R help - Apr 2009 - Matrix package,solve() errors and crashes

Hello All,

  I am working on graph object using IGRAPH package wanted to do Bonacich
Power.  This is my graph object.

The file 'Graph.RData' (4.2 MB) is available for download at
http://dropbox.unl.edu/uploads/20090424/cfe4fcb854bb17f2/Graph.RData

Graph size

Vertices: 20984
Edges: 326033
Directed: FALSE
No graph attributes.
Vertex attributes: name.
No edge attributes.

When I use bonacich power it goes out of memory

Error in get.adjacency.dense(graph, type = type, attr = attr, names names,  :
  At vector.pmt:409 : cannot reserve space for vector, Out of memory

I got help from IGRAPH community to use sparse Matrix

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

bonpow.sparse <- function(graph, nodes=V(graph), loops=FALSE,
                          exponent=1, rescale=FALSE, tol=1e-07) {

  ## remove loops if requested
  if (!loops) {
    graph <- simplify(graph, remove.multiple=FALSE, remove.loops=TRUE)
  }

  ## sparse adjacency matrix
  d <- get.adjacency(graph, sparse=TRUE)

  ## sparse identity matrix
  id <- spMatrix(vcount(graph), vcount(graph),
                 i=1:vcount(graph), j=1:vcount(graph),
                 x=rep(1, vcount(graph)))
  id <- as(id, "dgCMatrix")

  ## solve it
  ev <- solve(id - exponent * d, tol=tol) %*% degree(graph,
mode="out")

  if (rescale) {
    ev <- ev/sum(ev)
  } else {
    ev <- ev * sqrt(vcount(graph)/sum((ev)^2))
  }

  ev[as.numeric(nodes) + 1]
}

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

## test run
system.time(bp1 <- bonpow(test.g))
system.time(bp2 <- bonpow.sparse(test.g))

## check that they are the same
max(abs(bp1-bp2)) I get following error and sometime it crashes.

In solve(id - exponent * d, tol = tol) :
Reached total allocation of 1535Mb: see help(memory.size).I increased the
memory size and still it is not helpful

Help on this would be great.

These are steps I followed

1. Created graph object using Igraph version 0.6 on R 2.8.1 windows XP
2. Bonpow(g)
3. Bonpow.sparse function

sessionInfo()

R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] Matrix_0.999375-23 lattice_0.17-20    igraph_0.6
loaded via a namespace (and not attached):
[1] grid_2.8.1

Thanks in advance

Nathan

	[[alternative HTML version deleted]]

>>>>> "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]]

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    SS> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
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    SS> commented, minimal, self-contained, reproducible code.