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,PetscInt *ia[],PetscInt *ja[],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 PetscErrorCode ierr; 72 73 PetscFunctionBegin; 74 *nn = n; 75 if (!ia) PetscFunctionReturn(0); 76 if (!blockcompressed) { 77 /* malloc & create the natural set of indices */ 78 ierr = PetscMalloc2((n+1)*bs,PetscInt,ia,nz*bs,PetscInt,ja);CHKERRQ(ierr); 79 for (i=0; i<n+1; i++) { 80 for (j=0; j<bs; j++) { 81 *ia[i*bs+j] = a->i[i]*bs+j+oshift; 82 } 83 } 84 for (i=0; i<nz; i++) { 85 for (j=0; j<bs; j++) { 86 *ja[i*bs+j] = a->j[i]*bs+j+oshift; 87 } 88 } 89 } else { /* blockcompressed */ 90 if (oshift == 1) { 91 /* temporarily add 1 to i and j indices */ 92 for (i=0; i<nz; i++) a->j[i]++; 93 for (i=0; i<n+1; i++) a->i[i]++; 94 } 95 *ia = a->i; *ja = a->j; 96 } 97 98 PetscFunctionReturn(0); 99 } 100 101 #undef __FUNCT__ 102 #define __FUNCT__ "MatRestoreRowIJ_SeqSBAIJ" 103 static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscBool *done) 104 { 105 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 106 PetscInt i,n = a->mbs,nz = a->i[n]; 107 PetscErrorCode ierr; 108 109 PetscFunctionBegin; 110 if (!ia) PetscFunctionReturn(0); 111 112 if (!blockcompressed) { 113 ierr = PetscFree2(*ia,*ja);CHKERRQ(ierr); 114 } else if (oshift == 1) { /* blockcompressed */ 115 for (i=0; i<nz; i++) a->j[i]--; 116 for (i=0; i<n+1; i++) a->i[i]--; 117 } 118 119 PetscFunctionReturn(0); 120 } 121 122 #undef __FUNCT__ 123 #define __FUNCT__ "MatDestroy_SeqSBAIJ" 124 PetscErrorCode MatDestroy_SeqSBAIJ(Mat A) 125 { 126 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 127 PetscErrorCode ierr; 128 129 PetscFunctionBegin; 130 #if defined(PETSC_USE_LOG) 131 PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz); 132 #endif 133 ierr = MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);CHKERRQ(ierr); 134 if (a->free_diag){ierr = PetscFree(a->diag);CHKERRQ(ierr);} 135 ierr = ISDestroy(&a->row);CHKERRQ(ierr); 136 ierr = ISDestroy(&a->col);CHKERRQ(ierr); 137 ierr = ISDestroy(&a->icol);CHKERRQ(ierr); 138 ierr = PetscFree(a->idiag);CHKERRQ(ierr); 139 ierr = PetscFree(a->inode.size);CHKERRQ(ierr); 140 if (a->free_imax_ilen) {ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr);} 141 ierr = PetscFree(a->solve_work);CHKERRQ(ierr); 142 ierr = PetscFree(a->sor_work);CHKERRQ(ierr); 143 ierr = PetscFree(a->solves_work);CHKERRQ(ierr); 144 ierr = PetscFree(a->mult_work);CHKERRQ(ierr); 145 ierr = PetscFree(a->saved_values);CHKERRQ(ierr); 146 ierr = PetscFree(a->xtoy);CHKERRQ(ierr); 147 if (a->free_jshort) {ierr = PetscFree(a->jshort);CHKERRQ(ierr);} 148 ierr = PetscFree(a->inew);CHKERRQ(ierr); 149 ierr = MatDestroy(&a->parent);CHKERRQ(ierr); 150 ierr = PetscFree(A->data);CHKERRQ(ierr); 151 152 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 153 ierr = PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C","",PETSC_NULL);CHKERRQ(ierr); 154 ierr = PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C","",PETSC_NULL);CHKERRQ(ierr); 155 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C","",PETSC_NULL);CHKERRQ(ierr); 156 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C","",PETSC_NULL);CHKERRQ(ierr); 157 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C","",PETSC_NULL);CHKERRQ(ierr); 158 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C","",PETSC_NULL);CHKERRQ(ierr); 159 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqsbstrm_C","",PETSC_NULL);CHKERRQ(ierr); 160 PetscFunctionReturn(0); 161 } 162 163 #undef __FUNCT__ 164 #define __FUNCT__ "MatSetOption_SeqSBAIJ" 165 PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool flg) 166 { 167 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 168 PetscErrorCode ierr; 169 170 PetscFunctionBegin; 171 switch (op) { 172 case MAT_ROW_ORIENTED: 173 a->roworiented = flg; 174 break; 175 case MAT_KEEP_NONZERO_PATTERN: 176 a->keepnonzeropattern = flg; 177 break; 178 case MAT_NEW_NONZERO_LOCATIONS: 179 a->nonew = (flg ? 0 : 1); 180 break; 181 case MAT_NEW_NONZERO_LOCATION_ERR: 182 a->nonew = (flg ? -1 : 0); 183 break; 184 case MAT_NEW_NONZERO_ALLOCATION_ERR: 185 a->nonew = (flg ? -2 : 0); 186 break; 187 case MAT_UNUSED_NONZERO_LOCATION_ERR: 188 a->nounused = (flg ? -1 : 0); 189 break; 190 case MAT_NEW_DIAGONALS: 191 case MAT_IGNORE_OFF_PROC_ENTRIES: 192 case MAT_USE_HASH_TABLE: 193 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 194 break; 195 case MAT_HERMITIAN: 196 if (!A->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first"); 197 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 198 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort; 199 } else if (A->cmap->bs == 1) { 200 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian; 201 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1"); 202 break; 203 case MAT_SPD: 204 A->spd_set = PETSC_TRUE; 205 A->spd = flg; 206 if (flg) { 207 A->symmetric = PETSC_TRUE; 208 A->structurally_symmetric = PETSC_TRUE; 209 A->symmetric_set = PETSC_TRUE; 210 A->structurally_symmetric_set = PETSC_TRUE; 211 } 212 break; 213 case MAT_SYMMETRIC: 214 case MAT_STRUCTURALLY_SYMMETRIC: 215 case MAT_SYMMETRY_ETERNAL: 216 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix must be symmetric"); 217 ierr = PetscInfo1(A,"Option %s not relevent\n",MatOptions[op]);CHKERRQ(ierr); 218 break; 219 case MAT_IGNORE_LOWER_TRIANGULAR: 220 a->ignore_ltriangular = flg; 221 break; 222 case MAT_ERROR_LOWER_TRIANGULAR: 223 a->ignore_ltriangular = flg; 224 break; 225 case MAT_GETROW_UPPERTRIANGULAR: 226 a->getrow_utriangular = flg; 227 break; 228 default: 229 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 230 } 231 PetscFunctionReturn(0); 232 } 233 234 #undef __FUNCT__ 235 #define __FUNCT__ "MatGetRow_SeqSBAIJ" 236 PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *ncols,PetscInt **cols,PetscScalar **v) 237 { 238 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 239 PetscErrorCode ierr; 240 PetscInt itmp,i,j,k,M,*ai,*aj,bs,bn,bp,*cols_i,bs2; 241 MatScalar *aa,*aa_i; 242 PetscScalar *v_i; 243 244 PetscFunctionBegin; 245 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()"); 246 /* Get the upper triangular part of the row */ 247 bs = A->rmap->bs; 248 ai = a->i; 249 aj = a->j; 250 aa = a->a; 251 bs2 = a->bs2; 252 253 if (row < 0 || row >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Row %D out of range", row); 254 255 bn = row/bs; /* Block number */ 256 bp = row % bs; /* Block position */ 257 M = ai[bn+1] - ai[bn]; 258 *ncols = bs*M; 259 260 if (v) { 261 *v = 0; 262 if (*ncols) { 263 ierr = PetscMalloc((*ncols+row)*sizeof(PetscScalar),v);CHKERRQ(ierr); 264 for (i=0; i<M; i++) { /* for each block in the block row */ 265 v_i = *v + i*bs; 266 aa_i = aa + bs2*(ai[bn] + i); 267 for (j=bp,k=0; j<bs2; j+=bs,k++) {v_i[k] = aa_i[j];} 268 } 269 } 270 } 271 272 if (cols) { 273 *cols = 0; 274 if (*ncols) { 275 ierr = PetscMalloc((*ncols+row)*sizeof(PetscInt),cols);CHKERRQ(ierr); 276 for (i=0; i<M; i++) { /* for each block in the block row */ 277 cols_i = *cols + i*bs; 278 itmp = bs*aj[ai[bn] + i]; 279 for (j=0; j<bs; j++) {cols_i[j] = itmp++;} 280 } 281 } 282 } 283 284 /*search column A(0:row-1,row) (=A(row,0:row-1)). Could be expensive! */ 285 /* this segment is currently removed, so only entries in the upper triangle are obtained */ 286 #ifdef column_search 287 v_i = *v + M*bs; 288 cols_i = *cols + M*bs; 289 for (i=0; i<bn; i++){ /* for each block row */ 290 M = ai[i+1] - ai[i]; 291 for (j=0; j<M; j++){ 292 itmp = aj[ai[i] + j]; /* block column value */ 293 if (itmp == bn){ 294 aa_i = aa + bs2*(ai[i] + j) + bs*bp; 295 for (k=0; k<bs; k++) { 296 *cols_i++ = i*bs+k; 297 *v_i++ = aa_i[k]; 298 } 299 *ncols += bs; 300 break; 301 } 302 } 303 } 304 #endif 305 PetscFunctionReturn(0); 306 } 307 308 #undef __FUNCT__ 309 #define __FUNCT__ "MatRestoreRow_SeqSBAIJ" 310 PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 311 { 312 PetscErrorCode ierr; 313 314 PetscFunctionBegin; 315 if (idx) {ierr = PetscFree(*idx);CHKERRQ(ierr);} 316 if (v) {ierr = PetscFree(*v);CHKERRQ(ierr);} 317 PetscFunctionReturn(0); 318 } 319 320 #undef __FUNCT__ 321 #define __FUNCT__ "MatGetRowUpperTriangular_SeqSBAIJ" 322 PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A) 323 { 324 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 325 326 PetscFunctionBegin; 327 a->getrow_utriangular = PETSC_TRUE; 328 PetscFunctionReturn(0); 329 } 330 #undef __FUNCT__ 331 #define __FUNCT__ "MatRestoreRowUpperTriangular_SeqSBAIJ" 332 PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A) 333 { 334 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 335 336 PetscFunctionBegin; 337 a->getrow_utriangular = PETSC_FALSE; 338 PetscFunctionReturn(0); 339 } 340 341 #undef __FUNCT__ 342 #define __FUNCT__ "MatTranspose_SeqSBAIJ" 343 PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B) 344 { 345 PetscErrorCode ierr; 346 PetscFunctionBegin; 347 if (reuse == MAT_INITIAL_MATRIX || *B != A) { 348 ierr = MatDuplicate(A,MAT_COPY_VALUES,B);CHKERRQ(ierr); 349 } 350 PetscFunctionReturn(0); 351 } 352 353 #undef __FUNCT__ 354 #define __FUNCT__ "MatView_SeqSBAIJ_ASCII" 355 static PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer) 356 { 357 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 358 PetscErrorCode ierr; 359 PetscInt i,j,bs = A->rmap->bs,k,l,bs2=a->bs2; 360 PetscViewerFormat format; 361 PetscInt *diag; 362 363 PetscFunctionBegin; 364 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 365 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 366 ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); 367 } else if (format == PETSC_VIEWER_ASCII_MATLAB) { 368 Mat aij; 369 if (A->factortype && bs>1){ 370 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); 371 PetscFunctionReturn(0); 372 } 373 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);CHKERRQ(ierr); 374 ierr = MatView(aij,viewer);CHKERRQ(ierr); 375 ierr = MatDestroy(&aij);CHKERRQ(ierr); 376 } else if (format == PETSC_VIEWER_ASCII_COMMON) { 377 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 378 for (i=0; i<a->mbs; i++) { 379 for (j=0; j<bs; j++) { 380 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 381 for (k=a->i[i]; k<a->i[i+1]; k++) { 382 for (l=0; l<bs; l++) { 383 #if defined(PETSC_USE_COMPLEX) 384 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 385 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l, 386 PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 387 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 388 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l, 389 PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 390 } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 391 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 392 } 393 #else 394 if (a->a[bs2*k + l*bs + j] != 0.0) { 395 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 396 } 397 #endif 398 } 399 } 400 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 401 } 402 } 403 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 404 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 405 PetscFunctionReturn(0); 406 } else { 407 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 408 ierr = PetscObjectPrintClassNamePrefixType((PetscObject)A,viewer,"Matrix Object");CHKERRQ(ierr); 409 if (A->factortype){ /* for factored matrix */ 410 if (bs>1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"matrix is factored with bs>1. Not implemented yet"); 411 412 diag=a->diag; 413 for (i=0; i<a->mbs; i++) { /* for row block i */ 414 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); 415 /* diagonal entry */ 416 #if defined(PETSC_USE_COMPLEX) 417 if (PetscImaginaryPart(a->a[diag[i]]) > 0.0) { 418 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); 419 } else if (PetscImaginaryPart(a->a[diag[i]]) < 0.0) { 420 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); 421 } else { 422 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[diag[i]],PetscRealPart(1.0/a->a[diag[i]]));CHKERRQ(ierr); 423 } 424 #else 425 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[diag[i]],1.0/a->a[diag[i]]);CHKERRQ(ierr); 426 #endif 427 /* off-diagonal entries */ 428 for (k=a->i[i]; k<a->i[i+1]-1; k++) { 429 #if defined(PETSC_USE_COMPLEX) 430 if (PetscImaginaryPart(a->a[k]) > 0.0) { 431 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k],PetscRealPart(a->a[k]),PetscImaginaryPart(a->a[k]));CHKERRQ(ierr); 432 } else if (PetscImaginaryPart(a->a[k]) < 0.0) { 433 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k],PetscRealPart(a->a[k]),-PetscImaginaryPart(a->a[k]));CHKERRQ(ierr); 434 } else { 435 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k],PetscRealPart(a->a[k]));CHKERRQ(ierr); 436 } 437 #else 438 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[k],a->a[k]);CHKERRQ(ierr); 439 #endif 440 } 441 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 442 } 443 444 } else { /* for non-factored matrix */ 445 for (i=0; i<a->mbs; i++) { /* for row block i */ 446 for (j=0; j<bs; j++) { /* for row bs*i + j */ 447 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 448 for (k=a->i[i]; k<a->i[i+1]; k++) { /* for column block */ 449 for (l=0; l<bs; l++) { /* for column */ 450 #if defined(PETSC_USE_COMPLEX) 451 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) { 452 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l, 453 PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 454 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) { 455 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l, 456 PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 457 } else { 458 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 459 } 460 #else 461 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 462 #endif 463 } 464 } 465 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 466 } 467 } 468 } 469 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 470 } 471 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 472 PetscFunctionReturn(0); 473 } 474 475 #undef __FUNCT__ 476 #define __FUNCT__ "MatView_SeqSBAIJ_Draw_Zoom" 477 static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa) 478 { 479 Mat A = (Mat) Aa; 480 Mat_SeqSBAIJ *a=(Mat_SeqSBAIJ*)A->data; 481 PetscErrorCode ierr; 482 PetscInt row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2; 483 PetscMPIInt rank; 484 PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r; 485 MatScalar *aa; 486 MPI_Comm comm; 487 PetscViewer viewer; 488 489 PetscFunctionBegin; 490 /* 491 This is nasty. If this is called from an originally parallel matrix 492 then all processes call this,but only the first has the matrix so the 493 rest should return immediately. 494 */ 495 ierr = PetscObjectGetComm((PetscObject)draw,&comm);CHKERRQ(ierr); 496 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 497 if (rank) PetscFunctionReturn(0); 498 499 ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr); 500 501 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 502 PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric"); 503 504 /* loop over matrix elements drawing boxes */ 505 color = PETSC_DRAW_BLUE; 506 for (i=0,row=0; i<mbs; i++,row+=bs) { 507 for (j=a->i[i]; j<a->i[i+1]; j++) { 508 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 509 x_l = a->j[j]*bs; x_r = x_l + 1.0; 510 aa = a->a + j*bs2; 511 for (k=0; k<bs; k++) { 512 for (l=0; l<bs; l++) { 513 if (PetscRealPart(*aa++) >= 0.) continue; 514 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 515 } 516 } 517 } 518 } 519 color = PETSC_DRAW_CYAN; 520 for (i=0,row=0; i<mbs; i++,row+=bs) { 521 for (j=a->i[i]; j<a->i[i+1]; j++) { 522 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 523 x_l = a->j[j]*bs; x_r = x_l + 1.0; 524 aa = a->a + j*bs2; 525 for (k=0; k<bs; k++) { 526 for (l=0; l<bs; l++) { 527 if (PetscRealPart(*aa++) != 0.) continue; 528 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 529 } 530 } 531 } 532 } 533 534 color = PETSC_DRAW_RED; 535 for (i=0,row=0; i<mbs; i++,row+=bs) { 536 for (j=a->i[i]; j<a->i[i+1]; j++) { 537 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 538 x_l = a->j[j]*bs; x_r = x_l + 1.0; 539 aa = a->a + j*bs2; 540 for (k=0; k<bs; k++) { 541 for (l=0; l<bs; l++) { 542 if (PetscRealPart(*aa++) <= 0.) continue; 543 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 544 } 545 } 546 } 547 } 548 PetscFunctionReturn(0); 549 } 550 551 #undef __FUNCT__ 552 #define __FUNCT__ "MatView_SeqSBAIJ_Draw" 553 static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer) 554 { 555 PetscErrorCode ierr; 556 PetscReal xl,yl,xr,yr,w,h; 557 PetscDraw draw; 558 PetscBool isnull; 559 560 PetscFunctionBegin; 561 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 562 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 563 564 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);CHKERRQ(ierr); 565 xr = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0; 566 xr += w; yr += h; xl = -w; yl = -h; 567 ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr); 568 ierr = PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);CHKERRQ(ierr); 569 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",PETSC_NULL);CHKERRQ(ierr); 570 PetscFunctionReturn(0); 571 } 572 573 #undef __FUNCT__ 574 #define __FUNCT__ "MatView_SeqSBAIJ" 575 PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer) 576 { 577 PetscErrorCode ierr; 578 PetscBool iascii,isdraw; 579 FILE *file = 0; 580 581 PetscFunctionBegin; 582 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 583 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 584 if (iascii){ 585 ierr = MatView_SeqSBAIJ_ASCII(A,viewer);CHKERRQ(ierr); 586 } else if (isdraw) { 587 ierr = MatView_SeqSBAIJ_Draw(A,viewer);CHKERRQ(ierr); 588 } else { 589 Mat B; 590 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 591 ierr = MatView(B,viewer);CHKERRQ(ierr); 592 ierr = MatDestroy(&B);CHKERRQ(ierr); 593 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 594 if (file) { 595 fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs); 596 } 597 } 598 PetscFunctionReturn(0); 599 } 600 601 602 #undef __FUNCT__ 603 #define __FUNCT__ "MatGetValues_SeqSBAIJ" 604 PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[]) 605 { 606 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 607 PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j; 608 PetscInt *ai = a->i,*ailen = a->ilen; 609 PetscInt brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2; 610 MatScalar *ap,*aa = a->a; 611 612 PetscFunctionBegin; 613 for (k=0; k<m; k++) { /* loop over rows */ 614 row = im[k]; brow = row/bs; 615 if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */ 616 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); 617 rp = aj + ai[brow] ; ap = aa + bs2*ai[brow] ; 618 nrow = ailen[brow]; 619 for (l=0; l<n; l++) { /* loop over columns */ 620 if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */ 621 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); 622 col = in[l] ; 623 bcol = col/bs; 624 cidx = col%bs; 625 ridx = row%bs; 626 high = nrow; 627 low = 0; /* assume unsorted */ 628 while (high-low > 5) { 629 t = (low+high)/2; 630 if (rp[t] > bcol) high = t; 631 else low = t; 632 } 633 for (i=low; i<high; i++) { 634 if (rp[i] > bcol) break; 635 if (rp[i] == bcol) { 636 *v++ = ap[bs2*i+bs*cidx+ridx]; 637 goto finished; 638 } 639 } 640 *v++ = 0.0; 641 finished:; 642 } 643 } 644 PetscFunctionReturn(0); 645 } 646 647 648 #undef __FUNCT__ 649 #define __FUNCT__ "MatSetValuesBlocked_SeqSBAIJ" 650 PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 651 { 