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 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 PetscErrorCode ierr; 1156 1157 PetscFunctionBegin; 1158 /* Set the number of nonzeros in the new matrix */ 1159 ierr = MatAXPYGetPreallocation_SeqX_private(mbs,x->i,x->j,y->i,y->j,nnz);CHKERRQ(ierr); 1160 PetscFunctionReturn(0); 1161 } 1162 1163 #undef __FUNCT__ 1164 #define __FUNCT__ "MatAXPY_SeqSBAIJ" 1165 PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 1166 { 1167 Mat_SeqSBAIJ *x=(Mat_SeqSBAIJ*)X->data, *y=(Mat_SeqSBAIJ*)Y->data; 1168 PetscErrorCode ierr; 1169 PetscInt i,bs=Y->rmap->bs,bs2=bs*bs,j; 1170 PetscBLASInt one = 1; 1171 1172 PetscFunctionBegin; 1173 if (str == SAME_NONZERO_PATTERN) { 1174 PetscScalar alpha = a; 1175 PetscBLASInt bnz; 1176 ierr = PetscBLASIntCast(x->nz*bs2,&bnz);CHKERRQ(ierr); 1177 PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one)); 1178 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 1179 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 1180 if (y->xtoy && y->XtoY != X) { 1181 ierr = PetscFree(y->xtoy);CHKERRQ(ierr); 1182 ierr = MatDestroy(&y->XtoY);CHKERRQ(ierr); 1183 } 1184 if (!y->xtoy) { /* get xtoy */ 1185 ierr = MatAXPYGetxtoy_Private(x->mbs,x->i,x->j,NULL, y->i,y->j,NULL, &y->xtoy);CHKERRQ(ierr); 1186 y->XtoY = X; 1187 } 1188 for (i=0; i<x->nz; i++) { 1189 j = 0; 1190 while (j < bs2) { 1191 y->a[bs2*y->xtoy[i]+j] += a*(x->a[bs2*i+j]); 1192 j++; 1193 } 1194 } 1195 ierr = PetscObjectStateIncrease((PetscObject)Y);CHKERRQ(ierr); 1196 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); 1197 } else { 1198 Mat B; 1199 PetscInt *nnz; 1200 if (bs != X->rmap->bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrices must have same block size"); 1201 ierr = MatGetRowUpperTriangular(X);CHKERRQ(ierr); 1202 ierr = MatGetRowUpperTriangular(Y);CHKERRQ(ierr); 1203 ierr = PetscMalloc1(Y->rmap->N,&nnz);CHKERRQ(ierr); 1204 ierr = MatCreate(PetscObjectComm((PetscObject)Y),&B);CHKERRQ(ierr); 1205 ierr = PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);CHKERRQ(ierr); 1206 ierr = MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);CHKERRQ(ierr); 1207 ierr = MatSetBlockSizesFromMats(B,Y,Y);CHKERRQ(ierr); 1208 ierr = MatSetType(B,(MatType) ((PetscObject)Y)->type_name);CHKERRQ(ierr); 1209 ierr = MatAXPYGetPreallocation_SeqSBAIJ(Y,X,nnz);CHKERRQ(ierr); 1210 ierr = MatSeqSBAIJSetPreallocation(B,bs,0,nnz);CHKERRQ(ierr); 1211 1212 ierr = MatAXPY_BasicWithPreallocation(B,Y,a,X,str);CHKERRQ(ierr); 1213 1214 ierr = MatHeaderReplace(Y,B);CHKERRQ(ierr); 1215 ierr = PetscFree(nnz);CHKERRQ(ierr); 1216 ierr = MatRestoreRowUpperTriangular(X);CHKERRQ(ierr); 1217 ierr = MatRestoreRowUpperTriangular(Y);CHKERRQ(ierr); 1218 } 1219 PetscFunctionReturn(0); 1220 } 1221 1222 #undef __FUNCT__ 1223 #define __FUNCT__ "MatIsSymmetric_SeqSBAIJ" 1224 PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1225 { 1226 PetscFunctionBegin; 1227 *flg = PETSC_TRUE; 1228 PetscFunctionReturn(0); 1229 } 1230 1231 #undef __FUNCT__ 1232 #define __FUNCT__ "MatIsStructurallySymmetric_SeqSBAIJ" 1233 PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool *flg) 1234 { 1235 PetscFunctionBegin; 1236 *flg = PETSC_TRUE; 1237 PetscFunctionReturn(0); 1238 } 1239 1240 #undef __FUNCT__ 1241 #define __FUNCT__ "MatIsHermitian_SeqSBAIJ" 1242 PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1243 { 1244 PetscFunctionBegin; 1245 *flg = PETSC_FALSE; 1246 PetscFunctionReturn(0); 1247 } 1248 1249 #undef __FUNCT__ 1250 #define __FUNCT__ "MatRealPart_SeqSBAIJ" 1251 PetscErrorCode MatRealPart_SeqSBAIJ(Mat A) 1252 { 1253 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1254 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1255 MatScalar *aa = a->a; 1256 1257 PetscFunctionBegin; 1258 for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]); 1259 PetscFunctionReturn(0); 1260 } 1261 1262 #undef __FUNCT__ 1263 #define __FUNCT__ "MatImaginaryPart_SeqSBAIJ" 1264 PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A) 1265 { 1266 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1267 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1268 MatScalar *aa = a->a; 1269 1270 PetscFunctionBegin; 1271 for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]); 1272 PetscFunctionReturn(0); 1273 } 1274 1275 #undef __FUNCT__ 1276 #define __FUNCT__ "MatZeroRowsColumns_SeqSBAIJ" 1277 PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b) 1278 { 1279 Mat_SeqSBAIJ *baij=(Mat_SeqSBAIJ*)A->data; 1280 PetscErrorCode ierr; 1281 PetscInt i,j,k,count; 1282 PetscInt bs =A->rmap->bs,bs2=baij->bs2,row,col; 1283 PetscScalar zero = 0.0; 1284 MatScalar *aa; 1285 const PetscScalar *xx; 1286 PetscScalar *bb; 1287 PetscBool *zeroed,vecs = PETSC_FALSE; 1288 1289 PetscFunctionBegin; 1290 /* fix right hand side if needed */ 1291 if (x && b) { 1292 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1293 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1294 vecs = PETSC_TRUE; 1295 } 1296 1297 /* zero the columns */ 1298 ierr = PetscCalloc1(A->rmap->n,&zeroed);CHKERRQ(ierr); 1299 for (i=0; i<is_n; i++) { 1300 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]); 1301 zeroed[is_idx[i]] = PETSC_TRUE; 1302 } 1303 if (vecs) { 1304 for (i=0; i<A->rmap->N; i++) { 1305 row = i/bs; 1306 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1307 for (k=0; k<bs; k++) { 1308 col = bs*baij->j[j] + k; 1309 if (col <= i) continue; 1310 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1311 if (!zeroed[i] && zeroed[col]) bb[i] -= aa[0]*xx[col]; 1312 if (zeroed[i] && !zeroed[col]) bb[col] -= aa[0]*xx[i]; 1313 } 1314 } 1315 } 1316 for (i=0; i<is_n; i++) bb[is_idx[i]] = diag*xx[is_idx[i]]; 