[gmx-developers] GROMACS 4.6 error in file src/gromacs/analysisdata/analysisdata.cpp:45:0

Christoph Junghans junghans at votca.org
Fri Aug 24 21:16:57 CEST 2012

2012/8/24 Thomas Evangelidis <tevang3 at gmail.com>:
>> >> If you could provide us more information of why your gcc doesn't
>> >> understand -mavx that would be useful. Is gcc really 4.7 as cmake
>> >> prints?
>> >> Gcc 4.7 should support 4.7 thus this is confusing. How did you obtain
>> >> gcc?
>> >> Is it from your distribution (if so which one) or did you download and
>> >> compile gcc yourself? If so how?
>> >>
>> >
>> > Yes, its the precompiled gcc 4.7 from Fedora 17 86_64 repositories.
>> That odd. Anyone has access to Fedora 17 and can try to reproduce
>> this? It seems it would be really nice to have more distributions on
>> Jenkins.
>> >
>> > Both command lines failed. cmake is looking for a file a library named
>> > "libfftw3f" which does not exist in my fftw installation. What configure
>> > options do you use to compile fftw?
>> You probably compiled fftw without "--enable-float". You can also use
>> the fftw library without sse from before. It will work it just isn't
>> won't be quite as fast.
> Actually I did. This is the command line I used the last time:
> ./configure --enable-float --enable-threads
> --prefix=`pwd`/single_precision_installation_dir --enable-sse
> Here's the list of files in my fftw installation directory matching the
> pattern "libfftw3f". I couldn't find any "libfftw3f.so" as the error says.
> $ find ../fftw-3.3.2/single_precision_installation_dir/ -wholename
> "*libfftw3f*"
> ../fftw-3.3.2/single_precision_installation_dir/lib/libfftw3f_threads.la
> ../fftw-3.3.2/single_precision_installation_dir/lib/libfftw3f.la
> ../fftw-3.3.2/single_precision_installation_dir/lib/libfftw3f_threads.a
> ../fftw-3.3.2/single_precision_installation_dir/lib/libfftw3f.a
Is there a  fftw3f.pc in single_precision_installation_dir? If so, add
to your PKG_CONFIG_PATH that will help pkg-config to find the custom
Otherwise you will have to set  FFTW_LIBRARY and FFTW_INCLUDE_DIR by
hand. And never ever mix FFTW_LIBRARY and FFTW_INCLUDE_DIR of
different fftw installations like your did above that will lead to all
kind of strange errors.

I would always use the system libfftw in the first attempt to compile.
You may have to install Fedora's fftw-dev package as well.
The error "Your fftw3 seems to be compiled without SSE!" only tells
you that the performance is influence a bit.

Btw. as far as I remember Gromacs only supports OpenMM version 2.0.
(Other developers please correct me!)


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Christoph Junghans
Web: http://www.compphys.de

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