AMBER Archive (2007)

Subject: Re: AMBER: REMD error

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue May 22 2007 - 16:15:43 CDT

I'm puzzled- can you send me the actual input files? there could be some
typo etc when you
write what you think you are running- for example, is it really sander_mpi
or is
it sander.MPI ?
carlos

On 5/21/07, Jason K <jmk9jmk_at_gmail.com> wrote:
>
>
> Dear AMBER,
>
> I have been trying to run a replica exchange simulation on our
> departmental cluster (on which parallel jobs can be run on up to 12
> four-processor nodes). The command that I use is - essentially - the
> following
>
> mpirun -np 8 -machinefile {machine file} $AMBERHOME/exe/sander_mpi -ng 2
> -groupfile groupfile
>
> the groupfile being the one exemplified in the test cases (I have checked
> that it does not contain any errors)
>
> Nevertheless, when I submit the job I get error messages similar to these:
>
>
> Error: specified more groups ( 2 ) than the number of
> processors (
> 1 ) !
> p0_2936: p4_error: : 1
>
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
>
>
> Can anyone suggest what may be the cause of this behaviour? Is this a
> message generated by sander, or is it a failure with either MPI or the
> queueing system?
>
> I can attach the actual files containing the standard output / error as
> well as the input files if that can be any help.
>
> All help will be greatly appreciated.
>
> Jason
>
>
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
===================================================================

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