Hi,
Ensure prod_80ns.rst is the same length as other restart files. If it's
truncated, that could cause problems (in which case, you should rerun the
60-80 ns step).
James
On Fri, May 9, 2014 at 1:59 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> I've been running a 100ns MD production, using a 60ns restart file. The
> program aborts generating a a 100ns output as shown below.
>
> -------------------------------------------------------
> Amber 11 SANDER 2010
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 11
>
> | Run on 05/09/2014 at 07:03:32
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: prod.in
> | MDOUT: prod_100ns.out
> | INPCRD: prod_80ns.rst
> | PARM: 3n7h_oct_solv.prmtop
> | RESTRT: prod_100ns.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: prod_100ns.mdcrd
> | MDINFO: mdinfo
> |LOGFILE: logfile
>
> Here is the input file:
>
> production Agam(3n7h)-7octenoic acid (OCT)
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=10000000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=2.0,
> ntpr=5000, ntwx=5000,
> ntt=3, gamma_ln=2.0, ig=-1,
> temp0=300.0,
> /
>
>
> Note: ig = -1. Setting random seed based on wallclock time in microseconds
> and disabling the synchronization of random numbers between tasks
> to improve performance.
>
> | ERROR: I could not understand line 6472
> -13.9576165 77.1599087-108.8341833
>
>
> The application called
> MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> [mpiexec.r1i0n15] HYD_pmcd_pmiserv_send_signal
> (./pm/pmiserv/pmiserv_cb.c:221):
> assert (!closed) failed
> [mpiexec.r1i0n15] ui_cmd_cb (./pm/pmiserv/pmiserv_pmci.c:128): unable to
> send SI
> GUSR1 downstream
> [mpiexec.r1i0n15] HYDT_dmxu_poll_wait_for_event
> (./tools/demux/demux_poll.c:77):
> callback returned error status
> [mpiexec.r1i0n15] HYD_pmci_wait_for_completion
> (./pm/pmiserv/pmiserv_pmci.c:388)
> : error waiting for event
> [mpiexec.r1i0n15] main (./ui/mpich/mpiexec.c:718): process manager error
> waiting
> for completion
> georgios.itvds0:~/MD/OCTENOIC/3n7h-OCT-1/7_Production/100ns> more
> teste.e6423
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> [mpiexec.r1i0n15] HYD_pmcd_pmiserv_send_signal
> (./pm/pmiserv/pmiserv_cb.c:221):
> assert (!closed) failed
> [mpiexec.r1i0n15] ui_cmd_cb (./pm/pmiserv/pmiserv_pmci.c:128): unable to
> send SI
> GUSR1 downstream
> [mpiexec.r1i0n15] HYDT_dmxu_poll_wait_for_event
> (./tools/demux/demux_poll.c:77):
> callback returned error status
> [mpiexec.r1i0n15] HYD_pmci_wait_for_completion
> (./pm/pmiserv/pmiserv_pmci.c:388)
> : error waiting for event
> [mpiexec.r1i0n15] main (./ui/mpich/mpiexec.c:718): process manager error
> waiting
> for completion
>
>
> Any help on how to overcome this problem will be greatly appreciated.
>
> Thanks in advance
>
> George
>
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>
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Received on Fri May 09 2014 - 11:30:03 PDT
