[gmx-users] Change default "nice" option for mdrun (was: Can not find file: topol.tpr)
guillem_pg at hotmail.com
Thu Apr 27 16:11:30 CEST 2006
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
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
How do i do it?
Thank you very much !
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