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 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,PetscTruth); 15 #define CHUNKSIZE 10 16 17 18 /* 19 Checks for missing diagonals 20 */ 21 #undef __FUNCT__ 22 #define __FUNCT__ "MatMissingDiagonal_SeqSBAIJ" 23 PetscErrorCode MatMissingDiagonal_SeqSBAIJ(Mat A,PetscTruth *missing,PetscInt *dd) 24 { 25 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 26 PetscErrorCode ierr; 27 PetscInt *diag,*jj = a->j,i; 28 29 PetscFunctionBegin; 30 ierr = MatMarkDiagonal_SeqSBAIJ(A);CHKERRQ(ierr); 31 diag = a->diag; 32 *missing = PETSC_FALSE; 33 for (i=0; i<a->mbs; i++) { 34 if (jj[diag[i]] != i) { 35 *missing = PETSC_TRUE; 36 if (dd) *dd = i; 37 break; 38 } 39 } 40 PetscFunctionReturn(0); 41 } 42 43 #undef __FUNCT__ 44 #define __FUNCT__ "MatMarkDiagonal_SeqSBAIJ" 45 PetscErrorCode MatMarkDiagonal_SeqSBAIJ(Mat A) 46 { 47 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 48 PetscErrorCode ierr; 49 PetscInt i; 50 51 PetscFunctionBegin; 52 if (!a->diag) { 53 ierr = PetscMalloc(a->mbs*sizeof(PetscInt),&a->diag);CHKERRQ(ierr); 54 ierr = PetscLogObjectMemory(A,a->mbs*sizeof(PetscInt));CHKERRQ(ierr); 55 a->free_diag = PETSC_TRUE; 56 } 57 for (i=0; i<a->mbs; i++) a->diag[i] = a->i[i]; 58 PetscFunctionReturn(0); 59 } 60 61 #undef __FUNCT__ 62 #define __FUNCT__ "MatGetRowIJ_SeqSBAIJ" 63 static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscTruth symmetric,PetscTruth blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscTruth *done) 64 { 65 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 66 PetscInt i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs; 67 PetscErrorCode ierr; 68 69 PetscFunctionBegin; 70 *nn = n; 71 if (!ia) PetscFunctionReturn(0); 72 if (!blockcompressed) { 73 /* malloc & create the natural set of indices */ 74 ierr = PetscMalloc2((n+1)*bs,PetscInt,ia,nz*bs,PetscInt,ja);CHKERRQ(ierr); 75 for (i=0; i<n+1; i++) { 76 for (j=0; j<bs; j++) { 77 *ia[i*bs+j] = a->i[i]*bs+j+oshift; 78 } 79 } 80 for (i=0; i<nz; i++) { 81 for (j=0; j<bs; j++) { 82 *ja[i*bs+j] = a->j[i]*bs+j+oshift; 83 } 84 } 85 } else { /* blockcompressed */ 86 if (oshift == 1) { 87 /* temporarily add 1 to i and j indices */ 88 for (i=0; i<nz; i++) a->j[i]++; 89 for (i=0; i<n+1; i++) a->i[i]++; 90 } 91 *ia = a->i; *ja = a->j; 92 } 93 94 PetscFunctionReturn(0); 95 } 96 97 #undef __FUNCT__ 98 #define __FUNCT__ "MatRestoreRowIJ_SeqSBAIJ" 99 static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscTruth symmetric,PetscTruth blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscTruth *done) 100 { 101 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 102 PetscInt i,n = a->mbs,nz = a->i[n]; 103 PetscErrorCode ierr; 104 105 PetscFunctionBegin; 106 if (!ia) PetscFunctionReturn(0); 107 108 if (!blockcompressed) { 109 ierr = PetscFree2(*ia,*ja);CHKERRQ(ierr); 110 } else if (oshift == 1) { /* blockcompressed */ 111 for (i=0; i<nz; i++) a->j[i]--; 112 for (i=0; i<n+1; i++) a->i[i]--; 113 } 114 115 PetscFunctionReturn(0); 116 } 117 118 #undef __FUNCT__ 119 #define __FUNCT__ "MatDestroy_SeqSBAIJ" 120 PetscErrorCode MatDestroy_SeqSBAIJ(Mat A) 121 { 122 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 123 PetscErrorCode ierr; 124 125 PetscFunctionBegin; 126 #if defined(PETSC_USE_LOG) 127 PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz); 128 #endif 129 ierr = MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);CHKERRQ(ierr); 130 if (a->free_diag){ierr = PetscFree(a->diag);CHKERRQ(ierr);} 131 if (a->row) {ierr = ISDestroy(a->row);CHKERRQ(ierr);} 132 if (a->col){ierr = ISDestroy(a->col);CHKERRQ(ierr);} 133 if (a->icol) {ierr = ISDestroy(a->icol);CHKERRQ(ierr);} 134 if (a->idiag) {ierr = PetscFree(a->idiag);CHKERRQ(ierr);} 135 if (a->inode.size) {ierr = PetscFree(a->inode.size);CHKERRQ(ierr);} 136 if (a->free_diag) {ierr = PetscFree(a->diag);CHKERRQ(ierr);} 137 if (a->free_imax_ilen) {ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr);} 138 ierr = PetscFree(a->solve_work);CHKERRQ(ierr); 139 ierr = PetscFree(a->sor_work);CHKERRQ(ierr); 140 ierr = PetscFree(a->solves_work);CHKERRQ(ierr); 141 ierr = PetscFree(a->mult_work);CHKERRQ(ierr); 142 ierr = PetscFree(a->saved_values);CHKERRQ(ierr); 143 ierr = PetscFree(a->xtoy);CHKERRQ(ierr); 144 if (a->free_jshort) {ierr = PetscFree(a->jshort);CHKERRQ(ierr);} 145 ierr = PetscFree(a->inew);CHKERRQ(ierr); 146 if (a->parent) {ierr = MatDestroy(a->parent);CHKERRQ(ierr);} 147 ierr = PetscFree(a);CHKERRQ(ierr); 148 149 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 150 ierr = PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C","",PETSC_NULL);CHKERRQ(ierr); 151 ierr = PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C","",PETSC_NULL);CHKERRQ(ierr); 152 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C","",PETSC_NULL);CHKERRQ(ierr); 153 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C","",PETSC_NULL);CHKERRQ(ierr); 154 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C","",PETSC_NULL);CHKERRQ(ierr); 155 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C","",PETSC_NULL);CHKERRQ(ierr); 156 PetscFunctionReturn(0); 157 } 158 159 #undef __FUNCT__ 160 #define __FUNCT__ "MatSetOption_SeqSBAIJ" 161 PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscTruth flg) 162 { 163 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 164 PetscErrorCode ierr; 165 166 PetscFunctionBegin; 167 switch (op) { 168 case MAT_ROW_ORIENTED: 169 a->roworiented = flg; 170 break; 171 case MAT_KEEP_NONZERO_PATTERN: 172 a->keepnonzeropattern = flg; 173 break; 174 case MAT_NEW_NONZERO_LOCATIONS: 175 a->nonew = (flg ? 0 : 1); 176 break; 177 case MAT_NEW_NONZERO_LOCATION_ERR: 178 a->nonew = (flg ? -1 : 0); 179 break; 180 case MAT_NEW_NONZERO_ALLOCATION_ERR: 181 a->nonew = (flg ? -2 : 0); 182 break; 183 case MAT_UNUSED_NONZERO_LOCATION_ERR: 184 a->nounused = (flg ? -1 : 0); 185 break; 186 case MAT_NEW_DIAGONALS: 187 case MAT_IGNORE_OFF_PROC_ENTRIES: 188 case MAT_USE_HASH_TABLE: 189 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 190 break; 191 case MAT_HERMITIAN: 192 if (!A->assembled) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first"); 193 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 194 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort; 195 } else if (A->cmap->bs == 1) { 196 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian; 197 } else SETERRQ(PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1"); 198 break; 199 case MAT_SYMMETRIC: 200 case MAT_STRUCTURALLY_SYMMETRIC: 201 case MAT_SYMMETRY_ETERNAL: 202 if (!flg) SETERRQ(PETSC_ERR_SUP,"Matrix must be symmetric"); 203 ierr = PetscInfo1(A,"Option %s not relevent\n",MatOptions[op]);CHKERRQ(ierr); 204 break; 205 case MAT_IGNORE_LOWER_TRIANGULAR: 206 a->ignore_ltriangular = flg; 207 break; 208 case MAT_ERROR_LOWER_TRIANGULAR: 209 a->ignore_ltriangular = flg; 210 break; 211 case MAT_GETROW_UPPERTRIANGULAR: 212 a->getrow_utriangular = flg; 213 break; 214 default: 215 SETERRQ1(PETSC_ERR_SUP,"unknown option %d",op); 216 } 217 PetscFunctionReturn(0); 218 } 219 220 #undef __FUNCT__ 221 #define __FUNCT__ "MatGetRow_SeqSBAIJ" 222 PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *ncols,PetscInt **cols,PetscScalar **v) 223 { 224 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 225 PetscErrorCode ierr; 226 PetscInt itmp,i,j,k,M,*ai,*aj,bs,bn,bp,*cols_i,bs2; 227 MatScalar *aa,*aa_i; 228 PetscScalar *v_i; 229 230 PetscFunctionBegin; 231 if (A && !a->getrow_utriangular) SETERRQ(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()"); 232 /* Get the upper triangular part of the row */ 233 bs = A->rmap->bs; 234 ai = a->i; 235 aj = a->j; 236 aa = a->a; 237 bs2 = a->bs2; 238 239 if (row < 0 || row >= A->rmap->N) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE, "Row %D out of range", row); 240 241 bn = row/bs; /* Block number */ 242 bp = row % bs; /* Block position */ 243 M = ai[bn+1] - ai[bn]; 244 *ncols = bs*M; 245 246 if (v) { 247 *v = 0; 248 if (*ncols) { 249 ierr = PetscMalloc((*ncols+row)*sizeof(PetscScalar),v);CHKERRQ(ierr); 250 for (i=0; i<M; i++) { /* for each block in the block row */ 251 v_i = *v + i*bs; 252 aa_i = aa + bs2*(ai[bn] + i); 253 for (j=bp,k=0; j<bs2; j+=bs,k++) {v_i[k] = aa_i[j];} 254 } 255 } 256 } 257 258 if (cols) { 259 *cols = 0; 260 if (*ncols) { 261 ierr = PetscMalloc((*ncols+row)*sizeof(PetscInt),cols);CHKERRQ(ierr); 262 for (i=0; i<M; i++) { /* for each block in the block row */ 263 cols_i = *cols + i*bs; 264 itmp = bs*aj[ai[bn] + i]; 265 for (j=0; j<bs; j++) {cols_i[j] = itmp++;} 266 } 267 } 268 } 269 270 /*search column A(0:row-1,row) (=A(row,0:row-1)). Could be expensive! */ 271 /* this segment is currently removed, so only entries in the upper triangle are obtained */ 272 #ifdef column_search 273 v_i = *v + M*bs; 274 cols_i = *cols + M*bs; 275 for (i=0; i<bn; i++){ /* for each block row */ 276 M = ai[i+1] - ai[i]; 277 for (j=0; j<M; j++){ 278 itmp = aj[ai[i] + j]; /* block column value */ 279 if (itmp == bn){ 280 aa_i = aa + bs2*(ai[i] + j) + bs*bp; 281 for (k=0; k<bs; k++) { 282 *cols_i++ = i*bs+k; 283 *v_i++ = aa_i[k]; 284 } 285 *ncols += bs; 286 break; 287 } 288 } 289 } 290 #endif 291 PetscFunctionReturn(0); 292 } 293 