<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On 15.06.2008, at 20:19, ha salem wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><table cellspacing="0" cellpadding="0" border="0" style="position: static; z-index: auto; "><tbody><tr><td valign="top" style="font: inherit;">dear users<br> I have encouneterd a problem with mpirun I have 2 pc (every pc has 1 intel <br> quad core cpu) ,when I run mdrun on 1 machine with "-np 4 " option the calculation<br> run on 4 cores and goes faster ,system monitor show all 4 cores of this cpu are working<br> every core has 90% cpu usage,and every thing is ok<br> but now I connect 2 computer to LAN and I executed lamboot -v lamhosts<br> then I run mpirun -np 8 but I see the all 8 cores of 2 machines are workinng with<br> 20 % 10% cpu usage and speed is lower than 4 cores of 1 cpu!!!!</td></tr></tbody></table></blockquote>This could have a lot of reasons. What kind of interconnect do you use? If it is gigabit </div><div>Ethernet, you will need at least 80000 particles to be faster on two 4 CPU machines compared </div><div>to one. With only fast ethernet, do not expect any scaling at all on today's fast processors.</div><div><br></div><div>Try grompp -shuffle -sort, this will help increase the scaling a bit. </div><div><br></div><div>Regards,</div><div> Carsten</div><div><br></div><div><blockquote type="cite"><table cellspacing="0" cellpadding="0" border="0" style="position: static; z-index: auto; "><tbody><tr><td valign="top" style="font: inherit;"><br> can you help me ?my molecule is part of hsa and is macro molecule<br> these are my commands<br>usr/local/share/gromacs_331/bin/grompp -np 8 -f prmd.mdp -c finalprsp.gro -r finalprsp.gro -p n.top <br>mpirun -np 8 /usr/local/share/gromacs_331/bin/mdrun -np 8 -s prmd.tpr -o prmd.trr -c finalprmd.gro -g prmd.log -e prmd.edr -n n.ndx<br><br></td></tr></tbody></table><br> _______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></body></html>