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,*ii = a->i,i; 26 27 PetscFunctionBegin; 28 ierr = MatMarkDiagonal_SeqSBAIJ(A);CHKERRQ(ierr); 29 *missing = PETSC_FALSE; 30 if (A->rmap->n > 0 && !ii) { 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 (diag[i] >= ii[i+1]) { 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,j; 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++) { 62 a->diag[i] = a->i[i+1]; 63 for (j=a->i[i]; j<a->i[i+1]; j++) { 64 if (a->j[j] == i) { 65 a->diag[i] = j; 66 break; 67 } 68 } 69 } 70 PetscFunctionReturn(0); 71 } 72 73 #undef __FUNCT__ 74 #define __FUNCT__ "MatGetRowIJ_SeqSBAIJ" 75 static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *inia[],const PetscInt *inja[],PetscBool *done) 76 { 77 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 78 PetscInt i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs; 79 PetscInt **ia = (PetscInt**)inia,**ja = (PetscInt**)inja; 80 PetscErrorCode ierr; 81 82 PetscFunctionBegin; 83 *nn = n; 84 if (!ia) PetscFunctionReturn(0); 85 if (!blockcompressed) { 86 /* malloc & create the natural set of indices */ 87 ierr = PetscMalloc2((n+1)*bs,ia,nz*bs,ja);CHKERRQ(ierr); 88 for (i=0; i<n+1; i++) { 89 for (j=0; j<bs; j++) { 90 *ia[i*bs+j] = a->i[i]*bs+j+oshift; 91 } 92 } 93 for (i=0; i<nz; i++) { 94 for (j=0; j<bs; j++) { 95 *ja[i*bs+j] = a->j[i]*bs+j+oshift; 96 } 97 } 98 } else { /* blockcompressed */ 99 if (oshift == 1) { 100 /* temporarily add 1 to i and j indices */ 101 for (i=0; i<nz; i++) a->j[i]++; 102 for (i=0; i<n+1; i++) a->i[i]++; 103 } 104 *ia = a->i; *ja = a->j; 105 } 106 PetscFunctionReturn(0); 107 } 108 109 #undef __FUNCT__ 110 #define __FUNCT__ "MatRestoreRowIJ_SeqSBAIJ" 111 static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscBool *done) 112 { 113 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 114 PetscInt i,n = a->mbs,nz = a->i[n]; 115 PetscErrorCode ierr; 116 117 PetscFunctionBegin; 118 if (!ia) PetscFunctionReturn(0); 119 120 if (!blockcompressed) { 121 ierr = PetscFree2(*ia,*ja);CHKERRQ(ierr); 122 } else if (oshift == 1) { /* blockcompressed */ 123 for (i=0; i<nz; i++) a->j[i]--; 124 for (i=0; i<n+1; i++) a->i[i]--; 125 } 126 PetscFunctionReturn(0); 127 } 128 129 #undef __FUNCT__ 130 #define __FUNCT__ "MatDestroy_SeqSBAIJ" 131 PetscErrorCode MatDestroy_SeqSBAIJ(Mat A) 132 { 133 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 134 PetscErrorCode ierr; 135 136 PetscFunctionBegin; 137 #if defined(PETSC_USE_LOG) 138 PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz); 139 #endif 140 ierr = MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);CHKERRQ(ierr); 141 if (a->free_diag) {ierr = PetscFree(a->diag);CHKERRQ(ierr);} 142 ierr = ISDestroy(&a->row);CHKERRQ(ierr); 143 ierr = ISDestroy(&a->col);CHKERRQ(ierr); 144 ierr = ISDestroy(&a->icol);CHKERRQ(ierr); 145 ierr = PetscFree(a->idiag);CHKERRQ(ierr); 146 ierr = PetscFree(a->inode.size);CHKERRQ(ierr); 147 if (a->free_imax_ilen) {ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr);} 148 ierr = PetscFree(a->solve_work);CHKERRQ(ierr); 149 ierr = PetscFree(a->sor_work);CHKERRQ(ierr); 150 ierr = PetscFree(a->solves_work);CHKERRQ(ierr); 151 ierr = PetscFree(a->mult_work);CHKERRQ(ierr); 152 ierr = PetscFree(a->saved_values);CHKERRQ(ierr); 153 ierr = PetscFree(a->xtoy);CHKERRQ(ierr); 154 if (a->free_jshort) {ierr = PetscFree(a->jshort);CHKERRQ(ierr);} 155 ierr = PetscFree(a->inew);CHKERRQ(ierr); 156 ierr = MatDestroy(&a->parent);CHKERRQ(ierr); 157 ierr = PetscFree(A->data);CHKERRQ(ierr); 158 159 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 160 ierr = PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C",NULL);CHKERRQ(ierr); 161 ierr = PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C",NULL);CHKERRQ(ierr); 162 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C",NULL);CHKERRQ(ierr); 163 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C",NULL);CHKERRQ(ierr); 164 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C",NULL);CHKERRQ(ierr); 165 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C",NULL);CHKERRQ(ierr); 166 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocationCSR_C",NULL);CHKERRQ(ierr); 167 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqsbstrm_C",NULL);CHKERRQ(ierr); 168 PetscFunctionReturn(0); 169 } 170 171 #undef __FUNCT__ 172 #define __FUNCT__ "MatSetOption_SeqSBAIJ" 173 PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool flg) 174 { 175 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 176 PetscErrorCode ierr; 177 178 PetscFunctionBegin; 179 switch (op) { 180 case MAT_ROW_ORIENTED: 181 a->roworiented = flg; 182 break; 183 case MAT_KEEP_NONZERO_PATTERN: 184 a->keepnonzeropattern = flg; 185 break; 186 case MAT_NEW_NONZERO_LOCATIONS: 187 a->nonew = (flg ? 0 : 1); 188 break; 189 case MAT_NEW_NONZERO_LOCATION_ERR: 190 a->nonew = (flg ? -1 : 0); 191 break; 192 case MAT_NEW_NONZERO_ALLOCATION_ERR: 193 a->nonew = (flg ? -2 : 0); 194 break; 195 case MAT_UNUSED_NONZERO_LOCATION_ERR: 196 a->nounused = (flg ? -1 : 0); 197 break; 198 case MAT_NEW_DIAGONALS: 199 case MAT_IGNORE_OFF_PROC_ENTRIES: 200 case MAT_USE_HASH_TABLE: 201 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 202 break; 203 case MAT_HERMITIAN: 204 if (!A->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first"); 205 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 206 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort; 207 } else if (A->cmap->bs == 1) { 208 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian; 209 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1"); 210 break; 211 case MAT_SPD: 212 /* These options are handled directly by MatSetOption() */ 213 break; 214 case MAT_SYMMETRIC: 215 case MAT_STRUCTURALLY_SYMMETRIC: 216 case MAT_SYMMETRY_ETERNAL: 217 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix must be symmetric"); 218 ierr = PetscInfo1(A,"Option %s not relevent\n",MatOptions[op]);CHKERRQ(ierr); 219 break; 220 case MAT_IGNORE_LOWER_TRIANGULAR: 221 a->ignore_ltriangular = flg; 222 break; 223 case MAT_ERROR_LOWER_TRIANGULAR: 224 a->ignore_ltriangular = flg; 225 break; 226 case MAT_GETROW_UPPERTRIANGULAR: 227 a->getrow_utriangular = flg; 228 break; 229 default: 230 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 231 } 232 PetscFunctionReturn(0); 233 } 234 235 #undef __FUNCT__ 236 #define __FUNCT__ "MatGetRow_SeqSBAIJ" 237 PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 238 { 239 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 240 PetscErrorCode ierr; 241 242 PetscFunctionBegin; 243 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()"); 244 245 /* Get the upper triangular part of the row */ 246 ierr = MatGetRow_SeqBAIJ_private(A,row,nz,idx,v,a->i,a->j,a->a);CHKERRQ(ierr); 247 PetscFunctionReturn(0); 248 } 249 250 #undef __FUNCT__ 251 #define __FUNCT__ "MatRestoreRow_SeqSBAIJ" 252 PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 253 { 254 PetscErrorCode ierr; 255 256 PetscFunctionBegin; 257 if (idx) {ierr = PetscFree(*idx);CHKERRQ(ierr);} 258 if (v) {ierr = PetscFree(*v);CHKERRQ(ierr);} 259 PetscFunctionReturn(0); 260 } 261 262 #undef __FUNCT__ 263 #define __FUNCT__ "MatGetRowUpperTriangular_SeqSBAIJ" 264 PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A) 265 { 266 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 267 268 PetscFunctionBegin; 269 a->getrow_utriangular = PETSC_TRUE; 270 PetscFunctionReturn(0); 271 } 272 #undef __FUNCT__ 273 #define __FUNCT__ "MatRestoreRowUpperTriangular_SeqSBAIJ" 274 PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A) 275 { 276 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 277 278 PetscFunctionBegin; 279 a->getrow_utriangular = PETSC_FALSE; 280 PetscFunctionReturn(0); 281 } 282 283 #undef __FUNCT__ 284 #define __FUNCT__ "MatTranspose_SeqSBAIJ" 285 PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B) 286 { 287 PetscErrorCode ierr; 288 289 PetscFunctionBegin; 290 if (reuse == MAT_INITIAL_MATRIX || *B != A) { 291 ierr = MatDuplicate(A,MAT_COPY_VALUES,B);CHKERRQ(ierr); 292 } 293 PetscFunctionReturn(0); 294 } 295 296 #undef __FUNCT__ 297 #define __FUNCT__ "MatView_SeqSBAIJ_ASCII" 298 PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer) 299 { 300 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 301 PetscErrorCode ierr; 302 PetscInt i,j,bs = A->rmap->bs,k,l,bs2=a->bs2; 303 PetscViewerFormat format; 304 PetscInt *diag; 305 306 PetscFunctionBegin; 307 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 308 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 309 ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); 310 } else if (format == PETSC_VIEWER_ASCII_MATLAB) { 311 Mat aij; 312 if (A->factortype && bs>1) { 313 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); 314 PetscFunctionReturn(0); 315 } 316 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);CHKERRQ(ierr); 317 ierr = MatView(aij,viewer);CHKERRQ(ierr); 318 ierr = MatDestroy(&aij);CHKERRQ(ierr); 319 } else if (format == PETSC_VIEWER_ASCII_COMMON) { 320 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 321 for (i=0; i<a->mbs; i++) { 322 for (j=0; j<bs; j++) { 323 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 324 for (k=a->i[i]; k<a->i[i+1]; k++) { 325 for (l=0; l<bs; l++) { 326 #if defined(PETSC_USE_COMPLEX) 327 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 328 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l, 329 (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 330 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 331 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l, 332 (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 333 } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 334 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 335 } 336 #else 337 if (a->a[bs2*k + l*bs + j] != 0.0) { 338 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 339 } 340 #endif 341 } 342 } 343 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 344 } 345 } 346 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 347 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 348 PetscFunctionReturn(0); 349 } else { 350 