[Dock-fans] Re: Dock parallel run tutorial

Scott Brozell sbrozell at scripps.edu
Tue May 22 17:25:55 PDT 2007


Hi,

Please use dock-fans instead of contacting developers directly.

andreyvoronkov wrote:

> is there any tutorial on DOCK parallel run?
> As far as I've  found no tutorial on this subject  I want  to ask you if you can send me the example of machinefile with node numbers and dock.mpi file?
>

There is no tutorial on the web.
One is mentioned as coming soon, but that ad is stale:
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm

There is a demo:
dock6/demo/mpi_demo

There is a test case:
dock6/install/test/mpi


Here is a brief review of using MPICH2
which will be added to the DOCK manual:

    MPICH2 QUICK START:
    MPICH2, unlike MPICH, requires command line initialization. If your system administrators have not initialized MPICH2 then follow these steps:
    Create a .mpd.conf file in your home directory containing secretword=mysecretword.
    Create a .mpd.hosts file in your home directory containing a list of machine names, one per line.
    Start the MPICH2 daemons by executing mpdboot.
    Verify the start up of the MPICH2 daemons by executing mpdtrace -l.
    Finally execute DOCK using mpiexec or mpirun. For further information see the MPICH2 README:
"http://www-unix.mcs.anl.gov/mpi/mpich/downloads/mpich2-doc-README.txt"


Scott



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