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,PetscTruth); 16 #define CHUNKSIZE 10 17 18 19 /* 20 Checks for missing diagonals 21 */ 22 #undef __FUNCT__ 23 #define __FUNCT__ "MatMissingDiagonal_SeqSBAIJ" 24 PetscErrorCode MatMissingDiagonal_SeqSBAIJ(Mat A,PetscTruth *missing,PetscInt *dd) 25 { 26 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 27 PetscErrorCode ierr; 28 PetscInt *diag,*jj = a->j,i; 29 30 PetscFunctionBegin; 31 ierr = MatMarkDiagonal_SeqSBAIJ(A);CHKERRQ(ierr); 32 diag = a->diag; 33 *missing = PETSC_FALSE; 34 for (i=0; i<a->mbs; i++) { 35 if (jj[diag[i]] != i) { 36 *missing = PETSC_TRUE; 37 if (dd) *dd = i; 38 break; 39 } 40 } 41 PetscFunctionReturn(0); 42 } 43 44 #undef __FUNCT__ 45 #define __FUNCT__ "MatMarkDiagonal_SeqSBAIJ" 46 PetscErrorCode MatMarkDiagonal_SeqSBAIJ(Mat A) 47 { 48 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 49 PetscErrorCode ierr; 50 PetscInt i; 51 52 PetscFunctionBegin; 53 if (!a->diag) { 54 ierr = PetscMalloc(a->mbs*sizeof(PetscInt),&a->diag);CHKERRQ(ierr); 55 ierr = PetscLogObjectMemory(A,a->mbs*sizeof(PetscInt));CHKERRQ(ierr); 56 a->free_diag = PETSC_TRUE; 57 } 58 for (i=0; i<a->mbs; i++) a->diag[i] = a->i[i]; 59 PetscFunctionReturn(0); 60 } 61 62 #undef __FUNCT__ 63 #define __FUNCT__ "MatGetRowIJ_SeqSBAIJ" 64 static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscTruth symmetric,PetscTruth blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscTruth *done) 65 { 66 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 67 PetscInt i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs; 68 PetscErrorCode ierr; 69 70 PetscFunctionBegin; 71 *nn = n; 72 if (!ia) PetscFunctionReturn(0); 73 if (!blockcompressed) { 74 /* malloc & create the natural set of indices */ 75 ierr = PetscMalloc2((n+1)*bs,PetscInt,ia,nz*bs,PetscInt,ja);CHKERRQ(ierr); 76 for (i=0; i<n+1; i++) { 77 for (j=0; j<bs; j++) { 78 *ia[i*bs+j] = a->i[i]*bs+j+oshift; 79 } 80 } 81 for (i=0; i<nz; i++) { 82 for (j=0; j<bs; j++) { 83 *ja[i*bs+j] = a->j[i]*bs+j+oshift; 84 } 85 } 86 } else { /* blockcompressed */ 87 if (oshift == 1) { 88 /* temporarily add 1 to i and j indices */ 89 for (i=0; i<nz; i++) a->j[i]++; 90 for (i=0; i<n+1; i++) a->i[i]++; 91 } 92 *ia = a->i; *ja = a->j; 93 } 94 95 PetscFunctionReturn(0); 96 } 97 98 #undef __FUNCT__ 99 #define __FUNCT__ "MatRestoreRowIJ_SeqSBAIJ" 100 static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscTruth symmetric,PetscTruth blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscTruth *done) 101 { 102 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 103 PetscInt i,n = a->mbs,nz = a->i[n]; 104 PetscErrorCode ierr; 105 106 PetscFunctionBegin; 107 if (!ia) PetscFunctionReturn(0); 108 109 if (!blockcompressed) { 110 ierr = PetscFree2(*ia,*ja);CHKERRQ(ierr); 111 } else if (oshift == 1) { /* blockcompressed */ 112 for (i=0; i<nz; i++) a->j[i]--; 113 for (i=0; i<n+1; i++) a->i[i]--; 114 } 115 116 PetscFunctionReturn(0); 117 } 118 119 #undef __FUNCT__ 120 #define __FUNCT__ "MatDestroy_SeqSBAIJ" 121 PetscErrorCode MatDestroy_SeqSBAIJ(Mat A) 122 { 123 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 124 PetscErrorCode ierr; 125 126 PetscFunctionBegin; 127 #if defined(PETSC_USE_LOG) 128 PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz); 129 #endif 130 ierr = MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);CHKERRQ(ierr); 131 if (a->free_diag){ierr = PetscFree(a->diag);CHKERRQ(ierr);} 132 if (a->row) {ierr = ISDestroy(a->row);CHKERRQ(ierr);} 133 if (a->col){ierr = ISDestroy(a->col);CHKERRQ(ierr);} 134 if (a->icol) {ierr = ISDestroy(a->icol);CHKERRQ(ierr);} 135 if (a->idiag) {ierr = PetscFree(a->idiag);CHKERRQ(ierr);} 136 if (a->inode.size) {ierr = PetscFree(a->inode.size);CHKERRQ(ierr);} 137 if (a->free_diag) {ierr = PetscFree(a->diag);CHKERRQ(ierr);} 138 if (a->free_imax_ilen) {ierr = PetscFree2(a->imax,a->ilen);CHKERRQ(ierr);} 139 ierr = PetscFree(a->solve_work);CHKERRQ(ierr); 140 ierr = PetscFree(a->sor_work);CHKERRQ(ierr); 141 ierr = PetscFree(a->solves_work);CHKERRQ(ierr); 142 ierr = PetscFree(a->mult_work);CHKERRQ(ierr); 143 ierr = PetscFree(a->saved_values);CHKERRQ(ierr); 144 ierr = PetscFree(a->xtoy);CHKERRQ(ierr); 145 if (a->free_jshort) {ierr = PetscFree(a->jshort);CHKERRQ(ierr);} 146 ierr = PetscFree(a->inew);CHKERRQ(ierr); 147 if (a->parent) {ierr = MatDestroy(a->parent);CHKERRQ(ierr);} 148 ierr = PetscFree(a);CHKERRQ(ierr); 149 150 ierr = PetscObjectChangeTypeName((PetscObject)A,0);CHKERRQ(ierr); 151 ierr = PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C","",PETSC_NULL);CHKERRQ(ierr); 