FILE * readHB_newind(
const char* filename,
int* M,
int* N, int* nonzeros, int** colptr, int** rowind
)
{
FILE *in_file;
int Nrhs;
int Ptrcrd, Indcrd, Valcrd;
int Rhscrd = 0;
char Title[73], Key[9], Type[4], Rhstype[4];
char Ptrfmt[17], Indfmt[17], Rhsfmt[21],Valfmt[21];
if ((in_file = fopen( filename, "r")) == NULL) {
fprintf(stderr,"Error: Cannot open file: %s\n",filename);
return 0;
}
readHB_header(
in_file, Title, Key, Type, M, N, nonzeros, &Nrhs,
Ptrfmt, Indfmt, Valfmt, Rhsfmt,
&Ptrcrd, &Indcrd, &Valcrd, &Rhscrd, Rhstype
);
fclose(in_file);
*colptr = (int *)malloc((*N+1)*sizeof(int));
if ( *colptr == NULL )
IOHBTerminate("Insufficient memory for colptr.\nhb2mtxstrm.c: Line 279 approx.");
*rowind = (int *)malloc(*nonzeros*sizeof(int));
if ( *rowind == NULL )
IOHBTerminate("Insufficient memory for rowind.\nhb2mtxstrm.c: Line 281 approx.");
return readHB_ind(filename, *colptr, *rowind);
}
int
dspio_readHB_mat_double( const char* filename,
int row_i, int row_f,
int** p_rowptr,
int* p_nnz,
int** p_colind,
double** p_val )
{
/****************************************************************************/
/* This function opens and reads the specified file, interpreting its */
/* contents as a sparse matrix stored in the Harwell/Boeing standard */
/* format and creating compressed column storage scheme vectors to hold */
/* the index and nonzero value information. */
/* */
/* ---------- */
/* **CAVEAT** */
/* ---------- */
/* Parsing real formats from Fortran is tricky, and this file reader */
/* does not claim to be foolproof. It has been tested for cases when */
/* the real values are printed consistently and evenly spaced on each */
/* line, with Fixed (F), and Exponential (E or D) formats. */
/* */
/* ** If the input file does not adhere to the H/B format, the ** */
/* ** results will be unpredictable. ** */
/* */
/****************************************************************************/
FILE *in_file;
int i,j,ind,col,offset,count,last,Nrhs;
int Ptrcrd, Indcrd, Valcrd, Rhscrd;
int Nrow, Ncol, Nnzero;
int Ptrperline, Ptrwidth, Indperline, Indwidth;
int Valperline, Valwidth, Valprec;
int Valflag; /* Indicates 'E','D', or 'F' float format */
char* ThisElement;
char Title[73], Key[9], Type[4], Rhstype[4];
char Ptrfmt[17], Indfmt[17], Valfmt[21], Rhsfmt[21];
char line[BUFSIZ];
int* rowptr;
int* colind;
int len_colind;
double* val;
int nr = row_f - row_i + 1;
int temp_elem;
int rownum;
int running_offset;
int new_insert_pos;
list_t* symm_entries; /* store list of symmetric entries to add */
int* all_rowptr;
int len_extra_symm; /* # of extra entries due to symmetry */
fpos_t save_pos;
dlist_t* symm_vals;
fpos_t val_save_pos;
FILE* val_in_file;
char val_line[BUFSIZ];
int val_col;
int val_ind;
int val_i;
int val_skip_lines;
char* val_ThisElement;
double val_temp_elem;
in_file = fopen( filename, "r");
assert( in_file != NULL );
readHB_header(in_file, Title, Key, Type, &Nrow, &Ncol, &Nnzero, &Nrhs,
Ptrfmt, Indfmt, Valfmt, Rhsfmt,
&Ptrcrd, &Indcrd, &Valcrd, &Rhscrd, Rhstype);
assert( Nrow == Ncol );
assert( Type[0] == 'R' || Type[0] == 'r' );
assert( Type[1] == 'S' || Type[1] == 's' );
