Update install texts (#4010)

* Update INSTALL_CMake.txt as necessary

* Update remaining docs that use HDF5_USE_GNU_DIRS

* Update options in HDFMacros in HDF5Examples

1 files changed, 558 insertions, 0 deletions

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+
+Instructions for the Installation of HDF5 Software
+==================================================
+
+This file provides instructions for installing the HDF5 software.
+
+For help with installing, questions can be posted to the HDF Forum or sent to the HDF Helpdesk:
+
+   HDF Forum:     https://forum.hdfgroup.org/
+   HDF Helpdesk:  https://hdfgroup.atlassian.net/servicedesk/customer/portals
+
+CONTENTS
+--------
+        1. Obtaining HDF5
+
+        2. Quick installation
+        2.1. Windows
+
+        3. HDF5 dependencies
+        3.1. Zlib
+        3.2  Szip (optional)
+        3.3. MPI and MPI-IO
+
+        4. Full installation instructions for source distributions
+        4.1. Unpacking the distribution
+        4.1.1. Non-compressed tar archive (*.tar)
+        4.1.2. Compressed tar archive (*.tar.Z)
+        4.1.3. Gzip'd tar archive (*.tar.gz)
+        4.1.4. Bzip'd tar archive (*.tar.bz2)
+        4.2. Source versus build directories
+        4.3. Configuring
+        4.3.1. Specifying the installation directories
+        4.3.2. Using an alternate C compiler
+        4.3.3. Additional compilation flags
+        4.3.4. Compiling HDF5 wrapper libraries
+        4.3.5. Specifying other programs
+        4.3.6. Specifying other libraries and headers
+        4.3.7. Static versus shared linking
+        4.3.8. Optimization versus symbolic debugging
+        4.3.9. Parallel versus serial library
+        4.3.10. Threadsafe capability
+        4.3.11. Backward compatibility
+        4.4. Building
+        4.5. Testing
+        4.6. Installing HDF5
+
+        5. Using the Library
+
+
+*****************************************************************************
+
+1. Obtaining HDF5
+        The latest supported public releases of HDF5 are available on
+        https://github.com/HDFGroup/hdf5.
+
+
+2. Quick installation
+        For those who 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. For example, to install HDF5 version X.Y.Z at
+        location /usr/local/hdf5, use the following steps.
+
+            $ cd hdf5-X.Y.Z
+            $ ./configure --prefix=/usr/local/hdf5 <more configure_flags>
+            $ make
+            $ make check                # run test suite.
+            $ make install
+            $ make check-install        # verify installation.
+
+
+        <configure_flags> above refers to the configure flags appropriate
+        to your installation.  For example, to install HDF5 with the
+        Fortran and C++ interfaces and with SZIP compression, the
+        configure line might read as follows:
+
+            $ ./configure --prefix=/usr/local/hdf5 --enable-fortran \
+                          --enable-cxx --with-szlib=PATH_TO_SZIP
+
+        In this case, PATH_TO_SZIP would be replaced with the path to the
+        installed location of the SZIP library.
+
+2.1. Windows
+        Users of Microsoft Windows should see the INSTALL_Windows files for
+        detailed instructions.
+
+
+3. HDF5 dependencies
+3.1. Zlib
+        The HDF5 library includes a predefined compression filter that
+        uses the "deflate" method for chunked datasets. If zlib-1.1.2 or
+        later is found, 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.
+
+3.2. Szip (optional)
+        The HDF5 library includes a predefined compression filter that
+        uses the extended-Rice lossless compression algorithm for chunked
+        datasets. For information on Szip compression, license terms,
+        and obtaining the Szip source code, see:
+
+           https://portal.hdfgroup.org/display/HDF5/Szip+Compression+in+HDF+Products
+
+        Building instructions are available with the Szip source code.
+
+        The HDF Group does not distribute separate Szip precompiled libraries,
+        but the HDF5 pre-built binaries provided on The HDF Group download page
+        include the Szip library with the encoder enabled. These can be found
+        here:
+
+           https://www.hdfgroup.org/downloads/hdf5/
+
+        To configure the HDF5 library with the Szip compression filter, use
+        the '--with-szlib=/PATH_TO_SZIP' flag. For more information, see
+        section 4.3.7, "Specifying other libraries and headers."
+
+        Please notice that if HDF5 configure cannot find a valid Szip library,
+        configure will not fail; in this case, the compression filter will
+        not be available to the applications.
+
+        To check if Szip compression was successfully configured in,
+        check the "I/O filters (external):" line in the configure output,
+        summary section, printed to the standard output.
+
+3.3. 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, only a serial version of HDF5 can be built.
+
+
+4. Full installation instructions for source distributions
+
+4.1. 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-X.Y.Z' directory, where X.Y.Z is the HDF5 version numbers.
+
+4.1.1. Non-compressed tar archive (*.tar)
+
+            $ tar xf hdf5-X.Y.Z.tar
+
+4.1.2. Compressed tar archive (*.tar.Z)
+
+            $ uncompress -c < hdf5-X.Y.Z.tar.Z | tar xf -
+            Or
+            $ tar Zxf hdf5-X.Y.Z.tar.Z
+
+4.1.3. Gzip'd tar archive (*.tar.gz)
+
+            $ gunzip < hdf5-X.Y.Z.tar.gz | tar xf -
+            Or
+            $ tar zxf hdf5-X.Y.Z.tar.gz
+
+4.1.4. Bzip'd tar archive (*.tar.bz2)
+
+            $ bunzip2 < hdf5-X.Y.Z.tar.bz2 | tar xf -
+            Or
+            $ tar jxf hdf5-X.Y.Z.tar.bz2
+
