path: root/release_docs/INSTALL

	Instructions for the Installation of HDF5 Software
	==================================================

	CONTENTS
	--------
	1. Obtaining HDF5

	2. Warnings about compilers
	2.1. GNU (Intel platforms)
	2.2. DEC
	2.3. SGI (Irix64 6.2)
	2.4. Windows/NT

	3. Quick installation
	3.1. TFLOPS
	3.2. Windows
	3.3. Certain Virtual File Layer(VFL)

	4. HDF5 dependencies
	4.1. Zlib
	4.2  Szip
	4.3. MPI and MPI-IO

	5. Full installation instructions for source distributions
	5.1. Unpacking the distribution
	5.1.1. Non-compressed tar archive (*.tar)
	5.1.2. Compressed tar archive (*.tar.Z)
	5.1.3. Gzip'd tar archive (*.tar.gz)
	5.1.4. Bzip'd tar archive (*.tar.bz2)
	5.2. Source vs. Build Directories
	5.3. Configuring
	5.3.1. Specifying the installation directories
	5.3.2. Using an alternate C compiler
	5.3.3. Additional compilation flags
	5.3.4. Compiling HDF5 wrapper libraries
	5.3.5. Specifying other programs
	5.3.6. Specifying other libraries and headers
	5.3.7. Static versus shared linking
	5.3.8. Optimization versus symbolic debugging
	5.3.9. Large (>2GB) vs. small (<2GB) file capability
	5.3.10. Parallel vs. serial library
	5.4. Building
	5.5. Testing
	5.6. Installing
	5.7  Building and testing with Intel compilers
	5.8  Building and testing with PGI compilers

	6. Using the Library

	7. Support

*****************************************************************************

1. Obtaining HDF5
	The latest supported public release of HDF5 is available from
	ftp://hdf.ncsa.uiuc.edu/pub/dist/HDF5.  For Unix platforms, it is
	available in tar format uncompressed or compressed with compress,
	gzip, or bzip2.  For Microsoft Windows, it is in ZIP format.

	The HDF team also makes snapshots of the source code available on
	a regular basis. 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 of formats.


2. 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.

2.1. 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.

2.2. COMPAQ/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 *'.
        The fortran module (5.4.1a) fails in compiling some fortran
        programs.  Need to use 5.5.0 or more.

2.3. 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.

2.4. 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.

	A link warning: defaultlib "LIBC" conflicts with use of other libs
	appears for debug version of VC++ 6.0. This warning will not affect
	building and testing hdf5 libraries. 


3. 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 < hdf5-1.6.0.tar.gz | tar xf -
	    $ cd hdf5-1.6.0
	    $ make check
	    $ make install

3.1. TFLOPS
	Users of the Intel TFLOPS machine, after reading this file,
	should see the INSTALL_TFLOPS for more instructions.

3.2. Windows
	Users of Microsoft Windows should see the INSTALL_Windows for
	detailed instructions.

3.3. Certain Virtual File Layer(VFL)
	If users want to install with special Virtual File Layer(VFL),
	please go to read INSTALL_VFL file.  SRB and Globus-GASS have
	been documented. 


4. HDF5 dependencies
4.1. 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).

4.2. Szip
	The HDF5 library has a predefined compression filter that uses
	the extended-Rice lossless compression algorithm for chunked 
        datatsets. For more information about Szip compression and license terms
        see http://hdf.ncsa.uiuc.edu/HDF5/doc_resource/SZIP/index.html.
        Precompiled szip binaries for each supported platform and source tar ball
        file can be found at ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/

4.3. 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.


5. Full installation instructions for source distributions
5.1. 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 `hdf5-1.6.0' directory.

5.1.1. Non-compressed tar archive (*.tar)

	    $ tar xf hdf5-1.6.0.tar

5.1.2. Compressed tar archive (*.tar.Z)

	    $ uncompress -c < hdf5-1.6.0.tar.Z | tar xf -

5.1.3. Gzip'd tar archive (*.tar.gz)

	    $ gunzip < hdf5-1.6.0.tar.gz | tar xf -

5.1.4. Bzip'd tar archive (*.tar.bz2)

	    $ bunzip2 < hdf5-1.6.0.tar.bz2 | tar xf -

5.2. Source vs. Build Directories
	On most systems the build can occur in a directory other than the
	source directory, allowing multiple concurrent builds and/or
	read-only source code. In order to accomplish this, one should
	create a build directory, cd into that directory, and run the
	`configure' script found in the source directory (configure
	details are below).

