Instructions for the Installation of HDF5 Software ================================================== CONTENTS -------- 1. Obtaining HDF5 2. Warnings about compilers 2.1. GNU (Intel platforms) 2.2. DEC 2.3. SGI (Irix64 6.2) 2.4. Windows/NT 3. Quick installation 3.1. TFLOPS 3.2. Windows 3.3. Certain Virtual File Layer(VFL) 4. HDF5 dependencies 4.1. Zlib 4.2 Szip 4.3. MPI and MPI-IO 5. Full installation instructions for source distributions 5.1. Unpacking the distribution 5.1.1. Non-compressed tar archive (*.tar) 5.1.2. Compressed tar archive (*.tar.Z) 5.1.3. Gzip'd tar archive (*.tar.gz) 5.1.4. Bzip'd tar archive (*.tar.bz2) 5.2. Source vs. Build Directories 5.3. Configuring 5.3.1. Specifying the installation directories 5.3.2. Using an alternate C compiler 5.3.3. Additional compilation flags 5.3.4. Compiling HDF5 wrapper libraries 5.3.5. Specifying other programs 5.3.6. Specifying other libraries and headers 5.3.7. Static versus shared linking 5.3.8. Optimization versus symbolic debugging 5.3.9. Large (>2GB) vs. small (<2GB) file capability 5.3.10. Parallel vs. serial library 5.4. Building 5.5. Testing 5.6. Installing 5.7 Building and testing with Intel compilers 5.8 Building and testing with PGI compilers 6. Using the Library 7. Support ***************************************************************************** 1. Obtaining HDF5 The latest supported public release of HDF5 is available from ftp://hdf.ncsa.uiuc.edu/pub/dist/HDF5. For Unix platforms, it is available in tar format uncompressed or compressed with compress, gzip, or bzip2. For Microsoft Windows, it is in ZIP format. 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://hdf.ncsa.uiuc.edu/pub/outgoing/hdf5/snapshots in a limited number of formats. 2. Warnings about compilers OUTPUT FROM THE FOLLOWING COMPILERS SHOULD BE EXTREMELY SUSPECT WHEN USED TO COMPILE THE HDF5 LIBRARY, ESPECIALLY IF OPTIMIZATIONS ARE ENABLED. IN ALL CASES, HDF5 ATTEMPTS TO WORK AROUND THE COMPILER BUGS BUT THE HDF5 DEVELOPMENT TEAM MAKES NO GUARANTEES THAT THERE ARE OTHER CODE GENERATION PROBLEMS. 2.1. GNU (Intel platforms) Versions before 2.8.1 have serious problems allocating registers when functions contain operations on `long long' data types. Supplying the `--disable-hsizet' switch to configure (documented below) will prevent hdf5 from using `long long' data types in situations that are known not to work, but it limits the hdf5 address space to 2GB. 2.2. COMPAQ/DEC The V5.2-038 compiler (and possibly others) occasionally generates incorrect code for memcpy() calls when optimizations are enabled, resulting in unaligned access faults. HDF5 works around the problem by casting the second argument to `char *'. The fortran module (5.4.1a) fails in compiling some fortran programs. Need to use 5.5.0 or more. 2.3. SGI (Irix64 6.2) The Mongoose 7.00 compiler has serious optimization bugs and should be upgraded to MIPSpro 7.2.1.2m. Patches are available from SGI. 2.4. Windows/NT The MicroSoft Win32 5.0 compiler is unable to cast unsigned long long values to doubles. HDF5 works around this bug by first casting to signed long long and then to double. A link warning: defaultlib "LIBC" conflicts with use of other libs appears for debug version of VC++ 6.0. This warning will not affect building and testing hdf5 libraries. 3. Quick installation For those that 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. $ gunzip < hdf5-1.6.0.tar.gz | tar xf - $ cd hdf5-1.6.0 $ make check $ make install 3.1. TFLOPS Users of the Intel TFLOPS machine, after reading this file, should see the INSTALL_TFLOPS for more instructions. 3.2. Windows Users of Microsoft Windows should see the INSTALL_Windows for detailed instructions. 3.3. Certain Virtual File Layer(VFL) If users want to install with special Virtual File Layer(VFL), please go to read INSTALL_VFL file. SRB and Globus-GASS have been documented. 4. HDF5 dependencies 4.1. Zlib The HDF5 library has a predefined compression filter that uses the "deflate" method for chunked datatsets. If zlib-1.1.2 or later is found then 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). 4.2. Szip The HDF5 library has a predefined compression filter that uses the extended-Rice lossless compression algorithm for chunked datatsets. For more information about Szip compression and license terms see http://hdf.ncsa.uiuc.edu/HDF5/doc_resource/SZIP/index.html. Precompiled szip binaries for each supported platform and source tar ball file can be found at ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/ 4.3. 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 then only a serial version of HDF5 can be built. 5. Full installation instructions for source distributions 5.1. 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 `hdf5-1.6.0' directory. 