[gmx-users] Domain decomposition error

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> 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.

I don't know.  The DD algorithm is rather complex, and beyond the information in 
the manual, I can't really comment.  There are additional bonded interactions in 
ethanol relative to methanol, which could influence several factors in setting 
up the DD algorithm, which you could identify by comparing the DD information 
from both the log files.

-Justin

> 
> 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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> 
> 
> 

-- 
========================================

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

========================================