[phenixbb] Autobuild submitted jobs

[Tom Terwilliger]

Hi Mark,
I'm glad you got this job running on your big cluster!  In answer to  
your question, Autobuild tries the test run_command even if it doesn't  
need it, that's all.
All the best,
Tom T

On May 26, 2010, at 8:16 PM, Mark A Saper wrote:

> 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.
>
> saper at umich.edu     phone (734) 764-3353     fax (734) 764-3323
> http://www.biochem.med.umich.edu/?q=saper	http://www.strucbio.umich.edu/
>
>
>
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
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