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

Richard Pearson richard.pearson at postgrad.manchester.ac.uk
Thu Feb 28 18:46:05 CET 2008

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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