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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