[gmx-users] No domain decomposition
Justin Lemkul
jalemkul at vt.edu
Mon Sep 28 14:55:07 CEST 2015
On 9/28/15 8:49 AM, Chandan Choudhury wrote:
> g_tune_pme would give some useful information.
>
>
>
> On Mon, Sep 28, 2015 at 6:05 PM, soumadwip ghosh <soumadwipghosh at gmail.com>
> wrote:
>
>> Hi Chandan,
>> I tried it once using -nt option but it failed . I
>> kept it 8 although I dont know how to change the number of nodes for
>> mdrun correctly. How do I know the value of x if I want to run say
>> mdun -deffnm mdfinal -nt x. It is worth mentioning here that for my
>> NPT and NVT mdrun proceeded smoothly and I am being troubled only in
>> the production run stage. i would appreciate any sort of help. One
>> more question - from the crashed mdfinal.log file is it possible to
>> have some information about domain decomposition or the approximate
>> value of -nt x?
>>
The DD failure is symptomatic of unstable physics, not causative of it.
Regardless of how many threads/cores you use, an unstable system will always
crash. You need to have a thorough look through
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
-Justin
--
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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