[gmx-developers] Error configuring 5.0.5 with GMX_BUILD_OWN_FFTW=yes
Berk Hess
hess at kth.se
Thu May 14 10:20:56 CEST 2015
Hi,
I filed a redmine:
http://redmine.gromacs.org/issues/1735
Cheers,
Berk
On 05/13/2015 10:50 PM, Berk Hess wrote:
> On 05/13/2015 10:43 PM, Mark Abraham wrote:
>>
>>
>> On Wed, May 13, 2015 at 10:24 PM Berk Hess <hess at kth.se
>> <mailto:hess at kth.se>> wrote:
>>
>> Hi,
>>
>> 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 :-(
>>
>>
>> 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...
> 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.
>
> Berk
>>
>> Anyway, bring on the day when we can do our own FFTs! ;-)
>>
>> Mark
>>
>>
>>
>> Berk
>>
>>
>> On 05/13/2015 10:21 PM, Mark Abraham wrote:
>>> Hi,
>>>
>>> On Wed, May 13, 2015 at 8:54 PM Berk Hess <hess at kth.se
>>> <mailto:hess at kth.se>> wrote:
>>>
>>> Hi,
>>>
>>> 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.
>>>
>>>
>>> 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.
>>>
>>> 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 :-(
>>>
>>> Mark
>>>
>>> Cheers,
>>>
>>> Berk
>>>
>>>
>>> On 05/13/2015 05:54 PM, Mark Abraham wrote:
>>>> Hi,
>>>>
>>>> Thanks for the email.
>>>>
>>>> On Wed, May 13, 2015 at 5:34 PM Hardy, Adam <ah259 at hw.ac.uk
>>>> <mailto:ah259 at hw.ac.uk>> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> 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:
>>>>
>>>> "
>>>> CMake Warning at cmake/gmxManageFFTLibraries.cmake:93
>>>> (message):
>>>> The FFTW library was compiled with neither
>>>> --enable-sse nor --enable-sse2;
>>>> those would have enabled SSE(2) SIMD instructions.
>>>> This will give
>>>> suboptimal performance. You should (re)compile the
>>>> FFTW library with both
>>>> SSE2 and AVX instruction support (use both
>>>> --enable-sse2 and --enable-avx).
>>>> The FFTW library will determine at runtime which
>>>> SIMD instruction set is
>>>> fastest for different parts of the FFTs.
>>>> Call Stack (most recent call first):
>>>> CMakeLists.txt:742 (include)
>>>>
>>>> "
>>>>
>>>> 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.
>>>>
>>>> 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.
>>>>
>>>> This configuration works as expected with 5.0.4.
>>>>
>>>> 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.
>>>>
>>>>
>>>> Hmm that could be a minor problem, but none of us have
>>>> tried a build on a machine without FFTW, for the obvious
>>>> reason. :-)
>>>>
>>>> The error I get in 5.0.4 for this scenario is:
>>>>
>>>> "
>>>> Could not find fftw3f library named libfftw3f, please
>>>> specify its location in CMAKE_PREFIX_PATH or
>>>> FFTWF_LIBRARY by hand (e.g.
>>>> -DFFTWF_LIBRARY='/path/to/libfftw3f.so')
>>>>
>>>> CMake Error at cmake/gmxManageFFTLibraries.cmake:76
>>>> (MESSAGE):
>>>> Cannot find FFTW 3 (with correct precision -
>>>> libfftw3f for mixed-precision
>>>> GROMACS or libfftw3 for double-precision GROMACS).
>>>> Either choose the right
>>>> precision, choose another FFT(W) library
>>>> (-DGMX_FFT_LIBRARY), enable the
>>>> advanced option to let GROMACS build FFTW 3 for you
>>>> (-GMX_BUILD_OWN_FFTW=ON), or use the really slow
>>>> GROMACS built-in fftpack
>>>> library (-DGMX_FFT_LIBRARY=fftpack).
>>>> Call Stack (most recent call first):
>>>> CMakeLists.txt:738 (include)
>>>> "
>>>>
>>>> I see some in the release notes some changes were made
>>>> to the cmake warnings for AVX capable processors which
>>>> I belive mine is
>>>>
>>>> (AMD fx-8350).
>>>>
>>>>
>>>> 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).
>>>>
>>>> Mark
>>>>
>>>> Thanks,
>>>>
>>>> Adam Hardy
>>>> PhD Student
>>>> School of Engineering and Physical Sciences
>>>> Heriot-Watt University
>>>> Edinburgh EH14 4AS, UK
>>>>
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>>>
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>
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>
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