On 15/02/2012 1:44 AM, lloyd riggs wrote:
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?
This is not really the issue. You can read in the OP's output that there
are 20 PP and 12 PME nodes, which is a normal enough ratio, and fine for
a 0.29 PME load...
If the OP is confident that his initial configuration really doesn't
have such a long bond (no input checkpoint file messing things up?) he
should try again with GROMACS 4.5.5.
Mark
Stephan Watkins
-------- Original-Nachricht --------
Datum: Tue, 14 Feb 2012 18:01:24 +0400
Von: Alexey Zeifman<az...@mail.ru>
An: gmx-users@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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