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 = PetscMalloc1(a->mbs,&a->diag);CHKERRQ(ierr); 58 ierr = PetscLogObjectMemory((PetscObject)A,a->mbs*sizeof(PetscInt));CHKERRQ(ierr); 59 a->free_diag = PETSC_TRUE; 60 } 61 for (i=0; i<a->mbs; i++) a->diag[i] = a->i[i]; 62 PetscFunctionReturn(0); 63 } 64 65 #undef __FUNCT__ 66 #define __FUNCT__ "MatGetRowIJ_SeqSBAIJ" 67 static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *inia[],const PetscInt *inja[],PetscBool *done) 68 { 69 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 70 PetscInt i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs; 71 PetscInt **ia = (PetscInt**)inia,**ja = (PetscInt**)inja; 72 PetscErrorCode ierr; 73 74 PetscFunctionBegin; 75 *nn = n; 76 if (!ia) PetscFunctionReturn(0); 77 if (!blockcompressed) { 78 /* malloc & create the natural set of indices */ 79 ierr = PetscMalloc2((n+1)*bs,ia,nz*bs,ja);CHKERRQ(ierr); 80 for (i=0; i<n+1; i++) { 81 for (j=0; j<bs; j++) { 82 *ia[i*bs+j] = a->i[i]*bs+j+oshift; 83 } 84 } 85 for (i=0; i<nz; i++) { 86 for (j=0; j<bs; j++) { 87 *ja[i*bs+j] = a->j[i]*bs+j+oshift; 88 } 89 } 90 } else { /* blockcompressed */ 91 if (oshift == 1) { 92 /* temporarily add 1 to i and j indices */ 93 for (i=0; i<nz; i++) a->j[i]++; 94 for (i=0; i<n+1; i++) a->i[i]++; 95 } 96 *ia = a->i; *ja = a->j; 97 } 98 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,const PetscInt *ia[],const 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 PetscFunctionReturn(0); 119 } 120 121 #undef __FUNCT__ 122 #define __FUNCT__ "MatDestroy_SeqSBAIJ" 123 PetscErrorCode MatDestroy_SeqSBAIJ(Mat A) 124 { 125 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 126 PetscErrorCode ierr; 127 128 PetscFunctionBegin; 129 #if defined(PETSC_USE_LOG) 130 PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz); 131 #endif 132 ierr = MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);CHKERRQ(ierr); 133 if (a->free_diag) {ierr = PetscFree(a->diag);CHKERRQ(ierr);} 134 ierr = ISDestroy(&a->row);CHKERRQ(ierr); 135 ierr = ISDestroy(&a->col);CHKERRQ(ierr); 136 ierr = ISDestroy(&a->icol);CHKERRQ(ierr); 137 ierr = PetscFree(a->idiag);CHKERRQ(ierr); 138 ierr = PetscFree(a->inode.size);CHKERRQ(ierr); 139 if (a->free_imax_ilen) {ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr);} 140 ierr = PetscFree(a->solve_work);CHKERRQ(ierr); 141 ierr = PetscFree(a->sor_work);CHKERRQ(ierr); 142 ierr = PetscFree(a->solves_work);CHKERRQ(ierr); 143 ierr = PetscFree(a->mult_work);CHKERRQ(ierr); 144 ierr = PetscFree(a->saved_values);CHKERRQ(ierr); 145 ierr = PetscFree(a->xtoy);CHKERRQ(ierr); 146 if (a->free_jshort) {ierr = PetscFree(a->jshort);CHKERRQ(ierr);} 147 ierr = PetscFree(a->inew);CHKERRQ(ierr); 148 ierr = MatDestroy(&a->parent);CHKERRQ(ierr); 149 ierr = PetscFree(A->data);CHKERRQ(ierr); 150 151 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 152 ierr = PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C",NULL);CHKERRQ(ierr); 153 ierr = PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 154 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C",NULL);CHKERRQ(ierr); 155 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C",NULL);CHKERRQ(ierr); 156 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C",NULL);CHKERRQ(ierr); 157 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 158 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 159 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqsbstrm_C",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 = PetscMalloc1((*ncols+row),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 = PetscMalloc1((*ncols+row),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 #if defined(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; 339 340 PetscFunctionBegin; 341 if (reuse == MAT_INITIAL_MATRIX || *B != A) { 342 ierr = MatDuplicate(A,MAT_COPY_VALUES,B);CHKERRQ(ierr); 343 } 344 PetscFunctionReturn(0); 345 } 346 347 #undef __FUNCT__ 348 #define __FUNCT__ "MatView_SeqSBAIJ_ASCII" 349 PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer) 350 { 351 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 352 PetscErrorCode ierr; 353 PetscInt i,j,bs = A->rmap->bs,k,l,bs2=a->bs2; 354 PetscViewerFormat format; 355 PetscInt *diag; 356 357 PetscFunctionBegin; 358 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 359 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 360 ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); 361 } else if (format == PETSC_VIEWER_ASCII_MATLAB) { 362 Mat aij; 363 if (A->factortype && bs>1) { 364 ierr = PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored with bs>1. MatView() with PETSC_VIEWER_ASCII_MATLAB is not supported and ignored!\n");CHKERRQ(ierr); 365 PetscFunctionReturn(0); 366 } 367 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);CHKERRQ(ierr); 368 ierr = MatView(aij,viewer);CHKERRQ(ierr); 369 ierr = MatDestroy(&aij);CHKERRQ(ierr); 370 } else if (format == PETSC_VIEWER_ASCII_COMMON) { 371 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 372 for (i=0; i<a->mbs; i++) { 373 for (j=0; j<bs; j++) { 374 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 375 for (k=a->i[i]; k<a->i[i+1]; k++) { 376 for (l=0; l<bs; l++) { 377 #if defined(PETSC_USE_COMPLEX) 378 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 379 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l, 380 (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 381 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 382 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l, 383 (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 384 } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 385 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 386 } 387 #else 388 if (a->a[bs2*k + l*bs + j] != 0.0) { 389 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 390 } 391 #endif 392 } 393 } 394 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 395 } 396 } 397 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 398 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 399 PetscFunctionReturn(0); 400 } else { 401 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 402 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]],(double)PetscRealPart(1.0/a->a[diag[i]]),(double)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]],(double)PetscRealPart(1.0/a->a[diag[i]]),-(double)PetscImaginaryPart(1.0/a->a[diag[i]]));CHKERRQ(ierr); 414 } else { 415 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]));CHKERRQ(ierr); 416 } 417 #else 418 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)(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],(double)PetscRealPart(a->a[k]),(double)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],(double)PetscRealPart(a->a[k]),-(double)PetscImaginaryPart(a->a[k]));CHKERRQ(ierr); 427 } else { 428 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k],(double)PetscRealPart(a->a[k]));CHKERRQ(ierr); 429 } 430 #else 431 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[k],(double)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 (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)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 (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 450 } else { 451 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 452 } 453 #else 454 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)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 #include <petscdraw.h> 469 #undef __FUNCT__ 470 #define __FUNCT__ "MatView_SeqSBAIJ_Draw_Zoom" 471 static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa) 472 { 473 Mat A = (Mat) Aa; 474 Mat_SeqSBAIJ *a=(Mat_SeqSBAIJ*)A->data; 475 PetscErrorCode ierr; 476 PetscInt row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2; 477 PetscMPIInt rank; 478 PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r; 479 MatScalar *aa; 480 MPI_Comm comm; 481 PetscViewer viewer; 482 483 PetscFunctionBegin; 484 /* 485 This is nasty. If this is called from an originally parallel matrix 486 then all processes call this,but only the first has the matrix so the 487 rest should return immediately. 488 */ 489 ierr = PetscObjectGetComm((PetscObject)draw,&comm);CHKERRQ(ierr); 490 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 491 if (rank) PetscFunctionReturn(0); 492 493 ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr); 494 495 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 496 PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric"); 497 498 /* loop over matrix elements drawing boxes */ 499 color = PETSC_DRAW_BLUE; 500 for (i=0,row=0; i<mbs; i++,row+=bs) { 501 for (j=a->i[i]; j<a->i[i+1]; j++) { 502 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 503 x_l = a->j[j]*bs; x_r = x_l + 1.0; 504 aa = a->a + j*bs2; 505 for (k=0; k<bs; k++) { 506 for (l=0; l<bs; l++) { 507 if (PetscRealPart(*aa++) >= 0.) continue; 508 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 509 } 510 } 511 } 512 } 513 color = PETSC_DRAW_CYAN; 514 for (i=0,row=0; i<mbs; i++,row+=bs) { 515 for (j=a->i[i]; j<a->i[i+1]; j++) { 516 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 517 x_l = a->j[j]*bs; x_r = x_l + 1.0; 518 aa = a->a + j*bs2; 519 for (k=0; k<bs; k++) { 520 for (l=0; l<bs; l++) { 521 if (PetscRealPart(*aa++) != 0.) continue; 522 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 523 } 524 } 525 } 526 } 527 528 color = PETSC_DRAW_RED; 529 for (i=0,row=0; i<mbs; i++,row+=bs) { 530 for (j=a->i[i]; j<a->i[i+1]; j++) { 531 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 532 x_l = a->j[j]*bs; x_r = x_l + 1.0; 533 aa = a->a + j*bs2; 534 for (k=0; k<bs; k++) { 535 for (l=0; l<bs; l++) { 536 if (PetscRealPart(*aa++) <= 0.) continue; 537 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 538 } 539 } 540 } 541 } 542 PetscFunctionReturn(0); 543 } 544 545 #undef __FUNCT__ 546 #define __FUNCT__ "MatView_SeqSBAIJ_Draw" 547 static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer) 548 { 549 PetscErrorCode ierr; 550 PetscReal xl,yl,xr,yr,w,h; 551 PetscDraw draw; 552 PetscBool isnull; 553 554 PetscFunctionBegin; 555 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 556 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 557 558 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);CHKERRQ(ierr); 559 xr = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0; 560 xr += w; yr += h; xl = -w; yl = -h; 561 ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr); 562 ierr = PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);CHKERRQ(ierr); 563 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",NULL);CHKERRQ(ierr); 564 PetscFunctionReturn(0); 565 } 566 567 #undef __FUNCT__ 568 #define __FUNCT__ "MatView_SeqSBAIJ" 569 PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer) 570 { 571 PetscErrorCode ierr; 572 PetscBool iascii,isdraw; 573 FILE *file = 0; 574 575 PetscFunctionBegin; 576 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 577 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 578 if (iascii) { 579 ierr = MatView_SeqSBAIJ_ASCII(A,viewer);CHKERRQ(ierr); 580 } else if (isdraw) { 581 ierr = MatView_SeqSBAIJ_Draw(A,viewer);CHKERRQ(ierr); 582 } else { 583 Mat B; 584 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 585 ierr = MatView(B,viewer);CHKERRQ(ierr); 586 ierr = MatDestroy(&B);CHKERRQ(ierr); 587 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 588 if (file) { 589 fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs); 590 } 591 } 592 PetscFunctionReturn(0); 593 } 594 595 596 #undef __FUNCT__ 597 #define __FUNCT__ "MatGetValues_SeqSBAIJ" 598 PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[]) 599 { 600 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 601 PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j; 602 PetscInt *ai = a->i,*ailen = a->ilen; 603 PetscInt brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2; 604 MatScalar *ap,*aa = a->a; 605 606 PetscFunctionBegin; 607 for (k=0; k<m; k++) { /* loop over rows */ 608 row = im[k]; brow = row/bs; 609 if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */ 610 if (row >= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1); 611 rp = aj + ai[brow]; ap = aa + bs2*ai[brow]; 612 nrow = ailen[brow]; 613 for (l=0; l<n; l++) { /* loop over columns */ 614 if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */ 615 if (in[l] >= A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->cmap->n-1); 616 col = in[l]; 617 bcol = col/bs; 618 cidx = col%bs; 619 ridx = row%bs; 620 high = nrow; 621 low = 0; /* assume unsorted */ 622 while (high-low > 5) { 623 t = (low+high)/2; 624 if (rp[t] > bcol) high = t; 625 else low = t; 626 } 627 for (i=low; i<high; i++) { 628 if (rp[i] > bcol) break; 629 if (rp[i] == bcol) { 630 *v++ = ap[bs2*i+bs*cidx+ridx]; 631 goto finished; 632 } 633 } 634 *v++ = 0.0; 635 finished:; 636 } 637 } 638 PetscFunctionReturn(0); 639 } 640 641 642 #undef __FUNCT__ 643 #define __FUNCT__ "MatSetValuesBlocked_SeqSBAIJ" 644 PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 645 { 646 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 647 PetscErrorCode ierr; 648 PetscInt *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1; 649 PetscInt *imax =a->imax,*ai=a->i,*ailen=a->ilen; 650 PetscInt *aj =a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval; 651 PetscBool roworiented=a->roworiented; 652 const PetscScalar *value = v; 653 MatScalar *ap,*aa = a->a,*bap; 654 655 PetscFunctionBegin; 656 if (roworiented) stepval = (n-1)*bs; 657 else stepval = (m-1)*bs; 658 659 for (k=0; k<m; k++) { /* loop over added rows */ 660 row = im[k]; 661 if (row < 0) continue; 662 #if defined(PETSC_USE_DEBUG) 663 if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1); 664 #endif 665 rp = aj + ai[row]; 666 ap = aa + bs2*ai[row]; 667 rmax = imax[row]; 668 nrow = ailen[row]; 669 low = 0; 670 high = nrow; 671 for (l=0; l<n; l++) { /* loop over added columns */ 672 if (in[l] < 0) continue; 673 col = in[l]; 674 #if defined(PETSC_USE_DEBUG) 675 if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1); 676 #endif 677 if (col < row) { 678 if (a->ignore_ltriangular) continue; /* ignore lower triangular block */ 679 else 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)"); 680 } 681 if (roworiented) value = v + k*(stepval+bs)*bs + l*bs; 682 else value = v + l*(stepval+bs)*bs + k*bs; 683 684 if (col <= lastcol) low = 0; 685 else high = nrow; 686 687 lastcol = col; 688 while (high-low > 7) { 689 t = (low+high)/2; 690 if (rp[t] > col) high = t; 691 else low = t; 692 } 693 for (i=low; i<high; i++) { 694 if (rp[i] > col) break; 695 if (rp[i] == col) { 696 bap = ap + bs2*i; 697 if (roworiented) { 698 if (is == ADD_VALUES) { 699 for (ii=0; ii<bs; ii++,value+=stepval) { 700 for (jj=ii; jj<bs2; jj+=bs) { 701 bap[jj] += *value++; 702 } 703 } 704 } else { 705 for (ii=0; ii<bs; ii++,value+=stepval) { 706 for (jj=ii; jj<bs2; jj+=bs) { 707 bap[jj] = *value++; 708 } 709 } 710 } 711 } else { 712 if (is == ADD_VALUES) { 713 for (ii=0; ii<bs; ii++,value+=stepval) { 714 for (jj=0; jj<bs; jj++) { 715 *bap++ += *value++; 716 } 717 } 718 } else { 719 for (ii=0; ii<bs; ii++,value+=stepval) { 720 for (jj=0; jj<bs; jj++) { 721 *bap++ = *value++; 722 } 723 } 724 } 725 } 726 goto noinsert2; 727 } 728 } 729 if (nonew == 1) goto noinsert2; 730 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 731 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 732 N = nrow++ - 1; high++; 733 /* shift up all the later entries in this row */ 734 for (ii=N; ii>=i; ii--) { 735 rp[ii+1] = rp[ii]; 736 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 737 } 738 if (N >= i) { 739 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 740 } 741 rp[i] = col; 742 bap = ap + bs2*i; 743 if (roworiented) { 744 for (ii=0; ii<bs; ii++,value+=stepval) { 745 for (jj=ii; jj<bs2; jj+=bs) { 746 bap[jj] = *value++; 747 } 748 } 749 } else { 750 for (ii=0; ii<bs; ii++,value+=stepval) { 751 for (jj=0; jj<bs; jj++) { 752 *bap++ = *value++; 753 } 754 } 755 } 756 noinsert2:; 757 low = i; 758 } 759 ailen[row] = nrow; 760 } 761 PetscFunctionReturn(0); 762 } 763 764 /* 765 This is not yet used 766 */ 767 #undef __FUNCT__ 768 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode" 769 PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A) 770 { 771 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 772 PetscErrorCode ierr; 773 const PetscInt *ai = a->i, *aj = a->j,*cols; 774 PetscInt i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts; 775 PetscBool flag; 776 777 PetscFunctionBegin; 778 ierr = PetscMalloc1(m,&ns);CHKERRQ(ierr); 779 while (i < m) { 780 nzx = ai[i+1] - ai[i]; /* Number of nonzeros */ 781 /* Limits the number of elements in a node to 'a->inode.limit' */ 782 for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) { 783 nzy = ai[j+1] - ai[j]; 784 if (nzy != (nzx - j + i)) break; 785 ierr = PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);CHKERRQ(ierr); 786 if (!flag) break; 787 } 788 ns[node_count++] = blk_size; 789 790 i = j; 791 } 792 if (!a->inode.size && m && node_count > .9*m) { 793 ierr = PetscFree(ns);CHKERRQ(ierr); 794 ierr = PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);CHKERRQ(ierr); 795 } else { 796 a->inode.node_count = node_count; 797 798 ierr = PetscMalloc1(node_count,&a->inode.size);CHKERRQ(ierr); 799 ierr = PetscLogObjectMemory((PetscObject)A,node_count*sizeof(PetscInt));CHKERRQ(ierr); 800 ierr = PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt));CHKERRQ(ierr); 801 ierr = PetscFree(ns);CHKERRQ(ierr); 802 ierr = PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);CHKERRQ(ierr); 803 804 /* count collections of adjacent columns in each inode */ 805 row = 0; 806 cnt = 0; 807 for (i=0; i<node_count; i++) { 808 cols = aj + ai[row] + a->inode.size[i]; 809 nz = ai[row+1] - ai[row] - a->inode.size[i]; 810 for (j=1; j<nz; j++) { 811 if (cols[j] != cols[j-1]+1) cnt++; 812 } 813 cnt++; 814 row += a->inode.size[i]; 815 } 816 ierr = PetscMalloc1(2*cnt,&counts);CHKERRQ(ierr); 817 cnt = 0; 818 row = 0; 819 for (i=0; i<node_count; i++) { 820 cols = aj + ai[row] + a->inode.size[i]; 821 counts[2*cnt] = cols[0]; 822 nz = ai[row+1] - ai[row] - a->inode.size[i]; 823 cnt2 = 1; 824 for (j=1; j<nz; j++) { 825 if (cols[j] != cols[j-1]+1) { 826 counts[2*(cnt++)+1] = cnt2; 827 counts[2*cnt] = cols[j]; 828 cnt2 = 1; 829 } else cnt2++; 830 } 831 counts[2*(cnt++)+1] = cnt2; 832 row += a->inode.size[i]; 833 } 834 ierr = PetscIntView(2*cnt,counts,0);CHKERRQ(ierr); 835 } 836 PetscFunctionReturn(0); 837 } 838 839 #undef __FUNCT__ 840 