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************************************************************************
HDF5 Build and Install Instructions for Cygwin
************************************************************************
This document is an instruction on how to build, test and install HDF5 library on
Cygwin. See detailed information in hdf5/INSTALL.
NOTE: hdf5 can be built with CMake, see the INSTALL_CMake.txt file for more guidance.
Preconditions:
--------------
1. Installed Cygwin 1.7.25 or higher
To install the Cygwin net release, go to http://www.cygwin.com and
click on "setup-x86.exe" (32-bit installation) under the heading
"Current Cygwin DLL version". This will download a GUI
installer called setup-x86.exe which can be run to download a complete
Cygwin installation via the internet. Then follow the instructions
on each screen to install Cygwin.
Cygwin uses packages to manage installing various software. Users can
choose to install or uninstall certain packages by running setup.exe.
http://www.cygwin.com/packages/ provides detailed information about
Cygwin packages.
Most required dependencies can be satisfied by installing all packages in
the "Devel" category. However, please verify that you have installed all
packages listed below.
2. Compilers, Libraries and Utilities Installed
2.1 Compilers Supported
The following compilers are supported by HDF5 and included in the Cygwin
package system:
gcc (4.7.3 and 4.9.2), which includes:
gcc4-core : C compiler
gcc4-g++ : C++ compiler
gcc4-fortran : fortran compiler
2.1.1 Using Compilers Not Supported
By default the current configuration uses vendor compilers; to use
another compiler run the following commands before running
configure:
setenv CC "foo -flags"
setenv FC "fffoo -flags"
For example, if users want to use pgf90 as fortran compiler, then
setenv FC pgf90
See the configure help page (configure --help) for a list of
environment variables that have an affect on building the
library.
2.2 HDF5 External Library Dependencies
2.2.1 Zlib
zlib-1.2.5 or later is supported and tested on Cygwin.
2.2.2 Szip
The HDF5 library has a predefined compression filter that uses
the extended-Rice lossless compression algorithm for chunked
datasets. For more information on Szip compression, license terms,
and obtaining the Szip source code, see:
https://portal.hdfgroup.org/display/HDF5/Szip+Compression+in+HDF+Products
2.3 Additional Utilities
The following standard utilities are also required to build and test HDF5:
bison : yacc implementation
flex : flex utility
make : make utility
2.4 Alternate Build Process
Download the CMake package and follow the notes in the "INSTALL_CMake.txt"
file to build HDF5 with the CMake utilities.
Build, Test and Install HDF5 on Cygwin
--------------------------------------
1. Get HDF5 source code package
Users can download HDF5 source code package from HDF website
(http://hdfgroup.org).
2. 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 `hdf5-1.13.x' directory.
2.1 Non-compressed tar archive (*.tar)
$ tar xf hdf5-1.13.x.tar
2.2 Gzip'd tar archive (*.tar.gz)
$ gunzip < hdf5-1.13.x.tar.gz | tar xf -
2.3 Bzip'd tar archive (*.tar.bz2)
$ bunzip2 < hdf5-1.13.x.tar.bz2 | tar xf -
2. Setup Environment
In Cygwin, most compilers and setting are automatically detected during
the configure script. However, if you are building Fortran we recommend
that you explicitly set the "FC" variable in your environment to use the
gfortran compiler. For example, issue the command:
$ export FC=gfortran
4. Configuring
Notes: See detailed information in hdf5/release_docs/INSTALL,
part 5. Full installation instructions for source
distributions
The host configuration file for cygwin i686-pc-cygwin is located
in the `config' directory and are based on architecture name,
vendor name, and 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.
In short,
To configure HDF5 C Library, using
$ ./configure
To configure HDF5 C/C++ Library, using
$ ./configure --enable-cxx
To configure HDF5 C/Fortran Library, using
$ ./configure --enable-fortran
To configure HDF5 C with Szip library, using
$ ./configure --with-szlib="path to szlib"
For example, if szip library was installed in the directory
/cygdrive/c/szip, which is parent directory of "include" and
"lib", then the following command will configure HDF5 C library
with szip enabled:
$ ./configure --with-szlib=/cygdrive/c/szip
To configure HDF5 C without Zlib,
To disable zlib, using
$ ./configure --without-zlib
Two ways to configure HDF5 C with specified Zlib
Using
$ ./configure --with-zlib=INCDIR,LIBDIR
For example, if the zlib library is installed in
/cygdrive/c/usr, which is the parent directory of directories
"include" and "lib",
$ ./configure --with-zlib=/cygdrive/c/usr/include,/cygdrive/c/usr/lib
Through the CPPFLAGS and LDFLAGS Variables
For example, if zlib was installed in the directory
/cygdrive/c/usr then using the following command to configure
HDF5 with zib
$ CPPFLAGS=-I/cygdrive/c/usr/include \
$ LDFLAGS=-L/cygdrive/c/usr/lib \
$ ./configure
To specify the installation directories, using
$ ./configure --prefix="path for installation"
By default, HDF5 library, header files, examples, and
support programs will be installed 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 as in the above
command.
Combination of Switches
All of the above switches can be combined together. For
example, if users want to configure HDF5 C/C++/Fortran
library with szip library enabled, with zlib library at
/cygdrive/c/usr/, and install HDF5 into directory
/cygdrive/c/hdf5 using gcc/g++ as C/C++ compiler and gfortran
as fortran compiler
$ ./configure
--with-szlib=/cygdrive/c/szip
--with-zlib=/cygdrive/c/usr/include,/cygdrive/c/usr/lib
--prefix=/cygdrive/c/hdf5
--enable-cxx
--enable-fortran
<"If no more switches, then hit Enter">
Notes: The command format above is for readilibity. In practice,
please type in the command above with at least one
space between each line, No "Enter" until users finish
the switches and want to run the configure.
or do it through CPPFLAGS and LDFLAGS variables:
$ CPPFLAGS=-I/cygdrive/c/usr/include \
$ LDFLAGS=-L/cygdrive/c/usr/lib \
$ ./configure
--with-szlib=/cygdrive/c/szip
--prefix=/cygdrive/c/hdf5
--enable-cxx
--enable-fortran
<"If no more switches, then hit Enter">
5. Make and Make Check
After configuration is done successfully, run the following series of
commands to build, test and install HDF5
$ make > "output file name"
$ make check > "output file name"
Before run "make install", check output file for "make check", there
should be no failures at all.
6. Make Install
$ make install > "output file name"
7. Check installed HDF5 library
After step 6, go to your installation directory, there should be
three subdirectories: "bin" "include" and "lib".
8. Known Problems
dt_arith tests may fail due to the use of fork. This is a known issue
with cygwin on Windows.
"make check" fails when building shared lib files is enabled. The default
on Cygwin has been changed to disable shared. It can be enabled with
the --enable-shared configure option but is likely to fail "make check"
with GCC compilers.
-----------------------------------------------------------------------
HDF Forum: https://forum.hdfgroup.org/
HDF Helpdesk: https://portal.hdfgroup.org/display/support/The+HDF+Help+Desk
|
