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
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