assert( Type[2] == 'A' || Type[2] == 'a' );
/* Parse the array input formats from Line 3 of HB file */
ParseIfmt(Ptrfmt,&Ptrperline,&Ptrwidth);
ParseIfmt(Indfmt,&Indperline,&Indwidth);
ParseRfmt(Valfmt,&Valperline,&Valwidth,&Valprec,&Valflag);
/* Read row pointer array: */
offset = 1;
rowptr = (int *)malloc( sizeof(int)*(nr + 1) );
*p_rowptr = rowptr;
if( rowptr == NULL )
IOHBTerminate( "Out of memory allocating row pointer" );
all_rowptr = (int *)malloc( sizeof(int)*(row_f+2) );
if( all_rowptr == NULL )
IOHBTerminate( "Out of memory allocating all row pointer" );
symm_entries = (list_t *)malloc( sizeof(list_t)*(row_f+1) );
symm_vals = (dlist_t *)malloc( sizeof(dlist_t)*(row_f+1) );
if( symm_entries == NULL || symm_vals == NULL )
IOHBTerminate( "Out of memory allocating symmetric entries" );
for( i = 0; i < (row_f+1); i++ ) {
lst_init( &(symm_entries[i]) );
dlst_init( &(symm_vals[i]) );
}
ThisElement = (char *) malloc(Ptrwidth+1);
if ( ThisElement == NULL )
IOHBTerminate("Insufficient memory for ThisElement (1).");
*(ThisElement+Ptrwidth) = (char) NULL;
count = 0;
for( i = 0; i < Ptrcrd; i++ ) {
fgets( line, BUFSIZ, in_file );
if ( sscanf(line, "%*s") < 0 )
IOHBTerminate("--- Null (or blank) line in ptr data region ---\n");
col = 0;
for( ind = 0; ind < Ptrperline; ind++ ) {
if( count > Ncol || count > row_f+1 )
break;
/* copy and convert index */
strncpy( ThisElement, line+col, Ptrwidth );
temp_elem = atoi(ThisElement) - offset;
if( count >= row_i ) {
/* only save elements in the proper range for this processor */
rowptr[ count - row_i ] = temp_elem;
}
all_rowptr[ count ] = temp_elem;
count++;
col += Ptrwidth;
}
}
free(ThisElement);
#ifndef NDEBUG_IO
fprintf( stderr, "printing rowptr...\n" );
for( i = 0; i <= nr; i++ )
fprintf( stderr, "rowptr[%d]==%d\n", i, rowptr[i] );
fprintf( stderr, "printing all_rowptr...\n" );
for( i = 0; i <= row_f+1; i++ )
fprintf( stderr, "all_rowptr[%d]==%d\n", i, all_rowptr[i] );
#endif
/* alloc space for column indices and values */
ThisElement = (char *) malloc(Indwidth+1);
if ( ThisElement == NULL )
IOHBTerminate("Insufficient memory for ThisElement (2).");
*(ThisElement+Indwidth) = (char) NULL;
val_ThisElement = (char *) malloc(Valwidth+2);
if ( val_ThisElement == NULL )
IOHBTerminate("Insufficient memory for val_ThisElement (2).");
*(val_ThisElement+Valwidth) = (char) NULL;
*(val_ThisElement+Valwidth+1) = (char) NULL;
len_extra_symm = 0;
fgetpos( in_file, &save_pos );
rownum = 0;
/* position at analogous place in file for values */
val_in_file = fopen( filename, "r" );
assert( val_in_file != NULL );
val_skip_lines = 4 + (Rhscrd > 0) + Ptrcrd + Indcrd;
#ifndef NDEBUG_IO
fprintf( stderr, "header lines: %d (%d), ptr lines: %d, ind lines: %d\n",
4 + (Rhscrd>0), Rhscrd, Ptrcrd, Indcrd );
fprintf( stderr, "skipping %d lines to get to vals...\n", val_skip_lines );
#endif
for( i = 0; i < val_skip_lines; i++ ) {
fgets( line, BUFSIZ, val_in_file );
}
fgetpos( val_in_file, &val_save_pos );
count = 0;
/* for( i = 0; i < Indcrd; i++ ) {*/
i = 0; /* line number */
col = 0; /* column number on a given line */
