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

Reuti reuti at staff.uni-marburg.de
Thu Jul 16 17:47:15 CEST 2015


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.

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

-- 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.

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