1 #define PETSCMAT_DLL 2 3 /* 4 Defines the basic matrix operations for the SBAIJ (compressed row) 5 matrix storage format. 6 */ 7 #include "../src/mat/impls/baij/seq/baij.h" /*I "petscmat.h" I*/ 8 #include "../src/mat/impls/sbaij/seq/sbaij.h" 9 #include "petscblaslapack.h" 10 11 #include "../src/mat/impls/sbaij/seq/relax.h" 12 #define USESHORT 13 #include "../src/mat/impls/sbaij/seq/relax.h" 14 15 extern PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat,PetscBool ); 16 17 /* 18 Checks for missing diagonals 19 */ 20 #undef __FUNCT__ 21 #define __FUNCT__ "MatMissingDiagonal_SeqSBAIJ" 22 PetscErrorCode MatMissingDiagonal_SeqSBAIJ(Mat A,PetscBool *missing,PetscInt *dd) 23 { 24 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 25 PetscErrorCode ierr; 26 PetscInt *diag,*jj = a->j,i; 27 28 PetscFunctionBegin; 29 ierr = MatMarkDiagonal_SeqSBAIJ(A);CHKERRQ(ierr); 30 diag = a->diag; 31 *missing = PETSC_FALSE; 32 for (i=0; i<a->mbs; i++) { 33 if (jj[diag[i]] != i) { 34 *missing = PETSC_TRUE; 35 if (dd) *dd = i; 36 break; 37 } 38 } 39 PetscFunctionReturn(0); 40 } 41 42 #undef __FUNCT__ 43 #define __FUNCT__ "MatMarkDiagonal_SeqSBAIJ" 44 PetscErrorCode MatMarkDiagonal_SeqSBAIJ(Mat A) 45 { 46 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 47 PetscErrorCode ierr; 48 PetscInt i; 49 50 PetscFunctionBegin; 51 if (!a->diag) { 52 ierr = PetscMalloc(a->mbs*sizeof(PetscInt),&a->diag);CHKERRQ(ierr); 53 ierr = PetscLogObjectMemory(A,a->mbs*sizeof(PetscInt));CHKERRQ(ierr); 54 a->free_diag = PETSC_TRUE; 55 } 56 for (i=0; i<a->mbs; i++) a->diag[i] = a->i[i]; 57 PetscFunctionReturn(0); 58 } 59 60 #undef __FUNCT__ 61 #define __FUNCT__ "MatGetRowIJ_SeqSBAIJ" 62 static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscBool *done) 63 { 64 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 65 PetscInt i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs; 66 PetscErrorCode ierr; 67 68 PetscFunctionBegin; 69 *nn = n; 70 if (!ia) PetscFunctionReturn(0); 71 if (!blockcompressed) { 72 /* malloc & create the natural set of indices */ 73 ierr = PetscMalloc2((n+1)*bs,PetscInt,ia,nz*bs,PetscInt,ja);CHKERRQ(ierr); 74 for (i=0; i<n+1; i++) { 75 for (j=0; j<bs; j++) { 76 *ia[i*bs+j] = a->i[i]*bs+j+oshift; 77 } 78 } 79 for (i=0; i<nz; i++) { 80 for (j=0; j<bs; j++) { 81 *ja[i*bs+j] = a->j[i]*bs+j+oshift; 82 } 83 } 84 } else { /* blockcompressed */ 85 if (oshift == 1) { 86 /* temporarily add 1 to i and j indices */ 87 for (i=0; i<nz; i++) a->j[i]++; 88 for (i=0; i<n+1; i++) a->i[i]++; 89 } 90 *ia = a->i; *ja = a->j; 91 } 92 93 PetscFunctionReturn(0); 94 } 95 96 #undef __FUNCT__ 97 #define __FUNCT__ "MatRestoreRowIJ_SeqSBAIJ" 98 static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscBool *done) 99 { 100 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 101 PetscInt i,n = a->mbs,nz = a->i[n]; 102 PetscErrorCode ierr; 103 104 PetscFunctionBegin; 105 if (!ia) PetscFunctionReturn(0); 106 107 if (!blockcompressed) { 108 ierr = PetscFree2(*ia,*ja);CHKERRQ(ierr); 109 } else if (oshift == 1) { /* blockcompressed */ 110 for (i=0; i<nz; i++) a->j[i]--; 111 for (i=0; i<n+1; i++) a->i[i]--; 112 } 113 114 PetscFunctionReturn(0); 115 } 116 117 #undef __FUNCT__ 118 #define __FUNCT__ "MatDestroy_SeqSBAIJ" 119 PetscErrorCode MatDestroy_SeqSBAIJ(Mat A) 120 { 121 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 122 PetscErrorCode ierr; 123 124 PetscFunctionBegin; 125 #if defined(PETSC_USE_LOG) 126 PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz); 127 #endif 128 ierr = MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);CHKERRQ(ierr); 129 if (a->free_diag){ierr = PetscFree(a->diag);CHKERRQ(ierr);} 130 if (a->row) {ierr = ISDestroy(a->row);CHKERRQ(ierr);} 131 if (a->col){ierr = ISDestroy(a->col);CHKERRQ(ierr);} 132 if (a->icol) {ierr = ISDestroy(a->icol);CHKERRQ(ierr);} 133 if (a->idiag) {ierr = PetscFree(a->idiag);CHKERRQ(ierr);} 134 if (a->inode.size) {ierr = PetscFree(a->inode.size);CHKERRQ(ierr);} 135 if (a->free_diag) {ierr = PetscFree(a->diag);CHKERRQ(ierr);} 136 if (a->free_imax_ilen) {ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr);} 137 ierr = PetscFree(a->solve_work);CHKERRQ(ierr); 138 ierr = PetscFree(a->sor_work);CHKERRQ(ierr); 139 ierr = PetscFree(a->solves_work);CHKERRQ(ierr); 140 ierr = PetscFree(a->mult_work);CHKERRQ(ierr); 141 ierr = PetscFree(a->saved_values);CHKERRQ(ierr); 142 ierr = PetscFree(a->xtoy);CHKERRQ(ierr); 143 if (a->free_jshort) {ierr = PetscFree(a->jshort);CHKERRQ(ierr);} 144 ierr = PetscFree(a->inew);CHKERRQ(ierr); 145 if (a->parent) {ierr = MatDestroy(a->parent);CHKERRQ(ierr);} 146 ierr = PetscFree(a);CHKERRQ(ierr); 147 148 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 149 ierr = PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C","",PETSC_NULL);CHKERRQ(ierr); 150 ierr = PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C","",PETSC_NULL);CHKERRQ(ierr); 151 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C","",PETSC_NULL);CHKERRQ(ierr); 152 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C","",PETSC_NULL);CHKERRQ(ierr); 153 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C","",PETSC_NULL);CHKERRQ(ierr); 154 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C","",PETSC_NULL);CHKERRQ(ierr); 155 PetscFunctionReturn(0); 156 } 157 158 #undef __FUNCT__ 159 #define __FUNCT__ "MatSetOption_SeqSBAIJ" 160 PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool flg) 161 { 162 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 163 PetscErrorCode ierr; 164 165 PetscFunctionBegin; 166 switch (op) { 167 case MAT_ROW_ORIENTED: 168 a->roworiented = flg; 169 break; 170 case MAT_KEEP_NONZERO_PATTERN: 171 a->keepnonzeropattern = flg; 172 break; 173 case MAT_NEW_NONZERO_LOCATIONS: 174 a->nonew = (flg ? 0 : 1); 175 break; 176 case MAT_NEW_NONZERO_LOCATION_ERR: 177 a->nonew = (flg ? -1 : 0); 178 break; 179 case MAT_NEW_NONZERO_ALLOCATION_ERR: 180 a->nonew = (flg ? -2 : 0); 181 break; 182 case MAT_UNUSED_NONZERO_LOCATION_ERR: 183 a->nounused = (flg ? -1 : 0); 184 break; 185 case MAT_NEW_DIAGONALS: 186 case MAT_IGNORE_OFF_PROC_ENTRIES: 187 case MAT_USE_HASH_TABLE: 188 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 189 break; 190 case MAT_HERMITIAN: 191 if (!A->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first"); 192 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 193 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort; 194 } else if (A->cmap->bs == 1) { 195 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian; 196 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1"); 197 break; 198 case MAT_SPD: 199 A->spd_set = PETSC_TRUE; 200 A->spd = flg; 201 if (flg) { 202 A->symmetric = PETSC_TRUE; 203 A->structurally_symmetric = PETSC_TRUE; 204 A->symmetric_set = PETSC_TRUE; 205 A->structurally_symmetric_set = PETSC_TRUE; 206 } 207 break; 208 case MAT_SYMMETRIC: 209 case MAT_STRUCTURALLY_SYMMETRIC: 210 case MAT_SYMMETRY_ETERNAL: 211 if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix must be symmetric"); 212 ierr = PetscInfo1(A,"Option %s not relevent\n",MatOptions[op]);CHKERRQ(ierr); 213 break; 214 case MAT_IGNORE_LOWER_TRIANGULAR: 215 a->ignore_ltriangular = flg; 216 break; 217 case MAT_ERROR_LOWER_TRIANGULAR: 218 a->ignore_ltriangular = flg; 219 break; 220 case MAT_GETROW_UPPERTRIANGULAR: 221 a->getrow_utriangular = flg; 222 break; 223 default: 224 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op); 225 } 226 PetscFunctionReturn(0); 227 } 228 229 #undef __FUNCT__ 230 #define __FUNCT__ "MatGetRow_SeqSBAIJ" 231 PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *ncols,PetscInt **cols,PetscScalar **v) 232 { 233 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 234 PetscErrorCode ierr; 235 PetscInt itmp,i,j,k,M,*ai,*aj,bs,bn,bp,*cols_i,bs2; 236 MatScalar *aa,*aa_i; 237 PetscScalar *v_i; 238 239 PetscFunctionBegin; 240 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()"); 241 /* Get the upper triangular part of the row */ 242 bs = A->rmap->bs; 243 ai = a->i; 244 aj = a->j; 245 aa = a->a; 246 bs2 = a->bs2; 247 248 if (row < 0 || row >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Row %D out of range", row); 249 250 bn = row/bs; /* Block number */ 251 bp = row % bs; /* Block position */ 252 M = ai[bn+1] - ai[bn]; 253 *ncols = bs*M; 254 255 if (v) { 256 *v = 0; 257 if (*ncols) { 258 ierr = PetscMalloc((*ncols+row)*sizeof(PetscScalar),v);CHKERRQ(ierr); 259 for (i=0; i<M; i++) { /* for each block in the block row */ 260 v_i = *v + i*bs; 261 aa_i = aa + bs2*(ai[bn] + i); 262 for (j=bp,k=0; j<bs2; j+=bs,k++) {v_i[k] = aa_i[j];} 263 } 264 } 265 } 266 267 if (cols) { 268 *cols = 0; 269 if (*ncols) { 270 ierr = PetscMalloc((*ncols+row)*sizeof(PetscInt),cols);CHKERRQ(ierr); 271 for (i=0; i<M; i++) { /* for each block in the block row */ 272 cols_i = *cols + i*bs; 273 itmp = bs*aj[ai[bn] + i]; 274 for (j=0; j<bs; j++) {cols_i[j] = itmp++;} 275 } 276 } 277 } 278 279 /*search column A(0:row-1,row) (=A(row,0:row-1)). Could be expensive! */ 280 /* this segment is currently removed, so only entries in the upper triangle are obtained */ 281 #ifdef column_search 282 v_i = *v + M*bs; 283 cols_i = *cols + M*bs; 284 for (i=0; i<bn; i++){ /* for each block row */ 285 M = ai[i+1] - ai[i]; 286 for (j=0; j<M; j++){ 287 itmp = aj[ai[i] + j]; /* block column value */ 288 if (itmp == bn){ 289 aa_i = aa + bs2*(ai[i] + j) + bs*bp; 290 for (k=0; k<bs; k++) { 291 *cols_i++ = i*bs+k; 292 *v_i++ = aa_i[k]; 293 } 294 *ncols += bs; 295 break; 296 } 297 } 298 } 299 #endif 300 PetscFunctionReturn(0); 301 } 302 303 #undef __FUNCT__ 304 #define __FUNCT__ "MatRestoreRow_SeqSBAIJ" 305 PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 306 { 307 PetscErrorCode ierr; 308 309 PetscFunctionBegin; 310 if (idx) {ierr = PetscFree(*idx);CHKERRQ(ierr);} 