[svn-r11601] Purpose:

Added additional targets to build-all

Description:
Surveyed files to find out which ones are not built.
Added test/space_overflow and perform/benchpar to programs built with
--enable-build-all.
Discovered that tools/misc/pdb2hdf5 and tools/misc/h5import were
obsolete and deleted them.

Platforms tested:
mir, modi4, sol

Misc. update:
Update of release file and removal of --enable-pdb2hdf5 to follow.

7 files changed, 64 insertions, 705 deletions

diff --git a/perform/Makefile.am b/perform/Makefile.am
index c10a80e..a43e925 100644
--- a/perform/Makefile.am
+++ b/perform/Makefile.am
@@ -30,17 +30,19 @@ endif
 # always installed with the tools during make install.
 bin_PROGRAMS=h5perf
 
-# mpi-perf is not built or run by default, but can be built by hand or by
+# Some programs are not built or run by default, but can be built by hand or by
 # specifying --enable-build-all at configure time.
+# Also, some of these programs should only be built in parallel.
+if BUILD_PARALLEL_CONDITIONAL
+  PARA_BUILD_ALL=benchpar mpi-perf
+endif
 if BUILD_ALL_CONDITIONAL
-  MPI_PERF=mpi-perf
-else
-  MPI_PERF=
+  BUILD_ALL_PROGS=$(PARA_BUILD_ALL)
 endif
 
 # These are the programs that `make all' or `make tests' will build and which
 # `make check' will run. List them in the order they should be run.
-TEST_PROG = iopipe chunk overhead zip_perf perf_meta $(MPI_PERF)
+TEST_PROG = iopipe chunk overhead zip_perf perf_meta $(BUILD_ALL_PROGS)
 check_PROGRAMS=$(TEST_PROG_PARA) $(TEST_PROG) perf
 
 h5perf_SOURCES=pio_perf.c pio_engine.c pio_timer.c
diff --git a/perform/Makefile.in b/perform/Makefile.in
index caff887..70e53b5 100644
--- a/perform/Makefile.in
+++ b/perform/Makefile.in
@@ -30,7 +30,7 @@
 # HDF5 Library Performance Makefile(.in)
 #
 
-SOURCES = chunk.c $(h5perf_SOURCES) iopipe.c mpi-perf.c overhead.c perf.c perf_meta.c zip_perf.c
+SOURCES = benchpar.c chunk.c $(h5perf_SOURCES) iopipe.c mpi-perf.c overhead.c perf.c perf_meta.c zip_perf.c
 
 srcdir = @srcdir@
 top_srcdir = @top_srcdir@
@@ -58,7 +58,7 @@ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
 	$(top_srcdir)/config/commence.am \
 	$(top_srcdir)/config/conclude.am
 bin_PROGRAMS = h5perf$(EXEEXT)
-check_PROGRAMS = $(am__EXEEXT_1) $(am__EXEEXT_3) perf$(EXEEXT)
+check_PROGRAMS = $(am__EXEEXT_1) $(am__EXEEXT_4) perf$(EXEEXT)
 subdir = perform
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/configure.in
@@ -70,14 +70,20 @@ CONFIG_CLEAN_FILES =
 am__installdirs = "$(DESTDIR)$(bindir)"
 binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
 @BUILD_PARALLEL_CONDITIONAL_TRUE@am__EXEEXT_1 = h5perf$(EXEEXT)
-@BUILD_ALL_CONDITIONAL_TRUE@am__EXEEXT_2 = mpi-perf$(EXEEXT)
-am__EXEEXT_3 = iopipe$(EXEEXT) chunk$(EXEEXT) overhead$(EXEEXT) \
-	zip_perf$(EXEEXT) perf_meta$(EXEEXT) $(am__EXEEXT_2)
+@BUILD_PARALLEL_CONDITIONAL_TRUE@am__EXEEXT_2 = benchpar$(EXEEXT) \
+@BUILD_PARALLEL_CONDITIONAL_TRUE@	mpi-perf$(EXEEXT)
+@BUILD_ALL_CONDITIONAL_TRUE@am__EXEEXT_3 = $(am__EXEEXT_2)
+am__EXEEXT_4 = iopipe$(EXEEXT) chunk$(EXEEXT) overhead$(EXEEXT) \
+	zip_perf$(EXEEXT) perf_meta$(EXEEXT) $(am__EXEEXT_3)
 PROGRAMS = $(bin_PROGRAMS)
+benchpar_SOURCES = benchpar.c
+benchpar_OBJECTS = benchpar.$(OBJEXT)
+benchpar_LDADD = $(LDADD)
+am__DEPENDENCIES_1 = $(top_builddir)/src/libhdf5.la
+benchpar_DEPENDENCIES = $(am__DEPENDENCIES_1)
 chunk_SOURCES = chunk.c
 chunk_OBJECTS = chunk.$(OBJEXT)
 chunk_LDADD = $(LDADD)
-am__DEPENDENCIES_1 = $(top_builddir)/src/libhdf5.la
 chunk_DEPENDENCIES = $(am__DEPENDENCIES_1)
 am_h5perf_OBJECTS = pio_perf.$(OBJEXT) pio_engine.$(OBJEXT) \
 	pio_timer.$(OBJEXT)
@@ -118,10 +124,10 @@ LTCOMPILE = $(LIBTOOL) --tag=CC --mode=compile $(CC) $(DEFS) \
 CCLD = $(CC)
 LINK = $(LIBTOOL) --tag=CC --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
 	$(AM_LDFLAGS) $(LDFLAGS) -o $@
-SOURCES = chunk.c $(h5perf_SOURCES) iopipe.c mpi-perf.c overhead.c \
-	perf.c perf_meta.c zip_perf.c
-DIST_SOURCES = chunk.c $(h5perf_SOURCES) iopipe.c mpi-perf.c \
+SOURCES = benchpar.c chunk.c $(h5perf_SOURCES) iopipe.c mpi-perf.c \
 	overhead.c perf.c perf_meta.c zip_perf.c
+DIST_SOURCES = benchpar.c chunk.c $(h5perf_SOURCES) iopipe.c \
+	mpi-perf.c overhead.c perf.c perf_meta.c zip_perf.c
 ETAGS = etags
 CTAGS = ctags
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
@@ -353,15 +359,16 @@ H5FC_PP = $(bindir)/h5pfc
 CHECK_CLEANFILES = *.chkexe *.chklog *.clog
 INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/tools/lib
 @BUILD_PARALLEL_CONDITIONAL_TRUE@TEST_PROG_PARA = h5perf
-@BUILD_ALL_CONDITIONAL_FALSE@MPI_PERF = 
 
