[svn-r1431]

Example was modified to use references to different objects.
Missing calls to release dataset handles and to free memory buffers were
added.

Tested on  baldric.

COPYING

@@ -1,48 +1,39 @@
-/*=======================================================================
+Copyright Notice and Statement for NCSA Hierarchical Data Format (HDF)
+Software Library and Utilities
 
-Copyright Notice and Statement for
-NCSA Hierarchical Data Format (HDF) Software Library and Utilities 
+NCSA Hierarchical Data Format (HDF) Software Library and Utilities Copyright
+1998 the Board of Trustees of the University of Illinois. All rights reserved.
 
-
-NCSA Hierarchical Data Format (HDF) Software Library and Utilities
-Copyright 1998 the Board of Trustees of the University of Illinois
-All rights reserved.
-
-Contributors:   National Center for Supercomputing Applications (NCSA) at
-the University of Illinois, Lawrence Livermore Nat'l Laboratory (LLNL),
-Sandia National Laboratories (SNL), Los Alamos National Laboratory (LANL),
-Jean-loup Gailly and Mark Adler (gzip library)
+Contributors: National Center for Supercomputing Applications (NCSA) at the
+University of Illinois, Lawrence Livermore Nat'l Laboratory (LLNL), Sandia
+National Laboratories (SNL), Los Alamos National Laboratory (LANL).
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted for any purpose (including commercial purposes)
 provided that the following conditions are met:
 
-1.	Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
+1.  Redistributions of source code must retain the above copyright notice,
+    this list of conditions and the following disclaimer.
 
-2.	Redistributions in binary form must reproduce the above copyright
-notice, this list of conditions and the following disclaimer in the
-documentation and/or materials provided with the distribution.
+2.  Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or materials provided with the distribution.
 
-3.	In addition, redistributions of modified forms of the source or binary
-code must carry prominent notices stating that the original code was
-changed and the date of the change.
+3.  In addition, redistributions of modified forms of the source or binary
+    code must carry prominent notices stating that the original code was
+    changed and the date of the change.
 
-4.	All publications or advertising materials mentioning features or use of
-this software must acknowledge that it was developed by the National Center
-for Supercomputing Applications at the University of Illinois, and credit
-the Contributors.
+4.  All publications or advertising materials mentioning features or use of
+    this software must acknowledge that it was developed by the National
+    Center for Supercomputing Applications at the University of Illinois, and
+    credit the Contributors.
 
-5.	Neither the name of the University nor the names of the Contributors may
-be used to endorse or promote products derived from this software without
-specific prior written permission from the University or the Contributors.
-
-6.	THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY AND THE CONTRIBUTORS "AS IS"
-WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no event
-shall the University or the Contributors be liable for any damages suffered
-by the users arising out of the use of this software, even if advised of
-the possibility of such damage.
-
-
-=======================================================================*/
+5.  Neither the name of the University nor the names of the Contributors may
+    be used to endorse or promote products derived from this software without
+    specific prior written permission from the University or the Contributors.
 
+6.  THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY AND THE CONTRIBUTORS "AS IS"
+    WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no event
+    shall the University or the Contributors be liable for any damages
+    suffered by the users arising out of the use of this software, even if
+    advised of the possibility of such damage.

INSTALL

@@ -1,149 +1,410 @@
+-*- outline -*-
+
 This file contains instructions for the installation of HDF5 on
-Unix-like systems.  First, one must obtain a tarball of the HDF5
-release from the ftp://hdf.ncsa.uiuc.edu/pub/dist/HDF5 repository.
-The files are available in uncompressed tar, gzip, bzip2, and compress
-formats.
+Unix-like systems. Users of the Intel TFLOPS machine should see the
+INSTALL.ascired for instructions.
 
-For those that like to live dangerously and don't like to read ;-) you
-can do the following:
+* Obtaining HDF5
+	The latest supported public release of HDF5 is available from
+	ftp://hdf.ncsa.uiuc.edu/pub/dist/HDF5 and is available in tar
+	format uncompressed or compressed with compress, gzip, or
+	bzip2.
 
-	$ tar xf hdf5-1.0.0a.tar
-	$ cd hdf5-1.0.0a
-	$ make test
-	$ make install		# Optional
+	The HDF team also makes snapshots of the source code available 
+	on a regular basis but these. These snapshots are unsupported
+	(that is, the HDF team will not release a bug-fix on a
+	particular snapshot; rather any bug fixes will be rolled into
+	the next snapshot). Furthermore, the snapshots have only been
+	tested on a few machines and may not test correctly for
+	parallel applications. Snapshots can be found at
+	ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/snapshots in a
+	limited number for formats.
 
-Note:
-For the users of the Intel TFLOPS machine, a special sequence of steps
-for the install may be found in the file:  INSTALL.ascired.
+* Warnings about compilers
+	OUTPUT FROM THE FOLLOWING COMPILERS SHOULD BE EXTREMELY
+	SUSPECT WHEN USED TO COMPILE THE HDF5 LIBRARY, ESPECIALLY IF
+	OPTIMIZATIONS ARE ENABLED. IN ALL CASES, HDF5 ATTEMPTS TO WORK
+	AROUND THE COMPILER BUGS BUT THE HDF5 DEVELOPMENT TEAM MAKES
+	NO GUARANTEES THAT THERE ARE OTHER CODE GENERATION PROBLEMS.
 
-=======
-Step 0: Install optional third-party packages.
+** GNU (Intel platforms)
+	Versions before 2.8.1 have serious problems allocating
+	registers when functions contain operations on `long long'
+	data types. Supplying the `--disable-hsizet' switch to
+	configure (documented below) will prevent hdf5 from using
+	`long long' data types in situations that are known not to
+	work, but it limits the hdf5 address space to 2GB.
 
-    * GNU zlib compression library, version 1.0.2 or later is used for
-      the `deflate' compression method. If libz.a cannot be found then
-      this form of compression is not compiled into the library.
+** DEC
+	The V5.2-038 compiler (and possibly others) occasionally
+	generates incorrect code for memcpy() calls when optimizations
+	are enabled, resulting in unaligned access faults. HDF5 works
+	around the problem by casting the second argument to `char*'.
 
-Step 1. Unpack the source tree.
+** SGI (Irix64 6.2)
+	The Mongoose 7.00 compiler has serious optimization bugs and
+	should be upgraded to MIPSpro 7.2.1.2m. Patches are available
+	from SGI.
 
-    * The tarball will unpack into an hdf5-1.0.0a directory with one of
-      the following commands:
-
-	$ tar xf hdf5-1.0.0a.tar				OR
-	$ gunzip <hdf5-1.0.0a.tar.gz |tar xf -			OR
-	$ bunzip2 <hdf5-1.0.0a.tar.bz2 |tar xf -		OR
-	$ uncompress -c <hdf5-1.0.0a.tar.Z |tar xf -
-
-Step 2. Configure.
-
-    * HDF5 uses the GNU autoconf program for configuration.  Most
-      installations can be configured by typing just (from the
-      hdf5-1.0.0a directory)
-
-	$ sh configure
+** Windows/NT
+	The MicroSoft Win32 5.0 compiler is unable to cast unsigned
+	long long values to doubles. HDF5 works around this bug by
+	first casting to signed long long and then to double.
 
 
-    * The configuration process can be controlled through environment
-      variables, command-line switches, and host configuration files.
-      For a complete list of switches say `sh configure --help'.
+* Quick installation
+	For those that don't like to read ;-) the following steps can
+	be used to configure, build, test, and install the HDF5
+	library, header files, and support programs.
 
-    * Host configuration files are located in the `config' directory
-      and are based on architecture name, vendor name, and/or operating
-      system which are displayed near the beginning of the `configure'
-      output. Not all hosts require a host configuration file.
 
-    * The C compiler and flags, the `ar' and `ranlib' program names,
-      and the `make' program can be specified with environment
-      variables if configure doesn't properly detect them and they are 
-      not defined in a host config file.
+	$ gunzip <hdf5-1.0.0.tar.gz |tar xf -
+	$ cd hdf5-1.0.0
+	$ make check
+	$ make install
 
-	CC	  Name of the C compiler.
-	CFLAGS	  Switches for the C compiler.
-	CPPFLAGS  Additional switches for the .c -> .o step.
-	AR	  Name of the `ar' program.
-	RANLIB	  Name of the `ranlib' program or `:' if none.
-	MAKE	  Name of the `make' program (GNU make is preferred)
+* HDF5 dependencies
+** Zlib
+	The HDF5 library has a predefined compression filter that uses 
+	the "deflate" method for chunked datatsets. If zlib-1.1.2 or
+	later is found then hdf5 will use it, otherwise HDF5's
+	predefined compression method will degenerate to a no-op (the
+	compression filter will succeed but the data will not be
+	compressed).
 
-    * This version of HDF5 is normally built with various debugging
-      code enabled.  To turn it off add the `--disable-debug' switch
-      to the configure command.
+** MPI and MPI-IO
+	The parallel version of the library is built upon the
+	foundation provided by MPI and MPI-IO. If these libraries are
+	not available when HDF5 is configured then only a serial
+	version of HDF5 can be built.
 
-    * This version of HDF5 is normally built with support for symbolic 
-      debugging with dbx or gdb and without compiler optimization
-      switches.  To disable symbolic debugging and enable
-      optimizations add `--enable-production' to the configure
-      command.
+* Full installation instructions for source distributions
+** Unpacking the distribution
+	The HDF5 source code is distributed in a variety of formats
+	which can be unpacked with the following commands, each of
+	which creates an `hdf5-1.0.0' directory.
 
-    * This version of HDF5 is normally built with the ability to print 
-      the names, arguments, and return values of all API functions
-      when they're called.  For more information refer to the
-      doc/html/tracing.html file.  To disable tracing support add
-      `--disable-trace' to the configure command.
+*** Non-compressed tar archive (*.tar)
+	$ tar xf hdf5-1.0.0.tar
 
-    * Old versions of gcc (<2.8.0) may experience register allocation
-      problems on some architectures.  If this happens then the
-      `--disable-hsizet' can be given but the resulting library will
-      be unable to handle datasets larger than 4GB.
+*** Compressed tar archive (*.tar.Z)
+	$ uncompress -c <hdf5-1.0.0.tar.Z |tar xf -
 
-    * By default libraries, include files, programs, and documentation
-      are installed (when one says `make install') under
-      /usr/local/lib, /usr/local/include, /usr/local/bin, and
-      /usr/local/man.  However, if you want them in some other
-      location you can specify a prefix to use instead of /usr/local.
-      For instance, to install in /usr/lib, /usr/include, /usr/bin,
-      and /usr/man one would say
+*** Gzip'd tar archive (*.tar.gz)
+	$ gunzip <hdf5-1.0.0.tar.gz |tar xf -
 
-	$ ./configure --prefix=/usr
+*** Bzip'd tar archive (*.tar.bz2)
+	$ bunzip2 <hdf5-1.0.0.tar.gz |tar xf -
 
-      The library can be used directly from the source tree without
-      installing it.
+** Configuring
+	HDF5 uses the GNU autoconf system for configuration, which
+	detects various features of the host system and creates the
+	Makefiles.  On most systems it should be sufficient to say:
 
-Step 3. Compile library, tests, and programs.
+	    $ ./configure		OR
+	    $ sh configure
 
-    * Build library targets by saying
+    	The configuration process can be controlled through
+	environment variables, command-line switches, and host
+	configuration files. For a complete list of switches say
+	`./configure --help'. The host configuration files are located
+	in the `config' directory and are based on architecture name,
+	vendor name, and/or operating system which are displayed near
+	the beginning of the `configure' output. The host config file
+	influences the behavior of configure by setting or augmenting
+	shell variables.
 
-        $ make
+*** Specifying the installation directories
+	Typing `make install' will install the HDF5 library, header
+	files, and support programs in /usr/local/lib,
+	/usr/local/include, and /usr/local/bin.  To use a path other
+	than /usr/local specify the path with the `--prefix=PATH'
+	switch:
 
-      Note: If you supplied some other make command through the MAKE
-      environment variable in the previous step then use that command
-      instead. The same applies below.
+	    $ ./configure --prefix=/home/robb
 
-      Note: When using GNU make you can add `-j -l6' to the make
-      command to compile in parallel on SMP machines.  Do not give a
-      number after the `-j' since GNU make will turn it off for
-      recursive invocations of make.
+	If shared libraries are being built (the default) then the
+	final home of the shared library must be specified with this
+	switch before the library and executables are built.
 
-Step 4. Run confidence tests.
+*** Using an alternate C compiler
+	By default, configure will look for the C compiler by trying
+	`gcc' and `cc'. However, if the environment variable "CC" is
+	set then its value is used as the C compiler (users of csh and
+	derivatives will need to prefix the commands below with
+	`env'). For instance, to use the native C compiler on a system 
+	which also has the GNU gcc compiler:
 
-    * All confidence tests should be run by saying
+	    $ CC=cc ./configure
 
-	$ make test
+	A parallel version of hdf5 can be built by specifying `mpicc'
+	as the C compiler (the `--enable-parallel' flag documented
+	below is optional).  Using the `mpicc' compiler will insure
+	that the correct MPI and MPI-IO header files and libraries are 
+	used.
 
-      The command will fail if any test fails, and one will see the
-      word "*FAIL*" in the output.
+	    $ CC=/usr/local/mpi/bin/mpicc ./configure
 
-      Note: some old versions of make will report that `test is up to
-      date'. If this happens then run `make _test' instead or run
-      `make test' from within the test directory.
+	On Irix64 the default compiler is `cc -64'. To use an
+	alternate compiler specify it with the CC variable:
 
-      Temporary files will be deleted by each test when it completes,
-      but may continue to exist in an incomplete state if the test
-      fails. To prevent deletion of the files define the
-      HDF5_NOCLEANUP environment variable.
+	    $ CC='cc -o32' ./configure
 
-Step 5. Install public files.
+*** Additional compilation flags
+	If addtional flags must be passed to the compilation commands
+	then specify those flags with the CFLAGS variable. For
+	instance, to enable symbolic debugging of a production version 
+	of HDF5 one might say:
 
-    * Install the library, header files, and programs by saying:
+	    $ CFLAGS=-g ./confgure --enable-production
 
-        $ make install
+*** Specifying other programs
+	The build system has been tuned for use with GNU make but
+	works also with other versions of make.  If the `make' command 
+	runs a non-GNU version but a GNU version is available under a
+	different name (perhaps `gmake') then HDF5 can be configured
+	to use it by setting the MAKE variable. Note that whatever
+	value is used for MAKE must also be used as the make command
+	when building the library:
 
-     This step will fail unless you have permission to write to the
-     installation directories.  Of course, you can use the header
-     files, library, and programs directly out of the source tree if
-     you like, skipping this step.  The directory specified for the
-     --prefix switch (or "/usr/local") must exist, but the directories
-     under it are created automatically by make.
+	    $ MAKE=gmake ./configure
+	    $ gmake
 
-Step 6. Subscribe to mailing lists.
+	The `AR' and `RANLIB' variables can also be set to the names
+	of the `ar' and `ranlib' (or `:') commands to override values
+	detected by configure.
 
-    * Subscribe to the mailing lists described in the README file.
+	The HDF5 library, include files, and utilities are installed
+	during `make install' (described below) with a BSD-compatible
+	install program detected automatically by configure. If none
+	is found then the shell script bin/install-sh is
+	used. Configure doesn't check that the install script actually 
+	works, but if a bad install is detected on your system (e.g.,
+	on the ASCI blue machine as of March 2, 1999) you have two
+	choices:
+
+	    1. Copy the bin/install-sh program to your $HOME/bin
+	       directory, name it `install', and make sure that
+	       $HOME/bin is searched before the system bin
+	       directories.
+
+	    2. Specify the full path name of the `install-sh' program
+	       as the value of the INSTALL environment variable. Note:
+	       do not use `cp' or some other program in place of
+	       install because the HDF5 makefiles also use the install
+	       program to also change file ownership and/or access
+	       permissions.
+
+*** Specifying other libraries and headers
+	Configure searches the standard places (those places known by
+	the systems compiler) for include files and header
+	files. However, additional directories can be specified by
+	using the CPPFLAGS and/or LDFLAGS variables:
+
+	    $ CPPFLAGS=-I/home/robb/include \
+              LDFLAGS=-L/home/robb/lib \
+	      ./configure
+
+	HDF5 uses the zlib library for two purposes: it provides
+	support for the HDF5 deflate data compression filter, and it
+	is used by the h5toh4 converter in support of HDF4. Configure
+	searches the standard places (plus those specified above with
+	CPPFLAGS and LDFLAGS variables) for the zlib headers and
+	library. The search can be disabled by specifying
+	`--without-zlib' or alternate directories can be specified
+	with `--with-zlib=INCDIR,LIBDIR' or through the CPPFLAGS and
+	LDFLAGS variables:
+
+	    $ ./configure --with-zlib=/usr/unsup/include,/usr/unsup/lib
+
+	    $ CPPFLAGS=-I/usr/unsup/include \
+	      LDFLAGS=-L/usr/unsup/lib \
+	      ./configure
+
+        The HDF5-to-HDF4 conversion tool requires the HDF4 library and 
+        header files which are detected the same way as zlib. The
+        switch to give to configure is `--with-hdf4'.  Note that HDF5
+        requires a newer version of zlib than the one shipped with
+        some versions of HDF4. Also, unless you have the "correct"
+        version of hdf4 the confidence testing will fail in the tools
+        directory.
+
+*** Static versus shared linking
+	The build process will create static libraries on all systems
+	and shared libraries on systems that support dynamic linking
+	to a sufficient degree.  Either form of library may be
+	suppressed by saying `--disable-static' or `--disable-shared'.
+
+	    $ ./configure --disable-shared
+
+*** Optimization versus symbolic debugging
+	The library can be compiled to provide symbolic debugging
+	support so it can be debugged with gdb, dbx, ddd, etc or it
+	can be compiled with various optimizations.  To compile for
+	symbolic debugging (the default for snapshots) say
+	`--disable-production'; to compile with optimizations (the
+	default for supported public releases) say
+	`--enable-production'.  On some systems the library can also
+	be compiled for profiling with gprof by saying
+	`--enable-production=profile'.
+
+	    $ ./configure --disable-production         #symbolic debugging
+	    $ ./configure --enable-production          #optimized code
+	    $ ./configure --enable-production=profile  #for use with gprof
+
+	Regardless of whether support for symbolic debugging is
+	enabled, the library also is able to perform runtime debugging
+	of certain packages (such as type conversion execution times,
+	and extensive invariant condition checking). To enable this
+	debugging supply a comma-separated list of package names to to
+	the `--enable-debug' switch (see Debugging.html for a list of
+	package names). Debugging can be disabled by saying
+	`--disable-debug'. The default debugging level for snapshots
+	is a subset of the available packages; the default for
+	supported releases is no debugging (debugging can incur a
+	significant runtime penalty).
+
+	    $ ./configure --enable-debug=s,t  #debug only H5S and H5T
+	    $ ./configure --enable-debug      #debug normal packages
+	    $ ./configure --enable-debug=all  #debug all packages
+	    $ ./configure --disable-debug     #no debugging
+
+	HDF5 is also able to print a trace of all API function calls,
+	their arguments, and the return values. To enable or disable
+	the ability to trace the API say `--enable-trace' (the default
+	for snapthots) or `--disable-trace' (the default for public
+	releases). The tracing must also be enabled at runtime to see
+	any output (see Debugging.html).
+
+*** Large (>2GB) vs. small (<2GB) file capability
+	In order to read or write files that could potentially be
+	larger than 2GB it is necessary to use the non-ANSI `long
+	long' data type on some platforms. However, some compilers
+	(e.g., GNU gcc versions before 2.8.1 on Intel platforms)
+	are unable to produce correct machine code for this data
+	type. To disable use of the `long long' type on these machines 
+	say:
+
+	    $ ./configure --disable-hsizet
+
+*** Parallel vs. serial library
+	The HDF5 library can be configured to use MPI and MPI-IO for
+	parallelizm on a distributed multi-processor system. The easy
+	way to do this is to have a properly installed parallel
+	compiler (e.g., MPICH's mpicc or IBM's mpcc) and supply that
+	executable as the value of the CC environment variable:
+
+	    $ CC=mpcc ./configure
+	    $ CC=/usr/local/mpi/bin/mpicc ./configure
+
+	If no such wrapper script is available then you must specify
+	your normal C compiler along with the distribution of
+	MPI/MPI-IO which is to be used (values other than `mpich' will 
+	be added at a later date):
+
+	    $ ./configure --enable-parallel=mpich
+
+	If the MPI/MPI-IO include files and/or libraries cannot be
+	found by the compiler then their directories must be given as
+	arguments to CPPFLAGS and/or LDFLAGS:
+
+	    $ CPPFLAGS=-I/usr/local/mpi/include \
+	      LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \
+	      ./configure --enable-parallel=mpich
+
+	If a parallel library is being built then configure attempts
+	to determine how to run a parallel application on one
+	processor and on many processors.  If the compiler is mpicc
+	and the user hasn't specified values for RUNSERIAL and
+	RUNPARALLEL then configure chooses `mpirun' from the same
+	directory as `mpicc':
+
+	    RUNSERIAL:    /usr/local/mpi/bin/mpirun -np 1
+	    RUNPARALLEL:  /usr/local/mpi/bin/mpirun -np $${NPROCS:=2}
+
+	The `$${NPROCS:=2}' will be substituted with the value of the
+	NPROCS environment variable at the time `make check' is run
+	(or the value 2).
+
+** Building
+	The library, confidence tests, and programs can be build by
+	saying just
+
+	    $ make
+
+	Note that if you supplied some other make command via the MAKE 
+	variable during the configuration step then that same command
+	must be used here.
+
+	When using GNU make you can add `-j -l6' to the make command
+	to compile in arallel on SMP machines. Do not give a number
+	after th `-j' since GNU make will turn it off for recursive
+	invocations of make.
+
+	    $ make -j -l6
+
+** Testing
+	HDF5 comes with various test suites, all of which can be run
+	by saying
+
+	    $ make check
+
+	To run only the tests for the library change to the `test'
+	directory before issuing the command. Similarly, tests for the 
+	parallel aspects of the library are in `testpar' and tests for 
+	the support programs are in `tools'.
+
+	Temporary files will be deleted by each test when it complets, 
+	but may continue to exist in an incomplete state if the test
+	fails. To prevent deletion of the files define the
+	HDF5_NOCLEANUP environment variable.
+
+** Installing
+	The HDF5 library, include files, and support programs can be
+	installed in a (semi-)public place by saying `make
+	install'. The files are installed under the directory
+	specified with `--prefix=DIR' (or '/usr/local') in directories 
+	named `lib', `include', and `bin'. The prefix directory must
+	exist prior to `make install', but its subdirectories are
+	created automatically.
+
+	The library can be used without installing it by pointing the
+	compiler at the `src' directory for both include files and
+	libraries.  However, the minimum which must be installed to
+	make the library publically available is:
+
+	    The library:
+		./src/libhdf5.a
+
+	    The public header files:
+		./src/H5*public.h
+
+	    The main header file:
+		./src/hdf5.h
+
+	    The configuration information:
+		./src/H5config.h
+	
+    	The support programs that are useful are:
+	    ./tools/h5ls	(list file contents)
+	    ./tools/h5dump	(dump file contents)
+	    ./tools/h5repart	(repartition file families)
+	    ./tools/h5toh4	(hdf5 to hdf4 file converter)
+	    ./tools/h5debug	(low-level file debugging)
+	    ./tools/h5import	(a demo)
+
+* Using the Library
+	Please see the User Manual in the doc/html directory.
+
+	Most programs will include <hdf5.h> and link with
+	-lhdf5. Additional libraries may also be necessary depending
+	on whether support for compression, etc. was compiled into the 
+	hdf5 library.
+
+	A summary of the hdf5 installation can be found in the
+	libhdf5.settings file in the same directory as the static
+	and/or shared hdf5 libraries.
+
+* Support
+	Support is described in the README file.
 

INSTALL.ascired

@@ -17,9 +17,9 @@ effort is shown here at steps 9) and steps 10).
 The total required steps are something similar to:
 FROM SASN100,
 
-1) uncompress hdf5-1.0.0a.tar.Z
+1) uncompress hdf5-1.1.0.tar.Z
 
-2) tar xvf hdf5-1.0.0a.tar
+2) tar xvf hdf5-1.1.0.tar
 
 3) cd ./hdf5
 
@@ -73,9 +73,9 @@ execution of parallel tests described in steps 12) through 16).
 The total required steps are something similar to:
 FROM SASN100,
 
-1) uncompress hdf5-1.0.0a.tar.Z
+1) uncompress hdf5-1.1.0.tar.Z
 
-2) tar xvf hdf5-1.0.0a.tar
+2) tar xvf hdf5-1.1.0.tar
 
 3) cd ./hdf5
 
@@ -111,18 +111,11 @@ FROM SASN100,
 
 12) cd testpar
 
-13) /* edit testphdf5.c, change the following lines */
-    char    *filenames[]={ "pfs:/pfs/multi/tmp_1/your_own/ParaEg1.h5f",
-                           "pfs:/pfs/multi/tmp_1/your_own/ParaEg2.h5f",
-                           "pfs:/pfs/multi/tmp_1/your_own/ParaEg3.h5f" };
-
-    /* change "your_own" to your own directory name */
-    char    *filenames[]={ "pfs:/pfs/multi/tmp_1/my_dir/ParaEg1.h5f",
-                           "pfs:/pfs/multi/tmp_1/my_dir/ParaEg2.h5f",
-                           "pfs:/pfs/multi/tmp_1/my_dir/ParaEg3.h5f" };
+13) go through the README file.
 
 14) make -f Makefile.ascired
 
+
 When everything is finished compiling and linking,
 FROM JANUS, 
 

INSTALL.ibm.sp.parallel

@@ -37,7 +37,9 @@
 # (We use csh here, but of course you can adapt to whatever shell you like.)
 
 # compile for MPI jobs
-setenv CC mpcc
+# setenv CC mpcc						(for IBM's MPI)
+# setenv CC "/usr/local/mpich-1.1.1/lib/rs6000/ch_mpl/mpicc"	(for mpich)
+setenv CC "/usr/local/mpich-1.1.1/lib/rs6000/ch_mpl/mpicc"
 
 # These compiler flags work on ASCI baby blue pacific (IBM SP),
 # using IBM's MPI and Argonne's MPI-IO (ROMIO):
@@ -47,9 +49,9 @@ setenv CC mpcc
 # The following flags are only needed when compiling/linking a user program
 # for execution.
 #  -bI:/usr/include/piofs/piofs.exp	this MPI-IO uses PIOFS file system
-#  -L/usr/local/mpio/lib/ibm -lmpio	link to this MPI-IO lib
+#  -L/usr  /local/mpio/lib/ibm -lmpio	link to this MPI-IO lib
 #
-setenv CFLAGS "-g -D_LARGE_FILES -DHAVE_FUNCTION -I/usr/local/mpio/include/ibm -bI:/usr/include/piofs/piofs.exp -L/usr/local/mpio/lib/ibm -lmpio"
+setenv CFLAGS "-g -qfullpath -bnoobjreorder -D_LARGE_FILES -DHAVE_FUNCTION"
 
 # The configure/make process needs to be able to run some programs,
 # need to specify a processor pool.

INSTALL.parallel

@@ -0,0 +1,28 @@
+This file contains instructions for the installation a version of HDF5 
+that uses the parallel file I/O facilities of the MPI-IO library. A
+parallel version of HDF5 can run in a serial environment as long as
+the appropriate MPI-IO and MPI header files and libraries are
+available.
+
+The parallel version of hdf5 can be build by generally following the
+instructions in the INSTALL file for building a serial version and
+using `mpicc' as the C compiler.  This can be done by setting the CC
+environment variable before invoking configure as with:
+
+    $ CC=mpicc ./configure
+
+If the mpicc compiler is not available then a parallel library can
+still be built as long as the appropriate header files and libraries
+can be found.  If these files are part of the default compiler search
+paths then configuration is as simple as:
+
+    $ ./configure --enable-parallel
+
+Otherwise, if the MPI and MPI-IO header files or library cannot be
+found then the compiler search paths can be corrected, the files can
+be moved, or configure can be told about the file locations.  The
+latter is done with something like:
+
+    $ CPPFLAGS=-I/usr/local/mpi/include \
+      LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \
+      ./configure --enable-parallel

INSTALL_MAINT

@@ -97,3 +97,15 @@ Information for HDF5 maintainers:
 
   which limits the number of children to two (this doesn't work at the
   top level because the `-j2' is not passed to recursive makes).
+
+* To create a release tarball go to the top-level directory and run
+  ./bin/release.  You can optionally supply one or more of the words
+  `tar', `gzip', `bzip2' or `compress' on the command line.  The
+  result will be a (compressed) tar file(s) in the `releases'
+  directory.  The README file is updated to contain the release date
+  and version number.
+
+* To create a tarball of all the files which are part of HDF5 go to
+  the top-level directory and type:
+
+      tar cvf foo.tar `grep '^\.' MANIFEST |unexpand |cut -f1`

INSTALL_parallel

@@ -1,19 +1,17 @@
 	    Installation instructions for Parallel HDF5
 	    -------------------------------------------
-		(last updated: April 22, 1998)
+		(last updated: May 21, 1999)
 
+1. Overview
+-----------
 This file contains instructions for the installation of parallel
 HDF5.  Platforms supported by this release are SGI Origin 2000,
 IBM SP2, and the Intel TFLOP.  The steps are kind of unnatural and
 will be more automized in the next release.   If you have difficulties
 installing the software in your system, please send mail to
 	hdfparallel@ncsa.uiuc.edu
-
-Note:
-For the users of the Intel TFLOPS machine, a special sequence of steps
-for the parallel install may be found in the file:  INSTALL.ascired.
-Also, MPI/MPIO information similar to that found below may be found in
-INSTALL_parallel.ascired.
+In your mail, please enclose the output of "uname -a".  Also attach the
+content of "config.log" if you have run the "configure" command.
 
 First, you must obtain and unpack the HDF5 source as
 described in the file INSTALL.  You also need to obtain the
@@ -21,21 +19,69 @@ information of the include and library paths of MPI and MPIO
 software installed in your system since the parallel HDF5 library
 uses them for parallel I/O access.
 
-For an IBM SP2 system, follow the instructions in INSTALL.ibm.sp.parallel.
-For an SGI Origin 2000 system, use the following shell commands.  (The
-one shown here is what works in the NCSA O2K machine in which MPI library
-is installed in system area but no official MPIO software is available.
-I use a private installation of ROMIO for it.)
 
-mpi1_inc=""					#mpi-1 include
-mpi1_lib=""					#mpi-1 library
-mpio_inc="-I$HOME/ROMIO/include"		#mpio include
-mpio_lib="-L$HOME/ROMIO/lib/IRIX64/"		#mpio library
+2. Quick Instruction for known systems
+--------------------------------------
+The following shows particular steps to run the parallel HDF5
+configure for a few machines we tested.  If your particular platform
+is not shown or somehow the steps do not work for yours, please go
+to the next section for more detail explanations.
+
+IBM SP2: follow the instructions in INSTALL.ibm.sp.parallel.
+
+TFLOPS: follow the instuctions in INSTALL.ascired.
+
+SGI Origin 2000:
+Cray T3E:
+(where MPI-IO is part of system MPI library such as mpt 1.3)
+
+#!/bin/sh
+
+RUNPARALLEL="mpirun -np 2"
+export RUNPARALLEL
+LIBS="-lmpi"
+export LIBS
+./configure --enable-parallel --disable-shared --prefix=$PWD/installdir
+make
+make check
+make install
+
+
+SGI Origin 2000:
+Cray T3E:
+(where MPI-IO is not part of system MPI library or I want to
+use my own version of MPIO)
+
+
+mpi1_inc=""                                     #mpi-1 include
+mpi1_lib=""                                     #mpi-1 library
+mpio_inc=-I$HOME/ROMIO/include                  #mpio include
+mpio_lib="-L$HOME/ROMIO/lib/IRIX64"             #mpio library
+
+MPI_INC="$mpio_inc $mpi1_inc"
+MPI_LIB="$mpio_lib $mpi1_lib"
+
+#for version 1.1
+CPPFLAGS=$MPI_INC
+export CPPFLAGS
+LDFLAGS=$MPI_LIB
+export LDFLAGS
+RUNPARALLEL="mpirun -np 2"
+export RUNPARALLEL
+LIBS="-lmpio -lmpi"
+export LIBS
+
+./configure --enable-parallel --disable-shared --prefix=$PWD/installdir
+make
+make check
+make install
+
+
+3. Detail explanation
+---------------------
+[Work in progress.  Please send mail to hdfparallel@ncsa.uiuc.edu.]
+
+
 
-MPI_INC="$mpi1_inc $mpio_inc"
-export MPI_INC
-MPI_LIB="$mpi1_lib $mpio_lib"
-export MPI_LIB
 
-./configure --enable-parallel
 

INSTALL_parallel.ascired

@@ -18,7 +18,7 @@
 # (We use sh here, but of course you can adapt to whatever shell you like.)
 
 # compile for MPI jobs
-CC=cicc
+#CC=cicc
 
 # The following flags are only needed when compiling/linking a user program
 # for execution.
@@ -26,19 +26,32 @@ CC=cicc
 debug="-g -UH5O_DEBUG -DH5F_OPT_SEEK=0"
 default_mode="-DDOS386 $debug -DH5F_LOW_DFLT=H5F_LOW_SEC2"
 
-MPICH=""
-ROMIO="/usr/community/mpi-io/romio/current"
+# Using the MPICH libary by Daniel Sands.
+# It contains both MPI-1 and MPI-IO functions.
+ROMIO="${HOME}/MPIO/mpich"
+if [ ! -d $ROMIO ]
+then
+    echo "ROMIO directory ($ROMIO) not found"
+    echo "Aborted"
+    exit 1
+fi
 mpi1_inc=""
 mpi1_lib=""
 mpio_inc="-I$ROMIO/include"
-mpio_lib="-L$ROMIO/lib/tflop"
+mpio_lib="-L$ROMIO/lib"
+
 
 MPI_INC="$mpi1_inc $mpio_inc"
 MPI_LIB="$mpi1_lib $mpio_lib"
 
-CFLAGS="$default_mode"
+#for version 1.1 and later
+RUNSERIAL="yod -sz 1"
+export RUNSERIAL
+RUNPARALLEL="yod -sz 8"
+export RUNPARALLEL
+LIBS="-lmpich"
+export LIBS
 
-export CC CFLAGS MPI_INC MPI_LIB
 
 # Once these variables are set to the proper values for your installation,
 # you can run the configure program (i.e., ./configure tflop --enable-parallel=mpio)
@@ -49,5 +62,7 @@ export CC CFLAGS MPI_INC MPI_LIB
 # cicc and link to the MPI-IO library and the parallel version of the HDF5
 # library (that was created and installed with the configure/make process).
 
-./configure tflop --enable-parallel=mpio
-
+CFLAGS="$default_mode" \
+CPPFLAGS=$MPI_INC \
+LDFLAGS=$MPI_LIB \
+./configure --enable-parallel --disable-shared tflop 

MANIFEST

@@ -1,3 +1,10 @@
+#------------------------------------------------------------------------------
+# This is the list of files that are part of HDF5.  All files have a
+# `./' prefix and appear in lexicographic order.  Lines that end with
+# _DO_NOT_DISTRIBUTE_ will not be included in a release.  Blank lines
+# and comments are ignored.  Comments must start in column one.
+#------------------------------------------------------------------------------
+
 ./COPYING
 ./INSTALL
 ./INSTALL.ascired
@@ -11,57 +18,97 @@
 ./README
 ./RELEASE
 ./acconfig.h
-./bin/checkposix
-./bin/config.guess
-./bin/config.sub
-./bin/distdep
-./bin/errors
-./bin/install-sh
-./bin/release
-./bin/trace
-./bin/versinc
-./config/BlankForm
-./config/alpha-dec
-./config/commence.in
-./config/conclude.in
-./config/depend.in
-./config/freebsd2.2.1
-./config/hpux10.20
-./config/intel-osf1
-./config/irix5.3
-./config/irix6.2
-./config/irix64
-./config/linux
-./config/powerpc-ibm-aix4.2.1.0
-./config/rs6000-ibm-aix4.1.4.0
-./config/solaris2.5
+./aclocal.m4
 ./configure
 ./configure.in
-./doc/html/ddl.html
+./all.zip
+
+./bin/checkapi				_DO_NOT_DISTRIBUTE_
+./bin/checkposix			_DO_NOT_DISTRIBUTE_
+./bin/config.guess
+./bin/config.sub
+./bin/debug-ohdr			_DO_NOT_DISTRIBUTE_
+./bin/distdep
+./bin/errors				_DO_NOT_DISTRIBUTE_
+./bin/h5vers
+./bin/install-sh
+./bin/iostats
+./bin/ltconfig
+./bin/ltmain.sh
+./bin/release
+./bin/snapshot
+./bin/trace
+./bin/versinc				_DO_NOT_DISTRIBUTE_
+
+./config/BlankForm
+./config/commence.in
+./config/conclude.in
+./config/dec-flags
+./config/dec-osf4.x
+./config/depend.in
+./config/freebsd
+./config/gnu-flags
+./config/hpux10.20
+./config/hpux9.03
+./config/intel-osf1
+./config/irix5.x
+./config/irix6.x
+./config/linux-gnu
+./config/linux-gnulibc1
+./config/linux-gnulibc2
+./config/powerpc-ibm-aix4.x
+./config/rs6000-ibm-aix4.x
+./config/solaris2.x
+./config/unicosmk
+
 ./doc/html/Attributes.html
 ./doc/html/Big.html
 ./doc/html/Caching.html
-./doc/html/CodeReview.html
+./doc/html/Chunking.html
+./doc/html/Chunk_f1.gif
+./doc/html/Chunk_f1.obj			_DO_NOT_DISTRIBUTE_
+./doc/html/Chunk_f2.gif
+./doc/html/Chunk_f2.obj			_DO_NOT_DISTRIBUTE_
+./doc/html/Chunk_f3.gif
+./doc/html/Chunk_f4.gif
+./doc/html/Chunk_f5.gif
+./doc/html/Chunk_f6.gif
+./doc/html/Chunk_f6.obj			_DO_NOT_DISTRIBUTE_
+./doc/html/CodeReview.html		_DO_NOT_DISTRIBUTE_
 ./doc/html/Coding.html
-./doc/html/Compression.html
+./doc/html/Copyright.html
 ./doc/html/Datasets.html
 ./doc/html/Dataspaces.html
 ./doc/html/Datatypes.html
+./doc/html/DatatypesEnum.html
+./doc/html/ddl.html
+./doc/html/Debugging.html
+./doc/html/EnumMap.gif
+./doc/html/Environment.html
 ./doc/html/Errors.html
-./doc/html/ExternalFiles.html
+./doc/html/ExternalFiles.html		_DO_NOT_DISTRIBUTE_
 ./doc/html/Files.html
+./doc/html/Filters.html
 ./doc/html/Glossary.html
 ./doc/html/Groups.html
-./doc/html/H5.api.html
 ./doc/html/H5.api_map.html
 ./doc/html/H5.format.html
 ./doc/html/H5.intro.html
 ./doc/html/H5.sample_code.html
 ./doc/html/H5.user.html
+./doc/html/IH_map1.gif
+./doc/html/IH_map2.gif
+./doc/html/IH_map3.gif
+./doc/html/IH_map4.gif
+./doc/html/IH_mapFoot.gif
+./doc/html/IH_mapHead.gif
 ./doc/html/IOPipe.html
-./doc/html/MemoryManagement.html
-./doc/html/ObjectHeader.txt
+./doc/html/MemoryManagement.html	_DO_NOT_DISTRIBUTE_
+./doc/html/NCSAfooterlogo.gif
+./doc/html/ObjectHeader.txt		_DO_NOT_DISTRIBUTE_
 ./doc/html/Properties.html
+./doc/html/Ragged.html
+./doc/html/References.html
 ./doc/html/RM_H5.html
 ./doc/html/RM_H5A.html
 ./doc/html/RM_H5D.html
@@ -69,76 +116,76 @@
 ./doc/html/RM_H5F.html
 ./doc/html/RM_H5Front.html
 ./doc/html/RM_H5G.html
+./doc/html/RM_H5I.html
 ./doc/html/RM_H5P.html
+./doc/html/RM_H5R.html
+./doc/html/RM_H5RA.html
 ./doc/html/RM_H5S.html
 ./doc/html/RM_H5T.html
 ./doc/html/RM_H5Z.html
+./doc/html/Tools.html
 ./doc/html/Version.html
 ./doc/html/chunk1.gif
-./doc/html/chunk1.obj
+./doc/html/chunk1.obj			_DO_NOT_DISTRIBUTE_
 ./doc/html/compat.html
 ./doc/html/dataset_p1.gif
 ./doc/html/dataset_p1.obj
 ./doc/html/extern1.gif
-./doc/html/extern1.obj
+./doc/html/extern1.obj			_DO_NOT_DISTRIBUTE_
 ./doc/html/extern2.gif
-./doc/html/extern2.obj
+./doc/html/extern2.obj			_DO_NOT_DISTRIBUTE_
 ./doc/html/group_p1.gif
-./doc/html/group_p1.obj
+./doc/html/group_p1.obj			_DO_NOT_DISTRIBUTE_
 ./doc/html/group_p2.gif
-./doc/html/group_p2.obj
+./doc/html/group_p2.obj			_DO_NOT_DISTRIBUTE_
 ./doc/html/group_p3.gif
-./doc/html/group_p3.obj
+./doc/html/group_p3.obj			_DO_NOT_DISTRIBUTE_
 ./doc/html/h5s.examples
+./doc/html/hdf2.jpg
 ./doc/html/ph5design.html
 ./doc/html/ph5example.c
 ./doc/html/ph5implement.txt
 ./doc/html/pipe1.gif
-./doc/html/pipe1.obj
+./doc/html/pipe1.obj			_DO_NOT_DISTRIBUTE_
 ./doc/html/pipe2.gif
-./doc/html/pipe2.obj
+./doc/html/pipe2.obj			_DO_NOT_DISTRIBUTE_
 ./doc/html/pipe3.gif
-./doc/html/pipe3.obj
+./doc/html/pipe3.obj			_DO_NOT_DISTRIBUTE_
 ./doc/html/pipe4.gif
-./doc/html/pipe4.obj
+./doc/html/pipe4.obj			_DO_NOT_DISTRIBUTE_
 ./doc/html/pipe5.gif
-./doc/html/pipe5.obj
-./doc/html/heap.txt
+./doc/html/pipe5.obj			_DO_NOT_DISTRIBUTE_
+./doc/html/heap.txt			_DO_NOT_DISTRIBUTE_
 ./doc/html/index.html
-./doc/html/move.html
-./doc/html/review1.html
-./doc/html/review1a.html
-./doc/html/storage.html
-./doc/html/study.html
-./doc/html/study_1000x1000.gif
-./doc/html/study_250x250.gif
-./doc/html/study_499x499.gif
-./doc/html/study_5000x1000.gif
-./doc/html/study_500x500.gif
-./doc/html/study_p1.gif
-./doc/html/study_p1.obj
-./doc/html/symtab
-./doc/html/tracing.html
+./doc/html/move.html			_DO_NOT_DISTRIBUTE_
+./doc/html/review1.html			_DO_NOT_DISTRIBUTE_
+./doc/html/review1a.html		_DO_NOT_DISTRIBUTE_
+./doc/html/storage.html			_DO_NOT_DISTRIBUTE_
+./doc/html/symtab			_DO_NOT_DISTRIBUTE_
 ./doc/html/version.gif
-./doc/html/version.obj
-./doc/src/Glossary.html
-./doc/src/H5.intro.doc
-./doc/src/RM_H5.html
-./doc/src/RM_H5A.html
-./doc/src/RM_H5D.html
-./doc/src/RM_H5E.html
-./doc/src/RM_H5F.html
-./doc/src/RM_H5Front.html
-./doc/src/RM_H5G.html
-./doc/src/RM_H5P.html
-./doc/src/RM_H5S.html
-./doc/src/RM_H5T.html
-./doc/src/RM_H5Z.html
-./doc/tgif/APIGrammar.obj
-./doc/tgif/FileGrammar.obj
-./doc/tgif/IOPipe.obj
-./doc/tgif/RobbPipe.obj
-./doc/tgif/UserView.obj
+./doc/html/version.obj			_DO_NOT_DISTRIBUTE_
+./doc/src/Copyright.html		_DO_NOT_DISTRIBUTE_
+./doc/src/Glossary.html			_DO_NOT_DISTRIBUTE_
+./doc/src/H5.intro.doc			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5.html			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5A.html			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5D.html			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5E.html			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5F.html			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5Front.html		_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5G.html			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5P.html			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5R.html			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5S.html			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5T.html			_DO_NOT_DISTRIBUTE_
+./doc/src/RM_H5Z.html			_DO_NOT_DISTRIBUTE_
+./doc/src/Tools.html			_DO_NOT_DISTRIBUTE_
+./doc/tgif/APIGrammar.obj		_DO_NOT_DISTRIBUTE_
+./doc/tgif/FileGrammar.obj		_DO_NOT_DISTRIBUTE_
+./doc/tgif/IOPipe.obj			_DO_NOT_DISTRIBUTE_
+./doc/tgif/RobbPipe.obj			_DO_NOT_DISTRIBUTE_
+./doc/tgif/UserView.obj			_DO_NOT_DISTRIBUTE_
+
 ./examples/Attributes.txt
 ./examples/Makefile.in
 ./examples/h5_chunk_read.c
@@ -147,9 +194,29 @@
 ./examples/h5_group.c
 ./examples/h5_read.c
 ./examples/h5_write.c
+./examples/h5_select.c
+./examples/h5_attribute.c
+./examples/h5_mount.c
+./examples/h5_reference.c
+
+./pablo/HDFIOTrace.h
+./pablo/HDFTrace.h
+./pablo/HDFmpioProtos.h
+./pablo/HDFrecord_RT.h
+./pablo/Makefile.in
+./pablo/PabloHDF.c
+./pablo/PabloHDF_RT.c
+./pablo/PabloHDF_SDDF.c
+./pablo/ProcIDs.h
+./pablo/PabloSedscr
+./pablo/ProcTrace.h
+./pablo/ProcTrace.inc
+./pablo/READ_ME
+
 ./src/.distdep
-./src/.indent.pro
+./src/.indent.pro			_DO_NOT_DISTRIBUTE_
 ./src/H5.c
+./src/H5api_adpt.h
 ./src/H5A.c
 ./src/H5Aprivate.h
 ./src/H5Apublic.h
@@ -206,7 +273,9 @@
 ./src/H5Ocont.c
 ./src/H5Odtype.c
 ./src/H5Oefl.c
+./src/H5Ofill.c
 ./src/H5Olayout.c
+./src/H5Omtime.c
 ./src/H5Oname.c
 ./src/H5Onull.c
 ./src/H5Oprivate.h
@@ -217,13 +286,20 @@
 ./src/H5P.c
 ./src/H5Pprivate.h
 ./src/H5Ppublic.h
+./src/H5R.c
+./src/H5Rprivate.h
+./src/H5Rpublic.h
+./src/H5RA.c
+./src/H5RAprivate.h
+./src/H5RApublic.h
 ./src/H5S.c
 ./src/H5Sall.c
 ./src/H5Shyper.c
+./src/H5Smpio.c
+./src/H5Snone.c
 ./src/H5Spoint.c
 ./src/H5Sprivate.h
 ./src/H5Spublic.h
-./src/H5Ssimp.c
 ./src/H5Sselect.c
 ./src/H5T.c
 ./src/H5Tbit.c
@@ -231,6 +307,7 @@
 ./src/H5Tpkg.h
 ./src/H5Tprivate.h
 ./src/H5Tpublic.h
+./src/H5Tvlen.c
 ./src/H5TB.c
 ./src/H5TBprivate.h
 ./src/H5V.c
@@ -244,6 +321,8 @@
 ./src/H5public.h
 ./src/Makefile.in
 ./src/hdf5.h
+./src/libhdf5.settings.in
+
 ./test/.distdep
 ./test/Makefile.in
 ./test/big.c
@@ -252,33 +331,118 @@
 ./test/cmpd_dset.c
 ./test/dsets.c
 ./test/dtypes.c
+./test/enum.c
 ./test/extend.c
 ./test/external.c
+./test/fillval.c
+./test/flush1.c
+./test/flush2.c
 ./test/gheap.c
+./test/h5test.c
+./test/h5test.h
 ./test/hyperslab.c
 ./test/iopipe.c
 ./test/istore.c
+./test/lheap.c
 ./test/links.c
-./test/shtype.c
+./test/mount.c
+./test/mtime.c
+./test/ohdr.c
+./test/overhead.c
+./test/ragged.c
+./test/space_overflow.c			_DO_NOT_DISTRIBUTE_
+./test/stab.c
 ./test/testhdf5.c
 ./test/testhdf5.h
 ./test/tattr.c
 ./test/tfile.c
 ./test/th5s.c
-./test/theap.c
+./test/th5s.h5
 ./test/tmeta.c
-./test/tohdr.c
+./test/trefer.c
 ./test/tselect.c
-./test/tstab.c
-./testpar/Makefile.ascired
-./testpar/Makefile.irix64
+./test/tvltypes.c
+./test/unlink.c
+
+./testpar/Makefile.in
+./testpar/Makefile.ibmsp
 ./testpar/README
 ./testpar/t_dset.c
 ./testpar/t_file.c
+./testpar/t_mpi.c
 ./testpar/testphdf5.c
 ./testpar/testphdf5.h
+
 ./tools/Makefile.in
 ./tools/h5debug.c
+./tools/h5dump.c
+./tools/h5dump.h
+./tools/h5dumptst.c
+./tools/h5dumputil.c
+./tools/h5findshd.c
 ./tools/h5import.c
 ./tools/h5ls.c
 ./tools/h5repart.c
+./tools/h5toh4.c
+./tools/h5toh4.h
+./tools/h5tools.c
+./tools/h5tools.h
+./tools/testh5dump.sh
+./tools/testh5toh4
+
+./tools/testfiles/tall-1.ddl
+./tools/testfiles/tall-2.ddl
+./tools/testfiles/tall-3.ddl
+./tools/testfiles/tall.h5
+./tools/testfiles/tattr-1.ddl
+./tools/testfiles/tattr-2.ddl
+./tools/testfiles/tattr-3.ddl
+./tools/testfiles/tattr.h5
+./tools/testfiles/tcomp-1.ddl
+./tools/testfiles/tcomp-2.ddl
+./tools/testfiles/tcomp-3.ddl
+./tools/testfiles/tcompound.h5
+./tools/testfiles/tcompound2.h5
+./tools/testfiles/tdatareg.h5
+./tools/testfiles/tdatareg.ddl 
+./tools/testfiles/tdset-1.ddl
+./tools/testfiles/tdset-2.ddl
+./tools/testfiles/tdset.h5
+./tools/testfiles/tdset2.h5
+./tools/testfiles/tenum.h5
+./tools/testfiles/tenum.ddl
+./tools/testfiles/tgroup-1.ddl
+./tools/testfiles/tgroup-2.ddl
+./tools/testfiles/tgroup.h5
+./tools/testfiles/thlink-1.ddl
+./tools/testfiles/thlink-2.ddl
+./tools/testfiles/thlink-3.ddl
+./tools/testfiles/thlink-4.ddl
+./tools/testfiles/thlink-5.ddl
+./tools/testfiles/thlink.h5
+./tools/testfiles/tloop-1.ddl
+./tools/testfiles/tloop.h5
+./tools/testfiles/tloop2.h5
+./tools/testfiles/tmany.h5
+./tools/testfiles/tobjref.h5
+./tools/testfiles/tobjref.ddl
+./tools/testfiles/tslink-1.ddl
+./tools/testfiles/tslink-2.ddl
+./tools/testfiles/tslink.h5
+./tools/testfiles/tstr-1.ddl
+./tools/testfiles/tstr.h5
+./tools/testfiles/tstr2.h5
+
+./tools/testfiles/Expected/tall.hdf
+./tools/testfiles/Expected/tattr.hdf
+./tools/testfiles/Expected/tcompound.hdf
+./tools/testfiles/Expected/tcompound2.hdf
+./tools/testfiles/Expected/tdset.hdf
+./tools/testfiles/Expected/tdset2.hdf
+./tools/testfiles/Expected/tgroup.hdf
+./tools/testfiles/Expected/thlink.hdf
+./tools/testfiles/Expected/tloop.hdf
+./tools/testfiles/Expected/tmany.hdf
+./tools/testfiles/Expected/tslink.hdf
+./tools/testfiles/Expected/tstr.hdf
+./tools/testfiles/Expected/tstr2.hdf

Makefile.dist

@@ -11,7 +11,7 @@
 
 SHELL=/bin/sh
 
-all lib progs test _test install uninstall dep depend: _config
+all lib progs check test _test install uninstall dep depend: _config
 	$(MAKE) $@
 
 clean mostlyclean distclean maintainer-clean TAGS: _config

Makefile.in

@@ -1,4 +1,4 @@
-# Top-level HDF5 Makefile(.in)				       -*- makefile -*-
+# Top-level HDF5 Makefile(.in)
 #
 # Copyright (C) 1997 National Center for Supercomputing Applications.
 #                    All rights reserved.
@@ -8,10 +8,14 @@
 # but does so in the correct order.  You can alternatively invoke make from
 # each subdirectory manually.
 #
+top_srcdir=@top_srcdir@
+top_builddir=.
+srcdir=@srcdir@
+VPATH=.:@srcdir@
 @COMMENCE@
 
-# Subdirectories in build-order
-SUBDIRS=src test tools
+# Subdirectories in build-order (not including `examples')
+SUBDIRS=src test tools @TESTPARALLEL@
 
 ##############################################################################
 #			    T A R G E T S
@@ -21,7 +25,10 @@ SUBDIRS=src test tools
 #		library, header files, or programs.  The components can be
 #		built individually with the targets lib, progs, and tests.
 #
-# test:		Test the uninstalled library to make sure it works.
+# check:	Test the uninstalled library to make sure it works. You may
+#		also say `test' or `_test' (`test' doesn't work from the top
+#		level directory for some versions of make because `test' is
+#		also a directory).
 #
 # install:	Installs libraries, header files, programs, and documentation
 #		in the various directories under the prefix directory (lib,
@@ -59,11 +66,22 @@ SUBDIRS=src test tools
 #		make used in combination with gcc will maintain dependency
 #		information automatically.
 #
-lib progs tests test _test install uninstall TAGS dep depend:
+lib progs check test _test uninstall:
 	@@SETX@; for d in $(SUBDIRS); do				      \
 	   (cd $$d && $(MAKE) $@) || exit 1;				      \
 	done
 
+tests TAGS dep depend:
+	@@SETX@; for d in $(SUBDIRS) examples; do			      \
+	   (cd $$d && $(MAKE) $@) || exit 1;				      \
+	done
+
+install:
+	@@SETX@; for d in $(SUBDIRS); do				      \
+	   (cd $$d && $(MAKE) $@) || exit 1;				      \
+	done
+	@$(LT) --mode=finish $(libdir);
+
 # Number format detection
 H5detect: 
 	(cd src && $(MAKE) $@)
@@ -75,24 +93,26 @@ H5Tinit.c:
 	mostlyclean distclean maintainer-clean
 
 clean mostlyclean:
-	@@SETX@; for d in $(SUBDIRS); do				      \
-	   (cd $$d && $(MAKE) $@) || exit 1;				      \
+	@@SETX@; for d in $(SUBDIRS) examples pablo; do			      \
+	   (cd $$d && $(MAKE) $@);					      \
 	done
+	-$(RM) conftest conftest.c
 
 distclean:
-	@@SETX@; for d in $(SUBDIRS); do				      \
-	   (cd $$d && $(MAKE) $@) || exit 1;				      \
+	@@SETX@; for d in $(SUBDIRS) examples pablo; do			      \
+	   (cd $$d && $(MAKE) $@);					      \
 	done
-	$(RM) config/commence config/conclude config/depend
-	$(RM) config.cache config.log config.status src/H5config.h
-	$(RM) Makefile
-	$(CP) Makefile.dist Makefile
+	-$(RM) config/commence config/conclude config/depend
+	-$(RM) config.cache config.log config.status src/H5config.h
+	-$(RM) config/stamp1 config/stamp2 libtool Makefile
+	-$(CP) Makefile.dist Makefile
 
 maintainer-clean:
 	@echo "This command is intented for maintainers to use;"
 	@echo "it deletes files that may require special tools to rebuild."
-	@@SETX@; for d in $(SUBDIRS); do				      \
-	   (cd $$d && $(MAKE) $@) || exit 1;				      \
+	@@SETX@; for d in $(SUBDIRS) examples pablo; do			      \
+	   (cd $$d && $(MAKE) $@);					      \
 	done
-	$(RM) config.cache config.log config.status src/H5config.h
-	$(RM) configure src/H5config.h.in
+	-$(RM) config.cache config.log config.status src/H5config.h
+	-$(RM) configure src/H5config.h.in
+

README

@@ -1,4 +1,4 @@
-This is hdf5-1.0.23a released on 1998-06-15 05:41 UTC
+This is hdf5-1.1.110 currently under development
 Please refer to the INSTALL file for installation instructions.
 ------------------------------------------------------------------------------
 

RELEASE

@@ -1,5 +1,59 @@
-Release information for hdf5-1.0.23a
------------------------------------
+Release information for hdf5-1.1.x
+------------------------------------
+
+		    CHANGES SINCE THE Version 1.0.0 RELEASE
+
+* [Improvement]: configure sets up the Makefile in the parallel tests
+  suit (testpar/) correctly.  (Tested for O2K only.)
+
+* [Bug-Fix]: Configure failed for all IRIX versions other than 6.3.
+  It now configures correctly for all IRIX 6.x version.
+
+		    CHANGES SINCE THE BETA RELEASE
+
+* Added fill values for datasets.  For contiguous datasets fill value
+  performance may be quite poor since the fill value is written to the 
+  entire dataset when the dataset is created.  This will be remedied
+  in a future version.  Chunked datasets using fill values do not
+  incur any additional overhead. See H5Pset_fill_value().
+
+* Multiple hdf5 files can be "mounted" on one another to create a
+  larger virtual file. See H5Fmount().
+
+* Object names can be removed or changed but objects are never
+  actually removed from the file yet. See H5Gunlink() and H5Gmove().
+
+* Added a tuning mechanism for B-trees to insure that sequential
+  writes to chunked datasets use less overhead.  See H5Pset_btree_ratios().
+
+* Various optimizations and bug fixes.
+
+
+		    CHANGES SINCE THE SECOND ALPHA
+
+* Strided hyperslab selections in dataspaces now working.
+
+* The compression API has been replaced with a more general filter
+  API.  See doc/html/Filters.html for details.
+
+* Alpha-quality 2d ragged arrays are implemented as a layer built on
+  top of other hdf5 objects.  The API and storage format will almost
+  certainly change.
+
+* More debugging support including API tracing.  See Debugging.html.
+
+* C and Fortran style 8-bit fixed-length character string types are
+  supported with space or null padding or null termination and
+  translations between them.
+
+* Added function H5Fflush() to write all cached data immediately to
+  the file.
+
+* Datasets maintain a modification time which can be retrieved with
+  H5Gstat().
+
+* The h5ls tool can display much more information, including all the
+  values of a dataset.
 
