[svn-r398] Changes since 19980501

----------------------

./src/H5Bprivate.h
./src/H5F.c
./src/H5Ffamily.c
./src/H5Fprivate.h
./src/H5Gpkg.h
./src/H5MF.c
./src/H5P.c
./src/H5Ppublic.h
./test/big.c
./html/Big.html
./html/Files.html
	Family members can now be any size >1kB.  Got rid of some
	places where we were reading a property list after it was
	closed.

./MANIFEST
./src/Makefile.in
./src/h5repart.c
	A program to repartition file families.  The source and/or
	destination may be files or file families.  Examples:

	   testhdf5 -c -o stab
	   h5repart -m 1m   tstab2.h5 x%05d.h5
	   h5repart -m 100k x%05d.h5  y%05d.h5
	   h5repart         y%05d.h5  z.h5
	   diff tstab2.h5 z.h5

./src/h5ls.c
	Added a usage message, replaced assertions with error
	messages.

./config/linux
	Made a warning message more obvious.  Added better
	optimization flags for Pentium-Pro's.

1 files changed, 388 insertions, 0 deletions

diff --git a/src/h5repart.c b/src/h5repart.c
new file mode 100644
index 0000000..8faa9ea
--- /dev/null
+++ b/src/h5repart.c
@@ -0,0 +1,388 @@
+/*
+ * Copyright (C) 1998 NCSA
+ *                    All rights reserved.
+ *
+ * Programmer:  Robb Matzke <matzke@llnl.gov>
+ *              Wednesday, May 13, 1998
+ *
+ * Purpose:	Repartitions a file family.  This program can be used to
+ *		split a single file into a family of files, join a family of
+ *		files into a single file, or copy one family to another while
+ *		changing the size of the family members.  It can also be used
+ *		to copy a single file to a single file with holes.
+ */
+#include <ctype.h>
+#include <errno.h>
+#include <fcntl.h>
+#include <hdf5.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/stat.h>
+#include <unistd.h>
+
+#define FALSE	0
+#define TRUE	1
+#define NAMELEN	4096
+#define GB	*1024*1024*1024
+
+#define MIN(X,Y)	((X)<(Y)?(X):(Y))
+#define MIN3(X,Y,Z)	MIN(MIN(X,Y),Z)
+
+
+/*-------------------------------------------------------------------------
+ * Function:	usage
+ *
+ * Purpose:	Prints a usage message.
+ *
+ * Return:	void
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, May 13, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage (const char *progname)
+{
+    fprintf (stderr, "usage: %s [-[b|m] N[g|m|k]] SRC DST\n", progname);
+    fprintf (stderr, "   -b N   The I/O block size, defaults to 1kB\n");
+    fprintf (stderr, "   -m N   The destination member size or 1GB\n");
+    fprintf (stderr, "   SRC    The name of the source file\n");
+    fprintf (stderr, "   DST	The name of the destination files\n");
+    fprintf (stderr, "Sizes may be suffixed with `g' for GB, `m' for MB or "
+	     "`k' for kB.\n");
+    fprintf (stderr, "File family names include an integer printf "
+	     "format such as `%%d'\n");
+    exit (1);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	get_size
+ *
+ * Purpose:	Reads a size option of the form `-XNS' where `X' is any
+ *		letter, `N' is a multi-character positive decimal number, and
+ *		`S' is an optional suffix letter in the set [GgMmk].  The
+ *		option may also be split among two arguments as: `-X NS'.
+ *		The input value of ARGNO is the argument number for the
+ *		switch in the ARGV vector and ARGC is the number of entries
+ *		in that vector.
+ *
+ * Return:	Success:	The value N multiplied according to the
+ *				suffix S.  On return ARGNO will be the number
+ *				of the next argument to process.
+ *
+ *		Failure:	Calls usage() which exits with a non-zero
+ *				status.
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, May 13, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static off_t
+get_size (const char *progname, int *argno, int argc, char *argv[])
+{
+    off_t	retval;
+    char	*suffix;
+    
+    if (isdigit (argv[*argno][2])) {
+	retval = strtol (argv[*argno]+2, &suffix, 10);
+	(*argno)++;
+    } else if (argv[*argno][2] || *argno+1>=argc) {
+	usage (progname);
+    } else {
+	retval = strtol (argv[*argno+1], &suffix, 0);
+	if (suffix==argv[*argno+1]) usage (progname);
