[BioC] Running Pumacomb on both cores of dual-core machine
richard.pearson at postgrad.manchester.ac.uk
Thu Feb 28 22:37:11 CET 2008
Paul, glad you got this working. The speed up you've seen looks similar
to what I've seen running 2 cores rather than 1. Yes, I would highly
recommend using the same versions of all packages on all machines - in
fact, I think the general rule with Bioconductor is to always use the
latest release versions of everything.
Paul Geeleher wrote:
> 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
>> 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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