AMBER Archive (2007)

Subject: Re: AMBER: REMD error

From: Jason K (jmk9jmk_at_gmail.com)
Date: Thu May 24 2007 - 10:31:17 CDT

Hello,
I have attached the exact input files; the oREMD2.bash is the script that is
actually submitted.
The parallel sander excecutable actually appears in the $AMBERHOME/exe /
directory as sander_mpi

Of course, I did simplify for command for clarity, if there is something
evidently wrong I would really appreciate if you could point it out.

Many thanks,

Jason

On 5/22/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
>
> 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
> ===================================================================



  • application/octet-stream attachment: groupfile


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