocal_IS; 2317 A->ops->setvaluesblockedlocal = MatSetValuesBlockedLocal_IS; 2318 A->ops->zerorows = MatZeroRows_IS; 2319 A->ops->zerorowscolumns = MatZeroRowsColumns_IS; 2320 A->ops->assemblybegin = MatAssemblyBegin_IS; 2321 A->ops->assemblyend = MatAssemblyEnd_IS; 2322 A->ops->view = MatView_IS; 2323 A->ops->zeroentries = MatZeroEntries_IS; 2324 A->ops->scale = MatScale_IS; 2325 A->ops->getdiagonal = MatGetDiagonal_IS; 2326 A->ops->setoption = MatSetOption_IS; 2327 A->ops->ishermitian = MatIsHermitian_IS; 2328 A->ops->issymmetric = MatIsSymmetric_IS; 2329 A->ops->isstructurallysymmetric = MatIsStructurallySymmetric_IS; 2330 A->ops->duplicate = MatDuplicate_IS; 2331 A->ops->missingdiagonal = MatMissingDiagonal_IS; 2332 A->ops->copy = MatCopy_IS; 2333 A->ops->getlocalsubmatrix = MatGetLocalSubMatrix_IS; 2334 A->ops->createsubmatrix = MatCreateSubMatrix_IS; 2335 A->ops->axpy = MatAXPY_IS; 2336 A->ops->diagonalset = MatDiagonalSet_IS; 2337 A->ops->shift = MatShift_IS; 2338 A->ops->transpose = MatTranspose_IS; 2339 A->ops->getinfo = MatGetInfo_IS; 2340 A->ops->diagonalscale = MatDiagonalScale_IS; 2341 A->ops->setfromoptions = MatSetFromOptions_IS; 2342 2343 /* special MATIS functions */ 2344 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetLocalMat_C",MatISGetLocalMat_IS);CHKERRQ(ierr); 2345 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISRestoreLocalMat_C",MatISRestoreLocalMat_IS);CHKERRQ(ierr); 2346 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetLocalMat_C",MatISSetLocalMat_IS);CHKERRQ(ierr); 2347 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetMPIXAIJ_C",MatISGetMPIXAIJ_IS);CHKERRQ(ierr); 2348 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetPreallocation_C",MatISSetPreallocation_IS);CHKERRQ(ierr); 2349 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetUpSF_C",MatISSetUpSF_IS);CHKERRQ(ierr); 2350 ierr = PetscObjectChangeTypeName((PetscObject)A,MATIS);CHKERRQ(ierr); 2351 PetscFunctionReturn(0); 2352 } 2353