I have been working on a Java project from my local machine using Eclipse. I am trying to run this on a remote machine. The remote machine is a cluster running on Linux. Rig
Target management/Remote System Explorer provides plugins to keep a remote directory in sync with your project. See http://www.eclipse.org/tm/
To run your program remotely, you would probably have to set up an External Tool launch config (from the Run>External Tools menu) and use a program like ssh to launch your java app remotely on the linux cluster.