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, 0 insertions, 566 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
-        2.2. RedStorm (Cray XT3)
-
-        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.
-
-2.2. RedStorm (Cray XT3)
-        Users of the Red Storm machine, after reading this file, should read
-        the Red Storm section in the INSTALL_parallel file for specific
-        instructions for the Red Storm machine.  The same instructions would
-        probably work for other Cray XT3 systems, but they have not been
-        verified.
-
-
-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.
-
-
-