[gmx-users] gromacs 4.0 on CRAY-XT4

[BIN ZHANG]

Dear mark, and Roland:

Thanks for all the suggestions.
I was confused gromacs4 paper with another one by Erik Lindahl. (http://www.ncbi.nlm.nih.gov/pubmed/19229308 
) Since there they studied the same system (Kv1.2 voltage-gated ion  
channel), and they mentioned about the same speed as the benckmark, on  
a cray-xt4 machine. Here is also a link for the machine I'm working  
on: http://www.nersc.gov/nusers/systems/franklin/

Bin.


On Mar 17, 2010, at 1:39 AM, Roland Schulz wrote:

>
>
> 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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