[Dock-fans] Re: Dock parallel run tutorial

Philip Crawford p.crawford at unsw.edu.au
Wed May 23 00:04:09 PDT 2007


Scott,
On large clusters where hosts are allocated dynamically, using something
like PBS, it will probably be necessary to copy the list of hosts provided
as part of the submit script. This may be system implementation dependent so
contact with system administrators will be necessary.

Cheers,

Phil Crawford

_____________________________________________
Philip Crawford B Comp Sc, MIEEE
Medicine Computer Support Unit
The University of NSW, Sydney, NSW, 2052
Phone: +61-2-9385 2564
Fax: +61-2-9385 1258
Email: p.crawford at unsw.edu.au
_____________________________________________

-----Original Message-----
From: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org]
On Behalf Of Scott Brozell
Sent: Wednesday, 23 May 2007 10:26 AM
To: dock-fans at docking.org
Subject: [Dock-fans] Re: Dock parallel run tutorial

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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