[svn-r3487] Purpose:

    Code Movement
Description:
    Moved the tools into their own separate directories (except for these
    small tools which are REALLY small, not tested, or documented,
    really...They just get put into the misc/ directory).
Platforms tested:
    Linux and Kelgia

6 files changed, 1318 insertions, 0 deletions

diff --git a/tools/misc/Dependencies b/tools/misc/Dependencies
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/tools/misc/Dependencies
diff --git a/tools/misc/Makefile.in b/tools/misc/Makefile.in
new file mode 100644
index 0000000..def8f48
--- /dev/null
+++ b/tools/misc/Makefile.in
@@ -0,0 +1,71 @@
+## HDF5 Library Makefile(.in)
+##
+## Copyright (C) 2001 National Center for Supercomputing Applications.
+##                    All rights reserved.
+##
+## 
+top_srcdir=@top_srcdir@
+top_builddir=../..
+srcdir=@srcdir@
+SUBDIRS=
+@COMMENCE@
+
+## Add include directory to the C preprocessor flags, add -lh5tools and
+## -lhdf5 to the list of libraries.
+##
+CPPFLAGS=-I. -I$(srcdir) -I$(top_builddir)/src -I$(top_srcdir)/src  \
+         -I$(top_srcdir)/tools/lib @CPPFLAGS@
+
+## Test programs and scripts.
+##
+TEST_PROGS=
+TEST_SCRIPTS=
+
+## These are our main targets: library and tools.
+##
+LIBTOOLS=../lib/libh5tools.la
+LIBHDF5=$(top_builddir)/src/libhdf5.la
+
+PUB_PROGS=h5debug h5import h5repart @PDB2HDF@
+PROGS=$(PUB_PROGS) $(TEST_PROGS)
+
+## Source and object files for the library; do not install
+##
+LIB_SRC=
+LIB_OBJ=$(LIB_SRC:.c=.lo)
+PUB_LIB=
+
+## Source and object files for programs...
+##
+PROG_SRC=h5debug.c h5import.c h5repart.c pdb2hdf.c
+PROG_OBJ=$(PROG_SRC:.c=.lo)
+
+PRIVATE_HDR=
+
+## Source and object files for the tests
+##
+TEST_SRC=
+TEST_OBJ=$(TEST_SRC:.c=.lo)
+
+## Programs have to be built before they can be tested!
+##
+check test _test: $(PROGS)
+
+## How to build the programs...They all depend on the hdf5 library and
+## the tools library compiled in this directory.
+##
+$(PROGS): $(LIBTOOLS) $(LIBHDF5)
+
+h5debug: h5debug.lo
+	@$(LT_LINK_EXE) $(CFLAGS) -o $@ h5debug.lo $(LIBTOOLS) $(LIBHDF5) $(LDFLAGS) $(LIBS)
+
+h5import: h5import.lo
+	@$(LT_LINK_EXE) $(CFLAGS) -o $@ h5import.lo $(LIBTOOLS) $(LIBHDF5) $(LDFLAGS) $(LIBS)
+
+h5repart: h5repart.lo
+	@$(LT_LINK_EXE) $(CFLAGS) -o $@ h5repart.lo $(LIBTOOLS) $(LIBHDF5) $(LDFLAGS) $(LIBS)
+
+pdb2hdf: pdb2hdf.lo
+	@$(LT_LINK_EXE) $(CFLAGS) -o $@ pdb2hdf.lo $(LIBTOOLS) $(LIBHDF5) $(LDFLAGS) $(LIBS)
+
+@CONCLUDE@
diff --git a/tools/misc/h5debug.c b/tools/misc/h5debug.c
new file mode 100644
index 0000000..76eb472
--- /dev/null
+++ b/tools/misc/h5debug.c
@@ -0,0 +1,185 @@
+/*-------------------------------------------------------------------------
+ * Copyright (C) 1997   National Center for Supercomputing Applications.
+ *                      All rights reserved.
+ *
+ *-------------------------------------------------------------------------
+ *
+ * Created:             debug.c
+ *                      Jul 18 1997
+ *                      Robb Matzke <matzke@llnl.gov>
+ *
+ * Purpose:             Debugs an existing HDF5 file at a low level.
+ *
+ * Modifications:       
+ *
+ *-------------------------------------------------------------------------
+ */
+#define H5F_PACKAGE		/*suppress error about including H5Fpkg	  */
+
+#include <H5private.h>
+#include <H5Iprivate.h>
+#include <H5Bprivate.h>
+#include <H5Pprivate.h>
+#include <H5Fpkg.h>
+#include <H5Gprivate.h>
+#include <H5HGprivate.h>
+#include <H5HLprivate.h>
+#include <H5Oprivate.h>
+
+/* File drivers */
+#include <H5FDfamily.h>
+
+#define INDENT  3
+#define VCOL    50
+
+
+/*-------------------------------------------------------------------------
+ * Function:    main
+ *
+ * Usage:       debug FILENAME [OFFSET]
+ *
+ * Return:      Success:        exit (0)
+ *
+ *              Failure:        exit (non-zero)
+ *
+ * Programmer:  Robb Matzke
+ *              matzke@llnl.gov
+ *              Jul 18 1997
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(int argc, char *argv[])
+{
+    hid_t	fid, plist=H5P_DEFAULT;
+    H5F_t       *f;
+    haddr_t     addr=0, extra=0;
+    uint8_t     sig[16];
+    intn        i, ndims;
+    herr_t      status = SUCCEED;
+
+    if (argc == 1) {
+	fprintf(stderr,
+		"Usage: %s filename [signature addr [extra]]\n", argv[0]);
+	HDexit(1);
+    }
+
+    /*
+     * Open the file and get the file descriptor.
+     */
+    if (strchr (argv[1], '%')) {
+	plist = H5Pcreate (H5P_FILE_ACCESS);
+	H5Pset_fapl_family (plist, (hsize_t)0, H5P_DEFAULT);
+    }
+    if ((fid = H5Fopen(argv[1], H5F_ACC_RDONLY, plist)) < 0) {
+        fprintf(stderr, "cannot open file\n");
+        HDexit(1);
+    }
+    if (NULL == (f = H5I_object(fid))) {
+        fprintf(stderr, "cannot obtain H5F_t pointer\n");
+        HDexit(2);
+    }
+    
+    /*
+     * Parse command arguments.
+     */
+    if (argc > 2) {
+        printf("New address: %s\n", argv[2]);
+        addr = HDstrtoll(argv[2], NULL, 0);
+    }
+    if (argc > 3) {
+        extra = HDstrtoll(argv[3], NULL, 0);
+    }
+    /*
+     * Read the signature at the specified file position.
+     */
+    HDfprintf(stdout, "Reading signature at address %a (rel)\n", addr);
+    if (H5F_block_read(f, H5FD_MEM_SUPER, addr, (hsize_t)sizeof(sig), H5P_DEFAULT, sig)<0) {
+        fprintf(stderr, "cannot read signature\n");
+        HDexit(3);
+    }
+    if (!HDmemcmp(sig, H5F_SIGNATURE, H5F_SIGNATURE_LEN)) {
+        /*
+         * Debug the boot block.
+         */
+        status = H5F_debug(f, addr, stdout, 0, VCOL);
+
+    } else if (!HDmemcmp(sig, H5HL_MAGIC, H5HL_SIZEOF_MAGIC)) {
+        /*
+         * Debug a local heap.
+         */
+        status = H5HL_debug(f, addr, stdout, 0, VCOL);
+	
+    } else if (!HDmemcmp (sig, H5HG_MAGIC, H5HG_SIZEOF_MAGIC)) {
+	/*
+	 * Debug a global heap collection.
