1 2 /* 3 Defines the basic matrix operations for the SBAIJ (compressed row) 4 matrix storage format. 5 */ 6 #include <../src/mat/impls/baij/seq/baij.h> /*I "petscmat.h" I*/ 7 #include <../src/mat/impls/sbaij/seq/sbaij.h> 8 #include <petscblaslapack.h> 9 10 #include <../src/mat/impls/sbaij/seq/relax.h> 11 #define USESHORT 12 #include <../src/mat/impls/sbaij/seq/relax.h> 13 14 extern PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat,PetscBool ); 15 16 /* 17 Checks for missing diagonals 18 */ 19 #undef __FUNCT__ 20 #define __FUNCT__ "MatMissingDiagonal_SeqSBAIJ" 21 PetscErrorCode MatMissingDiagonal_SeqSBAIJ(Mat A,PetscBool *missing,PetscInt *dd) 22 { 23 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 24 PetscErrorCode ierr; 25 PetscInt *diag,*jj = a->j,i; 26 27 PetscFunctionBegin; 28 ierr = MatMarkDiagonal_SeqSBAIJ(A);CHKERRQ(ierr); 29 *missing = PETSC_FALSE; 30 if (A->rmap->n > 0 && !jj) { 31 *missing = PETSC_TRUE; 32 if (dd) *dd = 0; 33 PetscInfo(A,"Matrix has no entries therefore is missing diagonal"); 34 } else { 35 diag = a->diag; 36 for (i=0; i<a->mbs; i++) { 37 if (jj[diag[i]] != i) { 38 *missing = PETSC_TRUE; 39 if (dd) *dd = i; 40 break; 41 } 42 } 43 } 44 PetscFunctionReturn(0); 45 } 46 47 #undef __FUNCT__ 48 #define __FUNCT__ "MatMarkDiagonal_SeqSBAIJ" 49 PetscErrorCode MatMarkDiagonal_SeqSBAIJ(Mat A) 50 { 51 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 52 PetscErrorCode ierr; 53 PetscInt i; 54 55 PetscFunctionBegin; 56 if (!a->diag) { 57 ierr = PetscMalloc(a->mbs*sizeof(PetscInt),&a->diag);CHKERRQ(ierr); 58 ierr = PetscLogObjectMemory(A,a->mbs*sizeof(PetscInt));CHKERRQ(ierr); 59 a->free_diag = PETSC_TRUE; 60 } 61 for (i=0; i<a->mbs; i++) a->diag[i] = a->i[i]; 62 PetscFunctionReturn(0); 63 } 64 65 #undef __FUNCT__ 66 #define __FUNCT__ "MatGetRowIJ_SeqSBAIJ" 67 static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *inia[],const PetscInt *inja[],PetscBool *done) 68 { 69 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 70 PetscInt i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs; 71 PetscInt **ia = (PetscInt**)inia,**ja = (PetscInt**)inja; 72 PetscErrorCode ierr; 73 74 PetscFunctionBegin; 75 *nn = n; 76 if (!ia) PetscFunctionReturn(0); 77 if (!blockcompressed) { 78 /* malloc & create the natural set of indices */ 79 ierr = PetscMalloc2((n+1)*bs,PetscInt,ia,nz*bs,PetscInt,ja);CHKERRQ(ierr); 80 for (i=0; i<n+1; i++) { 81 for (j=0; j<bs; j++) { 82 *ia[i*bs+j] = a->i[i]*bs+j+oshift; 83 } 84 } 85 for (i=0; i<nz; i++) { 86 for (j=0; j<bs; j++) { 87 *ja[i*bs+j] = a->j[i]*bs+j+oshift; 88 } 89 } 90 } else { /* blockcompressed */ 91 if (oshift == 1) { 92 /* temporarily add 1 to i and j indices */ 93 for (i=0; i<nz; i++) a->j[i]++; 94 for (i=0; i<n+1; i++) a->i[i]++; 95 } 96 *ia = a->i; *ja = a->j; 97 } 98 99 PetscFunctionReturn(0); 100 } 101 102 #undef __FUNCT__ 103 #define __FUNCT__ "MatRestoreRowIJ_SeqSBAIJ" 104 static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscBool *done) 105 { 106 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 107 PetscInt i,n = a->mbs,nz = a->i[n]; 108 PetscErrorCode ierr; 109 110 PetscFunctionBegin; 111 if (!ia) PetscFunctionReturn(0); 112 113 if (!blockcompressed) { 114 ierr = PetscFree2(*ia,*ja);CHKERRQ(ierr); 115 } else if (oshift == 1) { /* blockcompressed */ 116 for (i=0; i<nz; i++) a->j[i]--; 117 for (i=0; i<n+1; i++) a->i[i]--; 118 } 119 120 PetscFunctionReturn(0); 121 } 122 123 #undef __FUNCT__ 124 #define __FUNCT__ "MatDestroy_SeqSBAIJ" 125 PetscErrorCode MatDestroy_SeqSBAIJ(Mat A) 126 { 127 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 128 PetscErrorCode ierr; 129 130 PetscFunctionBegin; 131 #if defined(PETSC_USE_LOG) 132 PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz); 133 #endif 134 ierr = MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);CHKERRQ(ierr); 135 if (a->free_diag){ierr = PetscFree(a->diag);CHKERRQ(ierr);} 136 ierr = ISDestroy(&a->row);CHKERRQ(ierr); 137 ierr = ISDestroy(&a->col);CHKERRQ(ierr); 138 ierr = ISDestroy(&a->icol);CHKERRQ(ierr); 139 ierr = PetscFree(a->idiag);CHKERRQ(ierr); 140 ierr = PetscFree(a->inode.size);CHKERRQ(ierr); 141 if (a->free_imax_ilen) {ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr);} 142 ierr = PetscFree(a->solve_work);CHKERRQ(ierr); 143 ierr = PetscFree(a->sor_work);CHKERRQ(ierr); 144 ierr = PetscFree(a->solves_work);CHKERRQ(ierr); 145 ierr = PetscFree(a->mult_work);CHKERRQ(ierr); 146 ierr = PetscFree(a->saved_values);CHKERRQ(ierr); 147 ierr = PetscFree(a->xtoy);CHKERRQ(ierr); 148 if (a->free_jshort) {ierr = PetscFree(a->jshort);CHKERRQ(ierr);} 149 ierr = PetscFree(a->inew);CHKERRQ(ierr); 150 ierr = MatDestroy(&a->parent);CHKERRQ(ierr); 151 ierr = PetscFree(A->data);CHKERRQ(ierr); 152 153 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 154 ierr = PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C","",PETSC_NULL);CHKERRQ(ierr); 155 ierr = PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C","",PETSC_NULL);CHKERRQ(ierr); 156 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C","",PETSC_NULL);CHKERRQ(ierr); 157 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C","",PETSC_NULL);CHKERRQ(ierr); 158 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C","",PETSC_NULL);CHKERRQ(ierr); 159 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C","",PETSC_NULL);CHKERRQ(ierr); 160 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqsbstrm_C","",PETSC_NULL);CHKERRQ(ierr); 161 PetscFunctionReturn(0); 162 } 163 164 #undef __FUNCT__ 165 #define __FUNCT__ "MatSetOption_SeqSBAIJ" 166 PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool flg) 167 { 168 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 169 PetscErrorCode ierr; 170 171 PetscFunctionBegin; 172 switch (op) { 173 case MAT_ROW_ORIENTED: 174 a->roworiented = flg; 175 break; 176 case MAT_KEEP_NONZERO_PATTERN: 177 a->keepnonzeropattern = flg; 178 break; 179 case MAT_NEW_NONZERO_LOCATIONS: 180 a->nonew = (flg ? 0 : 1); 181 break; 182 case MAT_NEW_NONZERO_LOCATION_ERR: 183 a->nonew = (flg ? -1 : 0); 184 break; 185 case MAT_NEW_NONZERO_ALLOCATION_ERR: 186 a->nonew = (flg ? -2 : 0); 187 break; 188 case MAT_UNUSED_NONZERO_LOCATION_ERR: 189 a->nounused = (flg ? -1 : 0); 190 break; 191 case MAT_NEW_DIAGONALS: 192 case MAT_IGNORE_OFF_PROC_ENTRIES: 193 case MAT_USE_HASH_TABLE: 194 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 195 break; 196 case MAT_HERMITIAN: 197 if (!A->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first"); 198 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 199 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort; 200 } else if (A->cmap->bs == 1) { 201 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian; 202 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1"); 203 break; 204 case MAT_SPD: 205 /* These options are handled directly by MatSetOption() */ 206 break; 207 case MAT_SYMMETRIC: 208 case MAT_STRUCTURALLY_SYMMETRIC: 209 case MAT_SYMMETRY_ETERNAL: 210 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix must be symmetric"); 211 ierr = PetscInfo1(A,"Option %s not relevent\n",MatOptions[op]);CHKERRQ(ierr); 212 break; 213 case MAT_IGNORE_LOWER_TRIANGULAR: 214 a->ignore_ltriangular = flg; 215 break; 216 case MAT_ERROR_LOWER_TRIANGULAR: 217 a->ignore_ltriangular = flg; 218 break; 219 case MAT_GETROW_UPPERTRIANGULAR: 220 a->getrow_utriangular = flg; 221 break; 222 default: 223 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 224 } 225 PetscFunctionReturn(0); 226 } 227 228 #undef __FUNCT__ 229 #define __FUNCT__ "MatGetRow_SeqSBAIJ" 230 PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *ncols,PetscInt **cols,PetscScalar **v) 231 { 232 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 233 PetscErrorCode ierr; 234 PetscInt itmp,i,j,k,M,*ai,*aj,bs,bn,bp,*cols_i,bs2; 235 MatScalar *aa,*aa_i; 236 PetscScalar *v_i; 237 238 PetscFunctionBegin; 239 if (A && !a->getrow_utriangular) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MatGetRow is not supported for SBAIJ matrix format. Getting the upper triangular part of row, run with -mat_getrow_uppertriangular, call MatSetOption(mat,MAT_GETROW_UPPERTRIANGULAR,PETSC_TRUE) or MatGetRowUpperTriangular()"); 240 /* Get the upper triangular part of the row */ 241 bs = A->rmap->bs; 242 ai = a->i; 243 aj = a->j; 244 aa = a->a; 245 bs2 = a->bs2; 246 247 if (row < 0 || row >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Row %D out of range", row); 248 249 bn = row/bs; /* Block number */ 250 bp = row % bs; /* Block position */ 251 M = ai[bn+1] - ai[bn]; 252 *ncols = bs*M; 253 254 if (v) { 255 *v = 0; 256 if (*ncols) { 257 ierr = PetscMalloc((*ncols+row)*sizeof(PetscScalar),v);CHKERRQ(ierr); 258 for (i=0; i<M; i++) { /* for each block in the block row */ 259 v_i = *v + i*bs; 260 aa_i = aa + bs2*(ai[bn] + i); 261 for (j=bp,k=0; j<bs2; j+=bs,k++) {v_i[k] = aa_i[j];} 262 } 263 } 264 } 265 266 if (cols) { 267 *cols = 0; 268 if (*ncols) { 269 ierr = PetscMalloc((*ncols+row)*sizeof(PetscInt),cols);CHKERRQ(ierr); 270 for (i=0; i<M; i++) { /* for each block in the block row */ 271 cols_i = *cols + i*bs; 272 itmp = bs*aj[ai[bn] + i]; 273 for (j=0; j<bs; j++) {cols_i[j] = itmp++;} 274 } 275 } 276 } 277 278 /*search column A(0:row-1,row) (=A(row,0:row-1)). Could be expensive! */ 279 /* this segment is currently removed, so only entries in the upper triangle are obtained */ 280 #ifdef column_search 281 v_i = *v + M*bs; 282 cols_i = *cols + M*bs; 283 for (i=0; i<bn; i++){ /* for each block row */ 284 M = ai[i+1] - ai[i]; 285 for (j=0; j<M; j++){ 286 itmp = aj[ai[i] + j]; /* block column value */ 287 if (itmp == bn){ 288 aa_i = aa + bs2*(ai[i] + j) + bs*bp; 289 for (k=0; k<bs; k++) { 290 *cols_i++ = i*bs+k; 291 *v_i++ = aa_i[k]; 292 } 293 *ncols += bs; 294 break; 295 } 296 } 297 } 298 #endif 299 PetscFunctionReturn(0); 300 } 301 302 #undef __FUNCT__ 303 #define __FUNCT__ "MatRestoreRow_SeqSBAIJ" 304 PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 305 { 306 PetscErrorCode ierr; 307 308 PetscFunctionBegin; 309 if (idx) {ierr = PetscFree(*idx);CHKERRQ(ierr);} 310 if (v) {ierr = PetscFree(*v);CHKERRQ(ierr);} 311 PetscFunctionReturn(0); 312 } 313 314 #undef __FUNCT__ 315 #define __FUNCT__ "MatGetRowUpperTriangular_SeqSBAIJ" 316 PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A) 317 { 318 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 319 320 PetscFunctionBegin; 321 a->getrow_utriangular = PETSC_TRUE; 322 PetscFunctionReturn(0); 323 } 324 #undef __FUNCT__ 325 #define __FUNCT__ "MatRestoreRowUpperTriangular_SeqSBAIJ" 326 PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A) 327 { 328 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 329 330 PetscFunctionBegin; 331 a->getrow_utriangular = PETSC_FALSE; 332 PetscFunctionReturn(0); 333 } 334 335 #undef __FUNCT__ 336 #define __FUNCT__ "MatTranspose_SeqSBAIJ" 337 PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B) 338 { 339 PetscErrorCode ierr; 340 PetscFunctionBegin; 341 if (reuse == MAT_INITIAL_MATRIX || *B != A) { 342 ierr = MatDuplicate(A,MAT_COPY_VALUES,B);CHKERRQ(ierr); 343 } 344 PetscFunctionReturn(0); 345 } 346 347 #undef __FUNCT__ 348 #define __FUNCT__ "MatView_SeqSBAIJ_ASCII" 349 static PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer) 350 { 351 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 352 PetscErrorCode ierr; 353 PetscInt i,j,bs = A->rmap->bs,k,l,bs2=a->bs2; 354 PetscViewerFormat format; 355 PetscInt *diag; 356 357 PetscFunctionBegin; 358 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 359 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 360 ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); 361 } else if (format == PETSC_VIEWER_ASCII_MATLAB) { 362 Mat aij; 363 if (A->factortype && bs>1){ 364 ierr = PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored with bs>1. MatView() with PETSC_VIEWER_ASCII_MATLAB is not supported and ignored!\n");CHKERRQ(ierr); 365 PetscFunctionReturn(0); 366 } 367 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);CHKERRQ(ierr); 368 ierr = MatView(aij,viewer);CHKERRQ(ierr); 369 ierr = MatDestroy(&aij);CHKERRQ(ierr); 370 } else if (format == PETSC_VIEWER_ASCII_COMMON) { 371 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 372 for (i=0; i<a->mbs; i++) { 373 for (j=0; j<bs; j++) { 374 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 375 for (k=a->i[i]; k<a->i[i+1]; k++) { 376 for (l=0; l<bs; l++) { 377 #if defined(PETSC_USE_COMPLEX) 378 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 379 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l, 380 PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 381 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 382 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l, 383 PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 384 } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 385 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 386 } 387 #else 388 if (a->a[bs2*k + l*bs + j] != 0.0) { 389 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 390 } 391 #endif 392 } 393 } 394 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 395 } 396 } 397 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 398 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 399 PetscFunctionReturn(0); 400 } else { 401 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 402 ierr = PetscObjectPrintClassNamePrefixType((PetscObject)A,viewer,"Matrix Object");CHKERRQ(ierr); 403 if (A->factortype){ /* for factored matrix */ 404 if (bs>1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"matrix is factored with bs>1. Not implemented yet"); 405 406 diag=a->diag; 407 for (i=0; i<a->mbs; i++) { /* for row block i */ 408 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); 409 /* diagonal entry */ 410 #if defined(PETSC_USE_COMPLEX) 411 if (PetscImaginaryPart(a->a[diag[i]]) > 0.0) { 412 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",a->j[diag[i]],PetscRealPart(1.0/a->a[diag[i]]),PetscImaginaryPart(1.0/a->a[diag[i]]));CHKERRQ(ierr); 413 } else if (PetscImaginaryPart(a->a[diag[i]]) < 0.0) { 414 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",a->j[diag[i]],PetscRealPart(1.0/a->a[diag[i]]),-PetscImaginaryPart(1.0/a->a[diag[i]]));CHKERRQ(ierr); 415 } else { 416 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[diag[i]],PetscRealPart(1.0/a->a[diag[i]]));CHKERRQ(ierr); 417 } 418 #else 419 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[diag[i]],1.0/a->a[diag[i]]);CHKERRQ(ierr); 420 #endif 421 /* off-diagonal entries */ 422 for (k=a->i[i]; k<a->i[i+1]-1; k++) { 423 #if defined(PETSC_USE_COMPLEX) 424 if (PetscImaginaryPart(a->a[k]) > 0.0) { 425 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k],PetscRealPart(a->a[k]),PetscImaginaryPart(a->a[k]));CHKERRQ(ierr); 426 } else if (PetscImaginaryPart(a->a[k]) < 0.0) { 427 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k],PetscRealPart(a->a[k]),-PetscImaginaryPart(a->a[k]));CHKERRQ(ierr); 428 } else { 429 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k],PetscRealPart(a->a[k]));CHKERRQ(ierr); 430 } 431 #else 432 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[k],a->a[k]);CHKERRQ(ierr); 433 #endif 434 } 435 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 436 } 437 438 } else { /* for non-factored matrix */ 439 for (i=0; i<a->mbs; i++) { /* for row block i */ 440 for (j=0; j<bs; j++) { /* for row bs*i + j */ 441 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 442 for (k=a->i[i]; k<a->i[i+1]; k++) { /* for column block */ 443 for (l=0; l<bs; l++) { /* for column */ 444 #if defined(PETSC_USE_COMPLEX) 445 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) { 446 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l, 447 PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 448 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) { 449 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l, 450 PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 451 } else { 452 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 453 } 454 #else 455 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 456 #endif 457 } 458 } 459 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 460 } 461 } 462 } 463 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 464 } 465 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 466 PetscFunctionReturn(0); 467 } 468 469 #undef __FUNCT__ 470 #define __FUNCT__ "MatView_SeqSBAIJ_Draw_Zoom" 471 static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa) 472 { 473 Mat A = (Mat) Aa; 474 Mat_SeqSBAIJ *a=(Mat_SeqSBAIJ*)A->data; 475 PetscErrorCode ierr; 476 PetscInt row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2; 477 PetscMPIInt rank; 478 PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r; 479 MatScalar *aa; 480 MPI_Comm comm; 481 PetscViewer viewer; 482 483 PetscFunctionBegin; 484 /* 485 This is nasty. If this is called from an originally parallel matrix 486 then all processes call this,but only the first has the matrix so the 487 rest should return immediately. 488 */ 489 ierr = PetscObjectGetComm((PetscObject)draw,&comm);CHKERRQ(ierr); 490 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 491 if (rank) PetscFunctionReturn(0); 492 493 ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr); 494 495 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 496 PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric"); 497 498 /* loop over matrix elements drawing boxes */ 499 color = PETSC_DRAW_BLUE; 500 for (i=0,row=0; i<mbs; i++,row+=bs) { 501 for (j=a->i[i]; j<a->i[i+1]; j++) { 502 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 503 x_l = a->j[j]*bs; x_r = x_l + 1.0; 504 aa = a->a + j*bs2; 505 for (k=0; k<bs; k++) { 506 for (l=0; l<bs; l++) { 507 if (PetscRealPart(*aa++) >= 0.) continue; 508 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 509 } 510 } 511 } 512 } 513 color = PETSC_DRAW_CYAN; 514 for (i=0,row=0; i<mbs; i++,row+=bs) { 515 for (j=a->i[i]; j<a->i[i+1]; j++) { 516 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 517 x_l = a->j[j]*bs; x_r = x_l + 1.0; 518 aa = a->a + j*bs2; 519 for (k=0; k<bs; k++) { 520 for (l=0; l<bs; l++) { 521 if (PetscRealPart(*aa++) != 0.) continue; 522 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 523 } 524 } 525 } 526 } 527 528 color = PETSC_DRAW_RED; 529 for (i=0,row=0; i<mbs; i++,row+=bs) { 530 for (j=a->i[i]; j<a->i[i+1]; j++) { 531 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 532 x_l = a->j[j]*bs; x_r = x_l + 1.0; 533 aa = a->a + j*bs2; 534 for (k=0; k<bs; k++) { 535 for (l=0; l<bs; l++) { 536 if (PetscRealPart(*aa++) <= 0.) continue; 537 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 538 } 539 } 540 } 541 } 542 PetscFunctionReturn(0); 543 } 544 545 #undef __FUNCT__ 546 #define __FUNCT__ "MatView_SeqSBAIJ_Draw" 547 static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer) 548 { 549 PetscErrorCode ierr; 550 PetscReal xl,yl,xr,yr,w,h; 551 PetscDraw draw; 552 PetscBool isnull; 553 554 PetscFunctionBegin; 555 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 556 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 557 558 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);CHKERRQ(ierr); 559 xr = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0; 560 xr += w; yr += h; xl = -w; yl = -h; 561 ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr); 562 ierr = PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);CHKERRQ(ierr); 563 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",PETSC_NULL);CHKERRQ(ierr); 564 PetscFunctionReturn(0); 565 } 566 567 #undef __FUNCT__ 568 #define __FUNCT__ "MatView_SeqSBAIJ" 569 PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer) 570 { 571 PetscErrorCode ierr; 572 PetscBool iascii,isdraw; 573 FILE *file = 0; 574 575 PetscFunctionBegin; 576 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 577 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 578 if (iascii){ 579 ierr = MatView_SeqSBAIJ_ASCII(A,viewer);CHKERRQ(ierr); 580 } else if (isdraw) { 581 ierr = MatView_SeqSBAIJ_Draw(A,viewer);CHKERRQ(ierr); 582 } else { 583 Mat B; 584 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 585 ierr = MatView(B,viewer);CHKERRQ(ierr); 586 ierr = MatDestroy(&B);CHKERRQ(ierr); 587 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 588 if (file) { 589 fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs); 590 } 591 } 592 PetscFunctionReturn(0); 593 } 594 595 596 #undef __FUNCT__ 597 #define __FUNCT__ "MatGetValues_SeqSBAIJ" 598 PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[]) 599 { 600 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 601 PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j; 602 PetscInt *ai = a->i,*ailen = a->ilen; 603 PetscInt brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2; 604 MatScalar *ap,*aa = a->a; 605 606 PetscFunctionBegin; 607 for (k=0; k<m; k++) { /* loop over rows */ 608 row = im[k]; brow = row/bs; 609 if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */ 610 if (row >= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1); 611 rp = aj + ai[brow] ; ap = aa + bs2*ai[brow] ; 612 nrow = ailen[brow]; 613 for (l=0; l<n; l++) { /* loop over columns */ 614 if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */ 615 if (in[l] >= A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->cmap->n-1); 616 col = in[l] ; 617 bcol = col/bs; 618 cidx = col%bs; 619 ridx = row%bs; 620 high = nrow; 621 low = 0; /* assume unsorted */ 622 while (high-low > 5) { 623 t = (low+high)/2; 624 if (rp[t] > bcol) high = t; 625 else low = t; 626 } 627 for (i=low; i<high; i++) { 628 if (rp[i] > bcol) break; 629 if (rp[i] == bcol) { 630 *v++ = ap[bs2*i+bs*cidx+ridx]; 631 goto finished; 632 } 633 } 634 *v++ = 0.0; 635 finished:; 636 } 637 } 638 PetscFunctionReturn(0); 639 } 640 641 642 #undef __FUNCT__ 643 #define __FUNCT__ "MatSetValuesBlocked_SeqSBAIJ" 644 PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 645 { 646 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 647 PetscErrorCode ierr; 648 PetscInt *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1; 649 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen; 650 PetscInt *aj=a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval; 651 PetscBool roworiented=a->roworiented; 652 const PetscScalar *value = v; 653 MatScalar *ap,*aa = a->a,*bap; 654 655 PetscFunctionBegin; 656 if (roworiented) { 657 stepval = (n-1)*bs; 658 } else { 659 stepval = (m-1)*bs; 660 } 661 for (k=0; k<m; k++) { /* loop over added rows */ 662 row = im[k]; 663 if (row < 0) continue; 664 #if defined(PETSC_USE_DEBUG) 665 if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1); 666 #endif 667 rp = aj + ai[row]; 668 ap = aa + bs2*ai[row]; 669 rmax = imax[row]; 670 nrow = ailen[row]; 671 low = 0; 672 high = nrow; 673 for (l=0; l<n; l++) { /* loop over added columns */ 674 if (in[l] < 0) continue; 675 col = in[l]; 676 #if defined(PETSC_USE_DEBUG) 677 if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1); 678 #endif 679 if (col < row) { 680 if (a->ignore_ltriangular) { 681 continue; /* ignore lower triangular block */ 682 } else { 683 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Lower triangular value cannot be set for sbaij format. Ignoring these values, run with -mat_ignore_lower_triangular or call MatSetOption(mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE)"); 684 } 685 } 686 if (roworiented) { 687 value = v + k*(stepval+bs)*bs + l*bs; 688 } else { 689 value = v + l*(stepval+bs)*bs + k*bs; 690 } 691 if (col <= lastcol) low = 0; else high = nrow; 692 lastcol = col; 693 while (high-low > 7) { 694 t = (low+high)/2; 695 if (rp[t] > col) high = t; 696 else low = t; 697 } 698 for (i=low; i<high; i++) { 699 if (rp[i] > col) break; 700 if (rp[i] == col) { 701 bap = ap + bs2*i; 702 if (roworiented) { 703 if (is == ADD_VALUES) { 704 for (ii=0; ii<bs; ii++,value+=stepval) { 705 for (jj=ii; jj<bs2; jj+=bs) { 706 bap[jj] += *value++; 707 } 708 } 709 } else { 710 for (ii=0; ii<bs; ii++,value+=stepval) { 711 for (jj=ii; jj<bs2; jj+=bs) { 712 bap[jj] = *value++; 713 } 714 } 715 } 716 } else { 717 if (is == ADD_VALUES) { 718 for (ii=0; ii<bs; ii++,value+=stepval) { 719 for (jj=0; jj<bs; jj++) { 720 *bap++ += *value++; 721 } 722 } 723 } else { 724 for (ii=0; ii<bs; ii++,value+=stepval) { 725 for (jj=0; jj<bs; jj++) { 726 *bap++ = *value++; 727 } 728 } 729 } 730 } 731 goto noinsert2; 732 } 733 } 734 if (nonew == 1) goto noinsert2; 735 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 736 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 737 N = nrow++ - 1; high++; 738 /* shift up all the later entries in this row */ 739 for (ii=N; ii>=i; ii--) { 740 rp[ii+1] = rp[ii]; 741 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 742 } 743 if (N >= i) { 744 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 745 } 746 rp[i] = col; 747 bap = ap + bs2*i; 748 if (roworiented) { 749 for (ii=0; ii<bs; ii++,value+=stepval) { 750 for (jj=ii; jj<bs2; jj+=bs) { 751 bap[jj] = *value++; 752 } 753 } 754 } else { 755 for (ii=0; ii<bs; ii++,value+=stepval) { 756 for (jj=0; jj<bs; jj++) { 757 *bap++ = *value++; 758 } 759 } 760 } 761 noinsert2:; 762 low = i; 763 } 764 ailen[row] = nrow; 765 } 766 PetscFunctionReturn(0); 767 } 768 769 /* 770 This is not yet used 771 */ 772 #undef __FUNCT__ 773 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode" 774 PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A) 775 { 776 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 777 PetscErrorCode ierr; 778 const PetscInt *ai = a->i, *aj = a->j,*cols; 779 PetscInt i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts; 780 PetscBool flag; 781 782 PetscFunctionBegin; 783 ierr = PetscMalloc(m*sizeof(PetscInt),&ns);CHKERRQ(ierr); 784 while (i < m){ 785 nzx = ai[i+1] - ai[i]; /* Number of nonzeros */ 786 /* Limits the number of elements in a node to 'a->inode.limit' */ 787 for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) { 788 nzy = ai[j+1] - ai[j]; 789 if (nzy != (nzx - j + i)) break; 790 ierr = PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);CHKERRQ(ierr); 791 if (!flag) break; 792 } 793 ns[node_count++] = blk_size; 794 i = j; 795 } 796 if (!a->inode.size && m && node_count > .9*m) { 797 ierr = PetscFree(ns);CHKERRQ(ierr); 798 ierr = PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);CHKERRQ(ierr); 799 } else { 800 a->inode.node_count = node_count; 801 ierr = PetscMalloc(node_count*sizeof(PetscInt),&a->inode.size);CHKERRQ(ierr); 802 ierr = PetscLogObjectMemory(A,node_count*sizeof(PetscInt));CHKERRQ(ierr); 803 ierr = PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt)); 804 ierr = PetscFree(ns);CHKERRQ(ierr); 805 ierr = PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);CHKERRQ(ierr); 806 807 /* count collections of adjacent columns in each inode */ 808 row = 0; 809 cnt = 0; 810 for (i=0; i<node_count; i++) { 811 cols = aj + ai[row] + a->inode.size[i]; 812 nz = ai[row+1] - ai[row] - a->inode.size[i]; 813 for (j=1; j<nz; j++) { 814 if (cols[j] != cols[j-1]+1) { 815 cnt++; 816 } 817 } 818 cnt++; 819 row += a->inode.size[i]; 820 } 821 ierr = PetscMalloc(2*cnt*sizeof(PetscInt),&counts);CHKERRQ(ierr); 822 cnt = 0; 823 row = 0; 824 for (i=0; i<node_count; i++) { 825 cols = aj + ai[row] + a->inode.size[i]; 826 CHKMEMQ; 827 counts[2*cnt] = cols[0]; 828 CHKMEMQ; 829 nz = ai[row+1] - ai[row] - a->inode.size[i]; 830 cnt2 = 1; 831 for (j=1; j<nz; j++) { 832 if (cols[j] != cols[j-1]+1) { 833 CHKMEMQ; 834 counts[2*(cnt++)+1] = cnt2; 835 counts[2*cnt] = cols[j]; 836 CHKMEMQ; 837 cnt2 = 1; 838 } else cnt2++; 839 } 840 CHKMEMQ; 841 counts[2*(cnt++)+1] = cnt2; 842 CHKMEMQ; 843 row += a->inode.size[i]; 844 } 845 ierr = PetscIntView(2*cnt,counts,0); 846 } 847 PetscFunctionReturn(0); 848 } 849 850 #undef __FUNCT__ 851 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ" 852 PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode) 853 { 854 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 855 PetscErrorCode ierr; 856 PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax; 857 PetscInt m = A->rmap->N,*ip,N,*ailen = a->ilen; 858 PetscInt mbs = a->mbs,bs2 = a->bs2,rmax = 0; 859 MatScalar *aa = a->a,*ap; 860 861 PetscFunctionBegin; 862 if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); 863 864 if (m) rmax = ailen[0]; 865 for (i=1; i<mbs; i++) { 866 /* move each row back by the amount of empty slots (fshift) before it*/ 867 fshift += imax[i-1] - ailen[i-1]; 868 rmax = PetscMax(rmax,ailen[i]); 869 if (fshift) { 870 ip = aj + ai[i]; ap = aa + bs2*ai[i]; 871 N = ailen[i]; 872 for (j=0; j<N; j++) { 873 ip[j-fshift] = ip[j]; 874 ierr = PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 875 } 876 } 877 ai[i] = ai[i-1] + ailen[i-1]; 878 } 879 if (mbs) { 880 fshift += imax[mbs-1] - ailen[mbs-1]; 881 ai[mbs] = ai[mbs-1] + ailen[mbs-1]; 882 } 883 /* reset ilen and imax for each row */ 884 for (i=0; i<mbs; i++) { 885 ailen[i] = imax[i] = ai[i+1] - ai[i]; 886 } 887 a->nz = ai[mbs]; 888 889 /* diagonals may have moved, reset it */ 890 if (a->diag) { 891 ierr = PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));CHKERRQ(ierr); 892 } 893 if (fshift && a->nounused == -1) { 894 SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Unused space detected in matrix: %D X %D block size %D, %D unneeded", m, A->cmap->n, A->rmap->bs, fshift*bs2); 895 } 896 ierr = PetscInfo5(A,"Matrix size: %D X %D, block size %D; storage space: %D unneeded, %D used\n",m,A->rmap->N,A->rmap->bs,fshift*bs2,a->nz*bs2);CHKERRQ(ierr); 897 ierr = PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);CHKERRQ(ierr); 898 ierr = PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);CHKERRQ(ierr); 899 A->info.mallocs += a->reallocs; 900 a->reallocs = 0; 901 A->info.nz_unneeded = (PetscReal)fshift*bs2; 902 a->idiagvalid = PETSC_FALSE; 903 904 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 905 if (a->jshort && a->free_jshort){ 906 /* when matrix data structure is changed, previous jshort must be replaced */ 907 ierr = PetscFree(a->jshort);CHKERRQ(ierr); 908 } 909 ierr = PetscMalloc(a->i[A->rmap->n]*sizeof(unsigned short),&a->jshort);CHKERRQ(ierr); 910 ierr = PetscLogObjectMemory(A,a->i[A->rmap->n]*sizeof(unsigned short));CHKERRQ(ierr); 911 for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i]; 912 A->ops->mult = MatMult_SeqSBAIJ_1_ushort; 913 A->ops->sor = MatSOR_SeqSBAIJ_ushort; 914 a->free_jshort = PETSC_TRUE; 915 } 916 PetscFunctionReturn(0); 917 } 918 919 /* 920 This function returns an array of flags which indicate the locations of contiguous 921 blocks that should be zeroed. for eg: if bs = 3 and is = [0,1,2,3,5,6,7,8,9] 922 then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)] 923 Assume: sizes should be long enough to hold all the values. 924 */ 925 #undef __FUNCT__ 926 #define __FUNCT__ "MatZeroRows_SeqSBAIJ_Check_Blocks" 927 PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max) 928 { 929 PetscInt i,j,k,row; 930 PetscBool flg; 931 932 PetscFunctionBegin; 933 for (i=0,j=0; i<n; j++) { 934 row = idx[i]; 935 if (row%bs!=0) { /* Not the begining of a block */ 936 sizes[j] = 1; 937 i++; 938 } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */ 939 sizes[j] = 1; /* Also makes sure atleast 'bs' values exist for next else */ 940 i++; 941 } else { /* Begining of the block, so check if the complete block exists */ 942 flg = PETSC_TRUE; 943 for (k=1; k<bs; k++) { 944 if (row+k != idx[i+k]) { /* break in the block */ 945 flg = PETSC_FALSE; 946 break; 947 } 948 } 949 if (flg) { /* No break in the bs */ 950 sizes[j] = bs; 951 i+= bs; 952 } else { 953 sizes[j] = 1; 954 i++; 955 } 956 } 957 } 958 *bs_max = j; 959 PetscFunctionReturn(0); 960 } 961 962 963 /* Only add/insert a(i,j) with i<=j (blocks). 964 Any a(i,j) with i>j input by user is ingored. 965 */ 966 967 #undef __FUNCT__ 968 #define __FUNCT__ "MatSetValues_SeqSBAIJ" 969 PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 970 { 971 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 972 PetscErrorCode ierr; 973 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1; 974 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented; 975 PetscInt *aj=a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol; 976 PetscInt ridx,cidx,bs2=a->bs2; 977 MatScalar *ap,value,*aa=a->a,*bap; 978 979 PetscFunctionBegin; 980 if (v) PetscValidScalarPointer(v,6); 981 for (k=0; k<m; k++) { /* loop over added rows */ 982 row = im[k]; /* row number */ 983 brow = row/bs; /* block row number */ 984 if (row < 0) continue; 985 #if defined(PETSC_USE_DEBUG) 986 if (row >= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1); 987 #endif 988 rp = aj + ai[brow]; /*ptr to beginning of column value of the row block*/ 989 ap = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/ 990 rmax = imax[brow]; /* maximum space allocated for this row */ 991 nrow = ailen[brow]; /* actual length of this row */ 992 low = 0; 993 994 for (l=0; l<n; l++) { /* loop over added columns */ 995 if (in[l] < 0) continue; 996 #if defined(PETSC_USE_DEBUG) 997 if (in[l] >= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->rmap->N-1); 998 #endif 999 col = in[l]; 1000 bcol = col/bs; /* block col number */ 1001 1002 if (brow > bcol) { 1003 if (a->ignore_ltriangular){ 1004 continue; /* ignore lower triangular values */ 1005 } else { 1006 SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Lower triangular value cannot be set for sbaij format. Ignoring these values, run with -mat_ignore_lower_triangular or call MatSetOption(mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE)"); 1007 } 1008 } 1009 1010 ridx = row % bs; cidx = col % bs; /*row and col index inside the block */ 1011 if ((brow==bcol && ridx<=cidx) || (brow<bcol)){ 1012 /* element value a(k,l) */ 1013 if (roworiented) { 1014 value = v[l + k*n]; 1015 } else { 1016 value = v[k + l*m]; 1017 } 1018 1019 /* move pointer bap to a(k,l) quickly and add/insert value */ 1020 if (col <= lastcol) low = 0; high = nrow; 1021 lastcol = col; 1022 while (high-low > 7) { 1023 t = (low+high)/2; 1024 if (rp[t] > bcol) high = t; 1025 else low = t; 1026 } 1027 for (i=low; i<high; i++) { 1028 if (rp[i] > bcol) break; 1029 if (rp[i] == bcol) { 1030 bap = ap + bs2*i + bs*cidx + ridx; 1031 if (is == ADD_VALUES) *bap += value; 1032 else *bap = value; 1033 /* for diag block, add/insert its symmetric element a(cidx,ridx) */ 1034 if (brow == bcol && ridx < cidx){ 1035 bap = ap + bs2*i + bs*ridx + cidx; 1036 if (is == ADD_VALUES) *bap += value; 1037 else *bap = value; 1038 } 1039 goto noinsert1; 1040 } 1041 } 1042 1043 if (nonew == 1) goto noinsert1; 1044 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 1045 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 1046 1047 N = nrow++ - 1; high++; 1048 /* shift up all the later entries in this row */ 1049 for (ii=N; ii>=i; ii--) { 1050 rp[ii+1] = rp[ii]; 1051 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 1052 } 1053 if (N>=i) { 1054 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1055 } 1056 rp[i] = bcol; 1057 ap[bs2*i + bs*cidx + ridx] = value; 1058 noinsert1:; 1059 low = i; 1060 } 1061 } /* end of loop over added columns */ 1062 ailen[brow] = nrow; 1063 } /* end of loop over added rows */ 1064 PetscFunctionReturn(0); 1065 } 1066 1067 #undef __FUNCT__ 1068 #define __FUNCT__ "MatICCFactor_SeqSBAIJ" 1069 PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info) 1070 { 1071 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)inA->data; 1072 Mat outA; 1073 PetscErrorCode ierr; 1074 PetscBool row_identity; 1075 1076 PetscFunctionBegin; 1077 if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc"); 1078 ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr); 1079 if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported"); 1080 if (inA->rmap->bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix block size %D is not supported",inA->rmap->bs); /* Need to replace MatCholeskyFactorSymbolic_SeqSBAIJ_MSR()! */ 1081 1082 outA = inA; 1083 inA->factortype = MAT_FACTOR_ICC; 1084 1085 ierr = MatMarkDiagonal_SeqSBAIJ(inA);CHKERRQ(ierr); 1086 ierr = MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);CHKERRQ(ierr); 1087 1088 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1089 ierr = ISDestroy(&a->row);CHKERRQ(ierr); 1090 a->row = row; 1091 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1092 ierr = ISDestroy(&a->col);CHKERRQ(ierr); 1093 a->col = row; 1094 1095 /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */ 1096 if (a->icol) {ierr = ISInvertPermutation(row,PETSC_DECIDE, &a->icol);CHKERRQ(ierr);} 1097 ierr = PetscLogObjectParent(inA,a->icol);CHKERRQ(ierr); 1098 1099 if (!a->solve_work) { 1100 ierr = PetscMalloc((inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar),&a->solve_work);CHKERRQ(ierr); 1101 ierr = PetscLogObjectMemory(inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));CHKERRQ(ierr); 1102 } 1103 1104 ierr = MatCholeskyFactorNumeric(outA,inA,info);CHKERRQ(ierr); 1105 PetscFunctionReturn(0); 1106 } 1107 1108 EXTERN_C_BEGIN 1109 #undef __FUNCT__ 1110 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices_SeqSBAIJ" 1111 PetscErrorCode MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices) 1112 { 1113 Mat_SeqSBAIJ *baij = (Mat_SeqSBAIJ *)mat->data; 1114 PetscInt i,nz,n; 1115 PetscErrorCode ierr; 1116 1117 PetscFunctionBegin; 1118 nz = baij->maxnz; 1119 n = mat->cmap->n; 1120 for (i=0; i<nz; i++) { 1121 baij->j[i] = indices[i]; 1122 } 1123 baij->nz = nz; 1124 for (i=0; i<n; i++) { 1125 baij->ilen[i] = baij->imax[i]; 1126 } 1127 ierr = MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1128 PetscFunctionReturn(0); 1129 } 1130 EXTERN_C_END 1131 1132 #undef __FUNCT__ 1133 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices" 1134 /*@ 1135 MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows 1136 in the matrix. 1137 1138 Input Parameters: 1139 + mat - the SeqSBAIJ matrix 1140 - indices - the column indices 1141 1142 Level: advanced 1143 1144 Notes: 1145 This can be called if you have precomputed the nonzero structure of the 1146 matrix and want to provide it to the matrix object to improve the performance 1147 of the MatSetValues() operation. 1148 1149 You MUST have set the correct numbers of nonzeros per row in the call to 1150 MatCreateSeqSBAIJ(), and the columns indices MUST be sorted. 1151 1152 MUST be called before any calls to MatSetValues() 1153 1154 .seealso: MatCreateSeqSBAIJ 1155 @*/ 1156 PetscErrorCode MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices) 1157 { 1158 PetscErrorCode ierr; 1159 1160 PetscFunctionBegin; 1161 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1162 PetscValidPointer(indices,2); 1163 ierr = PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt *),(mat,indices));CHKERRQ(ierr); 1164 PetscFunctionReturn(0); 1165 } 1166 1167 #undef __FUNCT__ 1168 #define __FUNCT__ "MatCopy_SeqSBAIJ" 1169 PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str) 1170 { 1171 PetscErrorCode ierr; 1172 1173 PetscFunctionBegin; 1174 /* If the two matrices have the same copy implementation, use fast copy. */ 1175 if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) { 1176 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1177 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1178 1179 if (a->i[A->rmap->N] != b->i[B->rmap->N]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of nonzeros in two matrices are different"); 1180 ierr = PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));CHKERRQ(ierr); 1181 } else { 1182 ierr = MatGetRowUpperTriangular(A);CHKERRQ(ierr); 1183 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 1184 ierr = MatRestoreRowUpperTriangular(A);CHKERRQ(ierr); 1185 } 1186 PetscFunctionReturn(0); 1187 } 1188 1189 #undef __FUNCT__ 1190 #define __FUNCT__ "MatSetUp_SeqSBAIJ" 1191 PetscErrorCode MatSetUp_SeqSBAIJ(Mat A) 1192 { 1193 PetscErrorCode ierr; 1194 1195 PetscFunctionBegin; 1196 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,A->rmap->bs,PETSC_DEFAULT,0);CHKERRQ(ierr); 1197 PetscFunctionReturn(0); 1198 } 1199 1200 #undef __FUNCT__ 1201 #define __FUNCT__ "MatSeqSBAIJGetArray_SeqSBAIJ" 1202 PetscErrorCode MatSeqSBAIJGetArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1203 { 1204 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1205 PetscFunctionBegin; 1206 *array = a->a; 1207 PetscFunctionReturn(0); 1208 } 1209 1210 #undef __FUNCT__ 1211 #define __FUNCT__ "MatSeqSBAIJRestoreArray_SeqSBAIJ" 1212 PetscErrorCode MatSeqSBAIJRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1213 { 1214 PetscFunctionBegin; 1215 PetscFunctionReturn(0); 1216 } 1217 1218 #undef __FUNCT__ 1219 #define __FUNCT__ "MatAXPY_SeqSBAIJ" 1220 PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 1221 { 1222 Mat_SeqSBAIJ *x=(Mat_SeqSBAIJ *)X->data, *y=(Mat_SeqSBAIJ *)Y->data; 1223 PetscErrorCode ierr; 1224 PetscInt i,bs=Y->rmap->bs,bs2=bs*bs,j; 1225 PetscBLASInt one = 1; 1226 1227 PetscFunctionBegin; 1228 if (str == SAME_NONZERO_PATTERN) { 1229 PetscScalar alpha = a; 1230 PetscBLASInt bnz = PetscBLASIntCast(x->nz*bs2); 