From schmidb at ibe.med.uni-muenchen.de  Fri Jul 18 14:23:46 2008
From: schmidb at ibe.med.uni-muenchen.de (Markus Schmidberger)
Date: Fri, 18 Jul 2008 14:23:46 +0200
Subject: [Rd] experinental revision of the 'snow' package
In-Reply-To: <alpine.LFD.1.10.0807071244250.2699@nokomis.stat.uiowa.edu>
References: <alpine.DEB.1.00.0807041822230.11721@luke-inspiron>
	<4871FE38.6060509@ibe.med.uni-muenchen.de>
	<alpine.LFD.1.10.0807071244250.2699@nokomis.stat.uiowa.edu>
Message-ID: <48808B52.50405@ibe.med.uni-muenchen.de>

Hello Luke,

at our windows cluster everything is working very well. We have 8 nodes, 
WindowsServer2003 and mpich2 (1.0.7).
Attached a small testcode and sessionInfo()

I did some bigger tests using my "afyPara" package. There were no problems.
There was an other discussion at the Rd list. Giuseppe confirmed, that 
DeinoMPI & Rmpi & the new version of snow is working very well.

See you in Seattle at the BioC2008 or Developer Day? I will fly to 
Seattle tomorrow.

Best regards
Markus



 > library(Rmpi)
 > library(snow)
 > c1<-makeCluster(3)
        3 slaves are spawned successfully. 0 failed.
 > clusterEvalQ(c1, Sys.info()["nodename"])
[[1]]
nodename
   "CL1"

[[2]]
nodename
   "CL2"

[[3]]
nodename
   "CL3"

 > stopCluster(c1)
[1] 1
 >
 > sessionInfo()
R version 2.7.1 (2008-06-23)
i386-pc-mingw32

locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252

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

other attached packages:
[1] snow_0.3-3 Rmpi_0.5-5




Luke Tierney schrieb:
> Thanks.
>
> Did you have a chance to check this on your WIndows setup?
>
> Best,
>
> luke
>
> On Mon, 7 Jul 2008, Markus Schmidberger wrote:
>
>> Hello Luke,
>>
>> I did several test with our affyPara Testcode. Everything was working 
>> very well. I think you improved error-handling?
>> It would be great to have a kind of change log in the package. To 
>> know the latest changes.
>>
>> Our system:
>> Linux, Suse, max. 120 nodes, LAM/MPI: 7.1.3
>>
>> R version 2.7.1 (2008-06-23)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C 
>>
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets  
>> methods [8] base other attached packages:
>> [1] hgu95acdf_2.2.0      Rmpi_0.5-6           affyPara_1.1.5     [4] 
>> snow_0.3-3           affy_1.18.2          preprocessCore_1.2.0
>> [7] affyio_1.8.0         Biobase_2.0.1
>> Best regards form Munich
>> Markus
>>
>>
>>
>> Luke Tierney schrieb:
>>> A new version of the 'snow' package for parallel computing in R is
>>> available at
>>>
>>>      http://www.stat.uiowa.edu/~luke/R/cluster/snow_0.3-3.tar.gz
>>>
>>> This substantially revises the way in which worker processes are
>>> started to allow snow to be used on Windows and Mac/Windows/Linux
>>> combinations. I have successfully used the SOCK version on a
>>> standalone Windows machine and combinations of Windows and Linux; the
>>> MPI version also works for me with DeinoMPI and the Rmpi verision for
>>> DeinoMPI.
>>>
>>> I would welcome it if some current snow users could try this verison
>>> in their settings to help iron out any major issues I missed before
>>> release to CRAN.
>>>
>>> Thanks,
>>>
>>> luke
>>>
>>
>>
>>
>


-- 
Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universit?t M?nchen
IBE - Institut f?r medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://ibe.web.med.uni-muenchen.de 
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4599



[Rd] experinental revision of the 'snow' package
Markus Schmidberger