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

Richard Pearson 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.
> -Paul.
> 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...?
>>  >
>>  >
>> _______________________________________________
>>  Bioconductor mailing list
>>  Bioconductor at stat.math.ethz.ch
>>  https://stat.ethz.ch/mailman/listinfo/bioconductor
>>  Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list