[AMBER] MPI_ABORT errorcode 1 sander

From: Erin Kelly <erkelly4572.gmail.com>
Date: Wed, 15 Jun 2011 14:58:40 -0500


**this is reposted because some emails may have been lost when the web page
was down.**

I've been attempting to complete "Tutorial 1: Molecular dynamics simulation
of protein" with 3OGP.pdb I was able to make it through the minimizaton,
heating, and equilibration steps but was stopped at the production step. I
was given the following error in an BATCH_ERROR file:

MPI_ABORT was invoked on rank 0 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 0 with PID 26869 on
node node169 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

I have attempted to find the source of this error. I have run sander a few
times before this and haven't seen anything similar. I've seen similar
threads that indicate that sander was used instead of sander.MPI however
this isn't the case here. I've attached all of my files, including the .out
that seems to have a problem with my .inpcrd file---none of the previous
simulations seemed to have this error.

I should mention that these simulations fail immediately when I submit them,
I don't even have time to see it listed in the job que

I would really appreciate any advice.

Erin Kelly

ps: In previous runs I have broken up this simulation into 500 ps
increments, I've left it as the full 10 ns here just to show the error
(which is the same for both approaches).


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Received on Wed Jun 15 2011 - 13:00:05 PDT
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