1317 } 1318 1319 for (i=0; i<A->rmap->N; i++) { 1320 if (!zeroed[i]) { 1321 row = i/bs; 1322 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1323 for (k=0; k<bs; k++) { 1324 col = bs*baij->j[j] + k; 1325 if (zeroed[col]) { 1326 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1327 aa[0] = 0.0; 1328 } 1329 } 1330 } 1331 } 1332 } 1333 ierr = PetscFree(zeroed);CHKERRQ(ierr); 1334 if (vecs) { 1335 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1336 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1337 } 1338 1339 /* zero the rows */ 1340 for (i=0; i<is_n; i++) { 1341 row = is_idx[i]; 1342 count = (baij->i[row/bs +1] - baij->i[row/bs])*bs; 1343 aa = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs); 1344 for (k=0; k<count; k++) { 1345 aa[0] = zero; 1346 aa += bs; 1347 } 1348 if (diag != 0.0) { 1349 ierr = (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); 1350 } 1351 } 1352 ierr = MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1353 PetscFunctionReturn(0); 1354 } 1355 1356 /* -------------------------------------------------------------------*/ 1357 static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ, 1358 MatGetRow_SeqSBAIJ, 1359 MatRestoreRow_SeqSBAIJ, 1360 MatMult_SeqSBAIJ_N, 1361 /* 4*/ MatMultAdd_SeqSBAIJ_N, 1362 MatMult_SeqSBAIJ_N, /* transpose versions are same as non-transpose versions */ 1363 MatMultAdd_SeqSBAIJ_N, 1364 0, 1365 0, 1366 0, 1367 /* 10*/ 0, 1368 0, 1369 MatCholeskyFactor_SeqSBAIJ, 1370 MatSOR_SeqSBAIJ, 1371 MatTranspose_SeqSBAIJ, 1372 /* 15*/ MatGetInfo_SeqSBAIJ, 1373 MatEqual_SeqSBAIJ, 1374 MatGetDiagonal_SeqSBAIJ, 1375 MatDiagonalScale_SeqSBAIJ, 1376 MatNorm_SeqSBAIJ, 1377 /* 20*/ 0, 1378 MatAssemblyEnd_SeqSBAIJ, 1379 MatSetOption_SeqSBAIJ, 1380 MatZeroEntries_SeqSBAIJ, 1381 /* 24*/ 0, 1382 0, 1383 0, 1384 0, 1385 0, 1386 /* 29*/ MatSetUp_SeqSBAIJ, 1387 0, 1388 0, 1389 0, 1390 0, 1391 /* 34*/ MatDuplicate_SeqSBAIJ, 1392 0, 1393 0, 1394 0, 1395 MatICCFactor_SeqSBAIJ, 1396 /* 39*/ MatAXPY_SeqSBAIJ, 1397 MatGetSubMatrices_SeqSBAIJ, 1398 MatIncreaseOverlap_SeqSBAIJ, 1399 MatGetValues_SeqSBAIJ, 1400 MatCopy_SeqSBAIJ, 1401 /* 44*/ 0, 1402 MatScale_SeqSBAIJ, 1403 0, 1404 0, 1405 MatZeroRowsColumns_SeqSBAIJ, 1406 /* 49*/ 0, 1407 MatGetRowIJ_SeqSBAIJ, 1408 MatRestoreRowIJ_SeqSBAIJ, 1409 0, 1410 0, 1411 /* 54*/ 0, 1412 0, 1413 0, 1414 0, 1415 MatSetValuesBlocked_SeqSBAIJ, 1416 /* 59*/ MatGetSubMatrix_SeqSBAIJ, 1417 0, 1418 0, 1419 0, 1420 0, 1421 /* 64*/ 0, 1422 0, 1423 0, 1424 0, 1425 0, 1426 /* 69*/ MatGetRowMaxAbs_SeqSBAIJ, 1427 0, 1428 0, 1429 0, 1430 0, 1431 /* 74*/ 0, 1432 0, 1433 0, 1434 0, 1435 0, 1436 /* 79*/ 0, 1437 0, 1438 0, 1439 MatGetInertia_SeqSBAIJ, 1440 MatLoad_SeqSBAIJ, 1441 /* 84*/ MatIsSymmetric_SeqSBAIJ, 1442 MatIsHermitian_SeqSBAIJ, 1443 MatIsStructurallySymmetric_SeqSBAIJ, 1444 0, 1445 0, 1446 /* 89*/ 0, 1447 0, 1448 0, 1449 0, 1450 0, 1451 /* 94*/ 0, 1452 0, 1453 0, 1454 0, 1455 0, 1456 /* 99*/ 0, 1457 0, 1458 0, 1459 0, 1460 0, 1461 /*104*/ 0, 1462 MatRealPart_SeqSBAIJ, 1463 MatImaginaryPart_SeqSBAIJ, 1464 MatGetRowUpperTriangular_SeqSBAIJ, 1465 MatRestoreRowUpperTriangular_SeqSBAIJ, 1466 /*109*/ 0, 1467 0, 1468 0, 1469 0, 1470 MatMissingDiagonal_SeqSBAIJ, 1471 /*114*/ 0, 1472 0, 1473 0, 1474 0, 1475 0, 1476 /*119*/ 0, 1477 0, 1478 0, 1479 0, 1480 0, 1481 /*124*/ 0, 1482 0, 1483 0, 1484 0, 1485 0, 1486 /*129*/ 0, 1487 0, 1488 0, 1489 0, 1490 0, 1491 /*134*/ 0, 1492 0, 1493 0, 1494 0, 1495 0, 1496 /*139*/ 0, 1497 0, 1498 0 1499 }; 1500 1501 #undef __FUNCT__ 1502 #define __FUNCT__ "MatStoreValues_SeqSBAIJ" 1503 PetscErrorCode MatStoreValues_SeqSBAIJ(Mat mat) 1504 { 1505 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)mat->data; 1506 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1507 PetscErrorCode ierr; 1508 1509 PetscFunctionBegin; 1510 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1511 1512 /* allocate space for values if not already there */ 1513 if (!aij->saved_values) { 1514 ierr = PetscMalloc1((nz+1),&aij->saved_values);CHKERRQ(ierr); 1515 } 1516 1517 /* copy values over */ 1518 ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1519 PetscFunctionReturn(0); 1520 } 1521 1522 #undef __FUNCT__ 1523 #define __FUNCT__ "MatRetrieveValues_SeqSBAIJ" 1524 PetscErrorCode MatRetrieveValues_SeqSBAIJ(Mat mat) 1525 { 1526 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)mat->data; 1527 PetscErrorCode ierr; 1528 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1529 1530 PetscFunctionBegin; 1531 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1532 if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first"); 1533 1534 /* copy values over */ 1535 ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1536 PetscFunctionReturn(0); 1537 } 1538 1539 #undef __FUNCT__ 1540 #define __FUNCT__ "MatSeqSBAIJSetPreallocation_SeqSBAIJ" 1541 PetscErrorCode MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz) 1542 { 1543 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1544 PetscErrorCode ierr; 1545 PetscInt i,mbs,bs2; 1546 PetscBool skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE; 1547 1548 PetscFunctionBegin; 1549 if (nz >= 0 || nnz) realalloc = PETSC_TRUE; 1550 B->preallocated = PETSC_TRUE; 1551 1552 ierr = MatSetBlockSize(B,PetscAbs(bs));CHKERRQ(ierr); 1553 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 1554 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 1555 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 1556 1557 mbs = B->rmap->N/bs; 1558 bs2 = bs*bs; 1559 1560 if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize"); 1561 1562 if (nz == MAT_SKIP_ALLOCATION) { 1563 skipallocation = PETSC_TRUE; 1564 nz = 0; 1565 } 1566 1567 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3; 1568 if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz); 1569 if (nnz) { 1570 for (i=0; i<mbs; i++) { 1571 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]); 1572 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); 1573 } 1574 } 1575 1576 B->ops->mult = MatMult_SeqSBAIJ_N; 1577 B->ops->multadd = MatMultAdd_SeqSBAIJ_N; 1578 B->ops->multtranspose = MatMult_SeqSBAIJ_N; 1579 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N; 1580 1581 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);CHKERRQ(ierr); 1582 if (!flg) { 1583 switch (bs) { 1584 case 1: 1585 B->ops->mult = MatMult_SeqSBAIJ_1; 1586 B->ops->multadd = MatMultAdd_SeqSBAIJ_1; 1587 B->ops->multtranspose = MatMult_SeqSBAIJ_1; 1588 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1; 1589 break; 1590 case 2: 1591 B->ops->mult = MatMult_SeqSBAIJ_2; 1592 B->ops->multadd = MatMultAdd_SeqSBAIJ_2; 1593 B->ops->multtranspose = MatMult_SeqSBAIJ_2; 1594 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2; 1595 break; 1596 case 3: 1597 B->ops->mult = MatMult_SeqSBAIJ_3; 1598 B->ops->multadd = MatMultAdd_SeqSBAIJ_3; 1599 B->ops->multtranspose = MatMult_SeqSBAIJ_3; 1600 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3; 1601 break; 1602 case 4: 1603 B->ops->mult = MatMult_SeqSBAIJ_4; 1604 B->ops->multadd = MatMultAdd_SeqSBAIJ_4; 1605 B->ops->multtranspose = MatMult_SeqSBAIJ_4; 1606 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4; 1607 break; 1608 case 5: 1609 B->ops->mult = MatMult_SeqSBAIJ_5; 1610 B->ops->multadd = MatMultAdd_SeqSBAIJ_5; 1611 B->ops->multtranspose = MatMult_SeqSBAIJ_5; 1612 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5; 1613 break; 1614 case 6: 1615 B->ops->mult = MatMult_SeqSBAIJ_6; 1616 B->ops->multadd = MatMultAdd_SeqSBAIJ_6; 1617 B->ops->multtranspose = MatMult_SeqSBAIJ_6; 1618 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6; 1619 break; 1620 case 7: 1621 B->ops->mult = MatMult_SeqSBAIJ_7; 1622 B->ops->multadd = MatMultAdd_SeqSBAIJ_7; 1623 B->ops->multtranspose = MatMult_SeqSBAIJ_7; 1624 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7; 1625 break; 1626 } 1627 } 1628 1629 b->mbs = mbs; 1630 b->nbs = mbs; 1631 if (!skipallocation) { 1632 if (!b->imax) { 1633 ierr = PetscMalloc2(mbs,&b->imax,mbs,&b->ilen);CHKERRQ(ierr); 1634 1635 b->free_imax_ilen = PETSC_TRUE; 1636 1637 ierr = PetscLogObjectMemory((PetscObject)B,2*mbs*sizeof(PetscInt));CHKERRQ(ierr); 1638 } 1639 if (!nnz) { 1640 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5; 1641 else if (nz <= 0) nz = 1; 1642 for (i=0; i<mbs; i++) b->imax[i] = nz; 1643 nz = nz*mbs; /* total nz */ 1644 } else { 1645 nz = 0; 1646 for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];} 1647 } 1648 /* b->ilen will count nonzeros in each block row so far. */ 1649 for (i=0; i<mbs; i++) b->ilen[i] = 0; 1650 /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */ 1651 1652 /* allocate the matrix space */ 1653 ierr = MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);CHKERRQ(ierr); 1654 ierr = PetscMalloc3(bs2*nz,&b->a,nz,&b->j,B->rmap->N+1,&b->i);CHKERRQ(ierr); 1655 ierr = PetscLogObjectMemory((PetscObject)B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr); 1656 ierr = PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 1657 ierr = PetscMemzero(b->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 1658 1659 b->singlemalloc = PETSC_TRUE; 1660 1661 /* pointer to beginning of each row */ 1662 b->i[0] = 0; 1663 for (i=1; i<mbs+1; i++) b->i[i] = b->i[i-1] + b->imax[i-1]; 1664 1665 b->free_a = PETSC_TRUE; 1666 b->free_ij = PETSC_TRUE; 1667 } else { 1668 b->free_a = PETSC_FALSE; 1669 b->free_ij = PETSC_FALSE; 1670 } 1671 1672 B->rmap->bs = bs; 1673 b->bs2 = bs2; 1674 b->nz = 0; 1675 b->maxnz = nz; 1676 1677 b->inew = 0; 1678 b->jnew = 0; 1679 b->anew = 0; 1680 b->a2anew = 0; 1681 b->permute = PETSC_FALSE; 1682 if (realalloc) {ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);} 1683 PetscFunctionReturn(0); 1684 } 1685 1686 #undef __FUNCT__ 1687 #define __FUNCT__ "MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ" 1688 PetscErrorCode MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[], const PetscScalar V[]) 1689 { 1690 PetscInt i,j,m,nz,nz_max=0,*nnz; 1691 PetscScalar *values=0; 1692 PetscBool roworiented = ((Mat_SeqSBAIJ*)B->data)->roworiented; 1693 PetscErrorCode ierr; 1694 PetscFunctionBegin; 1695 if (bs < 1) SETERRQ1(PetscObjectComm((PetscObject)B),PETSC_ERR_ARG_OUTOFRANGE,"Invalid block size specified, must be positive but it is %D",bs); 1696 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 1697 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 1698 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 1699 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 1700 ierr = PetscLayoutGetBlockSize(B->rmap,&bs);CHKERRQ(ierr); 1701 m = B->rmap->n/bs; 1702 1703 if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]); 1704 ierr = PetscMalloc1((m+1),&nnz);CHKERRQ(ierr); 1705 for (i=0; i<m; i++) { 1706 nz = ii[i+1] - ii[i]; 1707 if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D has a negative number of columns %D",i,nz); 1708 nz_max = PetscMax(nz_max,nz); 1709 nnz[i] = nz; 1710 } 1711 ierr = MatSeqSBAIJSetPreallocation(B,bs,0,nnz);CHKERRQ(ierr); 1712 ierr = PetscFree(nnz);CHKERRQ(ierr); 1713 1714 values = (PetscScalar*)V; 1715 if (!values) { 1716 ierr = PetscCalloc1(bs*bs*nz_max,&values);CHKERRQ(ierr); 1717 } 1718 for (i=0; i<m; i++) { 1719 PetscInt ncols = ii[i+1] - ii[i]; 1720 const PetscInt *icols = jj + ii[i]; 1721 if (!roworiented || bs == 1) { 1722 