Re: NAMD 2.8 job submission script for queenbee: ManyJobs

From: Thomas Bishop (
Date: Tue Jul 26 2011 - 08:46:29 CDT

here's what I use on queenbee.

the attached "quenamd_qb.tcsh"
takes four command line arguments
representing the system, the basename for the inputs and the outputs,
and the number of nodes to use.
Of course you'll have to use your own allocation :-)

(e.g. quenamd-qb.tcsh 1kx5-AA dyn3 dyn4 8 would submit a simulation
that takes files prefixed with dyn3 as input and
creates ones prefixed with dyn4 as output using a system I already built
up. The parm/top, pdb/psf are transferred from a remote server
to /work/bishop/1kx5-AA. The job uses 8x8 cores)

quenamd-qb.tcsh calls runnamd_qb.tcsh which in addition to firing up namd
gets the inputs from a remote filesystem (petashare in this case) and
puts the outputs back onto the remote filesystem.
(these are the pget and pput commands you can substitute with any remote
transfer supported by you fileserver)

Organizing my simulations this way has enabled me to get 1000's of
simulations done relatively easily
and by rolling petashare directly into my jobs I can easily move my
simulations from one computer to any other. If queenbee is busy I simply
go elsewhere.

We've developed some python tools to coordinate the workflow.
They aren't necessarily pretty but they work on LONI, local machines and
many teragrid machines... you just have to develop the
equivalents of quenamd and runnamd scripts for your machine of interest.
With ManyJobs we leave the command line arguments undefined until the
job starts
to run. Since the system, inputs and outputs are defined only at run
time we've created a so-called Pilot-Job. ManyJobs is gsi-ssh enabled.



On 07/25/2011 06:29 PM, cnu gromacs wrote:
> Hi
> Does any body has NAMD 2.8 job submission script for

    Thomas C. Bishop
     Tel: 318-257-5209
     Fax: 318-257-3823

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