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<div class="moz-cite-prefix">Hi,<br>
<br>
I filed a redmine:<br>
<a class="moz-txt-link-freetext" href="http://redmine.gromacs.org/issues/1735">http://redmine.gromacs.org/issues/1735</a><br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 05/13/2015 10:50 PM, Berk Hess wrote:<br>
</div>
<blockquote cite="mid:5553B913.302@kth.se" type="cite">
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<div class="moz-cite-prefix">On 05/13/2015 10:43 PM, Mark Abraham
wrote:<br>
</div>
<blockquote
cite="mid:CAMNuMAT5FWL7gi307ZWLJWCLd1Zbz40Fwvz4OLVNwV5duKroDg@mail.gmail.com"
type="cite">
<div dir="ltr"><br>
<br>
<div class="gmail_quote">On Wed, May 13, 2015 at 10:24 PM Berk
Hess <<a moz-do-not-send="true" href="mailto:hess@kth.se">hess@kth.se</a>>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi,<br>
<br>
I also noticed only now that there is more logic on
line 158 of FindFFTW.cmake that probably should have
been updated (as well as the documentation at the
top). I should have stayed out of the business of
editing cmake files :-(</div>
</div>
</blockquote>
<div><br>
</div>
<div>It's not exactly your fault that nobody thought to
comment anywhere that FindFFTW.cmake and the own-fftw
build are supposed to fulfil the same contract...</div>
</div>
</div>
</blockquote>
I already thought they would need to fulfill the same contract,
but I thought that would happen through the same test, since it
tests for HAVE_SIMD as well. I still don't understand how
HAVE_SIMD gets set (and HAVE_SSE not) when we build our own FFT.
Anyhow, it's probably better if someone else looks into fixing
this.<br>
<br>
Berk<br>
<blockquote
cite="mid:CAMNuMAT5FWL7gi307ZWLJWCLd1Zbz40Fwvz4OLVNwV5duKroDg@mail.gmail.com"
type="cite">
<div dir="ltr">
<div class="gmail_quote">
<div><br>
</div>
<div>Anyway, bring on the day when we can do our own FFTs!
;-)</div>
<div><br>
</div>
<div>Mark</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div><br>
<br>
Berk</div>
</div>
<div bgcolor="#FFFFFF" text="#000000">
<div><br>
<br>
On 05/13/2015 10:21 PM, Mark Abraham wrote:<br>
</div>
</div>
<div bgcolor="#FFFFFF" text="#000000">
<blockquote type="cite">
<div dir="ltr">Hi,<br>
<br>
<div class="gmail_quote">On Wed, May 13, 2015 at
8:54 PM Berk Hess <<a moz-do-not-send="true"
href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi,<br>
<br>
I had a look at my change to the FFTW
checks, but I don't see how something can go
wrong here. As far as I can see the order
and essential logic have not changed
compared to 5.0.4.<br>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>The issue is on line 91. The new AND NOT
works only under the assumption that FFTWF_FOUND
means that we ran the SIMD-flavour trycompile
tests. But the auto-download sets FFTWF_FOUND
*and* FFTWF_HAVE_SIMD (because it will have
SIMD) and runs/fakes none of the tests. The
previous logic was positive, so the issue did
not arise. One fix is to change
src/contrib/fftw/CMakeLists.txt to set a fake
${FFTW}_HAVE_SSE2.</div>
<div><br>
</div>
<div>Ideally, we could have a sane test that the
auto-download works, but even if we'd had one,
the build would have worked and we likely
wouldn't have verified the warning-issuing
behaviour :-(</div>
<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">
<div bgcolor="#FFFFFF" text="#000000">
<div> Cheers,<br>
<br>
Berk</div>
</div>
<div bgcolor="#FFFFFF" text="#000000">
<div><br>
<br>
On 05/13/2015 05:54 PM, Mark Abraham wrote:<br>
</div>
</div>
<div bgcolor="#FFFFFF" text="#000000">
<blockquote type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>Thanks for the email.</div>
