[gmx-developers] FFTW 3.1.2 and wisdom

Allen Smith easmith at beatrice.rutgers.edu
Tue Jul 31 19:42:10 CEST 2007

Has anyone worked on using a system "wisdom" file for FFTW 3.1.2 usage by
GROMACS and/or having GROMACS do more extensive planning for FFTW3 -
e.g., FFTW_PATIENT instead of FFTW_MEASURE - but save the resulting
"wisdom"? In the former case, one could make some pre-done
system "wisdom" created using fftwf-wisdom running with the routines that
GROMACS uses, with the -x (FFTW_EXHAUSTIVE) flag used. The latter might be
the best if the code alignment is considerably different between
fftwf-wisdom and GROMACS (more so than any differences due to GROMACS not
planning on the same-allocated arrays (or FFTW malloced arrays) than
the execution is taking place on; I am wondering as to why plans are not
done for unaligned arrays with the FFTW_UNALIGNED planner
flag... alternatively, could fftw_malloc be used in place of
gmx_alloc_aligned?), according to the FFTW documentation ("Caveats in Using



P.S. The systems that we'd be using this on would be a mix of Redhat Linux
boxes (2.4.21-27.ELhugemem or 2.4.21-27.ELsmp, dual P4 Xeon (Foster)) and
SGIs (IRIX 6.5.28m-6.5.30m, generally dual-processor R12000/IP30).

Allen Smith                       http://cesario.rutgers.edu/easmith/
February 1, 2003                               Space Shuttle Columbia
Ad Astra Per Aspera                     To The Stars Through Asperity

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