[gmx-users] Domain decomposition error
nishap.patel at utoronto.ca
nishap.patel at utoronto.ca
Mon May 17 17:12:19 CEST 2010
Thanks Mark, I did play around with the -npme option a little and
turns out using -npme 1 works for the system this is mdrun command I
have in the script file
mdrun_openmpi -nosum -dlb yes -npme 1 -cpt 40 -maxh 48 -deffnm md
Quoting Mark Abraham <mark.abraham at anu.edu.au>:
> ----- Original Message -----
> From: nishap.patel at utoronto.ca
> Date: Monday, May 17, 2010 10:28
> Subject: Re: [gmx-users] Domain decomposition error
> To: gmx-users at gromacs.org
>> 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'd guess that the greater size of ethanol in combination with
> constraints is running afoul of the DD minimum cell-size
> requirements. As you will see in reading the .log file, for your
> ethanol, P-LINCS requires at least 0.497nm given the initial
> condition of your system. DD fudges that up by a factor of 1.25 to
> give some flexibility. Given that minimimum size requirement, only 6
> cells can result from a partition in any dimension of a 4nm x 4nm x
> 4nm box. You've probably artificially required DD to use 14
> processors with -npme 2. That requires a 14x1x1 or 7x2x1 DD, neither
> of which can be consistent with the combination of your box size
> and constraint usage. Methanol will have a smaller constraint (see
> its .log file to compare), so the DD will be legal. If you'd given
> your full mdrun command line in your post, then I wouldn't be
> guessing as much...
> The .log file recommends a range of useful solutions for you to
> consider - but it makes no suggests regarding your .mdp file.
> Roughly speaking, the .mdp file normally describes the model physics
> and controls the output conditions, and the (sometimes implicit)
> arguments of mdrun describe the implemention of the resulting
> algorithm. You're requiring an impossible implementation.
> Simplest is to not specify -npme unless you know you need to. For
> efficiency, both -npme and "-np less -npme" need to be sufficiently
> composite and preferably with a high common factor of two of their
> factors. If you leave mdrun alone, it will guess reasonably. For
> example, -npme=4 giving 12 DD nodes decomposed 4x3x1 will work
> admirably in your case, and I bet that's what mdrun picks.
>> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> >nishap.patel at utoronto.ca wrote:
>> >> 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.
>> >>-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
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