+	 */
+	status = H5HG_debug (f, addr, stdout, 0, VCOL);
+
+    } else if (!HDmemcmp(sig, H5G_NODE_MAGIC, H5G_NODE_SIZEOF_MAGIC)) {
+        /*
+         * Debug a symbol table node.
+         */
+        status = H5G_node_debug(f, addr, stdout, 0, VCOL, extra);
+
+    } else if (!HDmemcmp(sig, H5B_MAGIC, H5B_SIZEOF_MAGIC)) {
+        /*
+         * Debug a B-tree.  B-trees are debugged through the B-tree
+         * subclass.  The subclass identifier is the byte immediately
+         * after the B-tree signature.
+         */
+        H5B_subid_t subtype = (H5B_subid_t)sig[H5B_SIZEOF_MAGIC];
+	
+        switch (subtype) {
+        case H5B_SNODE_ID:
+            status = H5G_node_debug(f, addr, stdout, 0, VCOL, extra);
+            break;
+
+	case H5B_ISTORE_ID:
+	    ndims = (int)extra;
+	    status = H5F_istore_debug (f, addr, stdout, 0, VCOL, ndims);
+	    break;
+
+        default:
+            fprintf(stderr, "Unknown B-tree subtype %u\n",
+		    (unsigned)(subtype));
+            HDexit(4);
+        }
+
+    } else if (sig[0] == H5O_VERSION) {
+        /*
+         * This could be an object header.  Since they don't have a signature
+         * it's a somewhat "ify" detection.
+         */
+        status = H5O_debug(f, addr, stdout, 0, VCOL);
+
+    } else {
+        /*
+         * Got some other unrecognized signature.
+         */
+        printf("%-*s ", VCOL, "Signature:");
+        for (i = 0; i < 8; i++) {
+            if (sig[i] > ' ' && sig[i] <= '~' && '\\' != sig[i]) {
+                HDputchar(sig[i]);
+            } else if ('\\' == sig[i]) {
+                HDputchar('\\');
+                HDputchar('\\');
+            } else {
+                printf("\\%03o", sig[i]);
+            }
+        }
+        HDputchar('\n');
+
+        fprintf(stderr, "unknown signature\n");
+        HDexit(4);
+    }
+
+    if (status < 0) {
+        fprintf(stderr, "An error occurred\n");
+        HDexit(5);
+    }
+    H5Fclose(fid);
+    return 0;
+}
diff --git a/tools/misc/h5import.c b/tools/misc/h5import.c
new file mode 100644
index 0000000..e896feb
--- /dev/null
+++ b/tools/misc/h5import.c
@@ -0,0 +1,141 @@
+/*
+ * Copyright (C) 1998 NCSA
+ *                    All rights reserved.
+ *
+ * Programmer:  Robb Matzke <matzke@llnl.gov>
+ *              Thursday, June 11, 1998
+ *
+ * Purpose:	Create an hdf5 file with a 1d dataset of uint8.
