[gmx-users] unexpexted stop of simulation

Florian Dommert dommert at icp.uni-stuttgart.de
Wed Nov 3 15:50:25 CET 2010

Hash: SHA1

On 11/03/2010 03:38 PM, Hong, Liang wrote:
> 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
> Liang
> 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).

Perhaps the queueing system of your cluster does not allow running a job
longer than 24h. Or the default is 24h and you have to supply the
corresponding information to the submission script.


- -- 
Florian Dommert

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
Fax:   +49-(0)711/685-6-3658

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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