const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0); 1723 ierr = MatSetValuesBlocked_SeqSBAIJ(B,1,&i,ncols,icols,svals,INSERT_VALUES);CHKERRQ(ierr); 1724 } else { 1725 for (j=0; j<ncols; j++) { 1726 const PetscScalar *svals = values + (V ? (bs*bs*(ii[i]+j)) : 0); 1727 ierr = MatSetValuesBlocked_SeqSBAIJ(B,1,&i,1,&icols[j],svals,INSERT_VALUES);CHKERRQ(ierr); 1728 } 1729 } 1730 } 1731 if (!V) { ierr = PetscFree(values);CHKERRQ(ierr); } 1732 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1733 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1734 ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 1735 PetscFunctionReturn(0); 1736 } 1737 1738 /* 1739 This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization 1740 */ 1741 #undef __FUNCT__ 1742 #define __FUNCT__ "MatSeqSBAIJSetNumericFactorization_inplace" 1743 PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural) 1744 { 1745 PetscErrorCode ierr; 1746 PetscBool flg = PETSC_FALSE; 1747 PetscInt bs = B->rmap->bs; 1748 1749 PetscFunctionBegin; 1750 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);CHKERRQ(ierr); 1751 if (flg) bs = 8; 1752 1753 if (!natural) { 1754 switch (bs) { 1755 case 1: 1756 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace; 1757 break; 1758 case 2: 1759 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2; 1760 break; 1761 case 3: 1762 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3; 1763 break; 1764 case 4: 1765 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4; 1766 break; 1767 case 5: 1768 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5; 1769 break; 1770 case 6: 1771 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6; 1772 break; 1773 case 7: 1774 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7; 1775 break; 1776 default: 1777 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N; 1778 break; 1779 } 1780 } else { 1781 switch (bs) { 1782 case 1: 1783 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace; 1784 break; 1785 case 2: 1786 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering; 1787 break; 1788 case 3: 1789 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering; 1790 break; 1791 case 4: 1792 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering; 1793 break; 1794 case 5: 1795 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering; 1796 break; 1797 case 6: 1798 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering; 1799 break; 1800 case 7: 1801 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering; 1802 break; 1803 default: 1804 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering; 1805 break; 1806 } 1807 } 1808 PetscFunctionReturn(0); 1809 } 1810 1811 PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*); 1812 PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*); 1813 1814 #undef __FUNCT__ 1815 #define __FUNCT__ "MatGetFactor_seqsbaij_petsc" 1816 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B) 1817 { 1818 PetscInt n = A->rmap->n; 1819 PetscErrorCode ierr; 1820 1821 PetscFunctionBegin; 1822 #if defined(PETSC_USE_COMPLEX) 1823 if (A->hermitian) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported"); 1824 #endif 1825 ierr = MatCreate(PetscObjectComm((PetscObject)A),B);CHKERRQ(ierr); 1826 ierr = MatSetSizes(*B,n,n,n,n);CHKERRQ(ierr); 1827 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1828 ierr = MatSetType(*B,MATSEQSBAIJ);CHKERRQ(ierr); 1829 ierr = MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,NULL);CHKERRQ(ierr); 1830 1831 (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ; 1832 (*B)->ops->iccfactorsymbolic = MatICCFactorSymbolic_SeqSBAIJ; 1833 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported"); 1834 (*B)->factortype = ftype; 1835 PetscFunctionReturn(0); 1836 } 1837 1838 #undef __FUNCT__ 1839 #define __FUNCT__ "MatGetFactorAvailable_seqsbaij_petsc" 1840 PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool *flg) 1841 { 1842 PetscFunctionBegin; 1843 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1844 *flg = PETSC_TRUE; 1845 } else { 1846 *flg = PETSC_FALSE; 1847 } 1848 PetscFunctionReturn(0); 1849 } 1850 1851 #if defined(PETSC_HAVE_MUMPS) 1852 PETSC_EXTERN PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*); 1853 #endif 1854 #if defined(PETSC_HAVE_PASTIX) 1855 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*); 1856 #endif 1857 #if defined(PETSC_HAVE_SUITESPARSE) 1858 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*); 1859 #endif 1860 PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_sbstrm(Mat,MatFactorType,Mat*); 1861 1862 /*MC 1863 MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices, 1864 based on block compressed sparse row format. Only the upper triangular portion of the matrix is stored. 1865 1866 For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you 1867 can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd() 1868 1869 Options Database Keys: 1870 . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions() 1871 1872 Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not 1873 stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use 1874 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. 