The nsec/day metric was added to mdinfo, I think by Ross Walker's group. It
is intended to be a quick check, not the final word, on run performance, I
believe. The final word on run performance is in all the performance data
at the end of the mdout file, as well as the logfile. I have not looked at
how they implemented the mdinfo timer and don't use it myself.
Regards - Bob Duke
----- Original Message -----
From: "Mayank Daga" <mdaga.vt.edu>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Tuesday, August 17, 2010 11:55 AM
Subject: Re: [AMBER] Question about mdinfo file.
> What I am concerned is how would the ns/day be affected if and if not the
> simulations run to the entirety. The mdinfo file states ns/day obtained
> due
> to last 'x' steps, hence if the 'x' = 10000 and not 1000, is there a
> chance
> the average would be better for 10000 steps??
> ~mayank
>
> On Tue, Aug 17, 2010 at 11:31 AM, Jason Swails
> <jason.swails.gmail.com>wrote:
>
>> Hello,
>>
>> I believe that pmemd does not update the mdinfo file as often as it
>> updates
>> the mdout file due to performance implications. You can figure out the
>> source of this discrepancy by digging through the pmemd code, but this
>> has
>> no effect on your results.
>>
>> Hope this helps,
>> Jason
>>
>> On Tue, Aug 17, 2010 at 11:10 AM, Mayank Daga <mdaga.vt.edu> wrote:
>>
>> > Hi,
>> >
>> > I am a newbie using AMBER on the GPUs.
>> > When I run my simulations, I see two output files, mdout and mdinfo. In
>> the
>> > mdinfo file, I see the timing details as to how many ns/day I get. The
>> > issue
>> > is some steps are always uncompleted according to this file while mdout
>> > lists that all the steps have been completed. Why is this discrepancy?
>> > For example, if I run a simulation for 10000 steps, mdinfo shows 9000
>> steps
>> > remaining while mdout list energy values for all 10000 steps.
>> >
>> > I am using the input files as downloaded from the AMBER website and to
>> run
>> > the simulation:
>> > ~/amber11/bin/pmemd.cuda -O -i mdin -o mdout -p prmtop -c inpcrd -r
>> restrt
>> > -x mdcrd -gpu 0
>> >
>> > Please explain this behaviour.
>> >
>> > Thanks,
>> > ~mayank
>> >
>> >
>> > --
>> > Mayank Daga | SyNeRGy Laboratory | Dept. of Computer Science
>> > Virginia Tech | http://synergy.cs.vt.edu | http://www.cs.vt.edu
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Mayank Daga | SyNeRGy Laboratory | Dept. of Computer Science
> Virginia Tech | http://synergy.cs.vt.edu | http://www.cs.vt.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Aug 17 2010 - 09:00:08 PDT
