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

[Richard Pearson]

Paul

Can you now ssh without a password from the unix command line on your 
SUSE box?

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!

Thanks

Richard.


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.
>
> -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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