ah I see I thought Bob was talking about frequency of dumping coordinates of
any type. I'm not sure why changing ntwr would affect performance but ntwx
would not- is the the open/close on the restart file, or the communications
to collect all coordinates?
thanks
carlos
On Tue, Dec 15, 2009 at 12:10 PM, Jason Swails <jason.swails.gmail.com>wrote:
> I think he just scales ntwr, not ntwx. I see the problem in scaling
> ntwx as far as assuming you're pulling snapshots every ps, but if ntwx
> is scaled to processor count it won't be the case. However, ntwr
> should have no bearing at all on the frequency with which frames are
> written to the trajectory.
>
> >From the pmemd source, it appears that only ntwr is scaled
>
> #ifdef MPI
> if (numtasks .gt. 10) ntwr = 50 * numtasks
> #endif
>
> Also, setting ntwr in the mdin fixes it (overriding the scaling)
> (fixes as in makes it constant, not makes it unbroken :) ). ntwx is
> set to 0 by default (in both sander and pmemd), at least in mdread.f
> for sander and mdin_ctrl_dat.fpp for pmemd. I'm not exactly sure what
> a value of 0 does, or if it's overridden somewhere else, but I'm
> pretty sure we're arguing different variables here. I always set ntwx
> in my simulations anyway, whether using sander or pmemd, so following
> that procedure it's all a non-issue.
>
> On Tue, Dec 15, 2009 at 11:53 AM, Carlos Simmerling
> <carlos.simmerling.gmail.com> wrote:
> > I mean that if changing processor count changes ntwx, then you need to be
> > very careful in a project with multiple trajectory files since the time
> per
> > frame increment is not constant. correct?
> > I don't mean the data will be wrong, just that one must be careful in
> > processing the data, such as when combining multiple trajectory files.
> > that's why I said it can be confusing- not incorrect.
> >
> >
> > On Tue, Dec 15, 2009 at 9:55 AM, Robert Duke <rduke.email.unc.edu>
> wrote:
> >
> >> Hi Carlos,
> >> Sorry, but I don't understand the problem here... Changing the
> processor
> >> count should have close to zero impact on what is happening in the runs
> (not
> >> completely true, as increasing the processor count probably does ever so
> >> slightly increase rounding error in the force summation). In the case
> of
> >> the restart files, unless there is a disaster the only one you should be
> >> interested in ever is the last one written, always the last step
> executed.
> >> So perhaps there is additional grief with things like REMD or LES that
> you
> >> are more involved with? I need to understand why you would say this, so
> I
> >> can understand and attempt to fix any real limitations.
> >> Regards - Bob
> >> (I change processor count all the time, really...)
> >>
> >> ----- Original Message ----- From: "Carlos Simmerling" <
> >> carlos.simmerling.gmail.com>
> >> To: "AMBER Mailing List" <amber.ambermd.org>
> >> Sent: Tuesday, December 15, 2009 8:31 AM
> >> Subject: Re: [AMBER] Number of Cycles
> >>
> >>
> >> the automatic scaling is great but people should be careful not to
> change
> >>> processor count during a project - which I often do based on partition
> >>> availability at run time. it can make things very confusing later.
> >>>
> >>>
> >>> On Tue, Dec 15, 2009 at 8:23 AM, Robert Duke <rduke.email.unc.edu>
> wrote:
> >>>
> >>> And I forgot to mention, but of course if you actually specify a value
> >>>> for
> >>>> ntwr in &cntrl, that value overrides the "default"
> >>>> scaled-by-processor-count
> >>>> value in pmemd. Actually, a great way to screw performance in pmemd
> is
> >>>> to
> >>>> specify some small number for ntwr and then throw your job at a couple
> >>>> hundred processors... So I don't recommend putting a value for ntwr
> into
> >>>> &cntrl unless you have a reason.
> >>>> Regards - Bob Duke
> >>>> ----- Original Message ----- From: "Robert Duke" <rduke.email.unc.edu
> >
> >>>> To: "AMBER Mailing List" <amber.ambermd.org>
> >>>> Sent: Tuesday, December 15, 2009 8:16 AM
> >>>> Subject: Re: [AMBER] Number of Cycles
> >>>>
> >>>>
> >>>> I presume that for sander there is indeed a simple "default" ntwr
> value,
> >>>>
> >>>>> giving a rewrite every 500 steps. In pmemd, the value is actually
> >>>>> scaled as
> >>>>> a function of processor count once you have more than 10 processors,
> in
> >>>>> order to not increase the frequency in time of rewriting restart
> files
> >>>>> as
> >>>>> you run on more and more processors. This keeps you from getting
> into a
> >>>>> situation where writing this file has a significant performance
> impact.
> >>>>> Regards - Bob Duke
> >>>>> ----- Original Message ----- From: "Jason Swails" <
> >>>>> jason.swails.gmail.com
> >>>>> >
> >>>>> To: "AMBER Mailing List" <amber.ambermd.org>
> >>>>> Sent: Tuesday, December 15, 2009 7:10 AM
> >>>>> Subject: Re: [AMBER] Number of Cycles
> >>>>>
> >>>>>
> >>>>> Hello,
> >>>>>
> >>>>> The exact step that the MD died on is fairly irrelevant. The only
> >>>>> thing that really matters is the last step of the MD in which a
> >>>>> restart file was written (this is ntwr, which has a default of 500 I
> >>>>> believe). If ntpr is greater than ntwr (especially by multiples of
> >>>>> ntwr), then there is no way of isolating exactly which step your
> >>>>> calculation ended on. This is why I typically use the same values
> for
> >>>>> ntwr and ntpr (and ntwx for MD simulations). If you do use the same
> >>>>> value for ntwr and ntpr, and the last step printed for ntpr is 66000,
> >>>>> then your restart corresponds to MD step 66000, and you'll need to
> run
> >>>>> an additional 34000 steps to reach 100000 (66000 + 34000 = 100000).
> >>>>>
> >>>>> Hope this helps!
> >>>>> Jason
> >>>>>
> >>>>> On Tue, Dec 15, 2009 at 3:31 AM, s. Bill <s_bill36.yahoo.co.uk>
> wrote:
> >>>>>
> >>>>> Dear AMBER
> >>>>>> How can I complete my total number of cycles?
> >>>>>> Say, I had submitted my job for 100000 cycle (nstlim=100000), and
> due
> >>>>>> to
> >>>>>> the wall clock time my job stopped at cycle number 66000, I asked to
> >>>>>> write
> >>>>>> out the output every 5000 cycle (NTPR=5000, NTWX=5000). The problem
> >>>>>> here is
> >>>>>> how to complete the remaining steps. I am not sure if the remaining
> >>>>>> steps
> >>>>>> are 44000, it may be in between 44000 and 43500, where my output
> >>>>>> written
> >>>>>> every 5000.
> >>>>>> So, how can I complete my number of cycles? is there any keyword
> manage
> >>>>>> this problem?
> >>>>>> Thanks in advance
> >>>>>> S. Bill
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> 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
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
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> >>>>
> >>>> _______________________________________________
> >>> AMBER mailing list
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> >>>
> >>
> >>
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>
>
> --
> ---------------------------------------
> 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
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Received on Tue Dec 15 2009 - 09:30:04 PST
