[gmx-developers] Reproducible runs with DLB

[XAvier Periole]

On Jul 21, 2011, at 3:43 PM, Shirts, Michael (mrs5pt) wrote:

>>> 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!
That is what I thought! But mark seem to suggest it is possible.
>
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
>
>
>>> XAvier.
>>>
>>> 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 
>>>> >
>>>> wrote:
>>>>> 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
>>>> together.
>>>>
>>>>> 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.
>>>>
>>>> Cheers,
>>>> Bogdan
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>>>
>>
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