[gmx-users] gromacs 4.0 on CRAY-XT4

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 17 08:55:40 CET 2010

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/
> 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.


> 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
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list