1875 1876 1877 Level: beginner 1878 1879 .seealso: MatCreateSeqSBAIJ 1880 M*/ 1881 1882 PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*); 1883 1884 #undef __FUNCT__ 1885 #define __FUNCT__ "MatCreate_SeqSBAIJ" 1886 PETSC_EXTERN PetscErrorCode MatCreate_SeqSBAIJ(Mat B) 1887 { 1888 Mat_SeqSBAIJ *b; 1889 PetscErrorCode ierr; 1890 PetscMPIInt size; 1891 PetscBool no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE; 1892 1893 PetscFunctionBegin; 1894 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);CHKERRQ(ierr); 1895 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1"); 1896 1897 ierr = PetscNewLog(B,&b);CHKERRQ(ierr); 1898 B->data = (void*)b; 1899 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 1900 1901 B->ops->destroy = MatDestroy_SeqSBAIJ; 1902 B->ops->view = MatView_SeqSBAIJ; 1903 b->row = 0; 1904 b->icol = 0; 1905 b->reallocs = 0; 1906 b->saved_values = 0; 1907 b->inode.limit = 5; 1908 b->inode.max_limit = 5; 1909 1910 b->roworiented = PETSC_TRUE; 1911 b->nonew = 0; 1912 b->diag = 0; 1913 b->solve_work = 0; 1914 b->mult_work = 0; 1915 B->spptr = 0; 1916 B->info.nz_unneeded = (PetscReal)b->maxnz*b->bs2; 1917 b->keepnonzeropattern = PETSC_FALSE; 1918 b->xtoy = 0; 1919 b->XtoY = 0; 1920 1921 b->inew = 0; 1922 b->jnew = 0; 1923 b->anew = 0; 1924 b->a2anew = 0; 1925 b->permute = PETSC_FALSE; 1926 1927 b->ignore_ltriangular = PETSC_TRUE; 1928 1929 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,NULL);CHKERRQ(ierr); 1930 1931 b->getrow_utriangular = PETSC_FALSE; 1932 1933 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,NULL);CHKERRQ(ierr); 1934 1935 #if defined(PETSC_HAVE_PASTIX) 1936 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_pastix_C",MatGetFactor_seqsbaij_pastix);CHKERRQ(ierr); 1937 #endif 1938 #if defined(PETSC_HAVE_MUMPS) 1939 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_mumps_C",MatGetFactor_sbaij_mumps);CHKERRQ(ierr); 1940 #endif 1941 #if defined(PETSC_HAVE_SUITESPARSE) 1942 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_cholmod_C",MatGetFactor_seqsbaij_cholmod);CHKERRQ(ierr); 1943 #endif 1944 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactorAvailable_petsc_C",MatGetFactorAvailable_seqsbaij_petsc);CHKERRQ(ierr); 1945 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_petsc_C",MatGetFactor_seqsbaij_petsc);CHKERRQ(ierr); 1946 ierr = PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_sbstrm_C",MatGetFactor_seqsbaij_sbstrm);CHKERRQ(ierr); 1947 ierr = PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqSBAIJ);CHKERRQ(ierr); 1948 ierr = PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqSBAIJ);CHKERRQ(ierr); 1949 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",MatSeqSBAIJSetColumnIndices_SeqSBAIJ);CHKERRQ(ierr); 1950 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",MatConvert_SeqSBAIJ_SeqAIJ);CHKERRQ(ierr); 1951 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",MatConvert_SeqSBAIJ_SeqBAIJ);CHKERRQ(ierr); 1952 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",MatSeqSBAIJSetPreallocation_SeqSBAIJ);CHKERRQ(ierr); 1953 ierr = PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocationCSR_C",MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ);CHKERRQ(ierr); 1954 ierr = PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C",MatConvert_SeqSBAIJ_SeqSBSTRM);CHKERRQ(ierr); 1955 1956 B->symmetric = PETSC_TRUE; 1957 B->structurally_symmetric = PETSC_TRUE; 1958 B->symmetric_set = PETSC_TRUE; 1959 B->structurally_symmetric_set = PETSC_TRUE; 1960 1961 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);CHKERRQ(ierr); 1962 1963 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)B),((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");CHKERRQ(ierr); 1964 ierr = PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",NULL,no_unroll,&no_unroll,NULL);CHKERRQ(ierr); 1965 if (no_unroll) { 1966 ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");CHKERRQ(ierr); 1967 } 1968 ierr = PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",NULL,no_inode,&no_inode,NULL);CHKERRQ(ierr); 1969 if (no_inode) { 1970 ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");CHKERRQ(ierr); 1971 } 1972 ierr = PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",NULL,b->inode.limit,&b->inode.limit,NULL);CHKERRQ(ierr); 1973 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1974 b->inode.use = (PetscBool)(!(no_unroll || no_inode)); 1975 if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit; 1976 PetscFunctionReturn(0); 1977 } 1978 1979 #undef __FUNCT__ 1980 #define __FUNCT__ "MatSeqSBAIJSetPreallocation" 1981 /*@C 1982 MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block 1983 compressed row) format. For good matrix assembly performance the 1984 user should preallocate the matrix storage by setting the parameter nz 1985 (or the array nnz). By setting these parameters accurately, performance 1986 during matrix assembly can be increased by more than a factor of 50. 1987 1988 Collective on Mat 1989 1990 Input Parameters: 1991 + B - the symmetric matrix 1992 . bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row 1993 blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs() 1994 . nz - number of block nonzeros per block row (same for all rows) 1995 - nnz - array containing the number of block nonzeros in the upper triangular plus 1996 diagonal portion of each block (possibly different for each block row) or NULL 1997 1998 Options Database Keys: 1999 . -mat_no_unroll - uses code that does not unroll the loops in the 2000 block calculations (much slower) 2001 . -mat_block_size - size of the blocks to use (only works if a negative bs is passed in 2002 2003 Level: intermediate 2004 2005 Notes: 2006 Specify the preallocated storage with either nz or nnz (not both). 2007 Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory 2008 allocation. See Users-Manual: ch_mat for details. 2009 2010 You can call MatGetInfo() to get information on how effective the preallocation was; 2011 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 2012 You can also run with the option -info and look for messages with the string 2013 malloc in them to see if additional memory allocation was needed. 