You need the C/C version of Eclipse and a JRE Runtime Environment (if not already installed).
http://www.eclipse.org/downloads/packages/eclipse-ide-cc-developers/junosr1

Create a new C Makefile-Project in Eclipse. This is the right choice because you want to use the
existing LPJmL Makefiles.
http://help.eclipse.org/indigo/index.jsp?topic=%2Forg.eclipse.cdt.doc.user%2Fgetting\_started%2Fcdt\_w\_newproj.htm

If Eclipse now does not compile the LPJmL code without errors, it might lack some compiler settings or the path to your
libraries, e.g. /usr/bin on Linux systems.

Check out the screenshots below to see a working configuration.

Note that some variables are set in the Project Properties (right-click on project name, select Properties), whereas others are set in the Preferences Dialog (Menu entry Window > Preferences).
Some more explanations about the very complex preferences dialog are given here:
http://help.eclipse.org/juno/index.jsp?topic=%2Forg.eclipse.platform.doc.user%2FwhatsNew%2Fplatform\_whatsnew.html

Hint: Eclipse tooltips Tooltips in Eclipse (pop-up window in editor) running on OS Ubuntu 11 and later appear with black font on black background. This cannot be changed within Eclipse, because it is a system-specific setting. Yet, it's easily tackled by installing 'GNOME Color Chooser' through the Software Center. Within that GNOME Color Chooser GUI go to -> Specific -> Tooltips and tick Foreground -> 'black' and Background -> e.g. 'pale yellow', -> apply.