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ" 841 PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode) 842 { 843 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 844 PetscErrorCode ierr; 845 PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax; 846 PetscInt m = A->rmap->N,*ip,N,*ailen = a->ilen; 847 PetscInt mbs = a->mbs,bs2 = a->bs2,rmax = 0; 848 MatScalar *aa = a->a,*ap; 849 850 PetscFunctionBegin; 851 if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); 852 853 if (m) rmax = ailen[0]; 854 for (i=1; i<mbs; i++) { 855 /* move each row back by the amount of empty slots (fshift) before it*/ 856 fshift += imax[i-1] - ailen[i-1]; 857 rmax = PetscMax(rmax,ailen[i]); 858 if (fshift) { 859 ip = aj + ai[i]; ap = aa + bs2*ai[i]; 860 N = ailen[i]; 861 for (j=0; j<N; j++) { 862 ip[j-fshift] = ip[j]; 863 ierr = PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 864 } 865 } 866 ai[i] = ai[i-1] + ailen[i-1]; 867 } 868 if (mbs) { 869 fshift += imax[mbs-1] - ailen[mbs-1]; 870 ai[mbs] = ai[mbs-1] + ailen[mbs-1]; 871 } 872 /* reset ilen and imax for each row */ 873 for (i=0; i<mbs; i++) { 874 ailen[i] = imax[i] = ai[i+1] - ai[i]; 875 } 876 a->nz = ai[mbs]; 877 878 /* diagonals may have moved, reset it */ 879 if (a->diag) { 880 ierr = PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));CHKERRQ(ierr); 881 } 882 if (fshift && a->nounused == -1) 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); 883 884 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); 885 ierr = PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);CHKERRQ(ierr); 886 ierr = PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);CHKERRQ(ierr); 887 888 A->info.mallocs += a->reallocs; 889 a->reallocs = 0; 890 A->info.nz_unneeded = (PetscReal)fshift*bs2; 891 a->idiagvalid = PETSC_FALSE; 892 893 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 894 if (a->jshort && a->free_jshort) { 895 /* when matrix data structure is changed, previous jshort must be replaced */ 896 ierr = PetscFree(a->jshort);CHKERRQ(ierr); 897 } 898 ierr = PetscMalloc1(a->i[A->rmap->n],&a->jshort);CHKERRQ(ierr); 899 ierr = PetscLogObjectMemory((PetscObject)A,a->i[A->rmap->n]*sizeof(unsigned short));CHKERRQ(ierr); 900 for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i]; 901 A->ops->mult = MatMult_SeqSBAIJ_1_ushort; 902 A->ops->sor = MatSOR_SeqSBAIJ_ushort; 903 a->free_jshort = PETSC_TRUE; 904 } 905 PetscFunctionReturn(0); 906 } 907 908 /* 909 This function returns an array of flags which indicate the locations of contiguous 910 blocks that should be zeroed. for eg: if bs = 3 and is = [0,1,2,3,5,6,7,8,9] 911 then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)] 912 Assume: sizes should be long enough to hold all the values. 913 */ 914 #undef __FUNCT__ 915 #define __FUNCT__ "MatZeroRows_SeqSBAIJ_Check_Blocks" 916 PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max) 917 { 918 PetscInt i,j,k,row; 919 PetscBool flg; 920 921 PetscFunctionBegin; 922 for (i=0,j=0; i<n; j++) { 923 row = idx[i]; 924 if (row%bs!=0) { /* Not the begining of a block */ 925 sizes[j] = 1; 926 i++; 927 } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */ 928 sizes[j] = 1; /* Also makes sure atleast 'bs' values exist for next else */ 929 i++; 930 } else { /* Begining of the block, so check if the complete block exists */ 931 flg = PETSC_TRUE; 932 for (k=1; k<bs; k++) { 933 if (row+k != idx[i+k]) { /* break in the block */ 934 flg = PETSC_FALSE; 935 break; 936 } 937 } 938 if (flg) { /* No break in the bs */ 939 sizes[j] = bs; 940 i += bs; 941 } else { 942 sizes[j] = 1; 943 i++; 944 } 945 } 946 } 947 *bs_max = j; 948 PetscFunctionReturn(0); 949 } 950 951 952 /* Only add/insert a(i,j) with i<=j (blocks). 953 Any a(i,j) with i>j input by user is ingored. 954 */ 955 956 #undef __FUNCT__ 957 #define __FUNCT__ "MatSetValues_SeqSBAIJ" 958 PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 959 { 960 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 961 PetscErrorCode ierr; 962 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1; 963 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented; 964 PetscInt *aj =a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol; 965 PetscInt ridx,cidx,bs2=a->bs2; 966 MatScalar *ap,value,*aa=a->a,*bap; 967 968 PetscFunctionBegin; 969 for (k=0; k<m; k++) { /* loop over added rows */ 970 row = im[k]; /* row number */ 971 brow = row/bs; /* block row number */ 972 if (row < 0) continue; 973 #if defined(PETSC_USE_DEBUG) 974 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); 975 #endif 976 rp = aj + ai[brow]; /*ptr to beginning of column value of the row block*/ 977 ap = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/ 978 rmax = imax[brow]; /* maximum space allocated for this row */ 979 nrow = ailen[brow]; /* actual length of this row */ 980 low = 0; 981 982 for (l=0; l<n; l++) { /* loop over added columns */ 983 if (in[l] < 0) continue; 984 #if defined(PETSC_USE_DEBUG) 985 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); 986 #endif 987 col = in[l]; 988 bcol = col/bs; /* block col number */ 989 990 if (brow > bcol) { 991 if (a->ignore_ltriangular) continue; /* ignore lower triangular values */ 992 else 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)"); 993 } 994 995 ridx = row % bs; cidx = col % bs; /*row and col index inside the block */ 996 if ((brow==bcol && ridx<=cidx) || (brow<bcol)) { 997 /* element value a(k,l) */ 998 if (roworiented) value = v[l + k*n]; 999 else value = v[k + l*m]; 1000 1001 /* move pointer bap to a(k,l) quickly and add/insert value */ 1002 if (col <= lastcol) low = 0; 1003 high = nrow; 1004 lastcol = col; 1005 while (high-low > 7) { 1006 t = (low+high)/2; 1007 if (rp[t] > bcol) high = t; 1008 else low = t; 1009 } 1010 for (i=low; i<high; i++) { 1011 if (rp[i] > bcol) break; 1012 if (rp[i] == bcol) { 1013 bap = ap + bs2*i + bs*cidx + ridx; 1014 if (is == ADD_VALUES) *bap += value; 1015 else *bap = value; 1016 /* for diag block, add/insert its symmetric element a(cidx,ridx) */ 1017 if (brow == bcol && ridx < cidx) { 1018 bap = ap + bs2*i + bs*ridx + cidx; 1019 if (is == ADD_VALUES) *bap += value; 1020 else *bap = value; 1021 } 1022 goto noinsert1; 1023 } 1024 } 1025 1026 if (nonew == 1) goto noinsert1; 1027 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 1028 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 1029 1030 N = nrow++ - 1; high++; 1031 /* shift up all the later entries in this row */ 1032 for (ii=N; ii>=i; ii--) { 1033 rp[ii+1] = rp[ii]; 1034 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 1035 } 1036 if (N>=i) { 1037 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1038 } 1039 rp[i] = bcol; 1040 ap[bs2*i + bs*cidx + ridx] = value; 1041 A->nonzerostate++; 1042 noinsert1:; 1043 low = i; 1044 } 1045 } /* end of loop over added columns */ 1046 ailen[brow] = nrow; 1047 } /* end of loop over added rows */ 1048 PetscFunctionReturn(0); 1049 } 1050 1051 #undef __FUNCT__ 1052 #define __FUNCT__ "MatICCFactor_SeqSBAIJ" 1053 PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info) 1054 { 1055 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)inA->data; 1056 Mat outA; 1057 PetscErrorCode ierr; 1058 PetscBool row_identity; 1059 1060 PetscFunctionBegin; 1061 if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc"); 1062 ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr); 1063 if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported"); 1064 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()! */ 1065 1066 outA = inA; 1067 inA->factortype = MAT_FACTOR_ICC; 1068 1069 ierr = MatMarkDiagonal_SeqSBAIJ(inA);CHKERRQ(ierr); 1070 ierr = MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);CHKERRQ(ierr); 1071 1072 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1073 ierr = ISDestroy(&a->row);CHKERRQ(ierr); 1074 a->row = row; 1075 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1076 ierr = ISDestroy(&a->col);CHKERRQ(ierr); 1077 a->col = row; 1078 1079 /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */ 1080 if (a->icol) {ierr = ISInvertPermutation(row,PETSC_DECIDE, &a->icol);CHKERRQ(ierr);} 1081 ierr = PetscLogObjectParent((PetscObject)inA,(PetscObject)a->icol);CHKERRQ(ierr); 1082 1083 if (!a->solve_work) { 1084 ierr = PetscMalloc1((inA->rmap->N+inA->rmap->bs),&a->solve_work);CHKERRQ(ierr); 1085 ierr = PetscLogObjectMemory((PetscObject)inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));CHKERRQ(ierr); 1086 } 1087 1088 ierr = MatCholeskyFactorNumeric(outA,inA,info);CHKERRQ(ierr); 1089 PetscFunctionReturn(0); 1090 } 1091 1092 #undef __FUNCT__ 1093 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices_SeqSBAIJ" 1094 PetscErrorCode MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices) 1095 { 1096 Mat_SeqSBAIJ *baij = (Mat_SeqSBAIJ*)mat->data; 1097 PetscInt i,nz,n; 1098 PetscErrorCode ierr; 1099 1100 PetscFunctionBegin; 1101 nz = baij->maxnz; 1102 n = mat->cmap->n; 1103 for (i=0; i<nz; i++) baij->j[i] = indices[i]; 1104 1105 baij->nz = nz; 1106 for (i=0; i<n; i++) baij->ilen[i] = baij->imax[i]; 1107 1108 ierr = MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1109 PetscFunctionReturn(0); 1110 } 1111 1112 #undef __FUNCT__ 1113 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices" 1114 /*@ 1115 MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows 1116 in the matrix. 1117 1118 Input Parameters: 1119 + mat - the SeqSBAIJ matrix 1120 - indices - the column indices 1121 1122 Level: advanced 1123 1124 Notes: 1125 This can be called if you have precomputed the nonzero structure of the 1126 matrix and want to provide it to the matrix object to improve the performance 1127 of the MatSetValues() operation. 1128 1129 You MUST have set the correct numbers of nonzeros per row in the call to 1130 MatCreateSeqSBAIJ(), and the columns indices MUST be sorted. 1131 1132 MUST be called before any calls to MatSetValues() 1133 1134 .seealso: MatCreateSeqSBAIJ 1135 @*/ 1136 PetscErrorCode MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices) 1137 { 1138 PetscErrorCode ierr; 1139 1140 PetscFunctionBegin; 1141 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1142 PetscValidPointer(indices,2); 1143 ierr = PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt*),(mat,indices));CHKERRQ(ierr); 1144 PetscFunctionReturn(0); 1145 } 1146 1147 #undef __FUNCT__ 1148 #define __FUNCT__ "MatCopy_SeqSBAIJ" 1149 PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str) 1150 { 1151 PetscErrorCode ierr; 1152 1153 PetscFunctionBegin; 1154 /* If the two matrices have the same copy implementation, use fast copy. */ 1155 if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) { 1156 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1157 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1158 1159 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"); 1160 ierr = PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));CHKERRQ(ierr); 1161 } else { 1162 ierr = MatGetRowUpperTriangular(A);CHKERRQ(ierr); 1163 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 1164 ierr = MatRestoreRowUpperTriangular(A);CHKERRQ(ierr); 1165 } 1166 PetscFunctionReturn(0); 1167 } 1168 1169 #undef __FUNCT__ 1170 #define __FUNCT__ "MatSetUp_SeqSBAIJ" 1171 PetscErrorCode MatSetUp_SeqSBAIJ(Mat A) 1172 { 1173 PetscErrorCode ierr; 1174 1175 PetscFunctionBegin; 1176 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,A->rmap->bs,PETSC_DEFAULT,0);CHKERRQ(ierr); 1177 PetscFunctionReturn(0); 1178 } 1179 1180 #undef __FUNCT__ 1181 #define __FUNCT__ "MatSeqSBAIJGetArray_SeqSBAIJ" 1182 PetscErrorCode MatSeqSBAIJGetArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1183 { 1184 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1185 1186 PetscFunctionBegin; 1187 *array = a->a; 1188 PetscFunctionReturn(0); 1189 } 1190 1191 #undef __FUNCT__ 1192 #define __FUNCT__ "MatSeqSBAIJRestoreArray_SeqSBAIJ" 1193 PetscErrorCode MatSeqSBAIJRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1194 { 1195 PetscFunctionBegin; 1196 PetscFunctionReturn(0); 1197 } 1198 1199 #undef __FUNCT__ 1200 #define __FUNCT__ "MatAXPY_SeqSBAIJ" 1201 PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 1202 { 1203 Mat_SeqSBAIJ *x=(Mat_SeqSBAIJ*)X->data, *y=(Mat_SeqSBAIJ*)Y->data; 1204 PetscErrorCode ierr; 1205 PetscInt i,bs=Y->rmap->bs,bs2=bs*bs,j; 1206 PetscBLASInt one = 1; 1207 1208 PetscFunctionBegin; 1209 if (str == SAME_NONZERO_PATTERN) { 1210 PetscScalar alpha = a; 1211 PetscBLASInt bnz; 1212 ierr = PetscBLASIntCast(x->nz*bs2,&bnz);CHKERRQ(ierr); 1213 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 1214 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 1215 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 1216 if (y->xtoy && y->XtoY != X) { 1217 ierr = PetscFree(y->xtoy);CHKERRQ(ierr); 1218 ierr = MatDestroy(&y->XtoY);CHKERRQ(ierr); 1219 } 1220 if (!y->xtoy) { /* get xtoy */ 1221 ierr = MatAXPYGetxtoy_Private(x->mbs,x->i,x->j,NULL, y->i,y->j,NULL, &y->xtoy);CHKERRQ(ierr); 1222 y->XtoY = X; 1223 } 1224 for (i=0; i<x->nz; i++) { 1225 j = 0; 1226 while (j < bs2) { 1227 y->a[bs2*y->xtoy[i]+j] += a*(x->a[bs2*i+j]); 1228 j++; 1229 } 1230 } 1231 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 1232 ierr = PetscInfo3(Y,"ratio of nnz_s(X)/nnz_s(Y): %D/%D = %g\n",bs2*x->nz,bs2*y->nz,(double)((PetscReal)(bs2*x->nz)/(PetscReal)(bs2*y->nz)));CHKERRQ(ierr); 1233 } else { 1234 ierr = MatGetRowUpperTriangular(X);CHKERRQ(ierr); 1235 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 1236 ierr = MatRestoreRowUpperTriangular(X);CHKERRQ(ierr); 1237 } 1238 PetscFunctionReturn(0); 1239 } 1240 1241 #undef __FUNCT__ 1242 #define __FUNCT__ "MatIsSymmetric_SeqSBAIJ" 1243 PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1244 { 1245 PetscFunctionBegin; 1246 *flg = PETSC_TRUE; 1247 PetscFunctionReturn(0); 1248 } 1249 1250 #undef __FUNCT__ 1251 #define __FUNCT__ "MatIsStructurallySymmetric_SeqSBAIJ" 1252 PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool *flg) 1253 { 1254 PetscFunctionBegin; 1255 *flg = PETSC_TRUE; 1256 PetscFunctionReturn(0); 1257 } 1258 1259 #undef __FUNCT__ 1260 #define __FUNCT__ "MatIsHermitian_SeqSBAIJ" 1261 PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1262 { 1263 PetscFunctionBegin; 1264 *flg = PETSC_FALSE; 1265 PetscFunctionReturn(0); 1266 } 1267 1268 #undef __FUNCT__ 1269 #define __FUNCT__ "MatRealPart_SeqSBAIJ" 1270 PetscErrorCode MatRealPart_SeqSBAIJ(Mat A) 1271 { 1272 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1273 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1274 MatScalar *aa = a->a; 1275 1276 PetscFunctionBegin; 1277 for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]); 1278 PetscFunctionReturn(0); 1279 } 1280 1281 #undef __FUNCT__ 1282 #define __FUNCT__ "MatImaginaryPart_SeqSBAIJ" 1283 PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A) 1284 { 1285 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1286 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1287 MatScalar *aa = a->a; 1288 1289 PetscFunctionBegin; 1290 for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]); 1291 PetscFunctionReturn(0); 1292 } 1293 1294 #undef __FUNCT__ 1295 #define __FUNCT__ "MatZeroRowsColumns_SeqSBAIJ" 1296 PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b) 1297 { 1298 Mat_SeqSBAIJ *baij=(Mat_SeqSBAIJ*)A->data; 1299 PetscErrorCode ierr; 1300 PetscInt i,j,k,count; 1301 PetscInt bs =A->rmap->bs,bs2=baij->bs2,row,col; 1302 PetscScalar zero = 0.0; 1303 MatScalar *aa; 1304 const PetscScalar *xx; 1305 PetscScalar *bb; 1306 PetscBool *zeroed,vecs = PETSC_FALSE; 1307 1308 PetscFunctionBegin; 1309 /* fix right hand side if needed */ 1310 if (x && b) { 1311 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1312 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1313 vecs = PETSC_TRUE; 1314 } 1315 1316 /* zero the columns */ 1317 ierr = PetscCalloc1(A->rmap->n,&zeroed);CHKERRQ(ierr); 1318 for (i=0; i<is_n; i++) { 1319 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]); 1320 zeroed[is_idx[i]] = PETSC_TRUE; 1321 } 1322 if (vecs) { 1323 for (i=0; i<A->rmap->N; i++) { 1324 row = i/bs; 1325 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1326 for (k=0; k<bs; k++) { 1327 col = bs*baij->j[j] + k; 1328 if (col <= i) continue; 1329 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1330 if (!zeroed[i] && zeroed[col]) bb[i] -= aa[0]*xx[col]; 1331 if (zeroed[i] && !zeroed[col]) bb[col] -= aa[0]*xx[i]; 1332 } 1333 } 1334 } 1335 for (i=0; i<is_n; i++) bb[is_idx[i]] = diag*xx[is_idx[i]]; 1336 } 1337 1338 for (i=0; i<A->rmap->N; i++) { 1339 if (!zeroed[i]) { 1340 row = i/bs; 1341 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1342 for (k=0; k<bs; k++) { 1343 col = bs*baij->j[j] + k; 1344 if (zeroed[col]) { 1345 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1346 aa[0] = 0.0; 1347 } 1348 } 1349 } 1350 } 1351 } 1352 ierr = PetscFree(zeroed);CHKERRQ(ierr); 1353 if (vecs) { 1354 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1355 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1356 } 1357 1358 /* zero the rows */ 1359 for (i=0; i<is_n; i++) { 1360 row = is_idx[i]; 1361 count = (baij->i[row/bs +1] - baij->i[row/bs])*bs; 1362 aa = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs); 1363 for (k=0; k<count; k++) { 1364 aa[0] = zero; 1365 aa += bs; 1366 } 1367 if (diag != 0.0) { 1368 ierr = (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); 1369 } 1370 } 1371 ierr = MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1372 PetscFunctionReturn(0); 1373 } 1374 1375 /* -------------------------------------------------------------------*/ 1376 static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ, 1377 MatGetRow_SeqSBAIJ, 1378 MatRestoreRow_SeqSBAIJ, 1379 MatMult_SeqSBAIJ_N, 1380 /* 4*/ MatMultAdd_SeqSBAIJ_N, 1381 MatMult_SeqSBAIJ_N, /* transpose versions are same as non-transpose versions */ 1382 MatMultAdd_SeqSBAIJ_N, 1383 0, 1384 0, 1385 0, 1386 /* 10*/ 0, 1387 0, 1388 MatCholeskyFactor_SeqSBAIJ, 1389 MatSOR_SeqSBAIJ, 1390 MatTranspose_SeqSBAIJ, 1391 /* 15*/ MatGetInfo_SeqSBAIJ, 1392 MatEqual_SeqSBAIJ, 1393 MatGetDiagonal_SeqSBAIJ, 1394 MatDiagonalScale_SeqSBAIJ, 1395 MatNorm_SeqSBAIJ, 1396 /* 20*/ 0, 1397 MatAssemblyEnd_SeqSBAIJ, 1398 MatSetOption_SeqSBAIJ, 1399 MatZeroEntries_SeqSBAIJ, 1400 /* 24*/ 0, 1401 0, 1402 0, 1403 0, 1404 0, 1405 /* 29*/ MatSetUp_SeqSBAIJ, 1406 0, 1407 0, 1408 0, 1409 0, 1410 /* 34*/ MatDuplicate_SeqSBAIJ, 1411 0, 1412 0, 1413 0, 1414 MatICCFactor_SeqSBAIJ, 1415 /* 39*/ MatAXPY_SeqSBAIJ, 1416 MatGetSubMatrices_SeqSBAIJ, 1417 MatIncreaseOverlap_SeqSBAIJ, 1418 