+ */
+
+/* See H5private.h for how to include system headers */
+#include <hdf5.h>
+#ifdef H5_STDC_HEADERS
+#   include <fcntl.h>
+#   include <string.h>
+#   include <stdlib.h>
+#   include <stdio.h>
+#endif
+
+#ifdef H5_HAVE_UNISTD_H
+#   include <sys/types.h>
+#   include <unistd.h>
+#endif
+
+#ifdef H5_HAVE_SYS_STAT_H
+#   include <sys/stat.h>
+#endif
+
+#ifdef WIN32
+#include <io.h>
+#endif
+
+
+/*-------------------------------------------------------------------------
+ * Function:	usage
+ *
+ * Purpose:	Print a usage message and exit with non-zero status
+ *
+ * Return:	never returns
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, June 11, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage (const char *argv0)
+{
+    fprintf (stderr, "Usage: %s -f HDF5-FILE FILES...\n", argv0);
+    exit (1);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	main
+ *
+ * Purpose:	
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	1
+ *
+ * Programmer:	Robb Matzke
+ *              Thursday, June 11, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main (int argc, char *argv[])
+{
+    hid_t	file, space=-1, dset=-1;
+    const char	*output_name, *dset_name;
+    int		argno, fd=-1;
+    hsize_t	size[1];
+    struct stat sb;
+
+    /* Parse arguments */
+    if (argc<4) usage (argv[0]);
+    if (strcmp (argv[1], "-f")) usage (argv[0]);
+    output_name = argv[2];
+
+    /* create the file */
+    H5E_BEGIN_TRY {
+	if ((file = H5Fcreate (output_name, H5F_ACC_EXCL,
+			       H5P_DEFAULT, H5P_DEFAULT))<0 &&
+	    (file = H5Fopen (output_name, H5F_ACC_RDWR, H5P_DEFAULT)<0)) {
+	    fprintf (stderr, "%s: unable to create or open hdf5 file\n",
+		     output_name);
+	    exit (1);
+	}
+    } H5E_END_TRY;
+    
+    /* process files from command-line */
+    for (argno=3;  argno<argc; argno++) {
+
+	/* Open the file */
+	if ((dset_name=strrchr (argv[argno], '/'))) dset_name++;
+	else dset_name = argv[argno];
+	fprintf (stderr, "%s\n", dset_name);
+	if ((fd=open (argv[argno], O_RDONLY))<0) {
+	    perror (argv[argno]);
+	    goto next;
+	}
+	if (fstat (fd, &sb)<0) {
+	    perror (argv[argno]);
+	    goto next;
+	}
+
+	/* Data space */
+	size[0] = sb.st_size;
+	if ((space = H5Screate_simple (1, size, size))<0) goto next;
+
+	/* Dataset */
+	if ((dset=H5Dcreate (file, dset_name, H5T_NATIVE_SCHAR,
+			     space, H5P_DEFAULT))<0) goto next;
+
+	
+	
+    next:
+	if (fd>=0) close (fd);
+	fd = -1;
+	H5E_BEGIN_TRY {
+	    if (space>=0) {
+		H5Sclose (space);
+		space = -1;
+	    }
+	    if (dset>=0) {
+		H5Dclose (dset);
+		dset = -1;
+	    }
+	} H5E_END_TRY;
+    }
+
+    /* Close the file */
+    H5Fclose (file);
+    return 0;
+}
diff --git a/tools/misc/h5repart.c b/tools/misc/h5repart.c
new file mode 100644
index 0000000..de7b3df
--- /dev/null
+++ b/tools/misc/h5repart.c
@@ -0,0 +1,418 @@
+/*
+ * 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.
+ */
+
+/* See H5private.h for how to include system headers */
+#include <hdf5.h>
+#ifdef H5_STDC_HEADERS
+#   include <ctype.h>
+#   include <errno.h>
+#   include <fcntl.h>
+#   include <stdio.h>
+#   include <stdlib.h>
+#   include <string.h>
+#endif
+
+#ifdef H5_HAVE_UNISTD_H
+#   include <sys/types.h>
+#   include <unistd.h>
+#endif
+
+#ifdef H5_HAVE_SYS_STAT_H
+#   include <sys/stat.h>
+#endif
+
+#ifdef WIN32
+#include <io.h>
+#endif
+
+#ifndef FALSE
+#define FALSE	0
+#endif
+#ifndef TRUE
+#define TRUE	1
+#endif
+#define NAMELEN	4096
+#define GB	*1024*1024*1024
+
+#ifndef MIN
+#define MIN(X,Y)	((X)<(Y)?(X):(Y))
+#endif
+#ifndef MIN3
+#define MIN3(X,Y,Z)	MIN(MIN(X,Y),Z)
+#endif
+
+
+/*-------------------------------------------------------------------------
+ * 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 [-v] [-V] [-[b|m] N[g|m|k]] SRC DST\n",
+	    progname);
+    fprintf(stderr, "   -v     Produce verbose output\n");
+    fprintf(stderr, "   -V     Print a version number and exit\n");
+    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=-1;
+    char	*suffix;
+    
+    if (isdigit ((int)(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 (!strcmp(argv[argno], "-V")) {
+	    printf("This is %s version %u.%u release %u\n",
+		   prog_name, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE);
+	    exit(0);
+	} 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;
+}
diff --git a/tools/misc/pdb2hdf.c b/tools/misc/pdb2hdf.c
new file mode 100644
index 0000000..7ecd28e
--- /dev/null
+++ b/tools/misc/pdb2hdf.c
@@ -0,0 +1,503 @@
+/*
+ * Copyright ©  1999 NCSA
+ *              All rights reserved.
