hdf5/INSTALL

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This file contains instructions for the installation of HDF5 on
Unix-like systems. First, one must obtain a tarball of the HDF5
release from the ftp://hdf.ncsa.uiuc.edu/pub/dist/HDF5 repository.
The files are available in uncompressed tar, gzip, bzip2, and compress
formats.
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For those that like to live dangerously and don't like to read ;-) you
can do the following:
$ tar xf hdf5-1.0.0a.tar
$ cd hdf5-1.0.0a
$ make test
$ make install # Optional
Note:
For the users of the Intel TFLOPS machine, a special sequence of steps
for the install may be found in the file: INSTALL.ascired.
=======
Step 0: Install optional third-party packages.
* GNU zlib compression library, version 1.0.2 or later is used for
[svn-r435] ./INSTALL ./INSTALL_MAINT ./README ./RELEASE Partially updated for second alpha, but haven't updated version numbers yet. ./src/H5.c ./src/H5A.c ./src/H5AC.c ./src/H5B.c ./src/H5D.c ./src/H5F.c ./src/H5Fcore.c ./src/H5Ffamily.c ./src/H5Fistore.c ./src/H5Fmpio.c ./src/H5Fsec2.c ./src/H5Fsplit.c ./src/H5Fstdio.c ./src/H5G.c ./src/H5Gnode.c ./src/H5HG.c ./src/H5HL.c ./src/H5I.c ./src/H5MM.c ./src/H5MMprivate.h ./src/H5O.c ./src/H5Oattr.c ./src/H5Ocomp.c ./src/H5Ocont.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Olayout.c ./src/H5Oname.c ./src/H5Osdspace.c ./src/H5Oshared.c ./src/H5Ostab.c ./src/H5P.c ./src/H5S.c ./src/H5T.c ./src/H5Tconv.c ./src/H5detect.c ./test/hyperslab.c ./test/istore.c Changed memory allocation functions so they fail instead of dumping core. The `x' was removed from the name to remind us of that: H5MM_xmalloc() -> H5MM_malloc(), etc. H5MM_calloc() takes one argument like H5MM_malloc() instead of two like calloc() because we almost always called it with `1' for one of the arguments anyway. The only difference between the two functions is that H5MM_calloc() returns memory which is initialized to zero. ./src/H5Gent.c ./src/H5Gprivate.h Removed H5G_ent_calloc() since it wasn't used. ./src/H5Fistore.c Fixed a bug found by Albert. Thanks, Albert! This fix combined with the changes to memory allocation prevent the library from failing an assertion if the application uses an unreasonable size for chunks (like Alberts 10000x10000x4). ./src/H5MF.c ./src/H5MFprivate.h Changed H5MF_free() to H5MF_xfree() since calling it with an undefined address is allowed.
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the `deflate' compression method. If libz.a cannot be found then
this form of compression is not compiled into the library.
Step 1. Unpack the source tree.
* The tarball will unpack into an hdf5-1.0.0a directory with one of
the following commands:
$ tar xf hdf5-1.0.0a.tar OR
[svn-r435] ./INSTALL ./INSTALL_MAINT ./README ./RELEASE Partially updated for second alpha, but haven't updated version numbers yet. ./src/H5.c ./src/H5A.c ./src/H5AC.c ./src/H5B.c ./src/H5D.c ./src/H5F.c ./src/H5Fcore.c ./src/H5Ffamily.c ./src/H5Fistore.c ./src/H5Fmpio.c ./src/H5Fsec2.c ./src/H5Fsplit.c ./src/H5Fstdio.c ./src/H5G.c ./src/H5Gnode.c ./src/H5HG.c ./src/H5HL.c ./src/H5I.c ./src/H5MM.c ./src/H5MMprivate.h ./src/H5O.c ./src/H5Oattr.c ./src/H5Ocomp.c ./src/H5Ocont.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Olayout.c ./src/H5Oname.c ./src/H5Osdspace.c ./src/H5Oshared.c ./src/H5Ostab.c ./src/H5P.c ./src/H5S.c ./src/H5T.c ./src/H5Tconv.c ./src/H5detect.c ./test/hyperslab.c ./test/istore.c Changed memory allocation functions so they fail instead of dumping core. The `x' was removed from the name to remind us of that: H5MM_xmalloc() -> H5MM_malloc(), etc. H5MM_calloc() takes one argument like H5MM_malloc() instead of two like calloc() because we almost always called it with `1' for one of the arguments anyway. The only difference between the two functions is that H5MM_calloc() returns memory which is initialized to zero. ./src/H5Gent.c ./src/H5Gprivate.h Removed H5G_ent_calloc() since it wasn't used. ./src/H5Fistore.c Fixed a bug found by Albert. Thanks, Albert! This fix combined with the changes to memory allocation prevent the library from failing an assertion if the application uses an unreasonable size for chunks (like Alberts 10000x10000x4). ./src/H5MF.c ./src/H5MFprivate.h Changed H5MF_free() to H5MF_xfree() since calling it with an undefined address is allowed.
