On Fri, 2014-09-12 at 16:45 +0000, Lawrenz, Morgan wrote:
> Hi all,
> What are the ramifications of building amber - serial or parallel -
> without fftw (i.e. the -nofftw3 flag for configure)?
> I see that it "disables RISM and the FFT solver in pbsa," so does this
> only affect mmpb/gbsa calculations? Not standard MD?
> I will need both, and installation with that flag is the only one
> successfully compiling for me right now.
If you don't plan on using RISM, the FFT solver in PBSA, or the mdgx
simulation engine, then you can safely skip the FFTW3 build.
Specifically -- it builds PBSA without the fft solver, it skips the MDGX
build, and it skips all RISM functionality.
Of course you could always tell us what error you're receiving and we
can try to help fix it. I helped someone else with an FFTW3-related
issue (something about not being able to open fftw3.f03) -- an issue we
were able to fix. Was this the problem you're having?
This problem exists in AmberTools 14 as far as I can tell, so I'll put
together the fix we implemented recently.
If that _is_ the problem (that I described), you should be able to work
around it by running the command:
make -C AmberTools/src/fftw-3.3 install
after running configure but before running "make install" -- that should
force the FFTW3 build (the dependencies were slightly wrong in one place
such that FFTW3 may not be built when it's needed).
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 12 2014 - 10:30:02 PDT