311 if (v) {ierr = PetscFree(*v);CHKERRQ(ierr);} 312 PetscFunctionReturn(0); 313 } 314 315 #undef __FUNCT__ 316 #define __FUNCT__ "MatGetRowUpperTriangular_SeqSBAIJ" 317 PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A) 318 { 319 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 320 321 PetscFunctionBegin; 322 a->getrow_utriangular = PETSC_TRUE; 323 PetscFunctionReturn(0); 324 } 325 #undef __FUNCT__ 326 #define __FUNCT__ "MatRestoreRowUpperTriangular_SeqSBAIJ" 327 PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A) 328 { 329 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 330 331 PetscFunctionBegin; 332 a->getrow_utriangular = PETSC_FALSE; 333 PetscFunctionReturn(0); 334 } 335 336 #undef __FUNCT__ 337 #define __FUNCT__ "MatTranspose_SeqSBAIJ" 338 PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B) 339 { 340 PetscErrorCode ierr; 341 PetscFunctionBegin; 342 if (reuse == MAT_INITIAL_MATRIX || *B != A) { 343 ierr = MatDuplicate(A,MAT_COPY_VALUES,B);CHKERRQ(ierr); 344 } 345 PetscFunctionReturn(0); 346 } 347 348 #undef __FUNCT__ 349 #define __FUNCT__ "MatView_SeqSBAIJ_ASCII" 350 static PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer) 351 { 352 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 353 PetscErrorCode ierr; 354 PetscInt i,j,bs = A->rmap->bs,k,l,bs2=a->bs2; 355 PetscViewerFormat format; 356 357 PetscFunctionBegin; 358 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 359 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 360 ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); 361 } else if (format == PETSC_VIEWER_ASCII_MATLAB) { 362 Mat aij; 363 if (A->factortype && bs>1){ 364 ierr = PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored with bs>1. MatView() with PETSC_VIEWER_ASCII_MATLAB is not supported and ignored!\n");CHKERRQ(ierr); 365 PetscFunctionReturn(0); 366 } 367 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);CHKERRQ(ierr); 368 ierr = MatView(aij,viewer);CHKERRQ(ierr); 369 ierr = MatDestroy(aij);CHKERRQ(ierr); 370 } else if (format == PETSC_VIEWER_ASCII_COMMON) { 371 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 372 for (i=0; i<a->mbs; i++) { 373 for (j=0; j<bs; j++) { 374 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 375 for (k=a->i[i]; k<a->i[i+1]; k++) { 376 for (l=0; l<bs; l++) { 377 #if defined(PETSC_USE_COMPLEX) 378 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 379 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l, 380 PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 381 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 382 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l, 383 PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 384 } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 385 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 386 } 387 #else 388 if (a->a[bs2*k + l*bs + j] != 0.0) { 389 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 390 } 391 #endif 392 } 393 } 394 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 395 } 396 } 397 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 398 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 399 PetscFunctionReturn(0); 400 } else { 401 if (A->factortype && bs>1){ 402 ierr = PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored. MatView_SeqSBAIJ_ASCII() may not display complete or logically correct entries!\n");CHKERRQ(ierr); 403 } 404 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 405 ierr = PetscObjectPrintClassNamePrefixType((PetscObject)A,viewer,"Matrix Object");CHKERRQ(ierr); 406 for (i=0; i<a->mbs; i++) { 407 for (j=0; j<bs; j++) { 408 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 409 for (k=a->i[i]; k<a->i[i+1]; k++) { 410 for (l=0; l<bs; l++) { 411 #if defined(PETSC_USE_COMPLEX) 412 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) { 413 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l, 414 PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 415 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) { 416 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l, 417 PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 418 } else { 419 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 420 } 421 #else 422 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 423 #endif 424 } 425 } 426 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 427 } 428 } 429 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 430 } 431 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 432 PetscFunctionReturn(0); 433 } 434 435 #undef __FUNCT__ 436 #define __FUNCT__ "MatView_SeqSBAIJ_Draw_Zoom" 437 static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa) 438 { 439 Mat A = (Mat) Aa; 440 Mat_SeqSBAIJ *a=(Mat_SeqSBAIJ*)A->data; 441 PetscErrorCode ierr; 442 PetscInt row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2; 443 PetscMPIInt rank; 444 PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r; 445 MatScalar *aa; 446 MPI_Comm comm; 447 PetscViewer viewer; 448 449 PetscFunctionBegin; 450 /* 451 This is nasty. If this is called from an originally parallel matrix 452 then all processes call this,but only the first has the matrix so the 453 rest should return immediately. 454 */ 455 ierr = PetscObjectGetComm((PetscObject)draw,&comm);CHKERRQ(ierr); 456 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 457 if (rank) PetscFunctionReturn(0); 458 459 ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr); 460 461 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 462 PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric"); 463 464 /* loop over matrix elements drawing boxes */ 465 color = PETSC_DRAW_BLUE; 466 for (i=0,row=0; i<mbs; i++,row+=bs) { 467 for (j=a->i[i]; j<a->i[i+1]; j++) { 468 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 469 x_l = a->j[j]*bs; x_r = x_l + 1.0; 470 aa = a->a + j*bs2; 471 for (k=0; k<bs; k++) { 472 for (l=0; l<bs; l++) { 473 if (PetscRealPart(*aa++) >= 0.) continue; 474 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 475 } 476 } 477 } 478 } 479 color = PETSC_DRAW_CYAN; 480 for (i=0,row=0; i<mbs; i++,row+=bs) { 481 for (j=a->i[i]; j<a->i[i+1]; j++) { 482 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 483 x_l = a->j[j]*bs; x_r = x_l + 1.0; 484 aa = a->a + j*bs2; 485 for (k=0; k<bs; k++) { 486 for (l=0; l<bs; l++) { 487 if (PetscRealPart(*aa++) != 0.) continue; 488 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 489 } 490 } 491 } 492 } 493 494 color = PETSC_DRAW_RED; 495 for (i=0,row=0; i<mbs; i++,row+=bs) { 496 for (j=a->i[i]; j<a->i[i+1]; j++) { 497 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 498 x_l = a->j[j]*bs; x_r = x_l + 1.0; 499 aa = a->a + j*bs2; 500 for (k=0; k<bs; k++) { 501 for (l=0; l<bs; l++) { 502 if (PetscRealPart(*aa++) <= 0.) continue; 503 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 504 } 505 } 506 } 507 } 508 PetscFunctionReturn(0); 509 } 510 511 #undef __FUNCT__ 512 #define __FUNCT__ "MatView_SeqSBAIJ_Draw" 513 static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer) 514 { 515 PetscErrorCode ierr; 516 PetscReal xl,yl,xr,yr,w,h; 517 PetscDraw draw; 518 PetscBool isnull; 519 520 PetscFunctionBegin; 521 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 522 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 523 524 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);CHKERRQ(ierr); 525 xr = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0; 526 xr += w; yr += h; xl = -w; yl = -h; 527 ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr); 528 ierr = PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);CHKERRQ(ierr); 529 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",PETSC_NULL);CHKERRQ(ierr); 530 PetscFunctionReturn(0); 531 } 532 533 #undef __FUNCT__ 534 #define __FUNCT__ "MatView_SeqSBAIJ" 535 PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer) 536 { 537 PetscErrorCode ierr; 538 PetscBool iascii,isdraw; 539 FILE *file = 0; 540 541 PetscFunctionBegin; 542 ierr = PetscTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); 543 ierr = PetscTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr); 544 if (iascii){ 545 ierr = MatView_SeqSBAIJ_ASCII(A,viewer);CHKERRQ(ierr); 546 } else if (isdraw) { 547 ierr = MatView_SeqSBAIJ_Draw(A,viewer);CHKERRQ(ierr); 548 } else { 549 Mat B; 550 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 551 ierr = MatView(B,viewer);CHKERRQ(ierr); 552 ierr = MatDestroy(B);CHKERRQ(ierr); 553 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 554 if (file) { 555 fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs); 556 } 557 } 558 PetscFunctionReturn(0); 559 } 560 561 562 #undef __FUNCT__ 563 #define __FUNCT__ "MatGetValues_SeqSBAIJ" 564 PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[]) 565 { 566 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 567 PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j; 568 PetscInt *ai = a->i,*ailen = a->ilen; 569 PetscInt brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2; 570 MatScalar *ap,*aa = a->a; 571 572 PetscFunctionBegin; 573 for (k=0; k<m; k++) { /* loop over rows */ 574 row = im[k]; brow = row/bs; 575 if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */ 576 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); 577 rp = aj + ai[brow] ; ap = aa + bs2*ai[brow] ; 578 nrow = ailen[brow]; 579 for (l=0; l<n; l++) { /* loop over columns */ 580 if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */ 581 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); 582 col = in[l] ; 583 bcol = col/bs; 584 cidx = col%bs; 585 ridx = row%bs; 586 high = nrow; 587 low = 0; /* assume unsorted */ 588 while (high-low > 5) { 589 t = (low+high)/2; 590 if (rp[t] > bcol) high = t; 591 else low = t; 592 } 593 for (i=low; i<high; i++) { 594 