[gmx-developers] Error configuring 5.0.5 with GMX_BUILD_OWN_FFTW=yes

Wed May 13 22:43:50 CEST 2015

On Wed, May 13, 2015 at 10:24 PM Berk Hess <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...

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> 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> 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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