Instructions for the Installation of HDF5 Software ================================================== 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. Disabling high-level C APIs 4.3.11. Threadsafe capability 4.3.12. Backward compatibility with HDF5 1.4* releases 4.4. Building 4.5. Testing 4.6. Installing 5. Using the Library 5.1. Using the C++ API 6. Support ***************************************************************************** 1. Obtaining HDF5 The latest supported public release of HDF5 is available from ftp://ftp.hdfgroup.org/HDF5/current/src. It is available in tar format compressed with gzip. The HDF team also makes snapshots of the source code available on a regular basis. These snapshots are unsupported (that is, the HDF team will not release a bug-fix on a particular snapshot; rather any bug fixes will be rolled into the next snapshot). Furthermore, the snapshots have only been tested on a few machines and may not test correctly for parallel applications. Snapshots can be found at ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots in a limited number of formats. 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. The "#" symbol in "hdf5-1.6.#" below stands for the release number and/or the subrelease version. (For example, use "3" for hdf5-1.6.3 or "3-snap4" for hdf5-1.6.3-snap4.) $ gunzip < hdf5-1.6.#.tar.gz | tar xf - $ cd hdf5-1.6.# $ ./configure $ make $ make check $ make install $ make check-install The last step above verifies your installation. 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 --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 one of 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 more information about Szip compression and license terms, see http://hdfgroup.org/doc_resource/SZIP/index.html. Precompiled szip binaries for each supported platform and a source tar ball file can be found at ftp://ftp.hdfgroup.org/lib-external/szip/. To configure the HDF5 Library with the Szip compression filter, use the '--enable-szlib=/PATH_TO_SZIP' flag. For more information, see section 4.3.6, "Specifying other libraries and headers." Starting with release 1.6.3, Szip library binaries are distributed with the encoder enabled (a license may be required to use this binary) and with the encoder disabled (freely usable without a license). Depending on which Szip binary is used, Szip compression is available or is not available for an HDF5 application. Szip decoding is always available, i.e., an HDF5 application can always read Szip compressed data, if the Szip filter is present. 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 'hdf5-1.6.#' directory. 4.1.1. Non-compressed tar archive (*.tar) $ tar xf hdf5-1.6.#.tar 4.1.2. Compressed tar archive (*.tar.Z) $ uncompress -c < hdf5-1.6.#.tar.Z | tar xf - 4.1.3. Gzip'd tar archive (*.tar.gz) $ gunzip < hdf5-1.6.#.tar.gz | tar xf - 4.1.4. Bzip'd tar archive (*.tar.bz2) $ bunzip2 < hdf5-1.6.#.tar.bz2 | tar xf - 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). Unfortunately, this does not work on recent Irix platforms (6.5 and later) because that 'make' does not understand the VPATH variable. However, HDF5 also supports Irix 'pmake' which has a .PATH target that serves a similar purpose. Here's what the man pages say about VPATH, which is the facility used by HDF5 makefiles for this feature: The VPATH facility is a derivation of the undocumented VPATH feature in the System V Release 3 version of make. System V Release 4 has a new VPATH implementation, much like the pmake(1) .PATH feature. This new feature is also undocumented in the standard System V Release 4 manual pages. For this reason it is not available in the IRIX version of make. The VPATH facility should not be used with the new parallel make option. 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 Typing 'make install' will install the HDF5 Library, header files, examples, and support programs in hdf5/lib, hdf5/include, hdf5/examples, and hdf5/bin under the directory where it was built (hdf5-1.6.# or the build directory mentioned in section 4.2, "Source versus build directories"). To use a path other than hdf5/, specify the path with the '--prefix=PATH' switch: $ ./configure --prefix=$HOME 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. 4.3.2. Using an alternate C compiler By default, configure will look for the C compiler specified in the host configuration file in the config directory or by trying 'gcc' and 'cc'. However, if the environment variable "CC" is set, then its value is used as the C compiler (users of csh and derivatives will need to prefix the commands below with 'env'). For instance, to use the native C compiler on a system which also has the GNU gcc compiler: $ CC=cc ./configure A parallel version of HDF5 can be built by specifying a parallel compiler, usually '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 On Irix64, the default compiler is 'cc'. To use an alternate compiler, specify it with the CC variable: $ CC='cc -n32' ./configure Similarly, users compiling on a Solaris machine and desiring to build the distribution with 64-bit support should specify the correct flags with the CC variable: $ CC='cc -xarch=v9' ./configure To configure AIX 64-bit, including the Fortran and C++ APIs, set the compilation flags as follows (note the requirement to hardset $AR to 'ar -X 64') and run configure with the appropriate flags as follows: Serial: $ CFLAGS=-q64 FFLAGS=-q64 CXXFLAGS=-q64 AR='ar -X 64'\ $ ./configure --enable-fortran Parallel: $ CFLAGS=-q64 FFLAGS=-q64 AR='ar -X 64'\ $ ./configure --enable-fortran --enable-parallel 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-production 4.3.4. Compiling HDF5 wrapper libraries One can optionally build the Fortran and/or C++ interface to the HDF5 C library. By default, both options are disabled. To build one or both, specify '--enable-fortran' and/or '--enable-cxx', respectively. $ ./configure --enable-fortran $ ./configure --enable-cxx $ ./configure --enable-fortran --enable-cxx Configure uses the Fortran compiler specified in the host configuration file in the fortran/config directory and the C++ compiler specified in the host configuration file under the c++/config directory. 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 Fortran compiler, specify it with the F9X variable. For example: $ F9X=/mycompiler/bin/g95 ./configure --enable-fortran To use an alternate C++ compiler, specify it with the CXX variable: $ CXX=/mycompiler/bin/c++ ./configure --enable-cxx Note: The Fortran interface supports parallel HDF5 while the C++ interface does not. 4.3.5. Specifying other programs The build system has been tuned for use with GNU make but works also with other versions of make. If the 'make' command runs a non-GNU version but a GNU version is available under a different name (perhaps 'gmake'), then HDF5 can be configured to use it by setting the MAKE variable. Note that whatever value is used for MAKE must also be used as the make command when building the library: $ MAKE=gmake ./configure $ gmake The 'AR' and 'RANLIB' variables can also be set to the names of the 'ar' and 'ranlib' (or ':') commands to override values detected by configure. The HDF5 Library, include files, and utilities are installed during 'make install' (described below) with a BSD-compatible install program detected automatically by configure. If none is found, the shell script bin/install-sh is used. Configure does NOT check that the install program actually works; if a bad install is detected on your system, 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 system 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 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=/PATH_TO_ZLIB' or through the CPPFLAGS and LDFLAGS variables: $ ./configure --with-zlib=/PATH_TO_ZLIB $ CPPFLAGS=-I/PATH_TO_ZLIB/include \ LDFLAGS=-L/PATH_TO_ZLIB/lib \ ./configure HDF5 also provides a predefined Szip compression method (see section 3.2, "Szip"). To enable Szip compression, the HDF5 Library has to be configured and built using the Szip Library: $ ./configure --with-szlib=/PATH_TO_SZIP 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 To build only statically linked executables on platforms that 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 '--disable-production'; to compile with optimizations (the default for supported public releases), say '--enable-production'. On some systems, the library can also be compiled for profiling with gprof by saying '--enable-production=profile'. $ ./configure --disable-production #symbolic debugging $ ./configure --enable-production #optimized code $ ./configure --enable-production=profile #for use with gprof Regardless of whether support for symbolic debugging is enabled, the library 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-debug' switch. (See "Debugging HDF5 Applications" for a list of package names. In the documentation distributed with this release, that document is in doc/html/Debugging.html. In the HDF5 documentation at http://hdfgroup.org/HDF5/doc1.6/, select "HDF5 User's Guide from Release 1.4.5," then select "Debugging.") Debugging can be disabled by saying '--disable-debug'. The default