[BioC] Running Pumacomb on both cores of dual-core machine

Paul Geeleher paulgeeleher at gmail.com
Thu Feb 28 18:56:45 CET 2008

Yes Richard it seems that updating R and Puma has succeeded on Ubuntu.
Still no idea what's going on with SUSE, but my gut instinct is that
it could be an SSH problem.

Running on both cores of the Pentium D has reduces execution time for
the Estrogen dataset from about and hour and a half to around an hour,
which makes a lot more sense that what I was seeing previously.

My next step is to try to get this working between two networked
machines and maybe scale up from there, as the datasets we'll be
analyzing seem to take up to 10 hours on a single core. I'm presuming
both machines should be running the same version of R and Puma etc?

Anyway I'll give it a go and see what happens.


On Thu, Feb 28, 2008 at 5:46 PM, Richard Pearson
<richard.pearson at postgrad.manchester.ac.uk> wrote:
> Hi Atro
>  The parallel functionality of pumaComb was really developed in order to
>  run the function much more quickly on large clusters. I wanted this to
>  be as generic as possible, which is why I've made use of the
>  functionality from the snow package (this means, for example, the
>  function can be run utilising either MPI or a simple network of
>  workstations connected via socket connections). When testing this on my
>  laptop I realised the function could be sped up by running on a simple
>  2-node network on the same machine, so thought I'd include some
>  instructions for how to do this in the vignette. I'm sure there are far
>  better solutions to maximising the speed on a single machine (e.g. your
>  suggestion of simply starting another process in the same session, or
>  the suggestion from Martin Morgan on this thread), which I hope to chase
>  up when I get the time.
>  Best wishes
>  Richard.
>  Atro Tossavainen wrote:
>  >> makeCluster is a function from the snow package, and I also can't find
>  >> much information about setting up "socket" clusters. However, I think
>  >> the fundamental problem here is that you can't ssh to localhost without
>  >> a password.
>  >>
>  >
>  > Of course this begs the question of why does one need to ssh to
>  > localhost at all rather than just start another process in the
>  > session that is already logged in...?
>  >
>  >
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