AMBER Archive (2007)

Subject: AMBER: REMD error

From: Jason K (jmk9jmk_at_gmail.com)
Date: Mon May 21 2007 - 10:20:12 CDT

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

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