[gmx-users] Setting rcon according to system

[Mark Abraham]

Hi,

On Wed, Nov 14, 2018 at 3:18 AM Sergio Perez <sperezconesa at gmail.com> wrote:

> Hello,
> First of all thanks for the help :)
> I don't necessarily need to run it with 100 processors, I just want to know
> how much I can reduce rcon taking into account the knowledge of my system
> without compromising the accuracy. Let me give some more details of my
> system. The system is a sodium montmorillonite clay with two solid
> alumino-silicate layers with two aqueous interlayers between them. The
>

I assume the silicate network has many bonds over large space - these
adjacent bonds are the issue, not uranyl. (You would have the same problem
with a clay-only system.)


> system has TIP4P waters, some OH bonds within the clay and the bonds of the
> uranyl hydrated ion described in my previous email as constraints. The
> system is orthorrhombic 4.67070x4.49090x3.77930 and has 9046 atoms.
>
> This is the ouput of gromacs:
>
> Initializing Domain Decomposition on 100 ranks
> Dynamic load balancing: locked
> Initial maximum inter charge-group distances:
>    two-body bonded interactions: 0.470 nm, Tab. Bonds NC, atoms 10 13
> Minimum cell size due to bonded interactions: 0.000 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.842 nm
> Estimated maximum distance required for P-LINCS: 0.842 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Guess for relative PME load: 0.04
> Will use 90 particle-particle and 10 PME only ranks
>

GROMACS has guessed to use 90 ranks in the real-space domain decomposition,
e.g. as an array of 6x5x3 ranks.


> This is a guess, check the performance at the end of the log file
> Using 10 separate PME ranks, as guessed by mdrun
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 90 cells with a minimum initial size of 1.052 nm
> The maximum allowed number of cells is: X 4 Y 4 Z 3
>

... but only 4x4x3=48 ranks can work with the connectivity of your input.
Thus you are simply using too many ranks for a small system. You'd have to
relax the tolerances quite a lot to get to use 90 ranks. Just follow the
first part of the message advice and use fewer ranks :-)

Mark

-------------------------------------------------------
> Program:     mdrun_mpi, version 2018.1
> Source file: src/gromacs/domdec/domdec.cpp (line 6571)
> MPI rank:    0 (out of 100)
>
> Fatal error:
> There is no domain decomposition for 90 ranks that is compatible with the
> given box and a minimum cell size of 1.05193 nm
> Change the number of ranks 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
> -------------------------------------------------------
>
>
> Thank you for your help!
>
> On Wed, Nov 14, 2018 at 5:28 AM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Possibly. It would be simpler to use fewer processors, such that the
> > domains can be larger.
> >
> > What does mdrun think it needs for -rcon?
> >
> > Mark
> >
> > On Tue, Nov 13, 2018 at 7:06 AM Sergio Perez <sperezconesa at gmail.com>
> > wrote:
> >
> > > Dear gmx comunity,
> > >
> > > I have been running my system without any problems with 100 processors.
> > But
> > > I decided to make some of the bonds of my main molecule constrains. My
> > > molecule is not an extended chain, it is a molecular hydrated ion, in
> > > particular the uranyl cation with 5 water molecules forming a
> pentagonal
> > by
> > > bipyramid. At this point I get a domain decomposition error and I would
> > > like to reduce rcon in order to run with 100 processors. Since I know
> > that
> > > by the shape of my molecule, two atoms connected by several constraints
> > > will never be further appart than 0.6nm, can I use this safely for
> -rcon?
> > >
> > > Thank you very much!
> > > Best regards,
> > > Sergio Pérez-Conesa
> > > --
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