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41
doc/Section_accelerate.html
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@ -101,28 +101,33 @@ simply trying them out.
<LI>processor command for layout
<LI>OMP when lots of cores
</UL>
<P>2-FFT PPPM, also called <I>analytic differentiation</I> or <I>ad</I> PPPM, uses 2 FFTs
instead of the 4 FFTs used by the default <I>ik differentiation</I> 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.
<P>2-FFT PPPM, also called <I>analytic differentiation</I> or <I>ad</I> PPPM, uses
2 FFTs instead of the 4 FFTs used by the default <I>ik differentiation</I>
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.
</P>
<P>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.
<P>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.
</P>
<CENTER><IMG SRC = "JPG/rhodo_staggered.jpg">
</CENTER>
<P>IMPORTANT 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.
<P>IMPORTANT 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.
</P>
<HR>

41
doc/Section_accelerate.txt
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@ -97,28 +97,33 @@ load-balancing: balance and fix balance
processor command for layout
OMP when lots of cores :ul
2-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.
2-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.
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)
IMPORTANT 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.
IMPORTANT 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.
:line