AMBER Archive (2007)

Subject: AMBER: Error at Equilibration....

From: Sandeep Kaushik (sandy.thesmitten_at_gmail.com)
Date: Mon Apr 02 2007 - 02:14:17 CDT

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.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu