Hi,
I am using parallel version of sander on Gmac5, with mpich.
I have just finished minimizing my protein which is solvated.
And when i tried putting it for equilibration i get following error.
THE COMMAND :
mpirun -np 4 sander.MPI -O -i equi1.in -o equi1.out -c Min1.rst -p
Achain.top -r Equi1.rst -x equi.mdcrd &
THE OUTPUT :
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()
[2] Exit 1 mpirun -np 4 sander.MPI -O -i equi1.in-o
equi1.out -c Min1.rst -p Achain.top ...
.............
Please tell me what is wrong and what could be the solution.
I haven't attached the equilbn input file coz this error appeared to be more
technical to me rather than input error.
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Received on Wed Apr 04 2007 - 06:07:25 PDT