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 351 if (A->factortype) { /* for factored matrix */ 352 if (bs>1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"matrix is factored with bs>1. Not implemented yet"); 353 354 diag=a->diag; 355 for (i=0; i<a->mbs; i++) { /* for row block i */ 356 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i);CHKERRQ(ierr); 357 /* diagonal entry */ 358 #if defined(PETSC_USE_COMPLEX) 359 if (PetscImaginaryPart(a->a[diag[i]]) > 0.0) { 360 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); 361 } else if (PetscImaginaryPart(a->a[diag[i]]) < 0.0) { 362 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); 363 } else { 364 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]));CHKERRQ(ierr); 365 } 366 #else 367 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)(1.0/a->a[diag[i]]));CHKERRQ(ierr); 368 #endif 369 /* off-diagonal entries */ 370 for (k=a->i[i]; k<a->i[i+1]-1; k++) { 371 #if defined(PETSC_USE_COMPLEX) 372 if (PetscImaginaryPart(a->a[k]) > 0.0) { 373 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),(double)PetscImaginaryPart(a->a[k]));CHKERRQ(ierr); 374 } else if (PetscImaginaryPart(a->a[k]) < 0.0) { 375 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),-(double)PetscImaginaryPart(a->a[k]));CHKERRQ(ierr); 376 } else { 377 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k],(double)PetscRealPart(a->a[k]));CHKERRQ(ierr); 378 } 379 #else 380 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[k],(double)a->a[k]);CHKERRQ(ierr); 381 #endif 382 } 383 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 384 } 385 386 } else { /* for non-factored matrix */ 387 for (i=0; i<a->mbs; i++) { /* for row block i */ 388 for (j=0; j<bs; j++) { /* for row bs*i + j */ 389 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 390 for (k=a->i[i]; k<a->i[i+1]; k++) { /* for column block */ 391 for (l=0; l<bs; l++) { /* for column */ 392 #if defined(PETSC_USE_COMPLEX) 393 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) { 394 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l, 395 (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 396 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) { 397 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l, 398 (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 399 } else { 400 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 401 } 402 #else 403 ierr = PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 404 #endif 405 } 406 } 407 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 408 } 409 } 410 } 411 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 412 } 413 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 414 PetscFunctionReturn(0); 415 } 416 417 #include <petscdraw.h> 418 #undef __FUNCT__ 419 #define __FUNCT__ "MatView_SeqSBAIJ_Draw_Zoom" 420 static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa) 421 { 422 Mat A = (Mat) Aa; 423 Mat_SeqSBAIJ *a=(Mat_SeqSBAIJ*)A->data; 424 PetscErrorCode ierr; 425 PetscInt row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2; 426 PetscMPIInt rank; 427 PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r; 428 MatScalar *aa; 429 MPI_Comm comm; 430 PetscViewer viewer; 431 432 PetscFunctionBegin; 433 /* 434 This is nasty. If this is called from an originally parallel matrix 435 then all processes call this,but only the first has the matrix so the 436 rest should return immediately. 437 */ 438 ierr = PetscObjectGetComm((PetscObject)draw,&comm);CHKERRQ(ierr); 439 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 440 if (rank) PetscFunctionReturn(0); 441 442 ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr); 443 444 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 445 PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric"); 446 447 /* loop over matrix elements drawing boxes */ 448 color = PETSC_DRAW_BLUE; 449 for (i=0,row=0; i<mbs; i++,row+=bs) { 450 for (j=a->i[i]; j<a->i[i+1]; j++) { 451 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 452 x_l = a->j[j]*bs; x_r = x_l + 1.0; 453 aa = a->a + j*bs2; 454 for (k=0; k<bs; k++) { 455 for (l=0; l<bs; l++) { 456 if (PetscRealPart(*aa++) >= 0.) continue; 457 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 458 } 459 } 460 } 461 } 462 color = PETSC_DRAW_CYAN; 463 for (i=0,row=0; i<mbs; i++,row+=bs) { 464 for (j=a->i[i]; j<a->i[i+1]; j++) { 465 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 466 x_l = a->j[j]*bs; x_r = x_l + 1.0; 467 aa = a->a + j*bs2; 468 for (k=0; k<bs; k++) { 469 for (l=0; l<bs; l++) { 470 if (PetscRealPart(*aa++) != 0.) continue; 471 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 472 } 473 } 474 } 475 } 476 477 color = PETSC_DRAW_RED; 478 for (i=0,row=0; i<mbs; i++,row+=bs) { 479 for (j=a->i[i]; j<a->i[i+1]; j++) { 480 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 481 x_l = a->j[j]*bs; x_r = x_l + 1.0; 482 aa = a->a + j*bs2; 483 for (k=0; k<bs; k++) { 484 for (l=0; l<bs; l++) { 485 if (PetscRealPart(*aa++) <= 0.) continue; 486 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 487 } 488 } 489 } 490 } 491 PetscFunctionReturn(0); 492 } 493 494 #undef __FUNCT__ 495 #define __FUNCT__ "MatView_SeqSBAIJ_Draw" 496 static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer) 497 { 498 PetscErrorCode ierr; 499 PetscReal xl,yl,xr,yr,w,h; 500 PetscDraw draw; 501 PetscBool isnull; 502 503 PetscFunctionBegin; 504 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 505 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 506 507 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);CHKERRQ(ierr); 508 xr = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0; 509 xr += w; yr += h; xl = -w; yl = -h; 510 ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr); 511 ierr = PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);CHKERRQ(ierr); 512 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",NULL);CHKERRQ(ierr); 513 PetscFunctionReturn(0); 514 } 515 516 #undef __FUNCT__ 517 #define __FUNCT__ "MatView_SeqSBAIJ" 518 PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer) 519 { 520 PetscErrorCode ierr; 521 PetscBool iascii,isdraw; 522 FILE *file = 0; 523 524 PetscFunctionBegin; 525 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 526 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 527 if (iascii) { 528 ierr = MatView_SeqSBAIJ_ASCII(A,viewer);CHKERRQ(ierr); 529 } else if (isdraw) { 530 ierr = MatView_SeqSBAIJ_Draw(A,viewer);CHKERRQ(ierr); 531 } else { 532 Mat B; 533 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 534 ierr = MatView(B,viewer);CHKERRQ(ierr); 535 ierr = MatDestroy(&B);CHKERRQ(ierr); 536 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 537 if (file) { 538 fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs); 539 } 540 } 541 PetscFunctionReturn(0); 542 } 543 544 545 #undef __FUNCT__ 546 #define __FUNCT__ "MatGetValues_SeqSBAIJ" 547 PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[]) 548 { 549 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 550 PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j; 551 PetscInt *ai = a->i,*ailen = a->ilen; 552 PetscInt brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2; 553 MatScalar *ap,*aa = a->a; 554 555 PetscFunctionBegin; 556 for (k=0; k<m; k++) { /* loop over rows */ 557 row = im[k]; brow = row/bs; 558 if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */ 559 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); 560 rp = aj + ai[brow]; ap = aa + bs2*ai[brow]; 561 nrow = ailen[brow]; 562 for (l=0; l<n; l++) { /* loop over columns */ 563 if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */ 564 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); 565 col = in[l]; 566 bcol = col/bs; 567 cidx = col%bs; 568 ridx = row%bs; 569 high = nrow; 570 low = 0; /* assume unsorted */ 571 while (high-low > 5) { 572 t = (low+high)/2; 573 if (rp[t] > bcol) high = t; 574 else low = t; 575 } 576 for (i=low; i<high; i++) { 577 if (rp[i] > bcol) break; 578 if (rp[i] == bcol) { 579 *v++ = ap[bs2*i+bs*cidx+ridx]; 580 goto finished; 581 } 582 } 583 *v++ = 0.0; 584 finished:; 585 } 586 } 587 PetscFunctionReturn(0); 588 } 589 590 591 #undef __FUNCT__ 592 #define __FUNCT__ "MatSetValuesBlocked_SeqSBAIJ" 593 PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 594 { 595 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 596 PetscErrorCode ierr; 597 PetscInt *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1; 598 PetscInt *imax =a->imax,*ai=a->i,*ailen=a->ilen; 599 PetscInt *aj =a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval; 600 PetscBool roworiented=a->roworiented; 601 const PetscScalar *value = v; 602 MatScalar *ap,*aa = a->a,*bap; 603 604 PetscFunctionBegin; 605 if (roworiented) stepval = (n-1)*bs; 606 else stepval = (m-1)*bs; 607 608 for (k=0; k<m; k++) { /* loop over added rows */ 609 row = im[k]; 610 if (row < 0) continue; 611 #if defined(PETSC_USE_DEBUG) 612 if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1); 613 #endif 614 rp = aj + ai[row]; 615 ap = aa + bs2*ai[row]; 616 rmax = imax[row]; 617 nrow = ailen[row]; 618 low = 0; 619 high = nrow; 620 for (l=0; l<n; l++) { /* loop over added columns */ 621 if (in[l] < 0) continue; 622 col = in[l]; 623 #if defined(PETSC_USE_DEBUG) 624 if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1); 625 #endif 626 if (col < row) { 627 if (a->ignore_ltriangular) continue; /* ignore lower triangular block */ 628 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)"); 629 } 630 if (roworiented) value = v + k*(stepval+bs)*bs + l*bs; 631 else value = v + l*(stepval+bs)*bs + k*bs; 632 633 if (col <= lastcol) low = 0; 634 else high = nrow; 635 636 lastcol = col; 637 while (high-low > 7) { 638 t = (low+high)/2; 639 if (rp[t] > col) high = t; 640 else low = t; 641 } 642 for (i=low; i<high; i++) { 643 if (rp[i] > col) break; 644 if (rp[i] == col) { 645 bap = ap + bs2*i; 646 if (roworiented) { 647 if (is == ADD_VALUES) { 648 for (ii=0; ii<bs; ii++,value+=stepval) { 649 for (jj=ii; jj<bs2; jj+=bs) { 650 bap[jj] += *value++; 651 } 652 } 653 } else { 654 for (ii=0; ii<bs; ii++,value+=stepval) { 655 for (jj=ii; jj<bs2; jj+=bs) { 656 