[gmx-users] error while running grompp

[Ragothaman Yennamalli]

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.

Regards,
Raghu

--- Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> Ragothaman Yennamalli wrote:
> > Dear all,
> > We are trying running Gromacs in different systems
> > with different number of processors. In sun
> opteron
> > cluster we checked and it ran perectly fine. When,
> > using the same input files, to run in apple g5
> system
> > with same number of processors. I get the
> following
> > message when I run grompp:
> >  creating statusfile for 4 nodes...
> > 
> > Back Off! I just backed up mdout.mdp to
> > ./#mdout.mdp.9#
> > checking input for internal consistency...
> > calling /lib/cpp...
> > sh: line 1: /lib/cpp: No such file or directory
> > cpp exit code: 32512
> > Tried to execute: '/lib/cpp 
> > -I/Users/swadha/new_gromacs/share/top  master.top
> >
> > gromppOC6J5h'
> > The '/lib/cpp' command is defined in the .mdp file
> > processing topology...
> > processing coordinates...
> > Fatal error: number of coordinates in coordinate
> file
> > (confout.gro, 78268)
> >              does not match topology (master.top,
> 0)
> > 
> > 
> > I made new toplogy files, there is nil difference
> > between the new and old .top file used in grompp.
> > Still I get the same error message.
> 
> Check out 
>
http://wiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
> 
> Mark
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