[gmx-users] problem to execute the parallelized CPMD in Gromacs/CPMD interface

[Christian Seifert]

Hi Yun-an Yan.

Am Dienstag, 3. Juni 2008 14:30:23 schrieb Yun-an Yan:
> Dear all,
>
> I have problems to execute the parallelized CPMD in Gromacs/CPMD
> interface.
> The Gromacs is build without support of parallelization and CPMD is
> parallelized.
> mdrun exits after displaying the error message:
>
> yunan at baldwin$ cat output_long.md
> ..........
> .........
>
> ****************************************************************
> *   ATOM       MASS   RAGGIO NLCC              PSEUDOPOTENTIAL *
> *     H      1.0080        1.2000   NO              VANDERBILT      *
> *     O     15.9994      1.2000   NO              VANDERBILT      *
> *     C     12.0112      1.2000   NO              VANDERBILT      *
> ****************************************************************
>
> PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA
> mpiexec_baldwin.mpg.uni-rostock.de: mpd_uncaught_except_tb handling:
>   <type 'exceptions.IOError'>: [Errno 9] Bad file descriptor
>     /usr/local/mpich64/bin/mpirun  1065  handle_stdin_input
>         sys.stdin.flush()  # probably does nothing
>     /usr/local/mpich64/bin/mpdlib.py  762  handle_active_streams
>         handler(stream,*args)
>     /usr/local/mpich64/bin/mpirun  515  mpiexec
>         rv = streamHandler.handle_active_streams(timeout=1.0)
>     /usr/local/mpich64/bin/mpirun  1423  <module>
>         mpiexec()

There seems to be someting wrong with you mpi library. You should recompile  
(on the machine, which really executes the mpi command later) and test it. 
After that, you should recompile cpmd and gromacs (--with-qmmm-cpmd).

That should do it.

>
>
> The content of the runcpmd is like that:
> yunan at baldwin$ cat runcpmd
> #! /bin/sh
>
> /usr/local/mpich64/bin/mpirun -np 4 /usr/local/bin/cpmd_mpi.x
> CPMD_inp.run .
>
> It runs well when I touch the file QMSTART and execute runcpmd directly.
>
> Does anyone have some ideas to figure it out?

Which command did you use to start gromacs? You have to start mdrun 
without /usr/local/mpich64/bin/mpirun!

>
> Thank you so much for your consideration.
>
> Best wishes,
> Yun-an Yan
>
>
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Regards,
Christian Seifert.

-- 
M. Sc. Christian Seifert
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: cseifert at bph.rub.de
Web: http://www.bph.rub.de