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
thanks for your help,
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"
19 "Madix"
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
9 27 1 c blue
9 24 1 c blue
9 5 1 c blue
9 37 1 c blue
9 11 1 c blue
9 14 1 c blue
37 10 1 c blue
37 27 1 c blue
37 24 1 c blue
37 5 1 c blue
37 11 1 c blue
37 9 1 c blue
37 14 1 c blue
10 27 1 c blue
10 24 1 c blue
10 5 1 c blue
10 37 1 c blue
10 11 1 c blue
10 9 1 c blue
10 14 1 c blue
8 10 1 c blue
8 19 1 c blue
8 5 1 c blue
8 40 1 c blue
8 26 1 c blue
8 11 1 c blue
8 16 1 c blue
5 10 1 c blue
5 19 1 c blue
5 40 1 c blue
5 8 1 c blue
5 26 1 c blue
5 11 1 c blue
5 16 1 c blue
40 9 1 c blue
40 16 1 c blue
11 10 1 c blue
11 19 1 c blue
11 5 1 c blue
11 40 1 c blue
11 8 1 c blue
11 26 1 c blue
11 16 1 c blue
11 27 1 c blue
11 24 1 c blue
11 37 1 c blue
11 9 1 c blue
11 14 1 c blue
26 10 1 c blue
26 19 1 c blue
26 5 1 c blue
26 40 1 c blue
26 8 1 c blue
26 11 1 c blue
26 16 1 c blue
26 39 1 c blue
26 9 1 c blue
10 19 1 c blue
10 40 1 c blue
10 8 1 c blue
10 26 1 c blue
10 16 1 c blue
39 5 1 c blue
39 40 1 c blue
39 26 1 c blue
39 9 1 c blue
5 39 1 c blue
5 9 1 c blue
40 39 1 c blue
40 5 1 c blue
40 26 1 c blue
9 39 1 c blue
9 40 1 c blue
9 26 1 c blue
12 10 1 c blue
12 27 1 c blue
12 15 1 c blue
12 16 1 c blue
10 15 1 c blue
10 12 1 c blue
16 40 1 c blue
16 9 1 c blue
16 10 1 c blue
16 27 1 c blue
16 15 1 c blue
16 12 1 c blue
15 10 1 c blue
15 27 1 c blue
15 12 1 c blue
15 16 1 c blue
9 16 1 c blue
27 10 1 c blue
27 15 1 c blue
27 12 1 c blue
27 16 1 c blue
16 19 1 c blue
16 5 1 c blue
16 8 1 c blue
16 26 1 c blue
16 11 1 c blue
19 10 1 c blue
19 5 1 c blue
19 40 1 c blue
19 8 1 c blue
19 26 1 c blue
19 11 1 c blue
19 16 1 c blue
40 10 1 c blue
40 19 1 c blue
40 8 1 c blue
40 11 1 c blue
34 10 1 c blue
34 5 1 c blue
34 40 1 c blue
34 11 1 c blue
10 34 1 c blue
37 19 1 c blue
37 40 1 c blue
37 8 1 c blue
37 26 1 c blue
37 21 1 c blue
37 31 1 c blue
27 19 1 c blue
27 5 1 c blue
27 40 1 c blue
27 8 1 c blue
27 26 1 c blue
27 37 1 c blue
27 21 1 c blue
27 31 1 c blue
8 27 1 c blue
8 37 1 c blue
8 21 1 c blue
8 31 1 c blue
31 5 1 c blue
31 11 1 c blue
5 27 1 c blue
5 37 1 c blue
5 21 1 c blue
5 31 1 c blue
5 34 1 c blue
21 10 1 c blue
21 27 1 c blue
21 19 1 c blue
21 5 1 c blue
21 40 1 c blue
21 8 1 c blue
21 26 1 c blue
21 37 1 c blue
21 31 1 c blue
40 27 1 c blue
40 37 1 c blue
40 21 1 c blue
40 31 1 c blue
10 21 1 c blue
10 31 1 c blue
11 34 1 c blue
11 31 1 c blue
40 34 1 c blue
31 10 1 c blue
31 27 1 c blue
31 19 1 c blue
31 40 1 c blue
31 8 1 c blue
31 26 1 c blue
31 37 1 c blue
31 21 1 c blue
19 27 1 c blue
19 37 1 c blue
