[gmx-users] genconf and bonded interactions

[Fabio Affinito]

Ok, the problem is solved.
Thank you.

Fabio
On 07/27/2011 05:17 PM, Justin A. Lemkul wrote:
>
>
> 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
>>> GROMACS
>>> 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.
>
> http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
>
>
> -Justin
>


-- 
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198