if (rp[i] > bcol) break; 595 if (rp[i] == bcol) { 596 *v++ = ap[bs2*i+bs*cidx+ridx]; 597 goto finished; 598 } 599 } 600 *v++ = 0.0; 601 finished:; 602 } 603 } 604 PetscFunctionReturn(0); 605 } 606 607 608 #undef __FUNCT__ 609 #define __FUNCT__ "MatSetValuesBlocked_SeqSBAIJ" 610 PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 611 { 612 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 613 PetscErrorCode ierr; 614 PetscInt *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1; 615 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen; 616 PetscInt *aj=a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval; 617 PetscBool roworiented=a->roworiented; 618 const PetscScalar *value = v; 619 MatScalar *ap,*aa = a->a,*bap; 620 621 PetscFunctionBegin; 622 if (roworiented) { 623 stepval = (n-1)*bs; 624 } else { 625 stepval = (m-1)*bs; 626 } 627 for (k=0; k<m; k++) { /* loop over added rows */ 628 row = im[k]; 629 if (row < 0) continue; 630 #if defined(PETSC_USE_DEBUG) 631 if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1); 632 #endif 633 rp = aj + ai[row]; 634 ap = aa + bs2*ai[row]; 635 rmax = imax[row]; 636 nrow = ailen[row]; 637 low = 0; 638 high = nrow; 639 for (l=0; l<n; l++) { /* loop over added columns */ 640 if (in[l] < 0) continue; 641 col = in[l]; 642 #if defined(PETSC_USE_DEBUG) 643 if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1); 644 #endif 645 if (col < row) { 646 if (a->ignore_ltriangular) { 647 continue; /* ignore lower triangular block */ 648 } else { 649 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)"); 650 } 651 } 652 if (roworiented) { 653 value = v + k*(stepval+bs)*bs + l*bs; 654 } else { 655 value = v + l*(stepval+bs)*bs + k*bs; 656 } 657 if (col <= lastcol) low = 0; else high = nrow; 658 lastcol = col; 659 while (high-low > 7) { 660 t = (low+high)/2; 661 if (rp[t] > col) high = t; 662 else low = t; 663 } 664 for (i=low; i<high; i++) { 665 if (rp[i] > col) break; 666 if (rp[i] == col) { 667 bap = ap + bs2*i; 668 if (roworiented) { 669 if (is == ADD_VALUES) { 670 for (ii=0; ii<bs; ii++,value+=stepval) { 671 for (jj=ii; jj<bs2; jj+=bs) { 672 bap[jj] += *value++; 673 } 674 } 675 } else { 676 for (ii=0; ii<bs; ii++,value+=stepval) { 677 for (jj=ii; jj<bs2; jj+=bs) { 678 bap[jj] = *value++; 679 } 680 } 681 } 682 } else { 683 if (is == ADD_VALUES) { 684 for (ii=0; ii<bs; ii++,value+=stepval) { 685 for (jj=0; jj<bs; jj++) { 686 *bap++ += *value++; 687 } 688 } 689 } else { 690 for (ii=0; ii<bs; ii++,value+=stepval) { 691 for (jj=0; jj<bs; jj++) { 692 *bap++ = *value++; 693 } 694 } 695 } 696 } 697 goto noinsert2; 698 } 699 } 700 if (nonew == 1) goto noinsert2; 701 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 702 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 703 N = nrow++ - 1; high++; 704 /* shift up all the later entries in this row */ 705 for (ii=N; ii>=i; ii--) { 706 rp[ii+1] = rp[ii]; 707 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 708 } 709 if (N >= i) { 710 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 711 } 712 rp[i] = col; 713 bap = ap + bs2*i; 714 if (roworiented) { 715 for (ii=0; ii<bs; ii++,value+=stepval) { 716 for (jj=ii; jj<bs2; jj+=bs) { 717 bap[jj] = *value++; 718 } 719 } 720 } else { 721 for (ii=0; ii<bs; ii++,value+=stepval) { 722 for (jj=0; jj<bs; jj++) { 723 *bap++ = *value++; 724 } 725 } 726 } 727 noinsert2:; 728 low = i; 729 } 730 ailen[row] = nrow; 731 } 732 PetscFunctionReturn(0); 733 } 734 735 /* 736 This is not yet used 737 */ 738 #undef __FUNCT__ 739 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode" 740 PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A) 741 { 742 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 743 PetscErrorCode ierr; 744 const PetscInt *ai = a->i, *aj = a->j,*cols; 745 PetscInt i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts; 746 PetscBool flag; 747 748 PetscFunctionBegin; 749 ierr = PetscMalloc(m*sizeof(PetscInt),&ns);CHKERRQ(ierr); 750 while (i < m){ 751 nzx = ai[i+1] - ai[i]; /* Number of nonzeros */ 752 /* Limits the number of elements in a node to 'a->inode.limit' */ 753 for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) { 754 nzy = ai[j+1] - ai[j]; 755 if (nzy != (nzx - j + i)) break; 756 ierr = PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);CHKERRQ(ierr); 757 if (!flag) break; 758 } 759 ns[node_count++] = blk_size; 760 i = j; 761 } 762 if (!a->inode.size && m && node_count > .9*m) { 763 ierr = PetscFree(ns);CHKERRQ(ierr); 764 ierr = PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);CHKERRQ(ierr); 765 } else { 766 a->inode.node_count = node_count; 767 ierr = PetscMalloc(node_count*sizeof(PetscInt),&a->inode.size);CHKERRQ(ierr); 768 ierr = PetscLogObjectMemory(A,node_count*sizeof(PetscInt));CHKERRQ(ierr); 769 ierr = PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt)); 770 ierr = PetscFree(ns);CHKERRQ(ierr); 771 ierr = PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);CHKERRQ(ierr); 772 773 /* count collections of adjacent columns in each inode */ 774 row = 0; 775 cnt = 0; 776 for (i=0; i<node_count; i++) { 777 cols = aj + ai[row] + a->inode.size[i]; 778 nz = ai[row+1] - ai[row] - a->inode.size[i]; 779 for (j=1; j<nz; j++) { 780 if (cols[j] != cols[j-1]+1) { 781 cnt++; 782 } 783 } 784 cnt++; 785 row += a->inode.size[i]; 786 } 787 ierr = PetscMalloc(2*cnt*sizeof(PetscInt),&counts);CHKERRQ(ierr); 788 cnt = 0; 789 row = 0; 790 for (i=0; i<node_count; i++) { 791 cols = aj + ai[row] + a->inode.size[i]; 792 CHKMEMQ; 793 counts[2*cnt] = cols[0]; 794 CHKMEMQ; 795 nz = ai[row+1] - ai[row] - a->inode.size[i]; 796 cnt2 = 1; 797 for (j=1; j<nz; j++) { 798 if (cols[j] != cols[j-1]+1) { 799 CHKMEMQ; 800 counts[2*(cnt++)+1] = cnt2; 801 counts[2*cnt] = cols[j]; 802 CHKMEMQ; 803 cnt2 = 1; 804 } else cnt2++; 805 } 806 CHKMEMQ; 807 counts[2*(cnt++)+1] = cnt2; 808 CHKMEMQ; 809 row += a->inode.size[i]; 810 } 811 ierr = PetscIntView(2*cnt,counts,0); 812 } 813 PetscFunctionReturn(0); 814 } 815 816 #undef __FUNCT__ 817 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ" 818 PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode) 819 { 820 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 821 PetscErrorCode ierr; 822 PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax; 823 PetscInt m = A->rmap->N,*ip,N,*ailen = a->ilen; 824 PetscInt mbs = a->mbs,bs2 = a->bs2,rmax = 0; 825 MatScalar *aa = a->a,*ap; 826 827 PetscFunctionBegin; 828 if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); 829 830 if (m) rmax = ailen[0]; 831 for (i=1; i<mbs; i++) { 832 /* move each row back by the amount of empty slots (fshift) before it*/ 833 fshift += imax[i-1] - ailen[i-1]; 834 rmax = PetscMax(rmax,ailen[i]); 835 if (fshift) { 836 ip = aj + ai[i]; ap = aa + bs2*ai[i]; 837 N = ailen[i]; 838 for (j=0; j<N; j++) { 839 ip[j-fshift] = ip[j]; 840 ierr = PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 841 } 842 } 843 ai[i] = ai[i-1] + ailen[i-1]; 844 } 845 if (mbs) { 846 fshift += imax[mbs-1] - ailen[mbs-1]; 847 ai[mbs] = ai[mbs-1] + ailen[mbs-1]; 848 } 849 /* reset ilen and imax for each row */ 850 for (i=0; i<mbs; i++) { 851 ailen[i] = imax[i] = ai[i+1] - ai[i]; 852 } 853 a->nz = ai[mbs]; 854 855 /* diagonals may have moved, reset it */ 856 if (a->diag) { 857 ierr = PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));CHKERRQ(ierr); 858 } 859 if (fshift && a->nounused == -1) { 860 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); 861 } 862 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); 863 ierr = PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);CHKERRQ(ierr); 864 ierr = PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);CHKERRQ(ierr); 865 A->info.mallocs += a->reallocs; 866 a->reallocs = 0; 867 A->info.nz_unneeded = (PetscReal)fshift*bs2; 868 a->idiagvalid = PETSC_FALSE; 869 870 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 871 if (!a->jshort) { 872 ierr = PetscMalloc(a->i[A->rmap->n]*sizeof(unsigned short),&a->jshort);CHKERRQ(ierr); 873 ierr = PetscLogObjectMemory(A,a->i[A->rmap->n]*sizeof(unsigned short));CHKERRQ(ierr); 874 for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i]; 875 A->ops->mult = MatMult_SeqSBAIJ_1_ushort; 876 A->ops->sor = MatSOR_SeqSBAIJ_ushort; 877 a->free_jshort = PETSC_TRUE; 878 } 879 } 880 PetscFunctionReturn(0); 881 } 882 883 /* 884 This function returns an array of flags which indicate the locations of contiguous 885 blocks that should be zeroed. for eg: if bs = 3 and is = [0,1,2,3,5,6,7,8,9] 886 then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)] 887 Assume: sizes should be long enough to hold all the values. 888 */ 889 #undef __FUNCT__ 890 #define __FUNCT__ "MatZeroRows_SeqSBAIJ_Check_Blocks" 891 PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max) 892 { 893 PetscInt i,j,k,row; 894 PetscBool flg; 895 896 PetscFunctionBegin; 897 for (i=0,j=0; i<n; j++) { 898 row = idx[i]; 899 if (row%bs!=0) { /* Not the begining of a block */ 900 sizes[j] = 1; 901 i++; 902 } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */ 903 sizes[j] = 1; /* Also makes sure atleast 'bs' values exist for next else */ 904 i++; 905 } else { /* Begining of the block, so check if the complete block exists */ 906 flg = PETSC_TRUE; 907 for (k=1; k<bs; k++) { 908 if (row+k != idx[i+k]) { /* break in the block */ 909 flg = PETSC_FALSE; 910 break; 911 } 912 } 913 if (flg) { /* No break in the bs */ 914 sizes[j] = bs; 915 i+= bs; 916 } else { 917 sizes[j] = 1; 918 i++; 919 } 920 } 921 } 922 *bs_max = j; 923 PetscFunctionReturn(0); 924 } 925 926 927 /* Only add/insert a(i,j) with i<=j (blocks). 928 Any a(i,j) with i>j input by user is ingored. 