-# mpi-perf is not built or run by default, but can be built by hand or by
+# Some programs are not built or run by default, but can be built by hand or by
 # specifying --enable-build-all at configure time.
-@BUILD_ALL_CONDITIONAL_TRUE@MPI_PERF = mpi-perf
+# Also, some of these programs should only be built in parallel.
+@BUILD_PARALLEL_CONDITIONAL_TRUE@PARA_BUILD_ALL = benchpar mpi-perf
+@BUILD_ALL_CONDITIONAL_TRUE@BUILD_ALL_PROGS = $(PARA_BUILD_ALL)
 
 # These are the programs that `make all' or `make tests' will build and which
 # `make check' will run. List them in the order they should be run.
-TEST_PROG = iopipe chunk overhead zip_perf perf_meta $(MPI_PERF)
+TEST_PROG = iopipe chunk overhead zip_perf perf_meta $(BUILD_ALL_PROGS)
 h5perf_SOURCES = pio_perf.c pio_engine.c pio_timer.c
 
 # These are the files that `make clean' (and derivatives) will remove from
@@ -461,6 +468,9 @@ clean-checkPROGRAMS:
 	  echo " rm -f $$p $$f"; \
 	  rm -f $$p $$f ; \
 	done
+benchpar$(EXEEXT): $(benchpar_OBJECTS) $(benchpar_DEPENDENCIES) 
+	@rm -f benchpar$(EXEEXT)
+	$(LINK) $(benchpar_LDFLAGS) $(benchpar_OBJECTS) $(benchpar_LDADD) $(LIBS)
 chunk$(EXEEXT): $(chunk_OBJECTS) $(chunk_DEPENDENCIES) 
 	@rm -f chunk$(EXEEXT)
 	$(LINK) $(chunk_LDFLAGS) $(chunk_OBJECTS) $(chunk_LDADD) $(LIBS)
@@ -492,6 +502,7 @@ mostlyclean-compile:
 distclean-compile:
 	-rm -f *.tab.c
 
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/benchpar.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/chunk.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/iopipe.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mpi-perf.Po@am__quote@
diff --git a/perform/benchpar.c b/perform/benchpar.c
index e5b6690..947a20c 100644
--- a/perform/benchpar.c
+++ b/perform/benchpar.c
@@ -16,11 +16,23 @@
 #include <stdlib.h>
 #include <assert.h>
 #include <math.h>
+#include <float.h>
+#include <string.h>
 
 #include "hdf5.h"
 