+ *
+ * Programmer:  Robb Matzke <matzke@llnl.gov>
+ *              Tuesday, October 12, 1999
+ *
+ * Purpose:	Creates an HDF5 file from a PDB file.  The raw data can be
+ *		left in the PDB file, creating an HDF5 file that contains
+ *		meta data that points into the PDB file.
+ */
+#include <assert.h>
+#include <hdf5.h>
+#include <pdb.h>
+#include <score.h>
+#include <stdio.h>
+#include <string.h>
+
+/*
+ * libsilo renames all the PDB functions. However, this source files uses
+ * their documented names, so we have #define's to translate them to Silo
+ * terminology.
+ */
+#ifdef H5_HAVE_LIBSILO
+#   define PD_open			lite_PD_open
+#   define PD_close			lite_PD_close
+#   define PD_ls			lite_PD_ls
+#   define PD_cd			lite_PD_cd
+#   define PD_inquire_entry		lite_PD_inquire_entry
+#   define PD_read			lite_PD_read
+#   define _PD_fixname			_lite_PD_fixname
+#   define _PD_rl_defstr		_lite_PD_rl_defstr
+#   define SC_free			lite_SC_free
+#endif
+
+static int verbose_g = 0;		/*verbose output?		*/
+static int cached_g = 0;		/*use core file driver?		*/
+
+
+/*-------------------------------------------------------------------------
+ * Function:	usage
+ *
+ * Purpose:	Print a usage message.
+ *
+ * Return:	void
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage(const char *arg0)
+{
+    char	*progname;
+
+    if ((progname=strrchr(arg0, '/')) && progname[1]) progname++;
+    else progname = arg0;
+
+    fprintf(stderr, "\
+usage: %s [OPTIONS] [PDBFILE ...]\n\
+   OPTIONS\n\
+      -h, -?, --help   Print a usage message and exit\n\
+      -c, --cached     Cache all data in memory before writing the output\n\
+      -v, --verbose    Print the name of each object processed\n\
+      -V, --version    Show the version number of this program\n\
+\n\
+   The options and PDB file names may be interspersed and are processed from\n\
+   left to right.\n\
+\n\
+   The name of the HDF5 file is generated by taking the basename of the PDB\n\
+   file and replacing the last extension (or appending if no extension) with\n\
+   the characters \".h5\". For example, \"/tmp/test/eos.data\" would result\n\
+   in an HDF5 file called \"eos.h5\" in the current directory.\n",
+	    progname);
+    
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	version
+ *
+ * Purpose:	Print the version number.
+ *
+ * Return:	void
+ *
+ * Programmer:	Robb Matzke
+ *              Friday, October 15, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+version(const char *arg0)
+{
+    const char	*progname;
+
+    if ((progname=strrchr(arg0, '/')) && progname[1]) progname++;
+    else progname = arg0;
+    print_version(progname);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	fix_name
+ *
+ * Purpose:	Given a PDB file name create the corresponding HDF5 file
+ *		name. This is done by taking the base name of the PDB file
+ *		and replacing (or appending) the last extension with ".h5".
