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

Richard Pearson richard.pearson at postgrad.manchester.ac.uk
Wed Feb 27 13:58:36 CET 2008

Hi Paul

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. The following instructions (taken from 
http://linuxproblem.org/art_9.html) should allow you password-free ssh 
access to localhost. Could you try this and see if this solves your 
problem? Post back to list to let me know how you get on - if you're 
still having problems I'll investigate further:

ssh-keygen -t rsa
(press enter 3 times for each of the questions asked)
cat .ssh/id_rsa.pub | ssh <username>@localhost 'cat >> .ssh/authorized_keys'
(enter your password)

You should then be able to "ssh localhost" without having to enter a 

Best wishes


Paul Geeleher wrote:
> Dear Members,
> I've followed the instructions as per the Puma Vignette in an attempt
> to get the pumacomb() function to run on both cores of my dual core
> notebook.
> I run the command "cl <- makeCluster(c('localhost', 'localhost'),
> type='SOCK')", to create the cluster.
> This appears to open an SSH connection and prompts for a password. If
> I type in the wrong password it re-prompts for the password, if I use
> the correct one it seems to accept it but nothing happens. I can type
> stuff on the screen but there is no response and I seem unable to
> issue any subsequent commands.
> I've tried this in Ubuntu and OpenSUSE to the same result. Obviously
> I'm missing something here? There seems to be virtually no
> documentation out there other than the package vignette.
> Thanks,
> -Paul.
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