[gmx-users] high load imbalance in GMX5.1 using MARTINI FF

Linda Song wlsonglinda at gmail.com
Thu Aug 9 10:13:31 CEST 2018


I am running some coarse grained simulations of a membrane-protein system using Martini force field. 
If I ran it using GMX5.1 and the mdp file provided by Martini website for GMX5, the load imbalance will gradually increase to over 80% from 4-10% at the beginning in a few hours. When I kill the job and restart from where it stopped, the load imbalance will go back to 4-10% at the start but increase again. 
If I ran the same simulation using GMX4.6 and the mdp file provided by Martini website for GMX4.x and the same number cores, such load imbalance issue will disappear. The imbalance will remain stable at 4-10%.

Both GMX4.6 and GMX5.1 I was using were not compiled with GPU acceleration. I wondered what gives rise to this load imbalance in GMX5. Is it because the domain decomposition is dealt with differently in GMX5 than GMX4.6? 

Thanks :)


More information about the gromacs.org_gmx-users mailing list