[gmx-users] gromacs 4.0 on CRAY-XT4

[Mark Abraham]

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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>