294 #undef __FUNCT__ 295 #define __FUNCT__ "MatRestoreRow_SeqSBAIJ" 296 PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 297 { 298 PetscErrorCode ierr; 299 300 PetscFunctionBegin; 301 if (idx) {ierr = PetscFree(*idx);CHKERRQ(ierr);} 302 if (v) {ierr = PetscFree(*v);CHKERRQ(ierr);} 303 PetscFunctionReturn(0); 304 } 305 306 #undef __FUNCT__ 307 #define __FUNCT__ "MatGetRowUpperTriangular_SeqSBAIJ" 308 PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A) 309 { 310 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 311 312 PetscFunctionBegin; 313 a->getrow_utriangular = PETSC_TRUE; 314 PetscFunctionReturn(0); 315 } 316 #undef __FUNCT__ 317 #define __FUNCT__ "MatRestoreRowUpperTriangular_SeqSBAIJ" 318 PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A) 319 { 320 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 321 322 PetscFunctionBegin; 323 a->getrow_utriangular = PETSC_FALSE; 324 PetscFunctionReturn(0); 325 } 326 327 #undef __FUNCT__ 328 #define __FUNCT__ "MatTranspose_SeqSBAIJ" 329 PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B) 330 { 331 PetscErrorCode ierr; 332 PetscFunctionBegin; 333 if (reuse == MAT_INITIAL_MATRIX || *B != A) { 334 ierr = MatDuplicate(A,MAT_COPY_VALUES,B);CHKERRQ(ierr); 335 } 336 PetscFunctionReturn(0); 337 } 338 339 #undef __FUNCT__ 340 #define __FUNCT__ "MatView_SeqSBAIJ_ASCII" 341 static PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer) 342 { 343 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 344 PetscErrorCode ierr; 345 PetscInt i,j,bs = A->rmap->bs,k,l,bs2=a->bs2; 346 const char *name; 347 PetscViewerFormat format; 348 349 PetscFunctionBegin; 350 ierr = PetscObjectGetName((PetscObject)A,&name);CHKERRQ(ierr); 351 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 352 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 353 ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); 354 } else if (format == PETSC_VIEWER_ASCII_MATLAB) { 355 Mat aij; 356 357 if (A->factor && bs>1){ 358 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); 359 PetscFunctionReturn(0); 360 } 361 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);CHKERRQ(ierr); 362 ierr = MatView(aij,viewer);CHKERRQ(ierr); 363 ierr = MatDestroy(aij);CHKERRQ(ierr); 364 } else if (format == PETSC_VIEWER_ASCII_COMMON) { 365 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 366 for (i=0; i<a->mbs; i++) { 367 for (j=0; j<bs; j++) { 368 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 369 for (k=a->i[i]; k<a->i[i+1]; k++) { 370 for (l=0; l<bs; l++) { 371 #if defined(PETSC_USE_COMPLEX) 372 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 373 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l, 374 PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 375 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 376 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l, 377 PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 378 } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 379 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 380 } 381 #else 382 if (a->a[bs2*k + l*bs + j] != 0.0) { 383 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 384 } 385 #endif 386 } 387 } 388 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 389 } 390 } 391 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 392 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 393 PetscFunctionReturn(0); 394 } else { 395 if (A->factor && bs>1){ 396 ierr = PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored. MatView_SeqSBAIJ_ASCII() may not display complete or logically correct entries!\n");CHKERRQ(ierr); 397 } 398 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 399 for (i=0; i<a->mbs; i++) { 400 for (j=0; j<bs; j++) { 401 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 402 for (k=a->i[i]; k<a->i[i+1]; k++) { 403 for (l=0; l<bs; l++) { 404 #if defined(PETSC_USE_COMPLEX) 405 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) { 406 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l, 407 PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 408 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) { 409 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l, 410 PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 411 } else { 412 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 413 } 414 #else 415 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 416 #endif 417 } 418 } 419 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 420 } 421 } 422 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 423 } 424 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 425 PetscFunctionReturn(0); 426 } 427 428 #undef __FUNCT__ 429 #define __FUNCT__ "MatView_SeqSBAIJ_Draw_Zoom" 430 static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa) 431 { 432 Mat A = (Mat) Aa; 433 Mat_SeqSBAIJ *a=(Mat_SeqSBAIJ*)A->data; 434 PetscErrorCode ierr; 435 PetscInt row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2; 436 PetscMPIInt rank; 437 PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r; 438 MatScalar *aa; 439 MPI_Comm comm; 440 PetscViewer viewer; 441 442 PetscFunctionBegin; 443 /* 444 This is nasty. If this is called from an originally parallel matrix 445 then all processes call this,but only the first has the matrix so the 446 rest should return immediately. 447 */ 448 ierr = PetscObjectGetComm((PetscObject)draw,&comm);CHKERRQ(ierr); 449 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 450 if (rank) PetscFunctionReturn(0); 451 452 ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr); 453 454 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 455 PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric"); 456 457 /* loop over matrix elements drawing boxes */ 458 color = PETSC_DRAW_BLUE; 459 for (i=0,row=0; i<mbs; i++,row+=bs) { 460 for (j=a->i[i]; j<a->i[i+1]; j++) { 461 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 462 x_l = a->j[j]*bs; x_r = x_l + 1.0; 463 aa = a->a + j*bs2; 464 for (k=0; k<bs; k++) { 465 for (l=0; l<bs; l++) { 466 if (PetscRealPart(*aa++) >= 0.) continue; 467 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 468 } 469 } 470 } 471 } 472 color = PETSC_DRAW_CYAN; 473 for (i=0,row=0; i<mbs; i++,row+=bs) { 474 for (j=a->i[i]; j<a->i[i+1]; j++) { 475 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 476 x_l = a->j[j]*bs; x_r = x_l + 1.0; 477 aa = a->a + j*bs2; 478 for (k=0; k<bs; k++) { 479 for (l=0; l<bs; l++) { 480 if (PetscRealPart(*aa++) != 0.) continue; 481 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 482 } 483 } 484 } 485 } 486 487 color = PETSC_DRAW_RED; 488 for (i=0,row=0; i<mbs; i++,row+=bs) { 489 for (j=a->i[i]; j<a->i[i+1]; j++) { 490 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 491 x_l = a->j[j]*bs; x_r = x_l + 1.0; 492 aa = a->a + j*bs2; 493 for (k=0; k<bs; k++) { 494 for (l=0; l<bs; l++) { 495 if (PetscRealPart(*aa++) <= 0.) continue; 496 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 497 } 498 } 499 } 500 } 501 PetscFunctionReturn(0); 502 } 503 504 #undef __FUNCT__ 505 #define __FUNCT__ "MatView_SeqSBAIJ_Draw" 506 static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer) 507 { 508 PetscErrorCode ierr; 509 PetscReal xl,yl,xr,yr,w,h; 510 PetscDraw draw; 511 PetscTruth isnull; 512 513 PetscFunctionBegin; 514 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 515 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 516 517 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);CHKERRQ(ierr); 518 xr = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0; 519 xr += w; yr += h; xl = -w; yl = -h; 520 ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr); 521 ierr = PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);CHKERRQ(ierr); 522 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",PETSC_NULL);CHKERRQ(ierr); 523 PetscFunctionReturn(0); 524 } 525 526 #undef __FUNCT__ 527 #define __FUNCT__ "MatView_SeqSBAIJ" 528 PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer) 529 { 530 PetscErrorCode ierr; 531 PetscTruth iascii,isdraw; 532 FILE *file = 0; 533 534 PetscFunctionBegin; 535 ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_ASCII,&iascii);CHKERRQ(ierr); 536 ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_DRAW,&isdraw);CHKERRQ(ierr); 537 if (iascii){ 538 ierr = MatView_SeqSBAIJ_ASCII(A,viewer);CHKERRQ(ierr); 539 } else if (isdraw) { 540 ierr = MatView_SeqSBAIJ_Draw(A,viewer);CHKERRQ(ierr); 541 } else { 542 Mat B; 543 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 544 ierr = MatView(B,viewer);CHKERRQ(ierr); 545 ierr = MatDestroy(B);CHKERRQ(ierr); 546 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 547 if (file) { 548 fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs); 549 } 550 } 551 PetscFunctionReturn(0); 552 } 553 554 555 #undef __FUNCT__ 556 #define __FUNCT__ "MatGetValues_SeqSBAIJ" 557 PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[]) 558 { 559 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 560 PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j; 561 PetscInt *ai = a->i,*ailen = a->ilen; 562 PetscInt brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2; 563 MatScalar *ap,*aa = a->a; 564 565 PetscFunctionBegin; 