[gmx-users] High load imbalance: 31.8%

[Mark Abraham]

Hi,

In cases like this, it's good to describe what's in your simulation, and
share the full .log file on a file-sharing service, so we can see both the
things mdrun reports early and late.

Mark

On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony <a.nash at ucl.ac.uk> wrote:

> Hi all,
>
> I appear to have a very high load imbalance on some of my runs. Values
> starting from approx. 7% up to 31.8% with reported vol min/aver of around
> 0.6 (I haven¹t found one under half yet).
>
> When I look through the .log file at the start of the run I see:
>
> Initializing Domain Decomposition on 8 ranks
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 0.514 nm, LJ-14, atoms 3116 3123
>   multi-body bonded interactions: 0.429 nm, Proper Dih., atoms 3116 3123
> Minimum cell size due to bonded interactions: 0.472 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.862 nm
> Estimated maximum distance required for P-LINCS: 0.862 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Using 0 separate PME ranks, as there are too few total
>  ranks for efficient splitting
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 8 cells with a minimum initial size of 1.077 nm
> The maximum allowed number of cells is: X 12 Y 12 Z 12
> Domain decomposition grid 4 x 2 x 1, separate PME ranks 0
> PME domain decomposition: 4 x 2 x 1
> Domain decomposition rank 0, coordinates 0 0 0
> Using 8 MPI processes
> Using 1 OpenMP thread per MPI process
>
>
>
>
> Having a quick look through the documentation and I see that I should
> consider implementing the verlet cut-off (which I am) and adjust the
> number of PME nodes/cut-off and PME grid spacing. Would this simply be a
> case of throwing more cores at the simulation or must I play around with
> P-LINCS parameters?
>
> Thanks
> Anthony
>
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