It could be system-specific. Could you try out dppc in tutor/gmxbench or
download gmxbench from gromacs' website (section Benchmark)?
Regards,
Yang Ye
Dr. Bernd Rupp wrote:
same problem as mpich2.
regards,
Bernd
Am Mittwoch, 25. Juni 2008 schrieb Yang Ye:
I don't think Python is to be blamed.
How about lam-mpi?
Regards,
Yang Ye
Dr. Bernd Rupp wrote:
Dear all,
CPU: Intel(R) Core(TM)2 Extreme CPU Q6850 @ 3.00GHz
System: fedora 8
Kernel: 2.6.25.6-27.fc8 #1 SMP
gromacs 3.3.3 correct compiled
MPI : mpich or mpich2
We had the same problem with mpich2.
single processor run CPU load 100%
double processor run CPU load around 70%
quad processor run CPU load around 40%
With mpich we have no problem:
quad processor run CPU load around 95%
We think that implementation of python are the reason of the bad scaling
of mpich2. Because mpiexec and mpdboot of mipch2 are python scipts.
May be we are wrong, but mpich dont use python and runs well!?
see you
Bernd
Am Samstag, 21. Juni 2008 schrieb ha salem:
Dear users
my gromacs is 3.3.3 my cpus are intel core2quad 2.4
GHz and my mpi is
LAM 7.0.6
I can get the cpu usage of 4 cores on one node but
when I run on 2
node the cpu usage of cores is low
I have installed gromacs with these instructions
Compile LAM 7
./configure --prefix=/usr/local/share/lam7
--enable-static
make |tee make.log
make install
make clean
Compile fftw
export MPI_HOME=/usr/local/share/lam7
export LAMHOME=/usr/local/share/lam7
export PATH=/usr/local/share/lam7/bin:$PATH
./configure --prefix=/usr/local/share/fftw3
--enable-mpi
make |tee make.log
make install
make distclean
Compile Gromacs
export MPI_HOME=/usr/local/share/lam7
export LAMHOME=/usr/local/share/lam7
export PATH=/usr/local/share/lam7/bin:$PATH
./configure --prefix=/usr/local/share/gromacs_333
--exec-prefix=/usr/local/share/gromacs_333
--program-prefix=""
--program-suffix="" --enable-static
--enable-mpi --disable-float
make |tee make.log
make install
make distclean
lamboot -v lamhosts
Run Gromacs on 2 machine (each machine has 1
core2quad)
/usr/local/share/gromacs_333/bin/grompp -f md.mdp -po
mdout.mdp -c
md.gro -r md_out.gro -n md.ndx -p md.top -o topol.tpr
-np 2
mpirun -np 2 /usr/local/share/gromacs_333/bin/mdrun
-np 2-f topol.tpr
-o md.trr -c md_out.gro -e md.edr -g md.log &
I also test with -np 8 but my cpu usage is low and the
speed is less
than single run!!!
thank you in your advance
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