[R] Bonpower Crashes Trying Sparse Matrix (Igraph)

[Gábor Csárdi]

Nathan,

please do not crosspost, it is actually lowers your chances to get a
reply. Thanks.

On Tue, Apr 7, 2009 at 10:20 PM, Surendar Swaminathan
<surendar.swaminathan at gmail.com> wrote:
> Hello Gabor,
>
>  Thank you very much for the reply.I tried working on the code. I have
> total of 5 different graphs and Bonpow function in Igraph works for 2 graphs
> and for the other it goes out of memory.It is the same case using sparse
> matrix. The graphs that did not work for Bonpow function in Igraph does not
> work using the sparse.And for one of the graph R crashes.

How does it crash? Which operating system do you use? Which R version
do you use? Which igraph version do you use?

> This is the error I get.Help on this would be great.
>
> *bonpow.sparse(g)*
>
> Error: cannot allocate vector of size 3.3 Gb
> In addition: Warning messages:
> 1: In solve(id - exponent * d, tol = tol) :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 2: In solve(id - exponent * d, tol = tol) :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 3: In solve(id - exponent * d, tol = tol) :
>  Reached total allocation of 1535Mb: see help(memory.size)
> 4: In solve(id - exponent * d, tol = tol) :
>  Reached total allocation of 1535Mb: see help(memory.size)

How many vertices and edges do your graphs have? Can you upload a
graph somewhere so that I can reproduce this problem?

G.

> Nathan
>
>
> On Tue, Apr 7, 2009 at 1:07 AM, Gábor Csárdi <csardi at rmki.kfki.hu> wrote:
>
>> For the records, the possible solution is here:
>> http://igraph.wikidot.com/r-recipes#toc6
>>
>> Gabor
>>
>> On Mon, Apr 6, 2009 at 9:22 PM, Surendar Swaminathan
>> <surendar.swaminathan at gmail.com> wrote:
>> > Hello All,
>> >
>> > I have been trying to do bonpow for a while now.Bonpow works for few
>> graphs
>> > and for few others it goes out of memory.
>> >
>> > I did see reply to one of the posting Alph Centrality Crashed in Igraph
>> > memory error.
>> >
>> > The solution in the posting was to use sparse matrix. This is the link of
>> > the message.
>> >
>> > http://lists.gnu.org/archive/html/igraph-help/2008-04/msg00071.html
>> > I was able to obtain edgelist for the graph and I do not know how to
>> convert
>> > that to sparse matrix and obtain bonpow.
>> > Can someone help me.
>> >  This is what I tried
>> >
>> > Summary(g)
>> >
>> > Vertices: 8047
>> > Edges: 99060
>> > Directed: FALSE
>> > No graph attributes.
>> > Vertex attributes: name.
>> > No edge attributes.
>> > I use get.adjacency( graph,Sparse=TR
>> >
>> > UE) to obtain the sparse matrix.Converted the sparse matrix to graph and
>> fed
>> > the graph object to bonpow.
>> > Can someone help me with this.I know I am making a big mistake but I do
>> not
>> > know how to solve them.
>> >
>> > Please find the attached graph object along with this mail.
>> >
>> > Nathan.
>> >
>> > ______________________________________________
>> > R-help at 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<http://www.r-project.org/posting-guide.html>
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>> >
>>
>>
>>
>> --
>> Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM
>>
>> ______________________________________________
>> R-help at 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<http://www.r-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
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>
>
> ______________________________________________
> R-help at 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.
>
>



-- 
Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM