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We have a Ubuntu server (mainly a compute server), which does not have X-server installed on it.

One can use something like Byobu or Screen to have programs running on the server even after the SSH connection is closed. However when one runs GUI based applications (using ssh -X), the application gets killed when the SSH connection is closed. Is there a work around this where the GUI based application (like say eclipse) keeps running even when the SSH connection is closed.

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Try xpra.

This is similar to ssh -X, except it is faster and you can disconnect and re-connect to the session as many times as you like.

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