929 */ 930 931 #undef __FUNCT__ 932 #define __FUNCT__ "MatSetValues_SeqSBAIJ" 933 PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 934 { 935 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 936 PetscErrorCode ierr; 937 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1; 938 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented; 939 PetscInt *aj=a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol; 940 PetscInt ridx,cidx,bs2=a->bs2; 941 MatScalar *ap,value,*aa=a->a,*bap; 942 943 PetscFunctionBegin; 944 if (v) PetscValidScalarPointer(v,6); 945 for (k=0; k<m; k++) { /* loop over added rows */ 946 row = im[k]; /* row number */ 947 brow = row/bs; /* block row number */ 948 if (row < 0) continue; 949 #if defined(PETSC_USE_DEBUG) 950 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); 951 #endif 952 rp = aj + ai[brow]; /*ptr to beginning of column value of the row block*/ 953 ap = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/ 954 rmax = imax[brow]; /* maximum space allocated for this row */ 955 nrow = ailen[brow]; /* actual length of this row */ 956 low = 0; 957 958 for (l=0; l<n; l++) { /* loop over added columns */ 959 if (in[l] < 0) continue; 960 #if defined(PETSC_USE_DEBUG) 961 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); 962 #endif 963 col = in[l]; 964 bcol = col/bs; /* block col number */ 965 966 if (brow > bcol) { 967 if (a->ignore_ltriangular){ 968 continue; /* ignore lower triangular values */ 969 } else { 970 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)"); 971 } 972 } 973 974 ridx = row % bs; cidx = col % bs; /*row and col index inside the block */ 975 if ((brow==bcol && ridx<=cidx) || (brow<bcol)){ 976 /* element value a(k,l) */ 977 if (roworiented) { 978 value = v[l + k*n]; 979 } else { 980 value = v[k + l*m]; 981 } 982 983 /* move pointer bap to a(k,l) quickly and add/insert value */ 984 if (col <= lastcol) low = 0; high = nrow; 985 lastcol = col; 986 while (high-low > 7) { 987 t = (low+high)/2; 988 if (rp[t] > bcol) high = t; 989 else low = t; 990 } 991 for (i=low; i<high; i++) { 992 if (rp[i] > bcol) break; 993 if (rp[i] == bcol) { 994 bap = ap + bs2*i + bs*cidx + ridx; 995 if (is == ADD_VALUES) *bap += value; 996 else *bap = value; 997 /* for diag block, add/insert its symmetric element a(cidx,ridx) */ 998 if (brow == bcol && ridx < cidx){ 999 bap = ap + bs2*i + bs*ridx + cidx; 1000 if (is == ADD_VALUES) *bap += value; 1001 else *bap = value; 1002 } 1003 goto noinsert1; 1004 } 1005 } 1006 1007 if (nonew == 1) goto noinsert1; 1008 if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 1009 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 1010 1011 N = nrow++ - 1; high++; 1012 /* shift up all the later entries in this row */ 1013 for (ii=N; ii>=i; ii--) { 1014 rp[ii+1] = rp[ii]; 1015 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 1016 } 1017 if (N>=i) { 1018 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1019 } 1020 rp[i] = bcol; 1021 ap[bs2*i + bs*cidx + ridx] = value; 1022 noinsert1:; 1023 low = i; 1024 } 1025 } /* end of loop over added columns */ 1026 ailen[brow] = nrow; 1027 } /* end of loop over added rows */ 1028 PetscFunctionReturn(0); 1029 } 1030 1031 #undef __FUNCT__ 1032 #define __FUNCT__ "MatICCFactor_SeqSBAIJ" 1033 PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info) 1034 { 1035 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)inA->data; 1036 Mat outA; 1037 PetscErrorCode ierr; 1038 PetscBool row_identity; 1039 1040 PetscFunctionBegin; 1041 if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc"); 1042 ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr); 1043 if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported"); 1044 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()! */ 1045 1046 outA = inA; 1047 inA->factortype = MAT_FACTOR_ICC; 1048 1049 ierr = MatMarkDiagonal_SeqSBAIJ(inA);CHKERRQ(ierr); 1050 ierr = MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);CHKERRQ(ierr); 1051 1052 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1053 if (a->row) { ierr = ISDestroy(a->row);CHKERRQ(ierr); } 1054 a->row = row; 1055 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1056 if (a->col) { ierr = ISDestroy(a->col);CHKERRQ(ierr); } 1057 a->col = row; 1058 1059 /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */ 1060 if (a->icol) {ierr = ISInvertPermutation(row,PETSC_DECIDE, &a->icol);CHKERRQ(ierr);} 1061 ierr = PetscLogObjectParent(inA,a->icol);CHKERRQ(ierr); 1062 1063 if (!a->solve_work) { 1064 ierr = PetscMalloc((inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar),&a->solve_work);CHKERRQ(ierr); 1065 ierr = PetscLogObjectMemory(inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));CHKERRQ(ierr); 1066 } 1067 1068 ierr = MatCholeskyFactorNumeric(outA,inA,info);CHKERRQ(ierr); 1069 PetscFunctionReturn(0); 1070 } 1071 1072 EXTERN_C_BEGIN 1073 #undef __FUNCT__ 1074 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices_SeqSBAIJ" 1075 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices) 1076 { 1077 Mat_SeqSBAIJ *baij = (Mat_SeqSBAIJ *)mat->data; 1078 PetscInt i,nz,n; 1079 1080 PetscFunctionBegin; 1081 nz = baij->maxnz; 1082 n = mat->cmap->n; 1083 for (i=0; i<nz; i++) { 1084 baij->j[i] = indices[i]; 1085 } 1086 baij->nz = nz; 1087 for (i=0; i<n; i++) { 1088 baij->ilen[i] = baij->imax[i]; 1089 } 1090 PetscFunctionReturn(0); 1091 } 1092 EXTERN_C_END 1093 1094 #undef __FUNCT__ 1095 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices" 1096 /*@ 1097 MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows 1098 in the matrix. 1099 1100 Input Parameters: 1101 + mat - the SeqSBAIJ matrix 1102 - indices - the column indices 1103 1104 Level: advanced 1105 1106 Notes: 1107 This can be called if you have precomputed the nonzero structure of the 1108 matrix and want to provide it to the matrix object to improve the performance 1109 of the MatSetValues() operation. 1110 1111 You MUST have set the correct numbers of nonzeros per row in the call to 1112 MatCreateSeqSBAIJ(), and the columns indices MUST be sorted. 1113 1114 MUST be called before any calls to MatSetValues() 1115 1116 .seealso: MatCreateSeqSBAIJ 1117 @*/ 1118 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices) 1119 { 1120 PetscErrorCode ierr; 1121 1122 PetscFunctionBegin; 1123 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 1124 PetscValidPointer(indices,2); 1125 ierr = PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt *),(mat,indices));CHKERRQ(ierr); 1126 PetscFunctionReturn(0); 1127 } 1128 1129 #undef __FUNCT__ 1130 #define __FUNCT__ "MatCopy_SeqSBAIJ" 1131 PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str) 1132 { 1133 PetscErrorCode ierr; 1134 1135 PetscFunctionBegin; 1136 /* If the two matrices have the same copy implementation, use fast copy. */ 1137 if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) { 1138 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1139 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1140 1141 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"); 1142 ierr = PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));CHKERRQ(ierr); 1143 } else { 1144 ierr = MatGetRowUpperTriangular(A);CHKERRQ(ierr); 1145 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 1146 ierr = MatRestoreRowUpperTriangular(A);CHKERRQ(ierr); 1147 } 1148 PetscFunctionReturn(0); 1149 } 1150 1151 #undef __FUNCT__ 1152 #define __FUNCT__ "MatSetUpPreallocation_SeqSBAIJ" 1153 PetscErrorCode MatSetUpPreallocation_SeqSBAIJ(Mat A) 1154 { 1155 PetscErrorCode ierr; 1156 1157 PetscFunctionBegin; 1158 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,-PetscMax(A->rmap->bs,1),PETSC_DEFAULT,0);CHKERRQ(ierr); 1159 PetscFunctionReturn(0); 1160 } 1161 1162 #undef __FUNCT__ 1163 #define __FUNCT__ "MatGetArray_SeqSBAIJ" 1164 PetscErrorCode MatGetArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1165 { 1166 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1167 PetscFunctionBegin; 1168 *array = a->a; 1169 PetscFunctionReturn(0); 1170 } 1171 1172 #undef __FUNCT__ 1173 #define __FUNCT__ "MatRestoreArray_SeqSBAIJ" 1174 PetscErrorCode MatRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1175 { 1176 PetscFunctionBegin; 1177 PetscFunctionReturn(0); 1178 } 1179 1180 #undef __FUNCT__ 1181 #define __FUNCT__ "MatAXPY_SeqSBAIJ" 1182 PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str) 1183 { 1184 Mat_SeqSBAIJ *x=(Mat_SeqSBAIJ *)X->data, *y=(Mat_SeqSBAIJ *)Y->data; 1185 PetscErrorCode ierr; 1186 PetscInt i,bs=Y->rmap->bs,bs2,j; 1187 PetscBLASInt one = 1,bnz = PetscBLASIntCast(x->nz); 1188 1189 PetscFunctionBegin; 1190 if (str == SAME_NONZERO_PATTERN) { 1191 PetscScalar alpha = a; 1192 BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one); 1193 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 1194 if (y->xtoy && y->XtoY != X) { 1195 ierr = PetscFree(y->xtoy);CHKERRQ(ierr); 1196 ierr = MatDestroy(y->XtoY);CHKERRQ(ierr); 1197 } 1198 if (!y->xtoy) { /* get xtoy */ 1199 ierr = MatAXPYGetxtoy_Private(x->mbs,x->i,x->j,PETSC_NULL, y->i,y->j,PETSC_NULL, &y->xtoy);CHKERRQ(ierr); 1200 y->XtoY = X; 1201 } 1202 bs2 = bs*bs; 1203 for (i=0; i<x->nz; i++) { 1204 j = 0; 1205 while (j < bs2){ 1206 y->a[bs2*y->xtoy[i]+j] += a*(x->a[bs2*i+j]); 1207 j++; 1208 } 1209 } 1210 ierr = PetscInfo3(Y,"ratio of nnz_s(X)/nnz_s(Y): %D/%D = %G\n",bs2*x->nz,bs2*y->nz,(PetscReal)(bs2*x->nz)/(bs2*y->nz));CHKERRQ(ierr); 1211 } else { 1212 ierr = MatGetRowUpperTriangular(X);CHKERRQ(ierr); 1213 ierr = MatAXPY_Basic(Y,a,X,str);CHKERRQ(ierr); 1214 ierr = MatRestoreRowUpperTriangular(X);CHKERRQ(ierr); 1215 } 1216 PetscFunctionReturn(0); 1217 } 1218 1219 #undef __FUNCT__ 1220 #define __FUNCT__ "MatSetBlockSize_SeqSBAIJ" 1221 PetscErrorCode MatSetBlockSize_SeqSBAIJ(Mat A,PetscInt bs) 1222 { 1223 PetscInt rbs,cbs; 1224 PetscErrorCode ierr; 1225 1226 PetscFunctionBegin; 1227 ierr = PetscLayoutGetBlockSize(A->rmap,&rbs);CHKERRQ(ierr); 