Less than 24 hours ago
http://www.gromacs.org/pipermail/gmx-users/2008-June/034719.html, I said
"Please put GROMACS-related correspondence on the list. That way
multiple people can have a chance to reply, and the answer is archived
for all to search."
The details you provide are useful, but not complete. There is a lot
more to running a parallel calculation than the number and type of your
CPUs. The kind of network is much more critical. See the many posts on
this list by Carsten Kutzner on this topic.
-------- Original Message --------
Subject: low cpu usage
Date: Sat, 21 Jun 2008 05:16:37 -0700 (PDT)
From: ha salem <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
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
On June 5
http://www.gromacs.org/pipermail/gmx-users/2008-June/034430.html, I
suggested you check out
http://wiki.gromacs.org/index.php/grompp#Parallel_calculations, and on
June 6 I felt the need to give you the same advice and point out that
the command line you've given in your email would not have been
effective, had you actually used it.
The same goes for the above command line... "-np 2-f topol.tpr" was not
the command line you used if mdrun actually ran. We're not interested in
reconstructions... we're interested in what you actually did. :-)
For certainty of correct function, all three -np options require the
number of MPI processes you wish to run. In your case, it sounds like
they should be 4*2=8 in all cases. Your text does not make it clear what
you've actually done.
Mark
_______________________________________________
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
