Dear Mark:
Thanks for your reply and sorry for my less info.
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
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
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
--
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/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
