RE: AMBER: Problems with Machine file for sander.MPI

From: Ross Walker <>
Date: Thu, 19 Apr 2007 14:02:24 -0700

Hi Terry,

> 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?

> MPICH2-1.0.5p2
> Debian OS on i686 Linux boxes

I suspect that this may be a permission issue with your system.

Can you run any simple mpich2 test cases and/or do other mpi jobs run? If
you rsh or ssh to one of the nodes specified in the machine file can you do
so without a password? Perhaps this part of the operation is just hanging. I
assume you don't see any output from sander.MPI which imply it never even
gets started.

The reason it probably works on 4 local processors is that the mpiexec
command doesn't have to rsh/ssh to another node to fire up the necessary

I would go back to the mpich2 setup and make sure you can run some test jobs
correctly and have setup your system as specified in the installation
instructions for mpich2.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Sun Apr 22 2007 - 06:07:34 PDT
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