[R] Bonpower Crashes Trying Sparse Matrix (Igraph)

Gábor Csárdi csardi at rmki.kfki.hu
Tue Apr 7 23:04:51 CEST 2009


On Tue, Apr 7, 2009 at 10:46 PM, Surendar Swaminathan
<surendar.swaminathan at gmail.com> wrote:
> Hello Gabor,
>
>  Thank you very much for the reply.With respect to  the cross post.I
> replied to the thread that was created I must have made a mistake.

And replied alternately to r-help and igraph-help.

> I tried
> working on the code.

Meaning exactly what?

> 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.
>
> This is the error I get.Help on this would be great.

But you haven't answered any of the questions I have asked in the
previous emails. Please do so, it would be great.

G.

> 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)
>
> Nathan
>
> On Mon, Apr 6, 2009 at 12:22 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.
>>
>
>        [[alternative HTML version deleted]]
>
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>



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




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