19 21 1 c blue
19 31 1 c blue
37 2 1 c blue
26 27 1 c blue
26 37 1 c blue
26 21 1 c blue
26 31 1 c blue
16 37 1 c blue
10 2 1 c blue
37 16 1 c blue
5 2 1 c blue
37 18 1 c blue
31 16 1 c blue
7 10 1 c blue
7 27 1 c blue
7 16 1 c blue
31 18 1 c blue
10 7 1 c blue
16 31 1 c blue
16 18 1 c blue
16 7 1 c blue
5 18 1 c blue
36 19 1 c blue
36 5 1 c blue
36 16 1 c blue
5 36 1 c blue
16 36 1 c blue
16 29 1 c blue
16 6 1 c blue
6 29 1 c blue
6 5 1 c blue
6 18 1 c blue
6 16 1 c blue
29 5 1 c blue
29 18 1 c blue
29 6 1 c blue
29 16 1 c blue
27 7 1 c blue
19 36 1 c blue
19 18 1 c blue
5 29 1 c blue
5 6 1 c blue
18 29 1 c blue
18 5 1 c blue
18 6 1 c blue
18 16 1 c blue
18 19 1 c blue
18 37 1 c blue
18 31 1 c blue
24 10 1 c blue
24 27 1 c blue
24 5 1 c blue
24 37 1 c blue
24 11 1 c blue
24 9 1 c blue
24 14 1 c blue
8 6 1 c blue
8 9 1 c blue
9 8 1 c blue
9 6 1 c blue
10 6 1 c blue
27 6 1 c blue
27 9 1 c blue
37 20 1 c blue
20 10 1 c blue
20 5 1 c blue
20 37 1 c blue
10 20 1 c blue
5 20 1 c blue
37 6 1 c blue
26 6 1 c blue
26 20 1 c blue
6 10 1 c blue
6 27 1 c blue
6 8 1 c blue
6 9 1 c blue
6 19 1 c blue
6 26 1 c blue
6 37 1 c blue
6 20 1 c blue
20 19 1 c blue
20 26 1 c blue
20 6 1 c blue
10 39 1 c blue
10 17 1 c blue
5 17 1 c blue
6 39 1 c blue
6 11 1 c blue
6 17 1 c blue
6 34 1 c blue
27 39 1 c blue
27 11 1 c blue
27 17 1 c blue
27 34 1 c blue
16 39 1 c blue
16 17 1 c blue
16 34 1 c blue
39 10 1 c blue
39 27 1 c blue
39 19 1 c blue
39 8 1 c blue
39 6 1 c blue
39 37 1 c blue
39 11 1 c blue
39 17 1 c blue
39 16 1 c blue
39 34 1 c blue
10 36 1 c blue
5 15 1 c blue
9 19 1 c blue
9 17 1 c blue
9 34 1 c blue
39 31 1 c blue
31 39 1 c blue
6 15 1 c blue
6 31 1 c blue
6 36 1 c blue
36 10 1 c blue
36 27 1 c blue
36 26 1 c blue
36 6 1 c blue
36 15 1 c blue
36 11 1 c blue
36 31 1 c blue
31 2 1 c blue
15 5 1 c blue
15 26 1 c blue
15 6 1 c blue
15 11 1 c blue
15 31 1 c blue
15 36 1 c blue
31 6 1 c blue
31 15 1 c blue
31 36 1 c blue
11 6 1 c blue
11 15 1 c blue
11 36 1 c blue
11 39 1 c blue
11 17 1 c blue
19 6 1 c blue
19 20 1 c blue
19 39 1 c blue
19 9 1 c blue
19 17 1 c blue
19 34 1 c blue
27 36 1 c blue
8 2 1 c blue
10 18 1 c blue
10 25 1 c blue
10 3 1 c blue
17 10 1 c blue
17 27 1 c blue
17 39 1 c blue
17 19 1 c blue
17 5 1 c blue
17 8 1 c blue
17 26 1 c blue
17 6 1 c blue
17 37 1 c blue
17 11 1 c blue
17 9 1 c blue
17 16 1 c blue
17 34 1 c blue
34 27 1 c blue
34 39 1 c blue
34 19 1 c blue
34 8 1 c blue
34 26 1 c blue
34 6 1 c blue
34 37 1 c blue
34 9 1 c blue
34 17 1 c blue
34 16 1 c blue
2 10 1 c blue
2 5 1 c blue
2 8 1 c blue
2 31 1 c blue
9 18 1 c blue
9 15 1 c blue
9 25 1 c blue
9 31 1 c blue
9 3 1 c blue
39 24 1 c blue
39 18 1 c blue
