[gmx-users] Setting Up "Equivalent" Runs With -notunepme
tconnolly at ucmerced.edu
Sat Mar 18 03:08:42 CET 2017
From my understanding of the release notes for the gromacs-2016
versions, pretty much all of the settings that are tuned by tunepme can
now be modified manually (modifying some of these settings still caused
errors all the way up to gromacs-5.1.7).
I'm not trying to make runs that are truly reproducible nor am I even
going for something that is perfectly equivalent. However, for both the
sake of performance and accuracy, I'm trying to avoid situations where,
for example, gromacs automatically runs two replicates of the same
system on the same compute node with automatically chosen coulomb
cutoffs of 1.3 and 2.0+ nm (which has in fact happened to me).
If I'm doing this manual tuning, I'd like to make sure that I'm doing it
properly, so I wanted to see if there is anyone who might catch any
obvious mistakes that I'm making. I *believe* that the options that need
to be set manually are:
1. rlist (though I've never had an issue with gromacs picking "strange"
values for this)
2. nstlist (gromacs will almost always pick the same values for this
unless the same system is run on drastically different hardware)
3. rcoulomb (this is the main thing that I'm trying to make "equivalent")
4. fourierspacing (manually scaled by the same amount as rcoulomb)
5. -notunepme as an option to mdrun
Are there any other significant settings that I'm missing? In general,
before running my production runs I perform several benchmarks where I
allow gromacs to do its own thing with multiple different settings. It
will usually choose several different optimizations. Then I'll compare
the benchmarks to see which set of values actually perform the best.
What I'd like to do is then use those automatically chosen optimizations
for all of my future runs for that system. I think that I remember at
one point finding at least one other setting that was automatically
changed during the tuning. I might be wrong, but now I'm a bit paranoid
that I'm missing something important.
Since I think the general consensus is that even with the tuning on, the
runs are "equivalent enough", I expect that at least some answers will
just be to leave things as they are without doing any manual tuning.
However, here are a couple things that happen to me on a somewhat
1. I do several benchmark runs before I start any major production runs,
so I usually have a general idea of what the optimal values should be
for maximum performance. Gromacs sometimes chooses values that are off
by quite a bit leading to losses of performance on the order of 10-20%.
2. Gromacs may optimize two replicates with different values on
equivalent hardware leading one run to finish days before another. This
can be inconvenient for my work schedule.
3. Hot and cold machines do NOT have the same optimal settings. Heat is
rarely a limiting factor for the CPUs in our nodes, but it is always a
limiting factor for our GPUs. This leads to the tuning oftentimes being
slightly imbalanced as the GPUs eventually reach a temperature that
reduces their clock speeds. The opposite may be true for other users.
4. Sometimes the most efficient setup is to run multiple jobs on a
single compute node if that node has specs that are overkill for a
single job. These multiple jobs may not even be the same system. It is
VERY difficult to get gromacs to properly optimize multiple jobs on the
same node. This sometimes leads to massive performance losses on the
order of 50%. I used to sometimes "trick" gromacs in to picking more
optimal settings by starting one job, starting a second job after the
optimization period, restarting the first job after the optimization
period, etc. However, this obviously becomes very complicated for more
than two runs per node. It also makes it impossible to start one run
after another has been going.
Thanks for any comments and corrections,
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