Hi Ross,
many thanks for your advice!
All the best,
Nick
----------------------------------------------------------------------
Message: 1
Date: Fri, 20 Apr 2018 17:43:34 -0400
From: Ross Walker <ross.rosswalker.co.uk>
Subject: Re: [AMBER] Brand new GPU card testing
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <24E2BA76-6EA7-4A4E-9CB2-4AD26B792E52.rosswalker.co.uk>
Content-Type: text/plain; charset=us-ascii
Hi Nikola,
No 24 hours total is normally sufficient to uncover any issues.. So run say
8 hours for each size.
All the best
Ross
> On Apr 20, 2018, at 07:25, Nikolay N. Kuzmich <nnkuzmich.gmail.com> wrote:
>
> Hello Ross,
>
> are 24 hours supposed to be spent for repeated runs of each set/system (so
> 24x3=72 hours for all the testing) - did I get right?
> And the identical results for each system - that means the same enegry,
> temperature, density, pressure, etc for every ntpr steps?
>
> Kind regards,
> Nick
>
>
> ------------------------------
>
> Message: 9
> Date: Thu, 19 Apr 2018 08:11:50 -0400
> From: Ross Walker <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] Brand new GPU card testing
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <08633E49-A2F3-44AC-A0A3-80B73B96EAAC.rosswalker.co.uk>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Nikolay,
>
> I suggest running the same calculation, with the same random seed,
> repeatedly for about 24 hours and check that you get identical results in
> each case. I typically run 3 sets of calculations. One around 25000 atoms,
> one around 1 million atoms and one around 3.5 million atoms. The 3.5
> million atom calculation is designed to use the majority of the cards
> memory but it isn't as simple as just testing all the memory, the actual
> workload matters. I've seen cases where the 3.5 million atom calculation
> works fine but the 25000 atom run gives errors.
>
> I typically set nstlim such that each calculation takes about 30 mins - so
> 50 or so repeats gives you ~ 24 hours.
>
> Hope that helps.
> All the best
> Ross
>
>> On Apr 19, 2018, at 03:28, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
>>
>> Dear Amber users and developers,
>>
>> how a brand new graphic card (1080Ti GTX, for instance)
>> should be tested to make sure it's quite suitable for running the
>> simulations?
>>
>> Kind regards,
>> Nick
>>
>> Nikolay Kuzmich
>> Department of Drug Safety,
>> Research Institute of Influenza,
>> WHO National Influenza Centre of Russia,
>> 15/17 Professor Popov St.,
>> Saint-Petersburg
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Apr 23 2018 - 03:30:02 PDT
