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

[Paul Geeleher]

Hi again,

For the sake of completeness I might as well say that I've installed
pnmath and it doesn't seem to make any noticeable difference to the
speed of the PUMA functions. Also looking at the Gnome System Monitor,
R seems to only be using one core. Unless I've made a mistake
somewhere I can assume that PUMA isn't too reliant on R's math
routines.

-Paul

On Wed, Feb 27, 2008 at 3:51 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> Depending on how puma is doing things, it might be useful to install
>  pnmath from
>
>  http://www.stat.uiowa.edu/~luke/R/experimental/
>
>  This parallelizes the math routines in R's core code. There's a read-me
>  file in the top level directory with instructions. It's not super-hard
>  to get working, but not as simple as biocLite. There's an extra config
>  step on Windows, but again the readme has tips.
>
>  Once installed, you wouldn't do anything differently to get the
>  performance benefit of multiple cores.
>
>  It would be interesting to know how this influences performance, if you
>  pursue this to the point of getting it working.
>
>  Martin
>
>
>
>  Richard Pearson 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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>  >>
>  >
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