[BioC] Running Pumacomb on both cores of dual-core machine
Richard Pearson
richard.pearson at postgrad.manchester.ac.uk
Thu Feb 28 15:20:28 CET 2008
Hi Paul
I'm almost certain your "Error in data.frame" error is due to a bug I
fixed a while ago. You need to upgrade to the latest release of puma
(1.4.3), but for this you will first need R version 2.6.x installed (you
should really go for 2.6.2).
My guess is that this won't solve your SUSE problem, but its certainly
the first thing to try. Let me know how you get on.
Hope that helps!
Richard.
Paul Geeleher wrote:
> 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
>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>>
>>>>>
>>>>
>>>
>
>
More information about the Bioconductor
mailing list