AMBER Archive (2008)

Subject: RE: AMBER: Amber 9 run error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 08 2008 - 16:52:30 CDT

Hi Andrew,

Search through your restart file looking for a series of *'s. It is likely
that one of the water molecules has diffused beyond the limit of the restart
file. You need to roll back 2ns and then reimage the restart file to place
everything back in the central box. You can do this using ptraj or
alternatively you can set

iwrap=1

in your input file and run the 48 to 50ns run. You can then keep iwrap=1 set
for the remainder of your runs.

Good luck,
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Andrew Borgert
> Sent: Tuesday, April 08, 2008 14:28
> To: amber_at_scripps.edu
> Subject: AMBER: Amber 9 run error
>
> Amber users,
> I am running an mpi version of sander (amber 9 version) on an
> SGI linux
> cluster using 16 processors. My simulation has been running
> fine in 2ns
> chunks for a total of ~50ns, however for some reason the
> current 2ns run
> will not execute properly. The run starts without error, but ends
> shortly thereafter. The script error file (returned by the queuing
> system I presume) contains a rather cryptic message:
>
> forrtl: error (76): IOT trap signal
> Timeout for rank 0 hostname 'cl1n246'. Job is not finalized there.
> Cleaning up all processes ...
> Some rank on 'cl1n246' exited without finalize.
> done.
>
>
> The sander output file lists no errors, however it appears to
> stop when
> reading in the restart file:
> ...
> ...
> ...
> --------------------------------------------------------------
> ------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------
> ------------------
>
> | Flags:
> MPI
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
>
> This is the end of the 'out' file.
>
> Upon examination, there appears to be nothing wrong with the restart
> file. It is the same size as the previous restart files for
> this system
> and contains the correct timestamp and number of atoms at the
> beginning
> of the file, along with the correct box information at the end.
>
> I am running other systems with the same sander executable, so I know
> the program is functioning properly.
>
> Any thoughts?
>
> For what it's worth, this is my input file:
>
> EA2 MD initial run up
> &cntrl
> imin=0,
> irest = 1,
> ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1, taup = 2.0,
> cut = 10,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 2000000, dt = 0.001,
> ntpr = 200, ntwx = 200, ntwr = 200
> /
>
>
>
> Andrew Borgert
>
> --------------------------------------------------------------
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