[Rsiena-help] Running RSiena on a computer cluster with Rmpi

[Ruth Ripley]

Dear Mikko,

I think changing RSiena to use Rmpi would be fairly straightforward. I
changed siena07 to allow an extra cluster type of "MPI" and sent the
code through the same path as "FORK" and this apparently ran successfully.

I was using a Mac for my tests.

Specific edits:

R/robmon.r:

change
		if (clusterType == "FORK")
to
 		if (clusterType %in% c("FORK", "MPI"))

R/siena07.r:

change
		clusterType=c("PSOCK", "FORK"), ...)

to
		clusterType=c("PSOCK", "FORK", "MPI"), ...)

Since the changes only involve R, you could make these changes in an
installed version of RSiena using

insertSource('path to siena07.r',package="RSiena")

and similarly for robmon.r. (You will need to do this in each session.)

You also need to have the packages snow and Rmpi. snow is easy to
install, but Rmpi needs to be compiled from source. On my Mac I set the
environment variable Rmpi_TYPE to OPENMPI (I was using Open MPI) and
then used, at the command line,

R CMD INSTALL path-to-Rmpi

although I suspect this could be done within R using

install.packages("Rmpi", type="source")

Regards,

Ruth


On 24/03/2014 20:15, Tom Snijders wrote:
> Dear Mikko,
> 
> Thanks for all your posts!
> I do not think that at this moment any work is planned on improving or extending the facilities for cluster computing in RSiena.
> 
> Best wishes,
> Tom
> 
> 
> ================================================================
> Tom A.B. Snijders
> Professor of Statistics in the Social Sciences
> Department of Politics and Department of Statistics
> Nuffield College
> University of Oxford
> tel. +44-01865-278599
> 
> 
> -----Original Message-----
> From: rsiena-help-bounces at lists.r-forge.r-project.org [mailto:rsiena-help-bounces at lists.r-forge.r-project.org] On Behalf Of Rönkkö Mikko
> Sent: 11 March 2014 08:11
> To: rsiena-help at lists.r-forge.r-project.org
> Subject: [Rsiena-help] Running RSiena on a computer cluster with Rmpi
> 
> Hi
> 
> There has been some discussion on this list regarding using RSiena on a computer cluster. The manual states that "To use more than one machine is more complicated, but it can be done by using, in addition, the clusterString parameter. The computers need to be running incoming ssh." (p. 31)
> 
> Is support for Rmpi planned? The cluster that I have does not allow ssh login to the slave nodes. I think that it is a fairly common scenario that the the slaves are managed by a work load manager and made available through Rmpi, but not direct login.
> 
> Mikko
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