[gmx-users] mpi error

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 11 14:10:13 CEST 2008

Ragothaman Yennamalli wrote:
> Dear all,
> I had been running many runs of mdrun in a Sun opteron
> cluster with each node having 4 processors.
> When I ran my latest mdrun after 15ns run, I get the
> following error and mdrun exits without any error
> message on other log files. 
> *******************************************************
> mpiexec_compute-0-1.local: mpd_uncaught_except_tb
> handling:
>   exceptions.IOError: [Errno 5] Input/output error
>     /home/deb/mpich2-install/bin/mpirun  1051 
> handle_cli_stderr_input
>         sys.stderr.write(msg)
>     /home/deb/mpich2-install/bin/mpdlib.py  762 
> handle_active_streams
>         handler(stream,*args)
>     /home/deb/mpich2-install/bin/mpirun  515  mpiexec
>         rv =
> streamHandler.handle_active_streams(timeout=1.0)
>     /home/deb/mpich2-install/bin/mpirun  1423  ?
>         mpiexec()
> *******************************************************
> Please tell me how to troubleshoot this problem as it 
> repeated when ran again.

There's nothing GROMACS-specific about this error, so we're unlikely to 
be able to help you further. All I can guess is that the "Input/output 
error" suggests that a filesystem is full, or not mounted, or otherwise 

In particular, GROMACS usage with MPICH2 has been known to have many 
more problems than LAM. In extremis, please install LAM and recompile 
GROMACS accordingly.


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