1228 ierr = PetscLayoutGetBlockSize(A->cmap,&cbs);CHKERRQ(ierr); 1229 if (rbs != bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Attempt to set block size %d with SBAIJ %d",bs,rbs); 1230 if (cbs != bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Attempt to set block size %d with SBAIJ %d",bs,cbs); 1231 PetscFunctionReturn(0); 1232 } 1233 1234 #undef __FUNCT__ 1235 #define __FUNCT__ "MatIsSymmetric_SeqSBAIJ" 1236 PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1237 { 1238 PetscFunctionBegin; 1239 *flg = PETSC_TRUE; 1240 PetscFunctionReturn(0); 1241 } 1242 1243 #undef __FUNCT__ 1244 #define __FUNCT__ "MatIsStructurallySymmetric_SeqSBAIJ" 1245 PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool *flg) 1246 { 1247 PetscFunctionBegin; 1248 *flg = PETSC_TRUE; 1249 PetscFunctionReturn(0); 1250 } 1251 1252 #undef __FUNCT__ 1253 #define __FUNCT__ "MatIsHermitian_SeqSBAIJ" 1254 PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg) 1255 { 1256 PetscFunctionBegin; 1257 *flg = PETSC_FALSE; 1258 PetscFunctionReturn(0); 1259 } 1260 1261 #undef __FUNCT__ 1262 #define __FUNCT__ "MatRealPart_SeqSBAIJ" 1263 PetscErrorCode MatRealPart_SeqSBAIJ(Mat A) 1264 { 1265 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1266 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1267 MatScalar *aa = a->a; 1268 1269 PetscFunctionBegin; 1270 for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]); 1271 PetscFunctionReturn(0); 1272 } 1273 1274 #undef __FUNCT__ 1275 #define __FUNCT__ "MatImaginaryPart_SeqSBAIJ" 1276 PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A) 1277 { 1278 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1279 PetscInt i,nz = a->bs2*a->i[a->mbs]; 1280 MatScalar *aa = a->a; 1281 1282 PetscFunctionBegin; 1283 for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]); 1284 PetscFunctionReturn(0); 1285 } 1286 1287 #undef __FUNCT__ 1288 #define __FUNCT__ "MatZeroRowsColumns_SeqSBAIJ" 1289 PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b) 1290 { 1291 Mat_SeqSBAIJ *baij=(Mat_SeqSBAIJ*)A->data; 1292 PetscErrorCode ierr; 1293 PetscInt i,j,k,count; 1294 PetscInt bs=A->rmap->bs,bs2=baij->bs2,row,col; 1295 PetscScalar zero = 0.0; 1296 MatScalar *aa; 1297 const PetscScalar *xx; 1298 PetscScalar *bb; 1299 PetscBool *zeroed; 1300 1301 PetscFunctionBegin; 1302 /* fix right hand side if needed */ 1303 if (x && b) { 1304 ierr = VecGetArrayRead(x,&xx);CHKERRQ(ierr); 1305 ierr = VecGetArray(b,&bb);CHKERRQ(ierr); 1306 for (i=0; i<is_n; i++) { 1307 bb[is_idx[i]] = diag*xx[is_idx[i]]; 1308 } 1309 ierr = VecRestoreArrayRead(x,&xx);CHKERRQ(ierr); 1310 ierr = VecRestoreArray(b,&bb);CHKERRQ(ierr); 1311 } 1312 A->same_nonzero = PETSC_TRUE; 1313 1314 /* zero the columns */ 1315 ierr = PetscMalloc(A->rmap->n*sizeof(PetscBool),&zeroed);CHKERRQ(ierr); 1316 ierr = PetscMemzero(zeroed,A->rmap->n*sizeof(PetscBool));CHKERRQ(ierr); 1317 for (i=0; i<is_n; i++) { 1318 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]); 1319 zeroed[is_idx[i]] = PETSC_TRUE; 1320 } 1321 for (i=0; i<A->rmap->N; i++) { 1322 if (!zeroed[i]) { 1323 row = i/bs; 1324 for (j=baij->i[row]; j<baij->i[row+1]; j++) { 1325 for (k=0; k<bs; k++) { 1326 col = bs*baij->j[j] + k; 1327 if (zeroed[col]) { 1328 aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k; 1329 aa[0] = 0.0; 1330 } 1331 } 1332 } 1333 } 1334 } 1335 ierr = PetscFree(zeroed);CHKERRQ(ierr); 1336 1337 /* zero the rows */ 1338 for (i=0; i<is_n; i++) { 1339 row = is_idx[i]; 1340 count = (baij->i[row/bs +1] - baij->i[row/bs])*bs; 1341 aa = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs); 1342 for (k=0; k<count; k++) { 1343 aa[0] = zero; 1344 aa += bs; 1345 } 1346 if (diag != 0.0) { 1347 ierr = (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);CHKERRQ(ierr); 1348 } 1349 } 1350 ierr = MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1351 PetscFunctionReturn(0); 1352 } 1353 1354 /* -------------------------------------------------------------------*/ 1355 static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ, 1356 MatGetRow_SeqSBAIJ, 1357 MatRestoreRow_SeqSBAIJ, 1358 MatMult_SeqSBAIJ_N, 1359 /* 4*/ MatMultAdd_SeqSBAIJ_N, 1360 MatMult_SeqSBAIJ_N, /* transpose versions are same as non-transpose versions */ 1361 MatMultAdd_SeqSBAIJ_N, 1362 0, 1363 0, 1364 0, 1365 /*10*/ 0, 1366 0, 1367 MatCholeskyFactor_SeqSBAIJ, 1368 MatSOR_SeqSBAIJ, 1369 MatTranspose_SeqSBAIJ, 1370 /*15*/ MatGetInfo_SeqSBAIJ, 1371 MatEqual_SeqSBAIJ, 1372 MatGetDiagonal_SeqSBAIJ, 1373 MatDiagonalScale_SeqSBAIJ, 1374 MatNorm_SeqSBAIJ, 1375 /*20*/ 0, 1376 MatAssemblyEnd_SeqSBAIJ, 1377 MatSetOption_SeqSBAIJ, 1378 MatZeroEntries_SeqSBAIJ, 1379 /*24*/ 0, 1380 0, 1381 0, 1382 0, 1383 0, 1384 /*29*/ MatSetUpPreallocation_SeqSBAIJ, 1385 0, 1386 0, 1387 MatGetArray_SeqSBAIJ, 1388 MatRestoreArray_SeqSBAIJ, 1389 /*34*/ MatDuplicate_SeqSBAIJ, 1390 0, 1391 0, 1392 0, 1393 MatICCFactor_SeqSBAIJ, 1394 /*39*/ MatAXPY_SeqSBAIJ, 1395 MatGetSubMatrices_SeqSBAIJ, 1396 MatIncreaseOverlap_SeqSBAIJ, 1397 MatGetValues_SeqSBAIJ, 1398 MatCopy_SeqSBAIJ, 1399 /*44*/ 0, 1400 MatScale_SeqSBAIJ, 1401 0, 1402 0, 1403 MatZeroRowsColumns_SeqSBAIJ, 1404 /*49*/ MatSetBlockSize_SeqSBAIJ, 1405 MatGetRowIJ_SeqSBAIJ, 1406 MatRestoreRowIJ_SeqSBAIJ, 1407 0, 1408 0, 1409 /*54*/ 0, 1410 0, 1411 0, 1412 0, 1413 MatSetValuesBlocked_SeqSBAIJ, 1414 /*59*/ MatGetSubMatrix_SeqSBAIJ, 1415 0, 1416 0, 1417 0, 1418 0, 1419 /*64*/ 0, 1420 0, 1421 0, 1422 0, 1423 0, 1424 /*69*/ MatGetRowMaxAbs_SeqSBAIJ, 1425 0, 1426 0, 1427 0, 1428 0, 1429 /*74*/ 0, 1430 0, 1431 0, 1432 0, 1433 0, 1434 /*79*/ 0, 1435 0, 1436 0, 1437 MatGetInertia_SeqSBAIJ, 1438 MatLoad_SeqSBAIJ, 1439 /*84*/ MatIsSymmetric_SeqSBAIJ, 1440 MatIsHermitian_SeqSBAIJ, 1441 MatIsStructurallySymmetric_SeqSBAIJ, 1442 0, 1443 0, 1444 /*89*/ 0, 1445 0, 1446 0, 1447 0, 1448 0, 1449 /*94*/ 0, 1450 0, 1451 0, 1452 0, 1453 0, 1454 /*99*/ 0, 1455 0, 1456 0, 1457 0, 1458 0, 1459 /*104*/0, 1460 MatRealPart_SeqSBAIJ, 1461 MatImaginaryPart_SeqSBAIJ, 1462 MatGetRowUpperTriangular_SeqSBAIJ, 1463 MatRestoreRowUpperTriangular_SeqSBAIJ, 1464 /*109*/0, 1465 0, 1466 0, 1467 0, 1468 MatMissingDiagonal_SeqSBAIJ, 1469 /*114*/0, 1470 0, 1471 0, 1472 0, 1473 0, 1474 /*119*/0, 1475 0, 1476 0, 1477 0 1478 }; 1479 1480 EXTERN_C_BEGIN 1481 #undef __FUNCT__ 1482 #define __FUNCT__ "MatStoreValues_SeqSBAIJ" 1483 PetscErrorCode PETSCMAT_DLLEXPORT MatStoreValues_SeqSBAIJ(Mat mat) 1484 { 1485 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ *)mat->data; 1486 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1487 PetscErrorCode ierr; 1488 1489 PetscFunctionBegin; 1490 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1491 1492 /* allocate space for values if not already there */ 1493 if (!aij->saved_values) { 1494 ierr = PetscMalloc((nz+1)*sizeof(PetscScalar),&aij->saved_values);CHKERRQ(ierr); 1495 } 1496 1497 /* copy values over */ 1498 ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1499 PetscFunctionReturn(0); 1500 } 1501 EXTERN_C_END 1502 1503 EXTERN_C_BEGIN 1504 #undef __FUNCT__ 1505 #define __FUNCT__ "MatRetrieveValues_SeqSBAIJ" 1506 PetscErrorCode PETSCMAT_DLLEXPORT MatRetrieveValues_SeqSBAIJ(Mat mat) 1507 { 1508 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ *)mat->data; 1509 PetscErrorCode ierr; 1510 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1511 1512 PetscFunctionBegin; 1513 if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1514 if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first"); 1515 1516 /* copy values over */ 1517 ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1518 PetscFunctionReturn(0); 1519 } 1520 EXTERN_C_END 1521 1522 EXTERN_C_BEGIN 1523 #undef __FUNCT__ 1524 #define __FUNCT__ "MatSeqSBAIJSetPreallocation_SeqSBAIJ" 1525 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz) 1526 { 1527 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1528 PetscErrorCode ierr; 1529 PetscInt i,mbs,bs2, newbs = PetscAbs(bs); 1530 PetscBool skipallocation = PETSC_FALSE,flg = PETSC_FALSE; 1531 1532 PetscFunctionBegin; 1533 B->preallocated = PETSC_TRUE; 1534 if (bs < 0) { 1535 ierr = PetscOptionsBegin(((PetscObject)B)->comm,((PetscObject)B)->prefix,"Options for MPISBAIJ matrix","Mat");CHKERRQ(ierr); 1536 ierr = PetscOptionsInt("-mat_block_size","Set the blocksize used to store the matrix","MatSeqSBAIJSetPreallocation",newbs,&newbs,PETSC_NULL);CHKERRQ(ierr); 1537 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1538 bs = PetscAbs(bs); 1539 } 1540 if (nnz && newbs != bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Cannot change blocksize from command line if setting nnz"); 1541 bs = newbs; 1542 1543 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 1544 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 1545 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 1546 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 1547 1548 mbs = B->rmap->N/bs; 1549 bs2 = bs*bs; 1550 1551 if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize"); 1552 1553 if (nz == MAT_SKIP_ALLOCATION) { 1554 skipallocation = PETSC_TRUE; 1555 nz = 0; 1556 } 1557 1558 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3; 1559 if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz); 1560 if (nnz) { 1561 for (i=0; i<mbs; i++) { 1562 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]); 1563 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); 1564 } 1565 } 1566 1567 B->ops->mult = MatMult_SeqSBAIJ_N; 1568 B->ops->multadd = MatMultAdd_SeqSBAIJ_N; 1569 B->ops->multtranspose = MatMult_SeqSBAIJ_N; 1570 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N; 1571 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);CHKERRQ(ierr); 1572 if (!flg) { 1573 switch (bs) { 1574 case 1: 1575 B->ops->mult = MatMult_SeqSBAIJ_1; 1576 B->ops->multadd = MatMultAdd_SeqSBAIJ_1; 