R help - Nov 2007 - snow and Rmpi, delayed starting-times at nodes

Hello,

we use R version 2.6.0, Rmpi_0.5-5 and snow_0.2-9 and have a parallel 
call like this:

clusterApply(cluster, input.list, function(input, data1, type) {  ....   
}, data1, type )

We now have the problem, that the processes at the nodes start delayed. 
This means for example, node 4 starts its calculation when node 1 is 
finished.(see the attached figure)
Therefore we have a lot of loss in our computation time.

Our messages are not very big:
input.list = list of vectors. Each vector has 10 strings
data1 = one integer
type = one string

What can we do to improve the speed?

Thanks
Markus

-- 
Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universit?t M?nchen
IBE - Institut f?r medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://ibe.web.med.uni-muenchen.de 
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de

On Fri, 2 Nov 2007, Markus Schmidberger wrote:
> Hello,
>
> we use R version 2.6.0, Rmpi_0.5-5 and snow_0.2-9 and have a parallel call 
> like this:
>
> clusterApply(cluster, input.list, function(input, data1, type) {  ....   },
> data1, type )
Most likely the problem is the direct use of function(...) ... here.
This captures the local environment in ist closure, which is probably
very large.  Try defining the function you want to call at top level,
or define a top level function to create your function if you do want
a closure with specific tada captured.

luke
>
> We now have the problem, that the processes at the nodes start delayed.
This
> means for example, node 4 starts its calculation when node 1 is
finished.(see
> the attached figure)
> Therefore we have a lot of loss in our computation time.
>
> Our messages are not very big:
> input.list = list of vectors. Each vector has 10 strings
> data1 = one integer
> type = one string
>
> What can we do to improve the speed?
>
> Thanks
> Markus
>
>
-- 
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