152 ierr = PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C","",PETSC_NULL);CHKERRQ(ierr); 153 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C","",PETSC_NULL);CHKERRQ(ierr); 154 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C","",PETSC_NULL);CHKERRQ(ierr); 155 ierr = PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C","",PETSC_NULL);CHKERRQ(ierr); 156 ierr = PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C","",PETSC_NULL);CHKERRQ(ierr); 157 PetscFunctionReturn(0); 158 } 159 160 #undef __FUNCT__ 161 #define __FUNCT__ "MatSetOption_SeqSBAIJ" 162 PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscTruth flg) 163 { 164 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 165 PetscErrorCode ierr; 166 167 PetscFunctionBegin; 168 switch (op) { 169 case MAT_ROW_ORIENTED: 170 a->roworiented = flg; 171 break; 172 case MAT_KEEP_NONZERO_PATTERN: 173 a->keepnonzeropattern = flg; 174 break; 175 case MAT_NEW_NONZERO_LOCATIONS: 176 a->nonew = (flg ? 0 : 1); 177 break; 178 case MAT_NEW_NONZERO_LOCATION_ERR: 179 a->nonew = (flg ? -1 : 0); 180 break; 181 case MAT_NEW_NONZERO_ALLOCATION_ERR: 182 a->nonew = (flg ? -2 : 0); 183 break; 184 case MAT_UNUSED_NONZERO_LOCATION_ERR: 185 a->nounused = (flg ? -1 : 0); 186 break; 187 case MAT_NEW_DIAGONALS: 188 case MAT_IGNORE_OFF_PROC_ENTRIES: 189 case MAT_USE_HASH_TABLE: 190 ierr = PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);CHKERRQ(ierr); 191 break; 192 case MAT_HERMITIAN: 193 if (!A->assembled) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first"); 194 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 195 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort; 196 } else if (A->cmap->bs == 1) { 197 A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian; 198 } else SETERRQ(PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1"); 199 break; 200 case MAT_SYMMETRIC: 201 case MAT_STRUCTURALLY_SYMMETRIC: 202 case MAT_SYMMETRY_ETERNAL: 203 if (!flg) SETERRQ(PETSC_ERR_SUP,"Matrix must be symmetric"); 204 ierr = PetscInfo1(A,"Option %s not relevent\n",MatOptions[op]);CHKERRQ(ierr); 205 break; 206 case MAT_IGNORE_LOWER_TRIANGULAR: 207 a->ignore_ltriangular = flg; 208 break; 209 case MAT_ERROR_LOWER_TRIANGULAR: 210 a->ignore_ltriangular = flg; 211 break; 212 case MAT_GETROW_UPPERTRIANGULAR: 213 a->getrow_utriangular = flg; 214 break; 215 default: 216 SETERRQ1(PETSC_ERR_SUP,"unknown option %d",op); 217 } 218 PetscFunctionReturn(0); 219 } 220 221 #undef __FUNCT__ 222 #define __FUNCT__ "MatGetRow_SeqSBAIJ" 223 PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *ncols,PetscInt **cols,PetscScalar **v) 224 { 225 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 226 PetscErrorCode ierr; 227 PetscInt itmp,i,j,k,M,*ai,*aj,bs,bn,bp,*cols_i,bs2; 228 MatScalar *aa,*aa_i; 229 PetscScalar *v_i; 230 231 PetscFunctionBegin; 232 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()"); 233 /* Get the upper triangular part of the row */ 234 bs = A->rmap->bs; 235 ai = a->i; 236 aj = a->j; 237 aa = a->a; 238 bs2 = a->bs2; 239 240 if (row < 0 || row >= A->rmap->N) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE, "Row %D out of range", row); 241 242 bn = row/bs; /* Block number */ 243 bp = row % bs; /* Block position */ 244 M = ai[bn+1] - ai[bn]; 245 *ncols = bs*M; 246 247 if (v) { 248 *v = 0; 249 if (*ncols) { 250 ierr = PetscMalloc((*ncols+row)*sizeof(PetscScalar),v);CHKERRQ(ierr); 251 for (i=0; i<M; i++) { /* for each block in the block row */ 252 v_i = *v + i*bs; 253 aa_i = aa + bs2*(ai[bn] + i); 254 for (j=bp,k=0; j<bs2; j+=bs,k++) {v_i[k] = aa_i[j];} 255 } 256 } 257 } 258 259 if (cols) { 260 *cols = 0; 261 if (*ncols) { 262 ierr = PetscMalloc((*ncols+row)*sizeof(PetscInt),cols);CHKERRQ(ierr); 263 for (i=0; i<M; i++) { /* for each block in the block row */ 264 cols_i = *cols + i*bs; 265 itmp = bs*aj[ai[bn] + i]; 266 for (j=0; j<bs; j++) {cols_i[j] = itmp++;} 267 } 268 } 269 } 270 271 /*search column A(0:row-1,row) (=A(row,0:row-1)). Could be expensive! */ 272 /* this segment is currently removed, so only entries in the upper triangle are obtained */ 273 #ifdef column_search 274 v_i = *v + M*bs; 275 cols_i = *cols + M*bs; 276 for (i=0; i<bn; i++){ /* for each block row */ 277 M = ai[i+1] - ai[i]; 278 for (j=0; j<M; j++){ 279 itmp = aj[ai[i] + j]; /* block column value */ 280 if (itmp == bn){ 281 aa_i = aa + bs2*(ai[i] + j) + bs*bp; 282 for (k=0; k<bs; k++) { 283 *cols_i++ = i*bs+k; 284 *v_i++ = aa_i[k]; 285 } 286 *ncols += bs; 287 break; 288 } 289 } 290 } 291 #endif 292 PetscFunctionReturn(0); 293 } 294 