 		    CHANGES SINCE THE FIRST ALPHA
 
@@ -37,12 +91,12 @@ Release information for hdf5-1.0.23a
   which correspond to the standard C types like H5T_NATIVE_INT.
 
 * More debugging support was added.  If tracing is enabled at
-  configuration time and the HDF5_TRACE environment variable is set to 
-  a file descriptor then all API calls will emit the function name,
-  argument names and values, and return value on that file number.
-  There is an html document that describes this.  If appropriate
-  debugging options are enabled at configuration time, some packages
-  will display performance information on stderr.
+  configuration time (the default) and the HDF5_TRACE environment
+  variable is set to a file descriptor then all API calls will emit
+  the function name, argument names and values, and return value on
+  that file number.  There is an html document that describes this.
+  If appropriate debugging options are enabled at configuration time,
+  some packages will display performance information on stderr.
 
 * Data types can be stored in the file as independent objects and
   multiple datasets can share a data type.
@@ -60,7 +114,7 @@ Release information for hdf5-1.0.23a
   HDF5.
 
 * Hard and soft (symbolic) links are implemented which allow groups to 
-  share objects.
+  share objects. Dangling and recursive symbolic links are supported.
 
 * User-defined data compression is implemented although we may
   generalize the interface to allow arbitrary user-defined filters
@@ -113,8 +167,8 @@ Library
    H5open		- initialize library (happens automatically)
    H5close		- shut down the library (happens automatically)
    H5dont_atexit	- don't call H5close on exit
-   H5version		- retrieve library version info
-   H5version_check	- check for specific library version
+   H5get_libversion	- retrieve library version info
+   H5check_version	- check for specific library version
 
 Property Lists
    H5Pclose		- release template resources
@@ -156,10 +210,10 @@ Property Lists
    H5Pset_buffer	- set raw-data I/O pipe buffer properties
    H5Pget_preserve	- get type conversion preservation properties
    H5Pset_preserve	- set type conversion preservation properties
-   H5Pget_compression	- get raw data compression properties
-   H5Pset_compression	- set raw data compression properties
-   H5Pget_deflate	- get deflate compression properties
-   H5Pset_deflate	- set deflate compression properties
+   H5Pget_nfilters	- get number of raw data filters
+   H5Pget_filter	- get raw data filter properties
+   H5Pset_filter	- set raw data filter properties
+   H5Pset_deflate	- set deflate compression filter properties
    H5Pget_mpi		- get MPI-IO properties
    H5Pset_mpi		- set MPI-IO properties
    H5Pget_xfer		- get data transfer properties
@@ -177,64 +231,74 @@ Datasets
    H5Dextend		- extend a dataset
 
 Attributes
-   H5Acreate	- create a new attribute
-   H5Aopen_name	- open an attribute by name
-   H5Aopen_idx	- open an attribute by number
+   H5Acreate		- create a new attribute
+   H5Aopen_name		- open an attribute by name
+   H5Aopen_idx		- open an attribute by number
    H5Awrite		- write values into an attribute
    H5Aread		- read values from an attribute
-   H5Aget_space	- get attribute data space
-   H5Aget_type	- get attribute data type
-   H5Aget_name	- get attribute name
-   H5Anum_attrs	- return the number of attributes for an object
-   H5Aiterate	- iterate over an object's attributes
-   H5Adelete	- delete an attribute
+   H5Aget_space		- get attribute data space
+   H5Aget_type		- get attribute data type
+   H5Aget_name		- get attribute name
+   H5Anum_attrs		- return the number of attributes for an object
+   H5Aiterate		- iterate over an object's attributes
+   H5Adelete		- delete an attribute
    H5Aclose		- close an attribute
 
 Errors
    H5Eclear		- clear the error stack
    H5Eprint		- print an error stack
-   H5Eget_auto	- get automatic error reporting settings
-   H5Eset_auto	- set automatic error reporting
+   H5Eget_auto		- get automatic error reporting settings
+   H5Eset_auto		- set automatic error reporting
    H5Ewalk		- iterate over the error stack
-   H5Ewalk_cb	- the default error stack iterator function
-   H5Eget_major	- get the message for the major error number
-   H5Eget_minor	- get the message for the minor error number
+   H5Ewalk_cb		- the default error stack iterator function
+   H5Eget_major		- get the message for the major error number
+   H5Eget_minor		- get the message for the minor error number
 
 Files
-   H5Fclose		    - close a file and release resources
+   H5Fclose		- close a file and release resources
    H5Fcreate		- create a new file
-   H5Fget_create_template- get file creation property list
-   H5Fget_access_template- get file access property list
+   H5Fget_create_plist	- get file creation property list
+   H5Fget_access_plist	- get file access property list
    H5Fis_hdf5		- determine if a file is an hdf5 file
-   H5Fopen		    - open an existing file
+   H5Fopen		- open an existing file
 
 Groups
    H5Gclose		- close a group and release resources
-   H5Gcreate    - create a new group
+   H5Gcreate    	- create a new group
    H5Gopen		- open an existing group
    H5Gpop		- pop a group from the cwg stack
    H5Gpush		- push a group onto the cwg stack
    H5Gset		- set the current working group (cwg)
-   H5Giterate   - iterate over the contents of a group
+   H5Giterate   	- iterate over the contents of a group
    H5Gmove		- change the name of some object
    H5Glink		- create a hard or soft link to an object
-   H5Gunlink    - break the link between a name and an object
-   H5Gstat		- get information about a group entry
+   H5Gunlink    	- break the link between a name and an object
+   H5Gget_objinfo	- get information about a group entry
    H5Gget_linkval	- get the value of a soft link
+   H5Gget_comment	- get the comment string for an object
+   H5Gset_comment	- set the comment string for an object
 
 Dataspaces
-   H5Sclose		        - release dataspace
-   H5Screate	        - create a new dataspace
-   H5Screate_simple	    - create a new simple dataspace
-   H5Sextent_dims		- get dataspace size
+   H5Screate	        - create a new data space
+   H5Scopy		- copy a data space
+   H5Sclose		- release data space
+   H5Screate_simple	- create a new simple data space
+   H5Sset_space		- set simple data space extents
+   H5Sis_simple		- determine if data space is simple
+   H5Sset_extent_simple	- set simple data space dimensionality and size
+   H5Sget_simple_extent_npoints	- get number of points in simple extent
+   H5Sget_simple_extent_ndims - get simple data space dimensionality
+   H5Sget_simple_extent_dims - get simple data space size
+   H5Sget_simple_extent_type - get type of simple extent
+   H5Sset_extent_none	- reset extent to be empty
+   H5Sextent_copy	- copy the extent from one data space to another
+   H5Sget_select_npoints - get number of points selected for I/O
    H5Sselect_hyperslab	- set hyperslab dataspace selection
    H5Sselect_elements   - set element sequence dataspace selection
-   H5Sextent_ndims		- get dataspace dimensionality
-   H5Sextent_npoints	- get number of points in extent of dataspace
-   H5Sselect_npoints	- get number of selected points in dataspace
-   H5Sis_simple		    - determine if dataspace is simple
-   H5Sset_extent_simple	- set simple dataspace dimensionality and size
-   H5Scopy		        - copy a dataspace
+   H5Sselect_all	- select entire extent for I/O
+   H5Sselect_none	- deselect all elements of extent
+   H5Soffset_simple	- set selection offset
+   H5Sselect_valid	- determine if selection is valid for extent
 
 Datatypes
    H5Tclose		- release data type resources
@@ -244,8 +308,14 @@ Datatypes
    H5Tcopy		- copy a data type
    H5Tcreate		- create a new data type
    H5Tequal		- compare two data types
+   H5Tlock		- lock type to prevent changes
    H5Tfind		- find a data type conversion function
    H5Tconvert		- convert data from one type to another
+   H5Tregister_hard	- register specific type conversion function
+   H5Tregister_soft	- register general type conversion function
+   H5Tunregister	- remove a type conversion function
+   H5Tget_overflow	- get function that handles overflow conv. cases
+   H5Tset_overflow	- set function to handle overflow conversion cases
    H5Tget_class		- get data type class
    H5Tget_cset		- get character set
    H5Tget_ebias		- get exponent bias
@@ -264,11 +334,9 @@ Datatypes
    H5Tget_sign		- get integer sign type
    H5Tget_size		- get size in bytes
    H5Tget_strpad	- get string padding
-   H5Tinsert		- insert struct member
-   H5Tlock		- lock type to prevent changes
+   H5Tinsert		- insert scalar struct member
+   H5Tinsert_array	- insert array struct member
    H5Tpack		- pack struct members
-   H5Tregister_hard	- register specific type conversion function
-   H5Tregister_soft	- register general type conversion function
    H5Tset_cset		- set character set
    H5Tset_ebias		- set exponent bias
    H5Tset_fields	- set floating point fields
@@ -281,36 +349,54 @@ Datatypes
    H5Tset_sign		- set integer sign type
    H5Tset_size		- set size in bytes
    H5Tset_strpad	- set string padding
-   H5Tunregister	- remove a type conversion function
 
-Compression
-   H5Tregister		- register a new compression method
+Filters
+   H5Tregister		- register a new filter method
+
+Ragged Arrays (alpha)
+   H5Rcreate		- create a new ragged array
+   H5Ropen		- open an existing array
+   H5Rclose		- close a ragged array
+   H5Rwrite		- write to an array
+   H5Rread		- read from an array
 
 This release has been tested on UNIX platforms only; specifically:
 Linux, FreedBSD, IRIX, Solaris & Dec UNIX.
 
 
-Release information for parallel HDF5
--------------------------------------
+		RELEASE INFORMATION FOR PARALLEL HDF5
+		-------------------------------------
 
-+) Current release supports independent access to fixed dimension datasets
-   only.
+* Current release supports independent access to fixed dimension datasets
+  only.
 
-+) The comm and info arguments of H5Cset_mpi are not used.  All parallel
-   I/O are done via MPI_COMM_WORLD.  Access_mode for H5Cset_mpi can be
-   H5ACC_INDEPENDENT only.
+* The comm and info arguments of H5Cset_mpi are not used.  All parallel
+  I/O are done via MPI_COMM_WORLD.  Access_mode for H5Cset_mpi can be
+  H5ACC_INDEPENDENT only.
 
-+) This release of parallel HDF5 has been tested on IBM SP2 and SGI
-   Origin 2000 systems.  It uses the ROMIO version of MPIO interface
-   for parallel I/O supports.
+* This release of parallel HDF5 has been tested on IBM SP2 and SGI
+  Origin 2000 systems.  It uses the ROMIO version of MPIO interface
+  for parallel I/O supports.
 
-+) Useful URL's.
-   Parallel HDF webpage: "http://hdf.ncsa.uiuc.edu/Parallel_HDF/"
-   ROMIO webpage: "http://www.mcs.anl.gov/home/thakur/romio/"
+* Useful URL's.
+  Parallel HDF webpage: "http://hdf.ncsa.uiuc.edu/Parallel_HDF/"
+  ROMIO webpage: "http://www.mcs.anl.gov/home/thakur/romio/"
 
-+) Some to-do items for future releases
-      support for Intel Teraflop platform.
-      support for unlimited dimension datasets.
-      support for file access via a communicator besides MPI_COMM_WORLD.
-      support for collective access to datasets.
-      support for independent create/open of datasets.
+* Some to-do items for future releases
+     support for Intel Teraflop platform.
+     support for unlimited dimension datasets.
+     support for file access via a communicator besides MPI_COMM_WORLD.
+     support for collective access to datasets.
+     support for independent create/open of datasets.
+
+
+
+			PLATFORMS SUPPORTED
+			-------------------
+
+  Platform(OS)                    C-Compiler       Fortran-Compiler   
+  ------------                    ----------       ---------------- 
+  Sun4(Solaris 2.5)               CC SC4.0         f77 SC4.0            
+  SGI (IRIX v6.5)                 CC 7.21          f77 7.21
+  SGI-Origin(IRIX64 v6.4-n32)     CC 7.2.1.2m      f77 7.2.1.2m     
+  SGI-Origin(IRIX64 v6.4-64)      CC 7.2.1.2m      f77 7.2.1.2m    

acconfig.h

@@ -10,5 +10,32 @@
 /* Define if it's safe to use `long long' for hsize_t and hssize_t */
 #undef HAVE_LARGE_HSIZET
 
-/* The width parameter for printf formats for type `long long', us. `ll' */
+/* Width for printf() for type `long long' or `__int64', us. `ll' */
 #undef PRINTF_LL_WIDTH
+
+/* Define if `tm_gmtoff' is a member of `struct tm' */
+#undef HAVE_TM_GMTOFF
+
+/* Define if `__tm_gmtoff' is a member of `struct tm' */
+#undef HAVE___TM_GMTOFF
+
+/* Define if `timezone' is a global variable */
+#undef HAVE_TIMEZONE
+
+/* Define if `struct timezone' is defined */
+#undef HAVE_STRUCT_TIMEZONE
+
+/* Define if `struct stat' has the `st_blocks' field */
+#undef HAVE_STAT_ST_BLOCKS
+
+/* Define if `struct text_info' is defined */
+#undef HAVE_STRUCT_TEXT_INFO
+
+/* Define if `struct videoconfig' is defined */
+#undef HAVE_STRUCT_VIDEOCONFIG
+
+/* Define if the ioctl TIOCGETD is defined */
+#undef HAVE_TIOCGETD
+
+/* Define if the ioctl TIOCGWINSZ is defined */
+#undef HAVE_TIOCGWINSZ

aclocal.m4

@@ -0,0 +1,259 @@
+## libtool.m4 - Configure libtool for the target system. -*-Shell-script-*-
+## Copyright (C) 1996-1998 Free Software Foundation, Inc.
+## Gordon Matzigkeit <gord@gnu.ai.mit.edu>, 1996
+##
+## This program is free software; you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation; either version 2 of the License, or
+## (at your option) any later version.
+##
+## This program is distributed in the hope that it will be useful, but
+## WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+## General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with this program; if not, write to the Free Software
+## Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+##
+## As a special exception to the GNU General Public License, if you
+## distribute this file as part of a program that contains a
+## configuration script generated by Autoconf, you may include it under
+## the same distribution terms that you use for the rest of that program.
+
+# serial 24 AM_PROG_LIBTOOL
+AC_DEFUN(AM_PROG_LIBTOOL,
+[AC_REQUIRE([AM_ENABLE_SHARED])dnl
+AC_REQUIRE([AM_ENABLE_STATIC])dnl
+AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_PROG_RANLIB])dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([AM_PROG_LD])dnl
+AC_REQUIRE([AM_PROG_NM])dnl
+AC_REQUIRE([AC_PROG_LN_S])dnl
+dnl
+# Always use our own libtool.
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+AC_SUBST(LIBTOOL)dnl
+
+# Check for any special flags to pass to ltconfig.
+libtool_flags=
+test "$enable_shared" = no && libtool_flags="$libtool_flags --disable-shared"
+test "$enable_static" = no && libtool_flags="$libtool_flags --disable-static"
+test "$silent" = yes && libtool_flags="$libtool_flags --silent"
+test "$ac_cv_prog_gcc" = yes && libtool_flags="$libtool_flags --with-gcc"
+test "$ac_cv_prog_gnu_ld" = yes && libtool_flags="$libtool_flags --with-gnu-ld"
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case "$host" in
+*-*-irix6*)
+  # Find out which ABI we are using.
+  echo '[#]line __oline__ "configure"' > conftest.$ac_ext
+  if AC_TRY_EVAL(ac_compile); then
+    case "`/usr/bin/file conftest.o`" in
+    *32-bit*)
+      LD="${LD-ld} -32"
+      ;;
+    *N32*)
+      LD="${LD-ld} -n32"
+      ;;
+    *64-bit*)
+      LD="${LD-ld} -64"
+      ;;
+    esac
+  fi
+  rm -rf conftest*
+  ;;
+
+*-*-sco3.2v5*)
+  # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+  CFLAGS="$CFLAGS -belf"
+  ;;
+esac
+
+# Actually configure libtool.  ac_aux_dir is where install-sh is found.
+AR="$AR" CC="$CC" CFLAGS="$CFLAGS" CPPFLAGS="$CPPFLAGS" \
+LD="$LD" NM="$NM" RANLIB="$RANLIB" LN_S="$LN_S" \
+${CONFIG_SHELL-/bin/sh} $ac_aux_dir/ltconfig \
+$libtool_flags --no-verify $ac_aux_dir/ltmain.sh $host \
+|| AC_MSG_ERROR([libtool configure failed])
+])
+
+# AM_ENABLE_SHARED - implement the --enable-shared flag
+# Usage: AM_ENABLE_SHARED[(DEFAULT)]
+#   Where DEFAULT is either `yes' or `no'.  If omitted, it defaults to
+#   `yes'.
+AC_DEFUN(AM_ENABLE_SHARED,
+[define([AM_ENABLE_SHARED_DEFAULT], ifelse($1, no, no, yes))dnl
+AC_ARG_ENABLE(shared,
+changequote(<<, >>)dnl
+<<  --enable-shared         build shared libraries [default=>>AM_ENABLE_SHARED_DEFAULT]
+changequote([, ])dnl
+[  --enable-shared=PKGS    only build shared libraries if the current package
+                          appears as an element in the PKGS list],
+[p=${PACKAGE-default}
+case "$enableval" in
+yes) enable_shared=yes ;;
+no) enable_shared=no ;;
+*)
+  enable_shared=no
+  # Look at the argument we got.  We use all the common list separators.
+  IFS="${IFS= 	}"; ac_save_ifs="$IFS"; IFS="${IFS}:,"
+  for pkg in $enableval; do
+    if test "X$pkg" = "X$p"; then
+      enable_shared=yes
+    fi
+  done
+  IFS="$ac_save_ifs"
+  ;;
+esac],
+enable_shared=AM_ENABLE_SHARED_DEFAULT)dnl
+])
+
+# AM_DISABLE_SHARED - set the default shared flag to --disable-shared
+AC_DEFUN(AM_DISABLE_SHARED,
+[AM_ENABLE_SHARED(no)])
+
+# AM_DISABLE_STATIC - set the default static flag to --disable-static
+AC_DEFUN(AM_DISABLE_STATIC,
+[AM_ENABLE_STATIC(no)])
+
+# AM_ENABLE_STATIC - implement the --enable-static flag
+# Usage: AM_ENABLE_STATIC[(DEFAULT)]
+#   Where DEFAULT is either `yes' or `no'.  If omitted, it defaults to
+#   `yes'.
+AC_DEFUN(AM_ENABLE_STATIC,
+[define([AM_ENABLE_STATIC_DEFAULT], ifelse($1, no, no, yes))dnl
+AC_ARG_ENABLE(static,
+changequote(<<, >>)dnl
+<<  --enable-static         build static libraries [default=>>AM_ENABLE_STATIC_DEFAULT]
+changequote([, ])dnl
+[  --enable-static=PKGS    only build shared libraries if the current package
+                          appears as an element in the PKGS list],
+[p=${PACKAGE-default}
+case "$enableval" in
+yes) enable_static=yes ;;
+no) enable_static=no ;;
+*)
+  enable_static=no
+  # Look at the argument we got.  We use all the common list separators.
+  IFS="${IFS= 	}"; ac_save_ifs="$IFS"; IFS="${IFS}:,"
+  for pkg in $enableval; do
+    if test "X$pkg" = "X$p"; then
+      enable_static=yes
+    fi
+  done
+  IFS="$ac_save_ifs"
+  ;;
+esac],
+enable_static=AM_ENABLE_STATIC_DEFAULT)dnl
+])
+
+
+# AM_PROG_LD - find the path to the GNU or non-GNU linker
+AC_DEFUN(AM_PROG_LD,
+[AC_ARG_WITH(gnu-ld,
+[  --with-gnu-ld           assume the C compiler uses GNU ld [default=no]],
+test "$withval" = no || with_gnu_ld=yes, with_gnu_ld=no)
+AC_REQUIRE([AC_PROG_CC])
+ac_prog=ld
+if test "$ac_cv_prog_gcc" = yes; then
+  # Check if gcc -print-prog-name=ld gives a path.
+  AC_MSG_CHECKING([for ld used by GCC])
+  ac_prog=`($CC -print-prog-name=ld) 2>&5`
+  case "$ac_prog" in
+  # Accept absolute paths.
+  /* | [A-Za-z]:\\*)
+    test -z "$LD" && LD="$ac_prog"
+    ;;
+  "")
+    # If it fails, then pretend we aren't using GCC.
+    ac_prog=ld
+    ;;
+  *)
+    # If it is relative, then search for the first ld in PATH.
+    with_gnu_ld=unknown
+    ;;
+  esac
+elif test "$with_gnu_ld" = yes; then
+  AC_MSG_CHECKING([for GNU ld])
+else
+  AC_MSG_CHECKING([for non-GNU ld])
+fi
+AC_CACHE_VAL(ac_cv_path_LD,
+[if test -z "$LD"; then
+  IFS="${IFS= 	}"; ac_save_ifs="$IFS"; IFS="${IFS}:"
+  for ac_dir in $PATH; do
+    test -z "$ac_dir" && ac_dir=.
+    if test -f "$ac_dir/$ac_prog"; then
+      ac_cv_path_LD="$ac_dir/$ac_prog"
+      # Check to see if the program is GNU ld.  I'd rather use --version,
+      # but apparently some GNU ld's only accept -v.
+      # Break only if it was the GNU/non-GNU ld that we prefer.
+      if "$ac_cv_path_LD" -v 2>&1 < /dev/null | egrep '(GNU|with BFD)' > /dev/null; then
+	test "$with_gnu_ld" != no && break
+      else
+        test "$with_gnu_ld" != yes && break
+      fi
+    fi
+  done
+  IFS="$ac_save_ifs"
+else
+  ac_cv_path_LD="$LD" # Let the user override the test with a path.
+fi])
+LD="$ac_cv_path_LD"
+if test -n "$LD"; then
+  AC_MSG_RESULT($LD)
+else
+  AC_MSG_RESULT(no)
+fi
+test -z "$LD" && AC_MSG_ERROR([no acceptable ld found in \$PATH])
+AC_SUBST(LD)
+AM_PROG_LD_GNU
+])
+
+AC_DEFUN(AM_PROG_LD_GNU,
+[AC_CACHE_CHECK([if the linker ($LD) is GNU ld], ac_cv_prog_gnu_ld,
+[# I'd rather use --version here, but apparently some GNU ld's only accept -v.
+if $LD -v 2>&1 </dev/null | egrep '(GNU|with BFD)' 1>&5; then
+  ac_cv_prog_gnu_ld=yes
+else
+  ac_cv_prog_gnu_ld=no
+fi])
+])
+
+# AM_PROG_NM - find the path to a BSD-compatible name lister
+AC_DEFUN(AM_PROG_NM,
+[AC_MSG_CHECKING([for BSD-compatible nm])
+AC_CACHE_VAL(ac_cv_path_NM,
+[case "$NM" in
+/* | [A-Za-z]:\\*)
+  ac_cv_path_NM="$NM" # Let the user override the test with a path.
+  ;;
+*)
+  IFS="${IFS= 	}"; ac_save_ifs="$IFS"; IFS="${IFS}:"
+  for ac_dir in /usr/ucb /usr/ccs/bin $PATH /bin; do
+    test -z "$ac_dir" && ac_dir=.
+    if test -f $ac_dir/nm; then
+      # Check to see if the nm accepts a BSD-compat flag.
+      # Adding the `sed 1q' prevents false positives on HP-UX, which says:
+      #   nm: unknown option "B" ignored
+      if ($ac_dir/nm -B /dev/null 2>&1 | sed '1q'; exit 0) | egrep /dev/null >/dev/null; then
+        ac_cv_path_NM="$ac_dir/nm -B"
+      elif ($ac_dir/nm -p /dev/null 2>&1 | sed '1q'; exit 0) | egrep /dev/null >/dev/null; then
+        ac_cv_path_NM="$ac_dir/nm -p"
+      else
+        ac_cv_path_NM="$ac_dir/nm"
+      fi
+      break
+    fi
+  done
+  IFS="$ac_save_ifs"
+  test -z "$ac_cv_path_NM" && ac_cv_path_NM=nm
+  ;;
+esac])
+NM="$ac_cv_path_NM"
+AC_MSG_RESULT([$NM])
+AC_SUBST(NM)
+])

bin/checkapi

@@ -0,0 +1,35 @@
+#!/usr/bin/perl -w
+require 5.003;
+
+# Purpose: insures that API functions aren't called internally.
+# Usage:   checkapi H5*.c
+my $comment = 0;
+while (<>) {
+
+  # Remove comments within the line.
+  s/\/\*.*?\*\///g;
+
+  # Process comment begin and end tokens on this line.
+  $comment-- if /\*\//;		# count comment ends
+  next if $comment;		# skip line if in comment
+  $comment++ if /\/\*/;		# count comment starts
+  s/(.*)\/\*.*/$1/;		# remove comments that begin on this line
+
+  # Remove character strings
+  s/\\.//g;			# remove escaped characters
+  s/\".*?\"//g;			# remove string constants
+
+  # Disregard the following hits
+  next if /^H5/;
+  next if /^\#/;
+  next if /FUNC_ENTER/;
+
+  next unless /(H5[A-Z]{1,2}[a-z]\w*)/;
+  print "$ARGV:$.: $1\n";
+} continue {
+  if (eof) {
+    print "$ARGV:$.: bad comment nesting\n" if $comment;
+    $comment = 0;
+    close ARGV;		# reset line number
+  }
+}

bin/checkposix

@@ -35,6 +35,8 @@ while (<>) {
    # Get rid of string constants if they begin and end on this line.
    s/([\'\"])([^\1]|\\\1)*?\1/$1$1/g;
 
+   # Get rid of preprocessor directives
+   s/^\#.*//;
 
    # Now find all function calls on this line
    while (($name)=/\b([a-gi-z_A-GI-Z]\w*)\s*\(/) {
@@ -44,14 +46,19 @@ while (<>) {
       # calls.
       next if $name =~ /^(if|for|return|sizeof|switch|while|void)$/;
 
+      # Ignore things that get misdetected because of the simplified
+      # parsing that takes place here.
+      next if $name =~ /^int$/;
+
       # These are really HDF5 functions/macros even though they don't
       # start with `h' or `H'.
       next if $name =~ /^FUNC_(ENTER|LEAVE)(_INIT)?$/;
       next if $name =~ /^U?INT(8|16|32|64)(ENCODE|DECODE)$/;
-      next if $name =~ /^(MIN|MAX3?|NELMTS|BOUND|CONSTR)$/;
+      next if $name =~ /^(MIN3?|MAX3?|NELMTS|BOUND|CONSTR)$/;
+      next if $name =~ /^addr_defined$/;
 
       # These functions/macros are exempt.
-      next if $name =~ /^(assert|main|[fs]?printf)$/;
+      next if $name =~ /^(assert|main|[fs]?printf|va_(start|arg|end))$/;
 
       print "$ARGV:$.: $name\n";
    }

bin/config.guess

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Attempt to guess a canonical system name.
-#   Copyright (C) 1992, 1993, 1994, 1995 Free Software Foundation, Inc.
+#   Copyright (C) 1992, 93, 94, 95, 96, 1997 Free Software Foundation, Inc.
 #
 # This file is free software; you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by
@@ -51,35 +51,110 @@ trap 'rm -f dummy.c dummy.o dummy; exit 1' 1 2 15
 # Note: order is significant - the case branches are not exclusive.
 
 case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
-    alpha:OSF1:V*:*)
-	# After 1.2, OSF1 uses "V1.3" for uname -r.
-	echo alpha-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^V//'`
-	exit 0 ;;
     alpha:OSF1:*:*)
+	if test $UNAME_RELEASE = "V4.0"; then
+		UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
+	fi
+	# A Vn.n version is a released version.
+	# A Tn.n version is a released field test version.
+	# A Xn.n version is an unreleased experimental baselevel.
 	# 1.2 uses "1.2" for uname -r.
-	echo alpha-dec-osf${UNAME_RELEASE}
-        exit 0 ;;
+	cat <<EOF >dummy.s
+	.globl main
+	.ent main
+main:
+	.frame \$30,0,\$26,0
+	.prologue 0
+	.long 0x47e03d80 # implver $0
+	lda \$2,259
+	.long 0x47e20c21 # amask $2,$1
+	srl \$1,8,\$2
+	sll \$2,2,\$2
+	sll \$0,3,\$0
+	addl \$1,\$0,\$0
+	addl \$2,\$0,\$0
+	ret \$31,(\$26),1
+	.end main
+EOF
+	${CC-cc} dummy.s -o dummy 2>/dev/null
+	if test "$?" = 0 ; then
+		./dummy
+		case "$?" in
+			7)
+				UNAME_MACHINE="alpha"
+				;;
+			15)
+				UNAME_MACHINE="alphaev5"
+				;;
+			14)
+				UNAME_MACHINE="alphaev56"
+				;;
+			10)
+				UNAME_MACHINE="alphapca56"
+				;;
+			16)
+				UNAME_MACHINE="alphaev6"
+				;;
+		esac
+	fi
+	rm -f dummy.s dummy
+	echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[VTX]//' | tr [[A-Z]] [[a-z]]`
+	exit 0 ;;
     21064:Windows_NT:50:3)
 	echo alpha-dec-winnt3.5
 	exit 0 ;;
+    Amiga*:UNIX_System_V:4.0:*)
+	echo m68k-cbm-sysv4
+	exit 0;;
     amiga:NetBSD:*:*)
       echo m68k-cbm-netbsd${UNAME_RELEASE}
       exit 0 ;;
+    amiga:OpenBSD:*:*)
+	echo m68k-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
+    arc64:OpenBSD:*:*)
+	echo mips64el-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
+    arc:OpenBSD:*:*)
+	echo mipsel-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
+    hkmips:OpenBSD:*:*)
+	echo mips-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
+    pmax:OpenBSD:*:*)
+	echo mipsel-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
+    sgi:OpenBSD:*:*)
+	echo mips-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
+    wgrisc:OpenBSD:*:*)
+	echo mipsel-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
     arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
 	echo arm-acorn-riscix${UNAME_RELEASE}
 	exit 0;;
-    Pyramid*:OSx*:*:*)
+    arm32:NetBSD:*:*)
+	echo arm-unknown-netbsd`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
+	exit 0 ;;
+    SR2?01:HI-UX/MPP:*:*)
+	echo hppa1.1-hitachi-hiuxmpp
+	exit 0;;
+    Pyramid*:OSx*:*:*|MIS*:OSx*:*:*)
+	# akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
 	if test "`(/bin/universe) 2>/dev/null`" = att ; then
 		echo pyramid-pyramid-sysv3
 	else
 		echo pyramid-pyramid-bsd
 	fi
 	exit 0 ;;
-    sun4*:SunOS:5.*:*)
+    NILE:*:*:dcosx)
+	echo pyramid-pyramid-svr4
+	exit 0 ;;
+    sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
 	echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
 	exit 0 ;;
     i86pc:SunOS:5.*:*)
-	echo i386-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+	echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
 	exit 0 ;;
     sun4*:SunOS:6*:*)
 	# According to config.sub, this is the proper way to canonicalize
@@ -99,27 +174,86 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
     sun3*:SunOS:*:*)
 	echo m68k-sun-sunos${UNAME_RELEASE}
 	exit 0 ;;
+    sun*:*:4.2BSD:*)
+	UNAME_RELEASE=`(head -1 /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
+	test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
+	case "`/bin/arch`" in
+	    sun3)
+		echo m68k-sun-sunos${UNAME_RELEASE}
+		;;
+	    sun4)
+		echo sparc-sun-sunos${UNAME_RELEASE}
+		;;
+	esac
+	exit 0 ;;
+    aushp:SunOS:*:*)
+	echo sparc-auspex-sunos${UNAME_RELEASE}
+	exit 0 ;;
     atari*:NetBSD:*:*)
 	echo m68k-atari-netbsd${UNAME_RELEASE}
 	exit 0 ;;
+    atari*:OpenBSD:*:*)
+	echo m68k-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
     sun3*:NetBSD:*:*)
 	echo m68k-sun-netbsd${UNAME_RELEASE}
 	exit 0 ;;
+    sun3*:OpenBSD:*:*)
+	echo m68k-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
     mac68k:NetBSD:*:*)
 	echo m68k-apple-netbsd${UNAME_RELEASE}
 	exit 0 ;;
+    mac68k:OpenBSD:*:*)
+	echo m68k-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
+    mvme68k:OpenBSD:*:*)
+	echo m68k-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
+    mvme88k:OpenBSD:*:*)
+	echo m88k-unknown-openbsd${UNAME_RELEASE}
+	exit 0 ;;
+    powerpc:machten:*:*)
+	echo powerpc-apple-machten${UNAME_RELEASE}
+	exit 0 ;;
+    RISC*:Mach:*:*)
+	echo mips-dec-mach_bsd4.3
+	exit 0 ;;
     RISC*:ULTRIX:*:*)
 	echo mips-dec-ultrix${UNAME_RELEASE}
 	exit 0 ;;
     VAX*:ULTRIX*:*:*)
 	echo vax-dec-ultrix${UNAME_RELEASE}
 	exit 0 ;;
-    mips:*:4*:UMIPS)
-	echo mips-mips-riscos4sysv
+    2020:CLIX:*:*)
+	echo clipper-intergraph-clix${UNAME_RELEASE}
 	exit 0 ;;
-    mips:*:5*:RISCos)
+    mips:*:*:UMIPS | mips:*:*:RISCos)
+	sed 's/^	//' << EOF >dummy.c
+	int main (argc, argv) int argc; char **argv; {
+	#if defined (host_mips) && defined (MIPSEB)
+	#if defined (SYSTYPE_SYSV)
+	  printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
+	#endif
+	#if defined (SYSTYPE_SVR4)
+	  printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
+	#endif
+	#if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
+	  printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
+	#endif
+	#endif
+	  exit (-1);
+	}
+EOF
+	${CC-cc} dummy.c -o dummy \
+	  && ./dummy `echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` \
+	  && rm dummy.c dummy && exit 0
+	rm -f dummy.c dummy
 	echo mips-mips-riscos${UNAME_RELEASE}
 	exit 0 ;;
+    Night_Hawk:Power_UNIX:*:*)
+	echo powerpc-harris-powerunix
+	exit 0 ;;
     m88k:CX/UX:7*:*)
 	echo m88k-harris-cxux7
 	exit 0 ;;
@@ -130,12 +264,17 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
 	echo m88k-motorola-sysv3
 	exit 0 ;;
     AViiON:dgux:*:*)
+        # DG/UX returns AViiON for all architectures
+        UNAME_PROCESSOR=`/usr/bin/uname -p`
+        if [ $UNAME_PROCESSOR = mc88100 -o $UNAME_PROCESSOR = mc88110 ] ; then
 	if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx \
 	     -o ${TARGET_BINARY_INTERFACE}x = x ] ; then
 		echo m88k-dg-dgux${UNAME_RELEASE}
 	else
 		echo m88k-dg-dguxbcs${UNAME_RELEASE}
 	fi
+        else echo i586-dg-dgux${UNAME_RELEASE}
+        fi
  	exit 0 ;;
     M88*:DolphinOS:*:*)	# DolphinOS (SVR3)
 	echo m88k-dolphin-sysv3
@@ -150,16 +289,13 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
     Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
 	echo m68k-tektronix-bsd
 	exit 0 ;;
-    *:IRIX64:*:*)
-	echo mips-sgi-irix64
-	exit 0 ;;
     *:IRIX*:*:*)
 	echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
 	exit 0 ;;
-   ????????:AIX?:[12].1:2)   # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
+    ????????:AIX?:[12].1:2)   # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
 	echo romp-ibm-aix      # uname -m gives an 8 hex-code CPU id
 	exit 0 ;;              # Note that: echo "'`uname -s`'" gives 'AIX '
-    i[34]86:AIX:*:*)
+    i?86:AIX:*:*)
 	echo i386-ibm-aix
 	exit 0 ;;
     *:AIX:2:3)
@@ -204,7 +340,7 @@ EOF
 	echo romp-ibm-bsd4.4
 	exit 0 ;;
     ibmrt:*BSD:*|romp-ibm:BSD:*)            # covers RT/PC NetBSD and
-	echo romp-ibm-bsd${UNAME_RELEASE}   # 4.3 with uname added to 
+	echo romp-ibm-bsd${UNAME_RELEASE}   # 4.3 with uname added to
 	exit 0 ;;                           # report: romp-ibm BSD 4.3
     *:BOSX:*:*)
 	echo rs6000-bull-bosx
@@ -222,7 +358,7 @@ EOF
 	case "${UNAME_MACHINE}" in
 	    9000/31? )            HP_ARCH=m68000 ;;
 	    9000/[34]?? )         HP_ARCH=m68k ;;
-	    9000/7?? | 9000/8?[79] ) HP_ARCH=hppa1.1 ;;
+	    9000/7?? | 9000/8?[1679] ) HP_ARCH=hppa1.1 ;;
 	    9000/8?? )            HP_ARCH=hppa1.0 ;;
 	esac
 	HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
@@ -270,6 +406,13 @@ EOF
     hp8??:OSF1:*:*)
 	echo hppa1.0-hp-osf
 	exit 0 ;;
+    i?86:OSF1:*:*)
+	if [ -x /usr/sbin/sysversion ] ; then
+	    echo ${UNAME_MACHINE}-unknown-osf1mk
+	else
+	    echo ${UNAME_MACHINE}-unknown-osf1
+	fi
+	exit 0 ;;
     parisc*:Lites*:*:*)
 	echo hppa1.1-hp-lites
 	exit 0 ;;
@@ -297,20 +440,36 @@ EOF
     CRAY*Y-MP:*:*:*)
 	echo ymp-cray-unicos${UNAME_RELEASE}
 	exit 0 ;;
-    CRAY*C90:*:*:*)
-	echo c90-cray-unicos${UNAME_RELEASE}
+    CRAY*[A-Z]90:*:*:*)
+	echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
+	| sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
+	      -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/
 	exit 0 ;;
+    CRAY*TS:*:*:*)
+	echo t90-cray-unicos${UNAME_RELEASE}
+	exit 0 ;;
+    CRAY*T3E:*:*:*)
+        echo t3e-cray-unicosmk
+        exit 0 ;;
     CRAY-2:*:*:*)
 	echo cray2-cray-unicos
         exit 0 ;;
+    F300:UNIX_System_V:*:*)
+        FUJITSU_SYS=`uname -p | tr [A-Z] [a-z] | sed -e 's/\///'`
+        FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+        echo "f300-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+        exit 0 ;;
+    F301:UNIX_System_V:*:*)
+       echo f301-fujitsu-uxpv`echo $UNAME_RELEASE | sed 's/ .*//'`
+       exit 0 ;;
     hp3[0-9][05]:NetBSD:*:*)
 	echo m68k-hp-netbsd${UNAME_RELEASE}
 	exit 0 ;;
-    i[3456]86:Paragon*:*:*)
-	echo ${UNAME_MACHINE}-intel-osf1
+    hp300:OpenBSD:*:*)
+	echo m68k-unknown-openbsd${UNAME_RELEASE}
 	exit 0 ;;
-    i[34]86:BSD/386:*:* | *:BSD/OS:*:*)
-	echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
+    i?86:BSD/386:*:* | *:BSD/OS:*:*)
+	echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
 	exit 0 ;;
     *:FreeBSD:*:*)
 	echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
@@ -318,36 +477,143 @@ EOF
     *:NetBSD:*:*)
 	echo ${UNAME_MACHINE}-unknown-netbsd`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
 	exit 0 ;;
+    *:OpenBSD:*:*)
+	echo ${UNAME_MACHINE}-unknown-openbsd`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
+	exit 0 ;;
+    i*:CYGWIN*:*)
+	echo i386-pc-cygwin32
+	exit 0 ;;
+    i*:MINGW*:*)
+	echo i386-pc-mingw32
+	exit 0 ;;
+    p*:CYGWIN*:*)
+	echo powerpcle-unknown-cygwin32
+	exit 0 ;;
+    prep*:SunOS:5.*:*)
+	echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+	exit 0 ;;
     *:GNU:*:*)
-	echo `echo ${UNAME_MACHINE}|sed -e 's,/.*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+	echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
 	exit 0 ;;
     *:Linux:*:*)
 	# The BFD linker knows what the default object file format is, so
 	# first see if it will tell us.
 	ld_help_string=`ld --help 2>&1`
-	if echo $ld_help_string | grep >/dev/null 2>&1 "supported emulations: elf_i[345]86"; then
-	  echo "${UNAME_MACHINE}-unknown-linux" ; exit 0
-	elif echo $ld_help_string | grep >/dev/null 2>&1 "supported emulations: i[345]86linux"; then
-	  echo "${UNAME_MACHINE}-unknown-linuxaout" ; exit 0
-	elif echo $ld_help_string | grep >/dev/null 2>&1 "supported emulations: i[345]86coff"; then
-	  echo "${UNAME_MACHINE}-unknown-linuxcoff" ; exit 0
-	elif test "${UNAME_MACHINE}" = "alpha" ; then
-	  echo alpha-unknown-linux ; exit 0
-	else
-	  # Either a pre-BFD a.out linker (linuxoldld) or one that does not give us
-	  # useful --help.  Gcc wants to distinguish between linuxoldld and linuxaout.
-	  test ! -d /usr/lib/ldscripts/. \
-	    && echo "${UNAME_MACHINE}-unknown-linuxoldld" && exit 0
-	  # Determine whether the default compiler is a.out or elf
+	ld_supported_emulations=`echo $ld_help_string \
+			 | sed -ne '/supported emulations:/!d
+				    s/[ 	][ 	]*/ /g
+				    s/.*supported emulations: *//
+				    s/ .*//
+				    p'`
+        case "$ld_supported_emulations" in
+	  i?86linux)  echo "${UNAME_MACHINE}-pc-linux-gnuaout"      ; exit 0 ;;
+	  i?86coff)   echo "${UNAME_MACHINE}-pc-linux-gnucoff"      ; exit 0 ;;
+	  sparclinux) echo "${UNAME_MACHINE}-unknown-linux-gnuaout" ; exit 0 ;;
+	  m68klinux)  echo "${UNAME_MACHINE}-unknown-linux-gnuaout" ; exit 0 ;;
+	  elf32ppc)   echo "powerpc-unknown-linux-gnu"              ; exit 0 ;;
+	esac
+
+	if test "${UNAME_MACHINE}" = "alpha" ; then
+		sed 's/^	//'  <<EOF >dummy.s
+		.globl main
+		.ent main
+	main:
+		.frame \$30,0,\$26,0
+		.prologue 0
+		.long 0x47e03d80 # implver $0
+		lda \$2,259
+		.long 0x47e20c21 # amask $2,$1
+		srl \$1,8,\$2
+		sll \$2,2,\$2
+		sll \$0,3,\$0
+		addl \$1,\$0,\$0
+		addl \$2,\$0,\$0
+		ret \$31,(\$26),1
+		.end main
+EOF
+		LIBC=""
+		${CC-cc} dummy.s -o dummy 2>/dev/null
+		if test "$?" = 0 ; then
+			./dummy
+			case "$?" in
+			7)
+				UNAME_MACHINE="alpha"
+				;;
+			15)
+				UNAME_MACHINE="alphaev5"
+				;;
+			14)
+				UNAME_MACHINE="alphaev56"
+				;;
+			10)
+				UNAME_MACHINE="alphapca56"
+				;;
+			16)
+				UNAME_MACHINE="alphaev6"
+				;;
+			esac	
+
+			objdump --private-headers dummy | \
+			  grep ld.so.1 > /dev/null
+			if test "$?" = 0 ; then
+				LIBC="libc1"
+			fi
+		fi	
+		rm -f dummy.s dummy
+		echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} ; exit 0
+	elif test "${UNAME_MACHINE}" = "mips" ; then
 	  cat >dummy.c <<EOF
 main(argc, argv)
-int argc;
-char *argv[];
+     int argc;
+     char *argv[];
+{
+#ifdef __MIPSEB__
+  printf ("%s-unknown-linux-gnu\n", argv[1]);
+#endif
+#ifdef __MIPSEL__
+  printf ("%sel-unknown-linux-gnu\n", argv[1]);
+#endif
+  return 0;
+}
+EOF
+	  ${CC-cc} dummy.c -o dummy 2>/dev/null && ./dummy "${UNAME_MACHINE}" && rm dummy.c dummy && exit 0
+	  rm -f dummy.c dummy
+	else
+	  # Either a pre-BFD a.out linker (linux-gnuoldld)
+	  # or one that does not give us useful --help.
+	  # GCC wants to distinguish between linux-gnuoldld and linux-gnuaout.
+	  # If ld does not provide *any* "supported emulations:"
+	  # that means it is gnuoldld.
+	  echo "$ld_help_string" | grep >/dev/null 2>&1 "supported emulations:"
+	  test $? != 0 && echo "${UNAME_MACHINE}-pc-linux-gnuoldld" && exit 0
+
+	  case "${UNAME_MACHINE}" in
+	  i?86)
+	    VENDOR=pc;
+	    ;;
+	  *)
+	    VENDOR=unknown;
+	    ;;
+	  esac
+	  # Determine whether the default compiler is a.out or elf
+	  cat >dummy.c <<EOF
+#include <features.h>
+main(argc, argv)
+     int argc;
+     char *argv[];
 {
 #ifdef __ELF__
-  printf ("%s-unknown-linux\n", argv[1]);
+# ifdef __GLIBC__
+#  if __GLIBC__ >= 2
+    printf ("%s-${VENDOR}-linux-gnu\n", argv[1]);
+#  else
+    printf ("%s-${VENDOR}-linux-gnulibc1\n", argv[1]);
+#  endif
+# else
+   printf ("%s-${VENDOR}-linux-gnulibc1\n", argv[1]);
+# endif
 #else
-  printf ("%s-unknown-linuxaout\n", argv[1]);
+  printf ("%s-${VENDOR}-linux-gnuaout\n", argv[1]);
 #endif
   return 0;
 }
@@ -357,30 +623,45 @@ EOF
 	fi ;;
 # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.  earlier versions
 # are messed up and put the nodename in both sysname and nodename.
-    i[34]86:DYNIX/ptx:4*:*)
+    i?86:DYNIX/ptx:4*:*)
 	echo i386-sequent-sysv4
 	exit 0 ;;
-    i[34]86:*:4.*:* | i[34]86:SYSTEM_V:4.*:*)
+    i?86:UNIX_SV:4.2MP:2.*)
+        # Unixware is an offshoot of SVR4, but it has its own version
+        # number series starting with 2...
+        # I am not positive that other SVR4 systems won't match this,
+	# I just have to hope.  -- rms.
+        # Use sysv4.2uw... so that sysv4* matches it.
+	echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
+	exit 0 ;;
+    i?86:*:4.*:* | i?86:SYSTEM_V:4.*:*)
 	if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
 		echo ${UNAME_MACHINE}-univel-sysv${UNAME_RELEASE}
 	else
-		echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}
+		echo ${UNAME_MACHINE}-pc-sysv${UNAME_RELEASE}
 	fi
 	exit 0 ;;
-    i[34]86:*:3.2:*)
+    i?86:*:3.2:*)
 	if test -f /usr/options/cb.name; then
 		UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
-		echo ${UNAME_MACHINE}-unknown-isc$UNAME_REL
+		echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
 	elif /bin/uname -X 2>/dev/null >/dev/null ; then
 		UNAME_REL=`(/bin/uname -X|egrep Release|sed -e 's/.*= //')`
 		(/bin/uname -X|egrep i80486 >/dev/null) && UNAME_MACHINE=i486
-		echo ${UNAME_MACHINE}-unknown-sco$UNAME_REL
+		(/bin/uname -X|egrep '^Machine.*Pentium' >/dev/null) \
+			&& UNAME_MACHINE=i586
+		echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
 	else
-		echo ${UNAME_MACHINE}-unknown-sysv32
+		echo ${UNAME_MACHINE}-pc-sysv32
 	fi
 	exit 0 ;;
+    pc:*:*:*)
+        # uname -m prints for DJGPP always 'pc', but it prints nothing about
+        # the processor, so we play safe by assuming i386.
+	echo i386-pc-msdosdjgpp
+        exit 0 ;;
     Intel:Mach:3*:*)
-	echo i386-unknown-mach3
+	echo i386-pc-mach3
 	exit 0 ;;
     paragon:*:*:*)
 	echo i860-intel-osf1
@@ -396,28 +677,36 @@ EOF
 	# "miniframe"
 	echo m68010-convergent-sysv
 	exit 0 ;;
-    M680[234]0:*:R3V[567]*:*)
+    M68*:*:R3V[567]*:*)
 	test -r /sysV68 && echo 'm68k-motorola-sysv' && exit 0 ;;
-    3[34]??:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0)
-        uname -p 2>/dev/null | grep 86 >/dev/null \
-          && echo i486-ncr-sysv4.3 && exit 0 ;;
+    3[34]??:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 4850:*:4.0:3.0)
+	OS_REL=''
+	test -r /etc/.relid \
+	&& OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+	/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+	  && echo i486-ncr-sysv4.3${OS_REL} && exit 0
+	/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+	  && echo i586-ncr-sysv4.3${OS_REL} && exit 0 ;;
     3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
-        uname -p 2>/dev/null | grep 86 >/dev/null \
+        /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
           && echo i486-ncr-sysv4 && exit 0 ;;
-    m680[234]0:LynxOS:2.[23]*:*)
-	echo m68k-lynx-lynxos${UNAME_RELEASE}
+    m68*:LynxOS:2.*:*)
+	echo m68k-unknown-lynxos${UNAME_RELEASE}
 	exit 0 ;;
     mc68030:UNIX_System_V:4.*:*)
 	echo m68k-atari-sysv4
 	exit 0 ;;
-    i[34]86:LynxOS:2.[23]*:*)
-	echo i386-lynx-lynxos${UNAME_RELEASE}
+    i?86:LynxOS:2.*:*)
+	echo i386-unknown-lynxos${UNAME_RELEASE}
 	exit 0 ;;
-    TSUNAMI:LynxOS:2.[23]*:*)
-	echo sparc-lynx-lynxos${UNAME_RELEASE}
+    TSUNAMI:LynxOS:2.*:*)
+	echo sparc-unknown-lynxos${UNAME_RELEASE}
 	exit 0 ;;
-    rs6000:LynxOS:2.[23]*:*)
-	echo rs6000-lynx-lynxos${UNAME_RELEASE}
+    rs6000:LynxOS:2.*:* | PowerPC:LynxOS:2.*:*)
+	echo rs6000-unknown-lynxos${UNAME_RELEASE}
+	exit 0 ;;
+    SM[BE]S:UNIX_SV:*:*)
+	echo mips-dde-sysv${UNAME_RELEASE}
 	exit 0 ;;
     RM*:SINIX-*:*:*)
 	echo mips-sni-sysv4
@@ -430,6 +719,32 @@ EOF
 		echo ns32k-sni-sysv
 	fi
 	exit 0 ;;
+    PENTIUM:CPunix:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+                           # says <Richard.M.Bartel@ccMail.Census.GOV>
+        echo i586-unisys-sysv4
+        exit 0 ;;
+    *:UNIX_System_V:4*:FTX*)
+	# From Gerald Hewes <hewes@openmarket.com>.
+	# How about differentiating between stratus architectures? -djm
+	echo hppa1.1-stratus-sysv4
+	exit 0 ;;
+    *:*:*:FTX*)
+	# From seanf@swdc.stratus.com.
+	echo i860-stratus-sysv4
+	exit 0 ;;
+    mc68*:A/UX:*:*)
+	echo m68k-apple-aux${UNAME_RELEASE}
+	exit 0 ;;
+    news*:NEWS-OS:*:6*)
+	echo mips-sony-newsos6
+	exit 0 ;;
+    R3000:*System_V*:*:* | R4000:UNIX_SYSV:*:*)
+	if [ -d /usr/nec ]; then
+	        echo mips-nec-sysv${UNAME_RELEASE}
+	else
+	        echo mips-unknown-sysv${UNAME_RELEASE}
+	fi
+        exit 0 ;;
 esac
 