bap[jj] = *value++; 657 } 658 } 659 } 660 } else { 661 if (is == ADD_VALUES) { 662 for (ii=0; ii<bs; ii++,value+=stepval) { 663 for (jj=0; jj<bs; jj++) { 664 *bap++ += *value++; 665 } 666 } 667 } else { 668 for (ii=0; ii<bs; ii++,value+=stepval) { 669 for (jj=0; jj<bs; jj++) { 670 *bap++ = *value++; 671 } 672 } 673 } 674 } 675 goto noinsert2; 676 } 677 } 678 if (nonew == 1) goto noinsert2; 679 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 680 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 681 N = nrow++ - 1; high++; 682 /* shift up all the later entries in this row */ 683 for (ii=N; ii>=i; ii--) { 684 rp[ii+1] = rp[ii]; 685 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 686 } 687 if (N >= i) { 688 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 689 } 690 rp[i] = col; 691 bap = ap + bs2*i; 692 if (roworiented) { 693 for (ii=0; ii<bs; ii++,value+=stepval) { 694 for (jj=ii; jj<bs2; jj+=bs) { 695 bap[jj] = *value++; 696 } 697 } 698 } else { 699 for (ii=0; ii<bs; ii++,value+=stepval) { 700 for (jj=0; jj<bs; jj++) { 701 *bap++ = *value++; 702 } 703 } 704 } 705 noinsert2:; 706 low = i; 707 } 708 ailen[row] = nrow; 709 } 710 PetscFunctionReturn(0); 711 } 712 713 /* 714 This is not yet used 715 */ 716 #undef __FUNCT__ 717 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode" 718 PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A) 719 { 720 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 721 PetscErrorCode ierr; 722 const PetscInt *ai = a->i, *aj = a->j,*cols; 723 PetscInt i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts; 724 PetscBool flag; 725 726 PetscFunctionBegin; 727 ierr = PetscMalloc1(m,&ns);CHKERRQ(ierr); 728 while (i < m) { 729 nzx = ai[i+1] - ai[i]; /* Number of nonzeros */ 730 /* Limits the number of elements in a node to 'a->inode.limit' */ 731 for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) { 732 nzy = ai[j+1] - ai[j]; 733 if (nzy != (nzx - j + i)) break; 734 ierr = PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);CHKERRQ(ierr); 735 if (!flag) break; 736 } 737 ns[node_count++] = blk_size; 738 739 i = j; 740 } 741 if (!a->inode.size && m && node_count > .9*m) { 742 ierr = PetscFree(ns);CHKERRQ(ierr); 743 ierr = PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);CHKERRQ(ierr); 744 } else { 745 a->inode.node_count = node_count; 746 747 ierr = PetscMalloc1(node_count,&a->inode.size);CHKERRQ(ierr); 748 ierr = PetscLogObjectMemory((PetscObject)A,node_count*sizeof(PetscInt));CHKERRQ(ierr); 749 ierr = PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt));CHKERRQ(ierr); 750 ierr = PetscFree(ns);CHKERRQ(ierr); 751 ierr = PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);CHKERRQ(ierr); 752 753 /* count collections of adjacent columns in each inode */ 754 row = 0; 755 cnt = 0; 756 for (i=0; i<node_count; i++) { 757 cols = aj + ai[row] + a->inode.size[i]; 758 nz = ai[row+1] - ai[row] - a->inode.size[i]; 759 for (j=1; j<nz; j++) { 760 if (cols[j] != cols[j-1]+1) cnt++; 761 } 762 cnt++; 763 row += a->inode.size[i]; 764 } 765 ierr = PetscMalloc1(2*cnt,&counts);CHKERRQ(ierr); 766 cnt = 0; 767 row = 0; 768 for (i=0; i<node_count; i++) { 769 cols = aj + ai[row] + a->inode.size[i]; 770 counts[2*cnt] = cols[0]; 771 nz = ai[row+1] - ai[row] - a->inode.size[i]; 772 cnt2 = 1; 773 for (j=1; j<nz; j++) { 774 if (cols[j] != cols[j-1]+1) { 775 counts[2*(cnt++)+1] = cnt2; 776 counts[2*cnt] = cols[j]; 777 cnt2 = 1; 778 } else cnt2++; 779 } 780 counts[2*(cnt++)+1] = cnt2; 781 row += a->inode.size[i]; 782 } 783 ierr = PetscIntView(2*cnt,counts,0);CHKERRQ(ierr); 784 } 785 PetscFunctionReturn(0); 786 } 787 788 #undef __FUNCT__ 789 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ" 790 PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode) 791 { 792 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 793 PetscErrorCode ierr; 794 PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax; 795 PetscInt m = A->rmap->N,*ip,N,*ailen = a->ilen; 796 PetscInt mbs = a->mbs,bs2 = a->bs2,rmax = 0; 797 MatScalar *aa = a->a,*ap; 798 799 PetscFunctionBegin; 800 if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); 801 802 if (m) rmax = ailen[0]; 803 for (i=1; i<mbs; i++) { 804 /* move each row back by the amount of empty slots (fshift) before it*/ 805 fshift += imax[i-1] - ailen[i-1]; 806 rmax = PetscMax(rmax,ailen[i]); 807 if (fshift) { 808 ip = aj + ai[i]; ap = aa + bs2*ai[i]; 809 N = ailen[i]; 810 for (j=0; j<N; j++) { 811 ip[j-fshift] = ip[j]; 812 ierr = PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 813 } 814 } 815 ai[i] = ai[i-1] + ailen[i-1]; 816 } 817 if (mbs) { 818 fshift += imax[mbs-1] - ailen[mbs-1]; 819 ai[mbs] = ai[mbs-1] + ailen[mbs-1]; 820 } 821 /* reset ilen and imax for each row */ 822 for (i=0; i<mbs; i++) { 823 ailen[i] = imax[i] = ai[i+1] - ai[i]; 824 } 825 a->nz = ai[mbs]; 826 827 /* diagonals may have moved, reset it */ 828 if (a->diag) { 829 ierr = PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));CHKERRQ(ierr); 830 } 831 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); 832 833 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); 834 ierr = PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);CHKERRQ(ierr); 835 ierr = PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);CHKERRQ(ierr); 836 837 A->info.mallocs += a->reallocs; 838 a->reallocs = 0; 839 A->info.nz_unneeded = (PetscReal)fshift*bs2; 840 a->idiagvalid = PETSC_FALSE; 841 842 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 843 if (a->jshort && a->free_jshort) { 844 /* when matrix data structure is changed, previous jshort must be replaced */ 845 ierr = PetscFree(a->jshort);CHKERRQ(ierr); 846 } 847 ierr = PetscMalloc1(a->i[A->rmap->n],&a->jshort);CHKERRQ(ierr); 848 ierr = PetscLogObjectMemory((PetscObject)A,a->i[A->rmap->n]*sizeof(unsigned short));CHKERRQ(ierr); 849 for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i]; 850 A->ops->mult = MatMult_SeqSBAIJ_1_ushort; 851 A->ops->sor = MatSOR_SeqSBAIJ_ushort; 852 a->free_jshort = PETSC_TRUE; 853 } 854 PetscFunctionReturn(0); 855 } 856 857 /* 858 This function returns an array of flags which indicate the locations of contiguous 859 blocks that should be zeroed. for eg: if bs = 3 and is = [0,1,2,3,5,6,7,8,9] 860 then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)] 861 Assume: sizes should be long enough to hold all the values. 862 */ 863 #undef __FUNCT__ 864 #define __FUNCT__ "MatZeroRows_SeqSBAIJ_Check_Blocks" 865 PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max) 866 { 867 PetscInt i,j,k,row; 868 PetscBool flg; 869 870 PetscFunctionBegin; 871 for (i=0,j=0; i<n; j++) { 872 row = idx[i]; 873 if (row%bs!=0) { /* Not the begining of a block */ 874 sizes[j] = 1; 875 i++; 876 } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */ 877 sizes[j] = 1; /* Also makes sure atleast 'bs' values exist for next else */ 878 i++; 879 } else { /* Begining of the block, so check if the complete block exists */ 880 flg = PETSC_TRUE; 881 for (k=1; k<bs; k++) { 882 if (row+k != idx[i+k]) { /* break in the block */ 883 flg = PETSC_FALSE; 884 break; 885 } 886 } 887 if (flg) { /* No break in the bs */ 888 sizes[j] = bs; 889 i += bs; 890 } else { 891 sizes[j] = 1; 892 i++; 893 } 894 } 895 } 896 *bs_max = j; 897 PetscFunctionReturn(0); 898 } 899 900 901 /* Only add/insert a(i,j) with i<=j (blocks). 902 Any a(i,j) with i>j input by user is ingored. 903 */ 904 905 #undef __FUNCT__ 906 #define __FUNCT__ "MatSetValues_SeqSBAIJ" 907 PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 908 { 909 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 910 PetscErrorCode ierr; 911 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1; 912 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented; 913 PetscInt *aj =a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol; 914 PetscInt ridx,cidx,bs2=a->bs2; 915 MatScalar *ap,value,*aa=a->a,*bap; 916 917 PetscFunctionBegin; 918 for (k=0; k<m; k++) { /* loop over added rows */ 919 row = im[k]; /* row number */ 920 brow = row/bs; /* block row number */ 921 if (row < 0) continue; 922 #if defined(PETSC_USE_DEBUG) 923 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); 924 #endif 925 rp = aj + ai[brow]; /*ptr to beginning of column value of the row block*/ 926 ap = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/ 927 rmax = imax[brow]; /* maximum space allocated for this row */ 928 nrow = ailen[brow]; /* actual length of this row */ 929 low = 0; 930 931 for (l=0; l<n; l++) { /* loop over added columns */ 932 if (in[l] < 0) continue; 933 #if defined(PETSC_USE_DEBUG) 934 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); 935 #endif 936 col = in[l]; 937 bcol = col/bs; /* block col number */ 938 939 if (brow > bcol) { 940 if (a->ignore_ltriangular) continue; /* ignore lower triangular values */ 941 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)"); 942 } 943 944 ridx = row % bs; cidx = col % bs; /*row and col index inside the block */ 945 if ((brow==bcol && ridx<=cidx) || (brow<bcol)) { 946 /* element value a(k,l) */ 947 if (roworiented) value = v[l + k*n]; 948 else value = v[k + l*m]; 949 950 /* move pointer bap to a(k,l) quickly and add/insert value */ 951 if (col <= lastcol) low = 0; 952 high = nrow; 953 lastcol = col; 954 while (high-low > 7) { 955 t = (low+high)/2; 956 if (rp[t] > bcol) high = t; 957 else low = t; 958 } 959 for (i=low; i<high; i++) { 960 if (rp[i] > bcol) break; 961 if (rp[i] == bcol) { 962 bap = ap + bs2*i + bs*cidx + ridx; 963 if (is == ADD_VALUES) *bap += value; 964 else *bap = value; 965 /* for diag block, add/insert its symmetric element a(cidx,ridx) */ 966 if (brow == bcol && ridx < cidx) { 967 bap = ap + bs2*i + bs*ridx + cidx; 968 if (is == ADD_VALUES) *bap += value; 969 else *bap = value; 970 } 971 goto noinsert1; 972 } 973 } 974 975 if (nonew == 1) goto noinsert1; 976 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 977 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 978 979 N = nrow++ - 1; high++; 980 /* shift up all the later entries in this row */ 981 for (ii=N; ii>=i; ii--) { 982 rp[ii+1] = rp[ii]; 983 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 