[gmx-users] unexpexted stop of simulation

[Carsten Kutzner]

Hi,

there was also an issue with the locking of the general md.log
output file which was resolved for 4.5.2. An update might help.

Carsten


On Nov 3, 2010, at 3:50 PM, Florian Dommert wrote:

> -----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: dommert at icp.uni-stuttgart.de
> 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    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists