Re: [gmx-users] Benchmarking gromacs over large number of cores

2011-04-28 Thread Roland Schulz
On Thu, Apr 28, 2011 at 10:05 AM, Bruno Monnet wrote: > Hi, > > I'm not really a Gromacs user, but I'm currently benchmarking Gromacs 4.5.4 > on a large cluster. It seems that my communication (PME) is really high and > gromacs keeps complaining for more PME nodes : > >Average load imbalance

Re: [gmx-users] Benchmarking gromacs over large number of cores

2011-04-28 Thread Peter C. Lai
how many particles is your system? if the number per domain is too low there is not much you can do about the load imbalance...but it did report only an overall 3.2% overhead for this so... you can modify the PP/PME ratio during mdrun by manually specifying the domain decomposition yourself. so

[gmx-users] Benchmarking gromacs over large number of cores

2011-04-28 Thread Bruno Monnet
Hi, I'm not really a Gromacs user, but I'm currently benchmarking Gromacs 4.5.4 on a large cluster. It seems that my communication (PME) is really high and gromacs keeps complaining for more PME nodes : Average load imbalance: 113.6 % Part of the total run time spent waiting due t