984 } 985 if (N>=i) { 986 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 987 } 988 rp[i] = bcol; 989 ap[bs2*i + bs*cidx + ridx] = value; 990 A->nonzerostate++; 991 noinsert1:; 992 low = i; 993 } 994 } /* end of loop over added columns */ 995 ailen[brow] = nrow; 996 } /* end of loop over added rows */ 997 PetscFunctionReturn(0); 998 } 999 1000 #undef __FUNCT__ 1001 #define __FUNCT__ "MatICCFactor_SeqSBAIJ" 1002 PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info) 1003 { 1004 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)inA->data; 1005 Mat outA; 1006 PetscErrorCode ierr; 1007 PetscBool row_identity; 1008 1009 PetscFunctionBegin; 1010 if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc"); 1011 ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr); 1012 if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported"); 1013 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()! */ 1014 1015 outA = inA; 1016 inA->factortype = MAT_FACTOR_ICC; 1017 1018 ierr = MatMarkDiagonal_SeqSBAIJ(inA);CHKERRQ(ierr); 1019 ierr = MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);CHKERRQ(ierr); 1020 1021 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1022 ierr = ISDestroy(&a->row);CHKERRQ(ierr); 1023 a->row = row; 1024 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1025 ierr = ISDestroy(&a->col);CHKERRQ(ierr); 1026 a->col = row; 1027 1028 /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */ 1029 if (a->icol) {ierr = ISInvertPermutation(row,PETSC_DECIDE, &a->icol);CHKERRQ(ierr);} 1030 ierr = PetscLogObjectParent((PetscObject)inA,(PetscObject)a->icol);CHKERRQ(ierr); 1031 1032 if (!a->solve_work) { 1033 ierr = PetscMalloc1((inA->rmap->N+inA->rmap->bs),&a->solve_work);CHKERRQ(ierr); 1034 ierr = PetscLogObjectMemory((PetscObject)inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));CHKERRQ(ierr); 1035 } 1036 1037 ierr = MatCholeskyFactorNumeric(outA,inA,info);CHKERRQ(ierr); 1038 PetscFunctionReturn(0); 1039 } 1040 1041 #undef __FUNCT__ 1042 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices_SeqSBAIJ" 1043 PetscErrorCode MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices) 1044 { 1045 Mat_SeqSBAIJ *baij = (Mat_SeqSBAIJ*)mat->data; 1046 PetscInt i,nz,n; 1047 PetscErrorCode ierr; 1048 1049 PetscFunctionBegin; 1050 nz = baij->maxnz; 1051 n = mat->cmap->n; 1052 for (i=0; i<nz; i++) baij->j[i] = indices[i]; 1053 1054 baij->nz = nz; 1055 for (i=0; i<n; i++) baij->ilen[i] = baij->imax[i]; 1056 1057 ierr = MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1058 PetscFunctionReturn(0); 1059 } 1060 1061 #undef __FUNCT__ 1062 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices" 1063 /*@ 1064 MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows 1065 in the matrix. 1066 1067 Input Parameters: 1068 + mat - the SeqSBAIJ matrix 1069 - indices - the column indices 1070 1071 Level: advanced 1072 1073 Notes: 1074 This can be called if you have precomputed the nonzero structure of the 1075 matrix and want to provide it to the matrix object to improve the performance 1076 of the MatSetValues() operation. 1077 1078 You MUST have set the correct numbers of nonzeros per row in the call to 1079 MatCreateSeqSBAIJ(), and the columns indices MUST be sorted. 1080 1081 MUST be called before any calls to MatSetValues() 1082 1083 .seealso: MatCreateSeqSBAIJ 1084 @*/ 1085 PetscErrorCode MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices) 1086 { 1087 PetscErrorCode ierr; 1088 1089 PetscFunctionBegin; 1090 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1091 PetscValidPointer(indices,2); 1092 ierr = PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt*),(mat,indices));CHKERRQ(ierr); 1093 PetscFunctionReturn(0); 1094 } 1095 1096 #undef __FUNCT__ 1097 #define __FUNCT__ "MatCopy_SeqSBAIJ" 1098 PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str) 1099 { 1100 PetscErrorCode ierr; 1101 1102 PetscFunctionBegin; 1103 /* If the two matrices have the same copy implementation, use fast copy. */ 1104 if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) { 1105 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1106 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1107 1108 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"); 1109 ierr = PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));CHKERRQ(ierr); 1110 } else { 1111 ierr = MatGetRowUpperTriangular(A);CHKERRQ(ierr); 1112 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 1113 ierr = MatRestoreRowUpperTriangular(A);CHKERRQ(ierr); 1114 } 1115 PetscFunctionReturn(0); 1116 } 1117 1118 #undef __FUNCT__ 1119 #define __FUNCT__ "MatSetUp_SeqSBAIJ" 1120 PetscErrorCode MatSetUp_SeqSBAIJ(Mat A) 1121 { 1122 PetscErrorCode ierr; 1123 1124 PetscFunctionBegin; 1125 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,A->rmap->bs,PETSC_DEFAULT,0);CHKERRQ(ierr); 1126 PetscFunctionReturn(0); 1127 } 1128 1129 #undef __FUNCT__ 1130 #define __FUNCT__ "MatSeqSBAIJGetArray_SeqSBAIJ" 1131 PetscErrorCode MatSeqSBAIJGetArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1132 { 1133 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1134 1135 PetscFunctionBegin; 1136 *array = a->a; 1137 PetscFunctionReturn(0); 1138 } 1139 1140 #undef __FUNCT__ 1141 #define __FUNCT__ "MatSeqSBAIJRestoreArray_SeqSBAIJ" 1142 PetscErrorCode MatSeqSBAIJRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1143 { 1144 PetscFunctionBegin; 1145 PetscFunctionReturn(0); 1146 } 1147 1148 #undef __FUNCT__ 1149 #define __FUNCT__ "MatAXPYGetPreallocation_SeqSBAIJ" 1150 PetscErrorCode MatAXPYGetPreallocation_SeqSBAIJ(Mat Y,Mat X,PetscInt *nnz) 1151 { 1152 PetscInt i,bs=Y->rmap->bs,mbs=Y->rmap->N/bs; 1153 Mat_SeqSBAIJ *x = (Mat_SeqSBAIJ*)X->data; 1154 Mat_SeqSBAIJ *y = (Mat_SeqSBAIJ*)Y->data; 1155 const PetscInt *xi = x->i,*yi = y->i; 1156 1157 PetscFunctionBegin; 1158 /* Set the number of nonzeros in the new matrix */ 1159 for (i=0; i<mbs; i++) { 1160 PetscInt j,k,nzx = xi[i+1] - xi[i],nzy = yi[i+1] - yi[i]; 1161 const PetscInt *xj = x->j+xi[i],*yj = y->j+yi[i]; 1162 nnz[i] = 0; 1163 for (j=0,k=0; j<nzx; j++) { /* Point in X */ 1164 for (; k<nzy && yj[k]<xj[j]; k++) nnz[i]++; /* Catch up to X */ 1165 if (k<nzy && yj[k]==xj[j]) k++; /* Skip duplicate */ 1166 nnz[i]++; 1167 } 1168 for (; k<nzy; k++) nnz[i]++; 1169 } 1170 PetscFunctionReturn(0); 1171 } 1172 1173 #undef __FUNCT__ 1174 #define __FUNCT__ "MatAXPY_SeqSBAIJ" 1175 PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 1176 { 1177 Mat_SeqSBAIJ *x=(Mat_SeqSBAIJ*)X->data, *y=(Mat_SeqSBAIJ*)Y->data; 1178 PetscErrorCode ierr; 1179 PetscInt i,bs=Y->rmap->bs,bs2=bs*bs,j; 1180 PetscBLASInt one = 1; 1181 1182 PetscFunctionBegin; 1183 if (str == SAME_NONZERO_PATTERN) { 1184 PetscScalar alpha = a; 1185 PetscBLASInt bnz; 1186 ierr = PetscBLASIntCast(x->nz*bs2,&bnz);CHKERRQ(ierr); 1187 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 1188 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 1189 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 1190 if (y->xtoy && y->XtoY != X) { 1191 ierr = PetscFree(y->xtoy);CHKERRQ(ierr); 1192 ierr = MatDestroy(&y->XtoY);CHKERRQ(ierr); 1193 } 1194 if (!y->xtoy) { /* get xtoy */ 1195 ierr = MatAXPYGetxtoy_Private(x->mbs,x->i,x->j,NULL, y->i,y->j,NULL, &y->xtoy);CHKERRQ(ierr); 1196 y->XtoY = X; 1197 } 1198 for (i=0; i<x->nz; i++) { 1199 j = 0; 1200 while (j < bs2) { 1201 y->a[bs2*y->xtoy[i]+j] += a*(x->a[bs2*i+j]); 1202 j++; 1203 } 1204 } 1205 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 1206 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); 1207 } else { 1208 Mat B; 1209 PetscInt *nnz; 1210 if (bs != X->rmap->bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrices must have same block size"); 1211 ierr = MatGetRowUpperTriangular(X);CHKERRQ(ierr); 1212 ierr = MatGetRowUpperTriangular(Y);CHKERRQ(ierr); 1213 ierr = PetscMalloc1(Y->rmap->N,&nnz);CHKERRQ(ierr); 1214 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 1215 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 1216 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 1217 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 1218 ierr = MatSetType(B,(MatType) ((PetscObject)Y)->type_name);CHKERRQ(ierr); 1219 ierr = MatAXPYGetPreallocation_SeqSBAIJ(Y,X,nnz);CHKERRQ(ierr); 1220 ierr = MatSeqSBAIJSetPreallocation(B,bs,0,nnz);CHKERRQ(ierr); 1221 1222 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 1223 1224 ierr = MatHeaderReplace(Y,B);CHKERRQ(ierr); 1225 ierr = PetscFree(nnz);CHKERRQ(ierr); 1226 ierr = MatRestoreRowUpperTriangular(X);CHKERRQ(ierr); 1227 ierr = MatRestoreRowUpperTriangular(Y);CHKERRQ(ierr); 1228 } 1229 PetscFunctionReturn(0); 1230 } 1231 1232 #undef __FUNCT__ 1233 #define __FUNCT__ "MatIsSymmetric_SeqSBAIJ" 1234 PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1235 { 1236 PetscFunctionBegin; 1237 *flg = PETSC_TRUE; 1238 PetscFunctionReturn(0); 1239 } 1240 1241 #undef __FUNCT__ 1242 #define __FUNCT__ "MatIsStructurallySymmetric_SeqSBAIJ" 1243 PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool *flg) 1244 { 1245 PetscFunctionBegin; 1246 *flg = PETSC_TRUE; 1247 PetscFunctionReturn(0); 1248 } 1249 1250 #undef __FUNCT__ 1251 #define __FUNCT__ "MatIsHermitian_SeqSBAIJ" 1252 PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1253 { 1254 PetscFunctionBegin; 1255 *flg = PETSC_FALSE; 1256 PetscFunctionReturn(0); 1257 } 1258 1259 #undef __FUNCT__ 1260 #define __FUNCT__ "MatRealPart_SeqSBAIJ" 1261 PetscErrorCode MatRealPart_SeqSBAIJ(Mat A) 1262 { 1263 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1264 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1265 MatScalar *aa = a->a; 1266 1267 PetscFunctionBegin; 1268 for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]); 1269 PetscFunctionReturn(0); 1270 } 1271 1272 #undef __FUNCT__ 1273 #define __FUNCT__ "MatImaginaryPart_SeqSBAIJ" 1274 PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A) 1275 { 1276 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1277 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1278 MatScalar *aa = a->a; 1279 1280 PetscFunctionBegin; 1281 for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]); 1282 