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
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Received on Mon Apr 18 2011 - 09:30:05 PDT
