On Wed, Aug 20, 2014 at 3:17 PM, Hallel Freedman <hfreedma.ualberta.ca>
wrote:
> Hi Jason,
> We were in fact using a serial version of MMPBSA.py, and it passes all of
> the serial tests. Do you have any other suggestions for me please?
>
What intermediate files _were_ made?
> Thanks,
> Holly
>
>
> On Wed, Aug 20, 2014 at 11:41 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Wed, Aug 20, 2014 at 1:37 PM, Hallel Freedman <hfreedma.ualberta.ca>
> > wrote:
> >
> > > It doesn't seem to be getting that far - there is no file with that
> name.
> > > Maybe I should mention that I am getting a warning:
> > > An MPI process has executed an operation involving a call to the
> > > "fork()" system call to create a child process. Open MPI is currently
> > > operating in a condition that could result in memory corruption or
> > > other system errors; your MPI job may hang, crash, or produce silent
> > > data corruption. The use of fork() (or system() or other calls that
> > > create child processes) is strongly discouraged.
> > >
> > > The process that invoked fork was:
> > >
> > > Local host: jasper.westgrid.ca (PID 19790)
> > > MPI_COMM_WORLD rank: 0
> > >
> > > Could this be related to the problem?
> > >
> >
> > If you're having trouble in parallel, the first thing to do (if
> possible)
> > is to run in serial. It's a very simple way to help reduce the number of
> > places one has to look for the source of the problem.
> >
> > I can't recall the exact name of the output file off the top of my head,
> > but the name should indicate it is the mdout file of rank 0 (.mdout.0)
> for
> > the complex. The output files often hide the true error messages.
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
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> > AMBER.ambermd.org
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> >
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 20 2014 - 14:30:02 PDT
