[gmx-users] low cpu usage

[Dr. Bernd Rupp]

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
> >>>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 189 bytes
Desc: This is a digitally signed message part.
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080625/b5dfba20/attachment.sig>