295 #undef __FUNCT__ 296 #define __FUNCT__ "MatRestoreRow_SeqSBAIJ" 297 PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v) 298 { 299 PetscErrorCode ierr; 300 301 PetscFunctionBegin; 302 if (idx) {ierr = PetscFree(*idx);CHKERRQ(ierr);} 303 if (v) {ierr = PetscFree(*v);CHKERRQ(ierr);} 304 PetscFunctionReturn(0); 305 } 306 307 #undef __FUNCT__ 308 #define __FUNCT__ "MatGetRowUpperTriangular_SeqSBAIJ" 309 PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A) 310 { 311 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 312 313 PetscFunctionBegin; 314 a->getrow_utriangular = PETSC_TRUE; 315 PetscFunctionReturn(0); 316 } 317 #undef __FUNCT__ 318 #define __FUNCT__ "MatRestoreRowUpperTriangular_SeqSBAIJ" 319 PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A) 320 { 321 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 322 323 PetscFunctionBegin; 324 a->getrow_utriangular = PETSC_FALSE; 325 PetscFunctionReturn(0); 326 } 327 328 #undef __FUNCT__ 329 #define __FUNCT__ "MatTranspose_SeqSBAIJ" 330 PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B) 331 { 332 PetscErrorCode ierr; 333 PetscFunctionBegin; 334 if (reuse == MAT_INITIAL_MATRIX || *B != A) { 335 ierr = MatDuplicate(A,MAT_COPY_VALUES,B);CHKERRQ(ierr); 336 } 337 PetscFunctionReturn(0); 338 } 339 340 #undef __FUNCT__ 341 #define __FUNCT__ "MatView_SeqSBAIJ_ASCII" 342 static PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer) 343 { 344 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 345 PetscErrorCode ierr; 346 PetscInt i,j,bs = A->rmap->bs,k,l,bs2=a->bs2; 347 const char *name; 348 PetscViewerFormat format; 349 350 PetscFunctionBegin; 351 ierr = PetscObjectGetName((PetscObject)A,&name);CHKERRQ(ierr); 352 ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); 353 if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 354 ierr = PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);CHKERRQ(ierr); 355 } else if (format == PETSC_VIEWER_ASCII_MATLAB) { 356 Mat aij; 357 358 if (A->factor && bs>1){ 359 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); 360 PetscFunctionReturn(0); 361 } 362 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);CHKERRQ(ierr); 363 ierr = MatView(aij,viewer);CHKERRQ(ierr); 364 ierr = MatDestroy(aij);CHKERRQ(ierr); 365 } else if (format == PETSC_VIEWER_ASCII_COMMON) { 366 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 367 for (i=0; i<a->mbs; i++) { 368 for (j=0; j<bs; j++) { 369 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 370 for (k=a->i[i]; k<a->i[i+1]; k++) { 371 for (l=0; l<bs; l++) { 372 #if defined(PETSC_USE_COMPLEX) 373 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 374 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l, 375 PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 376 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 377 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l, 378 PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 379 } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) { 380 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 381 } 382 #else 383 if (a->a[bs2*k + l*bs + j] != 0.0) { 384 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 385 } 386 #endif 387 } 388 } 389 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 390 } 391 } 392 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 393 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 394 PetscFunctionReturn(0); 395 } else { 396 if (A->factor && bs>1){ 397 ierr = PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored. MatView_SeqSBAIJ_ASCII() may not display complete or logically correct entries!\n");CHKERRQ(ierr); 398 } 399 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_NO);CHKERRQ(ierr); 400 for (i=0; i<a->mbs; i++) { 401 for (j=0; j<bs; j++) { 402 ierr = PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);CHKERRQ(ierr); 403 for (k=a->i[i]; k<a->i[i+1]; k++) { 404 for (l=0; l<bs; l++) { 405 #if defined(PETSC_USE_COMPLEX) 406 if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) { 407 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l, 408 PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 409 } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) { 410 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l, 411 PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 412 } else { 413 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));CHKERRQ(ierr); 414 } 415 #else 416 ierr = PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);CHKERRQ(ierr); 417 #endif 418 } 419 } 420 ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); 