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 <maech...@stat.math.ethz.ch > wrote: > >>>>> "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<http://www.r-project.org/posting-guide.html>and > provide > SS> commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ 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.