652 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 653 PetscErrorCode ierr; 654 PetscInt *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1; 655 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen; 656 PetscInt *aj=a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval; 657 PetscBool roworiented=a->roworiented; 658 const PetscScalar *value = v; 659 MatScalar *ap,*aa = a->a,*bap; 660 661 PetscFunctionBegin; 662 if (roworiented) { 663 stepval = (n-1)*bs; 664 } else { 665 stepval = (m-1)*bs; 666 } 667 for (k=0; k<m; k++) { /* loop over added rows */ 668 row = im[k]; 669 if (row < 0) continue; 670 #if defined(PETSC_USE_DEBUG) 671 if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1); 672 #endif 673 rp = aj + ai[row]; 674 ap = aa + bs2*ai[row]; 675 rmax = imax[row]; 676 nrow = ailen[row]; 677 low = 0; 678 high = nrow; 679 for (l=0; l<n; l++) { /* loop over added columns */ 680 if (in[l] < 0) continue; 681 col = in[l]; 682 #if defined(PETSC_USE_DEBUG) 683 if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1); 684 #endif 685 if (col < row) { 686 if (a->ignore_ltriangular) { 687 continue; /* ignore lower triangular block */ 688 } else { 689 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)"); 690 } 691 } 692 if (roworiented) { 693 value = v + k*(stepval+bs)*bs + l*bs; 694 } else { 695 value = v + l*(stepval+bs)*bs + k*bs; 696 } 697 if (col <= lastcol) low = 0; else high = nrow; 698 lastcol = col; 699 while (high-low > 7) { 700 t = (low+high)/2; 701 if (rp[t] > col) high = t; 702 else low = t; 703 } 704 for (i=low; i<high; i++) { 705 if (rp[i] > col) break; 706 if (rp[i] == col) { 707 bap = ap + bs2*i; 708 if (roworiented) { 709 if (is == ADD_VALUES) { 710 for (ii=0; ii<bs; ii++,value+=stepval) { 711 for (jj=ii; jj<bs2; jj+=bs) { 712 bap[jj] += *value++; 713 } 714 } 715 } else { 716 for (ii=0; ii<bs; ii++,value+=stepval) { 717 for (jj=ii; jj<bs2; jj+=bs) { 718 bap[jj] = *value++; 719 } 720 } 721 } 722 } else { 723 if (is == ADD_VALUES) { 724 for (ii=0; ii<bs; ii++,value+=stepval) { 725 for (jj=0; jj<bs; jj++) { 726 *bap++ += *value++; 727 } 728 } 729 } else { 730 for (ii=0; ii<bs; ii++,value+=stepval) { 731 for (jj=0; jj<bs; jj++) { 732 *bap++ = *value++; 733 } 734 } 735 } 736 } 737 goto noinsert2; 738 } 739 } 740 if (nonew == 1) goto noinsert2; 741 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 742 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 743 N = nrow++ - 1; high++; 744 /* shift up all the later entries in this row */ 745 for (ii=N; ii>=i; ii--) { 746 rp[ii+1] = rp[ii]; 747 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 748 } 749 if (N >= i) { 750 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 751 } 752 rp[i] = col; 753 bap = ap + bs2*i; 754 if (roworiented) { 755 for (ii=0; ii<bs; ii++,value+=stepval) { 756 for (jj=ii; jj<bs2; jj+=bs) { 757 bap[jj] = *value++; 758 } 759 } 760 } else { 761 for (ii=0; ii<bs; ii++,value+=stepval) { 762 for (jj=0; jj<bs; jj++) { 763 *bap++ = *value++; 764 } 765 } 766 } 767 noinsert2:; 768 low = i; 769 } 770 ailen[row] = nrow; 771 } 772 PetscFunctionReturn(0); 773 } 774 775 /* 776 This is not yet used 777 */ 778 #undef __FUNCT__ 779 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode" 780 PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A) 781 { 782 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 783 PetscErrorCode ierr; 784 const PetscInt *ai = a->i, *aj = a->j,*cols; 785 PetscInt i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts; 786 PetscBool flag; 787 788 PetscFunctionBegin; 789 ierr = PetscMalloc(m*sizeof(PetscInt),&ns);CHKERRQ(ierr); 790 while (i < m){ 791 nzx = ai[i+1] - ai[i]; /* Number of nonzeros */ 792 /* Limits the number of elements in a node to 'a->inode.limit' */ 793 for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) { 794 nzy = ai[j+1] - ai[j]; 795 if (nzy != (nzx - j + i)) break; 796 ierr = PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);CHKERRQ(ierr); 797 if (!flag) break; 798 } 799 ns[node_count++] = blk_size; 800 i = j; 801 } 802 if (!a->inode.size && m && node_count > .9*m) { 803 ierr = PetscFree(ns);CHKERRQ(ierr); 804 ierr = PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);CHKERRQ(ierr); 805 } else { 806 a->inode.node_count = node_count; 807 ierr = PetscMalloc(node_count*sizeof(PetscInt),&a->inode.size);CHKERRQ(ierr); 808 ierr = PetscLogObjectMemory(A,node_count*sizeof(PetscInt));CHKERRQ(ierr); 809 ierr = PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt)); 810 ierr = PetscFree(ns);CHKERRQ(ierr); 811 ierr = PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);CHKERRQ(ierr); 812 813 /* count collections of adjacent columns in each inode */ 814 row = 0; 815 cnt = 0; 816 for (i=0; i<node_count; i++) { 817 cols = aj + ai[row] + a->inode.size[i]; 818 nz = ai[row+1] - ai[row] - a->inode.size[i]; 819 for (j=1; j<nz; j++) { 820 if (cols[j] != cols[j-1]+1) { 821 cnt++; 822 } 823 } 824 cnt++; 825 row += a->inode.size[i]; 826 } 827 ierr = PetscMalloc(2*cnt*sizeof(PetscInt),&counts);CHKERRQ(ierr); 828 cnt = 0; 829 row = 0; 830 for (i=0; i<node_count; i++) { 831 cols = aj + ai[row] + a->inode.size[i]; 832 CHKMEMQ; 833 counts[2*cnt] = cols[0]; 834 CHKMEMQ; 835 nz = ai[row+1] - ai[row] - a->inode.size[i]; 836 cnt2 = 1; 837 for (j=1; j<nz; j++) { 838 if (cols[j] != cols[j-1]+1) { 839 CHKMEMQ; 840 counts[2*(cnt++)+1] = cnt2; 841 counts[2*cnt] = cols[j]; 842 CHKMEMQ; 843 cnt2 = 1; 844 } else cnt2++; 845 } 846 CHKMEMQ; 847 counts[2*(cnt++)+1] = cnt2; 848 CHKMEMQ; 849 row += a->inode.size[i]; 850 } 851 ierr = PetscIntView(2*cnt,counts,0); 852 } 853 PetscFunctionReturn(0); 854 } 855 856 #undef __FUNCT__ 857 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ" 858 PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode) 859 { 860 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 861 PetscErrorCode ierr; 862 PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax; 863 PetscInt m = A->rmap->N,*ip,N,*ailen = a->ilen; 864 PetscInt mbs = a->mbs,bs2 = a->bs2,rmax = 0; 865 MatScalar *aa = a->a,*ap; 866 867 PetscFunctionBegin; 868 if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); 869 870 if (m) rmax = ailen[0]; 871 for (i=1; i<mbs; i++) { 872 /* move each row back by the amount of empty slots (fshift) before it*/ 873 fshift += imax[i-1] - ailen[i-1]; 874 rmax = PetscMax(rmax,ailen[i]); 875 if (fshift) { 876 ip = aj + ai[i]; ap = aa + bs2*ai[i]; 877 N = ailen[i]; 878 for (j=0; j<N; j++) { 879 ip[j-fshift] = ip[j]; 880 ierr = PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 881 } 882 } 883 ai[i] = ai[i-1] + ailen[i-1]; 884 } 885 if (mbs) { 886 fshift += imax[mbs-1] - ailen[mbs-1]; 887 ai[mbs] = ai[mbs-1] + ailen[mbs-1]; 888 } 889 /* reset ilen and imax for each row */ 890 for (i=0; i<mbs; i++) { 891 ailen[i] = imax[i] = ai[i+1] - ai[i]; 892 } 893 a->nz = ai[mbs]; 894 895 /* diagonals may have moved, reset it */ 896 if (a->diag) { 897 ierr = PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));CHKERRQ(ierr); 898 } 899 if (fshift && a->nounused == -1) { 900 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); 901 } 902 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); 903 ierr = PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);CHKERRQ(ierr); 904 ierr = PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);CHKERRQ(ierr); 905 A->info.mallocs += a->reallocs; 906 a->reallocs = 0; 907 A->info.nz_unneeded = (PetscReal)fshift*bs2; 908 a->idiagvalid = PETSC_FALSE; 909 910 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 911 if (a->jshort && a->free_jshort){ 912 /* when matrix data structure is changed, previous jshort must be replaced */ 913 ierr = PetscFree(a->jshort);CHKERRQ(ierr); 914 } 915 ierr = PetscMalloc(a->i[A->rmap->n]*sizeof(unsigned short),&a->jshort);CHKERRQ(ierr); 916 ierr = PetscLogObjectMemory(A,a->i[A->rmap->n]*sizeof(unsigned short));CHKERRQ(ierr); 917 for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i]; 918 A->ops->mult = MatMult_SeqSBAIJ_1_ushort; 919 A->ops->sor = MatSOR_SeqSBAIJ_ushort; 920 a->free_jshort = PETSC_TRUE; 921 } 922 PetscFunctionReturn(0); 923 } 924 925 /* 926 This function returns an array of flags which indicate the locations of contiguous 927 blocks that should be zeroed. for eg: if bs = 3 and is = [0,1,2,3,5,6,7,8,9] 928 then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)] 929 Assume: sizes should be long enough to hold all the values. 930 */ 931 #undef __FUNCT__ 932 #define __FUNCT__ "MatZeroRows_SeqSBAIJ_Check_Blocks" 933 PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max) 934 { 935 PetscInt i,j,k,row; 936 PetscBool flg; 937 938 PetscFunctionBegin; 939 for (i=0,j=0; i<n; j++) { 940 row = idx[i]; 941 if (row%bs!=0) { /* Not the begining of a block */ 942 sizes[j] = 1; 943 i++; 944 } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */ 945 sizes[j] = 1; /* Also makes sure atleast 'bs' values exist for next else */ 946 i++; 947 } else { /* Begining of the block, so check if the complete block exists */ 948 flg = PETSC_TRUE; 949 for (k=1; k<bs; k++) { 950 if (row+k != idx[i+k]) { /* break in the block */ 951 flg = PETSC_FALSE; 952 break; 953 } 954 } 955 if (flg) { /* No break in the bs */ 956 sizes[j] = bs; 957 i+= bs; 958 } else { 959 sizes[j] = 1; 960 i++; 961 } 962 } 963 } 964 *bs_max = j; 965 PetscFunctionReturn(0); 966 } 967 968 969 /* Only add/insert a(i,j) with i<=j (blocks). 970 Any a(i,j) with i>j input by user is ingored. 