Dear Roland:
Thank you very much for the reply. Since I'm planning to play with
the source code a little bit, I would prefer to compile my own
version ;-) Aslo, I don't think I have the permission to look at your
config.log file.
After using the configuration you suggested, I got some strange error
as attached. I will try to contact the help-desk for more compiler info.
Sincerely,
Bin
===============================================================
/opt/cray/xt-asyncpe/3.3/bin/cc: INFO: linux target is being used
/opt/cray/xt-asyncpe/3.3/bin/cc: INFO: WARNING: gcc/4.2.3 does not
support barcelona options.
/opt/cray/xt-asyncpe/3.3/bin/cc: INFO: Swap gcc/4.2.3 for gcc/
420quadcore or a post 4.3 gcc version.
/usr/bin/ld: attempted static link of dynamic object `/opt/fftw/3.2.2/
lib/libfftw3f.so'
collect2: ld returned 1 exit status
make[3]: *** [grompp] Error 1
make[3]: Leaving directory `/global/u2/b/bingo/bin/gromacs-4.0.7/src/
kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/global/u2/b/bingo/bin/gromacs-4.0.7/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/global/u2/b/bingo/bin/gromacs-4.0.7/src'
make: *** [all-recursive] Error 1
On Mar 17, 2010, at 11:04 AM, Roland Schulz wrote:
Hi,
gromacs is installed on Franklin. (module load gromacs). But I don't
recommend the installed version. It is compiled only in double
precision and with FFTW2 and PGI.
You are welcome to use the version I have installed there:
/global/homes/r/rschulz/software/gromacs (4.0.7)
/global/homes/r/rschulz/software/gromacs.head/ (GIT master)
You can also look at the config.log and env.sh in /global/homes/r/
rschulz/download/ to look how it is compiled.
Of course if you do you do that on your own risk and I don't support
it there. Also I recompile it there frequently so you probably want
to make a copy if you want to keep the same binary during your
simulation.
It is probably better to ask the help-desk to compile with single
precision, fftw3 (to make it faster) and gcc (there were problems
with Gromacs and PGI before).
Roland
On Wed, Mar 17, 2010 at 1:27 PM, BIN ZHANG <zhn...@gmail.com> wrote:
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.abra...@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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