[gmx-users] gromacs 4.0 on CRAY-XT4

BIN ZHANG zhngbn at gmail.com
Wed Mar 17 08:19:47 CET 2010

Dear Mark:

Thanks for your reply and sorry for my less info.

Here is the configuration line I used:
module load fftw/
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.


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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