[NetCDF][] (Network Common Data Form) is an open standard for
self-describing, machine-independent data formats for array-oriented
scientific data.  The standard and a good deal of associated software
are developed by the [Unidata][] program at the [University
Corporation for Atmospheric Research][UCAR] (UCAR).

I needed one of their libraries ([ucar.ma2][]) to build [[HDFView]]
from source.  Because I have very little [[Java]] experience, figuring
out how to do this took the better part of today.  Here are my notes,
so things will be faster the next time around…

Note that the `hdf-java` source (containing the HDFView source) comes
with a few precompiled JARs, including `netcdf.jar`.  However, Gentoo
[wants to compile everything from source][why-source]), so we remove
those JARs before compiling `hdf-java`, forcing a reliance on versions
that have already been installed from source using [Portage][].

Java develoment kit
-------------------

You'll need both a Java development kit (JDK, think "compiler") and
runtime environment (JRE, think "bytecode interpreter").  Install the
default implementations with

    # emerge virtual/jdk

The [Gentoo Java team][team] publishes a [Java guide][guide] with more
details if you're interested.

Maven
-----

You'll also need [Maven][], [Apache]'s Java pacakge manager.

    # emerge dev-java/maven-bin

There's a from-source [dev-java/maven] in [java-overlay][], but I'll
wait until that has been merged into the main Portage tree before
checking it out.  NetCDF will probabaly not depend on any
bleeding-edge Maven features.

NetCDF
------

NetCDF is currently versioned with [[Git]] ([hosted on
GitHub][github]), so you can grab the source with

    $ git clone git://github.com/Unidata/thredds.git

Unfortunately, this repository bundles a number of related Unidata
packages besides netCDF, so the 95 megabyte cdm directory comes with
an additional 432 megabytes of additional stuff.  This means that it's
a good idea to run the clone over a fast connection, and probably
useful to use `git clone --depth 10` or similar to limit the amount of
history you clone.

Now that you've got the source, just tell Maven to install it for you.
First, you'll need to install the `common utilities:

    $ cd thredds/common
    $ mvn-2.2 install

Next, install the `cdm` module itself

    $ cd thredds
    $ mvn-2.2 install

For more details, see the [netCDF documentation][docs] and [build
instructions][build].

Compiling HDFView
-----------------

To install HDFView on Gentoo, just emerge `dev-java/hdf-java` from my
[[wtk overlay|Gentoo overlay]] with the `hdfview` `USE` flag enabled.

[NetCDF]: http://www.unidata.ucar.edu/software/netcdf/
[Unidata]: http://www.unidata.ucar.edu/about/
[UCAR]: http://www2.ucar.edu/
[ucar.ma2]: http://www.unidata.ucar.edu/software/netcdf-java/v4.0/javadoc/ucar/ma2/package-summary.html
[why-source]: http://www.gentoo.org/proj/en/java/why-build-from-source.xml
[Portage]: http://www.gentoo.org/proj/en/portage/
[team]: http://www.gentoo.org/proj/en/java/
[guide]: http://www.gentoo.org/doc/en/java.xml
[Maven]: http://maven.apache.org/
[Apache]: http://apache.org/
[dev-java/maven]: http://gpo.zugaina.org/dev-java/maven
[java-overlay]: http://overlays.gentoo.org/proj/java/wiki/Overlays
[github]: https://github.com/Unidata/thredds/
[docs]: http://www.unidata.ucar.edu/software/netcdf-java/documentation.htm
[build]: http://www.unidata.ucar.edu/software/netcdf-java/tutorial/buildFromSource.html