[gmx-users] pp/pme ratio differences between gromacs 5.0.x and 5.1.x

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 9 08:59:30 CET 2016


On Sun, Feb 7, 2016 at 8:00 PM Johannes Wagner <johannes.wagner at h-its.org>

> hey guys,
> came across an issue with pp/pme ratio difference from 5.0 to 5.1. For a
> system running on 2 nodes with a pp/pme ratio of 80:16 on 5.0, the same
> thing starts with 72:24 on gromacs 5.1. The 5.1 run has a much higher load
> imbalance and is hence slower. Are there known changes from 5.0 to 5.1 in
> the pp/pme ratio that cause this?

Yes and no. Even on only two nodes, your observations can be affected by
network congestion, so I would investigate whether you can reproduce the
observations. The changes that I identified that had the capacity to change
performance are noted at
For example, if you're using LINCS then the SIMD improvements there affect
only the PP ranks so it might seem to the auto-tuner that it's more
efficient to use fewer PP ranks. Then later some kind of load imbalance has
a stronger effect. The interactions of DD DLB and PME tuning are complex,
and we can't rule out that there's a problem that we should fix. But we
can't say much without being able to compare some (reproducible) log files.


cheers, johannes
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