[gmx-users] mdrun fatal error

Beniamino Sciacca superbenji83 at gmail.com
Tue Jun 6 09:54:01 CEST 2006

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"
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.


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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