[gmx-users] Intel MKL taken in preference of the specified FFT library

[Mark Abraham]

Hi,

On Thu, Jul 16, 2015 at 5:47 PM Reuti <reuti at staff.uni-marburg.de> wrote:

> Hi,
>
> I just downloaded Gromacs 5.1-rc1 and want to compile it using the GNU
> compilers and a self compiled FFTW*. I configured Gromacs with:
>
> $ cmake .. -DCMAKE_INSTALL_PREFIX=/home/reuti/local/gromacs-5.1-rc1
> -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=/home/reuti/local/fftw-3.3.4
>
> As there was now shared version of FFTW it complains about it, and hence I
> compiled FFTW again - this time with shared library flag and the configure
> step of Gromacs succeeded. But after `make` and `make install` I faced the
> result, that the binary `gmx` like the library in "lib64" were linked
> against Intel MKL. Well, there is an old version of the Intel MKL on the
> system and hence in the LD_LIBRARY_PATH. Once I cleared the LD_LIBRARY_PATH
> I got the result I expected.
>

Older MKL had a "feature" of providing headers that look like FFTW but
execute MKL, and programs will find that if it precedes real FFTW in the
lookup path.


> Question: is this the intended behavior? IMO the GMX_FFT_LIBRARY=fftw3
> flag should be honored first and any set LD_LIBRARY_PATH ignored.
>

Yes, but Intel decided to be "compatible" a.k.a. "deceptive." IIRC enough
people complained that it got fixed for subsequent MKL. Meanwhile, our
CMake code is quite complicated enough without double-checking for every
possible rare case ;-) Meanwhile, there are ways of forcing the find
mechanism to find the FFTW you really want.


>
> -- Reuti
>
> *) The automatic download (like outlined in the INSTALL:
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON) of FFTW and the
> regression tests points to the Gromacs site, but AFAICS they were moved to
> box.com, hence the automatic download fails.
>

No, the FFTW download goes to its site, and the tests download goes to
gerrit.gromacs.org. None of that has changed.

Mark


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