>>>>> "SS" == Surendar Swaminathan <surendar.swaminat...@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 and provide SS> commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.