1577 B->ops->multtranspose = MatMult_SeqSBAIJ_1; 1578 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1; 1579 break; 1580 case 2: 1581 B->ops->mult = MatMult_SeqSBAIJ_2; 1582 B->ops->multadd = MatMultAdd_SeqSBAIJ_2; 1583 B->ops->multtranspose = MatMult_SeqSBAIJ_2; 1584 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2; 1585 break; 1586 case 3: 1587 B->ops->mult = MatMult_SeqSBAIJ_3; 1588 B->ops->multadd = MatMultAdd_SeqSBAIJ_3; 1589 B->ops->multtranspose = MatMult_SeqSBAIJ_3; 1590 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3; 1591 break; 1592 case 4: 1593 B->ops->mult = MatMult_SeqSBAIJ_4; 1594 B->ops->multadd = MatMultAdd_SeqSBAIJ_4; 1595 B->ops->multtranspose = MatMult_SeqSBAIJ_4; 1596 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4; 1597 break; 1598 case 5: 1599 B->ops->mult = MatMult_SeqSBAIJ_5; 1600 B->ops->multadd = MatMultAdd_SeqSBAIJ_5; 1601 B->ops->multtranspose = MatMult_SeqSBAIJ_5; 1602 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5; 1603 break; 1604 case 6: 1605 B->ops->mult = MatMult_SeqSBAIJ_6; 1606 B->ops->multadd = MatMultAdd_SeqSBAIJ_6; 1607 B->ops->multtranspose = MatMult_SeqSBAIJ_6; 1608 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6; 1609 break; 1610 case 7: 1611 B->ops->mult = MatMult_SeqSBAIJ_7; 1612 B->ops->multadd = MatMultAdd_SeqSBAIJ_7; 1613 B->ops->multtranspose = MatMult_SeqSBAIJ_7; 1614 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7; 1615 break; 1616 } 1617 } 1618 1619 b->mbs = mbs; 1620 b->nbs = mbs; 1621 if (!skipallocation) { 1622 if (!b->imax) { 1623 ierr = PetscMalloc2(mbs,PetscInt,&b->imax,mbs,PetscInt,&b->ilen);CHKERRQ(ierr); 1624 b->free_imax_ilen = PETSC_TRUE; 1625 ierr = PetscLogObjectMemory(B,2*mbs*sizeof(PetscInt));CHKERRQ(ierr); 1626 } 1627 if (!nnz) { 1628 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5; 1629 else if (nz <= 0) nz = 1; 1630 for (i=0; i<mbs; i++) { 1631 b->imax[i] = nz; 1632 } 1633 nz = nz*mbs; /* total nz */ 1634 } else { 1635 nz = 0; 1636 for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];} 1637 } 1638 /* b->ilen will count nonzeros in each block row so far. */ 1639 for (i=0; i<mbs; i++) { b->ilen[i] = 0;} 1640 /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */ 1641 1642 /* allocate the matrix space */ 1643 ierr = MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);CHKERRQ(ierr); 1644 ierr = PetscMalloc3(bs2*nz,PetscScalar,&b->a,nz,PetscInt,&b->j,B->rmap->N+1,PetscInt,&b->i);CHKERRQ(ierr); 1645 ierr = PetscLogObjectMemory(B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr); 1646 ierr = PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 1647 ierr = PetscMemzero(b->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 1648 b->singlemalloc = PETSC_TRUE; 1649 1650 /* pointer to beginning of each row */ 1651 b->i[0] = 0; 1652 for (i=1; i<mbs+1; i++) { 1653 b->i[i] = b->i[i-1] + b->imax[i-1]; 1654 } 1655 b->free_a = PETSC_TRUE; 1656 b->free_ij = PETSC_TRUE; 1657 } else { 1658 b->free_a = PETSC_FALSE; 1659 b->free_ij = PETSC_FALSE; 1660 } 1661 1662 B->rmap->bs = bs; 1663 b->bs2 = bs2; 1664 b->nz = 0; 1665 b->maxnz = nz; 1666 1667 b->inew = 0; 1668 b->jnew = 0; 1669 b->anew = 0; 1670 b->a2anew = 0; 1671 b->permute = PETSC_FALSE; 1672 PetscFunctionReturn(0); 1673 } 1674 EXTERN_C_END 1675 1676 /* 1677 This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization 1678 */ 1679 #undef __FUNCT__ 1680 #define __FUNCT__ "MatSeqSBAIJSetNumericFactorization_inplace" 1681 PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural) 1682 { 1683 PetscErrorCode ierr; 1684 PetscBool flg = PETSC_FALSE; 1685 PetscInt bs = B->rmap->bs; 1686 1687 PetscFunctionBegin; 1688 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);CHKERRQ(ierr); 1689 if (flg) bs = 8; 1690 1691 if (!natural) { 1692 switch (bs) { 1693 case 1: 1694 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace; 1695 break; 1696 case 2: 1697 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2; 1698 break; 1699 case 3: 1700 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3; 1701 break; 1702 case 4: 1703 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4; 1704 break; 1705 case 5: 1706 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5; 1707 break; 1708 case 6: 1709 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6; 1710 break; 1711 case 7: 1712 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7; 1713 break; 1714 default: 1715 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N; 1716 break; 1717 } 1718 } else { 1719 switch (bs) { 1720 case 1: 1721 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace; 1722 break; 1723 case 2: 1724 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering; 1725 break; 1726 case 3: 1727 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering; 1728 break; 1729 case 4: 1730 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering; 1731 break; 1732 case 5: 1733 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering; 1734 break; 1735 case 6: 1736 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering; 1737 break; 1738 case 7: 1739 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering; 1740 break; 1741 default: 1742 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering; 1743 break; 1744 } 1745 } 1746 PetscFunctionReturn(0); 1747 } 1748 1749 EXTERN_C_BEGIN 1750 EXTERN PetscErrorCode PETSCMAT_DLLEXPORT MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*); 1751 EXTERN PetscErrorCode PETSCMAT_DLLEXPORT MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*); 1752 EXTERN_C_END 1753 1754 1755 EXTERN_C_BEGIN 1756 #undef __FUNCT__ 1757 #define __FUNCT__ "MatGetFactor_seqsbaij_petsc" 1758 PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B) 1759 { 1760 PetscInt n = A->rmap->n; 1761 PetscErrorCode ierr; 1762 1763 PetscFunctionBegin; 1764 ierr = MatCreate(((PetscObject)A)->comm,B);CHKERRQ(ierr); 1765 ierr = MatSetSizes(*B,n,n,n,n);CHKERRQ(ierr); 1766 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1767 ierr = MatSetType(*B,MATSEQSBAIJ);CHKERRQ(ierr); 1768 ierr = MatSeqSBAIJSetPreallocation(*B,1,MAT_SKIP_ALLOCATION,PETSC_NULL);CHKERRQ(ierr); 1769 (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ; 1770 (*B)->ops->iccfactorsymbolic = MatICCFactorSymbolic_SeqSBAIJ; 1771 } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported"); 1772 (*B)->factortype = ftype; 1773 PetscFunctionReturn(0); 1774 } 1775 EXTERN_C_END 1776 1777 EXTERN_C_BEGIN 1778 #undef __FUNCT__ 1779 #define __FUNCT__ "MatGetFactorAvailable_seqsbaij_petsc" 1780 PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool *flg) 1781 { 1782 PetscFunctionBegin; 1783 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1784 *flg = PETSC_TRUE; 1785 } else { 1786 *flg = PETSC_FALSE; 1787 } 1788 PetscFunctionReturn(0); 1789 } 1790 EXTERN_C_END 1791 1792 EXTERN_C_BEGIN 1793 #if defined(PETSC_HAVE_MUMPS) 1794 extern PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*); 1795 #endif 1796 #if defined(PETSC_HAVE_SPOOLES) 1797 extern PetscErrorCode MatGetFactor_seqsbaij_spooles(Mat,MatFactorType,Mat*); 1798 #endif 1799 #if defined(PETSC_HAVE_PASTIX) 1800 extern PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*); 1801 #endif 1802 #if defined(PETSC_HAVE_CHOLMOD) 1803 extern PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*); 1804 #endif 1805 EXTERN_C_END 1806 1807 /*MC 1808 MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices, 1809 based on block compressed sparse row format. Only the upper triangular portion of the matrix is stored. 1810 1811 Options Database Keys: 1812 . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions() 1813 1814 Level: beginner 1815 1816 .seealso: MatCreateSeqSBAIJ 1817 M*/ 1818 1819 EXTERN_C_BEGIN 1820 #undef __FUNCT__ 1821 #define __FUNCT__ "MatCreate_SeqSBAIJ" 1822 PetscErrorCode PETSCMAT_DLLEXPORT MatCreate_SeqSBAIJ(Mat B) 1823 { 1824 Mat_SeqSBAIJ *b; 1825 PetscErrorCode ierr; 1826 PetscMPIInt size; 1827 PetscBool no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE; 1828 1829 PetscFunctionBegin; 1830 ierr = MPI_Comm_size(((PetscObject)B)->comm,&size);CHKERRQ(ierr); 1831 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1"); 1832 1833 ierr = PetscNewLog(B,Mat_SeqSBAIJ,&b);CHKERRQ(ierr); 1834 B->data = (void*)b; 1835 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 1836 B->ops->destroy = MatDestroy_SeqSBAIJ; 1837 B->ops->view = MatView_SeqSBAIJ; 1838 B->mapping = 0; 1839 b->row = 0; 1840 b->icol = 0; 1841 b->reallocs = 0; 1842 b->saved_values = 0; 1843 b->inode.limit = 5; 1844 b->inode.max_limit = 5; 1845 1846 b->roworiented = PETSC_TRUE; 1847 b->nonew = 0; 1848 b->diag = 0; 1849 b->solve_work = 0; 1850 b->mult_work = 0; 1851 B->spptr = 0; 1852 B->info.nz_unneeded = (PetscReal)b->maxnz*b->bs2; 1853 b->keepnonzeropattern = PETSC_FALSE; 1854 b->xtoy = 0; 1855 b->XtoY = 0; 1856 1857 b->inew = 0; 1858 b->jnew = 0; 1859 b->anew = 0; 1860 b->a2anew = 0; 1861 b->permute = PETSC_FALSE; 1862 1863 b->ignore_ltriangular = PETSC_FALSE; 1864 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,PETSC_NULL);CHKERRQ(ierr); 1865 1866 b->getrow_utriangular = PETSC_FALSE; 1867 ierr = PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,PETSC_NULL);CHKERRQ(ierr); 1868 1869 #if defined(PETSC_HAVE_PASTIX) 1870 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_pastix_C", 1871 "MatGetFactor_seqsbaij_pastix", 1872 MatGetFactor_seqsbaij_pastix);CHKERRQ(ierr); 1873 #endif 1874 #if defined(PETSC_HAVE_SPOOLES) 1875 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_spooles_C", 1876 "MatGetFactor_seqsbaij_spooles", 1877 MatGetFactor_seqsbaij_spooles);CHKERRQ(ierr); 1878 #endif 1879 #if defined(PETSC_HAVE_MUMPS) 1880 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_mumps_C", 1881 "MatGetFactor_sbaij_mumps", 1882 