AMBER: Problems with Machine file for sander.MPI

From: Terry Lang <>
Date: Thu, 19 Apr 2007 13:15:45 -0700

Hey Everyone,

       I am trying to run a parallel job using the following command:

mpiexec -machinefile <my_path>/machines -np 4 sander.MPI -O -i
-o run_gb.out -p ptpb_gb.prm \
    -c run_gb.rst -r run_gb.rst -x run_gb.crd < /dev/null

but, when launched, the job just hangs. I am able to launch the job
successfully onto 4 processors using the command without the machine
file option. Has anyone had a similar experience?

I am running the following versions:

Amber version 9 up to bugfix 31
Intel compiler version 9.1
Debian OS on i686 Linux boxes


P. Therese Lang
Post Doc
Alber Lab, UC Berkeley
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Received on Sun Apr 22 2007 - 06:07:33 PDT
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