[gmx-users] mdrun fatal error
superbenji83 at gmail.com
Tue Jun 6 12:08:54 CEST 2006
So you are saying that also in the Desktop (because I not use "mpirun") it
is working with only one cpu??
2006/6/6, David van der Spoel <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 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
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