debugging level for snapshots is a subset of the available packages; the default for supported releases is no debugging (debugging can incur a significant runtime penalty). $ ./configure --enable-debug=s,t #debug only H5S and H5T $ ./configure --enable-debug #debug normal packages $ ./configure --enable-debug=all #debug all packages $ ./configure --disable-debug #no debugging HDF5 is also able to print a trace of all API function calls, their arguments, and the return values. To enable or disable the ability to trace the API, say '--enable-trace' (the default for snapthots) or '--disable-trace' (the default for public releases). The tracing must also be enabled at runtime to see any output (see Debugging.html). 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 explanations. 4.3.10. Disabling high-level C APIs By default, the HDF5 Library is configured to build the high-level C APIs. If this feature is not desired, use the '--disable-hl' configuration flag to bypass building and testing high-level C APIs. 4.3.11. 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' flag (or '--with-pthread=DIR') to the configure script. (For further details, see "Thread Safe HDF5 Library Implementation" in the "HDF5 Technical Notes." This document is included in the HDF5 documentation set distributed with this release and posted at http://hdfgroup.org/HDF5/doc1.6/.) 4.3.12. Backward compatibility with HDF5 1.4* releases The 1.6 version of the HDF5 Library can be configured to operate identically to the v1.4 library with the '--enable-hdf5v1_4' configure flag. This allows existing code to be compiled with the v1.6 library without requiring immediate changes to the application source code. This flag will only be supported in the v1.6 branch of the library; it will not be available in v1.8+. 4.4. Building The library, confidence tests, and programs can be built by saying just: $ make Note that if you 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 4.5. Testing HDF5 comes with various test suites, all of which can be run by saying $ make check To run only the tests for the library, change to the 'test' directory before issuing the command. Similarly, tests for the parallel aspects of the library are in 'testpar' and tests for the support programs are in 'tools'. Temporary files will be deleted by each test when it 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. 4.6. Installing The HDF5 Library, include files, and support programs can be installed in a (semi-)public place by saying 'make install'. The files are installed under the directory specified with '--prefix=DIR' (or under 'hdf5/' in the build directory) in directories named 'lib', 'include', 'doc', and 'bin'. The prefix directory DIR must exist prior to 'make install', but its subdirectories are created automatically. If no prefix is defined, an 'hdf5' directory is automatically created under the build directory. If 'make install' fails because the install command at your site somehow fails, you may use the install-sh script that comes with the source. You need to run ./configure again: $ INSTALL="$PWD/bin/install-sh -c" ./configure ... $ make install The library can be used without installing it by pointing the compiler at the 'src' 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 (lists file contents) ./tools/h5dump/h5dump (dumps file contents) ./tools/h5repack/h5repack (repacks HDF5 file) ./tools/h5jam/h5jam(unjam) (adds/removes user block to/from HDF5 file) ./tools/misc/h5repart (repartitions file families) ./tools/misc/h5debug (low-level file debugging) ./tools/h5import/h5import (imports data to HDF5 file) ./tools/h5diff/h5diff (compares two HDF5 files) ./hl//tools/h52gif/h52gif (HDF5 to GIF converter) ./hl//tools/gif2h5/gif2h5 (GIF to HDF5 converter) 5. Using the Library Please see the HDF5 User's Guide and the HDF5 Reference Manual in the HDF5 documentation. C programs must include and link with the HDF5 Libraries. Additional libraries may also be necessary depending on whether support for compression, etc., was compiled into the HDF5 Library. A summary of the current HDF5 installation can be found in the libhdf5.settings and libhdf5_fortran.settings files in the bin subdirectory. Users are encouraged to use the helper compiler scripts h5cc, h5fc, and h5c++ to build HDF5 C, Fortran, and C++ applications, respectively. Those scripts are installed under the bin subdirectory when 'make install' is run. Scripts inherit flags used during library compilation. Users may examine these and other flags used by a script by typing the script name with the '-echo' option: