[gmx-users] Re: question about fftw3 in gromacs 4.6 installation

[Tomek Wlodarski]

Thanks Szilárd, good idea:)
I tried to build gromacs and I got errors..:

/tmp/ccBvi1my.s: Assembler messages:
/tmp/ccBvi1my.s:110: Error: no such instruction: `vpcmov
%xmm13,%xmm5,%xmm14,%xmm10'
[...]
make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/ewald_util.c.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/tmp/ccncRj9M.s: Assembler messages:
/tmp/ccncRj9M.s:431: Error: no such instruction: `vpshad %xmm3,%xmm0,%xmm1'
[....]
make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/bondfree.c.o] Error 1
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
make: *** [all] Error 2

Any idea?
Gromacs confirguration with cmake went ok appart from:

-- Check size of bool - failed
-- Performing Test _isfinite_compile_ok - Failed
-- Performing Test _finite_compile_ok - Failed

I do not know if those are related to building errors..
Thanks!
Best!

tomek


On Sat, Feb 2, 2013 at 3:40 PM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:

> On Sat, Feb 2, 2013 at 2:38 PM, Tomek Wlodarski
> <tomek.wlodarski at gmail.com>wrote:
>
> > On Sat, Feb 2, 2013 at 12:34 PM, Mark Abraham <mark.j.abraham at gmail.com
> > >wrote:
> >
> > > On Sat, Feb 2, 2013 at 1:00 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> > >
> > > >
> > > >
> > > > On 2/1/13 5:26 PM, didymos wrote:
> > > >
> > > >> Hi Justin!
> > > >>
> > > >> I had the same problem and I used your advise but I am not sure if
> > this
> > > >> entirely worked for me...
> > > >>
> > > >> I used:
> > > >> cmake -DGMX_MPI=ON DCMAKE_INSTALL_PREFIX=$HOME/**gromacs
> > > >> -DFFTWF_INCLUDE_DIR=$HOME/**fftw/include
> > > >> -DFFTWF_LIBRARY=$HOME/fftw/**lib/libfftw3f.so
> > > -DCMAKE_PREFIX_PATH=$HOME/*
> > > >> *fftw/
> > > >> ..
> > > >>
> > > >>
> > > > The use of -DCMAKE_PREFIX_PATH eliminates the need for
> > > -DFFTWF_INCLUDE_DIR
> > > > and -DFFTWF_LIBRARY.  Not that this is the source of your problem,
> but
> > > you
> > > > can certainly trim down your command.
> > >
> > >
> > > Indeed. Also missing hyphen before "DCMAKE_INSTALL_PREFIX"
> > >
> >
> > Thanks a lot Mark and Justin - I fixed it.
> >
> > >
> > >  and I got:
> > > >> -- checking for module 'fftw3f'
> > > >> --   found fftw3f, version 3.2.2
> > > >> -- Looking for fftwf_plan_r2r_1d in
> > > >> /home/users/didymos/fftw/lib/**libfftw3f.so
> > > >> -- Looking for fftwf_plan_r2r_1d in
> > > >> /home/users/didymos/fftw/lib/**libfftw3f.so - found
> > > >> -- Looking for fftwf_have_simd_avx in
> > > >> /home/users/didymos/fftw/lib/**libfftw3f.so
> > > >> -- Looking for fftwf_have_simd_avx in
> > > >> /home/users/didymos/fftw/lib/**libfftw3f.so - not found
> > > >> -- Looking for fftwf_have_simd_sse2 in
> > > >> /home/users/didymos/fftw/lib/**libfftw3f.so
> > > >> -- Looking for fftwf_have_simd_sse2 in
> > > >> /home/users/didymos/fftw/lib/**libfftw3f.so - found
> > > >>
> > > >> So it seems ok but I am not sure about first two lines:
> > > >> -- checking for module 'fftw3f'
> > > >> --   found fftw3f, version 3.2.2
> > > >> it should be 3.3.3
> > > >>
> > > >
> > > > Is there a different FFTW installed anywhere else on your system?  I
> > > > believe the first "found fftw3f" statement comes from pkgconfig
> > > detection,
> > > > but this is superseded by what you specify manually.  Perhaps someone
> > who
> > > > is more familiar with this element of the build system can comment.
> > >
> > >
> > > Yeah the first message is CMake finding a system fftw via pkgconfig,
> but
> > > then there is further detection and the one found via pkconfig need not
> > be
> > > the one used. I guess if we have the two layers of detection we need to
> > be
> > > more clear about what is going on.
> > >
> >
> >
> > Yes, I am installing gromacs on a server and I want to use my local
> version
> > of FFTW rather than the one founded by pkgconfig.
> > So to make it clear for me :), which version of FFTW in the end will be
> > used in my case? this detected by pkgconfig or from DCMAKE_PREFIX_PATH
> > Thanks!
> >
>
> I can't tell, but you can check it yourself by having a look at the "mdrun
> -version" output which contains the FFTW version. :)
>
>
> >
> > tomek
> >
> >
> > > Mark
> > > --
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