1231 BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one); 1232 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 1233 if (y->xtoy && y->XtoY != X) { 1234 ierr = PetscFree(y->xtoy);CHKERRQ(ierr); 1235 ierr = MatDestroy(&y->XtoY);CHKERRQ(ierr); 1236 } 1237 if (!y->xtoy) { /* get xtoy */ 1238 ierr = MatAXPYGetxtoy_Private(x->mbs,x->i,x->j,PETSC_NULL, y->i,y->j,PETSC_NULL, &y->xtoy);CHKERRQ(ierr); 1239 y->XtoY = X; 1240 } 1241 for (i=0; i<x->nz; i++) { 1242 j = 0; 1243 while (j < bs2){ 1244 y->a[bs2*y->xtoy[i]+j] += a*(x->a[bs2*i+j]); 1245 j++; 1246 } 1247 } 1248 ierr = PetscInfo3(Y,"ratio of nnz_s(X)/nnz_s(Y): %D/%D = %G\n",bs2*x->nz,bs2*y->nz,(PetscReal)(bs2*x->nz)/(bs2*y->nz));CHKERRQ(ierr); 1249 } else { 1250 ierr = MatGetRowUpperTriangular(X);CHKERRQ(ierr); 1251 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 1252 ierr = MatRestoreRowUpperTriangular(X);CHKERRQ(ierr); 1253 } 1254 PetscFunctionReturn(0); 1255 } 1256 1257 #undef __FUNCT__ 1258 #define __FUNCT__ "MatIsSymmetric_SeqSBAIJ" 1259 PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1260 { 1261 PetscFunctionBegin; 1262 *flg = PETSC_TRUE; 1263 PetscFunctionReturn(0); 1264 } 1265 1266 #undef __FUNCT__ 1267 #define __FUNCT__ "MatIsStructurallySymmetric_SeqSBAIJ" 1268 PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool *flg) 1269 { 1270 PetscFunctionBegin; 1271 *flg = PETSC_TRUE; 1272 PetscFunctionReturn(0); 1273 } 1274 1275 #undef __FUNCT__ 1276 #define __FUNCT__ "MatIsHermitian_SeqSBAIJ" 1277 PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1278 { 1279 PetscFunctionBegin; 1280 *flg = PETSC_FALSE; 1281 PetscFunctionReturn(0); 1282 } 1283 1284 #undef __FUNCT__ 1285 #define __FUNCT__ "MatRealPart_SeqSBAIJ" 1286 PetscErrorCode MatRealPart_SeqSBAIJ(Mat A) 1287 { 1288 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1289 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1290 MatScalar *aa = a->a; 1291 1292 PetscFunctionBegin; 1293 for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]); 1294 PetscFunctionReturn(0); 1295 } 1296 1297 #undef __FUNCT__ 1298 #define __FUNCT__ "MatImaginaryPart_SeqSBAIJ" 1299 PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A) 1300 { 1301 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1302 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1303 MatScalar *aa = a->a; 1304 1305 PetscFunctionBegin; 1306 for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]); 1307 PetscFunctionReturn(0); 1308 } 1309 1310 #undef __FUNCT__ 1311 #define __FUNCT__ "MatZeroRowsColumns_SeqSBAIJ" 1312 PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b) 1313 { 1314 Mat_SeqSBAIJ *baij=(Mat_SeqSBAIJ*)A->data; 1315 PetscErrorCode ierr; 1316 PetscInt i,j,k,count; 1317 PetscInt bs=A->rmap->bs,bs2=baij->bs2,row,col; 1318 PetscScalar zero = 0.0; 1319 MatScalar *aa; 1320 const PetscScalar *xx; 1321 PetscScalar *bb; 1322 PetscBool *zeroed,vecs = PETSC_FALSE; 1323 1324 PetscFunctionBegin; 1325 /* fix right hand side if needed */ 1326 if (x && b) { 1327 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1328 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1329 vecs = PETSC_TRUE; 1330 } 1331 A->same_nonzero = PETSC_TRUE; 1332 1333 /* zero the columns */ 1334 ierr = PetscMalloc(A->rmap->n*sizeof(PetscBool),&zeroed);CHKERRQ(ierr); 1335 ierr = PetscMemzero(zeroed,A->rmap->n*sizeof(PetscBool));CHKERRQ(ierr); 1336 for (i=0; i<is_n; i++) { 1337 if (is_idx[i] < 0 || is_idx[i] >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range",is_idx[i]); 1338 zeroed[is_idx[i]] = PETSC_TRUE; 1339 } 1340 if (vecs) { 1341 for (i=0; i<A->rmap->N; i++) { 1342 row = i/bs; 1343 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1344 for (k=0; k<bs; k++) { 1345 col = bs*baij->j[j] + k; 1346 if (col <= i) continue; 1347 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1348 if (!zeroed[i] && zeroed[col]) { 1349 bb[i] -= aa[0]*xx[col]; 1350 } 1351 if (zeroed[i] && !zeroed[col]) { 1352 bb[col] -= aa[0]*xx[i]; 1353 } 1354 } 1355 } 1356 } 1357 for (i=0; i<is_n; i++) { 1358 bb[is_idx[i]] = diag*xx[is_idx[i]]; 1359 } 1360 } 1361 1362 for (i=0; i<A->rmap->N; i++) { 1363 if (!zeroed[i]) { 1364 row = i/bs; 1365 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1366 for (k=0; k<bs; k++) { 1367 col = bs*baij->j[j] + k; 1368 if (zeroed[col]) { 1369 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1370 aa[0] = 0.0; 1371 } 1372 } 1373 } 1374 } 1375 } 1376 ierr = PetscFree(zeroed);CHKERRQ(ierr); 1377 if (vecs) { 1378 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1379 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1380 } 1381 1382 /* zero the rows */ 1383 for (i=0; i<is_n; i++) { 1384 row = is_idx[i]; 1385 count = (baij->i[row/bs +1] - baij->i[row/bs])*bs; 1386 aa = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs); 1387 for (k=0; k<count; k++) { 1388 aa[0] = zero; 1389 aa += bs; 1390 } 1391 if (diag != 0.0) { 1392 ierr = (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); 1393 } 1394 } 1395 ierr = MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1396 PetscFunctionReturn(0); 1397 } 1398 1399 /* -------------------------------------------------------------------*/ 1400 static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ, 1401 MatGetRow_SeqSBAIJ, 1402 MatRestoreRow_SeqSBAIJ, 1403 MatMult_SeqSBAIJ_N, 1404 /* 4*/ MatMultAdd_SeqSBAIJ_N, 1405 MatMult_SeqSBAIJ_N, /* transpose versions are same as non-transpose versions */ 1406 MatMultAdd_SeqSBAIJ_N, 1407 0, 1408 0, 1409 0, 1410 /*10*/ 0, 1411 0, 1412 MatCholeskyFactor_SeqSBAIJ, 1413 MatSOR_SeqSBAIJ, 1414 MatTranspose_SeqSBAIJ, 1415 /*15*/ MatGetInfo_SeqSBAIJ, 1416 MatEqual_SeqSBAIJ, 1417 MatGetDiagonal_SeqSBAIJ, 1418 MatDiagonalScale_SeqSBAIJ, 1419 MatNorm_SeqSBAIJ, 1420 /*20*/ 0, 1421 MatAssemblyEnd_SeqSBAIJ, 1422 MatSetOption_SeqSBAIJ, 1423 MatZeroEntries_SeqSBAIJ, 1424 /*24*/ 0, 1425 0, 1426 0, 1427 0, 1428 0, 1429 /*29*/ MatSetUp_SeqSBAIJ, 1430 0, 1431 0, 1432 0, 1433 0, 1434 /*34*/ MatDuplicate_SeqSBAIJ, 1435 0, 1436 0, 1437 0, 1438 MatICCFactor_SeqSBAIJ, 1439 /*39*/ MatAXPY_SeqSBAIJ, 1440 MatGetSubMatrices_SeqSBAIJ, 1441 MatIncreaseOverlap_SeqSBAIJ, 1442 MatGetValues_SeqSBAIJ, 1443 MatCopy_SeqSBAIJ, 1444 /*44*/ 0, 1445 MatScale_SeqSBAIJ, 1446 0, 1447 0, 1448 MatZeroRowsColumns_SeqSBAIJ, 1449 /*49*/ 0, 1450 MatGetRowIJ_SeqSBAIJ, 1451 MatRestoreRowIJ_SeqSBAIJ, 1452 0, 1453 0, 1454 /*54*/ 0, 1455 0, 1456 0, 1457 0, 1458 MatSetValuesBlocked_SeqSBAIJ, 1459 /*59*/ MatGetSubMatrix_SeqSBAIJ, 1460 0, 1461 0, 1462 0, 1463 0, 1464 /*64*/ 0, 1465 0, 1466 0, 1467 0, 1468 0, 1469 /*69*/ MatGetRowMaxAbs_SeqSBAIJ, 1470 0, 1471 0, 1472 0, 1473 0, 1474 /*74*/ 0, 1475 0, 1476 0, 1477 0, 1478 0, 1479 /*79*/ 0, 1480 0, 1481 0, 1482 MatGetInertia_SeqSBAIJ, 1483 MatLoad_SeqSBAIJ, 1484 /*84*/ MatIsSymmetric_SeqSBAIJ, 1485 MatIsHermitian_SeqSBAIJ, 1486 MatIsStructurallySymmetric_SeqSBAIJ, 1487 0, 1488 0, 1489 /*89*/ 0, 1490 0, 1491 0, 1492 0, 1493 0, 1494 /*94*/ 0, 1495 0, 1496 0, 1497 0, 1498 0, 1499 /*99*/ 0, 1500 0, 1501 0, 1502 0, 1503 0, 1504 /*104*/0, 1505 MatRealPart_SeqSBAIJ, 1506 MatImaginaryPart_SeqSBAIJ, 1507 MatGetRowUpperTriangular_SeqSBAIJ, 1508 MatRestoreRowUpperTriangular_SeqSBAIJ, 1509 /*109*/0, 1510 0, 1511 0, 1512 0, 1513 MatMissingDiagonal_SeqSBAIJ, 1514 /*114*/0, 1515 0, 1516 0, 1517 0, 1518 0, 1519 /*119*/0, 1520 0, 1521 0, 1522 0 1523 }; 1524 1525 EXTERN_C_BEGIN 1526 #undef __FUNCT__ 1527 #define __FUNCT__ "MatStoreValues_SeqSBAIJ" 1528 PetscErrorCode MatStoreValues_SeqSBAIJ(Mat mat) 1529 { 1530 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ *)mat->data; 1531 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1532 PetscErrorCode ierr; 1533 1534 PetscFunctionBegin; 1535 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1536 1537 /* allocate space for values if not already there */ 1538 if (!aij->saved_values) { 1539 ierr = PetscMalloc((nz+1)*sizeof(PetscScalar),&aij->saved_values);CHKERRQ(ierr); 1540 } 1541 1542 /* copy values over */ 1543 ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1544 PetscFunctionReturn(0); 1545 } 1546 EXTERN_C_END 1547 1548 EXTERN_C_BEGIN 1549 #undef __FUNCT__ 1550 #define __FUNCT__ "MatRetrieveValues_SeqSBAIJ" 1551 PetscErrorCode MatRetrieveValues_SeqSBAIJ(Mat mat) 1552 { 1553 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ *)mat->data; 1554 PetscErrorCode ierr; 1555 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1556 1557 PetscFunctionBegin; 1558 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1559 if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first"); 1560 1561 /* copy values over */ 1562 ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1563 PetscFunctionReturn(0); 1564 } 1565 EXTERN_C_END 1566 1567 EXTERN_C_BEGIN 1568 #undef __FUNCT__ 1569 #define __FUNCT__ "MatSeqSBAIJSetPreallocation_SeqSBAIJ" 1570 PetscErrorCode MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz) 1571 { 1572 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1573 PetscErrorCode ierr; 1574 PetscInt i,mbs,bs2; 1575 PetscBool skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE; 1576 1577 PetscFunctionBegin; 1578 if (nz >= 0 || nnz) realalloc = PETSC_TRUE; 1579 B->preallocated = PETSC_TRUE; 1580 1581 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 1582 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 1583 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 1584 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 1585 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 1586 1587 mbs = B->rmap->N/bs; 1588 bs2 = bs*bs; 1589 1590 if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize"); 1591 1592 if (nz == MAT_SKIP_ALLOCATION) { 1593 skipallocation = PETSC_TRUE; 1594 nz = 0; 1595 } 1596 1597 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3; 1598 if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz); 1599 if (nnz) { 1600 for (i=0; i<mbs; i++) { 1601 if (nnz[i] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be less than 0: local row %D value %D",i,nnz[i]); 1602 if (nnz[i] > mbs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than block row length: local row %D value %D rowlength %D",i,nnz[i],mbs); 1603 } 1604 } 1605 1606 B->ops->mult = MatMult_SeqSBAIJ_N; 1607 B->ops->multadd = MatMultAdd_SeqSBAIJ_N; 1608 