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Re: [igraph] help with cohesion.blocks (again...)
|
From: |
Gabor Csardi |
|
Subject: |
Re: [igraph] help with cohesion.blocks (again...) |
|
Date: |
Wed, 30 Jan 2008 22:20:23 +0100 |
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User-agent: |
Mutt/1.5.13 (2006-08-11) |
On Wed, Jan 30, 2008 at 03:05:57PM -0600, address@hidden wrote:
> 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.
I don't think that would help much with this graph, you need at least 5Gb
of memory, and that is a very optimistic guess. The main problem is
not that graph.antichains() is slow, but that the memory requirements
are very high. Btw. it can be speeded up easily by not using
combn() for generating the combination, but something faster, i did
tmp <- get.edgelist(graph.full(acount))+1
which is kind of a hack, and that made it run into the memory limit.
Peter, can you summarize in five lines what graph.antichains() is
supposed to do? Just to see if it is worth thinking on a less
demanding implementation.
Thanks,
G.
> 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
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> >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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--
Csardi Gabor <address@hidden> UNIL DGM