Yes, I'll agree that stderr is not helpful here. I'm guessing that it's
something related to vlimit, and i'm assuming that your new setup/simulation
hasn't run into the same issue? Particularly, SHAKE failed and took the
rest of the simulation with it.
All the best,
Jason
On Thu, Aug 12, 2010 at 3:19 PM, <Don.Bashford.stjude.org> wrote:
> At Wed, 11 Aug 2010 16:45:41 -0500,
> Jason Swails wrote:
> >
> > What did stderr say, if anything?
> >
>
> Stderr says:
>
> Warning: Permanently added the RSA host key for IP address
> '172.20.101.10' to the list of known hosts.
> Warning: Permanently added the RSA host key for IP address
> '172.20.101.14' to the list of known hosts.
> Warning: No xauth data; using fake authentication data for X11
> forwarding.
> /usr/bin/xauth: error in locking authority file
> /home/bashford/.Xauthority
>
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
> --------------------------------------------------------------------------
>
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 3 with PID 23556 on
> node node020 exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
>
> The stuff about RSA and xauth is "normal" on our system.
>
> -Don
>
> Email Disclaimer: www.stjude.org/emaildisclaimer
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 12 2010 - 12:30:04 PDT
