[gmx-users] Re: low cpu usage

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list, so 
everyone can benefit from the information and make suggestions.

-Justin

ha salem wrote:
> Dear Dr
> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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