[gmx-users] gromacs 4.0 on CRAY-XT4
roland at utk.edu
Wed Mar 17 09:39:53 CET 2010
On Wed, Mar 17, 2010 at 3:55 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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/184.108.40.206
>> 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
> 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.
No. These are standard AMD CPUs and thus SSE2 works find.
module swap PrgEnv-pgi PrgEnv-gnu
module swap gcc gcc/4.2.4
./configure '--enable-mpi' '--without-x' 'CC=cc' 'CPP=cpp' 'CXXCPP=cpp'
'LDFLAGS=-L/sw/xt5/fftw/3.1.2/sles10.1_gnu4.2.4/lib -lfftw3f' 'CFLAGS=-O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
> 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.
If you want to scale to larger number of CPUs you probably need 2D PME. It
is available in the 2dpme git branch. (That it is in a branch means it is at
the moment considered experimental - even more than mast that is)
> 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.
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