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,
> Chris.
> --
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