Dear Jason,
The mdout file "equil10.out" can be found in the attachment. Thanks.
Aimin
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Friday, August 05, 2011 7:23 PM
To: AMBER Mailing List
Subject: Re: [AMBER] How to know whether the sander is running parallel
Can you attach your mdout file here?
On Fri, Aug 5, 2011 at 4:41 PM, Aimin <aimin.guo.csun.edu> wrote:
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Aug 06 2011 - 21:00:03 PDT