971 */ 972 973 #undef __FUNCT__ 974 #define __FUNCT__ "MatSetValues_SeqSBAIJ" 975 PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 976 { 977 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 978 PetscErrorCode ierr; 979 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1; 980 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented; 981 PetscInt *aj=a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol; 982 PetscInt ridx,cidx,bs2=a->bs2; 983 MatScalar *ap,value,*aa=a->a,*bap; 984 985 PetscFunctionBegin; 986 if (v) PetscValidScalarPointer(v,6); 987 for (k=0; k<m; k++) { /* loop over added rows */ 988 row = im[k]; /* row number */ 989 brow = row/bs; /* block row number */ 990 if (row < 0) continue; 991 #if defined(PETSC_USE_DEBUG) 992 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); 993 #endif 994 rp = aj + ai[brow]; /*ptr to beginning of column value of the row block*/ 995 ap = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/ 996 rmax = imax[brow]; /* maximum space allocated for this row */ 997 nrow = ailen[brow]; /* actual length of this row */ 998 low = 0; 999 1000 for (l=0; l<n; l++) { /* loop over added columns */ 1001 if (in[l] < 0) continue; 1002 #if defined(PETSC_USE_DEBUG) 1003 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); 1004 #endif 1005 col = in[l]; 1006 bcol = col/bs; /* block col number */ 1007 1008 if (brow > bcol) { 1009 if (a->ignore_ltriangular){ 1010 continue; /* ignore lower triangular values */ 1011 } else { 1012 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)"); 1013 } 1014 } 1015 1016 ridx = row % bs; cidx = col % bs; /*row and col index inside the block */ 1017 if ((brow==bcol && ridx<=cidx) || (brow<bcol)){ 1018 /* element value a(k,l) */ 1019 if (roworiented) { 1020 value = v[l + k*n]; 1021 } else { 1022 value = v[k + l*m]; 1023 } 1024 1025 /* move pointer bap to a(k,l) quickly and add/insert value */ 1026 if (col <= lastcol) low = 0; high = nrow; 1027 lastcol = col; 1028 while (high-low > 7) { 1029 t = (low+high)/2; 1030 if (rp[t] > bcol) high = t; 1031 else low = t; 1032 } 1033 for (i=low; i<high; i++) { 1034 if (rp[i] > bcol) break; 1035 if (rp[i] == bcol) { 1036 bap = ap + bs2*i + bs*cidx + ridx; 1037 if (is == ADD_VALUES) *bap += value; 1038 else *bap = value; 1039 /* for diag block, add/insert its symmetric element a(cidx,ridx) */ 1040 if (brow == bcol && ridx < cidx){ 1041 bap = ap + bs2*i + bs*ridx + cidx; 1042 if (is == ADD_VALUES) *bap += value; 1043 else *bap = value; 1044 } 1045 goto noinsert1; 1046 } 1047 } 1048 1049 if (nonew == 1) goto noinsert1; 1050 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 1051 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 1052 1053 N = nrow++ - 1; high++; 1054 /* shift up all the later entries in this row */ 1055 for (ii=N; ii>=i; ii--) { 1056 rp[ii+1] = rp[ii]; 1057 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 1058 } 1059 if (N>=i) { 1060 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1061 } 1062 rp[i] = bcol; 1063 ap[bs2*i + bs*cidx + ridx] = value; 1064 noinsert1:; 1065 low = i; 1066 } 1067 } /* end of loop over added columns */ 1068 ailen[brow] = nrow; 1069 } /* end of loop over added rows */ 1070 PetscFunctionReturn(0); 1071 } 1072 1073 #undef __FUNCT__ 1074 #define __FUNCT__ "MatICCFactor_SeqSBAIJ" 1075 PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info) 1076 { 1077 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)inA->data; 1078 Mat outA; 1079 PetscErrorCode ierr; 1080 PetscBool row_identity; 1081 1082 PetscFunctionBegin; 1083 if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc"); 1084 ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr); 1085 if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported"); 1086 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()! */ 1087 1088 outA = inA; 1089 inA->factortype = MAT_FACTOR_ICC; 1090 1091 ierr = MatMarkDiagonal_SeqSBAIJ(inA);CHKERRQ(ierr); 1092 ierr = MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);CHKERRQ(ierr); 1093 1094 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1095 ierr = ISDestroy(&a->row);CHKERRQ(ierr); 1096 a->row = row; 1097 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1098 ierr = ISDestroy(&a->col);CHKERRQ(ierr); 1099 a->col = row; 1100 1101 /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */ 1102 if (a->icol) {ierr = ISInvertPermutation(row,PETSC_DECIDE, &a->icol);CHKERRQ(ierr);} 1103 ierr = PetscLogObjectParent(inA,a->icol);CHKERRQ(ierr); 1104 1105 if (!a->solve_work) { 1106 ierr = PetscMalloc((inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar),&a->solve_work);CHKERRQ(ierr); 1107 ierr = PetscLogObjectMemory(inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));CHKERRQ(ierr); 1108 } 1109 1110 ierr = MatCholeskyFactorNumeric(outA,inA,info);CHKERRQ(ierr); 1111 PetscFunctionReturn(0); 1112 } 1113 1114 EXTERN_C_BEGIN 1115 #undef __FUNCT__ 1116 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices_SeqSBAIJ" 1117 PetscErrorCode MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices) 1118 { 1119 Mat_SeqSBAIJ *baij = (Mat_SeqSBAIJ *)mat->data; 1120 PetscInt i,nz,n; 1121 PetscErrorCode ierr; 1122 1123 PetscFunctionBegin; 1124 nz = baij->maxnz; 1125 n = mat->cmap->n; 1126 for (i=0; i<nz; i++) { 1127 baij->j[i] = indices[i]; 1128 } 1129 baij->nz = nz; 1130 for (i=0; i<n; i++) { 1131 baij->ilen[i] = baij->imax[i]; 1132 } 1133 ierr = MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1134 PetscFunctionReturn(0); 1135 } 1136 EXTERN_C_END 1137 1138 #undef __FUNCT__ 1139 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices" 1140 /*@ 1141 MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows 1142 in the matrix. 1143 1144 Input Parameters: 1145 + mat - the SeqSBAIJ matrix 1146 - indices - the column indices 1147 1148 Level: advanced 1149 1150 Notes: 1151 This can be called if you have precomputed the nonzero structure of the 1152 matrix and want to provide it to the matrix object to improve the performance 1153 of the MatSetValues() operation. 1154 1155 You MUST have set the correct numbers of nonzeros per row in the call to 1156 MatCreateSeqSBAIJ(), and the columns indices MUST be sorted. 1157 1158 MUST be called before any calls to MatSetValues() 1159 1160 .seealso: MatCreateSeqSBAIJ 1161 @*/ 1162 PetscErrorCode MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices) 1163 { 1164 PetscErrorCode ierr; 1165 1166 PetscFunctionBegin; 1167 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1168 PetscValidPointer(indices,2); 1169 ierr = PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt *),(mat,indices));CHKERRQ(ierr); 1170 PetscFunctionReturn(0); 1171 } 1172 1173 #undef __FUNCT__ 1174 #define __FUNCT__ "MatCopy_SeqSBAIJ" 1175 PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str) 1176 { 1177 PetscErrorCode ierr; 1178 1179 PetscFunctionBegin; 1180 /* If the two matrices have the same copy implementation, use fast copy. */ 1181 if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) { 1182 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1183 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1184 1185 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"); 1186 ierr = PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));CHKERRQ(ierr); 1187 } else { 1188 ierr = MatGetRowUpperTriangular(A);CHKERRQ(ierr); 1189 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 1190 ierr = MatRestoreRowUpperTriangular(A);CHKERRQ(ierr); 1191 } 1192 PetscFunctionReturn(0); 1193 } 1194 1195 #undef __FUNCT__ 1196 #define __FUNCT__ "MatSetUp_SeqSBAIJ" 1197 PetscErrorCode MatSetUp_SeqSBAIJ(Mat A) 1198 { 1199 PetscErrorCode ierr; 1200 1201 PetscFunctionBegin; 1202 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,A->rmap->bs,PETSC_DEFAULT,0);CHKERRQ(ierr); 1203 PetscFunctionReturn(0); 1204 } 1205 1206 #undef __FUNCT__ 1207 #define __FUNCT__ "MatSeqSBAIJGetArray_SeqSBAIJ" 1208 PetscErrorCode MatSeqSBAIJGetArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1209 { 1210 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1211 PetscFunctionBegin; 1212 *array = a->a; 1213 PetscFunctionReturn(0); 1214 } 1215 1216 #undef __FUNCT__ 1217 #define __FUNCT__ "MatSeqSBAIJRestoreArray_SeqSBAIJ" 1218 PetscErrorCode MatSeqSBAIJRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1219 { 1220 PetscFunctionBegin; 1221 PetscFunctionReturn(0); 1222 } 1223 1224 #undef __FUNCT__ 1225 #define __FUNCT__ "MatAXPY_SeqSBAIJ" 1226 PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 1227 { 1228 Mat_SeqSBAIJ *x=(Mat_SeqSBAIJ *)X->data, *y=(Mat_SeqSBAIJ *)Y->data; 1229 PetscErrorCode ierr; 1230 PetscInt i,bs=Y->rmap->bs,bs2=bs*bs,j; 1231 PetscBLASInt one = 1; 1232 1233 PetscFunctionBegin; 1234 if (str == SAME_NONZERO_PATTERN) { 1235 PetscScalar alpha = a; 1236 PetscBLASInt bnz = PetscBLASIntCast(x->nz*bs2); 1237 BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one); 1238 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 1239 if (y->xtoy && y->XtoY != X) { 1240 ierr = PetscFree(y->xtoy);CHKERRQ(ierr); 1241 ierr = MatDestroy(&y->XtoY);CHKERRQ(ierr); 1242 } 1243 if (!y->xtoy) { /* get xtoy */ 1244 ierr = MatAXPYGetxtoy_Private(x->mbs,x->i,x->j,PETSC_NULL, y->i,y->j,PETSC_NULL, &y->xtoy);CHKERRQ(ierr); 1245 y->XtoY = X; 1246 } 1247 for (i=0; i<x->nz; i++) { 1248 j = 0; 1249 while (j < bs2){ 1250 y->a[bs2*y->xtoy[i]+j] += a*(x->a[bs2*i+j]); 1251 j++; 1252 } 1253 } 1254 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); 1255 } else { 1256 ierr = MatGetRowUpperTriangular(X);CHKERRQ(ierr); 1257 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 1258 ierr = MatRestoreRowUpperTriangular(X);CHKERRQ(ierr); 1259 } 1260 PetscFunctionReturn(0); 1261 } 1262 1263 #undef __FUNCT__ 1264 #define __FUNCT__ "MatIsSymmetric_SeqSBAIJ" 1265 PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1266 { 1267 PetscFunctionBegin; 1268 *flg = PETSC_TRUE; 1269 PetscFunctionReturn(0); 1270 } 1271 1272 #undef __FUNCT__ 1273 #define __FUNCT__ "MatIsStructurallySymmetric_SeqSBAIJ" 1274 PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool *flg) 1275 { 1276 PetscFunctionBegin; 1277 *flg = PETSC_TRUE; 1278 PetscFunctionReturn(0); 1279 } 1280 1281 #undef __FUNCT__ 1282 #define __FUNCT__ "MatIsHermitian_SeqSBAIJ" 1283 PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1284 { 1285 PetscFunctionBegin; 1286 *flg = PETSC_FALSE; 1287 PetscFunctionReturn(0); 1288 } 1289 1290 #undef __FUNCT__ 1291 #define __FUNCT__ "MatRealPart_SeqSBAIJ" 1292 PetscErrorCode MatRealPart_SeqSBAIJ(Mat A) 1293 { 1294 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1295 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1296 MatScalar *aa = a->a; 1297 1298 PetscFunctionBegin; 1299 for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]); 1300 PetscFunctionReturn(0); 1301 } 1302 1303 #undef __FUNCT__ 1304 #define __FUNCT__ "MatImaginaryPart_SeqSBAIJ" 1305 PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A) 1306 { 1307 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1308 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1309 MatScalar *aa = a->a; 1310 1311 PetscFunctionBegin; 1312 for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]); 1313 PetscFunctionReturn(0); 1314 } 1315 1316 #undef __FUNCT__ 1317 #define __FUNCT__ "MatZeroRowsColumns_SeqSBAIJ" 1318 PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b) 1319 { 1320 Mat_SeqSBAIJ *baij=(Mat_SeqSBAIJ*)A->data; 1321 PetscErrorCode ierr; 1322 PetscInt i,j,k,count; 1323 PetscInt bs=A->rmap->bs,bs2=baij->bs2,row,col; 1324 PetscScalar zero = 0.0; 1325 MatScalar *aa; 1326 const PetscScalar *xx; 1327 PetscScalar *bb; 1328 PetscBool *zeroed,vecs = PETSC_FALSE; 1329 1330 PetscFunctionBegin; 1331 /* fix right hand side if needed */ 1332 if (x && b) { 1333 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1334 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1335 vecs = PETSC_TRUE; 1336 } 1337 A->same_nonzero = PETSC_TRUE; 1338 1339 /* zero the columns */ 1340 ierr = PetscMalloc(A->rmap->n*sizeof(PetscBool),&zeroed);CHKERRQ(ierr); 1341 ierr = PetscMemzero(zeroed,A->rmap->n*sizeof(PetscBool));CHKERRQ(ierr); 1342 for (i=0; i<is_n; i++) { 1343 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]); 1344 zeroed[is_idx[i]] = PETSC_TRUE; 1345 } 1346 if (vecs) { 1347 for (i=0; i<A->rmap->N; i++) { 1348 row = i/bs; 1349 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1350 for (k=0; k<bs; k++) { 1351 col = bs*baij->j[j] + k; 1352 if (col <= i) continue; 1353 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1354 if (!zeroed[i] && zeroed[col]) { 1355 bb[i] -= aa[0]*xx[col]; 1356 } 1357 if (zeroed[i] && !zeroed[col]) { 1358 bb[col] -= aa[0]*xx[i]; 1359 } 1360 } 1361 } 1362 } 1363 for (i=0; i<is_n; i++) { 1364 bb[is_idx[i]] = diag*xx[is_idx[i]]; 1365 } 1366 } 1367 1368 for (i=0; i<A->rmap->N; i++) { 1369 if (!zeroed[i]) { 1370 row = i/bs; 1371 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1372 for (k=0; k<bs; k++) { 1373 col = bs*baij->j[j] + k; 1374 if (zeroed[col]) { 1375 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1376 aa[0] = 0.0; 1377 } 1378 } 1379 } 1380 } 1381 } 1382 ierr = PetscFree(zeroed);CHKERRQ(ierr); 1383 if (vecs) { 1384 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1385 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1386 } 1387 1388 /* zero the rows */ 1389 for (i=0; i<is_n; i++) { 1390 row = is_idx[i]; 1391 count = (baij->i[row/bs +1] - baij->i[row/bs])*bs; 1392 aa = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs); 1393 for (k=0; k<count; k++) { 1394 aa[0] = zero; 1395 aa += bs; 1396 } 1397 if (diag != 0.0) { 1398 ierr = (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); 1399 } 1400 } 1401 ierr = MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1402 PetscFunctionReturn(0); 1403 } 1404 1405 /* -------------------------------------------------------------------*/ 1406 static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ, 1407 MatGetRow_SeqSBAIJ, 1408 MatRestoreRow_SeqSBAIJ, 1409 MatMult_SeqSBAIJ_N, 1410 /* 4*/ MatMultAdd_SeqSBAIJ_N, 1411 MatMult_SeqSBAIJ_N, /* transpose versions are same as non-transpose versions */ 1412 MatMultAdd_SeqSBAIJ_N, 1413 0, 1414 0, 1415 0, 1416 /*10*/ 0, 1417 0, 1418 MatCholeskyFactor_SeqSBAIJ, 1419 MatSOR_SeqSBAIJ, 1420 MatTranspose_SeqSBAIJ, 1421 /*15*/ MatGetInfo_SeqSBAIJ, 1422 MatEqual_SeqSBAIJ, 1423 MatGetDiagonal_SeqSBAIJ, 1424 MatDiagonalScale_SeqSBAIJ, 1425 MatNorm_SeqSBAIJ, 1426 /*20*/ 0, 1427 MatAssemblyEnd_SeqSBAIJ, 1428 MatSetOption_SeqSBAIJ, 1429 MatZeroEntries_SeqSBAIJ, 1430 /*24*/ 0, 1431 0, 1432 0, 1433 0, 1434 0, 1435 /*29*/ MatSetUp_SeqSBAIJ, 1436 0, 1437 0, 1438 0, 1439 0, 1440 /*34*/ MatDuplicate_SeqSBAIJ, 1441 0, 1442 0, 1443 0, 1444 MatICCFactor_SeqSBAIJ, 1445 /*39*/ MatAXPY_SeqSBAIJ, 1446 MatGetSubMatrices_SeqSBAIJ, 1447 MatIncreaseOverlap_SeqSBAIJ, 1448 MatGetValues_SeqSBAIJ, 1449 MatCopy_SeqSBAIJ, 1450 /*44*/ 0, 1451 MatScale_SeqSBAIJ, 1452 0, 1453 0, 1454 MatZeroRowsColumns_SeqSBAIJ, 1455 /*49*/ 0, 1456 MatGetRowIJ_SeqSBAIJ, 1457 MatRestoreRowIJ_SeqSBAIJ, 1458 0, 1459 0, 1460 /*54*/ 0, 1461 0, 1462 0, 1463 0, 1464 MatSetValuesBlocked_SeqSBAIJ, 1465 /*59*/ MatGetSubMatrix_SeqSBAIJ, 1466 0, 1467 0, 1468 0, 1469 0, 1470 /*64*/ 0, 1471 0, 1472 0, 1473 0, 1474 0, 1475 /*69*/ MatGetRowMaxAbs_SeqSBAIJ, 1476 0, 1477 0, 1478 0, 1479 0, 1480 /*74*/ 0, 1481 0, 1482 0, 1483 0, 1484 0, 1485 /*79*/ 0, 1486 0, 1487 0, 1488 MatGetInertia_SeqSBAIJ, 1489 MatLoad_SeqSBAIJ, 1490 /*84*/ MatIsSymmetric_SeqSBAIJ, 1491 MatIsHermitian_SeqSBAIJ, 1492 MatIsStructurallySymmetric_SeqSBAIJ, 1493 0, 1494 0, 1495 /*89*/ 0, 1496 0, 1497 0, 1498 0, 1499 0, 1500 /*94*/ 0, 1501 0, 1502 0, 1503 0, 1504 0, 1505 /*99*/ 0, 1506 0, 1507 0, 1508 0, 1509 0, 1510 /*104*/0, 1511 MatRealPart_SeqSBAIJ, 1512 MatImaginaryPart_SeqSBAIJ, 1513 MatGetRowUpperTriangular_SeqSBAIJ, 1514 MatRestoreRowUpperTriangular_SeqSBAIJ, 1515 /*109*/0, 1516 0, 1517 0, 1518 0, 1519 MatMissingDiagonal_SeqSBAIJ, 1520 /*114*/0, 1521 0, 1522 0, 1523 0, 1524 0, 1525 /*119*/0, 1526 0, 1527 0, 1528 0 1529 }; 1530 1531 EXTERN_C_BEGIN 1532 #undef __FUNCT__ 1533 #define __FUNCT__ "MatStoreValues_SeqSBAIJ" 1534 PetscErrorCode MatStoreValues_SeqSBAIJ(Mat mat) 1535 { 1536 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ *)mat->data; 1537 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1538 PetscErrorCode ierr; 1539 1540 PetscFunctionBegin; 1541 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1542 1543 /* allocate space for values if not already there */ 1544 if (!aij->saved_values) { 1545 ierr = PetscMalloc((nz+1)*sizeof(PetscScalar),&aij->saved_values);CHKERRQ(ierr); 1546 } 1547 1548 /* copy values over */ 1549 ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1550 PetscFunctionReturn(0); 1551 } 1552 EXTERN_C_END 1553 1554 EXTERN_C_BEGIN 1555 #undef __FUNCT__ 1556 #define __FUNCT__ "MatRetrieveValues_SeqSBAIJ" 1557 PetscErrorCode MatRetrieveValues_SeqSBAIJ(Mat mat) 1558 { 1559 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ *)mat->data; 1560 PetscErrorCode ierr; 1561 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1562 1563 PetscFunctionBegin; 1564 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1565 if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first"); 1566 1567 /* copy values over */ 1568 ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1569 PetscFunctionReturn(0); 1570 } 1571 EXTERN_C_END 1572 1573 EXTERN_C_BEGIN 1574 #undef __FUNCT__ 1575 #define __FUNCT__ "MatSeqSBAIJSetPreallocation_SeqSBAIJ" 1576 PetscErrorCode MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz) 1577 { 1578 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1579 PetscErrorCode ierr; 1580 PetscInt i,mbs,bs2; 1581 PetscBool skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE; 1582 1583 PetscFunctionBegin; 1584 if (nz >= 0 || nnz) realalloc = PETSC_TRUE; 1585 B->preallocated = PETSC_TRUE; 1586 1587 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 1588 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 1589 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 1590 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 1591 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 1592 1593 mbs = B->rmap->N/bs; 1594 bs2 = bs*bs; 1595 1596 if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize"); 1597 1598 if (nz == MAT_SKIP_ALLOCATION) { 1599 skipallocation = PETSC_TRUE; 1600 nz = 0; 1601 } 1602 1603 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3; 1604 if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz); 1605 if (nnz) { 1606 for (i=0; i<mbs; i++) { 1607 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]); 1608 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); 1609 } 1610 } 1611 1612 B->ops->mult = MatMult_SeqSBAIJ_N; 1613 B->ops->multadd = MatMultAdd_SeqSBAIJ_N; 1614 B->ops->multtranspose = MatMult_SeqSBAIJ_N; 1615 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N; 1616 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);CHKERRQ(ierr); 1617 if (!flg) { 1618 switch (bs) { 1619 case 1: 1620 B->ops->mult = MatMult_SeqSBAIJ_1; 1621 B->ops->multadd = MatMultAdd_SeqSBAIJ_1; 1622 B->ops->multtranspose = MatMult_SeqSBAIJ_1; 1623 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1; 1624 break; 1625 case 2: 1626 B->ops->mult = MatMult_SeqSBAIJ_2; 1627 B->ops->multadd = MatMultAdd_SeqSBAIJ_2; 1628 B->ops->multtranspose = MatMult_SeqSBAIJ_2; 1629 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2; 1630 break; 1631 case 3: 1632 B->ops->mult = MatMult_SeqSBAIJ_3; 1633 B->ops->multadd = MatMultAdd_SeqSBAIJ_3; 1634 B->ops->multtranspose = MatMult_SeqSBAIJ_3; 1635 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3; 1636 break; 1637 case 4: 1638 B->ops->mult = MatMult_SeqSBAIJ_4; 1639 B->ops->multadd = MatMultAdd_SeqSBAIJ_4; 1640 B->ops->multtranspose = MatMult_SeqSBAIJ_4; 1641 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4; 1642 break; 1643 case 5: 1644 B->ops->mult = MatMult_SeqSBAIJ_5; 1645 B->ops->multadd = MatMultAdd_SeqSBAIJ_5; 1646 B->ops->multtranspose = MatMult_SeqSBAIJ_5; 1647 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5; 1648 break; 1649 case 6: 1650 B->ops->mult = MatMult_SeqSBAIJ_6; 1651 B->ops->multadd = MatMultAdd_SeqSBAIJ_6; 1652 B->ops->multtranspose = MatMult_SeqSBAIJ_6; 1653 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6; 1654 break; 1655 case 7: 1656 B->ops->mult = MatMult_SeqSBAIJ_7; 1657 B->ops->multadd = MatMultAdd_SeqSBAIJ_7; 1658 B->ops->multtranspose = MatMult_SeqSBAIJ_7; 1659 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7; 1660 break; 1661 } 1662 } 1663 1664 b->mbs = mbs; 1665 b->nbs = mbs; 1666 if (!skipallocation) { 1667 if (!b->imax) { 1668 ierr = PetscMalloc2(mbs,PetscInt,&b->imax,mbs,PetscInt,&b->ilen);CHKERRQ(ierr); 1669 b->free_imax_ilen = PETSC_TRUE; 1670 ierr = PetscLogObjectMemory(B,2*mbs*sizeof(PetscInt));CHKERRQ(ierr); 1671 } 1672 if (!nnz) { 1673 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5; 1674 else if (nz <= 0) nz = 1; 1675 for (i=0; i<mbs; i++) { 1676 b->imax[i] = nz; 1677 } 1678 nz = nz*mbs; /* total nz */ 1679 } else { 1680 nz = 0; 1681 for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];} 1682 } 1683 /* b->ilen will count nonzeros in each block row so far. */ 1684 for (i=0; i<mbs; i++) { b->ilen[i] = 0;} 1685 /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */ 1686 1687 /* allocate the matrix space */ 1688 ierr = MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);CHKERRQ(ierr); 1689 ierr = PetscMalloc3(bs2*nz,PetscScalar,&b->a,nz,PetscInt,&b->j,B->rmap->N+1,PetscInt,&b->i);CHKERRQ(ierr); 1690 ierr = PetscLogObjectMemory(B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr); 1691 ierr = PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 1692 ierr = PetscMemzero(b->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 1693 b->singlemalloc = PETSC_TRUE; 1694 1695 /* pointer to beginning of each row */ 1696 b->i[0] = 0; 1697 for (i=1; i<mbs+1; i++) { 1698 b->i[i] = b->i[i-1] + b->imax[i-1]; 1699 } 1700 b->free_a = PETSC_TRUE; 1701 b->free_ij = PETSC_TRUE; 1702 } else { 1703 b->free_a = PETSC_FALSE; 1704 b->free_ij = PETSC_FALSE; 1705 } 1706 1707 B->rmap->bs = bs; 1708 b->bs2 = bs2; 1709 b->nz = 0; 1710 b->maxnz = nz; 1711 1712 b->inew = 0; 1713 b->jnew = 0; 1714 b->anew = 0; 1715 b->a2anew = 0; 1716 b->permute = PETSC_FALSE; 1717 if (realalloc) {ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);} 1718 PetscFunctionReturn(0); 1719 } 1720 EXTERN_C_END 1721 1722 /* 1723 This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization 1724 */ 1725 #undef __FUNCT__ 1726 #define __FUNCT__ "MatSeqSBAIJSetNumericFactorization_inplace" 1727 PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural) 1728 { 1729 PetscErrorCode ierr; 1730 PetscBool flg = PETSC_FALSE; 1731 PetscInt bs = B->rmap->bs; 1732 1733 PetscFunctionBegin; 1734 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);CHKERRQ(ierr); 1735 if (flg) bs = 8; 1736 1737 if (!natural) { 1738 switch (bs) { 1739 case 1: 1740 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace; 1741 break; 1742 case 2: 1743 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2; 1744 break; 1745 case 3: 1746 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3; 1747 break; 1748 case 4: 1749 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4; 1750 break; 1751 case 5: 1752 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5; 1753 break; 1754 case 6: 1755 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6; 1756 break; 1757 case 7: 1758 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7; 1759 break; 1760 default: 1761 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N; 1762 break; 1763 } 1764 } else { 1765 switch (bs) { 1766 case 1: 1767 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace; 1768 break; 1769 case 2: 1770 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering; 1771 break; 1772 case 3: 1773 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering; 1774 break; 1775 case 4: 1776 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering; 1777 break; 1778 case 5: 1779 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering; 1780 break; 1781 case 6: 1782 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering; 1783 break; 1784 case 7: 1785 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering; 1786 break; 1787 default: 1788 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering; 1789 break; 1790 } 1791 } 1792 PetscFunctionReturn(0); 1793 } 1794 1795 EXTERN_C_BEGIN 1796 extern PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*); 1797 extern PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*); 1798 EXTERN_C_END 1799 1800 1801 EXTERN_C_BEGIN 1802 #undef __FUNCT__ 1803 #define __FUNCT__ "MatGetFactor_seqsbaij_petsc" 1804 PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B) 1805 { 1806 PetscInt n = A->rmap->n; 1807 PetscErrorCode ierr; 1808 1809 PetscFunctionBegin; 1810 #if defined(PETSC_USE_COMPLEX) 1811 if (A->hermitian)SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported"); 1812 #endif 1813 ierr = MatCreate(((PetscObject)A)->comm,B);CHKERRQ(ierr); 1814 ierr = MatSetSizes(*B,n,n,n,n);CHKERRQ(ierr); 1815 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1816 ierr = MatSetType(*B,MATSEQSBAIJ);CHKERRQ(ierr); 1817 ierr = MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,PETSC_NULL);CHKERRQ(ierr); 1818 (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ; 1819 (*B)->ops->iccfactorsymbolic = MatICCFactorSymbolic_SeqSBAIJ; 1820 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported"); 1821 (*B)->factortype = ftype; 1822 PetscFunctionReturn(0); 1823 } 1824 EXTERN_C_END 1825 1826 EXTERN_C_BEGIN 1827 #undef __FUNCT__ 1828 #define __FUNCT__ "MatGetFactorAvailable_seqsbaij_petsc" 1829 PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool *flg) 1830 { 1831 PetscFunctionBegin; 1832 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1833 *flg = PETSC_TRUE; 1834 } else { 1835 *flg = PETSC_FALSE; 1836 } 1837 PetscFunctionReturn(0); 1838 } 1839 EXTERN_C_END 1840 1841 EXTERN_C_BEGIN 1842 #if defined(PETSC_HAVE_MUMPS) 1843 extern PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*); 1844 #endif 1845 #if defined(PETSC_HAVE_PASTIX) 1846 extern PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*); 1847 #endif 1848 #if defined(PETSC_HAVE_CHOLMOD) 1849 extern PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*); 1850 #endif 1851 extern PetscErrorCode MatGetFactor_seqsbaij_sbstrm(Mat,MatFactorType,Mat*); 1852 EXTERN_C_END 1853 1854 /*MC 1855 MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices, 1856 based on block compressed sparse row format. Only the upper triangular portion of the matrix is stored. 1857 1858 For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you 1859 can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd() 1860 1861 Options Database Keys: 1862 . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions() 1863 1864 Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not 1865 stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use 1866 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. 1867 1868 1869 Level: beginner 1870 1871 .seealso: MatCreateSeqSBAIJ 1872 M*/ 1873 1874 EXTERN_C_BEGIN 1875 extern PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*); 1876 EXTERN_C_END 1877 1878 1879 EXTERN_C_BEGIN 1880 #undef __FUNCT__ 1881 #define __FUNCT__ "MatCreate_SeqSBAIJ" 1882 PetscErrorCode MatCreate_SeqSBAIJ(Mat B) 1883 { 1884 Mat_SeqSBAIJ *b; 1885 PetscErrorCode ierr; 1886 PetscMPIInt size; 1887 PetscBool no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE; 1888 1889 PetscFunctionBegin; 1890 ierr = MPI_Comm_size(((PetscObject)B)->comm,&size);CHKERRQ(ierr); 1891 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1"); 1892 1893 ierr = PetscNewLog(B,Mat_SeqSBAIJ,&b);CHKERRQ(ierr); 1894 B->data = (void*)b; 1895 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 1896 B->ops->destroy = MatDestroy_SeqSBAIJ; 1897 B->ops->view = MatView_SeqSBAIJ; 1898 b->row = 0; 1899 b->icol = 0; 1900 b->reallocs = 0; 1901 b->saved_values = 0; 1902 b->inode.limit = 5; 1903 b->inode.max_limit = 5; 1904 1905 b->roworiented = PETSC_TRUE; 1906 b->nonew = 0; 1907 b->diag = 0; 1908 b->solve_work = 0; 1909 b->mult_work = 0; 1910 B->spptr = 0; 1911 B->info.nz_unneeded = (PetscReal)b->maxnz*b->bs2; 1912 b->keepnonzeropattern = PETSC_FALSE; 1913 b->xtoy = 0; 1914 b->XtoY = 0; 1915 1916 b->inew = 0; 1917 b->jnew = 0; 1918 b->anew = 0; 1919 b->a2anew = 0; 1920 b->permute = PETSC_FALSE; 1921 1922 b->ignore_ltriangular = PETSC_TRUE; 1923 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,PETSC_NULL);CHKERRQ(ierr); 1924 1925 b->getrow_utriangular = PETSC_FALSE; 1926 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,PETSC_NULL);CHKERRQ(ierr); 1927 1928 #if defined(PETSC_HAVE_PASTIX) 1929 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_pastix_C", 1930 "MatGetFactor_seqsbaij_pastix", 1931 MatGetFactor_seqsbaij_pastix);CHKERRQ(ierr); 1932 #endif 1933 #if defined(PETSC_HAVE_MUMPS) 1934 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_mumps_C", 1935 "MatGetFactor_sbaij_mumps", 1936 MatGetFactor_sbaij_mumps);CHKERRQ(ierr); 1937 #endif 1938 #if defined(PETSC_HAVE_CHOLMOD) 1939 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_cholmod_C", 1940 "MatGetFactor_seqsbaij_cholmod", 1941 MatGetFactor_seqsbaij_cholmod);CHKERRQ(ierr); 1942 #endif 1943 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactorAvailable_petsc_C", 1944 "MatGetFactorAvailable_seqsbaij_petsc", 1945 MatGetFactorAvailable_seqsbaij_petsc);CHKERRQ(ierr); 1946 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_petsc_C", 1947 "MatGetFactor_seqsbaij_petsc", 1948 MatGetFactor_seqsbaij_petsc);CHKERRQ(ierr); 1949 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_sbstrm_C", 1950 "MatGetFactor_seqsbaij_sbstrm", 1951 MatGetFactor_seqsbaij_sbstrm);CHKERRQ(ierr); 1952 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatStoreValues_C", 1953 "MatStoreValues_SeqSBAIJ", 1954 MatStoreValues_SeqSBAIJ);CHKERRQ(ierr); 1955 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatRetrieveValues_C", 1956 "MatRetrieveValues_SeqSBAIJ", 1957 (void*)MatRetrieveValues_SeqSBAIJ);CHKERRQ(ierr); 1958 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C", 1959 "MatSeqSBAIJSetColumnIndices_SeqSBAIJ", 1960 MatSeqSBAIJSetColumnIndices_SeqSBAIJ);CHKERRQ(ierr); 1961 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqaij_C", 1962 "MatConvert_SeqSBAIJ_SeqAIJ", 1963 MatConvert_SeqSBAIJ_SeqAIJ);CHKERRQ(ierr); 1964 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C", 1965 "MatConvert_SeqSBAIJ_SeqBAIJ", 1966 MatConvert_SeqSBAIJ_SeqBAIJ);CHKERRQ(ierr); 1967 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetPreallocation_C", 1968 "MatSeqSBAIJSetPreallocation_SeqSBAIJ", 1969 MatSeqSBAIJSetPreallocation_SeqSBAIJ);CHKERRQ(ierr); 1970 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C", 1971 "MatConvert_SeqSBAIJ_SeqSBSTRM", 1972 MatConvert_SeqSBAIJ_SeqSBSTRM);CHKERRQ(ierr); 1973 1974 B->symmetric = PETSC_TRUE; 1975 B->structurally_symmetric = PETSC_TRUE; 1976 B->symmetric_set = PETSC_TRUE; 1977 B->structurally_symmetric_set = PETSC_TRUE; 1978 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);CHKERRQ(ierr); 1979 1980 ierr = PetscOptionsBegin(((PetscObject)B)->comm,((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");CHKERRQ(ierr); 1981 ierr = PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",PETSC_NULL,no_unroll,&no_unroll,PETSC_NULL);CHKERRQ(ierr); 1982 if (no_unroll) {ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");CHKERRQ(ierr);} 1983 ierr = PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",PETSC_NULL,no_inode,&no_inode,PETSC_NULL);CHKERRQ(ierr); 1984 if (no_inode) {ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");CHKERRQ(ierr);} 1985 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); 1986 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1987 b->inode.use = (PetscBool)(!(no_unroll || no_inode)); 1988 if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit; 1989 1990 PetscFunctionReturn(0); 1991 } 1992 EXTERN_C_END 1993 1994 #undef __FUNCT__ 1995 #define __FUNCT__ "MatSeqSBAIJSetPreallocation" 1996 /*@C 1997 MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block 1998 compressed row) format. For good matrix assembly performance the 1999 user should preallocate the matrix storage by setting the parameter nz 2000 (or the array nnz). By setting these parameters accurately, performance 2001 during matrix assembly can be increased by more than a factor of 50. 2002 2003 Collective on Mat 2004 2005 Input Parameters: 2006 + A - the symmetric matrix 2007 . bs - size of block 2008 . nz - number of block nonzeros per block row (same for all rows) 2009 - nnz - array containing the number of block nonzeros in the upper triangular plus 2010 diagonal portion of each block (possibly different for each block row) or PETSC_NULL 2011 2012 Options Database Keys: 2013 . -mat_no_unroll - uses code that does not unroll the loops in the 2014 block calculations (much slower) 2015 . -mat_block_size - size of the blocks to use (only works if a negative bs is passed in 2016 2017 Level: intermediate 2018 2019 Notes: 2020 Specify the preallocated storage with either nz or nnz (not both). 2021 Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 2022 allocation. See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details. 2023 2024 You can call MatGetInfo() to get information on how effective the preallocation was; 2025 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 2026 You can also run with the option -info and look for messages with the string 2027 malloc in them to see if additional memory allocation was needed. 2028 2029 If the nnz parameter is given then the nz parameter is ignored 2030 2031 2032 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() 2033 @*/ 2034 PetscErrorCode MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[]) 2035 { 2036 PetscErrorCode ierr; 2037 2038 PetscFunctionBegin; 2039 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2040 PetscValidType(B,1); 2041 PetscValidLogicalCollectiveInt(B,bs,2); 2042 ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));CHKERRQ(ierr); 2043 PetscFunctionReturn(0); 2044 } 2045 2046 #undef __FUNCT__ 2047 #define __FUNCT__ "MatCreateSeqSBAIJ" 2048 /*@C 2049 MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block 2050 compressed row) format. For good matrix assembly performance the 2051 user should preallocate the matrix storage by setting the parameter nz 2052 (or the array nnz). By setting these parameters accurately, performance 2053 during matrix assembly can be increased by more than a factor of 50. 2054 2055 Collective on MPI_Comm 2056 2057 Input Parameters: 2058 + comm - MPI communicator, set to PETSC_COMM_SELF 2059 . bs - size of block 2060 . m - number of rows, or number of columns 2061 . nz - number of block nonzeros per block row (same for all rows) 2062 - nnz - array containing the number of block nonzeros in the upper triangular plus 2063 diagonal portion of each block (possibly different for each block row) or PETSC_NULL 2064 2065 Output Parameter: 2066 . A - the symmetric matrix 2067 2068 Options Database Keys: 2069 . -mat_no_unroll - uses code that does not unroll the loops in the 2070 block calculations (much slower) 2071 . -mat_block_size - size of the blocks to use 2072 2073 Level: intermediate 2074 2075 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 2076 MatXXXXSetPreallocation() paradgm instead of this routine directly. 2077 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 2078 2079 Notes: 2080 The number of rows and columns must be divisible by blocksize. 2081 This matrix type does not support complex Hermitian operation. 2082 2083 Specify the preallocated storage with either nz or nnz (not both). 2084 Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 2085 allocation. See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details. 2086 2087 If the nnz parameter is given then the nz parameter is ignored 2088 2089 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() 2090 @*/ 2091 PetscErrorCode MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A) 2092 { 2093 PetscErrorCode ierr; 2094 2095 PetscFunctionBegin; 2096 ierr = MatCreate(comm,A);CHKERRQ(ierr); 2097 ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); 2098 ierr = MatSetType(*A,MATSEQSBAIJ);CHKERRQ(ierr); 2099 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);CHKERRQ(ierr); 2100 PetscFunctionReturn(0); 2101 } 2102 2103 #undef __FUNCT__ 2104 #define __FUNCT__ "MatDuplicate_SeqSBAIJ" 2105 PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B) 2106 { 2107 Mat C; 2108 Mat_SeqSBAIJ *c,*a = (Mat_SeqSBAIJ*)A->data; 2109 PetscErrorCode ierr; 2110 PetscInt i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2; 2111 2112 PetscFunctionBegin; 2113 if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix"); 2114 2115 *B = 0; 2116 ierr = MatCreate(((PetscObject)A)->comm,&C);CHKERRQ(ierr); 2117 ierr = MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);CHKERRQ(ierr); 2118 ierr = MatSetType(C,MATSEQSBAIJ);CHKERRQ(ierr); 2119 ierr = PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2120 c = (Mat_SeqSBAIJ*)C->data; 2121 2122 C->preallocated = PETSC_TRUE; 2123 C->factortype = A->factortype; 2124 c->row = 0; 2125 c->icol = 0; 2126 c->saved_values = 0; 2127 c->keepnonzeropattern = a->keepnonzeropattern; 2128 C->assembled = PETSC_TRUE; 2129 2130 ierr = PetscLayoutReference(A->rmap,&C->rmap);CHKERRQ(ierr); 2131 ierr = PetscLayoutReference(A->cmap,&C->cmap);CHKERRQ(ierr); 2132 c->bs2 = a->bs2; 2133 c->mbs = a->mbs; 2134 c->nbs = a->nbs; 2135 2136 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2137 c->imax = a->imax; 2138 c->ilen = a->ilen; 2139 c->free_imax_ilen = PETSC_FALSE; 2140 } else { 2141 ierr = PetscMalloc2((mbs+1),PetscInt,&c->imax,(mbs+1),PetscInt,&c->ilen);CHKERRQ(ierr); 2142 ierr = PetscLogObjectMemory(C,2*(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2143 for (i=0; i<mbs; i++) { 2144 c->imax[i] = a->imax[i]; 2145 c->ilen[i] = a->ilen[i]; 2146 } 2147 c->free_imax_ilen = PETSC_TRUE; 2148 } 2149 2150 /* allocate the matrix space */ 2151 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2152 ierr = PetscMalloc(bs2*nz*sizeof(MatScalar),&c->a);CHKERRQ(ierr); 2153 ierr = PetscLogObjectMemory(C,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 2154 c->i = a->i; 2155 c->j = a->j; 2156 c->singlemalloc = PETSC_FALSE; 2157 c->free_a = PETSC_TRUE; 2158 c->free_ij = PETSC_FALSE; 2159 c->parent = A; 2160 ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr); 2161 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2162 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2163 } else { 2164 ierr = PetscMalloc3(bs2*nz,MatScalar,&c->a,nz,PetscInt,&c->j,mbs+1,PetscInt,&c->i);CHKERRQ(ierr); 2165 ierr = PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2166 ierr = PetscLogObjectMemory(C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));CHKERRQ(ierr); 2167 c->singlemalloc = PETSC_TRUE; 2168 c->free_a = PETSC_TRUE; 2169 c->free_ij = PETSC_TRUE; 2170 } 2171 if (mbs > 0) { 2172 if (cpvalues != MAT_SHARE_NONZERO_PATTERN) { 2173 ierr = PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 