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## Re: [igraph] help with cohesion.blocks (again...)

 From: Simone Gabbriellini Subject: Re: [igraph] help with cohesion.blocks (again...) Date: Wed, 30 Jan 2008 23:38:19 +0100

```Peter, Gabor,

```
thank you for your help... I am not sure I got everything from your explanations, but it seems to me that I can do two things:
```
```
- use parallel processing option (I can use it since my iMac has two processors, but only 2GB of memory.. btw, how to check that option? is something I have to do in R or a flag in the function or what? could you please point me to some useful links?) - wait for Gabor's hack - I did not understand where to put that line of code (tmp <- get.edgelist(graph.full(acount))+1)..
```
I'll try both! :)

Simone

```
Il giorno 30/gen/08, alle ore 22:05, address@hidden ha scritto:
```
```
```Hi Simone,

```
I checked out your network, and it is taking a very long time. The hangup is in the graph.antichains() function, which is part of the algorithm for finding all minimal-size cutsets of a graph. Things run quickly with your network until you get to the 7th subgraph with cohesion 14. I don't remember precisely, but the best known algorithm for finding all minimal-size cutsets is around O(k^5) for a k-cohesive graph. Your network is very dense and has a maximally- cohesive subgraph of over 14.
```
```
Basically, I don't think it's a bug, I just think that it's a tricky network to run cohesive blocking on. I've run the code on some graphs with aobut 170 nodes, but much less dense than yours, and it has taken days to finish running parallel on two 2.2Ghz processors. Cohesive blocking is an inherently slow process. (This is one of the reasons that k-cores are more widely used in the network literature: they are trivial to compute and often map very close to cohesive blocks on real networks.) I've considered rewriting some of the trickier bits of code in C instead of interpreted R, which would speed things up considerably, but that's a ways down the road if ever.
```
My suggestions for you now are:
```
1) try out using the parallel processing options if you have a multi-core machine or access to an MPI network on multiple computers. Other than that there is not much that can be done. 2) try running the function with verbose output ("cohesive.blocks(mynet,verbose=T)") and see if it's getting hung up on one subgraph for more than a couple of hours or if it's progresing slowly.
```
Sorry I can't be of more help.
Peter

```
On Jan 30, 2008, at 5:10 AM, Simone Gabbriellini simone.gabbriellini- at-......... |igraph-help| wrote:
```
```
```Hello list,

I am experiencing a problem with cohesion.blocks().. I have 25
```
multiplex networks, and everything runs ok for almost all of them, but
```with 6 of them there is a problem: the computation starts but never
ends... I leave the computer calculating the blocks even for 30
minutes, but no result appear..
I have no clue what's happening, I receive no error message from R

simone

this is one of the "incriminated" network (.net format):

*Vertices 41
1 "Aiken"
2 "Ainon"
3 "Aniat"
4 "azor"
5 "Brenn Tantor"
6 "Bube"
7 "Fds"
8 "Flazzer"
9 "Frederick Brae"
10 "Gae"
11 "ginkobiloba"
12 "Hunter999"
13 "Iced"
14 "ilBestio"
15 "Klingo"
16 "Kveldersen"
17 "Lej"
18 "Lukenet"
20 "Manand"
21 "Marco_Rsr"
22 "milordz"
23 "Mondovich"
24 "Nemi"
25 "Nimion"
26 "OrkoPazZo"
27 "Ouba"
28 "Pendragon"
29 "Quill"
30 "reasae"
31 "rukwa"
32 "Sephi"
33 "Shariz"
34 "Shin Xaqer"
35 "Shiny"
36 "Simus"
37 "skyline"
38 "Stryker"
39 "Sualtan"
40 "Tremors"
41 "Yusaku"
*Arcs
9    10    1    c blue
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24    27    1    c red
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26    37    1    c red
26    32    1    c red
26    40    1    c red
26    33    1    c red
26    39    1    c red
26    5    1    c red
26    15    1    c red
26    29    1    c red
26    16    1    c red
26    27    1    c red
26    10    1    c red
27    15    1    c red
27    40    1    c red
27    29    1    c red
27    14    1    c red
27    24    1    c red
27    39    1    c red
27    5    1    c red
27    26    1    c red
27    37    1    c red
27    33    1    c red
27    32    1    c red
27    10    1    c red
29    39    1    c red
29    26    1    c red
29    15    1    c red
29    10    1    c red
29    33    1    c red
29    27    1    c red
32    26    1    c red
32    15    1    c red
32    39    1    c red
32    27    1    c red
32    14    1    c red
32    10    1    c red
33    27    1    c red
33    29    1    c red
33    26    1    c red
37    5    1    c red
37    27    1    c red
37    26    1    c red
37    40    1    c red
39    32    1    c red
39    16    1    c red
39    29    1    c red
39    14    1    c red
39    15    1    c red
39    26    1    c red
39    27    1    c red
39    10    1    c red
40    5    1    c red
40    27    1    c red
40    26    1    c red
40    15    1    c red
40    37    1    c red

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```

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```