[gmx-users] GMX-PLUMED speed

[Szilárd Páll]

For what is worth, I'm not surprised by the impact of PLUMED. It's
quite easy to ruin the GROMACS performance by doing a ton of serial
work on a single rank. Unless I'm mistaken, PLUMED does that quite a
bit and there is very little parallelization -- it does have limited
multi-threading but no domain decompostion. Hence, the more work
PLUMED needs to do
 i) per rank (when mdrun runs with many threads/rank) or
 ii) on the master rank,
the higher the impact on simulation performance.

Cheers,
--
Szilárd


On Sun, Feb 5, 2017 at 11:08 PM,  <jkrieger at mrc-lmb.cam.ac.uk> wrote:
> Interesting finding. Have you tried leaving out the two options
> independently? Also would be good to try that with gromacs-2016.
>
> What is your system size and cluster usage? This sounds a phenomenal speed
> as well as speed up.
>
> You should probably share this on the plumed google group too.
>
> Best wishes
> James
>
>>
>> Dears,
>>
>> I am using gromacs v5.1.4 with PLUMED v2.3.0.
>>
>> Through my experience as a novice in using PLUMED, I have noticed that not
>> writing the restraint/forces info in a file and not using a STRIDE
>> accelerate the code significantly.
>>
>> Using a line such as follows in the plumed parameters set:
>> PRINT ARG=restraint.bias
>>
>> instead of the most correct:
>> PRINT STRIDE=10000 ARG=restraint.bias FILE=bias
>>
>> would make gmx run at 950 ns/day instead of 550 ns/day.
>>
>> The inconvenient is that the log file becomes large (all the restraint are
>> written in it) and messy (the values are mixing with the rest of the info
>> on exchanges), but the speed up is considerable.
>>
>> Note that I still print the values of the restraint in a file, which I
>> haven’t tried to remove but it could also speed up the run.
>>
>> Someone should may be look at this as he speed up applies on XX replicas
>> so lots of CPU time (cooling system, energy, climat change, …) is
>> wasted.
>>
>> I hope this helps.
>> X-
>> --
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