[gmx-developers] Reproducible runs with DLB

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jul 21 23:35:58 CEST 2011

On 22/07/2011 2:02 AM, XAvier Periole wrote:
> Hi,
> nothing I can help with here but having the reprod mode running with the
> dlb would be really useful!

It relies on observing timings... how can that be reproducible?

> 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.

Hacking some environment variable to do this seems feasible.


> 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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