diff options
Diffstat (limited to 'release_docs/INSTALL_Auto.txt')
| -rw-r--r-- | release_docs/INSTALL_Auto.txt | 556 |
1 files changed, 556 insertions, 0 deletions
diff --git a/release_docs/INSTALL_Auto.txt b/release_docs/INSTALL_Auto.txt new file mode 100644 index 0000000..969fbac --- /dev/null +++ b/release_docs/INSTALL_Auto.txt @@ -0,0 +1,556 @@ + +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 1.14 version of the HDF5 library can be configured to operate + 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 + v1.14 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. + + + |