+ *
+ * Return:	Success:	HDF_NAME
+ *
+ *		Failure:	NULL
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static char *
+fix_name(const char *pdb_name, char *hdf_name, size_t size)
+{
+    char	*s;
+    const char	*ext;
+    
+    if (!pdb_name || !hdf_name) return NULL;
+    if ((s=strrchr(pdb_name, '/'))) pdb_name = s;
+    if (NULL==(ext=strrchr(pdb_name, '.'))) ext = pdb_name + strlen(pdb_name);
+    if ((size_t)((ext-pdb_name)+4) > size) return NULL; /*overflow*/
+    memcpy(hdf_name, pdb_name, ext-pdb_name);
+    strcpy(hdf_name+(ext-pdb_name), ".h5");
+    return hdf_name;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	fix_type
+ *
+ * Purpose:	Given a PDB datatype return a corresponding hdf5 datatype.
+ *		The hdf5 datatype should be closed when the caller is
+ *		finished using it.
+ *
+ * Return:	Success:	HDF5 datatype
+ *
+ *		Failure:	negative
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static hid_t
+fix_type(PDBfile *pdb, const char *s)
+{
+    hid_t	type = -1;
+    defstr 	*d = _lite_PD_lookup_type((char*)s, pdb->chart);
+
+    /* PDB checking */
+    assert(d);
+    assert(d->size>0);
+    if (d->onescmp) return -1;
+    
+    
+    if (!strcmp(s, "char")) {
+	/*
+	 * Character datatypes. Use whatever sign the native system uses by
+	 * default.
+	 */
+	type = H5Tcopy(H5T_NATIVE_CHAR);
+	
+    } else if (!strcmp(s, "integer")) {
+	/*
+	 * Integer datatypes. PDB supports various sizes of signed or
+	 * unsigned integers.
+	 */
+	type = H5Tcopy(d->unsgned?H5T_NATIVE_UINT:H5T_NATIVE_INT);
+	H5Tset_size(type, d->size);
+	H5Tset_precision(type, 8*d->size);
+	assert(NORMAL_ORDER==d->order_flag || REVERSE_ORDER==d->order_flag);
+	H5Tset_order(type,
+		     NORMAL_ORDER==d->order_flag?H5T_ORDER_BE:H5T_ORDER_LE);
+	
+    } else if (!strcmp(s, "float") || !strcmp(s, "double")) {
+	/*
+	 * Floating-point datatypes
+	 */
+	size_t	nbits, spos, epos, esize, mpos, msize;
+
+	type = H5Tcopy(H5T_NATIVE_FLOAT);
+	H5Tset_size(type, d->size);
+	H5Tset_precision(type, 8*d->size);
+	assert(d->order);
+	H5Tset_order(type, 1==d->order[0]?H5T_ORDER_BE:H5T_ORDER_LE);
+	
+	/*
+	 * format[0] = # of bits per number                     
+	 * format[1] = # of bits in exponent                    
+	 * format[2] = # of bits in mantissa                    
+	 * format[3] = start bit of sign                        
+	 * format[4] = start bit of exponent                    
+	 * format[5] = start bit of mantissa                    
+	 * format[6] = high order mantissa bit (CRAY needs this)
+	 * format[7] = bias of exponent
+	 */
+	assert(d->format && d->format[0] == 8*d->size);
+	nbits = d->format[0];
+	spos = nbits - (d->format[3]+1);
+	esize = d->format[1];
+	epos = nbits - (d->format[4]+esize);
+	msize = d->format[2];
+	mpos = nbits - (d->format[5]+msize);
+	H5Tset_fields(type, spos, epos, esize, mpos, msize);
+	H5Tset_ebias(type, d->format[7]);
+    }
+    return type;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	fix_space
+ *
+ * Purpose:	Convert a PDB dimension list into an HDF5 data space.