 /* Local macros */
 
+/*      
+ * HDF Boolean type.
+ */
+#ifndef FALSE
+#   define FALSE 0
+#endif
+#ifndef TRUE
+#   define TRUE 1 
+#endif 
+
 /* defines for type of VFL driver to use */
 #define FACC_DEFAULT    0
 #define FACC_MPIO       1
diff --git a/test/Makefile.am b/test/Makefile.am
index f4e986d..89ce616 100644
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -56,7 +56,8 @@ check_PROGRAMS=$(TEST_PROG) error_test err_compat testmeta
 # so do not appear in this list.
 if BUILD_ALL_CONDITIONAL
   BUILD_ALL_PROGS=gen_deflate gen_filters gen_new_array gen_new_fill   \
-                  gen_new_mtime gen_new_super gen_noencoder gen_nullspace
+                  gen_new_mtime gen_new_super gen_noencoder gen_nullspace \
+                  space_overflow
 else
   BUILD_ALL_PROGS=
 endif
diff --git a/test/Makefile.in b/test/Makefile.in
index 3c8588d..32af5f6 100644
--- a/test/Makefile.in
+++ b/test/Makefile.in
@@ -31,7 +31,7 @@
 #
 
 
-SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c blocktrack.c btree2.c cache.c cmpd_dset.c dangle.c dsets.c dt_arith.c dtransform.c dtypes.c enum.c err_compat.c error_test.c extend.c external.c fillval.c flush1.c flush2.c gen_deflate.c gen_filters.c gen_new_array.c gen_new_fill.c gen_new_mtime.c gen_new_super.c gen_noencoder.c gen_nullspace.c getname.c gheap.c hyperslab.c istore.c lheap.c links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c set_extent.c sheap.c stab.c stream_test.c $(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
+SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c blocktrack.c btree2.c cache.c cmpd_dset.c dangle.c dsets.c dt_arith.c dtransform.c dtypes.c enum.c err_compat.c error_test.c extend.c external.c fillval.c flush1.c flush2.c gen_deflate.c gen_filters.c gen_new_array.c gen_new_fill.c gen_new_mtime.c gen_new_super.c gen_noencoder.c gen_nullspace.c getname.c gheap.c hyperslab.c istore.c lheap.c links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c set_extent.c sheap.c space_overflow.c stab.c stream_test.c $(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
 
 srcdir = @srcdir@
 top_srcdir = @top_srcdir@
@@ -92,7 +92,8 @@ am__EXEEXT_1 = testhdf5$(EXEEXT) lheap$(EXEEXT) ohdr$(EXEEXT) \
 @BUILD_ALL_CONDITIONAL_TRUE@	gen_new_mtime$(EXEEXT) \
 @BUILD_ALL_CONDITIONAL_TRUE@	gen_new_super$(EXEEXT) \
 @BUILD_ALL_CONDITIONAL_TRUE@	gen_noencoder$(EXEEXT) \
-@BUILD_ALL_CONDITIONAL_TRUE@	gen_nullspace$(EXEEXT)
+@BUILD_ALL_CONDITIONAL_TRUE@	gen_nullspace$(EXEEXT) \
+@BUILD_ALL_CONDITIONAL_TRUE@	space_overflow$(EXEEXT)
 PROGRAMS = $(noinst_PROGRAMS)
 b_tree_SOURCES = b+tree.c
 b_tree_OBJECTS = b+tree.$(OBJEXT)
@@ -263,6 +264,10 @@ sheap_SOURCES = sheap.c
 sheap_OBJECTS = sheap.$(OBJEXT)
 sheap_LDADD = $(LDADD)
 sheap_DEPENDENCIES = libh5test.la $(am__DEPENDENCIES_1)
+space_overflow_SOURCES = space_overflow.c
+space_overflow_OBJECTS = space_overflow.$(OBJEXT)
+space_overflow_LDADD = $(LDADD)
+space_overflow_DEPENDENCIES = libh5test.la $(am__DEPENDENCIES_1)
 stab_SOURCES = stab.c
 stab_OBJECTS = stab.$(OBJEXT)
 stab_LDADD = $(LDADD)
@@ -319,8 +324,9 @@ SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c \
 	gen_new_mtime.c gen_new_super.c gen_noencoder.c \
 	gen_nullspace.c getname.c gheap.c hyperslab.c istore.c lheap.c \
 	links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c \
-	set_extent.c sheap.c stab.c stream_test.c $(testhdf5_SOURCES) \
-	testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
+	set_extent.c sheap.c space_overflow.c stab.c stream_test.c \
+	$(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c \
+	vfd.c
 DIST_SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c \
 	blocktrack.c btree2.c cache.c cmpd_dset.c dangle.c dsets.c \
 	dt_arith.c dtransform.c dtypes.c enum.c err_compat.c \
@@ -329,8 +335,9 @@ DIST_SOURCES = $(libh5test_la_SOURCES) b+tree.c big.c bittests.c \
 	gen_new_mtime.c gen_new_super.c gen_noencoder.c \
 	gen_nullspace.c getname.c gheap.c hyperslab.c istore.c lheap.c \
 	links.c mount.c mtime.c ntypes.c ohdr.c pool.c reserved.c \
-	set_extent.c sheap.c stab.c stream_test.c $(testhdf5_SOURCES) \
-	testmeta.c $(ttsafe_SOURCES) unlink.c vfd.c
+	set_extent.c sheap.c space_overflow.c stab.c stream_test.c \
+	$(testhdf5_SOURCES) testmeta.c $(ttsafe_SOURCES) unlink.c \
+	vfd.c
 ETAGS = etags
 CTAGS = ctags
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
@@ -610,7 +617,8 @@ TEST_PROG = testhdf5 lheap ohdr stab gheap btree2 cache b+tree blocktrack sheap
 # The gen_old_* files can only be compiled with older versions of the library
 # so do not appear in this list.
 @BUILD_ALL_CONDITIONAL_TRUE@BUILD_ALL_PROGS = gen_deflate gen_filters gen_new_array gen_new_fill   \
-@BUILD_ALL_CONDITIONAL_TRUE@                  gen_new_mtime gen_new_super gen_noencoder gen_nullspace
+@BUILD_ALL_CONDITIONAL_TRUE@                  gen_new_mtime gen_new_super gen_noencoder gen_nullspace \
+@BUILD_ALL_CONDITIONAL_TRUE@                  space_overflow
 
