Tom --
It turns out that each of the omit region's jobs submits another job, but that latter job is only the "test run_command" job. Why test the run_command if no subsequent jobs are submitted?
Our solution, thanks to an extremely savvy cluster manager, was to install the qsub (Torque?) package on each of the computing nodes (117). Also we ran the top-level process on the head (scheduler) node, so as not to tie up a computing node while it waits for its sibling jobs (the omit regions) to finish the calculation. Overall wall-time with a separate node allocated for each omit region was about 50 minutes. Interestingly, although each node has 8 processors, the OMIT region jobs seems to only use one processor! Interestingly when phenix.refine jobs are run on my Macbook Pro, the operating system is savvy enough to spread it over 2 processors.
-Mark
______________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
University of Michigan
Biophysics, 3040 Chemistry Building
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.