I am using gpt on a linux server (Ubuntu 14.04/64bit with SNAP 2.0 Beta 05). When running with a multi-step graph, gpt needs to write (intermediate?) target.dim and target.data to the installation directory (/usr/local/snap in my case) which is normally read only for the user running gpt (I install as sudo).
I checked all configuration files on /usr/local/snap/config but none seem to allow me to change this behavior. For now, I have made /usr/local/snap writable.
PS. Since the server does not run a graphics environment, I have to add the following to /usr/local/snap/bin/gpt.vmoptions
otherwise, the JAI classes will not work (this is a very old JAI issue).