+4.2. Source versus 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). For example,
+            $ mkdir built-fortran
+            $ cd build-fortran
+            $ ../hdf5-X.Y.Z/configure --enable-fortran ...
+
+
+4.3. 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.
+
+4.3.1. Specifying the installation directories
+        The default installation location is the HDF5 directory created in
+        the build directory. Typing `make install' will install the HDF5
+        library, header files, examples, and support programs in hdf5/lib,
+        hdf5/include, hdf5/doc/hdf5/examples, and hdf5/bin. To use a path
+        other than hdf5, specify the path with the `--prefix=PATH' switch:
+
+            $ ./configure --prefix=/usr/local
+
+        If shared libraries are being built (the default), the final
+        home of the shared library must be specified with this switch
+        before the library and executables are built.
+
+        HDF5 can be installed into a different location than the prefix
+        specified at configure time; see section 4.6, "Installing HDF5,"
+        for more details.
+
+4.3.2. 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.  For instance, one would
+        use the following line to specify the native C compiler on a system
+        that also has the GNU gcc compiler (users of csh and derivatives
+        will need to prefix the commands below with `env'):
+
+            $ 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
+
+
+4.3.3. Additional compilation flags
+        If additional flags must be passed to the compilation commands,
+        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-build-mode=production
+
+4.3.4. Compiling HDF5 wrapper libraries
+        One can optionally build the Fortran, C++, and Java interfaces to
+        the HDF5 C library. By default, these options are disabled. To build
+        them, specify '--enable-fortran', '--enable-cxx', or '--enable-java',
+        respectively.
+
+            $ ./configure --enable-fortran
+            $ ./configure --enable-cxx
+            $ ./configure --enable-java
+
+        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
+        alternate compiler specify it with the FC variable:
+
+            $ FC=/usr/local/bin/g95 ./configure --enable-fortran
+
+
+4.3.5. Specifying other programs
+        The build system has been tuned for use with GNU make but also
+        works 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, the shell script bin/install-sh is used. Configure does not
+        check that the install script actually works; 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
+               change file ownership and/or access permissions.
+
+4.3.6. 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 to support the HDF5 deflate
+        data compression filter.  Configure searches the standard places
+        (plus those specified above with the 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
+
+        HDF5 includes Szip as a predefined compression method (see 3.2).
+        To enable Szip compression, the HDF5 library must be configured
+        and built using the Szip library:
+
+            $ ./configure --with-szlib=/Szip_Install_Directory
+
+4.3.7. 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 the library may be suppressed by
+        saying `--disable-static' or `--disable-shared'.
+
+            $ ./configure --disable-shared
+
+        Shared C++ and Fortran libraries will be built if shared libraries
+        are enabled.
+
+        To build only statically linked executables on platforms which
+        support shared libraries, use the `--enable-static-exec' flag.
+
+            $ ./configure --enable-static-exec
+
+4.3.8. 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
+        `--enable-build-mode=debug'; to compile with optimizations
+        (the default for supported public releases),
+        say `--enable-build-mode=production'. For a 'clean slate' configuration
+        with optimization disabled and nothing turned on,
+        say `--enable-build-mode=clean'. On some systems the
+        library can also be compiled for profiling with gprof by saying
+        `--enable-profiling'.
+
+            $ ./configure --enable-build-mode=debug       #symbolic debugging
+            $ ./configure --enable-build-mode=production  #optimized code
+            $ ./configure --enable-build-mode=clean       #'clean slate'
+            $ ./configure --enable-profiling              #for use with gprof
+
+        Regardless of whether support for symbolic debugging is enabled,
+        the library can also 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 the `--enable-internal-debug'
+        switch.
+
+        Debugging can be disabled by saying `--disable-internal-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-internal-debug=s,t  #debug only H5S and H5T
+            $ ./configure --enable-internal-debug      #debug normal packages
+            $ ./configure --enable-internal-debug=all  #debug all packages
+            $ ./configure --disable-internal-debug     #no debugging
+
+        HDF5 can also 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.
+
+4.3.9. Parallel versus serial library
+        The HDF5 library can be configured to use MPI and MPI-IO for
+        parallelism on a distributed multi-processor system.  Read the
+        file INSTALL_parallel for detailed information.
+
+        The threadsafe, C++ and Java interfaces are not compatible
+        with the parallel option.
+        Unless --enable-unsupported has been specified on the configure line,
+        the following options must be disabled:
+            --enable-threadsafe, --enable-cxx, --enable-java
+
+
+4.3.10. Threadsafe capability