B->ops->multtranspose = MatMult_SeqSBAIJ_N; 1609 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N; 1610 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);CHKERRQ(ierr); 1611 if (!flg) { 1612 switch (bs) { 1613 case 1: 1614 B->ops->mult = MatMult_SeqSBAIJ_1; 1615 B->ops->multadd = MatMultAdd_SeqSBAIJ_1; 1616 B->ops->multtranspose = MatMult_SeqSBAIJ_1; 1617 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1; 1618 break; 1619 case 2: 1620 B->ops->mult = MatMult_SeqSBAIJ_2; 1621 B->ops->multadd = MatMultAdd_SeqSBAIJ_2; 1622 B->ops->multtranspose = MatMult_SeqSBAIJ_2; 1623 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2; 1624 break; 1625 case 3: 1626 B->ops->mult = MatMult_SeqSBAIJ_3; 1627 B->ops->multadd = MatMultAdd_SeqSBAIJ_3; 1628 B->ops->multtranspose = MatMult_SeqSBAIJ_3; 1629 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3; 1630 break; 1631 case 4: 1632 B->ops->mult = MatMult_SeqSBAIJ_4; 1633 B->ops->multadd = MatMultAdd_SeqSBAIJ_4; 1634 B->ops->multtranspose = MatMult_SeqSBAIJ_4; 1635 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4; 1636 break; 1637 case 5: 1638 B->ops->mult = MatMult_SeqSBAIJ_5; 1639 B->ops->multadd = MatMultAdd_SeqSBAIJ_5; 1640 B->ops->multtranspose = MatMult_SeqSBAIJ_5; 1641 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5; 1642 break; 1643 case 6: 1644 B->ops->mult = MatMult_SeqSBAIJ_6; 1645 B->ops->multadd = MatMultAdd_SeqSBAIJ_6; 1646 B->ops->multtranspose = MatMult_SeqSBAIJ_6; 1647 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6; 1648 break; 1649 case 7: 1650 B->ops->mult = MatMult_SeqSBAIJ_7; 1651 B->ops->multadd = MatMultAdd_SeqSBAIJ_7; 1652 B->ops->multtranspose = MatMult_SeqSBAIJ_7; 1653 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7; 1654 break; 1655 } 1656 } 1657 1658 b->mbs = mbs; 1659 b->nbs = mbs; 1660 if (!skipallocation) { 1661 if (!b->imax) { 1662 ierr = PetscMalloc2(mbs,PetscInt,&b->imax,mbs,PetscInt,&b->ilen);CHKERRQ(ierr); 1663 b->free_imax_ilen = PETSC_TRUE; 1664 ierr = PetscLogObjectMemory(B,2*mbs*sizeof(PetscInt));CHKERRQ(ierr); 1665 } 1666 if (!nnz) { 1667 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5; 1668 else if (nz <= 0) nz = 1; 1669 for (i=0; i<mbs; i++) { 1670 b->imax[i] = nz; 1671 } 1672 nz = nz*mbs; /* total nz */ 1673 } else { 1674 nz = 0; 1675 for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];} 1676 } 1677 /* b->ilen will count nonzeros in each block row so far. */ 1678 for (i=0; i<mbs; i++) { b->ilen[i] = 0;} 1679 /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */ 1680 1681 /* allocate the matrix space */ 1682 ierr = MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);CHKERRQ(ierr); 1683 ierr = PetscMalloc3(bs2*nz,PetscScalar,&b->a,nz,PetscInt,&b->j,B->rmap->N+1,PetscInt,&b->i);CHKERRQ(ierr); 1684 ierr = PetscLogObjectMemory(B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr); 1685 ierr = PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 1686 ierr = PetscMemzero(b->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 1687 b->singlemalloc = PETSC_TRUE; 1688 1689 /* pointer to beginning of each row */ 1690 b->i[0] = 0; 1691 for (i=1; i<mbs+1; i++) { 1692 b->i[i] = b->i[i-1] + b->imax[i-1]; 1693 } 1694 b->free_a = PETSC_TRUE; 1695 b->free_ij = PETSC_TRUE; 1696 } else { 1697 b->free_a = PETSC_FALSE; 1698 b->free_ij = PETSC_FALSE; 1699 } 1700 1701 B->rmap->bs = bs; 1702 b->bs2 = bs2; 1703 b->nz = 0; 1704 b->maxnz = nz; 1705 1706 b->inew = 0; 1707 b->jnew = 0; 1708 b->anew = 0; 1709 b->a2anew = 0; 1710 b->permute = PETSC_FALSE; 1711 if (realalloc) {ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);} 1712 PetscFunctionReturn(0); 1713 } 1714 EXTERN_C_END 1715 1716 /* 1717 This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization 1718 */ 1719 #undef __FUNCT__ 1720 #define __FUNCT__ "MatSeqSBAIJSetNumericFactorization_inplace" 1721 PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural) 1722 { 1723 PetscErrorCode ierr; 1724 PetscBool flg = PETSC_FALSE; 1725 PetscInt bs = B->rmap->bs; 1726 1727 PetscFunctionBegin; 1728 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);CHKERRQ(ierr); 1729 if (flg) bs = 8; 1730 1731 if (!natural) { 1732 switch (bs) { 1733 case 1: 1734 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace; 1735 break; 1736 case 2: 1737 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2; 1738 break; 1739 case 3: 1740 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3; 1741 break; 1742 case 4: 1743 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4; 1744 break; 1745 case 5: 1746 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5; 1747 break; 1748 case 6: 1749 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6; 1750 break; 1751 case 7: 1752 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7; 1753 break; 1754 default: 1755 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N; 1756 break; 1757 } 1758 } else { 1759 switch (bs) { 1760 case 1: 1761 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace; 1762 break; 1763 case 2: 1764 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering; 1765 break; 1766 case 3: 1767 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering; 1768 break; 1769 case 4: 1770 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering; 1771 break; 1772 case 5: 1773 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering; 1774 break; 1775 case 6: 1776 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering; 1777 break; 1778 case 7: 1779 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering; 1780 break; 1781 default: 1782 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering; 1783 break; 1784 } 1785 } 1786 PetscFunctionReturn(0); 1787 } 1788 1789 EXTERN_C_BEGIN 1790 extern PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*); 1791 extern PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*); 1792 EXTERN_C_END 1793 1794 1795 EXTERN_C_BEGIN 1796 #undef __FUNCT__ 1797 #define __FUNCT__ "MatGetFactor_seqsbaij_petsc" 1798 PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B) 1799 { 1800 PetscInt n = A->rmap->n; 1801 PetscErrorCode ierr; 1802 1803 PetscFunctionBegin; 1804 #if defined(PETSC_USE_COMPLEX) 1805 if (A->hermitian)SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported"); 1806 #endif 1807 ierr = MatCreate(((PetscObject)A)->comm,B);CHKERRQ(ierr); 1808 ierr = MatSetSizes(*B,n,n,n,n);CHKERRQ(ierr); 1809 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1810 ierr = MatSetType(*B,MATSEQSBAIJ);CHKERRQ(ierr); 1811 ierr = MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,PETSC_NULL);CHKERRQ(ierr); 1812 (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ; 1813 (*B)->ops->iccfactorsymbolic = MatICCFactorSymbolic_SeqSBAIJ; 1814 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported"); 1815 (*B)->factortype = ftype; 1816 PetscFunctionReturn(0); 1817 } 1818 EXTERN_C_END 1819 1820 EXTERN_C_BEGIN 1821 #undef __FUNCT__ 1822 #define __FUNCT__ "MatGetFactorAvailable_seqsbaij_petsc" 1823 PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool *flg) 1824 { 1825 PetscFunctionBegin; 1826 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1827 *flg = PETSC_TRUE; 1828 } else { 1829 *flg = PETSC_FALSE; 1830 } 1831 PetscFunctionReturn(0); 1832 } 1833 EXTERN_C_END 1834 1835 EXTERN_C_BEGIN 1836 #if defined(PETSC_HAVE_MUMPS) 1837 extern PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*); 1838 #endif 1839 #if defined(PETSC_HAVE_PASTIX) 1840 extern PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*); 1841 #endif 1842 #if defined(PETSC_HAVE_CHOLMOD) 1843 extern PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*); 1844 #endif 1845 extern PetscErrorCode MatGetFactor_seqsbaij_sbstrm(Mat,MatFactorType,Mat*); 1846 EXTERN_C_END 1847 1848 /*MC 1849 MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices, 1850 based on block compressed sparse row format. Only the upper triangular portion of the matrix is stored. 1851 1852 For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you 1853 can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd() 1854 1855 Options Database Keys: 1856 . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions() 1857 1858 Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not 1859 stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use 1860 the options database -mat_ignore_lower_triangular false it will generate an error if you try to set a value in the lower triangular portion. 1861 1862 1863 Level: beginner 1864 1865 .seealso: MatCreateSeqSBAIJ 1866 M*/ 1867 1868 EXTERN_C_BEGIN 1869 extern PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*); 1870 EXTERN_C_END 1871 1872 1873 EXTERN_C_BEGIN 1874 #undef __FUNCT__ 1875 #define __FUNCT__ "MatCreate_SeqSBAIJ" 1876 PetscErrorCode MatCreate_SeqSBAIJ(Mat B) 1877 { 1878 Mat_SeqSBAIJ *b; 1879 PetscErrorCode ierr; 1880 PetscMPIInt size; 1881 PetscBool no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE; 1882 1883 PetscFunctionBegin; 1884 ierr = MPI_Comm_size(((PetscObject)B)->comm,&size);CHKERRQ(ierr); 1885 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1"); 1886 1887 ierr = PetscNewLog(B,Mat_SeqSBAIJ,&b);CHKERRQ(ierr); 1888 B->data = (void*)b; 1889 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 1890 B->ops->destroy = MatDestroy_SeqSBAIJ; 1891 B->ops->view = MatView_SeqSBAIJ; 1892 b->row = 0; 1893 b->icol = 0; 1894 b->reallocs = 0; 1895 b->saved_values = 0; 1896 b->inode.limit = 5; 1897 b->inode.max_limit = 5; 1898 1899 b->roworiented = PETSC_TRUE; 1900 b->nonew = 0; 1901 b->diag = 0; 1902 b->solve_work = 0; 1903 b->mult_work = 0; 1904 B->spptr = 0; 1905 B->info.nz_unneeded = (PetscReal)b->maxnz*b->bs2; 1906 b->keepnonzeropattern = PETSC_FALSE; 1907 b->xtoy = 0; 1908 b->XtoY = 0; 1909 1910 b->inew = 0; 1911 b->jnew = 0; 1912 b->anew = 0; 1913 b->a2anew = 0; 1914 b->permute = PETSC_FALSE; 1915 1916 b->ignore_ltriangular = PETSC_TRUE; 1917 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,PETSC_NULL);CHKERRQ(ierr); 1918 1919 b->getrow_utriangular = PETSC_FALSE; 1920 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,PETSC_NULL);CHKERRQ(ierr); 1921 1922 #if defined(PETSC_HAVE_PASTIX) 1923 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_pastix_C", 1924 "MatGetFactor_seqsbaij_pastix", 1925 