MatGetValues_SeqSBAIJ, 1419 MatCopy_SeqSBAIJ, 1420 /* 44*/ 0, 1421 MatScale_SeqSBAIJ, 1422 0, 1423 0, 1424 MatZeroRowsColumns_SeqSBAIJ, 1425 /* 49*/ 0, 1426 MatGetRowIJ_SeqSBAIJ, 1427 MatRestoreRowIJ_SeqSBAIJ, 1428 0, 1429 0, 1430 /* 54*/ 0, 1431 0, 1432 0, 1433 0, 1434 MatSetValuesBlocked_SeqSBAIJ, 1435 /* 59*/ MatGetSubMatrix_SeqSBAIJ, 1436 0, 1437 0, 1438 0, 1439 0, 1440 /* 64*/ 0, 1441 0, 1442 0, 1443 0, 1444 0, 1445 /* 69*/ MatGetRowMaxAbs_SeqSBAIJ, 1446 0, 1447 0, 1448 0, 1449 0, 1450 /* 74*/ 0, 1451 0, 1452 0, 1453 0, 1454 0, 1455 /* 79*/ 0, 1456 0, 1457 0, 1458 MatGetInertia_SeqSBAIJ, 1459 MatLoad_SeqSBAIJ, 1460 /* 84*/ MatIsSymmetric_SeqSBAIJ, 1461 MatIsHermitian_SeqSBAIJ, 1462 MatIsStructurallySymmetric_SeqSBAIJ, 1463 0, 1464 0, 1465 /* 89*/ 0, 1466 0, 1467 0, 1468 0, 1469 0, 1470 /* 94*/ 0, 1471 0, 1472 0, 1473 0, 1474 0, 1475 /* 99*/ 0, 1476 0, 1477 0, 1478 0, 1479 0, 1480 /*104*/ 0, 1481 MatRealPart_SeqSBAIJ, 1482 MatImaginaryPart_SeqSBAIJ, 1483 MatGetRowUpperTriangular_SeqSBAIJ, 1484 MatRestoreRowUpperTriangular_SeqSBAIJ, 1485 /*109*/ 0, 1486 0, 1487 0, 1488 0, 1489 MatMissingDiagonal_SeqSBAIJ, 1490 /*114*/ 0, 1491 0, 1492 0, 1493 0, 1494 0, 1495 /*119*/ 0, 1496 0, 1497 0, 1498 0, 1499 0, 1500 /*124*/ 0, 1501 0, 1502 0, 1503 0, 1504 0, 1505 /*129*/ 0, 1506 0, 1507 0, 1508 0, 1509 0, 1510 /*134*/ 0, 1511 0, 1512 0, 1513 0, 1514 0, 1515 /*139*/ 0, 1516 0, 1517 0 1518 }; 1519 1520 #undef __FUNCT__ 1521 #define __FUNCT__ "MatStoreValues_SeqSBAIJ" 1522 PetscErrorCode MatStoreValues_SeqSBAIJ(Mat mat) 1523 { 1524 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)mat->data; 1525 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1526 PetscErrorCode ierr; 1527 1528 PetscFunctionBegin; 1529 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1530 1531 /* allocate space for values if not already there */ 1532 if (!aij->saved_values) { 1533 ierr = PetscMalloc1((nz+1),&aij->saved_values);CHKERRQ(ierr); 1534 } 1535 1536 /* copy values over */ 1537 ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1538 PetscFunctionReturn(0); 1539 } 1540 1541 #undef __FUNCT__ 1542 #define __FUNCT__ "MatRetrieveValues_SeqSBAIJ" 1543 PetscErrorCode MatRetrieveValues_SeqSBAIJ(Mat mat) 1544 { 1545 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)mat->data; 1546 PetscErrorCode ierr; 1547 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1548 1549 PetscFunctionBegin; 1550 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1551 if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first"); 1552 1553 /* copy values over */ 1554 ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1555 PetscFunctionReturn(0); 1556 } 1557 1558 #undef __FUNCT__ 1559 #define __FUNCT__ "MatSeqSBAIJSetPreallocation_SeqSBAIJ" 1560 PetscErrorCode MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz) 1561 { 1562 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1563 PetscErrorCode ierr; 1564 PetscInt i,mbs,bs2; 1565 PetscBool skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE; 1566 1567 PetscFunctionBegin; 1568 if (nz >= 0 || nnz) realalloc = PETSC_TRUE; 1569 B->preallocated = PETSC_TRUE; 1570 1571 ierr = MatSetBlockSize(B,PetscAbs(bs));CHKERRQ(ierr); 1572 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 1573 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 1574 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 1575 1576 mbs = B->rmap->N/bs; 1577 bs2 = bs*bs; 1578 1579 if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize"); 1580 1581 if (nz == MAT_SKIP_ALLOCATION) { 1582 skipallocation = PETSC_TRUE; 1583 nz = 0; 1584 } 1585 1586 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3; 1587 if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz); 1588 if (nnz) { 1589 for (i=0; i<mbs; i++) { 1590 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]); 1591 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); 1592 } 1593 } 1594 1595 B->ops->mult = MatMult_SeqSBAIJ_N; 1596 B->ops->multadd = MatMultAdd_SeqSBAIJ_N; 1597 B->ops->multtranspose = MatMult_SeqSBAIJ_N; 1598 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N; 1599 1600 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);CHKERRQ(ierr); 1601 if (!flg) { 1602 switch (bs) { 1603 case 1: 1604 B->ops->mult = MatMult_SeqSBAIJ_1; 1605 B->ops->multadd = MatMultAdd_SeqSBAIJ_1; 1606 B->ops->multtranspose = MatMult_SeqSBAIJ_1; 1607 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1; 1608 break; 1609 case 2: 1610 B->ops->mult = MatMult_SeqSBAIJ_2; 1611 B->ops->multadd = MatMultAdd_SeqSBAIJ_2; 1612 B->ops->multtranspose = MatMult_SeqSBAIJ_2; 1613 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2; 1614 break; 1615 case 3: 1616 B->ops->mult = MatMult_SeqSBAIJ_3; 1617 B->ops->multadd = MatMultAdd_SeqSBAIJ_3; 1618 B->ops->multtranspose = MatMult_SeqSBAIJ_3; 1619 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3; 1620 break; 1621 case 4: 1622 B->ops->mult = MatMult_SeqSBAIJ_4; 1623 B->ops->multadd = MatMultAdd_SeqSBAIJ_4; 1624 B->ops->multtranspose = MatMult_SeqSBAIJ_4; 1625 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4; 1626 break; 1627 case 5: 1628 B->ops->mult = MatMult_SeqSBAIJ_5; 1629 B->ops->multadd = MatMultAdd_SeqSBAIJ_5; 1630 B->ops->multtranspose = MatMult_SeqSBAIJ_5; 1631 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5; 1632 break; 1633 case 6: 1634 B->ops->mult = MatMult_SeqSBAIJ_6; 1635 B->ops->multadd = MatMultAdd_SeqSBAIJ_6; 1636 B->ops->multtranspose = MatMult_SeqSBAIJ_6; 1637 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6; 1638 break; 1639 case 7: 1640 B->ops->mult = MatMult_SeqSBAIJ_7; 1641 B->ops->multadd = MatMultAdd_SeqSBAIJ_7; 1642 B->ops->multtranspose = MatMult_SeqSBAIJ_7; 1643 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7; 1644 break; 1645 } 1646 } 1647 1648 b->mbs = mbs; 1649 b->nbs = mbs; 1650 if (!skipallocation) { 1651 if (!b->imax) { 1652 ierr = PetscMalloc2(mbs,&b->imax,mbs,&b->ilen);CHKERRQ(ierr); 1653 1654 b->free_imax_ilen = PETSC_TRUE; 1655 1656 ierr = PetscLogObjectMemory((PetscObject)B,2*mbs*sizeof(PetscInt));CHKERRQ(ierr); 1657 } 1658 if (!nnz) { 1659 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5; 1660 else if (nz <= 0) nz = 1; 1661 for (i=0; i<mbs; i++) b->imax[i] = nz; 1662 nz = nz*mbs; /* total nz */ 1663 } else { 1664 nz = 0; 1665 for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];} 1666 } 1667 /* b->ilen will count nonzeros in each block row so far. */ 1668 for (i=0; i<mbs; i++) b->ilen[i] = 0; 1669 /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */ 1670 1671 /* allocate the matrix space */ 1672 ierr = MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);CHKERRQ(ierr); 1673 ierr = PetscMalloc3(bs2*nz,&b->a,nz,&b->j,B->rmap->N+1,&b->i);CHKERRQ(ierr); 1674 ierr = PetscLogObjectMemory((PetscObject)B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr); 1675 ierr = PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 1676 ierr = PetscMemzero(b->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 1677 1678 b->singlemalloc = PETSC_TRUE; 1679 1680 /* pointer to beginning of each row */ 1681 b->i[0] = 0; 1682 for (i=1; i<mbs+1; i++) b->i[i] = b->i[i-1] + b->imax[i-1]; 1683 1684 b->free_a = PETSC_TRUE; 1685 b->free_ij = PETSC_TRUE; 1686 } else { 1687 b->free_a = PETSC_FALSE; 1688 b->free_ij = PETSC_FALSE; 1689 } 1690 1691 B->rmap->bs = bs; 1692 b->bs2 = bs2; 1693 b->nz = 0; 1694 b->maxnz = nz; 1695 1696 b->inew = 0; 1697 b->jnew = 0; 1698 b->anew = 0; 1699 b->a2anew = 0; 1700 b->permute = PETSC_FALSE; 1701 if (realalloc) {ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);} 1702 PetscFunctionReturn(0); 1703 } 1704 1705 #undef __FUNCT__ 1706 #define __FUNCT__ "MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ" 1707 PetscErrorCode MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[], const PetscScalar V[]) 1708 { 1709 PetscInt i,j,m,nz,nz_max=0,*nnz; 1710 PetscScalar *values=0; 1711 PetscBool roworiented = ((Mat_SeqSBAIJ*)B->data)->roworiented; 1712 PetscErrorCode ierr; 1713 PetscFunctionBegin; 1714 if (bs < 1) SETERRQ1(PetscObjectComm((PetscObject)B),PETSC_ERR_ARG_OUTOFRANGE,"Invalid block size specified, must be positive but it is %D",bs); 1715 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 1716 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 1717 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 1718 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 1719 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 1720 m = B->rmap->n/bs; 1721 1722 if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]); 1723 ierr = PetscMalloc1((m+1),&nnz);CHKERRQ(ierr); 1724 for (i=0; i<m; i++) { 1725 nz = ii[i+1] - ii[i]; 1726 if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D has a negative number of columns %D",i,nz); 1727 nz_max = PetscMax(nz_max,nz); 1728 nnz[i] = nz; 1729 } 1730 ierr = MatSeqSBAIJSetPreallocation(B,bs,0,nnz);CHKERRQ(ierr); 1731 ierr = PetscFree(nnz);CHKERRQ(ierr); 1732 1733 values = (PetscScalar*)V; 1734 if (!values) { 1735 ierr = PetscCalloc1(bs*bs*nz_max,&values);CHKERRQ(ierr); 1736 } 1737 for (i=0; i<m; i++) { 1738 PetscInt ncols = ii[i+1] - ii[i]; 1739 const PetscInt *icols = jj + ii[i]; 1740 if (!roworiented || bs == 1) { 1741 const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0); 1742 