MatGetFactor_sbaij_mumps);CHKERRQ(ierr); 1883 #endif 1884 #if defined(PETSC_HAVE_CHOLMOD) 1885 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_cholmod_C", 1886 "MatGetFactor_seqsbaij_cholmod", 1887 MatGetFactor_seqsbaij_cholmod);CHKERRQ(ierr); 1888 #endif 1889 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactorAvailable_petsc_C", 1890 "MatGetFactorAvailable_seqsbaij_petsc", 1891 MatGetFactorAvailable_seqsbaij_petsc);CHKERRQ(ierr); 1892 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_petsc_C", 1893 "MatGetFactor_seqsbaij_petsc", 1894 MatGetFactor_seqsbaij_petsc);CHKERRQ(ierr); 1895 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatStoreValues_C", 1896 "MatStoreValues_SeqSBAIJ", 1897 MatStoreValues_SeqSBAIJ);CHKERRQ(ierr); 1898 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatRetrieveValues_C", 1899 "MatRetrieveValues_SeqSBAIJ", 1900 (void*)MatRetrieveValues_SeqSBAIJ);CHKERRQ(ierr); 1901 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C", 1902 "MatSeqSBAIJSetColumnIndices_SeqSBAIJ", 1903 MatSeqSBAIJSetColumnIndices_SeqSBAIJ);CHKERRQ(ierr); 1904 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqaij_C", 1905 "MatConvert_SeqSBAIJ_SeqAIJ", 1906 MatConvert_SeqSBAIJ_SeqAIJ);CHKERRQ(ierr); 1907 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C", 1908 "MatConvert_SeqSBAIJ_SeqBAIJ", 1909 MatConvert_SeqSBAIJ_SeqBAIJ);CHKERRQ(ierr); 1910 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetPreallocation_C", 1911 "MatSeqSBAIJSetPreallocation_SeqSBAIJ", 1912 MatSeqSBAIJSetPreallocation_SeqSBAIJ);CHKERRQ(ierr); 1913 1914 B->symmetric = PETSC_TRUE; 1915 B->structurally_symmetric = PETSC_TRUE; 1916 B->symmetric_set = PETSC_TRUE; 1917 B->structurally_symmetric_set = PETSC_TRUE; 1918 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);CHKERRQ(ierr); 1919 1920 ierr = PetscOptionsBegin(((PetscObject)B)->comm,((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");CHKERRQ(ierr); 1921 ierr = PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",PETSC_NULL,no_unroll,&no_unroll,PETSC_NULL);CHKERRQ(ierr); 1922 if (no_unroll) {ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");CHKERRQ(ierr);} 1923 ierr = PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",PETSC_NULL,no_inode,&no_inode,PETSC_NULL);CHKERRQ(ierr); 1924 if (no_inode) {ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");CHKERRQ(ierr);} 1925 ierr = PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",PETSC_NULL,b->inode.limit,&b->inode.limit,PETSC_NULL);CHKERRQ(ierr); 1926 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1927 b->inode.use = (PetscBool)(!(no_unroll || no_inode)); 1928 if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit; 1929 1930 PetscFunctionReturn(0); 1931 } 1932 EXTERN_C_END 1933 1934 #undef __FUNCT__ 1935 #define __FUNCT__ "MatSeqSBAIJSetPreallocation" 1936 /*@C 1937 MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block 1938 compressed row) format. For good matrix assembly performance the 1939 user should preallocate the matrix storage by setting the parameter nz 1940 (or the array nnz). By setting these parameters accurately, performance 1941 during matrix assembly can be increased by more than a factor of 50. 1942 1943 Collective on Mat 1944 1945 Input Parameters: 1946 + A - the symmetric matrix 1947 . bs - size of block 1948 . nz - number of block nonzeros per block row (same for all rows) 1949 - nnz - array containing the number of block nonzeros in the upper triangular plus 1950 diagonal portion of each block (possibly different for each block row) or PETSC_NULL 1951 1952 Options Database Keys: 1953 . -mat_no_unroll - uses code that does not unroll the loops in the 1954 block calculations (much slower) 1955 . -mat_block_size - size of the blocks to use (only works if a negative bs is passed in 1956 1957 Level: intermediate 1958 1959 Notes: 1960 Specify the preallocated storage with either nz or nnz (not both). 1961 Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 1962 allocation. See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details. 1963 1964 You can call MatGetInfo() to get information on how effective the preallocation was; 1965 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 1966 You can also run with the option -info and look for messages with the string 1967 malloc in them to see if additional memory allocation was needed. 1968 1969 If the nnz parameter is given then the nz parameter is ignored 1970 1971 1972 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateMPISBAIJ() 1973 @*/ 1974 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[]) 1975 { 1976 PetscErrorCode ierr; 1977 1978 PetscFunctionBegin; 1979 ierr = PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));CHKERRQ(ierr); 1980 PetscFunctionReturn(0); 1981 } 1982 1983 #undef __FUNCT__ 1984 #define __FUNCT__ "MatCreateSeqSBAIJ" 1985 /*@C 1986 MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block 1987 compressed row) format. For good matrix assembly performance the 1988 user should preallocate the matrix storage by setting the parameter nz 1989 (or the array nnz). By setting these parameters accurately, performance 1990 during matrix assembly can be increased by more than a factor of 50. 1991 1992 Collective on MPI_Comm 1993 1994 Input Parameters: 1995 + comm - MPI communicator, set to PETSC_COMM_SELF 1996 . bs - size of block 1997 . m - number of rows, or number of columns 1998 . nz - number of block nonzeros per block row (same for all rows) 1999 - nnz - array containing the number of block nonzeros in the upper triangular plus 2000 diagonal portion of each block (possibly different for each block row) or PETSC_NULL 2001 2002 Output Parameter: 2003 . A - the symmetric matrix 2004 2005 Options Database Keys: 2006 . -mat_no_unroll - uses code that does not unroll the loops in the 2007 block calculations (much slower) 2008 . -mat_block_size - size of the blocks to use 2009 2010 Level: intermediate 2011 2012 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 2013 MatXXXXSetPreallocation() paradgm instead of this routine directly. 2014 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 2015 2016 Notes: 2017 The number of rows and columns must be divisible by blocksize. 2018 This matrix type does not support complex Hermitian operation. 2019 2020 Specify the preallocated storage with either nz or nnz (not both). 2021 Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 2022 allocation. See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details. 2023 2024 If the nnz parameter is given then the nz parameter is ignored 2025 2026 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateMPISBAIJ() 2027 @*/ 2028 PetscErrorCode PETSCMAT_DLLEXPORT MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A) 2029 { 2030 PetscErrorCode ierr; 2031 2032 PetscFunctionBegin; 2033 ierr = MatCreate(comm,A);CHKERRQ(ierr); 2034 ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); 2035 ierr = MatSetType(*A,MATSEQSBAIJ);CHKERRQ(ierr); 2036 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);CHKERRQ(ierr); 2037 PetscFunctionReturn(0); 2038 } 2039 2040 #undef __FUNCT__ 2041 #define __FUNCT__ "MatDuplicate_SeqSBAIJ" 2042 PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B) 2043 { 2044 Mat C; 2045 Mat_SeqSBAIJ *c,*a = (Mat_SeqSBAIJ*)A->data; 2046 PetscErrorCode ierr; 2047 PetscInt i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2; 2048 2049 PetscFunctionBegin; 2050 if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix"); 2051 2052 *B = 0; 2053 ierr = MatCreate(((PetscObject)A)->comm,&C);CHKERRQ(ierr); 2054 ierr = MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);CHKERRQ(ierr); 2055 ierr = MatSetType(C,MATSEQSBAIJ);CHKERRQ(ierr); 2056 ierr = PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 2057 c = (Mat_SeqSBAIJ*)C->data; 2058 2059 C->preallocated = PETSC_TRUE; 2060 C->factortype = A->factortype; 2061 c->row = 0; 2062 c->icol = 0; 2063 c->saved_values = 0; 2064 c->keepnonzeropattern = a->keepnonzeropattern; 2065 C->assembled = PETSC_TRUE; 2066 2067 ierr = PetscLayoutCopy(A->rmap,&C->rmap);CHKERRQ(ierr); 2068 ierr = PetscLayoutCopy(A->cmap,&C->cmap);CHKERRQ(ierr); 2069 c->bs2 = a->bs2; 2070 c->mbs = a->mbs; 2071 c->nbs = a->nbs; 2072 2073 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2074 c->imax = a->imax; 2075 c->ilen = a->ilen; 2076 c->free_imax_ilen = PETSC_FALSE; 2077 } else { 2078 ierr = PetscMalloc2((mbs+1),PetscInt,&c->imax,(mbs+1),PetscInt,&c->ilen);CHKERRQ(ierr); 2079 ierr = PetscLogObjectMemory(C,2*(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2080 for (i=0; i<mbs; i++) { 2081 c->imax[i] = a->imax[i]; 2082 c->ilen[i] = a->ilen[i]; 2083 } 2084 c->free_imax_ilen = PETSC_TRUE; 2085 } 2086 2087 /* allocate the matrix space */ 2088 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2089 ierr = PetscMalloc(bs2*nz*sizeof(MatScalar),&c->a);CHKERRQ(ierr); 2090 ierr = PetscLogObjectMemory(C,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 2091 c->singlemalloc = PETSC_FALSE; 2092 c->free_ij = PETSC_FALSE; 2093 c->parent = A; 2094 ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr); 2095 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2096 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2097 } else { 2098 ierr = PetscMalloc3(bs2*nz,MatScalar,&c->a,nz,PetscInt,&c->j,mbs+1,PetscInt,&c->i);CHKERRQ(ierr); 2099 ierr = PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2100 ierr = PetscLogObjectMemory(C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));CHKERRQ(ierr); 2101 c->singlemalloc = PETSC_TRUE; 2102 c->free_ij = PETSC_TRUE; 2103 } 2104 if (mbs > 0) { 2105 if (cpvalues != MAT_SHARE_NONZERO_PATTERN) { 2106 ierr = PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 2107 } 2108 if (cpvalues == MAT_COPY_VALUES) { 