PetscFunctionReturn(0); 1283 } 1284 1285 #undef __FUNCT__ 1286 #define __FUNCT__ "MatZeroRowsColumns_SeqSBAIJ" 1287 PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b) 1288 { 1289 Mat_SeqSBAIJ *baij=(Mat_SeqSBAIJ*)A->data; 1290 PetscErrorCode ierr; 1291 PetscInt i,j,k,count; 1292 PetscInt bs =A->rmap->bs,bs2=baij->bs2,row,col; 1293 PetscScalar zero = 0.0; 1294 MatScalar *aa; 1295 const PetscScalar *xx; 1296 PetscScalar *bb; 1297 PetscBool *zeroed,vecs = PETSC_FALSE; 1298 1299 PetscFunctionBegin; 1300 /* fix right hand side if needed */ 1301 if (x && b) { 1302 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1303 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1304 vecs = PETSC_TRUE; 1305 } 1306 1307 /* zero the columns */ 1308 ierr = PetscCalloc1(A->rmap->n,&zeroed);CHKERRQ(ierr); 1309 for (i=0; i<is_n; i++) { 1310 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]); 1311 zeroed[is_idx[i]] = PETSC_TRUE; 1312 } 1313 if (vecs) { 1314 for (i=0; i<A->rmap->N; i++) { 1315 row = i/bs; 1316 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1317 for (k=0; k<bs; k++) { 1318 col = bs*baij->j[j] + k; 1319 if (col <= i) continue; 1320 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1321 if (!zeroed[i] && zeroed[col]) bb[i] -= aa[0]*xx[col]; 1322 if (zeroed[i] && !zeroed[col]) bb[col] -= aa[0]*xx[i]; 1323 } 1324 } 1325 } 1326 for (i=0; i<is_n; i++) bb[is_idx[i]] = diag*xx[is_idx[i]]; 1327 } 1328 1329 for (i=0; i<A->rmap->N; i++) { 1330 if (!zeroed[i]) { 1331 row = i/bs; 1332 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1333 for (k=0; k<bs; k++) { 1334 col = bs*baij->j[j] + k; 1335 if (zeroed[col]) { 1336 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1337 aa[0] = 0.0; 1338 } 1339 } 1340 } 1341 } 1342 } 1343 ierr = PetscFree(zeroed);CHKERRQ(ierr); 1344 if (vecs) { 1345 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1346 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1347 } 1348 1349 /* zero the rows */ 1350 for (i=0; i<is_n; i++) { 1351 row = is_idx[i]; 1352 count = (baij->i[row/bs +1] - baij->i[row/bs])*bs; 1353 aa = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs); 1354 for (k=0; k<count; k++) { 1355 aa[0] = zero; 1356 aa += bs; 1357 } 1358 if (diag != 0.0) { 1359 ierr = (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); 1360 } 1361 } 1362 ierr = MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1363 PetscFunctionReturn(0); 1364 } 1365 1366 /* -------------------------------------------------------------------*/ 1367 static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ, 1368 MatGetRow_SeqSBAIJ, 1369 MatRestoreRow_SeqSBAIJ, 1370 MatMult_SeqSBAIJ_N, 1371 /* 4*/ MatMultAdd_SeqSBAIJ_N, 1372 MatMult_SeqSBAIJ_N, /* transpose versions are same as non-transpose versions */ 1373 MatMultAdd_SeqSBAIJ_N, 1374 0, 1375 0, 1376 0, 1377 /* 10*/ 0, 1378 0, 1379 MatCholeskyFactor_SeqSBAIJ, 1380 MatSOR_SeqSBAIJ, 1381 MatTranspose_SeqSBAIJ, 1382 /* 15*/ MatGetInfo_SeqSBAIJ, 1383 MatEqual_SeqSBAIJ, 1384 MatGetDiagonal_SeqSBAIJ, 1385 MatDiagonalScale_SeqSBAIJ, 1386 MatNorm_SeqSBAIJ, 1387 /* 20*/ 0, 1388 MatAssemblyEnd_SeqSBAIJ, 1389 MatSetOption_SeqSBAIJ, 1390 MatZeroEntries_SeqSBAIJ, 1391 /* 24*/ 0, 1392 0, 1393 0, 1394 0, 1395 0, 1396 /* 29*/ MatSetUp_SeqSBAIJ, 1397 0, 1398 0, 1399 0, 1400 0, 1401 /* 34*/ MatDuplicate_SeqSBAIJ, 1402 0, 1403 0, 1404 0, 1405 MatICCFactor_SeqSBAIJ, 1406 /* 39*/ MatAXPY_SeqSBAIJ, 1407 MatGetSubMatrices_SeqSBAIJ, 1408 MatIncreaseOverlap_SeqSBAIJ, 1409 MatGetValues_SeqSBAIJ, 1410 MatCopy_SeqSBAIJ, 1411 /* 44*/ 0, 1412 MatScale_SeqSBAIJ, 1413 0, 1414 0, 1415 MatZeroRowsColumns_SeqSBAIJ, 1416 /* 49*/ 0, 1417 MatGetRowIJ_SeqSBAIJ, 1418 MatRestoreRowIJ_SeqSBAIJ, 1419 0, 1420 0, 1421 /* 54*/ 0, 1422 0, 1423 0, 1424 0, 1425 MatSetValuesBlocked_SeqSBAIJ, 1426 /* 59*/ MatGetSubMatrix_SeqSBAIJ, 1427 0, 1428 0, 1429 0, 1430 0, 1431 /* 64*/ 0, 1432 0, 1433 0, 1434 0, 1435 0, 1436 /* 69*/ MatGetRowMaxAbs_SeqSBAIJ, 1437 0, 1438 0, 1439 0, 1440 0, 1441 /* 74*/ 0, 1442 0, 1443 0, 1444 0, 1445 0, 1446 /* 79*/ 0, 1447 0, 1448 0, 1449 MatGetInertia_SeqSBAIJ, 1450 MatLoad_SeqSBAIJ, 1451 /* 84*/ MatIsSymmetric_SeqSBAIJ, 1452 MatIsHermitian_SeqSBAIJ, 1453 MatIsStructurallySymmetric_SeqSBAIJ, 1454 0, 1455 0, 1456 /* 89*/ 0, 1457 0, 1458 0, 1459 0, 1460 0, 1461 /* 94*/ 0, 1462 0, 1463 0, 1464 0, 1465 0, 1466 /* 99*/ 0, 1467 0, 1468 0, 1469 0, 1470 0, 1471 /*104*/ 0, 1472 MatRealPart_SeqSBAIJ, 1473 MatImaginaryPart_SeqSBAIJ, 1474 MatGetRowUpperTriangular_SeqSBAIJ, 1475 MatRestoreRowUpperTriangular_SeqSBAIJ, 1476 /*109*/ 0, 1477 0, 1478 0, 1479 0, 1480 MatMissingDiagonal_SeqSBAIJ, 1481 /*114*/ 0, 1482 0, 1483 0, 1484 0, 1485 0, 1486 /*119*/ 0, 1487 0, 1488 0, 1489 0, 1490 0, 1491 /*124*/ 0, 1492 0, 1493 0, 1494 0, 1495 0, 1496 /*129*/ 0, 1497 0, 1498 0, 1499 0, 1500 0, 1501 /*134*/ 0, 1502 0, 1503 0, 1504 0, 1505 0, 1506 /*139*/ 0, 1507 0, 1508 0 1509 }; 1510 1511 #undef __FUNCT__ 1512 #define __FUNCT__ "MatStoreValues_SeqSBAIJ" 1513 PetscErrorCode MatStoreValues_SeqSBAIJ(Mat mat) 1514 { 1515 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)mat->data; 1516 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1517 PetscErrorCode ierr; 1518 1519 PetscFunctionBegin; 1520 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1521 1522 /* allocate space for values if not already there */ 1523 if (!aij->saved_values) { 1524 ierr = PetscMalloc1((nz+1),&aij->saved_values);CHKERRQ(ierr); 1525 } 1526 1527 /* copy values over */ 1528 ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1529 PetscFunctionReturn(0); 1530 } 1531 1532 #undef __FUNCT__ 1533 #define __FUNCT__ "MatRetrieveValues_SeqSBAIJ" 1534 PetscErrorCode MatRetrieveValues_SeqSBAIJ(Mat mat) 1535 { 1536 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)mat->data; 1537 PetscErrorCode ierr; 1538 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1539 1540 PetscFunctionBegin; 1541 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1542 if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first"); 1543 1544 /* copy values over */ 1545 ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1546 PetscFunctionReturn(0); 1547 } 1548 1549 #undef __FUNCT__ 1550 #define __FUNCT__ "MatSeqSBAIJSetPreallocation_SeqSBAIJ" 1551 PetscErrorCode MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz) 1552 { 1553 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1554 PetscErrorCode ierr; 1555 PetscInt i,mbs,bs2; 1556 PetscBool skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE; 1557 1558 PetscFunctionBegin; 1559 if (nz >= 0 || nnz) realalloc = PETSC_TRUE; 1560 B->preallocated = PETSC_TRUE; 1561 1562 ierr = MatSetBlockSize(B,PetscAbs(bs));CHKERRQ(ierr); 1563 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 1564 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 1565 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 1566 1567 mbs = B->rmap->N/bs; 1568 bs2 = bs*bs; 1569 1570 if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize"); 1571 1572 if (nz == MAT_SKIP_ALLOCATION) { 1573 skipallocation = PETSC_TRUE; 1574 nz = 0; 1575 } 1576 1577 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3; 1578 if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz); 1579 if (nnz) { 1580 for (i=0; i<mbs; i++) { 1581 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]); 1582 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); 1583 } 1584 } 1585 1586 B->ops->mult = MatMult_SeqSBAIJ_N; 1587 B->ops->multadd = MatMultAdd_SeqSBAIJ_N; 1588 B->ops->multtranspose = MatMult_SeqSBAIJ_N; 1589 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N; 1590 1591 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);CHKERRQ(ierr); 1592 if (!flg) { 1593 switch (bs) { 1594 case 1: 1595 B->ops->mult = MatMult_SeqSBAIJ_1; 1596 B->ops->multadd = MatMultAdd_SeqSBAIJ_1; 1597 B->ops->multtranspose = MatMult_SeqSBAIJ_1; 1598 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1; 1599 break; 1600 case 2: 1601 B->ops->mult = MatMult_SeqSBAIJ_2; 1602 B->ops->multadd = MatMultAdd_SeqSBAIJ_2; 1603 B->ops->multtranspose = MatMult_SeqSBAIJ_2; 1604 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2; 1605 break; 1606 case 3: 1607 B->ops->mult = MatMult_SeqSBAIJ_3; 1608 B->ops->multadd = MatMultAdd_SeqSBAIJ_3; 1609 B->ops->multtranspose = MatMult_SeqSBAIJ_3; 1610 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3; 1611 break; 1612 case 4: 1613 B->ops->mult = MatMult_SeqSBAIJ_4; 1614 B->ops->multadd = MatMultAdd_SeqSBAIJ_4; 1615 B->ops->multtranspose = MatMult_SeqSBAIJ_4; 1616 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4; 1617 break; 1618 case 5: 1619 B->ops->mult = MatMult_SeqSBAIJ_5; 1620 B->ops->multadd = MatMultAdd_SeqSBAIJ_5; 1621 B->ops->multtranspose = MatMult_SeqSBAIJ_5; 1622 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5; 1623 break; 1624 case 6: 1625 B->ops->mult = MatMult_SeqSBAIJ_6; 1626 B->ops->multadd = MatMultAdd_SeqSBAIJ_6; 1627 B->ops->multtranspose = MatMult_SeqSBAIJ_6; 1628 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6; 1629 break; 1630 case 7: 1631 B->ops->mult = MatMult_SeqSBAIJ_7; 1632 B->ops->multadd = MatMultAdd_SeqSBAIJ_7; 1633 B->ops->multtranspose = MatMult_SeqSBAIJ_7; 1634 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7; 1635 break; 1636 } 1637 } 1638 1639 b->mbs = mbs; 1640 b->nbs = mbs; 1641 if (!skipallocation) { 1642 if (!b->imax) { 1643 ierr = PetscMalloc2(mbs,&b->imax,mbs,&b->ilen);CHKERRQ(ierr); 1644 1645 b->free_imax_ilen = PETSC_TRUE; 1646 1647 ierr = PetscLogObjectMemory((PetscObject)B,2*mbs*sizeof(PetscInt));CHKERRQ(ierr); 1648 } 1649 if (!nnz) { 1650 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5; 1651 else if (nz <= 0) nz = 1; 1652 for (i=0; i<mbs; i++) b->imax[i] = nz; 1653 nz = nz*mbs; /* total nz */ 1654 } else { 1655 nz = 0; 1656 for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];} 1657 } 1658 /* b->ilen will count nonzeros in each block row so far. */ 1659 for (i=0; i<mbs; i++) b->ilen[i] = 0; 1660 /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */ 1661 1662 /* allocate the matrix space */ 1663 ierr = MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);CHKERRQ(ierr); 