AMBER Archive (2004)

Subject: RE: AMBER:

From: Ross Walker (
Date: Thu Sep 23 2004 - 12:36:45 CDT

Dear Jiten,
It is hard to tell what is going on from the error message you are seeing.
It is certainly not an error from Amber, it is being printed from your
system. Probably something to do with the way your cluster is configured -
are you using a batch queuing system? I would contact whoever maintains your
What is probably happening is all of the mpi threads are running on the same
machine - run 'top' and see if you see 4 copies of sander running. This will
tell you if you are running multi-cpu. You should be, just maybe not on the
machines you expect.
All the best
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |


From: [] On Behalf Of
Sent: 23 September 2004 01:45
Subject: AMBER:

Hello Amber users,
I have compiled amber8 serial in PC Cluster using ifort option. Serial
compilation and test - no problem. Test runs are all passed.
Again for parallel compilation, completed successfully. But when I run the
test.sander and test.sander.LES - all were passed. But I see one massge on
the screen
cd cytosine; ./Run.cytosine
This account is currently not available.
This account is currently not available.
diffing with cytosine.out
cd nonper; ./Run.nonper
This account is currently not available.
This account is currently not available.
diffing with mdout.nonper
I use two processor : setenv DO_PARALLEL 'mpirun -np 2'

If I use four processors, then I see four of the following massege, test run
This account is currently not available.

Can anybody tell me if I am using parallel processors.
N. Jiten Singh
C/O Prof. Kwang S. Kim
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : and
Home Page :

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