[gmx-users] error while running grompp

[Mark Abraham]

Ragothaman Yennamalli wrote:
> Dear Mark,
> Thanks for the mail. I was able to solve the problem,
> by changing the path of cpp from /lib/cpp to
> /usr/bin/cpp.
> With the same system, When I run mdrun calling mpirun
> I get the following error message and the program
> exits.
> 
> mpiexec_bicg5quad.local: mpd_uncaught_except_tb
> handling:
>   exceptions.IOError: [Errno 9] Bad file descriptor
>     /Users/deb/mpich2-install/bin/mpirun  1035 
> handle_stdin_input
>         sys.stdin.flush()  # probably does nothing
>     /Users/deb/mpich2-install/bin/mpdlib.py  527 
> handle_active_streams
>         handler(stream,*args)
>     /Users/deb/mpich2-install/bin/mpirun  493  mpiexec
>         rv =
> streamHandler.handle_active_streams(timeout=1.0)
>     /Users/deb/mpich2-install/bin/mpirun  1393  ?
>         mpiexec()
> 
> Please let em know how can I solve this? Just a
> reminder that the system is a 4 processor apple G5
> system.

Something's broken with your MPI setup. Re-initialize the mpi system, 
try again. Maybe recompile gromacs if you've updated the MPI libraries.

Mark