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