<table cellspacing='0' cellpadding='0' border='0' ><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!!!!<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></table><br>