On 17/03/2010 6:19 PM, BIN ZHANG wrote:
Dear Mark:
Thanks for your reply and sorry for my less info.
I'm confused about your statement "I was trying to build gromacs 4.0 on
a cray-xt4 machine, the same one as the benchmark in the gromacs4 paper"
because I can't see any mention of results on such a machine in J. Chem.
Theory Comput. 2008, 4, 435-447
Here is the configuration line I used:
module load fftw/2.1.5.1
module load libxml2
CXX=CC CC=cc F77=ftn MPICC=cc LIBS="$XML2_LIBDIR -L/usr/X11/lib64"
./configure --enable-mpi --enable-double --enable-fortran
--prefix=$HOME/gmx/para --disable-nice --with-fft=fftw2
--program-suffix=_mpi
The use of double precision and the absence of hardware-optimized inner
loops (--enable-fortran, since AFAIK there's no alternative on XT4) will
slow things down compared to an Intel machine.
Also, I searched the maillist and added ddorder in the mdrun line, but
that doesn't seem to help much.
aprun -n 128 $gmxdir/mdrun_mpi -deffnm npt_02 -g npt_02.log -ddorder
cartesian -npme 32
You will need to experiment with npme and ddorder to find what's best.
Also consider g_tune_pme in the git codebase.
Mark
The system is a membrane protein and I'm using berger lipid/OPLS-AA
force filed.
Thanks
Bin
On Mar 17, 2010, at 12:02 AM, Mark Abraham wrote:
On 17/03/2010 5:43 PM, BIN ZHANG wrote:
Dear all:
I was trying to build gromacs 4.0 on a cray-xt4 machine, the same one as
the benchmark in the gromacs4 paper (). However, my timing for a similar
system, ~100,000 atoms, is almost 3 times slower than in the paper. For
example, I only got ~25 ns/day with 128 cpus. So is there any special
flags, or tricks I can use during the configuration for detailed tuning?
Probably. You've made it hard to help you when you haven't provided
(at least) your configure command, compiler and version, mdrun command
line and simulation system composition.
Mark
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