[Dock-fans] Re: Dock parallel run tutorial

Scott Brozell sbrozell at scripps.edu
Wed May 23 08:55:36 PDT 2007


Yes, Philip refers to something like this, eg

#PBS -l nodes=10:ppn=2
mpirun -v -machinefile $PBS_NODEFILE -np 20 ./a.out

Note that their example could be further automated like this:
setenv NPROCS \
    `wc -l $PBS_NODEFILE | sed 's/^[ \t]*//' | cut -d' ' -f1`
echo "Number of processors is $NPROCS"
mpirun -v -machinefile $PBS_NODEFILE -np $NPROCS ./a.out

At some centers mpirun is wrapped to hide the details, eg

#PBS -l nodes=12:ppn=2:myrinet
mpiexec ./a.out

I think that the DOCK manual clearly indicates that the
quick start is for users that have to roll their own.
But I'll proof read it with an eye to clarification.


On Wed, 23 May 2007, Philip Crawford wrote:

> 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.
> -----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, 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"

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