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$ gunzip <hdf5-1.0.0a.tar.gz |tar xf - OR
$ bunzip2 <hdf5-1.0.0a.tar.bz2 |tar xf - OR
[svn-r435] ./INSTALL ./INSTALL_MAINT ./README ./RELEASE Partially updated for second alpha, but haven't updated version numbers yet. ./src/H5.c ./src/H5A.c ./src/H5AC.c ./src/H5B.c ./src/H5D.c ./src/H5F.c ./src/H5Fcore.c ./src/H5Ffamily.c ./src/H5Fistore.c ./src/H5Fmpio.c ./src/H5Fsec2.c ./src/H5Fsplit.c ./src/H5Fstdio.c ./src/H5G.c ./src/H5Gnode.c ./src/H5HG.c ./src/H5HL.c ./src/H5I.c ./src/H5MM.c ./src/H5MMprivate.h ./src/H5O.c ./src/H5Oattr.c ./src/H5Ocomp.c ./src/H5Ocont.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Olayout.c ./src/H5Oname.c ./src/H5Osdspace.c ./src/H5Oshared.c ./src/H5Ostab.c ./src/H5P.c ./src/H5S.c ./src/H5T.c ./src/H5Tconv.c ./src/H5detect.c ./test/hyperslab.c ./test/istore.c Changed memory allocation functions so they fail instead of dumping core. The `x' was removed from the name to remind us of that: H5MM_xmalloc() -> H5MM_malloc(), etc. H5MM_calloc() takes one argument like H5MM_malloc() instead of two like calloc() because we almost always called it with `1' for one of the arguments anyway. The only difference between the two functions is that H5MM_calloc() returns memory which is initialized to zero. ./src/H5Gent.c ./src/H5Gprivate.h Removed H5G_ent_calloc() since it wasn't used. ./src/H5Fistore.c Fixed a bug found by Albert. Thanks, Albert! This fix combined with the changes to memory allocation prevent the library from failing an assertion if the application uses an unreasonable size for chunks (like Alberts 10000x10000x4). ./src/H5MF.c ./src/H5MFprivate.h Changed H5MF_free() to H5MF_xfree() since calling it with an undefined address is allowed.
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$ uncompress -c <hdf5-1.0.0a.tar.Z |tar xf -
Step 2. Configure.
* HDF5 uses the GNU autoconf program for configuration. Most
installations can be configured by typing just (from the
hdf5-1.0.0a directory)
$ sh configure
* The configuration process can be controlled through environment
variables, command-line switches, and host configuration files.
For a complete list of switches say `sh configure --help'.
* 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. Not all hosts require a host configuration file.
* The C compiler and flags, the `ar' and `ranlib' program names,
and the `make' program can be specified with environment
variables if configure doesn't properly detect them and they are
not defined in a host config file.
CC Name of the C compiler.
CFLAGS Switches for the C compiler.
CPPFLAGS Additional switches for the .c -> .o step.
AR Name of the `ar' program.
RANLIB Name of the `ranlib' program or `:' if none.
MAKE Name of the `make' program (GNU make is preferred)
* This version of HDF5 is normally built with various debugging
code enabled. To turn it off add the `--disable-debug' switch
to the configure command. Even if debugging support is compiled
into the library one must still enable the code at runtime with
the HDF5_DEBUG environment variable (see Debugging.html).
