AMBER Archive (2009)

Subject: Re: [AMBER] Number of Cycles

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Dec 15 2009 - 07:31:09 CST

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_at_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_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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER_at_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
>>
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>
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