Add timeout configuration on atom

A build could potentially take a long time, but the ClusterRunner is made for breaking up a large task into small chunks. That being said, the expectation is that a sub job should finish within a reasonable amount of time. If it does not finish in a short period of time, nodes will not be deallocating in a timely manner, if at all, which can severely impact the cluster. For example, there have been occurrences where a single subjob has been stuck indefinitely.

I think that subjob durations should be restricted to a finite time limit.