<div dir="ltr">Hi,<div><br></div><div>If so, then we might want a helper function like as_rvec_array, but as_real_array instead.</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Mar 23, 2016 at 10:51 AM Berk Hess <<a href="mailto:hess@kth.se">hess@kth.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#FFFFFF">
<div>On 2016-03-23 10:50, Erik Lindahl
wrote:<br>
</div>
<blockquote type="cite">
Hi,
<div><br>
</div>
<div>I haven’t followed the discussion in detail, but a
long time ago I remember having simliar issues in the kernels
when using a list[] of rvec[] (in plain-old-c, no c++) instead
of extracting the pointer and handling the multiply-by-3
manually. Could it be something similar here, e.g. that the
compiler things it does not know enough about RVec rather than
something going from with the outer list?</div>
</blockquote></div><div text="#000000" bgcolor="#FFFFFF">
That would be my guess. The index used in the same loop comes from a
vector as well and doesn't seem to affect performance.</div><div text="#000000" bgcolor="#FFFFFF"><br>
<br>
Berk</div><div text="#000000" bgcolor="#FFFFFF"><br>
<blockquote type="cite">
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Erik</div>
<div><br>
</div>
<div>
<div>
<blockquote type="cite">
<div>On 23 Mar 2016, at 10:44, Berk Hess <<a href="mailto:hess@kth.se" target="_blank"><a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a></a>> wrote:</div>
<br>
<div>
<div text="#000000" bgcolor="#FFFFFF">
<div>On 2016-03-23 10:42, Mark
Abraham wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi,<br>
<br>
<div class="gmail_quote">
<div dir="ltr">On Wed, Mar 23, 2016 at
9:44 AM Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
Luckily Szilard does thorough testing and
noticed a performance<br>
degradation in change set 25 of <a href="https://gerrit.gromacs.org/#/c/5232/" rel="noreferrer" target="_blank"><a href="https://gerrit.gromacs.org/#/c/5232/" target="_blank">https://gerrit.gromacs.org/#/c/5232/</a></a>
The<br>
only signifcant change with respect to previous
sets is replacing C<br>
pointers by std::vector. I traced the
performance difference back to a<br>
single loop, which must have become several
factors slower to explain<br>
the time difference. I get the performance back
when replacing the<br>
vector by a pointer extracted with .data(), see
below. I looked at the<br>
assembly code from gcc 5.3.1 and the vector case
generated 200 extra<br>
instructions, which makes it difficult to see
what the actual difference<br>
is. The pointer case uses a lot of vmovss and
vaddss, which the vector<br>
one does much less, but this is only serial SIMD
instruction. I thought<br>
that [] in vector might does bounds checking,</blockquote>
<div><br>
</div>
<div>Definitely not in release builds.</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> but it seems it does
not.<br>
Can anyone explain why the vector case can be so
slow?</blockquote>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> If this is a general
issue (with RVec or more?), we need to always
extra<br>
a pointer with .data() for use in all
inner-loops. This is pretty<br>
annoying and difficult to enforce.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
const
std::vector<RVec> f_foreign =<br>
idt_foreign->force<br>
</blockquote>
<div><br>
</div>
<div>This does a copy of the vector, and
doesn't seem to be in any version of this patch
in gerrit. Is this what you meant to write?</div>
</div>
</div>
</blockquote>
I tried this. But my original "vectorized" patch set
took a pointer from idt_foreign and did not copy the
vector, that gives the same, slow, performance.<br>
<br>
Berk<br>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_quote">
<div><br>
</div>
<div>Mark</div>
<div><br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> or<br>
const RVec
*f_foreign =<br>
idt_foreign->force.data();<br>
<br>
int natom =
atomList->atom.size();<br>
for (int i = 0; i <
natom; i++)<br>
{<br>
int ind =
atomList->atom[i];<br>
rvec_inc(f[ind],
f_foreign[ind]);<br>
}<br>
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