[gmx-users] GROMACS mpirun with extremely high load imbalance in output (vol 0.43! imb F 15- 53%)

Marc Hoemberger hoemberg at brandeis.edu
Thu Mar 1 18:58:19 CET 2018

Hi gromacs-users,

I am currently running a set of TMD simulations with gromacs 5.1.4 +
plumed_2.4.0. The system for all four runs is identical, the only
difference is the force constant for bias applied by plumed.

I am using gromacs with mpi support, starting it with 32 processes on my
32core processors. While two of the four runs take a relatively short time,
the other two are estimated to be done 5 days later. The only difference I
can make out in the gromacs output is that for runs that are running at
normal speed the output of gromacs reports low imbalance, i.e. fluctuating
between 0 and 2% :

vol 0.39! imb F  1% pme/F 0.20 step 224700, will finish Wed Mar

However, in the two simulations that are running much slower the imbalance
reported is much higher, i.e. fluctuating between 10 and 50+%:

vol 0.39! imb F 15% pme/F 0.81 step 4222700, will finish Wed Mar

I left -dlb option of mdrun to auto. Could this difference indeed explain
the vast difference in calculation time of the different runs, and if so is
there anything I could do to alleviate this?

Marc Hoemberger

More information about the gromacs.org_gmx-users mailing list