Re: [AMBER] How to know whether the sander is running parallel

From: Aimin <aimin.guo.csun.edu>
Date: Fri, 5 Aug 2011 13:41:50 -0700

Hi,

The command I used is as follows:

mpirun -np 4 $AMBERHOME/bin/sander.MPI -O -i equil.in -p TC5b.prmtop -c equil9.rst -r equil10.rst -o equil10.out -x equil10.mdcrd

I cannot find the word "node" in the output files, i.e., equil10.rst, equil10.out, and equil10.mdcrd. Is it normal?

Aimin

________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Friday, August 05, 2011 11:50 AM
To: AMBER Mailing List
Subject: Re: [AMBER] How to know whether the sander is running parallel

Even if sander.MPI was running on one node it would still say "node" somewhere in your output file. Are you sure this word is not in your output file?

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Aug 5, 2011, at 1:03 PM, Aimin <aimin.guo.csun.edu> wrote:
> Hi David,
>
> It still does not work. I have used sander.MPI, but I can not find pmemd.MPI. I can not find out the reason why the sander can not be running parallel.
>
> Aimin
>
> ________________________________________
> From: David A Case [case.biomaps.rutgers.edu]
> Sent: Friday, August 05, 2011 9:49 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] How to know whether the sander is running parallel
>
> On Fri, Aug 05, 2011, Aimin wrote:
>>
>> I cannot find the word "nodes" in the mdout file.
>
> This means you are not running in parallel.  Be sure you are calling
> sander.MPI or pmemd.MPI, with an appropriate mpirun command.  Do the parallel
> test cases work?
>
> ...dac
>
>
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Received on Fri Aug 05 2011 - 14:00:02 PDT