Thatz ok. Thank you very much.
Sajeewa Dewage
On Sat, Feb 9, 2013 at 12:27 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sat, Feb 9, 2013 at 11:45 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> >
> >
> > On Sat, Feb 9, 2013 at 12:30 AM, Sajeewa Pemasinghe <sajeewasp.gmail.com
> >wrote:
> >
> >> Yeah it had been a problem with compiler mismatch. Now it is running
> >> fine.One last question. The contents of the rem.log is NOT dynamically
> >> updated
> >> right? Will the contents be written to it when thw whole calculation is
> >> over? coz although there is a em.log file, currently it is empty.
> >>
> >
> > This depends on the file system (and perhaps operating system as well --
> > I'm not sure of everything that is responsible for file writing
> behavior).
> > Many file writes are buffered -- that is, data is written to a chunk of
> > memory and stored until one of two things happens:
> >
> > 1) The buffer fills up so the buffer empties into the file.
> > 2) The buffer is forcibly flushed to the file. Most languages have a
> > "flush" command to do this (although perhaps unreliably). Closing the
> file
> > flushes the buffer as well.
> >
> > The file will be closed (and the buffer) flushed at the end of the file,
> >
>
> At the end of the calculation*
>
> My mistake.
>
>
> > but for long runs the buffer should fill up and flush at some point
> during
> > the calculation. Note, though, if your simulation is killed before it
> > finishes you may lose some data that was stored in the buffer and never
> > flushed.
> >
> > HTH,
> > Jason
> >
> >
> >>
> >> Thank you
> >>
> >> Sajeewa Dewage
> >>
> >> On Fri, Feb 8, 2013 at 4:37 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com
> >> >wrote:
> >>
> >> > Thank you very much. Now that I know where the problem lies, I will
> keep
> >> > on working on that.
> >> >
> >> >
> >> > On Fri, Feb 8, 2013 at 4:17 PM, Ross Walker <ross.rosswalker.co.uk>
> >> wrote:
> >> >
> >> >> >know why it fails now. If there is a mismatching in MPIs above MD
> >> >> >calculations should also have given errors right?
> >> >>
> >> >> Not necessarily - they would just run on 1 core. Have you checked the
> >> >> output of your regular MD runs to see how many nodes sander reports
> it
> >> is
> >> >> using?
> >> >>
> >> >> All the best
> >> >> Ross
> >> >>
> >> >> >
> >> >>
> >> >>
> >> >>
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> >> >
> >> >
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> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Feb 09 2013 - 10:00:02 PST