+ *
+ * Return:	Success:	HDF5 data space
+ *
+ *		Failure:	negative
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static hid_t
+fix_space(const dimdes *dim)
+{
+    hsize_t	size[H5S_MAX_RANK];
+    int		rank;
+
+    for (rank=0; rank<H5S_MAX_RANK && dim; rank++, dim=dim->next) {
+	size[rank] = dim->number;
+    }
+    if (rank>=H5S_MAX_RANK) return -1;
+    return H5Screate_simple(rank, size, NULL);
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	fix_external
+ *
+ * Purpose:	Sets the external file information for a dataset creation
+ *		property list based on information from PDB.
+ *
+ * Return:	Success:	non-negative
+ *
+ *		Failure:	negative
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+fix_external(hid_t dcpl, const char *pdb_file_name, long nelmts,
+	     hsize_t elmt_size, symblock *block)
+{
+    int		i;
+    
+    for (i=0; nelmts>0; i++) {
+	hsize_t nbytes = block[i].number * elmt_size;
+	H5Pset_external(dcpl, pdb_file_name, block[i].diskaddr, nbytes);
+	nelmts -= block[i].number;
+    }
+    return 0;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	traverse
+ *
+ * Purpose:	Traverse the current working directory of the PDB file.
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	-1
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+traverse(PDBfile *pdb, const char *pdb_file_name, hid_t hdf)
+{
+    int			nitems, i, in_subdir=FALSE;
+    char		**list=NULL;
+    hid_t		group=-1, h_type=-1, h_space=-1, dset=-1, dcpl=-1;
+    hsize_t		elmt_size;
+    const syment	*ep=NULL;
+
+    if (NULL==(list=PD_ls(pdb, ".", NULL, &nitems))) {
+	fprintf(stderr, "cannot obtain PDB directory contents\n");
+	goto error;
+    }
+
+    for (i=0; i<nitems; i++) {
+	ep = PD_inquire_entry(pdb, list[i], TRUE, NULL);
+	if (verbose_g) {
+	    printf("%s %s\n", _PD_fixname(pdb, list[i]), ep->type);
+	    fflush(stdout);
+	}
+	
+
+	if ('/'==list[i][strlen(list[i])-1]) {
+	    /*
+	     * This is a PDB directory. Make a corresponding HDF5 group and
+	     * traverse into that PDB directory and HDF5 group
+	     */
+	    if ((group=H5Gcreate(hdf, list[i], 0))<0) {
+		fprintf(stderr, "cannot create HDF group %s\n", list[i]);
+		goto error;
+	    }
+	    if (!PD_cd(pdb, list[i])) {
+		fprintf(stderr, "cannot cd into PDB directory %s\n", list[i]);
+		goto error;
+	    } else {
+		in_subdir = TRUE;
+	    }
+	    
+	    traverse(pdb, pdb_file_name, group);
+	    if (!PD_cd(pdb, "..")) {
+		fprintf(stderr, "cannot traverse out of PDB %s\n", list[i]);
+		goto error;
+	    }
+	    H5Gclose(group);
+	    
+	} else {
+	    /* This is some non-directory PDB object */
+
+	    /* Create an HDF5 datatype from the PDB type */
+	    if ((h_type=fix_type(pdb, ep->type))<0) {
+		fprintf(stderr, "cannot create datatype for %s (%s)\n",
+		       list[i], ep->type);
+		continue;
+	    }
+	    elmt_size = H5Tget_size(h_type);
+
+	    /* Create an HDF5 dataspace from the PDB dimensions */
+	    if ((h_space=fix_space(ep->dimensions))<0) {
+		fprintf(stderr, "cannot create datatype for %s\n", list[i]);
+		continue;
+	    }
+
+	    /* Create pointers to the external PDB data */
+	    dcpl = H5Pcreate(H5P_DATASET_CREATE);
+	    fix_external(dcpl, pdb_file_name, ep->number, elmt_size,
+			 ep->blocks);
+
+	    /* Create the dataset */
+	    if ((dset=H5Dcreate(hdf, list[i], h_type, h_space, dcpl))<0) {
+		fprintf(stderr, "cannot create dataset for %s\n", list[i]);
+	    }
+
+	    H5Pclose(dcpl);
+	    H5Dclose(dset);
+	    H5Sclose(h_space);
+	    H5Tclose(h_type);
+	}
+	
+    }
+
+    for (i=0; i<nitems; i++) {
+	SC_free(list[i]);
+    }
+    SC_free(list);
+    return 0;
+
+ error:
+    if (group>=0) H5Gclose(group);
+    if (in_subdir) PD_cd(pdb, "..");
+    if (list) {
+	for (i=0; i<nitems; i++) {
+	    SC_free(list[i]);
+	}
+	SC_free(list);
+    }
+    return -1;
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function:	main
+ *
+ * Purpose:	Create an HDF5 file from a PDB file.
