Thank you, Now the job seems to be running. But why is it strange to use 25
cpu for the process. Somewhere in amber forum i have read once that for
sander one needs to give no. of cpu's in powers of 2 but for pmemd any no.
of cpu can be given. Is this still the case ?
On Mon, Apr 18, 2011 at 6:11 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Bala,
>
> Try redirecting stdin from /dev/null - some MPI implementations require
> this. As an aside 25 MPI threads is a strange number to be using. You
> really
> have 25 cores allocated to this job?
>
> nohup mpirun -np 25 pmemd.MPI -O -i md1 -o md1.out -r md1.rst -p ALL.top
> -c min1.rst -ref min1.rst </dev/null &
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Bala subramanian [mailto:bala.biophysics.gmail.com]
> > Sent: Monday, April 18, 2011 8:44 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] strange background job crash
> >
> > Friends,
> > When i submit a job using pmemd.MPI (amber 11), it runs fine (following
> > syntax)
> >
> > mpirun -np 25 pmemd.MPI -O -i md1 -o md1.out -r md1.rst -p ALL.top -
> > c
> > min1.rst -ref min1.rst
> >
> > But when i submit the same job in background with & symbol at the end
> > and if
> > i press any key after the job submission, the job gets terminated.
> > Could you
> > please write me what would be the problem. The following was the
> > message the
> > termination throws.
> >
> > HYDU_sock_read (./utils/sock/sock.c:223): read errno (Input/output
> > error)
> > control_cb (./pm/pmiserv/pmiserv_cb.c:249): assert (!closed) failed
> > HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback
> > returned error status
> > HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:206): error
> > waiting for event
> > main (./ui/mpich/mpiexec.c:404): process manager error waiting for
> > completion
> >
> > I am submitting the job in SUSE Linux Enterprise Server 11.
> >
> > Thanks,
> > Bala
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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Received on Mon Apr 18 2011 - 09:30:06 PDT
