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Installing HDF-EOS5 using Autoconf/Automake
-------------------------------------------
Prerequisite
------------
The HDF-EOS5 library requires HDF5 library version 1.8.19 or later. You can download HDF5
from the HDF Group:
https://www.hdfgroup.org/downloads/hdf5/
or, depending upon your system, you may be able to install it from a package. The HDF5
libary may depend upon other libraries, such as szip, z (compress). The HDF-EOS5
configure script will do its best to determine these dependencies and find the appropriate
libraries, but it may occasionally need help. Please refer to the troubleshooting section
at the bottom of this document.
Configuring
-----------
After downloading and unpacking the tar file, 'cd' into the hdfeos5 directory and type
./configure
This will run a series of tests to determine the necessary library dependencies, and
configure the makefiles accordingly. The configure script will output a summary of the
configuration options at completion. These can be useful for troubleshooting.
By default, the HDF-EOS5 libraries and include headers will be installed in /usr/local. This
can be changed by using the --prefix option when running configure, e.g.
./configure --prefix=/custom/install/location
A number of other options may be provided to the configure script. You can get details
of these options using the command:
./configure --help
Building
--------
Once configured, you can build HDF-EOS5 by simply type
make
from the hdfeos5 directory.
Tests
-----
The HDF-EOS5 library comes with some tests. You can run these using the command
make check
from the hdfeos5 directory. These test may provide useful examples, but USE AT YOUR
OWN RISK.
Installing
--------
To install HDF-EOS5, simply type
make install
from the hdfeos5 directory. You need to make sure you have the necessary permissions to
install the files in the chosen location.
Troubleshooting
---------------
General
-------
This section contains general troubleshooting tips. Additional sections below detail
known issues for specific platforms.
* Determining HDF5 Dependencies
It can be difficult to find out what additional libraries HDF5 depends upon. This is usually
just libz, but may also include libsz. You can get an idea of the dependencies
by using the h5cc tool (you may have to search for this):
h5cc -show
This will produce output similar to the following:
gcc -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE -O0 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4
-grecord-gcc-switches -m64 -mtune=generic -L/usr/lib64 /usr/lib64/libhdf5_hl.a
/usr/lib64/libhdf5.a -Wl,-z,relro -lsz -lz -ldl -lm -Wl,-rpath -Wl,/usr/lib64
It lists the libraries that HDF5 (and hence HDF-EOS5) programs will need to link against.
In this case we can see both -lsz (libsz) and -lz (libz).
* Finding libraries
Most of the libraries need by HDF5 and HDF-EOS5 should be found automatically by
the configure script, but if it cannot find them, you will need to provide that
information to the configure script explicitly. If you need to find a library on
your system, you can do this with a simple command: e.g. To find the sz library:
find / -name 'libsz.*'
This might produce output as follows:
/usr/lib64/libsz.so
/usr/lib64/libsz.so.2
/usr/lib64/libsz.so.2.0.1
In this case, we have a dynamic (shared) sz library in /usr/lib64 We can tell configure
where to find it as follows:
./configure --with-szlib=/usr/lib64
If you cannot find a particular library, you will need to install the appropriate
package.
* Installing missing packages
Linux distributions generally use a package manager to install software packages, though
the specific tool varies depending upon the distribution. For example, Centos may use
'yum' while Ubuntu may use 'apt'.
Max OSX systems, while 'Linux like', does not have an official package management tool like
the Linux systems. However, there are independently developed tools such as
MacPorts (https://www.macports.org/) and HomeBrew (https://brew.sh/) which are just
as capable, and can provide everything you need.
Packages often come in two different 'flavors' - regular, and 'devel'. The regular versions
contain the libraries needed to run programs that use them. The 'devel' packages are
developer oriented packages that include headers files needed to compile your own
programs using that use the libraries. The following is a list of the key packages
needed by HDF-EOS5:
hdf5 The main HDF5 package. A 'devel' version is needed since HDF-EOS5 compiles
against this library and needs the header files.
zlib Compression library. A regular version can be used since HDF-EOS5 does not
explicity invoke compression functions.
aec Adaptive Entropy Encoding library (szip). This may or may not be needed,
depending upon how HDF5 was built. If you have access to the h5cc commmand,
you can use 'h5cc -show' to determine whether or not it is needed. If
the output contains '-lsz', then you need aec. Most package versions of
HDF5 do not use aec. If required, a regular version can be used.
Examples of command to install packages on some of the common linux distributions are
given below.
Linux (Ubuntu/Debian)
---------------------
* Finding/Installing packages
These distributions tend to use 'apt' as the package manager. You can search for packages
using apt as follows:
apt-cache search hdf
A package can be installed as follows:
apt-get install libhdf4-dev
One of the advantages of package managers is that if you install a package in this way, it
will also install all the dependencies required by the package. You can see which additional
packages a given package depends on as follows:
apt-cache depends libhdf4-dev
This is also a good way to determine whether or not aec is required.
Linux (Redhat/Centos)
---------------------
* Finding/Installing packages
These distributions tend to use 'yum' as the package manager. You can search for packages
using yum as follows:
yum search hdf5
A package can be installed as follows:
yum install hdf5-devel
One of the advantages of package managers is that if you install a package in this way, it
will also install all the dependencies required by the package. You can see which additional
packages a given package depends on as follows:
yum deplist hdf5-devel
This is also a good way to determine whether or not aec is required.
Mac OSX
-------
* Finding/Installing packages using MacPorts
You can search for packages using MacPorts as follows:
port search --name "*hdf5*"
A package can be installed as follows (you may need to run this using sudo):
port install hdf5
As with Linux base package managers, MacPorts will also install all the depenencies required
by a package. You can see which additional packages a given package depends on as follows:
port info hdf5
Look for a line beginning 'Library Dependencies'. You can ignore any line beginning with
'Build Dependencies' since you will not be building HDF5.
* Missing library 'System'.
If your build fails with a message indicating it cannot find a library called 'System',
try adding the following configure option:
./configure LDFLAGS=-L/usr/local
This gives the location of the library to the linker.
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