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Amber PMEMD MPI Error

posted Jun 17, 2011, 11:02 AM by Dong Xu
If you get errors like these:

[mpiexec@chili] HYDU_sock_read (./utils/sock/sock.c:222): read errno (Bad file descriptor)
[mpiexec@chili] control_cb (./pm/pmiserv/pmiserv_cb.c:249): assert (!closed) failed
[mpiexec@chili] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:77): callback returned error status
[mpiexec@chili] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:206): error waiting for event
[mpiexec@chili] main (./ui/mpich/mpiexec.c:404): process manager error waiting for completion

Try redirecting stdin from /dev/null - some MPI implementations require this.

nohup mpirun -np 8 $AMBERHOME/bin/pmemd.MPI -O -i mdin.min -p PEG50.bondi.prmtop -c PEG50.bondi.inpcrd -suffix min </dev/null &

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