[gmx-users] Change default "nice" option for mdrun (was: Can not find file: topol.tpr)

[Guillem Plasencia]

Hello again gmxers,

i've found the problem i had (Can not find file: topol.tpr). Silly problem 
with easy answer, i didn't had a local copy of this file in each node.

I still have one more question. I'm using 2 boxes with 2 Intel P4 3Ghz  
processors (with hyperthreading on), but right now i'm just using only one 
of them because the other is busy (and it wouldn't be a reliable benchmark).

I've done the test with lysozyme (cutoff) using only one of the CPUs in one 
of my machines, and got the  low performance of 3,256 ps /day (it should be 
1494).  I'd like to know how it scalates, by running it using both physical 
CPUs inside this same machine, but when i do

grompp <files> -np 2
and
mpirun n0 -np 2 mdrun <files> -np 2

it complains that it was processed for two nodes, not just one. How do i run 
this job in parallel between the two CPUs in my box? I suppose that if i 
remove the second node in my LAM-MPI configuration it will still complain 
that it was prepared for two nodes, not just one. Also, i've read in the 
archives that threads aren't yet implemented, so using option -nt 2 doesn't 
work neither.

How do i do it?

Thank you very much !

Guillem Plasencia