[phenixbb] Autobuild submitted jobs
terwilliger at lanl.gov
Thu May 27 08:51:03 PDT 2010
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,
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 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/
> phenixbb mailing list
> phenixbb at phenix-online.org
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
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb