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

[Paul Geeleher]

Well Richard,

That does seemed to have solved the problem on my Ubuntu desktop. The
same problem is still however occurring with SUSE so I'm guessing it
might be some kind of problem with the SSH server on SUSE?

To my amazement, running pumacomb parallel (on the estrogen dataset)
cut the estimated time of execution from over an hour, to just 15
minutes on my Pentuim D 2.8 GHz.

Unfortunately though pumacomb() has thrown up an error at the very end
of its execution and has failed to output any data:

" Error in data.frame(numeric(n), row.names = nms) :
        duplicate row.names: "

Any ideas what might be causing this? I've run it twice now with the
same result. It runs fine on the single core, without using the
cluster, although about 4 or 5 times slower.

-Paul



On Wed, Feb 27, 2008 at 12:58 PM, Richard Pearson
<richard.pearson at postgrad.manchester.ac.uk> wrote:
> 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
>  password.
>
>  Best wishes
>
>  Richard
>
>
>
>
>  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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