[R] Matrix package,solve() errors and crashes

[Martin Maechler]

>>>>> "SS" == Surendar Swaminathan <surendar.swaminathan at 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 at 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 and provide
    SS> commented, minimal, self-contained, reproducible code.