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<div class="moz-cite-prefix">On 2016-03-23 10:42, Mark Abraham
wrote:<br>
</div>
<blockquote
cite="mid:CAMNuMAT8Wgv4ZroixK-JqNxvyYhpZzWNr7R8AK4rgetgFeEjrQ@mail.gmail.com"
type="cite">
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<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
moz-do-not-send="true" href="mailto:hess@kth.se"><a class="moz-txt-link-abbreviated" href="mailto:hess@kth.se">hess@kth.se</a></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 moz-do-not-send="true"
href="https://gerrit.gromacs.org/#/c/5232/"
rel="noreferrer" target="_blank">https://gerrit.gromacs.org/#/c/5232/</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
cite="mid:CAMNuMAT8Wgv4ZroixK-JqNxvyYhpZzWNr7R8AK4rgetgFeEjrQ@mail.gmail.com"
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>
--<br>
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