[gmx-users] mdrun fatal error
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jun 6 10:19:30 CEST 2006
Beniamino Sciacca wrote:
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"
> 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
>>> I know it's possible because I' ve another pc that is working in this
>> 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.
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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
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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