2174 } 2175 if (cpvalues == MAT_COPY_VALUES) { 2176 ierr = PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2177 } else { 2178 ierr = PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2179 } 2180 if (a->jshort) { 2181 /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */ 2182 /* if the parent matrix is reassembled, this child matrix will never notice */ 2183 ierr = PetscMalloc(nz*sizeof(unsigned short),&c->jshort);CHKERRQ(ierr); 2184 ierr = PetscLogObjectMemory(C,nz*sizeof(unsigned short));CHKERRQ(ierr); 2185 ierr = PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));CHKERRQ(ierr); 2186 c->free_jshort = PETSC_TRUE; 2187 } 2188 } 2189 2190 c->roworiented = a->roworiented; 2191 c->nonew = a->nonew; 2192 2193 if (a->diag) { 2194 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2195 c->diag = a->diag; 2196 c->free_diag = PETSC_FALSE; 2197 } else { 2198 ierr = PetscMalloc(mbs*sizeof(PetscInt),&c->diag);CHKERRQ(ierr); 2199 ierr = PetscLogObjectMemory(C,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2200 for (i=0; i<mbs; i++) { 2201 c->diag[i] = a->diag[i]; 2202 } 2203 c->free_diag = PETSC_TRUE; 2204 } 2205 } 2206 c->nz = a->nz; 2207 c->maxnz = a->nz; /* Since we allocate exactly the right amount */ 2208 c->solve_work = 0; 2209 c->mult_work = 0; 2210 *B = C; 2211 ierr = PetscFListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);CHKERRQ(ierr); 2212 PetscFunctionReturn(0); 2213 } 2214 2215 #undef __FUNCT__ 2216 #define __FUNCT__ "MatLoad_SeqSBAIJ" 2217 PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer) 2218 { 2219 Mat_SeqSBAIJ *a; 2220 PetscErrorCode ierr; 2221 int fd; 2222 PetscMPIInt size; 2223 PetscInt i,nz,header[4],*rowlengths=0,M,N,bs=1; 2224 PetscInt *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount; 2225 PetscInt kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols; 2226 PetscInt *masked,nmask,tmp,bs2,ishift; 2227 PetscScalar *aa; 2228 MPI_Comm comm = ((PetscObject)viewer)->comm; 2229 2230 PetscFunctionBegin; 2231 ierr = PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,PETSC_NULL);CHKERRQ(ierr); 2232 bs2 = bs*bs; 2233 2234 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2235 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor"); 2236 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2237 ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr); 2238 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object"); 2239 M = header[1]; N = header[2]; nz = header[3]; 2240 2241 if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ"); 2242 2243 if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices"); 2244 2245 /* 2246 This code adds extra rows to make sure the number of rows is 2247 divisible by the blocksize 2248 */ 2249 mbs = M/bs; 2250 extra_rows = bs - M + bs*(mbs); 2251 if (extra_rows == bs) extra_rows = 0; 2252 else mbs++; 2253 if (extra_rows) { 2254 ierr = PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");CHKERRQ(ierr); 2255 } 2256 2257 /* Set global sizes if not already set */ 2258 if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) { 2259 ierr = MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);CHKERRQ(ierr); 2260 } else { /* Check if the matrix global sizes are correct */ 2261 ierr = MatGetSize(newmat,&rows,&cols);CHKERRQ(ierr); 2262 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); 2263 } 2264 2265 /* read in row lengths */ 2266 ierr = PetscMalloc((M+extra_rows)*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr); 2267 ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); 2268 for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1; 2269 2270 /* read in column indices */ 2271 ierr = PetscMalloc((nz+extra_rows)*sizeof(PetscInt),&jj);CHKERRQ(ierr); 2272 ierr = PetscBinaryRead(fd,jj,nz,PETSC_INT);CHKERRQ(ierr); 2273 for (i=0; i<extra_rows; i++) jj[nz+i] = M+i; 2274 2275 /* loop over row lengths determining block row lengths */ 2276 ierr = PetscMalloc(mbs*sizeof(PetscInt),&s_browlengths);CHKERRQ(ierr); 2277 ierr = PetscMemzero(s_browlengths,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2278 ierr = PetscMalloc2(mbs,PetscInt,&mask,mbs,PetscInt,&masked);CHKERRQ(ierr); 2279 ierr = PetscMemzero(mask,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2280 rowcount = 0; 2281 nzcount = 0; 2282 for (i=0; i<mbs; i++) { 2283 nmask = 0; 2284 for (j=0; j<bs; j++) { 2285 kmax = rowlengths[rowcount]; 2286 for (k=0; k<kmax; k++) { 2287 tmp = jj[nzcount++]/bs; /* block col. index */ 2288 if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;} 2289 } 2290 rowcount++; 2291 } 2292 s_browlengths[i] += nmask; 2293 2294 /* zero out the mask elements we set */ 2295 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2296 } 2297 2298 /* Do preallocation */ 2299 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);CHKERRQ(ierr); 2300 a = (Mat_SeqSBAIJ*)newmat->data; 2301 2302 /* set matrix "i" values */ 2303 a->i[0] = 0; 2304 for (i=1; i<= mbs; i++) { 2305 a->i[i] = a->i[i-1] + s_browlengths[i-1]; 2306 a->ilen[i-1] = s_browlengths[i-1]; 2307 } 2308 a->nz = a->i[mbs]; 2309 2310 /* read in nonzero values */ 2311 ierr = PetscMalloc((nz+extra_rows)*sizeof(PetscScalar),&aa);CHKERRQ(ierr); 2312 ierr = PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);CHKERRQ(ierr); 2313 for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0; 2314 2315 /* set "a" and "j" values into matrix */ 2316 nzcount = 0; jcount = 0; 2317 for (i=0; i<mbs; i++) { 2318 nzcountb = nzcount; 2319 nmask = 0; 2320 for (j=0; j<bs; j++) { 2321 kmax = rowlengths[i*bs+j]; 2322 for (k=0; k<kmax; k++) { 2323 tmp = jj[nzcount++]/bs; /* block col. index */ 2324 if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;} 2325 } 2326 } 2327 /* sort the masked values */ 2328 ierr = PetscSortInt(nmask,masked);CHKERRQ(ierr); 2329 2330 /* set "j" values into matrix */ 2331 maskcount = 1; 2332 for (j=0; j<nmask; j++) { 2333 a->j[jcount++] = masked[j]; 2334 mask[masked[j]] = maskcount++; 2335 } 2336 2337 /* set "a" values into matrix */ 2338 ishift = bs2*a->i[i]; 2339 for (j=0; j<bs; j++) { 2340 kmax = rowlengths[i*bs+j]; 2341 for (k=0; k<kmax; k++) { 2342 tmp = jj[nzcountb]/bs ; /* block col. index */ 2343 if (tmp >= i){ 2344 block = mask[tmp] - 1; 2345 point = jj[nzcountb] - bs*tmp; 2346 idx = ishift + bs2*block + j + bs*point; 2347 a->a[idx] = aa[nzcountb]; 2348 } 2349 nzcountb++; 2350 } 2351 } 2352 /* zero out the mask elements we set */ 2353 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2354 } 2355 if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix"); 2356 2357 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2358 ierr = PetscFree(s_browlengths);CHKERRQ(ierr); 2359 ierr = PetscFree(aa);CHKERRQ(ierr); 2360 ierr = PetscFree(jj);CHKERRQ(ierr); 2361 ierr = PetscFree2(mask,masked);CHKERRQ(ierr); 2362 2363 ierr = MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2364 ierr = MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2365 ierr = MatView_Private(newmat);CHKERRQ(ierr); 2366 PetscFunctionReturn(0); 2367 } 2368 2369 #undef __FUNCT__ 2370 #define __FUNCT__ "MatCreateSeqSBAIJWithArrays" 2371 /*@ 2372 MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements 2373 (upper triangular entries in CSR format) provided by the user. 2374 2375 Collective on MPI_Comm 2376 2377 Input Parameters: 2378 + comm - must be an MPI communicator of size 1 2379 . bs - size of block 2380 . m - number of rows 2381 . n - number of columns 2382 . i - row indices 2383 . j - column indices 2384 - a - matrix values 2385 2386 Output Parameter: 2387 . mat - the matrix 2388 2389 Level: advanced 2390 2391 Notes: 2392 The i, j, and a arrays are not copied by this routine, the user must free these arrays 2393 once the matrix is destroyed 2394 2395 You cannot set new nonzero locations into this matrix, that will generate an error. 2396 2397 The i and j indices are 0 based 2398 2399 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 2400 it is the regular CSR format excluding the lower triangular elements. 2401 2402 .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ() 2403 2404 @*/ 2405 PetscErrorCode MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt* i,PetscInt*j,PetscScalar *a,Mat *mat) 2406 { 2407 PetscErrorCode ierr; 2408 PetscInt ii; 2409 Mat_SeqSBAIJ *sbaij; 2410 2411 PetscFunctionBegin; 2412 if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs); 2413 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 2414 2415 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 2416 ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); 2417 ierr = MatSetType(*mat,MATSEQSBAIJ);CHKERRQ(ierr); 2418 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);CHKERRQ(ierr); 2419 sbaij = (Mat_SeqSBAIJ*)(*mat)->data; 2420 ierr = PetscMalloc2(m,PetscInt,&sbaij->imax,m,PetscInt,&sbaij->ilen);CHKERRQ(ierr); 2421 ierr = PetscLogObjectMemory(*mat,2*m*sizeof(PetscInt));CHKERRQ(ierr); 2422 2423 sbaij->i = i; 2424 sbaij->j = j; 2425 sbaij->a = a; 2426 sbaij->singlemalloc = PETSC_FALSE; 2427 sbaij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/ 2428 sbaij->free_a = PETSC_FALSE; 2429 sbaij->free_ij = PETSC_FALSE; 2430 2431 for (ii=0; ii<m; ii++) { 2432 sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii]; 2433 #if defined(PETSC_USE_DEBUG) 2434 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]); 2435 #endif 2436 } 2437 #if defined(PETSC_USE_DEBUG) 2438 for (ii=0; ii<sbaij->i[m]; ii++) { 2439 if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]); 2440 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]); 2441 } 2442 #endif 2443 2444 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2445 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2446 PetscFunctionReturn(0); 2447 } 2448 2449 2450 2451 2452 2453