[gmx-developers] warning Emulating FMA instructions - this is probably not what you want!

Roland Schulz roland at utk.edu
Wed Oct 17 22:37:54 CEST 2012 

On Wed, Oct 17, 2012 at 4:12 PM, Jochen Hub <jhub at gwdg.de> wrote:

> Hi all,
>
> many thanks for the help. I now compiled with gcc 4.7 and with manually
> adding export CFLAGS=-mfma4 (that is what you meant, right?). Now the
> warning does not appear any more.
>
> I am not sure though how Gromacs performed on this hardware using these
> settings, as the AVX kernels are apparently not in release-4.6.
>
The verlet kernels are . The group kernels not yet. So you need to
use "cutoff-scheme = Verlet" if you want to try that (
http://www.gromacs.org/Documentation/Cut-off_schemes).

Roland


> Thanks,
> Jochen
>
>
> Am 10/17/12 5:12 PM, schrieb Szilárd Páll:
> > On Wed, Oct 17, 2012 at 4:46 PM, Berk Hess <hess at kth.se
> > <mailto:hess at kth.se>> wrote:
> >
> >     Hi,
> >
> >     Apparently icc can compile the code, so than it's not strange that
> >     you end up in this situation. But we should avoid this from
> happening.
> >     SSE4.1 would be the next supported level, but you really want the
> >     vex instructions and not plain SSE, as the latter is much slower.
> >
> >
> > AMD explicitly states that only up to -msse3 should be used on Bulldozer
> > and I have never tried to generate SSE4.1 instructions with icc and run
> > it on AMD. I would not be surprised if it didn't work.
> >
> > --
> > Szilárd
> >
> >     The best thing would be to use gcc, preferably 4.7.
> >
> >     Cheers,
> >
> >     Berk
> >
> >     ----- Reply message -----
> >     From: "Szilárd Páll" <szilard.pall at cbr.su.se
> >     <mailto:szilard.pall at cbr.su.se>>
> >     To: "Discussion list for GROMACS development"
> >     <gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>>
> >     Subject: [gmx-developers] warning Emulating FMA instructions - this
> >     is probably not what you want!
> >     Date: Wed, Oct 17, 2012 15:25
> >
> >
> >     Hi,
> >
> >     First of all, as far as I know, the new icc 13 can not generate
> >     AMD-compatible FMA4/XOP (v12 surely cant:
> >     http://developer.amd.com/Assets/CompilerOptQuickRef-62004200.pdf),
> >     so I find it strange that you've ended up with
> >     GMX_ACCELERATION=AVX_128_FMA using an Intel compiler -- unless you
> >     set the acceleration manually. To get FMA4 support you need to use a
> >     recent gcc version, the newer the better. The Verlet kernels don't
> >     benefit much from FMA4, so if you want to, you can use Intel
> >     Compiler, but then you need to set the acceleration to SSE2 (max
> >     SSE3 works, but we don't use these instructions).
> >
> >     On Wed, Oct 17, 2012 at 11:14 AM, Jochen Hub <jhub at gwdg.de
> >     <mailto:jhub at gwdg.de>> wrote:
> >
> >         Hi developers,
> >
> >         does anyone know how to interpret this icc warning:
> >
> >         [  8%]
> >         /home/jhub/src/gromacs/__include/gmx_x86_avx_128_fma.h(__88):
> >         warning #1224: #warning directive: Emulating FMA instructions -
> >         this is probably not what you want!
> >
> >            #warning Emulating FMA instructions - this is probably not
> >         what you want!
> >
> >
> >     This warning is related to a bug in the build system, you'll need to
> >     add the -mfma4 flag to the compiler flags manually.
> >
> >     --
> >     Szilard
> >
> >
> >         I am compiling 46-release on a Interlagos 6378 with OpenMPI and
> >         icc 13.0.0 20120731. My cmake line is:
> >
> >         cmake $gmxsrc \
> >              -DFFTW_LIBRARY=$FFTW_LOCATION/__lib/libfftw3f.a \
> >              -DFFTW3F_INCLUDE_DIR=$FFTW___LOCATION/include \
> >              -DFFTW3F_LIBRARIES=$FFTW___LOCATION/lib/libfftw3f.a \
> >              -DCMAKE_INSTALL_PREFIX=$(pwd) \
> >              -DGMX_X11=OFF \
> >              -DCMAKE_CXX_COMPILER=$MPICXX \
> >              -DCMAKE_C_COMPILER=$MPICC \
> >              -DGMX_MPI=ON \
> >              -DGMX_PREFER_STATIC_LIBS=ON \
> >              -DGMX_GPU=OFF
> >
> >         and cmake reported:
> >
> >         -- Performing Test GNU_AVX_CFLAG
> >         -- Performing Test GNU_AVX_CFLAG - Success
> >         -- Enabling 128-bit AVX Gromacs acceleration (with
> >         fused-multiply add), and it will help compiler optimization.
> >
> >         Thanks a lot,
> >         Jochen
> >
> >
> >
> >
> >         --
> >         ------------------------------__---------------------
> >         Dr. Jochen Hub
> >         Computational Molecular Biophysics Group
> >         Institute for Microbiology and Genetics
> >         Georg-August-University of Göttingen
> >         Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
> >         Phone: +49-551-39-14189 <tel:%2B49-551-39-14189>
> >         http://cmb.bio.uni-goettingen.__de/
> >         <http://cmb.bio.uni-goettingen.de/>
> >         ------------------------------__---------------------
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> >
>
> --
> ---------------------------------------------------
> Dr. Jochen Hub
> Computational Molecular Biophysics Group
> Institute for Microbiology and Genetics
> Georg-August-University of Göttingen
> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
> Phone: +49-551-39-14189
> http://cmb.bio.uni-goettingen.de/
> ---------------------------------------------------
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