Hello, Read_Edgelist() won't work because that assumes that the vertex IDs are in the range [0; |V|-1] so it would create lots of isolated vertices if your vertex ID range has "gaps" in it. Read_Ncol() is the way to go, but it has an additional space penalty as it has to maintain a mapping from the numeric IDs in the file to the range [0; |V|-1].
igraph requires 32 bytes per edge and 16 bytes per vertex to store the graph itself, plus additional data structures to store the vertex/edge attributes. Therefore, a graph of your size would require ~2.5 GB of memory plus the attributes. 8 GB of RAM should therefore be enough -- however, note that Python might not be able to utilize all that memory. In particular, 32-bit Python on Windows is limited to 2 or 3 GBs of memory (see https://msdn.microsoft.com/en-us/library/aa366778(v=vs.85).aspx#memory_limits ). If you happen to use a 32-bit Python on a 64-bit machine, you will need to install a 64-bit Python with a corresponding igraph package that is also built for 64-bit, and then try again. Best, T. On Mon, Aug 1, 2016 at 9:52 AM, Raphael C <[email protected]> wrote: > I have 8GB of RAM and I have a simple edge list text file of size > 1.2GB. It was 62500000 edges and about half that many vertices. Each > line looks like > > 287111206 357850135 > > I would like to read in the graph and output a sparse adjacency > matrix. I am failing on all counts. I have tried > > > g = Graph.Read_Edgelist('edges.txt') > > but this fails immediately with > > MemoryError: Error at vector.pmt:439: cannot reserve space for vector, > Out of memory > > This seems unrelated to the size of the graph is just a function of > the node ids being large. > > So instead I tried > > g = Graph.Read_Ncol('edges.txt') > > This eats up all the RAM in my PC forcing me to kill the code. > > I fact I tested g = Graph.Read_Ncol('edges.txt') with the first 1/5 of > the edges and have the same memory problem. > > Each node id is a 32 bit integer so the graph should fit easily in 8GB of RAM. > > What can I do? > > Thanks very much for any help. > Raphael > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