1664 ierr = PetscMalloc3(bs2*nz,&b->a,nz,&b->j,B->rmap->N+1,&b->i);CHKERRQ(ierr); 1665 ierr = PetscLogObjectMemory((PetscObject)B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr); 1666 ierr = PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 1667 ierr = PetscMemzero(b->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 1668 1669 b->singlemalloc = PETSC_TRUE; 1670 1671 /* pointer to beginning of each row */ 1672 b->i[0] = 0; 1673 for (i=1; i<mbs+1; i++) b->i[i] = b->i[i-1] + b->imax[i-1]; 1674 1675 b->free_a = PETSC_TRUE; 1676 b->free_ij = PETSC_TRUE; 1677 } else { 1678 b->free_a = PETSC_FALSE; 1679 b->free_ij = PETSC_FALSE; 1680 } 1681 1682 B->rmap->bs = bs; 1683 b->bs2 = bs2; 1684 b->nz = 0; 1685 b->maxnz = nz; 1686 1687 b->inew = 0; 1688 b->jnew = 0; 1689 b->anew = 0; 1690 b->a2anew = 0; 1691 b->permute = PETSC_FALSE; 1692 if (realalloc) {ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);} 1693 PetscFunctionReturn(0); 1694 } 1695 1696 #undef __FUNCT__ 1697 #define __FUNCT__ "MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ" 1698 PetscErrorCode MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[], const PetscScalar V[]) 1699 { 1700 PetscInt i,j,m,nz,nz_max=0,*nnz; 1701 PetscScalar *values=0; 1702 PetscBool roworiented = ((Mat_SeqSBAIJ*)B->data)->roworiented; 1703 PetscErrorCode ierr; 1704 PetscFunctionBegin; 1705 if (bs < 1) SETERRQ1(PetscObjectComm((PetscObject)B),PETSC_ERR_ARG_OUTOFRANGE,"Invalid block size specified, must be positive but it is %D",bs); 1706 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 1707 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 1708 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 1709 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 1710 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 1711 m = B->rmap->n/bs; 1712 1713 if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]); 1714 ierr = PetscMalloc1((m+1),&nnz);CHKERRQ(ierr); 1715 for (i=0; i<m; i++) { 1716 nz = ii[i+1] - ii[i]; 1717 if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D has a negative number of columns %D",i,nz); 1718 nz_max = PetscMax(nz_max,nz); 1719 nnz[i] = nz; 1720 } 1721 ierr = MatSeqSBAIJSetPreallocation(B,bs,0,nnz);CHKERRQ(ierr); 1722 ierr = PetscFree(nnz);CHKERRQ(ierr); 1723 1724 values = (PetscScalar*)V; 1725 if (!values) { 1726 ierr = PetscCalloc1(bs*bs*nz_max,&values);CHKERRQ(ierr); 1727 } 1728 for (i=0; i<m; i++) { 1729 PetscInt ncols = ii[i+1] - ii[i]; 1730 const PetscInt *icols = jj + ii[i]; 1731 if (!roworiented || bs == 1) { 1732 const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0); 1733 ierr = MatSetValuesBlocked_SeqSBAIJ(B,1,&i,ncols,icols,svals,INSERT_VALUES);CHKERRQ(ierr); 1734 } else { 1735 for (j=0; j<ncols; j++) { 1736 const PetscScalar *svals = values + (V ? (bs*bs*(ii[i]+j)) : 0); 1737 ierr = MatSetValuesBlocked_SeqSBAIJ(B,1,&i,1,&icols[j],svals,INSERT_VALUES);CHKERRQ(ierr); 1738 } 1739 } 1740 } 1741 if (!V) { ierr = PetscFree(values);CHKERRQ(ierr); } 1742 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1743 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1744 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1745 PetscFunctionReturn(0); 1746 } 1747 1748 /* 1749 This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization 1750 */ 1751 #undef __FUNCT__ 1752 #define __FUNCT__ "MatSeqSBAIJSetNumericFactorization_inplace" 1753 PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural) 1754 { 1755 PetscErrorCode ierr; 1756 PetscBool flg = PETSC_FALSE; 1757 PetscInt bs = B->rmap->bs; 1758 1759 PetscFunctionBegin; 1760 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);CHKERRQ(ierr); 1761 if (flg) bs = 8; 1762 1763 if (!natural) { 1764 switch (bs) { 1765 case 1: 1766 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace; 1767 break; 1768 case 2: 1769 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2; 1770 break; 1771 case 3: 1772 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3; 1773 break; 1774 case 4: 1775 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4; 1776 break; 1777 case 5: 1778 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5; 1779 break; 1780 case 6: 1781 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6; 1782 break; 1783 case 7: 1784 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7; 1785 break; 1786 default: 1787 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N; 1788 break; 1789 } 1790 } else { 1791 switch (bs) { 1792 case 1: 1793 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace; 1794 break; 1795 case 2: 1796 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering; 1797 break; 1798 case 3: 1799 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering; 1800 break; 1801 case 4: 1802 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering; 1803 break; 1804 case 5: 1805 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering; 1806 break; 1807 case 6: 1808 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering; 1809 break; 1810 case 7: 1811 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering; 1812 break; 1813 default: 1814 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering; 1815 break; 1816 } 1817 } 1818 PetscFunctionReturn(0); 1819 } 1820 1821 PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*); 1822 PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*); 1823 1824 #undef __FUNCT__ 1825 #define __FUNCT__ "MatGetFactor_seqsbaij_petsc" 1826 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B) 1827 { 1828 PetscInt n = A->rmap->n; 1829 PetscErrorCode ierr; 1830 1831 PetscFunctionBegin; 1832 #if defined(PETSC_USE_COMPLEX) 1833 if (A->hermitian) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported"); 1834 #endif 1835 ierr = MatCreate(PetscObjectComm((PetscObject)A),B);CHKERRQ(ierr); 1836 ierr = MatSetSizes(*B,n,n,n,n);CHKERRQ(ierr); 1837 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1838 ierr = MatSetType(*B,MATSEQSBAIJ);CHKERRQ(ierr); 1839 ierr = MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,NULL);CHKERRQ(ierr); 1840 1841 (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ; 1842 (*B)->ops->iccfactorsymbolic = MatICCFactorSymbolic_SeqSBAIJ; 1843 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported"); 1844 (*B)->factortype = ftype; 1845 PetscFunctionReturn(0); 1846 } 1847 1848 #undef __FUNCT__ 1849 #define __FUNCT__ "MatGetFactorAvailable_seqsbaij_petsc" 1850 PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool *flg) 1851 { 1852 PetscFunctionBegin; 1853 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1854 *flg = PETSC_TRUE; 1855 } else { 1856 *flg = PETSC_FALSE; 1857 } 1858 PetscFunctionReturn(0); 1859 } 1860 1861 #if defined(PETSC_HAVE_MUMPS) 1862 PETSC_EXTERN PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*); 1863 #endif 1864 #if defined(PETSC_HAVE_PASTIX) 1865 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*); 1866 #endif 1867 #if defined(PETSC_HAVE_SUITESPARSE) 1868 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*); 1869 #endif 1870 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_sbstrm(Mat,MatFactorType,Mat*); 1871 1872 /*MC 1873 MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices, 1874 based on block compressed sparse row format. Only the upper triangular portion of the matrix is stored. 1875 1876 For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you 1877 can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd() 1878 1879 Options Database Keys: 1880 . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions() 1881 1882 Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not 1883 stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use 1884 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. 1885 1886 1887 Level: beginner 1888 1889 .seealso: MatCreateSeqSBAIJ 1890 M*/ 1891 1892 PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*); 1893 1894 #undef __FUNCT__ 1895 #define __FUNCT__ "MatCreate_SeqSBAIJ" 1896 PETSC_EXTERN PetscErrorCode MatCreate_SeqSBAIJ(Mat B) 1897 { 1898 Mat_SeqSBAIJ *b; 1899 PetscErrorCode ierr; 1900 PetscMPIInt size; 1901 PetscBool no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE; 1902 1903 PetscFunctionBegin; 1904 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 1905 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1"); 1906 1907 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 1908 B->data = (void*)b; 1909 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 1910 1911 B->ops->destroy = MatDestroy_SeqSBAIJ; 1912 B->ops->view = MatView_SeqSBAIJ; 1913 b->row = 0; 1914 b->icol = 0; 1915 b->reallocs = 0; 1916 b->saved_values = 0; 1917 b->inode.limit = 5; 1918 b->inode.max_limit = 5; 1919 1920 b->roworiented = PETSC_TRUE; 1921 b->nonew = 0; 1922 b->diag = 0; 1923 b->solve_work = 0; 1924 b->mult_work = 0; 1925 B->spptr = 0; 1926 B->info.nz_unneeded = (PetscReal)b->maxnz*b->bs2; 1927 b->keepnonzeropattern = PETSC_FALSE; 1928 b->xtoy = 0; 1929 b->XtoY = 0; 1930 1931 b->inew = 0; 1932 b->jnew = 0; 1933 b->anew = 0; 1934 b->a2anew = 0; 1935 b->permute = PETSC_FALSE; 1936 1937 b->ignore_ltriangular = PETSC_TRUE; 1938 1939 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,NULL);CHKERRQ(ierr); 1940 1941 b->getrow_utriangular = PETSC_FALSE; 1942 1943 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,NULL);CHKERRQ(ierr); 1944 1945 #if defined(PETSC_HAVE_PASTIX) 1946 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_pastix_C",MatGetFactor_seqsbaij_pastix);CHKERRQ(ierr); 1947 #endif 1948 #if defined(PETSC_HAVE_MUMPS) 1949 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_mumps_C",MatGetFactor_sbaij_mumps);CHKERRQ(ierr); 1950 #endif 1951 #if defined(PETSC_HAVE_SUITESPARSE) 1952 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_cholmod_C",MatGetFactor_seqsbaij_cholmod);CHKERRQ(ierr); 1953 #endif 1954 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactorAvailable_petsc_C",MatGetFactorAvailable_seqsbaij_petsc);CHKERRQ(ierr); 1955 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_petsc_C",MatGetFactor_seqsbaij_petsc);CHKERRQ(ierr); 1956 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_sbstrm_C",MatGetFactor_seqsbaij_sbstrm);CHKERRQ(ierr); 