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

Thu Feb 28 15:09:15 CET 2008

Ya I found the 4x increase rather suspicious myself.

I can indeed now ssh to localhost on the SUSE box. In R pretty much
the same thing as before happens, except that it doesn't prompt for a
password. I'll email you a screenshot actually.

At the moment I'm just using the Estrogen data set to test this so the
script is as simple as:

library(puma)
library(pumadata)
library(snow)

data(eset_estrogen_mmgmos)
cl <- makeCluster(c("localhost", "localhost"), type="SOCK")
eset_estrogen_comb <- pumaComb(eset_estrogen_mmgmos, cl=cl)

The output of session info on Ubuntu, after running the above, is as follows:

R version 2.5.1 (2007-06-27)
i486-pc-linux-gnu

locale:
LC_CTYPE=en_IE.UTF-8;LC_NUMERIC=C;LC_TIME=en_IE.UTF-8;LC_COLLATE=en_IE.UTF-8;LC_MONETARY=en_IE.UTF-8;LC_MESSAGES=en_IE.UTF-8;LC_PAPER=en_IE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"

other attached packages:
    snow pumadata     puma     ROCR   gplots    gdata   gtools annotate
 "0.2-9"  "1.0.0"  "1.2.3"  "1.0-2"  "2.3.2"  "2.4.0"  "2.4.0" "1.14.1"
   limma     affy   affyio  Biobase
"2.10.5" "1.14.2"  "1.4.1" "1.14.1"

And on SUSE, which only makes it as far as the "cl <-
makeCluster(c("localhost", "localhost"), type="SOCK")" line before
going blank:

R version 2.5.1 (2007-06-27)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"

other attached packages:
    snow pumadata     puma     ROCR   gplots    gdata   gtools annotate
 "0.2-9"  "1.0.0"  "1.2.3"  "1.0-2"  "2.3.2"  "2.4.0"  "2.4.0" "1.14.1"
   limma     affy   affyio  Biobase
"2.10.5" "1.14.2"  "1.4.1" "1.14.1"

-Paul

On Wed, Feb 27, 2008 at 8:52 PM, Richard Pearson
<richard.pearson at postgrad.manchester.ac.uk> wrote:
> 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.
> >> >
> >>
> >>
> >>
> >>> _______________________________________________
> >>>
> >> > Bioconductor mailing list
> >> > Bioconductor at stat.math.ethz.ch
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
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> >> >
> >> >
> >>
> >>
> >
> >
>