Hi,
Pathscale seems to be as fast as gcc 4.5 on AMD Barcelona and the
-march=barcelona option unfortunately doesn't seem to help much.
However, I didn't try any other compiler optimization options.
We do have several Magny-Cours machines around we can benchmark on,
but thanks for the offer!
Cheers,
--
Szilárd
On Fri, Dec 2, 2011 at 2:24 AM, <chris.ne...@utoronto.ca> wrote:
> Dear Szilárd:
>
> Thank you for the advice. I made a mistake when I said that I was using new
> Xeons. The new cluster is actually composed of AMD Opteron Magny-cours 6172
> (12-cores at 2.1 or 2.2 GHz grouped as 24-cores per node). It was because of
> the AMD architecture that I was trying with the pathscale and PGI compilers
> in addition to Intel. For the one system that I have checked, the intel
> compilation is 20% faster than the pathscale compilation, although I didn't
> provide any special compilation options to either. I will continue to look
> into using pathscale optimizations for gromacs on AMDs.
>
> If you are still interested in benchmark speeds on the opterons, then please
> point me to system and mdp files that people are using nowadays for
> comparisons and I will reply back with the benchmark information.
>
> Thank you,
> Chris.
>
> -- original message --
>
> Hi,
>
> I've personally never heard of anybody using gromacs compiled with PGI.
>
>> I am using a new cluster of Xeons and, to get the most efficient
>> compilation, I have compiled gromacs-4.5.4 separately with the intel,
>> pathscale, and pgi compilers.
>
>
> I did try Pathscale a few months ago and AFAIR it wasn't very
> difficult to get it working - although I do remember getting some
> segfaults from time to time. The Intel Compiler support in CMake is
> kind of broken in 4.5, you need to fiddle with the flags a bit, but it
> should be quite straightforward.
>
>> With the pgi compiler, I am most concerned about this floating point
>> overflow warning:
>>
>> ...
>> [ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o
>> [ 19%] Building C object
>> src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o
>> [ 19%] Building C object
>> src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o
>> PGC-W-0129-Floating point overflow. Check constants and constant
>> expressions
>>
>> (/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/gmxlib/trajana/nbsearch.c:
>> 166)
>
>
> That looks like a bug, in case of real==float HUGE_VALF should be used
> instead of HUGE_VAL.
>
>> PGC/x86-64 Linux 11.8-0: compilation completed with warnings
>> [ 19%] Building C object
>> src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o
>> [ 19%] Building C object
>> src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o
>> ...
>>
>>
>> There are also a lot of warnings about a type cast, which seems less like
>> a
>> real problem:
>
>
> Looks like all of them are enum to string-related stuff, they are harmless.
>
>> I compiled like this:
>>
>> module purge
>> module load pgi64/11.8 openmpi_pgi64/1.4.3_ofed
>> module load cmake/2.8.5
>> export CCDIR=/opt/pgi/linux86-64/11.8/bin
>>
>> ## set the location of the single precision FFTW isntallation
>> export FFTW_LOCATION=/home/nealechr/exe/pgi/fftw-3.1.2/exec
>>
>> ##### Nothing below this line usually needs to be changed
>>
>> export CXX=pgCC
>> export CC=pgcc
>>
>> cmake ../source/ \
>> -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include \
>> -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a \
>> -DCMAKE_INSTALL_PREFIX=$(pwd) \
>> -DGMX_X11=OFF \
>> -DCMAKE_CXX_COMPILER=${CCDIR}/pgCC \
>> -DCMAKE_C_COMPILER=${CCDIR}/pgcc \
>> -DGMX_PREFER_STATIC_LIBS=ON \
>> -DGMX_MPI=OFF
>>
>>
>> make
>>
>> make install
>
>
> That looks fine, if you're benchmarking you might want to try the arch
> specific flags - I assume PGI does have something, even if not
> specific for Xeon E5.
>
>> ##########
>>
>> I don't get any similar errors with the intel or pathscale compilers
>> (although intel gives me "icc: command line warning #10159: invalid
>> argument
>> for option '-m'" a lot) and the pathscale compilation appears to be hung
>> on
>
>
> Yeah, as I sad that's kind of broken.
>
>> If anybody has run into this warning, or knows enough to be sure that I
>> don't need to worry about it during mdrun (it seems to be in an analysis
>> file, but I'm not entirely sure), then I would be happy to hear about it.
>> A
>> gmx-users search for PGI returned zero results. I saw something here, but
>> it
>> was not very specific about the problem with pgi (
>> http://www.levlafayette.com/node/175 ).
>
>
> The overflow error is in the trajectory analysis tool's source files
> and doesn't concern mdrun (btw, you can do make mdrun and even make
> install-mdrun ;).
>
> Would it be possible for you to share some performance numbers you're
> getting on the E5?
>
> Cheers,
> --
> Szilárd
>
>> Thank you,
>
>
> --
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