39 15 1 c blue
39 25 1 c blue
39 3 1 c blue
3 10 1 c blue
3 27 1 c blue
3 39 1 c blue
3 24 1 c blue
3 5 1 c blue
3 40 1 c blue
3 18 1 c blue
3 8 1 c blue
3 26 1 c blue
3 6 1 c blue
3 15 1 c blue
3 9 1 c blue
3 25 1 c blue
3 31 1 c blue
3 16 1 c blue
37 39 1 c blue
37 17 1 c blue
37 34 1 c blue
26 24 1 c blue
26 18 1 c blue
26 15 1 c blue
26 25 1 c blue
26 3 1 c blue
26 36 1 c blue
26 17 1 c blue
26 34 1 c blue
6 24 1 c blue
6 40 1 c blue
6 25 1 c blue
6 3 1 c blue
5 24 1 c blue
5 25 1 c blue
5 3 1 c blue
8 39 1 c blue
8 17 1 c blue
8 34 1 c blue
8 24 1 c blue
8 18 1 c blue
8 15 1 c blue
8 25 1 c blue
8 3 1 c blue
27 24 1 c blue
27 18 1 c blue
27 25 1 c blue
27 3 1 c blue
24 39 1 c blue
24 40 1 c blue
24 18 1 c blue
24 8 1 c blue
24 26 1 c blue
24 6 1 c blue
24 15 1 c blue
24 25 1 c blue
24 31 1 c blue
24 16 1 c blue
24 3 1 c blue
15 39 1 c blue
15 24 1 c blue
15 40 1 c blue
15 18 1 c blue
15 8 1 c blue
15 9 1 c blue
15 25 1 c blue
15 3 1 c blue
37 30 1 c blue
5 30 1 c blue
31 24 1 c blue
31 9 1 c blue
31 25 1 c blue
31 3 1 c blue
30 10 1 c blue
30 19 1 c blue
30 5 1 c blue
30 37 1 c blue
19 30 1 c blue
25 10 1 c blue
25 27 1 c blue
25 39 1 c blue
25 24 1 c blue
25 5 1 c blue
25 40 1 c blue
25 18 1 c blue
25 8 1 c blue
25 26 1 c blue
25 6 1 c blue
25 15 1 c blue
25 9 1 c blue
25 31 1 c blue
25 16 1 c blue
25 3 1 c blue
18 10 1 c blue
18 26 1 c blue
18 23 1 c blue
26 23 1 c blue
18 27 1 c blue
18 39 1 c blue
18 24 1 c blue
18 40 1 c blue
18 8 1 c blue
18 15 1 c blue
18 9 1 c blue
18 25 1 c blue
18 3 1 c blue
10 30 1 c blue
5 23 1 c blue
16 24 1 c blue
16 25 1 c blue
16 3 1 c blue
10 23 1 c blue
40 24 1 c blue
40 18 1 c blue
40 6 1 c blue
40 15 1 c blue
40 25 1 c blue
40 3 1 c blue
37 36 1 c blue
31 30 1 c blue
31 13 1 c blue
37 13 1 c blue
30 26 1 c blue
30 31 1 c blue
30 2 1 c blue
30 36 1 c blue
30 13 1 c blue
26 30 1 c blue
26 2 1 c blue
26 13 1 c blue
5 13 1 c blue
20 9 1 c blue
9 20 1 c blue
2 26 1 c blue
2 37 1 c blue
2 30 1 c blue
2 36 1 c blue
2 13 1 c blue
6 23 1 c blue
36 37 1 c blue
36 30 1 c blue
36 2 1 c blue
36 13 1 c blue
23 10 1 c blue
23 5 1 c blue
23 18 1 c blue
23 26 1 c blue
23 6 1 c blue
13 5 1 c blue
13 26 1 c blue
13 37 1 c blue
13 30 1 c blue
13 31 1 c blue
13 2 1 c blue
13 36 1 c blue
31 34 1 c blue
13 10 1 c blue
13 11 1 c blue
11 13 1 c blue
18 20 1 c blue
10 13 1 c blue
20 18 1 c blue
34 31 1 c blue
15 19 1 c blue
15 37 1 c blue
41 10 1 c blue
41 27 1 c blue
41 5 1 c blue
41 26 1 c blue
27 41 1 c blue
26 41 1 c blue
10 41 1 c blue
37 15 1 c blue
18 11 1 c blue
5 41 1 c blue
11 18 1 c blue
38 27 1 c blue
38 5 1 c blue
5 38 1 c blue
27 38 1 c blue
19 15 1 c blue
15 28 1 c blue
