static gmx_bool gmx_one_before_eof(FILE *fp)
{
char data[4];
gmx_bool beof;
if ((beof = fread(data, 1, 1, fp)) == 1)
{
gmx_fseek(fp, -1, SEEK_CUR);
}
return !beof;
}
gmx_bool gmx_eof(FILE *fp)
{
char data[4];
gmx_bool beof;
if (is_pipe(fp))
return feof(fp);
else {
if ((beof=fread(data,1,1,fp))==1)
gmx_fseek(fp,-1,SEEK_CUR);
return !beof;
}
}
int gmx_fio_seek(t_fileio* fio, gmx_off_t fpos)
{
int rc;
gmx_fio_lock(fio);
if (fio->fp)
{
rc = gmx_fseek(fio->fp, fpos, SEEK_SET);
}
else
{
gmx_file(fio->fn);
rc = -1;
}
gmx_fio_unlock(fio);
return rc;
}
/* internal variant of get_file_md5 that operates on a locked file */
static int gmx_fio_int_get_file_md5(t_fileio *fio, gmx_off_t offset,
unsigned char digest[])
{
/*1MB: large size important to catch almost identical files */
#define CPT_CHK_LEN 1048576
md5_state_t state;
unsigned char buf[CPT_CHK_LEN];
gmx_off_t read_len;
gmx_off_t seek_offset;
int ret = -1;
seek_offset = offset - CPT_CHK_LEN;
if (seek_offset < 0)
{
seek_offset = 0;
}
read_len = offset - seek_offset;
if (fio->fp && fio->bReadWrite)
{
ret = gmx_fseek(fio->fp, seek_offset, SEEK_SET);
if (ret)
{
gmx_fseek(fio->fp, 0, SEEK_END);
}
}
if (ret) /*either no fp, not readwrite, or fseek not successful */
{
return -1;
}
/* the read puts the file position back to offset */
if ((gmx_off_t)fread(buf, 1, read_len, fio->fp) != read_len)
{
/* not fatal: md5sum check to prevent overwriting files
* works (less safe) without
* */
if (ferror(fio->fp))
{
fprintf(stderr, "\nTrying to get md5sum: %s: %s\n", fio->fn,
strerror(errno));
}
else if (feof(fio->fp))
{
/*
* For long runs that checkpoint frequently but write e.g. logs
* infrequently we don't want to issue lots of warnings before we
* have written anything to the log.
*/
if (0)
{
fprintf(stderr, "\nTrying to get md5sum: EOF: %s\n", fio->fn);
}
}
else
{
fprintf(
stderr,
"\nTrying to get md5sum: Unknown reason for short read: %s\n",
fio->fn);
}
gmx_fseek(fio->fp, 0, SEEK_END);
ret = -1;
}
gmx_fseek(fio->fp, 0, SEEK_END); /*is already at end, but under windows
it gives problems otherwise*/
if (debug)
{
fprintf(debug, "chksum %s readlen %ld\n", fio->fn, (long int)read_len);
}
if (!ret)
{
md5_init(&state);
md5_append(&state, buf, read_len);
md5_finish(&state, digest);
return read_len;
}
else
{
return ret;
}
}
/*****************************************************************
*
* EXPORTED SECTION
*
*****************************************************************/
t_fileio *gmx_fio_open(const char *fn, const char *mode)
{
t_fileio *fio = NULL;
int i;
char newmode[5];
gmx_bool bRead, bReadWrite;
int xdrid;
if (fn2ftp(fn) == efTPA)
{
strcpy(newmode, mode);
}
else
{
/* sanitize the mode string */
if (strncmp(mode, "r+", 2) == 0)
{
strcpy(newmode, "r+");
}
else if (mode[0] == 'r')
{
strcpy(newmode, "r");
}
else if (strncmp(mode, "w+", 2) == 0)
{
strcpy(newmode, "w+");
}
else if (mode[0] == 'w')
{
strcpy(newmode, "w");
}
else if (strncmp(mode, "a+", 2) == 0)
{
strcpy(newmode, "a+");
}
else if (mode[0] == 'a')
{
strcpy(newmode, "a");
}
else
{
gmx_fatal(FARGS, "DEATH HORROR in gmx_fio_open, mode is '%s'", mode);
}
}
/* Check if it should be opened as a binary file */
if (strncmp(ftp2ftype(fn2ftp(fn)), "ASCII", 5))
{
/* Not ascii, add b to file mode */
if ((strchr(newmode, 'b') == NULL) && (strchr(newmode, 'B') == NULL))
{
strcat(newmode, "b");
}
}
snew(fio, 1);
#ifdef GMX_THREAD_MPI
tMPI_Lock_init(&(fio->mtx));
#endif
bRead = (newmode[0] == 'r' && newmode[1] != '+');
bReadWrite = (newmode[1] == '+');
fio->fp = NULL;
fio->xdr = NULL;
if (fn)
{
fio->iFTP = fn2ftp(fn);
fio->fn = strdup(fn);
fio->bStdio = FALSE;
/* If this file type is in the list of XDR files, open it like that */
if (in_ftpset(fio->iFTP, asize(ftpXDR), ftpXDR))
{
/* First check whether we have to make a backup,
* only for writing, not for read or append.
*/
if (newmode[0] == 'w')
{
#ifndef GMX_FAHCORE
/* only make backups for normal gromacs */
make_backup(fn);
#endif
}
else
{
/* Check whether file exists */
if (!gmx_fexist(fn))
{
gmx_open(fn);
}
}
/* Open the file */
fio->fp = ffopen(fn, newmode);
/* determine the XDR direction */
if (newmode[0] == 'w' || newmode[0] == 'a')
{
fio->xdrmode = XDR_ENCODE;
}
else
{
fio->xdrmode = XDR_DECODE;
}
snew(fio->xdr, 1);
xdrstdio_create(fio->xdr, fio->fp, fio->xdrmode);
}
else
{
/* If it is not, open it as a regular file */
fio->fp = ffopen(fn, newmode);
}
/* for appending seek to end of file to make sure ftell gives correct position
* important for checkpointing */
if (newmode[0] == 'a')
{
gmx_fseek(fio->fp, 0, SEEK_END);
}
}
else
{
/* Use stdin/stdout for I/O */
fio->iFTP = efTPA;
fio->fp = bRead ? stdin : stdout;
fio->fn = strdup("STDIO");
fio->bStdio = TRUE;
}
fio->bRead = bRead;
fio->bReadWrite = bReadWrite;
fio->bDouble = (sizeof(real) == sizeof(double));
fio->bDebug = FALSE;
fio->bOpen = TRUE;
fio->bLargerThan_off_t = FALSE;
/* set the reader/writer functions */
gmx_fio_set_iotype(fio);
/* and now insert this file into the list of open files. */
gmx_fio_insert(fio);
return fio;
}
static gmx_bool do_binread(t_fileio *fio, void *item, int nitem, int eio,
const char *desc, const char *srcfile, int line)
{
size_t size = 0, rsize;
int ssize;
gmx_fio_check_nitem(fio, eio, nitem, srcfile, line);
switch (eio)
{
case eioREAL:
if (fio->bDouble)
{
size = sizeof(double);
}
else
{
size = sizeof(float);
}
break;
case eioFLOAT:
size = sizeof(float);
break;
case eioDOUBLE:
size = sizeof(double);
break;
case eioINT:
size = sizeof(int);
break;
case eioGMX_LARGE_INT:
size = sizeof(gmx_large_int_t);
break;
case eioUCHAR:
size = sizeof(unsigned char);
break;
case eioNUCHAR:
size = sizeof(unsigned char);
break;
case eioUSHORT:
size = sizeof(unsigned short);
break;
case eioRVEC:
case eioNRVEC:
if (fio->bDouble)
{
size = sizeof(double) * DIM;
}
else
{
size = sizeof(float) * DIM;
}
break;
case eioIVEC:
size = sizeof(ivec);
break;
case eioSTRING:
do_binread(fio, &ssize, 1, eioINT, desc, srcfile, line);
size = ssize;
break;
default:
gmx_fio_fe(fio, eio, desc, srcfile, line);
}
if (item)
{
rsize = fread(item, size, nitem, fio->fp);
}
else
{
/* Skip over it if we have a NULL pointer here */
gmx_fseek(fio->fp, (gmx_off_t)(size*nitem), SEEK_CUR);
rsize = nitem;
}
if ((rsize != nitem) && (fio->bDebug))
{
fprintf(stderr,
"Error reading %s %s from file %s (source %s, line %d)\n",
eioNames[eio], desc, fio->fn, srcfile, line);
}
return (rsize == nitem);
}
