Hi Jason,
thanks for the help and file. The only problem is...the whole package is
installed on a Super Computer Center and I have no access to either
installation or update... I will contact them to see what I could do...
Best,
Guqin
2016-01-13 11:40 GMT-05:00 Jason Swails <jason.swails.gmail.com>:
> On Wed, Jan 13, 2016 at 11:40 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> >
> >
> > On Wed, Jan 13, 2016 at 10:46 AM, Guqin Shi <shi.293.osu.edu> wrote:
> >
> >> Hi Pallavi,
> >>
> >> I'm 100% sure all .dat files are out and whole job is done.
> >> I had finished around ren mmpbsa.MPI jobs on Super Computer, about half
> of
> >> them didn't terminate by themselves after all .dat files are produced. I
> >> requested #PBS -j oe so I had all xxx.o12345678 file when job is done or
> >> aborted due to wall time limit. It showed that mmpbsa job is done.
> >>
> >> I also got reply back from Super Computer Tech Support. They said
> >> according
> >> to their log, mmpbsa.MPI was running after all .dat files have been
> done.
> >> They claimed that the pbs platform worked all right and they thought
> it's
> >> because something is stuck in program.
> >>
> >> What I can do right now is to restrict the wall time limit to minimum so
> >> that I can save resource units (charged by super computer center) if the
> >> program has to be aborted.
> >> According to Kenneth's post, it happened to her, too. It might because
> >> some
> >> minor issues in mmpbsa.MPI itself...
> >>
> >> Thank you for the help! Overall, I think it's not a big problem. It will
> >> be
> >> better if any developer could have a look and fix that.
> >>
> >
> > I made a change that I *think* should fix this problem, but since I
> > haven't observed this behavior before specifically with MMPBSA.py.MPI, I
> > have no way of testing that my change really does resolve this. I've
> > attached a patch with my changes. You can apply this patch by going to
> > $AMBERHOME and running the command
> >
>
> ​Only I didn't attach the patch. Here it is:
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Guqin SHI
The Ohio State University
College of Pharmacy
500 W. 12th Ave.
Columbus, OH, 43210
(614)688-3531
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Received on Thu Jan 14 2016 - 09:00:04 PST
