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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 09 2014 - 11:30:02 PDT
