-----BEGIN PGP SIGNED MESSAGE----- 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. /Flo - -- Florian Dommert Dipl.-Phys. 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: [email protected] Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzRdrEACgkQLpNNBb9GiPm1sgCg3LkRUWgiZvOOH/GIjp5ifbZI bJcAn1aamCMWlWTokD1+eDCLG1WhT/rd =4Vs3 -----END PGP SIGNATURE----- -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
