AMBER Archive (2009)

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

From: michael bane (michael.bane_at_manchester.ac.uk)
Date: Mon Nov 09 2009 - 06:51:17 CST

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
> <sander.MPI.out-15750>_______________________________________________
> 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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