5.1.1. Non-compressed tar archive (*.tar) $ tar xf hdf5-1.6.0.tar 5.1.2. Compressed tar archive (*.tar.Z) $ uncompress -c < hdf5-1.6.0.tar.Z | tar xf - 5.1.3. Gzip'd tar archive (*.tar.gz) $ gunzip < hdf5-1.6.0.tar.gz | tar xf - 5.1.4. Bzip'd tar archive (*.tar.bz2) $ bunzip2 < hdf5-1.6.0.tar.bz2 | tar xf - 5.2. Source vs. 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' doesn't understand the VPATH variable. However, hdf5 also supports Irix `pmake' which has a .PATH target which 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. 5.3. 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. 5.3.1. Specifying the installation directories Typing `make install' will install the HDF5 library, header files, examples, and support programs in /usr/local/lib, /usr/local/include, /usr/local/doc/hdf5/examples, and /usr/local/bin. To use a path other than /usr/local specify the path with the `--prefix=PATH' switch: $ ./configure --prefix=$HOME If shared libraries are being built (the default) then the final home of the shared library must be specified with this switch before the library and executables are built. 5.3.2. 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 (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 `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 bits including fortran API, (Remark: need to hardset $AR to 'ar -X 64'.) Serial: $ CC='xlc -q64' F9X='xlf -q64' AR='ar -X 64'\ $ ./configure --enable-fortran Parallel: $ CC='mpcc_r -q64' F9X='mpxlf_r -q64' AR='ar -X 64'\ $ ./configure --enable-fortran Specifying these machine architecture flags in the CFLAGS variable (see below) will not work correctly. 5.3.3. Additional compilation flags If addtional flags must be passed to the compilation commands then 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 5.3.4. 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 them, specify `--enable-fortran' and `--enable-cxx' respectively. $ ./configure --enable-fortran $ ./configure --enable-cxx 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 alternative compiler specify it with the F9X variable: $ F9X=/usr/local/bin/g95 ./configure --enable-fortran Note: The Fortran and C++ interfaces are not supported on all the platforms the main HDF5 library supports. Also, the Fortran interface supports parallel HDF5 while the C++ interface does not. Note: On Crays the following files should be modified before building the Fortran Library: fortran/src/H5Dff.f90 fortran/src/H5Aff.f90 fortran/src/H5Pff.f90 Check for "Comment if on T3E ..." comment and comment out specified lines or use a patch from HDF FTP server ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/ Note: See sections 5.7 and 5.8 for how to build Fortran Library with PGI or Intel compilers. 5.3.5. 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 then the shell script bin/install-sh is used. Configure doesn't check that the install script actually works, but 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 also change file ownership and/or access permissions. 5.3.6. 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 for two purposes: it provides support for the HDF5 deflate data compression filter, and it is used by the h5toh4 converter and the h4toh5 converter in support of HDF4. 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=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 The HDF5-to-HDF4 and HDF4-to-HDF5 conversion tool requires the HDF4 library and header files which are detected the same way as zlib. The switch to give to configure is `--with-hdf4'. Note that HDF5 requires a newer version of zlib than the one shipped with some versions of HDF4. Also, unless you have the "correct" version of hdf4 the confidence testing will fail in the tools directory. HDF5 has Szip predefined compression method (see 4.2). To enable Szip compression, HDF5 library has to be configured and build using Szip Library $ ./configure --with-szlib=/Szip_Install_Directory 5.3.7. 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 library may be suppressed by saying `--disable-static' or `--disable-shared'. $ ./configure --disable-shared The C++ and Fortran libraries are currently only available in the static format. To build only statically linked executables on platforms which support shared libraries, use the `--enable-static-exec' flag. $ ./configure --enable-static-exec 5.3.8. 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 also is able to 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 to the `--enable-debug' switch (see Debugging.html for a list of package names). 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). 5.3.9. Large (>2GB) vs. small (<2GB) file capability In order to read or write files that could potentially be larger than 2GB it is necessary to use the non-ANSI `long long' data type on some platforms. However, some compilers (e.g., GNU gcc versions before 2.8.1 on Intel platforms) are unable to produce correct machine code for this data type. To disable use of the `long long' type on these machines say: $ ./configure --disable-hsizet 5.3.10. Parallel vs. serial library The HDF5 library can be configured to use MPI and MPI-IO for parallelizm on a distributed multi-processor system. Read the file INSTALL_parallel for detailed explanations. 