[gmx-users] mdrun fatal error

[David van der Spoel]

Beniamino Sciacca wrote:
> So you are saying that also in the Desktop (because I not use "mpirun") 
> it is working with only one cpu??
> 
yes.


> Beniamino
> 
> 2006/6/6, David van der Spoel < spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>>:
> 
>     Beniamino Sciacca wrote:
> 
>     two points:
> 
>     you can not do constraints in parallel in 3.3
>     you can not run in parallel without mpirun
> 
>     ergo you are comparing apples and oranges.
> 
> 
> 
> 
> 
>      > 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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> 
>     --
>     David.
>     ________________________________________________________________________
>     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>     Dept. of Cell and Molecular Biology, Uppsala University.
>     Husargatan 3, Box 596,          75124 Uppsala, Sweden
>     phone:  46 18 471 4205          fax: 46 18 511 755
>     spoel at xray.bmc.uu.se
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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