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-rw-r--r--tools/misc/Dependencies0
-rw-r--r--tools/misc/Makefile.in71
-rw-r--r--tools/misc/h5debug.c185
-rw-r--r--tools/misc/h5import.c141
-rw-r--r--tools/misc/h5repart.c418
-rw-r--r--tools/misc/pdb2hdf.c503
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;
+}