[gmx-users] Domain decomposition

[Sergio Manzetti]

Checked the link, nothing written here on rcon and dds... 


Sergio Manzetti 

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From: "Justin Lemkul" <jalemkul at vt.edu> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Thursday, June 22, 2017 3:21:28 PM 
Subject: Re: [gmx-users] Domain decomposition 

On 6/22/17 9:16 AM, Sergio Manzetti wrote: 
> Hi, I have (also) a system of one molecule in water box of 3 3 3 dimensions, the procedure goes well all the way till the simulation starts, getting: 
> 
> Will use 20 particle-particle and 4 PME only ranks 
> This is a guess, check the performance at the end of the log file 
> 
> ------------------------------------------------------- 
> Program gmx mdrun, VERSION 5.1.2 
> Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/domdec/domdec.cpp, line: 6987 
> 
> Fatal error: 
> There is no domain decomposition for 20 ranks that is compatible with the given box and a minimum cell size of 2.0777 nm 
> Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings 
> Look in the log file for details on the domain decomposition 
> For more information and tips for troubleshooting, please check the GROMACS 
> website at http://www.gromacs.org/Documentation/Errors 
> ------------------------------------------------------- 
> 
> 
> Not sure what to do here.. 
> 

Follow the link provided in the error message. 

-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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