	Unfortunately, this does not work on recent Irix platforms (6.5?
	and later) because that `make' doesn't understand the VPATH
	variable. However, hdf5 also supports Irix `pmake' which has a
	.PATH target which serves a similar purpose. Here's what the man
	pages say about VPATH, which is the facility used by HDF5
	makefiles for this feature:

		The VPATH facility is a derivation of the undocumented
		VPATH feature in the System V Release 3 version of make.
		System V Release 4 has a new VPATH implementation, much
		like the pmake(1) .PATH feature. This new feature is also
		undocumented in the standard System V Release 4 manual
		pages.  For this reason it is not available in the IRIX
		version of make. The VPATH facility should not be used
		with the new parallel make option.

5.3. 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 type:

	    $ ./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.

5.3.1. Specifying the installation directories
	Typing `make install' will install the HDF5 library, header
	files, examples, and support programs in /usr/local/lib,
	/usr/local/include, /usr/local/doc/hdf5/examples, and 
        /usr/local/bin. To use a path other than
	/usr/local specify the path with the `--prefix=PATH' switch:

	    $ ./configure --prefix=$HOME

	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.

5.3.2. 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 in this case).  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'. To use an alternate
	compiler specify it with the CC variable:

	    $ CC='cc -n32' ./configure

	Similarly, users compiling on a Solaris machine and desiring to
	build the distribution with 64-bit support should specify the
	correct flags with the CC variable:

	    $ CC='cc -xarch=v9' ./configure

	To configure AIX 64 bits including fortran API,
	(Remark: need to hardset $AR to 'ar -X 64'.)
	Serial:
	    $ CC='xlc -q64' F9X='xlf -q64' AR='ar -X 64'\
	    $ ./configure --enable-fortran
	Parallel:
	    $ CC='mpcc_r -q64' F9X='mpxlf_r -q64' AR='ar -X 64'\
	    $ ./configure --enable-fortran

	Specifying these machine architecture flags in the CFLAGS variable
	(see below) will not work correctly.

5.3.3. 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 ./configure --enable-production

5.3.4. Compiling HDF5 wrapper libraries
	One can optionally build the Fortran and/or C++ interface to the
	HDF5 C library. By default, both options are disabled. To build
	them, specify `--enable-fortran' and `--enable-cxx' respectively.

	    $ ./configure --enable-fortran
	    $ ./configure --enable-cxx
	
	Configuration will halt if a working Fortran 90 or 95 compiler or
	C++ compiler is not found. Currently, the Fortran configure tests
	for these compilers in order: f90, pgf90, f95. To use an
	alternative compiler specify it with the F9X variable:

	    $ F9X=/usr/local/bin/g95 ./configure --enable-fortran

	Note: The Fortran and C++ interfaces are not supported on all the
	platforms the main HDF5 library supports. Also, the Fortran
	interface supports parallel HDF5 while the C++ interface does
	not.
          
        Note:  On Crays the following files should be modified before
               building the Fortran Library:
                 fortran/src/H5Dff.f90
                 fortran/src/H5Aff.f90
                 fortran/src/H5Pff.f90
               Check for "Comment if on T3E ..." comment and comment out 
               specified lines or use a patch from HDF FTP server
        ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/hdf5-1.6.0/F90_source_for_Crays       
        Note: See sections 5.7 and 5.8 for how to build Fortran Library with
              PGI or Intel compilers. 

5.3.5. 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.

5.3.6. 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 and  the h4toh5 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 and HDF4-to-HDF5 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.
        
        HDF5 has szip predefined compression method (see 4.2).  To enable
        szip compression, HDF5 library has to be configured and build using 
        SZIP Library

        $ ./configure --with-szlib=/SZIP_Install_directory

5.3.7. 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

	The C++ and Fortran libraries are currently only available in the
	static format.

	To build only statically linked executables on platforms which
	support shared libraries, use the `--enable-static-exec' flag.

	    $ ./configure --enable-static-exec

5.3.8. 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).

5.3.9. 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

5.3.10. Parallel vs. serial library
	The HDF5 library can be configured to use MPI and MPI-IO for
	parallelizm on a distributed multi-processor system.  Read the
	file INSTALL_parallel for detailed explanations.

5.3.11. Threadsafe capability
	The HDF5 library can be configured to be thread-safe (on a very
	large scale) with the with the `--enable-threadsafe' flag to
	configure. Read the file doc/TechNotes/ThreadSafeLibrary.html for
	further details.

