[phenixbb] Autobuild submitted jobs

Tom Terwilliger terwilliger at lanl.gov
Wed May 26 09:29:40 PDT 2010

Hi Mark,

Hmmm...I hadn't thought of that situation.  Right now you can only  
specify one type of "run_command", either specifying a submitted job  
or a subprocess, but not both in one run, I'm afraid.   In your case  
I'd suggest two options:

1. Set nproc= the smaller of ( the number of nodes on your cluster,  
the number of omit regions in your composit omit job)
2. Run a separate job for each omit region with omit_box_start and  
omit_box_end ,specify run-command="csh -f" and nproc=8:
     omit_box_start = 0
       .help = "   To only carry out omit in some of the omit boxes,  
               "omit_box_start and omit_box_end "
       .type = int
     omit_box_end = 0
       .help = "   To only carry out omit in some of the omit boxes,  
               "omit_box_start and omit_box_end "
       .type = int

I hope that helps!
All the best,
Tom T

On May 26, 2010, at 10:06 AM, Mark A Saper wrote:

> Dear Tom and colleagues,
> We're running Autobuild composite omit on a large cluster, each node  
> has 8 processors.  Autobuild submits jobs with the "run_command".   
> And it appears that each of those jobs submit other jobs. Are the  
> latter jobs necessary?  That is, are there situtations where they  
> wouldn't be submitted as separate jobs but run as subprocesses?   
> Currently nodes in our cluster don't have capability of qsubing new  
> jobs, but we are in the process of changing this.
> Thanks, 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
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