1957 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqSBAIJ);CHKERRQ(ierr); 1958 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqSBAIJ);CHKERRQ(ierr); 1959 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",MatSeqSBAIJSetColumnIndices_SeqSBAIJ);CHKERRQ(ierr); 1960 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",MatConvert_SeqSBAIJ_SeqAIJ);CHKERRQ(ierr); 1961 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",MatConvert_SeqSBAIJ_SeqBAIJ);CHKERRQ(ierr); 1962 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",MatSeqSBAIJSetPreallocation_SeqSBAIJ);CHKERRQ(ierr); 1963 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocationCSR_C",MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ);CHKERRQ(ierr); 1964 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C",MatConvert_SeqSBAIJ_SeqSBSTRM);CHKERRQ(ierr); 1965 1966 B->symmetric = PETSC_TRUE; 1967 B->structurally_symmetric = PETSC_TRUE; 1968 B->symmetric_set = PETSC_TRUE; 1969 B->structurally_symmetric_set = PETSC_TRUE; 1970 1971 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);CHKERRQ(ierr); 1972 1973 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)B),((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");CHKERRQ(ierr); 1974 ierr = PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",NULL,no_unroll,&no_unroll,NULL);CHKERRQ(ierr); 1975 if (no_unroll) { 1976 ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");CHKERRQ(ierr); 1977 } 1978 ierr = PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",NULL,no_inode,&no_inode,NULL);CHKERRQ(ierr); 1979 if (no_inode) { 1980 ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");CHKERRQ(ierr); 1981 } 1982 ierr = PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",NULL,b->inode.limit,&b->inode.limit,NULL);CHKERRQ(ierr); 1983 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1984 b->inode.use = (PetscBool)(!(no_unroll || no_inode)); 1985 if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit; 1986 PetscFunctionReturn(0); 1987 } 1988 1989 #undef __FUNCT__ 1990 #define __FUNCT__ "MatSeqSBAIJSetPreallocation" 1991 /*@C 1992 MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block 1993 compressed row) format. For good matrix assembly performance the 1994 user should preallocate the matrix storage by setting the parameter nz 1995 (or the array nnz). By setting these parameters accurately, performance 1996 during matrix assembly can be increased by more than a factor of 50. 1997 1998 Collective on Mat 1999 2000 Input Parameters: 2001 + B - the symmetric matrix 2002 . bs - size of block 2003 . nz - number of block nonzeros per block row (same for all rows) 2004 - nnz - array containing the number of block nonzeros in the upper triangular plus 2005 diagonal portion of each block (possibly different for each block row) or NULL 2006 2007 Options Database Keys: 2008 . -mat_no_unroll - uses code that does not unroll the loops in the 2009 block calculations (much slower) 2010 . -mat_block_size - size of the blocks to use (only works if a negative bs is passed in 2011 2012 Level: intermediate 2013 2014 Notes: 2015 Specify the preallocated storage with either nz or nnz (not both). 2016 Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory 2017 allocation. See Users-Manual: ch_mat for details. 2018 2019 You can call MatGetInfo() to get information on how effective the preallocation was; 2020 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 2021 You can also run with the option -info and look for messages with the string 2022 malloc in them to see if additional memory allocation was needed. 2023 2024 If the nnz parameter is given then the nz parameter is ignored 2025 2026 2027 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() 2028 @*/ 2029 PetscErrorCode MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[]) 2030 { 2031 PetscErrorCode ierr; 2032 2033 PetscFunctionBegin; 2034 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2035 PetscValidType(B,1); 2036 PetscValidLogicalCollectiveInt(B,bs,2); 2037 ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));CHKERRQ(ierr); 2038 PetscFunctionReturn(0); 2039 } 2040 2041 #undef __FUNCT__ 2042 #define __FUNCT__ "MatSeqSBAIJSetPreallocationCSR" 2043 /*@C 2044 MatSeqSBAIJSetPreallocationCSR - Allocates memory for a sparse sequential matrix in symmetric block AIJ format. 2045 2046 Input Parameters: 2047 + B - the matrix 2048 . i - the indices into j for the start of each local row (starts with zero) 2049 . j - the column indices for each local row (starts with zero) these must be sorted for each row 2050 - v - optional values in the matrix 2051 2052 Level: developer 2053 2054 Notes: 2055 The order of the entries in values is specified by the MatOption MAT_ROW_ORIENTED. For example, C programs 2056 may want to use the default MAT_ROW_ORIENTED=PETSC_TRUE and use an array v[nnz][bs][bs] where the second index is 2057 over rows within a block and the last index is over columns within a block row. Fortran programs will likely set 2058 MAT_ROW_ORIENTED=PETSC_FALSE and use a Fortran array v(bs,bs,nnz) in which the first index is over rows within a 2059 block column and the second index is over columns within a block. 2060 2061 .keywords: matrix, block, aij, compressed row, sparse 2062 2063 .seealso: MatCreate(), MatCreateSeqSBAIJ(), MatSetValuesBlocked(), MatSeqSBAIJSetPreallocation(), MATSEQSBAIJ 2064 @*/ 2065 PetscErrorCode MatSeqSBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 2066 { 2067 PetscErrorCode ierr; 2068 2069 PetscFunctionBegin; 2070 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2071 PetscValidType(B,1); 2072 PetscValidLogicalCollectiveInt(B,bs,2); 2073 ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));CHKERRQ(ierr); 2074 PetscFunctionReturn(0); 2075 } 2076 2077 #undef __FUNCT__ 2078 #define __FUNCT__ "MatCreateSeqSBAIJ" 2079 /*@C 2080 MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block 2081 compressed row) format. For good matrix assembly performance the 2082 user should preallocate the matrix storage by setting the parameter nz 2083 (or the array nnz). By setting these parameters accurately, performance 2084 during matrix assembly can be increased by more than a factor of 50. 2085 2086 Collective on MPI_Comm 2087 2088 Input Parameters: 2089 + comm - MPI communicator, set to PETSC_COMM_SELF 2090 . bs - size of block 2091 . m - number of rows, or number of columns 2092 . nz - number of block nonzeros per block row (same for all rows) 2093 - nnz - array containing the number of block nonzeros in the upper triangular plus 2094 diagonal portion of each block (possibly different for each block row) or NULL 2095 2096 Output Parameter: 2097 . A - the symmetric matrix 2098 2099 Options Database Keys: 2100 . -mat_no_unroll - uses code that does not unroll the loops in the 2101 block calculations (much slower) 2102 . -mat_block_size - size of the blocks to use 2103 2104 Level: intermediate 2105 2106 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 2107 MatXXXXSetPreallocation() paradgm instead of this routine directly. 2108 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 2109 2110 Notes: 2111 The number of rows and columns must be divisible by blocksize. 2112 This matrix type does not support complex Hermitian operation. 2113 2114 Specify the preallocated storage with either nz or nnz (not both). 2115 Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory 2116 allocation. See Users-Manual: ch_mat for details. 2117 2118 If the nnz parameter is given then the nz parameter is ignored 2119 2120 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() 2121 @*/ 2122 PetscErrorCode MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A) 2123 { 2124 PetscErrorCode ierr; 2125 2126 PetscFunctionBegin; 2127 ierr = MatCreate(comm,A);CHKERRQ(ierr); 2128 ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); 2129 ierr = MatSetType(*A,MATSEQSBAIJ);CHKERRQ(ierr); 2130 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);CHKERRQ(ierr); 2131 PetscFunctionReturn(0); 2132 } 2133 2134 #undef __FUNCT__ 2135 #define __FUNCT__ "MatDuplicate_SeqSBAIJ" 2136 PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B) 2137 { 2138 Mat C; 2139 Mat_SeqSBAIJ *c,*a = (Mat_SeqSBAIJ*)A->data; 2140 PetscErrorCode ierr; 2141 PetscInt i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2; 2142 2143 PetscFunctionBegin; 2144 if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix"); 2145 2146 *B = 0; 2147 ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr); 2148 ierr = MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);CHKERRQ(ierr); 2149 ierr = MatSetType(C,MATSEQSBAIJ);CHKERRQ(ierr); 2150 ierr = PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2151 c = (Mat_SeqSBAIJ*)C->data; 2152 2153 C->preallocated = PETSC_TRUE; 2154 C->factortype = A->factortype; 2155 c->row = 0; 2156 c->icol = 0; 2157 c->saved_values = 0; 2158 c->keepnonzeropattern = a->keepnonzeropattern; 2159 C->assembled = PETSC_TRUE; 2160 2161 ierr = PetscLayoutReference(A->rmap,&C->rmap);CHKERRQ(ierr); 2162 ierr = PetscLayoutReference(A->cmap,&C->cmap);CHKERRQ(ierr); 2163 c->bs2 = a->bs2; 2164 c->mbs = a->mbs; 2165 c->nbs = a->nbs; 2166 2167 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2168 c->imax = a->imax; 2169 c->ilen = a->ilen; 2170 c->free_imax_ilen = PETSC_FALSE; 2171 } else { 2172 ierr = PetscMalloc2((mbs+1),&c->imax,(mbs+1),&c->ilen);CHKERRQ(ierr); 2173 ierr = PetscLogObjectMemory((PetscObject)C,2*(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2174 for (i=0; i<mbs; i++) { 2175 c->imax[i] = a->imax[i]; 2176 c->ilen[i] = a->ilen[i]; 2177 } 2178 c->free_imax_ilen = PETSC_TRUE; 2179 } 2180 2181 /* allocate the matrix space */ 2182 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2183 ierr = PetscMalloc1(bs2*nz,&c->a);CHKERRQ(ierr); 2184 ierr = PetscLogObjectMemory((PetscObject)C,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 2185 c->i = a->i; 2186 c->j = a->j; 2187 c->singlemalloc = PETSC_FALSE; 2188 c->free_a = PETSC_TRUE; 2189 c->free_ij = PETSC_FALSE; 2190 c->parent = A; 2191 ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr); 