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 Fri Apr 20 2018 - 04:30:01 PDT
