Randall C Johnson [Contr.]
2006-Nov-07 14:56 UTC
[R] snow's makeCluster hanging (using Rmpi)
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? 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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html and provide commented, minimal, > self-contained, reproducible code.-- Ram?n D?az-Uriarte Bioinformatics Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}}
The most likely culprit is firewall settings. Something like tcpdump may help to confirm that. Working with a stand-alone example from Rmpi may also help. Best, luke On Tue, 7 Nov 2006, 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? > > 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 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics and Fax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke at stat.uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu