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From: Paul Cochrane (paultcochrane_at_[hidden])
Date: 2007-09-08 03:20:25


On 08/09/07, Ashley Dowling <ashley.dowling_at_[hidden]> wrote:
>
>
> Hi all
>
> I am very much a novice at all this so please forgive my ignorance. I am
> trying to set up a piece of analytical software for parallel processing of
> my datasets on two quad core Mac Pros. I have managed to install OpenMPI on
> the Macs, compile the software, and get it to run in parallel across the
> four nodes within each Mac. My sticking point now is how to get it to run on
> all eight nodes (two Macs) in parallel. The instructions on the webpage for
> the software use Lam and are as follows:
>
> Running MrBayes
>
> First we have to start the 'lam' by creating a text file called lamhost. If
> you are using one quad G5 machine, you need only one line "localhost cpu=4",
> e.g. by typing in the terminal window
> echo "localhost cpu=4" > lamhosts
>
>
> When you have multiple machines, you need a line for every machine in the
> lamhost file and the full machine name instead of localhost. The file might
> look like
> $ cat lamhosts
> mac01 cpu=4
> mac02 cpu=4
> mac03 cpu=4
>
>
> To start the lam you can type
> lamboot lamhosts
>
>
> from a terminal window.
>
> To run mrbayes on N processors, you use
> mpirun -np N ./mb
>
>
> N is typically four times the number of machines you are using.
>
> To stop the lam type
> wipe lamhosts
>
>
> in a terminal window.
>
> Retrieved from "
> http://mrbayes.csit.fsu.edu/wiki/index.php/FAQ_3.2"
>
>
>
> Obviously this doesn't work on MPI since there is no lamboot. Is there an
> equivalent command to use? Or better yet, how do I go about getting these
> two machines to communicate in parallel? I have scoured the web looking for
> advice on this, but as I mentioned, I am new at this and I think some of the
> things I have found are just way over my head right now and have hit the
> point where I am giving up and asking for help. Any info/instructions/advice
> (written in terms I can understand) would be greatly appreciated.

Ashley,

Did you try the OpenMPI web page? (http://www.openmpi.org). There's
lots of info there, and help for running MPI jobs can be found in the
FAQ:

http://www.open-mpi.org/faq/?category=running

HTH

Paul