

-------- Original Message --------
Subject: 	Re: [R-sig-hpc] snowfall error
Date: 	Wed, 23 Jun 2010 09:06:28 +0100
From: 	Unger Kristian <k.unger@imperial.ac.uk>
To: 	Gottardo Raphaël <Raphael.Gottardo@ircm.qc.ca>





I updated R and updated all packages.

here the sessionInfo:

 > sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu

locale:
  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] Rmpi_0.5-8     CGHcall_2.8.0  CGHbase_1.6.0  marray_1.26.0  
limma_3.4.3
  [6] Biobase_2.8.0  DNAcopy_1.22.1 impute_1.22.0  snowfall_1.84  
snow_0.3-3

loaded via a namespace (and not attached):
[1] tools_2.11.1

After running: sfInit(parallel=TRUE,cpus=2,type="MPI"):

Library Rmpi loaded.
     2 slaves are spawned successfully. 0 failed.
snowfall 1.84 initialized (using snow 0.3-3): parallel execution on 2 CPUs.

BUT R crashes when I try to run the command:

calldata <- sfLapply(1:2,wrapper)

Error message:

[ip-10-228-169-140:09871] [[20253,1],0] routed:binomial: Connection to 
lifeline [[20253,0],0] lost

Any ideas?

Best wishes

Kristian



On 22/06/10 15:56, Gottardo Raphaël wrote:
> First of all you are running R 2.10.1. You should update to R 2.11 and update all packages at the same time. By default, sfInit() uses socket type connections.
> You could try' type="MPI"' (or something else) when calling sfInit which is way more stable.
>
> Have  you tried
>
> sfInit(parallel=FALSE,cpus=2)
> calldata<- sfLapply(1:2,wrapper) #parallel
>
> to see if it works using the serial version of snowfall.
>
> On Jun 22, 2010, at 10:45 AM, Unger Kristian wrote:
>
> I tried on two different systems:
>
> a) a dual core laptop with Ubuntu Lucid
>
> sessionInfo:
>
>    
>> sessionInfo()
>>      
> R version 2.10.1 (2009-12-14)
> i486-pc-linux-gnu
>
> locale:
>   [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>   [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8
>   [7] LC_PAPER=en_GB.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] CGHcall_2.6.0  CGHbase_1.4.0  marray_1.24.0  limma_3.2.3    Biobase_2.6.1
> [6] DNAcopy_1.20.0 impute_1.22.0  snowfall_1.84  snow_0.3-3
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
>
> b) EC2 cloud m1.large instance (7.5 GB memory, 4 EC2 Compute Units (2 virtual cores with 2 EC2 Compute Units each), 850 GB instance storage (2×420 GB plus 10 GB root partition), 64-bit platform, I/O Performance: High
>      API name: m1.large) running Ubuntu Lucid 64bit AMD (standard official image published by Ubuntu).
>    
>> sessionInfo()
>>      
> R version 2.10.1 (2009-12-14)
> x86_64-pc-linux-gnu
>
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] CGHcall_2.6.0  CGHbase_1.4.0  marray_1.24.0  limma_3.2.3    Biobase_2.6.1
> [6] DNAcopy_1.20.0 impute_1.20.0  snowfall_1.84  snow_0.3-3
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
>
> The code I am trying to run is the following:
>
> require(snowfall)
> require(CGHcall)
>
> sfInit(parallel=TRUE,cpus=2)
> sfLibrary(CGHcall)
>
> segdata<- "CGHcallPtest.Rdata"
>
>
> load(segdata)
> sfExport("segnorm")
>
> calldata<- vector("list",ncol(segnorm))
>
> segcghdata<- segnorm
> wrapper<- function(ii)
> {
>      return(CGHcall(segcghdata[,ii]))
> }
>
> calldata<- sfLapply(1:2,wrapper) #parallel
>
> calldata<- lapply(1:2,wrapper)
>
> Error message:
>    
>> calldata<- sfLapply(1:2,wrapper)
>>      
> Error in unserialize(node$con) : error reading from connection
>
> running calldata<- lapply(1:2,wrapper) works perfectly alright.
>
> I cannot answer your question on which I connection is used. How can I find out?
>
> Many thanks
>
> Kristian
>
>
>
>
>
>
>
> On 22/06/10 15:13, Raphael Gottardo wrote:
> In that case, send us the command and more details about your configuration. What sort of cluster are you using? (i.e. several machines, one machine with multiple cores).
> What type of connection? Sockets, etc.
> Also what's your session Info?
> On Jun 22, 2010, at 10:07 AM, Unger Kristian wrote:
>
> Thanks you Raphael. Unfortunately deleting ~/.sfCluster does not help.
>
> Kristian
>
> On 22/06/10 14:18, Raphael Gottardo wrote:
>
> This can happen sometimes, try to remove the ~/.sfCluster directory, quit R and try again.
>
> Raphael
>
> On Jun 22, 2010, at 8:32 AM, Unger Kristian wrote:
>
>
>
> Hi!
>
> I am a quite new user of the snowfall package and when I try to run a
> wrapper function (which works fine in normal serial mode) in parallel
> mode I get the following error message:
>
> R snowfall Error in serialize(node$con) : error reading from connection
>
> Looking this error message up in Google did not help much so I would
> appreciate if I could get any advice from here.
>
> Best wishes
>
> Kristian
>
> --
> _____
>
> Dr Kristian Unger
>
> Bioinformaticist Chernobyl Tissue Bank
>
> Department of Surgery and Cancer
>
> Imperial College London
>
> Rm G02, Ground floor G Block
> Hammersmith Hospital
> Du Cane Road,
> London W12 0HS
>
> Tel +44-20-8383-2443
>
> Mob +44-795-1080619
>
> http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
> http://www.chernobyltissuebank.com<http://www.chernobyltissuebank.com/>
>
>
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>
> _______________________________________________
> R-sig-hpc mailing list
> R-sig-hpc@r-project.org<mailto:R-sig-hpc@r-project.org>
> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>
>
>
>
>
> --
> _____
>
> Dr Kristian Unger
>
> Bioinformaticist Chernobyl Tissue Bank
>
> Department of Surgery and Cancer
>
> Imperial College London
>
> Rm G02, Ground floor G Block
> Hammersmith Hospital
> Du Cane Road,
> London W12 0HS
>
> Tel +44-20-8383-2443
>
> Mob +44-795-1080619
>
> http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
> http://www.chernobyltissuebank.com<http://www.chernobyltissuebank.com/>
>
>
>
>
> --
> _____
>
> Dr Kristian Unger
>
> Bioinformaticist Chernobyl Tissue Bank
>
> Department of Surgery and Cancer
>
> Imperial College London
>
> Rm G02, Ground floor G Block
> Hammersmith Hospital
> Du Cane Road,
> London W12 0HS
>
> Tel +44-20-8383-2443
>
> Mob +44-795-1080619
>
> http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
> http://www.chernobyltissuebank.com<http://www.chernobyltissuebank.com/>
>
>
>
>
> ------------------------------------------------------------------
> Raphael Gottardo, PhD
> Research Unit Director in Computational Biology
> Clinical Research Institute of Montreal (IRCM)
> 110, avenue des Pins Ouest
> Montréal (Québec) H2W 1R7
> url:http://www.rglab.org<http://www.rglab.org/>
> phone: 514-987-5747
> fax: 514-987-5546
> email:raphael.gottardo@ircm.qc.ca<mailto:raphael.gottardo@ircm.qc.ca>
>
>    

-- 
_____

Dr Kristian Unger

Bioinformaticist Chernobyl Tissue Bank

Department of Surgery and Cancer

Imperial College London

Rm G02, Ground floor G Block
Hammersmith Hospital
Du Cane Road,
London W12 0HS

Tel +44-20-8383-2443

Mob +44-795-1080619

http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
http://www.chernobyltissuebank.com


-- 
_____

Dr Kristian Unger

Bioinformaticist Chernobyl Tissue Bank

Department of Surgery and Cancer

Imperial College London

Rm G02, Ground floor G Block
Hammersmith Hospital
Du Cane Road,
London W12 0HS

Tel +44-20-8383-2443

Mob +44-795-1080619

http://www1.imperial.ac.uk/medicine/about/divisions/is/histo/
http://www.chernobyltissuebank.com


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