ierr = MatSetValuesBlocked_SeqSBAIJ(B,1,&i,ncols,icols,svals,INSERT_VALUES);CHKERRQ(ierr); 1743 } else { 1744 for (j=0; j<ncols; j++) { 1745 const PetscScalar *svals = values + (V ? (bs*bs*(ii[i]+j)) : 0); 1746 ierr = MatSetValuesBlocked_SeqSBAIJ(B,1,&i,1,&icols[j],svals,INSERT_VALUES);CHKERRQ(ierr); 1747 } 1748 } 1749 } 1750 if (!V) { ierr = PetscFree(values);CHKERRQ(ierr); } 1751 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1752 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1753 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1754 PetscFunctionReturn(0); 1755 } 1756 1757 /* 1758 This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization 1759 */ 1760 #undef __FUNCT__ 1761 #define __FUNCT__ "MatSeqSBAIJSetNumericFactorization_inplace" 1762 PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural) 1763 { 1764 PetscErrorCode ierr; 1765 PetscBool flg = PETSC_FALSE; 1766 PetscInt bs = B->rmap->bs; 1767 1768 PetscFunctionBegin; 1769 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);CHKERRQ(ierr); 1770 if (flg) bs = 8; 1771 1772 if (!natural) { 1773 switch (bs) { 1774 case 1: 1775 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace; 1776 break; 1777 case 2: 1778 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2; 1779 break; 1780 case 3: 1781 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3; 1782 break; 1783 case 4: 1784 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4; 1785 break; 1786 case 5: 1787 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5; 1788 break; 1789 case 6: 1790 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6; 1791 break; 1792 case 7: 1793 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7; 1794 break; 1795 default: 1796 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N; 1797 break; 1798 } 1799 } else { 1800 switch (bs) { 1801 case 1: 1802 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace; 1803 break; 1804 case 2: 1805 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering; 1806 break; 1807 case 3: 1808 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering; 1809 break; 1810 case 4: 1811 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering; 1812 break; 1813 case 5: 1814 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering; 1815 break; 1816 case 6: 1817 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering; 1818 break; 1819 case 7: 1820 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering; 1821 break; 1822 default: 1823 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering; 1824 break; 1825 } 1826 } 1827 PetscFunctionReturn(0); 1828 } 1829 1830 PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*); 1831 PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*); 1832 1833 #undef __FUNCT__ 1834 #define __FUNCT__ "MatGetFactor_seqsbaij_petsc" 1835 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B) 1836 { 1837 PetscInt n = A->rmap->n; 1838 PetscErrorCode ierr; 1839 1840 PetscFunctionBegin; 1841 #if defined(PETSC_USE_COMPLEX) 1842 if (A->hermitian) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported"); 1843 #endif 1844 ierr = MatCreate(PetscObjectComm((PetscObject)A),B);CHKERRQ(ierr); 1845 ierr = MatSetSizes(*B,n,n,n,n);CHKERRQ(ierr); 1846 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1847 ierr = MatSetType(*B,MATSEQSBAIJ);CHKERRQ(ierr); 1848 ierr = MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,NULL);CHKERRQ(ierr); 1849 1850 (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ; 1851 (*B)->ops->iccfactorsymbolic = MatICCFactorSymbolic_SeqSBAIJ; 1852 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported"); 1853 (*B)->factortype = ftype; 1854 PetscFunctionReturn(0); 1855 } 1856 1857 #undef __FUNCT__ 1858 #define __FUNCT__ "MatGetFactorAvailable_seqsbaij_petsc" 1859 PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool *flg) 1860 { 1861 PetscFunctionBegin; 1862 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1863 *flg = PETSC_TRUE; 1864 } else { 1865 *flg = PETSC_FALSE; 1866 } 1867 PetscFunctionReturn(0); 1868 } 1869 1870 #if defined(PETSC_HAVE_MUMPS) 1871 PETSC_EXTERN PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*); 1872 #endif 1873 #if defined(PETSC_HAVE_PASTIX) 1874 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*); 1875 #endif 1876 #if defined(PETSC_HAVE_SUITESPARSE) 1877 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*); 1878 #endif 1879 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_sbstrm(Mat,MatFactorType,Mat*); 1880 1881 /*MC 1882 MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices, 1883 based on block compressed sparse row format. Only the upper triangular portion of the matrix is stored. 1884 1885 For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you 1886 can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd() 1887 1888 Options Database Keys: 1889 . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions() 1890 1891 Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not 1892 stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use 1893 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. 1894 1895 1896 Level: beginner 1897 1898 .seealso: MatCreateSeqSBAIJ 1899 M*/ 1900 1901 PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*); 1902 1903 #undef __FUNCT__ 1904 #define __FUNCT__ "MatCreate_SeqSBAIJ" 1905 PETSC_EXTERN PetscErrorCode MatCreate_SeqSBAIJ(Mat B) 1906 { 1907 Mat_SeqSBAIJ *b; 1908 PetscErrorCode ierr; 1909 PetscMPIInt size; 1910 PetscBool no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE; 1911 1912 PetscFunctionBegin; 1913 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 1914 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1"); 1915 1916 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 1917 B->data = (void*)b; 1918 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 1919 1920 B->ops->destroy = MatDestroy_SeqSBAIJ; 1921 B->ops->view = MatView_SeqSBAIJ; 1922 b->row = 0; 1923 b->icol = 0; 1924 b->reallocs = 0; 1925 b->saved_values = 0; 1926 b->inode.limit = 5; 1927 b->inode.max_limit = 5; 1928 1929 b->roworiented = PETSC_TRUE; 1930 b->nonew = 0; 1931 b->diag = 0; 1932 b->solve_work = 0; 1933 b->mult_work = 0; 1934 B->spptr = 0; 1935 B->info.nz_unneeded = (PetscReal)b->maxnz*b->bs2; 1936 b->keepnonzeropattern = PETSC_FALSE; 1937 b->xtoy = 0; 1938 b->XtoY = 0; 1939 1940 b->inew = 0; 1941 b->jnew = 0; 1942 b->anew = 0; 1943 b->a2anew = 0; 1944 b->permute = PETSC_FALSE; 1945 1946 b->ignore_ltriangular = PETSC_TRUE; 1947 1948 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,NULL);CHKERRQ(ierr); 1949 1950 b->getrow_utriangular = PETSC_FALSE; 1951 1952 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,NULL);CHKERRQ(ierr); 1953 1954 #if defined(PETSC_HAVE_PASTIX) 1955 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_pastix_C",MatGetFactor_seqsbaij_pastix);CHKERRQ(ierr); 1956 #endif 1957 #if defined(PETSC_HAVE_MUMPS) 1958 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_mumps_C",MatGetFactor_sbaij_mumps);CHKERRQ(ierr); 1959 #endif 1960 #if defined(PETSC_HAVE_SUITESPARSE) 1961 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_cholmod_C",MatGetFactor_seqsbaij_cholmod);CHKERRQ(ierr); 1962 #endif 1963 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactorAvailable_petsc_C",MatGetFactorAvailable_seqsbaij_petsc);CHKERRQ(ierr); 1964 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_petsc_C",MatGetFactor_seqsbaij_petsc);CHKERRQ(ierr); 1965 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_sbstrm_C",MatGetFactor_seqsbaij_sbstrm);CHKERRQ(ierr); 1966 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqSBAIJ);CHKERRQ(ierr); 1967 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqSBAIJ);CHKERRQ(ierr); 1968 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",MatSeqSBAIJSetColumnIndices_SeqSBAIJ);CHKERRQ(ierr); 1969 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",MatConvert_SeqSBAIJ_SeqAIJ);CHKERRQ(ierr); 1970 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",MatConvert_SeqSBAIJ_SeqBAIJ);CHKERRQ(ierr); 1971 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",MatSeqSBAIJSetPreallocation_SeqSBAIJ);CHKERRQ(ierr); 1972 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocationCSR_C",MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ);CHKERRQ(ierr); 1973 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C",MatConvert_SeqSBAIJ_SeqSBSTRM);CHKERRQ(ierr); 1974 1975 B->symmetric = PETSC_TRUE; 1976 B->structurally_symmetric = PETSC_TRUE; 1977 B->symmetric_set = PETSC_TRUE; 1978 B->structurally_symmetric_set = PETSC_TRUE; 1979 1980 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);CHKERRQ(ierr); 1981 1982 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)B),((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");CHKERRQ(ierr); 1983 ierr = PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",NULL,no_unroll,&no_unroll,NULL);CHKERRQ(ierr); 1984 if (no_unroll) { 1985 ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");CHKERRQ(ierr); 1986 } 1987 ierr = PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",NULL,no_inode,&no_inode,NULL);CHKERRQ(ierr); 1988 if (no_inode) { 1989 ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");CHKERRQ(ierr); 1990 } 1991 ierr = PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",NULL,b->inode.limit,&b->inode.limit,NULL);CHKERRQ(ierr); 1992 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1993 b->inode.use = (PetscBool)(!