It's difficult to comment in too much detail based on the information
you have given. What version of ptraj are you running, and what
compilers did you use to build it? How big is the system you are
running ptraj on, and how long is the trajectory you are processing?
What sort of actions are you performing (I assume at least an RMSD
calculation from the name of your input file). What output does ptraj
give, if any? Also, why are you using 'mpirun' for a single processor
job? If you don't use 'mpirun' does it complete faster?
-Dan
On Fri, Aug 27, 2010 at 12:33 PM, Andrew Voronkov <drugdesign.yandex.ru> wrote:
> It's a bit strange but while running on clusted in a single processor mode ptraj runs for hours:
> mpirun -as single -np 1 -maxtime 360 ptraj fzd5-7_w.prmtop < fzd5_w_ca.calc_rms
> while on central node just several minutes.
> I am not sure if this is a question to Amber mailing list or cluster admins, but I don't understand what causes such a difference.
>
> Sincerely yours,
> Andrew
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Aug 27 2010 - 13:30:07 PDT
