Thank you very much for your quick replies,
Seems there is no wall clock set:
d47fvj@milano:~/VOTCA-play_around$ grep mdrun inverse.log
run_gromacs.sh: No walltime defined, so time limitation given to mdrun
Running critical command 'mdrun -s topol.tpr -c confout.gro -o
traj.trr -x traj.xtc'
:-) mdrun (-:
starting mdrun 'cg-c12'
And if I look into the inverse.log the last thing is:
d47fvj@milano:~/VOTCA-play_around$ tail inverse.log
NODE (s) Real (s) (%)
Time: 44.510 70.053 63.5
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 3.327 502.271 7.772 3.088
gcq#356: "Never, I said never, compare with experiment" (Magnus Bergh)
Simulation is not finished, but a checkpoint was found, so it seems
walltime is nearly up, stopping now, resume csg_inverse whenever you
want.
d47fvj@milano:~/VOTCA-play_around$
I have also tried running mmdrun before submitting for the iterations
and it was running. (Going to try in the step 001 now)
On Aug 18, 4:07 pm, Christoph Junghans <[email protected]> wrote:
> Hi Valentina,
>
> have a look at inverse.log to see if and how mdrun was executed:
> $grep mdrun inverse.log
>
> if no walltime is given, the output should look like:
> run_gromacs.sh: No walltime defined, so time limitation given to mdrun
> Running critical command 'mdrun -s topol.tpr -c confout.gro -o
> traj.trr -x traj.xtc'
> :-) mdrun (-:
> starting mdrun 'CG water'
>
> You can also go in step_001 and run mdrun by hand to see what happens.
>
> Cheers,
>
> Christoph
>
> 2011/8/18 Valentina <[email protected]>:
>
>
>
> > Hello, sorry for so many questions.
>
> > I am currently trying to run csg_inverse. I am not setting any
> > walltime and I am getting the following:
>
> > Doing iteration 1 (dir step_001)
> > Incomplete step 1
> > Simulation with gromacs
> > Simulation is not finished, but a checkpoint was found, so it seems
> > walltime is nearly up, stopping now, resume csg_inverse whenever you
> > want.
>
> > Seems I cannot get further then step 1, even if I restart the
> > calculation or do it with a set wall time for a large number. It is
> > only a tryal run, so there are nto many steps to be done, so the
> > calculation itself is taking very little time.
>
> > Thank you very much for your help,
> > V
>
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> --
> Dr. Christoph Junghans
> Votca Core Developer
>
> Web:http://www.votca.org
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