On Fri, Jan 15, 2010 at 10:31 PM,
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Today's Topics:
1. Question about vector (zhengjun chen)
2. Re: Question about vector (Tamas Nepusz)
3. question about installing C packages (gunce orman)
4. Re: question about installing C packages (Tamas Nepusz)
5. Re: question about installing C packages (gunce orman)
6. Re: question about installing C packages (Tamas Nepusz)
7. Re: question about installing C packages (gunce orman)
8. segfault in self-test (Neal Becker)
9. Re: question about installing C packages (Tamas Nepusz)
10. Re: question about installing C packages (gunce orman)
11. Re: Question about vector (zhengjun chen)
12. edge_betweenness community detection (zhengjun chen)
13. Re: edge_betweenness community detection (G?bor Cs?rdi)
14. Re: edge_betweenness community detection (Tamas Nepusz)
15. Re: edge_betweenness community detection (G?bor Cs?rdi)
16. Query regarding modularity calculations (Vijaykumar Muley)
17. Re: Query regarding modularity calculations (G?bor Cs?rdi)
----------------------------------------------------------------------
Message: 1
Date: Thu, 14 Jan 2010 22:17:00 -0500
From: zhengjun chen <zhjchen.sa@gmail.com>
Subject: [igraph] Question about vector
To: Help for igraph users <address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I have a problem with vector data type. After using community structure
detection algorithm, I got the membership of vertices. This information is
written into file.
Then I want to calculate the modularity for this community division.
So I extract membership information from the file, and assign them to a
vector. The code is in the following:
int member[12000] ;
..........
for(j=0; j<nodes; j++) // nodes is the number of nodes in the graph
{
igraph_vector_set( &membership, j, (double) member [j] ); // member
array stores the membership of vertices
printf( "%f\n", (double)VECTOR(membership)[j] );
}
igraph_modularity( &graph, &membership, &modu, NULL );
The vector membership is initialized correctly. But when running
igraph_modularity() function, it reports the following errors:
*** glibc detected *** ./modularity: malloc(): memory corruption (fast):
0x08084318 ***
======= Backtrace: =========
/lib/i686/nosegneg/libc.so.6[0x45dbfc6e]
/lib/i686/nosegneg/libc.so.6(__libc_calloc+0x94)[0x45dc0874]
/usr/local/lib/libigraph.so.0(igraph_vector_init+0x33)[0xeb1143]
/usr/local/lib/libigraph.so.0(igraph_modularity+0x5f)[0xf0600f]
./modularity[0x8048980]
/lib/i686/nosegneg/libc.so.6(__libc_start_main+0xdc)[0x45d6ddec]
./modularity[0x8048691]
So, I am a bit confused. Where is wrong?
--
Thanks
zhengjun
Graduate research assistant
Dept of Computer Science and Engineering
Lehigh University
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Message: 2
Date: Fri, 15 Jan 2010 10:30:52 +0000
From: Tamas Nepusz <address@hidden>
Subject: Re: [igraph] Question about vector
To: Help for igraph users <address@hidden>
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii
Hi,
Please send a full code that reproduces the error. It might have
happened that your membership vector is not initialized properly for
instance. By the way, there is an easier way to treat a C array as an
igraph_vector_t, see:
http://igraph.sourceforge.net/doc-0.5/html/ch06s02s05.html
Make sure that you neither modify nor destroy vectors created this way.
Modifying the underlying array is fine.
--
Tamas
> vector. The code is in the following:
>
> int member[12000] ;
> ..........
> for(j=0; j<nodes; j++) // nodes is the number of nodes in the graph
> {
> igraph_vector_set( &membership, j, (double) member [j] ); // member
> array stores the membership of vertices
> printf( "%f\n", (double)VECTOR(membership)[j] );
> }
> igraph_modularity( &graph, &membership, &modu, NULL );
>
> The vector membership is initialized correctly. But when running
> igraph_modularity() function, it reports the following errors:
>
> *** glibc detected *** ./modularity: malloc(): memory corruption (fast):
> 0x08084318 ***
> ======= Backtrace: =========
> /lib/i686/nosegneg/libc.so.6[0x45dbfc6e]
> /lib/i686/nosegneg/libc.so.6(__libc_calloc+0x94)[0x45dc0874]
> /usr/local/lib/libigraph.so.0(igraph_vector_init+0x33)[0xeb1143]
> /usr/local/lib/libigraph.so.0(igraph_modularity+0x5f)[0xf0600f]
> ./modularity[0x8048980]
> /lib/i686/nosegneg/libc.so.6(__libc_start_main+0xdc)[0x45d6ddec]
> ./modularity[0x8048691]
>
> So, I am a bit confused. Where is wrong?
> --
> Thanks
> zhengjun
>
> Graduate research assistant
> Dept of Computer Science and Engineering
> Lehigh University
> _______________________________________________
> igraph-help mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/igraph-help
------------------------------
Message: 3
Date: Fri, 15 Jan 2010 12:47:30 +0200
From: gunce orman <address@hidden>
Subject: [igraph] question about installing C packages
To: Help for igraph users <address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="utf-8"
hello, I'm trying to install C packages of igraph for ubuntu 9.10, 64 bit
system... I've added the packages repository to my /etc/apt/source.list as
mentioned your web page but I can't see any of the igraph packages in
synaptic manager... Is there something wrong?
Thank you very much
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Message: 4
Date: Fri, 15 Jan 2010 11:50:24 +0000
From: Tamas Nepusz <address@hidden>
Subject: Re: [igraph] question about installing C packages
To: Help for igraph users <address@hidden>
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii
> hello, I'm trying to install C packages of igraph for ubuntu 9.10, 64 bit
> system... I've added the packages repository to my /etc/apt/source.list as
> mentioned your web page but I can't see any of the igraph packages in
> synaptic manager... Is there something wrong?