 #echo '(No uname command or uname output not recognized.)' 1>&2
@@ -473,7 +788,7 @@ main ()
 #endif
   int version;
   version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
-  printf ("%s-next-nextstep%s\n", __ARCHITECTURE__,  version==2 ? "2" : "3");
+  printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
   exit (0);
 #endif
 
@@ -490,7 +805,7 @@ main ()
 #endif
 
 #if defined (__386BSD__)
-  printf ("i386-unknown-bsd\n"); exit (0);
+  printf ("i386-pc-bsd\n"); exit (0);
 #endif
 
 #if defined (sequent)

bin/config.sub

@@ -1,9 +1,9 @@
 #! /bin/sh
 # Configuration validation subroutine script, version 1.1.
-#   Copyright (C) 1991, 1992, 1993, 1994, 1995 Free Software Foundation, Inc.
+#   Copyright (C) 1991, 92, 93, 94, 95, 96, 1997 Free Software Foundation, Inc.
 # This file is (in principle) common to ALL GNU software.
 # The presence of a machine in this file suggests that SOME GNU software
-# can handle that machine.  It does not imply ALL GNU software can. 
+# can handle that machine.  It does not imply ALL GNU software can.
 #
 # This file is free software; you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -41,10 +41,9 @@
 # The goal of this file is to map all the various variations of a given
 # machine specification into a single specification in the form:
 #	CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
+# or in some cases, the newer four-part form:
+#	CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
 # It is wrong to echo any other type of specification.
-#
-# Robb Matzke, 24 Sep 1997
-# Changed i[345]86 to i[3456]86 so pentium pro processors are recognized.
 
 if [ x$1 = x ]
 then
@@ -65,11 +64,21 @@ case $1 in
 	;;
 esac
 
-# Separate what the user gave into CPU-COMPANY and OS (if any).
-basic_machine=`echo $1 | sed 's/-[^-]*$//'`
-if [ $basic_machine != $1 ]
-then os=`echo $1 | sed 's/.*-/-/'`
-else os=; fi
+# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
+# Here we must recognize all the valid KERNEL-OS combinations.
+maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
+case $maybe_os in
+  linux-gnu*)
+    os=-$maybe_os
+    basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
+    ;;
+  *)
+    basic_machine=`echo $1 | sed 's/-[^-]*$//'`
+    if [ $basic_machine != $1 ]
+    then os=`echo $1 | sed 's/.*-/-/'`
+    else os=; fi
+    ;;
+esac
 
 ### Let's recognize common machines as not being operating systems so
 ### that things like config.sub decstation-3100 work.  We also
@@ -84,38 +93,43 @@ case $os in
 	-unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
 	-convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
 	-c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
-	-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp )
+	-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
+	-apple)
 		os=
 		basic_machine=$1
 		;;
 	-hiux*)
 		os=-hiuxwe2
 		;;
+	-sco5)
+		os=sco3.2v5
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+		;;
 	-sco4)
 		os=-sco3.2v4
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-unknown/'`
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
 		;;
 	-sco3.2.[4-9]*)
 		os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-unknown/'`
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
 		;;
 	-sco3.2v[4-9]*)
 		# Don't forget version if it is 3.2v4 or newer.
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-unknown/'`
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
 		;;
 	-sco*)
 		os=-sco3.2v2
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-unknown/'`
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
 		;;
 	-isc)
 		os=-isc2.2
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-unknown/'`
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
 		;;
 	-clix*)
 		basic_machine=clipper-intergraph
 		;;
 	-isc*)
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-unknown/'`
+		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
 		;;
 	-lynx*)
 		os=-lynxos
@@ -126,35 +140,49 @@ case $os in
 	-windowsnt*)
 		os=`echo $os | sed -e 's/windowsnt/winnt/'`
 		;;
+	-psos*)
+		os=-psos
+		;;
 esac
 
 # Decode aliases for certain CPU-COMPANY combinations.
 case $basic_machine in
 	# Recognize the basic CPU types without company name.
 	# Some are omitted here because they have special meanings below.
-	tahoe | i[3456]86 | i860 | m68k | m68000 | m88k | ns32k | arm \
-		| arme[lb] | pyramid \
-		| tron | a29k | 580 | i960 | h8300 | hppa1.0 | hppa1.1 \
-		| alpha | we32k | ns16k | clipper | sparclite | i370 | sh \
-		| powerpc | powerpcle | sparc64 | 1750a | dsp16xx | mips64 | mipsel \
-		| pdp11 | mips64el | mips64orion | mips64orionel \
-		| sparc)
+	tahoe | i860 | m32r | m68k | m68000 | m88k | ns32k | arc | arm \
+		| arme[lb] | pyramid | mn10200 | mn10300 \
+		| tron | a29k | 580 | i960 | h8300 | hppa | hppa1.0 | hppa1.1 \
+		| alpha | alphaev5 | alphaev56 | we32k | ns16k | clipper \
+		| i370 | sh | powerpc | powerpcle | 1750a | dsp16xx | pdp11 \
+		| mips64 | mipsel | mips64el | mips64orion | mips64orionel \
+		| mipstx39 | mipstx39el \
+		| sparc | sparclet | sparclite | sparc64 | v850)
 		basic_machine=$basic_machine-unknown
 		;;
+	# We use `pc' rather than `unknown'
+	# because (1) that's what they normally are, and
+	# (2) the word "unknown" tends to confuse beginning users.
+	i[3456]86)
+	  basic_machine=$basic_machine-pc
+	  ;;
 	# Object if more than one company name word.
 	*-*-*)
 		echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
 		exit 1
 		;;
 	# Recognize the basic CPU types with company name.
-	vax-* | tahoe-* | i[3456]86-* | i860-* | m68k-* | m68000-* | m88k-* \
-	      | sparc-* | ns32k-* | fx80-* | arm-* | c[123]* \
-	      | mips-* | pyramid-* | tron-* | a29k-* | romp-* | rs6000-* | power-* \
-	      | none-* | 580-* | cray2-* | h8300-* | i960-* | xmp-* | ymp-* \
-	      | hppa1.0-* | hppa1.1-* | alpha-* | we32k-* | cydra-* | ns16k-* \
-	      | pn-* | np1-* | xps100-* | clipper-* | orion-* | sparclite-* \
-	      | pdp11-* | sh-* | powerpc-* | powerpcle-* | sparc64-* | mips64-* | mipsel-* \
-	      | mips64el-* | mips64orion-* | mips64orionel-*)
+	vax-* | tahoe-* | i[3456]86-* | i860-* | m32r-* | m68k-* | m68000-* \
+	      | m88k-* | sparc-* | ns32k-* | fx80-* | arc-* | arm-* | c[123]* \
+	      | mips-* | pyramid-* | tron-* | a29k-* | romp-* | rs6000-* \
+	      | power-* | none-* | 580-* | cray2-* | h8300-* | i960-* \
+	      | xmp-* | ymp-* | hppa-* | hppa1.0-* | hppa1.1-* \
+	      | alpha-* | alphaev5-* | alphaev56-* | we32k-* | cydra-* \
+	      | ns16k-* | pn-* | np1-* | xps100-* | clipper-* | orion-* \
+	      | sparclite-* | pdp11-* | sh-* | powerpc-* | powerpcle-* \
+	      | sparc64-* | mips64-* | mipsel-* \
+	      | mips64el-* | mips64orion-* | mips64orionel-*  \
+	      | mipstx39-* | mipstx39el-* \
+	      | f301-*)
 		;;
 	# Recognize the various machine names and aliases which stand
 	# for a CPU type and a company and sometimes even an OS.
@@ -181,9 +209,9 @@ case $basic_machine in
 	amiga | amiga-*)
 		basic_machine=m68k-cbm
 		;;
-	amigados)
+	amigaos | amigados)
 		basic_machine=m68k-cbm
-		os=-amigados
+		os=-amigaos
 		;;
 	amigaunix | amix)
 		basic_machine=m68k-cbm
@@ -193,6 +221,10 @@ case $basic_machine in
 		basic_machine=m68k-apollo
 		os=-sysv
 		;;
+	aux)
+		basic_machine=m68k-apple
+		os=-aux
+		;;
 	balance)
 		basic_machine=ns32k-sequent
 		os=-dynix
@@ -225,6 +257,14 @@ case $basic_machine in
 		basic_machine=cray2-cray
 		os=-unicos
 		;;
+        cray-t3e | t3e | t3e-cray)
+                basic_machine=t3e-cray
+                os=-unicosmk
+                ;;
+	[ctj]90-cray)
+		basic_machine=c90-cray
+		os=-unicos
+		;;
 	crds | unos)
 		basic_machine=m68k-crds
 		;;
@@ -306,25 +346,28 @@ case $basic_machine in
 	hp9k8[0-9][0-9] | hp8[0-9][0-9])
 		basic_machine=hppa1.0-hp
 		;;
+	hppa-next)
+		os=-nextstep3
+		;;
 	i370-ibm* | ibm*)
 		basic_machine=i370-ibm
 		os=-mvs
 		;;
 # I'm not sure what "Sysv32" means.  Should this be sysv3.2?
 	i[3456]86v32)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-unknown/'`
+		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
 		os=-sysv32
 		;;
 	i[3456]86v4*)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-unknown/'`
+		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
 		os=-sysv4
 		;;
 	i[3456]86v)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-unknown/'`
+		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
 		os=-sysv
 		;;
 	i[3456]86sol2)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-unknown/'`
+		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
 		os=-solaris2
 		;;
 	iris | iris4d)
@@ -355,6 +398,14 @@ case $basic_machine in
 	miniframe)
 		basic_machine=m68000-convergent
 		;;
+	mipsel*-linux*)
+		basic_machine=mipsel-unknown
+		os=-linux-gnu
+		;;
+	mips*-linux*)
+		basic_machine=mips-unknown
+		os=-linux-gnu
+		;;
 	mips3*-*)
 		basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
 		;;
@@ -413,10 +464,10 @@ case $basic_machine in
 		basic_machine=i860-intel
 		os=-osf
 		;;
-	janus | tflop)
-		basic_machine=i386-intel
-		os=-osf1
-		;;
+        tflop*)
+                basic_machine=i386-intel
+                os=-osf1
+                ;;
 	pbd)
 		basic_machine=sparc-tti
 		;;
@@ -426,14 +477,18 @@ case $basic_machine in
         pc532 | pc532-*)
 		basic_machine=ns32k-pc532
 		;;
-	pentium | p5 | p6)
-		# We don't have specific support for the Intel Pentium (p6) followon yet, so just call it a Pentium
+	pentium | p5)
 		basic_machine=i586-intel
 		;;
-	pentium-* | p5-* | p6-*)
-		# We don't have specific support for the Intel Pentium (p6) followon yet, so just call it a Pentium
+	pentiumpro | p6)
+		basic_machine=i686-intel
+		;;
+	pentium-* | p5-*)
 		basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
 		;;
+	pentiumpro-* | p6-*)
+		basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+		;;
 	k5)
 		# We don't have specific support for AMD's K5 yet, so just call it a Pentium
 		basic_machine=i586-amd
@@ -524,6 +579,12 @@ case $basic_machine in
 		basic_machine=i386-sequent
 		os=-dynix
 		;;
+	tx39)
+		basic_machine=mipstx39-unknown
+		;;
+	tx39el)
+		basic_machine=mipstx39el-unknown
+		;;
 	tower | tower-32)
 		basic_machine=m68k-ncr
 		;;
@@ -543,6 +604,9 @@ case $basic_machine in
 		basic_machine=vax-dec
 		os=-vms
 		;;
+	vpp*|vx|vx-*)
+               basic_machine=f301-fujitsu
+               ;;
 	vxworks960)
 		basic_machine=i960-wrs
 		os=-vxworks
@@ -570,7 +634,11 @@ case $basic_machine in
 # Here we handle the default manufacturer of certain CPU types.  It is in
 # some cases the only manufacturer, in others, it is the most popular.
 	mips)
-		basic_machine=mips-mips
+		if [ x$os = x-linux-gnu ]; then
+			basic_machine=mips-unknown
+		else
+			basic_machine=mips-mips
+		fi
 		;;
 	romp)
 		basic_machine=romp-ibm
@@ -622,6 +690,8 @@ esac
 if [ x"$os" != x"" ]
 then
 case $os in
+        # First match some system type aliases
+        # that might get confused with valid system types.
 	# -solaris* is a basic system type, with this one exception.
 	-solaris1 | -solaris1.*)
 		os=`echo $os | sed -e 's|solaris1|sunos4|'`
@@ -629,28 +699,37 @@ case $os in
 	-solaris)
 		os=-solaris2
 		;;
-	-unixware* | svr4*)
+	-svr4*)
 		os=-sysv4
 		;;
+	-unixware*)
+		os=-sysv4.2uw
+		;;
 	-gnu/linux*)
-		os=`echo $os | sed -e 's|gnu/linux|linux|'`
+		os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
 		;;
 	# First accept the basic system types.
 	# The portable systems comes first.
 	# Each alternative MUST END IN A *, to match a version number.
 	# -sysv* is not here because it comes later, after sysvr4.
 	-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
-	      | -vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[345]* \
+	      | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\
 	      | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
-	      | -amigados* | -msdos* | -newsos* | -unicos* | -aos* \
-	      | -nindy* | -vxworks* | -ebmon* | -hms* | -mvs* | -clix* \
-	      | -riscos* | -linux* | -uniplus* | -iris* | -rtu* | -xenix* \
-	      | -hiux* | -386bsd* | -netbsd* | -freebsd* | -riscix* \
+	      | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
+	      | -aos* \
+	      | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
+	      | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
+	      | -hiux* | -386bsd* | -netbsd* | -openbsd* | -freebsd* | -riscix* \
 	      | -lynxos* | -bosx* | -nextstep* | -cxux* | -aout* | -elf* \
 	      | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
-	      | -udi* | -eabi* | -lites* )
+	      | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
+	      | -cygwin32* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+	      | -mingw32* | -linux-gnu* | -uxpv*)
 	# Remember, each alternative MUST END IN *, to match a version number.
 		;;
+	-linux*)
+		os=`echo $os | sed -e 's|linux|linux-gnu|'`
+		;;
 	-sunos5*)
 		os=`echo $os | sed -e 's|sunos5|solaris2|'`
 		;;
@@ -675,6 +754,9 @@ case $os in
 	-ctix* | -uts*)
 		os=-sysv
 		;;
+	-ns2 )
+	        os=-nextstep2
+		;;
 	# Preserve the version number of sinix5.
 	-sinix5.*)
 		os=`echo $os | sed -e 's|sinix|sysv|'`
@@ -768,7 +850,7 @@ case $basic_machine in
 		os=-sysv
 		;;
 	*-cbm)
-		os=-amigados
+		os=-amigaos
 		;;
 	*-dg)
 		os=-dgux
@@ -782,6 +864,9 @@ case $basic_machine in
 	m88k-omron*)
 		os=-luna
 		;;
+	*-next )
+		os=-nextstep
+		;;
 	*-sequent)
 		os=-ptx
 		;;
@@ -815,6 +900,9 @@ case $basic_machine in
 	*-masscomp)
 		os=-rtu
 		;;
+	f301-fujitsu)
+		os=-uxpv
+		;;
 	*)
 		os=-none
 		;;
@@ -833,9 +921,6 @@ case $basic_machine in
 			-sunos*)
 				vendor=sun
 				;;
-			-lynxos*)
-				vendor=lynx
-				;;
 			-aix*)
 				vendor=ibm
 				;;
@@ -863,9 +948,12 @@ case $basic_machine in
 			-ptx*)
 				vendor=sequent
 				;;
-			-vxworks*)
+			-vxsim* | -vxworks*)
 				vendor=wrs
 				;;
+			-aux*)
+				vendor=apple
+				;;
 		esac
 		basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
 		;;

bin/debug-ohdr

@@ -0,0 +1,26 @@
+#!/usr/bin/perl
+require 5.003;
+
+# Looks for lines emitted by H5O_open() and H5O_close() and tries to
+# determine which objects were not properly closed.
+
+while (<>) {
+   next unless /^([<>])(0x[\da-f]+|\d+)$/;
+   my ($op, $addr) = ($1, $2);
+
+   if ($op eq ">") {
+      # Open object
+      $obj{$addr} += 1;
+   } else {
+      # Close object
+      die unless $obj{$addr}>0;
+      $obj{$addr} -= 1;
+      delete $obj{$addr} unless $obj{$addr};
+   }
+}
+
+for (sort keys %obj) {
+   printf "%3d %s\n", $obj{$_}, $_;
+}
+
+exit 0;

bin/errors

@@ -2,6 +2,9 @@
 require 5.003;
 use Text::Tabs;
 
+# NOTE: THE FORMAT OF HRETURN_ERROR AND HGOTO_ERROR MACROS HAS
+# CHANGED. THIS SCRIPT NO LONGER WORKS! --rpm
+
 # Copyright (C) 1997 National Center for Supercomputing Applications.
 #		All rights reserved.
 #

bin/h5vers

@@ -0,0 +1,202 @@
+#!/usr/bin/perl -w
+require 5.003;
+
+### Copyright © 1998 NCSA.
+# Robb Matzke <matzke@llnl.gov>
+# 17 July 1998
+
+### Purpose
+# Increments the hdf5 version number by changing the value of
+# constants in the src/H5public.h file.  The new version number is
+# printed on the standard output. An alternate source file name can be
+# specified as an argument.  In any case, the original file is saved
+# by appending a tilde `~' to the name.
+
+### Usage:
+# h5vers [OPTIONS] [FILE]
+
+# Without options this program only displays the current version and
+# doesn't modify any files or create backups.  The default is to print
+# the version number as a dotted triple like `1.0.24' but with the
+# `-v' option the version will be printed as `version 1.0 release 24'.
+#
+# The `-s VERSION' switch will set the version as specified.  If the
+# string contains a dotted triple then it will be used as the version
+# number, otherwise up to three numbers will be read from the end of
+# the string and used as the major version, minor version, and release
+# number.  If any numbers are missing then zero is assumed.  This
+# allows versions to be specified like `-s "version 2.1 release 8"' or
+# `-s hdf5-2.1.8.tar.bz2'.  If the new version is less than the old
+# version then a warning message is generated on standard error.
+#
+# The `-i [major|minor|release]' option increments the major, minor,
+# or release (the default) number.  If the minor number is incremented
+# then the release number is set to zero; if the major number is
+# incremented then the minor and release numbers are set to zero.
+#
+# If a file is specified then that file is used instead of
+# ./H5public.h or ./src/H5public.h.
+#
+# If the version number is changed (either `-s' or `-i' was used on
+# the command line) then the first line of the README file one
+# directory above the H5public.h file is also modified so it looks
+# something like: This is hdf5-1.2.3 currently under development.
+##############################################################################
+
+sub getvers {
+  local ($_) = @_;
+  my (@vers);
+
+  ($vers[0]) = /^\#\s*define\s+H5_VERS_MAJOR\s+(\d+)/m;
+  ($vers[1]) = /^\#\s*define\s+H5_VERS_MINOR\s+(\d+)/m;
+  ($vers[2]) = /^\#\s*define\s+H5_VERS_RELEASE\s+(\d+)/m;
+  return @vers;
+}
+
+sub setvers {
+  my ($contents, @vers) = @_;
+  $_[0] =~ s/^(\#\s*define\s+H5_VERS_MAJOR\s+)\d+/$1$vers[0]/m;
+  $_[0] =~ s/^(\#\s*define\s+H5_VERS_MINOR\s+)\d+/$1$vers[1]/m;
+  $_[0] =~ s/^(\#\s*define\s+H5_VERS_RELEASE\s+)\d+/$1$vers[2]/m;
+}
+
+sub usage {
+  my ($prog) = $0 =~ /([^\/]+)$/;
+  print STDERR <<EOF;
+Usage: $prog [OPTS] [FILE]
+    -i major|minor|release
+        Increment specified version component and set following components
+        to zero.
+    -s VERSION
+        Set the version as specified. The version number can be embedded in
+        some other string such as \"hdf5-1.1.0.tar.bz2\" or even \"this is
+        hdf5 version 1.1 release 0\" for convenience.
+    -v
+        Instead of displaying only a dotted triple version number a line such
+        as \"version 1.1 release 0\" will be printed.
+    FILE
+        The name of the file that contains version information.  This is
+        seldom necessary since files H5public.h, src/H5public.h and
+        ../src/H5public.h are automatically checked.
+EOF
+  exit 1;
+}
+
+# Parse arguments
+my ($verbose, $set, $inc, $file);
+my (@files) = ("H5public.h", "src/H5public.h", "../src/H5public.h");
+while ($_ = shift) {
+  $_ eq "-s" && do {
+    die "-s switch needs a version number\n" unless @ARGV;
+    $set = shift;
+    next;
+  };
+
+  $_ eq "-i" && do {
+    if (@ARGV && $ARGV[1]=~/^(major|minor|release)$/) {
+      $inc = shift;
+    } else {
+      $inc = "release";
+    }
+    next;
+  };
+
+  $_ eq "-v" && do {
+    $verbose = 1;
+    next;
+  };
+
+  /^-(h|\?|-?help)$/ && usage;
+  /^-/ && die "unrecognized option: $_\n";
+  die "only one file name can be specified\n" if $file;
+  $file = $_;
+}
+die "mutually exclusive options given\n" if $set && $inc;
+
+# Determine file to use as H5public.h and README. The README file is
+# always in the directory above H5public.h
+unless ($file) {
+  for (@files) {
+    ($file=$_,last) if -f $_;
+  }
+}
+die "unable to read file: $file\n" unless -r $file;
+$README = $file;
+$README =~ s/[^\/]*$/..\/README/;
+die "unable to read file: $README\n" unless -r $file;
+
+# Get the current version number.
+open FILE, $file or die "unable to open $file: $!\n";
+my ($contents) = join "", <FILE>;
+close FILE;
+my (@curver) = getvers $contents;
+
+# Determine the new version number.
+if ($set) {
+  if ($set =~ /(\d+)\.(\d+)\.(\d+)/) {
+    @newver = ($1, $2, $3);
+  } elsif ($set =~ /(\d+)\D+(\d+)\D+(\d+)\D*$/) {
+    @newver = ($1, $2, $3);
+  } elsif ($set =~ /(\d+)\D+(\d+)\D*$/) {
+    @newver = ($1, $2, 0);
+  } elsif ($set =~ /(\d+)\D*$/) {
+    @newver = ($1, 0, 0);
+  } else {
+    die "illegal version number specified: $set\n";
+  }
+} elsif ($inc && $inc eq "major") {
+  $newver[0] = $curver[0]+1;
+  @newver[1,2] = (0,0);
+} elsif ($inc && $inc eq "minor") {
+  $newver[0] = $curver[0];
+  $newver[1] = $curver[1]+1;
+  $newver[2] = 0;
+} elsif ($inc && $inc eq "release") {
+  @newver[0,1] = @curver[0,1];
+  $newver[2] = $curver[2]+1;
+} elsif ($inc) {
+  die "unknown increment field: $inc\n";
+} else {
+  # Nothing to do but print result
+  $README = "";
+  @newver = @curver;
+}
+
+# Print a warning if the version got smaller.
+if ($newver[0]*1000000 + $newver[1]*1000 + $newver[2] <
+    $curver[0]*1000000 + $curver[1]*1000 + $curver[2]) {
+  printf STDERR "Warning: version decreased from %d.%d.%d to %d.%d.%d\n",
+    @curver, @newver;
+}
+
+# Update the version number if it changed.
+if ($newver[0]!=$curver[0] ||
+    $newver[1]!=$curver[1] ||
+    $newver[2]!=$curver[2]) {
+  setvers $contents, @newver or die "unable to set version\n";
+  rename $file, "$file~" or die "unable to save backup file\n";
+  open FILE, ">$file" or die "unable to open $file but backup saved!\n";
+  print FILE $contents;
+  close FILE;
+}
+
+# Update the README file
+if ($README) {
+  open FILE, $README or die "$README: $!\n";
+  @contents = <FILE>;
+  close FILE;
+  $contents[0] = sprintf("This is hdf5-%d.%d.%d currently under development\n",
+			 @newver);
+  open FILE, ">$README" or die "$README: $!\n";
+  print FILE @contents;
+  close FILE;
+}
+
+# Print the new version number
+if ($verbose) {
+  printf "version %d.%d release %d\n", @newver;
+} else {
+  printf "%d.%d.%d\n", @newver;
+}
+
+exit 0;

bin/iostats

@@ -0,0 +1,83 @@
+#!/usr/bin/perl
+
+# Usage: pipe the output of Linux's `strace' program into the stdin of
+# this command, and the output of this command into gnuplot.
+
+my ($fast,$npasses);
+if ($ARGV[0] =~ /^--?fast$/) {
+  $fast = 1;
+  shift;
+}
+
+my $filename = shift || "tstab2.h5";
+my $total = 0;
+my %What;			# What{pos}{nbytes}{r|w} = naccesses
+my($total_writes, $total_bytes_out, $total_reads, $total_bytes_in);
+
+while (<>) {
+  if (!defined $fd) {
+    if (/^open\("(.*?)".*=\s+(\d+)/ && $1 eq $filename) {
+      $fd = $2;
+      $pos = 0;
+    }
+  } elsif (/^close\((\d+)/ && $1==$fd) {
+    $fd = undef;
+  } elsif (!$fast &&
+	   /^lseek\((\d+), -?\d+,.*= (\d+)/ &&
+	   $1==$fd && $2>=0) {
+    $pos = $2;
+  } elsif (!$fast && /^lseek\((\d+),/ && $1==$fd) {
+    die $_;
+  } elsif (/^write\((\d+), ".*?"(\.\.\.)?, \d+\)\s*= (\d+)/ &&
+	   $1==$fd && $3>=0) {
+    my $nbytes = $3;
+    if ($fast) {
+      $total_writes++;
+      $total_bytes_out += $nbytes;
+    } else {
+      $What{$pos}{$nbytes}{w}++;
+      printf "%d %d\n", $total, $pos;
+      $pos += $nbytes;
+      $total += $nbytes;
+    }
+  } elsif (/^write\((\d+),/ && $1==$fd) {
+    die $_;
+  } elsif (/^read\((\d+), ".*?"(\.\.\.)?, \d+\)\s*= (\d+)/ &&
+	   $1==$fd && $3>=0) {
+    my $nbytes = $3;
+    if ($fast) {
+      $total_reads++;
+      $total_bytes_in += $nbytes;
+    } else {
+      $What{$pos}{$nbytes}{r}++;
+      printf "%d %d\n", $total, $pos;
+      $pos += $nbytes;
+      $total += $nbytes;
+    }
+  } elsif (/^read\((\d+),/ && $1==$fd) {
+    die $_;
+  }
+}
+     
+
+if (!$fast) {
+  print "="x36, "\n"; 
+  printf "%8s %8s %8s %8s\n","Position","NBytes","NReads","NWrites";
+  for $pos (sort {$a<=>$b} keys %What) {
+    for $nbytes (sort {$a<=>$b} keys %{$What{$pos}}) {
+      printf("%8d %8d %8d %8d\n", $pos, $nbytes,
+	     $What{$pos}{$nbytes}{r},
+	     $What{$pos}{$nbytes}{w});
+      $total_writes += $What{$pos}{$nbytes}{w};
+      $total_reads  += $What{$pos}{$nbytes}{r};
+      $total_bytes_out += $What{$pos}{$nbytes}{w} * $nbytes;
+      $total_bytes_in  += $What{$pos}{$nbytes}{r} * $nbytes;
+    }
+  }
+}
+
+print "="x36, "\n";
+printf("Write: %8d calls, %10d total bytes, %10g average bytes\n",
+       $total_writes, $total_bytes_out, $total_bytes_out/$total_writes);
+printf("Read:  %8d calls, %10d total bytes, %10g average bytes\n",
+       $total_reads, $total_bytes_in, $total_bytes_in/$total_reads);

bin/release

@@ -1,249 +1,165 @@
-#! /usr/local/bin/perl -w
-require 5.003;
-use Cwd;
+#!/bin/sh
 
-# Builds a release.  Arguments are zero or more of the words.
+# Make a release of hdf5.  The command-line switches are:
 #
-#	tar		-- build a tar file			*.tar
-#	compress	-- build a compressed tar file		*.tar.Z
-#	gzip		-- build a compressed tar file		*.tar.gz
-#	bzip2		-- build a compressed tar file		*.tar.bz2
+#  -d DIR	The name of the directory where the releas(es) should be
+#               placed.  By default, the directory is ./releases
 #
-# If no arguments are given then `gzip' is assumed.  If the only argument
-# is the word `all' then all forms are used.
-
-$releases = "./releases";	# Directory for release tarballs
-
-##############################################################################
-# Read version info, return an array (MAJOR,MINOR,RELEASE,PATCHLEVEL) or
-# a string "MAJOR.MINOR.RELEASE PATCHLEVEL"
+#  --nocheck	Ignore errors in MANIFEST file.
+#          
+# The other command-line options are the names of the programs to use
+# for compressing the resulting tar archive (if none are given then
+# `tar' is assumed):
 #
-sub getver () {
-   my @ver;
-
-   open SRC, "./src/H5public.h" or die "cannot read HDF5 version";
-   while (<SRC>) {
-      $ver[0] = $1 if /define\s+H5_VERS_MAJOR\s+(\d+)/;
-      $ver[1] = $1 if /define\s+H5_VERS_MINOR\s+(\d+)/;
-      $ver[2] = $1 if /define\s+H5_VERS_RELEASE\s+(\d+)/;
-      $ver[3] = $1 if /define\s+H5_VERS_PATCH\s+(\d+)/;
-   }
-   close SRC;
-   wantarray ? @ver : "$ver[0].$ver[1].$ver[2]".chr(ord('a')+$ver[3]);
-}
-
-##############################################################################
-# Set version information.  Input is a string or an array.
+#   tar		-- use tar and don't do any compressing.
+#   compress	-- use compress and append `.Z' to the output name.
+#   gzip	-- use gzip with `-9' and append `.gz' to the output name.
+#   bzip2       -- use bzip2 with `-9' and append `.bz2' to the output name.
 #
-sub setver ($;$$$) {
-   my @ver = @_;
-   local $_;
-
-   if ($ver[0]=~/\D/) {
-      @ver = $ver[0] =~ /^(\d+)\.(\d+)\.(\d+)([a-z])$/ or return "";
-      $ver[3] = ord($ver[3])-ord('a');
-   }
-
-   $_ = `cat ./src/H5public.h`;
-   s/(define\s+H5_VERS_MAJOR\s+)(\d+)/$1$ver[0]/;
-   s/(define\s+H5_VERS_MINOR\s+)(\d+)/$1$ver[1]/;
-   s/(define\s+H5_VERS_RELEASE\s+)(\d+)/$1$ver[2]/;
-   s/(define\s+H5_VERS_PATCH\s+)(\d+)/$1$ver[3]/;
-   open SRC, "> ./src/H5public.h" or return "";
-   print SRC $_;
-   close SRC;
-
-   return 1;
-}
-
-##############################################################################
-# Make sure MANIFEST contains all the necessary files.  If we are running
-# under CVS then look at the CVS/Entries files to get the names that should
-# be in the manifest.  Otherwise we really can't do anything.
+# Examples:
 #
-sub manifest () {
-    my ($fname, %manifest);
-    my $nprobs=0;
-
-    # We can't do anything if we're not running under cvs.
-    return "" unless -d "CVS";
-
-    # Read the files from the manifest.
-    open MANIFEST, "MANIFEST" or die "unable to read manifest";
-    while (<MANIFEST>) {
-	chomp;
-	$manifest{$_} = 1;
-    }
-    close MANIFEST;
-
-    # Read files from CVS/Entries
-    open FIND, "find . -name Entries -print | sort |" or
-	die "unable to find CVS entries";
-    while (defined($fname=<FIND>)) {
-	chomp $fname;
-	my ($dir) = $fname =~ m%(.*)/CVS/Entries%;
-	open ENTRIES, $fname or die "unable to open $fname";
-	while (<ENTRIES>) {
-	    my ($ename);
-	    next unless ($ename) = m%^/([^/]+)/[^-]%;
-	    $ename = "$dir/" . $ename;
-	    if (exists $manifest{$ename}) {
-		delete $manifest{$ename};
-	    } else {
-		print "NEW: $ename\n";
-		$nprobs++;
-	    }
-	}
-	close ENTRIES;
-    }
-    close FIND;
-
-    for (sort keys %manifest) {
-	print "OLD: $_\n";
-	$nprobs++;
-    }
-
-    if ($nprobs) {
-	print "Please add the new files to MANIFEST and remove the old\n";
-	print "files and try again.  The MANIFEST should contain all files\n";
-	print "that are to be distributed for a release.\n";
-	exit 1;
-    }
-}
-
-
-##############################################################################
-# Build a release
+#   $ release
+#   releases/hdf5-1.0.38.tar
+#
+#   $ release gzip
+#   releases/hdf5-1.0.38.tar.gz
+#
+#   $ release -d /tmp tar compress gzip bzip2
+#   /tmp/hdf5-1.0.38.tar
+#   /tmp/hdf5-1.0.38.tar.Z
+#   /tmp/hdf5-1.0.38.tar.gz
+#   /tmp/hdf5-1.0.38.tar.bz2
 #
-sub release (@) {
-   my @types = @_;
-   my ($ver, $status, $created_symlink);
-   my ($batch) = 0;
-   local $_;
 
-   if (@types>0 && $types[0] =~ /^-?-batch$/) {
-     $batch = 1;
-     shift @types;
-   }
+# Defaults
+DEST=releases
+VERS=`perl bin/h5vers`
+test "$VERS" || exit 1
+verbose=yes
+check=yes
 
-   # Make sure no one forgot to update MANIFEST
-   manifest;
+# Command-line arguments
+while [ -n "$1" ]; do
+    arg=$1
+    shift
+    case "$arg" in
+	-d)
+	    DEST=$1
+	    shift
+	    ;;
+	--nocheck)
+	    check=no
+	    ;;
+	-*)
+	    echo "Unknown switch: $arg" 1>&2
+	    exit 1
+	    ;;
+	*)
+	    methods="$methods $arg"
+	    ;;
+    esac
+done
 
-   # Make sure the version number is correct.
-   $ver = getver;
-   if ($batch) {
-     print "Releasing version $ver\n";
-   } else {
-     print "HDF version to release [$ver] ";
-     return "" unless defined ($_=<STDIN>);
-     chomp;
-     (setver ($ver=$_) or die "cannot set version") if /\S/;
-   }
+# Default method is tar
+if [ "X$methods" = "X" ]; then
+    methods=tar
+fi
 
-   # Update the README file to contain the new version and date
-   # information.
-   my $today = sprintf "19%02d-%02d-%02d %02d:%02d UTC", (gmtime)[5,4,3,2,1];
-   $_ = `cat README`;
-   s[^(This is hdf5-)\d+.\d+.\d+[a-z]( released on )(\d+-?){3} \d+:\d+ UTC]
-    [$1$ver$2$today]s;
-   system ("cp -p README README~");
-   open README, ">README" or die "unable to open README: $!\n";
-   print README;
-   close README;
-   
-   # Move default top-level makefile into place.
-   $status = system "cp Makefile.dist Makefile";
-   die "cannot install default Makefile" if $status >> 8;
 
-   # Make sure release directory exists
-   (mkdir $releases, 0777 or die "cannot create $releases")
-       unless -d $releases;
-   die "no manifest" unless -r "MANIFEST";
+test "$verbose" && echo "Releasing hdf5-$VERS to $DEST" 1>&2
+if [ ! -d $DEST ]; then
+    echo "   Destination directory $DEST does not exist" 1>&2
+    exit 1
+fi
 
-   # We build the release from above the root of the source tree so the
-   # hdf5 directory appears as part of the name in the tar file. We create
-   # a temporary symlink called something like `hdf5-1.0.0a' that points to
-   # our current working directory.
-   $_ = cwd;
-   my ($parent,$root) = m%(.*)/(.*)$% or die "cannot split directory";
-   if ($root ne "hdf5-$ver" && ! -e "../hdf5-$ver") {
-      symlink $root, "../hdf5-$ver" or die "cannot create link";
-      $created_symlink = 1;
-   }
-   my $name = "$root/$releases/hdf5-$ver";
+# Copy the manifest file to get a list of file names.
+MANIFEST=/tmp/H5_MANIFEST.$$
+grep '^\.' MANIFEST | expand | cut -f1 -d' ' >$MANIFEST
 
-   # Build the releases.
-   @types = ("gzip") unless @types;
-   @types = qw/tar gzip compress bzip2/ if 1==@types && "all" eq $types[0];
-   $_ = `cat MANIFEST`;
-   s/^\.\///mg;
-   @filelist = ("Makefile", split /\s*\n/, $_);
-   $filelist = join " ", map {"hdf5-$ver/$_"} @filelist;
-
-   chdir ".." or die;
-   for (@types) {
-      print "Compressing with $_...\n";
-
-      /^tar$/ && do {
-	 $status = system "tar cf $name.tar $filelist";
-	 next;
-      };
-
-      /^gzip$/ && do {
-	 $status = system "tar cf - $filelist |gzip -9 >$name.tar.gz";
-	 next;
-      };
-
-      /^compress$/ && do {
-	 $status = system "tar cf - $filelist |compress -c >$name.tar.Z";
-	 next;
-      };
-
-      /^bzip2$/ && do {
-	 $status = system "tar cf - $filelist |bzip2 -9 >$name.tar.bz2";
-	 next;
-      };
-   } continue {
-      print STDERR "$_ failed\n" if $status >> 8;
-   }
-   chdir $root or die;
-
-   # Remove the temporary symlink we created above.
-   unlink "../hdf5-$ver" if $created_symlink;
-   
-
-   # Update version info
-   if ($batch) {
-     my ($v1,$v2,$v3,$v4) = $ver =~ /^(\d+)\.(\d+)\.(\d+)([a-z])$/;
-     $v3 += 1;
-     setver ($ver = "$v1.$v2.${v3}a") or die "cannot set version";
-     print "Development version set to $ver\n";
-   } else {
-     print <<EOF;
-
-If this is a real release then the version number for continued development
-should be incremented.  Otherwise just press return.
+# Check that all the files in MANIFEST exist and that (if this is a
+# CVS checkout) that all the CVS-managed files appear in the
+# MANIFEST.
+test "$verbose" && echo "   Checking manifest..." 1>&2
+test -f $MANIFEST || exit 1
+for file in `cat $MANIFEST`; do
+    if [ ! -f $file ]; then
+       echo "- $file"
+       fail=yes
+    fi
+done
+for cvs in `find . -type d -name CVS -print`; do
+    path=`echo $cvs |sed s+/CVS++`
+    for file in `grep '^\/' $cvs/Entries |cut -d/ -f2`; do
+	if (grep $path/$file $MANIFEST >/dev/null); then
+	    :
+	else
+	    echo "+ $path/$file"
+	    fail=yes
+	fi
+    done
+done
+# for file in ./Changes `sh -c 'svf ls' 2>/dev/null`; do
+#     if (grep $file $MANIFEST >/dev/null); then
+# 	:
+#     elif [ $file = ./Changes ]; then
+#         :
+#     else
+# 	echo "+ $file"
+# 	fail=yes
+#     fi
+# done
 
+if [ "X$fail" = "Xyes" ]; then
+    cat 1>&2 <<EOF
+The MANIFEST is out of date. Files marked with a minus sign (-) no
+longer exist; files marked with a plus sign (+) are CVS-managed but do
+not appear in the MANIFEST.  Please remedy the situation and try again.
 EOF
-     print "Set development version to [", ($ver=getver), "] ";
-     return "" unless defined ($_ = <STDIN>);
-     chomp;
-     (setver ($ver=$_) or die "cannot set version") if /\S/;
+    if [ $check = yes ]; then
+        exit 1
+    else
+	echo "Continuing anyway..."
+    fi
+fi
 
-     if (-d "CVS") {
-       my $tag = $ver;
-       $tag =~ s/\./-/g;
-       print "Tag CVS sources with \"$tag\"? [n] ";
-       chomp ($_ = <STDIN>);
-       if ($_ eq 'y') {
-	 print "Tagging CVS sources...\n";
-	 my $status = system "cvs tag -R $tag";
-	 die "cvs tag failed" if $status >> 8;
-       }
-     }
-   }
+# Create a manifest that contains only files for distribution.
+grep '^\.' MANIFEST | grep -v _DO_NOT_DISTRIBUTE_ >$MANIFEST
 
-   return 1;
-}
+# Prepare the source tree for a release.
+test -h ../hdf5-$VERS && rm ../hdf5-$VERS
+ln -s `pwd` ../hdf5-$VERS || exit 1
+mv Makefile ../Makefile.x 2>/dev/null #might fail
+cp -p Makefile.dist Makefile
+echo "This is hdf5-$VERS released on `date`" >README.x
+tail -n +2 <README >>README.x
+mv README.x README
+test "$verbose" && echo "   Running tar..." 1>&2
+( \
+    cd ..; \
+    tar cf x.tar hdf5-$VERS/Makefile \
+	`sed s+^.+hdf5-$VERS+ $MANIFEST` || exit 1 \
+)
 
-release @ARGV;
+# Compress
+for comp in $methods; do
+    case $comp in
+	tar)
+	    cp -p ../x.tar $DEST/hdf5-$VERS.tar;;
+	compress)
+	    test "$verbose" && echo "   Running compress..." 1>&2
+	    compress -c <../x.tar >$DEST/hdf5-$VERS.tar.Z;;
+	gzip)
+	    test "$verbose" && echo "   Running gzip..." 1>&2
+	    gzip -9 <../x.tar >$DEST/hdf5-$VERS.tar.gz;;
+	bzip2)
+	    test "$verbose" && echo "   Running bzip2..." 1>&2
+	    bzip2 -9 <../x.tar >$DEST/hdf5-$VERS.tar.bz2;;
+    esac
+done
+
+# Remove temporary things
+test -f ../Makefile.x && mv ../Makefile.x Makefile
+rm -f $MANIFEST
+rm -f ../hdf5-$VERS
+rm -f ../x.tar
+exit 0

bin/snapshot

@@ -0,0 +1,192 @@
+#!/bin/sh
+set -x
+date
+#
+# This script should be run nightly from cron.  It checks out hdf5
+# from the CVS source tree and compares it against the previous
+# snapshot.  If anything significant changed then a new snapshot is
+# created, the minor version number is incremented, and the change is
+# checked back into the CVS repository.
+#
+
+# The path isn't properly initialized on hawkwind -- /usr/local/bin is
+# either missing or is after /usr/bin when it should be before.
+PATH="/usr/local/bin:$PATH"
+
+# Where are the snapshots stored?
+ARCHIVES_default=/afs/ncsa/ftp/HDF/pub/outgoing/hdf5/snapshots
+ARCHIVES=$ARCHIVES_default
+
+# Where are the HDF4 library?
+# At NCSA, the standard place to find HDF4 software is in /usr/ncsa/.
+HDF4LIB_default="/usr/ncsa/include,/usr/ncsa/lib"
+HDF4LIB=$HDF4LIB_default
+
+# What compression methods to use?
+METHODS="gzip bzip2"
+
+# Make sure cvs would work
+if [ -z "$CVSROOT" ]; then
+    echo "Where is the CVS repository?" 1>&2
+    exit 1
+fi
+
+#
+# Command options
+cmd="all"
+errcode=0
+echo '$#=' $# '$*="' $* '"'
+while [ $# -gt 0 ] ; do
+    case "$1" in
+	all)	
+	    cmd="all"
+	    ;;
+	checkout)
+	    cmdcheckout="checkout"
+	    cmd=""
+	    ;;
+	test)
+	    cmdtest="test"
+	    cmd=""
+	    ;;
+	release)
+	    cmdrel="release"
+	    cmd=""
+	    ;;
+	help)
+	    cmd="help"
+	    break
+	    ;;
+	hdf4)
+	    shift
+	    if [ $# -lt 1 ]; then
+		echo "HDF4LIB information missing"
+		errcode=1
+		cmd="help"
+		break
+	    fi
+	    HDF4LIB="$1"
+	    ;;
+	archive)
+	    shift
+	    if [ $# -lt 1 ]; then
+		echo "Archive pathname missing"
+		errcode=1
+		cmd="help"
+		break
+	    fi
+	    ARCHIVES="$1"
+	    ;;
+	*)
+	    echo "Unkown option $1"
+	    errcode=1
+	    cmd="help"
+	    break
+	    ;;
+    esac
+    shift
+done
+
+if [ "$cmd" = help ]; then
+    set -
+    echo "Usage: $0 [all] [checkout] [test] [release] [help] [hdf4 <hdf4lib_path>] [archive <arch_path> ]"
+    echo "    all:      Run all commands (checkout, test & release)"
+    echo "              [Default is all]"
+    echo "    checkout: Run cvs checkout"
+    echo "    test:     Run test"
+    echo "    release:  Run release"
+    echo "    help:     Print this message"
+    echo "    hdf4 <hdf4lib_path>:"
+    echo "              Use <hdf4lib_path> as the HDF4LIB locations"
+    echo "              [Default is $HDF4LIB_default]"
+    echo "    archive <arch_path>: "
+    echo "              Use <arch_path> as the release ARCHIVE area"
+    echo "              [<arch_path> default as $ARCHIVES_default]"
+    exit $errcode
+fi
+
+# Setup the proper configure option (--with-hdf4) to use hdf4 library
+# provide HDF4LIB is non-empty.
+HDF4LIB=${HDF4LIB:+"--with-hdf4="$HDF4LIB}
+CONFIGURE="./configure $HDF4LIB"
+
+# Execute the requests
+snapshot=yes
+
+# Show all settings right before execution.
+# set
+# exit 0
+
+
+#=============================
+# Run CVS checkout
+#=============================
+if [ "$cmd" = "all" -o -n "$cmdcheckout" ]; then
+    # Create a working directory.  Hopefully one is left over from last
+    # time that still has the contents of the previous release.  But if
+    # not, just create one and assume that a snapshot is necessary.
+    COMPARE=${HOME}/hdf5-snapshots
+    test -d ${COMPARE} || mkdir -p ${COMPARE} || exit 1
+
+    # Check out the current version from CVS
+    cvs -Q co -d ${COMPARE}/current hdf5 || exit 1
+fi # Do CVS checkout
+
+
+#=============================
+# Run Test the HDF5 library
+#=============================
+if [ "$cmd" = "all" -o -n "$cmdtest" ]; then
+    # Compare it with the previous version.  Compare only files listed in
+    # the MANIFEST plus the MANIFEST itself.
+    if [ -d ${COMPARE}/previous ]; then
+	if (diff -c ${COMPARE}/previous/MANIFEST ${COMPARE}/current/MANIFEST); then
+	    snapshot=no
+	    for src in `grep '^\.' ${COMPARE}/current/MANIFEST|expand|cut -f1 -d' '`; do
+		diff -I H5_VERS_RELEASE -I " released on " \
+		    -I " currently under development" \
+		    ${COMPARE}/previous/$src ${COMPARE}/current/$src || \
+		    snapshot=yes
+		    # Don't break because we want to see all the diffs.
+	    done
+	fi
+    fi
+
+    # Make sure all the serial tests work.
+    if [ "$snapshot" = "yes" ]; then
+	if (cd ${COMPARE}/current; \
+	    ${CONFIGURE}; \
+	    make _test); then
+	    :
+	else
+	    snapshot=no
+	fi
+    fi
+fi # Test the HDF5 library
+
+
+#=============================
+# Run Release snapshot, update version, and commit to cvs and tag
+#=============================
+if [ "$cmd" = "all" -o -n "$cmdrel" ]; then
+    if [ "$snapshot" = "yes" ]; then
+	(cd ${COMPARE}/current; make distclean)
+	(
+	    # Turn on exit on error in the sub-shell so that it does not
+	    # cvs commit if errors encounter here.
+	    set -e
+	    cd ${COMPARE}/current
+	    cvs -Q tag hdf5-`perl -w bin/h5vers |tr . _`
+	    bin/release -d $ARCHIVES $METHODS
+	    RELEASE_VERSION="`perl -w bin/h5vers -v`"
+	    perl -w bin/h5vers -i
+	    cvs -Q commit -m "Snapshot $RELEASE_VERSION"
+	)
+    fi
+
+    # Replace the previous version with the current version.
+    rm -rf ${COMPARE}/previous
+    mv ${COMPARE}/current ${COMPARE}/previous
+fi #Release snapshot
+
+exit 0

bin/trace

@@ -15,6 +15,7 @@ $Source = "";
 # usually the same as the package name.
 #
 %TypeString = ("hbool_t"                   => "b",
+               "htri_t"                    => "b",
                "double"                    => "d",
                "H5D_layout_t"              => "Dl",
                "H5D_transfer_t"            => "Dt",
@@ -22,6 +23,7 @@ $Source = "";
                "H5E_direction_t"           => "Ed",
                "H5E_error_t*"              => "Ee",
 	       "H5F_driver_t"              => "Fd",
+	       "H5F_scope_t"               => "Fs",
                "H5G_link_t"                => "Gl",
                "H5G_stat_t*"               => "Gs",
                "hsize_t"                   => "h",
@@ -30,10 +32,13 @@ $Source = "";
                "int"                       => "Is",
                "unsigned"                  => "Iu",
                "unsigned int"              => "Iu",
+               "H5I_type_t"                => "It",
                "MPI_Comm"                  => "Mc",
                "MPI_Info"                  => "Mi",
                "off_t"                     => "o",
                "H5P_class_t"               => "p",
+               "href_t"                    => "r",
+               "H5R_type_t"                => "Rt",
                "char*"                     => "s",
 	       "H5S_class_t"               => "Sc",
 	       "H5S_seloper_t"             => "Ss",
@@ -41,6 +46,7 @@ $Source = "";
                "H5T_norm_t"                => "Tn",
                "H5T_order_t"               => "To",
                "H5T_pad_t"                 => "Tp",
+	       "H5T_pers_t"		   => "Te",
                "H5T_sign_t"                => "Ts",
                "H5T_class_t"               => "Tt",
                "H5T_str_t"                 => "Tz",
@@ -55,7 +61,7 @@ $Source = "";
 	       "H5T_overflow_t"            => "x",
                "H5Z_func_t"                => "x",
                "size_t"                    => "z",
-               "H5Z_method_t"              => "Zm",
+               "H5Z_filter_t"              => "Zf",
                "ssize_t"                   => "Zs",
               );
 
@@ -80,17 +86,21 @@ sub errmesg ($$@) {
 #
 sub argstring ($$$) {
   my ($file, $func, $atype) = @_;
-  my ($ptr, $tstr) = (0,"!");
+  my ($ptr, $tstr, $array) = (0, "!", "");
   my ($fq_atype);
 
   # Normalize the data type by removing redundant white space,
   # certain type qualifiers, and indirection.
   $atype =~ s/^\bconst\b//;
-  $atype =~ s/\b__unused__\b//g;
+  $atype =~ s/\bUNUSED\b//g;
   $atype =~ s/\s+/ /g;
   $ptr = length $1 if  $atype =~ s/(\*+)//;
   $atype =~ s/^\s+//;
   $atype =~ s/\s+$//;
+  if ($atype =~ /(.*)\[(.*)\]$/) {
+    ($array, $atype) = ($2, $1);
+    $atype =~ s/\s+$//;
+  }
   $fq_atype = $atype . ('*' x $ptr);
 
   if ($ptr>0 && exists $TypeString{$fq_atype}) {
@@ -104,7 +114,7 @@ sub argstring ($$$) {
   } else {
     $tstr = $TypeString{$atype};
   }
-  return ("*" x $ptr) . $tstr;
+  return ("*" x $ptr) . ($array?"[$array]":"") . $tstr;
 }
 
 ##############################################################################
@@ -129,15 +139,18 @@ sub rewrite_func ($$$$$) {
     # comma, then split the arguments on commas.
     $args =~ s/(\/\*\s*in),\s*(out\s*\*\/)/$1_$2/g;
     my @args = split /,[\s\n]*/, $args;
+    my $argno = 0;
+    my %names;
 
     for $arg (@args) {
       unless ($arg=~/^(([a-z_A-Z]\w*\s+)+\**)
-	      ([a-z_A-Z]\w*)(\[\])?
+	      ([a-z_A-Z]\w*)(\[.*?\])?
 	      (\s*\/\*\s*(in|out|in_out)\s*\*\/)?\s*$/x) {
 	errmesg $file, $name, "unable to parse \`$arg\'";
 	goto error;
       } else {
 	my ($atype, $aname, $array, $adir) = ($1, $3, $4, $6);
+	$names{$aname} = $argno++;
 	$adir ||= "in";
 	$atype =~ s/\s+$//;
 	push @arg_name, $aname;
@@ -145,7 +158,18 @@ sub rewrite_func ($$$$$) {
 	if ($adir eq "out") {
 	  push @arg_str, "x";
 	} else {
-	  $atype .= "*" if $array;
+	  if (defined $array) {
+	    $atype .= "*";
+	    if ($array =~ /^\[\/\*([a-z_A-Z]\w*)\*\/\]$/) {
+	      my $asize = $1;
+	      if (exists $names{$asize}) {
+		$atype .= '[a' . $names{$asize} . ']';
+	      } else {
+		warn "bad array size: $asize";
+		$atype .= "*";
+	      }
+	    }
+	  }
 	  push @arg_str, argstring $file, $name, $atype;
 	}
       }
@@ -154,7 +178,7 @@ sub rewrite_func ($$$$$) {
     $trace .= join("", @arg_str) . "\"";
     my $len = 4 + length $trace;
     for (@arg_name) {
-      if ($len + length >= 78) {
+      if ($len + length >= 77) {
 	$trace .= ",\n             $_";
 	$len = 13 + length;
       } else {
@@ -185,7 +209,7 @@ sub rewrite_func ($$$$$) {
 
   
  error:
-  return "\n$type\n$name ($args)$body";
+  return "\n$type\n$name($args)\n$body";
 }
 
 ##############################################################################
@@ -203,8 +227,8 @@ for $file (@ARGV) {
   my $original = $Source;
   my $napi = $Source =~ s/\n([A-Za-z]\w*(\s+[a-z]\w*)*)\s*\n #type
                             (H5[A-Z]{1,2}[^_A-Z]\w*)      #name
-                            \s*\((.*?)\)                  #args
-                            (.*?\n\}[^\n]*)               #body
+                            \s*\((.*?)\)\s*               #args
+                            (\{.*?\n\}[^\n]*)             #body
                          /rewrite_func($file,$1,$3,$4,$5)/segx;
   $total_api += $napi;
   

config/BlankForm

@@ -9,31 +9,109 @@
 # Compiler flags. The CPPFLAGS values should not include package debug
 # flags like `-DH5G_DEBUG' since these are added with the
 # `--enable-debug' switch of configure.
-
-# Sometimes a particular compiler must be used.  If that's the case
-# then uncomment the following line.  Otherwise the main configure
-# script will try to detect the compiler automatically.
-#CC=gcc
-
-# What must *always* be present for things to compile correctly?
-#CFLAGS="$CFLAGS -ansi"
-#CPPFLAGS="$CPPFLAGS -I."
-
-# What compiler flags should be used for code development?
-DEBUG_CFLAGS=-g
-DEBUG_CPPFLAGS=
-
-# What compiler flags should be used for building a production
-# library?
-PROD_CFLAGS=-O
-PROD_CPPFLAGS=
-
-# What compiler flags enable code profiling?
-PROFILE_CFLAGS=-pg
-PROFILE_CPPFLAGS=
-
-
 #----------------------------------------------------------------------------
+
+
+# Choosing a C Compiler
+# ---------------------
+#
+# The user should be able to specify the compiler by setting the CC
+# environment variable to the name of the compiler and any switches it 
+# requires for proper operation.  If CC is unset then this script may
+# set it.  If CC is unset by time this script completes then configure 
+# will try `gcc' and `cc' in that order (perhaps some others too).
+#
+# Note: Code later in this file may depend on the value of $CC_BASENAME
+#       in order to distinguish between different compilers when
+#       deciding which compiler command-line switches to use.  This
+#       variable is set based on the incoming value of $CC and is only
+#       used within this file.
+
+if test "X-" =  "X-$CC"; then
+    CC="/some/default/compiler/named/foo -ansi"
+    CC_BASENAME=foo
+fi
+
+
+# C Compiler and Preprocessor Flags
+# ---------------------------------
+#
+# Flags that end with `_CFLAGS' are always passed to the compiler.
+# Flags that end with `_CPPFLAGS' are passed to the compiler when
+# compiling but not when linking.
+#
+# DEBUG_CFLAGS		Flags to pass to the compiler to create a
+# DEBUG_CPPFLAGS	library suitable for use with debugging
+#			tools. Usually this list will exclude
+#			optimization switches (like `-O') and include
+#			switches that turn on symbolic debugging
+#			support (like `-g').
+#
+# PROD_CFLAGS		Flags to pass to the compiler to create a
+# PROD_CPPFLAGS		production version of the library.  These
+#			usualy exclude symbolic debugging switches
+#			(like `-g') and include optimization switches
+#			(like `-O').
+#
+# PROFILE_CFLAGS	Flags to pass to the compiler to create a
+# PROFILE_CPPFLAGS	library suitable for performance testing (like 
+# 			`-pg').  This may or may not include debugging 
+# 			or production flags.
+#			
+# CFLAGS		Flags can be added to this variable which
+#			might already be partially initialized.  These 
+#			flags will always be passed to the compiler
+#			and should include switches to turn on full
+#			warnings.  HDF5 attempts to be ANSI and Posix
+#			compliant and employ good programming
+#			practices resulting in few if any
+#			warnings.
+#
+#			Warning flags do not have to be added to CFLAGS
+#			variable if the compiler is the GNU gcc
+#			compiler or a descendent of gcc such as EGCS or PGCC.
+#
+#			The CFLAGS should contains *something* or else 
+#			configure will probably add `-g'.  For most
+#			systems this isn't a problem but some systems
+#			will disable optimizations in favor of the
+#			`-g'.
+#			
+#
+# These flags should be set according to the compiler being used.
+# There are two ways to check the compiler.  You can try using `-v' or 
+# `--version' to see if the compiler will print a version string.  You 
+# can use the value of $CC_BASENAME which is the base name of the
+# first word in $CC (note that the value of CC may have changed
+# above).
+
+case $CC_BASENAME in
+    gcc)
+	CFLAGS="$CFLAGS -Wsign-compare" #Only works for some versions
+	DEBUG_CFLAGS="-g -fverbose-asm"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+	PROD_CFLAGS="-O3 -fomit-frame-pointer"
+	PROD_CPPFLAGS=
+	PROFILE_CFLAGS="-pg"
+	PROFILE_CPPFLAGS=
+	;;
+
+    *)
+	CFLAGS="$CFLAGS -ansi"
+	DEBUG_CFLAGS="-g"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+	PROD_CFLAGS="-O"
+	PROD_CPPFLAGS=
+	PROFILE_CFLAGS="-pg"
+	PROFILE_CPPFLAGS=
+	;;
+esac
+
+
+
+# Overriding Configure Tests
+# --------------------------
+#
 # Values for overriding configuration tests when cross compiling.
 # This includes compiling on some machines where the serial front end
 # compiles for a parallel back end.

config/alpha-dec

@@ -1,38 +0,0 @@
-#							-*- shell-script -*-
-#
-# This file is part of the HDF5 build script.  It is processed shortly
-# after configure starts and defines, among other things, flags for
-# the various compile modes.
-
-
-#----------------------------------------------------------------------------
-# Compiler flags. The CPPFLAGS values should not include package debug
-# flags like `-DH5G_DEBUG' since these are added with the
-# `--enable-debug' switch of configure.
-
-# What must *always* be present for things to compile correctly?
-#CFLAGS="$CFLAGS -ansi"
-#CPPFLAGS="$CPPFLAGS -I."
-
-# What compiler flags should be used for code development?
-DEBUG_CFLAGS=-g
-DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
-
-# What compiler flags should be used for building a production
-# library?
-PROD_CFLAGS=-O
-PROD_CPPFLAGS=
-
-# What compiler flags enable code profiling?
-PROFILE_CFLAGS=-pg
-PROFILE_CPPFLAGS=
-
-
-#----------------------------------------------------------------------------
-# Values for overriding configuration tests when cross compiling.
-# This includes compiling on some machines where the serial front end
-# compiles for a parallel back end.
-
-# Set this to `yes' or `no' depending on whether the target is big
-# endian or little endian.
-#ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}

config/commence.in

@@ -6,7 +6,7 @@
 
 # Things that Make needs
 .SUFFIXES:
-.SUFFIXES: .c .o
+.SUFFIXES: .c .o .lo
 @SET_MAKE@
 
 # Programs
@@ -14,6 +14,7 @@ SHELL=/bin/sh
 CC=@CC@
 CFLAGS=@CFLAGS@
 CPPFLAGS=@CPPFLAGS@
+LDFLAGS=@LDFLAGS@
 LIBS=@LIBS@
 AR=@AR@
 RANLIB=@RANLIB@
@@ -22,19 +23,36 @@ CP=cp
 INSTALL=@INSTALL@
 INSTALL_PROGRAM=@INSTALL_PROGRAM@
 INSTALL_DATA=@INSTALL_DATA@
-RUNTEST=@RUNTEST@
+RUNSERIAL=@RUNSERIAL@
+RUNPARALLEL=@RUNPARALLEL@
+RUNTEST=$(RUNSERIAL)
 TRACE=:
 
 # Installation points
-ROOT=@ROOT@
 prefix=@prefix@
 exec_prefix=@exec_prefix@
 bindir=@bindir@
 libdir=@libdir@
 includedir=@includedir@
+PUB_LIB=$(LIB)
 
-# The default is to build the library and/or programs
-all: lib tests progs
+# Shared libraries
+LT=$(top_builddir)/libtool
+LT_COMPILE=$(LT) --mode=compile $(CC)
+LT_LINK_LIB=$(LT) --mode=link $(CC) -rpath $(libdir)
+LT_LINK_EXE=$(LT) --mode=link $(CC) -rpath $(bindir)
+LT_RUN=$(LT) --mode=execute
+LT_INSTALL_PROG=$(LT) --mode=install $(INSTALL_PROGRAM)
+LT_INSTALL_LIB=$(LT) --mode=install $(INSTALL_DATA)
+LT_UNINSTALL=$(LT) --mode=uninstall $(RM)
+
+
+# The default is to build the library and/or programs.  We must build
+# them sequentially.
+all:
+	$(MAKE) lib
+	$(MAKE) progs
+	$(MAKE) tests
 
 # The following rules insure that the Makefile is up-to-date by rerunning
 # various autoconf components (although not all versions of make assume
@@ -45,22 +63,25 @@ all: lib tests progs
 #
 # Graphically, the dependencies are:
 #
-#			    configure.in
-#                              |  |
-#         +--------------------+  +-------------------+
-#         |                                           |
-#      stamp1                                     configure
-#         |                                           |
-#         |                                     config.status
-#         |                                       |   |
-#         | +-------------------------------------+   |
-#         | |                                         |
-#       stamp2          Makefile.in et al             |
-#          |                    |                     |
-#          |                    +-----------+  +------+
-#          +-----------------------------+  |  |
-#                                        |  |  |
-#                                        Makefile
+#		         configure.in
+#                           |  |
+#         +-----------------+  +------------+
+#         |                                 |
+#      stamp1                           configure
+#   (H5config.h.in)                         |
+#       |  |                                |
+#       |  +---------------+    +-----------+
+#       |                  |    |
+#       |               config.status
+#       |                     |
+#       |  +------------------+
+#       |  |
+#      stamp2
+#    (H5config.h)                   Makefile.in et al
+#         |                                 |
+#         +------------------+  +-----------+
+#                            |  |
+#                          Makefile
 #
 # A side effect of updating stamp1 is to generate H5config.h.in and a
 # side effect of updating stamp2 is to generate H5config.h.  When using
@@ -68,30 +89,31 @@ all: lib tests progs
 # the user may want to occassionally type `make Makefile' in any source
 # directory.
 #
-STAMP1=$(ROOT)/config/stamp1
-STAMP2=$(ROOT)/config/stamp2
+STAMP1=$(top_builddir)/config/stamp1
+STAMP2=$(top_builddir)/config/stamp2
 
-MAKEFILE_PARTS=$(ROOT)/config/commence.in Makefile.in			      \
-	       $(ROOT)/config/conclude.in $(ROOT)/config/depend.in
+MAKEFILE_PARTS=$(srcdir)/Makefile.in					      \
+	       $(top_srcdir)/config/commence.in				      \
+	       $(top_srcdir)/config/conclude.in				      \
+	       $(top_srcdir)/config/depend.in
 
-$(STAMP1): $(ROOT)/configure.in
-	-(cd $(ROOT);							      \
-	  touch $(STAMP1);						      \
-	  autoheader)
+$(STAMP1): $(top_srcdir)/configure.in
+	touch $(STAMP1)
+	-cd $(top_srcdir); autoheader
 
-$(STAMP2): $(STAMP1) $(ROOT)/config.status
-	-(cd $(ROOT);							      \
-	  touch $(STAMP2);						      \
-	  CONFIG_FILES= CONFIG_HEADERS=src/H5config.h ./config.status)
+$(STAMP2): $(STAMP1) $(top_builddir)/config.status
+	touch $(STAMP2)
+	-cd $(top_builddir); \
+	   CONFIG_FILES= CONFIG_HEADERS=src/H5config.h ./config.status
 
-$(ROOT)/configure: $(ROOT)/configure.in
-	-(cd $(ROOT); autoconf)
+$(top_srcdir)/configure: $(top_srcdir)/configure.in
+	-cd $(top_srcdir); autoconf
 
-$(ROOT)/config.status: $(ROOT)/configure
-	-(cd $(ROOT); ./config.status --recheck)
+$(top_builddir)/config.status: $(top_srcdir)/configure $(STAMP1)
+	-cd $(top_builddir); ./config.status --recheck
 
-Makefile: $(MAKEFILE_PARTS) $(ROOT)/config.status $(STAMP2)
-	-(cd $(ROOT); CONFIG_HEADERS= ./config.status)
+Makefile: $(MAKEFILE_PARTS) $(STAMP2)
+	-cd $(top_builddir); CONFIG_HEADERS= ./config.status
 
 #------------------------------------------------------------------------------
 # The following section of this makefile comes from the middle of `Makefile.in'

config/conclude.in

@@ -9,10 +9,9 @@
 #
 lib: $(LIB)
 $(LIB) __no_library__: $(LIB_OBJ)
-	$(AR) -rc $@ $(LIB_OBJ)
-	$(RANLIB) $@
+	@$(LT_LINK_LIB) -o $@ $(CFLAGS) $(LIB_OBJ) $(LIBS)
 
-progs: $(PROGS)
+progs: $(LIB) $(PROGS)
 
 # Build a tags file in this directory.
 TAGS: $(LIB_SRC)
@@ -20,60 +19,99 @@ TAGS: $(LIB_SRC)
 	-etags $(LIB_SRC)
 
 # Runs each test in order, passing $(TEST_FLAGS) to the program.
-tests: $(TESTS)
-test _test: tests
-	@for test in $(TESTS) dummy; do			                      \
+tests: $(TEST_PROGS) $(LIB)
+check test _test: tests
+	@for test in $(TEST_PROGS) dummy; do                                  \
 	   if test $$test != dummy; then				      \
+	      echo "============================";			      \
 	      echo "Testing $$test $(TEST_FLAGS)";			      \
-	      $(RUNTEST) ./$$test $(TEST_FLAGS) || exit 1;		      \
+	      echo "============================";			      \
+	      PATH=".:$$PATH" srcdir=$(srcdir)				      \
+		 $(RUNTEST) $$test $(TEST_FLAGS) ||			      \
+		 exit 1;						      \
+	      echo "";							      \
+	   fi;								      \
+	done;
+	@for test in $(TEST_SCRIPTS) dummy; do                                \
+	   if test $$test != dummy; then				      \
+	      echo "============================";			      \
+	      echo "Testing $$test $(TEST_FLAGS)";			      \
+	      echo "============================";			      \
+	      RUNSERIAL="$(RUNSERIAL)" RUNPARALLEL="$(RUNPARALLEL)"           \
+	      srcdir=$(srcdir)						      \
+		 /bin/sh $$test $(TEST_FLAGS) ||		              \
+		 exit 1;						      \
+	      echo "";							      \
 	   fi;								      \
 	done;
 
+# Make installation directories directories if they don't exist.
+$(libdir):
+	mkdir $@ && chmod 755 $@
+
+$(includedir):
+	mkdir $@ && chmod 755 $@
+
+$(bindir):
+	mkdir $@ && chmod 755 $@
+
 # Install the library, the public header files, and programs.
-install: $(LIB) $(PUB_HDR) $(PROGS)
-	@test -d $(libdir) || mkdir $(libdir)
-	@for f in X $(LIB); do						      \
+install: $(PUB_LIB) $(PUB_HDR) $(PROGS) $(libdir) $(includedir) $(bindir)
+	@for f in X $(PUB_LIB); do					      \
 	   if test $$f != X; then					      \
-	      (set -x; $(INSTALL_DATA) $$f $(libdir)/. || exit 1);	      \
+	      ($(LT_INSTALL_LIB) $$f $(libdir)/. || exit 1);		      \
 	   fi;								      \
 	done
-	@test -d $(includedir) || mkdir $(includedir)
+	@if test -f libhdf5.settings; then				      \
+	   (set -x; $(INSTALL_DATA) libhdf5.settings $(libdir)/. || exit 1);  \
+	fi
 	@for f in X $(PUB_HDR); do					      \
 	   if test $$f != X; then					      \
-	      (set -x; $(INSTALL_DATA) $$f $(includedir)/. || exit 1);        \
-	   fi								      \
+	      if test -f $$f; then					      \
+		 (set -x; $(INSTALL_DATA) $$f $(includedir)/. || exit 1);     \
+	      else							      \
+	         (set -x; $(INSTALL_DATA) $(srcdir)/$$f $(includedir)/. ||    \
+		    exit 1);						      \
+	      fi;							      \
+	   fi;								      \
 	done
-	@test -d $(bindir) || mkdir $(bindir)
 	@for f in X $(PROGS); do					      \
 	   if test $$f != X; then					      \
-	     (set -x; $(INSTALL_PROGRAM) $$f $(bindir)/. || exit 1);	      \
+	     ($(LT_INSTALL_PROG) $$f $(bindir)/. || exit 1);		      \
 	   fi;							              \
 	done
 
 # Removes those things that `make install' (would have) installed.
 uninstall:
 	@if test "X$(LIB)" != X; then					      \
-           set -x; cd $(libdir) && $(RM) $(LIB);			      \
+	   for f in $(LIB); do						      \
+	      $(LT_UNINSTALL) $(libdir)/$$f;				      \
+	   done;							      \
 	fi
-	@if test "X$(PUBHDR)" != X; then				      \
+	@if test "X$(PUB_HDR)" != X; then				      \
 	   set -x; cd $(includedir) && $(RM) $(PUB_HDR);		      \
 	fi
 	@if test "X$(PROGS)" != X; then					      \
-	   set -x; cd $(bindir) && $(RM) $(PROGS);			      \
+	   for f in $(PROGS); do					      \
+	      $(LT_UNINSTALL) $(bindir)/$$f;				      \
+	   done;							      \
 	fi
 
 # Removes temporary files without removing the final target files.  That is,
 # remove things like object files but not libraries or executables.
 #
 mostlyclean:
-	$(RM) $(LIB_OBJ) $(PROG_OBJ) $(MOSTLYCLEAN)
+	-$(RM) $(LIB_OBJ) $(LIB_OBJ:.lo=.o)
+	-$(RM) $(TEST_OBJ) $(TEST_OBJ:.lo=.o)
+	-$(RM) $(PROG_OBJ) $(PROG_OBJ:.lo=.o) $(MOSTLYCLEAN)
 
 # Like `mostlyclean' except it also removes the final targets: things like
 # libraries and executables.  This target doesn't remove any file that
 # is part of the HDF5 distribution.
 #
 clean: mostlyclean
-	$(RM) $(LIB) $(TESTS) $(PROGS) $(CLEAN)
+	-$(RM) $(LIB) $(TEST_PROGS) $(PROGS) $(CLEAN)
+	-$(RM) -r .libs
 
 # Like `clean' except it also removes files that were created by running
 # configure.  If you've unpacked the source and built HDF5 without creating
@@ -81,26 +119,25 @@ clean: mostlyclean
 # in the distribution.
 #
 distclean: clean
-	$(RM) .depend TAGS *~ core *.core *.bak *.old *.new $(DISTCLEAN)
-	@if test -f Makefile.in; then					      \
+	-$(RM) .depend TAGS *~ core *.core *.bak *.old *.new $(DISTCLEAN)
+	@if test -f $(srcdir)/Makefile.in; then				      \
 	   (set -x; $(RM) Makefile);					      \
 	fi
 
+
 # Like `distclean' except it deletes all files that can be regenerated from
 # the makefile, including those generated from autoheader and autoconf.
 #
 maintainer-clean: distclean
-	$(RM) *~ core core.* *.core *.bak *.contrib gmon.out
+	-$(RM) *~ core core.* *.core *.bak *.contrib gmon.out
 
 # Implicit rules
-.c.a:
-	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
-	$(AR) -rc $@ $*.o
-	$(RM) $*.o
-
 .c.o:
 	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
 
+.c.lo:
+	@$(LT_COMPILE) $(CFLAGS) $(CPPFLAGS) -c $<
+
 #------------------------------------------------------------------------------
 # The following section of this makefile contains dependencies between the
 # source files and the header files.  If GNU make and GCC are being used then
@@ -113,3 +150,5 @@ maintainer-clean: distclean
 
 @DEPEND1@
 @DEPEND2@
+@DEPEND3@
+@DEPEND4@

config/dec-flags

@@ -0,0 +1,62 @@
+#							-*- shell-script -*-
+#
+# This file should be sourced into configure if the compiler is a DEC
+# compiler.  It is careful not to do anything if the compiler is not
+# DEC; otherwise `cc_flags_set' is set to `yes'
+#
+
+# Get the compiler version unless it's already known.
+#
+#   cc_vendor:    The compiler vendor: DEC
+#   cc_version:   Version number, like: V5.2-038
+#
+if test X = "X$cc_flags_set"; then
+    cc_vendor=DEC
+    cc_version="`$CC $CFLAGS -V 2>&1 |head -1 |\
+	        sed 's/.*DEC C \(V[0-9][-\.0-9]*\).*/\1/'`"
+    if test X != "$gcc_version"; then
+	echo "compiler '$CC' is $cc_vendor-$cc_version"
+    else
+        cc_vendor=
+    fi
+fi
+
+# Warn about old compilers that don't work right.
+case "$cc_vendor-$cc_version" in
+    DEC-V5.2-038)
+        cat <<EOF
+    **
+    ** This compiler may generate incorrect code when optimizations are
+    ** enabled. Please upgrade to a newer version (we're not sure which
+    ** version actually works) before reporting bugs to the HDF5 team.
+    **
+EOF
+	sleep 5
+	;;
+esac
+
+# Compiler flags
+case "$cc_vendor-$cc_version" in
+    DEC-V5.*)
+	# Production
+	PROD_CFLAGS="-g0 -verbose -warnprotos -std -O4 $ARCH -ansi_args -fp_reorder -readonly_strings -inline speed"
+	PROD_CPPFLAGS="-D_INTRINSICS -D_INLINE_INTRINSICS"
+
+	# Debug
+	DEBUG_CFLAGS="-g -std -verbose -warnprotos"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+
+	# Profile
+	PROFILE_CFLAGS="-pg -std -verbose -warnprotos"
+	PROFILE_CPPFLAGS=
+
+	# Flags are set
+	cc_flags_set=yes
+	;;
+esac
+
+# If no flags were set then clear the compiler vendor and version info.
+if test X = "X$cc_flags_set"; then
+    cc_vendor=
+    cc_version=
+fi

config/dec-osf4.x

@@ -0,0 +1,20 @@
+#							-*- shell-script -*-
+#
+# This file is part of the HDF5 build script.  It is processed shortly
+# after configure starts and defines, among other things, flags for
+# the various compile modes.
+#
+# See BlankForm in this directory for detailed information.
+
+# The default compiler is `cc'
+if test "X-" =  "X-$CC"; then
+    CC=cc
+    CC_BASENAME=cc
+fi
+
+# Try GNU compiler flags.
+. $srcdir/config/gnu-flags
+
+# Try native DEC compiler
+ARCH=${ARCH:='-arch host -tune host'}
+. $srcdir/config/dec-flags

config/depend.in

@@ -25,20 +25,20 @@ dep depend: .distdep
 
 .distdep: .depend
 	touch .distdep
-	-perl -p $(ROOT)/bin/distdep .depend >.distdep
+	-srcdir=$(srcdir) perl -p $(top_srcdir)/bin/distdep .depend >.distdep
 
 .depend: $(LIB_SRC) $(TEST_SRC) $(PROG_SRC)
 	@touch .depend
 	@for dep in $? dummy; do					      \
 	   if [ $$dep != "dummy" ]; then				      \
 	      echo Building dependencies for $$dep;			      \
-	      obj=`echo $$dep | sed 's/\.c/\\\\.o/'`;			      \
-	      sed "/$$obj/,/[^\\]$$/d" <$@ >$@- && mv $@- $@;		      \
+	      obj=`echo $$dep | sed 's/\.c/\\\\.lo/'`;			      \
+	      sed '\%$$obj%,\%[^\\]$$%d' <$@ >$@- && mv $@- $@;		      \
 	      $(TRACE) $$dep;						      \
-	      $(CC) -M -MG $(CPPFLAGS) $$dep >>$@;			      \
+	      $(CC) -M -MG $(CPPFLAGS) $$dep |sed 's/\.o/.lo/' >>$@;	      \
 	   fi;								      \
 	done;
-	-perl -p $(ROOT)/bin/distdep .depend >.distdep
+	-perl -p $(top_srcdir)/bin/distdep .depend >$(srcdir)/.distdep
 
 -include .depend
 

config/freebsd

@@ -0,0 +1,21 @@
+#							-*- shell-script -*-
+# This file is part of the HDF5 build script.  It is processed shortly
+# after configure starts and defines, among other things, flags for
+# the various compile modes.
+#
+# See BlankForm in this directory for details.
+
+# The default compiler is `gcc'
+if test "X-" = "X-$CC"; then
+    CC=gcc
+    CC_BASENAME=gcc
+fi
+
+# Architecture-specific flags
+ARCH=
+
+# Omit frame pointer for optimized code?
+NOFP=${NOFP:=-fomit-frame-pointer}
+
+# Figure out compiler flags
+. $srcdir/config/gnu-flags

config/gnu-flags

@@ -0,0 +1,156 @@
+#							-*- shell-script -*-
+#
+# This file should be sourced into configure if the compiler is the
+# GNU gcc compiler or a derivative.  It is careful not to do anything
+# if the compiler is not GNU; otherwise `cc_flags_set' is set to `yes'
+#
+
+# Get the compiler version in a way that works for gcc, egcs, and
+# pgcc unless a compiler version is already known
+#
+#   cc_vendor:    The compiler name: gcc, egcs, or pgcc
+#   cc_version:   Version number: 2.91.60, 2.7.2.1
+#
+if test X = "X$cc_flags_set"; then
+    cc_version="`$CC $CFLAGS -v 2>&1 |grep 'gcc version' |\
+	        sed 's/.*gcc version \([-a-z0-9\.]*\).*/\1/'`"
+    cc_vendor=`echo $cc_version |sed 's/\([a-z]*\).*/\1/'`
+    cc_version=`echo $cc_version |sed 's/[-a-z]//g'`
+    if test X = "X$cc_vendor" -a X != "X$cc_version"; then
+	cc_vendor=gcc
+    fi
+    if test "-" != "$cc_vendor-$cc_version"; then
+	echo "compiler '$CC' is GNU $cc_vendor-$cc_version"
+    fi
+fi
+
+# Warn about old GNU compilers that don't work right.
+case "$cc_vendor-$cc_version" in
+    gcc-2.7.*)
+	cat <<EOF
+    **
+    ** This compiler may be unable to properly compile the long long
+    ** data type used extensively by hdf5, although specifying
+    ** --disable-hsizet for configure may work around those bugs.
+    ** There may be other code generation problems also, especially
+    ** when optimizations are enabled.  Please upgrade to at least GNU
+    ** gcc version 2.8.1 before reporting bugs to the HDF5 team.
+    **
+EOF
+	sleep 5
+	;;
+	    
+    pgcc-2.*)
+        v2=`echo $cc_version |cut -f2 -d.`
+	v3=`echo $cc_version |cut -f3 -d.`
+	v=`expr $v2 '*' 1000 + $v3`
+	if test $v -le 91066; then
+	    cat <<EOF
+    **
+    ** This compiler may have problems allocating registers for long
+    ** long data types when optimizations are enabled. There may be
+    ** other code generation problems as well. We know of no version
+    ** of pgcc which is capable of compiling HDF5 in production mode.
+    ** Please use gcc-2.8 or egcs-1.1.1 before reporting bugs.
+    **
+EOF
+	    sleep 5
+	fi
+	;;
+esac
+
+# Architecture-specific flags
+case "$host_cpu" in
+    i686)
+	ARCH=${ARCH:="-mcpu=pentiumpro -march=pentiumpro -malign-double"}
+	;;
+esac
+
+# Compiler flags
+case "$cc_vendor-$cc_version" in
+    gcc-2.7*)
+	# General
+	CFLAGS="$CFLAGS -ansi"
+
+	# Production
+	PROC_CFLAGS="-O3 $NOFP -finline-functions -Wno-shadow"
+	PROD_CPPFLAGS=
+
+	# Debug
+	DEBUG_CFLAGS="-g -fverbose-asm -Wno-shadow"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+
+	# Profile
+	PROFILE_CFLAGS=-pg
+	PROFILE_CPPFLAGS=
+
+	# Flags are set
+	cc_flags_set=yes
+	;;
+
+    gcc-2.8.*)
+        # General
+        CFLAGS="$CFLAGS -Wsign-compare"
+
+	# Production
+	PROD_CFLAGS="$ARCH -O3 $NOFP -finline-functions -fschedule-insns2 -Wno-shadow"
+	PROD_CPPFLAGS=
+
+	# Debug
+	DEBUG_CFLAGS="-g -fverbose-asm -Wno-shadow"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+
+	# Profile
+	PROFILE_CFLAGS=-pg
+	PROFILE_CPPFLAGS=
+
+	# Flags are set
+	cc_flags_set=yes
+	;;
+
+    egcs-2.*|pgcc-2.*)
+	# General
+	CFLAGS="$CFLAGS -Wsign-compare"
+
+	# Production
+	PROD_CFLAGS="$ARCH -O6 $NOFP -Wno-shadow"
+	PROD_CPPFLAGS=
+
+	# Debug
+	DEBUG_CFLAGS="-g -fverbose-asm -Wno-shadow"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+
+	# Profile
+	PROFILE_CFLAGS=-pg
+	PROFILE_CPPFLAGS=
+
+	# Flags are set
+	cc_flags_set=yes
+	;;
+
+    gcc-*|egcs-*|pgcc-*)
+        # This must be some other GNU compiler that we don't know about.
+        # Just use fairly generic flags.
+
+	# Production
+	PROD_CFLAGS=-O
+	PROD_CPPFLAGS=
+
+	# Debug
+	DEBUG_CFLAGS=-g
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+
+	# Profile
+	PROFILE_CFLAGS=-pg
+	PROFILE_CPPFLAGS=
+
+	# Flags are set
+	cc_flags_set=yes
+	;;
+esac
+
+# Clear cc info if no flags set
+if test X = "X$cc_flags_set"; then
+    cc_vendor=
+    cc_version=
+fi

config/hpux10.20

@@ -3,36 +3,34 @@
 # This file is part of the HDF5 build script.  It is processed shortly
 # after configure starts and defines, among other things, flags for
 # the various compile modes.
+#
+# See BlankForm in this directory for details.
 
+# Default compiler is `cc'
+if test "X-" =  "X-$CC"; then
+    CC=cc
+    CC_BASENAME=cc
+fi
 
-#----------------------------------------------------------------------------
-# Compiler flags. The CPPFLAGS values should not include package debug
-# flags like `-DH5G_DEBUG' since these are added with the
-# `--enable-debug' switch of configure.
+# Flags
+case "X-$CC" in
+    X-gcc)
+	CFLAGS="$CFLAGS -Wsign-compare" #Only works for some versions
+	DEBUG_CFLAGS="-g -fverbose-asm"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+	PROD_CFLAGS="-O3"
+	PROD_CPPFLAGS=
+	PROFILE_CFLAGS="-pg"
+	PROFILE_CPPFLAGS=
+	;;
 
-# What must *always* be present for things to compile correctly?
-CFLAGS="$CFLAGS -Ae"
-#CPPFLAGS="$CPPFLAGS -I."
-
-# What compiler flags should be used for code development?
-DEBUG_CFLAGS=
-DEBUG_CPPFLAGS=
-
-# What compiler flags should be used for building a production
-# library?
-PROD_CFLAGS=
-PROD_CPPFLAGS=
-
-# What compiler flags enable code profiling?
-PROFILE_CFLAGS=
-PROFILE_CPPFLAGS=
-
-
-#----------------------------------------------------------------------------
-# Values for overriding configuration tests when cross compiling.
-# This includes compiling on some machines where the serial front end
-# compiles for a parallel back end.
-
-# Set this to `yes' or `no' depending on whether the target is big
-# endian or little endian.
-#ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}
+    *)
+	CFLAGS="$CFLAGS -Ae"
+	DEBUG_CFLAGS=-g
+	DEBUG_CPPFLAGS="-Ae"
+	PROD_CFLAGS=-O
+	PROD_CPPFLAGS="-Ae"
+	PROFILE_CFLAGS=
+	PROFILE_CPPFLAGS="-Ae"
+	;;
+esac

config/hpux9.03

@@ -0,0 +1,36 @@
+#							-*- shell-script -*-
+#
+# This file is part of the HDF5 build script.  It is processed shortly
+# after configure starts and defines, among other things, flags for
+# the various compile modes.
+#
+# See BlankForm in this directory for details
+
+# Default compiler is `cc'
+if test "X-" =  "X-$CC"; then
+    CC=cc
+    CC_BASENAME=cc
+fi
+
+# Flags
+case "X-$CC" in
+    X-gcc)
+	CFLAGS="$CFLAGS -Wsign-compare" #Only works for some versions
+	DEBUG_CFLAGS="-g -fverbose-asm"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+	PROD_CFLAGS="-O3"
+	PROD_CPPFLAGS=
+	PROFILE_CFLAGS="-pg"
+	PROFILE_CPPFLAGS=
+	;;
+
+    *)
+	CFLAGS="$CFLAGS -Ae"
+	DEBUG_CFLAGS=-g
+	DEBUG_CPPFLAGS=
+	PROD_CFLAGS=
+	PROD_CPPFLAGS=
+	PROFILE_CFLAGS=
+	PROFILE_CPPFLAGS=
+	;;
+esac

config/intel-osf1

@@ -3,24 +3,29 @@
 # This file is part of the HDF5 build script.  It is processed shortly
 # after configure starts and defines, among other things, flags for
 # the various compile modes.
+#
+# See BlankForm in this directory for details.
 
+# The default compiler is `cicc'
+if test "X-" =  "X-$CC"; then
+    CC=cicc
+    CC_BASENAME=cicc
+fi
 
-#----------------------------------------------------------------------------
-# Compiler flags. The CPPFLAGS values should not include package debug
-# flags like `-DH5G_DEBUG' since these are added with the
-# `--enable-debug' switch of configure.
+# The default archiver is `xar'
+AR=${AR:-xar}
 
-# Sometimes a particular compiler must be used.  If that's the case
-# then uncomment the following line.  Otherwise the main configure
-# script will try to detect the compiler automatically.
-CC=cicc
-AR=xar
+# There is no ranlib
 RANLIB=:
-LIBS="-L./ -L../ -lnoop_stubs"
-RUNTEST="yod -sz 1"
+
+# Additional libraries
+LDFLAGS="$LDFLAGS -lnoop_stubs"
+
+# How to run serial and parallel test programs
+RUNSERIAL="yod -sz 1"
+RUNPARALLEL="yod -sz 8"
 
 # What must *always* be present for things to compile correctly?
-CFLAGS="$CFLAGS -DDOS386"
 #CPPFLAGS="$CPPFLAGS -I."
 
 # What compiler flags should be used for code development?
@@ -36,17 +41,20 @@ PROD_CPPFLAGS=
 PROFILE_CFLAGS=-pg
 PROFILE_CPPFLAGS=
 
-
-#----------------------------------------------------------------------------
-# Values for overriding configuration tests when cross compiling.
-# This includes compiling on some machines where the serial front end
-# compiles for a parallel back end.
-
-# Set this to `yes' or `no' depending on whether the target is big
-# endian or little endian.
-#ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}
+# Turn off shared lib option.  It does not work for TFLOPS yet.
+enable_shared="${enable_shared:-no}"
 
 # Set this to the width required by printf() to print type `long
 # long'.  For instance, if the format would be `%lld' then set it to
 # `ll' or if the format would be `%qd' set it to `q'.
 hdf5_cv_printf_ll=${hdf5_cv_printf_ll='ll'}
+
+# Hard set sizeof_intn_t to 0 because they are not supported.
+ac_cv_sizeof_int16_t=${ac_cv_sizeof_int16_t='0'}
+ac_cv_sizeof_int32_t=${ac_cv_sizeof_int32_t='0'}
+ac_cv_sizeof_int64_t=${ac_cv_sizeof_int64_t='0'}
+ac_cv_sizeof_int8_t=${ac_cv_sizeof_int8_t='0'}
+ac_cv_sizeof_uint16_t=${ac_cv_sizeof_uint16_t='0'}
+ac_cv_sizeof_uint32_t=${ac_cv_sizeof_uint32_t='0'}
+ac_cv_sizeof_uint64_t=${ac_cv_sizeof_uint64_t='0'}
+ac_cv_sizeof_uint8_t=${ac_cv_sizeof_uint8_t='0'}

config/irix5.3

@@ -1,50 +0,0 @@
-#							-*- shell-script -*-
-#
-# This file is part of the HDF5 build script.  It is processed shortly
-# after configure starts and defines, among other things, flags for
-# the various compile modes.
-
-
-#----------------------------------------------------------------------------
-# Compiler flags. The CPPFLAGS values should not include package debug
-# flags like `-DH5G_DEBUG' since these are added with the
-# `--enable-debug' switch of configure.
-
-# Sometimes a particular compiler must be used.  If that's the case
-# then uncomment the following line.  Otherwise the main configure
-# script will try to detect the compiler automatically.
-CC=cc
-RANLIB=:
-
-# What must *always* be present for things to compile correctly?
-CFLAGS="$CFLAGS -ansi -fullwarn -woff 799"
-#CPPFLAGS="$CPPFLAGS -I."
-
-# What compiler flags should be used for code development?
-DEBUG_CFLAGS=-g
-DEBUG_CPPFLAGS=
-
-# What compiler flags should be used for building a production
-# library?
-PROD_CFLAGS=-O
-PROD_CPPFLAGS=
-
-# What compiler flags enable code profiling?
-PROFILE_CFLAGS=-pg
-PROFILE_CPPFLAGS=
-
-
-#----------------------------------------------------------------------------
-# Values for overriding configuration tests when cross compiling.
-# This includes compiling on some machines where the serial front end
-# compiles for a parallel back end.
-
-# Set this to `yes' or `no' depending on whether the target is big
-# endian or little endian.
-#ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}
-
-# Set this to the width required by printf() to print type `long
-# long'.  For instance, if the format would be `%lld' then set it to
-# `ll' or if the format would be `%qd' set it to `q'.
-#hdf5_cv_printf_ll=${hdf5_cv_printf_ll='ll'}
-

config/irix5.x

@@ -0,0 +1,50 @@
+#							-*- shell-script -*-
+#
+# This file is part of the HDF5 build script.  It is processed shortly
+# after configure starts and defines, among other things, flags for
+# the various compile modes.
+#
+# See BlankForm in this directory for details
+
+# The default compiler is `cc' and there is no ranlib.
+if test "X-" =  "X-$CC"; then
+    CC=cc
+    CC_BASENAME=cc
+fi
+RANLIB=:
+
+case "X-$CC_BASENAME" in
+    X-gcc)
+	CFLAGS="$CFLAGS -Wsign-compare" #Only works for some versions
+	DEBUG_CFLAGS="-g -fverbose-asm"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+	PROD_CFLAGS="-O3"
+	PROD_CPPFLAGS=
+	PROFILE_CFLAGS="-pg"
+	PROFILE_CPPFLAGS=
+	;;
+
+    *)
+        # Do *not* use -ansi because it prevents hdf5 from being able
+        # to read modification dates from the file. On some systems it
+        # can also result in compile errors in system header files
+        # since hdf5 includes a couple non-ANSI header files.
+        #CFLAGS="$CFLAGS -ansi"
+
+	# Always turn off these compiler warnings:
+        CFLAGS="$CFLAGS -woff 799"
+
+	# Extra debugging flags
+	DEBUG_CFLAGS=-g
+	DEBUG_CPPFLAGS=
+
+	# Extra production flags
+	# Note: higher optimizations relax alignment requirements needed.
+	PROD_CFLAGS=-O
+	PROD_CPPFLAGS=
+
+	# Extra profiling flags
+	PROFILE_CFLAGS=-pg
+	PROFILE_CPPFLAGS=
+	;;
+esac

config/irix6.2

@@ -1,39 +0,0 @@
-#							-*- shell-script -*-
-#
-# This file is part of the HDF5 build script.  It is processed shortly
-# after configure starts and defines, among other things, flags for
-# the various compile modes.
-
-
-#----------------------------------------------------------------------------
-# Compiler flags. The CPPFLAGS values should not include package debug
-# flags like `-DH5G_DEBUG' since these are added with the
-# `--enable-debug' switch of configure.
-RANLIB=:
-
-# What must *always* be present for things to compile correctly?
-CFLAGS="$CFLAGS -ansi -n32"
-#CPPFLAGS="$CPPFLAGS -I."
-
-# What compiler flags should be used for code development?
-DEBUG_CFLAGS=-g
-DEBUG_CPPFLAGS=
-
-# What compiler flags should be used for building a production
-# library?
-PROD_CFLAGS=-O
-PROD_CPPFLAGS=
-
-# What compiler flags enable code profiling?
-PROFILE_CFLAGS=-pg
-PROFILE_CPPFLAGS=
-
-
-#----------------------------------------------------------------------------
-# Values for overriding configuration tests when cross compiling.
-# This includes compiling on some machines where the serial front end
-# compiles for a parallel back end.
-
-# Set this to `yes' or `no' depending on whether the target is big
-# endian or little endian.
-#ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}

config/irix6.x

@@ -0,0 +1,87 @@
+#							-*- shell-script -*-
+#
+# This file is part of the HDF5 build script.  It is processed shortly
+# after configure starts and defines, among other things, flags for
+# the various compile modes.
+#
+# See BlankForm in this directory for details.
+
+# Use SGI supplied C compiler by default.  There is no ranlib
+if test "X-" =  "X-$CC"; then
+    CC='cc'
+    CC_BASENAME=cc
+fi
+RANLIB=:
+
+# Compiler flags
+case "X-$CC_BASENAME" in
+    X-gcc)
+	CFLAGS="$CFLAGS -Wsign-compare" #Only works for some versions
+	DEBUG_CFLAGS="-g -fverbose-asm"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+	PROD_CFLAGS="-O3"
+	PROD_CPPFLAGS=
+	PROFILE_CFLAGS="-pg"
+	PROFILE_CPPFLAGS=
+	;;
+
+    *)
+
+        # Check for old versions of the compiler that don't work right.
+        case "`$CC -version 2>&1 |head -1`" in
+	    "Mongoose Compilers: Version 7.00")
+		echo "  +---------------------------------------------------+"
+		echo "  | You have an old version of cc (Mongoose Compilers |"
+		echo "  | version 7.00).  Please upgrade to MIPSpro version |"
+		echo "  | 7.2.1.2m (patches are available from the SGI web  |"
+		echo "  | site).  The 7.00 version may generate incorrect   |"
+		echo "  | code, especially when optimizations are enabled.  |"
+		echo "  +---------------------------------------------------+"
+		sleep 5
+		;;
+	esac
+
+        # Do *not* use -ansi because it prevents hdf5 from being able
+        # to read modification dates from the file. On some systems it
+        # can also result in compile errors in system header files
+        # since hdf5 includes a couple non-ANSI header files.
+        #CFLAGS="$CFLAGS -ansi"
+
+	# Always turn off these compiler warnings for the -64 compiler:
+	#    1174:  function declared but not used
+	#    1429:  the `long long' type is not standard
+	#    1209:  constant expressions
+	#    1196:  __vfork() (this is an SGI config problem)
+	#    1685:  turn off warnings about turning off invalid warnings
+	CFLAGS="$CFLAGS -woff 1174,1429,1209,1196,1685"
+
+	# Always turn off these compiler warnings for the old compiler:
+	#    799:   the `long long' type is not standard
+	#    803:   turn off warnings about turning off invalid warnings
+        #    835:   __vfork() (this is an SGI config problem)
+	CFLAGS="$CFLAGS -woff 799,803,835"
+
+	# Always turn off these loader warnings:
+	# (notice the peculiar syntax)
+	#      47:  branch instructions that degrade performance on R4000
+	#      84:  a library is not used
+	#      85:  duplicate definition preemption (from -lnsl)
+	#     134:  duplicate weak definition preemption (from -lnsl)
+	CFLAGS="$CFLAGS -Wl,-woff,47,-woff,84,-woff,85,-woff,134"
+
+	# Extra debugging flags
+	DEBUG_CFLAGS="-g -fullwarn"
+	DEBUG_CPPFLAGS=
+
+	# Extra production flags
+	PROD_CFLAGS=-O
+	PROD_CPPFLAGS=
+
+	# Extra profiling flags
+	PROFILE_CFLAGS=-pg
+	PROFILE_CPPFLAGS=
+
+	# Turn off shared lib option.  It does not work for IRIX64 yet.
+	test `uname -s` = IRIX64 && enable_shared="${enable_shared:-no}"
+	;;
+esac

config/irix64

@@ -1,50 +0,0 @@
-#							-*- shell-script -*-
-#
-# This file is part of the HDF5 build script.  It is processed shortly
-# after configure starts and defines, among other things, flags for
-# the various compile modes.
-
-
-#----------------------------------------------------------------------------
-# Compiler flags. The CPPFLAGS values should not include package debug
-# flags like `-DH5G_DEBUG' since these are added with the
-# `--enable-debug' switch of configure.
-
-# Use SGI supplied C compiler
-CC="cc"
-RANLIB=:
-
-# What must *always* be present for things to compile correctly?
-# Always turn off these warnings:
-#    1174:  function declared but not used
-#    1429:  the `long long' type is not standard
-#    1209:  constant expressions
-#    1196:  __vfork() (this is an SGI config problem)
-#
-CFLAGS="$CFLAGS -fullwarn -ansi -64 -woff 1174,1429,1209,1196"
-#CPPFLAGS="$CPPFLAGS -I."
-
-# What compiler flags should be used for code development?
-DEBUG_CFLAGS=-g
-DEBUG_CPPFLAGS=
-
-# What compiler flags should be used for building a production
-# library?
-PROD_CFLAGS=-O
-PROD_CPPFLAGS=
-
-# What compiler flags enable code profiling?
-PROFILE_CFLAGS=-pg
-PROFILE_CPPFLAGS=
-
-
-#----------------------------------------------------------------------------
-# Values for overriding configuration tests when cross compiling.
-# This includes compiling on some machines where the serial front end
-# compiles for a parallel back end.
-
-# Set this to `yes' or `no' depending on whether the target is big
-# endian or little endian.
-#ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}
-#!/bin/sh
-

config/linux

@@ -1,58 +0,0 @@
-#							-*- shell-script -*-
-#
-# This file is part of the HDF5 build script.  It is processed shortly
-# after configure starts and defines, among other things, flags for
-# the various compile modes.
-
-
-#----------------------------------------------------------------------------
-# Compiler flags. The CPPFLAGS values should not include package debug
-# flags like `-DH5G_DEBUG' since these are added with the
-# `--enable-debug' switch of configure.
-CC=${CC:-gcc}
-case `$CC -v 2>&1 |tail -1 |sed 's/gcc version //'` in
-   2.7.*)
-       echo "  +------------------------------------------------+"
-       echo "  | You have an old version of gcc. Please upgrade |"
-       echo "  | to 2.8.1 or better.  Continuing anyway, but    |"
-       echo "  | code generation may be wrong on some platforms.|"
-       echo "  +------------------------------------------------+"
-       sleep 5
-       ;;
-   2.8.*)
-       CFLAGS="$CFLAGS -Wundef -Wsign-compare"
-       ;;
-esac
-
-# What must *always* be present for things to compile correctly?
-CFLAGS="$CFLAGS -ansi"
-#CPPFLAGS="$CPPFLAGS -I."
-
-# What compiler flags should be used for code development?
-DEBUG_CFLAGS="-g -fverbose-asm"
-DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
-
-# What compiler flags should be used for building a production
-# library?
-PROD_CFLAGS="-mcpu=pentiumpro -march=pentiumpro -O3 -finline-functions -malign-double -fomit-frame-pointer -fschedule-insns2"
-PROD_CPPFLAGS=
-
-# What compiler flags enable code profiling?
-PROFILE_CFLAGS=-pg
-PROFILE_CPPFLAGS=
-
-#----------------------------------------------------------------------------
-# Enable parallel support by default for Robb's development system.
-#
-if [ 'robb@arborea' = `whoami`@`hostname` ]; then
-    enable_parallel=${enable_parallel:-yes}
-fi
-
-#----------------------------------------------------------------------------
-# Values for overriding configuration tests when cross compiling.
-# This includes compiling on some machines where the serial front end
-# compiles for a parallel back end.
-
-# Set this to `yes' or `no' depending on whether the target is big
-# endian or little endian.
-#ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}

config/linux-gnu

@@ -0,0 +1,4 @@
+#							-*- shell-script -*-
+# This is the same as linux-gnulibc1
+
+. $srcdir/config/linux-gnulibc1

config/linux-gnulibc1

@@ -0,0 +1,19 @@
+#							-*- shell-script -*-
+#
+# This file is part of the HDF5 build script.  It is processed shortly
+# after configure starts and defines, among other things, flags for
+# the various compile modes.
+#
+# See BlankForm in this directory for details.
+
+# The default compiler is `gcc'.
+if test "X-" =  "X-$CC"; then
+    CC=gcc
+    CC_BASENAME=gcc
+fi
+
+# Omit frame pointer for optimized code?
+NOFP=${NOFP:=-fomit-frame-pointer}
+
+# Figure out compiler flags
+. $srcdir/config/gnu-flags

config/linux-gnulibc2

@@ -1,7 +1,10 @@
 #							-*- shell-script -*-
+#
 # This file is part of the HDF5 build script.  It is processed shortly
 # after configure starts and defines, among other things, flags for
 # the various compile modes.
+#
+# See BlankForm in this directory for details.
 
-. config/linux
-CPP=/usr/bin/cpp
+# Same as with gnulibc1 for now
+. $srcdir/config/linux-gnulibc1

config/powerpc-ibm-aix4.2.1.0

@@ -1,39 +0,0 @@
-#							-*- shell-script -*-
-#
-# This file is part of the HDF5 build script.  It is processed shortly
-# after configure starts and defines, among other things, flags for
-# the various compile modes.
-
-
-#----------------------------------------------------------------------------
-# Compiler flags. The CPPFLAGS values should not include package debug
-# flags like `-DH5G_DEBUG' since these are added with the
-# `--enable-debug' switch of configure.
-
-# What must *always* be present for things to compile correctly?
-#CFLAGS="$CFLAGS -ansi"
-#CPPFLAGS="$CPPFLAGS -I."
-
-# What compiler flags should be used for code development?
-DEBUG_CFLAGS=
-DEBUG_CPPFLAGS=
-
-# What compiler flags should be used for building a production
-# library?
-PROD_CFLAGS=
-PROD_CPPFLAGS=
-
-# What compiler flags enable code profiling?
-PROFILE_CFLAGS=
-PROFILE_CPPFLAGS=
-
-
-#----------------------------------------------------------------------------
-# Values for overriding configuration tests when cross compiling.
-# This includes compiling on some machines where the serial front end
-# compiles for a parallel back end.
-
-# Set this to `yes' or `no' depending on whether the target is big
-# endian or little endian.
-ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}
-

config/powerpc-ibm-aix4.x

@@ -0,0 +1,21 @@
+#							-*- shell-script -*-
+#
+# This file is part of the HDF5 build script.  It is processed shortly
+# after configure starts and defines, among other things, flags for
+# the various compile modes.
+#
+# See BlankForm in this directory for details.
+
+# Cross compiling defaults
+ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}
+ac_cv_header_stdc=${ac_cv_header_stdc='yes'}
+ac_cv_sizeof_short=${ac_cv_sizeof_short=2}
+ac_cv_sizeof_int=${ac_cv_sizeof_int=4}
+ac_cv_sizeof_long=${ac_cv_sizeof_long=4}
+ac_cv_sizeof_long_long=${ac_cv_sizeof_long_long=8}
+ac_cv_sizeof_float=${ac_cv_sizeof_float=4}
+ac_cv_sizeof_double=${ac_cv_sizeof_double=8}
+ac_cv_sizeof_long_double=${ac_cv_sizeof_long_double=8}
+ac_cv_sizeof_int=${ac_cv_sizeof_int=4}
+ac_cv_sizeof_size_t=${ac_cv_sizeof_size_t=4}
+ac_cv_sizeof_off_t=${ac_cv_sizeof_off_t=8}

config/rs6000-ibm-aix4.1.4.0

@@ -1,39 +0,0 @@
-#							-*- shell-script -*-
-#
-# This file is part of the HDF5 build script.  It is processed shortly
-# after configure starts and defines, among other things, flags for
-# the various compile modes.
-
-
-#----------------------------------------------------------------------------
-# Compiler flags. The CPPFLAGS values should not include package debug
-# flags like `-DH5G_DEBUG' since these are added with the
-# `--enable-debug' switch of configure.
-
-# What must *always* be present for things to compile correctly?
-#CFLAGS="$CFLAGS -ansi"
-#CPPFLAGS="$CPPFLAGS -I."
-
-# What compiler flags should be used for code development?
-DEBUG_CFLAGS=
-DEBUG_CPPFLAGS=
-
-# What compiler flags should be used for building a production
-# library?
-PROD_CFLAGS=
-PROD_CPPFLAGS=
-
-# What compiler flags enable code profiling?
-PROFILE_CFLAGS=
-PROFILE_CPPFLAGS=
-
-
-#----------------------------------------------------------------------------
-# Values for overriding configuration tests when cross compiling.
-# This includes compiling on some machines where the serial front end
-# compiles for a parallel back end.
-
-# Set this to `yes' or `no' depending on whether the target is big
-# endian or little endian.
-ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}
-

config/rs6000-ibm-aix4.x

@@ -0,0 +1,10 @@
+#							-*- shell-script -*-
+#
+# This file is part of the HDF5 build script.  It is processed shortly
+# after configure starts and defines, among other things, flags for
+# the various compile modes.
+#
+# See BlankForm in this directory for details.
+
+# Cross compiling defaults
+ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}

config/solaris2.5

@@ -1,41 +0,0 @@
-#							-*- shell-script -*-
-#
-# This file is part of the HDF5 build script.  It is processed shortly
-# after configure starts and defines, among other things, flags for
-# the various compile modes.
-
-
-#----------------------------------------------------------------------------
-# Compiler flags. The CPPFLAGS values should not include package debug
-# flags like `-DH5G_DEBUG' since these are added with the
-# `--enable-debug' switch of configure.
-
-# We can only use gcc
-CC=gcc
-
-# What must *always* be present for things to compile correctly?
-CFLAGS="$CFLAGS -ansi"
-#CPPFLAGS="$CPPFLAGS -I."
-
-# What compiler flags should be used for code development?
-DEBUG_CFLAGS=-g
-DEBUG_CPPFLAGS=
-
-# What compiler flags should be used for building a production
-# library?
-PROD_CFLAGS=-O2
-PROD_CPPFLAGS=
-
-# What compiler flags enable code profiling?
-PROFILE_CFLAGS=-pg
-PROFILE_CPPFLAGS=
-
-
-#----------------------------------------------------------------------------
-# Values for overriding configuration tests when cross compiling.
-# This includes compiling on some machines where the serial front end
-# compiles for a parallel back end.
-
-# Set this to `yes' or `no' depending on whether the target is big
-# endian or little endian.
-#ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}

config/solaris2.x

@@ -0,0 +1,28 @@
+#							-*- shell-script -*-
+#
+# This file is part of the HDF5 build script.  It is processed shortly
+# after configure starts and defines, among other things, flags for
+# the various compile modes.
+#
+# See BlankForm in this directory for details
+
+# The default compiler is `gcc'
+if test "X-" =  "X-$CC"; then
+    CC=gcc
+    CC_BASENAME=gcc
+fi
+
+# Try gcc compiler flags
+. $srcdir/config/gnu-flags
+
+# Try solaris native compiler flags
+if test "X-" = "X-$cc_flags_set"; then
+    CFLAGS="-erroff=%none"
+    DEBUG_CFLAGS=-g
+    DEBUG_CPPFLAGS="-DH5F_LOW_DFLT=H5F_LOW_SEC2"
+    PROD_CFLAGS=-xO2
+    PROD_CPPFLAGS=
+    PROFILE_CFLAGS=-xpg
+    PROFILE_CPPFLAGS=
+    cc_flags_set=yes
+fi

config/unicosmk

@@ -0,0 +1,138 @@
+#							-*- shell-script -*-
+#
+# This file is part of the HDF5 build script.  It is processed shortly
+# after configure starts and defines, among other things, flags for
+# the various compile modes.
+
+
+#----------------------------------------------------------------------------
+# Compiler flags. The CPPFLAGS values should not include package debug
+# flags like `-DH5G_DEBUG' since these are added with the
+# `--enable-debug' switch of configure.
+#----------------------------------------------------------------------------
+
+
+# Choosing a C Compiler
+# ---------------------
+#
+# The user should be able to specify the compiler by setting the CC
+# environment variable to the name of the compiler and any switches it 
+# requires for proper operation.  If CC is unset then this script may
+# set it.  If CC is unset by time this script completes then configure 
+# will try `gcc' and `cc' in that order (perhaps some others too).
+#
+# Note: Code later in this file may depend on the value of $CC_BASENAME
+#       in order to distinguish between different compilers when
+#       deciding which compiler command-line switches to use.  This
+#       variable is set based on the incoming value of $CC and is only
+#       used within this file.
+
+if test "X-" =  "X-$CC"; then
+    CC=cc
+    CC_BASENAME=cc
+fi
+# no need to use RANLIB
+RANLIB=:
+
+
+# C Compiler and Preprocessor Flags
+# ---------------------------------
+#
+# Flags that end with `_CFLAGS' are always passed to the compiler.
+# Flags that end with `_CPPFLAGS' are passed to the compiler when
+# compiling but not when linking.
+#
+# DEBUG_CFLAGS		Flags to pass to the compiler to create a
+# DEBUG_CPPFLAGS	library suitable for use with debugging
+#			tools. Usually this list will exclude
+#			optimization switches (like `-O') and include
+#			switches that turn on symbolic debugging
+#			support (like `-g').
+#
+# PROD_CFLAGS		Flags to pass to the compiler to create a
+# PROD_CPPFLAGS		production version of the library.  These
+#			usualy exclude symbolic debugging switches
+#			(like `-g') and include optimization switches
+#			(like `-O').
+#
+# PROFILE_CFLAGS	Flags to pass to the compiler to create a
+# PROFILE_CPPFLAGS	library suitable for performance testing (like 
+# 			`-pg').  This may or may not include debugging 
+# 			or production flags.
+#			
+# CFLAGS		Flags can be added to this variable which
+#			might already be partially initialized.  These 
+#			flags will always be passed to the compiler
+#			and should include switches to turn on full
+#			warnings.  HDF5 attempts to be ANSI and Posix
+#			compliant and employ good programming
+#			practices resulting in few if any
+#			warnings.
+#
+#			Warning flags do not have to be added to CFLAGS
+#			variable if the compiler is the GNU gcc
+#			compiler or a descendent of gcc such as EGCS or PGCC.
+#
+#			The CFLAGS should contains *something* or else 
+#			configure will probably add `-g'.  For most
+#			systems this isn't a problem but some systems
+#			will disable optimizations in favor of the
+#			`-g'.
+#			
+#
+# These flags should be set according to the compiler being used.
+# There are two ways to check the compiler.  You can try using `-v' or 
+# `--version' to see if the compiler will print a version string.  You 
+# can use the value of $CC_BASENAME which is the base name of the
+# first word in $CC (note that the value of CC may have changed
+# above).
+
+case $CC_BASENAME in
+    gcc)
+	CFLAGS="$CFLAGS -Wsign-compare" #Only works for some versions
+	DEBUG_CFLAGS="-g -fverbose-asm"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+	PROD_CFLAGS="-O3 -fomit-frame-pointer"
+	PROD_CPPFLAGS=
+	PROFILE_CFLAGS="-pg"
+	PROFILE_CPPFLAGS=
+	;;
+
+    cc)
+	CFLAGS="$CFLAGS"
+	DEBUG_CFLAGS="-g -h zero"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+	PROD_CFLAGS="-O2"
+	PROD_CPPFLAGS=
+	PROFILE_CFLAGS="-pg"
+	PROFILE_CPPFLAGS=
+	;;
+
+    *)
+	CFLAGS="$CFLAGS -ansi"
+	DEBUG_CFLAGS="-g"
+	DEBUG_CPPFLAGS="-DH5F_OPT_SEEK=0 -DH5F_LOW_DFLT=H5F_LOW_SEC2"
+	PROD_CFLAGS="-O"
+	PROD_CPPFLAGS=
+	PROFILE_CFLAGS="-pg"
+	PROFILE_CPPFLAGS=
+	;;
+esac
+
+
+
+# Overriding Configure Tests
+# --------------------------
+#
+# Values for overriding configuration tests when cross compiling.
+# This includes compiling on some machines where the serial front end
+# compiles for a parallel back end.
+
+# Set this to `yes' or `no' depending on whether the target is big
+# endian or little endian.
+#ac_cv_c_bigendian=${ac_cv_c_bigendian='yes'}
+
+# Set this to the width required by printf() to print type `long
+# long'.  For instance, if the format would be `%lld' then set it to
+# `ll' or if the format would be `%qd' set it to `q'.
+#hdf5_cv_printf_ll=${hdf5_cv_printf_ll='ll'}

configure.in

@@ -1,10 +1,8 @@
-dnl Process this file with autoconf to produce configure.  -*-indented-text-*-
+dnl Process this file with autoconf to produce configure.
 dnl
 dnl Copyright (C) 1997 National Center for Supercomputing Applications.
 dnl                    All rights reserved.
 
-
-
 dnl ----------------------------------------------------------------------
 dnl Initialize configure.
 dnl
@@ -15,6 +13,13 @@ AC_CONFIG_AUX_DIR(bin)
 AC_CANONICAL_HOST
 AC_SUBST(CPPFLAGS)
 
+dnl ----------------------------------------------------------------------
+dnl Dump all shell variables values.
+dnl
+AC_MSG_CHECKING(shell variables initial values)
+set >&5
+AC_MSG_RESULT(done)
+
 dnl ----------------------------------------------------------------------
 dnl Check that the cache file was build on the same host as what we're
 dnl running on now.
@@ -28,8 +33,6 @@ elif test $hdf5_cv_host != $host; then
    AC_MSG_ERROR(config.cache file is invalid)
 fi
 
-
-
 dnl ----------------------------------------------------------------------
 dnl Source any special files that we need.  These files normally aren't
 dnl present but can be used by the maintainers to fine tune things like
@@ -44,33 +47,65 @@ dnl	OS
 dnl	VENDOR
 dnl	CPU
 dnl
-AC_MSG_CHECKING(for host config file)
+dnl If the `OS' ends with a version number then remove it. For instance,
+dnl `freebsd3.1' would become `freebsd'
+case $host_os in
+    aix4.*)
+	host_os_novers=aix4.x
+	;;
+    freebsd*)
+	host_os_novers=freebsd
+	;;
+    irix5.*)
+	host_os_novers=irix5.x
+	;;
+    irix6.*)
+	host_os_novers=irix6.x
+	;;
+    osf4.*)
+	host_os_novers=osf4.x
+	;;
+    solaris2.*)
+	host_os_novers=solaris2.x
+	;;
+    *)
+	host_os_novers=$host_os
+	;;
+esac
+
 host_config="none"
-for f in $host \
-         $host_vendor-$host_os \
-         $host_cpu-$host_os \
+for f in $host_cpu-$host_vendor-$host_os \
+	 $host_cpu-$host_vendor-$host_os_novers \
+	 $host_vendor-$host_os \
+         $host_vendor-$host_os_novers \
+	 $host_cpu-$host_os \
+         $host_cpu-$host_os_novers \
          $host_cpu-$host_vendor \
 	 $host_os \
+	 $host_os_novers \
 	 $host_vendor \
 	 $host_cpu ; do
-   if test -f config/$f; then
-      host_config=config/$f
+   AC_MSG_CHECKING(for config $f)
+   if test -f $srcdir/config/$f; then
+      host_config=$srcdir/config/$f
+      AC_MSG_RESULT(found)
       break
    fi
+   AC_MSG_RESULT(no)
 done
-AC_MSG_RESULT($host_config)
 if test $host_config != "none"; then
+   CC_BASENAME="`echo $CC |cut -f1 -d' ' |xargs basename 2>/dev/null`"
    . $host_config
 fi
 
-
 dnl ----------------------------------------------------------------------
 dnl Check for programs.
 dnl
 AC_PROG_CC
+CC_BASENAME="`echo $CC |cut -f1 -d' ' |xargs basename 2>/dev/null`"
 AC_PROG_MAKE_SET
 AC_PROG_INSTALL
-AC_PROG_RANLIB
+AM_PROG_LIBTOOL
 
 if test "X$AR" = "X"; then
    AC_CHECK_PROGS(AR,ar xar,:,$PATH)
@@ -94,61 +129,116 @@ if test Xyes = "X$GCC"; then
 fi
 
 dnl ----------------------------------------------------------------------
-dnl Production flags?
+dnl Production flags?  Save the value in $CONFIG_MODE so we have it for
+dnl the record.
 dnl
 AC_MSG_CHECKING(for production mode)
 AC_ARG_ENABLE(production,
-  [--enable-production=yes|no  Determines how to run the compiler.])
+  [  --enable-production     Determines how to run the compiler.])
 
 case "X-$enableval" in
    X-yes)
       AC_MSG_RESULT("production")
+      CONFIG_MODE=production
       CFLAGS="$CFLAGS $PROD_CFLAGS"
       CPPFLAGS="$CPPFLAGS $PROD_CPPFLAGS"
       ;;
    X-|X-no)
       AC_MSG_RESULT("development")
+      CONFIG_MODE=development
       CFLAGS="$CFLAGS $DEBUG_CFLAGS"
       CPPFLAGS="$CPPFLAGS $DEBUG_CPPFLAGS"
       ;;
    X-pg|X-profile)
       AC_MSG_RESULT("profile")
+      CONFIG_MODE=profile
       CFLAGS="$CFLAGS $PROFILE_CFLAGS"
       CPPFLAGS="$CPPFLAGS $PROFILE_CPPFLAGS"
       ;;
    *)
       AC_MSG_RESULT("user-defined")
+      CONFIG_MODE="$X-enableval"
       ;;
 esac
 
-
 dnl ----------------------------------------------------------------------
-dnl Check for libraries.  (none required yet)
+dnl Check for system libraries.
 dnl
-AC_CHECK_LIB(m, ceil)
-AC_CHECK_LIB(coug, main)	dnl ...for ASCI/Red
-AC_CHECK_LIB(z, compress2)
+AC_CHECK_LIB(m,ceil)
+AC_CHECK_LIB(nsl,xdr_int)	dnl ...for Solaris and hdf4
+AC_CHECK_LIB(coug,main)		dnl ...for ASCI/Red
+AC_CHECK_LIB(jpeg,main)		dnl ...required for linking hdf4 apps
 
 dnl ----------------------------------------------------------------------
-dnl Check for header files.
+dnl Check for system header files.
 dnl
 AC_HEADER_STDC
-AC_CHECK_HEADERS(unistd.h zlib.h)
+AC_HEADER_TIME
+dnl Unix
+AC_CHECK_HEADERS(sys/resource.h sys/time.h unistd.h sys/ioctl.h sys/stat.h)
+AC_CHECK_HEADERS(stddef.h setjmp.h stdint.h)
+dnl Windows
+AC_CHECK_HEADERS(io.h winsock.h sys/timeb.h)
 
+case $host in
+    alpha*-dec*-osf*)
+	dnl The <sys/sysinfo.h> and <sys/proc.h> are needed on the DEC
+	dnl Alpha to turn off UAC fixing. We do *not* attempt to
+	dnl locate these files on other systems because there are too
+	dnl many problems with including them.
+	AC_CHECK_HEADERS(sys/sysinfo.h sys/proc.h)
+	;;
+esac
 
 dnl ----------------------------------------------------------------------
 dnl Data types and their sizes.
 dnl
 AC_TYPE_OFF_T
-AC_TYPE_SIZE_T
+AC_CHECK_TYPE(size_t, unsigned long)
+AC_CHECK_TYPE(ssize_t, long)
 AC_C_BIGENDIAN
+AC_CHECK_SIZEOF(char, 1)
 AC_CHECK_SIZEOF(short, 2)
 AC_CHECK_SIZEOF(int, 4)
 AC_CHECK_SIZEOF(long, 4)
 AC_CHECK_SIZEOF(long long, 8)
+AC_CHECK_SIZEOF(__int64, 8)
 AC_CHECK_SIZEOF(float, 4)
 AC_CHECK_SIZEOF(double, 8)
 AC_CHECK_SIZEOF(long double, 8)
+
+dnl Posix.1g types (C9x)
+cat >>confdefs.h <<\EOF
+#include <sys/types.h>
+EOF
+AC_CHECK_SIZEOF(        int8_t, 1)
+AC_CHECK_SIZEOF(       uint8_t, 1)
+AC_CHECK_SIZEOF(  int_least8_t, 1)
+AC_CHECK_SIZEOF( uint_least8_t, 1)
+AC_CHECK_SIZEOF(   int_fast8_t, 1)
+AC_CHECK_SIZEOF(  uint_fast8_t, 1)
+
+AC_CHECK_SIZEOF(       int16_t, 2)
+AC_CHECK_SIZEOF(      uint16_t, 2)
+AC_CHECK_SIZEOF( int_least16_t, 2)
+AC_CHECK_SIZEOF(uint_least16_t, 2)
+AC_CHECK_SIZEOF(  int_fast16_t, 2)
+AC_CHECK_SIZEOF( uint_fast16_t, 2)
+
+AC_CHECK_SIZEOF(       int32_t, 4)
+AC_CHECK_SIZEOF(      uint32_t, 4)
+AC_CHECK_SIZEOF( int_least32_t, 4)
+AC_CHECK_SIZEOF(uint_least32_t, 4)
+AC_CHECK_SIZEOF(  int_fast32_t, 4)
+AC_CHECK_SIZEOF( uint_fast32_t, 4)
+
+AC_CHECK_SIZEOF(       int64_t, 8)
+AC_CHECK_SIZEOF(      uint64_t, 8)
+AC_CHECK_SIZEOF( int_least64_t, 8)
+AC_CHECK_SIZEOF(uint_least64_t, 8)
+AC_CHECK_SIZEOF(  int_fast64_t, 8)
+AC_CHECK_SIZEOF( uint_fast64_t, 8)
+
 AC_CHECK_SIZEOF(size_t, 4)
 cat >>confdefs.h <<\EOF
 #include <sys/types.h> /*for off_t definition*/
@@ -156,30 +246,205 @@ EOF
 AC_CHECK_SIZEOF(off_t, 4)
 
 AC_ARG_ENABLE(hsizet,
-  [--disable-hsizet          Datasets can normally be larger than memory
-                             and/or files but some compilers are unable to
-                             handle this (including versions of GCC before
-                             2.8.0).  Disabling the feature causes dataset
-                             sizes to be restricted to the size of core memory,
-                             or 'size_t'.],
+  [  --disable-hsizet        Datasets can normally be larger than memory
+                          and/or files but some compilers are unable to
+                          handle this (including versions of GCC before
+                          2.8.0).  Disabling the feature causes dataset
+                          sizes to be restricted to the size of core memory,
+                          or 'size_t'.],
   HSIZET=$enableval)
 AC_MSG_CHECKING(for sizeof hsize_t and hssize_t)
+AC_SUBST(HSIZET)
 case $HSIZET in
     no|small)
 	AC_MSG_RESULT(small)
+	HSIZET=small
 	;;
     *)
         AC_MSG_RESULT(large)
+	HSIZET=large
         AC_DEFINE(HAVE_LARGE_HSIZET)
 	;;
 esac
 
+dnl ----------------------------------------------------------------------
+dnl Is the GNU zlib present?  It has a header file `zlib.h' and a library
+dnl `-lz' and their locations might be specified with the `--enable-zlib'
+dnl command-line switch.  The value is an include path and/or a library path.
+dnl If the library path is specified then it must be preceded by a comma.
+dnl
+
+AC_ARG_WITH(zlib,[  --with-zlib=INC,LIB     Use the GNU zlib compression],
+            ,withval=yes)
+case $withval in
+    yes)
+	AC_CHECK_HEADERS(zlib.h)
+	AC_CHECK_LIB(z, compress)
+	;;
+    no)
+	AC_MSG_CHECKING(for GNU zlib)
+	AC_MSG_RESULT(suppressed)
+	;;
+    *)
+	zlib_inc="`echo $withval |cut -f1 -d,`"
+	if test "X" != "$zlib_inc"; then
+	    saved_CPPFLAGS="$CPPFLAGS"
+	    CPPFLAGS="$CPPFLAGS -I$zlib_inc"
+	    AC_CHECK_HEADERS(zlib.h,,CPPFLAGS="$saved_CPPFLAGS")
+        else
+	    AC_CHECK_HEADERS(zlib.h)
+	fi
+
+	zlib_lib="`echo $withval |cut -f2 -d, -s`"
+	if test "X" != "$zlb_lib"; then
+	    saved_LDFLAGS="$LDFLAGS"
+	    LDFLAGS="$LDFLAGS -L$zlib_lib"
+	    AC_CHECK_LIB(z, compress,,LDFLAGS="$saved_LDFLAGS")
+	else
+	    AC_CHECK_LIB(z, compress)
+	fi
+	;;
+esac
+	
+dnl ----------------------------------------------------------------------
+dnl Is HDF4 present?  If so then we can compile the h5toh4 converter. We
+dnl assume h5toh4 can be compiled and then prove otherwise when we don't find
+dnl a header file or library.
+dnl
+AC_SUBST(H5TOH4)
+H5TOH4=h5toh4
+AC_SUBST(TESTH5TOH4)
+TESTH5TOH4='$(srcdir)/testh5toh4'
+
+AC_ARG_WITH(hdf4,[  --with-hdf4=INC,LIB     Use the HDF4 library],,withval=yes)
+case $withval in
+    yes)
+	AC_CHECK_HEADERS(mfhdf.h,,unset H5TOH4 TESTH5TOH4)
+	AC_CHECK_LIB(df,main,,unset H5TOH4 TESTH5TOH4)
+	AC_CHECK_LIB(mfhdf,main,,unset H5TOH4 TESTH5TOH4)
+	;;
+    no)
+	AC_MSG_CHECKING(for HDF4)
+	AC_MSG_RESULT(suppressed)
+	unset H5TOH4 TESTH5TOH4
+	;;
+    *)
+	hdf4_inc="`echo $withval |cut -f1 -d,`"
+	if test "X" != "$hdf4_inc"; then
+	    saved_CPPFLAGS="$CPPFLAGS"
+	    CPPFLAGS="$CPPFLAGS -I$hdf4_inc"
+	    AC_CHECK_HEADERS(mfhdf.h,,
+	        CPPFLAGS="$saved_CPPFLAGS"
+	        unset H5TOH4 TESTH5TOH4
+            )
+	else
+	    AC_CHECK_HEADERS(mfhdf.h)
+	fi
+	
+	hdf4_lib="`echo $withval |cut -f2 -d, -s`"
+	if test "X" != "$hdf4_lib"; then
+	    saved_LDFLAGS="$LDFLAGS"
+	    LDFLAGS="$LDFLAGS -L$hdf4_lib"
+	    AC_CHECK_LIB(df,main,,unset H5TOH4 TESTH5TOH4)
+	    AC_CHECK_LIB(mfhdf,main,,unset H5TOH4 TESTH5TOH4)
+	else
+	    AC_CHECK_LIB(df,main)
+	    AC_CHECK_LIB(mfhdf,main)
+	fi
+	;;
+esac
+
+
+dnl ----------------------------------------------------------------------
+dnl How does one figure out the local time zone?  Anyone know of a
+dnl Posix way to do this?
+dnl
+
+dnl First check if `struct tm' has a `tm_gmtoff' member.
+AC_MSG_CHECKING(for tm_gmtoff in struct tm)
+AC_TRY_COMPILE([
+#include <sys/time.h>
+#include <time.h>],[struct tm tm; tm.tm_gmtoff=0;],
+AC_DEFINE(HAVE_TM_GMTOFF)
+AC_MSG_RESULT(yes),
+AC_MSG_RESULT(no))
+
+dnl check if `struct tm' has a `__tm_gmtoff' member.
+AC_MSG_CHECKING(for __tm_gmtoff in struct tm)
+AC_TRY_COMPILE([
+#include <sys/time.h>
+#include <time.h>],[struct tm tm; tm.__tm_gmtoff=0;],
+AC_DEFINE(HAVE___TM_GMTOFF)
+AC_MSG_RESULT(yes),
+AC_MSG_RESULT(no))
+
+dnl Check whether the global variable `timezone' is defined.
+AC_MSG_CHECKING(for global timezone variable)
+AC_TRY_LINK([
+#include <sys/time.h>
+#include <time.h>], [timezone=0;],
+AC_DEFINE(HAVE_TIMEZONE)
+AC_MSG_RESULT(yes),
+AC_MSG_RESULT(no))
+
+dnl Check whether `struct timezone' is defined.
+AC_STRUCT_TIMEZONE
+AC_MSG_CHECKING(for struct timezone)
+AC_TRY_COMPILE([
+#include <sys/types.h>
+#include <sys/time.h>
+#include <time.h>],[struct timezone tz; tz.tz_minuteswest=0;],
+AC_DEFINE(HAVE_STRUCT_TIMEZONE)
+AC_MSG_RESULT(yes),
+AC_MSG_RESULT(no))
+
+dnl ----------------------------------------------------------------------
+dnl Does the struct stat have the st_blocks field?  This field is not Posix.
+dnl
+AC_MSG_CHECKING(for st_blocks in struct stat)
+AC_TRY_COMPILE([
+#include <sys/stat.h>],[struct stat sb; sb.st_blocks=0;],
+AC_DEFINE(HAVE_STAT_ST_BLOCKS)
+AC_MSG_RESULT(yes),
+AC_MSG_RESULT(no))
+
+dnl ----------------------------------------------------------------------
+dnl How do we figure out the width of a tty in characters?
+dnl
+AC_CHECK_FUNCS(_getvideoconfig gettextinfo GetConsoleScreenBufferInfo)
+AC_CHECK_FUNCS(_scrsize ioctl)
+
+AC_MSG_CHECKING(for struct videoconfig)
+AC_TRY_COMPILE(,[struct videoconfig w; w.numtextcols=0;],
+AC_DEFINE(HAVE_STRUCT_VIDEOCONFIG)
+AC_MSG_RESULT(yes),
+AC_MSG_RESULT(no))
+
+AC_MSG_CHECKING(for struct text_info)
+AC_TRY_COMPILE(,[struct text_info w; w.screenwidth=0;],
+AC_DEFINE(HAVE_STRUCT_TEXT_INFO)
+AC_MSG_RESULT(yes),
+AC_MSG_RESULT(no))
+
+AC_MSG_CHECKING(for TIOCGWINSZ)
+AC_TRY_COMPILE([#include <sys/ioctl.h>],[int w=TIOCGWINSZ;],
+AC_DEFINE(HAVE_TIOCGWINSZ)
+AC_MSG_RESULT(yes),
+AC_MSG_RESULT(no))
+
+AC_MSG_CHECKING(for TIOCGGETD)
+AC_TRY_COMPILE([#include <sys/ioctl.h>],[int w=TIOCGETD;],
+AC_DEFINE(HAVE_TIOCGETD)
+AC_MSG_RESULT(yes),
+AC_MSG_RESULT(no))
+
 
 dnl ----------------------------------------------------------------------
 dnl Check for functions.
 dnl
 AC_CHECK_FUNCS(getpwuid gethostname system getrusage fork waitpid)
-
+AC_CHECK_FUNCS(gettimeofday BSDgettimeofday difftime snprintf vsnprintf)
+AC_CHECK_FUNCS(compress2 setsysinfo longjmp signal sigaction)
 AC_TRY_COMPILE([#include<sys/types.h>],
 	       [off64_t n = 0;],
 	       AC_CHECK_FUNCS(lseek64 fseek64),
@@ -194,13 +459,13 @@ AC_C_CONST
 AC_C_INLINE
 
 AC_MSG_CHECKING(for __attribute__ extension)
-AC_TRY_COMPILE(,[int __attribute__((unused)) f(void){return 1;}],
+AC_TRY_COMPILE(,[int __attribute__((unused)) x],
 		     AC_DEFINE(HAVE_ATTRIBUTE)
 		     AC_MSG_RESULT(yes),
 		     AC_MSG_RESULT(no))
 
 AC_MSG_CHECKING(for __FUNCTION__ extension)
-AC_TRY_COMPILE(,[int f(void){return __FUNCTION__;}],
+AC_TRY_COMPILE(,[(void)__FUNCTION__],
 		     AC_DEFINE(HAVE_FUNCTION)
 		     AC_MSG_RESULT(yes),
 		     AC_MSG_RESULT(no))
@@ -212,7 +477,7 @@ dnl default in case none of the others work.
 dnl
 AC_MSG_CHECKING(how to print long long)
 AC_CACHE_VAL(hdf5_cv_printf_ll,
-             for hdf5_cv_printf_ll in ll q l; do
+             for hdf5_cv_printf_ll in l L q ll unknown; do
                 AC_TRY_RUN([
 #include <stdio.h>
 #include <stdlib.h>
@@ -223,24 +488,24 @@ AC_CACHE_VAL(hdf5_cv_printf_ll,
 	             exit (strcmp(s,"1099511627776"));}],
 		 break)
 	     done)
-AC_MSG_RESULT($hdf5_cv_printf_ll)
+AC_MSG_RESULT(%${hdf5_cv_printf_ll}d and %${hdf5_cv_printf_ll}u)
 AC_DEFINE_UNQUOTED(PRINTF_LL_WIDTH,"$hdf5_cv_printf_ll")
 
-
 dnl ----------------------------------------------------------------------
 dnl Turn on debugging by setting compiler flags
 dnl
 AC_MSG_CHECKING(for debug flags)
 AC_ARG_ENABLE(debug,
-  [--enable-debug=all        Turn on debugging in all packages.  One may also
+  [  --enable-debug[=all]    Turn on debugging in all packages.  One may also
                           specify a comma-separated list of package names
                           without the leading H5 or the word no.  The default
                           is most packages.],
   DEBUG_PKG=$enableval)
 
+AC_SUBST(DEBUG_PKG)
 all_packages="ac,b,d,e,f,g,hg,hl,i,mf,mm,o,p,s,t,v,z"
 if test X = "X$DEBUG_PKG" -o Xyes = "X$DEBUG_PKG"; then
-   DEBUG_PKG=ac,b,d,e,f,g,hg,i,mm,p,s,t,v,z
+   DEBUG_PKG="d,e,f,g,hg,i,mm,o,p,s,t,v,z"
    CPPFLAGS="$CPPFLAGS -UNDEBUG"
    AC_MSG_RESULT(default ($DEBUG_PKG))
 elif test Xall = "X$DEBUG_PKG"; then
@@ -266,53 +531,256 @@ dnl Enable tracing of the API
 dnl
 AC_MSG_CHECKING(for API tracing);
 AC_ARG_ENABLE(trace,
-  [--disable-trace           Disable API tracing capability],
+  [  --disable-trace         Disable API tracing capability],
   TRACE=$enableval)
 
+AC_SUBST(TRACE_API)
 if test X = "X$TRACE" -o Xyes = "X$TRACE"; then
    AC_MSG_RESULT(yes)
+   TRACE_API=yes
    CPPFLAGS="$CPPFLAGS -DH5_DEBUG_API"
 else
    AC_MSG_RESULT(no)
+   TRACE_API=no
    CPPFLAGS="$CPPFLAGS -UH5_DEBUG_API"
 fi
 
 dnl ----------------------------------------------------------------------
-dnl Check for parallel support
+dnl The following variables are used to distinguish between building a
+dnl serial and parallel library.
+dnl
+dnl    HAVE_PARALLEL	-- defined in H5config.h if we are building
+dnl			   a parallel library even if configure wasn't
+dnl			   able to find some header file or library that
+dnl			   might be required. This is defined if the
+dnl			   compiler looks like a parallel compiler (e.g.,
+dnl			   mpicc or mpcc) or if the user explicitly states
+dnl			   that a parallel library is being built by supplying
+dnl			   the `--enable-parallel' configure switch.
+dnl
+dnl    PARALLEL		-- This variable is set to a non-null value if
+dnl			   configure thinks we're compiling a parallel
+dnl			   version of the library.
+dnl
+dnl    RUNSERIAL	-- This is a command which will be prepended to
+dnl			   the executable name to run the executable using
+dnl			   a single process. For serial versions of the
+dnl			   library this will normally be empty. For parallel
+dnl			   versions it might be something like `mpirun -np 1'.
+dnl			   The value of this variable is substituted in *.in
+dnl			   files.
+dnl
+dnl    RUNPARALLEL	-- This is a command which will be prepended to
+dnl			   the executable name to run the executable on
+dnl			   multiple processors. For the serial library the
+dnl			   value will normally be the empty string. For
+dnl			   parallel library it should be something like
+dnl			   `mpi -np $$NPROCS' where NPROCS will eventually
+dnl			   contain the number of processors on which to run
+dnl			   the executable (the double dollarsigns are to
+dnl			   protect the expansion until make executes the
+dnl			   command).  The value of this variable is
+dnl			   substituted in *.in files.
+dnl
+AC_SUBST(PARALLEL)
+AC_SUBST(RUNSERIAL)
+AC_SUBST(RUNPARALLEL)
+AC_SUBST(TESTPARALLEL)
+
+dnl ----------------------------------------------------------------------
+dnl If the compiler is obviously a parallel compiler then we're building
+dnl a parallel version of hdf5 and should define HAVE_PARALLEL. Furthermore,
+dnl the name of the compiler might tell us how to run the resulting
+dnl executable. For `mpicc' the executable should be run with `mpirun' from
+dnl the same directory as mpicc if it exists.
+dnl
+case "$CC_BASENAME" in
+    mpicc)
+	# The mpich compiler. Use mpirun from the same directory if it
+	# exists.
+	PARALLEL=mpicc
+	AC_MSG_CHECKING(for mpirun)
+
+	# Find the path where mpicc is located.
+	cmd=`echo $CC |cut -f1 -d' '`
+        if (echo $cmd |grep / >/dev/null); then
+	    path="`echo $cmd |sed 's/\(.*\)\/.*$/\1/'`"
+	else
+	    for path in `echo $PATH |tr : ' '`; do
+		if test -x $path/$cmd; then
+		    break;
+		fi
+	    done
+	fi
+
+	# Is there an mpirun at that path?
+	if test -x $path/mpirun; then
+	    AC_MSG_RESULT($path/mpirun)
+	    RUNSERIAL="${RUNSERIAL:-none}"
+	    if test "X-" = "X-$RUNPARALLEL"; then
+	        RUNPARALLEL="$path/mpirun -np \$\${NPROCS:=2}"
+	    fi
+	else
+	    AC_MSG_RESULT(none)
+        fi
+	;;
+
+    mpcc|mpcc_r)
+	# The IBM compiler
+	PARALLEL="$CC_BASENAME"
+	;;
+
+    *)
+	# Probably not a parallel compiler, but if `--enable-parallel'
+	# is defined below then we're still building a parallel hdf5.
+	;;
+esac
+
+dnl ----------------------------------------------------------------------
+dnl What header files and libraries do we have to look for for parallel
+dnl support?  For the most part, search paths are already specified with
+dnl CPPFLAGS and LDFLAGS or are known to the compiler.  If the user says
+dnl `--disable-parallel' but specifies a known parallel compiler (like mpicc
+dnl or mpcc) then parallel support is enabled but configure doesn't search
+dnl for any parallel header files or libraries.
 dnl
 AC_ARG_ENABLE(parallel,
-  --enable-parallel=mpio    Enable parallel support with MPIO,
-  PARALLEL=$enableval)
-AC_MSG_CHECKING(for parallel support);
-AC_SUBST(RUNTEST)
+  [  --enable-parallel=TYPE  Search for MPI-IO and MPI support files])
 
-case "X-$PARALLEL" in
+AC_MSG_CHECKING(for parallel support files)
+case "X-$enable_parallel" in
+    X-|X-no|X-none)
+	# Either we are not compiling for parallel or the header and library
+	# files and locations are known to the compiler (this is the case
+	# for a correct installation of mpicc for instance).
+	AC_MSG_RESULT(skipped)
+	;;
 
-   X-|X-no)
-      # Parallel support is not enabled
-      AC_MSG_RESULT(disabled)
-      ;;
+    X-yes)
+	# We want to compile a parallel library with a compiler that
+	# already knows how to link with MPI and MPI-IO.
+	AC_MSG_RESULT(provided by compiler)
+	PARALLEL=yes
+	;;
 
-   X-mpio|X-yes)
-      # Use MPIO.  Define HAVE_PARALLEL in src/H5config.h (comes from
-      # ./acconfig.h) and augment the include and library search paths
-      # (it doesn't hurt to have extra paths).  Then check for header
-      # files and libraries. Some extra source files are added to the
-      # list also so we don't have to ifdef out the whole file.
-      AC_MSG_RESULT(mpio)
-      AC_DEFINE(HAVE_PARALLEL)
-      CPPFLAGS="$CPPFLAGS $MPI_INC"
-      CFLAGS="$CFLAGS $MPI_LIB"
-      RUNTEST="$RUNTEST"
-      AC_CHECK_LIB(mpi,main)  dnl Replace `main' with some function
-      AC_CHECK_LIB(mpio,main) dnl Replace `main' with some function
-      ;;
+    X-mpich)
+	# For normal mpich installation the compiler, mpicc, should know
+	# where the MPI and MPI-IO header files are located and know which
+	# extra libraries need to be linked and will supply appropriate
+	# flags to the underlying compiler.
+	AC_MSG_RESULT(mpich)
+	AC_MSG_WARN(*** Why aren't you using an mpicc compiler? ***)
 
-   *)
-      AC_MSG_ERROR(unknown parallel support: $PARALLEL)
-      ;;
+	# Apparently mpicc isn't installed correctly so configure must search
+	# for the header files and libraries. Actually we only have to search
+	# for the libraries in order to get the onto the link line, the user
+	# will have already told us about the locations. Fail if something
+	# is missing.
+	PARALLEL=mpich
+	AC_CHECK_LIB(mpich,MPI_Init,,AC_MSG_ERROR(no mpich library))
+	;;
+
+    *)
+	AC_MSG_RESULT(error)
+	AC_MSG_ERROR(\"$enable_parallel\" is not a valid parallel search type)
+	;;
 esac
-        
+
+dnl ----------------------------------------------------------------------
+dnl Should the `testpar' directory participate in the build?
+dnl
+if test "X-" != "X-$PARALLEL"; then
+    TESTPARALLEL=testpar
+fi
+
+dnl ----------------------------------------------------------------------
+dnl Print some other parallel information and do some sanity checks.
+dnl
+if test "X-" != "X-$PARALLEL"; then
+    # We are building a parallel library
+    AC_DEFINE(HAVE_PARALLEL)
+
+    # Display what we found about running programs
+    AC_MSG_CHECKING(prefix for running on one processor)
+    AC_MSG_RESULT($RUNSERIAL)
+    AC_MSG_CHECKING(prefix for running in parallel)
+    AC_MSG_RESULT($RUNPARALLEL)
+
+    # Check that we can link a simple MPI and MPI-IO application
+dnl    AC_MSG_CHECKING(whether a simple MPI-IO program can be linked)
+dnl    AC_TRY_LINK(,[MPI_Init();MPI_File_open();],
+dnl		AC_MSG_RESULT(yes),
+dnl		AC_MSG_RESULT(no)
+dnl	        AC_MSG_ERROR('unable to link a simple MPI-IO application'))
+
+
+    # There *must* be some way to run in parallel even if it's just the
+    # word `none'.
+    if test "X-" = "X-$RUNPARALLEL"; then
+	AC_MSG_ERROR(no way to run a parallel program)
+    fi
+
+    # If RUNSERIAL or RUNPARALLEL is the word `none' then replace it with
+    # the empty string.
+    if test "X-none" = "X-$RUNSERIAL"; then
+	RUNSERIAL=
+    fi
+    if test "X-none" = "X-$RUNPARALLEL"; then
+	RUNPARALLEL=
+    fi
+fi
+
+dnl ----------------------------------------------------------------------
+dnl Set some variables for general configuration information to be saved
+dnl and installed with the libraries.
+dnl
+
+# HDF5 version from the first line of the README file.
+H5_VERSION=`cut -d' ' -f3 $srcdir/README |head -1`
+AC_SUBST(H5_VERSION)
+
+# Configuration date
+AC_SUBST(CONFIG_DATE) CONFIG_DATE=`date`
+
+# User doing the configuration
+AC_SUBST(CONFIG_USER) CONFIG_USER="$USER@`hostname`"
+if test "X-$ORGANIZATION" != "X-"; then
+    CONFIG_USER="$CONFIG_USER at $ORGANIZATION"
+fi
+
+# Configuration mode (production, development, profile, etc) saved above.
+AC_SUBST(CONFIG_MODE)
+
+# Byte sex from the AC_C_BIGENDIAN macro.
+AC_SUBST(BYTESEX)
+if test "X-$WORDS_BIGENDIAN" = "X-"; then
+    BYTESEX="little-endian"
+else
+    BYTESEX="big-endian"
+fi
+
+# Are we compiling static libraries, shared libraries, or both?
+AC_SUBST(STATIC_SHARED)
+if test "X-$enable_static" = "X-yes" && test "X-$enable_shared" = "X-yes"; then
+    STATIC_SHARED="static, shared"
+elif test "X-$enable_static" = "X-yes"; then
+    STATIC_SHARED="static"
+elif test "X-$enable_shared" = "X-yes"; then
+    STATIC_SHARED="shared"
+else
+    STATIC_SHARED="none"
+fi
+
+# Parallel support? (set above except empty if none)
+PARALLEL=${PARALLEL:-no}
+
+# Compiler with version information
+AC_SUBST(CC_VERSION)
+if test "X-$cc_vendor" != "X-" && test "X-$cc_version" != "X-"; then
+    CC_VERSION="$CC ($cc_vendor-$cc_version)"
+else
+    CC_VERSION="$CC"
+fi
 
 
 dnl ----------------------------------------------------------------------
@@ -326,9 +794,13 @@ AC_SUBST_FILE(CONCLUDE) CONCLUDE=config/conclude
 if test "X$GCC" = "Xyes" && test "X$GMAKE" = "Xyes"; then
    AC_SUBST_FILE(DEPEND1) DEPEND1=config/depend
    AC_SUBST_FILE(DEPEND2) DEPEND2=/dev/null
+   AC_SUBST_FILE(DEPEND3) DEPEND3=/dev/null
+   AC_SUBST_FILE(DEPEND4) DEPEND4=/dev/null
 else
-   AC_SUBST_FILE(DEPEND1) DEPEND1=src/.distdep
-   AC_SUBST_FILE(DEPEND2) DEPEND2=test/.distdep
+   AC_SUBST_FILE(DEPEND1) DEPEND1=$srcdir/src/.distdep
+   AC_SUBST_FILE(DEPEND2) DEPEND2=$srcdir/test/.distdep
+   AC_SUBST_FILE(DEPEND3) DEPEND3=$srcdir/testpar/.distdep
+   AC_SUBST_FILE(DEPEND4) DEPEND4=$srcdirtools/.distdep
 fi
 
 dnl We don't need to say when we're entering directories if we're using
@@ -350,9 +822,28 @@ else
 fi
 AC_SUBST(ROOT) ROOT=`$pwd`
 
-dnl Touch the time-stamp files for src/H5config.h.in and src/H5config.h
-dnl before we generate them or the Makefiles.
-touch ./config/stamp1 ./config/stamp2
+dnl Some cleanup stuff
+rm -f conftest conftest.o conftest.c dummy.o
 
-AC_OUTPUT(config/depend config/commence config/conclude \
-          Makefile src/Makefile test/Makefile tools/Makefile examples/Makefile)
+dnl Build config.status, touch the stamp files, and build all the Makefiles.
+dnl The order is such that the first `make' does not need to update any
+dnl configuration information. See config/commence.in for the order in which
+dnl things need to be done.
+
+# First the stamp1 file for H5config.h.in
+mkdir ./config >/dev/null 2>&1
+touch ./config/stamp1
+
+# Then the config.status file (but not makefiles)
+saved_no_create=$no_create
+no_create=yes
+AC_OUTPUT(src/libhdf5.settings config/depend config/commence config/conclude \
+          Makefile src/Makefile pablo/Makefile test/Makefile \
+          testpar/Makefile tools/Makefile examples/Makefile)
+no_create=$saved_no_create
+
+# Then the stamp2 file for H5config.h
+touch ./config/stamp2
+
+# Finally the makefiles
+test "$no_create" = yes || ${CONFIG_SHELL-/bin/sh} $CONFIG_STATUS || exit 1

doc/html/Attributes.html

@@ -1,18 +1,80 @@
-<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+
 <html>
   <head>
     <title>Attributes</title>
   </head>
 
-  <body>
-    <h1>Attributes</h1>
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      Attributes&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
+    <h1>The Attribute Interface (H5A)</h1>
 
     <h2>1. Introduction</h2>
 
-    <p>The appribute API (H5A) is primarily designed to easily allow small
+    <p>The attribute API (H5A) is primarily designed to easily allow small
         datasets to be attached to primary datasets as metadata information.
         Additional goals for the H5A interface include keeping storage
-        requirement for each attribute to a minimum and easily sharing
+        requirements for each attribute to a minimum and easily sharing
         attributes among datasets.
     <p>Because attributes are intended to be small objects, large datasets
         intended as additional information for a primary dataset should be
@@ -21,7 +83,7 @@
         indicate a particular type of dataset with supplemental datasets is
         located in the group.  How small is "small" is not defined by the
         library and is up to the user's interpretation.
-    <p>Attributes are not seperate objects in the file, they are always
+    <p>Attributes are not separate objects in the file, they are always
         contained in the object header of the object they are attached to.  The
         I/O functions defined below are required to read or write attribute
         information, not the H5D I/O routines.
@@ -44,12 +106,12 @@
     and <em>space_id</em> are created with the H5T and H5S interfaces
     respectively.  Currently only simple dataspaces are allowed for attribute
     dataspaces.  The <em>create_plist_id</em> property list is currently
-    unused, but will be used int the future for optional properties of
+    unused, but will be used in the future for optional properties of
     attributes.  The attribute ID returned from this function must be released
     with H5Aclose or resource leaks will develop.  Attempting to create an
     attribute with the same name as an already existing attribute will fail,
     leaving the pre-existing attribute in place.
-    This function returns a attribute ID for success or negative for failure.
+    This function returns an attribute ID for success or negative for failure.
 
 	<br><br>
       <dt><code>hid_t H5Aopen_name (hid_t <em>loc_id</em>, const char
@@ -58,7 +120,7 @@
     specified with <em>loc_id</em>.  The name specified with <em>name</em>
     indicates the attribute to access.  The attribute ID returned from this
     function must be released with H5Aclose or resource leaks will develop.
-    This function returns a attribute ID for success or negative for failure.
+    This function returns an attribute ID for success or negative for failure.
 
 	<br><br>
       <dt><code>hid_t H5Aopen_idx (hid_t <em>loc_id</em>, unsigned
@@ -68,7 +130,7 @@
     indicates the <em>idx</em>th attribute to access, starting with '0'. The
     attribute ID returned from this function must be released with H5Aclose or
     resource leaks will develop.
-    This function returns a attribute ID for success or negative for failure.
+    This function returns an attribute ID for success or negative for failure.
 
 	<br><br>
       <dt><code>herr_t H5Aclose (hid_t <em>attr_id</em>)</code>
@@ -116,7 +178,7 @@
       unsigned *<em>attr_number</em>, 
       H5A_operator <em>operator</em>, 
 	  void *<em>operator_data</em>)</code>
-      <dd> This function interates over the attributes of dataset or group
+      <dd> This function iterates over the attributes of the dataset or group
     specified with <em>loc_id</em>.  For each attribute of the object, the
     <em>operator_data</em> and some additional information (specified below)
     are passed to the <em>operator</em> function.  The iteration begins with
@@ -156,7 +218,7 @@
     This function returns a datatype ID for success or negative for failure.
 	<br><br>
       <dt><code>size_t H5Aget_name (hid_t <em>attr_id</em>,
-          char *<em>buf</em>, size_t <em>buf_size</em>)</code>
+          size_t <em>buf_size</em>, char *<em>buf</em>)</code>
       <dd>This function retrieves the name of an attribute for an attribute ID.
     Up to <em>buf_size</em> characters are stored in <em>buf</em> followed by a
     '\0' string terminator.  If the name of the attribute is longer than
@@ -165,13 +227,78 @@
     This function returns the length of the attribute's name (which may be
     longer than <em>buf_size</em>) on success or negative for failure.
 	<br><br>
-      <dt><code>int H5Anum_attrs (hid_t <em>loc_id</em>)</code>
+      <dt><code>int H5Aget_num_attrs (hid_t <em>loc_id</em>)</code>
       <dd>This function returns the number of attributes attached to a dataset or
     group, <em>loc_id</em>.
     This function returns non-negative for success or negative for failure.
     </dl>
 
-    <hr>
-    <address><a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Support</a></address>
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      Attributes&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+
+<br>
+Last modified:  30 October 1998
+
   </body>
 </html>

doc/html/Big.html

@@ -24,10 +24,18 @@
 
     <h2>2. File Size Limits</h2>
 
-    <p>Some 32-bit operating systems have special file systems that
-      can support large (&gt;2GB) files and HDF5 will detect these and
-      use them automatically.  If this is the case, the output from
-      configure will show:
+    <p>Systems that have 64-bit file addresses will be able to access
+      those files automatically.  One should see the following output
+      from configure:
+
+    <p><code><pre>
+checking size of off_t... 8
+    </pre></code>
+
+    <p>Also, some 32-bit operating systems have special file systems
+      that can support large (&gt;2GB) files and HDF5 will detect
+      these and use them automatically.  If this is the case, the
+      output from configure will show:
 
     <p><code><pre>
 checking for lseek64... yes
@@ -42,25 +50,28 @@ checking for fseek64... yes
     <p><code><pre>
 hid_t plist, file;
 plist = H5Pcreate (H5P_FILE_ACCESS);
-H5Pset_family (plist, 1<<30, H5P_DEFAULT);
+H5Pset_family (plist, 1&lt;&lt;30, H5P_DEFAULT);
 file = H5Fcreate ("big%03d.h5", H5F_ACC_TRUNC, H5P_DEFAULT, plist);
     </code></pre>
 
-    <p>The second argument (<code>30</code>) to
+    <p>The second argument (<code>1&lt;&lt;30</code>) to
       <code>H5Pset_family()</code> indicates that the family members
-      are to be 2^30 bytes (1GB) each.  In general, family members
-      cannot be 2GB because writes to byte number 2,147,483,647 will
-      fail, so the largest safe value for a family member is
-      2,147,483,647.  HDF5 will create family members on demand as the
-      HDF5 address space increases, but since most Unix systems limit
-      the number of concurrently open files the effective maximum size
-      of the HDF5 address space will be limited.
+      are to be 2^30 bytes (1GB) each although we could have used any
+      reasonably large value.  In general, family members cannot be
+      2GB because writes to byte number 2,147,483,647 will fail, so
+      the largest safe value for a family member is 2,147,483,647.
+      HDF5 will create family members on demand as the HDF5 address
+      space increases, but since most Unix systems limit the number of
+      concurrently open files the effective maximum size of the HDF5
+      address space will be limited (the system on which this was
+      developed allows 1024 open files, so if each family member is
+      approx 2GB then the largest HDF5 file is approx 2TB).
 
     <p>If the effective HDF5 address space is limited then one may be
       able to store datasets as external datasets each spanning
       multiple files of any length since HDF5 opens external dataset
-      files one at a time.  To arrange storage for a 5TB dataset one
-      could say:
+      files one at a time.  To arrange storage for a 5TB dataset split
+      among 1GB files one could say:
 
     <p><code><pre>
 hid_t plist = H5Pcreate (H5P_DATASET_CREATE);
@@ -73,9 +84,9 @@ for (i=0; i&lt;5*1024; i++) {
     <h2>3. Dataset Size Limits</h2>
 
     <p>The second limit which must be overcome is that of
-      <code>sizeof(size_t)</code>.  HDF5 defines a new data type
-      called <code>hsize_t</code> which is used for sizes of datasets
-      and is, by default, defined as <code>unsigned long long</code>.
+      <code>sizeof(size_t)</code>.  HDF5 defines a data type called
+      <code>hsize_t</code> which is used for sizes of datasets and is,
+      by default, defined as <code>unsigned long long</code>.
 
