[gmx-users] Setting rcon according to system

Mark Abraham mark.j.abraham at gmail.com
Thu Nov 15 21:43:41 CET 2018 

Hi,

Ah I see. So unless your hydrated uranyl is modelled with bonded
interactions between uranyl atoms and water atoms, the only bonds in the
system are silicate hydroxyl, water, and uranyl. If so, then I suspect the
default value of lincs-order (which is 4, to suit highly connected
biomolecular use cases) is too high for the actual connectivity you have.
Reducing that to 3 will relax the minimum diameter that the domain
decomposition requires, which I feel is a more stable approach than
modifying -rcon. How does that work for you?

Perhaps we should automate such a check in grompp, to cater for such weakly
connected use cases.

Mark

On Thu, Nov 15, 2018 at 3:25 AM Sergio Perez <sperezconesa at gmail.com> wrote:

> Actually the clay has the clayFF force which has only bonds on OH units,
> the rest of atoms are just LJ spheres with a charge. I guess the conclusion
> is still the same?
>
> On Wed, Nov 14, 2018 at 8:47 PM Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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
> > > > > --
> > > > > Gromacs Users mailing list
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