Great to see how to run GNU Parallel on a PBS-cluster. @15:00 $PBS_NODEFILE repeats the hostname for each core reserved. GNU Parallel, however, ignores this the repeats. It detects the number of cores on the host . @20:50 There is no need to quote spaces. You only need to quote special shell characters (such as '>'). @22:45 Also try: '--workdir $PBS_O_WORKDIR'. This will make GNU Parallel 'cd' to '$PBS_O_WORKDIR' before running the command.