[BioC] Running Pumacomb on both cores of dual-core machine
richard.pearson at postgrad.manchester.ac.uk
Wed Feb 27 21:52:49 CET 2008
Can you now ssh without a password from the unix command line on your
Could you send me the script you ran and the output of sessionInfo()? It
sounds a bit suspicious getting over a 4-fold speed increase if you're
just using a 2-node cluster!
Paul Geeleher wrote:
> 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.
> 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
>> 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.
>> > 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
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