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]] ______________________________________________ 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.