+ *
+ * Return:	Success:	0
+ *
+ *		Failure:	non-zero
+ *
+ * Programmer:	Robb Matzke
+ *              Tuesday, October 12, 1999
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(int argc, char *argv[])
+{
+    int		argno;
+    char	_hdf_name[512], *hdf_name, *pdb_name, *s;
+    PDBfile	*pdb;
+    hid_t	hdf, fapl;
+
+    /* Print a help message if called with no arguments */
+    if (1==argc) {
+	usage(argv[0]);
+	exit(1);
+    }
+
+    /* Process arguments in order; switches interspersed with files */
+    for (argno=1; argno<argc; argno++) {
+	if (!strcmp("--help", argv[argno])) {
+	    usage(argv[0]);
+	    exit(1);
+	} else if (!strcmp("--verbose", argv[argno])) {
+	    verbose_g++;
+	} else if (!strcmp("--cached", argv[argno])) {
+	    cached_g++;
+	} else if (!strcmp("--version", argv[argno])) {
+	    version(argv[0]);
+	} else if ('-'==argv[argno][0] && '-'!=argv[argno][1]) {
+	    for (s=argv[argno]+1; *s; s++) {
+		switch (*s) {
+		case '?':
+		case 'h':		/*--help*/
+		    usage(argv[0]);
+		    exit(0);
+		case 'c':		/*--cached*/
+		    cached_g++;
+		    break;
+		case 'v':		/*--verbose*/
+		    verbose_g++;
+		    break;
+		case 'V':		/*--version*/
+		    version(argv[0]);
+		    break;
+		default:
+		    usage(argv[0]);
+		    exit(1);
+		}
+	    }
+	} else if ('-'==argv[argno][0]) {
+	    usage(argv[0]);
+	    exit(1);
+	} else {
+	    /* This must be a file name. Process it. */
+	    fapl = H5Pcreate(H5P_FILE_ACCESS);
+	    if (cached_g) H5Pset_fapl_core(fapl, 1024*1024, TRUE);
+
+	    pdb_name = argv[argno];
+	    hdf_name = fix_name(argv[argno], _hdf_name, sizeof _hdf_name);
+	    if (NULL==(pdb=PD_open(pdb_name, "r"))) {
+		fprintf(stderr, "%s: unable to open PDB file\n", pdb_name);
+		exit(1);
+	    }
+	    if ((hdf=H5Fcreate(hdf_name, H5F_ACC_TRUNC, H5P_DEFAULT,
+			       fapl))<0) {
+		fprintf(stderr, "%s: unable to open HDF file\n", hdf_name);
+		exit(1);
+	    }
+	    H5Pclose(fapl);
+	    
+	    /*
+	     * Traverse the PDB file to create the HDF5 file.
+	     */
+	    traverse(pdb, pdb_name, hdf);
+
+	    /* Close the files */
+	    if (!PD_close(pdb)) {
+		fprintf(stderr, "%s: problems closing PDB file\n", pdb_name);
+		exit(1);
+	    }
+	    if (H5Fclose(hdf)<0) {
+		fprintf(stderr, "%s: problems closing HDF file\n", hdf_name);
+		exit(1);
+	    }
+	}
+    }
+    return 0;
+}