[gmx-users] Restart simulation from checkpoint file with fewer nodes

[jkrieger at mrc-lmb.cam.ac.uk]

I have found that only some kinds of nodes on our cluster work for gromacs
4.6 (the ones we call m620, m620+ and m630 but not others - I can check
the details tomorrow). I haven't tested it again now I'm using 5.0 so
don't know if that's still an issue but if it is it could explain why your
restart failed even and the initial run didn't.

> thanks a lot for your fast response.
>
> I have tried it, and it failed. I ask in this forum just to make sure.
> However, there was something in my cluster that probably make it failed.
> I'll handle it first and then retry to restart again.
>
> Regards,
>
> Husen
>
> On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/13/16 8:53 PM, Husen R wrote:
>>
>>> Dear all
>>>
>>> Does simulation able to be restarted from checkpoint file with fewer
>>> nodes ?
>>> let's say, at the first time, I run simulation with 3 nodes. At running
>>> time, one of those nodes is crashed and the simulation is terminated.
>>>
>>> I want to restart that simulation immadiately based on checkpoint file
>>> with
>>> the remaining 2 nodes. does gromacs support such case ?
>>> I need help.
>>>
>>
>> Have you tried it?  It should work.  You will probably get a note about
>> the continuation not being exact due to a change in the number of cores,
>> but the run should proceed fine.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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