[gmx-users] RE: Re: loab imbalance

[lina]

> > > 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