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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