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+
+ 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. 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
+
+ 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. 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 *'.
+
+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 < hdf5-1.4.0.tar.gz | tar xf -
+ $ cd hdf5-1.4.0
+ $ 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. 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 `hdf5-1.2.0' directory.
+
+5.1.1. Non-compressed tar archive (*.tar)
+
+ $ tar xf hdf5-1.4.0.tar
+
+5.1.2. Compressed tar archive (*.tar.Z)
+
+ $ uncompress -c < hdf5-1.4.0.tar.Z | tar xf -
+
+5.1.3. Gzip'd tar archive (*.tar.gz)
+
+ $ gunzip < hdf5-1.4.0.tar.gz | tar xf -
+
+5.1.4. Bzip'd tar archive (*.tar.bz2)
+
+ $ bunzip2 < hdf5-1.2.0.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, 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
+
+ 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). 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 -o32' ./configure
+
+ One may also use various environment variables to change the
+ behavior of the compiler. E.g., to ask for -n32 ABI:
+
+ $ SGI_ABI=-n32
+ $ export SGI_ABI
+ $ ./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
+
+ 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 T3E and J90 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.
+
+
+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.
+
+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 1.4 version of the HDF5 library can be configured to operate
+ identically to the v1.2 library with the `--enable-hdf5v1_2'
+ configure flag. This allows existing code to be compiled with the
+ v1.4 library without requiring immediate changes to the
+ application source code. This flag will only be supported in the
+ v1.4 branch of the library, it will not be available in v1.5+.
+
+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
+
+ 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/H5pubconf.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)
+ ./tools/h4toh5 (hdf4 to hdf5 file converter)
+
+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.