[gmx-users] low cpu usage

[Dr. Bernd Rupp]

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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-- 
Dr. Bernd F. Rupp

Leibniz-Institut für Molekulare Pharmakologie (FMP)
Abt. NMR-unterstützte Strukturforschung
AG   Molecular Modeling/ Drug Design
Robert-Roessle-Str. 10
13125 Berlin
Germany

Tel.    +49/0-30-94793-279
FAX     +49/0-30-94793-169
Web     www.fmp-berlin.info/drug_design.html
E-Mail  rupp at fmp-berlin.de 
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