2014 2015 If the nnz parameter is given then the nz parameter is ignored 2016 2017 2018 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() 2019 @*/ 2020 PetscErrorCode MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[]) 2021 { 2022 PetscErrorCode ierr; 2023 2024 PetscFunctionBegin; 2025 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2026 PetscValidType(B,1); 2027 PetscValidLogicalCollectiveInt(B,bs,2); 2028 ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));CHKERRQ(ierr); 2029 PetscFunctionReturn(0); 2030 } 2031 2032 #undef __FUNCT__ 2033 #define __FUNCT__ "MatSeqSBAIJSetPreallocationCSR" 2034 /*@C 2035 MatSeqSBAIJSetPreallocationCSR - Allocates memory for a sparse sequential matrix in symmetric block AIJ format. 2036 2037 Input Parameters: 2038 + B - the matrix 2039 . i - the indices into j for the start of each local row (starts with zero) 2040 . j - the column indices for each local row (starts with zero) these must be sorted for each row 2041 - v - optional values in the matrix 2042 2043 Level: developer 2044 2045 Notes: 2046 The order of the entries in values is specified by the MatOption MAT_ROW_ORIENTED. For example, C programs 2047 may want to use the default MAT_ROW_ORIENTED=PETSC_TRUE and use an array v[nnz][bs][bs] where the second index is 2048 over rows within a block and the last index is over columns within a block row. Fortran programs will likely set 2049 MAT_ROW_ORIENTED=PETSC_FALSE and use a Fortran array v(bs,bs,nnz) in which the first index is over rows within a 2050 block column and the second index is over columns within a block. 2051 2052 .keywords: matrix, block, aij, compressed row, sparse 2053 2054 .seealso: MatCreate(), MatCreateSeqSBAIJ(), MatSetValuesBlocked(), MatSeqSBAIJSetPreallocation(), MATSEQSBAIJ 2055 @*/ 2056 PetscErrorCode MatSeqSBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[]) 2057 { 2058 PetscErrorCode ierr; 2059 2060 PetscFunctionBegin; 2061 PetscValidHeaderSpecific(B,MAT_CLASSID,1); 2062 PetscValidType(B,1); 2063 PetscValidLogicalCollectiveInt(B,bs,2); 2064 ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));CHKERRQ(ierr); 2065 PetscFunctionReturn(0); 2066 } 2067 2068 #undef __FUNCT__ 2069 #define __FUNCT__ "MatCreateSeqSBAIJ" 2070 /*@C 2071 MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block 2072 compressed row) format. For good matrix assembly performance the 2073 user should preallocate the matrix storage by setting the parameter nz 2074 (or the array nnz). By setting these parameters accurately, performance 2075 during matrix assembly can be increased by more than a factor of 50. 2076 2077 Collective on MPI_Comm 2078 2079 Input Parameters: 2080 + comm - MPI communicator, set to PETSC_COMM_SELF 2081 . bs - size of block, the blocks are ALWAYS square. One can use MatSetBlockSizes() to set a different row and column blocksize but the row 2082 blocksize always defines the size of the blocks. The column blocksize sets the blocksize of the vectors obtained with MatCreateVecs() 2083 . m - number of rows, or number of columns 2084 . nz - number of block nonzeros per block row (same for all rows) 2085 - nnz - array containing the number of block nonzeros in the upper triangular plus 2086 diagonal portion of each block (possibly different for each block row) or NULL 2087 2088 Output Parameter: 2089 . A - the symmetric matrix 2090 2091 Options Database Keys: 2092 . -mat_no_unroll - uses code that does not unroll the loops in the 2093 block calculations (much slower) 2094 . -mat_block_size - size of the blocks to use 2095 2096 Level: intermediate 2097 2098 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 2099 MatXXXXSetPreallocation() paradgm instead of this routine directly. 2100 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 2101 2102 Notes: 2103 The number of rows and columns must be divisible by blocksize. 2104 This matrix type does not support complex Hermitian operation. 2105 2106 Specify the preallocated storage with either nz or nnz (not both). 2107 Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory 2108 allocation. See Users-Manual: ch_mat for details. 2109 2110 If the nnz parameter is given then the nz parameter is ignored 2111 2112 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ() 2113 @*/ 2114 PetscErrorCode MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A) 2115 { 2116 PetscErrorCode ierr; 2117 2118 PetscFunctionBegin; 2119 ierr = MatCreate(comm,A);CHKERRQ(ierr); 2120 ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); 2121 ierr = MatSetType(*A,MATSEQSBAIJ);CHKERRQ(ierr); 2122 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);CHKERRQ(ierr); 2123 PetscFunctionReturn(0); 2124 } 2125 2126 #undef __FUNCT__ 2127 #define __FUNCT__ "MatDuplicate_SeqSBAIJ" 2128 PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B) 2129 { 2130 Mat C; 2131 Mat_SeqSBAIJ *c,*a = (Mat_SeqSBAIJ*)A->data; 2132 PetscErrorCode ierr; 2133 PetscInt i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2; 2134 2135 PetscFunctionBegin; 2136 if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix"); 2137 2138 *B = 0; 2139 ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr); 2140 ierr = MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);CHKERRQ(ierr); 2141 ierr = MatSetType(C,MATSEQSBAIJ);CHKERRQ(ierr); 2142 ierr = PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2143 c = (Mat_SeqSBAIJ*)C->data; 2144 2145 C->preallocated = PETSC_TRUE; 2146 C->factortype = A->factortype; 2147 c->row = 0; 2148 c->icol = 0; 2149 c->saved_values = 0; 2150 c->keepnonzeropattern = a->keepnonzeropattern; 2151 C->assembled = PETSC_TRUE; 2152 2153 ierr = PetscLayoutReference(A->rmap,&C->rmap);CHKERRQ(ierr); 2154 ierr = PetscLayoutReference(A->cmap,&C->cmap);CHKERRQ(ierr); 2155 c->bs2 = a->bs2; 2156 c->mbs = a->mbs; 2157 c->nbs = a->nbs; 2158 2159 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2160 c->imax = a->imax; 2161 c->ilen = a->ilen; 2162 c->free_imax_ilen = PETSC_FALSE; 2163 } else { 2164 ierr = PetscMalloc2((mbs+1),&c->imax,(mbs+1),&c->ilen);CHKERRQ(ierr); 2165 ierr = PetscLogObjectMemory((PetscObject)C,2*(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2166 for (i=0; i<mbs; i++) { 2167 c->imax[i] = a->imax[i]; 2168 c->ilen[i] = a->ilen[i]; 2169 } 2170 c->free_imax_ilen = PETSC_TRUE; 2171 } 2172 2173 /* allocate the matrix space */ 2174 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2175 ierr = PetscMalloc1(bs2*nz,&c->a);CHKERRQ(ierr); 2176 ierr = PetscLogObjectMemory((PetscObject)C,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 2177 c->i = a->i; 2178 c->j = a->j; 2179 c->singlemalloc = PETSC_FALSE; 2180 c->free_a = PETSC_TRUE; 2181 c->free_ij = PETSC_FALSE; 2182 c->parent = A; 2183 ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr); 2184 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2185 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2186 } else { 2187 ierr = PetscMalloc3(bs2*nz,&c->a,nz,&c->j,mbs+1,&c->i);CHKERRQ(ierr); 2188 ierr = PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2189 ierr = PetscLogObjectMemory((PetscObject)C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));CHKERRQ(ierr); 2190 c->singlemalloc = PETSC_TRUE; 2191 c->free_a = PETSC_TRUE; 2192 c->free_ij = PETSC_TRUE; 2193 } 2194 if (mbs > 0) { 2195 if (cpvalues != MAT_SHARE_NONZERO_PATTERN) { 2196 ierr = PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 2197 } 2198 if (cpvalues == MAT_COPY_VALUES) { 2199 ierr = PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2200 } else { 2201 ierr = PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2202 } 2203 if (a->jshort) { 2204 /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */ 2205 /* if the parent matrix is reassembled, this child matrix will never notice */ 2206 ierr = PetscMalloc1(nz,&c->jshort);CHKERRQ(ierr); 2207 ierr = PetscLogObjectMemory((PetscObject)C,nz*sizeof(unsigned short));CHKERRQ(ierr); 2208 ierr = PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));CHKERRQ(ierr); 2209 2210 c->free_jshort = PETSC_TRUE; 2211 } 2212 } 2213 2214 c->roworiented = a->roworiented; 2215 c->nonew = a->nonew; 2216 2217 if (a->diag) { 2218 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2219 c->diag = a->diag; 2220 c->free_diag = PETSC_FALSE; 2221 } else { 2222 ierr = PetscMalloc1(mbs,&c->diag);CHKERRQ(ierr); 2223 ierr = PetscLogObjectMemory((PetscObject)C,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2224 for (i=0; i<mbs; i++) c->diag[i] = a->diag[i]; 2225 c->free_diag = PETSC_TRUE; 2226 } 2227 } 2228 c->nz = a->nz; 2229 c->maxnz = a->nz; /* Since we allocate exactly the right amount */ 2230 c->solve_work = 0; 2231 c->mult_work = 0; 2232 2233 *B = C; 2234 ierr = PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);CHKERRQ(ierr); 2235 PetscFunctionReturn(0); 2236 } 2237 2238 #undef __FUNCT__ 2239 #define __FUNCT__ "MatLoad_SeqSBAIJ" 2240 PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer) 2241 { 2242 Mat_SeqSBAIJ *a; 2243 PetscErrorCode ierr; 2244 int fd; 2245 PetscMPIInt size; 2246 PetscInt i,nz,header[4],*rowlengths=0,M,N,bs=1; 2247 PetscInt *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount; 2248 PetscInt kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols; 2249 PetscInt *masked,nmask,tmp,bs2,ishift; 2250 PetscScalar *aa; 2251 MPI_Comm comm; 2252 2253 PetscFunctionBegin; 2254 ierr = PetscObjectGetComm((PetscObject)viewer,&comm);CHKERRQ(ierr); 2255 ierr = PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,NULL);CHKERRQ(ierr); 2256 bs2 = bs*bs; 2257 2258 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2259 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor"); 2260 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2261 ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr); 2262 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object"); 2263 M = header[1]; N = header[2]; nz = header[3]; 2264 2265 if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ"); 2266 2267 if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices"); 2268 2269 /* 2270 This code adds extra rows to make sure the number of rows is 2271 divisible by the blocksize 2272 */ 2273 mbs = M/bs; 2274 extra_rows = bs - M + bs*(mbs); 2275 if (extra_rows == bs) extra_rows = 0; 2276 else mbs++; 2277 if (extra_rows) { 2278 ierr = PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");CHKERRQ(ierr); 2279 } 2280 2281 /* Set global sizes if not already set */ 2282 if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) { 2283 ierr = MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);CHKERRQ(ierr); 2284 } else { /* Check if the matrix global sizes are correct */ 2285 ierr = MatGetSize(newmat,&rows,&cols);CHKERRQ(ierr); 2286 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); 2287 } 2288 2289 /* read in row lengths */ 2290 ierr = PetscMalloc1((M+extra_rows),&rowlengths);CHKERRQ(ierr); 2291 ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); 2292 for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1; 2293 2294 /* read in column indices */ 2295 ierr = PetscMalloc1((nz+extra_rows),&jj);CHKERRQ(ierr); 2296 ierr = PetscBinaryRead(fd,jj,nz,PETSC_INT);CHKERRQ(ierr); 2297 for (i=0; i<extra_rows; i++) jj[nz+i] = M+i; 2298 2299 /* loop over row lengths determining block