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, > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? 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