[gmx-users] Re: Restarting a simulation after replacing an empty md.trr file

[Justin Lemkul]

On 11/12/13 12:07 PM, arunjones wrote:
> Thank you Sir,
> initially i was running on 60 threads, now i changed it to 100. simulation
> is running with out any error, but i found a note in the log file as fallows
>
>    #nodes mismatch,
>      current program: 100
>      checkpoint file: 60
>
>    #PME-nodes mismatch,
>      current program: -1
>      checkpoint file: 12
>
> Gromacs binary or parallel settings not identical to previous run.
> Continuation is exact, but is not guaranteed to be binary identical.
>
> Initializing Domain Decomposition on 100 nodes
>
>
> is it a good idea to continue or shall i stick with 60 threads.
>

Like I said, I think it is a bad idea to switch settings haphazardly during the 
run.  As the note indicates, the continuation is exact, but not binary 
identical.  Check the website for what all that means if you're not sure.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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