[gmx-developers] warning Emulating FMA instructions - this is probably not what you want!
Roland Schulz
roland at utk.edu
Thu Oct 18 15:12:46 CEST 2012
On Thu, Oct 18, 2012 at 7:01 AM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:
> That's correct. The point I was trying to make is that we might end up
> hearing about this issue in the future if people use CFLAGS just by
> routine. I fact, I'm not even sure that cmake is not supposed to pick up
> CLAGS as well and it's some later cmake pass rewriting compiler options is
> that the current code is trying to overcome, but it ends up loosing some
> options when CFLAGS is set.
>
> Any comments? Should CFLAGS work?
>
Yes. And I think it mostly works like it should. Environment variables
should only be read the first time you run. And it should overwrite any of
the default settings. Thus I think we should not set any flags if CFLAGS is
set. Sander added that with 0ce2e62b72d2 to cmake/gmxCFlags.cmake. None of
the flags set in that file are added to CMAKE_C_FLAGS if CFLAGS is set..
But the new acceleration depending options (e.g. -mavx) are set even if
CFLAGS is set. I think this is wrong. If you agree I can fix that.
Roland
>
> --
> Szilárd
>
>
>
> On Thu, Oct 18, 2012 at 9:43 AM, Jochen Hub <jhub at gwdg.de> wrote:
>
>> Following Szilard, I tried to use
>>
>> cmake -DCMAKE_C_FLAGS=-mfma4 ...
>>
>> instead of export CFLAGS=-mfma4 to add the -mfma4 flag. Now, the only
>> difference in CMakeCache.txt is
>>
>> < CMAKE_C_FLAGS:STRING='-mavx -Wall -Wno-unused -Wunused-value '
>> ---
>> > CMAKE_C_FLAGS:STRING=-mavx -Wall -Wno-unused -Wunused-value -mfma4
>>
>> which is just what I wanted, right? (and the warning on emulating FMA
>> instructions does not appear any more).
>>
>> Jochen
>>
>>
>> Am 10/17/12 11:28 PM, schrieb Szilárd Páll:
>>
>>>
>>> That way of calling CMake triggers an interesting bug in the option
>>> generator and CFLAGS will essentially override part of the
>>> auto-generated compiler options. Diff of relevant lines in
>>> CMakeCache.txt are below, the only difference is that the second file
>>> ("+" in the diff) was generated by running "CFLAGS=-march=native
>>> cmake...":
>>>
>>> //Flags used by the compiler during all build types
>>> -CMAKE_C_FLAGS:STRING='-msse2 -Wall -Wno-unused -Wunused-value '
>>> +CMAKE_C_FLAGS:STRING='-msse2 -march=native '
>>> //Flags used by the compiler during debug builds.
>>> -CMAKE_C_FLAGS_DEBUG:STRING=-**fno-inline -g
>>> +CMAKE_C_FLAGS_DEBUG:STRING=-g
>>> -//Flags used by the compiler during release builds.
>>> -CMAKE_C_FLAGS_RELEASE:STRING=**-fomit-frame-pointer -funroll-all-loops
>>> -fexcess-precision=fast -O3 -DNDEBUG
>>> +//Flags used by the compiler during release builds (/MD /Ob1 /Oi
>>> +// /Ot /Oy /Gs will produce slightly less optimized but smaller
>>> +// files).
>>> +CMAKE_C_FLAGS_RELEASE:STRING=**-O3 -DNDEBUG
>>>
>>> As this messes with "considered to be best basic set of options", we
>>> could state that CFLAGS should not be used, but it might be a better
>>> alternative to make the configuration prepend the CFLAG to the
>>> CMAKE_C_FLAGS and keep our generated set of flags as well.
>>>
>>> I'm not sure which options is best. Thoughts?
>>>
>>> --
>>> Szilárd
>>>
>>>
>>> On Wed, Oct 17, 2012 at 10:12 PM, Jochen Hub <jhub at gwdg.de
>>> <mailto: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.
>>>
>>> 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>
>>> <mailto: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**>
>>> <mailto: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@**gromacs.org<gmx-developers at gromacs.org>
>>> >
>>> <mailto:gmx-developers at __groma**cs.org <http://gromacs.org>
>>> <mailto:gmx-developers@**gromacs.org<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<http://developer.amd.com/__Assets/CompilerOptQuickRef-__62004200.pdf>
>>> <http://developer.amd.com/**Assets/CompilerOptQuickRef-**
>>> 62004200.pdf<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>
>>> <mailto: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>
>>> <tel:%2B49-551-39-14189>
>>> http://cmb.bio.uni-goettingen.**____de/
>>> <http://cmb.bio.uni-__**goettingen.de/<http://cmb.bio.uni-__goettingen.de/>
>>> <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 <tel:%2B49-551-39-14189>
>>> http://cmb.bio.uni-goettingen.**__de/ <http://cmb.bio.uni-**
>>> goettingen.de/ <http://cmb.bio.uni-goettingen.de/>>
>>> ------------------------------**__---------------------
>>>
>>>
>>>
>> --
>> ------------------------------**---------------------
>> 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/ <http://cmb.bio.uni-goettingen.de/>
>> ------------------------------**---------------------
>> --
>> gmx-developers mailing list
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>
>
--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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