[gmx-users] low cpu usage

[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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