15 30 1 c blue
15 20 1 c blue
16 28 1 c blue
16 30 1 c blue
16 20 1 c blue
37 28 1 c blue
27 30 1 c blue
5 28 1 c blue
30 8 1 c blue
30 6 1 c blue
30 28 1 c blue
30 15 1 c blue
30 20 1 c blue
30 16 1 c blue
30 27 1 c blue
10 28 1 c blue
6 28 1 c blue
6 30 1 c blue
19 28 1 c blue
20 8 1 c blue
20 28 1 c blue
20 30 1 c blue
20 15 1 c blue
20 16 1 c blue
20 36 1 c blue
1 10 1 c blue
1 5 1 c blue
1 26 1 c blue
1 11 1 c blue
1 9 1 c blue
9 1 1 c blue
5 1 1 c blue
8 28 1 c blue
8 30 1 c blue
8 20 1 c blue
8 36 1 c blue
28 10 1 c blue
28 19 1 c blue
28 5 1 c blue
28 8 1 c blue
28 6 1 c blue
28 37 1 c blue
28 30 1 c blue
28 15 1 c blue
28 20 1 c blue
28 16 1 c blue
28 36 1 c blue
36 8 1 c blue
36 28 1 c blue
36 20 1 c blue
15 2 1 c blue
15 17 1 c blue
31 22 1 c blue
31 28 1 c blue
14 10 1 c blue
14 27 1 c blue
14 24 1 c blue
14 5 1 c blue
14 37 1 c blue
14 11 1 c blue
14 9 1 c blue
9 2 1 c blue
9 22 1 c blue
9 28 1 c blue
9 13 1 c blue
22 28 1 c blue
22 9 1 c blue
22 31 1 c blue
22 2 1 c blue
22 13 1 c blue
28 22 1 c blue
28 9 1 c blue
28 31 1 c blue
28 2 1 c blue
28 13 1 c blue
11 2 1 c blue
11 1 1 c blue
31 29 1 c blue
10 29 1 c blue
27 14 1 c blue
29 10 1 c blue
29 26 1 c blue
29 31 1 c blue
29 2 1 c blue
17 15 1 c blue
17 2 1 c blue
5 14 1 c blue
26 29 1 c blue
35 10 1 c blue
35 5 1 c blue
35 20 1 c blue
35 2 1 c blue
35 16 1 c blue
35 34 1 c blue
5 35 1 c blue
16 2 1 c blue
16 35 1 c blue
20 2 1 c blue
20 34 1 c blue
20 35 1 c blue
10 35 1 c blue
13 22 1 c blue
13 28 1 c blue
13 9 1 c blue
26 1 1 c blue
10 1 1 c blue
2 29 1 c blue
2 16 1 c blue
2 11 1 c blue
2 17 1 c blue
2 20 1 c blue
2 34 1 c blue
2 35 1 c blue
2 22 1 c blue
2 28 1 c blue
2 9 1 c blue
2 15 1 c blue
17 31 1 c blue
31 17 1 c blue
18 2 1 c blue
2 18 1 c blue
34 20 1 c blue
34 2 1 c blue
34 35 1 c blue
4 10 1 c red
4 16 1 c red
4 15 1 c red
5 37 1 c red
5 40 1 c red
5 27 1 c red
5 26 1 c red
10 39 1 c red
10 26 1 c red
10 32 1 c red
10 16 1 c red
10 15 1 c red
10 27 1 c red
10 14 1 c red
10 4 1 c red
10 29 1 c red
10 24 1 c red
14 15 1 c red
14 32 1 c red
14 39 1 c red
14 27 1 c red
14 10 1 c red
15 14 1 c red
15 26 1 c red
15 39 1 c red
15 4 1 c red
15 10 1 c red
15 40 1 c red
15 27 1 c red
15 32 1 c red
15 16 1 c red
15 29 1 c red
16 15 1 c red
16 26 1 c red
16 10 1 c red
16 4 1 c red
16 39 1 c red
24 27 1 c red
24 10 1 c red
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
_______________________________________________
igraph-help mailing list
address@hidden
http://lists.nongnu.org/mailman/listinfo/igraph-help
_______________________________________________
igraph-help mailing list
address@hidden
http://lists.nongnu.org/mailman/listinfo/igraph-help