[gmx-users] gromacs 4.0 on CRAY-XT4
zhngbn at gmail.com
Wed Mar 17 08:19:47 CET 2010
Thanks for your reply and sorry for my less info.
Here is the configuration line I used:
module load fftw/220.127.116.11
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
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
>> system, ~100,000 atoms, is almost 3 times slower than in the paper.
>> 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
> 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.
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