[gmx-users] load imbalance!!!

delara aghaie d_aghaie at yahoo.com
Wed Apr 13 11:02:04 CEST 2011

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?
Does it mean that because of load imbalance, I have lost almost 45 percentage of performance?
Thanks in advance
Best regards
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