+	*argno += 2;
+    }
+    if (suffix && suffix[0] && !suffix[1]) {
+	switch (*suffix) {
+	case 'G':
+	case 'g':
+	    retval *= 1024 * 1024 * 1024;
+	    break;
+	case 'M':
+	case 'm':
+	    retval *= 1024 * 1024;
+	    break;
+	case 'k':
+	    retval *= 1024;
+	    break;
+	default:
+	    usage (progname);
+	}
+    } else if (suffix && suffix[0]) {
+	usage (progname);
+    }
+    return retval;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	main
+ *
+ * Purpose:	Split an hdf5 file
+ *
+ * Return:	Success:	
+ *
+ *		Failure:	
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, May 13, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main (int argc, char *argv[])
+{
+    const char	*prog_name;		/*program name			*/
+    size_t	blk_size=1024;		/*size of each I/O block	*/
+    char	*buf=NULL;		/*I/O block buffer		*/
+    size_t	n, i;			/*counters			*/
+    ssize_t	nio;			/*I/O return value		*/
+    int		argno=1;		/*program argument number	*/
+    int		src, dst=-1;		/*source & destination files	*/
+    int		need_seek=FALSE;	/*destination needs to seek?	*/
+    int		need_write;		/*data needs to be written?	*/
+    struct stat	sb;			/*temporary file stat buffer	*/
+    int		verbose=FALSE;		/*display file names?		*/
+    size_t	left_overs=0;		/*amount of zeros left over	*/
+
+    const char	*src_gen_name;		/*general source name		*/
+    char	src_name[NAMELEN];	/*source member name		*/
+    off_t	src_offset=0;		/*offset in source member	*/
+    int		src_is_family;		/*is source name a family name?	*/
+    int		src_membno=0;		/*source member number		*/
+    off_t	src_size;		/*source logical member size	*/
+    off_t	src_act_size;		/*source actual member size	*/
+    
+    const char	*dst_gen_name;		/*general destination name	*/
+    char	dst_name[NAMELEN];	/*destination member name	*/
+    off_t	dst_offset=0;		/*offset in destination member	*/
+    int		dst_is_family;		/*is dst name a family name?	*/
+    int		dst_membno=0;		/*destination member number	*/
+    off_t	dst_size=1 GB;		/*destination logical memb size	*/
+
+    /*
+     * Get the program name from argv[0]. Use only the last component.
+     */
+    if ((prog_name=strrchr (argv[0], '/'))) prog_name++;
+    else prog_name = argv[0];
+
+    /*
+     * Parse switches.
+     */
+    while (argno<argc && '-'==argv[argno][0]) {
+	if (!strcmp (argv[argno], "-v")) {
+	    verbose = TRUE;
+	    argno++;
+	} else if ('b'==argv[argno][1]) {
+	    blk_size = get_size (prog_name, &argno, argc, argv);
+	} else if ('m'==argv[argno][1]) {
+	    dst_size = get_size (prog_name, &argno, argc, argv);
+	} else {
+	    usage (prog_name);
+	}
+    }
+
+    /*
+     * Get the name for the source file and open the first member.  The size
+     * of the first member determines the logical size of all the members.
+     */
+    if (argno>=argc) usage (prog_name);
+    src_gen_name = argv[argno++];
+    sprintf (src_name, src_gen_name, src_membno);
+    src_is_family = strcmp (src_name, src_gen_name);
+    if ((src=open (src_name, O_RDONLY))<0) {
+	perror (src_name);
+	exit (1);
+    }
+    if (fstat (src, &sb)<0) {
+	perror ("fstat");
+	exit (1);
+    }
+    src_size = src_act_size = sb.st_size;
+    if (verbose) fprintf (stderr, "< %s\n", src_name);
+
+    /*
+     * Get the name for the destination file and open the first member.
+     */
+    if (argno>=argc) usage (prog_name);
+    dst_gen_name = argv[argno++];
+    sprintf (dst_name, dst_gen_name, dst_membno);
+    dst_is_family = strcmp (dst_name, dst_gen_name);
+    if ((dst=open (dst_name, O_RDWR|O_CREAT|O_TRUNC, 0666))<0) {
+	perror (dst_name);
+	exit (1);
+    }
+    if (verbose) fprintf (stderr, "> %s\n", dst_name);
+
+    /* No more arguments */
+    if (argno<argc) usage (prog_name);
+
+    /* Now the real work, split the file */
+    buf = malloc (blk_size);
+    while (src_offset<src_size) {
+
+	/* Read a block.  The amount to read is the minimum of:
+	 *    1. The I/O block size
+	 *    2. What's left to write in the destination member