ind = 0; /* item number on a given line */
val_col = 0; /* analogous */
val_ind = 0;
val_i = 0;
while( i <= Indcrd ) {
/* read new lines, if necessary */
if( (ind % Indperline) == 0 ) {
fgets( line, BUFSIZ, in_file );
if ( sscanf(line,"%*s") < 0 )
IOHBTerminate("--- Null (or blank) line in index data region ---\n");
i++;
col = 0;
}
if( (val_ind % Valperline) == 0 ) {
fgets( val_line, BUFSIZ, val_in_file );
if( sscanf(val_line, "%*s") < 0 )
IOHBTerminate("--- Null (or blank) line in value region ---\n");
val_i++;
val_col = 0;
if( Valflag == 'D' ) {
while( strchr(val_line, 'D') ) *strchr(val_line,'D') = 'E';
}
}
if (count == Nnzero) break;
/* read an entry from this line */
strncpy( ThisElement, line+col, Indwidth );
col += Indwidth;
ind++;
strncpy( val_ThisElement, val_line + val_col, Valwidth );
*(val_ThisElement+Valwidth) = (char) NULL;
val_col += Valwidth;
val_ind++;
if ( Valflag != 'F' && strchr(val_ThisElement,'E') == NULL ) {
/* insert a char prefix for exp */
last = strlen(val_ThisElement);
for (j=last+1;j>=0;j--) {
val_ThisElement[j] = val_ThisElement[j-1];
if ( val_ThisElement[j] == '+' || val_ThisElement[j] == '-' ) {
val_ThisElement[j-1] = Valflag;
break;
}
}
}
/* done */
if( count >= rowptr[nr] )
break;
temp_elem = atoi( ThisElement ) - offset;
val_temp_elem = atof( val_ThisElement );
#ifndef NDEBUG_IO
fprintf( stderr, "found: %d (%f)\n", temp_elem, val_temp_elem );
#endif
if( temp_elem >= row_i && temp_elem <= row_f ) {
if( temp_elem != rownum ) { /* ignore diagonal entry */
#ifndef NDEBUG_IO
fprintf( stderr, "new entry: (%d, %d) == %f\n",
temp_elem, rownum, val_temp_elem );
#endif
len_extra_symm++;
lst_insert( &(symm_entries[temp_elem]), rownum );
dlst_insert( &(symm_vals[temp_elem]), val_temp_elem );
}
}
count++;
if( count >= all_rowptr[rownum+1] )
rownum++;
}
#ifndef NDEBUG_IO
fprintf( stderr, "extra entries due to symmetry: %d\n", len_extra_symm );
#endif
len_colind = rowptr[nr] - rowptr[0] + len_extra_symm;
*p_nnz = len_colind;
colind = (int *)malloc( sizeof(int)*len_colind );
*p_colind = colind;
#ifndef NDEBUG_IO
fprintf( stderr, "nnz == %d\n", len_colind );
#endif
val = (double *)malloc( sizeof(double)*len_colind );
*p_val = val;
assert( colind != NULL && val != NULL );
/* Read column index array: */
fsetpos( in_file, &save_pos );
i = 0;
col = 0;
ind = 0;
fsetpos( val_in_file, &val_save_pos );
val_i = 0;
val_col = 0;
val_ind = 0;
count = 0;
rownum = 0;
running_offset = 0;
while( i <= Indcrd ) {
/* read new lines, if necessary */
if( (ind % Indperline) == 0 ) {
fgets( line, BUFSIZ, in_file );
if ( sscanf(line,"%*s") < 0 )
IOHBTerminate("--- Null (or blank) line in index data region ---\n");
i++;
col = 0;
}
if( (val_ind % Valperline) == 0 ) {
fgets( val_line, BUFSIZ, val_in_file );
if( sscanf(val_line, "%*s") < 0 )
IOHBTerminate("--- Null (or blank) line in value region ---\n");
val_i++;
val_col = 0;
if( Valflag == 'D' ) {
while( strchr(val_line, 'D') ) *strchr(val_line,'D') = 'E';
}
}
if (count == Nnzero) break;
/* read an entry from this line */
strncpy( ThisElement, line+col, Indwidth );
col += Indwidth;
ind++;
strncpy( val_ThisElement, val_line + val_col, Valwidth );