<div><br>
<div class="gmail_quote">On Wed, May 13,
2015 at 5:34 PM Hardy, Adam <<a
moz-do-not-send="true"
href="mailto:ah259@hw.ac.uk"
target="_blank">ah259@hw.ac.uk</a>>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">Dear all,<br>
<br>
I'm having trouble installing the
latest release. Leaving all other
options default, but switching
GMX_BUILD_OWN_FFTW=yes results in a
cmake warning:<br>
<br>
"<br>
CMake Warning at
cmake/gmxManageFFTLibraries.cmake:93
(message):<br>
The FFTW library was compiled
with neither --enable-sse nor
--enable-sse2;<br>
those would have enabled SSE(2)
SIMD instructions. This will give<br>
suboptimal performance. You
should (re)compile the FFTW library
with both<br>
SSE2 and AVX instruction support
(use both --enable-sse2 and
--enable-avx).<br>
The FFTW library will determine
at runtime which SIMD instruction
set is<br>
fastest for different parts of
the FFTs.<br>
Call Stack (most recent call
first):<br>
CMakeLists.txt:742 (include) </blockquote>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">"</blockquote>
<div> </div>
<div>That's inconsistent and somewhat
embarassing, but not actually a
problem. FFTW hasn't been downloaded
or built by the time that warning is
issued, so we have some logic that
doesn't work correctly in the
auto-download case.</div>
<div><br>
</div>
<div>Later on, FFTW is built but is
still compiled with only
--enable-sse2. We may change that
behaviour for 5.1, if it is clear
that adding --enable-avx as well is
always neutral-or-useful, but
there's nothing wrong with the
resulting mdrun here.</div>
<div><br>
</div>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex"> This
configuration works as expected with
5.0.4.<br>
<br>
I get the same results with this
setting as "no". This message
doesn't make much sense in either
case as I do not have an FFTW
library on my machine.</blockquote>
<div><br>
</div>
<div>Hmm that could be a minor
problem, but none of us have tried a
build on a machine without FFTW, for
the obvious reason. :-)</div>
<div> </div>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">The error I
get in 5.0.4 for this scenario is:<br>
<br>
"<br>
Could not find fftw3f library named
libfftw3f, please specify its
location in CMAKE_PREFIX_PATH or
FFTWF_LIBRARY by hand (e.g.<br>
-DFFTWF_LIBRARY='/path/to/libfftw3f.so')<br>
<br>
CMake Error at
cmake/gmxManageFFTLibraries.cmake:76
(MESSAGE):<br>
Cannot find FFTW 3 (with correct
precision - libfftw3f for
mixed-precision<br>
GROMACS or libfftw3 for
double-precision GROMACS). Either
choose the right<br>
precision, choose another FFT(W)
library (-DGMX_FFT_LIBRARY), enable
the<br>
advanced option to let GROMACS
build FFTW 3 for you<br>
(-GMX_BUILD_OWN_FFTW=ON), or use
the really slow GROMACS built-in
fftpack<br>
library
(-DGMX_FFT_LIBRARY=fftpack).<br>
Call Stack (most recent call
first):<br>
CMakeLists.txt:738 (include)<br>
"<br>
<br>
I see some in the release notes some
changes were made to the cmake
warnings for AVX capable processors
which I belive mine is </blockquote>
<blockquote class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">(AMD
fx-8350).<br>
</blockquote>
<div><br>
</div>
<div>Yes, but we don't expect much/any
improvement on AMD cpus from adding
--enable-avx. Use --enable-sse2
always (which is what the
auto-download does).</div>
<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"> Thanks,<br>
<br>
Adam Hardy<br>
PhD Student<br>
School of Engineering and Physical
Sciences<br>
Heriot-Watt University<br>
Edinburgh EH14 4AS, UK<br>
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