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

[Szilárd Páll]

Tomek,

That looks like your assembler does not support the XOP instruction set (
http://goo.gl/nMSX0) and chokes on XOP instructions generated by the
compiler. As you did not post much detail on the compilers you are using
and cmake cache, but my guess is that you'll need to either update
your assembler or use SSE4.1 acceleration (AVX128_FMA also enables XOP).

Cheers,

--
Szilárd


On Sat, Feb 2, 2013 at 8:48 PM, Tomek Wlodarski
<tomek.wlodarski at gmail.com>wrote:

> 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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