[gmx-users] Domain decomposition in FEP

[lloyd riggs]

Dear Alexey Zeifman,

>From my experience it is just the nodes have to break down into some sort of even multiple by dividing the domain decomposition size or vise versi.  I think somone elses answere was just to try it with a couple sizes for the decomposition, as multiples of the number of nodes.

also your PME reserved nodes are probably too much or your wasting space, but I am not sure if this effects the domain decomposition or if all 20 nodes are thrown into that?

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Tue, 14 Feb 2012 18:01:24 +0400
> Von: Alexey Zeifman <azeif at mail.ru>
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] Domain decomposition in FEP

> Dear all,
> 
> I'm trying to run FEP calculation of the ligand in the protein in water.
> Performing NVT-dynamics for Lennard-Johnes perturbation using soft core
> results in the following error:
> 
> There is no domain decomposition for 20 nodes...
> 
> I've checked out the log-file and found this:
> 
> >Initial maximum inter charge-group distances:
> >    two-body bonded interactions: 1.474 nm, Bond, atoms 4371 4391
>  > multi-body bonded interactions: 0.522 nm, Ryckaert-Bell., atoms 3747
> 3756
> >Minimum cell size due to bonded interactions: 1.621 nm
> >Guess for relative PME load: 0.29
> >Will use 20 particle-particle and 12 PME only nodes
> >This is a guess, check the performance at the end of the log file
> >Using 12 separate PME nodes
> >Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> >Optimizing the DD grid for 20 cells with a minimum initial size of 2.026
> nm
> >The maximum allowed number of cells is: X 3 Y 3 Z 3
> >
> ->------------------------------------------------------
> >Program mdrun_mpi, VERSION 4.5.1
> >Source code file: domdec.c, line: 6428
> 
> >Fatal error:
> >There is no domain decomposition for 20 nodes that is compatible with the
> given box and a minimum cell size of 2.02621 nm
> >Change the number of nodes or mdrun option -rdd or -dds
> >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
> ->------------------------------------------------------>
> 
> I understand that distance of 1.474 nm is rather big for bond! BUT I can't
> find such a distance between atoms 4371 4391. The fragment of gro-file for
> such index interval looks like this:
> 
>   640LIG     C4 4371   2.897   3.416   3.072
>   640LIG     N3 4372   3.296   3.109   3.434
>   640LIG     N6 4373   3.416   2.999   3.595
>   640LIG     C6 4374   2.696   2.762   3.601
>   640LIG     C7 4375   3.025   3.232   3.150
>   640LIG     C8 4376   3.208   3.142   3.338
>   640LIG     C9 4377   2.758   2.644   3.649
>   640LIG    C10 4378   2.767   2.884   3.595
>   640LIG     N4 4379   3.319   2.826   3.731
>   640LIG    C11 4380   2.968   2.768   3.677
>   640LIG    C12 4381   2.894   2.648   3.686
>   640LIG    C13 4382   2.901   2.887   3.638
>   640LIG     N5 4383   3.100   2.766   3.707
>   640LIG    C14 4384   3.420   2.908   3.693
>   640LIG     O1 4385   3.018   3.627   3.068
>   640LIG    C15 4386   3.028   3.095   3.182
>   640LIG    C16 4387   3.123   3.049   3.275
>   640LIG     O2 4388   2.566   2.759   3.559
>   640LIG     O3 4389   2.699   2.993   3.545
>   640LIG     O4 4390   2.680   2.530   3.655
>   640LIG    C17 4391   2.791   3.426   3.184
>   640LIG    C18 4392   2.834   3.453   2.937
> 
> and the actual distance is 1.55 A - quite OK for single C-C bond. 
> 
> And another interesting fact is that it doesn't occur during FEP
> calculation of the same system without soft-core and aimed at only charge
> perturbation.
> 
> I will appreciate any help regarding this.
> 
> Alexey Zeifman
> 

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