hdf5/INSTALL

-*- outline -*-

This file contains instructions for the installation of HDF5 on
Unix-like systems. Users of the Intel TFLOPS machine should see the
INSTALL.ascired for instructions.

* 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.

	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.

* 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.

** 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.

** 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*'.

** 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.

** 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.


* 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.


	$ gunzip <hdf5-1.0.0.tar.gz |tar xf -
	$ cd hdf5-1.0.0
	$ make check
	$ make install

* 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).

** 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.

* 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.

*** Non-compressed tar archive (*.tar)
	$ tar xf hdf5-1.0.0.tar

*** Compressed tar archive (*.tar.Z)
	$ uncompress -c <hdf5-1.0.0.tar.Z |tar xf -

*** Gzip'd tar archive (*.tar.gz)
	$ gunzip <hdf5-1.0.0.tar.gz |tar xf -

*** Bzip'd tar archive (*.tar.bz2)
	$ bunzip2 <hdf5-1.0.0.tar.gz |tar xf -

** 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:

	    $ ./configure		OR
	    $ sh configure

    	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.

*** 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:

	    $ ./configure --prefix=/home/robb

	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.

*** 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:

	    $ CC=cc ./configure

	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.

	    $ CC=/usr/local/mpi/bin/mpicc ./configure

	On Irix64 the default compiler is `cc -64'. To use an
	alternate compiler specify it with the CC variable:

	    $ CC='cc -o32' ./configure

*** 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:

	    $ CFLAGS=-g ./confgure --enable-production

*** 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:

	    $ MAKE=gmake ./configure
	    $ gmake

	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.

	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)

* Support
	Support is described in the README file.