[gmx-users] gromacs 4.0 on CRAY-XT4

[Roland Schulz]

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/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.


No. These are standard AMD CPUs and thus SSE2 works find.

I use
module swap PrgEnv-pgi PrgEnv-gnu
module swap gcc gcc/4.2.4
./configure '--enable-mpi' '--without-x' 'CC=cc' 'CPP=cpp' 'CXXCPP=cpp'
'CXX=CC' '--without-xml'
'CPPFLAGS=-I/sw/xt5/fftw/3.1.2/sles10.1_gnu4.2.4/include'
'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
-funroll-all-loops -std=gnu99'

>
>
>  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)

Roland


>
> 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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>>
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