RE: Problem of running sander on Linux cluster

From: Thomas A. Spraggins <>
Date: Mon 19 Mar 2001 11:23:12 -0500

The problem is almost certainly in your machinefile. Processes are
allocated round-robin, using the entries in this file, which may be in a
place like /usr/local/mpich/utl/machines/machine.LINUX.

If you want two processes on the same machine, create a file like:


then run with: mpirun -np 2 -machinefile <whateveryoucalledyourfile>
and you'll get the desired result.

Tom Spraggins

-----Original Message-----
From: chomsri upkaew []
Sent: Monday, March 19, 2001 10:25 AM
Subject: Problem of running sander on Linux cluster

Dear Ross Walker and netters,

I can compile sander with parallel on Linux cluster as Ross's suggestion.
However, I have some problem.

My Linux cluster contains 12 boxes and 2 processors in each box (total 24
processors). When I submitted my job on box2 (or other boxes which are not
box1) with command

% mpirun -np 2 $AMBERHOME/exe/sander -O -i input -o output -c ...

I want to run 2 process on the same box (box2).I found that 1 process was
running on box2 and another process was running on box1. I don't know why?
Could you please give my the suggestion?

Sincerely Yours,

Ross Walker wrote:
>Hi Chomsri,
>Try the following:
>1) Resinstall MPICH manually specifing the compilers
> e.g ./configure -prefix=/usr/local/mpich-1.2.1 -fc=g77 -cc=gcc
>Then do make / make install etc.
>Then try recompiling amber. Make sure you do a make clean in ./amber6/src
>All the best
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Received on Mon Mar 19 2001 - 08:23:12 PST
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