421 } 422 } 423 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_YES);CHKERRQ(ierr); 424 } 425 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 426 PetscFunctionReturn(0); 427 } 428 429 #undef __FUNCT__ 430 #define __FUNCT__ "MatView_SeqSBAIJ_Draw_Zoom" 431 static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa) 432 { 433 Mat A = (Mat) Aa; 434 Mat_SeqSBAIJ *a=(Mat_SeqSBAIJ*)A->data; 435 PetscErrorCode ierr; 436 PetscInt row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2; 437 PetscMPIInt rank; 438 PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r; 439 MatScalar *aa; 440 MPI_Comm comm; 441 PetscViewer viewer; 442 443 PetscFunctionBegin; 444 /* 445 This is nasty. If this is called from an originally parallel matrix 446 then all processes call this,but only the first has the matrix so the 447 rest should return immediately. 448 */ 449 ierr = PetscObjectGetComm((PetscObject)draw,&comm);CHKERRQ(ierr); 450 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 451 if (rank) PetscFunctionReturn(0); 452 453 ierr = PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);CHKERRQ(ierr); 454 455 ierr = PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);CHKERRQ(ierr); 456 PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric"); 457 458 /* loop over matrix elements drawing boxes */ 459 color = PETSC_DRAW_BLUE; 460 for (i=0,row=0; i<mbs; i++,row+=bs) { 461 for (j=a->i[i]; j<a->i[i+1]; j++) { 462 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 463 x_l = a->j[j]*bs; x_r = x_l + 1.0; 464 aa = a->a + j*bs2; 465 for (k=0; k<bs; k++) { 466 for (l=0; l<bs; l++) { 467 if (PetscRealPart(*aa++) >= 0.) continue; 468 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 469 } 470 } 471 } 472 } 473 color = PETSC_DRAW_CYAN; 474 for (i=0,row=0; i<mbs; i++,row+=bs) { 475 for (j=a->i[i]; j<a->i[i+1]; j++) { 476 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 477 x_l = a->j[j]*bs; x_r = x_l + 1.0; 478 aa = a->a + j*bs2; 479 for (k=0; k<bs; k++) { 480 for (l=0; l<bs; l++) { 481 if (PetscRealPart(*aa++) != 0.) continue; 482 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 483 } 484 } 485 } 486 } 487 488 color = PETSC_DRAW_RED; 489 for (i=0,row=0; i<mbs; i++,row+=bs) { 490 for (j=a->i[i]; j<a->i[i+1]; j++) { 491 y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0; 492 x_l = a->j[j]*bs; x_r = x_l + 1.0; 493 aa = a->a + j*bs2; 494 for (k=0; k<bs; k++) { 495 for (l=0; l<bs; l++) { 496 if (PetscRealPart(*aa++) <= 0.) continue; 497 ierr = PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);CHKERRQ(ierr); 498 } 499 } 500 } 501 } 502 PetscFunctionReturn(0); 503 } 504 505 #undef __FUNCT__ 506 #define __FUNCT__ "MatView_SeqSBAIJ_Draw" 507 static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer) 508 { 509 PetscErrorCode ierr; 510 PetscReal xl,yl,xr,yr,w,h; 511 PetscDraw draw; 512 PetscTruth isnull; 513 514 PetscFunctionBegin; 515 ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); 516 ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); 517 518 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);CHKERRQ(ierr); 519 xr = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0; 520 xr += w; yr += h; xl = -w; yl = -h; 521 ierr = PetscDrawSetCoordinates(draw,xl,yl,xr,yr);CHKERRQ(ierr); 522 ierr = PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);CHKERRQ(ierr); 523 ierr = PetscObjectCompose((PetscObject)A,"Zoomviewer",PETSC_NULL);CHKERRQ(ierr); 524 PetscFunctionReturn(0); 525 } 526 527 #undef __FUNCT__ 528 #define __FUNCT__ "MatView_SeqSBAIJ" 529 PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer) 530 { 531 PetscErrorCode ierr; 532 PetscTruth iascii,isdraw; 533 FILE *file = 0; 534 535 PetscFunctionBegin; 536 ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_ASCII,&iascii);CHKERRQ(ierr); 537 ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_DRAW,&isdraw);CHKERRQ(ierr); 538 if (iascii){ 539 ierr = MatView_SeqSBAIJ_ASCII(A,viewer);CHKERRQ(ierr); 540 } else if (isdraw) { 541 ierr = MatView_SeqSBAIJ_Draw(A,viewer);CHKERRQ(ierr); 542 } else { 543 Mat B; 544 ierr = MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); 545 ierr = MatView(B,viewer);CHKERRQ(ierr); 546 ierr = MatDestroy(B);CHKERRQ(ierr); 547 ierr = PetscViewerBinaryGetInfoPointer(viewer,&file);CHKERRQ(ierr); 548 if (file) { 549 fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs); 550 } 551 } 552 PetscFunctionReturn(0); 553 } 554 555 556 #undef __FUNCT__ 557 #define __FUNCT__ "MatGetValues_SeqSBAIJ" 558 PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[]) 