*(val_ThisElement+Valwidth) = (char) NULL;
val_col += Valwidth;
val_ind++;
if ( Valflag != 'F' && strchr(val_ThisElement,'E') == NULL ) {
/* insert a char prefix for exp */
last = strlen(val_ThisElement);
for (j=last+1;j>=0;j--) {
val_ThisElement[j] = val_ThisElement[j-1];
if ( val_ThisElement[j] == '+' || val_ThisElement[j] == '-' ) {
val_ThisElement[j-1] = Valflag;
break;
}
}
}
/* done */
if( count >= all_rowptr[nr + row_i] )
break;
temp_elem = atoi( ThisElement ) - offset;
val_temp_elem = atof( val_ThisElement );
#ifndef NDEBUG_IO
fprintf( stderr, "entry: (%d, %d) == %f\n", rownum, temp_elem, val_temp_elem );
#endif
if( count >= all_rowptr[ row_i ] ) {
new_insert_pos = count - all_rowptr[row_i] + running_offset;
#ifndef NDEBUG_IO
fprintf( stderr, "inserting into colind[%d]: %d\n",
new_insert_pos, temp_elem );
#endif
colind[ new_insert_pos ] = temp_elem;
val[ new_insert_pos ] = val_temp_elem;
}
count++;
if( count >= all_rowptr[rownum+1] ) {
rownum++;
if( rownum >= row_i && rownum <= row_f+1 ) {
#ifndef NDEBUG_IO
fprintf( stderr, "rowptr[%d] (== %d) += %d\n", rownum - row_i, rowptr[ rownum - row_i ], running_offset );
#endif
rowptr[ rownum - row_i ] += running_offset;
}
if( rownum >= row_i && rownum <= row_f ) {
/* insert symmetric entries, if any */
int new_additions = 0;
list_node_t* trace = symm_entries[rownum].head;
dlist_node_t* dtrace = symm_vals[rownum].head;
#ifndef NDEBUG_IO
fprintf( stderr, "symm_entry[%d].length == %d\n", rownum, symm_entries[rownum].length );
#endif
new_insert_pos = count - all_rowptr[row_i] + running_offset;
while( trace != NULL ) {
assert( dtrace != NULL );
#ifndef NDEBUG_IO
fprintf( stderr, "inserting symmetric entry: colind[%d] = %d\n",
new_insert_pos + new_additions, trace->value );
fprintf( stderr, "inserting symmetric value: val[%d] = %f\n",
new_insert_pos + new_additions, dtrace->value );
#endif
colind[ new_insert_pos + new_additions ] = trace->value;
val[ new_insert_pos + new_additions ] = dtrace->value;
trace = trace->next;
dtrace = dtrace->next;
new_additions++;
} /* while */
assert( new_additions == symm_entries[rownum].length );
assert( new_additions == symm_vals[rownum].length );
running_offset += new_additions;
} /* rownum >= row_i ... */
} /* count >= ... */
}
free(ThisElement);
free(val_ThisElement);
for( i = 0; i < row_f+1; i++ ) {
lst_destroy( &(symm_entries[i]) );
}
for( i = 0; i < row_f+1; i++ ) {
dlst_destroy( &(symm_vals[i]) );
}
free( symm_entries );
free( symm_vals );
free( all_rowptr );
fclose( in_file );
fclose( val_in_file );
return 1;
}
void main(int argc, char *argv[])
{
FILE *in_file;
char Title[73], Key[9], Rhstype[4];
char Type[4];
char Ptrfmt[17], Indfmt[17], Valfmt[21], Rhsfmt[21];
int Ptrcrd, Indcrd, Valcrd, Rhscrd;
int Indperline, Indwidth;
int Valperline, Valwidth, Valprec;
int Valflag; /* Indicates 'E','D', or 'F' float format */
int Nrow, Ncol, Nnzero;
int Nrhs;
char* ThisElement;
char format[30];
char rformat[30];
int *colptr, *rowind;
int *colcount;
int i,j, repeat, count, col, ind, items, last;
char line[BUFSIZ];
MM_typecode matcode;
if (argc != 2) {
