AMBER Archive (2009)

Subject: Re: [AMBER] Number of Cycles

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Dec 15 2009 - 07:23:04 CST

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_at_email.unc.edu>
To: "AMBER Mailing List" <amber_at_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_at_gmail.com>
> To: "AMBER Mailing List" <amber_at_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_at_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
>>
>>
>>
>>
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>>
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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