+	 *    3. Left over zeros or what's left in the source member.
+	 */
+	n = blk_size;
+	if (dst_is_family) n = (size_t)MIN((off_t)n, dst_size-dst_offset);
+	if (left_overs) {
+	    n = MIN (n, left_overs);
+	    left_overs -= n;
+	    need_write = FALSE;
+	} else if (src_offset<src_act_size) {
+	    n = (size_t)MIN ((off_t)n, src_act_size-src_offset);
+	    if ((nio=read (src, buf, n))<0) {
+		perror ("read");
+		exit (1);
+	    } else if ((size_t)nio!=n) {
+		fprintf (stderr, "%s: short read\n", src_name);
+		exit (1);
+	    }
+	    for (i=0; i<n; i++) {
+		if (buf[i]) break;
+	    }
+	    need_write = (i<n);
+	} else {
+	    n = 0;
+	    left_overs = src_size - src_act_size;
+	    need_write = FALSE;
+	}
+
+	/*
+	 * If the block contains non-zero data then write it to the
+	 * destination, otherwise just remember that we'll have to do a seek
+	 * later in the destination when we finally get non-zero data.
+	 */
+	if (need_write) {
+	    if (need_seek && lseek (dst, dst_offset, SEEK_SET)<0) {
+		perror ("lseek");
+		exit (1);
+	    }
+	    if ((nio=write (dst, buf, n))<0) {
+		perror ("write");
+		exit (1);
+	    } else if ((size_t)nio!=n) {
+		fprintf (stderr, "%s: short write\n", dst_name);
+		exit (1);
+	    }
+	    need_seek = FALSE;
+	} else {
+	    need_seek = TRUE;
+	}
+
+	/*
+	 * Update the source offset and open the next source family member if
+	 * necessary.  The source stream ends at the first member which
+	 * cannot be opened because it doesn't exist.  At the end of the
+	 * source stream, update the destination offset and break out of the
+	 * loop.   The destination offset must be updated so we can fix
+	 * trailing holes.
+	 */
+	src_offset += n;
+	if (src_offset==src_act_size) {
+	    close (src);
+	    if (!src_is_family) {
+		dst_offset += n;
+		break;
+	    }
+	    sprintf (src_name, src_gen_name, ++src_membno);
+	    if ((src=open (src_name, O_RDONLY))<0 && ENOENT==errno) {
+		dst_offset += n;
+		break;
+	    } else if (src<0) {
+		perror (src_name);
+		exit (1);
+	    }
+	    if (fstat (src, &sb)<0) {
+		perror ("fstat");
+		exit (1);
+	    }
+	    src_act_size = sb.st_size;
+	    if (src_act_size>src_size) {
+		fprintf (stderr, "%s: member truncated to %lu bytes\n",
+			 src_name, (unsigned long)src_size);
+	    }
+	    src_offset = 0;
+	    if (verbose) fprintf (stderr, "< %s\n", src_name);
+	}
+
+	/*
+	 * Update the destination offset, opening a new member if one will be
+	 * needed. The first member is extended to the logical member size
+	 * but other members might be smaller if they end with a hole.
+	 */
+	dst_offset += n;
+	if (dst_is_family && dst_offset==dst_size) {
+	    if (0==dst_membno) {
+		if (lseek (dst, dst_size-1, SEEK_SET)<0) {
+		    perror ("lseek");
+		    exit (1);
+		}
+		if (read (dst, buf, 1)<0) {
+		    perror ("read");
+		    exit (1);
+		}
+		if (lseek (dst, dst_size-1, SEEK_SET)<0) {
+		    perror ("lseek");
+		    exit (1);
+		}
+		if (write (dst, buf, 1)<0) {
+		    perror ("write");
+		    exit (1);
+		}
+	    }
+	    close (dst);
+	    sprintf (dst_name, dst_gen_name, ++dst_membno);
+	    if ((dst=open (dst_name, O_RDWR|O_CREAT|O_TRUNC, 0666))<0) {
+		perror (dst_name);
+		exit (1);
+	    }
+	    dst_offset = 0;
+	    need_seek = FALSE;
+	    if (verbose) fprintf (stderr, "> %s\n", dst_name);
+	}
+    }
+
+    /*
+     * Make sure the last family member is the right size and then close it.
+     * The last member can't end with a hole or hdf5 will think that the
+     * family has been truncated.
+     */
+    if (need_seek) {
+	if (lseek (dst, dst_offset-1, SEEK_SET)<0) {
+	    perror ("lseek");
+	    exit (1);
+	}
+	if (read (dst, buf, 1)<0) {
+	    perror ("read");
+	    exit (1);
+	}
+	if (lseek (dst, dst_offset-1, SEEK_SET)<0) {
+	    perror ("lseek");
+	    exit (1);
+	}
+	if (write (dst, buf, 1)<0) {
+	    perror ("write");
+	    exit (1);
+	}
+    }
+    close (dst);
+    
+    /* Free resources and return */
+    free (buf);
+    return 0;
+}