printf("Usage: %s HBfile\n\n", argv[0]);
printf(" Sends Matrix Market formatted output to stdout\n");
exit(-1);
}
in_file = fopen( argv[1], "r");
if (in_file == NULL)
{
fprintf(stderr,"Error: Cannot open file: %s\n",argv[1]);
exit(1);
}
readHB_header(in_file, Title, Key, Type, &Nrow, &Ncol, &Nnzero, &Nrhs,
Ptrfmt, Indfmt, Valfmt, Rhsfmt,
&Ptrcrd, &Indcrd, &Valcrd, &Rhscrd, Rhstype);
fclose(in_file);
if (Type[0] == 'P' ) {
fprintf(stderr,"This is a streaming translator for LARGE files with ");
fprintf(stderr,"REAL or COMPLEX data. Use 'hbmat2mtx' for PATTERN matrices.\n");
exit(1);
}
in_file = readHB_newind(argv[1], &Nrow, &Ncol, &Nnzero, &colptr, &rowind);
ParseIfmt(Indfmt,&Indperline,&Indwidth);
sprintf(format,"%%%dd %%%dd ",Indwidth,Indwidth);
ParseRfmt(Valfmt,&Valperline,&Valwidth,&Valprec,&Valflag);
sprintf(rformat,"%%%ds ",Valwidth);
ThisElement = (char *) malloc(Valwidth+1);
/* Skip to values in hb file: */
mm_set_matrix(&matcode);
mm_set_coordinate(&matcode);
if ( Type[0] == 'R' )
mm_set_real(&matcode);
else if ( Type[0] == 'C' )
mm_set_complex(&matcode);
else if ( Type[0] == 'P' )
mm_set_pattern(&matcode);
else {
fprintf(stderr,"Unrecognized field in HB Type: %1s",Type);
exit(1);
}
if ( Type[1] == 'U' || Type[1] == 'R' )
mm_set_general(&matcode);
else if ( Type[1] == 'S' )
mm_set_symmetric(&matcode);
else if ( Type[1] == 'Z' )
mm_set_skew(&matcode);
else if ( Type[1] == 'H' )
mm_set_hermitian(&matcode);
else {
fprintf(stderr,"Unrecognized field in HB Type: %1s",&Type[1]);
exit(1);
}
if ( Type[2] != 'A' ){
fprintf(stderr,"Unrecognized format in HB Type: %1s",&Type[2]);
exit(1);
}
mm_write_banner(stdout, matcode);
fprintf(stdout,"%% RBTitle: %s\n",Title);
fprintf(stdout,"%% RBKey: %s\n",Key);
mm_write_mtx_crd_size(stdout, Nrow, Ncol, Nnzero);
if ( ThisElement == NULL ) IOHBTerminate("Insufficient memory for ThisElement.\nhb2mtxstrm.c: Line 117 approx.");
repeat=0;
if ( Type[0] == 'C') repeat=1;
count = 0;
colcount = &colptr[1];
items = 0;
for (i=0;i<Valcrd;i++)
{
fgets(line, BUFSIZ, in_file);
if ( sscanf(line,"%*s") < 0 ) {
fprintf(stderr,"iohb.c: Null (or blank) line in value data region of HB file.\n");
exit(1);
}
if (Valflag == 'D') {
while( strchr(line,'D') ) *strchr(line,'D') = 'E';
}
col = 0;
for (ind = 0;ind<Valperline;ind++)
{
if (count == Nnzero) break;
if (count == *colcount-1) colcount++;
strncpy(ThisElement,line+col,Valwidth);
*(ThisElement+Valwidth) = (char) NULL;
if ( Valflag != 'F' && strchr(ThisElement,'E') == NULL ) {
/* insert a char prefix for exp */
last = strlen(ThisElement);
for (j=last+1;j>=0;j--) {
ThisElement[j] = ThisElement[j-1];
if ( ThisElement[j] == '+' || ThisElement[j] == '-' ) {
ThisElement[j-1] = Valflag;
break;
}
}
}
items++;
if (items==1) fprintf(stdout,format,rowind[count],colcount-colptr);
if (items > repeat) {
fprintf(stdout,rformat,ThisElement);
fprintf(stdout,"\n");
count++;
items=0;
} else {
fprintf(stdout,rformat,ThisElement);
}
col += Valwidth;
}
}
}
FILE * readHB_ind(const char* filename, int colptr[], int rowind[])
{
/****************************************************************************/