566 for (k=0; k<m; k++) { /* loop over rows */ 567 row = im[k]; brow = row/bs; 568 if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */ 569 if (row >= A->rmap->N) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1); 570 rp = aj + ai[brow] ; ap = aa + bs2*ai[brow] ; 571 nrow = ailen[brow]; 572 for (l=0; l<n; l++) { /* loop over columns */ 573 if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */ 574 if (in[l] >= A->cmap->n) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->cmap->n-1); 575 col = in[l] ; 576 bcol = col/bs; 577 cidx = col%bs; 578 ridx = row%bs; 579 high = nrow; 580 low = 0; /* assume unsorted */ 581 while (high-low > 5) { 582 t = (low+high)/2; 583 if (rp[t] > bcol) high = t; 584 else low = t; 585 } 586 for (i=low; i<high; i++) { 587 if (rp[i] > bcol) break; 588 if (rp[i] == bcol) { 589 *v++ = ap[bs2*i+bs*cidx+ridx]; 590 goto finished; 591 } 592 } 593 *v++ = 0.0; 594 finished:; 595 } 596 } 597 PetscFunctionReturn(0); 598 } 599 600 601 #undef __FUNCT__ 602 #define __FUNCT__ "MatSetValuesBlocked_SeqSBAIJ" 603 PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 604 { 605 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 606 PetscErrorCode ierr; 607 PetscInt *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1; 608 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen; 609 PetscInt *aj=a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval; 610 PetscTruth roworiented=a->roworiented; 611 const PetscScalar *value = v; 612 MatScalar *ap,*aa = a->a,*bap; 613 614 PetscFunctionBegin; 615 if (roworiented) { 616 stepval = (n-1)*bs; 617 } else { 618 stepval = (m-1)*bs; 619 } 620 for (k=0; k<m; k++) { /* loop over added rows */ 621 row = im[k]; 622 if (row < 0) continue; 623 #if defined(PETSC_USE_DEBUG) 624 if (row >= a->mbs) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1); 625 #endif 626 rp = aj + ai[row]; 627 ap = aa + bs2*ai[row]; 628 rmax = imax[row]; 629 nrow = ailen[row]; 630 low = 0; 631 high = nrow; 632 for (l=0; l<n; l++) { /* loop over added columns */ 633 if (in[l] < 0) continue; 634 col = in[l]; 635 #if defined(PETSC_USE_DEBUG) 636 if (col >= a->nbs) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1); 637 #endif 638 if (col < row) { 639 if (a->ignore_ltriangular) { 640 continue; /* ignore lower triangular block */ 641 } else { 642 SETERRQ(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)"); 643 } 644 } 645 if (roworiented) { 646 value = v + k*(stepval+bs)*bs + l*bs; 647 } else { 648 value = v + l*(stepval+bs)*bs + k*bs; 649 } 650 if (col <= lastcol) low = 0; else high = nrow; 651 lastcol = col; 652 while (high-low > 7) { 653 t = (low+high)/2; 654 if (rp[t] > col) high = t; 655 else low = t; 656 } 657 for (i=low; i<high; i++) { 658 if (rp[i] > col) break; 659 if (rp[i] == col) { 660 bap = ap + bs2*i; 661 if (roworiented) { 662 if (is == ADD_VALUES) { 663 for (ii=0; ii<bs; ii++,value+=stepval) { 664 for (jj=ii; jj<bs2; jj+=bs) { 665 bap[jj] += *value++; 666 } 667 } 668 } else { 669 for (ii=0; ii<bs; ii++,value+=stepval) { 670 for (jj=ii; jj<bs2; jj+=bs) { 671 bap[jj] = *value++; 672 } 673 } 674 } 675 } else { 676 if (is == ADD_VALUES) { 677 for (ii=0; ii<bs; ii++,value+=stepval) { 678 for (jj=0; jj<bs; jj++) { 679 *bap++ += *value++; 680 } 681 } 682 } else { 683 for (ii=0; ii<bs; ii++,value+=stepval) { 684 for (jj=0; jj<bs; jj++) { 685 *bap++ = *value++; 686 } 687 } 688 } 689 } 690 goto noinsert2; 691 } 692 } 693 if (nonew == 1) goto noinsert2; 694 if (nonew == -1) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 695 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 696 N = nrow++ - 1; high++; 697 /* shift up all the later entries in this row */ 698 for (ii=N; ii>=i; ii--) { 699 rp[ii+1] = rp[ii]; 700 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 701 } 702 if (N >= i) { 703 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 704 } 705 rp[i] = col; 706 bap = ap + bs2*i; 707 if (roworiented) { 708 for (ii=0; ii<bs; ii++,value+=stepval) { 709 for (jj=ii; jj<bs2; jj+=bs) { 710 bap[jj] = *value++; 711 } 712 } 713 } else { 714 for (ii=0; ii<bs; ii++,value+=stepval) { 715 for (jj=0; jj<bs; jj++) { 716 *bap++ = *value++; 717 } 718 } 719 } 720 noinsert2:; 721 low = i; 722 } 723 ailen[row] = nrow; 724 } 725 PetscFunctionReturn(0); 726 } 727 728 /* 729 This is not yet used 730 */ 731 #undef __FUNCT__ 732 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode" 733 PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A) 734 { 735 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 736 PetscErrorCode ierr; 737 const PetscInt *ai = a->i, *aj = a->j,*cols; 738 PetscInt i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts; 739 PetscTruth flag; 740 741 PetscFunctionBegin; 742 ierr = PetscMalloc(m*sizeof(PetscInt),&ns);CHKERRQ(ierr); 743 while (i < m){ 744 nzx = ai[i+1] - ai[i]; /* Number of nonzeros */ 745 /* Limits the number of elements in a node to 'a->inode.limit' */ 746 for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) { 747 nzy = ai[j+1] - ai[j]; 748 if (nzy != (nzx - j + i)) break; 749 ierr = PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);CHKERRQ(ierr); 750 if (!flag) break; 751 } 752 ns[node_count++] = blk_size; 753 i = j; 754 } 755 if (!a->inode.size && m && node_count > .9*m) { 756 ierr = PetscFree(ns);CHKERRQ(ierr); 757 ierr = PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);CHKERRQ(ierr); 758 } else { 759 a->inode.node_count = node_count; 760 ierr = PetscMalloc(node_count*sizeof(PetscInt),&a->inode.size);CHKERRQ(ierr); 761 ierr = PetscLogObjectMemory(A,node_count*sizeof(PetscInt));CHKERRQ(ierr); 762 ierr = PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt)); 763 ierr = PetscFree(ns);CHKERRQ(ierr); 764 ierr = PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);CHKERRQ(ierr); 765 766 /* count collections of adjacent columns in each inode */ 767 row = 0; 768 cnt = 0; 769 for (i=0; i<node_count; i++) { 770 cols = aj + ai[row] + a->inode.size[i]; 771 nz = ai[row+1] - ai[row] - a->inode.size[i]; 772 for (j=1; j<nz; j++) { 773 if (cols[j] != cols[j-1]+1) { 774 cnt++; 775 } 776 } 777 cnt++; 778 row += a->inode.size[i]; 779 } 780 ierr = PetscMalloc(2*cnt*sizeof(PetscInt),&counts);CHKERRQ(ierr); 781 cnt = 0; 782 row = 0; 783 for (i=0; i<node_count; i++) { 784 cols = aj + ai[row] + a->inode.size[i]; 785 CHKMEMQ; 786 counts[2*cnt] = cols[0]; 787 CHKMEMQ; 788 nz = ai[row+1] - ai[row] - a->inode.size[i]; 789 cnt2 = 1; 790 for (j=1; j<nz; j++) { 791 if (cols[j] != cols[j-1]+1) { 792 CHKMEMQ; 793 counts[2*(cnt++)+1] = cnt2; 794 counts[2*cnt] = cols[j]; 795 CHKMEMQ; 796 cnt2 = 1; 797 } else cnt2++; 798 } 799 CHKMEMQ; 800 counts[2*(cnt++)+1] = cnt2; 801 CHKMEMQ; 802 row += a->inode.size[i]; 803 } 804 ierr = PetscIntView(2*cnt,counts,0); 805 } 806 PetscFunctionReturn(0); 807 } 808 809 #undef __FUNCT__ 810 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ" 811 PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode) 812 { 813 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 814 PetscErrorCode ierr; 815 PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax; 816 PetscInt m = A->rmap->N,*ip,N,*ailen = a->ilen; 817 PetscInt mbs = a->mbs,bs2 = a->bs2,rmax = 0; 818 MatScalar *aa = a->a,*ap; 819 820 PetscFunctionBegin; 821 if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); 822 823 if (m) rmax = ailen[0]; 824 for (i=1; i<mbs; i++) { 825 /* move each row back by the amount of empty slots (fshift) before it*/ 826 fshift += imax[i-1] - ailen[i-1]; 827 rmax = PetscMax(rmax,ailen[i]); 828 if (fshift) { 829 ip = aj + ai[i]; ap = aa + bs2*ai[i]; 830 N = ailen[i]; 831 for (j=0; j<N; j++) { 832 ip[j-fshift] = ip[j]; 833 ierr = PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 834 } 835 } 836 ai[i] = ai[i-1] + ailen[i-1]; 837 } 838 if (mbs) { 839 fshift += imax[mbs-1] - ailen[mbs-1]; 840 ai[mbs] = ai[mbs-1] + ailen[mbs-1]; 841 } 842 /* reset ilen and imax for each row */ 843 for (i=0; i<mbs; i++) { 844 ailen[i] = imax[i] = ai[i+1] - ai[i]; 845 } 846 a->nz = ai[mbs]; 847 848 /* diagonals may have moved, reset it */ 849 if (a->diag) { 850 ierr = PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));CHKERRQ(ierr); 851 } 852 if (fshift && a->nounused == -1) { 853 SETERRQ4(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); 854 } 855 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); 856 ierr = PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);CHKERRQ(ierr); 857 ierr = PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);CHKERRQ(ierr); 858 a->reallocs = 0; 859 A->info.nz_unneeded = (PetscReal)fshift*bs2; 860 a->idiagvalid = PETSC_FALSE; 861 862 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 863 if (!a->jshort) { 864 ierr = PetscMalloc(a->i[A->rmap->n]*sizeof(unsigned short),&a->jshort);CHKERRQ(ierr); 865 ierr = PetscLogObjectMemory(A,a->i[A->rmap->n]*sizeof(unsigned short));CHKERRQ(ierr); 866 for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i]; 867 A->ops->mult = MatMult_SeqSBAIJ_1_ushort; 868 A->ops->sor = MatSOR_SeqSBAIJ_ushort; 869 a->free_jshort = PETSC_TRUE; 870 } 871 } 872 PetscFunctionReturn(0); 873 } 874 875 /* 876 This function returns an array of flags which indicate the locations of contiguous 877 blocks that should be zeroed. for eg: if bs = 3 and is = [0,1,2,3,5,6,7,8,9] 878 then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)] 879 Assume: sizes should be long enough to hold all the values. 