[gmx-users] load imbalance!!!
Mark.Abraham at anu.edu.au
Wed Apr 13 14:01:18 CEST 2011
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
> 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.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users