[R] snow's makeCluster hanging (using Rmpi)

[Ramon Diaz-Uriarte]

On Tuesday 07 November 2006 15:56, Randall C Johnson [Contr.] wrote:
> Hello everyone,
> I've been fiddling around with the snow and Rmpi packages on my new Intel
> Mac, and have run into a few problems. When I make a cluster on my machine,
> both slaves start up just fine, and everything works as expected. When I
> try to make a cluster including another networked machine it hangs. I've
> followed the suggestions at
> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/83086.html and
> http://www.stat.uiowa.edu/~luke/R/cluster/cluster.html but to no avail.
> Everything seems to start up fine using lamboot, but then hangs when making
> the cluster in R. Making a cluster with 2 slaves seems to work fine, but if
> I increase the number (to use the networked machines) it hangs again.
>
> I've tried networking to another Mac, and also to a machine running Red Hat
> Linux. Both machines can set up their own local clusters. Does anyone have
> any ideas?

Dear Randy,

A few suggestions:

a) make sure there are no firewalls; I assume this is actually the case, but 
anyway;

b) what happens if you lamboot outside R (and create a universe with a local 
and a networked machine) and then you do: "lamexec -np 6 hostname"?

c) are the Rmpi and snow installed in the same directories in the different 
machines? are there version differences in Rmpi (or Snow) between machines?


HTH,

R.



>
> Thanks,
> Randy
>
> > sessionInfo()
>
> R version 2.4.0 Patched (2006-10-03 r39576)
> i386-apple-darwin8.8.2
>
> locale:
> C
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "base"
>
> other attached packages:
>    Rmpi    snow
> "0.5-3" "0.2-2"
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Randall C Johnson
> Bioinformatics Analyst
> SAIC-Frederick, Inc (Contractor)
> Laboratory of Genomic Diversity
> NCI-Frederick, P.O. Box B
> Bldg 560, Rm 11-85
> Frederick, MD 21702
> Phone: (301) 846-1304
> Fax: (301) 846-1686
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
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-- 
Ramón Díaz-Uriarte
Bioinformatics 
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
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