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author | Glenn Song <43005495+glennsong09@users.noreply.github.com> | 2024-02-14 13:37:18 (GMT) |
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committer | GitHub <noreply@github.com> | 2024-02-14 13:37:18 (GMT) |
commit | 14ed93e749d1b12acc9a43ba41911a8475366f60 (patch) | |
tree | d9187b95b10eaa7de67aa9919786423078efcb02 /release_docs/INSTALL | |
parent | be956ea3021ac733dcc9cdec025ed87ea109fe33 (diff) | |
download | hdf5-14ed93e749d1b12acc9a43ba41911a8475366f60.zip hdf5-14ed93e749d1b12acc9a43ba41911a8475366f60.tar.gz hdf5-14ed93e749d1b12acc9a43ba41911a8475366f60.tar.bz2 |
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
Diffstat (limited to 'release_docs/INSTALL')
-rw-r--r-- | release_docs/INSTALL | 566 |
1 files changed, 0 insertions, 566 deletions
diff --git a/release_docs/INSTALL b/release_docs/INSTALL deleted file mode 100644 index 369e270..0000000 --- a/release_docs/INSTALL +++ /dev/null @@ -1,566 +0,0 @@ - -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. - - - |