[R-sig-hpc] Problem Running 'snow' on Several Machines

[Stephen Weston]

Unfortunately, there are dozens of possible reasons that makeSOCKcluster
could hang, so it's impossible for us to guess what your particular problem is.
You may have several issues to resolve before you'll get this running if
you're unlucky.

However, one common problem is that one of the workers (in your case
"192.168.1.101") may be unable to connect back to the master process using
the default name used by makeSOCKcluster.  It may work better to use the
dot-separated IP address, which you might be able to compute using:

    > master <- nsl(Sys.info()["nodename"])

Then create the cluster with:

    > cl <- makeSOCKcluster(c("localhost", "192.168.1.101"), master=master)

But if that shot in the dark doesn't work, I suggest debugging it by setting
the manual argument to TRUE:

    > cl <- makeSOCKcluster(c("localhost", "192.168.1.101"), manual=TRUE)

It will then tell you the command to use to start each of the workers.
Open a terminal on each worker, and execute the commands as it prompts you.
Now, you should see the error message, and finding the solution will be
much easier.

- Steve


On Fri, Apr 22, 2011 at 5:30 AM, Michael Smith <my.r.help at gmail.com> wrote:
> All,
>
> I want to run the following program:
>
> library("snow")
> cl <- makeSOCKcluster(c("localhost", "192.168.1.101"))
> clusterCall(cl, function() Sys.info()[c("nodename","machine")])
> stopCluster(cl)
>
> I have set up SSH keys so I don't need to type a password when logging
> in to 192.168.1.101. I'm using Fedora 13 on both machines.
>
> What happens is that the program somehow hangs after 'makeSOCKcluster'
> because it does not return to the R prompt and I have to hit Ctrl-C. It
> also fails to establish the cluster:
>
> $ R -q
>> library("snow")
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>    enquote
>
>> cl <- makeSOCKcluster(c("localhost", "192.168.1.101"))
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>    enquote
>
>
> Attaching package: 'snow'
>
> The following object(s) are masked from 'package:base':
>
>    enquote
>
> ^C
>> clusterCall(cl, function() Sys.info()[c("nodename","machine")])
> Error in inherits(cl, "cluster") : object 'cl' not found
>
>
> When I use makeSOCKcluster(c("localhost", "localhost")) everything works
> fine locally.Below is more information on the system.
>
> Thanks,
> Michael
>
>
>
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] snow_0.3-3
>> Sys.getlocale()
> [1]
> "LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATION=C"
>> library(help=snow)
>
>
>
>
>                Information on package 'snow'
>
> Description:
>
> Package:       snow
> Title:         Simple Network of Workstations
> Version:       0.3-3
> Author:        Luke Tierney, A. J. Rossini, Na Li, H. Sevcikova
> Description:   Support for simple parallel computing in R.
> Maintainer:    Luke Tierney <luke at stat.uiowa.edu>
> Suggests:      Rmpi,rpvm,rlecuyer,rsprng,nws
> License:       GPL
> Depends:       R (>= 2.3), utils
> Packaged:      Fri Jul 4 18:07:30 2008; luke
> Built:         R 2.12.2; ; 2011-04-21 03:02:00 UTC; unix
>
> Index:
>
> clusterSetupRNG         Uniform Random Number Generation in SNOW
>                        Clusters
> clusterSplit            Cluster-Level SNOW Functions
> getMPIcluster           Starting and Stopping SNOW Clusters
> parLapply               Higher Level SNOW Functions
>
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