+        The HDF5 library can be configured to be thread-safe (on a very
+        large scale) with the `--enable-threadsafe' flag to the configure
+        script.  Some platforms may also require the '-with-pthread=INC,LIB'
+        (or '--with-pthread=DIR') flag to the configure script.
+        For further information, see:
+
+           https://portal.hdfgroup.org/display/knowledge/Questions+about+thread-safety+and+concurrent+access
+
+        The high-level, C++, Fortran and Java interfaces are not compatible
+        with the thread-safety option because the lock is not hoisted
+        into the higher-level API calls.
+        Unless --enable-unsupported has been specified on the configure line,
+        the following options must be disabled:
+            --enable-hl, --enable-cxx, --enable-fortran, --enable-java
+
+
+4.3.11. Backward compatibility
+        The 1.15 version of the HDF5 library can be configured to operate
+        identically to the v1.14 library with the
+            --with-default-api-version=v114
+        identically to the v1.12 library with the
+            --with-default-api-version=v112
+        configure flag, or identically to the v1.10 library with the
+            --with-default-api-version=v110
+        configure flag, or identically to the v1.8 library with the
+            --with-default-api-version=v18
+        configure flag, or identically to the v1.6 library with the
+            --with-default-api-version=v16
+        configure flag. This allows existing code to be compiled with the
+        v1.15 library without requiring immediate changes to the application
+        source code.  For additional configuration options and other details,
+        see "API Compatibility Macros":
+
+            https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros
+
+4.4. Building
+        The library, confidence tests, and programs can be built by
+        specifying:
+
+            $ make
+
+        Note that if you have supplied some other make command via the MAKE
+        variable during the configuration step, 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
+        the `-j' since GNU make will turn it off for recursive invocations
+        of make.
+
+            $ make -j -l6
+
+4.4. Building doxygen
+        One can optionally build the doxygen files for the HDF5 C library.
+        By default, this option is disabled. To build the html files, specify
+        '--enable-doxygen'.
+
+            $ ./configure --enable-doxygen
+
+        Configuration will halt if the required applications are not available.
+        To build:
+
+            $ make doxygen
+
+
+4.5. Testing
+        HDF5 comes with various test suites, all of which can be run by
+        specifying:
+
+            $ 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'.
+
+        The `check' consists of two sub-tests, check-s and check-p, which
+        are for serial and parallel tests, respectively.  Since serial tests
+        and parallel tests must be run with single and multiple processes
+        respectively, the two sub-tests work nicely for batch systems in
+        which the number of processes is fixed per batch job.  One may submit
+        one batch job, requesting 1 process, to run all the serial tests by
+        "make check-s"; and submit another batch job, requesting multiple
+        processes, to run all the parallel tests by "make check-p".
+
+        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.
+
+        The HDF5 tests can take a long time to run on some systems.  To perform
+        a faster (but less thorough) test, set the HDF5TestExpress environment
+        variable to 2 or 3 (with 3 being the shortest run).  To perform a
+        longer test, set HDF5TestExpress to 0.  3 is the default.
+
+4.6. Installing HDF5
+        The HDF5 library, include files, and support programs can be
+        installed by specifying `make install'. The files are installed under the
+        directory specified with `--prefix=DIR' (or if not specified, in 'hdf5'
+        in the top directory of the HDF5 source code). They will be
+        placed in directories named `lib', `include', and `bin'. The directories,
+        if not existing, will be created automatically, provided the mkdir command
+        supports the -p option.
+
+        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 will 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, `hdf5'), you can do that
+        by running the deploy script:
+
+            $ bin/deploy NEW_DIR
+
+        This will install HDF5 in NEW_DIR.  Alternately, you can do this
+        manually by issuing the command:
+
+            $ make install prefix=NEW_DIR
+
+        where NEW_DIR is the new directory where you wish to install HDF5.
+        If you do not use the deploy script, you should run h5redeploy in
+        NEW_DIR/bin directory.  This utility will fix the h5cc, h5fc and
+        h5c++ scripts to reflect the new NEW_DIR location.
+
+        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 publicly available is:
+
+            The library:
+                ./src/.libs/libhdf5.a
+
+            The public header files:
+                ./src/H5*public.h, ./src/H5public.h
+                ./src/H5FD*.h except ./src/H5FDprivate.h,
+                ./src/H5api_adpt.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. Using the Library
+
+        For information on using HDF5 see the documentation, tutorials and examples
+        found here:
+
+           https://portal.hdfgroup.org/display/HDF5/HDF5
+
+        A summary of the features included in the built HDF5 installation can be found
+        in the libhdf5.settings file in the same directory as the static and/or
+        shared HDF5 libraries.
+
+
+