<div dir="ltr">Hi,<br><br><div class="gmail_quote">On Wed, May 13, 2015 at 10:50 PM Berk Hess <<a 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>On 05/13/2015 10:43 PM, Mark Abraham
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr"><br>
<br>
<div class="gmail_quote">On Wed, May 13, 2015 at 10:24 PM Berk
Hess <<a 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 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></div><div bgcolor="#FFFFFF" text="#000000">
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.</div></blockquote><div><br></div><div>It can't happen through a CMake test, because the download and build of FFTW happens at make time, not configure time. So the old implementation faked it in the file I mentioned.</div><div><br></div><div>I uploaded a hack-fix for the release branch, and a refactoring on master that avoids the need for faking things just to avoid warnings.</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">
<br>
Berk</div><div bgcolor="#FFFFFF" text="#000000"><br>
<blockquote 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 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 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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