 
 # The libh5test library provides common support code for the tests.
@@ -831,6 +839,9 @@ set_extent$(EXEEXT): $(set_extent_OBJECTS) $(set_extent_DEPENDENCIES)
 sheap$(EXEEXT): $(sheap_OBJECTS) $(sheap_DEPENDENCIES) 
 	@rm -f sheap$(EXEEXT)
 	$(LINK) $(sheap_LDFLAGS) $(sheap_OBJECTS) $(sheap_LDADD) $(LIBS)
+space_overflow$(EXEEXT): $(space_overflow_OBJECTS) $(space_overflow_DEPENDENCIES) 
+	@rm -f space_overflow$(EXEEXT)
+	$(LINK) $(space_overflow_LDFLAGS) $(space_overflow_OBJECTS) $(space_overflow_LDADD) $(LIBS)
 stab$(EXEEXT): $(stab_OBJECTS) $(stab_DEPENDENCIES) 
 	@rm -f stab$(EXEEXT)
 	$(LINK) $(stab_LDFLAGS) $(stab_OBJECTS) $(stab_LDADD) $(LIBS)
@@ -902,6 +913,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/reserved.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/set_extent.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/sheap.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/space_overflow.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stab.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stream_test.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/tarray.Po@am__quote@
diff --git a/tools/misc/h5import.c b/tools/misc/h5import.c
deleted file mode 100644
index 4192821..0000000
--- a/tools/misc/h5import.c
+++ /dev/null
@@ -1,152 +0,0 @@
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Copyright by the Board of Trustees of the University of Illinois.         *
- * All rights reserved.                                                      *
- *                                                                           *
- * This file is part of HDF5.  The full HDF5 copyright notice, including     *
- * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
- * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-
-/*
- * 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/pdb2hdf.c b/tools/misc/pdb2hdf.c
deleted file mode 100644
index c3e93aa..0000000
--- a/tools/misc/pdb2hdf.c
+++ /dev/null
@@ -1,527 +0,0 @@
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Copyright by the Board of Trustees of the University of Illinois.         *
- * All rights reserved.                                                      *
- *                                                                           *
- * This file is part of HDF5.  The full HDF5 copyright notice, including     *
- * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
- * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-
-/*
- * 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 <stdio.h>
-#include <string.h>
-
-#include "hdf5.h"
-
-/* Strictly speaking, the "ifdef H5_HAVE_PDB_H" is unnecessary, since this
- * file won't be compiled unless PDB is available (see the Makefile.in for
- * this directory, as well as the PDB detection in the main configure.in).
- * However, the Intel C compiler, v7.1, seems to have problems generating
- * correct dependencies with the -MG flag when include files are not found
- * and having this ifdef here removes the PDB headers from its consideration.
- * QAK - 2004/02/07
- */
-#ifdef H5_HAVE_PDB_H
-
-#include "pdb.h"
-#include "score.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;
-}
-#endif /* H5_HAVE_PDB_H */