880 */ 881 #undef __FUNCT__ 882 #define __FUNCT__ "MatZeroRows_SeqSBAIJ_Check_Blocks" 883 PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max) 884 { 885 PetscInt i,j,k,row; 886 PetscTruth flg; 887 888 PetscFunctionBegin; 889 for (i=0,j=0; i<n; j++) { 890 row = idx[i]; 891 if (row%bs!=0) { /* Not the begining of a block */ 892 sizes[j] = 1; 893 i++; 894 } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */ 895 sizes[j] = 1; /* Also makes sure atleast 'bs' values exist for next else */ 896 i++; 897 } else { /* Begining of the block, so check if the complete block exists */ 898 flg = PETSC_TRUE; 899 for (k=1; k<bs; k++) { 900 if (row+k != idx[i+k]) { /* break in the block */ 901 flg = PETSC_FALSE; 902 break; 903 } 904 } 905 if (flg) { /* No break in the bs */ 906 sizes[j] = bs; 907 i+= bs; 908 } else { 909 sizes[j] = 1; 910 i++; 911 } 912 } 913 } 914 *bs_max = j; 915 PetscFunctionReturn(0); 916 } 917 918 919 /* Only add/insert a(i,j) with i<=j (blocks). 920 Any a(i,j) with i>j input by user is ingored. 921 */ 922 923 #undef __FUNCT__ 924 #define __FUNCT__ "MatSetValues_SeqSBAIJ" 925 PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 926 { 927 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 928 PetscErrorCode ierr; 929 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1; 930 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented; 931 PetscInt *aj=a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol; 932 PetscInt ridx,cidx,bs2=a->bs2; 933 MatScalar *ap,value,*aa=a->a,*bap; 934 935 PetscFunctionBegin; 936 if (v) PetscValidScalarPointer(v,6); 937 for (k=0; k<m; k++) { /* loop over added rows */ 938 row = im[k]; /* row number */ 939 brow = row/bs; /* block row number */ 940 if (row < 0) continue; 941 #if defined(PETSC_USE_DEBUG) 942 if (row >= A->rmap->N) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1); 943 #endif 944 rp = aj + ai[brow]; /*ptr to beginning of column value of the row block*/ 945 ap = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/ 946 rmax = imax[brow]; /* maximum space allocated for this row */ 947 nrow = ailen[brow]; /* actual length of this row */ 948 low = 0; 949 950 for (l=0; l<n; l++) { /* loop over added columns */ 951 if (in[l] < 0) continue; 952 #if defined(PETSC_USE_DEBUG) 953 if (in[l] >= A->rmap->N) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->rmap->N-1); 954 #endif 955 col = in[l]; 956 bcol = col/bs; /* block col number */ 957 958 if (brow > bcol) { 959 if (a->ignore_ltriangular){ 960 continue; /* ignore lower triangular values */ 961 } else { 962 SETERRQ(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)"); 963 } 964 } 965 966 ridx = row % bs; cidx = col % bs; /*row and col index inside the block */ 967 if ((brow==bcol && ridx<=cidx) || (brow<bcol)){ 968 /* element value a(k,l) */ 969 if (roworiented) { 970 value = v[l + k*n]; 971 } else { 972 value = v[k + l*m]; 973 } 974 975 /* move pointer bap to a(k,l) quickly and add/insert value */ 976 if (col <= lastcol) low = 0; high = nrow; 977 lastcol = col; 978 while (high-low > 7) { 979 t = (low+high)/2; 980 if (rp[t] > bcol) high = t; 981 else low = t; 982 } 983 for (i=low; i<high; i++) { 984 if (rp[i] > bcol) break; 985 if (rp[i] == bcol) { 986 bap = ap + bs2*i + bs*cidx + ridx; 987 if (is == ADD_VALUES) *bap += value; 988 else *bap = value; 989 /* for diag block, add/insert its symmetric element a(cidx,ridx) */ 990 if (brow == bcol && ridx < cidx){ 991 bap = ap + bs2*i + bs*ridx + cidx; 992 if (is == ADD_VALUES) *bap += value; 993 else *bap = value; 994 } 995 goto noinsert1; 996 } 997 } 998 999 if (nonew == 1) goto noinsert1; 1000 if (nonew == -1) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 1001 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 1002 1003 N = nrow++ - 1; high++; 1004 /* shift up all the later entries in this row */ 1005 for (ii=N; ii>=i; ii--) { 1006 rp[ii+1] = rp[ii]; 1007 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 1008 } 1009 if (N>=i) { 1010 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1011 } 1012 rp[i] = bcol; 1013 ap[bs2*i + bs*cidx + ridx] = value; 1014 noinsert1:; 1015 low = i; 1016 } 1017 } /* end of loop over added columns */ 1018 ailen[brow] = nrow; 1019 } /* end of loop over added rows */ 1020 PetscFunctionReturn(0); 1021 } 1022 1023 #undef __FUNCT__ 1024 #define __FUNCT__ "MatICCFactor_SeqSBAIJ" 1025 PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info) 1026 { 1027 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)inA->data; 1028 Mat outA; 1029 PetscErrorCode ierr; 1030 PetscTruth row_identity; 1031 1032 PetscFunctionBegin; 1033 if (info->levels != 0) SETERRQ(PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc"); 1034 ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr); 1035 if (!row_identity) SETERRQ(PETSC_ERR_SUP,"Matrix reordering is not supported"); 1036 if (inA->rmap->bs != 1) SETERRQ1(PETSC_ERR_SUP,"Matrix block size %D is not supported",inA->rmap->bs); /* Need to replace MatCholeskyFactorSymbolic_SeqSBAIJ_MSR()! */ 1037 1038 outA = inA; 1039 inA->factor = MAT_FACTOR_ICC; 1040 1041 ierr = MatMarkDiagonal_SeqSBAIJ(inA);CHKERRQ(ierr); 1042 ierr = MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);CHKERRQ(ierr); 1043 1044 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1045 if (a->row) { ierr = ISDestroy(a->row);CHKERRQ(ierr); } 1046 a->row = row; 1047 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1048 if (a->col) { ierr = ISDestroy(a->col);CHKERRQ(ierr); } 1049 a->col = row; 1050 1051 /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */ 1052 if (a->icol) {ierr = ISInvertPermutation(row,PETSC_DECIDE, &a->icol);CHKERRQ(ierr);} 1053 ierr = PetscLogObjectParent(inA,a->icol);CHKERRQ(ierr); 1054 1055 if (!a->solve_work) { 1056 ierr = PetscMalloc((inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar),&a->solve_work);CHKERRQ(ierr); 1057 ierr = PetscLogObjectMemory(inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));CHKERRQ(ierr); 1058 } 1059 1060 ierr = MatCholeskyFactorNumeric(outA,inA,info);CHKERRQ(ierr); 1061 PetscFunctionReturn(0); 1062 } 1063 1064 EXTERN_C_BEGIN 1065 #undef __FUNCT__ 1066 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices_SeqSBAIJ" 1067 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices) 1068 { 1069 Mat_SeqSBAIJ *baij = (Mat_SeqSBAIJ *)mat->data; 1070 PetscInt i,nz,n; 1071 1072 PetscFunctionBegin; 1073 nz = baij->maxnz; 1074 n = mat->cmap->n; 1075 for (i=0; i<nz; i++) { 1076 baij->j[i] = indices[i]; 1077 } 1078 baij->nz = nz; 1079 for (i=0; i<n; i++) { 1080 baij->ilen[i] = baij->imax[i]; 1081 } 1082 PetscFunctionReturn(0); 1083 } 1084 EXTERN_C_END 1085 1086 #undef __FUNCT__ 1087 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices" 1088 /*@ 1089 MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows 1090 in the matrix. 1091 1092 Input Parameters: 1093 + mat - the SeqSBAIJ matrix 1094 - indices - the column indices 1095 1096 Level: advanced 1097 1098 Notes: 1099 This can be called if you have precomputed the nonzero structure of the 1100 matrix and want to provide it to the matrix object to improve the performance 1101 of the MatSetValues() operation. 1102 1103 You MUST have set the correct numbers of nonzeros per row in the call to 1104 MatCreateSeqSBAIJ(), and the columns indices MUST be sorted. 1105 1106 MUST be called before any calls to MatSetValues() 1107 1108 .seealso: MatCreateSeqSBAIJ 1109 @*/ 1110 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices) 1111 { 1112 PetscErrorCode ierr,(*f)(Mat,PetscInt *); 1113 1114 PetscFunctionBegin; 1115 PetscValidHeaderSpecific(mat,MAT_COOKIE,1); 1116 PetscValidPointer(indices,2); 1117 ierr = PetscObjectQueryFunction((PetscObject)mat,"MatSeqSBAIJSetColumnIndices_C",(void (**)(void))&f);CHKERRQ(ierr); 1118 if (f) { 1119 ierr = (*f)(mat,indices);CHKERRQ(ierr); 1120 } else { 1121 SETERRQ(PETSC_ERR_SUP,"Wrong type of matrix to set column indices"); 1122 } 1123 PetscFunctionReturn(0); 1124 } 1125 1126 #undef __FUNCT__ 1127 #define __FUNCT__ "MatCopy_SeqSBAIJ" 1128 PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str) 1129 { 1130 PetscErrorCode ierr; 1131 1132 PetscFunctionBegin; 1133 /* If the two matrices have the same copy implementation, use fast copy. */ 1134 if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) { 1135 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1136 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1137 1138 if (a->i[A->rmap->N] != b->i[B->rmap->N]) { 1139 SETERRQ(PETSC_ERR_ARG_INCOMP,"Number of nonzeros in two matrices are different"); 1140 } 1141 ierr = PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));CHKERRQ(ierr); 1142 } else { 1143 ierr = MatGetRowUpperTriangular(A);CHKERRQ(ierr); 1144 ierr = MatCopy_Basic(A,B,str);CHKERRQ(ierr); 1145 ierr = MatRestoreRowUpperTriangular(A);CHKERRQ(ierr); 1146 } 1147 PetscFunctionReturn(0); 1148 } 1149 1150 #undef __FUNCT__ 1151 #define __FUNCT__ "MatSetUpPreallocation_SeqSBAIJ" 1152 PetscErrorCode