5.3.12. Backward compatibility
	The 1.6 version of the HDF5 library can be configured to operate
	identically to the v1.4 library with the `--enable-hdf5v1_4'
	configure flag. This allows existing code to be compiled with the
	v1.6 library without requiring immediate changes to the
	application source code. This flag will only be supported in the
	v1.6 branch of the library, it will not be available in v1.7+.

5.3.13. Network stream capability
	The HDF5 library can be configured with a network stream file
	driver with the `--enable-stream-vfd' configure flag. This option
	compiles the "stream" Virtual File Driver into the main library.
	See the documentation on the Virtual File Layer for more details
	about the use of this driver.

5.4. 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 parallel 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

5.5. 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.

5.6. 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.

	If `make install' fails because the install command at your site
	somehow fails, you may use the install-sh that comes with the
	source. You need to run ./configure again.

            $ INSTALL="$PWD/bin/install-sh -c" ./configure ...
            $ make install

	If you want to install HDF5 in a location other than the location
	specified by the `--prefix=DIR' flag during configuration (or
	instead of the default location, `/usr/local'), you can do that
	by issuing the command:

	    $ make install prefix=NEW_DIR

	where NEW_DIR is the new directory you wish to install HDF5. If
	you do this, you should also modify the installed "bin/h5cc"
	script. Change the "prefix=..." line to reflect the value of
	NEW_DIR.

	The library can be used without installing it by pointing the
	compiler at the `src' and 'src/.libs' directory for include files and
	libraries. However, the minimum which must be installed to make
	the library publically available is:

	    The library:
		./src/.libs/libhdf5.a

	    The public header files:
		./src/H5*public.h

	    The main header file:
		./src/hdf5.h

	    The configuration information:
		./src/H5pubconf.h
	
    	The support programs that are useful are:
	    ./tools/h5ls/h5ls		(list file contents)
	    ./tools/h5dump/h5dump	(dump file contents)
	    ./tools/misc/h5repart	(repartition file families)
	    ./tools/misc/h5debug	(low-level file debugging)
	    ./tools/h5import/h5import	(imports data to HDF5 file)
            ./tools/h5diff/h5diff       (compares two HDF5 files)
            ./tools/gifconv/h52gif	(HDF5 to GIF converter) 
            ./tools/gifconv/gif2h5      (GIF to HDF5 converter)

5.7  Building and testing with Intel compilers


     When Intel compilers are used (icc or ecc), you will need to 
     modify the generated "libtool" program after configuration is finished.
     On or around line 104 of the libtool file, there are lines which 
     look like:

          # How to pass a linker flag through the compiler.
          wl=""

      Change these lines to this:

          # How to pass a linker flag through the compiler.
          wl="-Wl,"

      UPDATE: This is now done automatically by the configure script. However,
      if you still experience a problem, you may want to check this line in
      the libtool file and make sure that it has the correct value.

    * To build the Fortran library using Intel compiler on Linux 2.4, one has to 
          x Use -fpp -DDEC$=DEC_ -DMS$=MS_ compiler flags to disable
            DEC and MS compiler directives in source files in fortran/src, fortran/test 
            and fortran/examples directories.
	    e.g., setenv F9X 'ifc -fpp -DDEC$=DEC_ -DMS$=MS_'
	    (do not use double quotes since $ is interpreted in them.)

          x If Version 6.0 of Fortran compiler is used, build fails in 
            the fortran/test directory and then in the
            fortran/examples directory; to proceed, edit the work.pcl files in
            those directories to contain two lines

                    work.pc
                    ../src/work.pc 

          x Do the same in fortran/examples directory
          x Problem with work.pc files was resolved for newest version of the compiler (7.0)

    * To build the Fortran Library on IA32 follow step described above, except 
      that DEC and MS compiler directives should be removed manually or 
      use a patch from HDF FTP server
      ftp://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/hdf5-1.6.0/F90_source_for_Intel


5.8  Building and testing with PGI compilers
     
     When PGI C and C++ compilers are used (pgcc or pgCC), you will need to 
     modify the generated "libtool" program after configuration is finished.
     On or around line 104 of the libtool file, there are lines which 
     look like:

          # How to pass a linker flag through the compiler.
          wl=""

      Change these lines to this:

          # How to pass a linker flag through the compiler.
          wl="-Wl,"

      UPDATE: This is now done automatically by the configure script. However,
      if you still experience a problem, you may want to check this line in
      the libtool file and make sure that it has the correct value.

      To build HDF5 C++ Library with pgCC (version 4.0 and later), set
      environment variable CXX to "pgCC -tlocal"
         setenv CXX "pgCC -tlocal"
      before running the configure script.


6. 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.


7. Support
	Support is described in the README file.