AMBER Archive (2009)

Subject: Re: [AMBER] Task is running on supercomputer without any output

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Thu Nov 12 2009 - 07:24:56 CST

No I just should use
mpirun -np 128 -p 10 $AMBERHOME/exe/sander.MPI -O -i
but not
mpirun -np 128 -p 10 $AMBERHOME/exe/sander.MPI sander -O -i
double command. My mistake but hope can help someone else reading this list.

09.11.09, 12:51, "michael bane" <michael.bane_at_manchester.ac.uk>:

> On 9 Nov 2009, at 12:39, Andrew Voronkov wrote:
> > Dear Amber users,
> > I don't understand the situation - the task is running on
> > supercomputer during 50 hours, no output is produced but log file
> > shows an error which has happened a day ago.
> >
> > The log files shows error but the task keeps runing. The command was
> > the next:
> >
> > mpirun -np 128 -p 10 $AMBERHOME/exe/sander.MPI sander -O -i
> > fzd10_w_md2.in -o fzd10_w_md2.out -p fzd10_w.prmtop -c
> > fzd10_w_md1.rst -r fzd9_w_md2.rst -x fzd10_w_md2.mdcrd
> >
> > Sincerely yours,
> > Andrey
> > _______________________________________________
> > A
> It looks as if MPI Abort did not stop the batch job. This is fair
> since MPI Abort "does it best" (or something very similar wording as
> per MPI standard). Always worth keeping an eye on batch jobs' output
> files!
> M
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