1 /* 2 Creates a matrix class for using the Neumann-Neumann type preconditioners. 3 This stores the matrices in globally unassembled form. Each processor 4 assembles only its local Neumann problem and the parallel matrix vector 5 product is handled "implicitly". 6 7 Currently this allows for only one subdomain per processor. 8 */ 9 10 #include <../src/mat/impls/is/matis.h> /*I "petscmat.h" I*/ 11 #include <../src/mat/impls/aij/mpi/mpiaij.h> 12 #include <petsc/private/sfimpl.h> 13 14 #define MATIS_MAX_ENTRIES_INSERTION 2048 15 16 static PetscErrorCode MatISContainerDestroyFields_Private(void *ptr) 17 { 18 MatISLocalFields lf = (MatISLocalFields)ptr; 19 PetscInt i; 20 PetscErrorCode ierr; 21 22 PetscFunctionBegin; 23 for (i=0;i<lf->nr;i++) { 24 ierr = ISDestroy(&lf->rf[i]);CHKERRQ(ierr); 25 } 26 for (i=0;i<lf->nc;i++) { 27 ierr = ISDestroy(&lf->cf[i]);CHKERRQ(ierr); 28 } 29 ierr = PetscFree2(lf->rf,lf->cf);CHKERRQ(ierr); 30 ierr = PetscFree(lf);CHKERRQ(ierr); 31 PetscFunctionReturn(0); 32 } 33 34 static PetscErrorCode MatISContainerDestroyArray_Private(void *ptr) 35 { 36 PetscErrorCode ierr; 37 38 PetscFunctionBeginUser; 39 ierr = PetscFree(ptr);CHKERRQ(ierr); 40 PetscFunctionReturn(0); 41 } 42 43 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_IS(Mat A,MatType type,MatReuse reuse,Mat *newmat) 44 { 45 Mat_MPIAIJ *aij = (Mat_MPIAIJ*)A->data; 46 Mat_SeqAIJ *diag = (Mat_SeqAIJ*)(aij->A->data); 47 Mat_SeqAIJ *offd = (Mat_SeqAIJ*)(aij->B->data); 48 Mat lA; 49 ISLocalToGlobalMapping rl2g,cl2g; 50 IS is; 51 MPI_Comm comm; 52 void *ptrs[2]; 53 const char *names[2] = {"_convert_csr_aux","_convert_csr_data"}; 54 PetscScalar *dd,*od,*aa,*data; 55 PetscInt *di,*dj,*oi,*oj; 56 PetscInt *aux,*ii,*jj; 57 PetscInt lc,dr,dc,oc,str,stc,nnz,i,jd,jo,cum; 58 PetscErrorCode ierr; 59 60 PetscFunctionBegin; 61 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 62 if (!aij->garray) SETERRQ(comm,PETSC_ERR_SUP,"garray not present"); 63 64 /* access relevant information from MPIAIJ */ 65 ierr = MatGetOwnershipRange(A,&str,NULL);CHKERRQ(ierr); 66 ierr = MatGetOwnershipRangeColumn(A,&stc,NULL);CHKERRQ(ierr); 67 ierr = MatGetLocalSize(A,&dr,&dc);CHKERRQ(ierr); 68 di = diag->i; 69 dj = diag->j; 70 dd = diag->a; 71 oc = aij->B->cmap->n; 72 oi = offd->i; 73 oj = offd->j; 74 od = offd->a; 75 nnz = diag->i[dr] + offd->i[dr]; 76 77 /* generate l2g maps for rows and cols */ 78 ierr = ISCreateStride(comm,dr,str,1,&is);CHKERRQ(ierr); 79 ierr = ISLocalToGlobalMappingCreateIS(is,&rl2g);CHKERRQ(ierr); 80 ierr = ISDestroy(&is);CHKERRQ(ierr); 81 if (dr) { 82 ierr = PetscMalloc1(dc+oc,&aux);CHKERRQ(ierr); 83 for (i=0; i<dc; i++) aux[i] = i+stc; 84 for (i=0; i<oc; i++) aux[i+dc] = aij->garray[i]; 85 ierr = ISCreateGeneral(comm,dc+oc,aux,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 86 lc = dc+oc; 87 } else { 88 ierr = ISCreateGeneral(comm,0,NULL,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 89 lc = 0; 90 } 91 ierr = ISLocalToGlobalMappingCreateIS(is,&cl2g);CHKERRQ(ierr); 92 ierr = ISDestroy(&is);CHKERRQ(ierr); 93 94 /* create MATIS object */ 95 ierr = MatCreate(comm,newmat);CHKERRQ(ierr); 96 ierr = MatSetSizes(*newmat,dr,dc,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); 97 ierr = MatSetType(*newmat,MATIS);CHKERRQ(ierr); 98 ierr = MatSetLocalToGlobalMapping(*newmat,rl2g,cl2g);CHKERRQ(ierr); 99 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 100 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 101 102 /* merge local matrices */ 103 ierr = PetscMalloc1(nnz+dr+1,&aux);CHKERRQ(ierr); 104 ierr = PetscMalloc1(nnz,&data);CHKERRQ(ierr); 105 ii = aux; 106 jj = aux+dr+1; 107 aa = data; 108 *ii = *(di++) + *(oi++); 109 for (jd=0,jo=0,cum=0;*ii<nnz;cum++) 110 { 111 for (;jd<*di;jd++) { *jj++ = *dj++; *aa++ = *dd++; } 112 for (;jo<*oi;jo++) { *jj++ = *oj++ + dc; *aa++ = *od++; } 113 *(++ii) = *(di++) + *(oi++); 114 } 115 for (;cum<dr;cum++) *(++ii) = nnz; 116 ii = aux; 117 jj = aux+dr+1; 118 aa = data; 119 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,dr,lc,ii,jj,aa,&lA);CHKERRQ(ierr); 120 121 /* create containers to destroy the data */ 122 ptrs[0] = aux; 123 ptrs[1] = data; 124 for (i=0; i<2; i++) { 125 PetscContainer c; 126 127 ierr = PetscContainerCreate(PETSC_COMM_SELF,&c);CHKERRQ(ierr); 128 ierr = PetscContainerSetPointer(c,ptrs[i]);CHKERRQ(ierr); 129 ierr = PetscContainerSetUserDestroy(c,MatISContainerDestroyArray_Private);CHKERRQ(ierr); 130 ierr = PetscObjectCompose((PetscObject)lA,names[i],(PetscObject)c);CHKERRQ(ierr); 131 ierr = PetscContainerDestroy(&c);CHKERRQ(ierr); 132 } 133 134 /* finalize matrix */ 135 ierr = MatISSetLocalMat(*newmat,lA);CHKERRQ(ierr); 136 ierr = MatDestroy(&lA);CHKERRQ(ierr); 137 ierr = MatAssemblyBegin(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 138 ierr = MatAssemblyEnd(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 139 PetscFunctionReturn(0); 140 } 141 142 /*@ 143 MatISSetUpSF - Setup star forest objects used by MatIS. 144 145 Collective on MPI_Comm 146 147 Input Parameters: 148 + A - the matrix 149 150 Level: advanced 151 152 Notes: This function does not need to be called by the user. 153 154 .keywords: matrix 155 156 .seealso: MatCreate(), MatCreateIS(), MatISSetPreallocation(), MatISGetLocalMat() 157 @*/ 158 PetscErrorCode MatISSetUpSF(Mat A) 159 { 160 PetscErrorCode ierr; 161 162 PetscFunctionBegin; 163 PetscValidHeaderSpecific(A,MAT_CLASSID,1); 164 PetscValidType(A,1); 165 ierr = PetscTryMethod(A,"MatISSetUpSF_C",(Mat),(A));CHKERRQ(ierr); 166 PetscFunctionReturn(0); 167 } 168 169 PETSC_INTERN PetscErrorCode MatConvert_Nest_IS(Mat A,MatType type,MatReuse reuse,Mat *newmat) 170 { 171 Mat **nest,*snest,**rnest,lA,B; 172 IS *iscol,*isrow,*islrow,*islcol; 173 ISLocalToGlobalMapping rl2g,cl2g; 174 MPI_Comm comm; 175 PetscInt *lr,*lc,*l2gidxs; 176 PetscInt i,j,nr,nc,rbs,cbs; 177 PetscBool convert,lreuse,*istrans; 178 PetscErrorCode ierr; 179 180 PetscFunctionBegin; 181 ierr = MatNestGetSubMats(A,&nr,&nc,&nest);CHKERRQ(ierr); 182 lreuse = PETSC_FALSE; 183 rnest = NULL; 184 if (reuse == MAT_REUSE_MATRIX) { 185 PetscBool ismatis,isnest; 186 187 ierr = PetscObjectTypeCompare((PetscObject)*newmat,MATIS,&ismatis);CHKERRQ(ierr); 188 if (!ismatis) SETERRQ1(PetscObjectComm((PetscObject)*newmat),PETSC_ERR_USER,"Cannot reuse matrix of type %s",((PetscObject)(*newmat))->type); 189 ierr = MatISGetLocalMat(*newmat,&lA);CHKERRQ(ierr); 190 ierr = PetscObjectTypeCompare((PetscObject)lA,MATNEST,&isnest);CHKERRQ(ierr); 191 if (isnest) { 192 ierr = MatNestGetSubMats(lA,&i,&j,&rnest);CHKERRQ(ierr); 193 lreuse = (PetscBool)(i == nr && j == nc); 194 if (!lreuse) rnest = NULL; 195 } 196 } 197 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 198 ierr = PetscCalloc2(nr,&lr,nc,&lc);CHKERRQ(ierr); 199 ierr = PetscCalloc6(nr,&isrow,nc,&iscol, 200 nr,&islrow,nc,&islcol, 201 nr*nc,&snest,nr*nc,&istrans);CHKERRQ(ierr); 202 ierr = MatNestGetISs(A,isrow,iscol);CHKERRQ(ierr); 203 for (i=0;i<nr;i++) { 204 for (j=0;j<nc;j++) { 205 PetscBool ismatis; 206 PetscInt l1,l2,lb1,lb2,ij=i*nc+j; 207 208 /* Null matrix pointers are allowed in MATNEST */ 209 if (!nest[i][j]) continue; 210 211 /* Nested matrices should be of type MATIS */ 212 ierr = PetscObjectTypeCompare((PetscObject)nest[i][j],MATTRANSPOSEMAT,&istrans[ij]);CHKERRQ(ierr); 213 if (istrans[ij]) { 214 Mat T,lT; 215 ierr = MatTransposeGetMat(nest[i][j],&T);CHKERRQ(ierr); 216 ierr = PetscObjectTypeCompare((PetscObject)T,MATIS,&ismatis);CHKERRQ(ierr); 217 if (!ismatis) SETERRQ2(comm,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) (transposed) is not of type MATIS",i,j); 218 ierr = MatISGetLocalMat(T,&lT);CHKERRQ(ierr); 219 ierr = MatCreateTranspose(lT,&snest[ij]);CHKERRQ(ierr); 220 } else { 221 ierr = PetscObjectTypeCompare((PetscObject)nest[i][j],MATIS,&ismatis);CHKERRQ(ierr); 222 if (!ismatis) SETERRQ2(comm,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) is not of type MATIS",i,j); 223 ierr = MatISGetLocalMat(nest[i][j],&snest[ij]);CHKERRQ(ierr); 224 } 225 226 /* Check compatibility of local sizes */ 227 ierr = MatGetSize(snest[ij],&l1,&l2);CHKERRQ(ierr); 228 ierr = MatGetBlockSizes(snest[ij],&lb1,&lb2);CHKERRQ(ierr); 229 if (!l1 || !l2) continue; 230 if (lr[i] && l1 != lr[i]) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid local size %D != %D",i,j,lr[i],l1); 231 if (lc[j] && l2 != lc[j]) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid local size %D != %D",i,j,lc[j],l2); 232 lr[i] = l1; 233 lc[j] = l2; 234 235 /* check compatibilty for local matrix reusage */ 236 if (rnest && !rnest[i][j] != !snest[ij]) lreuse = PETSC_FALSE; 237 } 238 } 239 240 #if defined (PETSC_USE_DEBUG) 241 /* Check compatibility of l2g maps for rows */ 242 for (i=0;i<nr;i++) { 243 rl2g = NULL; 244 for (j=0;j<nc;j++) { 245 PetscInt n1,n2; 246 247 if (!nest[i][j]) continue; 248 if (istrans[i*nc+j]) { 249 Mat T; 250 251 ierr = MatTransposeGetMat(nest[i][j],&T);CHKERRQ(ierr); 252 ierr = MatGetLocalToGlobalMapping(T,NULL,&cl2g);CHKERRQ(ierr); 253 } else { 254 ierr = MatGetLocalToGlobalMapping(nest[i][j],&cl2g,NULL);CHKERRQ(ierr); 255 } 256 ierr = ISLocalToGlobalMappingGetSize(cl2g,&n1);CHKERRQ(ierr); 257 if (!n1) continue; 258 if (!rl2g) { 259 rl2g = cl2g; 260 } else { 261 const PetscInt *idxs1,*idxs2; 262 PetscBool same; 263 264 ierr = ISLocalToGlobalMappingGetSize(rl2g,&n2);CHKERRQ(ierr); 265 if (n1 != n2) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid row l2gmap size %D != %D",i,j,n1,n2); 266 ierr = ISLocalToGlobalMappingGetIndices(cl2g,&idxs1);CHKERRQ(ierr); 267 ierr = ISLocalToGlobalMappingGetIndices(rl2g,&idxs2);CHKERRQ(ierr); 268 ierr = PetscMemcmp(idxs1,idxs2,n1*sizeof(PetscInt),&same);CHKERRQ(ierr); 269 ierr = ISLocalToGlobalMappingRestoreIndices(cl2g,&idxs1);CHKERRQ(ierr); 270 ierr = ISLocalToGlobalMappingRestoreIndices(rl2g,&idxs2);CHKERRQ(ierr); 271 if (!same) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid row l2gmap",i,j); 272 } 273 } 274 } 275 /* Check compatibility of l2g maps for columns */ 276 for (i=0;i<nc;i++) { 277 rl2g = NULL; 278 for (j=0;j<nr;j++) { 279 PetscInt n1,n2; 280 281 if (!nest[j][i]) continue; 282 if (istrans[j*nc+i]) { 283 Mat T; 284 285 ierr = MatTransposeGetMat(nest[j][i],&T);CHKERRQ(ierr); 286 ierr = MatGetLocalToGlobalMapping(T,&cl2g,NULL);CHKERRQ(ierr); 287 } else { 288 ierr = MatGetLocalToGlobalMapping(nest[j][i],NULL,&cl2g);CHKERRQ(ierr); 289 } 290 ierr = ISLocalToGlobalMappingGetSize(cl2g,&n1);CHKERRQ(ierr); 291 if (!n1) continue; 292 if (!rl2g) { 293 rl2g = cl2g; 294 } else { 295 const PetscInt *idxs1,*idxs2; 296 PetscBool same; 297 298 ierr = ISLocalToGlobalMappingGetSize(rl2g,&n2);CHKERRQ(ierr); 299 if (n1 != n2) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid column l2gmap size %D != %D",j,i,n1,n2); 300 ierr = ISLocalToGlobalMappingGetIndices(cl2g,&idxs1);CHKERRQ(ierr); 301 ierr = ISLocalToGlobalMappingGetIndices(rl2g,&idxs2);CHKERRQ(ierr); 302 ierr = PetscMemcmp(idxs1,idxs2,n1*sizeof(PetscInt),&same);CHKERRQ(ierr); 303 ierr = ISLocalToGlobalMappingRestoreIndices(cl2g,&idxs1);CHKERRQ(ierr); 304 ierr = ISLocalToGlobalMappingRestoreIndices(rl2g,&idxs2);CHKERRQ(ierr); 305 if (!same) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot convert from MATNEST to MATIS! Matrix block (%D,%D) has invalid column l2gmap",j,i); 306 } 307 } 308 } 309 #endif 310 311 B = NULL; 312 if (reuse != MAT_REUSE_MATRIX) { 313 PetscInt stl; 314 315 /* Create l2g map for the rows of the new matrix and index sets for the local MATNEST */ 316 for (i=0,stl=0;i<nr;i++) stl += lr[i]; 317 ierr = PetscMalloc1(stl,&l2gidxs);CHKERRQ(ierr); 318 for (i=0,stl=0;i<nr;i++) { 319 Mat usedmat; 320 Mat_IS *matis; 321 const PetscInt *idxs; 322 323 /* local IS for local NEST */ 324 ierr = ISCreateStride(PETSC_COMM_SELF,lr[i],stl,1,&islrow[i]);CHKERRQ(ierr); 325 326 /* l2gmap */ 327 j = 0; 328 usedmat = nest[i][j]; 329 while (!usedmat && j < nc-1) usedmat = nest[i][++j]; 330 if (!usedmat) SETERRQ(comm,PETSC_ERR_SUP,"Cannot find valid row mat"); 331 332 if (istrans[i*nc+j]) { 333 Mat T; 334 ierr = MatTransposeGetMat(usedmat,&T);CHKERRQ(ierr); 335 usedmat = T; 336 } 337 ierr = MatISSetUpSF(usedmat);CHKERRQ(ierr); 338 matis = (Mat_IS*)(usedmat->data); 339 ierr = ISGetIndices(isrow[i],&idxs);CHKERRQ(ierr); 340 if (istrans[i*nc+j]) { 341 ierr = PetscSFBcastBegin(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 342 ierr = PetscSFBcastEnd(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 343 } else { 344 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 345 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 346 } 347 ierr = ISRestoreIndices(isrow[i],&idxs);CHKERRQ(ierr); 348 stl += lr[i]; 349 } 350 ierr = ISLocalToGlobalMappingCreate(comm,1,stl,l2gidxs,PETSC_OWN_POINTER,&rl2g);CHKERRQ(ierr); 351 352 /* Create l2g map for columns of the new matrix and index sets for the local MATNEST */ 353 for (i=0,stl=0;i<nc;i++) stl += lc[i]; 354 ierr = PetscMalloc1(stl,&l2gidxs);CHKERRQ(ierr); 355 for (i=0,stl=0;i<nc;i++) { 356 Mat usedmat; 357 Mat_IS *matis; 358 const PetscInt *idxs; 359 360 /* local IS for local NEST */ 361 ierr = ISCreateStride(PETSC_COMM_SELF,lc[i],stl,1,&islcol[i]);CHKERRQ(ierr); 362 363 /* l2gmap */ 364 j = 0; 365 usedmat = nest[j][i]; 366 while (!usedmat && j < nr-1) usedmat = nest[++j][i]; 367 if (!usedmat) SETERRQ(comm,PETSC_ERR_SUP,"Cannot find valid column mat"); 368 if (istrans[j*nc+i]) { 369 Mat T; 370 ierr = MatTransposeGetMat(usedmat,&T);CHKERRQ(ierr); 371 usedmat = T; 372 } 373 ierr = MatISSetUpSF(usedmat);CHKERRQ(ierr); 374 matis = (Mat_IS*)(usedmat->data); 375 ierr = ISGetIndices(iscol[i],&idxs);CHKERRQ(ierr); 376 if (istrans[j*nc+i]) { 377 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 378 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 379 } else { 380 ierr = PetscSFBcastBegin(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 381 ierr = PetscSFBcastEnd(matis->csf,MPIU_INT,idxs,l2gidxs+stl);CHKERRQ(ierr); 382 } 383 ierr = ISRestoreIndices(iscol[i],&idxs);CHKERRQ(ierr); 384 stl += lc[i]; 385 } 386 ierr = ISLocalToGlobalMappingCreate(comm,1,stl,l2gidxs,PETSC_OWN_POINTER,&cl2g);CHKERRQ(ierr); 387 388 /* Create MATIS */ 389 ierr = MatCreate(comm,&B);CHKERRQ(ierr); 390 ierr = MatSetSizes(B,A->rmap->n,A->cmap->n,A->rmap->N,A->cmap->N);CHKERRQ(ierr); 391 ierr = MatGetBlockSizes(A,&rbs,&cbs);CHKERRQ(ierr); 392 ierr = MatSetBlockSizes(B,rbs,cbs);CHKERRQ(ierr); 393 ierr = MatSetType(B,MATIS);CHKERRQ(ierr); 394 ierr = MatSetLocalToGlobalMapping(B,rl2g,cl2g);CHKERRQ(ierr); 395 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 396 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 397 ierr = MatCreateNest(PETSC_COMM_SELF,nr,islrow,nc,islcol,snest,&lA);CHKERRQ(ierr); 398 for (i=0;i<nr*nc;i++) { 399 if (istrans[i]) { 400 ierr = MatDestroy(&snest[i]);CHKERRQ(ierr); 401 } 402 } 403 ierr = MatISSetLocalMat(B,lA);CHKERRQ(ierr); 404 ierr = MatDestroy(&lA);CHKERRQ(ierr); 405 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 406 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 407 if (reuse == MAT_INPLACE_MATRIX) { 408 ierr = MatHeaderReplace(A,&B);CHKERRQ(ierr); 409 } else { 410 *newmat = B; 411 } 412 } else { 413 if (lreuse) { 414 ierr = MatISGetLocalMat(*newmat,&lA);CHKERRQ(ierr); 415 for (i=0;i<nr;i++) { 416 for (j=0;j<nc;j++) { 417 if (snest[i*nc+j]) { 418 ierr = MatNestSetSubMat(lA,i,j,snest[i*nc+j]);CHKERRQ(ierr); 419 if (istrans[i*nc+j]) { 420 ierr = MatDestroy(&snest[i*nc+j]);CHKERRQ(ierr); 421 } 422 } 423 } 424 } 425 } else { 426 PetscInt stl; 427 for (i=0,stl=0;i<nr;i++) { 428 ierr = ISCreateStride(PETSC_COMM_SELF,lr[i],stl,1,&islrow[i]);CHKERRQ(ierr); 429 stl += lr[i]; 430 } 431 for (i=0,stl=0;i<nc;i++) { 432 ierr = ISCreateStride(PETSC_COMM_SELF,lc[i],stl,1,&islcol[i]);CHKERRQ(ierr); 433 stl += lc[i]; 434 } 435 ierr = MatCreateNest(PETSC_COMM_SELF,nr,islrow,nc,islcol,snest,&lA);CHKERRQ(ierr); 436 for (i=0;i<nr*nc;i++) { 437 if (istrans[i]) { 438 ierr = MatDestroy(&snest[i]);CHKERRQ(ierr); 439 } 440 } 441 ierr = MatISSetLocalMat(*newmat,lA);CHKERRQ(ierr); 442 ierr = MatDestroy(&lA);CHKERRQ(ierr); 443 } 444 ierr = MatAssemblyBegin(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 445 ierr = MatAssemblyEnd(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 446 } 447 448 /* Create local matrix in MATNEST format */ 449 convert = PETSC_FALSE; 450 ierr = PetscOptionsGetBool(NULL,((PetscObject)A)->prefix,"-matis_convert_local_nest",&convert,NULL);CHKERRQ(ierr); 451 if (convert) { 452 Mat M; 453 MatISLocalFields lf; 454 PetscContainer c; 455 456 ierr = MatISGetLocalMat(*newmat,&lA);CHKERRQ(ierr); 457 ierr = MatConvert(lA,MATAIJ,MAT_INITIAL_MATRIX,&M);CHKERRQ(ierr); 458 ierr = MatISSetLocalMat(*newmat,M);CHKERRQ(ierr); 459 ierr = MatDestroy(&M);CHKERRQ(ierr); 460 461 /* attach local fields to the matrix */ 462 ierr = PetscNew(&lf);CHKERRQ(ierr); 463 ierr = PetscCalloc2(nr,&lf->rf,nc,&lf->cf);CHKERRQ(ierr); 464 for (i=0;i<nr;i++) { 465 PetscInt n,st; 466 467 ierr = ISGetLocalSize(islrow[i],&n);CHKERRQ(ierr); 468 ierr = ISStrideGetInfo(islrow[i],&st,NULL);CHKERRQ(ierr); 469 ierr = ISCreateStride(comm,n,st,1,&lf->rf[i]);CHKERRQ(ierr); 470 } 471 for (i=0;i<nc;i++) { 472 PetscInt n,st; 473 474 ierr = ISGetLocalSize(islcol[i],&n);CHKERRQ(ierr); 475 ierr = ISStrideGetInfo(islcol[i],&st,NULL);CHKERRQ(ierr); 476 ierr = ISCreateStride(comm,n,st,1,&lf->cf[i]);CHKERRQ(ierr); 477 } 478 lf->nr = nr; 479 lf->nc = nc; 480 ierr = PetscContainerCreate(PetscObjectComm((PetscObject)(*newmat)),&c);CHKERRQ(ierr); 481 ierr = PetscContainerSetPointer(c,lf);CHKERRQ(ierr); 482 ierr = PetscContainerSetUserDestroy(c,MatISContainerDestroyFields_Private);CHKERRQ(ierr); 483 ierr = PetscObjectCompose((PetscObject)(*newmat),"_convert_nest_lfields",(PetscObject)c);CHKERRQ(ierr); 484 ierr = PetscContainerDestroy(&c);CHKERRQ(ierr); 485 } 486 487 /* Free workspace */ 488 for (i=0;i<nr;i++) { 489 ierr = ISDestroy(&islrow[i]);CHKERRQ(ierr); 490 } 491 for (i=0;i<nc;i++) { 492 ierr = ISDestroy(&islcol[i]);CHKERRQ(ierr); 493 } 494 ierr = PetscFree6(isrow,iscol,islrow,islcol,snest,istrans);CHKERRQ(ierr); 495 ierr = PetscFree2(lr,lc);CHKERRQ(ierr); 496 PetscFunctionReturn(0); 497 } 498 499 static PetscErrorCode MatDiagonalScale_IS(Mat A, Vec l, Vec r) 500 { 501 Mat_IS *matis = (Mat_IS*)A->data; 502 Vec ll,rr; 503 const PetscScalar *Y,*X; 504 PetscScalar *x,*y; 505 PetscErrorCode ierr; 506 507 PetscFunctionBegin; 508 ierr = MatISSetUpSF(A);CHKERRQ(ierr); 509 if (l) { 510 ll = matis->y; 511 ierr = VecGetArrayRead(l,&Y);CHKERRQ(ierr); 512 ierr = VecGetArray(ll,&y);CHKERRQ(ierr); 513 ierr = PetscSFBcastBegin(matis->sf,MPIU_SCALAR,Y,y);CHKERRQ(ierr); 514 } else { 515 ll = NULL; 516 } 517 if (r) { 518 rr = matis->x; 519 ierr = VecGetArrayRead(r,&X);CHKERRQ(ierr); 520 ierr = VecGetArray(rr,&x);CHKERRQ(ierr); 521 ierr = PetscSFBcastBegin(matis->csf,MPIU_SCALAR,X,x);CHKERRQ(ierr); 522 } else { 523 rr = NULL; 524 } 525 if (ll) { 526 ierr = PetscSFBcastEnd(matis->sf,MPIU_SCALAR,Y,y);CHKERRQ(ierr); 527 ierr = VecRestoreArrayRead(l,&Y);CHKERRQ(ierr); 528 ierr = VecRestoreArray(ll,&y);CHKERRQ(ierr); 529 } 530 if (rr) { 531 ierr = PetscSFBcastEnd(matis->csf,MPIU_SCALAR,X,x);CHKERRQ(ierr); 532 ierr = VecRestoreArrayRead(r,&X);CHKERRQ(ierr); 533 ierr = VecRestoreArray(rr,&x);CHKERRQ(ierr); 534 } 535 ierr = MatDiagonalScale(matis->A,ll,rr);CHKERRQ(ierr); 536 PetscFunctionReturn(0); 537 } 538 539 static PetscErrorCode MatGetInfo_IS(Mat A,MatInfoType flag,MatInfo *ginfo) 540 { 541 Mat_IS *matis = (Mat_IS*)A->data; 542 MatInfo info; 543 PetscReal isend[6],irecv[6]; 544 PetscInt bs; 545 PetscErrorCode ierr; 546 547 PetscFunctionBegin; 548 ierr = MatGetBlockSize(A,&bs);CHKERRQ(ierr); 549 if (matis->A->ops->getinfo) { 550 ierr = MatGetInfo(matis->A,MAT_LOCAL,&info);CHKERRQ(ierr); 551 isend[0] = info.nz_used; 552 isend[1] = info.nz_allocated; 553 isend[2] = info.nz_unneeded; 554 isend[3] = info.memory; 555 isend[4] = info.mallocs; 556 } else { 557 isend[0] = 0.; 558 isend[1] = 0.; 559 isend[2] = 0.; 560 isend[3] = 0.; 561 isend[4] = 0.; 562 } 563 isend[5] = matis->A->num_ass; 564 if (flag == MAT_LOCAL) { 565 ginfo->nz_used = isend[0]; 566 ginfo->nz_allocated = isend[1]; 567 ginfo->nz_unneeded = isend[2]; 568 ginfo->memory = isend[3]; 569 ginfo->mallocs = isend[4]; 570 ginfo->assemblies = isend[5]; 571 } else if (flag == MAT_GLOBAL_MAX) { 572 ierr = MPIU_Allreduce(isend,irecv,6,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 573 574 ginfo->nz_used = irecv[0]; 575 ginfo->nz_allocated = irecv[1]; 576 ginfo->nz_unneeded = irecv[2]; 577 ginfo->memory = irecv[3]; 578 ginfo->mallocs = irecv[4]; 579 ginfo->assemblies = irecv[5]; 580 } else if (flag == MAT_GLOBAL_SUM) { 581 ierr = MPIU_Allreduce(isend,irecv,5,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 582 583 ginfo->nz_used = irecv[0]; 584 ginfo->nz_allocated = irecv[1]; 585 ginfo->nz_unneeded = irecv[2]; 586 ginfo->memory = irecv[3]; 587 ginfo->mallocs = irecv[4]; 588 ginfo->assemblies = A->num_ass; 589 } 590 ginfo->block_size = bs; 591 ginfo->fill_ratio_given = 0; 592 ginfo->fill_ratio_needed = 0; 593 ginfo->factor_mallocs = 0; 594 PetscFunctionReturn(0); 595 } 596 597 PetscErrorCode MatTranspose_IS(Mat A,MatReuse reuse,Mat *B) 598 { 599 Mat C,lC,lA; 600 PetscErrorCode ierr; 601 602 PetscFunctionBegin; 603 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_INPLACE_MATRIX) { 604 ISLocalToGlobalMapping rl2g,cl2g; 605 ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr); 606 ierr = MatSetSizes(C,A->cmap->n,A->rmap->n,A->cmap->N,A->rmap->N);CHKERRQ(ierr); 607 ierr = MatSetBlockSizes(C,PetscAbs(A->cmap->bs),PetscAbs(A->rmap->bs));CHKERRQ(ierr); 608 ierr = MatSetType(C,MATIS);CHKERRQ(ierr); 609 ierr = MatGetLocalToGlobalMapping(A,&rl2g,&cl2g);CHKERRQ(ierr); 610 ierr = MatSetLocalToGlobalMapping(C,cl2g,rl2g);CHKERRQ(ierr); 611 } else { 612 C = *B; 613 } 614 615 /* perform local transposition */ 616 ierr = MatISGetLocalMat(A,&lA);CHKERRQ(ierr); 617 ierr = MatTranspose(lA,MAT_INITIAL_MATRIX,&lC);CHKERRQ(ierr); 618 ierr = MatISSetLocalMat(C,lC);CHKERRQ(ierr); 619 ierr = MatDestroy(&lC);CHKERRQ(ierr); 620 621 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 622 *B = C; 623 } else { 624 ierr = MatHeaderMerge(A,&C);CHKERRQ(ierr); 625 } 626 ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 627 ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 628 PetscFunctionReturn(0); 629 } 630 631 PetscErrorCode MatDiagonalSet_IS(Mat A,Vec D,InsertMode insmode) 632 { 633 Mat_IS *is = (Mat_IS*)A->data; 634 PetscErrorCode ierr; 635 636 PetscFunctionBegin; 637 if (!D) { /* this code branch is used by MatShift_IS */ 638 ierr = VecSet(is->y,1.);CHKERRQ(ierr); 639 } else { 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 PetscErrorCode ierr; 651 652 PetscFunctionBegin; 653 ierr = MatDiagonalSet_IS(A,NULL,ADD_VALUES);CHKERRQ(ierr); 654 PetscFunctionReturn(0); 655 } 656 657 static PetscErrorCode MatSetValuesLocal_SubMat_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 658 { 659 PetscErrorCode ierr; 660 Mat_IS *is = (Mat_IS*)A->data; 661 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 662 663 PetscFunctionBegin; 664 #if defined(PETSC_USE_DEBUG) 665 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); 666 #endif 667 ierr = ISLocalToGlobalMappingApply(A->rmap->mapping,m,rows,rows_l);CHKERRQ(ierr); 668 ierr = ISLocalToGlobalMappingApply(A->cmap->mapping,n,cols,cols_l);CHKERRQ(ierr); 669 ierr = MatSetValues(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 670 PetscFunctionReturn(0); 671 } 672 673 static PetscErrorCode MatSetValuesBlockedLocal_SubMat_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 674 { 675 PetscErrorCode ierr; 676 Mat_IS *is = (Mat_IS*)A->data; 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 = MatSetValuesBlocked(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; 807 MPI_Comm comm; 808 809 ierr = PetscObjectGetComm((PetscObject)mat,&comm);CHKERRQ(ierr); 810 ierr = ISGetLocalSize(irow,&m);CHKERRQ(ierr); 811 ierr = ISGetLocalSize(icol,&n);CHKERRQ(ierr); 812 ierr = MatCreate(comm,newmat);CHKERRQ(ierr); 813 ierr = MatSetType(*newmat,MATIS);CHKERRQ(ierr); 814 ierr = MatSetSizes(*newmat,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); 815 /* communicate irow to their owners in the layout */ 816 ierr = ISGetIndices(irow,&idxs);CHKERRQ(ierr); 817 ierr = PetscLayoutMapLocal_Private(mat->rmap,m,idxs,&ll,&lidxs,&lgidxs);CHKERRQ(ierr); 818 ierr = ISRestoreIndices(irow,&idxs);CHKERRQ(ierr); 819 ierr = MatISSetUpSF(mat);CHKERRQ(ierr); 820 ierr = PetscMemzero(matis->sf_rootdata,matis->sf->nroots*sizeof(PetscInt));CHKERRQ(ierr); 821 for (i=0;i<ll;i++) matis->sf_rootdata[lidxs[i]] = lgidxs[i]+1; 822 ierr = PetscFree(lidxs);CHKERRQ(ierr); 823 ierr = PetscFree(lgidxs);CHKERRQ(ierr); 824 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 825 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 826 for (i=0,newloc=0;i<matis->sf->nleaves;i++) if (matis->sf_leafdata[i]) newloc++; 827 ierr = PetscMalloc1(newloc,&newgidxs);CHKERRQ(ierr); 828 ierr = PetscMalloc1(newloc,&lidxs);CHKERRQ(ierr); 829 for (i=0,newloc=0;i<matis->sf->nleaves;i++) 830 if (matis->sf_leafdata[i]) { 831 lidxs[newloc] = i; 832 newgidxs[newloc++] = matis->sf_leafdata[i]-1; 833 } 834 ierr = ISCreateGeneral(comm,newloc,newgidxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 835 ierr = ISLocalToGlobalMappingCreateIS(is,&rl2g);CHKERRQ(ierr); 836 ierr = ISDestroy(&is);CHKERRQ(ierr); 837 /* local is to extract local submatrix */ 838 newmatis = (Mat_IS*)(*newmat)->data; 839 ierr = ISCreateGeneral(comm,newloc,lidxs,PETSC_OWN_POINTER,&newmatis->getsub_ris);CHKERRQ(ierr); 840 if (mat->congruentlayouts == -1) { /* first time we compare rows and cols layouts */ 841 PetscBool cong; 842 ierr = PetscLayoutCompare(mat->rmap,mat->cmap,&cong);CHKERRQ(ierr); 843 if (cong) mat->congruentlayouts = 1; 844 else mat->congruentlayouts = 0; 845 } 846 if (mat->congruentlayouts && irow == icol) { 847 ierr = MatSetLocalToGlobalMapping(*newmat,rl2g,rl2g);CHKERRQ(ierr); 848 ierr = PetscObjectReference((PetscObject)newmatis->getsub_ris);CHKERRQ(ierr); 849 newmatis->getsub_cis = newmatis->getsub_ris; 850 } else { 851 ISLocalToGlobalMapping cl2g; 852 853 /* communicate icol to their owners in the layout */ 854 ierr = ISGetIndices(icol,&idxs);CHKERRQ(ierr); 855 ierr = PetscLayoutMapLocal_Private(mat->cmap,n,idxs,&ll,&lidxs,&lgidxs);CHKERRQ(ierr); 856 ierr = ISRestoreIndices(icol,&idxs);CHKERRQ(ierr); 857 ierr = PetscMemzero(matis->csf_rootdata,matis->csf->nroots*sizeof(PetscInt));CHKERRQ(ierr); 858 for (i=0;i<ll;i++) matis->csf_rootdata[lidxs[i]] = lgidxs[i]+1; 859 ierr = PetscFree(lidxs);CHKERRQ(ierr); 860 ierr = PetscFree(lgidxs);CHKERRQ(ierr); 861 ierr = PetscSFBcastBegin(matis->csf,MPIU_INT,matis->csf_rootdata,matis->csf_leafdata);CHKERRQ(ierr); 862 ierr = PetscSFBcastEnd(matis->csf,MPIU_INT,matis->csf_rootdata,matis->csf_leafdata);CHKERRQ(ierr); 863 for (i=0,newloc=0;i<matis->csf->nleaves;i++) if (matis->csf_leafdata[i]) newloc++; 864 ierr = PetscMalloc1(newloc,&newgidxs);CHKERRQ(ierr); 865 ierr = PetscMalloc1(newloc,&lidxs);CHKERRQ(ierr); 866 for (i=0,newloc=0;i<matis->csf->nleaves;i++) 867 if (matis->csf_leafdata[i]) { 868 lidxs[newloc] = i; 869 newgidxs[newloc++] = matis->csf_leafdata[i]-1; 870 } 871 ierr = ISCreateGeneral(comm,newloc,newgidxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 872 ierr = ISLocalToGlobalMappingCreateIS(is,&cl2g);CHKERRQ(ierr); 873 ierr = ISDestroy(&is);CHKERRQ(ierr); 874 /* local is to extract local submatrix */ 875 ierr = ISCreateGeneral(comm,newloc,lidxs,PETSC_OWN_POINTER,&newmatis->getsub_cis);CHKERRQ(ierr); 876 ierr = MatSetLocalToGlobalMapping(*newmat,rl2g,cl2g);CHKERRQ(ierr); 877 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 878 } 879 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 880 } else { 881 ierr = MatISGetLocalMat(*newmat,&newlocmat);CHKERRQ(ierr); 882 } 883 ierr = MatISGetLocalMat(mat,&locmat);CHKERRQ(ierr); 884 newmatis = (Mat_IS*)(*newmat)->data; 885 ierr = MatCreateSubMatrix(locmat,newmatis->getsub_ris,newmatis->getsub_cis,scall,&newlocmat);CHKERRQ(ierr); 886 if (scall == MAT_INITIAL_MATRIX) { 887 ierr = MatISSetLocalMat(*newmat,newlocmat);CHKERRQ(ierr); 888 ierr = MatDestroy(&newlocmat);CHKERRQ(ierr); 889 } 890 ierr = MatAssemblyBegin(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 891 ierr = MatAssemblyEnd(*newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 892 PetscFunctionReturn(0); 893 } 894 895 static PetscErrorCode MatCopy_IS(Mat A,Mat B,MatStructure str) 896 { 897 Mat_IS *a = (Mat_IS*)A->data,*b; 898 PetscBool ismatis; 899 PetscErrorCode ierr; 900 901 PetscFunctionBegin; 902 ierr = PetscObjectTypeCompare((PetscObject)B,MATIS,&ismatis);CHKERRQ(ierr); 903 if (!ismatis) SETERRQ(PetscObjectComm((PetscObject)B),PETSC_ERR_SUP,"Need to be implemented"); 904 b = (Mat_IS*)B->data; 905 ierr = MatCopy(a->A,b->A,str);CHKERRQ(ierr); 906 ierr = PetscObjectStateIncrease((PetscObject)B);CHKERRQ(ierr); 907 PetscFunctionReturn(0); 908 } 909 910 static PetscErrorCode MatMissingDiagonal_IS(Mat A,PetscBool *missing,PetscInt *d) 911 { 912 Vec v; 913 const PetscScalar *array; 914 PetscInt i,n; 915 PetscErrorCode ierr; 916 917 PetscFunctionBegin; 918 *missing = PETSC_FALSE; 919 ierr = MatCreateVecs(A,NULL,&v);CHKERRQ(ierr); 920 ierr = MatGetDiagonal(A,v);CHKERRQ(ierr); 921 ierr = VecGetLocalSize(v,&n);CHKERRQ(ierr); 922 ierr = VecGetArrayRead(v,&array);CHKERRQ(ierr); 923 for (i=0;i<n;i++) if (array[i] == 0.) break; 924 ierr = VecRestoreArrayRead(v,&array);CHKERRQ(ierr); 925 ierr = VecDestroy(&v);CHKERRQ(ierr); 926 if (i != n) *missing = PETSC_TRUE; 927 if (d) { 928 *d = -1; 929 if (*missing) { 930 PetscInt rstart; 931 ierr = MatGetOwnershipRange(A,&rstart,NULL);CHKERRQ(ierr); 932 *d = i+rstart; 933 } 934 } 935 PetscFunctionReturn(0); 936 } 937 938 static PetscErrorCode MatISSetUpSF_IS(Mat B) 939 { 940 Mat_IS *matis = (Mat_IS*)(B->data); 941 const PetscInt *gidxs; 942 PetscInt nleaves; 943 PetscErrorCode ierr; 944 945 PetscFunctionBegin; 946 if (matis->sf) PetscFunctionReturn(0); 947 ierr = PetscSFCreate(PetscObjectComm((PetscObject)B),&matis->sf);CHKERRQ(ierr); 948 ierr = ISLocalToGlobalMappingGetIndices(B->rmap->mapping,&gidxs);CHKERRQ(ierr); 949 ierr = ISLocalToGlobalMappingGetSize(B->rmap->mapping,&nleaves);CHKERRQ(ierr); 950 ierr = PetscSFSetGraphLayout(matis->sf,B->rmap,nleaves,NULL,PETSC_OWN_POINTER,gidxs);CHKERRQ(ierr); 951 ierr = ISLocalToGlobalMappingRestoreIndices(B->rmap->mapping,&gidxs);CHKERRQ(ierr); 952 ierr = PetscMalloc2(matis->sf->nroots,&matis->sf_rootdata,matis->sf->nleaves,&matis->sf_leafdata);CHKERRQ(ierr); 953 if (B->rmap->mapping != B->cmap->mapping) { /* setup SF for columns */ 954 ierr = ISLocalToGlobalMappingGetSize(B->cmap->mapping,&nleaves);CHKERRQ(ierr); 955 ierr = PetscSFCreate(PetscObjectComm((PetscObject)B),&matis->csf);CHKERRQ(ierr); 956 ierr = ISLocalToGlobalMappingGetIndices(B->cmap->mapping,&gidxs);CHKERRQ(ierr); 957 ierr = PetscSFSetGraphLayout(matis->csf,B->cmap,nleaves,NULL,PETSC_OWN_POINTER,gidxs);CHKERRQ(ierr); 958 ierr = ISLocalToGlobalMappingRestoreIndices(B->cmap->mapping,&gidxs);CHKERRQ(ierr); 959 ierr = PetscMalloc2(matis->csf->nroots,&matis->csf_rootdata,matis->csf->nleaves,&matis->csf_leafdata);CHKERRQ(ierr); 960 } else { 961 matis->csf = matis->sf; 962 matis->csf_leafdata = matis->sf_leafdata; 963 matis->csf_rootdata = matis->sf_rootdata; 964 } 965 PetscFunctionReturn(0); 966 } 967 968 /*@ 969 MatISSetPreallocation - Preallocates memory for a MATIS parallel matrix. 970 971 Collective on MPI_Comm 972 973 Input Parameters: 974 + B - the matrix 975 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 976 (same value is used for all local rows) 977 . d_nnz - array containing the number of nonzeros in the various rows of the 978 DIAGONAL portion of the local submatrix (possibly different for each row) 979 or NULL, if d_nz is used to specify the nonzero structure. 980 The size of this array is equal to the number of local rows, i.e 'm'. 981 For matrices that will be factored, you must leave room for (and set) 982 the diagonal entry even if it is zero. 983 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 984 submatrix (same value is used for all local rows). 985 - o_nnz - array containing the number of nonzeros in the various rows of the 986 OFF-DIAGONAL portion of the local submatrix (possibly different for 987 each row) or NULL, if o_nz is used to specify the nonzero 988 structure. The size of this array is equal to the number 989 of local rows, i.e 'm'. 990 991 If the *_nnz parameter is given then the *_nz parameter is ignored 992 993 Level: intermediate 994 995 Notes: This function has the same interface as the MPIAIJ preallocation routine in order to simplify the transition 996 from the asssembled format to the unassembled one. It overestimates the preallocation of MATIS local 997 matrices; for exact preallocation, the user should set the preallocation directly on local matrix objects. 998 999 .keywords: matrix 1000 1001 .seealso: MatCreate(), MatCreateIS(), MatMPIAIJSetPreallocation(), MatISGetLocalMat(), MATIS 1002 @*/ 1003 PetscErrorCode MatISSetPreallocation(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 1004 { 1005 PetscErrorCode ierr; 1006 1007 PetscFunctionBegin; 1008 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 1009 PetscValidType(B,1); 1010 ierr = PetscTryMethod(B,"MatISSetPreallocation_C",(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[]),(B,d_nz,d_nnz,o_nz,o_nnz));CHKERRQ(ierr); 1011 PetscFunctionReturn(0); 1012 } 1013 1014 static PetscErrorCode MatISSetPreallocation_IS(Mat B,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 1015 { 1016 Mat_IS *matis = (Mat_IS*)(B->data); 1017 PetscInt bs,i,nlocalcols; 1018 PetscErrorCode ierr; 1019 1020 PetscFunctionBegin; 1021 if (!matis->A) SETERRQ(PetscObjectComm((PetscObject)B),PETSC_ERR_SUP,"You should first call MatSetLocalToGlobalMapping"); 1022 ierr = MatISSetUpSF(B);CHKERRQ(ierr); 1023 1024 if (!d_nnz) for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] = d_nz; 1025 else for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] = d_nnz[i]; 1026 1027 if (!o_nnz) for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] += o_nz; 1028 else for (i=0;i<matis->sf->nroots;i++) matis->sf_rootdata[i] += o_nnz[i]; 1029 1030 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1031 ierr = MatGetSize(matis->A,NULL,&nlocalcols);CHKERRQ(ierr); 1032 ierr = MatGetBlockSize(matis->A,&bs);CHKERRQ(ierr); 1033 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1034 1035 for (i=0;i<matis->sf->nleaves;i++) matis->sf_leafdata[i] = PetscMin(matis->sf_leafdata[i],nlocalcols); 1036 ierr = MatSeqAIJSetPreallocation(matis->A,0,matis->sf_leafdata);CHKERRQ(ierr); 1037 #if defined(PETSC_HAVE_HYPRE) 1038 ierr = MatHYPRESetPreallocation(matis->A,0,matis->sf_leafdata,0,NULL);CHKERRQ(ierr); 1039 #endif 1040 1041 for (i=0;i<matis->sf->nleaves/bs;i++) matis->sf_leafdata[i] = matis->sf_leafdata[i*bs]/bs; 1042 ierr = MatSeqBAIJSetPreallocation(matis->A,bs,0,matis->sf_leafdata);CHKERRQ(ierr); 1043 1044 for (i=0;i<matis->sf->nleaves/bs;i++) matis->sf_leafdata[i] = matis->sf_leafdata[i]-i; 1045 ierr = MatSeqSBAIJSetPreallocation(matis->A,bs,0,matis->sf_leafdata);CHKERRQ(ierr); 1046 1047 /* for other matrix types */ 1048 ierr = MatSetUp(matis->A);CHKERRQ(ierr); 1049 PetscFunctionReturn(0); 1050 } 1051 1052 PETSC_EXTERN PetscErrorCode MatISSetMPIXAIJPreallocation_Private(Mat A, Mat B, PetscBool maxreduce) 1053 { 1054 Mat_IS *matis = (Mat_IS*)(A->data); 1055 PetscInt *my_dnz,*my_onz,*dnz,*onz,*mat_ranges,*row_ownership; 1056 const PetscInt *global_indices_r,*global_indices_c; 1057 PetscInt i,j,bs,rows,cols; 1058 PetscInt lrows,lcols; 1059 PetscInt local_rows,local_cols; 1060 PetscMPIInt nsubdomains; 1061 PetscBool isdense,issbaij; 1062 PetscErrorCode ierr; 1063 1064 PetscFunctionBegin; 1065 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)A),&nsubdomains);CHKERRQ(ierr); 1066 ierr = MatGetSize(A,&rows,&cols);CHKERRQ(ierr); 1067 ierr = MatGetBlockSize(A,&bs);CHKERRQ(ierr); 1068 ierr = MatGetSize(matis->A,&local_rows,&local_cols);CHKERRQ(ierr); 1069 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQDENSE,&isdense);CHKERRQ(ierr); 1070 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQSBAIJ,&issbaij);CHKERRQ(ierr); 1071 ierr = ISLocalToGlobalMappingGetIndices(A->rmap->mapping,&global_indices_r);CHKERRQ(ierr); 1072 if (A->rmap->mapping != A->cmap->mapping) { 1073 ierr = ISLocalToGlobalMappingGetIndices(A->cmap->mapping,&global_indices_c);CHKERRQ(ierr); 1074 } else { 1075 global_indices_c = global_indices_r; 1076 } 1077 1078 if (issbaij) { 1079 ierr = MatGetRowUpperTriangular(matis->A);CHKERRQ(ierr); 1080 } 1081 /* 1082 An SF reduce is needed to sum up properly on shared rows. 1083 Note that generally preallocation is not exact, since it overestimates nonzeros 1084 */ 1085 ierr = MatISSetUpSF(A);CHKERRQ(ierr); 1086 ierr = MatGetLocalSize(A,&lrows,&lcols);CHKERRQ(ierr); 1087 ierr = MatPreallocateInitialize(PetscObjectComm((PetscObject)A),lrows,lcols,dnz,onz);CHKERRQ(ierr); 1088 /* All processes need to compute entire row ownership */ 1089 ierr = PetscMalloc1(rows,&row_ownership);CHKERRQ(ierr); 1090 ierr = MatGetOwnershipRanges(A,(const PetscInt**)&mat_ranges);CHKERRQ(ierr); 1091 for (i=0;i<nsubdomains;i++) { 1092 for (j=mat_ranges[i];j<mat_ranges[i+1];j++) { 1093 row_ownership[j] = i; 1094 } 1095 } 1096 ierr = MatGetOwnershipRangesColumn(A,(const PetscInt**)&mat_ranges);CHKERRQ(ierr); 1097 1098 /* 1099 my_dnz and my_onz contains exact contribution to preallocation from each local mat 1100 then, they will be summed up properly. This way, preallocation is always sufficient 1101 */ 1102 ierr = PetscCalloc2(local_rows,&my_dnz,local_rows,&my_onz);CHKERRQ(ierr); 1103 /* preallocation as a MATAIJ */ 1104 if (isdense) { /* special case for dense local matrices */ 1105 for (i=0;i<local_rows;i++) { 1106 PetscInt owner = row_ownership[global_indices_r[i]]; 1107 for (j=0;j<local_cols;j++) { 1108 PetscInt index_col = global_indices_c[j]; 1109 if (index_col > mat_ranges[owner]-1 && index_col < mat_ranges[owner+1] ) { /* diag block */ 1110 my_dnz[i] += 1; 1111 } else { /* offdiag block */ 1112 my_onz[i] += 1; 1113 } 1114 } 1115 } 1116 } else if (matis->A->ops->getrowij) { 1117 const PetscInt *ii,*jj,*jptr; 1118 PetscBool done; 1119 ierr = MatGetRowIJ(matis->A,0,PETSC_FALSE,PETSC_FALSE,&local_rows,&ii,&jj,&done);CHKERRQ(ierr); 1120 if (!done) SETERRQ(PetscObjectComm((PetscObject)(matis->A)),PETSC_ERR_PLIB,"Error in MatGetRowIJ"); 1121 jptr = jj; 1122 for (i=0;i<local_rows;i++) { 1123 PetscInt index_row = global_indices_r[i]; 1124 for (j=0;j<ii[i+1]-ii[i];j++,jptr++) { 1125 PetscInt owner = row_ownership[index_row]; 1126 PetscInt index_col = global_indices_c[*jptr]; 1127 if (index_col > mat_ranges[owner]-1 && index_col < mat_ranges[owner+1] ) { /* diag block */ 1128 my_dnz[i] += 1; 1129 } else { /* offdiag block */ 1130 my_onz[i] += 1; 1131 } 1132 /* same as before, interchanging rows and cols */ 1133 if (issbaij && index_col != index_row) { 1134 owner = row_ownership[index_col]; 1135 if (index_row > mat_ranges[owner]-1 && index_row < mat_ranges[owner+1] ) { 1136 my_dnz[*jptr] += 1; 1137 } else { 1138 my_onz[*jptr] += 1; 1139 } 1140 } 1141 } 1142 } 1143 ierr = MatRestoreRowIJ(matis->A,0,PETSC_FALSE,PETSC_FALSE,&local_rows,&ii,&jj,&done);CHKERRQ(ierr); 1144 if (!done) SETERRQ(PetscObjectComm((PetscObject)(matis->A)),PETSC_ERR_PLIB,"Error in MatRestoreRowIJ"); 1145 } else { /* loop over rows and use MatGetRow */ 1146 for (i=0;i<local_rows;i++) { 1147 const PetscInt *cols; 1148 PetscInt ncols,index_row = global_indices_r[i]; 1149 ierr = MatGetRow(matis->A,i,&ncols,&cols,NULL);CHKERRQ(ierr); 1150 for (j=0;j<ncols;j++) { 1151 PetscInt owner = row_ownership[index_row]; 1152 PetscInt index_col = global_indices_c[cols[j]]; 1153 if (index_col > mat_ranges[owner]-1 && index_col < mat_ranges[owner+1] ) { /* diag block */ 1154 my_dnz[i] += 1; 1155 } else { /* offdiag block */ 1156 my_onz[i] += 1; 1157 } 1158 /* same as before, interchanging rows and cols */ 1159 if (issbaij && index_col != index_row) { 1160 owner = row_ownership[index_col]; 1161 if (index_row > mat_ranges[owner]-1 && index_row < mat_ranges[owner+1] ) { 1162 my_dnz[cols[j]] += 1; 1163 } else { 1164 my_onz[cols[j]] += 1; 1165 } 1166 } 1167 } 1168 ierr = MatRestoreRow(matis->A,i,&ncols,&cols,NULL);CHKERRQ(ierr); 1169 } 1170 } 1171 if (global_indices_c != global_indices_r) { 1172 ierr = ISLocalToGlobalMappingRestoreIndices(A->cmap->mapping,&global_indices_c);CHKERRQ(ierr); 1173 } 1174 ierr = ISLocalToGlobalMappingRestoreIndices(A->rmap->mapping,&global_indices_r);CHKERRQ(ierr); 1175 ierr = PetscFree(row_ownership);CHKERRQ(ierr); 1176 1177 /* Reduce my_dnz and my_onz */ 1178 if (maxreduce) { 1179 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_dnz,dnz,MPI_MAX);CHKERRQ(ierr); 1180 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_onz,onz,MPI_MAX);CHKERRQ(ierr); 1181 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_dnz,dnz,MPI_MAX);CHKERRQ(ierr); 1182 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_onz,onz,MPI_MAX);CHKERRQ(ierr); 1183 } else { 1184 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_dnz,dnz,MPI_SUM);CHKERRQ(ierr); 1185 ierr = PetscSFReduceBegin(matis->sf,MPIU_INT,my_onz,onz,MPI_SUM);CHKERRQ(ierr); 1186 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_dnz,dnz,MPI_SUM);CHKERRQ(ierr); 1187 ierr = PetscSFReduceEnd(matis->sf,MPIU_INT,my_onz,onz,MPI_SUM);CHKERRQ(ierr); 1188 } 1189 ierr = PetscFree2(my_dnz,my_onz);CHKERRQ(ierr); 1190 1191 /* Resize preallocation if overestimated */ 1192 for (i=0;i<lrows;i++) { 1193 dnz[i] = PetscMin(dnz[i],lcols); 1194 onz[i] = PetscMin(onz[i],cols-lcols); 1195 } 1196 1197 /* Set preallocation */ 1198 ierr = MatMPIAIJSetPreallocation(B,0,dnz,0,onz);CHKERRQ(ierr); 1199 for (i=0;i<lrows/bs;i++) { 1200 dnz[i] = dnz[i*bs]/bs; 1201 onz[i] = onz[i*bs]/bs; 1202 } 1203 ierr = MatMPIBAIJSetPreallocation(B,bs,0,dnz,0,onz);CHKERRQ(ierr); 1204 ierr = MatMPISBAIJSetPreallocation(B,bs,0,dnz,0,onz);CHKERRQ(ierr); 1205 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 1206 if (issbaij) { 1207 ierr = MatRestoreRowUpperTriangular(matis->A);CHKERRQ(ierr); 1208 } 1209 PetscFunctionReturn(0); 1210 } 1211 1212 static PetscErrorCode MatISGetMPIXAIJ_IS(Mat mat, MatReuse reuse, Mat *M) 1213 { 1214 Mat_IS *matis = (Mat_IS*)(mat->data); 1215 Mat local_mat; 1216 /* info on mat */ 1217 PetscInt bs,rows,cols,lrows,lcols; 1218 PetscInt local_rows,local_cols; 1219 PetscBool isseqdense,isseqsbaij,isseqaij,isseqbaij; 1220 #if defined (PETSC_USE_DEBUG) 1221 PetscBool lb[4],bb[4]; 1222 #endif 1223 PetscMPIInt nsubdomains; 1224 /* values insertion */ 1225 PetscScalar *array; 1226 /* work */ 1227 PetscErrorCode ierr; 1228 1229 PetscFunctionBegin; 1230 /* get info from mat */ 1231 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)mat),&nsubdomains);CHKERRQ(ierr); 1232 if (nsubdomains == 1) { 1233 Mat B; 1234 IS rows,cols; 1235 IS irows,icols; 1236 const PetscInt *ridxs,*cidxs; 1237 1238 ierr = ISLocalToGlobalMappingGetIndices(mat->rmap->mapping,&ridxs);CHKERRQ(ierr); 1239 ierr = ISLocalToGlobalMappingGetIndices(mat->cmap->mapping,&cidxs);CHKERRQ(ierr); 1240 ierr = ISCreateGeneral(PETSC_COMM_SELF,mat->rmap->n,ridxs,PETSC_USE_POINTER,&rows);CHKERRQ(ierr); 1241 ierr = ISCreateGeneral(PETSC_COMM_SELF,mat->cmap->n,cidxs,PETSC_USE_POINTER,&cols);CHKERRQ(ierr); 1242 ierr = ISLocalToGlobalMappingRestoreIndices(mat->rmap->mapping,&ridxs);CHKERRQ(ierr); 1243 ierr = ISLocalToGlobalMappingRestoreIndices(mat->cmap->mapping,&cidxs);CHKERRQ(ierr); 1244 ierr = ISSetPermutation(rows);CHKERRQ(ierr); 1245 ierr = ISSetPermutation(cols);CHKERRQ(ierr); 1246 ierr = ISInvertPermutation(rows,mat->rmap->n,&irows);CHKERRQ(ierr); 1247 ierr = ISInvertPermutation(cols,mat->cmap->n,&icols);CHKERRQ(ierr); 1248 ierr = ISDestroy(&cols);CHKERRQ(ierr); 1249 ierr = ISDestroy(&rows);CHKERRQ(ierr); 1250 ierr = MatConvert(matis->A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 1251 ierr = MatCreateSubMatrix(B,irows,icols,reuse,M);CHKERRQ(ierr); 1252 ierr = MatDestroy(&B);CHKERRQ(ierr); 1253 ierr = ISDestroy(&icols);CHKERRQ(ierr); 1254 ierr = ISDestroy(&irows);CHKERRQ(ierr); 1255 PetscFunctionReturn(0); 1256 } 1257 ierr = MatGetSize(mat,&rows,&cols);CHKERRQ(ierr); 1258 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 1259 ierr = MatGetLocalSize(mat,&lrows,&lcols);CHKERRQ(ierr); 1260 ierr = MatGetSize(matis->A,&local_rows,&local_cols);CHKERRQ(ierr); 1261 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQDENSE,&isseqdense);CHKERRQ(ierr); 1262 ierr = PetscObjectBaseTypeCompare((PetscObject)matis->A,MATSEQAIJ,&isseqaij);CHKERRQ(ierr); 1263 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQBAIJ,&isseqbaij);CHKERRQ(ierr); 1264 ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQSBAIJ,&isseqsbaij);CHKERRQ(ierr); 1265 if (!isseqdense && !isseqaij && !isseqbaij && !isseqsbaij) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Not for matrix type %s",((PetscObject)(matis->A))->type_name); 1266 #if defined (PETSC_USE_DEBUG) 1267 lb[0] = isseqdense; 1268 lb[1] = isseqaij; 1269 lb[2] = isseqbaij; 1270 lb[3] = isseqsbaij; 1271 ierr = MPIU_Allreduce(lb,bb,4,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)mat));CHKERRQ(ierr); 1272 if (!bb[0] && !bb[1] && !bb[2] && !bb[3]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Local matrices must have the same type"); 1273 #endif 1274 1275 if (reuse == MAT_INITIAL_MATRIX) { 1276 ierr = MatCreate(PetscObjectComm((PetscObject)mat),M);CHKERRQ(ierr); 1277 ierr = MatSetSizes(*M,lrows,lcols,rows,cols);CHKERRQ(ierr); 1278 ierr = MatSetBlockSize(*M,bs);CHKERRQ(ierr); 1279 if (!isseqsbaij) { 1280 ierr = MatSetType(*M,MATAIJ);CHKERRQ(ierr); 1281 } else { 1282 ierr = MatSetType(*M,MATSBAIJ);CHKERRQ(ierr); 1283 } 1284 ierr = MatISSetMPIXAIJPreallocation_Private(mat,*M,PETSC_FALSE);CHKERRQ(ierr); 1285 } else { 1286 PetscInt mbs,mrows,mcols,mlrows,mlcols; 1287 /* some checks */ 1288 ierr = MatGetBlockSize(*M,&mbs);CHKERRQ(ierr); 1289 ierr = MatGetSize(*M,&mrows,&mcols);CHKERRQ(ierr); 1290 ierr = MatGetLocalSize(*M,&mlrows,&mlcols);CHKERRQ(ierr); 1291 if (mrows != rows) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of rows (%d != %d)",rows,mrows); 1292 if (mcols != cols) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of cols (%d != %d)",cols,mcols); 1293 if (mlrows != lrows) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of local rows (%d != %d)",lrows,mlrows); 1294 if (mlcols != lcols) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong number of local cols (%d != %d)",lcols,mlcols); 1295 if (mbs != bs) SETERRQ2(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse matrix. Wrong block size (%d != %d)",bs,mbs); 1296 ierr = MatZeroEntries(*M);CHKERRQ(ierr); 1297 } 1298 1299 if (isseqsbaij) { 1300 ierr = MatConvert(matis->A,MATSEQBAIJ,MAT_INITIAL_MATRIX,&local_mat);CHKERRQ(ierr); 1301 } else { 1302 ierr = PetscObjectReference((PetscObject)matis->A);CHKERRQ(ierr); 1303 local_mat = matis->A; 1304 } 1305 1306 /* Set values */ 1307 ierr = MatSetLocalToGlobalMapping(*M,mat->rmap->mapping,mat->cmap->mapping);CHKERRQ(ierr); 1308 if (isseqdense) { /* special case for dense local matrices */ 1309 PetscInt i,*dummy; 1310 1311 ierr = PetscMalloc1(PetscMax(local_rows,local_cols),&dummy);CHKERRQ(ierr); 1312 for (i=0;i<PetscMax(local_rows,local_cols);i++) dummy[i] = i; 1313 ierr = MatSetOption(*M,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr); 1314 ierr = MatDenseGetArray(local_mat,&array);CHKERRQ(ierr); 1315 ierr = MatSetValuesLocal(*M,local_rows,dummy,local_cols,dummy,array,ADD_VALUES);CHKERRQ(ierr); 1316 ierr = MatDenseRestoreArray(local_mat,&array);CHKERRQ(ierr); 1317 ierr = PetscFree(dummy);CHKERRQ(ierr); 1318 } else if (isseqaij) { 1319 PetscInt i,nvtxs,*xadj,*adjncy; 1320 PetscBool done; 1321 1322 ierr = MatGetRowIJ(local_mat,0,PETSC_FALSE,PETSC_FALSE,&nvtxs,(const PetscInt**)&xadj,(const PetscInt**)&adjncy,&done);CHKERRQ(ierr); 1323 if (!done) SETERRQ(PetscObjectComm((PetscObject)local_mat),PETSC_ERR_PLIB,"Error in MatGetRowIJ"); 1324 ierr = MatSeqAIJGetArray(local_mat,&array);CHKERRQ(ierr); 1325 for (i=0;i<nvtxs;i++) { 1326 ierr = MatSetValuesLocal(*M,1,&i,xadj[i+1]-xadj[i],adjncy+xadj[i],array+xadj[i],ADD_VALUES);CHKERRQ(ierr); 1327 } 1328 ierr = MatRestoreRowIJ(local_mat,0,PETSC_FALSE,PETSC_FALSE,&nvtxs,(const PetscInt**)&xadj,(const PetscInt**)&adjncy,&done);CHKERRQ(ierr); 1329 if (!done) SETERRQ(PetscObjectComm((PetscObject)local_mat),PETSC_ERR_PLIB,"Error in MatRestoreRowIJ"); 1330 ierr = MatSeqAIJRestoreArray(local_mat,&array);CHKERRQ(ierr); 1331 } else { /* very basic values insertion for all other matrix types */ 1332 PetscInt i; 1333 1334 for (i=0;i<local_rows;i++) { 1335 PetscInt j; 1336 const PetscInt *local_indices_cols; 1337 1338 ierr = MatGetRow(local_mat,i,&j,&local_indices_cols,(const PetscScalar**)&array);CHKERRQ(ierr); 1339 ierr = MatSetValuesLocal(*M,1,&i,j,local_indices_cols,array,ADD_VALUES);CHKERRQ(ierr); 1340 ierr = MatRestoreRow(local_mat,i,&j,&local_indices_cols,(const PetscScalar**)&array);CHKERRQ(ierr); 1341 } 1342 } 1343 ierr = MatAssemblyBegin(*M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1344 ierr = MatDestroy(&local_mat);CHKERRQ(ierr); 1345 ierr = MatAssemblyEnd(*M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1346 if (isseqdense) { 1347 ierr = MatSetOption(*M,MAT_ROW_ORIENTED,PETSC_TRUE);CHKERRQ(ierr); 1348 } 1349 PetscFunctionReturn(0); 1350 } 1351 1352 /*@ 1353 MatISGetMPIXAIJ - Converts MATIS matrix into a parallel AIJ format 1354 1355 Input Parameter: 1356 . mat - the matrix (should be of type MATIS) 1357 . reuse - either MAT_INITIAL_MATRIX or MAT_REUSE_MATRIX 1358 1359 Output Parameter: 1360 . newmat - the matrix in AIJ format 1361 1362 Level: developer 1363 1364 Notes: mat and *newmat cannot be the same object when MAT_REUSE_MATRIX is requested. 1365 1366 .seealso: MATIS 1367 @*/ 1368 PetscErrorCode MatISGetMPIXAIJ(Mat mat, MatReuse reuse, Mat *newmat) 1369 { 1370 PetscErrorCode ierr; 1371 1372 PetscFunctionBegin; 1373 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1374 PetscValidLogicalCollectiveEnum(mat,reuse,2); 1375 PetscValidPointer(newmat,3); 1376 if (reuse != MAT_INITIAL_MATRIX) { 1377 PetscValidHeaderSpecific(*newmat,MAT_CLASSID,3); 1378 PetscCheckSameComm(mat,1,*newmat,3); 1379 if (mat == *newmat) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot reuse the same matrix"); 1380 } 1381 ierr = PetscUseMethod(mat,"MatISGetMPIXAIJ_C",(Mat,MatReuse,Mat*),(mat,reuse,newmat));CHKERRQ(ierr); 1382 PetscFunctionReturn(0); 1383 } 1384 1385 PetscErrorCode MatDuplicate_IS(Mat mat,MatDuplicateOption op,Mat *newmat) 1386 { 1387 PetscErrorCode ierr; 1388 Mat_IS *matis = (Mat_IS*)(mat->data); 1389 PetscInt bs,m,n,M,N; 1390 Mat B,localmat; 1391 1392 PetscFunctionBegin; 1393 ierr = MatGetBlockSize(mat,&bs);CHKERRQ(ierr); 1394 ierr = MatGetSize(mat,&M,&N);CHKERRQ(ierr); 1395 ierr = MatGetLocalSize(mat,&m,&n);CHKERRQ(ierr); 1396 ierr = MatCreateIS(PetscObjectComm((PetscObject)mat),bs,m,n,M,N,mat->rmap->mapping,mat->cmap->mapping,&B);CHKERRQ(ierr); 1397 ierr = MatDuplicate(matis->A,op,&localmat);CHKERRQ(ierr); 1398 ierr = MatISSetLocalMat(B,localmat);CHKERRQ(ierr); 1399 ierr = MatDestroy(&localmat);CHKERRQ(ierr); 1400 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1401 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1402 *newmat = B; 1403 PetscFunctionReturn(0); 1404 } 1405 1406 static PetscErrorCode MatIsHermitian_IS(Mat A,PetscReal tol,PetscBool *flg) 1407 { 1408 PetscErrorCode ierr; 1409 Mat_IS *matis = (Mat_IS*)A->data; 1410 PetscBool local_sym; 1411 1412 PetscFunctionBegin; 1413 ierr = MatIsHermitian(matis->A,tol,&local_sym);CHKERRQ(ierr); 1414 ierr = MPIU_Allreduce(&local_sym,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1415 PetscFunctionReturn(0); 1416 } 1417 1418 static PetscErrorCode MatIsSymmetric_IS(Mat A,PetscReal tol,PetscBool *flg) 1419 { 1420 PetscErrorCode ierr; 1421 Mat_IS *matis = (Mat_IS*)A->data; 1422 PetscBool local_sym; 1423 1424 PetscFunctionBegin; 1425 ierr = MatIsSymmetric(matis->A,tol,&local_sym);CHKERRQ(ierr); 1426 ierr = MPIU_Allreduce(&local_sym,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1427 PetscFunctionReturn(0); 1428 } 1429 1430 static PetscErrorCode MatIsStructurallySymmetric_IS(Mat A,PetscBool *flg) 1431 { 1432 PetscErrorCode ierr; 1433 Mat_IS *matis = (Mat_IS*)A->data; 1434 PetscBool local_sym; 1435 1436 PetscFunctionBegin; 1437 if (A->rmap->mapping != A->cmap->mapping) { 1438 *flg = PETSC_FALSE; 1439 PetscFunctionReturn(0); 1440 } 1441 ierr = MatIsStructurallySymmetric(matis->A,&local_sym);CHKERRQ(ierr); 1442 ierr = MPIU_Allreduce(&local_sym,flg,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)A));CHKERRQ(ierr); 1443 PetscFunctionReturn(0); 1444 } 1445 1446 static PetscErrorCode MatDestroy_IS(Mat A) 1447 { 1448 PetscErrorCode ierr; 1449 Mat_IS *b = (Mat_IS*)A->data; 1450 1451 PetscFunctionBegin; 1452 ierr = MatDestroy(&b->A);CHKERRQ(ierr); 1453 ierr = VecScatterDestroy(&b->cctx);CHKERRQ(ierr); 1454 ierr = VecScatterDestroy(&b->rctx);CHKERRQ(ierr); 1455 ierr = VecDestroy(&b->x);CHKERRQ(ierr); 1456 ierr = VecDestroy(&b->y);CHKERRQ(ierr); 1457 ierr = VecDestroy(&b->counter);CHKERRQ(ierr); 1458 ierr = ISDestroy(&b->getsub_ris);CHKERRQ(ierr); 1459 ierr = ISDestroy(&b->getsub_cis);CHKERRQ(ierr); 1460 if (b->sf != b->csf) { 1461 ierr = PetscSFDestroy(&b->csf);CHKERRQ(ierr); 1462 ierr = PetscFree2(b->csf_rootdata,b->csf_leafdata);CHKERRQ(ierr); 1463 } 1464 ierr = PetscSFDestroy(&b->sf);CHKERRQ(ierr); 1465 ierr = PetscFree2(b->sf_rootdata,b->sf_leafdata);CHKERRQ(ierr); 1466 ierr = PetscFree(A->data);CHKERRQ(ierr); 1467 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 1468 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetLocalMat_C",NULL);CHKERRQ(ierr); 1469 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetLocalMat_C",NULL);CHKERRQ(ierr); 1470 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetMPIXAIJ_C",NULL);CHKERRQ(ierr); 1471 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetPreallocation_C",NULL);CHKERRQ(ierr); 1472 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetUpSF_C",NULL);CHKERRQ(ierr); 1473 PetscFunctionReturn(0); 1474 } 1475 1476 static PetscErrorCode MatMult_IS(Mat A,Vec x,Vec y) 1477 { 1478 PetscErrorCode ierr; 1479 Mat_IS *is = (Mat_IS*)A->data; 1480 PetscScalar zero = 0.0; 1481 1482 PetscFunctionBegin; 1483 /* scatter the global vector x into the local work vector */ 1484 ierr = VecScatterBegin(is->cctx,x,is->x,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1485 ierr = VecScatterEnd(is->cctx,x,is->x,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1486 1487 /* multiply the local matrix */ 1488 ierr = MatMult(is->A,is->x,is->y);CHKERRQ(ierr); 1489 1490 /* scatter product back into global memory */ 1491 ierr = VecSet(y,zero);CHKERRQ(ierr); 1492 ierr = VecScatterBegin(is->rctx,is->y,y,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1493 ierr = VecScatterEnd(is->rctx,is->y,y,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1494 PetscFunctionReturn(0); 1495 } 1496 1497 static PetscErrorCode MatMultAdd_IS(Mat A,Vec v1,Vec v2,Vec v3) 1498 { 1499 Vec temp_vec; 1500 PetscErrorCode ierr; 1501 1502 PetscFunctionBegin; /* v3 = v2 + A * v1.