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I don't know if the admins would consider a "repetitive" contribution for the forum this tutorial, but I've got some troubles with eclipse and NS-3 and I would like to help others users.
We have to configure the build toolchain to use waf instead the default make. Right-click to the project and select: Properties -> C/C++ Build
In the tab Builder Settings you have uncheck all the options checked and set the Build Command field to your waf path. In my case: ${workspace_loc:/ns3test/ns-3.21}/waf
And for the build directory my path is: ${workspace_loc:/ns3test/ns-3.21}/waf
For enable the configure options in waf we should to follow the next steps: Right-click to the project and select: Make Targets -> Create ... Select a name and fill the rest of the fields, there are different combinations for these example I've used: Make Target field configure --enable-examples --enable-tests
To run your compiled project: Right-click to the project and select: Run AS -> Run Configuration... Select C/C++ Application and New launch configuration http://s13.postimg.org/3txc02ivn/8ok.jpg
Just have to select a Name In the field project click on Browse and select ns3 in that case ns3 test ns3test
And then in C/C++ Application click on Search Project and select your file, in that case I called test ns-3.21/build/scratch/test
Most probably after click run is that you get a library error like this: error while loading shared libraries: libns3.21-lr-wpan-debug.so: cannot open shared object file: No such file or directory
As Yeison Camargo sais in his thread (https://groups.google.com/forum/#!topic/ns-3-users/EMnZk1UpLQY) we have to create a symbolic link, I advise create a symbolic link for all libraries: sudo ln -s /home/alumni/workspace/ns3test/ns-3.21/build/libns3.21-* /usr/lib/