559 { 560 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 561 PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j; 562 PetscInt *ai = a->i,*ailen = a->ilen; 563 PetscInt brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2; 564 MatScalar *ap,*aa = a->a; 565 566 PetscFunctionBegin; 567 for (k=0; k<m; k++) { /* loop over rows */ 568 row = im[k]; brow = row/bs; 569 if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */ 570 if (row >= A->rmap->N) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1); 571 rp = aj + ai[brow] ; ap = aa + bs2*ai[brow] ; 572 nrow = ailen[brow]; 573 for (l=0; l<n; l++) { /* loop over columns */ 574 if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */ 575 if (in[l] >= A->cmap->n) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->cmap->n-1); 576 col = in[l] ; 577 bcol = col/bs; 578 cidx = col%bs; 579 ridx = row%bs; 580 high = nrow; 581 low = 0; /* assume unsorted */ 582 while (high-low > 5) { 583 t = (low+high)/2; 584 if (rp[t] > bcol) high = t; 585 else low = t; 586 } 587 for (i=low; i<high; i++) { 588 if (rp[i] > bcol) break; 589 if (rp[i] == bcol) { 590 *v++ = ap[bs2*i+bs*cidx+ridx]; 591 goto finished; 592 } 593 } 594 *v++ = 0.0; 595 finished:; 596 } 597 } 598 PetscFunctionReturn(0); 599 } 600 601 602 #undef __FUNCT__ 603 #define __FUNCT__ "MatSetValuesBlocked_SeqSBAIJ" 604 PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 605 { 606 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 607 PetscErrorCode ierr; 608 PetscInt *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1; 609 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen; 610 PetscInt *aj=a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval; 611 PetscTruth roworiented=a->roworiented; 612 const PetscScalar *value = v; 613 MatScalar *ap,*aa = a->a,*bap; 614 615 PetscFunctionBegin; 616 if (roworiented) { 617 stepval = (n-1)*bs; 618 } else { 619 stepval = (m-1)*bs; 620 } 621 for (k=0; k<m; k++) { /* loop over added rows */ 622 row = im[k]; 623 if (row < 0) continue; 624 #if defined(PETSC_USE_DEBUG) 625 if (row >= a->mbs) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1); 626 #endif 627 rp = aj + ai[row]; 628 ap = aa + bs2*ai[row]; 629 rmax = imax[row]; 630 nrow = ailen[row]; 631 low = 0; 632 high = nrow; 633 for (l=0; l<n; l++) { /* loop over added columns */ 634 if (in[l] < 0) continue; 635 col = in[l]; 636 #if defined(PETSC_USE_DEBUG) 637 if (col >= a->nbs) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1); 638 #endif 639 if (col < row) { 640 if (a->ignore_ltriangular) { 641 continue; /* ignore lower triangular block */ 642 } else { 643 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)"); 644 } 645 } 646 if (roworiented) { 647 value = v + k*(stepval+bs)*bs + l*bs; 648 } else { 649 value = v + l*(stepval+bs)*bs + k*bs; 650 } 651 if (col <= lastcol) low = 0; else high = nrow; 652 lastcol = col; 653 while (high-low > 7) { 654 t = (low+high)/2; 655 if (rp[t] > col) high = t; 656 else low = t; 657 } 658 for (i=low; i<high; i++) { 659 if (rp[i] > col) break; 660 if (rp[i] == col) { 661 bap = ap + bs2*i; 662 if (roworiented) { 663 if (is == ADD_VALUES) { 664 for (ii=0; ii<bs; ii++,value+=stepval) { 665 for (jj=ii; jj<bs2; jj+=bs) { 666 bap[jj] += *value++; 667 } 668 } 669 } else { 670 for (ii=0; ii<bs; ii++,value+=stepval) { 671 for (jj=ii; jj<bs2; jj+=bs) { 672 bap[jj] = *value++; 673 } 674 } 675 } 676 } else { 677 if (is == ADD_VALUES) { 678 for (ii=0; ii<bs; ii++,value+=stepval) { 679 for (jj=0; jj<bs; jj++) { 680 *bap++ += *value++; 681 } 682 } 683 } else { 684 for (ii=0; ii<bs; ii++,value+=stepval) { 685 for (jj=0; jj<bs; jj++) { 686 *bap++ = *value++; 687 } 688 } 689 } 690 } 691 goto noinsert2; 692 } 693 } 694 if (nonew == 1) goto noinsert2; 695 if (nonew == -1) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 696 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 697 N = nrow++ - 1; high++; 698 /* shift up all the later entries in this row */ 699 for (ii=N; ii>=i; ii--) { 700 rp[ii+1] = rp[ii]; 701 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 702 } 703 if (N >= i) { 704 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 705 } 706 rp[i] = col; 707 bap = ap + bs2*i; 708 if (roworiented) { 709 for (ii=0; ii<bs; ii++,value+=stepval) { 710 for (jj=ii; jj<bs2; jj+=bs) { 711 bap[jj] = *value++; 712 } 713 } 714 } else { 715 for (ii=0; ii<bs; ii++,value+=stepval) { 716 for (jj=0; jj<bs; jj++) { 717 *bap++ = *value++; 718 } 719 } 720 } 721 noinsert2:; 722 low = i; 723 } 724 ailen[row] = nrow; 725 } 726 PetscFunctionReturn(0); 727 } 728 729 /* 730 This is not yet used 731 */ 732 #undef __FUNCT__ 733 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode" 734 PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A) 735 { 736 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 737 PetscErrorCode ierr; 738 const PetscInt *ai = a->i, *aj = a->j,*cols; 739 PetscInt i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts; 740 PetscTruth flag; 741 742 PetscFunctionBegin; 743 ierr = PetscMalloc(m*sizeof(PetscInt),&ns);CHKERRQ(ierr); 744 while (i < m){ 745 nzx = ai[i+1] - ai[i]; /* Number of nonzeros */ 746 /* Limits the number of elements in a node to 'a->inode.limit' */ 747 for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) { 748 nzy = ai[j+1] - ai[j]; 749 if (nzy != (nzx - j + i)) break; 750 ierr = PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);CHKERRQ(ierr); 751 if (!flag) break; 752 } 753 ns[node_count++] = blk_size; 754 i = j; 755 } 756 if (!a->inode.size && m && node_count > .9*m) { 757 ierr = PetscFree(ns);CHKERRQ(ierr); 758 ierr = PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);CHKERRQ(ierr); 759 } else { 760 a->inode.node_count = node_count; 761 ierr = PetscMalloc(node_count*sizeof(PetscInt),&a->inode.size);CHKERRQ(ierr); 762 ierr = PetscLogObjectMemory(A,node_count*sizeof(PetscInt));CHKERRQ(ierr); 763 ierr = PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt)); 764 ierr = PetscFree(ns);CHKERRQ(ierr); 765 ierr = PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);CHKERRQ(ierr); 766 767 /* count collections of adjacent columns in each inode */ 768 row = 0; 769 cnt = 0; 770 for (i=0; i<node_count; i++) { 771 cols = aj + ai[row] + a->inode.size[i]; 772 nz = ai[row+1] - ai[row] - a->inode.size[i]; 773 for (j=1; j<nz; j++) { 774 if (cols[j] != cols[j-1]+1) { 775 cnt++; 776 } 777 } 778 cnt++; 779 row += a->inode.size[i]; 780 } 781 ierr = PetscMalloc(2*cnt*sizeof(PetscInt),&counts);CHKERRQ(ierr); 782 cnt = 0; 783 row = 0; 784 for (i=0; i<node_count; i++) { 785 cols = aj + ai[row] + a->inode.size[i]; 786 CHKMEMQ; 787 counts[2*cnt] = cols[0]; 788 CHKMEMQ; 789 nz = ai[row+1] - ai[row] - a->inode.size[i]; 790 cnt2 = 1; 791 for (j=1; j<nz; j++) { 792 if (cols[j] != cols[j-1]+1) { 793 CHKMEMQ; 794 counts[2*(cnt++)+1] = cnt2; 795 counts[2*cnt] = cols[j]; 796 CHKMEMQ; 797 cnt2 = 1; 798 } else cnt2++; 799 } 800 CHKMEMQ; 801 counts[2*(cnt++)+1] = cnt2; 802 CHKMEMQ; 803 row += a->inode.size[i]; 804 } 805 ierr = PetscIntView(2*cnt,counts,0); 806 } 807 PetscFunctionReturn(0); 808 } 809 810 #undef __FUNCT__ 811 #define __FUNCT__ "MatAssemblyEnd_SeqSBAIJ" 812 PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode) 813 { 814 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 815 PetscErrorCode ierr; 816 PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax; 817 PetscInt m = A->rmap->N,*ip,N,*ailen = a->ilen; 818 PetscInt mbs = a->mbs,bs2 = a->bs2,rmax = 0; 819 MatScalar *aa = a->a,*ap; 820 821 PetscFunctionBegin; 822 if (mode == MAT_FLUSH_ASSEMBLY) PetscFunctionReturn(0); 823 824 if (m) rmax = ailen[0]; 825 for (i=1; i<mbs; i++) { 826 /* move each row back by the amount of empty slots (fshift) before it*/ 827 fshift += imax[i-1] - ailen[i-1]; 828 rmax = PetscMax(rmax,ailen[i]); 829 if (fshift) { 830 ip = aj + ai[i]; ap = aa + bs2*ai[i]; 831 N = ailen[i]; 832 for (j=0; j<N; j++) { 833 ip[j-fshift] = ip[j]; 834 ierr = PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 835 } 836 } 837 ai[i] = ai[i-1] + ailen[i-1]; 838 } 839 if (mbs) { 840 fshift += imax[mbs-1] - ailen[mbs-1]; 841 ai[mbs] = ai[mbs-1] + ailen[mbs-1]; 842 } 843 /* reset ilen and imax for each row */ 844 for (i=0; i<mbs; i++) { 845 ailen[i] = imax[i] = ai[i+1] - ai[i]; 846 } 847 a->nz = ai[mbs]; 848 849 /* diagonals may have moved, reset it */ 850 if (a->diag) { 851 ierr = PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));CHKERRQ(ierr); 852 } 853 if (fshift && a->nounused == -1) { 854 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); 855 } 856 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); 857 ierr = PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);CHKERRQ(ierr); 858 ierr = PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);CHKERRQ(ierr); 859 a->reallocs = 0; 860 A->info.nz_unneeded = (PetscReal)fshift*bs2; 861 a->idiagvalid = PETSC_FALSE; 862 863 if (A->cmap->n < 65536 && A->cmap->bs == 1) { 864 if (!a->jshort) { 865 ierr = PetscMalloc(a->i[A->rmap->n]*sizeof(unsigned short),&a->jshort);CHKERRQ(ierr); 866 ierr = PetscLogObjectMemory(A,a->i[A->rmap->n]*sizeof(unsigned short));CHKERRQ(ierr); 867 for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i]; 868 A->ops->mult = MatMult_SeqSBAIJ_1_ushort; 869 A->ops->sor = MatSOR_SeqSBAIJ_ushort; 870 a->free_jshort = PETSC_TRUE; 871 } 872 } 873 PetscFunctionReturn(0); 874 } 875 876 /* 877 This function returns an array of flags which indicate the locations of contiguous 878 blocks that should be zeroed. for eg: if bs = 3 and is = [0,1,2,3,5,6,7,8,9] 879 then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)] 880 Assume: sizes should be long enough to hold all the values. 