* This version of HDF5 is normally built with support for symbolic
debugging with dbx or gdb and without compiler optimization
switches. To disable symbolic debugging and enable
optimizations add `--enable-production' to the configure
command.
* This version of HDF5 is normally built with the ability to print
the names, arguments, and return values of all API functions
when they're called. For more information refer to the
Debugging.html file. To disable tracing support add
`--disable-trace' to the configure command.
* Old versions of gcc (<2.8.0) may experience register allocation
problems on some architectures. If this happens then the
`--disable-hsizet' can be given but the resulting library will
be unable to handle datasets larger than 4GB.
* By default libraries, include files, programs, and documentation
are installed (when one says `make install') under
/usr/local/lib, /usr/local/include, /usr/local/bin, and
/usr/local/man. However, if you want them in some other
location you can specify a prefix to use instead of /usr/local.
For instance, to install in /usr/lib, /usr/include, /usr/bin,
and /usr/man one would say
$ ./configure --prefix=/usr
The library can be used directly from the source tree without
installing it.
Step 3. Compile library, tests, and programs.
* Build library targets by saying
$ make
Note: If you supplied some other make command through the MAKE
environment variable in the previous step then use that command
instead. The same applies below.
Note: 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.
Step 4. Run confidence tests.
* All confidence tests should be run by saying
$ make test
[svn-r435] ./INSTALL ./INSTALL_MAINT ./README ./RELEASE Partially updated for second alpha, but haven't updated version numbers yet. ./src/H5.c ./src/H5A.c ./src/H5AC.c ./src/H5B.c ./src/H5D.c ./src/H5F.c ./src/H5Fcore.c ./src/H5Ffamily.c ./src/H5Fistore.c ./src/H5Fmpio.c ./src/H5Fsec2.c ./src/H5Fsplit.c ./src/H5Fstdio.c ./src/H5G.c ./src/H5Gnode.c ./src/H5HG.c ./src/H5HL.c ./src/H5I.c ./src/H5MM.c ./src/H5MMprivate.h ./src/H5O.c ./src/H5Oattr.c ./src/H5Ocomp.c ./src/H5Ocont.c ./src/H5Odtype.c ./src/H5Oefl.c ./src/H5Olayout.c ./src/H5Oname.c ./src/H5Osdspace.c ./src/H5Oshared.c ./src/H5Ostab.c ./src/H5P.c ./src/H5S.c ./src/H5T.c ./src/H5Tconv.c ./src/H5detect.c ./test/hyperslab.c ./test/istore.c Changed memory allocation functions so they fail instead of dumping core. The `x' was removed from the name to remind us of that: H5MM_xmalloc() -> H5MM_malloc(), etc. H5MM_calloc() takes one argument like H5MM_malloc() instead of two like calloc() because we almost always called it with `1' for one of the arguments anyway. The only difference between the two functions is that H5MM_calloc() returns memory which is initialized to zero. ./src/H5Gent.c ./src/H5Gprivate.h Removed H5G_ent_calloc() since it wasn't used. ./src/H5Fistore.c Fixed a bug found by Albert. Thanks, Albert! This fix combined with the changes to memory allocation prevent the library from failing an assertion if the application uses an unreasonable size for chunks (like Alberts 10000x10000x4). ./src/H5MF.c ./src/H5MFprivate.h Changed H5MF_free() to H5MF_xfree() since calling it with an undefined address is allowed.
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The command will fail if any test fails, and one will see the
word "*FAIL*" in the output.
Note: some old versions of make will report that `test is up to
date'. If this happens then run `make _test' instead or run
`make test' from within the test directory.
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.
Step 5. Install public files.
* Install the library, header files, and programs by saying:
$ make install
This step will fail unless you have permission to write to the
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installation directories. Of course, you can use the header
files, library, and programs directly out of the source tree if
you like, skipping this step. The directory specified for the
--prefix switch (or "/usr/local") must exist, but the directories
under it are created automatically by make.
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Step 6. Subscribe to mailing lists.
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* Subscribe to the mailing lists described in the README file.