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

[Mark Abraham]

Hi,

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

> 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
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/performance.html.
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.

Mark

cheers, johannes
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