     <p>To create a dataset with 8*2^30 4-byte integers for a total of
       32GB one first creates the dataspace.  We give two examples
@@ -105,7 +116,7 @@ hid_t space2 = H5Screate_simple (1, size2, size2};
     <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
 <!-- Created: Fri Apr 10 13:26:04 EDT 1998 -->
 <!-- hhmts start -->
-Last modified: Wed May 13 12:36:47 EDT 1998
+Last modified: Sun Jul 19 11:37:25 EDT 1998
 <!-- hhmts end -->
   </body>
 </html>

doc/html/Caching.html

@@ -4,7 +4,69 @@
     <title>Data Caching</title>
   </head>
 
-  <body>
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      Caching&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
     <h1>Meta Data Caching</h1>
 
     <p>The HDF5 library caches two types of data: meta data and raw
@@ -72,11 +134,83 @@
 	the pointer arguments may be null pointers.
     </dl>
 
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      Caching&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<!--
     <hr>
     <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
+-->
 <!-- Created: Tue May 26 15:20:14 EDT 1998 -->
 <!-- hhmts start -->
+<!--
 Last modified: Tue May 26 15:38:27 EDT 1998
+-->
 <!-- hhmts end -->
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
+
+Last modified:  30 October 1998
+
   </body>
 </html>

doc/html/Chunk_f1.obj

@@ -0,0 +1,252 @@
+%TGIF 3.0-p17
+state(0,33,100.000,0,0,0,16,1,9,1,1,0,0,0,1,1,1,'Courier',0,17,0,0,0,10,0,0,1,1,0,16,0,0,1,1,1,0,1088,1408,0,0,2880).
+%
+% @(#)$Header$
+% %W%
+%
+unit("1 pixel/pixel").
+color_info(11,65535,0,[
+	"magenta", 65535, 0, 65535, 65280, 0, 65280, 1,
+	"red", 65535, 0, 0, 65280, 0, 0, 1,
+	"green", 0, 65535, 0, 0, 65280, 0, 1,
+	"blue", 0, 0, 65535, 0, 0, 65280, 1,
+	"yellow", 65535, 65535, 0, 65280, 65280, 0, 1,
+	"pink", 65535, 49344, 52171, 65280, 49152, 51968, 1,
+	"cyan", 0, 65535, 65535, 0, 65280, 65280, 1,
+	"CadetBlue", 24415, 40606, 41120, 24320, 40448, 40960, 1,
+	"white", 65535, 65535, 65535, 65280, 65280, 65280, 1,
+	"black", 0, 0, 0, 0, 0, 0, 1,
+	"DarkSlateGray", 12079, 20303, 20303, 12032, 20224, 20224, 1
+]).
+page(1,"",1).
+text('black',432,272,'Courier',0,17,2,1,0,1,49,28,302,0,11,3,0,0,0,0,0,2,0,0,0,0,"",0,0,0,[
+	"Point",
+	"Written"]).
+box('black',256,288,320,352,0,3,1,70,0,0,0,0,0,'3',[
+]).
+text('black',288,272,'Courier',0,17,1,1,0,1,49,14,75,0,11,3,0,0,0,0,0,2,0,0,0,0,"",0,0,0,[
+	"Dataset"]).
+box('black',352,288,384,320,5,1,1,77,5,0,0,0,0,'1',[
+]).
+text('black',368,272,'Courier',0,17,1,1,0,1,35,14,80,0,11,3,0,0,0,0,0,2,0,0,0,0,"",0,0,0,[
+	"Chunk"]).
+box('black',96,32,544,384,0,1,1,118,0,0,0,0,0,'1',[
+]).
+box('black',128,64,256,128,5,1,1,131,5,0,0,0,0,'1',[
+]).
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doc/html/Chunking.html

@@ -0,0 +1,326 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<html>
+  <head>
+    <title>Dataset Chunking Issues</title>
+  </head>
+
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      Chunking&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
+    <h1>Dataset Chunking Issues</h1>
+
+    <h2>Table of Contents</h2>
+
+    <ul>
+      <li><a href="#S1">1. Introduction</a>
+      <li><a href="#S2">2. Raw Data Chunk Cache</a>
+      <li><a href="#S3">3. Cache Efficiency</a>
+      <li><a href="#S4">4. Fragmentation</a>
+      <li><a href="#S5">5. File Storage Overhead</a>
+    </ul>
+
+    <h2><a name="S1">1. Introduction</a></h2>
+
+
+    <p><em>Chunking</em> refers to a storage layout where a dataset is
+      partitioned into fixed-size multi-dimensional chunks.  The
+      chunks cover the dataset but the dataset need not be an integral
+      number of chunks.  If no data is ever written to a chunk then
+      that chunk isn't allocated on disk.  Figure 1 shows a 25x48
+      element dataset covered by nine 10x20 chunks and 11 data points
+      written to the dataset.  No data was written to the region of
+      the dataset covered by three of the chunks so those chunks were
+      never allocated in the file -- the other chunks are allocated at 
+      independent locations in the file and written in their entirety.
+
+      <center><image src="Chunk_f1.gif"><br><b>Figure 1</b></center>
+
+    <p>The HDF5 library treats chunks as atomic objects -- disk I/O is 
+      always in terms of complete chunks<a href="#fn1">(1)</a>. This
+      allows data filters to be defined by the application to perform
+      tasks such as compression, encryption, checksumming,
+      <em>etc</em>. on entire chunks. As shown in Figure 2, if
+      <code>H5Dwrite()</code> touches only a few bytes of the chunk,
+      the entire chunk is read from the file, the data passes upward
+      through the filter pipeline, the few bytes are modified, the
+      data passes downward through the filter pipeline, and the entire
+      chunk is written back to the file.
+
+      <center><image src="Chunk_f2.gif"><br><b>Figure 2</b></center>
+
+    <h2><a name="S2">2. The Raw Data Chunk Cache</a></h2>
+
+    <p>It's obvious from Figure 2 that calling <code>H5Dwrite()</code> 
+      many times from the application would result in poor performance
+      even if the data being written all falls within a single chunk.
+      A raw data chunk cache layer was added between the top of the
+      filter stack and the bottom of the byte modification layer<a
+      href="#fn2">(2)</a>. By default, the chunk cache will store 521
+      chunks or 1MB of data (whichever is less) but these values can
+      be modified with <code>H5Pset_cache()</code>.
+
+    <p>The preemption policy for the cache favors certain chunks and
+      tries not to preempt them.
+
+    <ul>
+      <li>Chunks that have been accessed frequently in the near past
+	are favored.
+      <li>A chunk which has just entered the cache is favored.
+      <li>A chunk which has been completely read or completely written 
+	but not partially read or written is penalized according to
+	some application specified weighting between zero and one.
+      <li>A chunk which is larger than the maximum cache size is not
+	eligible for caching.
+    </ul>
+
+    <h2><a name="S3">3. Cache Efficiency</a></h2>
+
+    <p>Now for some real numbers... A 2000x2000 element dataset is
+      created and covered by a 20x20 array of chunks (each chunk is 100x100
+      elements). The raw data cache is adjusted to hold at most 25 chunks by
+      setting the maximum number of bytes to 25 times the chunk size in
+      bytes. Then the application creates a square, two-dimensional memory
+      buffer and uses it as a window into the dataset, first reading and then
+      rewriting in row-major order by moving the window across the dataset
+      (the read and write tests both start with a cold cache).
+
+    <p>The measure of efficiency in Figure 3 is the number of bytes requested
+      by the application divided by the number of bytes transferred from the
+      file.  There are at least a couple ways to get an estimate of the cache
+      performance: one way is to turn on <a href="Debugging.html">cache
+      debugging</a> and look at the number of cache misses.  A more accurate
+      and specific way is to register a data filter whose sole purpose is to
+      count the number of bytes that pass through it (that's the method used
+      below).
+
+    <center><image src="Chunk_f3.gif"><br><b>Figure 3</b></center>
+
+    <p>The read efficiency is less than one for two reasons: collisions in the
+      cache are handled by preempting one of the colliding chunks, and the
+      preemption algorithm occasionally preempts a chunk which hasn't been
+      referenced for a long time but is about to be referenced in the near
+      future.
+
+    <p>The write test results in lower efficiency for most window
+      sizes because HDF5 is unaware that the application is about to
+      overwrite the entire dataset and must read in most chunks before 
+      modifying parts of them.
+
+    <p>There is a simple way to improve efficiency for this example.
+      It turns out that any chunk that has been completely read or
+      written is a good candidate for preemption.  If we increase the
+      penalty for such chunks from the default 0.75 to the maximum
+      1.00 then efficiency improves.
+
+      <center><image src="Chunk_f4.gif"><br><b>Figure 4</b></center>
+
+    <p>The read efficiency is still less than one because of
+      collisions in the cache.  The number of collisions can often be
+      reduced by increasing the number of slots in the cache.  Figure
+      5 shows what happens when the maximum number of slots is
+      increased by an order of magnitude from the default (this change 
+      has no major effect on memory used by the test since the byte
+      limit was not increased for the cache).
+
+      <center><image src="Chunk_f5.gif"><br><b>Figure 5</b></center>
+
+    <p>Although the application eventually overwrites every chunk
+      completely the library has know way of knowing this before hand
+      since most calls to <code>H5Dwrite()</code> modify only a
+      portion of any given chunk. Therefore, the first modification of 
+      a chunk will cause the chunk to be read from disk into the chunk 
+      buffer through the filter pipeline.  Eventually HDF5 might
+      contain a data set transfer property that can turn off this read 
+      operation resulting in write efficiency which is equal to read
+      efficiency.
+
+
+    <h2><a name="S4">4. Fragmentation</a></h2>
+
+    <p>Even if the application transfers the entire dataset contents with a
+      single call to <code>H5Dread()</code> or <code>H5Dwrite()</code> it's
+      possible the request will be broken into smaller, more manageable
+      pieces by the library.  This is almost certainly true if the data
+      transfer includes a type conversion.
+
+      <center><image src="Chunk_f6.gif"><br><b>Figure 6</b></center>
+
+    <p>By default the strip size is 1MB but it can be changed by calling
+      <code>H5Pset_buffer()</code>.
+
+
+    <h2><a name="S5">5. File Storage Overhead</a></h2>
+
+    <p>The chunks of the dataset are allocated at independent
+      locations throughout the HDF5 file and a B-tree maps chunk
+      N-dimensional addresses to file addresses. The more chunks that
+      are allocated for a dataset the larger the B-tree. Large B-trees
+      have two disadvantages:
+
+    <ul>
+      <li>The file storage overhead is higher and more disk I/O is
+	required to traverse the tree from root to leaves.
+      <li>The increased number of B-tree nodes will result in higher
+	contention for the meta data cache.
+    </ul>
+
+    <p>There are three ways to reduce the number of B-tree nodes.  The
+      obvious way is to reduce the number of chunks by choosing a larger chunk
+      size (doubling the chunk size will cut the number of B-tree nodes in
+      half).  Another method is to adjust the split ratios for the B-tree by
+      calling <code>H5Pset_split_ratios()</code>, but this method typically
+      results in only a slight improvement over the default settings.
+      Finally, the out-degree of each node can be increased by calling
+      <code>H5Pset_istore_k()</code> (increasing the out degree actually
+      increases file overhead while decreasing the number of nodes).
+
+    <hr>
+
+    <p><a name="fn1">Footnote 1:</a> Parallel versions of the library
+      can access individual bytes of a chunk when the underlying file
+      uses MPI-IO.
+
+    <p><a name="fn2">Footnote 2:</a> The raw data chunk cache was
+      added before the second alpha release.
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      Chunking&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<!--
+    <hr>
+    <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
+-->
+<!-- Created: Tue Oct 20 12:38:40 EDT 1998 -->
+<!-- hhmts start -->
+<!--
+Last modified: Fri Oct 23 10:30:52 EDT 1998
+-->
+<!-- hhmts end -->
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+
+<br>
+Last modified:  30 October 1998
+
+
+  </body>
+</html>

doc/html/Compression.html

@@ -1,409 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
-<html>
-  <head>
-    <title>Compression</title>
-  </head>
-
-  <body>
-    <h1>Compression</h1>
-
-    <h2>1. Introduction</h2>
-
-    <p>HDF5 supports compression of raw data by compression methods
-      built into the library or defined by an application.  A
-      compression method is associated with a dataset when the dataset
-      is created and is applied independently to each storage chunk of
-      the dataset.
-
-      The dataset must use the <code>H5D_CHUNKED</code> storage
-      layout. The library doesn't support compression for contiguous
-      datasets because of the difficulty of implementing random access
-      for partial I/O, and compact dataset compression is not
-      supported because it wouldn't produce significant results.
-      
-    <h2>2. Supported Compression Methods</h2>
-
-    <p>The library identifies compression methods with small
-      integers, with values less than 16 reserved for use by NCSA and
-      values between 16 and 255 (inclusive) available for general
-      use.  This range may be extended in the future if it proves to
-      be too small.
-
-    <p>
-      <center>
-	<table align=center width="80%">
-	  <tr>
-	    <th width="30%">Method Name</th>
-	    <th width="70%">Description</th>
-	  </tr>
-
-	  <tr valign=top>
-	    <td><code>H5Z_NONE</code></td>
-	    <td>The default is to not use compression.  Specifying
-	      <code>H5Z_NONE</code> as the compression method results
-	      in better perfomance than writing a function that just
-	      copies data because the library's I/O pipeline
-	      recognizes this method and is able to short circuit
-	      parts of the pipeline.</td>
-	  </tr>
-
-	  <tr valign=top>
-	    <td><code>H5Z_DEFLATE</code></td>
-	    <td>The <em>deflate</em> method is the algorithm used by
-	      the GNU <code>gzip</code>program.  It's a combination of
-	      a Huffman encoding followed by a 1977 Lempel-Ziv (LZ77)
-	      dictionary encoding.  The aggressiveness of the
-	      compression can be controlled by passing an integer value
-	      to the compressor with <code>H5Pset_deflate()</code>
-	      (see below).  In order for this compression method to be
-	      used, the HDF5 library must be configured and compiled
-	      in the presence of the GNU zlib version 1.1.2 or
-	      later.</td>
-	  </tr>
-
-	  <tr valign=top>
-	    <td><code>H5Z_RES_<em>N</em></code></td>
-	    <td>These compression methods (where <em>N</em> is in the
-	      range two through 15, inclusive) are reserved by NCSA
-	      for future use.</td>
-	  </tr>
-
-	  <tr valign=top>
-	    <td>Values of <em>N</em> between 16 and 255, inclusive</td>
-	    <td>These values can be used to represent application-defined 
-	      compression methods.  We recommend that methods under
-	      testing should be in the high range and when a method is
-	      about to be published it should be given a number near
-	      the low end of the range (or even below 16).  Publishing
-	      the compression method and its numeric ID will make a
-	      file sharable.</td>
-	  </tr>
-	</table>
-      </center>
-
-    <p>Setting the compression for a dataset to a method which was
-      not compiled into the library and/or not registered by the
-      application is allowed, but writing to such a dataset will
-      silently <em>not</em> compress the data.  Reading a compressed
-      dataset for a method which is not available will result in
-      errors (specifically, <code>H5Dread()</code> will return a
-      negative value).  The errors will be displayed in the
-      compression statistics if the library was compiled with
-      debugging turned on for the &quot;z&quot; package.  See the
-      section on diagnostics below for more details.
-
-    <h2>3. Application-Defined Methods</h2>
-
-    <p>Compression methods 16 through 255 can be defined by an
-      application. As mentioned above, methods that have not been
-      released should use high numbers in that range while methods
-      that have been published will be assigned an official number in
-      the low region of the range (possibly less than 16).  Users
-      should be aware that using unpublished compression methods
-      results in unsharable files.
-
-    <p>A compression method has two halves: one have handles
-      compression and the other half handles uncompression.  The
-      halves are implemented as functions
-      <code><em>method</em>_c</code> and
-      <code><em>method</em>_u</code> respectively.  One should not use
-      the names <code>compress</code> or <code>uncompress</code> since
-      they are likely to conflict with other compression libraries
-      (like the GNU zlib).
-
-    <p>Both the <code><em>method</em>_c</code> and
-      <code><em>method</em>_u</code> functions take the same arguments
-      and return the same values.  They are defined with the type:
-
-    <dl>
-      <dt><code>typedef size_t (*H5Z_func_t)(unsigned int
-	  <em>flags</em>, size_t <em>cd_size</em>, const void
-	  *<em>client_data</em>, size_t <em>src_nbytes</em>, const
-	  void *<em>src</em>, size_t <em>dst_nbytes</em>, void
-	  *<em>dst</em>/*out*/)</code>
-      <dd>The <em>flags</em> are an 8-bit vector which is stored in
-	the file and which is defined when the compression method is
-	defined.  The <em>client_data</em> is a pointer to
-	<em>cd_size</em> bytes of configuration data which is also
-	stored in the file.  The function compresses or uncompresses
-	<em>src_nbytes</em> from the source buffer <em>src</em> into
-	at most <em>dst_nbytes</em> of the result buffer <em>dst</em>.
-	The function returns the number of bytes written to the result
-	buffer or zero if an error occurs.  But if a result buffer
-	overrun occurs the function should return a value at least as
-	large as <em>dst_size</em> (the uncompressor will see an
-	overrun only for corrupt data).
-    </dl>
-
-    <p>The application associates the pair of functions with a name
-      and a method number by calling <code>H5Zregister()</code>.  This
-      function can also be used to remove a compression method from
-      the library by supplying null pointers for the functions.
-
-    <dl>
-      <dt><code>herr_t H5Zregister (H5Z_method_t <em>method</em>,
-	  const char *<em>name</em>, H5Z_func_t <em>method_c</em>,
-	  H5Z_func_t <em>method_u</em>)</code>
-      <dd>The pair of functions to be used for compression
-	(<em>method_c</em>) and uncompression (<em>method_u</em>) are
-	associated with a short <em>name</em> used for debugging and a
-	<em>method</em> number in the range 16 through 255.  This
-	function can be called as often as desired for a particular
-	compression method with each call replacing the information
-	stored by the previous call.  Sometimes it's convenient to
-	supply only one half of the compression, for instance in an
-	application that opens files for read-only. Compression
-	statistics for the method are accumulated across calls to this
-	function.
-    </dl>
-
-    <p>
-      <center>
-	<table border align=center width="100%">
-	  <caption align=bottom><h4>Example: Registering an
-	      Application-Defined Compression Method</h4></caption>
-	  <tr>
-	    <td>
-	      <p>Here's a simple-minded &quot;compression&quot; method
-		that just copies the input value to the output.  It's
-		similar to the <code>H5Z_NONE</code> method but
-		slower.  Compression and uncompression are performed
-		by the same function.
-
-	      <p><code><pre>
-size_t
-bogus (unsigned int flags,
-       size_t cd_size, const void *client_data,
-       size_t src_nbytes, const void *src,
-       size_t dst_nbytes, void *dst/*out*/)
-{
-    memcpy (dst, src, src_nbytes);
-    return src_nbytes;
-}
-	      </pre></code>
-
-	      <p>The function could be registered as method 250 as
-		follows:
-
-	      <p><code><pre>
-#define H5Z_BOGUS 250
-H5Zregister (H5Z_BOGUS, "bogus", bogus, bogus);
-	      </pre></code>
-
-	      <p>The function can be unregistered by saying:
-
-	      <p><code><pre>
-H5Zregister (H5Z_BUGUS, "bogus", NULL, NULL);
-	      </pre></code>
-
-	      <p>Notice that we kept the name &quot;bogus&quot; even
-		though we unregistered the functions that perform the
-		compression and uncompression.  This makes compression
-		statistics more understandable when they're printed.
-	    </td>
-	  </tr>
-	</table>
-      </center>
-	
-    <h2>4. Enabling Compression for a Dataset</h2>
-
-    <p>If a dataset is to be compressed then the compression
-      information must be specified when the dataset is created since
-      once a dataset is created compression parameters cannot be
-      adjusted.  The compression is specified through the dataset
-      creation property list (see <code>H5Pcreate()</code>).
-
-    <dl>
-      <dt><code>herr_t H5Pset_deflate (hid_t <em>plist</em>, int
-	  <em>level</em>)</code>
-      <dd>The compression method for dataset creation property list
-	<em>plist</em> is set to <code>H5Z_DEFLATE</code> and the
-	aggression level is set to <em>level</em>.  The <em>level</em>
-	must be a value between one and nine, inclusive, where one
-	indicates no (but fast) compression and nine is aggressive
-	compression.
-
-	<br><br>
-      <dt><code>int H5Pget_deflate (hid_t <em>plist</em>)</code>
-      <dd>If dataset creation property list <em>plist</em> is set to
-	use <code>H5Z_DEFLATE</code> compression then this function
-	will return the aggression level, an integer between one and
-	nine inclusive.  If <em>plist</em> isn't a valid dataset
-	creation property list or it isn't set to use the deflate
-        method then a negative value is returned.
-
-	<br><br>
-      <dt><code>herr_t H5Pset_compression (hid_t <em>plist</em>,
-	  H5Z_method_t <em>method</em>, unsigned int <em>flags</em>,
-	  size_t <em>cd_size</em>, const void *<em>client_data</em>)</code>
-      <dd>This is a catch-all function for defining compresion methods
-	and is intended to be called from a wrapper such as
-	<code>H5Pset_deflate()</code>. The dataset creation property
-	list <em>plist</em> is adjusted to use the specified
-	compression method.  The <em>flags</em> is an 8-bit vector
-	which is stored in the file as part of the compression message
-	and passed to the compress and uncompress functions.  The
-	<em>client_data</em> is a byte array of length
-	<em>cd_size</em> which is copied to the file and passed to the
-	compress and uncompress methods.
-
-	<br><br>
-      <dt><code>H5Z_method_t H5Pget_compression (hid_t <em>plist</em>,
-	  unsigned int *<em>flags</em>, size_t *<em>cd_size</em>, void
-	  *<em>client_data</em>)</code>
-      <dd>This is a catch-all function for querying the compression
-	method associated with dataset creation property list
-	<em>plist</em> and is intended to be called from a wrapper
-	function such as <code>H5Pget_deflate()</code>.  The
-	compression method (or a negative value on error) is returned
-	by value, and compression flags and client data is returned by
-	argument.  The application should allocate the
-	<em>client_data</em> and pass its size as the
-	<em>cd_size</em>.  On return, <em>cd_size</em> will contain
-	the actual size of the client data.  If <em>client_data</em>
-	is not large enough to hold the entire client data then
-	<em>cd_size</em> bytes are copied into <em>client_data</em>
-	and <em>cd_size</em> is set to the total size of the client
-	data, a value larger than the original.
-    </dl>
-
-    <p>It is possible to set the compression to a method which hasn't
-      been defined with <code>H5Zregister()</code> and which isn't
-      supported as a predefined method (for instance, setting the
-      method to <code>H5Z_DEFLATE</code> when the GNU zlib isn't
-      available).  If that happens then data will be written to the
-      file in its uncompressed form and the compression statistics
-      will show failures for the compression.
-
-    <p>
-      <center>
-	<table border align=center width="100%">
-	  <caption align=bottom><h4>Example: Statistics for an
-	      Unsupported Compression Method</h4></caption>
-	  <tr>
-	    <td>
-	      <p>If an application attempts to use an unsupported
-		method then the compression statistics will show large
-		numbers of compression errors and no data
-		uncompressed.
-
-	      <p><code><pre>
-H5Z: compression statistics accumulated over life of library:
-   Method      Total  Overrun  Errors  User  System  Elapsed Bandwidth
-   ------      -----  -------  ------  ----  ------  ------- ---------
-   deflate-c  160000        0  160000  0.00    0.01     0.01 1.884e+07
-   deflate-u       0        0       0  0.00    0.00     0.00       NaN
-	      </pre></code>
-
-	      <p>This example is from a program that tried to use
-		<code>H5Z_DEFLATE</code> on a system that didn't have
-		the GNU zlib to write to a dataset and then read the
-		result.  The read and write both succeeded but the
-		data was not compressed.
-	    </td>
-	  </tr>
-	</table>
-      </center>
-
-    <h2>5. Compression Diagnostics</h2>
-
-    <p>If the library is compiled with debugging turned on for the H5Z
-      layer (usually as a result of <code>configure --enable-debug=z</code>)
-      then statistics about data compression are printed when the
-      application exits normally or the library is closed.  The
-      statistics are written to the standard error stream and include
-      two lines for each compression method that was used:  the first
-      line shows compression statistics while the second shows
-      uncompression statistics.  The following fields are displayed:
-
-    <p>
-      <center>
-	<table align=center width="80%">
-	  <tr>
-	    <th width="30%">Field Name</th>
-	    <th width="70%">Description</th>
-	  </tr>
-
-	  <tr valign=top>
-	    <td>Method</td>
-	    <td>This is the name of the method as defined with
-	      <code>H5Zregister()</code> with the letters
-	      &quot;-c&quot; or &quot;-u&quot; appended to indicate
-	      compression or uncompression.</td>
-	  </tr>
-
-	  <tr valign=top>
-	    <td>Total</td>
-	    <td>The total number of bytes compressed or decompressed
-	      including buffer overruns and errors.  Bytes of
-	      non-compressed data are counted.</td>
-	  </tr>
-
-	  <tr valign=top>
-	    <td>Overrun</td>
-	    <td>During compression, if the algorithm causes the result
-	      to be at least as large as the input then a buffer
-	      overrun error occurs.  This field shows the total number
-	      of bytes from the Total column which can be attributed to
-	      overruns. Overruns for decompression can only happen if
-	      the data has been corrupted in some way and will result
-	      in failure of <code>H5Dread()</code>.</td>
-	  </tr>
-
-	  <tr valign=top>
-	    <td>Errors</td>
-	    <td>If an error occurs during compression the data is
-	      stored in it's uncompressed form; and an error during
-	      uncompression causes <code>H5Dread()</code> to return
-	      failure.  This field shows the number of bytes of the
-	      Total column which can be attributed to errors.</td>
-	  </tr>
-
-	  <tr valign=top>
-	    <td>User, System, Elapsed</td>
-	    <td>These are the amount of user time, system time, and
-	      elapsed time in seconds spent by the library to perform
-	      compression.  Elapsed time is sensitive to system
-	      load. These times may be zero on operating systems that
-	      don't support the required operations.</td>
-	  </tr>
-
-	  <tr valign=top>
-	    <td>Bandwidth</td>
-	    <td>This is the compression bandwidth which is the total
-	      number of bytes divided by elapsed time.  Since elapsed
-	      time is subject to system load the bandwidth numbers
-	      cannot always be trusted.  Furthermore, the bandwidth
-	      includes overrun and error bytes which may significanly
-	      taint the value.</td>
-	  </tr>
-	</table>
-      </center>
-
-    <p>
-      <center>
-	<table border align=center width="100%">
-	  <caption align=bottom><h4>Example: Compression
-	      Statistics</h4></caption>
-	  <tr>
-	    <td>
-	      <p><code><pre>
-H5Z: compression statistics accumulated over life of library:
-   Method      Total  Overrun  Errors  User  System  Elapsed Bandwidth
-   ------      -----  -------  ------  ----  ------  ------- ---------
-   deflate-c  160000      200       0  0.62    0.74     1.33 1.204e+05
-   deflate-u  120000        0       0  0.11    0.00     0.12 9.885e+05
-	      </pre></code>
-	    </td>
-	  </tr>
-	</table>
-      </center>
-
-    <hr>
-    <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
-<!-- Created: Fri Apr 17 13:39:35 EDT 1998 -->
-<!-- hhmts start -->
-Last modified: Fri Apr 17 16:15:21 EDT 1998
-<!-- hhmts end -->
-  </body>
-</html>

doc/html/Copyright.html

@@ -0,0 +1,76 @@
+<html>
+<head><title>
+HDF5 Copyright Notice
+</title></head>
+
+<body>
+
+
+<hr>               
+
+<h3>Copyright Notice and Statement for
+<br>
+NCSA Hierarchical Data Format (HDF) Software Library and Utilities</h3>
+<hr>               
+<p>
+
+
+NCSA Hierarchical Data Format (HDF) Software Library and Utilities
+<br>
+Copyright 1998 the Board of Trustees of the University of Illinois
+<br>
+<strong>All rights reserved.</strong>
+<p>
+
+Contributors:   National Center for Supercomputing Applications (NCSA) at
+the University of Illinois, Lawrence Livermore Nat'l Laboratory (LLNL),
+Sandia National Laboratories (SNL), Los Alamos National Laboratory (LANL),
+Jean-loup Gailly and Mark Adler (gzip library)
+<p>
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted for any purpose (including commercial purposes)
+provided that the following conditions are met:
+<p>
+
+<ol>
+<li>Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+<li>Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or materials provided with the distribution.
+
+<li>In addition, redistributions of modified forms of the source or binary
+code must carry prominent notices stating that the original code was
+changed and the date of the change.
+
+<li>All publications or advertising materials mentioning features or use of
+this software must acknowledge that it was developed by the National Center
+for Supercomputing Applications at the University of Illinois, and credit
+the Contributors.
+
+<li>Neither the name of the University nor the names of the Contributors may
+be used to endorse or promote products derived from this software without
+specific prior written permission from the University or the Contributors.
+
+<li>THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY AND THE CONTRIBUTORS "AS IS"
+WITH NO WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED.  In no event
+shall the University or the Contributors be liable for any damages suffered
+by the users arising out of the use of this software, even if advised of
+the possibility of such damage.
+
+</ol>
+
+
+<hr>
+
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+
+<br>
+Last modified:  8 September 1998
+
+</body>
+</html>
+

doc/html/Datasets.html

@@ -4,7 +4,67 @@
     <title>The Dataset Interface (H5D)</title>
   </head>
 
-  <body>
+  <body bgcolor="#FFFFFF">
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      Datasets&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
     <h1>The Dataset Interface (H5D)</h1>
 
     <h2>1. Introduction</h2>
@@ -829,11 +889,83 @@ H5Pset_external (plist, "scan3.data", 0, 16);
 	</table>
       </center>
 
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      Datasets&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<!--
     <hr>
     <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
+-->
 <!-- Created: Tue Dec  2 09:17:09 EST 1997 -->
 <!-- hhmts start -->
+<!--
 Last modified: Wed May 13 18:57:47 EDT 1998
+-->
 <!-- hhmts end -->
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
+
+Last modified:  30 October 1998
+
   </body>
 </html>

doc/html/Dataspaces.html

@@ -3,7 +3,68 @@
    <META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
    <TITLE>The Data Space Interface (H5S)</TITLE>
 </HEAD>
-<BODY>
+<body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      Dataspaces&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
 
 <H1>
 The Dataspace Interface (H5S)</H1>
@@ -162,14 +223,14 @@ would look like this:
       <br><strong>Example 3: Non-contiguous selection with 1,1 offset</strong>
     </center>
 
-<P>Selections also have an linearization ordering of the points selected
+<P>Selections also have a linearization ordering of the points selected
 (defaulting to "C" order, ie. last dimension changing fastest).  The
 linearization order may be specified for each point or it may be chosen by
 the axis of the dataspace.  For example, with the default "C" ordering,
-example 1's selected points are iterated through in this order: (1,1), (2,1),
-(3,1), (1,2), (2,2), etc.  With "FORTRAN" ordering, example 1's selected points 
-would be iterated through in this order: (1,1), (1,2), (1,3), (1,4), (1,5),
-(2,1), (2,2), etc.
+example 1's selected points are iterated through in this order: (1,1), (1,2),
+(1,3), (2,1), (2,2), etc.  With "FORTRAN" ordering, example 1's selected points 
+would be iterated through in this order: (1,1), (2,1), (3,1), (4,1), (5,1),
+(1,2), (2,2), etc.
 
 <P>A dataspace may be stored in the file as a permanent object, to allow many
 datasets to use a commonly defined dataspace.  Dataspaces with extendable
@@ -195,9 +256,8 @@ by calling <TT>H5Sclose()</TT>.
 
 <DD>
     This function creates a new dataspace of a particular <I>type</I>.  The
-types currently supported are H5S_SCALAR, H5S_SIMPLE, or H5S_NONE, although
-others are planned to be added later.  The H5S_NONE dataspace can only hold a
-selection, not an extent.
+types currently supported are H5S_SCALAR and H5S_SIMPLE; 
+others are planned to be added later.  
 </DD>
 
 <DT>
@@ -252,12 +312,12 @@ dataspace identifier after this call is undefined.
 </DD>
 
 <DT>
-<TT>H5S_class_t H5Sget_class (hid_t <I>space</I>)</TT></DT>
+<TT>H5S_class_t H5Sextent_class (hid_t <I>space</I>)</TT></DT>
 
 <DD>
 Query a dataspace to determine the current class of a dataspace.  The value
-which is returned is one of: H5S_SCALAR, H5S_SIMPLE, or H5S_NONE on success or
-FAIL on failure.
+which is returned is one of: H5S_SCALAR, H5S_SIMPLE on success or
+H5S_NO_CLASS on failure.
 </DD>
 </DL>
 
@@ -284,7 +344,7 @@ H5S_SIMPLE and the extent is set as specified.
 <TT>herr_t H5Sset_extent_none (hid_t <I>space</I>)</TT></DT>
 
 <DD>
-Removes the extent from a dataspace and sets the type to H5S_NONE.
+Removes the extent from a dataspace and sets the type to H5S_NO_CLASS.
 </DD>
 
 <DT>
@@ -298,7 +358,7 @@ failure.
 </DD>
 
 <DT>
-<TT>hsize_t H5Sextent_npoints (hid_t <I>space</I>)</TT></DT>
+<TT>hsize_t H5Sget_simple_extent_npoints (hid_t <I>space</I>)</TT></DT>
 
 <DD>
 This function determines the number of elements in a dataspace. For example, a
@@ -308,7 +368,7 @@ Returns the number of elements in the dataspace, negative on failure.
 </DD>
 
 <DT>
-<TT>int H5Sextent_ndims (hid_t <I>space</I>)</TT></DT>
+<TT>int H5Sget_simple_extent_ndims (hid_t <I>space</I>)</TT></DT>
 
 <DD>
 This function determines the dimensionality (or rank) of a dataspace. 
@@ -316,7 +376,7 @@ Returns the number of dimensions in the dataspace, negative on failure.
 </DD>
 
 <DT>
-<TT>herr_t H5Sextent_dims (hid_t <I>space</I>, hsize_t *<I>dims</I>,
+<TT>herr_t H5Sget_simple_extent_dims (hid_t <I>space</I>, hsize_t *<I>dims</I>,
     hsize_t *<I>max</I>)</TT></DT>
 
 <DD>
@@ -356,11 +416,24 @@ This function selects a hyperslab region to add to the current selected region
 for the <I>space</I> dataspace.  The <I>start</I>, <I>stride</I>, <I>count</I>
 and <I>block</I> arrays must be the same size as the rank of the dataspace.  
 The selection operator <I>op</I> determines how the new selection is to be
-combined with the already existing selection for the dataspace.  Currently,
-only the H5S_SELECT_SET operator is supported, which replaces the existing
-selection with the parameters from this call.  Overlapping blocks are not
-supported with the H5S_SELECT_SET operator.
-<P>The <I>start</I> array determines the starting coordinates of the hyperslab
+combined with the already existing selection for the dataspace.  
+Currently, The following operators are supported:
+  <dir>
+  <table width=80% border=0>
+    <tr><td valign=top>
+      <code>H5S_SELECT_SET</code>
+      </td><td valign=top>
+      Replaces the existing selection with the parameters from this call.  
+      Overlapping blocks are not supported with this operator.
+    </td></tr><tr><td valign=top>
+      <code>H5S_SELECT_OR</code>
+      </td><td valign=top>
+      Adds the new selection to the existing selection.
+    </td></tr>
+  </table>
+  </dir>
+<P>
+The <I>start</I> array determines the starting coordinates of the hyperslab
 to select.  The <I>stride</I> array chooses array locations from the dataspace
 with each value in the <I>stride</I> array determining how many elements to move
 in each dimension.  Setting a value in the <I>stride</I> array to 1 moves to
@@ -398,9 +471,23 @@ iterated through when I/O is performed.  Duplicate coordinate locations are not
 checked for.
 
 <P>The selection operator <I>op</I> determines how the new selection is to be
-combined with the already existing selection for the dataspace.  Currently,
-only the H5S_SELECT_SET operator is supported, which replaces the existing
-selection with the parameters from this call.  When operators other than
+combined with the already existing selection for the dataspace.  
+The following operators are supported:
+  <dir>
+  <table width=80% border=0>
+    <tr><td valign=top>
+      <code>H5S_SELECT_SET</code>
+      </td><td valign=top>
+      Replaces the existing selection with the parameters from this call.  
+      Overlapping blocks are not supported with this operator.
+    </td></tr><tr><td valign=top>
+      <code>H5S_SELECT_OR</code>
+      </td><td valign=top>
+      Adds the new selection to the existing selection.
+    </td></tr>
+  </table>
+  </dir>
+When operators other than
 H5S_SELECT_SET are used to combine a new selection with an existing selection,
 the selection ordering is reset to 'C' array ordering.
 </DD>
@@ -481,7 +568,7 @@ the selection or extent is not defined).
 </DD>
 
 <DT>
-<TT>hsize_t H5Sselect_npoints (hid_t <I>space</I>)</TT></DT>
+<TT>hsize_t H5Sget_select_npoints (hid_t <I>space</I>)</TT></DT>
 
 <DD>
 This function determines the number of elements in the current selection
@@ -555,14 +642,87 @@ is returned.
 
 </DL>
 
-<HR>
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      Dataspaces&nbsp;&nbsp;
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+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
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+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
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+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<!--
 <ADDRESS>
 <A HREF="mailto:matzke@llnl.gov">Robb Matzke</A></ADDRESS>
 
 <ADDRESS>
 <A HREF="mailto:koziol@ncsa.uiuc.edu">Quincey Koziol</A></ADDRESS>
 
-<BR><!-- Created: Thu Dec  4 14:57:32 EST 1997 --><!-- hhmts start -->Last
-modified: Thu May 28 15:12:04 EST 1998&nbsp;<!-- hhmts end -->
+<BR>
+-->
+<!-- Created: Thu Dec  4 14:57:32 EST 1997 --><!-- hhmts start -->
+<!--
+Last modified: Thu May 28 15:12:04 EST 1998&nbsp;
+-->
+<!-- hhmts end -->
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+
+<br>
+Last modified:  26 April 1999
+
 </BODY>
 </HTML>

doc/html/Datatypes.html

@@ -4,7 +4,69 @@
     <title>The Data Type Interface (H5T)</title>
   </head>
 
-  <body>
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      Data Types&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
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+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
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+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
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+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
     <h1>The Data Type Interface (H5T)</h1>
 
     <h2>1. Introduction</h2>
@@ -135,13 +197,12 @@
     <dl>
       <dt><code>H5T_class_t H5Tget_class (hid_t <em>type</em>)</code>
       <dd>This property holds one of the class names:
-	<code>H5T_INTEGER, H5T_FLOAT, H5T_TIME, H5T_STRING,
-	H5T_BITFIELD</code>, or <code>H5T_OPAQUE</code>.  This
-	property is read-only and is set when the datatype is
-	created or copied (see <code>H5Tcreate()</code>,
-	<code>H5Tcopy()</code>). If this function fails it returns
-	<code>H5T_NO_CLASS</code> which has a negative value (all
-	other class constants are non-negative).
+	<code>H5T_INTEGER, H5T_FLOAT, H5T_TIME, H5T_STRING, or
+	H5T_BITFIELD</code>.  This property is read-only and is set
+	when the datatype is created or copied (see
+	<code>H5Tcreate()</code>, <code>H5Tcopy()</code>). If this
+	function fails it returns <code>H5T_NO_CLASS</code> which has
+	a negative value (all other class constants are non-negative).
 
 	<br><br>
       <dt><code>size_t H5Tget_size (hid_t <em>type</em>)</code>
@@ -156,13 +217,11 @@
 	the significant part of the data still extends beyond the edge
 	of the data type then the <code>precision</code> property is
 	decremented a bit at a time.  Decreasing the size of a data
-	type may fail if the precesion must be decremented and the
-	data type is of the <code>H5T_OPAQUE</code> class or the
-	<code>H5T_FLOAT</code> bit fields would extend beyond the
-	significant part of the type.  Increasing the size of an
-	<code>H5T_STRING</code> automatically increases the precision
-	as well.  On error, <code>H5Tget_size()</code> returns zero
-	which is never a valid size.
+	type may fail if the <code>H5T_FLOAT</code> bit fields would
+	extend beyond the significant part of the type.  Adjusting the
+	size of an <code>H5T_STRING</code> automatically adjusts the
+	precision as well.  On error, <code>H5Tget_size()</code>
+	returns zero which is never a valid size.
 
 	<br><br>
       <dt><code>H5T_order_t H5Tget_order (hid_t <em>type</em>)</code>
@@ -358,9 +417,6 @@
       <em>19971205162530</em>; as an integer value in Unix time(2)
       format; or other variations.
 
-    <p>I'm deferring definition until later since they're probably not
-      as important as the other data types.
-
     <h3>3.4. Properties of Character String Atomic Types</h3>
 
     <p>Fixed-length character string types are used to store textual
@@ -388,9 +444,33 @@
 	programming language: C usually null terminates strings while
 	Fortran left-justifies and space-pads strings.  This property
 	defines the storage mechanism and can be
-	<code>H5T_STR_NULL</code> for C-style strings or
-	<code>H5T_STR_SPACE</code> for Fortran-style
-	strings. <code>H5Tget_strpad()</code> returns
+
+	<p>
+	<dl>
+	  <dt><code>H5T_STR_NULLTERM</code>
+	  <dd>A C-style string which is guaranteed to be null
+	    terminated.  When converting  from a longer string the
+	    value will be truncated and then a null character
+	    appended.
+
+	    <br><br>
+	  <dt><code>H5T_STR_NULLPAD</code>
+	  <dd>A C-style string which is padded with null characters
+	    but not necessarily null terminated.  Conversion from a
+	    long string to a shorter <code>H5T_STR_NULLPAD</code>
+	    string will truncate but not null terminate.  Conversion
+	    from a short value to a longer value will append null
+	    characters as with <code>H5T_STR_NULLTERM</code>.
+
+	    <br><br>
+	  <dt><code>H5T_STR_SPACEPAD</code>
+	  <dd>A Fortran-style string which is padded with space
+	    characters.  This is the same as
+	    <code>H5T_STR_NULLPAD</code> except the padding character
+	    is a space instead of a null.
+	</dl>
+
+	<p><code>H5Tget_strpad()</code> returns
 	<code>H5T_STR_ERROR</code> on failure, a negative value (all
 	successful return values are non-negative).
     </dl>
@@ -403,17 +483,100 @@
       Otherwise new bits are filled according to the <code>msb</code>
       padding type.
 
-    <h3>3.6. Properties of Opaque Atomic Types</h3>
+    <h3>3.6 Character and String Datatype Issues</h3>
 
-    <p>Opaque atomic types (<code>class=H5T_OPAQUE</code>) act like
-      bit fields except conversions which change the precision are not
-      allowed.  However, padding can be added or removed from either
-      end and the bytes can be reordered.  Opaque types can be used to
-      create novel data types not directly supported by the library,
-      but the application is responsible for data conversion of these
-      types.
+      The <code>H5T_NATIVE_CHAR</code> and <code>H5T_NATIVE_UCHAR</code> 
+      data types are actually numeric data (1-byte integers).  If the 
+      application wishes to store character data, then an HDF5 
+      <em>string</em> data type should be derived from 
+      <code>H5T_C_S1</code> instead.
 
-    <h2>4. Properties of Compound Types</h2>
+        <h4>Motivation</h4>
+
+          HDF5 defines at least three classes of data types: 
+          integer data, floating point data, and character data.  
+          However, the C language defines only integer and 
+          floating point data types; character data in C is 
+          overloaded on the 8- or 16-bit integer types and 
+          character strings are overloaded on arrays of those 
+          integer types which, by convention, are terminated with 
+          a zero element.
+
+          In C, the variable <code>unsigned char s[256]</code> is 
+          either an array of numeric data, a single character string 
+          with at most 255 characters, or an array of 256 characters, 
+          depending entirely on usage.  For uniformity with the 
+          other <code>H5T_NATIVE_</code> types, HDF5 uses the 
+          numeric interpretation of <code>H5T_NATIVE_CHAR</code> 
+          and <code>H5T_NATIVE_UCHAR</code>.
+
+
+        <h4>Usage</h4>
+
+          To store <code>unsigned char s[256]</code> data as an 
+          array of integer values, use the HDF5 data type 
+          <code>H5T_NATIVE_UCHAR</code> and a data space that 
+          describes the 256-element array. Some other application 
+          that reads the data will then be able to read, say, a 
+          256-element array of 2-byte integers and HDF5 will 
+          perform the numeric translation.
+
+          To store <code>unsigned char s[256]</code> data as a 
+          character string, derive a fixed length string data type 
+          from <code>H5T_C_S1</code> by increasing its size to 
+          256 characters. Some other application that reads the 
+          data will be able to read, say, a space padded string 
+          of 16-bit characters and HDF5 will perform the character 
+          and padding translations.
+
+          <pre>
+                hid_t s256 = H5Tcopy(H5T_C_S1);
+                             H5Tset_size(s256, 256);
+          </pre>
+
+          To store <code>unsigned char s[256]</code> data as 
+          an array of 256 ASCII characters, use an 
+          HDF5 data space to describe the array and derive a 
+          one-character string type from <code>H5T_C_S1</code>. 
+          Some other application will be able to read a subset 
+          of the array as 16-bit characters and HDF5 will 
+          perform the character translations.  
+          The <code>H5T_STR_NULLPAD</code> is necessary because 
+          if <code>H5T_STR_NULLTERM</code> were used 
+          (the default) then the single character of storage 
+          would be for the null terminator and no useful data 
+          would actually be stored (unless the length were 
+          incremented to more than one character).
+
+          <pre>
+                hid_t s1 = H5Tcopy(H5T_C_S1);
+                           H5Tset_strpad(s1, H5T_STR_NULLPAD);
+          </pre>
+
+        <h4>Summary</h4>
+
+          The C language uses the term <code>char</code> to 
+          represent one-byte numeric data and does not make 
+          character strings a first-class data type.  
+          HDF5 makes a distinction between integer and 
+          character data and maps the C <code>signed char</code> 
+          (<code>H5T_NATIVE_CHAR</code>) and 
+          <code>unsigned char</code> (<code>H5T_NATIVE_UCHAR</code>) 
+          data types to the HDF5 integer type class.
+
+    <h2>4. Properties of Opaque Types</h2>
+
+    <p>Opaque types (<code>class=H5T_OPAQUE</code>) provide the
+      application with a mechanism for describing data which cannot be 
+      otherwise described by HDF5. The only properties associated with 
+      opaque types are a size in bytes and an ASCII tag which is
+      manipulated with <code>H5Tset_tag()</code> and
+      <code>H5Tget_tag()</code> functions. The library contains no
+      predefined conversion functions but the application is free to
+      register conversions between any two opaque types or between an
+      opaque type and some other type.
+
+    <h2>5. Properties of Compound Types</h2>
 
     <p>A compound data type is similar to a <code>struct</code> in C
       or a common block in Fortran: it is a collection of one or more
@@ -507,7 +670,9 @@
       <code>H5Tinsert()</code>) and cannot be subsequently modified.
       This makes it imposible to define recursive data structures.
 
-    <h2>5. Predefined Atomic Data Types</h2>
+    <a name="DTypes-PredefinedAtomic">
+    <h2>6. Predefined Atomic Data Types</h2>
+    </a>
 
     <p>The library predefines a modest number of data types having
       names like <code>H5T_<em>arch</em>_<em>base</em></code> where
@@ -616,6 +781,10 @@
 	    <td align=center>I</td>
 	    <td>Signed integer</td>
 	  </tr>
+	  <tr>
+	    <td align=center>R</td>
+	    <td>References</td>
+	  </tr>
 	  <tr>
 	    <td align=center>S</td>
 	    <td>Character string</td>
@@ -687,6 +856,10 @@
 	    <td><code>H5T_CRAY_F64</code></td>
 	    <td>Eight-byte Cray floating point</td>
 	  </tr>
+	  <tr valign=top>
+	    <td><code>H5T_STD_ROBJ</code></td>
+	    <td>Reference to an entire object in a file</td>
+	  </tr>
 	</table>
       </center>
 
@@ -703,6 +876,10 @@
 	  </tr>
 	  <tr>
 	    <td><code>H5T_NATIVE_CHAR</code></td>
+	    <td><code>char</code></td>
+	  </tr>
+	  <tr>
+	    <td><code>H5T_NATIVE_SCHAR</code></td>
 	    <td><code>signed char</code></td>
 	  </tr>
 	  <tr>
@@ -753,6 +930,22 @@
 	    <td><code>H5T_NATIVE_LDOUBLE</code></td>
 	    <td><code>long double</code></td>
 	  </tr>
+	  <tr>
+	    <td><code>H5T_NATIVE_HSIZE</code></td>
+	    <td><code>hsize_t</code></td>
+	  </tr>
+	  <tr>
+	    <td><code>H5T_NATIVE_HSSIZE</code></td>
+	    <td><code>hssize_t</code></td>
+	  </tr>
+	  <tr>
+	    <td><code>H5T_NATIVE_HERR</code></td>
+	    <td><code>herr_t</code></td>
+	  </tr>
+	  <tr>
+	    <td><code>H5T_NATIVE_HBOOL</code></td>
+	    <td><code>hbool_t</code></td>
+	  </tr>
 	</table>
       </center>
 
@@ -799,7 +992,7 @@ H5Tset_size (str80, 80);
 	</table>
       </center>
 
-    <h2>6. Defining Compound Data Types</h2>
+    <h2>7. Defining Compound Data Types</h2>
 
     <p>Unlike atomic data types which are derived from other atomic
       data types, compound data types are created from scratch. First,
@@ -955,7 +1148,21 @@ H5Tinsert (surf_id, "y", HOFFSET(surf_t,y), complex_id);
 	</table>
       </center>
 
-    <h2>7. Sharing Data Types among Datasets</h2>
+    <a name="Datatypes_Enum">&nbsp;</a>
+    <h2>8. <a href="DatatypesEnum.html">Enumeration Data Types</a></h2>
+
+      An HDF5 enumeration data type is a 1:1 mapping between a set of
+      symbols and a set of integer values, and an order is imposed on
+      the symbols by their integer values.  The symbols are passed
+      between the application and library as character strings and all
+      the values for a particular enumeration type are of the same
+      integer type, which is not necessarily a native type.
+      <p>
+      Details of enumeration data types and the related functions
+      are discussed on a separate 
+      <a href="DatatypesEnum.html">Enumeration Data Types</a> page.
+
+    <h2>9. Sharing Data Types among Datasets</h2>
 
     <p>If a file has lots of datasets which have a common data type
       then the file could be made smaller by having all the datasets
@@ -1000,36 +1207,40 @@ hid_t dset4 = H5Dcreate (file, "dset4", t2, space, H5P_DEFAULT);
 	</table>
       </center>
 
-    <h2>8. Data Conversion</h2>
+    <a name="Datatypes-DataConversion">
+    <h2>10. Data Conversion</h2>
+    </a>
 
     <p>The library is capable of converting data from one type to
       another and does so automatically when reading or writing the
-      raw data of a dataset.  The data type interface does not provide
-      functions to the application for changing data types directly,
-      but the user is allowed a certain amount of control over the
-      conversion process.
+      raw data of a dataset, attribute data, or fill values. The
+      application can also change the type of data stored in an array.
 
     <p>In order to insure that data conversion exceeds disk I/O rates,
       common data conversion paths can be hand-tuned and optimized for
-      performance.  If a hand-tuned conversion function is not
+      performance.  The library contains very efficient code for
+      conversions between most native data types and a few non-native
+      data types, but if a hand-tuned conversion function is not
       available, then the library falls back to a slower but more
-      general conversion function.  Although conversion paths include
-      data space conversion, only data type conversions are described
-      here.  Most applications will not be concerned with data type
-      conversions since the library will contain hand-tuned conversion
-      functions for many common conversion paths.  In fact, if an
-      application does define a conversion function which would be of
-      general interest, we request that the function be submitted to
-      the HDF5 development team for inclusion in the library (there
-      might be less overhead involved with calling an internal
-      conversion functions than calling an application-defined
-      conversion function).
+      general conversion function.  The application programmer can
+      define additional conversion functions when the libraries
+      repertoire is insufficient. In fact, if an application does
+      define a conversion function which would be of general interest,
+      we request that the function be submitted to the HDF5
+      development team for inclusion in the library.
 
-    <p><b>Note:</b> The alpha version of the library does not contain
-      a full set of conversions.  It can convert from one integer
-      format to another and one struct to another.  It can also
-      perform byte swapping when the source and destination types are
-      otherwise the same.
+    <p><b>Note:</b> The HDF5 library contains a deliberately limited
+      set of conversion routines.  It can convert from one integer
+      format to another, from one floating point format to another,
+      and from one struct to another.  It can also perform byte
+      swapping when the source and destination types are otherwise the
+      same.  The library does not contain any functions for converting
+      data between integer and floating point formats.  It is
+      anticipated that some users will find it necessary to develop
+      float to integer or integer to float conversion functions at the
+      application level; users are invited to submit those functions
+      to be considered for inclusion in future versions of the
+      library.
 
     <p>A conversion path contains a source and destination data type
       and each path contains a <em>hard</em> conversion function
@@ -1041,7 +1252,7 @@ hid_t dset4 = H5Dcreate (file, "dset4", t2, space, H5P_DEFAULT);
       conversion path, then the hard function is favored and when
       multiple soft functions apply, the one defined last is favored.
 
-    <p>A data conversion function is of type <code>H5T_conv_t</em>
+    <p>A data conversion function is of type <code>H5T_conv_t</code>
 	which is defined as:
 
     <p>
@@ -1089,24 +1300,25 @@ typedef herr_t (*H5T_conv_t)(hid_t <em>src_type</em>,
 
 	<br><br>
       <dt><code>H5T_CONV_CONV</code>
-      <dd>This is the usually command which indicates that
-	data points should be converted.  The conversion function
-	should initialize the <code>priv</code> field of
-	<em>cdata</em> if it wasn't initialize during the
-	<code>H5T_CONV_INIT</code> command and then convert
-	<em>nelmts</em> instances of the <em>src_type</em> to the
-	<em>dst_type</em>. The <em>buffer</em> serves as both input
-	and output.  The <em>background</em> buffer is supplied
-	according to the value of the <code>need_bkg</code> field of
-	<em>cdata</em> (the values are described below).
+      <dd>This command indicates that data points should be converted.
+	The conversion function should initialize the
+	<code>priv</code> field of <em>cdata</em> if it wasn't
+	initialize during the <code>H5T_CONV_INIT</code> command and
+	then convert <em>nelmts</em> instances of the
+	<em>src_type</em> to the <em>dst_type</em>. The
+	<em>buffer</em> serves as both input and output.  The
+	<em>background</em> buffer is supplied according to the value
+	of the <code>need_bkg</code> field of <em>cdata</em> (the
+	values are described below).
 
