Thanks Jason.
Chinh
On Fri, Jun 5, 2015 at 11:32 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Jun 4, 2015 at 9:59 PM, Chinh Su Tran To <chinh.sutranto.gmail.com
> >
> wrote:
>
> > Thanks Jason and Prof. Monard.
> >
> > One more question. Sometimes I got the results regarding "Infinity".
> > For example, the results below I got from the .out file (running on GPU
> > installed in a server, using ALPB Implicit, amber14, ff12SB), as below:
> >
> >
> >
> --------------------------------------------------------------------------------
> > 5. TIMINGS
> >
> >
> --------------------------------------------------------------------------------
> >
> > | NonSetup CPU Time in Major Routines:
> > |
> > | Routine Sec %
> > | ------------------------------
> > | Nonbond 223686.99 79.15
> > | Bond 0.00 0.00
> > | Angle 0.00 0.00
> > | Dihedral 0.00 0.00
> > | Shake 2049.98 0.73
> > | RunMD 56857.13 20.12
> > | Other 0.00 0.00
> > | ------------------------------
> > | Total 282594.10
> >
> > | Generalized Born CPU Time:
> > |
> > | Routine Sec %
> > | ------------------------------------
> > | Radii Calc 0.00 0.00
> > | Diagonal Calc 0.00 0.00
> > | Off Diagonal Calc 0.00 0.00
> > | GBSA LCPO Calc 0.00 0.00
> > | ---------------------------------
> > | Total 0.00 0.00
> >
> > | Final Performance Info:
> > | -----------------------------------------------------
> > | Average timings for last 0 steps:
> > | Elapsed(s) = 0.03 Per Step(ms) = +Infinity
> > | ns/day = 0.00 seconds/ns = +Infinity
> >
>
> This is just performance (timing) information. Not related to results at
> all. If you look at the mdinfo file during the course of the simulation,
> it shows how fast the last chunk of simulation (between mdinfo prints) ran,
> and the overall efficiency. Then below it shows the timings for every
> step.
>
> It just so happens that the timing info was printed on the last step to the
> mdinfo file, so the end of the mdout file had the timing for the last "0"
> steps (as it says). Well, the time per step, when the total number of
> steps is 0, is infinity (because you're dividing a number very close to
> zero by zero). Same with the ns/day.
>
> These numbers are meaningless, and not a cause for concern.
>
>
>
> >
> > |
> >
> > | Average timings for all steps:
> >
> > | Elapsed(s) = 283573.63 Per Step(ms) = 5.67
> >
> > | ns/day = 30.47 seconds/ns = 2835.74
> >
> > | -----------------------------------------------------
> >
>
> And here you see the average timing over the whole run. These are more
> reliable performance measurements ;).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Thu Jun 04 2015 - 23:00:02 PDT
