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

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 16 20:43:17 CEST 2015


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:
> 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.


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