 	<br><br>
       <dt><code>H5T_CONV_FREE</code>
       <dd>The conversion function is about to be removed from some
 	path and the private data (the
 	<code><em>cdata</em>->priv</code> pointer) should be freed and
-	set to null.  All other pointer arguments are null and the
-	<em>nelmts</em> argument is zero.
+	set to null.  All other pointer arguments are null, the
+	<em>src_type</em> and <em>dst_type</em> are invalid
+	(negative), and the <em>nelmts</em> argument is zero.
 
 	<br><br>
       <dt><em>Others...</em>
@@ -1133,7 +1345,7 @@ typedef herr_t (*H5T_conv_t)(hid_t <em>src_type</em>,
 	initialized. This is useful for those functions requiring some
 	extra buffer space as the buffer can probably be allocated
 	more efficiently by the library (the application can supply
-	the buffer as part of the dataset transfer template).
+	the buffer as part of the dataset transfer property list).
 
 	<br><br>
       <dt><code>H5T_BKG_YES</code>
@@ -1148,64 +1360,56 @@ typedef herr_t (*H5T_conv_t)(hid_t <em>src_type</em>,
 	destination.
     </dl>
 
-    <p>Other fields of <em>cdata</em> can be read or written by
-      the conversion functions.  Many of these contain
-      performance-measuring fields which can be printed by the
-      conversion function during the <code>H5T_CONV_FREE</code>
-      command which is issued whenever the function is removed from a
-      conversion path.
-
-    <dl>
-      <dt><code>hbool_t recalc</code>
-      <dd>This field is set by the library when any other data type
-	conversion function is registered or unregistered.  It allows
-	conversion functions to cache pointers to other conversion
-	functions and be notified when the cache should be
-	recalculated.
-
-	<br><br>
-      <dt><code>unsigned long ncalls</code>
-      <dd>This field contains the number of times the conversion
-	function was called with the command
-	<code>H5T_CONV_CONV</code>.  It is updated automatically by
-	the library.
-
-	<br><br>
-      <dt><code>unsigned long nelmts</code>
-      <dd>This is the total number of data points converted by this
-	function and is updated automatically by the library.
-    </dl>
-
+    <p>The <code>recalc</code> field of <em>cdata</em> is set when the 
+      conversion path table changes. It can be used by conversion
+      function that cache other conversion paths so they know when
+      their cache needs to be recomputed.
 
 
     <p>Once a conversion function is written it can be registered and
       unregistered with these functions:
 
     <dl>
-      <dt><code>herr_t H5Tregister_hard (const char *<em>name</em>,
-	  hid_t <em>src_type</em>, hid_t <em>dest_type</em>,
-	  H5T_conv_t <em>func</em>)</code>
+      <dt><code>herr_t H5Tregister(H5T_pers_t <em>pers</em>, const
+	  char *<em>name</em>, hid_t <em>src_type</em>, hid_t
+	  <em>dest_type</em>, H5T_conv_t <em>func</em>)</code>
       <dd>Once a conversion function is written, the library must be
-	notified so it can be used.  The function can be registered as a
-	hard conversion for one or more conversion paths by calling
-	<code>H5Tregister_hard()</code>, displacing any previous hard
-	conversion for those paths.  The <em>name</em> is used only
-	for debugging but must be supplied.
+	notified so it can be used.  The function can be registered as
+	a hard (<code>H5T_PERS_HARD</code>) or soft
+	(<code>H5T_PERS_SOFT</code>) conversion depending on the value
+	of <em>pers</em>, displacing any previous conversions for all
+	applicable paths.  The <em>name</em> is used only for
+	debugging but must be supplied.  If <em>pers</em> is
+	<code>H5T_PERS_SOFT</code> then only the type classes of the
+	<em>src_type</em> and <em>dst_type</em> are used. For
+	instance, to register a general soft conversion function that
+	can be applied to any integer to integer conversion one could
+	say: <code>H5Tregister(H5T_PERS_SOFT, "i2i", H5T_NATIVE_INT,
+	H5T_NATIVE_INT, convert_i2i)</code>.  One special conversion
+	path called the "no-op" conversion path is always defined by
+	the library and used as the conversion function when no data
+	transformation is necessary. The application can redefine this 
+	path by specifying a new hard conversion function with a
+	negative value for both the source and destination data types, 
+	but the library might not call the function under certain
+	circumstances.
 
 	<br><br>
-      <dt><code>herr_t H5Tregister_soft (const char *<em>name</em>,
-	  H5T_class_t <em>src_class</em>, H5T_class_t <em>dest_class</em>,
-	  H5T_conv_t <em>func</em>)</code>
-      <dd>The function can be registered as a generic function which
-	will be automatically added to any conversion path for which
-	it returns an indication that it applies.  The name is used
-	only for debugging but must be supplied.
-
-	<br><br>
-      <dt><code>herr_t H5Tunregister (H5T_conv_t <em>func</em>)</code>
-      <dd>A function can be removed from the set of known conversion
-	functions by calling <code>H5Tunregister()</code>.  The
-	function is removed from all conversion paths.
+      <dt><code>herr_t H5Tunregister (H5T_pers_t <em>pers</em>, const
+	  char *<em>name</em>, hid_t <em>src_type</em>, hid_t
+	  <em>dest_type</em>, H5T_conv_t <em>func</em>)</code>
+      <dd>Any conversion path or function that matches the critera
+	specified by a call to this function is removed from the type
+	conversion table. All fields have the same interpretation as
+	for <code>H5Tregister()</code> with the added feature that any
+	(or all) may be wild cards.  The
+	<code>H5T_PERS_DONTCARE</code> constant should be used to
+	indicate a wild card for the <em>pers</em> argument. The wild
+	card <em>name</em> is the null pointer or empty string, the
+	wild card for the <em>src_type</em> and <em>dest_type</em>
+	arguments is any negative value, and the wild card for the
+	<em>func</em> argument is the null pointer.  The special no-op 
+	conversion path is never removed by this function.
     </dl>
 
     <p>
@@ -1334,7 +1538,9 @@ typedef herr_t (*H5T_conv_t)(hid_t <em>src_type</em>,
 		paths it can handle.
 
 	      <p><code><pre>
-H5Tregister_soft ("cus2be", H5T_INTEGER, H5T_INTEGER, cray_ushort2be);
+H5Tregister(H5T_PERS_SOFT, "cus2be",
+            H5T_NATIVE_INT, H5T_NATIVE_INT,
+            cray_ushort2be);
 	      </pre></code>
 
 	      <p>This causes it to be consulted for any conversion
@@ -1359,12 +1565,76 @@ H5Tregister_soft ("cus2be", H5T_INTEGER, H5T_INTEGER, cray_ushort2be);
       conversion path whether that conversion path was actually used
       or not.
 
-    <hr>
-    <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
-    <address><a href="mailto:koziol@ncsa.uiuc.edu">Quincey Koziol</a></address>
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
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+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
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+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
 <!-- Created: Thu Dec  4 14:57:32 EST 1997 -->
 <!-- hhmts start -->
-Last modified: Thu Jun 18 13:59:12 EDT 1998
+Last modified: Fri Jun  4 16:14:04 EDT 1999
 <!-- hhmts end -->
-  </body>
+
+
+</body>
 </html>

doc/html/DatatypesEnum.html

@@ -0,0 +1,921 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<html>
+  <head>
+    <title>Enumeration Data Types in the Data Type Interface (H5T)</title>
+  </head>
+
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
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+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
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+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
+    <h1>The Data Type Interface (H5T) <font size=-1><i>(contitnued)</i></font></h1>
+
+    <p align=right><font size=-1><i>
+    (Return to <a href="Datatypes.html#Datatypes_Enum">Data Types Interface (H5T)</a>.)
+    </font></i>
+
+    <h2>7. Enumeration Data Types</h2>
+
+    <h3>7.1. Introduction</h2>
+
+    <p>An HDF enumeration data type is a 1:1 mapping between a set of
+      symbols and a set of integer values, and an order is imposed on
+      the symbols by their integer values.  The symbols are passed
+      between the application and library as character strings and all
+      the values for a particular enumeration type are of the same
+      integer type, which is not necessarily a native type.
+
+    <h3>7.2. Creation</h2>
+    
+    <p>Creation of an enumeration data type resembles creation of a
+      compound data type: first an empty enumeration type is created,
+      then members are added to the type, then the type is optionally
+      locked.
+
+    <dl>
+      <dt><code>hid_t H5Tcreate(H5T_class_t <em>type_class</em>,
+	  size_t <em>size</em>)</code>
+      <dd>This function creates a new empty enumeration data type based 
+	on a native signed integer type. The first argument is the
+	constant <code>H5T_ENUM</code> and the second argument is the
+	size in bytes of the native integer on which the enumeration
+	type is based. If the architecture does not support a native
+	signed integer of the specified size then an error is
+	returned.
+
+	<pre>
+/* Based on a native signed short */
+hid_t hdf_en_colors = H5Tcreate(H5T_ENUM, sizeof(short));</pre>
+
+
+      <dt><code>hid_t H5Tenum_create(hid_t <em>base</em>)</code>
+      <dd>This function creates a new empty enumeration data type based 
+	on some integer data type <em>base</em> and is a
+	generalization of the <code>H5Tcreate()</code> function.  This 
+	function is useful when creating an enumeration type based on
+	some non-native integer data type, but it can be used for
+	native types as well.
+
+	<pre>
+/* Based on a native unsigned short */
+hid_t hdf_en_colors_1 = H5Tenum_create(H5T_NATIVE_USHORT);
+
+/* Based on a MIPS 16-bit unsigned integer */
+hid_t hdf_en_colors_2 = H5Tenum_create(H5T_MIPS_UINT16);
+
+/* Based on a big-endian 16-bit unsigned integer */
+hid_t hdf_en_colors_3 = H5Tenum_create(H5T_STD_U16BE);</pre>
+
+
+      <dt><code>herr_t H5Tenum_insert(hid_t <em>etype</em>, const char
+	  *<em>symbol</em>, void *<em>value</em>)</code>
+      <dd>Members are inserted into the enumeration data type
+	<em>etype</em> with this function.  Each member has a symbolic 
+	name <em>symbol</em> and some integer representation
+	<em>value</em>.  The <em>value</em> argument must point to a value
+	of the same data type as specified when the enumeration type
+	was created. The order of member insertion is not important
+	but all symbol names and values must be unique within a
+	particular enumeration type.
+
+	<pre>
+short val;
+H5Tenum_insert(hdf_en_colors, "RED",   (val=0,&amp;val));
+H5Tenum_insert(hdf_en_colors, "GREEN", (val=1,&amp;val));
+H5Tenum_insert(hdf_en_colors, "BLUE",  (val=2,&amp;val));
+H5Tenum_insert(hdf_en_colors, "WHITE", (val=3,&amp;val));
+H5Tenum_insert(hdf_en_colors, "BLACK", (val=4,&amp;val));</pre>
+
+
+      <dt><code>herr_t H5Tlock(hid_t <em>etype</em>)</code>
+      <dd>This function locks a data type so it cannot be modified or
+	freed unless the entire HDF5 library is closed.  Its use is
+	completely optional but using it on an application data type
+	makes that data type act like a predefined data type.
+
+	<pre>
+H5Tlock(hdf_en_colors);</pre>
+
+    </dl>
+
+    <h3>7.3. Integer Operations</h2>
+
+    <p>Because an enumeration data type is derived from an integer
+      data type, any operation which can be performed on integer data
+      types can also be performed on enumeration data types.  This
+      includes:
+
+    <p>
+      <center>
+	  <table>
+	    <tr>
+	      <td><code>H5Topen()</code></td>
+	      <td><code>H5Tcreate()</code></td>
+	      <td><code>H5Tcopy()</code></td>
+	      <td><code>H5Tclose()</code></td>
+	    </tr><tr>
+	      <td><code>H5Tequal()</code></td>
+	      <td><code>H5Tlock()</code></td>
+	      <td><code>H5Tcommit()</code></td>
+	      <td><code>H5Tcommitted()</code></td>
+	    </tr><tr>
+	      <td><code>H5Tget_class()</code></td>
+	      <td><code>H5Tget_size()</code></td>
+	      <td><code>H5Tget_order()</code></td>
+	      <td><code>H5Tget_pad()</code></td>
+	    </tr><tr>
+	      <td><code>H5Tget_precision()</code></td>
+	      <td><code>H5Tget_offset()</code></td>
+	      <td><code>H5Tget_sign()</code></td>
+	      <td><code>H5Tset_size()</code></td>
+	    </tr><tr>
+	      <td><code>H5Tset_order()</code></td>
+	      <td><code>H5Tset_precision()</code></td>
+	      <td><code>H5Tset_offset()</code></td>
+	      <td><code>H5Tset_pad()</code></td>
+	    </tr><tr>
+	      <td><code>H5Tset_sign()</code></td>
+	    </tr>
+	  </table>
+      </center>
+
+    <p>In addition, the new function <code>H5Tget_super()</code> will
+      be defined for all data types that are derived from existing
+      types (currently just enumeration types).
+
+    <dl>
+      <dt><code>hid_t H5Tget_super(hid_t <em>type</em>)</code>
+      <dd>Return the data type from which <em>type</em> is
+	derived. When <em>type</em> is an enumeration data type then
+	the returned value will be an integer data type but not
+	necessarily a native type.  One use of this function would be
+	to create a new enumeration type based on the same underlying
+	integer type and values but with possibly different symbols.
+
+	<pre>
+hid_t itype = H5Tget_super(hdf_en_colors);
+hid_t hdf_fr_colors = H5Tenum_create(itype);
+H5Tclose(itype);
+
+short val;
+H5Tenum_insert(hdf_fr_colors, "ouge",  (val=0,&amp;val));
+H5Tenum_insert(hdf_fr_colors, "vert",  (val=1,&amp;val));
+H5Tenum_insert(hdf_fr_colors, "bleu",  (val=2,&amp;val));
+H5Tenum_insert(hdf_fr_colors, "blanc", (val=3,&amp;val));
+H5Tenum_insert(hdf_fr_colors, "noir",  (val=4,&amp;val));
+H5Tlock(hdf_fr_colors);</pre>
+    </dl>
+
+    <h3>7.4. Type Functions</h2>
+
+    <p>A small set of functions is available for querying properties
+      of an enumeration type.  These functions are likely to be used
+      by browsers to display data type information.
+
+    <dl>
+      <dt><code>int H5Tget_nmembers(hid_t <em>etype</em>)</code>
+      <dd>When given an enumeration data type <em>etype</em> this
+	function returns the number of members defined for that
+	type. This function is already implemented for compound data
+	types.
+
+	<br><br>
+      <dt><code>char *H5Tget_member_name(hid_t <em>etype</em>, int
+	  <em>membno</em>)</code>
+      <dd>Given an enumeration data type <em>etype</em> this function
+	returns the symbol name for the member indexed by
+	<em>membno</em>. Members are numbered from zero to
+	<em>N</em>-1 where <em>N</em> is the return value from
+	<code>H5Tget_nmembers()</code>. The members are stored in no
+	particular order.  This function is already implemented for
+	compound data types.  If an error occurs then the null pointer 
+	is returned.  The return value should be freed by calling
+	<code>free()</code>.
+
+	<br><br>
+      <dt><code>herr_t H5Tget_member_value(hid_t <em>etype</em>, int
+	  <em>membno</em>, void *<em>value</em>/*out*/)</code>
+      <dd>Given an enumeration data type <em>etype</em> this function
+	returns the value associated with the member indexed by
+	<em>membno</em> (as described for
+	<code>H5Tget_member_name()</code>). The value returned
+	is in the domain of the underlying integer
+	data type which is often a native integer type. The
+	application should ensure that the memory pointed to by
+	<em>value</em> is large enough to contain the result (the size 
+	can be obtained by calling <code>H5Tget_size()</code> on
+	either the enumeration type or the underlying integer type
+	when the type is not known by the C compiler.
+
+	<pre>
+int i, n = H5Tget_nmembers(hdf_en_colors);
+for (i=0; i&lt;n; i++) {
+    char *symbol = H5Tget_member_name(hdf_en_colors, i);
+    short val;
+    H5Tget_member_value(hdf_en_colors, i, &amp;val);
+    printf("#%d %20s = %d\n", i, symbol, val);
+    free(symbol);
+}</pre>
+
+	  <p>
+          Output:
+	  <pre>
+#0                BLACK = 4
+#1                 BLUE = 2
+#2                GREEN = 1
+#3                  RED = 0
+#4                WHITE = 3</pre>
+    </dl>
+
+    <h3>7.5. Data Functions</h2>
+
+    <p>In addition to querying about the enumeration type properties,
+      an application may want to make queries about enumerated
+      data. These functions perform efficient mappings between symbol
+      names and values.
+
+    <dl>
+      <dt><code>herr_t H5Tenum_valueof(hid_t <em>etype</em>, const char 
+	  *<em>symbol</em>, void *<em>value</em>/*out*/)</code>
+      <dd>Given an enumeration data type <em>etype</em> this function
+      returns through <em>value</em> the bit pattern associated with
+      the symbol name <em>symbol</em>.  The <em>value</em> argument
+      should point to memory which is large enough to hold the result, 
+      which is returned as the underlying integer data type specified
+      when the enumeration type was created, often a native integer
+      type.
+
+	<br><br>
+      <dt><code>herr_t H5Tenum_nameof(hid_t <em>etype</em>, void
+	  *<em>value</em>, char *<em>symbol</em>, size_t
+	  <em>size</em>)</code>
+      <dd>This function translates a bit pattern pointed to by
+	<em>value</em> to a symbol name according to the mapping
+	defined in the enumeration data type <em>etype</em> and stores
+	at most <em>size</em> characters of that name (counting the
+	null terminator) to the <em>symbol</em> buffer. If the name is 
+	longer than the result buffer then the result is not null
+	terminated and the function returns failure. If <em>value</em> 
+	points to a bit pattern which is not in the domain of the
+	enumeration type then the first byte of the <em>symbol</em>
+	buffer is set to zero and the function fails.
+
+	<pre>
+short data[1000] = {4, 2, 0, 0, 5, 1, ...};
+int i;
+char symbol[32];
+
+for (i=0; i<1000; i++) {
+    if (H5Tenum_nameof(hdf_en_colors, data+i, symbol,
+                       sizeof symbol))&lt;0) {
+        if (symbol[0]) {
+            strcpy(symbol+sizeof(symbol)-4, "...");
+        } else {
+            strcpy(symbol, "UNKNOWN");
+        }
+    }
+    printf("%d %s\n", data[i], symbol);
+}
+printf("}\n");</pre>
+
+	  <p>
+          Output:
+	  <pre>
+
+4 BLACK
+2 BLUE
+0 RED
+0 RED
+5 UNKNOWN
+1 GREEN
+...</pre>
+    </dl>
+
+    <h3>7.6. Conversion</h2>
+
+    <p>Enumerated data can be converted from one type to another
+      provided the destination enumeration type contains all the
+      symbols of the source enumeration type. The conversion operates
+      by matching up the symbol names of the source and destination
+      enumeration types to build a mapping from source value to
+      destination value.  For instance, if we are translating from an
+      enumeration type that defines a sequence of integers as the
+      values for the colors to a type that defines a different bit for 
+      each color then the mapping might look like this:
+
+    <p><img src="EnumMap.gif" alt="Enumeration Mapping">
+
+    <p>That is, a source value of <code>2</code> which corresponds to
+      <code>BLUE</code> would be mapped to <code>0x0004</code>. The
+      following code snippet builds the second data type, then
+      converts a raw data array from one data type to another, and
+      then prints the result.
+
+      <pre>
+/* Create a new enumeration type */
+short val;
+hid_t bits = H5Tcreate(H5T_ENUM, sizeof val);
+H5Tenum_insert(bits, "RED",   (val=0x0001,&amp;val));
+H5Tenum_insert(bits, "GREEN", (val=0x0002,&amp;val));
+H5Tenum_insert(bits, "BLUE",  (val=0x0004,&amp;val));
+H5Tenum_insert(bits, "WHITE", (val=0x0008,&amp;val));
+H5Tenum_insert(bits, "BLACK", (val=0x0010,&amp;val));
+
+/* The data */
+short data[6] = {1, 4, 2, 0, 3, 5};
+
+/* Convert the data from one type to another */
+H5Tconvert(hdf_en_colors, bits, 5, data, NULL);
+
+/* Print the data */
+for (i=0; i&lt;6; i++) {
+    printf("0x%04x\n", (unsigned)(data[i]));
+}</pre>
+
+        <p>
+        Output:
+	<pre>
+
+0x0002
+0x0010
+0x0004
+0x0001
+0x0008
+0xffff</pre>
+
+    <p>If the source data stream contains values which are not in the
+      domain of the conversion map then an overflow exception is
+      raised within the library, causing the application defined
+      overflow handler to be invoked (see
+      <code>H5Tset_overflow()</code>). If no overflow handler is
+      defined then all bits of the destination value will be set.
+
+    <p>The HDF library will not provide conversions between enumerated 
+      data and integers although the application is free to do so
+      (this is a policy we apply to all classes of HDF data
+      types). However, since enumeration types are derived from
+      integer types it is permissible to treat enumerated data as
+      integers and perform integer conversions in that context.
+
+    <h3>7.7. Symbol Order</h2>
+
+    <p>Symbol order is determined by the integer values associated
+      with each symbol.  When the integer data type is a native type,
+      testing the relative order of two symbols is an easy process:
+      simply compare the values of the symbols.  If only the symbol
+      names are available then the values must first be determined by
+      calling <code>H5Tenum_valueof()</code>.
+
+      <pre>
+short val1, val2;
+H5Tenum_valueof(hdf_en_colors, "WHITE", &amp;val1);
+H5Tenum_valueof(hdf_en_colors, "BLACK", &amp;val2);
+if (val1 &lt; val2) ...</pre>
+
+    <p>When the underlying integer data type is not a native type then 
+      the easiest way to compare symbols is to first create a similar
+      enumeration type that contains all the same symbols but has a
+      native integer type (HDF type conversion features can be used to
+      convert the non-native values to native values). Once we have a
+      native type we can compare symbol order as just described.  If
+      <code>foreign</code> is some non-native enumeration type then a
+      native type can be created as follows:
+
+      <pre>
+int n = H5Tget_nmembers(foreign);
+hid_t itype = H5Tget_super(foreign);
+void *val = malloc(n * MAX(H5Tget_size(itype), sizeof(int)));
+char *name = malloc(n * sizeof(char*));
+int i;
+
+/* Get foreign type information */
+for (i=0; i&lt;n; i++) {
+    name[i] = H5Tget_member_name(foreign, i);
+    H5Tget_member_value(foreign, i,
+                        (char*)val+i*H5Tget_size(foreign));
+}
+
+/* Convert integer values to new type */
+H5Tconvert(itype, H5T_NATIVE_INT, n, val, NULL);
+
+/* Build a native type */
+hid_t native = H5Tenum_create(H5T_NATIVE_INT);
+for (i=0; i&lt;n; i++) {
+    H5Tenum_insert(native, name[i], ((int*)val)[i]);
+    free(name[i]);
+}
+free(name);
+free(val);</pre>
+
+    <p>It is also possible to convert enumerated data to a new type
+      that has a different order defined for the symbols.  For
+      instance, we can define a new type, <code>reverse</code> that
+      defines the same five colors but in the reverse order.
+
+      <pre>
+short val;
+int i;
+char sym[8];
+short data[5] = {0, 1, 2, 3, 4};
+
+hid_t reverse = H5Tenum_create(H5T_NATIVE_SHORT);
+H5Tenum_insert(reverse, "BLACK", (val=0,&amp;val));
+H5Tenum_insert(reverse, "WHITE", (val=1,&amp;val));
+H5Tenum_insert(reverse, "BLUE",  (val=2,&amp;val));
+H5Tenum_insert(reverse, "GREEN", (val=3,&amp;val));
+H5Tenum_insert(reverse, "RED",   (val=4,&amp;val));
+
+/* Print data */
+for (i=0; i<5; i++) {
+    H5Tenum_nameof(hdf_en_colors, data+i, sym, sizeof sym);
+    printf ("%d %s\n", data[i], sym);
+}
+
+puts("Converting...");
+H5Tconvert(hdf_en_colors, reverse, 5, data, NULL);
+
+/* Print data */
+for (i=0; i<5; i++) {
+    H5Tenum_nameof(reverse, data+i, sym, sizeof sym);
+    printf ("%d %s\n", data[i], sym);
+}</pre>
+	
+      <p>
+      Output:
+      <pre>
+0 RED
+1 GREEN
+2 BLUE
+3 WHITE
+4 BLACK
+Converting...
+4 RED
+3 GREEN
+2 BLUE
+1 WHITE
+0 BLACK</pre>
+
+    <h3>7.8. Equality</h2>
+
+    <p>The order that members are inserted into an enumeration type is 
+      unimportant; the important part is the associations between the
+      symbol names and the values.  Thus, two enumeration data types
+      will be considered equal if and only if both types have the same
+      symbol/value associations and both have equal underlying integer
+      data types. Type equality is tested with the
+      <code>H5Tequal()</code> function.
+
+    <h3>7.9. Interacting with C's <code>enum</code> Type</h2>
+
+    <p>Although HDF enumeration data types are similar to C
+      <code>enum</code> data types, there are some important
+      differences:
+
+    <p>
+      <center>
+	<table border width="80%">
+	  <tr>
+	    <th>Difference</th>
+	    <th>Motivation/Implications</th>
+	  </tr>
+
+	  <tr>
+	    <td valign=top>Symbols are unquoted in C but quoted in
+	      HDF.</td>
+	    <td valign=top>This allows the application to manipulate
+	      symbol names in ways that are not possible with C.</td>
+	  </tr>
+
+	  <tr>
+	    <td valign=top>The C compiler automatically replaces all
+	      symbols with their integer values but HDF requires
+	      explicit calls to do the same.</td>
+	    <td valign=top>C resolves symbols at compile time while
+	      HDF resolves symbols at run time.</td>
+	  </tr>
+
+	  <tr>
+	    <td valign=top>The mapping from symbols to integers is
+	      <em>N</em>:1 in C but 1:1 in HDF.</td>
+	    <td valign=top>HDF can translate from value to name
+	      uniquely and large <code>switch</code> statements are
+	      not necessary to print values in human-readable
+	      format.</td>
+	  </tr>
+
+	  <tr>
+	    <td valign=top>A symbol must appear in only one C
+	      <code>enum</code> type but may appear in multiple HDF
+	      enumeration types.</td>
+	    <td valign=top>The translation from symbol to value in HDF 
+	      requires the data type to be specified while in C the
+	      data type is not necessary because it can be inferred
+	      from the symbol.</td>
+	  </tr>
+
+	  <tr>
+	    <td valign=top>The underlying integer value is always a
+	      native integer in C but can be a foreign integer type in 
+	      HDF.</td>
+	    <td valign=top>This allows HDF to describe data that might 
+	      reside on a foreign architecture, such as data stored in 
+	      a file.</td>
+	  </tr>
+
+	  <tr>
+	    <td valign=top>The sign and size of the underlying integer 
+	      data type is chosen automatically by the C compiler but
+	      must be fully specified with HDF.</td>
+	    <td valign=top>Since HDF doesn't require finalization of a 
+	      data type, complete specification of the type must be
+	      supplied before the type is used.  Requiring that
+	      information at the time of type creation was a design
+	      decision to simplify the library.</td>
+	  </tr>
+	</table>
+      </center>
+
+    <p>The examples below use the following C data types:
+
+    <p>
+      <table width="90%" bgcolor="white">
+	<tr>
+	  <td>
+	    <code><pre>
+/* English color names */
+typedef enum {
+    RED,
+    GREEN,
+    BLUE,
+    WHITE,
+    BLACK
+} c_en_colors;
+
+/* Spanish color names, reverse order */
+typedef enum {
+    NEGRO
+    BLANCO,
+    AZUL,
+    VERDE,
+    ROJO,
+} c_sp_colors;
+
+/* No enum definition for French names */
+	    </pre></code>
+	  </td>
+	</tr>
+      </table>
+
+    <h4>Creating HDF Types from C Types</h3>
+
+    <p>An HDF enumeration data type can be created from a C
+      <code>enum</code> type simply by passing pointers to the C
+      <code>enum</code> values to <code>H5Tenum_insert()</code>.  For
+      instance, to create HDF types for the <code>c_en_colors</code>
+      type shown above:
+
+    <p>
+      <table width="90%" bgcolor="white">
+	<tr>
+	  <td>
+	    <code><pre>
+
+c_en_colors val;
+hid_t hdf_en_colors = H5Tcreate(H5T_ENUM, sizeof(c_en_colors));
+H5Tenum_insert(hdf_en_colors, "RED",   (val=RED,  &amp;val));
+H5Tenum_insert(hdf_en_colors, "GREEN", (val=GREEN,&amp;val));
+H5Tenum_insert(hdf_en_colors, "BLUE",  (val=BLUE, &amp;val));
+H5Tenum_insert(hdf_en_colors, "WHITE", (val=WHITE,&amp;val));
+H5Tenum_insert(hdf_en_colors, "BLACK", (val=BLACK,&amp;val));</pre></code>
+	  </td>
+	</tr>
+      </table>
+
+    <h4>Name Changes between Applications</h3>
+
+    <p>Occassionally two applicatons wish to exchange data but they
+      use different names for the constants they exchange.  For
+      instance, an English and a Spanish program may want to
+      communicate color names although they use different symbols in
+      the C <code>enum</code> definitions. The communication is still
+      possible although the applications must agree on common terms
+      for the colors. The following example shows the Spanish code to
+      read the values assuming that the applications have agreed that
+      the color information will be exchanged using Enlish color
+      names:
+
+    <p>
+      <table width="90%" bgcolor="white">
+	<tr>
+	  <td>
+	    <code><pre>
+
+c_sp_colors val, data[1000];
+hid_t hdf_sp_colors = H5Tcreate(H5T_ENUM, sizeof(c_sp_colors));
+H5Tenum_insert(hdf_sp_colors, "RED",   (val=ROJO,   &amp;val));
+H5Tenum_insert(hdf_sp_colors, "GREEN", (val=VERDE,  &amp;val));
+H5Tenum_insert(hdf_sp_colors, "BLUE",  (val=AZUL,   &amp;val));
+H5Tenum_insert(hdf_sp_colors, "WHITE", (val=BLANCO, &amp;val));
+H5Tenum_insert(hdf_sp_colors, "BLACK", (val=NEGRO,  &amp;val));
+
+H5Dread(dataset, hdf_sp_colors, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);</pre></code>
+	  </td>
+	</tr>
+      </table>
+
+
+    <h4>Symbol Ordering across Applications</h3>
+
+    <p>Since symbol ordering is completely determined by the integer values
+      assigned to each symbol in the <code>enum</code> definition,
+      ordering of <code>enum</code> symbols cannot be preserved across
+      files like with HDF enumeration types.  HDF can convert from one
+      application's integer values to the other's so a symbol in one
+      application's C <code>enum</code> gets mapped to the same symbol
+      in the other application's C <code>enum</code>, but the relative
+      order of the symbols is not preserved.
+
+    <p>For example, an application may be defined to use the
+      definition of <code>c_en_colors</code> defined above where
+      <code>WHITE</code> is less than <code>BLACK</code>, but some
+      other application might define the colors in some other
+      order. If each application defines an HDF enumeration type based 
+      on that application's C <code>enum</code> type then HDF will
+      modify the integer values as data is communicated from one
+      application to the other so that a <code>RED</code> value
+      in the first application is also a <code>RED</code> value in the
+      other application.
+
+    <p>A case of this reordering of symbol names was also shown in the 
+      previous code snippet (as well as a change of language), where
+      HDF changed the integer values so 0 (<code>RED</code>) in the
+      input file became 4 (<code>ROJO</code>) in the <code>data</code>
+      array. In the input file, <code>WHITE</code> was less than
+      <code>BLACK</code>; in the application the opposite is true.
+
+    <p>In fact, the ability to change the order of symbols is often
+      convenient when the enumeration type is used only to group
+      related symbols that don't have any well defined order
+      relationship.
+
+    <h4>Internationalization</h3>
+
+    <p>The HDF enumeration type conversion features can also be used
+      to provide internationalization of debugging output.  A program
+      written with the <code>c_en_colors</code> data type could define 
+      a separate HDF data type for languages such as English, Spanish, 
+      and French and cast the enumerated value to one of these HDF
+      types to print the result.
+
+    <p>
+      <table width="90%" bgcolor="white">
+	<tr>
+	  <td>
+	    <code><pre>
+
+c_en_colors val, *data=...;
+
+hid_t hdf_sp_colors = H5Tcreate(H5T_ENUM, sizeof val);
+H5Tenum_insert(hdf_sp_colors, "ROJO",   (val=RED,   &amp;val));
+H5Tenum_insert(hdf_sp_colors, "VERDE",  (val=GREEN, &amp;val));
+H5Tenum_insert(hdf_sp_colors, "AZUL",   (val=BLUE,  &amp;val));
+H5Tenum_insert(hdf_sp_colors, "BLANCO", (val=WHITE, &amp;val));
+H5Tenum_insert(hdf_sp_colors, "NEGRO",  (val=BLACK, &amp;val));
+
+hid_t hdf_fr_colors = H5Tcreate(H5T_ENUM, sizeof val);
+H5Tenum_insert(hdf_fr_colors, "OUGE",  (val=RED,   &amp;val));
+H5Tenum_insert(hdf_fr_colors, "VERT",  (val=GREEN, &amp;val));
+H5Tenum_insert(hdf_fr_colors, "BLEU",  (val=BLUE,  &amp;val));
+H5Tenum_insert(hdf_fr_colors, "BLANC", (val=WHITE, &amp;val));
+H5Tenum_insert(hdf_fr_colors, "NOIR",  (val=BLACK, &amp;val));
+
+void
+nameof(lang_t language, c_en_colors val, char *name, size_t size)
+{
+    switch (language) {
+    case ENGLISH:
+        H5Tenum_nameof(hdf_en_colors, &amp;val, name, size);
+        break;
+    case SPANISH:
+        H5Tenum_nameof(hdf_sp_colors, &amp;val, name, size);
+        break;
+    case FRENCH:
+        H5Tenum_nameof(hdf_fr_colors, &amp;val, name, size);
+        break;
+    }
+}</pre></code>
+	  </td>
+	</tr>
+      </table>
+
+    <h3>7.10. Goals That Have Been Met</h2>
+
+    <p>The main goal of enumeration types is to provide communication
+      of enumerated data using symbolic equivalence.  That is, a
+      symbol written to a dataset by one application should be read as
+      the same symbol by some other application.
+
+    <p>
+      <table width="90%">
+	<tr>
+	  <td valign=top><b>Architecture Independence</b></td>
+	  <td valign=top>Two applications shall be able to exchange
+	    enumerated data even when the underlying integer values
+	    have different storage formats. HDF accomplishes this for
+	    enumeration types by building them upon integer types.</td>
+	</tr>
+
+	<tr>
+	  <td valign=top><b>Preservation of Order Relationship</b></td>
+	  <td valign=top>The relative order of symbols shall be
+	    preserved between two applications that use equivalent
+	    enumeration data types. Unlike numeric values that have
+	    an implicit ordering, enumerated data has an explicit
+	    order defined by the enumeration data type and HDF
+	    records this order in the file.</td>
+	</tr>
+
+	<tr>
+	  <td valign=top><b>Order Independence</b></td>
+	  <td valign=top>An application shall be able to change the
+	    relative ordering of the symbols in an enumeration data
+	    type.  This is accomplished by defining a new type with
+	    different integer values and converting data from one type 
+	    to the other.</td>
+	</tr>
+
+	<tr>
+	  <td valign=top><b>Subsets</b></td>
+	  <td valign=top>An application shall be able to read
+	    enumerated data from an archived dataset even after the
+	    application has defined additional members for the
+	    enumeration type. An application shall be able to write
+	    to a dataset when the dataset contains a superset of the 
+	    members defined by the application.  Similar rules apply 
+	    for in-core conversions between enumerated data
+	    types.</td>
+	</tr>
+
+	<tr>
+	  <td valign=top><b>Targetable</b></td>
+	  <td valign=top>An application shall be able to target a
+	    particular architecture or application when storing
+	    enumerated data. This is accomplished by allowing
+	    non-native underlying integer types and converting the
+	    native data to non-native data.</td>
+	</tr>
+
+	<tr>
+	  <td valign=top><b>Efficient Data Transfer</b></td>
+	  <td valign=top>An application that defines a file dataset
+	    that corresponds to some native C enumerated data array
+	    shall be able to read and write to that dataset directly
+	    using only Posix read and write functions. HDF already
+	    optimizes this case for integers, so the same optimization 
+	    will apply to enumerated data.
+	</tr>
+
+	<tr>
+	  <td valign=top><b>Efficient Storage</b></td>
+	  <td valign=top>Enumerated data shall be stored in a manner 
+	    which is space efficient. HDF stores the enumerated data
+	    as integers and allows the application to chose the size
+	    and format of those integers.</td>
+	</tr>
+      </table>
+
+
+    <p align=right><font size=-1><i>
+    (Return to <a href="Datatypes.html#Datatypes_Enum">Data Types Interface (H5T)</a>.)
+    </font></i>
+
+<hr>
+<center>
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+
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+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
+<!-- Created: Thu Dec  4 14:57:32 EST 1997 -->
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+Last modified: 30 April 1999
+<!-- hhmts end -->
+
+
+</body>
+</html>

doc/html/Debugging.html

@@ -0,0 +1,544 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<html>
+  <head>
+    <title>Debugging HDF5 Applications</title>
+  </head>
+
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
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+<td valign=top align=right>
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+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
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+<hr>
+And in this document, the 
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+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
+    <h1>Debugging HDF5 Applications</h1>
+
+    <h2>Introduction</h2>
+
+    <p>The HDF5 library contains a number of debugging features to
+      make programmers' lives easier including the ability to print
+      detailed error messages, check invariant conditions, display
+      timings and other statistics, and trace API function calls and
+      return values.
+
+    <dl>
+      <dt><b>Error Messages</b>
+      <dd>Error messages are normally displayed automatically on the
+	standard error stream and include a stack trace of the library
+	including file names, line numbers, and function names. The
+	application has complete control over how error messages are
+	displayed and can disable the display on a permanent or
+	temporary basis. Refer to the documentation for the H5E error
+	handling package.
+
+	<br><br>
+      <dt><b>Invariant Conditions</b>
+      <dd>Unless <code>NDEBUG</code> is defined during compiling, the
+	library will include code to verify that invariant conditions
+	have the expected values.  When a problem is detected the
+	library will display the file and line number within the
+	library and the invariant condition that failed.  A core dump
+	may be generated for post mortem debugging. The code to
+	perform these checks can be included on a per-package bases.
+
+	<br><br>
+      <dt><b>Timings and Statistics</b>
+      <dd>The library can be configured to accumulate certain
+	statistics about things like cache performance, data type
+	conversion, data space conversion, and data filters. The code
+	is included on a per-package basis and enabled at runtime by
+	an environment variable.
+
+	<br><br>
+      <dt><b>API Tracing</b>
+      <dd>All API calls made by an application can be displayed and
+	include formal argument names and actual values and the
+	function return value. This code is also conditionally
+	included at compile time and enabled at runtime.
+    </dl>
+
+    <p>The statistics and tracing can be displayed on any output
+      stream (including streams opened by the shell) with output from
+      different packages even going to different streams.
+
+    <h2>Error Messages</h2>
+
+    <p>By default any API function that fails will print an error
+      stack to the standard error stream.
+
+    <p>
+      <center>
+	<table border align=center width="100%">
+	  <tr>
+	    <td>
+	      <p><code><pre>
+
+HDF5-DIAG: Error detected in thread 0.  Back trace follows.
+  #000: H5F.c line 1245 in H5Fopen(): unable to open file
+    major(04): File interface
+    minor(10): Unable to open file
+  #001: H5F.c line 846 in H5F_open(): file does not exist
+    major(04): File interface
+    minor(10): Unable to open file
+	      </code></pre>
+	    </td>
+	  </tr>
+	</table>
+      </center>
+
+    <p>The error handling package (H5E) is described
+      <a href="Errors.html">elsewhere</a>.
+
+    <h2>Invariant Conditions</h2>
+
+    <p>To include checks for invariant conditions the library should
+      be configured with <code>--disable-production</code>, the
+      default for versions before 1.2. The library designers have made
+      every attempt to handle error conditions gracefully but an
+      invariant condition assertion may fail in certain cases.  The
+      output from a failure usually looks something like this:
+
+    <p>
+      <center>
+	<table border align=center width="100%">
+	  <tr>
+	    <td>
+	      <p><code><pre>
+
+Assertion failed: H5.c:123: i&lt;NELMTS(H5_debug_g)
+IOT Trap, core dumped.
+	      </code></pre>
+	    </td>
+	  </tr>
+	</table>
+      </center>
+
+    <h2>Timings and Statistics</h2>
+
+    <p>Code to accumulate statistics is included at compile time by
+      using the <code>--enable-debug</code> configure switch. The
+      switch can be followed by an equal sign and a comma-separated
+      list of package names or else a default list is used.
+
+    <p>
+      <center>
+        <table border align=center width="80%">
+          <tr>
+            <th>Name</th>
+	    <th>Default</th>
+            <th>Description</th>
+          </tr>
+	  <tr>
+	    <td align=center>a</td>
+	    <td align=center>No</td>
+	    <td>Attributes</td>
+	  </tr>
+	  <tr>
+	    <td align=center>ac</td>
+	    <td align=center>Yes</td>
+	    <td>Meta data cache</td>
+	  </tr>
+	  <tr>
+	    <td align=center>b</td>
+	    <td align=center>Yes</td>
+	    <td>B-Trees</td>
+	  </tr>
+	  <tr>
+	    <td align=center>d</td>
+	    <td align=center>Yes</td>
+	    <td>Datasets</td>
+	  </tr>
+	  <tr>
+	    <td align=center>e</td>
+	    <td align=center>Yes</td>
+	    <td>Error handling</td>
+	  </tr>
+	  <tr>
+	    <td align=center>f</td>
+	    <td align=center>Yes</td>
+	    <td>Files</td>
+	  </tr>
+	  <tr>
+	    <td align=center>g</td>
+	    <td align=center>Yes</td>
+	    <td>Groups</td>
+	  </tr>
+	  <tr>
+	    <td align=center>hg</td>
+	    <td align=center>Yes</td>
+	    <td>Global heap</td>
+	  </tr>
+	  <tr>
+	    <td align=center>hl</td>
+	    <td align=center>No</td>
+	    <td>Local heaps</td>
+	  </tr>
+	  <tr>
+	    <td align=center>i</td>
+	    <td align=center>Yes</td>
+	    <td>Interface abstraction</td>
+	  </tr>
+	  <tr>
+	    <td align=center>mf</td>
+	    <td align=center>No</td>
+	    <td>File memory management</td>
+	  </tr>
+	  <tr>
+	    <td align=center>mm</td>
+	    <td align=center>Yes</td>
+	    <td>Library memory managment</td>
+	  </tr>
+	  <tr>
+	    <td align=center>o</td>
+	    <td align=center>No</td>
+	    <td>Object headers and messages</td>
+	  </tr>
+	  <tr>
+	    <td align=center>p</td>
+	    <td align=center>Yes</td>
+	    <td>Property lists</td>
+	  </tr>
+	  <tr>
+	    <td align=center>s</td>
+	    <td align=center>Yes</td>
+	    <td>Data spaces</td>
+	  </tr>
+	  <tr>
+	    <td align=center>t</td>
+	    <td align=center>Yes</td>
+	    <td>Data types</td>
+	  </tr>
+	  <tr>
+	    <td align=center>v</td>
+	    <td align=center>Yes</td>
+	    <td>Vectors</td>
+	  </tr>
+	  <tr>
+	    <td align=center>z</td>
+	    <td align=center>Yes</td>
+	    <td>Raw data filters</td>
+	  </tr>
+        </table>
+      </center>
+
+    <p>In addition to including the code at compile time the
+      application must enable each package at runtime.  This is done
+      by listing the package names in the <code>HDF5_DEBUG</code>
+      environment variable. That variable may also contain file
+      descriptor numbers (the default is `2') which control the output
+      for all following packages up to the next file number.  The
+      word <code>all</code> refers to all packages. Any word my be
+      preceded by a minus sign to turn debugging off for the package.
+
+    <p>
+      <center>
+	<table border align=center width="100%">
+	  <caption align=top><b>Sample debug specifications</b></caption>
+	  <tr valign=top>
+	    <td><code>all</code></td>
+	    <td>This causes debugging output from all packages to be
+	      sent to the standard error stream.</td>
+	  </tr>
+	  <tr valign=top>
+	    <td><code>all -t -s</code></td>
+	    <td>Debugging output for all packages except data types
+	      and data spaces will appear on the standard error
+	      stream.</td>
+	  </tr>
+	  <tr valign=top>
+	    <td><code>-all ac 255 t,s</code></td>
+	    <td>This disables all debugging even if the default was to
+	      debug something, then output from the meta data cache is
+	      send to the standard error stream and output from data
+	      types and spaces is sent to file descriptor 255 which
+	      should be redirected by the shell.</td>
+	  </tr>
+	</table>
+      </center>
+
+    <p>The components of the <code>HDF5_DEBUG</code> value may be
+      separated by any non-lowercase letter.
+
+    <h2>API Tracing</h2>
+
+    <p>The HDF5 library can trace API calls by printing the
+      function name, the argument names and their values, and the
+      return value. Some people like to see lots of output during
+      program execution instead of using a good symbolic debugger, and
+      this feature is intended for their consumption.  For example,
+      the output from <code>h5ls foo</code> after turning on tracing,
+      includes:
+
+    <p>
+      <center>
+	<table border align=center width="100%">
+	  <tr>
+	    <td>
+	      <code><pre>
+
+H5Tcopy(type=184549388) = 184549419 (type);
+H5Tcopy(type=184549392) = 184549424 (type);
+H5Tlock(type=184549424) = SUCCEED;
+H5Tcopy(type=184549393) = 184549425 (type);
+H5Tlock(type=184549425) = SUCCEED;
+H5Fopen(filename="foo", flags=0, access=H5P_DEFAULT) = FAIL;
+HDF5-DIAG: Error detected in thread 0.  Back trace follows.
+  #000: H5F.c line 1245 in H5Fopen(): unable to open file
+    major(04): File interface
+    minor(10): Unable to open file
+  #001: H5F.c line 846 in H5F_open(): file does not exist
+    major(04): File interface
+    minor(10): Unable to open file
+	      </pre></code>
+	    </td>
+	  </tr>
+	</table>
+      </center>
+
+    <p>The code that performs the tracing must be included in the
+      library by specifying the <code>--enable-trace</code>
+      configuration switch (the default for versions before 1.2). Then
+      the word <code>trace</code> must appear in the value of the
+      <code>HDF5_DEBUG</code> variable.  The output will appear on the
+      last file descriptor before the word <code>trace</code> or two
+      (standard error) by default.
+
+    <p>
+      <center>
+	<table border align=center width="100%">
+	  <tr>
+	    <td>To display the trace on the standard error stream:
+	      <code><pre>
+$ env HDF5_DEBUG=trace a.out
+	      </pre></code>
+	    </td>
+	  </tr>
+	  <tr>
+	    <td>To send the trace to a file:
+	      <code><pre>
+$ env HDF5_DEBUG="55 trace" a.out 55>trace-output
+	      </pre></code>
+	    </td>
+	  </tr>
+	</table>
+      </center>
+
+    <h3>Performance</h3>
+
+    <p>If the library was not configured for tracing then there is no
+      unnecessary overhead since all tracing code is excluded.
+      However, if tracing is enabled but not used there is a small
+      penalty. First, code size is larger because of extra
+      statically-declared character strings used to store argument
+      types and names and extra auto variable pointer in each
+      function.  Also, execution is slower because each function sets
+      and tests a local variable and each API function calls the
+      <code>H5_trace()</code> function.
+
+    <p>If tracing is enabled and turned on then the penalties from the 
+      previous paragraph apply plus the time required to format each
+      line of tracing information.  There is also an extra call to
+      H5_trace() for each API function to print the return value.
+
+    <h3>Safety</h3>
+
+    <p>The tracing mechanism is invoked for each API function before
+      arguments are checked for validity.  If bad arguments are passed 
+      to an API function it could result in a segmentation fault.
+      However, the tracing output is line-buffered so all previous
+      output will appear.
+
+    <h3>Completeness</h3>
+
+    <p>There are two API functions that don't participate in
+      tracing. They are <code>H5Eprint()</code> and
+      <code>H5Eprint_cb()</code> because their participation would
+      mess up output during automatic error reporting.
+
+    <p>On the other hand, a number of API functions are called during
+      library initialization and they print tracing information.
+
+    <h3>Implementation</h3>
+
+    <p>For those interested in the implementation here is a
+      description.  Each API function should have a call to one of the 
+      <code>H5TRACE()</code> macros immediately after the
+      <code>FUNC_ENTER()</code> macro.  The first argument is the
+      return type encoded as a string.  The second argument is the
+      types of all the function arguments encoded as a string.  The
+      remaining arguments are the function arguments.  This macro was
+      designed to be as terse and unobtrousive as possible.
+
+    <p>In order to keep the <code>H5TRACE()</code> calls synchronized
+      with the source code we've written a perl script which gets
+      called automatically just before Makefile dependencies are
+      calculated for the file.  However, this only works when one is
+      using GNU make.  To reinstrument the tracing explicitly, invoke
+      the <code>trace</code> program from the hdf5 bin directory with
+      the names of the source files that need to be updated.  If any
+      file needs to be modified then a backup is created by appending
+      a tilde to the file name.
+
+    <p>
+      <center>
+	<table border align=center width="100%">
+	  <caption align=top><b>Explicit Instrumentation</b></caption>
+	  <tr>
+	    <td>
+	      <code><pre>
+
+$ ../bin/trace *.c
+H5E.c: in function `H5Ewalk_cb':
+H5E.c:336: warning: trace info was not inserted
+	      </pre></code>
+	    </td>
+	  </tr>
+	</table>
+      </center>
+
+    <p>Note: The warning message is the result of a comment of the
+      form <code>/*NO TRACE*/</code> somewhere in the function
+      body. Tracing information will not be updated or inserted if
+      such a comment exists.
+
+    <p>Error messages have the same format as a compiler so that they
+      can be parsed from program development environments like
+      Emacs. Any function which generates an error will not be
+      modified.
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      Debugging&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<!--
+    <hr>
+    <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
+-->
+<!-- Created: Wed Jun 17 12:29:12 EDT 1998 -->
+<!-- hhmts start -->
+<!--
+Last modified: Thu Aug 20 10:43:42 PDT 1998
+-->
+<!-- hhmts end -->
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
+
+Last modified:  30 October 1998
+
+  </body>
+</html>

doc/html/Environment.html

@@ -0,0 +1,284 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<html>
+<<<<<<< Environment.html
+<head>
+<title>HDF5 Library Environment Variables and Configuration Parameters</title>
+</head>
+
+<body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      Environment&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
+<h1>HDF5 Library Environment Variables and Configuration Parameters</h1>
+
+<h2>1. Environment Variables</h2>
+
+The HDF5 library uses UNIX environment variables to control
+or adjust certain library features at runtime.  The variables and 
+their defined effects are as follows:
+
+<dir>
+<dl>
+    <dt><tt>HDF5_DEBUG</tt>
+        <dd>Defines a list of debugging switches documented in the
+            <a href="Debugging.html">Debugging</a> section of the
+            <cite>HDF5 User's Guide</cite>.
+
+    <dt><tt>HDF5_NOCLEANUP</tt>
+        <dd>When set to a non-empty value, the programs in the test
+            directory do not remove temporary HDF5 data files.
+            The default is for each test to remove the files before exit.
+
+    <dt><tt>HDF5_MPI_OPT_TYPES</tt> 
+            &nbsp;&nbsp;(for parallel beta version only)
+        <dd>When set to <code>1</code>, PHDF5 will use the MPI optimized 
+            code to perform parallel read/write accesses to datasets.
+            Currently, this optimization fails when accessing extendable
+            datasets.  The default is not to use the optimized code.
+
+    <dt><tt>HDF5_MPI_1_METAWRITE</tt> 
+            &nbsp;&nbsp;(for parallel beta version only)
+        <dd>When set to <code>1</code>, PHDF5 will write the metadata 
+            via process 0 of each opened parallel HDF5 file.  This should 
+            improve I/O throughput.  The default is not to use this 
+            optimization.
+
+</dl>
+</dir>
+
+<h2>2. Configuration Parameters</h2>
+
+The HDF5 configuration script accepts a list of parameters to control
+configuration features when creating the Makefiles for the library.  
+The command
+<br>
+<code>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;configure --help </code>
+<br>
+will display the current list of parameters and their effects.
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      Environment&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<hr>
+
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
+=======
+  <head>
+    <title>HDF5 Library Environment Variables
+      and Configuration Parameters</title>
+  </head>
+
+  <body>
+
+    <h1>HDF5 Library Environment Variables and Configuration Parameters</h1>
+
+    <h2>1. Environment Variables</h2>
+
+    The HDF5 library uses UNIX environment variables to control
+    or adjust certain library features at runtime.  The variables and 
+    their defined effects are as follows:
+
+    <center>
+      <table width="90%">
+	<tr>
+	  <th>Variable</th>
+	  <th>Description</th>
+	</tr>
+
+	<tr valign=top>
+	  <td><code>HDF5_DEBUG</code></td>
+	  <td>Defines a list of debugging switches documented in the
+	    <a href="Debugging.html">Debugging</a> section of the
+	    <cite>HDF5 User's Guide</cite>.</td>
+	</tr>
+
+	<tr valign=top>
+	  <td><code>HDF5_NOCLEANUP</code></td>
+	  <td>If set then programs in the test directories do not
+	    remove temporary files. The default is for each test to
+	    remove the files before exit if the test succeeds but to
+	    leave the files if the test fails.</td>
+	</tr>
+
+	<tr valign=top>
+	  <td><code>HDF5_PREFIX</code></td>
+	  <td>The value of this variable is prepended to all temporary 
+	    file names created by the test programs and separated from 
+	    the base name of the file by a slash. The default is no
+	    prefix.</td>
+	</tr>
+
+	<tr valign=top>
+	  <td><ode>HDF5_DRIVER</code></td>
+	  <td>This variable should hold the name of a low-level HDF5
+	    file driver such as <code>sec2</code>, <code>stdio</code>, 
+	    <code>core</code>, <code>split</code>, or
+	    <code>family</code>. The family driver also takes an
+	    optional real-valued family member size in MB which
+	    defaults to 1. If this variable is not set or empty then
+	    the library-defined default file driver is used (which can 
+	    be set at configuration time with the H5F_LOW_DFLT cpp
+	    constant, usually <code>sec2</code>).</td>
+	</tr>
+
+	<tr valign=top>
+	  <td><code>HDF5_MPI_OPT_TYPES</code></td>
+	  <td>When set to <code>1</code>, parallel HDF5 will use the
+	    MPI-optimized code to perform parallel read/write accesses
+	    to datasets. Currently, this optimization fails when
+	    accessing extendable datasets.  The default is not to use
+	    the optimized code.</td>
+	</tr>
+
+	<tr valign=top>
+	  <td><code>HDF5_MPI_1_METAWRITE</code></td>
+	  <td>When set to <code>1</code>, parallel HDF5 will write the
+	  metadata via process 0 of each opened parallel HDF5 file.
+	  This should improve I/O throughput.  The default is not to
+	  use this optimization.</td>
+	</tr>
+
+      </table>
+    </center>
+
+
+    <h2>2. Configuration Parameters</h2>
+
+    The HDF5 configuration script accepts a list of parameters to control
+    configuration features when creating the Makefiles for the library.  
+    The command
+    <br>
+    <code>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;configure --help </code>
+    <br>
+    will display the current list of parameters and their effects.
+
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
+
+Last modified: 25 November 1998
+
+
+</body>
+</html>
+

doc/html/Errors.html

@@ -4,7 +4,69 @@
     <title>The Error Handling Interface (H5E)</title>
   </head>
 
-  <body>
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      Error Handling&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
     <h1>The Error Handling Interface (H5E)</h1>
 
     <h2>1. Introduction</h2>
@@ -269,13 +331,83 @@ H5Ewalk_cb(int n, H5E_error_t *err_desc, void *client_data)
 	</table>
       </center>
 
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      Error Handling&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
 	
 
+<!--
     <hr>
     <address><a href="mailto:hdf5dev@ncsa.uiuc.edu">Robb Matzke</a></address>
+-->
 <!-- Created: Fri Feb 27 23:42:52 EST 1998 -->
 <!-- hhmts start -->
+<!--
 Last modified: Wed Mar  4 10:06:17 EST 1998
+-->
 <!-- hhmts end -->
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
+
+Last modified:  30 October 1998
+
   </body>
 </html>

doc/html/ExternalFiles.html

@@ -110,16 +110,16 @@
       Currently, the default low-level file driver is used for all
       family members (H5F_LOW_DFLT, usually set to be Section 2 I/O or
       Section 3 stdio), but we'll probably eventually want to pass
-      that as a parameter of the file access template, which hasn't
-      been implemented yet.  When creating a family, a default family
-      member size is used (defined at the top H5Ffamily.c, currently
-      64MB) but that also should be settable in the file access
-      template. When opening an existing family, the size of the first
-      member is used to determine the member size (flushing/closing a
-      family ensures that the first member is the correct size) but
-      the other family members don't have to be that large (the local
-      address space, however, is logically the same size for all
-      members).
+      that as a parameter of the file access property list, which
+      hasn't been implemented yet.  When creating a family, a default
+      family member size is used (defined at the top H5Ffamily.c,
+      currently 64MB) but that also should be settable in the file
+      access property list. When opening an existing family, the size
+      of the first member is used to determine the member size
+      (flushing/closing a family ensures that the first member is the
+      correct size) but the other family members don't have to be that
+      large (the local address space, however, is logically the same
+      size for all members).
 