MatSetUpPreallocation_SeqSBAIJ(Mat A) 1153 { 1154 PetscErrorCode ierr; 1155 1156 PetscFunctionBegin; 1157 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,-PetscMax(A->rmap->bs,1),PETSC_DEFAULT,0);CHKERRQ(ierr); 1158 PetscFunctionReturn(0); 1159 } 1160 1161 #undef __FUNCT__ 1162 #define __FUNCT__ "MatGetArray_SeqSBAIJ" 1163 PetscErrorCode MatGetArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1164 { 1165 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1166 PetscFunctionBegin; 1167 *array = a->a; 1168 PetscFunctionReturn(0); 1169 } 1170 1171 #undef __FUNCT__ 1172 #define __FUNCT__ "MatRestoreArray_SeqSBAIJ" 1173 PetscErrorCode MatRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[]) 1174 { 1175 PetscFunctionBegin; 1176 PetscFunctionReturn(0); 1177 } 1178 1179 #include "petscblaslapack.h" 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_ERR_ARG_SIZ,"Attempt to set block size %d with SBAIJ %d",bs,rbs); 1230 if (cbs != bs) SETERRQ2(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,PetscTruth *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,PetscTruth *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,PetscTruth *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 /* -------------------------------------------------------------------*/ 1288 static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ, 1289 MatGetRow_SeqSBAIJ, 1290 MatRestoreRow_SeqSBAIJ, 1291 MatMult_SeqSBAIJ_N, 1292 /* 4*/ MatMultAdd_SeqSBAIJ_N, 1293 MatMult_SeqSBAIJ_N, /* transpose versions are same as non-transpose versions */ 1294 MatMultAdd_SeqSBAIJ_N, 1295 0, 1296 0, 1297 0, 1298 /*10*/ 0, 1299 0, 1300 MatCholeskyFactor_SeqSBAIJ, 1301 MatSOR_SeqSBAIJ, 1302 MatTranspose_SeqSBAIJ, 1303 /*15*/ MatGetInfo_SeqSBAIJ, 1304 MatEqual_SeqSBAIJ, 1305 MatGetDiagonal_SeqSBAIJ, 1306 MatDiagonalScale_SeqSBAIJ, 1307 MatNorm_SeqSBAIJ, 1308 /*20*/ 0, 1309 MatAssemblyEnd_SeqSBAIJ, 1310 MatSetOption_SeqSBAIJ, 1311 MatZeroEntries_SeqSBAIJ, 1312 /*24*/ 0, 1313 0, 1314 0, 1315 0, 1316 0, 1317 /*29*/ MatSetUpPreallocation_SeqSBAIJ, 1318 0, 1319 0, 1320 MatGetArray_SeqSBAIJ, 1321 MatRestoreArray_SeqSBAIJ, 1322 /*34*/ MatDuplicate_SeqSBAIJ, 1323 0, 1324 0, 1325 0, 1326 MatICCFactor_SeqSBAIJ, 1327 /*39*/ MatAXPY_SeqSBAIJ, 1328 MatGetSubMatrices_SeqSBAIJ, 1329 MatIncreaseOverlap_SeqSBAIJ, 1330 MatGetValues_SeqSBAIJ, 1331 MatCopy_SeqSBAIJ, 1332 /*44*/ 0, 1333 MatScale_SeqSBAIJ, 1334 0, 1335 0, 1336 0, 1337 /*49*/ MatSetBlockSize_SeqSBAIJ, 1338 MatGetRowIJ_SeqSBAIJ, 1339 MatRestoreRowIJ_SeqSBAIJ, 1340 0, 1341 0, 1342 /*54*/ 0, 1343 0, 1344 0, 1345 0, 1346 MatSetValuesBlocked_SeqSBAIJ, 1347 /*59*/ MatGetSubMatrix_SeqSBAIJ, 1348 0, 1349 0, 1350 0, 1351 0, 1352 /*64*/ 0, 1353 0, 1354 0, 1355 0, 1356 0, 1357 /*69*/ MatGetRowMaxAbs_SeqSBAIJ, 1358 0, 1359 0, 1360 0, 1361 0, 1362 /*74*/ 0, 1363 0, 1364 0, 1365 0, 1366 0, 1367 /*79*/ 0, 1368 0, 1369 0, 1370 #if !defined(PETSC_USE_COMPLEX) 1371 MatGetInertia_SeqSBAIJ, 1372 #else 1373 0, 1374 #endif 1375 MatLoad_SeqSBAIJ, 1376 /*84*/ MatIsSymmetric_SeqSBAIJ, 1377 MatIsHermitian_SeqSBAIJ, 1378 MatIsStructurallySymmetric_SeqSBAIJ, 1379 0, 1380 0, 1381 /*89*/ 0, 1382 0, 1383 0, 1384 0, 1385 0, 1386 /*94*/ 0, 1387 0, 1388 0, 1389 0, 1390 0, 1391 /*99*/ 0, 1392 0, 1393 0, 1394 0, 1395 0, 1396 /*104*/0, 1397 MatRealPart_SeqSBAIJ, 1398 MatImaginaryPart_SeqSBAIJ, 1399 MatGetRowUpperTriangular_SeqSBAIJ, 1400 MatRestoreRowUpperTriangular_SeqSBAIJ, 1401 /*109*/0, 1402 0, 1403 0, 1404 0, 1405 MatMissingDiagonal_SeqSBAIJ, 1406 /*114*/0, 1407 0, 1408 0, 1409 0, 1410 0, 1411 /*119*/0, 1412 0, 1413 0 1414 }; 1415 1416 EXTERN_C_BEGIN 1417 #undef __FUNCT__ 1418 #define __FUNCT__ "MatStoreValues_SeqSBAIJ" 1419 PetscErrorCode PETSCMAT_DLLEXPORT MatStoreValues_SeqSBAIJ(Mat mat) 1420 { 1421 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ *)mat->data; 1422 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1423 PetscErrorCode ierr; 1424 1425 PetscFunctionBegin; 1426 if (aij->nonew != 1) { 1427 SETERRQ(PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1428 } 1429 1430 /* allocate space for values if not already there */ 1431 if (!aij->saved_values) { 1432 ierr = PetscMalloc((nz+1)*sizeof(PetscScalar),&aij->saved_values);CHKERRQ(ierr); 1433 } 1434 1435 /* copy values over */ 1436 ierr = PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1437 PetscFunctionReturn(0); 1438 } 1439 EXTERN_C_END 1440 1441 EXTERN_C_BEGIN 1442 #undef __FUNCT__ 1443 #define __FUNCT__ "MatRetrieveValues_SeqSBAIJ" 1444 PetscErrorCode PETSCMAT_DLLEXPORT MatRetrieveValues_SeqSBAIJ(Mat mat) 1445 { 1446 Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ *)mat->data; 1447 PetscErrorCode ierr; 1448 PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2; 1449 1450 PetscFunctionBegin; 1451 if (aij->nonew != 1) { 1452 SETERRQ(PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first"); 1453 } 1454 if (!aij->saved_values) { 1455 SETERRQ(PETSC_ERR_ORDER,"Must call MatStoreValues(A);first"); 1456 } 1457 1458 /* copy values over */ 1459 ierr = PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));CHKERRQ(ierr); 1460 PetscFunctionReturn(0); 1461 } 1462 EXTERN_C_END 1463 1464 EXTERN_C_BEGIN 1465 #undef __FUNCT__ 1466 #define __FUNCT__ "MatSeqSBAIJSetPreallocation_SeqSBAIJ" 1467 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz) 1468 { 1469 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1470 PetscErrorCode ierr; 1471 PetscInt i,mbs,bs2, newbs = PetscAbs(bs); 1472 PetscTruth skipallocation = PETSC_FALSE,flg = PETSC_FALSE; 1473 1474 PetscFunctionBegin; 1475 B->preallocated = PETSC_TRUE; 1476 if (bs < 0) { 1477 ierr = PetscOptionsBegin(((PetscObject)B)->comm,((PetscObject)B)->prefix,"Options for MPISBAIJ matrix","Mat");CHKERRQ(ierr); 1478 ierr = PetscOptionsInt("-mat_block_size","Set the blocksize used to store the matrix","MatSeqSBAIJSetPreallocation",newbs,&newbs,PETSC_NULL);CHKERRQ(ierr); 1479 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1480 bs = PetscAbs(bs); 1481 } 1482 if (nnz && newbs != bs) { 1483 SETERRQ(PETSC_ERR_ARG_WRONG,"Cannot change blocksize from command line if setting nnz"); 1484 } 1485 bs = newbs; 1486 1487 ierr = PetscLayoutSetBlockSize(B->rmap,bs);CHKERRQ(ierr); 1488 ierr = PetscLayoutSetBlockSize(B->cmap,bs);CHKERRQ(ierr); 1489 ierr = PetscLayoutSetUp(B->rmap);CHKERRQ(ierr); 1490 ierr = PetscLayoutSetUp(B->cmap);CHKERRQ(ierr); 1491 1492 mbs = B->rmap->N/bs; 1493 bs2 = bs*bs; 1494 1495 if (mbs*bs != B->rmap->N) { 1496 SETERRQ(PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize"); 1497 } 1498 1499 if (nz == MAT_SKIP_ALLOCATION) { 1500 skipallocation = PETSC_TRUE; 1501 nz = 0; 1502 } 1503 1504 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3; 1505 if (nz < 0) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz); 1506 if (nnz) { 1507 for (i=0; i<mbs; i++) { 1508 if (nnz[i] < 0) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be less than 0: local row %D value %D",i,nnz[i]); 1509 if (nnz[i] > mbs) SETERRQ3(PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than block row length: local row %D value %D rowlength %D",i,nnz[i],mbs); 1510 } 1511 } 1512 1513 B->ops->mult = MatMult_SeqSBAIJ_N; 1514 B->ops->multadd = MatMultAdd_SeqSBAIJ_N; 1515 B->ops->multtranspose = MatMult_SeqSBAIJ_N; 1516 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N; 1517 ierr = PetscOptionsGetTruth(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);CHKERRQ(ierr); 1518 if (!flg) { 1519 switch (bs) { 1520 case 1: 1521 B->ops->mult = MatMult_SeqSBAIJ_1; 1522 B->ops->multadd = MatMultAdd_SeqSBAIJ_1; 1523 B->ops->multtranspose = MatMult_SeqSBAIJ_1; 1524 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1; 1525 break; 1526 case 2: 1527 B->ops->mult = MatMult_SeqSBAIJ_2; 1528 B->ops->multadd = MatMultAdd_SeqSBAIJ_2; 1529 B->ops->multtranspose = MatMult_SeqSBAIJ_2; 1530 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2; 1531 break; 1532 case 3: 1533 B->ops->mult = MatMult_SeqSBAIJ_3; 1534 B->ops->multadd = MatMultAdd_SeqSBAIJ_3; 1535 B->ops->multtranspose = MatMult_SeqSBAIJ_3; 1536 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3; 1537 break; 1538 case 4: 1539 B->ops->mult = MatMult_SeqSBAIJ_4; 1540 B->ops->multadd = MatMultAdd_SeqSBAIJ_4; 1541 B->ops->multtranspose = MatMult_SeqSBAIJ_4; 1542 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4; 1543 break; 1544 case 5: 1545 B->ops->mult = MatMult_SeqSBAIJ_5; 1546 B->ops->multadd = MatMultAdd_SeqSBAIJ_5; 1547 B->ops->multtranspose = MatMult_SeqSBAIJ_5; 1548 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5; 1549 break; 1550 case 6: 1551 B->ops->mult = MatMult_SeqSBAIJ_6; 1552 B->ops->multadd = MatMultAdd_SeqSBAIJ_6; 1553 B->ops->multtranspose = MatMult_SeqSBAIJ_6; 1554 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6; 1555 break; 1556 case 7: 1557 B->ops->mult = MatMult_SeqSBAIJ_7; 1558 B->ops->multadd = MatMultAdd_SeqSBAIJ_7; 1559 B->ops->multtranspose = MatMult_SeqSBAIJ_7; 1560 B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7; 1561 break; 1562 } 1563 } 1564 1565 b->mbs = mbs; 1566 b->nbs = mbs; 1567 if (!skipallocation) { 1568 if (!b->imax) { 1569 ierr = PetscMalloc2(mbs,PetscInt,&b->imax,mbs,PetscInt,&b->ilen);CHKERRQ(ierr); 1570 