[gmx-users] RE: Re: loab imbalance

[Berk Hess]

> From: zhao0139 at ntu.edu.sg
> To: gmx-users at gromacs.org
> Date: Tue, 6 Apr 2010 20:31:18 +0800
> Subject: [gmx-users] RE: Re: loab imbalance
> 
> > > > On 6/04/2010 5:39 PM, lina wrote:
> > > > > Hi everyone,
> > > > >
> > > > > Here is the result of the mdrun which was performed on 16cpus. I am not
> > > > > clear about it, was it due to using MPI reason? or some other reasons.
> > > > >
> > > > > Writing final coordinates.
> > > > >   Average load imbalance: 1500.0 %
> > > > >   Part of the total run time spent waiting due to load imbalance: 187.5 %
> > > > >   Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
> > > > > X 0 % Y 0 %
> > > > > NOTE: 187.5 % performance was lost due to load imbalance
> > > > >        in the domain decomposition.
> > > > 
> > > > You ran an inefficient but otherwise valid computation. Check out the 
> > > > manual section on domain decomposition to learn why it was inefficient, 
> > > > and whether you can do better.
> > > > 
> > > > Mark
> > > 
> > > I search the "decomposition" keyword on Gromacs manual, no match found.
> > > Are you positive about that? Thanks any way, but can you make it more
> > > problem-solved-oriented, so I can easily understand.
> > > 
> > > Thanks and regards,
> > > 
> > > lina
> > 
> > This looks strange.
> > You have 1 core doing something and 15 cores doing nothing.
> > Do you only have one small molecule?
> > How many steps was this simulation?
> > 
> > Berk
> 
> 6,000,000steps. When I used htop to check the 16 cores, found they were
> all took 100%. I am surprised to be told that only 1 core working. 
> Below is part of the md.log
> 
> Initializing Domain Decomposition on 16 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 0.574 nm, LJ-14, atoms 330 338
>   multi-body bonded interactions: 0.572 nm, Proper Dih., atoms 934 942
> Minimum cell size due to bonded interactions: 0.629 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876
> nm
> Estimated maximum distance required for P-LINCS: 0.876 nm
> This distance will limit the DD cell size, you can override this with
> -rcon
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 16 cells with a minimum initial size of 1.095
> nm
> The maximum allowed number of cells is: X 5 Y 5 Z 4
> Domain decomposition grid 4 x 4 x 1, separate PME nodes 0
> Domain decomposition nodeid 0, coordinates 0 0 0
> 
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 0.9   Coulomb: 1.4   LJ: 1.4
> Reaction-Field:
> epsRF = 78, rc = 1.4, krf = 0.178734, crf = 1.0646, epsfac = 138.935
> The electrostatics potential has its minimum at r = 1.40903
> System total charge: 0.000
> Generated table with 4800 data points for 1-4 COUL.
> Tabscale = 2000 points/nm
> Generated table with 4800 data points for 1-4 LJ6.
> Tabscale = 2000 points/nm
> Generated table with 4800 data points for 1-4 LJ12.
> Tabscale = 2000 points/nm
> 
> Enabling SPC water optimization for 7729 molecules.
> 
> Configuring nonbonded kernels...
> Testing x86_64 SSE2 support... present.
> 
> Initializing Parallel LINear Constraint Solver.
> 
> Thanks advance.
> 
> lina

This all looks very normal.
I would guess the imbalance print in the output is incorrect.
Which version of Gromacs are you using?

You could run a short simulation (of a minute or so) on 1 or 2 cores
and compare the ns/day reported at the end of the log file to this run.

Berk

 		 	   		  
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