row lengths */ 2300 ierr = PetscCalloc1(mbs,&s_browlengths);CHKERRQ(ierr); 2301 ierr = PetscMalloc2(mbs,&mask,mbs,&masked);CHKERRQ(ierr); 2302 ierr = PetscMemzero(mask,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2303 rowcount = 0; 2304 nzcount = 0; 2305 for (i=0; i<mbs; i++) { 2306 nmask = 0; 2307 for (j=0; j<bs; j++) { 2308 kmax = rowlengths[rowcount]; 2309 for (k=0; k<kmax; k++) { 2310 tmp = jj[nzcount++]/bs; /* block col. index */ 2311 if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;} 2312 } 2313 rowcount++; 2314 } 2315 s_browlengths[i] += nmask; 2316 2317 /* zero out the mask elements we set */ 2318 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2319 } 2320 2321 /* Do preallocation */ 2322 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);CHKERRQ(ierr); 2323 a = (Mat_SeqSBAIJ*)newmat->data; 2324 2325 /* set matrix "i" values */ 2326 a->i[0] = 0; 2327 for (i=1; i<= mbs; i++) { 2328 a->i[i] = a->i[i-1] + s_browlengths[i-1]; 2329 a->ilen[i-1] = s_browlengths[i-1]; 2330 } 2331 a->nz = a->i[mbs]; 2332 2333 /* read in nonzero values */ 2334 ierr = PetscMalloc1((nz+extra_rows),&aa);CHKERRQ(ierr); 2335 ierr = PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);CHKERRQ(ierr); 2336 for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0; 2337 2338 /* set "a" and "j" values into matrix */ 2339 nzcount = 0; jcount = 0; 2340 for (i=0; i<mbs; i++) { 2341 nzcountb = nzcount; 2342 nmask = 0; 2343 for (j=0; j<bs; j++) { 2344 kmax = rowlengths[i*bs+j]; 2345 for (k=0; k<kmax; k++) { 2346 tmp = jj[nzcount++]/bs; /* block col. index */ 2347 if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;} 2348 } 2349 } 2350 /* sort the masked values */ 2351 ierr = PetscSortInt(nmask,masked);CHKERRQ(ierr); 2352 2353 /* set "j" values into matrix */ 2354 maskcount = 1; 2355 for (j=0; j<nmask; j++) { 2356 a->j[jcount++] = masked[j]; 2357 mask[masked[j]] = maskcount++; 2358 } 2359 2360 /* set "a" values into matrix */ 2361 ishift = bs2*a->i[i]; 2362 for (j=0; j<bs; j++) { 2363 kmax = rowlengths[i*bs+j]; 2364 for (k=0; k<kmax; k++) { 2365 tmp = jj[nzcountb]/bs; /* block col. index */ 2366 if (tmp >= i) { 2367 block = mask[tmp] - 1; 2368 point = jj[nzcountb] - bs*tmp; 2369 idx = ishift + bs2*block + j + bs*point; 2370 a->a[idx] = aa[nzcountb]; 2371 } 2372 nzcountb++; 2373 } 2374 } 2375 /* zero out the mask elements we set */ 2376 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2377 } 2378 if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix"); 2379 2380 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2381 ierr = PetscFree(s_browlengths);CHKERRQ(ierr); 2382 ierr = PetscFree(aa);CHKERRQ(ierr); 2383 ierr = PetscFree(jj);CHKERRQ(ierr); 2384 ierr = PetscFree2(mask,masked);CHKERRQ(ierr); 2385 2386 ierr = MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2387 ierr = MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2388 PetscFunctionReturn(0); 2389 } 2390 2391 #undef __FUNCT__ 2392 #define __FUNCT__ "MatCreateSeqSBAIJWithArrays" 2393 /*@ 2394 MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements 2395 (upper triangular entries in CSR format) provided by the user. 2396 2397 Collective on MPI_Comm 2398 2399 Input Parameters: 2400 + comm - must be an MPI communicator of size 1 2401 . bs - size of block 2402 . m - number of rows 2403 . n - number of columns 2404 . i - row indices 2405 . j - column indices 2406 - a - matrix values 2407 2408 Output Parameter: 2409 . mat - the matrix 2410 2411 Level: advanced 2412 2413 Notes: 2414 The i, j, and a arrays are not copied by this routine, the user must free these arrays 2415 once the matrix is destroyed 2416 2417 You cannot set new nonzero locations into this matrix, that will generate an error. 2418 2419 The i and j indices are 0 based 2420 2421 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 2422 it is the regular CSR format excluding the lower triangular elements. 2423 2424 .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ() 2425 2426 @*/ 2427 PetscErrorCode MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt *i,PetscInt *j,PetscScalar *a,Mat *mat) 2428 { 2429 PetscErrorCode ierr; 2430 PetscInt ii; 2431 Mat_SeqSBAIJ *sbaij; 2432 2433 PetscFunctionBegin; 2434 if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs); 2435 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 2436 2437 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 2438 ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); 2439 ierr = MatSetType(*mat,MATSEQSBAIJ);CHKERRQ(ierr); 2440 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);CHKERRQ(ierr); 2441 sbaij = (Mat_SeqSBAIJ*)(*mat)->data; 2442 ierr = PetscMalloc2(m,&sbaij->imax,m,&sbaij->ilen);CHKERRQ(ierr); 2443 ierr = PetscLogObjectMemory((PetscObject)*mat,2*m*sizeof(PetscInt));CHKERRQ(ierr); 2444 2445 sbaij->i = i; 2446 sbaij->j = j; 2447 sbaij->a = a; 2448 2449 sbaij->singlemalloc = PETSC_FALSE; 2450 sbaij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/ 2451 sbaij->free_a = PETSC_FALSE; 2452 sbaij->free_ij = PETSC_FALSE; 2453 2454 for (ii=0; ii<m; ii++) { 2455 sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii]; 2456 #if defined(PETSC_USE_DEBUG) 2457 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]); 2458 #endif 2459 } 2460 #if defined(PETSC_USE_DEBUG) 2461 for (ii=0; ii<sbaij->i[m]; ii++) { 2462 if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]); 2463 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]); 2464 } 2465 #endif 2466 2467 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2468 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2469 PetscFunctionReturn(0); 2470 } 2471 2472 2473 2474 2475 2476