[gmx-users] Domain decomposition error

[nishap.patel at utoronto.ca]

Thanks Justin. But how come it worked for methanol. The system is of  
the same size , and all the parameters are same, so I don't understand  
why it won't work for ethanol.

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> nishap.patel at utoronto.ca wrote:
>> Hello,
>>
>>   I got this following error when I was trying to run a simulation   
>> of ethanol-water box size 4*4*4 nm (~6530 atoms).
>>
>> Fatal error:
>> There is no domain decomposition for 14 nodes that is compatible   
>> with the given box and a minimum cell size of 0.62175 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.
>>
>> I looked into my log file and this is what I got:
>>
>> Initializing Domain Decomposition on 16 nodes
>> Dynamic load balancing: yes
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>>    two-body bonded interactions: 0.234 nm, LJ-14, atoms 1 9
>>  multi-body bonded interactions: 0.234 nm, Angle, atoms 2 5
>> Minimum cell size due to bonded interactions: 0.257 nm
>> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.497 nm
>> Estimated maximum distance required for P-LINCS: 0.497 nm
>> This distance will limit the DD cell size, you can override this with -rcon
>> Guess for relative PME load: 0.13
>> Will use 14 particle-particle and 2 PME only nodes
>> This is a guess, check the performance at the end of the log file
>> Using 2 separate PME nodes
>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>> Optimizing the DD grid for 14 cells with a minimum initial size of 0.622 nm
>> The maximum allowed number of cells is: X 6 Y 6 Z 6
>>
>> I am using the same .mdp file that I used for methanol, and it is   
>> working fine, I don't understand why it's giving me problem for   
>> ethanol. I am running my simulation on 2 nodes.
>>
>
> Not according to the log file messages.  You're running on 16 nodes,
> with 14 for PP and 2 for PME.  Your system is of insufficient size to
> be divided over this many PP nodes.  Check the list archive for tips,
> or simply use less nodes for the calculation.  There is also
> information in the manual about all of the settings that are mentioned
> in the log file.
>
> -Justin
>
>> Suggestions?
>>
>> Thanks
>> -Nisha P
>>
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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