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

Mark Abraham mark.j.abraham at gmail.com
Wed May 13 18:32:27 CEST 2015


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
>  -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


> Adam Hardy
> PhD Student
> School of Engineering and Physical Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS, UK
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