[gmx-users] Power6 @ 4.7 Ghz vs Xeon E5472 @ 3.00GHz

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 16 17:12:57 CET 2010

On 17/02/10 03:06, pim schravendijk wrote:
> Dear Gromacs users,
> I have been installing Gromacs on a Power6 4.7 GHz with Infiniband,
> GBit-Ethernet
> before calling configure, I set:
> export LDFLAGS="-L/gpfs/schraven/fftw3/lib"
> export CPPFLAGS="-I/gpfs/schraven/fftw3/include"
> export CC="mpcc_r -q64"
> export CFLAGS="-O3 -qstrict -qarch=auto -qtune=auto"
> export CXX="mpCC_r -q64"
> export CXXFLAGS="-O3 -qstrict -qarch=auto -qtune=auto"
> export F77="mpxlf_r -q64"
> ### O3 gives warning: The NOSTRICT option (default at OPT(3)) has the
> potential to alter the semantics of a program.
> export FFLAGS="-O3 -qstrict -qnoprefetch -qarch=auto -qtune=auto"
> export LIBS="-lmass"
> export FLIBS= "-xlf -xlf90"
> export OBJECT_MODE=64
> I run on both machines at 8 cores (so within the board), and find the 8
> power6 cores to be 4-5 times slower (!) than the 8 intel xeon cores.
> Does anyone have similar experience between these machines? Are there
> some things I should check?
> It's a bit useless to use the power6 at all with these kind of speeds,
> but they were already here anyway and amazon's 30 day refund on retour
> has expired already ;)
> Hopefully I'm doing something wrong and the situation can still be improved?

This issue might have been discussed on the list before, have a search. 
I suspect the issue is that there are no optimized inner loops for 
Power6 as there are for x86. You can see what GROMACS is finding and 
doing in the configure output. Probably GROMACS is finding nothing 
useful and falling back on generic C versions of such loops. You should 
experiment with --enable-fortran to try the generic FORTRAN versions.


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