From: Jason K <>
Date: Mon, 21 May 2007 16:20:12 +0100


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.


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Received on Wed May 23 2007 - 06:07:26 PDT
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