b->free_imax_ilen = PETSC_TRUE; 1571 ierr = PetscLogObjectMemory(B,2*mbs*sizeof(PetscInt));CHKERRQ(ierr); 1572 } 1573 if (!nnz) { 1574 if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5; 1575 else if (nz <= 0) nz = 1; 1576 for (i=0; i<mbs; i++) { 1577 b->imax[i] = nz; 1578 } 1579 nz = nz*mbs; /* total nz */ 1580 } else { 1581 nz = 0; 1582 for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];} 1583 } 1584 /* b->ilen will count nonzeros in each block row so far. */ 1585 for (i=0; i<mbs; i++) { b->ilen[i] = 0;} 1586 /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */ 1587 1588 /* allocate the matrix space */ 1589 ierr = MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);CHKERRQ(ierr); 1590 ierr = PetscMalloc3(bs2*nz,PetscScalar,&b->a,nz,PetscInt,&b->j,B->rmap->N+1,PetscInt,&b->i);CHKERRQ(ierr); 1591 ierr = PetscLogObjectMemory(B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));CHKERRQ(ierr); 1592 ierr = PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 1593 ierr = PetscMemzero(b->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 1594 b->singlemalloc = PETSC_TRUE; 1595 1596 /* pointer to beginning of each row */ 1597 b->i[0] = 0; 1598 for (i=1; i<mbs+1; i++) { 1599 b->i[i] = b->i[i-1] + b->imax[i-1]; 1600 } 1601 b->free_a = PETSC_TRUE; 1602 b->free_ij = PETSC_TRUE; 1603 } else { 1604 b->free_a = PETSC_FALSE; 1605 b->free_ij = PETSC_FALSE; 1606 } 1607 1608 B->rmap->bs = bs; 1609 b->bs2 = bs2; 1610 b->nz = 0; 1611 b->maxnz = nz*bs2; 1612 1613 b->inew = 0; 1614 b->jnew = 0; 1615 b->anew = 0; 1616 b->a2anew = 0; 1617 b->permute = PETSC_FALSE; 1618 PetscFunctionReturn(0); 1619 } 1620 EXTERN_C_END 1621 1622 /* 1623 This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization 1624 */ 1625 #undef __FUNCT__ 1626 #define __FUNCT__ "MatSeqSBAIJSetNumericFactorization_inplace" 1627 PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscTruth natural) 1628 { 1629 PetscErrorCode ierr; 1630 PetscTruth flg = PETSC_FALSE; 1631 PetscInt bs = B->rmap->bs; 1632 1633 PetscFunctionBegin; 1634 ierr = PetscOptionsGetTruth(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);CHKERRQ(ierr); 1635 if (flg) bs = 8; 1636 1637 if (!natural) { 1638 switch (bs) { 1639 case 1: 1640 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace; 1641 break; 1642 case 2: 1643 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2; 1644 break; 1645 case 3: 1646 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3; 1647 break; 1648 case 4: 1649 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4; 1650 break; 1651 case 5: 1652 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5; 1653 break; 1654 case 6: 1655 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6; 1656 break; 1657 case 7: 1658 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7; 1659 break; 1660 default: 1661 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N; 1662 break; 1663 } 1664 } else { 1665 switch (bs) { 1666 case 1: 1667 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace; 1668 break; 1669 case 2: 1670 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering; 1671 break; 1672 case 3: 1673 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering; 1674 break; 1675 case 4: 1676 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering; 1677 break; 1678 case 5: 1679 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering; 1680 break; 1681 case 6: 1682 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering; 1683 break; 1684 case 7: 1685 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering; 1686 break; 1687 default: 1688 B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering; 1689 break; 1690 } 1691 } 1692 PetscFunctionReturn(0); 1693 } 1694 1695 EXTERN_C_BEGIN 1696 EXTERN PetscErrorCode PETSCMAT_DLLEXPORT MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*); 1697 EXTERN PetscErrorCode PETSCMAT_DLLEXPORT MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*); 1698 EXTERN_C_END 1699 1700 1701 EXTERN_C_BEGIN 1702 #undef __FUNCT__ 1703 #define __FUNCT__ "MatGetFactor_seqsbaij_petsc" 1704 PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B) 1705 { 1706 PetscInt n = A->rmap->n; 1707 PetscErrorCode ierr; 1708 1709 PetscFunctionBegin; 1710 ierr = MatCreate(((PetscObject)A)->comm,B);CHKERRQ(ierr); 1711 ierr = MatSetSizes(*B,n,n,n,n);CHKERRQ(ierr); 1712 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1713 ierr = MatSetType(*B,MATSEQSBAIJ);CHKERRQ(ierr); 1714 ierr = MatSeqSBAIJSetPreallocation(*B,1,MAT_SKIP_ALLOCATION,PETSC_NULL);CHKERRQ(ierr); 1715 (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ; 1716 (*B)->ops->iccfactorsymbolic = MatICCFactorSymbolic_SeqSBAIJ; 1717 } else SETERRQ(PETSC_ERR_SUP,"Factor type not supported"); 1718 (*B)->factor = ftype; 1719 PetscFunctionReturn(0); 1720 } 1721 EXTERN_C_END 1722 1723 EXTERN_C_BEGIN 1724 #undef __FUNCT__ 1725 #define __FUNCT__ "MatGetFactorAvailable_seqsbaij_petsc" 1726 PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscTruth *flg) 1727 { 1728 PetscFunctionBegin; 1729 if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) { 1730 *flg = PETSC_TRUE; 1731 } else { 1732 *flg = PETSC_FALSE; 1733 } 1734 PetscFunctionReturn(0); 1735 } 1736 EXTERN_C_END 1737 1738 EXTERN_C_BEGIN 1739 #if defined(PETSC_HAVE_MUMPS) 1740 extern PetscErrorCode MatGetFactor_seqsbaij_mumps(Mat,MatFactorType,Mat*); 1741 #endif 1742 #if defined(PETSC_HAVE_SPOOLES) 1743 extern PetscErrorCode MatGetFactor_seqsbaij_spooles(Mat,MatFactorType,Mat*); 1744 #endif 1745 #if defined(PETSC_HAVE_PASTIX) 1746 extern PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*); 1747 #endif 1748 EXTERN_C_END 1749 1750 /*MC 1751 MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices, 1752 based on block compressed sparse row format. Only the upper triangular portion of the matrix is stored. 1753 1754 Options Database Keys: 1755 . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions() 1756 1757 Level: beginner 1758 1759 .seealso: MatCreateSeqSBAIJ 1760 M*/ 1761 1762 EXTERN_C_BEGIN 1763 #undef __FUNCT__ 1764 #define __FUNCT__ "MatCreate_SeqSBAIJ" 1765 PetscErrorCode PETSCMAT_DLLEXPORT MatCreate_SeqSBAIJ(Mat B) 1766 { 1767 Mat_SeqSBAIJ *b; 1768 PetscErrorCode ierr; 1769 PetscMPIInt size; 1770 PetscTruth no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE; 1771 1772 PetscFunctionBegin; 1773 ierr = MPI_Comm_size(((PetscObject)B)->comm,&size);CHKERRQ(ierr); 1774 if (size > 1) SETERRQ(PETSC_ERR_ARG_WRONG,"Comm must be of size 1"); 1775 1776 ierr = PetscNewLog(B,Mat_SeqSBAIJ,&b);CHKERRQ(ierr); 1777 B->data = (void*)b; 1778 ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); 1779 B->ops->destroy = MatDestroy_SeqSBAIJ; 1780 B->ops->view = MatView_SeqSBAIJ; 1781 B->mapping = 0; 1782 b->row = 0; 1783 b->icol = 0; 1784 b->reallocs = 0; 1785 b->saved_values = 0; 1786 b->inode.limit = 5; 1787 b->inode.max_limit = 5; 1788 1789 b->roworiented = PETSC_TRUE; 1790 b->nonew = 0; 1791 b->diag = 0; 1792 b->solve_work = 0; 1793 b->mult_work = 0; 1794 B->spptr = 0; 1795 b->keepnonzeropattern = PETSC_FALSE; 1796 b->xtoy = 0; 1797 b->XtoY = 0; 1798 1799 b->inew = 0; 1800 b->jnew = 0; 1801 b->anew = 0; 1802 b->a2anew = 0; 1803 b->permute = PETSC_FALSE; 1804 1805 b->ignore_ltriangular = PETSC_FALSE; 1806 ierr = PetscOptionsGetTruth(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,PETSC_NULL);CHKERRQ(ierr); 1807 1808 b->getrow_utriangular = PETSC_FALSE; 1809 ierr = PetscOptionsGetTruth(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,PETSC_NULL);CHKERRQ(ierr); 1810 1811 #if defined(PETSC_HAVE_PASTIX) 1812 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_pastix_C", 1813 "MatGetFactor_seqsbaij_pastix", 1814 MatGetFactor_seqsbaij_pastix);CHKERRQ(ierr); 1815 #endif 1816 #if defined(PETSC_HAVE_SPOOLES) 1817 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_spooles_C", 1818 "MatGetFactor_seqsbaij_spooles", 1819 MatGetFactor_seqsbaij_spooles);CHKERRQ(ierr); 1820 #endif 1821 #if defined(PETSC_HAVE_MUMPS) 1822 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_mumps_C", 1823 "MatGetFactor_seqsbaij_mumps", 1824 MatGetFactor_seqsbaij_mumps);CHKERRQ(ierr); 1825 #endif 1826 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactorAvailable_petsc_C", 1827 "MatGetFactorAvailable_seqsbaij_petsc", 1828 MatGetFactorAvailable_seqsbaij_petsc);CHKERRQ(ierr); 1829 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_petsc_C", 1830 "MatGetFactor_seqsbaij_petsc", 1831 MatGetFactor_seqsbaij_petsc);CHKERRQ(ierr); 1832 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatStoreValues_C", 1833 "MatStoreValues_SeqSBAIJ", 1834 MatStoreValues_SeqSBAIJ);CHKERRQ(ierr); 1835 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatRetrieveValues_C", 1836 "MatRetrieveValues_SeqSBAIJ", 1837 (void*)MatRetrieveValues_SeqSBAIJ);CHKERRQ(ierr); 1838 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C", 1839 "MatSeqSBAIJSetColumnIndices_SeqSBAIJ", 1840 MatSeqSBAIJSetColumnIndices_SeqSBAIJ);CHKERRQ(ierr); 1841 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqaij_C", 1842 "MatConvert_SeqSBAIJ_SeqAIJ", 1843 MatConvert_SeqSBAIJ_SeqAIJ);CHKERRQ(ierr); 1844 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C", 1845 "MatConvert_SeqSBAIJ_SeqBAIJ", 1846 MatConvert_SeqSBAIJ_SeqBAIJ);CHKERRQ(ierr); 1847 ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetPreallocation_C", 1848 "MatSeqSBAIJSetPreallocation_SeqSBAIJ", 1849 MatSeqSBAIJSetPreallocation_SeqSBAIJ);CHKERRQ(ierr); 1850 1851 B->symmetric = PETSC_TRUE; 1852 B->structurally_symmetric = PETSC_TRUE; 1853 B->symmetric_set = PETSC_TRUE; 1854 B->structurally_symmetric_set = PETSC_TRUE; 1855 ierr = PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);CHKERRQ(ierr); 1856 1857 ierr = PetscOptionsBegin(((PetscObject)B)->comm,((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");CHKERRQ(ierr); 1858 ierr = PetscOptionsTruth("-mat_no_unroll","Do not optimize for inodes (slower)",PETSC_NULL,no_unroll,&no_unroll,PETSC_NULL);CHKERRQ(ierr); 1859 if (no_unroll) {ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");CHKERRQ(ierr);} 1860 ierr = PetscOptionsTruth("-mat_no_inode","Do not optimize for inodes (slower)",PETSC_NULL,no_inode,&no_inode,PETSC_NULL);CHKERRQ(ierr); 1861 if (no_inode) {ierr = PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");CHKERRQ(ierr);} 1862 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); 1863 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1864 b->inode.use = (PetscTruth)(!