881 */ 882 #undef __FUNCT__ 883 #define __FUNCT__ "MatZeroRows_SeqSBAIJ_Check_Blocks" 884 PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max) 885 { 886 PetscInt i,j,k,row; 887 PetscTruth flg; 888 889 PetscFunctionBegin; 890 for (i=0,j=0; i<n; j++) { 891 row = idx[i]; 892 if (row%bs!=0) { /* Not the begining of a block */ 893 sizes[j] = 1; 894 i++; 895 } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */ 896 sizes[j] = 1; /* Also makes sure atleast 'bs' values exist for next else */ 897 i++; 898 } else { /* Begining of the block, so check if the complete block exists */ 899 flg = PETSC_TRUE; 900 for (k=1; k<bs; k++) { 901 if (row+k != idx[i+k]) { /* break in the block */ 902 flg = PETSC_FALSE; 903 break; 904 } 905 } 906 if (flg) { /* No break in the bs */ 907 sizes[j] = bs; 908 i+= bs; 909 } else { 910 sizes[j] = 1; 911 i++; 912 } 913 } 914 } 915 *bs_max = j; 916 PetscFunctionReturn(0); 917 } 918 919 920 /* Only add/insert a(i,j) with i<=j (blocks). 921 Any a(i,j) with i>j input by user is ingored. 922 */ 923 924 #undef __FUNCT__ 925 #define __FUNCT__ "MatSetValues_SeqSBAIJ" 926 PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is) 927 { 928 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 929 PetscErrorCode ierr; 930 PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1; 931 PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented; 932 PetscInt *aj=a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol; 933 PetscInt ridx,cidx,bs2=a->bs2; 934 MatScalar *ap,value,*aa=a->a,*bap; 935 936 PetscFunctionBegin; 937 if (v) PetscValidScalarPointer(v,6); 938 for (k=0; k<m; k++) { /* loop over added rows */ 939 row = im[k]; /* row number */ 940 brow = row/bs; /* block row number */ 941 if (row < 0) continue; 942 #if defined(PETSC_USE_DEBUG) 943 if (row >= A->rmap->N) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1); 944 #endif 945 rp = aj + ai[brow]; /*ptr to beginning of column value of the row block*/ 946 ap = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/ 947 rmax = imax[brow]; /* maximum space allocated for this row */ 948 nrow = ailen[brow]; /* actual length of this row */ 949 low = 0; 950 951 for (l=0; l<n; l++) { /* loop over added columns */ 952 if (in[l] < 0) continue; 953 #if defined(PETSC_USE_DEBUG) 954 if (in[l] >= A->rmap->N) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->rmap->N-1); 955 #endif 956 col = in[l]; 957 bcol = col/bs; /* block col number */ 958 959 if (brow > bcol) { 960 if (a->ignore_ltriangular){ 961 continue; /* ignore lower triangular values */ 962 } else { 963 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)"); 964 } 965 } 966 967 ridx = row % bs; cidx = col % bs; /*row and col index inside the block */ 968 if ((brow==bcol && ridx<=cidx) || (brow<bcol)){ 969 /* element value a(k,l) */ 970 if (roworiented) { 971 value = v[l + k*n]; 972 } else { 973 value = v[k + l*m]; 974 } 975 976 /* move pointer bap to a(k,l) quickly and add/insert value */ 977 if (col <= lastcol) low = 0; high = nrow; 978 lastcol = col; 979 while (high-low > 7) { 980 t = (low+high)/2; 981 if (rp[t] > bcol) high = t; 982 else low = t; 983 } 984 for (i=low; i<high; i++) { 985 if (rp[i] > bcol) break; 986 if (rp[i] == bcol) { 987 bap = ap + bs2*i + bs*cidx + ridx; 988 if (is == ADD_VALUES) *bap += value; 989 else *bap = value; 990 /* for diag block, add/insert its symmetric element a(cidx,ridx) */ 991 if (brow == bcol && ridx < cidx){ 992 bap = ap + bs2*i + bs*ridx + cidx; 993 if (is == ADD_VALUES) *bap += value; 994 else *bap = value; 995 } 996 goto noinsert1; 997 } 998 } 999 1000 if (nonew == 1) goto noinsert1; 1001 if (nonew == -1) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col); 1002 MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar); 1003 1004 N = nrow++ - 1; high++; 1005 /* shift up all the later entries in this row */ 1006 for (ii=N; ii>=i; ii--) { 1007 rp[ii+1] = rp[ii]; 1008 ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); 1009 } 1010 if (N>=i) { 1011 ierr = PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1012 } 1013 rp[i] = bcol; 1014 ap[bs2*i + bs*cidx + ridx] = value; 1015 noinsert1:; 1016 low = i; 1017 } 1018 } /* end of loop over added columns */ 1019 ailen[brow] = nrow; 1020 } /* end of loop over added rows */ 1021 PetscFunctionReturn(0); 1022 } 1023 1024 #undef __FUNCT__ 1025 #define __FUNCT__ "MatICCFactor_SeqSBAIJ" 1026 PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info) 1027 { 1028 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)inA->data; 1029 Mat outA; 1030 PetscErrorCode ierr; 1031 PetscTruth row_identity; 1032 1033 PetscFunctionBegin; 1034 if (info->levels != 0) SETERRQ(PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc"); 1035 ierr = ISIdentity(row,&row_identity);CHKERRQ(ierr); 1036 if (!row_identity) SETERRQ(PETSC_ERR_SUP,"Matrix reordering is not supported"); 1037 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()! */ 1038 1039 outA = inA; 1040 inA->factor = MAT_FACTOR_ICC; 1041 1042 ierr = MatMarkDiagonal_SeqSBAIJ(inA);CHKERRQ(ierr); 1043 ierr = MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);CHKERRQ(ierr); 1044 1045 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1046 if (a->row) { ierr = ISDestroy(a->row);CHKERRQ(ierr); } 1047 a->row = row; 1048 ierr = PetscObjectReference((PetscObject)row);CHKERRQ(ierr); 1049 if (a->col) { ierr = ISDestroy(a->col);CHKERRQ(ierr); } 1050 a->col = row; 1051 1052 /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */ 1053 if (a->icol) {ierr = ISInvertPermutation(row,PETSC_DECIDE, &a->icol);CHKERRQ(ierr);} 1054 ierr = PetscLogObjectParent(inA,a->icol);CHKERRQ(ierr); 1055 1056 if (!a->solve_work) { 1057 ierr = PetscMalloc((inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar),&a->solve_work);CHKERRQ(ierr); 1058 ierr = PetscLogObjectMemory(inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));CHKERRQ(ierr); 1059 } 1060 1061 ierr = MatCholeskyFactorNumeric(outA,inA,info);CHKERRQ(ierr); 1062 PetscFunctionReturn(0); 1063 } 1064 1065 EXTERN_C_BEGIN 1066 #undef __FUNCT__ 1067 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices_SeqSBAIJ" 1068 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices) 1069 { 1070 Mat_SeqSBAIJ *baij = (Mat_SeqSBAIJ *)mat->data; 1071 PetscInt i,nz,n; 1072 1073 PetscFunctionBegin; 1074 nz = baij->maxnz; 1075 n = mat->cmap->n; 1076 for (i=0; i<nz; i++) { 1077 baij->j[i] = indices[i]; 1078 } 1079 baij->nz = nz; 1080 for (i=0; i<n; i++) { 1081 baij->ilen[i] = baij->imax[i]; 1082 } 1083 PetscFunctionReturn(0); 1084 } 1085 EXTERN_C_END 1086 1087 #undef __FUNCT__ 1088 #define __FUNCT__ "MatSeqSBAIJSetColumnIndices" 1089 /*@ 1090 MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows 1091 in the matrix. 1092 1093 Input Parameters: 1094 + mat - the SeqSBAIJ matrix 1095 - indices - the column indices 1096 1097 Level: advanced 1098 1099 Notes: 1100 This can be called if you have precomputed the nonzero structure of the 1101 matrix and want to provide it to the matrix object to improve the performance 1102 of the MatSetValues() operation. 1103 1104 You MUST have set the correct numbers of nonzeros per row in the call to 1105 MatCreateSeqSBAIJ(), and the columns indices MUST be sorted. 1106 1107 MUST be called before any calls to MatSetValues() 1108 1109 .seealso: MatCreateSeqSBAIJ 1110 @*/ 1111 PetscErrorCode PETSCMAT_DLLEXPORT MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices) 1112 { 1113 PetscErrorCode ierr,(*f)(Mat,PetscInt *); 1114 1115 PetscFunctionBegin; 1116 PetscValidHeaderSpecific(mat,MAT_COOKIE,1); 1117 PetscValidPointer(indices,2); 1118 ierr = PetscObjectQueryFunction((PetscObject)mat,"MatSeqSBAIJSetColumnIndices_C",(void (**)(void))&f);CHKERRQ(ierr); 1119 if (f) { 1120 ierr = (*f)(mat,indices);CHKERRQ(ierr); 1121 } else { 1122 SETERRQ(PETSC_ERR_SUP,"Wrong type of matrix to set column indices"); 1123 } 1124 PetscFunctionReturn(0); 1125 } 1126 1127 #undef __FUNCT__ 1128 #define __FUNCT__ "MatCopy_SeqSBAIJ" 1129 PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str) 1130 { 1131 PetscErrorCode ierr; 1132 1133 PetscFunctionBegin; 1134 /* If the two matrices have the same copy implementation, use fast copy. */ 1135 if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) { 1136 Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data; 1137 Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data; 1138 1139 if (a->i[A->rmap->N] != b->i[B->rmap->N]) { 1140 SETERRQ(PETSC_ERR_ARG_INCOMP,"Number of nonzeros in two matrices are different"); 1141 } 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_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