/* This function opens and reads the specified file, interpreting its */
/* contents as a sparse matrix stored in the Harwell/Boeing standard */
/* format and creating compressed column storage scheme vectors to hold */
/* the index information. */
/* */
/* ---------- */
/* **CAVEAT** */
/* ---------- */
/* Parsing real formats from Fortran is tricky, and this file reader */
/* does not claim to be foolproof. It has been tested for cases when */
/* the real values are printed consistently and evenly spaced on each */
/* line, with Fixed (F), and Exponential (E or D) formats. */
/* */
/* ** If the input file does not adhere to the H/B format, the ** */
/* ** results will be unpredictable. ** */
/* */
/****************************************************************************/
FILE *in_file;
int i,ind,col,offset,count;
int Nrow,Ncol,Nnzero,Nrhs;
int Ptrcrd, Indcrd, Valcrd, Rhscrd;
int Ptrperline, Ptrwidth, Indperline, Indwidth;
int Valperline, Valwidth, Valprec;
int Valflag; /* Indicates 'E','D', or 'F' float format */
char* ThisElement;
char line[BUFSIZ];
char Title[73], Key[8], Type[4], Rhstype[4];
char Ptrfmt[17], Indfmt[17], Rhsfmt[21], Valfmt[21];
if ( (in_file = fopen( filename, "r")) == NULL ) {
fprintf(stderr,"Error: Cannot open file: %s\n",filename);
return 0;
}
readHB_header(in_file, Title, Key, Type, &Nrow, &Ncol, &Nnzero, &Nrhs,
Ptrfmt, Indfmt, Valfmt, Rhsfmt,
&Ptrcrd, &Indcrd, &Valcrd, &Rhscrd, Rhstype);
/* Parse the array input formats from Line 3 of HB file */
ParseIfmt(Ptrfmt,&Ptrperline,&Ptrwidth);
ParseIfmt(Indfmt,&Indperline,&Indwidth);
ParseRfmt(Valfmt,&Valperline,&Valwidth,&Valprec,&Valflag);
if (Valflag == 'D') {
*strchr(Valfmt,'D') = 'E';
}
/* Read column pointer array: */
offset = 1-_SP_base; /* if base 0 storage is declared (via macro definition), */
/* then storage entries are offset by 1 */
ThisElement = (char *) malloc(Ptrwidth+1);
if ( ThisElement == NULL ) IOHBTerminate("Insufficient memory for ThisElement.\nhb2mtxstrm.c: Line 216 approx.");
count=0;
for (i=0;i<Ptrcrd;i++)
{
fgets(line, BUFSIZ, in_file);
if ( sscanf(line,"%*s") < 0 )
IOHBTerminate("iohb.c: Null (or blank) line in pointer data region of HB file.\n");
col = 0;
for (ind = 0;ind<Ptrperline;ind++)
{
if (count > Ncol) break;
strncpy(ThisElement,line+col,Ptrwidth);
*(ThisElement+Ptrwidth) = (char) NULL;
/* ThisElement = substr(line,col,Ptrwidth); */
colptr[count] = atoi(ThisElement)-offset;
count++; col += Ptrwidth;
}
}
free(ThisElement);
/* Read row index array: */
ThisElement = (char *) malloc(Ptrwidth+1);
if ( ThisElement == NULL ) IOHBTerminate("Insufficient memory for ThisElement.\nhb2mtxstrm.c: Line 238 approx.");
count = 0;
for (i=0;i<Indcrd;i++)
{
fgets(line, BUFSIZ, in_file);
if ( sscanf(line,"%*s") < 0 )
IOHBTerminate("iohb.c: Null (or blank) line in index data region of HB file.\n");
col = 0;
for (ind = 0;ind<Indperline;ind++)
{
if (count == Nnzero) break;
strncpy(ThisElement,line+col,Indwidth);
*(ThisElement+Indwidth) = (char) NULL;
/* ThisElement = substr(line,col,Indwidth);*/
rowind[count] = atoi(ThisElement)-offset;
count++; col += Indwidth;
}
}
free(ThisElement);
return in_file;
}
