[gmx-developers] Reproducible runs with DLB
Shirts, Michael (mrs5pt)
mrs5pt at eservices.virginia.edu
Thu Jul 21 23:43:34 CEST 2011
>> And an even more useful option would be to be able to write out
>> conformations more often than in the original run. That would allow one
>> run long simulations and go back and zoom in a particular time
>> period of the simulation where some interesting event occurred.
I'll add the plug that having this sort of functionality would be great, if
possible. Could only really be done on the same machine, and may be
impossible since on restart, the order of operations might be different, and
chaos would get you very quickly, but it would be great!
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
>> On Jul 21, 2011, at 9:26 AM, Bogdan Costescu wrote:
>>> On Thu, Jul 21, 2011 at 16:30, Mark Abraham <Mark.Abraham at anu.edu.au>
>>>> Extending the checkpoint file format is not programmer-friendly,
>>>> never mind
>>>> writing save-and-restore code for DD.
>>> If it would have been programmer-friendly, wouldn't it have been done
>>> already ? :-)
>>> Saving DD state was meant to be done at the same time as the
>>> checkpoint to have a restart point for both the molecular system state
>>> and the distribution of the atoms on nodes. But it doesn't have to be
>>> in the same file - the checkpoint file can remain as it is and an
>>> additional one can contain the DD state, as long as they are named
>>> similarly (f.e. state_stepX.dd) to know which ones to be used
>>>> I suggest you look at the hidden options to mdrun that allow you to
>>>> impose a
>>>> particular DD grid that gives satisfactory performance. See "mdrun -h
>>>> -hidden". You might have to reverse engineer how to use these from
>>>> the code.
>>> I'm already using '-dd x y z' for both the tests with and without DLB.
>>> PME is not used in some of the simulations (so playing with -npme has
>>> no meaning) and -dlb and -reprod I've already mentioned in my previous
>>> message. Are there other options that you refer to ?
>>> I understand that saving of DD state is not an easy feat. Do you
>>> consider this to be a waste of time ? Even if the answer is positive I
>>> would still be interested in it, as it would allow significantly
>>> faster while also reproducible for my simulations.
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