     <p>I haven't implemented a split meta/raw family yet but am rather
       curious to see how it would perform. I was planning to use the
@@ -130,7 +130,7 @@
       then we'll chose the split family and use the default low level
       driver for each of the two family members.  Eventually we'll
       want to pass these kinds of things through the file access
-      template instead of relying on naming convention.
+      property list instead of relying on naming convention.
 
     <h3>External Raw Data</h3>
 
@@ -198,12 +198,13 @@ struct H5F_mount_t {
     </pre></code>
 
     <p>The <code>H5Fmount</code> function takes the ID of an open
-      file, the name of a to-be-mounted file, the name of the mount
-      point, and a file access template (like <code>H5Fopen</code>).
+      file or group, the name of a to-be-mounted file, the name of the mount
+      point, and a file access property list (like <code>H5Fopen</code>).
       It opens the new file and adds a record to the parent's mount
       table.  The <code>H5Funmount</code> function takes the parent
-      file ID and the name of the mount point and closes the file
-      that's mounted at that point.  The <code>H5Fclose</code>
+      file or group ID and the name of the mount point and disassociates
+      the mounted file from the mount point.  It does not close the 
+      mounted file.  The <code>H5Fclose</code>
       function closes/unmounts files recursively.
 
     <p>The <code>H5G_iname</code> function which translates a name to
@@ -272,7 +273,7 @@ struct H5F_mount_t {
     <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
 <!-- Created: Sat Nov  8 18:08:52 EST 1997 -->
 <!-- hhmts start -->
-Last modified: Wed Nov 12 15:01:14 EST 1997
+Last modified: Tue Sep  8 14:43:32 EDT 1998
 <!-- hhmts end -->
   </body>
 </html>

doc/html/Files.html

@@ -4,8 +4,68 @@
     <title>HDF5 Files</title>
   </head>
 
-  <body>
-    <h1>Files</h1>
+  <body bgcolor="#FFFFFF">
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      Files&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+    <h1>The File Interface (H5F)</h1>
 
     <h2>1. Introduction</h2>
 
@@ -61,7 +121,7 @@
 	set.  The <em>access_properties</em> is a file access property
 	list ID or <code>H5P_DEFAULT</code> for the default I/O access
         parameters.  Creating and changing the parameters for access
-        templates is documented further below.  Files which are opened
+        property lists is documented further below.  Files which are opened
         more than once return a unique identifier for each
         <code>H5Fopen()</code> call and can be accessed through all
         file IDs.  The return value is an ID for the open file and it
@@ -74,6 +134,15 @@
         opened by <code>H5Fcreate()</code> or <code>H5Fopen()</code>. After
         closing a file the <em>file_id</em> should not be used again.  This
         function returns zero for success or a negative value for failure.
+
+	<br><br>
+      <dt><code>herr_t H5Fflush (hid_t <em>object_id</em>, 
+          H5F_scope_t <em>scope</em>)</code>
+      <dd>This function will cause all buffers associated with a file
+	to be immediately flushed to the file.  The <em>object_id</em> 
+	can be any object which is associated with a file, including
+	the file itself.  <em>scope</em> specifies whether the flushing
+        action is to be global or local.
     </dl>
 
     <h2>4. File Property Lists</h2>
@@ -193,40 +262,40 @@
 	an address which is a multiple of some number.
     </dl> </ul>
 
-    <h2>5. Examples of using file templates</h2>
+    <h2>5. Examples of using file property lists</h2>
     
-    <h3>5.1. Example of using file creation templates</h3>
+    <h3>5.1. Example of using file creation property lists</h3>
     
     <p>This following example shows how to create a file with 64-bit object
       offsets and lengths:<br>
     <pre>
-        hid_t create_template;
+        hid_t create_plist;
         hid_t file_id;
 
-        create_template = H5Pcreate(H5P_FILE_CREATE);
-        H5Pset_sizes(create_template, 8, 8);
+        create_plist = H5Pcreate(H5P_FILE_CREATE);
+        H5Pset_sizes(create_plist, 8, 8);
 
         file_id = H5Fcreate("test.h5", H5F_ACC_TRUNC,
-                             create_template, H5P_DEFAULT);
+                             create_plist, H5P_DEFAULT);
         .
         .
         .
         H5Fclose(file_id);
     </pre>
         
-    <h3>5.2. Example of using file creation templates</h3>
+    <h3>5.2. Example of using file creation plist</h3>
 
     <p>This following example shows how to open an existing file for
       independent datasets access by MPI parallel I/O:<br>
     <pre>
-        hid_t access_template;
+        hid_t access_plist;
         hid_t file_id;
 
-        access_template = H5Pcreate(H5P_FILE_ACCESS);
-        H5Pset_mpi(access_template, MPI_COMM_WORLD, MPI_INFO_NULL);
+        access_plist = H5Pcreate(H5P_FILE_ACCESS);
+        H5Pset_mpi(access_plist, MPI_COMM_WORLD, MPI_INFO_NULL);
 
 	/* H5Fopen must be called collectively */
-        file_id = H5Fopen("test.h5", H5F_ACC_RDWR, access_template);
+        file_id = H5Fopen("test.h5", H5F_ACC_RDWR, access_plist);
         .
         .
         .
@@ -245,7 +314,7 @@
       referred to as an "HDF5 file" regardless of how the space is organized
       at the storage level.
 
-    <h3>6.1 Unbuffered Permanent Files</h3>
+    <h3>6.1. Unbuffered Permanent Files</h3>
 
     <p>The <em>sec2</em> driver uses functions from section 2 of the
       Posix manual to access files stored on a local file system.  These are
@@ -278,7 +347,7 @@
 	function to match those added to <code>H5Pset_sec2()</code>.
     </dl>
 
-    <h3>6.2 Buffered Permanent Files</h3>
+    <h3>6.2. Buffered Permanent Files</h3>
 
     <p>The <em>stdio</em> driver uses the functions declared in the
       <code>stdio.h</code> header file to access permanent files in a local
@@ -310,7 +379,7 @@
 	function to match those added to <code>H5Pset_stdio()</code>.
     </dl>
 
-    <h3>6.3 Buffered Temporary Files</h3>
+    <h3>6.3. Buffered Temporary Files</h3>
 
     <p>The <em>core</em> driver uses <code>malloc()</code> and
       <code>free()</code> to allocated space for a file in the heap. Reading
@@ -346,7 +415,7 @@
 	function to match those added to <code>H5Pset_core()</code>.
     </dl>
 
-    <h3>6.4 Parallel Files</h3>
+    <h3>6.4. Parallel Files</h3>
 
     <p>This driver uses MPI I/O to provide parallel access to a file.
 
@@ -376,7 +445,9 @@
 	added to <code>H5Pset_mpi()</code>.
     </dl>
 
-    <h3>6.4 File Families</h3>
+    <a name="Files_Families">
+    <h3>6.5. File Families</h3>
+    </a>
 
     <p>A single HDF5 address space may be split into multiple files which,
       together, form a file family.  Each member of the family must be the
@@ -458,7 +529,7 @@
 	match those added to <code>H5Pset_family()</code>.
     </dl>
 
-    <h3>6.5 Split Meta/Raw Files</h3>
+    <h3>6.6. Split Meta/Raw Files</h3>
 
     <p>On occasion, it might be useful to separate meta data from raw
       data. The <em>split</em> driver does this by creating two files: one for
@@ -518,12 +589,83 @@
     </dl>
 
 
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      Files&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<!--
     <hr>
     <address><a href="mailto:koziol@ncsa.uiuc.edu">Quincey Koziol</a></address>
     <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
+-->
 <!-- Created: Tue Jan 27 09:11:27 EST 1998 -->
 <!-- hhmts start -->
-Last modified: Tue Jun  9 15:03:44 EDT 1998
+<!--
+Last modified: Tue Sep  8 14:43:31 EDT 1998
+-->
 <!-- hhmts end -->
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
+
+Last modified:  30 October 1998
+
   </body>
 </html>

doc/html/Filters.html

@@ -0,0 +1,601 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<html>
+  <head>
+    <title>Filters</title>
+  </head>
+
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      Filters&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
+    <h1>Filters in HDF5</h1>
+
+    <b>Note: Transient pipelines described in this document have not
+      been implemented.</b>
+
+    <h2>1. Introduction</h2>
+
+    <p>HDF5 allows chunked data to pass through user-defined filters
+      on the way to or from disk.  The filters operate on chunks of an
+      <code>H5D_CHUNKED</code> dataset can be arranged in a pipeline
+      so output of one filter becomes the input of the next filter.
+
+    <p>Each filter has a two-byte identification number (type
+      <code>H5Z_filter_t</code>) allocated by NCSA and can also be
+      passed application-defined integer resources to control its
+      behavior.  Each filter also has an optional ASCII comment
+      string.
+
+    <p>
+      <center>
+	<table align=center width="80%">
+	  <caption alignment=top>
+	    <b>Values for <code>H5Z_filter_t</code></b>
+	  </caption>
+
+	  <tr>
+	    <th width="30%">Value</th>
+	    <th width="70%">Description</th>
+	  </tr>
+
+	  <tr valign=top>
+	    <td><code>0-255</code></td>
+	    <td>These values are reserved for filters predefined and
+	      registered by the HDF5 library and of use to the general 
+	      public.  They are described in a separate section
+	      below.</td>
+	  </tr>
+
+	  <tr valign=top>
+	    <td><code>256-511</code></td>
+	    <td>Filter numbers in this range are used for testing only 
+	      and can be used temporarily by any organization.  No
+	      attempt is made to resolve numbering conflicts since all 
+	      definitions are by nature temporary.</td>
+	  </tr>
+
+	  <tr valign=top>
+	    <td><code>512-65535</code></td>
+	    <td>Reserved for future assignment.  Please contact the
+	      <a href="mailto:hdf5dev@ncsa.uiuc.edu">HDF5 development
+	      team</a> to reserve a value or range of values for
+	      use by your filters.</td>
+	</table>
+      </center>
+
+    <h2>2. Defining and Querying the Filter Pipeline</h2>
+
+    <p>Two types of filters can be applied to raw data I/O: permanent
+      filters and transient filters.  The permanent filter pipeline is
+      defned when the dataset is created while the transient pipeline
+      is defined for each I/O operation.  During an
+      <code>H5Dwrite()</code> the transient filters are applied first
+      in the order defined and then the permanent filters are applied
+      in the order defined.  For an <code>H5Dread()</code> the
+      opposite order is used: permanent filters in reverse order, then
+      transient filters in reverse order.  An <code>H5Dread()</code>
+      must result in the same amount of data for a chunk as the
+      original <code>H5Dwrite()</code>.
+
+    <p>The permanent filter pipeline is defined by calling
+      <code>H5Pset_filter()</code> for a dataset creation property
+      list while the transient filter pipeline is defined by calling
+      that function for a dataset transfer property list.
+
+    <dl>
+      <dt><code>herr_t H5Pset_filter (hid_t <em>plist</em>,
+	  H5Z_filter_t <em>filter</em>, unsigned int <em>flags</em>,
+	  size_t <em>cd_nelmts</em>, const unsigned int
+	  <em>cd_values</em>[])</code>
+      <dd>This function adds the specified <em>filter</em> and
+	corresponding properties to the end of the transient or
+	permanent output filter pipeline (depending on whether
+	<em>plist</em> is a dataset creation or dataset transfer
+	property list).  The <em>flags</em> argument specifies certain
+	general properties of the filter and is documented below. The
+	<em>cd_values</em> is an array of <em>cd_nelmts</em> integers
+	which are auxiliary data for the filter.  The integer values
+	will be stored in the dataset object header as part of the
+	filter information.
+
+	<br><br>
+      <dt><code>int H5Pget_nfilters (hid_t <em>plist</em>)</code>
+      <dd>This function returns the number of filters defined in the
+	permanent or transient filter pipeline depending on whether
+	<em>plist</em> is a dataset creation or dataset transfer
+	property list.  In each pipeline the filters are numbered from
+	0 through <em>N</em>-1 where <em>N</em> is the value returned
+	by this function. During output to the file the filters of a
+	pipeline are applied in increasing order (the inverse is true
+	for input).  Zero is returned if there are no filters in the
+	pipeline and a negative value is returned for errors.
+
+	<br><br>
+      <dt><code>H5Z_filter_t H5Pget_filter (hid_t <em>plist</em>,
+	  int <em>filter_number</em>, unsigned int *<em>flags</em>,
+	  size_t *<em>cd_nelmts</em>, unsigned int
+	  *<em>cd_values</em>, size_t namelen, char name[])</code>
+      <dd>This is the query counterpart of
+	<code>H5Pset_filter()</code> and returns information about a
+	particular filter number in a permanent or transient pipeline
+	depending on whether <em>plist</em> is a dataset creation or
+	dataset transfer property list.  On input, <em>cd_nelmts</em>
+	indicates the number of entries in the <em>cd_values</em>
+	array allocated by the caller while on exit it contains the
+	number of values defined by the filter.  The
+	<em>filter_number</em> should be a value between zero and
+	<em>N</em>-1 as described for <code>H5Pget_nfilters()</code>
+	and the function will return failure (a negative value) if the
+	filter number is out of range.  If <em>name</em> is a pointer
+	to an array of at least <em>namelen</em> bytes then the filter 
+	name will be copied into that array.  The name will be null
+	terminated if the <em>namelen</em> is large enough.  The
+	filter name returned will be the name appearing in the file or 
+	else the name registered for the filter or else an empty string.
+    </dl>
+
+    <p>The flags argument to the functions above is a bit vector of
+      the following fields:
+
+    <p>
+      <center>
+	<table align=center width="80%">
+	  <caption align=top>
+	    <b>Values for the <em>flags</em> argument</b>
+	  </caption>
+
+	  <tr>
+	    <th width="30%">Value</th>
+	    <th width="70%">Description</th>
+	  </tr>
+
+	  <tr valign=top>
+	    <td><code>H5Z_FLAG_OPTIONAL</code></td>
+	    <td>If this bit is set then the filter is optional.  If
+	      the filter fails (see below) during an
+	      <code>H5Dwrite()</code> operation then the filter is
+	      just excluded from the pipeline for the chunk for which
+	      it failed; the filter will not participate in the
+	      pipeline during an <code>H5Dread()</code> of the chunk.
+	      This is commonly used for compression filters: if the
+	      compression result would be larger than the input then
+	      the compression filter returns failure and the
+	      uncompressed data is stored in the file.  If this bit is
+	      clear and a filter fails then the
+	      <code>H5Dwrite()</code> or <code>H5Dread()</code> also
+	      fails.</td>
+	  </tr>
+	</table>
+      </center>
+
+    <h2>3. Defining Filters</h2>
+
+    <p>Each filter is bidirectional, handling both input and output to 
+      the file, and a flag is passed to the filter to indicate the
+      direction.  In either case the filter reads a chunk of data from 
+      a buffer, usually performs some sort of transformation on the
+      data, places the result in the same or new buffer, and returns
+      the buffer pointer and size to the caller. If something goes
+      wrong the filter should return zero to indicate a failure.
+
+    <p>During output, a filter that fails or isn't defined and is
+      marked as optional is silently excluded from the pipeline and
+      will not be used when reading that chunk of data.  A required
+      filter that fails or isn't defined causes the entire output
+      operation to fail. During input, any filter that has not been
+      excluded from the pipeline during output and fails or is not
+      defined will cause the entire input operation to fail.
+
+    <p>Filters are defined in two phases.  The first phase is to
+      define a function to act as the filter and link the function
+      into the application.  The second phase is to register the
+      function, associating the function with an
+      <code>H5Z_filter_t</code> identification number and a comment.
+
+    <dl>
+      <dt><code>typedef size_t (*H5Z_func_t)(unsigned int
+	  <em>flags</em>, size_t <em>cd_nelmts</em>, const unsigned int
+	  <em>cd_values</em>[], size_t <em>nbytes</em>, size_t
+	  *<em>buf_size</em>, void **<em>buf</em>)</code>
+      <dd>The <em>flags</em>, <em>cd_nelmts</em>, and
+	<em>cd_values</em> are the same as for the
+	<code>H5Pset_filter()</code> function with the additional flag
+	<code>H5Z_FLAG_REVERSE</code> which is set when the filter is
+	called as part of the input pipeline. The input buffer is
+	pointed to by <em>*buf</em> and has a total size of
+	<em>*buf_size</em> bytes but only <em>nbytes</em> are valid
+	data. The filter should perform the transformation in place if
+	possible and return the number of valid bytes or zero for
+	failure.  If the transformation cannot be done in place then
+	the filter should allocate a new buffer with
+	<code>malloc()</code> and assign it to <em>*buf</em>,
+	assigning the allocated size of that buffer to
+	<em>*buf_size</em>. The old buffer should be freed
+	by calling <code>free()</code>.
+
+	<br><br>
+      <dt><code>herr_t H5Zregister (H5Z_filter_t <em>filter_id</em>,
+	  const char *<em>comment</em>, H5Z_func_t
+	  <em>filter</em>)</code>
+      <dd>The <em>filter</em> function is associated with a filter
+	number and a short ASCII comment which will be stored in the
+	hdf5 file if the filter is used as part of a permanent
+	pipeline during dataset creation.
+    </dl>
+    
+      
+    <h2>4. Predefined Filters</h2>
+
+    <p>If <code>zlib</code> version 1.1.2 or later was found
+      during configuration then the library will define a filter whose
+      <code>H5Z_filter_t</code> number is
+      <code>H5Z_FILTER_DEFLATE</code>. Since this compression method
+      has the potential for generating compressed data which is larger
+      than the original, the <code>H5Z_FLAG_OPTIONAL</code> flag
+      should be turned on so such cases can be handled gracefully by
+      storing the original data instead of the compressed data.  The
+      <em>cd_nvalues</em> should be one with <em>cd_value[0]</em>
+      being a compression agression level between zero and nine,
+      inclusive (zero is the fastest compression while nine results in
+      the best compression ratio).
+
+    <p>A convenience function for adding the
+      <code>H5Z_FILTER_DEFLATE</code> filter to a pipeline is:
+
+    <dl>
+      <dt><code>herr_t H5Pset_deflate (hid_t <em>plist</em>, unsigned
+	  <em>aggression</em>)</code>
+      <dd>The deflate compression method is added to the end of the
+	permanent or transient filter pipeline depending on whether
+	<em>plist</em> is a dataset creation or dataset transfer
+	property list. The <em>aggression</em> is a number between
+	zero and nine (inclusive) to indicate the tradeoff between
+	speed and compression ratio (zero is fastest, nine is best
+	ratio).
+    </dl>
+
+    <p>Even if the <code>zlib</code> isn't detected during
+      configuration the application can define
+      <code>H5Z_FILTER_DEFLATE</code> as a permanent filter.  If the
+      filter is marked as optional (as with
+      <code>H5Pset_deflate()</code>) then it will always fail and be
+      automatically removed from the pipeline.  Applications that read
+      data will fail only if the data is actually compressed; they
+      won't fail if <code>H5Z_FILTER_DEFLATE</code> was part of the
+      permanent output pipeline but was automatically excluded because
+      it didn't exist when the data was written.
+
+    <h2>5. Example</h2>
+
+    <p>This example shows how to define and register a simple filter
+      that adds a checksum capability to the data stream.
+
+    <p>The function that acts as the filter always returns zero
+      (failure) if the <code>md5()</code> function was not detected at 
+      configuration time (left as an excercise for the reader).
+      Otherwise the function is broken down to an input and output
+      half.  The output half calculates a checksum, increases the size 
+      of the output buffer if necessary, and appends the checksum to
+      the end of the buffer.  The input half calculates the checksum
+      on the first part of the buffer and compares it to the checksum
+      already stored at the end of the buffer.  If the two differ then 
+      zero (failure) is returned, otherwise the buffer size is reduced 
+      to exclude the checksum.
+
+    <p>
+      <center>
+	<table border align=center width="100%">
+	  <tr>
+	    <td>
+	      <p><code><pre>
+
+size_t
+md5_filter(unsigned int flags, size_t cd_nelmts,
+           const unsigned int cd_values[], size_t nbytes,
+           size_t *buf_size, void **buf)
+{
+#ifdef HAVE_MD5
+    unsigned char       cksum[16];
+
+    if (flags & H5Z_REVERSE) {
+        /* Input */
+        assert(nbytes>=16);
+        md5(nbytes-16, *buf, cksum);
+
+        /* Compare */
+        if (memcmp(cksum, (char*)(*buf)+nbytes-16, 16)) {
+            return 0; /*fail*/
+        }
+
+        /* Strip off checksum */
+        return nbytes-16;
+            
+    } else {
+        /* Output */
+        md5(nbytes, *buf, cksum);
+
+        /* Increase buffer size if necessary */
+        if (nbytes+16>*buf_size) {
+            *buf_size = nbytes + 16;
+            *buf = realloc(*buf, *buf_size);
+        }
+
+        /* Append checksum */
+        memcpy((char*)(*buf)+nbytes, cksum, 16);
+        return nbytes+16;
+    }
+#else
+    return 0; /*fail*/
+#endif
+}
+	      </pre></code>
+	    </td>
+	  </tr>
+	</table>
+      </center>
+
+    <p>Once the filter function is defined it must be registered so
+      the HDF5 library knows about it.  Since we're testing this
+      filter we choose one of the <code>H5Z_filter_t</code> numbers
+      from the reserved range.  We'll randomly choose 305.
+
+    <p>
+      <center>
+	<table border align=center width="100%">
+	  <tr>
+	    <td>
+	      <p><code><pre>
+
+#define FILTER_MD5 305
+herr_t status = H5Zregister(FILTER_MD5, "md5 checksum", md5_filter);
+	      </pre></code>
+	    </td>
+	  </tr>
+	</table>
+      </center>
+
+    <p>Now we can use the filter in a pipeline.  We could have added
+      the filter to the pipeline before defining or registering the
+      filter as long as the filter was defined and registered by time
+      we tried to use it (if the filter is marked as optional then we
+      could have used it without defining it and the library would
+      have automatically removed it from the pipeline for each chunk
+      written before the filter was defined and registered).
+
+    <p>
+      <center>
+	<table border align=center width="100%">
+	  <tr>
+	    <td>
+	      <p><code><pre>
+
+hid_t dcpl = H5Pcreate(H5P_DATASET_CREATE);
+hsize_t chunk_size[3] = {10,10,10};
+H5Pset_chunk(dcpl, 3, chunk_size);
+H5Pset_filter(dcpl, FILTER_MD5, 0, 0, NULL);
+hid_t dset = H5Dcreate(file, "dset", H5T_NATIVE_DOUBLE, space, dcpl);
+	      </pre></code>
+	    </td>
+	  </tr>
+	</table>
+      </center>
+
+    <h2>6. Filter Diagnostics</h2>
+
+    <p>If the library is compiled with debugging turned on for the H5Z
+      layer (usually as a result of <code>configure
+      --enable-debug=z</code>) then filter statistics are printed when
+      the application exits normally or the library is closed.  The
+      statistics are written to the standard error stream and include
+      two lines for each filter that was used: one for input and one
+      for output.  The following fields are displayed:
+
+    <p>
+      <center>
+	<table align=center width="80%">
+	  <tr>
+	    <th width="30%">Field Name</th>
+	    <th width="70%">Description</th>
+	  </tr>
+
+	  <tr valign=top>
+	    <td>Method</td>
+	    <td>This is the name of the method as defined with
+	      <code>H5Zregister()</code> with the charaters
+	      &quot;&lt; or &quot;&gt;&quot; prepended to indicate
+	      input or output.</td>
+	  </tr>
+
+	  <tr valign=top>
+	    <td>Total</td>
+	    <td>The total number of bytes processed by the filter
+	      including errors.  This is the maximum of the
+	      <em>nbytes</em> argument or the return value.
+	  </tr>
+
+	  <tr valign=top>
+	    <td>Errors</td>
+	    <td>This field shows the number of bytes of the Total
+	      column which can be attributed to errors.</td>
+	  </tr>
+
+	  <tr valign=top>
+	    <td>User, System, Elapsed</td>
+	    <td>These are the amount of user time, system time, and
+	      elapsed time in seconds spent in the filter function.
+	      Elapsed time is sensitive to system load. These times
+	      may be zero on operating systems that don't support the
+	      required operations.</td>
+	  </tr>
+
+	  <tr valign=top>
+	    <td>Bandwidth</td>
+	    <td>This is the filter bandwidth which is the total
+	      number of bytes processed divided by elapsed time.
+	      Since elapsed time is subject to system load the
+	      bandwidth numbers cannot always be trusted.
+	      Furthermore, the bandwidth includes bytes attributed to
+	      errors which may significanly taint the value if the
+	      function is able to detect errors without much
+	      expense.</td>
+	  </tr>
+	</table>
+      </center>
+
+    <p>
+      <center>
+	<table border align=center width="100%">
+	  <caption align=bottom>
+	    <b>Example: Filter Statistics</b>
+	  </caption>
+	  <tr>
+	    <td>
+	      <p><code><pre>
+H5Z: filter statistics accumulated over life of library:
+   Method     Total  Errors  User  System  Elapsed Bandwidth
+   ------     -----  ------  ----  ------  ------- ---------
+   >deflate  160000   40000  0.62    0.74     1.33 117.5 kBs
+   &lt;deflate  120000       0  0.11    0.00     0.12 1.000 MBs
+	      </pre></code>
+	    </td>
+	  </tr>
+	</table>
+      </center>
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      Filters&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<!--
+    <hr>
+    <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
+-->
+<!-- Created: Fri Apr 17 13:39:35 EDT 1998 -->
+<!-- hhmts start -->
+Last modified: Mon Jan 18 13:32:14 EST 1999
+<!-- hhmts end -->
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
+
+Last modified:  30 October 1998
+
+  </body>
+</html>

doc/html/Glossary.html

@@ -1,5 +1,5 @@
 <html><head><title>
-HDF5 Draft Glossary
+HDF5 Glossary
 </title></head>
 
 <body>
@@ -25,23 +25,29 @@ Glossary
 <h1>HDF5 Glossary</h1>
 </center>
 
-<i>(<b>Under construction!</b>  
-    This is the bare beginning of a Glossary to accompany the HDF5 documentation;
-    it is by no means complete.)</i>
+<i>(<b>Under construction!</b> 
+    This is the bare beginning of a Glossary to accompany the HDF5 
+    documentation; it is by no means complete.)</i>
 
-<ol type=A>
-    <li><a href="#Glossary-Basic">Basic Types</a>
-    <li><a href="#Glossary-Complex">Complex Types</a>
-    <li><a href="#Glossary-DiskIO">Disk I/O Types</a>
-</ol>
+<ul>
+    <li><a href="#Glossary-Basic">basic data types</a>
+    <li><a href="#Glossary-Complex">complex data types</a>
+    <li>data types
+<ul>
+        <li><a href="#Glossary-Basic">basic data types</a>
+        <li><a href="#Glossary-Complex">complex data types</a>
+        <li><a href="#Glossary-DiskIO">disk I/O data types</a>
+</ul>
+    <li><a href="#Glossary-DiskIO">disk I/O data types</a>
+</ul>
 
-<P>Since many of the typedefs in the HDF5 API are not well-defined yet,
-the types below may change radically en route to a final API...
 
 <hr>
 
-<a name="Glossary-Basic">Basic Types:</a>
+<a name="Glossary-Basic">basic data types:</a>
 <ul>
+    <li><em>(Some data types may change substantially en route to 
+        Release 1.0.)</em>
     <li>char     - 8-bit character (only for ASCII information)
     <li>int8     - 8-bit signed integer
     <li>uint8    - 8-bit unsigned integer
@@ -57,8 +63,10 @@ the types below may change radically en route to a final API...
     <li>float64  - 64-bit IEEE float
 </ul>
 
-<a name="Glossary-Complex">Complex Types:</a>
+<a name="Glossary-Complex">Complex data types:</a>
 <ul>
+    <li><em>(Some data types may change substantially en route to 
+        Release 1.0.)</em>
     <li>hid_t   - 32-bit unsigned integer used as ID for memory objects
     <li>hoid_t  - 32-bit unsigned integer (currently) used as ID for disk-based
                 objects
@@ -66,8 +74,10 @@ the types below may change radically en route to a final API...
     <li>herr_t  - 32-bit integer to indicate succeed/fail codes from functions
 </ul>
 
-<a name="Glossary-DiskIO">Disk I/O Types:</a>
+<a name="Glossary-DiskIO">disk I/O data types:</a>
 <ul>
+    <li><em>(Some data types may change substantially en route to 
+        Release 1.0.)</em>
     <li>hoff_t  - (64-bit?) offset on disk in bytes
     <li>hlen_t  - (64-bit?) length on disk in bytes
 </ul>

doc/html/Groups.html

@@ -4,8 +4,70 @@
     <title>Groups</title>
   </head>
 
-  <body>
-    <h1>Groups</h1>
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      Groups&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
+    <h1>The Group Interface (H5G)</h1>
 
     <h2>1. Introduction</h2>
 
@@ -51,7 +113,7 @@
       name which begins with a slash is an <em>absolute</em> name
       which is looked up beginning at the root group of the file while
       all other <em>relative</em> names are looked up beginning at the
-      current working group (described below) or a specified group.
+      specified group.
       Multiple consecutive slashes in a full name are treated as
       single slashes and trailing slashes are not significant.  A
       special case is the name "/" (or equivalent) which refers to the
@@ -75,7 +137,7 @@
 	    <td>File ID</td>
 	    <td><code>/foo/bar</code></td>
 	    <td>The object <code>bar</code> in group <code>foo</code>
-	      in the root group of the specified file.</td>
+	      in the root group.</td>
 	  </tr>
 
 	  <tr>
@@ -104,9 +166,7 @@
 	    <td>File ID</td>
 	    <td><code>foo/bar</code></td>
 	    <td>The object <code>bar</code> in group <code>foo</code>
-	      in the current working group of the specified file.  The
-	      initial current working group is the root group of the
-	      file as described below.</td>
+	      in the specified group.</td>
 	  </tr>
 
 	  <tr>
@@ -119,7 +179,7 @@
 	  <tr>
 	    <td>File ID</td>
 	    <td><code>.</code></td>
-	    <td>The current working group of the specified file.</td>
+	    <td>The root group of the file.</td>
 	  </tr>
 
 	  <tr>
@@ -181,51 +241,7 @@
 	returns zero for success or a negative value for failure.
     </dl>
 
-    <h2>4. Current Working Group</h2>
-
-    <p>Each file handle (<code>hid_t <em>file_id</em></code>) has a
-      current working group, initially the root group of the file.
-      Names which do not begin with a slash are relative to the
-      specified group or to the current working group as described
-      above.  For instance, the name "/Foo/Bar/Baz" is resolved by
-      first looking up "Foo" in the root group.  But the name
-      "Foo/Bar/Baz" is resolved by first looking up "Foo" in the
-      current working group.
-
-    <dl>
-      <dt><code>herr_t H5Gset (hid_t <em>location_id</em>, const char
-	  *<em>name</em>)</code>
-      <dd>The group with the specified name is made the current
-	working group for the file which contains it. The
-	<em>location_id</em> can be a file handle or a group handle
-	and the name is resolved as described above.  Each file handle
-	has it's own current working group and if the
-	<em>location_id</em> is a group handle then the file handle is
-	derived from the group handle. This function returns zero for
-	success or negative for failure.
-
-	<br><br>
-      <dt><code>herr_t H5Gpush (hid_t <em>location_id</em>, const char
-	  *<em>name</em>)</code>
-      <dd>Each file handle has a stack of groups and the top group on
-	that stack is the current working group.  The stack initially
-	contains only the root group.  This function pushes a new
-	group onto the stack and returns zero for success or negative
-	for failure.
-
-	<br><br>
-      <dt><code>herr_t H5Gpop (hid_t <em>location_id</em>)</code>
-      <dd>This function pops one group off the group stack for the
-	specified file (if the <em>location_id</em> is a group then
-	the file is derived from that group), changing the current
-	working group to the new top-of-stack group.  The function
-	returns zero for success or negative for failure (failure
-	includes attempting to pop from an empty stack).  If the last
-	item is popped from the stack then the current working group
-	is set to the root group.
-    </dl>
-
-    <h2>5. Objects with Multiple Names</h2>
+    <h2>4. Objects with Multiple Names</h2>
 
     <p>An object (including a group) can have more than one
       name. Creating the object gives it the first name, and then
@@ -263,8 +279,7 @@
 	<code>H5T_LINK_SOFT</code> a soft link is created which is an
 	alias for the <em>current_name</em>.  When creating a soft
 	link the object need not exist.  This function returns zero
-	for success or negative for failure. <b>This function is not
-	part of the prototype API.</b>
+	for success or negative for failure. 
 
 	<br><br>
       <dt><code>herr_t H5Gunlink (hid_t <em>file_id</em>, const char
@@ -274,15 +289,112 @@
 	to the object and when the hard link count reaches zero the
 	object can be removed from the file (but objects which are
 	open are not removed until all handles to the object are
-	closed).  <b>This function is not part of the prototype
-	API.</b>
+	closed).  
     </dl>
 
+    <h2>5. Comments</h2>
+
+    <p>Objects can have a comment associated with them.  The comment
+      is set and queried with these two functions:
+
+    <dl>
+      <dt><code>herr_t H5Gset_comment (hid_t <em>loc_id</em>, const
+	  char *<em>name</em>, const char *<em>comment</em>)</code>
+      <dd>The previous comment (if any) for the specified object is
+	replace with a new comment.  If the <em>comment</em> argument
+	is the empty string or a null pointer then the comment message 
+	is removed from the object.  Comments should be relatively
+	short, null-terminated, ASCII strings.
+
+	<br><br>
+      <dt><code>herr_t H5Gget_comment (hid_t <em>loc_id</em>, const
+	  char *<em>name</em>, size_t <em>bufsize</em>, char
+	  *<em>comment</em>)</code>
+      <dd>The comment string for an object is returned through the
+	<em>comment</em> buffer.  At most <em>bufsize</em> characters
+	including a null terminator are copied, and the result is
+	not null terminated if the comment is longer than the supplied 
+	buffer.  If an object doesn't have a comment then the empty
+	string is returned.
+    </dl>
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+   And in this document, the 
+   <a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      Groups&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<!--
     <hr>
     <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
+-->
 <!-- Created: Tue Jan 27 09:11:27 EST 1998 -->
 <!-- hhmts start -->
-Last modified: Tue Mar 24 15:52:14 EST 1998
+<!--
+Last modified: Wed Jul 22 14:24:34 EDT 1998
+-->
 <!-- hhmts end -->
+
+<hr>
+<address>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+</address>
+
+Last modified:  30 October 1998
+
   </body>
 </html>

doc/html/H5.sample_code.html

@@ -29,7 +29,7 @@ overwrite the previous file's information.
 <code> <pre>
     hid_t file_id;
 
-    file_id=<A HREF="H5.apiv2.html#File-Create">H5Fcreate</a>("example1.h5",H5F_ACC_EXCL,H5P_DEFAULT_TEMPLATE,H5P_DEFAULT_TEMPLATE);
+    file_id=<A HREF="H5.apiv2.html#File-Create">H5Fcreate</a>("example1.h5",H5F_ACC_EXCL,H5P_DEFAULT,H5P_DEFAULT);
 
     <A HREF="H5.apiv2.html#File-Close">H5Fclose</a>(file_id);
 

doc/html/H5.user.PrintGen.html

@@ -0,0 +1,135 @@
+<html>
+  <head>
+    <title>
+      HDF5 User's Guide -- Single Print
+    </title>
+  </head>
+
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+
+
+    <center><h1>A User's Guide for HDF5</h1></center>
+
+This page provides a means of printing the <cite>HDF5 User's Guide</cite>
+with a single print command as follows:
+<ol><li>Open this page in Internet Explorer, version 4.0 or or later.
+        (Sorry, but as of this writing, Netscape does not offer the required 
+        print feature.)
+    <li>On the <strong>File</strong> menu, select <strong>Print</strong>.
+    <li>In the <strong>Print</strong> dialogue box, select 
+        <strong>Print all linked documents</strong>.
+    <li>Select <strong>OK</strong>.  Depending on the print settings of your
+        browser, this will produce a 100- to 200-page set of documents, 
+        one chapter or section at a time.
+    <li>Once the print job is complete, discard the first page printed (this page).  
+        The rest of the printout should form a complete copy of the 
+        <cite>HDF5 User's Guide</cite>.
+</ol>
+
+
+<br><br>
+<center>
+<table border=0 width=85%>
+
+      <tr><td valign=top><a href="H5.user.PrintTpg.html" target="PrintWin">Title Page</a>
+	</td><td>&nbsp;&nbsp;&nbsp;&nbsp;</td>
+        <td valign=top>Title page.
+        </td></tr>
+      <tr><td valign=top><a href="Copyright.html" target="PrintWin">Copyright</a>
+	</td><td>&nbsp;&nbsp;&nbsp;&nbsp;</td>
+        <td valign=top>The HDF5 copyright notice, contact information, 
+           and other <i>back-of-the-title-page</i> material.
+        </td></tr>
+      <tr><td valign=top><a href="H5.user.html" target="PrintWin">TOC</a>
+	</td><td>&nbsp;&nbsp;&nbsp;&nbsp;</td>
+        <td valign=top>Table of contents.
+        </td></tr>
+      <tr><td valign=top><a href="Files.html" target="PrintWin">HDF5 Files</a>
+	</td><td>&nbsp;&nbsp;&nbsp;&nbsp;</td>
+        <td valign=top>A guide to the <strong>H5F</strong> interface.
+        </td></tr>
+      <tr><td valign=top><a href="Datasets.html" target="PrintWin">Datasets</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5D</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Datatypes.html" target="PrintWin">Data Types</a> and
+        <br>&nbsp;&nbsp;&nbsp;&nbsp;
+          <a href="DatatypesEnum.html" target="PrintWin">Enumeration Data Types</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5T</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Dataspaces.html" target="PrintWin">Dataspaces</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5S</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Groups.html" target="PrintWin">Groups</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5G</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="References.html" target="PrintWin">References and
+          Identifiers</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5R</strong> 
+          and <strong>H5I</strong> interfaces.
+        </td></tr>
+      <tr><td valign=top><a href="Attributes.html" target="PrintWin">Attributes</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5A</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Properties.html" target="PrintWin">Property Lists</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5P</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Errors.html" target="PrintWin">Error Handling</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5E</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Filters.html" target="PrintWin">Filters</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5Z</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Caching.html" target="PrintWin">Caching</a>
+	</td><td></td><td valign=top>A guide for meta and raw data caching.
+        </td></tr>
+      <tr><td valign=top><a href="Chunking.html" target="PrintWin">Dataset Chunking</a>
+	</td><td></td><td valign=top>A guide to the issues and pitfalls 
+          of dataset chunking.
+        </td></tr>
+      <tr><td valign=top><a href="Debugging.html" target="PrintWin">Debugging</a>
+	</td><td></td><td valign=top>A guide to debugging HDF5 API calls.
+        </td></tr>
+      <tr><td valign=top><a href="Environment.html" target="PrintWin">Environment Variables 
+          and Configuration Parameters</a>
+	</td><td></td><td valign=top>A list of HDF5 environment variables
+          and <br>&nbsp;&nbsp;&nbsp;configuration parameters.
+        </td></tr>
+      <tr><td valign=top><a href="ddl.html" target="PrintWin">DDL for HDF5</a>
+	</td><td></td><td valign=top>A DDL in BNF for HDF5.
+        </td></tr>
+      <tr><td valign=top><hr noshade size=1><a href="Ragged.html" target="PrintWin">Ragged Arrays</a>
+	</td><td></td><td valign=top><hr noshade size=1>A guide to the 
+          <strong>H5RA</strong> interface.
+	&nbsp;&nbsp;<em><font color=red>(Experimental)</font></em> 
+        </td></tr>
+</table>
+</center>
+
+
+<br><br>
+
+<hr>
+
+
+<address>
+<table width=100% border=0>
+<tr><td align=left valign=top>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+<br>
+Last modified:  1 June 1999
+
+</table>             
+
+  </body>
+</html>

doc/html/H5.user.PrintTpg.html

@@ -0,0 +1,75 @@
+<html>
+  <head>
+    <title>
+      HDF5 User's Guide
+    </title>
+  </head>
+
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<br>
+<br><br>
+
+<center>
+
+<font size=7>
+A User's Guide for HDF5
+</font>
+
+<br><br><br>
+<hr>
+<hr>
+<br><br><br>
+
+<font size=6>
+Release 1.0
+<br>
+January 1999
+</font>
+
+<br><br><br><br>
+
+<font size=3>
+Hierarchical Data Format (HDF) Group
+<br>
+National Center for Supercomputing Applications (NCSA)
+<br>
+University of Illinois at Urbana-Champaign (UIUC)
+</font>
+
+</center>
+
+<br><br><br>
+<hr>
+<hr>
+<br><br><br>
+<br><br><br>
+
+<blockquote>
+<strong>A Note to the Reader:</strong>
+The primary HDF5 user documents are the online HTML documents
+distributed with the HDF5 code and binaries and found on the HDF5 website.
+Several users have expressed a desire for documents in an alternative format:
+<ul>
+<li>Some have requested a version that can be reasonably printed in a 
+    single print operation.
+<li>Others have requested an easily searchable version.
+</ul>
+This PDF file has been created expressly to meet these needs.
+<p>
+The reader will note that each section of this document looks very much
+as the corresponding HTML page would look in a web browser.  That is not
+accidental as the HTML version remains the HDF5 development team's primary 
+documentation vehicle.
+</blockquote>
+
+
+<br><br>
+<hr>
+
+
+
+</body>
+</html>

doc/html/H5.user.html

@@ -1,39 +1,156 @@
 <html>
   <head>
     <title>
-      HDF5 Uer's Guide
+      HDF5 User's Guide
     </title>
   </head>
 
-  <body>
-    <center><h1>A User Guide for HDF5</h1></center>
+  <body bgcolor="#FFFFFF">
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
+
+<!--
+
+   And in this document, the 
+   HDF5 User's Guide:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
+      <a href="Groups.html">Groups</a>&nbsp;&nbsp;
+      <a href="References.html">References</a>&nbsp;&nbsp;
+      <br>
+      <a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
+      <a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
+      <a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
+      <a href="Filters.html">Filters</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+-->
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+<hr>
+
+
+    <center><h1>A User's Guide for HDF5</h1></center>
 
     <p>The following documents form a loosely organized user's guide
       to the HDF5 library.
 
-    <ul>
-      <li><a href="Files.html">HDF5 Files</a> -
-	A guide to the H5F interface.
-      <li><a href="Datasets.html">Datasets</a> -
-	A guide to the H5D interface.
-      <li><a href="Datatypes.html">Data types</a> -
-	A guide to the H5T interface.
-      <li><a href="Dataspaces.html">Data spaces</a> -
-	A guide to the H5S interface.
-      <li><a href="Groups.html">Groups</a> -
-	A guide to the H5G interface.
-      <li><a href="Attributes.html">Attributes</a> -
-	A guide to the H5A interface.
-      <li><a href="Properties.html">Property lists</a> -
-	A guide to the H5P interface.
-      <li><a href="Errors.html">Error handling</a> -
-	A guide to the H5E interface.
-      <li><a href="Caching.html">Caching</a> -
-	A guide for meta and raw data caching.
-      <li><a href="tracing.html">API Tracing</a> -
-	A guide to debugging HDF5 API calls.
-    </ul>
+<center>
+<table border=0>
 
+<tr><td valign=top><a href="Files.html">HDF5 Files</a>
+	</td><td>&nbsp;&nbsp;&nbsp;&nbsp;</td>
+        <td valign=top>A guide to the <strong>H5F</strong> interface.
+        </td></tr>
+      <tr><td valign=top><a href="Datasets.html">Datasets</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5D</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Datatypes.html">Data Types</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5T</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Dataspaces.html">Dataspaces</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5S</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Groups.html">Groups</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5G</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="References.html">References and
+          Identifiers</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5R</strong> 
+          and <strong>H5I</strong> interfaces.
+        </td></tr>
+      <tr><td valign=top><a href="Attributes.html">Attributes</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5A</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Properties.html">Property Lists</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5P</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Errors.html">Error Handling</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5E</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Filters.html">Filters</a>
+	</td><td></td><td valign=top>A guide to the <strong>H5Z</strong> 
+          interface.
+        </td></tr>
+      <tr><td valign=top><a href="Caching.html">Caching</a>
+	</td><td></td><td valign=top>A guide for meta and raw data caching.
+        </td></tr>
+      <tr><td valign=top><a href="Chunking.html">Dataset Chunking</a>
+	</td><td></td><td valign=top>A guide to the issues and pitfalls 
+          of dataset chunking.
+        </td></tr>
+      <tr><td valign=top><a href="Debugging.html">Debugging</a>
+	</td><td></td><td valign=top>A guide to debugging HDF5 API calls.
+        </td></tr>
+      <tr><td valign=top><a href="Environment.html">Environment Variables 
+          and</a>
+          <br>&nbsp;&nbsp;&nbsp;<a href="Environment.html">Configuration 
+          Parameters</a>
+	</td><td></td><td valign=top>A list of HDF5 environment variables
+          and <br>&nbsp;&nbsp;&nbsp;configuration parameters.
+        </td></tr>
+      <tr><td valign=top><a href="ddl.html">DDL for HDF5</a>
+	</td><td></td><td valign=top>A DDL in BNF for HDF5.
+        </td></tr>
+      <tr><td valign=top><hr noshade size=1><a href="Ragged.html">Ragged Arrays</a>
+	</td><td></td><td valign=top><hr noshade size=1>A guide to the 
+          <strong>H5RA</strong> interface.
+	&nbsp;&nbsp;<em><font color=red>(Experimental)</font></em> 
+        </td></tr>
+</table>
+</center>
+<br>
+
+<!--
     <p>The following documents form a loosely organized developer's guide to
       aspects of the HDF5 library. (Some of the following documents
       may be rather out of date as they were working papers for design
@@ -44,30 +161,109 @@
 	A description of HDF5 version numbers.
       <li><a href="IOPipe.html">I/O Pipeline</a> -
 	A description of the raw data I/O pipeline.
-      <li><a href="Compression.html">Compression</a> -
-	A guide to the use of compression for datasets.
-      <li><a href="ExternalFiles.html">Working with external files</a> -
+      <li><a href="ExternalFiles.html">Working with External Files</a> -
 	A guide to the use of multiple files with HDF5.
       <li><a href="Big.html">Large Datasets</a> -
 	A guide to accessing large datasets on small computers.
-      <li><a href="MemoryManagement.html">Memory management</a> -
+      <li><a href="MemoryManagement.html">Memory Management</a> -
 	A white	paper about memory management issues in HDF5.
-      <li><a href="Coding.html">Coding style</a> -
+      <li><a href="Coding.html">Coding Style</a> -
 	A white paper about coding style in the HDF5 library code.
-      <li><a href="compat.html">HDF4/HDF5 compatibility</a> -
+      <li><a href="compat.html">HDF4/HDF5 Compatibility</a> -
 	A white paper about compatibility issues between HDF4 and HDF5.
-      <li><a href="study.html">Chunking performance study</a> -
+      <li><a href="study.html">Chunking Performance Study</a> -
 	A white paper describing the HDF5 chunking performance.
     </ul>
+-->
 
 
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+   <a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
+   <a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+   <a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
+   <!--
+   <a href="Glossary.html">Glossary</a><br>
+   -->
+</td>
+<td valign=top align=right>
 
+<!--
+
+   And in this document, the 
+   HDF5 User's Guide:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Files.html">Files</a>&nbsp;&nbsp;
+      <br>
+      <a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">Data Types</a>&nbsp;&nbsp;
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+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <br>
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
+-->
+
+<!--
+<hr>
+And in this document, the 
+<a href="H5.user.html">HDF5 User's Guide</a>:&nbsp;&nbsp;&nbsp;&nbsp;
+      <a href="Attributes.html">H5A</a>&nbsp;&nbsp;
+      <a href="Datasets.html">H5D</a>&nbsp;&nbsp;
+      <a href="Errors.html">H5E</a>&nbsp;&nbsp;
+      <a href="Files.html">H5F</a>&nbsp;&nbsp;
+      <a href="Groups.html">H5G</a>&nbsp;&nbsp;
+      <a href="Properties.html">H5P</a>&nbsp;&nbsp;
+      <a href="References.html">H5R & H5I</a>&nbsp;&nbsp;
+      <a href="Ragged.html">H5RA</a>&nbsp;&nbsp;
+      <a href="Dataspaces.html">H5S</a>&nbsp;&nbsp;
+      <a href="Datatypes.html">H5T</a>&nbsp;&nbsp;
+      <a href="Filters.html">H5Z</a>&nbsp;&nbsp;
+      <a href="Caching.html">Caching</a>&nbsp;&nbsp;
+      <a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
+      <a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
+      <a href="Environment.html">Environment</a>&nbsp;&nbsp;
+      <a href="ddl.html">DDL</a>&nbsp;&nbsp;
+-->
+</td></tr>
+</table>
+</center>
+
+
+<!--
     <hr>
     <address><a href="mailto:koziol@ncsa.uiuc.edu">Quincey Koziol</a></address>
     <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
+-->
 <!-- hhmts start -->
-Last modified: Wed Jul  8 14:10:50 EDT 1998
+<!--
+Last modified: Wed Aug 19 15:29:11 PDT 1998
+-->
 <!-- hhmts end -->
 
+<hr>
+<address>
+<table width=100% border=0>
+<tr><td align=left valign=top>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+<br>
+Last modified:  30 October 1998
+
+</td><td align=right valign=top>
+<a href="Copyright.html">Copyright</a>&nbsp;&nbsp;
+</td></tr>
+</table>             
+
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 </html>