[igraph] igraph memory error

[Abby Rudolph]

Hello,

 

I have a graph with 23379 edges and 23295 vertices.  It is a simple, unconnected graph with 917 distinct clusters and a density of 4.26x10^-5.

I am able to load the graph without a problem.  However, I need to calculate shortest paths using R so that I can run a series of simulations and I am getting memory errors (64-bit machine) or the program is crashing (32-bit machine).

Using the code

sp<-shortest.paths(g1,mode=”all”)

 

I get the error:

Error in shortest.paths(g1) :

    At vector.pmt:409 : cannot reserve space for vector, Out of memory

 

I noticed that others have had similar errors, but I cannot find a solution to this problem that works for me.

 

On other occasions, when I run the same code, I get the following:

In addition: Warning messages:

1: In print.default(m, ..., quote = quote, right = right) :

  Reached total allocation of 3891Mb: see help(memory.size)

2: In print.default(m, ..., quote = quote, right = right) :

  Reached total allocation of 3891Mb: see help(memory.size)

3: In print.default(m, ..., quote = quote, right = right) :

  Reached total allocation of 3891Mb: see help(memory.size)

4: In print.default(m, ..., quote = quote, right = right) :

  Reached total allocation of 3891Mb: see help(memory.size)

> for (i in 1:vcount(g1)) sp<-shortest.paths(g1,v=i)

Error in shortest.paths(g1, v = i) : 

  At iterators.c:722 : Cannot create iterator, invalid vertex id, Invalid vertex id

In addition: Warning message:

In shortest.paths(g1, v = i) :

  Reached total allocation of 3891Mb: see help(memory.size)

 

 

Any help would be greatly appreciated.

 

Thanks!

 

Abby