Hello Martin,

 Thanks for looking in to the problem. My mistake, I pasted the code for
sparse matrix for the graph that was created by

test.g <- simplify(ba.game(1000,m=2))

What I was intending to show was I have a graph object "g" created by
IGRPAH. Please find the link that has the graph object.

http://dropbox.unl.edu/uploads/20090424/cfe4fcb854bb17f2/Graph.RData

Substituting this graph object to the argument in the sparse Matrix gives
the error.

Also I have pasted the link for the sparse Matrix code & the thread I had
posted to IGraph community about the error.

Code (http://igraph.wikidot.com/r-recipes#toc6)

Thread
http://www.google.com/search?q=bonpowe+crashes&sourceid=ie7&rls=com.microsoft:en-US&ie=utf8&oe=utf8&rlz=1I7DKUS_en

I substituted my Graph Object in the code.It says error.

Hope I have explained properly.

Thanks in advance Martin

Nathan







On Tue, Apr 21, 2009 at 6:13 AM, Martin Maechler <maechler@stat.math.ethz.ch
> wrote:

> >>>>> "SS" == Surendar Swaminathan <surendar.swaminathan@gmail.com>
> >>>>>     on Mon, 20 Apr 2009 12:10:47 -0700 writes:
>
>    SS> Hello All, I am working on graph object using IGRAPH
>    SS> package wanted to do Bonacich Power.  This is my graph
>    SS> object.
>
>    SS> The file 'Graph.RData' (4.2 MB) is available for
>    SS> download at
>    SS>
> http://dropbox.unl.edu/uploads/20090424/cfe4fcb854bb17f2/Graph.RData
>
>    SS> Graph size
>
>    SS> Vertices: 20984 Edges: 326033 Directed: FALSE No graph
>    SS> attributes.  Vertex attributes: name.  No edge
>    SS> attributes.
>
>    SS> When I use bonacich power it goes out of memory
>
>    SS> Error in get.adjacency.dense(graph, type = type, attr =
>    SS> attr, names = names, : At vector.pmt:409 : cannot
>    SS> reserve space for vector, Out of memory
>
> how much memory (RAM) has your computer?
>
> I have tried in a few ways to reproduce your problem,
> but have not got any errors, neither when using the 'test.g'
> example you use below, nor by using
>        bonpow.sparse(g)
> where 'g' comes from your  'Graph.RData' file (you mention above).
>
> But you have not provided (in your e-mail) a fully reproducible
> example, so I am not sure how exactly you got the memory problem
> (or even worse the "crash"es).
>
> Regards,
> Martin Maechler, ETH Zurich
> (co-maintainer of 'Matrix').
>
>    SS> I got help from IGRAPH community to use sparse Matrix
>
>    SS> http://igraph.wikidot.com/r-recipes#toc6
>
>    SS> bonpow.sparse <- function(graph, nodes=V(graph),
>    SS> loops=FALSE, exponent=1, rescale=FALSE, tol=1e-07) {
>
>    SS>   ## remove loops if requested if (!loops) { graph <-
>    SS> simplify(graph, remove.multiple=FALSE,
>    SS> remove.loops=TRUE) }
>
>    SS>   ## sparse adjacency matrix d <- get.adjacency(graph,
>    SS> sparse=TRUE)
>
>    SS>   ## sparse identity matrix id <-
>    SS> spMatrix(vcount(graph), vcount(graph),
>    SS> i=1:vcount(graph), j=1:vcount(graph), x=rep(1,
>    SS> vcount(graph))) id <- as(id, "dgCMatrix")
>
>    SS>   ## solve it ev <- solve(id - exponent * d, tol=tol)
>    SS> %*% degree(graph, mode="out")
>
>    SS>   if (rescale) { ev <- ev/sum(ev) } else { ev <- ev *
>    SS> sqrt(vcount(graph)/sum((ev)^2)) }
>
>    SS>   ev[as.numeric(nodes) + 1] }
>
>    SS> ## test graph test.g <- simplify(ba.game(1000,m=2))
>
>    SS> ## test run system.time(bp1 <- bonpow(test.g))
>    SS> system.time(bp2 <- bonpow.sparse(test.g))
>
>    SS> ## check that they are the same max(abs(bp1-bp2)) I get
>    SS> following error and sometime it crashes.
>
>    SS> In solve(id - exponent * d, tol = tol) : Reached total
>    SS> allocation of 1535Mb: see help(memory.size).I increased
>    SS> the memory size and still it is not helpful
>
>    SS> Help on this would be great.
>
>    SS> These are steps I followed
>
>    SS> 1. Created graph object using Igraph version 0.6 on R
>    SS> 2.8.1 windows XP 2. Bonpow(g) 3. Bonpow.sparse function
>
>    SS> sessionInfo()
>
>    SS> R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale:
>    SS> LC_COLLATE=English_United
>    SS> States.1252;LC_CTYPE=English_United
>    SS> States.1252;LC_MONETARY=English_United
>    SS> States.1252;LC_NUMERIC=C;LC_TIME=English_United
>    SS> States.1252 attached base packages: [1] stats graphics
>    SS> grDevices utils datasets methods base other attached
>    SS> packages: [1] Matrix_0.999375-23 lattice_0.17-20
>    SS> igraph_0.6 loaded via a namespace (and not attached):
>    SS> [1] grid_2.8.1
>
>    SS> Thanks in advance
>
>    SS> Nathan
>
>    SS>         [[alternative HTML version deleted]]
>
>    SS> ______________________________________________
>    SS> R-help@r-project.org mailing list
>    SS> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
>    SS> read the posting guide
>    SS> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>and provide
>    SS> commented, minimal, self-contained, reproducible code.
>

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