*/ 1503 if (v3 != v2) { 1504 ierr = MatMult(A,v1,v3);CHKERRQ(ierr); 1505 ierr = VecAXPY(v3,1.0,v2);CHKERRQ(ierr); 1506 } else { 1507 ierr = VecDuplicate(v2,&temp_vec);CHKERRQ(ierr); 1508 ierr = MatMult(A,v1,temp_vec);CHKERRQ(ierr); 1509 ierr = VecAXPY(temp_vec,1.0,v2);CHKERRQ(ierr); 1510 ierr = VecCopy(temp_vec,v3);CHKERRQ(ierr); 1511 ierr = VecDestroy(&temp_vec);CHKERRQ(ierr); 1512 } 1513 PetscFunctionReturn(0); 1514 } 1515 1516 static PetscErrorCode MatMultTranspose_IS(Mat A,Vec y,Vec x) 1517 { 1518 Mat_IS *is = (Mat_IS*)A->data; 1519 PetscErrorCode ierr; 1520 1521 PetscFunctionBegin; 1522 /* scatter the global vector x into the local work vector */ 1523 ierr = VecScatterBegin(is->rctx,y,is->y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1524 ierr = VecScatterEnd(is->rctx,y,is->y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1525 1526 /* multiply the local matrix */ 1527 ierr = MatMultTranspose(is->A,is->y,is->x);CHKERRQ(ierr); 1528 1529 /* scatter product back into global vector */ 1530 ierr = VecSet(x,0);CHKERRQ(ierr); 1531 ierr = VecScatterBegin(is->cctx,is->x,x,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1532 ierr = VecScatterEnd(is->cctx,is->x,x,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1533 PetscFunctionReturn(0); 1534 } 1535 1536 static PetscErrorCode MatMultTransposeAdd_IS(Mat A,Vec v1,Vec v2,Vec v3) 1537 { 1538 Vec temp_vec; 1539 PetscErrorCode ierr; 1540 1541 PetscFunctionBegin; /* v3 = v2 + A' * v1.*/ 1542 if (v3 != v2) { 1543 ierr = MatMultTranspose(A,v1,v3);CHKERRQ(ierr); 1544 ierr = VecAXPY(v3,1.0,v2);CHKERRQ(ierr); 1545 } else { 1546 ierr = VecDuplicate(v2,&temp_vec);CHKERRQ(ierr); 1547 ierr = MatMultTranspose(A,v1,temp_vec);CHKERRQ(ierr); 1548 ierr = VecAXPY(temp_vec,1.0,v2);CHKERRQ(ierr); 1549 ierr = VecCopy(temp_vec,v3);CHKERRQ(ierr); 1550 ierr = VecDestroy(&temp_vec);CHKERRQ(ierr); 1551 } 1552 PetscFunctionReturn(0); 1553 } 1554 1555 static PetscErrorCode MatView_IS(Mat A,PetscViewer viewer) 1556 { 1557 Mat_IS *a = (Mat_IS*)A->data; 1558 PetscErrorCode ierr; 1559 PetscViewer sviewer; 1560 PetscBool isascii,view = PETSC_TRUE; 1561 1562 PetscFunctionBegin; 1563 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&isascii);CHKERRQ(ierr); 1564 if (isascii) { 1565 PetscViewerFormat format; 1566 1567 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 1568 if (format == PETSC_VIEWER_ASCII_INFO) view = PETSC_FALSE; 1569 } 1570 if (!view) PetscFunctionReturn(0); 1571 ierr = PetscViewerGetSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1572 ierr = MatView(a->A,sviewer);CHKERRQ(ierr); 1573 ierr = PetscViewerRestoreSubViewer(viewer,PETSC_COMM_SELF,&sviewer);CHKERRQ(ierr); 1574 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 1575 PetscFunctionReturn(0); 1576 } 1577 1578 static PetscErrorCode MatSetLocalToGlobalMapping_IS(Mat A,ISLocalToGlobalMapping rmapping,ISLocalToGlobalMapping cmapping) 1579 { 1580 PetscErrorCode ierr; 1581 PetscInt nr,rbs,nc,cbs; 1582 Mat_IS *is = (Mat_IS*)A->data; 1583 IS from,to; 1584 Vec cglobal,rglobal; 1585 1586 PetscFunctionBegin; 1587 PetscCheckSameComm(A,1,rmapping,2); 1588 PetscCheckSameComm(A,1,cmapping,3); 1589 /* Destroy any previous data */ 1590 ierr = VecDestroy(&is->x);CHKERRQ(ierr); 1591 ierr = VecDestroy(&is->y);CHKERRQ(ierr); 1592 ierr = VecDestroy(&is->counter);CHKERRQ(ierr); 1593 ierr = VecScatterDestroy(&is->rctx);CHKERRQ(ierr); 1594 ierr = VecScatterDestroy(&is->cctx);CHKERRQ(ierr); 1595 ierr = MatDestroy(&is->A);CHKERRQ(ierr); 1596 if (is->csf != is->sf) { 1597 ierr = PetscSFDestroy(&is->csf);CHKERRQ(ierr); 1598 ierr = PetscFree2(is->csf_rootdata,is->csf_leafdata);CHKERRQ(ierr); 1599 } 1600 ierr = PetscSFDestroy(&is->sf);CHKERRQ(ierr); 1601 ierr = PetscFree2(is->sf_rootdata,is->sf_leafdata);CHKERRQ(ierr); 1602 1603 /* Setup Layout and set local to global maps */ 1604 ierr = PetscLayoutSetUp(A->rmap);CHKERRQ(ierr); 1605 ierr = PetscLayoutSetUp(A->cmap);CHKERRQ(ierr); 1606 ierr = PetscLayoutSetISLocalToGlobalMapping(A->rmap,rmapping);CHKERRQ(ierr); 1607 ierr = PetscLayoutSetISLocalToGlobalMapping(A->cmap,cmapping);CHKERRQ(ierr); 1608 1609 /* Create the local matrix A */ 1610 ierr = ISLocalToGlobalMappingGetSize(rmapping,&nr);CHKERRQ(ierr); 1611 ierr = ISLocalToGlobalMappingGetBlockSize(rmapping,&rbs);CHKERRQ(ierr); 1612 ierr = ISLocalToGlobalMappingGetSize(cmapping,&nc);CHKERRQ(ierr); 1613 ierr = ISLocalToGlobalMappingGetBlockSize(cmapping,&cbs);CHKERRQ(ierr); 1614 ierr = MatCreate(PETSC_COMM_SELF,&is->A);CHKERRQ(ierr); 1615 ierr = MatSetType(is->A,MATAIJ);CHKERRQ(ierr); 1616 ierr = MatSetSizes(is->A,nr,nc,nr,nc);CHKERRQ(ierr); 1617 ierr = MatSetBlockSizes(is->A,rbs,cbs);CHKERRQ(ierr); 1618 ierr = MatSetOptionsPrefix(is->A,((PetscObject)A)->prefix);CHKERRQ(ierr); 1619 ierr = MatAppendOptionsPrefix(is->A,"is_");CHKERRQ(ierr); 1620 ierr = MatSetFromOptions(is->A);CHKERRQ(ierr); 1621 ierr = PetscLayoutSetUp(is->A->rmap);CHKERRQ(ierr); 1622 ierr = PetscLayoutSetUp(is->A->cmap);CHKERRQ(ierr); 1623 1624 if (!is->islocalref) { /* setup scatters and local vectors for MatMult */ 1625 /* Create the local work vectors */ 1626 ierr = MatCreateVecs(is->A,&is->x,&is->y);CHKERRQ(ierr); 1627 1628 /* setup the global to local scatters */ 1629 ierr = MatCreateVecs(A,&cglobal,&rglobal);CHKERRQ(ierr); 1630 ierr = ISCreateStride(PETSC_COMM_SELF,nr,0,1,&to);CHKERRQ(ierr); 1631 ierr = ISLocalToGlobalMappingApplyIS(rmapping,to,&from);CHKERRQ(ierr); 1632 ierr = VecScatterCreate(rglobal,from,is->y,to,&is->rctx);CHKERRQ(ierr); 1633 if (rmapping != cmapping) { 1634 ierr = ISDestroy(&to);CHKERRQ(ierr); 1635 ierr = ISDestroy(&from);CHKERRQ(ierr); 1636 ierr = ISCreateStride(PETSC_COMM_SELF,nc,0,1,&to);CHKERRQ(ierr); 1637 ierr = ISLocalToGlobalMappingApplyIS(cmapping,to,&from);CHKERRQ(ierr); 1638 ierr = VecScatterCreate(cglobal,from,is->x,to,&is->cctx);CHKERRQ(ierr); 1639 } else { 1640 ierr = PetscObjectReference((PetscObject)is->rctx);CHKERRQ(ierr); 1641 is->cctx = is->rctx; 1642 } 1643 1644 /* interface counter vector (local) */ 1645 ierr = VecDuplicate(is->y,&is->counter);CHKERRQ(ierr); 1646 ierr = VecSet(is->y,1.);CHKERRQ(ierr); 1647 ierr = VecScatterBegin(is->rctx,is->y,rglobal,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1648 ierr = VecScatterEnd(is->rctx,is->y,rglobal,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1649 ierr = VecScatterBegin(is->rctx,rglobal,is->counter,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1650 ierr = VecScatterEnd(is->rctx,rglobal,is->counter,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1651 1652 /* free workspace */ 1653 ierr = VecDestroy(&rglobal);CHKERRQ(ierr); 1654 ierr = VecDestroy(&cglobal);CHKERRQ(ierr); 1655 ierr = ISDestroy(&to);CHKERRQ(ierr); 1656 ierr = ISDestroy(&from);CHKERRQ(ierr); 1657 } 1658 ierr = MatSetUp(A);CHKERRQ(ierr); 1659 PetscFunctionReturn(0); 1660 } 1661 1662 static PetscErrorCode MatSetValues_IS(Mat mat, PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols, const PetscScalar *values, InsertMode addv) 1663 { 1664 Mat_IS *is = (Mat_IS*)mat->data; 1665 PetscErrorCode ierr; 1666 #if defined(PETSC_USE_DEBUG) 1667 PetscInt i,zm,zn; 1668 #endif 1669 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 1670 1671 PetscFunctionBegin; 1672 #if defined(PETSC_USE_DEBUG) 1673 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); 1674 /* count negative indices */ 1675 for (i=0,zm=0;i<m;i++) if (rows[i] < 0) zm++; 1676 for (i=0,zn=0;i<n;i++) if (cols[i] < 0) zn++; 1677 #endif 1678 ierr = ISGlobalToLocalMappingApply(mat->rmap->mapping,IS_GTOLM_MASK,m,rows,&m,rows_l);CHKERRQ(ierr); 1679 ierr = ISGlobalToLocalMappingApply(mat->cmap->mapping,IS_GTOLM_MASK,n,cols,&n,cols_l);CHKERRQ(ierr); 1680 #if defined(PETSC_USE_DEBUG) 1681 /* count negative indices (should be the same as before) */ 1682 for (i=0;i<m;i++) if (rows_l[i] < 0) zm--; 1683 for (i=0;i<n;i++) if (cols_l[i] < 0) zn--; 1684 /* disable check when usesetlocal is true */ 1685 if (!is->usesetlocal && zm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the row indices can not be mapped! Maybe you should not use MATIS"); 1686 if (!is->usesetlocal && zn) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the column indices can not be mapped! Maybe you should not use MATIS"); 1687 #endif 1688 if (is->usesetlocal) { 1689 ierr = MatSetValuesLocal(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 1690 } else { 1691 ierr = MatSetValues(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 1692 } 1693 PetscFunctionReturn(0); 1694 } 1695 1696 static PetscErrorCode MatSetValuesBlocked_IS(Mat mat, PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols, const PetscScalar *values, InsertMode addv) 1697 { 1698 Mat_IS *is = (Mat_IS*)mat->data; 1699 PetscErrorCode ierr; 1700 #if defined(PETSC_USE_DEBUG) 1701 PetscInt i,zm,zn; 1702 #endif 1703 PetscInt rows_l[MATIS_MAX_ENTRIES_INSERTION],cols_l[MATIS_MAX_ENTRIES_INSERTION]; 1704 1705 PetscFunctionBegin; 1706 #if defined(PETSC_USE_DEBUG) 1707 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); 1708 /* count negative indices */ 1709 for (i=0,zm=0;i<m;i++) if (rows[i] < 0) zm++; 1710 for (i=0,zn=0;i<n;i++) if (cols[i] < 0) zn++; 1711 #endif 1712 ierr = ISGlobalToLocalMappingApplyBlock(mat->rmap->mapping,IS_GTOLM_MASK,m,rows,&m,rows_l);CHKERRQ(ierr); 1713 ierr = ISGlobalToLocalMappingApplyBlock(mat->cmap->mapping,IS_GTOLM_MASK,n,cols,&n,cols_l);CHKERRQ(ierr); 1714 #if defined(PETSC_USE_DEBUG) 1715 /* count negative indices (should be the same as before) */ 1716 for (i=0;i<m;i++) if (rows_l[i] < 0) zm--; 1717 for (i=0;i<n;i++) if (cols_l[i] < 0) zn--; 1718 if (zm) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the row indices can not be mapped! Maybe you should not use MATIS"); 1719 if (zn) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Some of the column indices can not be mapped! Maybe you should not use MATIS"); 1720 #endif 1721 ierr = MatSetValuesBlocked(is->A,m,rows_l,n,cols_l,values,addv);CHKERRQ(ierr); 1722 PetscFunctionReturn(0); 1723 } 1724 1725 static PetscErrorCode MatSetValuesLocal_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 1726 { 1727 PetscErrorCode ierr; 1728 Mat_IS *is = (Mat_IS*)A->data; 1729 1730 PetscFunctionBegin; 1731 if (is->usesetlocal) { 1732 ierr = MatSetValuesLocal(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr); 1733 } else { 1734 ierr = MatSetValues(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr); 1735 } 1736 PetscFunctionReturn(0); 1737 } 1738 1739 static PetscErrorCode MatSetValuesBlockedLocal_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv) 1740 { 1741 PetscErrorCode ierr; 1742 Mat_IS *is = (Mat_IS*)A->data; 1743 1744 PetscFunctionBegin; 1745 ierr = MatSetValuesBlocked(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr); 1746 PetscFunctionReturn(0); 1747 } 1748 1749 static PetscErrorCode MatISZeroRowsColumnsLocal_Private(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,PetscBool columns) 1750 { 1751 Mat_IS *is = (Mat_IS*)A->data; 1752 PetscErrorCode ierr; 1753 1754 PetscFunctionBegin; 1755 if (!n) { 1756 is->pure_neumann = PETSC_TRUE; 1757 } else { 1758 PetscInt i; 1759 is->pure_neumann = PETSC_FALSE; 1760 1761 if (columns) { 1762 ierr = MatZeroRowsColumns(is->A,n,rows,diag,0,0);CHKERRQ(ierr); 1763 } else { 1764 ierr = MatZeroRows(is->A,n,rows,diag,0,0);CHKERRQ(ierr); 1765 } 1766 if (diag != 0.) { 1767 const PetscScalar *array; 1768 ierr = VecGetArrayRead(is->counter,&array);CHKERRQ(ierr); 1769 for (i=0; i<n; i++) { 1770 ierr = MatSetValue(is->A,rows[i],rows[i],diag/(array[rows[i]]),INSERT_VALUES);CHKERRQ(ierr); 1771 } 1772 ierr = VecRestoreArrayRead(is->counter,&array);CHKERRQ(ierr); 1773 } 1774 ierr = MatAssemblyBegin(is->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1775 ierr = MatAssemblyEnd(is->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1776 } 1777 PetscFunctionReturn(0); 1778 } 1779 1780 static PetscErrorCode MatZeroRowsColumns_Private_IS(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,Vec x,Vec b,PetscBool columns) 1781 { 1782 Mat_IS *matis = (Mat_IS*)A->data; 1783 PetscInt nr,nl,len,i; 1784 PetscInt *lrows; 1785 PetscErrorCode ierr; 1786 1787 PetscFunctionBegin; 1788 #if defined(PETSC_USE_DEBUG) 1789 if (columns || diag != 0. || (x && b)) { 1790 PetscBool cong; 1791 ierr = PetscLayoutCompare(A->rmap,A->cmap,&cong);CHKERRQ(ierr); 1792 if (!cong && columns) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Columns can be zeroed if and only if A->rmap and A->cmap are congruent for MATIS"); 1793 if (!cong && diag != 0.) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"Nonzero diagonal value supported if and only if A->rmap and A->cmap are congruent for MATIS"); 1794 if (!cong && x && b) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_SUP,"A->rmap and A->cmap need to be congruent"); 1795 } 1796 #endif 1797 /* get locally owned rows */ 1798 ierr = PetscLayoutMapLocal_Private(A->rmap,n,rows,&len,&lrows,NULL);CHKERRQ(ierr); 1799 /* fix right hand side if needed */ 1800 if (x && b) { 1801 const PetscScalar *xx; 1802 PetscScalar *bb; 1803 1804 ierr = VecGetArrayRead(x, &xx);CHKERRQ(ierr); 1805 ierr = VecGetArray(b, &bb);CHKERRQ(ierr); 1806 for (i=0;i<len;++i) bb[lrows[i]] = diag*xx[lrows[i]]; 1807 ierr = VecRestoreArrayRead(x, &xx);CHKERRQ(ierr); 1808 ierr = VecRestoreArray(b, &bb);CHKERRQ(ierr); 1809 } 1810 /* get rows associated to the local matrices */ 1811 ierr = MatISSetUpSF(A);CHKERRQ(ierr); 1812 ierr = MatGetSize(matis->A,&nl,NULL);CHKERRQ(ierr); 1813 ierr = PetscMemzero(matis->sf_leafdata,nl*sizeof(PetscInt));CHKERRQ(ierr); 1814 ierr = PetscMemzero(matis->sf_rootdata,A->rmap->n*sizeof(PetscInt));CHKERRQ(ierr); 1815 for (i=0;i<len;i++) matis->sf_rootdata[lrows[i]] = 1; 1816 ierr = PetscFree(lrows);CHKERRQ(ierr); 1817 ierr = PetscSFBcastBegin(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1818 ierr = PetscSFBcastEnd(matis->sf,MPIU_INT,matis->sf_rootdata,matis->sf_leafdata);CHKERRQ(ierr); 1819 ierr = PetscMalloc1(nl,&lrows);CHKERRQ(ierr); 1820 for (i=0,nr=0;i<nl;i++) if (matis->sf_leafdata[i]) lrows[nr++] = i; 1821 ierr = MatISZeroRowsColumnsLocal_Private(A,nr,lrows,diag,columns);CHKERRQ(ierr); 1822 ierr = PetscFree(lrows);CHKERRQ(ierr); 1823 PetscFunctionReturn(0); 1824 } 1825 1826 static PetscErrorCode MatZeroRows_IS(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1827 { 1828 PetscErrorCode ierr; 1829 1830 PetscFunctionBegin; 1831 ierr = MatZeroRowsColumns_Private_IS(A,n,rows,diag,x,b,PETSC_FALSE);CHKERRQ(ierr); 1832 PetscFunctionReturn(0); 1833 } 1834 1835 static PetscErrorCode MatZeroRowsColumns_IS(Mat A,PetscInt n,const PetscInt rows[],PetscScalar diag,Vec x,Vec b) 1836 { 1837 PetscErrorCode ierr; 1838 1839 PetscFunctionBegin; 1840 ierr = MatZeroRowsColumns_Private_IS(A,n,rows,diag,x,b,PETSC_TRUE);CHKERRQ(ierr); 1841 PetscFunctionReturn(0); 1842 } 1843 1844 static PetscErrorCode MatAssemblyBegin_IS(Mat A,MatAssemblyType type) 1845 { 1846 Mat_IS *is = (Mat_IS*)A->data; 1847 PetscErrorCode ierr; 1848 1849 PetscFunctionBegin; 1850 ierr = MatAssemblyBegin(is->A,type);CHKERRQ(ierr); 1851 PetscFunctionReturn(0); 1852 } 1853 1854 static PetscErrorCode MatAssemblyEnd_IS(Mat A,MatAssemblyType type) 1855 { 1856 Mat_IS *is = (Mat_IS*)A->data; 1857 PetscErrorCode ierr; 1858 1859 PetscFunctionBegin; 1860 ierr = MatAssemblyEnd(is->A,type);CHKERRQ(ierr); 1861 /* fix for local empty rows/cols */ 1862 if (is->locempty && type == MAT_FINAL_ASSEMBLY) { 1863 Mat newlA; 1864 ISLocalToGlobalMapping l2g; 1865 IS tis; 1866 const PetscScalar *v; 1867 PetscInt i,n,cf,*loce,*locf; 1868 PetscBool sym; 1869 1870 ierr = MatGetRowMaxAbs(is->A,is->y,NULL);CHKERRQ(ierr); 1871 ierr = MatIsSymmetric(is->A,PETSC_SMALL,&sym);CHKERRQ(ierr); 1872 if (!sym) SETERRQ(PetscObjectComm((PetscObject)is->A),PETSC_ERR_SUP,"Not yet implemented for unsymmetric case"); 1873 ierr = VecGetLocalSize(is->y,&n);CHKERRQ(ierr); 1874 ierr = PetscMalloc1(n,&loce);CHKERRQ(ierr); 1875 ierr = PetscMalloc1(n,&locf);CHKERRQ(ierr); 1876 ierr = VecGetArrayRead(is->y,&v);CHKERRQ(ierr); 1877 for (i=0,cf=0;i<n;i++) { 1878 if (v[i] == 0.0) { 1879 loce[i] = -1; 1880 } else { 1881 loce[i] = cf; 1882 locf[cf++] = i; 1883 } 1884 } 1885 ierr = VecRestoreArrayRead(is->y,&v);CHKERRQ(ierr); 1886 /* extract valid submatrix */ 1887 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)is->A),cf,locf,PETSC_USE_POINTER,&tis);CHKERRQ(ierr); 1888 ierr = MatCreateSubMatrix(is->A,tis,tis,MAT_INITIAL_MATRIX,&newlA);CHKERRQ(ierr); 1889 ierr = ISDestroy(&tis);CHKERRQ(ierr); 1890 /* attach local l2g map for successive calls of MatSetValues */ 1891 ierr = ISLocalToGlobalMappingCreate(PetscObjectComm((PetscObject)is->A),1,n,loce,PETSC_OWN_POINTER,&l2g);CHKERRQ(ierr); 1892 ierr = MatSetLocalToGlobalMapping(newlA,l2g,l2g);CHKERRQ(ierr); 1893 ierr = ISLocalToGlobalMappingDestroy(&l2g);CHKERRQ(ierr); 1894 /* flag MatSetValues */ 1895 is->usesetlocal = PETSC_TRUE; 1896 /* attach new global l2g map */ 1897 ierr = ISLocalToGlobalMappingApply(A->rmap->mapping,cf,locf,locf);CHKERRQ(ierr); 1898 ierr = ISLocalToGlobalMappingCreate(PetscObjectComm((PetscObject)A),1,cf,locf,PETSC_OWN_POINTER,&l2g);CHKERRQ(ierr); 1899 ierr = MatSetLocalToGlobalMapping(A,l2g,l2g);CHKERRQ(ierr); 1900 ierr = MatISSetLocalMat(A,newlA);CHKERRQ(ierr); 1901 ierr = MatDestroy(&newlA);CHKERRQ(ierr); 1902 ierr = ISLocalToGlobalMappingDestroy(&l2g);CHKERRQ(ierr); 1903 } 1904 is->locempty = PETSC_FALSE; 1905 PetscFunctionReturn(0); 1906 } 1907 1908 static PetscErrorCode MatISGetLocalMat_IS(Mat mat,Mat *local) 1909 { 1910 Mat_IS *is = (Mat_IS*)mat->data; 1911 1912 PetscFunctionBegin; 1913 *local = is->A; 1914 PetscFunctionReturn(0); 1915 } 1916 1917 static PetscErrorCode MatISRestoreLocalMat_IS(Mat mat,Mat *local) 1918 { 1919 PetscFunctionBegin; 1920 *local = NULL; 1921 PetscFunctionReturn(0); 1922 } 1923 1924 /*@ 1925 MatISGetLocalMat - Gets the local matrix stored inside a MATIS matrix. 1926 1927 Input Parameter: 1928 . mat - the matrix 1929 1930 Output Parameter: 1931 . local - the local matrix 1932 1933 Level: advanced 1934 1935 Notes: 1936 This can be called if you have precomputed the nonzero structure of the 1937 matrix and want to provide it to the inner matrix object to improve the performance 1938 of the MatSetValues() operation. 1939 1940 Call MatISRestoreLocalMat() when finished with the local matrix. 1941 1942 .seealso: MATIS 1943 @*/ 1944 PetscErrorCode MatISGetLocalMat(Mat mat,Mat *local) 1945 { 1946 PetscErrorCode ierr; 1947 1948 PetscFunctionBegin; 1949 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1950 PetscValidPointer(local,2); 1951 ierr = PetscUseMethod(mat,"MatISGetLocalMat_C",(Mat,Mat*),(mat,local));CHKERRQ(ierr); 1952 PetscFunctionReturn(0); 1953 } 1954 1955 /*@ 1956 MatISRestoreLocalMat - Restores the local matrix obtained with MatISGetLocalMat() 1957 1958 Input Parameter: 1959 . mat - the matrix 1960 1961 Output Parameter: 1962 . local - the local matrix 1963 1964 Level: advanced 1965 1966 .seealso: MATIS 1967 @*/ 1968 PetscErrorCode MatISRestoreLocalMat(Mat mat,Mat *local) 1969 { 1970 PetscErrorCode ierr; 1971 1972 PetscFunctionBegin; 1973 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1974 PetscValidPointer(local,2); 1975 ierr = PetscUseMethod(mat,"MatISRestoreLocalMat_C",(Mat,Mat*),(mat,local));CHKERRQ(ierr); 1976 PetscFunctionReturn(0); 1977 } 1978 1979 static PetscErrorCode MatISSetLocalMat_IS(Mat mat,Mat local) 1980 { 1981 Mat_IS *is = (Mat_IS*)mat->data; 1982 PetscInt nrows,ncols,orows,ocols; 1983 PetscErrorCode ierr; 1984 1985 PetscFunctionBegin; 1986 if (is->A) { 1987 ierr = MatGetSize(is->A,&orows,&ocols);CHKERRQ(ierr); 1988 ierr = MatGetSize(local,&nrows,&ncols);CHKERRQ(ierr); 1989 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); 1990 } 1991 ierr = PetscObjectReference((PetscObject)local);CHKERRQ(ierr); 1992 ierr = MatDestroy(&is->A);CHKERRQ(ierr); 1993 is->A = local; 1994 PetscFunctionReturn(0); 1995 } 1996 1997 /*@ 1998 MatISSetLocalMat - Replace the local matrix stored inside a MATIS object. 1999 2000 Input Parameter: 2001 . mat - the matrix 2002 . local - the local matrix 2003 2004 Output Parameter: 2005 2006 Level: advanced 2007 2008 Notes: 2009 This can be called if you have precomputed the local matrix and 2010 want to provide it to the matrix object MATIS. 2011 2012 .seealso: MATIS 2013 @*/ 2014 PetscErrorCode MatISSetLocalMat(Mat mat,Mat local) 2015 { 2016 PetscErrorCode ierr; 2017 2018 PetscFunctionBegin; 2019 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 2020 PetscValidHeaderSpecific(local,MAT_CLASSID,2); 2021 ierr = PetscUseMethod(mat,"MatISSetLocalMat_C",(Mat,Mat),(mat,local));CHKERRQ(ierr); 2022 PetscFunctionReturn(0); 2023 } 2024 2025 static PetscErrorCode MatZeroEntries_IS(Mat A) 2026 { 2027 Mat_IS *a = (Mat_IS*)A->data; 2028 PetscErrorCode ierr; 2029 2030 PetscFunctionBegin; 2031 ierr = MatZeroEntries(a->A);CHKERRQ(ierr); 2032 PetscFunctionReturn(0); 2033 } 2034 2035 static PetscErrorCode MatScale_IS(Mat A,PetscScalar a) 2036 { 2037 Mat_IS *is = (Mat_IS*)A->data; 2038 PetscErrorCode ierr; 2039 2040 PetscFunctionBegin; 2041 ierr = MatScale(is->A,a);CHKERRQ(ierr); 2042 PetscFunctionReturn(0); 2043 } 2044 2045 static PetscErrorCode MatGetDiagonal_IS(Mat A, Vec v) 2046 { 2047 Mat_IS *is = (Mat_IS*)A->data; 2048 PetscErrorCode ierr; 2049 2050 PetscFunctionBegin; 2051 /* get diagonal of the local matrix */ 2052 ierr = MatGetDiagonal(is->A,is->y);CHKERRQ(ierr); 2053 2054 /* scatter diagonal back into global vector */ 2055 ierr = VecSet(v,0);CHKERRQ(ierr); 2056 ierr = VecScatterBegin(is->rctx,is->y,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 2057 ierr = VecScatterEnd(is->rctx,is->y,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 2058 PetscFunctionReturn(0); 2059 } 2060 2061 static PetscErrorCode MatSetOption_IS(Mat A,MatOption op,PetscBool flg) 2062 { 2063 Mat_IS *a = (Mat_IS*)A->data; 2064 PetscErrorCode ierr; 2065 2066 PetscFunctionBegin; 2067 ierr = MatSetOption(a->A,op,flg);CHKERRQ(ierr); 2068 PetscFunctionReturn(0); 2069 } 2070 2071 static PetscErrorCode MatAXPY_IS(Mat Y,PetscScalar a,Mat X,MatStructure str) 2072 { 2073 Mat_IS *y = (Mat_IS*)Y->data; 2074 Mat_IS *x; 2075 #if defined(PETSC_USE_DEBUG) 2076 PetscBool ismatis; 2077 #endif 2078 PetscErrorCode ierr; 2079 2080 PetscFunctionBegin; 2081 #if defined(PETSC_USE_DEBUG) 2082 ierr = PetscObjectTypeCompare((PetscObject)X,MATIS,&ismatis);CHKERRQ(ierr); 2083 if (!ismatis) SETERRQ(PetscObjectComm((PetscObject)Y),PETSC_ERR_SUP,"Cannot call MatAXPY(Y,a,X,str) with X not of type MATIS"); 2084 #endif 2085 x = (Mat_IS*)X->data; 2086 ierr = MatAXPY(y->A,a,x->A,str);CHKERRQ(ierr); 2087 PetscFunctionReturn(0); 2088 } 2089 2090 static PetscErrorCode MatGetLocalSubMatrix_IS(Mat A,IS row,IS col,Mat *submat) 2091 { 2092 Mat lA; 2093 Mat_IS *matis; 2094 ISLocalToGlobalMapping rl2g,cl2g; 2095 IS is; 2096 const PetscInt *rg,*rl; 2097 PetscInt nrg; 2098 PetscInt N,M,nrl,i,*idxs; 2099 PetscErrorCode ierr; 2100 2101 PetscFunctionBegin; 2102 ierr = ISLocalToGlobalMappingGetIndices(A->rmap->mapping,&rg);CHKERRQ(ierr); 2103 ierr = ISGetLocalSize(row,&nrl);CHKERRQ(ierr); 2104 ierr = ISGetIndices(row,&rl);CHKERRQ(ierr); 2105 ierr = ISLocalToGlobalMappingGetSize(A->rmap->mapping,&nrg);CHKERRQ(ierr); 2106 #if defined(PETSC_USE_DEBUG) 2107 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); 2108 #endif 2109 ierr = PetscMalloc1(nrg,&idxs);CHKERRQ(ierr); 2110 /* map from [0,nrl) to row */ 2111 for (i=0;i<nrl;i++) idxs[i] = rl[i]; 2112 #if defined(PETSC_USE_DEBUG) 2113 for (i=nrl;i<nrg;i++) idxs[i] = nrg; 2114 #else 2115 for (i=nrl;i<nrg;i++) idxs[i] = -1; 2116 #endif 2117 ierr = ISRestoreIndices(row,&rl);CHKERRQ(ierr); 2118 ierr = ISLocalToGlobalMappingRestoreIndices(A->rmap->mapping,&rg);CHKERRQ(ierr); 2119 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),nrg,idxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 2120 ierr = ISLocalToGlobalMappingCreateIS(is,&rl2g);CHKERRQ(ierr); 2121 ierr = ISDestroy(&is);CHKERRQ(ierr); 2122 /* compute new l2g map for columns */ 2123 if (col != row || A->rmap->mapping != A->cmap->mapping) { 2124 const PetscInt *cg,*cl; 2125 PetscInt ncg; 2126 PetscInt ncl; 2127 2128 ierr = ISLocalToGlobalMappingGetIndices(A->cmap->mapping,&cg);CHKERRQ(ierr); 2129 ierr = ISGetLocalSize(col,&ncl);CHKERRQ(ierr); 2130 ierr = ISGetIndices(col,&cl);CHKERRQ(ierr); 2131 ierr = ISLocalToGlobalMappingGetSize(A->cmap->mapping,&ncg);CHKERRQ(ierr); 2132 #if defined(PETSC_USE_DEBUG) 2133 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); 2134 #endif 2135 ierr = PetscMalloc1(ncg,&idxs);CHKERRQ(ierr); 2136 /* map from [0,ncl) to col */ 2137 for (i=0;i<ncl;i++) idxs[i] = cl[i]; 2138 #if defined(PETSC_USE_DEBUG) 2139 for (i=ncl;i<ncg;i++) idxs[i] = ncg; 2140 #else 2141 for (i=ncl;i<ncg;i++) idxs[i] = -1; 2142 #endif 2143 ierr = ISRestoreIndices(col,&cl);CHKERRQ(ierr); 2144 ierr = ISLocalToGlobalMappingRestoreIndices(A->cmap->mapping,&cg);CHKERRQ(ierr); 2145 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)A),ncg,idxs,PETSC_OWN_POINTER,&is);CHKERRQ(ierr); 2146 ierr = ISLocalToGlobalMappingCreateIS(is,&cl2g);CHKERRQ(ierr); 2147 ierr = ISDestroy(&is);CHKERRQ(ierr); 2148 } else { 2149 ierr = PetscObjectReference((PetscObject)rl2g);CHKERRQ(ierr); 2150 cl2g = rl2g; 2151 } 2152 /* create the MATIS submatrix */ 2153 ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr); 2154 ierr = MatCreate(PetscObjectComm((PetscObject)A),submat);CHKERRQ(ierr); 2155 ierr = MatSetSizes(*submat,PETSC_DECIDE,PETSC_DECIDE,M,N);CHKERRQ(ierr); 2156 ierr = MatSetType(*submat,MATIS);CHKERRQ(ierr); 2157 matis = (Mat_IS*)((*submat)->data); 2158 matis->islocalref = PETSC_TRUE; 2159 ierr = MatSetLocalToGlobalMapping(*submat,rl2g,cl2g);CHKERRQ(ierr); 2160 ierr = MatISGetLocalMat(A,&lA);CHKERRQ(ierr); 2161 ierr = MatISSetLocalMat(*submat,lA);CHKERRQ(ierr); 2162 ierr = MatSetUp(*submat);CHKERRQ(ierr); 2163 ierr = MatAssemblyBegin(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2164 ierr = MatAssemblyEnd(*submat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2165 ierr = ISLocalToGlobalMappingDestroy(&rl2g);CHKERRQ(ierr); 2166 ierr = ISLocalToGlobalMappingDestroy(&cl2g);CHKERRQ(ierr); 2167 /* remove unsupported ops */ 2168 ierr = PetscMemzero((*submat)->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2169 (*submat)->ops->destroy = MatDestroy_IS; 2170 (*submat)->ops->setvalueslocal = MatSetValuesLocal_SubMat_IS; 2171 (*submat)->ops->setvaluesblockedlocal = MatSetValuesBlockedLocal_SubMat_IS; 2172 (*submat)->ops->assemblybegin = MatAssemblyBegin_IS; 2173 (*submat)->ops->assemblyend = MatAssemblyEnd_IS; 2174 PetscFunctionReturn(0); 2175 } 2176 2177 static PetscErrorCode MatSetFromOptions_IS(PetscOptionItems *PetscOptionsObject, Mat A) 2178 { 2179 Mat_IS *a = (Mat_IS*)A->data; 2180 PetscErrorCode ierr; 2181 2182 PetscFunctionBegin; 2183 ierr = PetscOptionsHead(PetscOptionsObject,"MATIS options");CHKERRQ(ierr); 2184 ierr = PetscObjectOptionsBegin((PetscObject)A); 2185 ierr = PetscOptionsBool("-matis_fixempty","Fix local matrices in case of empty local rows/columns",NULL,a->locempty,&a->locempty,NULL);CHKERRQ(ierr); 2186 ierr = PetscOptionsEnd();CHKERRQ(ierr); 2187 PetscFunctionReturn(0); 2188 } 2189 2190 /*@ 2191 MatCreateIS - Creates a "process" unassembled matrix, assembled on each 2192 process but not across processes. 2193 2194 Input Parameters: 2195 + comm - MPI communicator that will share the matrix 2196 . bs - block size of the matrix 2197 . m,n,M,N - local and/or global sizes of the left and right vector used in matrix vector products 2198 . rmap - local to global map for rows 2199 - cmap - local to global map for cols 2200 2201 Output Parameter: 2202 . A - the resulting matrix 2203 2204 Level: advanced 2205 2206 Notes: See MATIS for more details. 2207 m and n are NOT related to the size of the map; they represent the size of the local parts of the vectors 2208 used in MatMult operations. The sizes of rmap and cmap define the size of the local matrices. 2209 If either rmap or cmap are NULL, then the matrix is assumed to be square. 2210 2211 .seealso: MATIS, MatSetLocalToGlobalMapping() 2212 @*/ 2213 PetscErrorCode MatCreateIS(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt M,PetscInt N,ISLocalToGlobalMapping rmap,ISLocalToGlobalMapping cmap,Mat *A) 2214 { 2215 PetscErrorCode ierr; 2216 2217 PetscFunctionBegin; 2218 if (!rmap && !cmap) SETERRQ(comm,PETSC_ERR_USER,"You need to provide at least one of the mappings"); 2219 ierr = MatCreate(comm,A);CHKERRQ(ierr); 2220 ierr = MatSetSizes(*A,m,n,M,N);CHKERRQ(ierr); 2221 if (bs > 0) { 2222 ierr = MatSetBlockSize(*A,bs);CHKERRQ(ierr); 2223 } 2224 ierr = MatSetType(*A,MATIS);CHKERRQ(ierr); 2225 if (rmap && cmap) { 2226 ierr = MatSetLocalToGlobalMapping(*A,rmap,cmap);CHKERRQ(ierr); 2227 } else if (!rmap) { 2228 ierr = MatSetLocalToGlobalMapping(*A,cmap,cmap);CHKERRQ(ierr); 2229 } else { 2230 ierr = MatSetLocalToGlobalMapping(*A,rmap,rmap);CHKERRQ(ierr); 2231 } 2232 PetscFunctionReturn(0); 2233 } 2234 2235 /*MC 2236 MATIS - MATIS = "is" - A matrix type to be used for using the non-overlapping domain decomposition methods (e.g. PCBDDC or KSPFETIDP). 2237 This stores the matrices in globally unassembled form. Each processor 2238 assembles only its local Neumann problem and the parallel matrix vector 2239 product is handled "implicitly". 2240 2241 Operations Provided: 2242 + MatMult() 2243 . MatMultAdd() 2244 . MatMultTranspose() 2245 . MatMultTransposeAdd() 2246 . MatZeroEntries() 2247 . MatSetOption() 2248 . MatZeroRows() 2249 . MatSetValues() 2250 . MatSetValuesBlocked() 2251 . MatSetValuesLocal() 2252 . MatSetValuesBlockedLocal() 2253 . MatScale() 2254 . MatGetDiagonal() 2255 . MatMissingDiagonal() 2256 . MatDuplicate() 2257 . MatCopy() 2258 . MatAXPY() 2259 . MatCreateSubMatrix() 2260 . MatGetLocalSubMatrix() 2261 . MatTranspose() 2262 - MatSetLocalToGlobalMapping() 2263 2264 Options Database Keys: 2265 . -mat_type is - sets the matrix type to "is" during a call to MatSetFromOptions() 2266 2267 Notes: Options prefix for the inner matrix are given by -is_mat_xxx 2268 2269 You must call MatSetLocalToGlobalMapping() before using this matrix type. 2270 2271 You can do matrix preallocation on the local matrix after you obtain it with 2272 MatISGetLocalMat(); otherwise, you could use MatISSetPreallocation() 2273 2274 Level: advanced 2275 2276 .seealso: Mat, MatISGetLocalMat(), MatSetLocalToGlobalMapping(), MatISSetPreallocation(), MatCreateIS(), PCBDDC, KSPFETIDP 2277 2278 M*/ 2279 2280 PETSC_EXTERN PetscErrorCode MatCreate_IS(Mat A) 2281 { 2282 PetscErrorCode ierr; 2283 Mat_IS *b; 2284 2285 PetscFunctionBegin; 2286 ierr = PetscNewLog(A,&b);CHKERRQ(ierr); 2287 A->data = (void*)b; 2288 2289 /* matrix ops */ 2290 ierr = PetscMemzero(A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2291 A->ops->mult = MatMult_IS; 2292 A->ops->multadd = MatMultAdd_IS; 2293 A->ops->multtranspose = MatMultTranspose_IS; 2294 A->ops->multtransposeadd = MatMultTransposeAdd_IS; 2295 A->ops->destroy = MatDestroy_IS; 2296 A->ops->setlocaltoglobalmapping = MatSetLocalToGlobalMapping_IS; 2297 A->ops->setvalues = MatSetValues_IS; 2298 A->ops->setvaluesblocked = MatSetValuesBlocked_IS; 2299 A->ops->setvalueslocal = MatSetValuesLocal_IS; 2300 A->ops->setvaluesblockedlocal = MatSetValuesBlockedLocal_IS; 2301 A->ops->zerorows = MatZeroRows_IS; 2302 A->ops->zerorowscolumns = MatZeroRowsColumns_IS; 2303 A->ops->assemblybegin = MatAssemblyBegin_IS; 2304 A->ops->assemblyend = MatAssemblyEnd_IS; 2305 A->ops->view = MatView_IS; 2306 A->ops->zeroentries = MatZeroEntries_IS; 2307 A->ops->scale = MatScale_IS; 2308 A->ops->getdiagonal = MatGetDiagonal_IS; 2309 A->ops->setoption = MatSetOption_IS; 2310 A->ops->ishermitian = MatIsHermitian_IS; 2311 A->ops->issymmetric = MatIsSymmetric_IS; 2312 A->ops->isstructurallysymmetric = MatIsStructurallySymmetric_IS; 2313 A->ops->duplicate = MatDuplicate_IS; 2314 A->ops->missingdiagonal = MatMissingDiagonal_IS; 2315 A->ops->copy = MatCopy_IS; 2316 A->ops->getlocalsubmatrix = MatGetLocalSubMatrix_IS; 2317 A->ops->createsubmatrix = MatCreateSubMatrix_IS; 2318 A->ops->axpy = MatAXPY_IS; 2319 A->ops->diagonalset = MatDiagonalSet_IS; 2320 A->ops->shift = MatShift_IS; 2321 A->ops->transpose = MatTranspose_IS; 2322 A->ops->getinfo = MatGetInfo_IS; 2323 A->ops->diagonalscale = MatDiagonalScale_IS; 2324 A->ops->setfromoptions = MatSetFromOptions_IS; 2325 2326 /* special MATIS functions */ 2327 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetLocalMat_C",MatISGetLocalMat_IS);CHKERRQ(ierr); 2328 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISRestoreLocalMat_C",MatISRestoreLocalMat_IS);CHKERRQ(ierr); 2329 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetLocalMat_C",MatISSetLocalMat_IS);CHKERRQ(ierr); 2330 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISGetMPIXAIJ_C",MatISGetMPIXAIJ_IS);CHKERRQ(ierr); 2331 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetPreallocation_C",MatISSetPreallocation_IS);CHKERRQ(ierr); 2332 ierr = PetscObjectComposeFunction((PetscObject)A,"MatISSetUpSF_C",MatISSetUpSF_IS);CHKERRQ(ierr); 2333 ierr = PetscObjectChangeTypeName((PetscObject)A,MATIS);CHKERRQ(ierr); 2334 PetscFunctionReturn(0); 2335 } 2336