Re: AMBER: REMD error

From: Carlos Simmerling <>
Date: Thu, 24 May 2007 13:23:02 -0400


the test ran fine for me but I do have a few comments:

1) make sure that ntwx is set to less than nstlim or you won't get
trajectory output.
The same goes for things like nscm. This is the same as what you would
need to do for a sander run. We will make this more flexible in Amber10.

2) make sure to specify a trajectory file name in the groupfile. Yours does
not, which makes
  all replicas default to mdcrd (the same file).

3) it seems to run ok, I get this output:
  Running multisander version of sander amber9
     Total processors = 8
     Number of groups = 2

and the remlog shows the exchanges are working fine.

The number of processors is passed to sander from MPI, I am not sure
why it is giving you 1 when it works ok for me and sander gets a value of 8.
Your script seems ok but you might try to simplify it a little or check the
machinefile that you generated to make sure it has 8 entries.


On 5/21/07, Jason K <> 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:
Stony Brook, NY 11794-5115          Web:
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Received on Sun May 27 2007 - 06:07:27 PDT
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