[gmx-users] genconf and bonded interactions

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 27 17:17:46 CEST 2011

Fabio Affinito wrote:
> Thanks.
> This actually solved the problem in grompp.
> I still have problems when running. This is the log of mdrun:
>> Initializing Domain Decomposition on 4096 nodes
>> Dynamic load balancing: auto
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>>     two-body bonded interactions: 0.583 nm, LJ-14, atoms 28051 28056
>>   multi-body bonded interactions: 0.583 nm, Proper Dih., atoms 28051 
>> 28056
>> Minimum cell size due to bonded interactions: 0.642 nm
>> Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 
>> 1.139 nm
>> Estimated maximum distance required for P-LINCS: 1.139 nm
>> This distance will limit the DD cell size, you can override this with 
>> -rcon
>> Guess for relative PME load: 0.43
>> Will use 2400 particle-particle and 1696 PME only nodes
>> This is a guess, check the performance at the end of the log file
>> Using 1696 separate PME nodes
>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>> Optimizing the DD grid for 2400 cells with a minimum initial size of 
>> 1.424 nm
>> The maximum allowed number of cells is: X 18 Y 18 Z 6
>> -------------------------------------------------------
>> Program mdrun_mpi_bg, VERSION 4.5.4
>> Source code file: domdec.c, line: 6438
>> Fatal error:
>> There is no domain decomposition for 2400 nodes that is compatible 
>> with the given box and a minimum cell size of 1.4242 nm
>> Change the number of nodes 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 
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> "Meet Me At the Coffee Shop" (Red Hot Chili Peppers)
> I imagine that now I have to tune the dds and rcon parameter. Am I right?

I've never touched those parameters and I do not know how they will affect 
performance or the stability of your systems.  The easier solution is to simply 
reduce the number of processors so that the cell sizes increase a bit.




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list