(no_unroll || no_inode)); 1865 if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit; 1866 1867 PetscFunctionReturn(0); 1868 } 1869 EXTERN_C_END 1870 1871 #undef __FUNCT__ 1872 #define __FUNCT__ "MatSeqSBAIJSetPreallocation" 1873 /*@C 1874 MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block 1875 compressed row) format. For good matrix assembly performance the 1876 user should preallocate the matrix storage by setting the parameter nz 1877 (or the array nnz). By setting these parameters accurately, performance 1878 during matrix assembly can be increased by more than a factor of 50. 1879 1880 Collective on Mat 1881 1882 Input Parameters: 1883 + A - the symmetric matrix 1884 . bs - size of block 1885 . nz - number of block nonzeros per block row (same for all rows) 1886 - nnz - array containing the number of block nonzeros in the upper triangular plus 1887 diagonal portion of each block (possibly different for each block row) or PETSC_NULL 1888 1889 Options Database Keys: 1890 . -mat_no_unroll - uses code that does not unroll the loops in the 1891 block calculations (much slower) 1892 . -mat_block_size - size of the blocks to use (only works if a negative bs is passed in 1893 1894 Level: intermediate 1895 1896 Notes: 1897 Specify the preallocated storage with either nz or nnz (not both). 1898 Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 1899 allocation. For additional details, see the users manual chapter on 1900 matrices. 1901 1902 You can call MatGetInfo() to get information on how effective the preallocation was; 1903 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 1904 You can also run with the option -info and look for messages with the string 1905 malloc in them to see if additional memory allocation was needed. 1906 1907 If the nnz parameter is given then the nz parameter is ignored 1908 1909 1910 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateMPISBAIJ() 1911 @*/ 1912 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[]) 1913 { 1914 PetscErrorCode ierr,(*f)(Mat,PetscInt,PetscInt,const PetscInt[]); 1915 1916 PetscFunctionBegin; 1917 ierr = PetscObjectQueryFunction((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",(void (**)(void))&f);CHKERRQ(ierr); 1918 if (f) { 1919 ierr = (*f)(B,bs,nz,nnz);CHKERRQ(ierr); 1920 } 1921 PetscFunctionReturn(0); 1922 } 1923 1924 #undef __FUNCT__ 1925 #define __FUNCT__ "MatCreateSeqSBAIJ" 1926 /*@C 1927 MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block 1928 compressed row) format. For good matrix assembly performance the 1929 user should preallocate the matrix storage by setting the parameter nz 1930 (or the array nnz). By setting these parameters accurately, performance 1931 during matrix assembly can be increased by more than a factor of 50. 1932 1933 Collective on MPI_Comm 1934 1935 Input Parameters: 1936 + comm - MPI communicator, set to PETSC_COMM_SELF 1937 . bs - size of block 1938 . m - number of rows, or number of columns 1939 . nz - number of block nonzeros per block row (same for all rows) 1940 - nnz - array containing the number of block nonzeros in the upper triangular plus 1941 diagonal portion of each block (possibly different for each block row) or PETSC_NULL 1942 1943 Output Parameter: 1944 . A - the symmetric matrix 1945 1946 Options Database Keys: 1947 . -mat_no_unroll - uses code that does not unroll the loops in the 1948 block calculations (much slower) 1949 . -mat_block_size - size of the blocks to use 1950 1951 Level: intermediate 1952 1953 It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(), 1954 MatXXXXSetPreallocation() paradgm instead of this routine directly. 1955 [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation] 1956 1957 Notes: 1958 The number of rows and columns must be divisible by blocksize. 1959 This matrix type does not support complex Hermitian operation. 1960 1961 Specify the preallocated storage with either nz or nnz (not both). 1962 Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory 1963 allocation. For additional details, see the users manual chapter on 1964 matrices. 1965 1966 If the nnz parameter is given then the nz parameter is ignored 1967 1968 .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateMPISBAIJ() 1969 @*/ 1970 PetscErrorCode PETSCMAT_DLLEXPORT MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A) 1971 { 1972 PetscErrorCode ierr; 1973 1974 PetscFunctionBegin; 1975 ierr = MatCreate(comm,A);CHKERRQ(ierr); 1976 ierr = MatSetSizes(*A,m,n,m,n);CHKERRQ(ierr); 1977 ierr = MatSetType(*A,MATSEQSBAIJ);CHKERRQ(ierr); 1978 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);CHKERRQ(ierr); 1979 PetscFunctionReturn(0); 1980 } 1981 1982 #undef __FUNCT__ 1983 #define __FUNCT__ "MatDuplicate_SeqSBAIJ" 1984 PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B) 1985 { 1986 Mat C; 1987 Mat_SeqSBAIJ *c,*a = (Mat_SeqSBAIJ*)A->data; 1988 PetscErrorCode ierr; 1989 PetscInt i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2; 1990 1991 PetscFunctionBegin; 1992 if (a->i[mbs] != nz) SETERRQ(PETSC_ERR_PLIB,"Corrupt matrix"); 1993 1994 *B = 0; 1995 ierr = MatCreate(((PetscObject)A)->comm,&C);CHKERRQ(ierr); 1996 ierr = MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);CHKERRQ(ierr); 1997 ierr = MatSetType(C,((PetscObject)A)->type_name);CHKERRQ(ierr); 1998 ierr = PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));CHKERRQ(ierr); 1999 c = (Mat_SeqSBAIJ*)C->data; 2000 2001 C->preallocated = PETSC_TRUE; 2002 C->factor = A->factor; 2003 c->row = 0; 2004 c->icol = 0; 2005 c->saved_values = 0; 2006 c->keepnonzeropattern = a->keepnonzeropattern; 2007 C->assembled = PETSC_TRUE; 2008 2009 ierr = PetscLayoutCopy(A->rmap,&C->rmap);CHKERRQ(ierr); 2010 ierr = PetscLayoutCopy(A->cmap,&C->cmap);CHKERRQ(ierr); 2011 c->bs2 = a->bs2; 2012 c->mbs = a->mbs; 2013 c->nbs = a->nbs; 2014 2015 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2016 c->imax = a->imax; 2017 c->ilen = a->ilen; 2018 c->free_imax_ilen = PETSC_FALSE; 2019 } else { 2020 ierr = PetscMalloc2((mbs+1),PetscInt,&c->imax,(mbs+1),PetscInt,&c->ilen);CHKERRQ(ierr); 2021 ierr = PetscLogObjectMemory(C,2*(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2022 for (i=0; i<mbs; i++) { 2023 c->imax[i] = a->imax[i]; 2024 c->ilen[i] = a->ilen[i]; 2025 } 2026 c->free_imax_ilen = PETSC_TRUE; 2027 } 2028 2029 /* allocate the matrix space */ 2030 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2031 ierr = PetscMalloc(bs2*nz*sizeof(MatScalar),&c->a);CHKERRQ(ierr); 2032 ierr = PetscLogObjectMemory(C,nz*bs2*sizeof(MatScalar));CHKERRQ(ierr); 2033 c->singlemalloc = PETSC_FALSE; 2034 c->free_ij = PETSC_FALSE; 2035 c->parent = A; 2036 ierr = PetscObjectReference((PetscObject)A);CHKERRQ(ierr); 2037 ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2038 ierr = MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr); 2039 } else { 2040 ierr = PetscMalloc3(bs2*nz,MatScalar,&c->a,nz,PetscInt,&c->j,mbs+1,PetscInt,&c->i);CHKERRQ(ierr); 2041 ierr = PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));CHKERRQ(ierr); 2042 ierr = PetscLogObjectMemory(C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));CHKERRQ(ierr); 2043 c->singlemalloc = PETSC_TRUE; 2044 c->free_ij = PETSC_TRUE; 2045 } 2046 if (mbs > 0) { 2047 if (cpvalues != MAT_SHARE_NONZERO_PATTERN) { 2048 ierr = PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));CHKERRQ(ierr); 2049 } 2050 if (cpvalues == MAT_COPY_VALUES) { 2051 ierr = PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2052 } else { 2053 ierr = PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));CHKERRQ(ierr); 2054 } 2055 if (a->jshort) { 2056 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2057 c->jshort = a->jshort; 2058 c->free_jshort = PETSC_FALSE; 2059 } else { 2060 ierr = PetscMalloc(nz*sizeof(unsigned short),&c->jshort);CHKERRQ(ierr); 2061 ierr = PetscLogObjectMemory(C,nz*sizeof(unsigned short));CHKERRQ(ierr); 2062 ierr = PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));CHKERRQ(ierr); 2063 c->free_jshort = PETSC_TRUE; 2064 } 2065 } 2066 } 2067 2068 c->roworiented = a->roworiented; 2069 c->nonew = a->nonew; 2070 2071 if (a->diag) { 2072 if (cpvalues == MAT_SHARE_NONZERO_PATTERN) { 2073 c->diag = a->diag; 2074 c->free_diag = PETSC_FALSE; 2075 } else { 2076 ierr = PetscMalloc(mbs*sizeof(PetscInt),&c->diag);CHKERRQ(ierr); 2077 ierr = PetscLogObjectMemory(C,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2078 for (i=0; i<mbs; i++) { 2079 c->diag[i] = a->diag[i]; 2080 } 2081 c->free_diag = PETSC_TRUE; 2082 } 2083 } else c->diag = 0; 2084 c->nz = a->nz; 2085 c->maxnz = a->maxnz; 2086 c->solve_work = 0; 2087 c->mult_work = 0; 2088 c->free_a = PETSC_TRUE; 2089 *B = C; 2090 ierr = PetscFListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);CHKERRQ(ierr); 2091 PetscFunctionReturn(0); 2092 } 2093 2094 #undef __FUNCT__ 2095 #define __FUNCT__ "MatLoad_SeqSBAIJ" 2096 PetscErrorCode MatLoad_SeqSBAIJ(PetscViewer viewer, const MatType type,Mat *A) 2097 { 2098 Mat_SeqSBAIJ *a; 2099 Mat B; 2100 PetscErrorCode ierr; 2101 int fd; 2102 PetscMPIInt size; 2103 PetscInt i,nz,header[4],*rowlengths=0,M,N,bs=1; 2104 PetscInt *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount; 2105 PetscInt kmax,jcount,block,idx,point,nzcountb,extra_rows; 2106 PetscInt *masked,nmask,tmp,bs2,ishift; 2107 PetscScalar *aa; 2108 MPI_Comm comm = ((PetscObject)viewer)->comm; 2109 2110 PetscFunctionBegin; 2111 ierr = PetscOptionsGetInt(PETSC_NULL,"-matload_block_size",&bs,PETSC_NULL);CHKERRQ(ierr); 2112 bs2 = bs*bs; 2113 2114 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 2115 if (size > 1) SETERRQ(PETSC_ERR_ARG_WRONG,"view must have one processor"); 2116 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 2117 ierr = PetscBinaryRead(fd,header,4,PETSC_INT);CHKERRQ(ierr); 2118 if (header[0] != MAT_FILE_COOKIE) SETERRQ(PETSC_ERR_FILE_UNEXPECTED,"not Mat object"); 2119 M = header[1]; N = header[2]; nz = header[3]; 2120 2121 if (header[3] < 0) { 2122 SETERRQ(PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ"); 2123 } 2124 2125 if (M != N) SETERRQ(PETSC_ERR_SUP,"Can only do square matrices"); 2126 2127 /* 2128 This code adds extra rows to make sure the number of rows is 2129 divisible by the blocksize 2130 */ 2131 mbs = M/bs; 2132 extra_rows = bs - M + bs*(mbs); 2133 if (extra_rows == bs) extra_rows = 0; 2134 else mbs++; 2135 if (extra_rows) { 2136 ierr = PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");CHKERRQ(ierr); 2137 } 2138 2139 /* read in row lengths */ 2140 ierr = PetscMalloc((M+extra_rows)*sizeof(PetscInt),&rowlengths);CHKERRQ(ierr); 2141 ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); 2142 for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1; 2143 2144 /* read in column indices */ 2145 ierr = PetscMalloc((nz+extra_rows)*sizeof(PetscInt),&jj);CHKERRQ(ierr); 2146 ierr = PetscBinaryRead(fd,jj,nz,PETSC_INT);CHKERRQ(ierr); 2147 for (i=0; i<extra_rows; i++) jj[nz+i] = M+i; 2148 2149 /* loop over row lengths determining block row lengths */ 2150 ierr = PetscMalloc(mbs*sizeof(PetscInt),&s_browlengths);CHKERRQ(ierr); 2151 ierr = PetscMemzero(s_browlengths,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2152 ierr = PetscMalloc2(mbs,PetscInt,&mask,mbs,PetscInt,&masked);CHKERRQ(ierr); 2153 ierr = PetscMemzero(mask,mbs*sizeof(PetscInt));CHKERRQ(ierr); 2154 rowcount = 0; 2155 nzcount = 0; 2156 for (i=0; i<mbs; i++) { 2157 nmask = 0; 2158 for (j=0; j<bs; j++) { 2159 kmax = rowlengths[rowcount]; 2160 for (k=0; k<kmax; k++) { 2161 tmp = jj[nzcount++]/bs; /* block col. index */ 2162 if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;} 2163 } 2164 rowcount++; 2165 } 2166 s_browlengths[i] += nmask; 2167 2168 /* zero out the mask elements we set */ 2169 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2170 } 2171 2172 /* create our matrix */ 2173 ierr = MatCreate(comm,&B);CHKERRQ(ierr); 2174 ierr = MatSetSizes(B,M+extra_rows,N+extra_rows,M+extra_rows,N+extra_rows);CHKERRQ(ierr); 2175 ierr = MatSetType(B,type);CHKERRQ(ierr); 2176 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(B,bs,0,s_browlengths);CHKERRQ(ierr); 2177 a = (Mat_SeqSBAIJ*)B->data; 2178 2179 /* set matrix "i" values */ 2180 a->i[0] = 0; 2181 for (i=1; i<= mbs; i++) { 2182 a->i[i] = a->i[i-1] + s_browlengths[i-1]; 2183 a->ilen[i-1] = s_browlengths[i-1]; 2184 } 2185 a->nz = a->i[mbs]; 2186 2187 /* read in nonzero values */ 2188 ierr = PetscMalloc((nz+extra_rows)*sizeof(PetscScalar),&aa);CHKERRQ(ierr); 2189 ierr = PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);CHKERRQ(ierr); 2190 for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0; 2191 2192 /* set "a" and "j" values into matrix */ 2193 nzcount = 0; jcount = 0; 2194 for (i=0; i<mbs; i++) { 2195 nzcountb = nzcount; 2196 nmask = 0; 2197 for (j=0; j<bs; j++) { 2198 kmax = rowlengths[i*bs+j]; 2199 for (k=0; k<kmax; k++) { 2200 tmp = jj[nzcount++]/bs; /* block col. index */ 2201 if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;} 2202 } 2203 } 2204 /* sort the masked values */ 2205 ierr = PetscSortInt(nmask,masked);CHKERRQ(ierr); 2206 2207 /* set "j" values into matrix */ 2208 maskcount = 1; 2209 for (j=0; j<nmask; j++) { 2210 a->j[jcount++] = masked[j]; 2211 mask[masked[j]] = maskcount++; 2212 } 2213 2214 /* set "a" values into matrix */ 2215 ishift = bs2*a->i[i]; 2216 for (j=0; j<bs; j++) { 2217 kmax = rowlengths[i*bs+j]; 2218 for (k=0; k<kmax; k++) { 2219 tmp = jj[nzcountb]/bs ; /* block col. index */ 2220 if (tmp >= i){ 2221 block = mask[tmp] - 1; 2222 point = jj[nzcountb] - bs*tmp; 2223 idx = ishift + bs2*block + j + bs*point; 2224 a->a[idx] = aa[nzcountb]; 2225 } 2226 nzcountb++; 2227 } 2228 } 2229 /* zero out the mask elements we set */ 2230 for (j=0; j<nmask; j++) mask[masked[j]] = 0; 2231 } 2232 if (jcount != a->nz) SETERRQ(PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix"); 2233 2234 ierr = PetscFree(rowlengths);CHKERRQ(ierr); 2235 ierr = PetscFree(s_browlengths);CHKERRQ(ierr); 2236 ierr = PetscFree(aa);CHKERRQ(ierr); 2237 ierr = PetscFree(jj);CHKERRQ(ierr); 2238 ierr = PetscFree2(mask,masked);CHKERRQ(ierr); 2239 2240 ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2241 ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2242 ierr = MatView_Private(B);CHKERRQ(ierr); 2243 *A = B; 2244 PetscFunctionReturn(0); 2245 } 2246 2247 #undef __FUNCT__ 2248 #define __FUNCT__ "MatCreateSeqSBAIJWithArrays" 2249 /*@ 2250 MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements 2251 (upper triangular entries in CSR format) provided by the user. 2252 2253 Collective on MPI_Comm 2254 2255 Input Parameters: 2256 + comm - must be an MPI communicator of size 1 2257 . bs - size of block 2258 . m - number of rows 2259 . n - number of columns 2260 . i - row indices 2261 . j - column indices 2262 - a - matrix values 2263 2264 Output Parameter: 2265 . mat - the matrix 2266 2267 Level: intermediate 2268 2269 Notes: 2270 The i, j, and a arrays are not copied by this routine, the user must free these arrays 2271 once the matrix is destroyed 2272 2273 You cannot set new nonzero locations into this matrix, that will generate an error. 2274 2275 The i and j indices are 0 based 2276 2277 .seealso: MatCreate(), MatCreateMPISBAIJ(), MatCreateSeqSBAIJ() 2278 2279 @*/ 2280 PetscErrorCode PETSCMAT_DLLEXPORT MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt* i,PetscInt*j,PetscScalar *a,Mat *mat) 2281 { 2282 PetscErrorCode ierr; 2283 PetscInt ii; 2284 Mat_SeqSBAIJ *sbaij; 2285 2286 PetscFunctionBegin; 2287 if (bs != 1) SETERRQ1(PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs); 2288 if (i[0]) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0"); 2289 2290 ierr = MatCreate(comm,mat);CHKERRQ(ierr); 2291 ierr = MatSetSizes(*mat,m,n,m,n);CHKERRQ(ierr); 2292 ierr = MatSetType(*mat,MATSEQSBAIJ);CHKERRQ(ierr); 2293 ierr = MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);CHKERRQ(ierr); 2294 sbaij = (Mat_SeqSBAIJ*)(*mat)->data; 2295 ierr = PetscMalloc2(m,PetscInt,&sbaij->imax,m,PetscInt,&sbaij->ilen);CHKERRQ(ierr); 2296 ierr = PetscLogObjectMemory(*mat,2*m*sizeof(PetscInt));CHKERRQ(ierr); 2297 2298 sbaij->i = i; 2299 sbaij->j = j; 2300 sbaij->a = a; 2301 sbaij->singlemalloc = PETSC_FALSE; 2302 sbaij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/ 2303 sbaij->free_a = PETSC_FALSE; 2304 sbaij->free_ij = PETSC_FALSE; 2305 2306 for (ii=0; ii<m; ii++) { 2307 sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii]; 2308 #if defined(PETSC_USE_DEBUG) 2309 if (i[ii+1] - i[ii] < 0) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Negative row length in i (row indices) row = %d length = %d",ii,i[ii+1] - i[ii]); 2310 #endif 2311 } 2312 #if defined(PETSC_USE_DEBUG) 2313 for (ii=0; ii<sbaij->i[m]; ii++) { 2314 if (j[ii] < 0) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]); 2315 if (j[ii] > n - 1) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column index to large at location = %d index = %d",ii,j[ii]); 2316 } 2317 #endif 2318 2319 ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2320 ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2321 PetscFunctionReturn(0); 2322 } 2323 2324 2325 2326 2327 2328