[gmx-developers] Possible problems with findFFTW

Wed Dec 5 11:52:16 CET 2012

The change broke fftw in an implicit way. Some Gromacs builds, including
the most popular one (non-mpi program set + mpi mdrun), must have been
broken too. But now everything works fine and eclasses accept old and new
variables, but if the ebuild currently executed happens to be using the old
ones, they issue a warning which, unfortunately, easily gets lost in the
sea of build information.
Gromacs ebuilds still use the old variables, but at least the recent change
gives some time to adjust them to the new rules.

Best,
Krzysztof Młynarczyk

2012/12/5 Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>

> Krzysztof Mlynarczyk писал 04-12-2012 22:37:
>
>> I see you are using Gentoo. This weekend there were updates to
>> autotools-utils.eclass and cmake-utils.eclass that broke
>> AUTOTOOL_BUILD_DIR and CMAKE_BUILD_DIR. If you ran emerge fftw:3.0
>> during that time, you may only have one version of fftw installed (the
>> one that was built at the end since they were all using the same
>> working directory) and hence only one *.pc file set is present.
>>  Today all ebuilds work, but still will have to be updated to use
>> BUILD_DIR instead of AUTOTOOL_BUILD_DIR and CMAKE_BUILD_DIR. Please
>> check https://bugs.gentoo.org/show_**bug.cgi?id=445800<https://bugs.gentoo.org/show_bug.cgi?id=445800>[3]. emerge
>>
>> --sync && emerge fftw:3.0 -v should do the trick.
>>  I spent half of the weekend fighting this issue since emerging
>> ambertools failed due to undefined references to fftw functions and
>> the problem was traced down to empty output of pkg-config fftw3 --libs
>> while configuring the build.
>>
>
> Ohh.. I know about this change but i didnt fugured out that its brake fftw
> =\
>
>  Best regards,
>> Krzysztof Młynarczyk
>>
>> 2012/12/4 Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>
>>
>>  Christoph Junghans писал 04-12-2012 21:34:
>>>
>>>  2012/12/2 Alexey Shvetsov <alexxy at omrb.pnpi.spb.ru>:
>>>>
>>>>  Hi all!
>>>>>
>>>>> With tag 4.6-beta1 i noticed that on 64bit multilib systems gromacs
>>>>> trying
>>>>> to find 32bit versions first and only then 64bit versions thats why it
>>>>> failes
>>>>>
>>>>> -- Enabling SSE4.1 Gromacs acceleration, and it will help compiler
>>>>> optimization.
>>>>> -- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1")
>>>>> -- checking for module 'fftw3f'
>>>>> --   package 'fftw3f' not found
>>>>>
>>>> Why is that fftw should have a pkg-config file. Can you run:
>>>> $ pkg-config --libs fftw3f
>>>>
>>>
>>> It didnt find it. fftw version is 3.3.3
>>>
>>>  -- Looking for fftwf_plan_r2r_1d in /usr/lib32/libfftw3f.so
>>>>> -- Looking for fftwf_plan_r2r_1d in /usr/lib32/libfftw3f.so - not found
>>>>> CMake Error at cmake/FindFFTW.cmake:102 (message):
>>>>>   Could not find fftwf_plan_r2r_1d in /usr/lib32/libfftw3f.so, take a
>>>>> look
>>>>> at
>>>>>   the error message in
>>>>>
>>>>>
>>>>> /var/tmp/portage/sci-**chemistry/gromacs-4.6.9999/**
>>>>> work/gromacs-4.6.9999_float/**CMakeFiles/CMakeError.log
>>>>>   to find out what went wrong.  If you are using a static lib (.a)
>>>>> make sure
>>>>>   you have specified all dependencies of fftw3f in FFTWF_LIBRARY by
>>>>> hand
>>>>>   (e.g.  -DFFTWF_LIBRARY='/path/to/**libfftw3f.so;/path/to/libm.so'**)
>>>>> !
>>>>> Call Stack (most recent call first):
>>>>>   CMakeLists.txt:948 (find_package)
>>>>>
>>>>> I have both versions present on this system
>>>>>
>>>>> x201 ~ # ls -l  /usr/lib*/libfftw3f.so.3
>>>>> lrwxrwxrwx 1 root root 18 May 25  2012 /usr/lib/libfftw3f.so.3 ->
>>>>> libfftw3f.so.3.3.2
>>>>> lrwxrwxrwx 1 root root 18 Nov  9 11:10 /usr/lib32/libfftw3f.so.3 ->
>>>>> libfftw3f.so.3.2.4
>>>>> lrwxrwxrwx 1 root root 18 May 25  2012 /usr/lib64/libfftw3f.so.3 ->
>>>>> libfftw3f.so.3.3.2
>>>>>
>>>>> PS cmake version is 2.8.10.2
>>>>>
>>>>> --
>>>>> Best Regards,
>>>>> Alexey 'Alexxy' Shvetsov
>>>>> Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
>>>>> Gatchina,
>>>>> Russia
>>>>> Department of Molecular and Radiation Biophysics
>>>>> Gentoo Team Ru
>>>>> Gentoo Linux Dev
>>>>> mailto:alexxyum at gmail.com
>>>>> mailto:alexxy at gentoo.org
>>>>> mailto:alexxy at omrb.pnpi.spb.ru
>>>>> --
>>>>> gmx-developers mailing list
>>>>> gmx-developers at gromacs.org
>>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-**developers<http://lists.gromacs.org/mailman/listinfo/gmx-developers>[1]
>>>>>
>>>>> Please don't post (un)subscribe requests to the list. Use the www
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>>>>> .
>>>>>
>>>>
>>>> --
>>>> Christoph Junghans
>>>> Web: http://www.compphys.de [2]
>>>>
>>>
>>> --
>>> Best Regards,
>>> Alexey 'Alexxy' Shvetsov
>>> Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina,
>>> Russia
>>> Department of Molecular and Radiation Biophysics
>>> Gentoo Team Ru
>>> Gentoo Linux Dev
>>> mailto:alexxyum at gmail.com
>>> mailto:alexxy at gentoo.org
>>> mailto:alexxy at omrb.pnpi.spb.ru
>>> --
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
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>>>
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>>>
>>
>>
>>
>> Links:
>> ------
>> [1] http://lists.gromacs.org/**mailman/listinfo/gmx-**developers<http://lists.gromacs.org/mailman/listinfo/gmx-developers>
>> [2] http://www.compphys.de
>> [3] https://bugs.gentoo.org/show_**bug.cgi?id=445800<https://bugs.gentoo.org/show_bug.cgi?id=445800>
>>
>
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina,
> Russia
> Department of Molecular and Radiation Biophysics
> Gentoo Team Ru
> Gentoo Linux Dev
> mailto:alexxyum at gmail.com
> mailto:alexxy at gentoo.org
> mailto:alexxy at omrb.pnpi.spb.ru
> --
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