MatGetFactor_seqsbaij_pastix);CHKERRQ(ierr); 1926 #endif 1927 #if defined(PETSC_HAVE_MUMPS) 1928 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_mumps_C", 1929 "MatGetFactor_sbaij_mumps", 1930 MatGetFactor_sbaij_mumps);CHKERRQ(ierr); 1931 #endif 1932 #if defined(PETSC_HAVE_CHOLMOD) 1933 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_cholmod_C", 1934 "MatGetFactor_seqsbaij_cholmod", 1935 MatGetFactor_seqsbaij_cholmod);CHKERRQ(ierr); 1936 #endif 1937 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactorAvailable_petsc_C", 1938 "MatGetFactorAvailable_seqsbaij_petsc", 1939 MatGetFactorAvailable_seqsbaij_petsc);CHKERRQ(ierr); 1940 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_petsc_C", 1941 "MatGetFactor_seqsbaij_petsc", 1942 MatGetFactor_seqsbaij_petsc);CHKERRQ(ierr); 1943 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_sbstrm_C", 1944 "MatGetFactor_seqsbaij_sbstrm", 1945 MatGetFactor_seqsbaij_sbstrm);CHKERRQ(ierr); 1946 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatStoreValues_C", 1947 "MatStoreValues_SeqSBAIJ", 1948 MatStoreValues_SeqSBAIJ);CHKERRQ(ierr); 1949 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatRetrieveValues_C", 1950 "MatRetrieveValues_SeqSBAIJ", 1951 (void*)MatRetrieveValues_SeqSBAIJ);CHKERRQ(ierr); 1952 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C", 1953 "MatSeqSBAIJSetColumnIndices_SeqSBAIJ", 1954 MatSeqSBAIJSetColumnIndices_SeqSBAIJ);CHKERRQ(ierr); 1955 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqaij_C", 1956 "MatConvert_SeqSBAIJ_SeqAIJ", 1957 MatConvert_SeqSBAIJ_SeqAIJ);CHKERRQ(ierr); 1958 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C", 1959 "MatConvert_SeqSBAIJ_SeqBAIJ", 1960 MatConvert_SeqSBAIJ_SeqBAIJ);CHKERRQ(ierr); 1961 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetPreallocation_C", 1962 "MatSeqSBAIJSetPreallocation_SeqSBAIJ", 1963 MatSeqSBAIJSetPreallocation_SeqSBAIJ);CHKERRQ(ierr); 1964 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C", 1965 "MatConvert_SeqSBAIJ_SeqSBSTRM", 1966 MatConvert_SeqSBAIJ_SeqSBSTRM);CHKERRQ(ierr); 1967 1968 B->symmetric = PETSC_TRUE; 1969 B->structurally_symmetric = PETSC_TRUE; 1970 B->symmetric_set = PETSC_TRUE; 1971 B->structurally_symmetric_set = PETSC_TRUE; 1972 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);CHKERRQ(ierr); 1973 1974 ierr = PetscOptionsBegin(((PetscObject)B)->comm,((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");CHKERRQ(ierr); 1975 ierr = PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",PETSC_NULL,no_unroll,&no_unroll,PETSC_NULL);CHKERRQ(ierr); 1976 if (no_unroll) {ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");CHKERRQ(ierr);} 1977 ierr = PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",PETSC_NULL,no_inode,&no_inode,PETSC_NULL);CHKERRQ(ierr); 1978 if (no_inode) {ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");CHKERRQ(ierr);} 1979 ierr = PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",PETSC_NULL,b->inode.limit,&b->inode.limit,PETSC_NULL);CHKERRQ(ierr); 1980 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1981 b->inode.use = (PetscBool)(!(no_unroll || no_inode)); 1982 if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit; 1983 1984 PetscFunctionReturn(0); 1985 } 1986 EXTERN_C_END 1987 1988 #undef __FUNCT__ 1989 #define __FUNCT__ "MatSeqSBAIJSetPreallocation" 1990 /*@C 1991 MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block 1992 compressed row) format. For good matrix assembly performance the 1993 user should preallocate the matrix storage by setting the parameter nz 1994 (or the array nnz). By setting these parameters accurately, performance 1995 during matrix assembly can be increased by more than a factor of 50. 1996 1997 Collective on Mat 1998 1999 Input Parameters: 2000 + A - the symmetric matrix 2001 . bs - size of block 2002 . nz - number of block nonzeros per block row (same for all rows) 2003 - nnz - array containing the number of block nonzeros in the upper triangular plus 2004 diagonal portion of each block (possibly different for each block row) or PETSC_NULL 2005 2006 Options Database Keys: 2007 . -mat_no_unroll - uses code that does not unroll the loops in the 2008 block calculations (much slower) 2009 . -mat_block_size - size of the blocks to use (only works if a negative bs is passed in 2010 2011 Level: intermediate 2012 2013 Notes: 2014 Specify the preallocated storage with either nz or nnz (not both). 2015 Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 2016 allocation. See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details. 2017 2018 You can call MatGetInfo() to get information on how effective the preallocation was; 2019 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 2020 You can also run with the option -info and look for messages with the string 2021 malloc in them to see if additional memory allocation was needed. 2022 2023 If the nnz parameter is given then the nz parameter is ignored 2024 2025 2026 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() 2027 @*/ 2028 PetscErrorCode MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[]) 2029 { 2030 PetscErrorCode ierr; 2031 2032 PetscFunctionBegin; 2033 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2034 PetscValidType(B,1); 2035 PetscValidLogicalCollectiveInt(B,bs,2); 2036 ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));CHKERRQ(ierr); 2037 PetscFunctionReturn(0); 2038 } 2039 2040 #undef __FUNCT__ 2041 #define __FUNCT__ "MatCreateSeqSBAIJ" 2042 /*@C 2043 MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block 2044 compressed row) format. For good matrix assembly performance the 2045 user should preallocate the matrix storage by setting the parameter nz 2046 (or the array nnz). By setting these parameters accurately, performance 2047 during matrix assembly can be increased by more than a factor of 50. 2048 2049 Collective on MPI_Comm 2050 2051 Input Parameters: 2052 + comm - MPI communicator, set to PETSC_COMM_SELF 2053 . bs - size of block 2054 . m - number of rows, or number of columns 2055 . nz - number of block nonzeros per block row (same for all rows) 2056 - nnz - array containing the number of block nonzeros in the upper triangular plus 2057 diagonal portion of each block (possibly different for each block row) or PETSC_NULL 2058 2059 Output Parameter: 2060 . A - the symmetric matrix 2061 2062 Options Database Keys: 2063 . -mat_no_unroll - uses code that does not unroll the loops in the 2064 block calculations (much slower) 2065 . -mat_block_size - size of the blocks to use 2066 2067 Level: intermediate 2068 2069 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 2070 MatXXXXSetPreallocation() paradgm instead of this routine directly. 2071 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 2072 2073 Notes: 2074 The number of rows and columns must be divisible by blocksize. 2075 This matrix type does not support complex Hermitian operation. 2076 2077 Specify the preallocated storage with either nz or nnz (not both). 2078 Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 2079 allocation. See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details. 2080 2081 If the nnz parameter is given then the nz parameter is ignored 2082 2083 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() 2084 @*/ 2085 PetscErrorCode MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A) 2086 { 2087 PetscErrorCode ierr; 2088 2089 PetscFunctionBegin; 2090 ierr = MatCreate(comm,A);CHKERRQ(ierr); 2091 ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); 2092 ierr = MatSetType(*A,MATSEQSBAIJ);CHKERRQ(ierr); 2093 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);CHKERRQ(ierr); 2094 PetscFunctionReturn(0); 2095 } 2096 2097 #undef __FUNCT__ 2098 #define __FUNCT__ "MatDuplicate_SeqSBAIJ" 2099 PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B) 2100 { 2101 Mat C; 2102 Mat_SeqSBAIJ *c,*a = (Mat_SeqSBAIJ*)A->data; 2103 PetscErrorCode ierr; 2104 PetscInt i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2; 2105 2106 PetscFunctionBegin; 2107 if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix"); 2108 2109 *B = 0; 2110 ierr = MatCreate(((PetscObject)A)->comm,&C);CHKERRQ(ierr); 2111 ierr = MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);CHKERRQ(ierr); 2112 ierr = MatSetType(C,MATSEQSBAIJ);CHKERRQ(ierr); 2113 ierr = PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2114 c = (Mat_SeqSBAIJ*)C->data; 2115 2116 C->preallocated = PETSC_TRUE; 2117 C->factortype = A->factortype; 2118 c->row = 0; 2119 c->icol = 0; 2120 c->saved_values = 0; 2121 c->keepnonzeropattern = a->keepnonzeropattern; 2122 C->assembled = PETSC_TRUE; 2123 2124 ierr = PetscLayoutReference(A->rmap,&C->rmap);CHKERRQ(ierr); 2125 ierr = PetscLayoutReference(A->cmap,&C->cmap);CHKERRQ(ierr); 2126 c->bs2 = a->bs2; 2127 c->mbs = a->mbs; 2128 c->nbs = a->nbs; 2129 2130 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2131 c->imax = a->imax; 2132 c->ilen = a->ilen; 2133 c->free_imax_ilen = PETSC_FALSE; 2134 } else { 2135 ierr = PetscMalloc2((mbs+1),PetscInt,&c->imax,(mbs+1),PetscInt,&c->ilen);CHKERRQ(ierr); 2136 ierr = PetscLogObjectMemory(C,2*(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2137 for (i=0; i<mbs; i++) { 2138 c->imax[i] = a->imax[i]; 2139 c->ilen[i] = a->ilen[i]; 2140 } 2141 c->free_imax_ilen = PETSC_TRUE; 2142 } 2143 2144 /* allocate the matrix space */ 2145 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2146 ierr = PetscMalloc(bs2*nz*sizeof(MatScalar),&c->a);CHKERRQ(ierr); 2147 ierr = PetscLogObjectMemory(C,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 2148 c->i = a->i; 2149 c->j = a->j; 2150 c->singlemalloc = PETSC_FALSE; 2151 c->free_a = PETSC_TRUE; 2152 c->free_ij = PETSC_FALSE; 2153 c->parent = A; 2154 ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr); 2155 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2156 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2157 } else { 2158 ierr = PetscMalloc3(bs2*nz,MatScalar,&c->a,nz,PetscInt,&c->j,mbs+1,PetscInt,&c->i);CHKERRQ(ierr); 2159 ierr = PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2160 ierr = PetscLogObjectMemory(C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));CHKERRQ(ierr); 2161 c->singlemalloc = PETSC_TRUE; 2162 c->free_a = PETSC_TRUE; 2163 c->free_ij = PETSC_TRUE; 2164 } 2165 if (mbs > 0) { 2166 if (cpvalues != MAT_SHARE_NONZERO_PATTERN) { 2167 ierr = PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 2168 } 2169 if (cpvalues == MAT_COPY_VALUES) { 2170 ierr = PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2171 } else { 2172 ierr = PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2173 } 2174 if (a->jshort) { 2175 /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */ 2176 /* if the parent matrix is reassembled, this child matrix will never notice */ 2177 ierr = PetscMalloc(nz*sizeof(unsigned short),&c->jshort);CHKERRQ(ierr); 2178 ierr = PetscLogObjectMemory(C,nz*sizeof(unsigned short));CHKERRQ(ierr); 2179 ierr = PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));CHKERRQ(ierr); 2180 c->free_jshort = PETSC_TRUE; 2181 } 2182 } 2183 2184 c->roworiented = a->roworiented; 2185 c->nonew = a->nonew; 2186 2187 if (a->diag) { 2188 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2189 c->diag = a->diag; 2190 c->free_diag = PETSC_FALSE; 2191 } else { 2192 ierr = PetscMalloc(mbs*sizeof(PetscInt),&c->diag);CHKERRQ(ierr); 2193 ierr = PetscLogObjectMemory(C,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2194 for (i=0; i<mbs; i++) { 2195 c->diag[i] = a->diag[i]; 2196 } 2197 c->free_diag = PETSC_TRUE; 2198 } 2199 } 2200 c->nz = a->nz; 2201 c->maxnz = a->nz; /* Since we allocate exactly the right amount */ 2202 c->solve_work = 0; 2203 c->mult_work = 0; 2204 *B = C; 2205 ierr = PetscFListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);CHKERRQ(ierr); 2206 PetscFunctionReturn(0); 2207 } 2208 2209 #undef __FUNCT__ 2210 #define __FUNCT__ "MatLoad_SeqSBAIJ" 2211 PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer) 2212 { 2213 Mat_SeqSBAIJ *a; 2214 PetscErrorCode ierr; 2215 int fd; 2216 PetscMPIInt size; 2217 PetscInt i,nz,header[4],*rowlengths=0,M,N,bs=1; 2218 PetscInt *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount; 2219 PetscInt kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols; 2220 PetscInt *masked,nmask,tmp,bs2,ishift; 2221 PetscScalar *aa; 2222 MPI_Comm comm = ((PetscObject)viewer)->comm; 2223 2224 PetscFunctionBegin; 2225 ierr = PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,PETSC_NULL);CHKERRQ(ierr); 2226 bs2 = bs*bs; 2227 2228 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2229 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor"); 2230 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2231 ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr); 2232 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object"); 2233 M = header[1]; N = header[2]; nz = header[3]; 2234 2235 if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ"); 2236 2237 if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices"); 2238 2239 /* 2240 This code adds extra rows to make sure the number of rows is 2241 divisible by the blocksize 2242 */ 2243 mbs = M/bs; 2244 extra_rows = bs - M + bs*(mbs); 2245 if (extra_rows == bs) extra_rows = 0; 2246 else mbs++; 2247 if (extra_rows) { 2248 ierr = PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");CHKERRQ(ierr); 2249 } 2250 2251 /* Set global sizes if not already set */ 2252 if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) { 2253 ierr = MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);CHKERRQ(ierr); 2254 } else { /* Check if the matrix global sizes are correct */ 2255 ierr = MatGetSize(newmat,&rows,&cols);CHKERRQ(ierr); 2256 if (M != rows || N != cols) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix in file of different length (%d, %d) than the input matrix (%d, %d)",M,N,rows,cols); 2257 } 2258 2259 /* read in row lengths */ 2260 ierr = PetscMalloc((M+extra_rows)*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr); 2261 ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); 2262 for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1; 2263 2264 /* read in column indices */ 2265 ierr = PetscMalloc((nz+extra_rows)*sizeof(PetscInt),&jj);CHKERRQ(ierr); 2266 ierr = PetscBinaryRead(fd,jj,nz,PETSC_INT);CHKERRQ(ierr); 2267 for (i=0; i<extra_rows; i++) jj[nz+i] = M+i; 2268 2269 /* loop over row lengths determining block row lengths */ 2270 ierr = PetscMalloc(mbs*sizeof(PetscInt),&s_browlengths);CHKERRQ(ierr); 2271 ierr = PetscMemzero(s_browlengths,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2272 ierr = PetscMalloc2(mbs,PetscInt,&mask,mbs,PetscInt,&masked);CHKERRQ(ierr); 2273 ierr = PetscMemzero(mask,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2274 rowcount = 0; 2275 nzcount = 0; 2276 for (i=0; i<mbs; i++) { 2277 nmask = 0; 2278 for (j=0; j<bs; j++) { 2279 kmax = rowlengths[rowcount]; 2280 for (k=0; k<kmax; k++) { 2281 tmp = jj[nzcount++]/bs; /* block col. index */ 2282 if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;} 2283 } 2284 rowcount++; 2285 } 2286 s_browlengths[i] += nmask; 2287 2288 /* zero out the mask elements we set */ 2289 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2290 } 2291 2292 /* Do preallocation */ 2293 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);CHKERRQ(ierr); 2294 a = (Mat_SeqSBAIJ*)newmat->data; 2295 2296 /* set matrix "i" values */ 2297 a->i[0] = 0; 2298 for (i=1; i<= mbs; i++) { 2299 a->i[i] = a->i[i-1] + s_browlengths[i-1]; 2300 a->ilen[i-1] = s_browlengths[i-1]; 2301 } 2302 a->nz = a->i[mbs]; 2303 2304 /* read in nonzero values */ 2305 ierr = PetscMalloc((nz+extra_rows)*sizeof(PetscScalar),&aa);CHKERRQ(ierr); 2306 ierr = PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);CHKERRQ(ierr); 2307 for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0; 2308 2309 /* set "a" and "j" values into matrix */ 2310 nzcount = 0; jcount = 0; 2311 for (i=0; i<mbs; i++) { 2312 nzcountb = nzcount; 2313 nmask = 0; 2314 for (j=0; j<bs; j++) { 2315 kmax = rowlengths[i*bs+j]; 2316 for (k=0; k<kmax; k++) { 2317 tmp = jj[nzcount++]/bs; /* block col. index */ 2318 if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;} 2319 } 2320 } 2321 /* sort the masked values */ 2322 ierr = PetscSortInt(nmask,masked);CHKERRQ(ierr); 2323 2324 /* set "j" values into matrix */ 2325 maskcount = 1; 2326 for (j=0; j<nmask; j++) { 2327 a->j[jcount++] = masked[j]; 2328 mask[masked[j]] = maskcount++; 2329 } 2330 2331 /* set "a" values into matrix */ 2332 ishift = bs2*a->i[i]; 2333 for (j=0; j<bs; j++) { 2334 kmax = rowlengths[i*bs+j]; 2335 for (k=0; k<kmax; k++) { 2336 tmp = jj[nzcountb]/bs ; /* block col. index */ 2337 if (tmp >= i){ 2338 block = mask[tmp] - 1; 2339 point = jj[nzcountb] - bs*tmp; 2340 idx = ishift + bs2*block + j + bs*point; 2341 a->a[idx] = aa[nzcountb]; 2342 } 2343 nzcountb++; 2344 } 2345 } 2346 /* zero out the mask elements we set */ 2347 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2348 } 2349 if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix"); 2350 2351 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2352 ierr = PetscFree(s_browlengths);CHKERRQ(ierr); 2353 ierr = PetscFree(aa);CHKERRQ(ierr); 2354 ierr = PetscFree(jj);CHKERRQ(ierr); 2355 ierr = PetscFree2(mask,masked);CHKERRQ(ierr); 2356 2357 ierr = MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2358 ierr = MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2359 PetscFunctionReturn(0); 2360 } 2361 2362 #undef __FUNCT__ 2363 #define __FUNCT__ "MatCreateSeqSBAIJWithArrays" 2364 /*@ 2365 MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements 2366 (upper triangular entries in CSR format) provided by the user. 2367 2368 Collective on MPI_Comm 2369 2370 Input Parameters: 2371 + comm - must be an MPI communicator of size 1 2372 . bs - size of block 2373 . m - number of rows 2374 . n - number of columns 2375 . i - row indices 2376 . j - column indices 2377 - a - matrix values 2378 2379 Output Parameter: 2380 . mat - the matrix 2381 2382 Level: advanced 2383 2384 Notes: 2385 The i, j, and a arrays are not copied by this routine, the user must free these arrays 2386 once the matrix is destroyed 2387 2388 You cannot set new nonzero locations into this matrix, that will generate an error. 2389 2390 The i and j indices are 0 based 2391 2392 When block size is greater than 1 the matrix values must be stored using the SBAIJ storage format (see the SBAIJ code to determine this). For block size of 1 2393 it is the regular CSR format excluding the lower triangular elements. 2394 2395 .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ() 2396 2397 @*/ 2398 PetscErrorCode MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt* i,PetscInt*j,PetscScalar *a,Mat *mat) 2399 { 2400 PetscErrorCode ierr; 2401 PetscInt ii; 2402 Mat_SeqSBAIJ *sbaij; 2403 2404 PetscFunctionBegin; 2405 if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs); 2406 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 2407 2408 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 2409 ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); 2410 ierr = MatSetType(*mat,MATSEQSBAIJ);CHKERRQ(ierr); 2411 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);CHKERRQ(ierr); 2412 sbaij = (Mat_SeqSBAIJ*)(*mat)->data; 2413 ierr = PetscMalloc2(m,PetscInt,&sbaij->imax,m,PetscInt,&sbaij->ilen);CHKERRQ(ierr); 2414 ierr = PetscLogObjectMemory(*mat,2*m*sizeof(PetscInt));CHKERRQ(ierr); 2415 2416 sbaij->i = i; 2417 sbaij->j = j; 2418 sbaij->a = a; 2419 sbaij->singlemalloc = PETSC_FALSE; 2420 sbaij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/ 2421 sbaij->free_a = PETSC_FALSE; 2422 sbaij->free_ij = PETSC_FALSE; 2423 2424 for (ii=0; ii<m; ii++) { 2425 sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii]; 2426 #if defined(PETSC_USE_DEBUG) 2427 if (i[ii+1] - i[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row length in i (row indices) row = %d length = %d",ii,i[ii+1] - i[ii]); 2428 #endif 2429 } 2430 #if defined(PETSC_USE_DEBUG) 2431 for (ii=0; ii<sbaij->i[m]; ii++) { 2432 if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]); 2433 if (j[ii] > n - 1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column index to large at location = %d index = %d",ii,j[ii]); 2434 } 2435 #endif 2436 2437 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2438 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2439 PetscFunctionReturn(0); 2440 } 2441 2442 2443 2444 2445 2446