2109 ierr = PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2110 } else { 2111 ierr = PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2112 } 2113 if (a->jshort) { 2114 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2115 c->jshort = a->jshort; 2116 c->free_jshort = PETSC_FALSE; 2117 } else { 2118 ierr = PetscMalloc(nz*sizeof(unsigned short),&c->jshort);CHKERRQ(ierr); 2119 ierr = PetscLogObjectMemory(C,nz*sizeof(unsigned short));CHKERRQ(ierr); 2120 ierr = PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));CHKERRQ(ierr); 2121 c->free_jshort = PETSC_TRUE; 2122 } 2123 } 2124 } 2125 2126 c->roworiented = a->roworiented; 2127 c->nonew = a->nonew; 2128 2129 if (a->diag) { 2130 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2131 c->diag = a->diag; 2132 c->free_diag = PETSC_FALSE; 2133 } else { 2134 ierr = PetscMalloc(mbs*sizeof(PetscInt),&c->diag);CHKERRQ(ierr); 2135 ierr = PetscLogObjectMemory(C,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2136 for (i=0; i<mbs; i++) { 2137 c->diag[i] = a->diag[i]; 2138 } 2139 c->free_diag = PETSC_TRUE; 2140 } 2141 } else c->diag = 0; 2142 c->nz = a->nz; 2143 c->maxnz = a->nz; /* Since we allocate exactly the right amount */ 2144 c->solve_work = 0; 2145 c->mult_work = 0; 2146 c->free_a = PETSC_TRUE; 2147 *B = C; 2148 ierr = PetscFListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);CHKERRQ(ierr); 2149 PetscFunctionReturn(0); 2150 } 2151 2152 #undef __FUNCT__ 2153 #define __FUNCT__ "MatLoad_SeqSBAIJ" 2154 PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer) 2155 { 2156 Mat_SeqSBAIJ *a; 2157 PetscErrorCode ierr; 2158 int fd; 2159 PetscMPIInt size; 2160 PetscInt i,nz,header[4],*rowlengths=0,M,N,bs=1; 2161 PetscInt *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount; 2162 PetscInt kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols; 2163 PetscInt *masked,nmask,tmp,bs2,ishift; 2164 PetscScalar *aa; 2165 MPI_Comm comm = ((PetscObject)viewer)->comm; 2166 2167 PetscFunctionBegin; 2168 ierr = PetscOptionsGetInt(PETSC_NULL,"-matload_block_size",&bs,PETSC_NULL);CHKERRQ(ierr); 2169 bs2 = bs*bs; 2170 2171 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2172 if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor"); 2173 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2174 ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr); 2175 if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object"); 2176 M = header[1]; N = header[2]; nz = header[3]; 2177 2178 if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ"); 2179 2180 if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices"); 2181 2182 /* 2183 This code adds extra rows to make sure the number of rows is 2184 divisible by the blocksize 2185 */ 2186 mbs = M/bs; 2187 extra_rows = bs - M + bs*(mbs); 2188 if (extra_rows == bs) extra_rows = 0; 2189 else mbs++; 2190 if (extra_rows) { 2191 ierr = PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");CHKERRQ(ierr); 2192 } 2193 2194 /* Set global sizes if not already set */ 2195 if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) { 2196 ierr = MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);CHKERRQ(ierr); 2197 } else { /* Check if the matrix global sizes are correct */ 2198 ierr = MatGetSize(newmat,&rows,&cols);CHKERRQ(ierr); 2199 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); 2200 } 2201 2202 /* read in row lengths */ 2203 ierr = PetscMalloc((M+extra_rows)*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr); 2204 ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); 2205 for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1; 2206 2207 /* read in column indices */ 2208 ierr = PetscMalloc((nz+extra_rows)*sizeof(PetscInt),&jj);CHKERRQ(ierr); 2209 ierr = PetscBinaryRead(fd,jj,nz,PETSC_INT);CHKERRQ(ierr); 2210 for (i=0; i<extra_rows; i++) jj[nz+i] = M+i; 2211 2212 /* loop over row lengths determining block row lengths */ 2213 ierr = PetscMalloc(mbs*sizeof(PetscInt),&s_browlengths);CHKERRQ(ierr); 2214 ierr = PetscMemzero(s_browlengths,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2215 ierr = PetscMalloc2(mbs,PetscInt,&mask,mbs,PetscInt,&masked);CHKERRQ(ierr); 2216 ierr = PetscMemzero(mask,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2217 rowcount = 0; 2218 nzcount = 0; 2219 for (i=0; i<mbs; i++) { 2220 nmask = 0; 2221 for (j=0; j<bs; j++) { 2222 kmax = rowlengths[rowcount]; 2223 for (k=0; k<kmax; k++) { 2224 tmp = jj[nzcount++]/bs; /* block col. index */ 2225 if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;} 2226 } 2227 rowcount++; 2228 } 2229 s_browlengths[i] += nmask; 2230 2231 /* zero out the mask elements we set */ 2232 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2233 } 2234 2235 /* Do preallocation */ 2236 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);CHKERRQ(ierr); 2237 a = (Mat_SeqSBAIJ*)newmat->data; 2238 2239 /* set matrix "i" values */ 2240 a->i[0] = 0; 2241 for (i=1; i<= mbs; i++) { 2242 a->i[i] = a->i[i-1] + s_browlengths[i-1]; 2243 a->ilen[i-1] = s_browlengths[i-1]; 2244 } 2245 a->nz = a->i[mbs]; 2246 2247 /* read in nonzero values */ 2248 ierr = PetscMalloc((nz+extra_rows)*sizeof(PetscScalar),&aa);CHKERRQ(ierr); 2249 ierr = PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);CHKERRQ(ierr); 2250 for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0; 2251 2252 /* set "a" and "j" values into matrix */ 2253 nzcount = 0; jcount = 0; 2254 for (i=0; i<mbs; i++) { 2255 nzcountb = nzcount; 2256 nmask = 0; 2257 for (j=0; j<bs; j++) { 2258 kmax = rowlengths[i*bs+j]; 2259 for (k=0; k<kmax; k++) { 2260 tmp = jj[nzcount++]/bs; /* block col. index */ 2261 if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;} 2262 } 2263 } 2264 /* sort the masked values */ 2265 ierr = PetscSortInt(nmask,masked);CHKERRQ(ierr); 2266 2267 /* set "j" values into matrix */ 2268 maskcount = 1; 2269 for (j=0; j<nmask; j++) { 2270 a->j[jcount++] = masked[j]; 2271 mask[masked[j]] = maskcount++; 2272 } 2273 2274 /* set "a" values into matrix */ 2275 ishift = bs2*a->i[i]; 2276 for (j=0; j<bs; j++) { 2277 kmax = rowlengths[i*bs+j]; 2278 for (k=0; k<kmax; k++) { 2279 tmp = jj[nzcountb]/bs ; /* block col. index */ 2280 if (tmp >= i){ 2281 block = mask[tmp] - 1; 2282 point = jj[nzcountb] - bs*tmp; 2283 idx = ishift + bs2*block + j + bs*point; 2284 a->a[idx] = aa[nzcountb]; 2285 } 2286 nzcountb++; 2287 } 2288 } 2289 /* zero out the mask elements we set */ 2290 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2291 } 2292 if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix"); 2293 2294 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2295 ierr = PetscFree(s_browlengths);CHKERRQ(ierr); 2296 ierr = PetscFree(aa);CHKERRQ(ierr); 2297 ierr = PetscFree(jj);CHKERRQ(ierr); 2298 ierr = PetscFree2(mask,masked);CHKERRQ(ierr); 2299 2300 ierr = MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2301 ierr = MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2302 ierr = MatView_Private(newmat);CHKERRQ(ierr); 2303 PetscFunctionReturn(0); 2304 } 2305 2306 #undef __FUNCT__ 2307 #define __FUNCT__ "MatCreateSeqSBAIJWithArrays" 2308 /*@ 2309 MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements 2310 (upper triangular entries in CSR format) provided by the user. 2311 2312 Collective on MPI_Comm 2313 2314 Input Parameters: 2315 + comm - must be an MPI communicator of size 1 2316 . bs - size of block 2317 . m - number of rows 2318 . n - number of columns 2319 . i - row indices 2320 . j - column indices 2321 - a - matrix values 2322 2323 Output Parameter: 2324 . mat - the matrix 2325 2326 Level: advanced 2327 2328 Notes: 2329 The i, j, and a arrays are not copied by this routine, the user must free these arrays 2330 once the matrix is destroyed 2331 2332 You cannot set new nonzero locations into this matrix, that will generate an error. 2333 2334 The i and j indices are 0 based 2335 2336 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 2337 it is the regular CSR format excluding the lower triangular elements. 2338 2339 .seealso: MatCreate(), MatCreateMPISBAIJ(), MatCreateSeqSBAIJ() 2340 2341 @*/ 2342 PetscErrorCode PETSCMAT_DLLEXPORT MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt* i,PetscInt*j,PetscScalar *a,Mat *mat) 2343 { 2344 PetscErrorCode ierr; 2345 PetscInt ii; 2346 Mat_SeqSBAIJ *sbaij; 2347 2348 PetscFunctionBegin; 2349 if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs); 2350 if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 2351 2352 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 2353 ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); 2354 ierr = MatSetType(*mat,MATSEQSBAIJ);CHKERRQ(ierr); 2355 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);CHKERRQ(ierr); 2356 sbaij = (Mat_SeqSBAIJ*)(*mat)->data; 2357 ierr = PetscMalloc2(m,PetscInt,&sbaij->imax,m,PetscInt,&sbaij->ilen);CHKERRQ(ierr); 2358 ierr = PetscLogObjectMemory(*mat,2*m*sizeof(PetscInt));CHKERRQ(ierr); 2359 2360 sbaij->i = i; 2361 sbaij->j = j; 2362 sbaij->a = a; 2363 sbaij->singlemalloc = PETSC_FALSE; 2364 sbaij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/ 2365 sbaij->free_a = PETSC_FALSE; 2366 sbaij->free_ij = PETSC_FALSE; 2367 2368 for (ii=0; ii<m; ii++) { 2369 sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii]; 2370 #if defined(PETSC_USE_DEBUG) 2371 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]); 2372 #endif 2373 } 2374 #if defined(PETSC_USE_DEBUG) 2375 for (ii=0; ii<sbaij->i[m]; ii++) { 2376 if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]); 2377 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]); 2378 } 2379 #endif 2380 2381 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2382 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2383 PetscFunctionReturn(0); 2384 } 2385 2386 2387 2388 2389 2390