(no_unroll || no_inode)); 1994 if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit; 1995 PetscFunctionReturn(0); 1996 } 1997 1998 #undef __FUNCT__ 1999 #define __FUNCT__ "MatSeqSBAIJSetPreallocation" 2000 /*@C 2001 MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block 2002 compressed row) format. For good matrix assembly performance the 2003 user should preallocate the matrix storage by setting the parameter nz 2004 (or the array nnz). By setting these parameters accurately, performance 2005 during matrix assembly can be increased by more than a factor of 50. 2006 2007 Collective on Mat 2008 2009 Input Parameters: 2010 + A - the symmetric matrix 2011 . bs - size of block 2012 . nz - number of block nonzeros per block row (same for all rows) 2013 - nnz - array containing the number of block nonzeros in the upper triangular plus 2014 diagonal portion of each block (possibly different for each block row) or NULL 2015 2016 Options Database Keys: 2017 . -mat_no_unroll - uses code that does not unroll the loops in the 2018 block calculations (much slower) 2019 . -mat_block_size - size of the blocks to use (only works if a negative bs is passed in 2020 2021 Level: intermediate 2022 2023 Notes: 2024 Specify the preallocated storage with either nz or nnz (not both). 2025 Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory 2026 allocation. See Users-Manual: ch_mat for details. 2027 2028 You can call MatGetInfo() to get information on how effective the preallocation was; 2029 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 2030 You can also run with the option -info and look for messages with the string 2031 malloc in them to see if additional memory allocation was needed. 2032 2033 If the nnz parameter is given then the nz parameter is ignored 2034 2035 2036 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() 2037 @*/ 2038 PetscErrorCode MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[]) 2039 { 2040 PetscErrorCode ierr; 2041 2042 PetscFunctionBegin; 2043 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2044 PetscValidType(B,1); 2045 PetscValidLogicalCollectiveInt(B,bs,2); 2046 ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));CHKERRQ(ierr); 2047 PetscFunctionReturn(0); 2048 } 2049 2050 #undef __FUNCT__ 2051 #define __FUNCT__ "MatSeqSBAIJSetPreallocationCSR" 2052 /*@C 2053 MatSeqSBAIJSetPreallocationCSR - Allocates memory for a sparse sequential matrix in symmetric block AIJ format. 2054 2055 Input Parameters: 2056 + A - the matrix 2057 . i - the indices into j for the start of each local row (starts with zero) 2058 . j - the column indices for each local row (starts with zero) these must be sorted for each row 2059 - v - optional values in the matrix 2060 2061 Level: developer 2062 2063 Notes: 2064 The order of the entries in values is specified by the MatOption MAT_ROW_ORIENTED. For example, C programs 2065 may want to use the default MAT_ROW_ORIENTED=PETSC_TRUE and use an array v[nnz][bs][bs] where the second index is 2066 over rows within a block and the last index is over columns within a block row. Fortran programs will likely set 2067 MAT_ROW_ORIENTED=PETSC_FALSE and use a Fortran array v(bs,bs,nnz) in which the first index is over rows within a 2068 block column and the second index is over columns within a block. 2069 2070 .keywords: matrix, block, aij, compressed row, sparse 2071 2072 .seealso: MatCreate(), MatCreateSeqSBAIJ(), MatSetValuesBlocked(), MatSeqSBAIJSetPreallocation(), MATSEQSBAIJ 2073 @*/ 2074 PetscErrorCode MatSeqSBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 2075 { 2076 PetscErrorCode ierr; 2077 2078 PetscFunctionBegin; 2079 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2080 PetscValidType(B,1); 2081 PetscValidLogicalCollectiveInt(B,bs,2); 2082 ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));CHKERRQ(ierr); 2083 PetscFunctionReturn(0); 2084 } 2085 2086 #undef __FUNCT__ 2087 #define __FUNCT__ "MatCreateSeqSBAIJ" 2088 /*@C 2089 MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block 2090 compressed row) format. For good matrix assembly performance the 2091 user should preallocate the matrix storage by setting the parameter nz 2092 (or the array nnz). By setting these parameters accurately, performance 2093 during matrix assembly can be increased by more than a factor of 50. 2094 2095 Collective on MPI_Comm 2096 2097 Input Parameters: 2098 + comm - MPI communicator, set to PETSC_COMM_SELF 2099 . bs - size of block 2100 . m - number of rows, or number of columns 2101 . nz - number of block nonzeros per block row (same for all rows) 2102 - nnz - array containing the number of block nonzeros in the upper triangular plus 2103 diagonal portion of each block (possibly different for each block row) or NULL 2104 2105 Output Parameter: 2106 . A - the symmetric matrix 2107 2108 Options Database Keys: 2109 . -mat_no_unroll - uses code that does not unroll the loops in the 2110 block calculations (much slower) 2111 . -mat_block_size - size of the blocks to use 2112 2113 Level: intermediate 2114 2115 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 2116 MatXXXXSetPreallocation() paradgm instead of this routine directly. 2117 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 2118 2119 Notes: 2120 The number of rows and columns must be divisible by blocksize. 2121 This matrix type does not support complex Hermitian operation. 2122 2123 Specify the preallocated storage with either nz or nnz (not both). 2124 Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory 2125 allocation. See Users-Manual: ch_mat for details. 2126 2127 If the nnz parameter is given then the nz parameter is ignored 2128 2129 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() 2130 @*/ 2131 PetscErrorCode MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A) 2132 { 2133 PetscErrorCode ierr; 2134 2135 PetscFunctionBegin; 2136 ierr = MatCreate(comm,A);CHKERRQ(ierr); 2137 ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); 2138 ierr = MatSetType(*A,MATSEQSBAIJ);CHKERRQ(ierr); 2139 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);CHKERRQ(ierr); 2140 PetscFunctionReturn(0); 2141 } 2142 2143 #undef __FUNCT__ 2144 #define __FUNCT__ "MatDuplicate_SeqSBAIJ" 2145 PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B) 2146 { 2147 Mat C; 2148 Mat_SeqSBAIJ *c,*a = (Mat_SeqSBAIJ*)A->data; 2149 PetscErrorCode ierr; 2150 PetscInt i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2; 2151 2152 PetscFunctionBegin; 2153 if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix"); 2154 2155 *B = 0; 2156 ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr); 2157 ierr = MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);CHKERRQ(ierr); 2158 ierr = MatSetType(C,MATSEQSBAIJ);CHKERRQ(ierr); 2159 ierr = PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2160 c = (Mat_SeqSBAIJ*)C->data; 2161 2162 C->preallocated = PETSC_TRUE; 2163 C->factortype = A->factortype; 2164 c->row = 0; 2165 c->icol = 0; 2166 c->saved_values = 0; 2167 c->keepnonzeropattern = a->keepnonzeropattern; 2168 C->assembled = PETSC_TRUE; 2169 2170 ierr = PetscLayoutReference(A->rmap,&C->rmap);CHKERRQ(ierr); 2171 ierr = PetscLayoutReference(A->cmap,&C->cmap);CHKERRQ(ierr); 2172 c->bs2 = a->bs2; 2173 c->mbs = a->mbs; 2174 c->nbs = a->nbs; 2175 2176 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2177 c->imax = a->imax; 2178 c->ilen = a->ilen; 2179 c->free_imax_ilen = PETSC_FALSE; 2180 } else { 2181 ierr = PetscMalloc2((mbs+1),&c->imax,(mbs+1),&c->ilen);CHKERRQ(ierr); 2182 ierr = PetscLogObjectMemory((PetscObject)C,2*(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2183 for (i=0; i<mbs; i++) { 2184 c->imax[i] = a->imax[i]; 2185 c->ilen[i] = a->ilen[i]; 2186 } 2187 c->free_imax_ilen = PETSC_TRUE; 2188 } 2189 2190 /* allocate the matrix space */ 2191 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2192 ierr = PetscMalloc1(bs2*nz,&c->a);CHKERRQ(ierr); 2193 ierr = PetscLogObjectMemory((PetscObject)C,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 2194 c->i = a->i; 2195 c->j = a->j; 2196 c->singlemalloc = PETSC_FALSE; 2197 c->free_a = PETSC_TRUE; 2198 c->free_ij = PETSC_FALSE; 2199 c->parent = A; 2200 ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr); 2201 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2202 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2203 } else { 2204 ierr = PetscMalloc3(bs2*nz,&c->a,nz,&c->j,mbs+1,&c->i);CHKERRQ(ierr); 2205 ierr = PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2206 ierr = PetscLogObjectMemory((PetscObject)C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));CHKERRQ(ierr); 2207 c->singlemalloc = PETSC_TRUE; 2208 c->free_a = PETSC_TRUE; 2209 c->free_ij = PETSC_TRUE; 2210 } 2211 if (mbs > 0) { 2212 if (cpvalues != MAT_SHARE_NONZERO_PATTERN) { 2213 ierr = PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 2214 } 2215 if (cpvalues == MAT_COPY_VALUES) { 2216 ierr = PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2217 } else { 2218 ierr = PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2219 } 2220 if (a->jshort) { 2221 /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */ 2222 /* if the parent matrix is reassembled, this child matrix will never notice */ 2223 ierr = PetscMalloc1(nz,&c->jshort);CHKERRQ(ierr); 2224 ierr = PetscLogObjectMemory((PetscObject)C,nz*sizeof(unsigned short));CHKERRQ(ierr); 2225 ierr = PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));CHKERRQ(ierr); 2226 2227 c->free_jshort = PETSC_TRUE; 2228 } 2229 } 2230 2231 c->roworiented = a->roworiented; 2232 c->nonew = a->nonew; 2233 2234 if (a->diag) { 2235 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2236 c->diag = a->diag; 2237 c->free_diag = PETSC_FALSE; 2238 } else { 2239 ierr = PetscMalloc1(mbs,&c->diag);CHKERRQ(ierr); 2240 ierr = PetscLogObjectMemory((PetscObject)C,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2241 for (i=0; i<mbs; i++) c->diag[i] = a->diag[i]; 2242 c->free_diag = PETSC_TRUE; 2243 } 2244 } 2245 c->nz = a->nz; 2246 c->maxnz = a->nz; /* Since we allocate exactly the right amount */ 2247 c->solve_work = 0; 2248 c->mult_work = 0; 2249 2250 *B = C; 2251 ierr = PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);CHKERRQ(ierr); 2252 PetscFunctionReturn(0); 2253 } 2254 2255 #undef __FUNCT__ 2256 #define __FUNCT__ "MatLoad_SeqSBAIJ" 2257 PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer) 2258 { 2259 Mat_SeqSBAIJ *a; 2260 PetscErrorCode ierr; 2261 int fd; 2262 PetscMPIInt size; 2263 PetscInt i,nz,header[4],*rowlengths=0,M,N,bs=1; 2264 PetscInt *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount; 2265 PetscInt kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols; 2266 PetscInt *masked,nmask,tmp,bs2,ishift; 2267 PetscScalar *aa; 2268 MPI_Comm comm; 2269 2270 PetscFunctionBegin; 2271 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2272 ierr = PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,NULL);CHKERRQ(ierr); 2273 bs2 = bs*bs; 2274 2275 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2276 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor"); 2277 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2278 ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr); 2279 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object"); 2280 M = header[1]; N = header[2]; nz = header[3]; 2281 2282 if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ"); 2283 2284 if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices"); 2285 2286 /* 2287 This code adds extra rows to make sure the number of rows is 2288 divisible by the blocksize 2289 */ 2290 mbs = M/bs; 2291 extra_rows = bs - M + bs*(mbs); 2292 if (extra_rows == bs) extra_rows = 0; 2293 else mbs++; 2294 if (extra_rows) { 2295 ierr = PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");CHKERRQ(ierr); 2296 } 2297 2298 /* Set global sizes if not already set */ 2299 if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) { 2300 ierr = MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);CHKERRQ(ierr); 2301 } else { /* Check if the matrix global sizes are correct */ 2302 ierr = MatGetSize(newmat,&rows,&cols);CHKERRQ(ierr); 2303 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); 2304 } 2305 2306 /* read in row lengths */ 2307 ierr = PetscMalloc1((M+extra_rows),&rowlengths);CHKERRQ(ierr); 2308 ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); 2309 for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1; 2310 2311 /* read in column indices */ 2312 ierr = PetscMalloc1((nz+extra_rows),&jj);CHKERRQ(ierr); 2313 ierr = PetscBinaryRead(fd,jj,nz,PETSC_INT);CHKERRQ(ierr); 2314 for (i=0; i<extra_rows; i++) jj[nz+i] = M+i; 2315 2316 /* loop over row lengths determining block row lengths */ 2317 ierr = PetscCalloc1(mbs,&s_browlengths);CHKERRQ(ierr); 2318 ierr = PetscMalloc2(mbs,&mask,mbs,&masked);CHKERRQ(ierr); 2319 ierr = PetscMemzero(mask,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2320 rowcount = 0; 2321 nzcount = 0; 2322 for (i=0; i<mbs; i++) { 2323 nmask = 0; 2324 for (j=0; j<bs; j++) { 2325 kmax = rowlengths[rowcount]; 2326 for (k=0; k<kmax; k++) { 2327 tmp = jj[nzcount++]/bs; /* block col. index */ 2328 if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;} 2329 } 2330 rowcount++; 2331 } 2332 s_browlengths[i] += nmask; 2333 2334 /* zero out the mask elements we set */ 2335 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2336 } 2337 2338 /* Do preallocation */ 2339 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);CHKERRQ(ierr); 2340 a = (Mat_SeqSBAIJ*)newmat->data; 2341 2342 /* set matrix "i" values */ 2343 a->i[0] = 0; 2344 for (i=1; i<= mbs; i++) { 2345 a->i[i] = a->i[i-1] + s_browlengths[i-1]; 2346 a->ilen[i-1] = s_browlengths[i-1]; 2347 } 2348 a->nz = a->i[mbs]; 2349 2350 /* read in nonzero values */ 2351 ierr = PetscMalloc1((nz+extra_rows),&aa);CHKERRQ(ierr); 2352 ierr = PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);CHKERRQ(ierr); 2353 for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0; 2354 2355 /* set "a" and "j" values into matrix */ 2356 nzcount = 0; jcount = 0; 2357 for (i=0; i<mbs; i++) { 2358 nzcountb = nzcount; 2359 nmask = 0; 2360 for (j=0; j<bs; j++) { 2361 kmax = rowlengths[i*bs+j]; 2362 for (k=0; k<kmax; k++) { 2363 tmp = jj[nzcount++]/bs; /* block col. index */ 2364 if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;} 2365 } 2366 } 2367 /* sort the masked values */ 2368 ierr = PetscSortInt(nmask,masked);CHKERRQ(ierr); 2369 2370 /* set "j" values into matrix */ 2371 maskcount = 1; 2372 for (j=0; j<nmask; j++) { 2373 a->j[jcount++] = masked[j]; 2374 mask[masked[j]] = maskcount++; 2375 } 2376 2377 /* set "a" values into matrix */ 2378 ishift = bs2*a->i[i]; 2379 for (j=0; j<bs; j++) { 2380 kmax = rowlengths[i*bs+j]; 2381 for (k=0; k<kmax; k++) { 2382 tmp = jj[nzcountb]/bs; /* block col. index */ 2383 if (tmp >= i) { 2384 block = mask[tmp] - 1; 2385 point = jj[nzcountb] - bs*tmp; 2386 idx = ishift + bs2*block + j + bs*point; 2387 a->a[idx] = aa[nzcountb]; 2388 } 2389 nzcountb++; 2390 } 2391 } 2392 /* zero out the mask elements we set */ 2393 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2394 } 2395 if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix"); 2396 2397 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2398 ierr = PetscFree(s_browlengths);CHKERRQ(ierr); 2399 ierr = PetscFree(aa);CHKERRQ(ierr); 2400 ierr = PetscFree(jj);CHKERRQ(ierr); 2401 ierr = PetscFree2(mask,masked);CHKERRQ(ierr); 2402 2403 ierr = MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2404 ierr = MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2405 PetscFunctionReturn(0); 2406 } 2407 2408 #undef __FUNCT__ 2409 #define __FUNCT__ "MatCreateSeqSBAIJWithArrays" 2410 /*@ 2411 MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements 2412 (upper triangular entries in CSR format) provided by the user. 2413 2414 Collective on MPI_Comm 2415 2416 Input Parameters: 2417 + comm - must be an MPI communicator of size 1 2418 . bs - size of block 2419 . m - number of rows 2420 . n - number of columns 2421 . i - row indices 2422 . j - column indices 2423 - a - matrix values 2424 2425 Output Parameter: 2426 . mat - the matrix 2427 2428 Level: advanced 2429 2430 Notes: 2431 The i, j, and a arrays are not copied by this routine, the user must free these arrays 2432 once the matrix is destroyed 2433 2434 You cannot set new nonzero locations into this matrix, that will generate an error. 2435 2436 The i and j indices are 0 based 2437 2438 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 2439 it is the regular CSR format excluding the lower triangular elements. 2440 2441 .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ() 2442 2443 @*/ 2444 PetscErrorCode MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt *i,PetscInt *j,PetscScalar *a,Mat *mat) 2445 { 2446 PetscErrorCode ierr; 2447 PetscInt ii; 2448 Mat_SeqSBAIJ *sbaij; 2449 2450 PetscFunctionBegin; 2451 if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs); 2452 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 2453 2454 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 2455 ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); 2456 ierr = MatSetType(*mat,MATSEQSBAIJ);CHKERRQ(ierr); 2457 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);CHKERRQ(ierr); 2458 sbaij = (Mat_SeqSBAIJ*)(*mat)->data; 2459 ierr = PetscMalloc2(m,&sbaij->imax,m,&sbaij->ilen);CHKERRQ(ierr); 2460 ierr = PetscLogObjectMemory((PetscObject)*mat,2*m*sizeof(PetscInt));CHKERRQ(ierr); 2461 2462 sbaij->i = i; 2463 sbaij->j = j; 2464 sbaij->a = a; 2465 2466 sbaij->singlemalloc = PETSC_FALSE; 2467 sbaij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/ 2468 sbaij->free_a = PETSC_FALSE; 2469 sbaij->free_ij = PETSC_FALSE; 2470 2471 for (ii=0; ii<m; ii++) { 2472 sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii]; 2473 #if defined(PETSC_USE_DEBUG) 2474 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]); 2475 #endif 2476 } 2477 #if defined(PETSC_USE_DEBUG) 2478 for (ii=0; ii<sbaij->i[m]; ii++) { 2479 if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]); 2480 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]); 2481 } 2482 #endif 2483 2484 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2485 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2486 PetscFunctionReturn(0); 2487 } 2488 2489 2490 2491 2492 2493