Need to remove timeouts and the "launch timed out and was terminated" message

You cannot turn them off. If your card runs a display manager, it will have a 5 second watchdog timer on any kernel. The only work-arounds are to use a dedicated card for computation or not use a display manager at all (both are possible under linux), or break the work up into small, short running kernels and run them many times. It seems that the second strategy should be possible, just provide a subset of the search space to each kernel and run lots of kernel executions. You can keep the accumulating results in GPU memory and periodically copy them back and write them to disk. Depending on what card you are using, you can even overlap the copying and kernel execution so that the copying and disk IO is effectively free.