5.3.11. Threadsafe capability The HDF5 library can be configured to be thread-safe (on a very large scale) with the with the `--enable-threadsafe' flag to configure. Read the file doc/TechNotes/ThreadSafeLibrary.html for further details. 5.3.12. Backward compatibility 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 v1.7+. 5.3.13. Network stream capability The HDF5 library can be configured with a network stream file driver with the `--enable-stream-vfd' configure flag. This option compiles the "stream" Virtual File Driver into the main library. See the documentation on the Virtual File Layer for more details about the use of this driver. 5.4. Building The library, confidence tests, and programs can be build by saying just: $ make Note that if you supplied some other make command via the MAKE variable during the configuration step then 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 th `-j' since GNU make will turn it off for recursive invocations of make. $ make -j -l6 5.5. 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 complets, 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. 5.6. 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 '/usr/local') in directories named `lib', `include', and `bin'. The prefix directory must exist prior to `make install', but its subdirectories are created automatically. 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 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, `/usr/local'), you can do that by issuing the command: $ make install prefix=NEW_DIR where NEW_DIR is the new directory you wish to install HDF5. If you do this, you should run h5redeploy in NEW_DIR/bin directory. This utility will fix h5cc, h5fc and h5c++ scripts to reflect 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 publically available is: The library: ./src/.libs/libhdf5.a The public header files: ./src/H5*public.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) 5.7 Building and testing with Intel compilers When Intel compilers are used (icc or ecc), you will need to modify the generated "libtool" program after configuration is finished. On or around line 104 of the libtool file, there are lines which look like: # How to pass a linker flag through the compiler. wl="" Change these lines to this: # How to pass a linker flag through the compiler. wl="-Wl," UPDATE: This is now done automatically by the configure script. However, if you still experience a problem, you may want to check this line in the libtool file and make sure that it has the correct value. * To build the Fortran library using Intel compiler on Linux 2.4, one has to x Use -fpp -DDEC$=DEC_ -DMS$=MS_ compiler flags to disable DEC and MS compiler directives in source files in fortran/src, fortran/test and fortran/examples directories. e.g., setenv F9X 'ifc -fpp -DDEC$=DEC_ -DMS$=MS_' (do not use double quotes since $ is interpreted in them.) x If Version 6.0 of Fortran compiler is used, build fails in the fortran/test directory and then in the fortran/examples directory; to proceed, edit the work.pcl files in those directories to contain two lines work.pc ../src/work.pc x Do the same in fortran/examples directory x Problem with work.pc files was resolved for newest version of the compiler (7.0) * To build the Fortran Library on IA32 follow step described above, except that DEC and MS compiler directives should be removed manually or use a patch from HDF FTP server ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/ 5.8 Building and testing with PGI compilers When PGI C and C++ compilers are used (pgcc or pgCC), you will need to modify the generated "libtool" program after configuration is finished. On or around line 104 of the libtool file, there are lines which look like: # How to pass a linker flag through the compiler. wl="" Change these lines to this: # How to pass a linker flag through the compiler. wl="-Wl," UPDATE: This is now done automatically by the configure script. However, if you still experience a problem, you may want to check this line in the libtool file and make sure that it has the correct value. To build HDF5 C++ Library with pgCC (version 4.0 and later), set environment variable CXX to "pgCC -tlocal" setenv CXX "pgCC -tlocal" before running the configure script. 6. Using the Library Please see the User Manual in the doc/html directory. Most programs will include and link with -lhdf5. Additional libraries may also be necessary depending on whether support for compression, etc. was compiled into the hdf5 library. A summary of the hdf5 installation can be found in the libhdf5.settings file in the same directory as the static and/or shared hdf5 libraries. 7. Support Support is described in the README file.