[gmx-users] unexpexted stop of simulation

Hong, Liang hongl at ornl.gov
Wed Nov 3 15:38:50 CET 2010

Dear all,
I'm performing a three-day simulation. It runs well for the first day, but stops for the second one. The error message is below. Does anyone know what might be the problem? Thanks

Program mdrun, VERSION 4.5.1-dev-20101008-e2cbc-dirty
Source code file: /home/z8g/download/gromacs.head/src/gmxlib/checkpoint.c, line: 1748

Fatal error:
Failed to lock: md100ns.log. Already running simulation?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

"Sitting on a rooftop watching molecules collide" (A Camp)

Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 32

gcq#348: "Sitting on a rooftop watching molecules collide" (A Camp)

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.
[node139:04470] [[37327,0],0]-[[37327,1],0] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104)
mpiexec has exited due to process rank 0 with PID 4471 on
node node139 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).

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