2192 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2193 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2194 } else { 2195 ierr = PetscMalloc3(bs2*nz,&c->a,nz,&c->j,mbs+1,&c->i);CHKERRQ(ierr); 2196 ierr = PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2197 ierr = PetscLogObjectMemory((PetscObject)C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));CHKERRQ(ierr); 2198 c->singlemalloc = PETSC_TRUE; 2199 c->free_a = PETSC_TRUE; 2200 c->free_ij = PETSC_TRUE; 2201 } 2202 if (mbs > 0) { 2203 if (cpvalues != MAT_SHARE_NONZERO_PATTERN) { 2204 ierr = PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 2205 } 2206 if (cpvalues == MAT_COPY_VALUES) { 2207 ierr = PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2208 } else { 2209 ierr = PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2210 } 2211 if (a->jshort) { 2212 /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */ 2213 /* if the parent matrix is reassembled, this child matrix will never notice */ 2214 ierr = PetscMalloc1(nz,&c->jshort);CHKERRQ(ierr); 2215 ierr = PetscLogObjectMemory((PetscObject)C,nz*sizeof(unsigned short));CHKERRQ(ierr); 2216 ierr = PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));CHKERRQ(ierr); 2217 2218 c->free_jshort = PETSC_TRUE; 2219 } 2220 } 2221 2222 c->roworiented = a->roworiented; 2223 c->nonew = a->nonew; 2224 2225 if (a->diag) { 2226 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2227 c->diag = a->diag; 2228 c->free_diag = PETSC_FALSE; 2229 } else { 2230 ierr = PetscMalloc1(mbs,&c->diag);CHKERRQ(ierr); 2231 ierr = PetscLogObjectMemory((PetscObject)C,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2232 for (i=0; i<mbs; i++) c->diag[i] = a->diag[i]; 2233 c->free_diag = PETSC_TRUE; 2234 } 2235 } 2236 c->nz = a->nz; 2237 c->maxnz = a->nz; /* Since we allocate exactly the right amount */ 2238 c->solve_work = 0; 2239 c->mult_work = 0; 2240 2241 *B = C; 2242 ierr = PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);CHKERRQ(ierr); 2243 PetscFunctionReturn(0); 2244 } 2245 2246 #undef __FUNCT__ 2247 #define __FUNCT__ "MatLoad_SeqSBAIJ" 2248 PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer) 2249 { 2250 Mat_SeqSBAIJ *a; 2251 PetscErrorCode ierr; 2252 int fd; 2253 PetscMPIInt size; 2254 PetscInt i,nz,header[4],*rowlengths=0,M,N,bs=1; 2255 PetscInt *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount; 2256 PetscInt kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols; 2257 PetscInt *masked,nmask,tmp,bs2,ishift; 2258 PetscScalar *aa; 2259 MPI_Comm comm; 2260 2261 PetscFunctionBegin; 2262 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2263 ierr = PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,NULL);CHKERRQ(ierr); 2264 bs2 = bs*bs; 2265 2266 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2267 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor"); 2268 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2269 ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr); 2270 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object"); 2271 M = header[1]; N = header[2]; nz = header[3]; 2272 2273 if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ"); 2274 2275 if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices"); 2276 2277 /* 2278 This code adds extra rows to make sure the number of rows is 2279 divisible by the blocksize 2280 */ 2281 mbs = M/bs; 2282 extra_rows = bs - M + bs*(mbs); 2283 if (extra_rows == bs) extra_rows = 0; 2284 else mbs++; 2285 if (extra_rows) { 2286 ierr = PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");CHKERRQ(ierr); 2287 } 2288 2289 /* Set global sizes if not already set */ 2290 if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) { 2291 ierr = MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);CHKERRQ(ierr); 2292 } else { /* Check if the matrix global sizes are correct */ 2293 ierr = MatGetSize(newmat,&rows,&cols);CHKERRQ(ierr); 2294 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); 2295 } 2296 2297 /* read in row lengths */ 2298 ierr = PetscMalloc1((M+extra_rows),&rowlengths);CHKERRQ(ierr); 2299 ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); 2300 for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1; 2301 2302 /* read in column indices */ 2303 ierr = PetscMalloc1((nz+extra_rows),&jj);CHKERRQ(ierr); 2304 ierr = PetscBinaryRead(fd,jj,nz,PETSC_INT);CHKERRQ(ierr); 2305 for (i=0; i<extra_rows; i++) jj[nz+i] = M+i; 2306 2307 /* loop over row lengths determining block row lengths */ 2308 ierr = PetscCalloc1(mbs,&s_browlengths);CHKERRQ(ierr); 2309 ierr = PetscMalloc2(mbs,&mask,mbs,&masked);CHKERRQ(ierr); 2310 ierr = PetscMemzero(mask,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2311 rowcount = 0; 2312 nzcount = 0; 2313 for (i=0; i<mbs; i++) { 2314 nmask = 0; 2315 for (j=0; j<bs; j++) { 2316 kmax = rowlengths[rowcount]; 2317 for (k=0; k<kmax; k++) { 2318 tmp = jj[nzcount++]/bs; /* block col. index */ 2319 if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;} 2320 } 2321 rowcount++; 2322 } 2323 s_browlengths[i] += nmask; 2324 2325 /* zero out the mask elements we set */ 2326 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2327 } 2328 2329 /* Do preallocation */ 2330 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);CHKERRQ(ierr); 2331 a = (Mat_SeqSBAIJ*)newmat->data; 2332 2333 /* set matrix "i" values */ 2334 a->i[0] = 0; 2335 for (i=1; i<= mbs; i++) { 2336 a->i[i] = a->i[i-1] + s_browlengths[i-1]; 2337 a->ilen[i-1] = s_browlengths[i-1]; 2338 } 2339 a->nz = a->i[mbs]; 2340 2341 /* read in nonzero values */ 2342 ierr = PetscMalloc1((nz+extra_rows),&aa);CHKERRQ(ierr); 2343 ierr = PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);CHKERRQ(ierr); 2344 for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0; 2345 2346 /* set "a" and "j" values into matrix */ 2347 nzcount = 0; jcount = 0; 2348 for (i=0; i<mbs; i++) { 2349 nzcountb = nzcount; 2350 nmask = 0; 2351 for (j=0; j<bs; j++) { 2352 kmax = rowlengths[i*bs+j]; 2353 for (k=0; k<kmax; k++) { 2354 tmp = jj[nzcount++]/bs; /* block col. index */ 2355 if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;} 2356 } 2357 } 2358 /* sort the masked values */ 2359 ierr = PetscSortInt(nmask,masked);CHKERRQ(ierr); 2360 2361 /* set "j" values into matrix */ 2362 maskcount = 1; 2363 for (j=0; j<nmask; j++) { 2364 a->j[jcount++] = masked[j]; 2365 mask[masked[j]] = maskcount++; 2366 } 2367 2368 /* set "a" values into matrix */ 2369 ishift = bs2*a->i[i]; 2370 for (j=0; j<bs; j++) { 2371 kmax = rowlengths[i*bs+j]; 2372 for (k=0; k<kmax; k++) { 2373 tmp = jj[nzcountb]/bs; /* block col. index */ 2374 if (tmp >= i) { 2375 block = mask[tmp] - 1; 2376 point = jj[nzcountb] - bs*tmp; 2377 idx = ishift + bs2*block + j + bs*point; 2378 a->a[idx] = aa[nzcountb]; 2379 } 2380 nzcountb++; 2381 } 2382 } 2383 /* zero out the mask elements we set */ 2384 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2385 } 2386 if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix"); 2387 2388 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2389 ierr = PetscFree(s_browlengths);CHKERRQ(ierr); 2390 ierr = PetscFree(aa);CHKERRQ(ierr); 2391 ierr = PetscFree(jj);CHKERRQ(ierr); 2392 ierr = PetscFree2(mask,masked);CHKERRQ(ierr); 2393 2394 ierr = MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2395 ierr = MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2396 PetscFunctionReturn(0); 2397 } 2398 2399 #undef __FUNCT__ 2400 #define __FUNCT__ "MatCreateSeqSBAIJWithArrays" 2401 /*@ 2402 MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements 2403 (upper triangular entries in CSR format) provided by the user. 2404 2405 Collective on MPI_Comm 2406 2407 Input Parameters: 2408 + comm - must be an MPI communicator of size 1 2409 . bs - size of block 2410 . m - number of rows 2411 . n - number of columns 2412 . i - row indices 2413 . j - column indices 2414 - a - matrix values 2415 2416 Output Parameter: 2417 . mat - the matrix 2418 2419 Level: advanced 2420 2421 Notes: 2422 The i, j, and a arrays are not copied by this routine, the user must free these arrays 2423 once the matrix is destroyed 2424 2425 You cannot set new nonzero locations into this matrix, that will generate an error. 2426 2427 The i and j indices are 0 based 2428 2429 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 2430 it is the regular CSR format excluding the lower triangular elements. 2431 2432 .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ() 2433 2434 @*/ 2435 PetscErrorCode MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt *i,PetscInt *j,PetscScalar *a,Mat *mat) 2436 { 2437 PetscErrorCode ierr; 2438 PetscInt ii; 2439 Mat_SeqSBAIJ *sbaij; 2440 2441 PetscFunctionBegin; 2442 if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs); 2443 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 2444 2445 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 2446 ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); 2447 ierr = MatSetType(*mat,MATSEQSBAIJ);CHKERRQ(ierr); 2448 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);CHKERRQ(ierr); 2449 sbaij = (Mat_SeqSBAIJ*)(*mat)->data; 2450 ierr = PetscMalloc2(m,&sbaij->imax,m,&sbaij->ilen);CHKERRQ(ierr); 2451 ierr = PetscLogObjectMemory((PetscObject)*mat,2*m*sizeof(PetscInt));CHKERRQ(ierr); 2452 2453 sbaij->i = i; 2454 sbaij->j = j; 2455 sbaij->a = a; 2456 2457 sbaij->singlemalloc = PETSC_FALSE; 2458 sbaij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/ 2459 sbaij->free_a = PETSC_FALSE; 2460 sbaij->free_ij = PETSC_FALSE; 2461 2462 for (ii=0; ii<m; ii++) { 2463 sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii]; 2464 #if defined(PETSC_USE_DEBUG) 2465 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]); 2466 #endif 2467 } 2468 #if defined(PETSC_USE_DEBUG) 2469 for (ii=0; ii<sbaij->i[m]; ii++) { 2470 if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]); 2471 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]); 2472 } 2473 #endif 2474 2475 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2476 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2477 PetscFunctionReturn(0); 2478 } 2479 2480 2481 2482 2483 2484