Also the machine (where now I've the problem) before worked as the other
machine... I don't know before "what".
However...I start from a file .gro where is my system ready for
constraint forces; I use grompp:
"grompp_d -f MD_Eq.mdp -c DNA5x3_min.gro -p DNAx3.top -o DNA6x3_MD.tpr
-n indexAcqua.ndx -po mdout.mdp"
"lamboot"
and later mdrun:
"mdrun_d -nice 0 -v -s DNA6x3_MD.tpr -pi pull.ppa -po pullout.ppa -pdo
pull.pdo -o mdEq_traj.trr -c DNA6x3_MD.gro -e mdEq_ener.edr -pn
indexAcqua.ndx -x mdEq_traj.xtc -g EqD.log"
I don't use mpirun.
There is no differences between the way to prepare calculations.
one machine is a notebook (centrino duo)
the other machine is a Desktop (AMD64 X2)
the kernel is the same (2.6) debian.
with the code written above notebook uses only one processor, Desktop
uses both the cpu.
I repeat...I also worked in this manner, and also the notebook has ever
worked until some week ago.
Now for use both the cpu I must use mpirun.
Desktop kernel is non smp
Laptop kernel has both smp and non-smp.
Beniamino
Mark Abraham ha scritto:
Beniamino Sciacca wrote:
Ok... the problem is certainly that I made two processes.
But if I made only one process mdrun uses only one cpu...
I want one process (and so I can use constraint forces) that use both
cpus.
I know it's possible because I' ve another pc that is working in this
manner.
So work out what is different between the two machines, their
configurations and how you're preparing the calculations. If you can't
identify a difference, then tell us what you have done and maybe we
can suggest something you haven't tried.
Mark
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