Re: [AMBER] Question about mdinfo file.

From: Mayank Daga <mdaga.vt.edu>
Date: Tue, 17 Aug 2010 12:42:21 -0400

Thanks for the replies.

I tried looking at the Timing values in mdout.

It contains the Total CPU Time as well as Total Wall Time. For my
simulation, both are 50 secs. I wanted to know do these times include the
time spent on the GPU? If not, where do I find the Total GPU Time? If I use
50secs to calculate ns/day, I am getting amazingly high numbers.

Thanks again,

~mayank

On Tue, Aug 17, 2010 at 12:00 PM, Jason Swails <jason.swails.gmail.com>wrote:

> It's certainly possible that the simulation becomes more efficient in later
> steps, especially since the first steps have the setup and such. However,
> it's trivial to calculate the ns/day that you achieve by looking at the
> mdout file. Simply look at how long it took to complete your 10000 steps
> and convert that into ns/day. (Simple dimensional analysis that we do in
> our 1st chemistry class). In fact, that's how it's done for the mdinfo.
>
> On Tue, Aug 17, 2010 at 11:55 AM, Mayank Daga <mdaga.vt.edu> wrote:
>
> > 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
> >
>
>
>
> --
> 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
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Received on Tue Aug 17 2010 - 10:30:13 PDT
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