[gmx-users] load imbalance!!!

[Mark Abraham]

On 13/04/2011 7:02 PM, delara aghaie wrote:
> Dear gromacs users
> I have Dppc monolayer on Tip4p2005 water layer.
> I use gromacs 4.0.7, tcoupl=v-rescale
> command line in .ll file:
> mpiexec mdrun -v -s topol.tpr
> (I have made topol.tpr with the following command:
> *grompp -c .gro -f .mdp -n .ndx -p .top -o .tpr*
> **
> *now submitting the .ll file with qsub, the run has finished but I see 
> this mesaage in the .e.ll file;*
> **
> NOTE: Turning on dynamic load balancing
> vol 0.69! imb F 149%
> Writing final coordinates.
> step 100, remaining runtime:     0 s
>  Average load imbalance: 184.7 %
>  Part of the total run time spent waiting due to load imbalance: 45.5 %
>  Steps where the load balancing was limited by -rdd, -rcon and/or 
> -dds: Z 5 %
> NOTE: 45.5 % performance was lost due to load imbalance
>       in the domain decomposition.
> Is there a way to fix this load imbalance to get the better performance?
>

Start using dynamic load balancing from the beginning of the run with 
-dlb yes.

> Does it mean that because of load imbalance, I have lost almost 45 
> percentage of performance?
>

Yes, but you simulated only 100 steps, so the time taken will be 
dominated by I/O and setup costs.

Some systems are intrinsically hard to treat in parallel. There's a lot 
of diagnostic data before step 0, some of which might help you 
trouble-shoot, once you demonstrate that load imbalance over a longer 
run doesn't become less significant.

Mark

Mark
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