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General tips :h3

NOTE: this page is still a work in progress

Here is a list of general ideas for improving simulation performance.
Most of them are only applicable to certain models and certain
bottlenecks in the current performance, so let the timing data you
generate be your guide.  It is hard, if not impossible, to predict how
much difference these options will make, since it is a function of
problem size, number of processors used, and your machine.  There is
no substitute for identifying performance bottlenecks, and trying out
various options.

rRESPA
Two-FFT PPPM
Staggered PPPM
single vs double PPPM
partial charge PPPM
verlet/split run style
processor command for proc layout and numa layout
load-balancing: balance and fix balance :ul

Two-FFT PPPM, also called {analytic differentiation} or {ad} PPPM,
uses 2 FFTs instead of the 4 FFTs used by the default {ik
differentiation} PPPM. However, 2-FFT PPPM also requires a slightly
larger mesh size to achieve the same accuracy as 4-FFT PPPM. For
problems where the FFT cost is the performance bottleneck (typically
large problems running on many processors), 2-FFT PPPM may be faster
than 4-FFT PPPM.

Staggered PPPM performs calculations using two different meshes, one
shifted slightly with respect to the other.  This can reduce force
aliasing errors and increase the accuracy of the method, but also
doubles the amount of work required. For high relative accuracy, using
staggered PPPM allows one to half the mesh size in each dimension as
compared to regular PPPM, which can give around a 4x speedup in the
kspace time. However, for low relative accuracy, using staggered PPPM
gives little benefit and can be up to 2x slower in the kspace
time. For example, the rhodopsin benchmark was run on a single
processor, and results for kspace time vs. relative accuracy for the
different methods are shown in the figure below.  For this system,
staggered PPPM (using ik differentiation) becomes useful when using a
relative accuracy of slightly greater than 1e-5 and above.

:c,image(JPG/rhodo_staggered.jpg)

NOTE: Using staggered PPPM may not give the same increase in accuracy
of energy and pressure as it does in forces, so some caution must be
used if energy and/or pressure are quantities of interest, such as
when using a barostat.
