[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,
use"
"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,
use"
"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/
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
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...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100526/1763f87e/attachment-0002.htm>
More information about the phenixbb
mailing list