AMBER Archive (2007)

Subject: Re: AMBER: REMD error

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon May 21 2007 - 10:41:53 CDT

have you run regular MD with more than 1 cpu using this code?
also, have you run non-REMD multisander using this code?

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
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu