[gmx-users] High load imbalance: 31.8%

Nash, Anthony a.nash at ucl.ac.uk
Thu Aug 20 08:21:45 CEST 2015

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?


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