Did you run apt-get update after adding the repositories to
/etc/apt/sources.list?
--
Tamas
------------------------------
Message: 5
Date: Fri, 15 Jan 2010 14:13:52 +0200
From: gunce orman <address@hidden>
Subject: Re: [igraph] question about installing C packages
To: Help for igraph users <address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="utf-8"
yes
On Fri, Jan 15, 2010 at 1:50 PM, Tamas Nepusz <address@hidden> wrote:
> > hello, I'm trying to install C packages of igraph for ubuntu 9.10, 64 bit
> > system... I've added the packages repository to my /etc/apt/source.list
> as
> > mentioned your web page but I can't see any of the igraph packages in
> > synaptic manager... Is there something wrong?
> Did you run apt-get update after adding the repositories to
> /etc/apt/sources.list?
>
> --
> Tamas
>
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/igraph-help
>
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Message: 6
Date: Fri, 15 Jan 2010 12:15:42 +0000
From: Tamas Nepusz <address@hidden>
Subject: Re: [igraph] question about installing C packages
To: Help for igraph users <address@hidden>
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii
> yes
In that case, I don't know what's wrong with Synaptic, but you can open
up a terminal and type:
apt-get install libigraph libigraph-dev
Does it work for you? If not, what's the error message?
--
Tamas
------------------------------
Message: 7
Date: Fri, 15 Jan 2010 14:23:13 +0200
From: gunce orman <address@hidden>
Subject: Re: [igraph] question about installing C packages
To: Help for igraph users <address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="utf-8"
it is not working
here the message:
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Couldn't find package libigraph
On Fri, Jan 15, 2010 at 2:15 PM, Tamas Nepusz <address@hidden> wrote:
> > yes
> In that case, I don't know what's wrong with Synaptic, but you can open
> up a terminal and type:
>
> apt-get install libigraph libigraph-dev
>
> Does it work for you? If not, what's the error message?
>
> --
> Tamas
>
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/igraph-help
>
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Message: 8
Date: Fri, 15 Jan 2010 07:32:01 -0500
From: Neal Becker <address@hidden>
Subject: [igraph] segfault in self-test
To: address@hidden
Message-ID: <address@hidden>
Content-Type: Text/Plain; charset="us-ascii"
I maintain igraph (and python-igraph) on Fedora. python-igraph is now failing
on (bleeding edge) rawhide builds. The report is here:
https://bugzilla.redhat.com/attachment.cgi?id=383932
failure is:
testAuthorityScore (igraph.test.structural.CentralityTests) ... /var/tmp/rpm-
tmp.tE6lTM: line 30: 22398 Segmentation fault (core dumped)
PYTHONPATH=$RPM_BUILD_ROOT/usr/lib64/python2.6/site-packages /usr/bin/python -
c 'import igraph.test; igraph.test.test();'
The build target was x86_64. igraph is 0.5.2.
I have no idea what might have changed in the enviroment that is causing this,
perhaps a newer gcc?
I have no direct access to a system configured in this way, these builds are
done remotely on systems I have no direct access to.
I wonder if anyone has seen a problem like this?
------------------------------
Message: 9
Date: Fri, 15 Jan 2010 12:42:45 +0000
From: Tamas Nepusz <address@hidden>
Subject: Re: [igraph] question about installing C packages
To: Help for igraph users <address@hidden>
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii
Can you please post the contents of your /etc/apt/sources.list file?
It definitely works for me, so there's something wrong on your
side.
--
Tamas
On Fri, Jan 15, 2010 at 02:23:13PM +0200, gunce orman wrote:
> it is not working
>
> here the message:
>
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> E: Couldn't find package libigraph
>
>
> On Fri, Jan 15, 2010 at 2:15 PM, Tamas Nepusz <address@hidden> wrote:
>
> > > yes
> > In that case, I don't know what's wrong with Synaptic, but you can open
> > up a terminal and type:
> >
> > apt-get install libigraph libigraph-dev
> >
> > Does it work for you? If not, what's the error message?
> >
> > --
> > Tamas
> >
> >
> > _______________________________________________
> > 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
------------------------------
Message: 10
Date: Fri, 15 Jan 2010 14:46:15 +0200
From: gunce orman <address@hidden>
Subject: Re: [igraph] question about installing C packages
To: Help for igraph users <address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="utf-8"
I've found the new repository for amd64 bits from your main page :
http://ppa.launchpad.net/igraph/ppa/ubuntu/pool/main/i/igraph/... I've
downloaded packages and now it's working... The problem was due to use old
repository... there wasn't suitable packages for my system... Now I
installed it... thank you very much
On Fri, Jan 15, 2010 at 2:42 PM, Tamas Nepusz <address@hidden> wrote:
> Can you please post the contents of your /etc/apt/sources.list file?
> It definitely works for me, so there's something wrong on your
> side.
>
> --
> Tamas
>
> On Fri, Jan 15, 2010 at 02:23:13PM +0200, gunce orman wrote:
> > it is not working
> >
> > here the message:
> >
> > Reading package lists... Done
> > Building dependency tree
> > Reading state information... Done
> > E: Couldn't find package libigraph
> >
> >
> > On Fri, Jan 15, 2010 at 2:15 PM, Tamas Nepusz <address@hidden> wrote:
> >
> > > > yes
> > > In that case, I don't know what's wrong with Synaptic, but you can open
> > > up a terminal and type:
> > >
> > > apt-get install libigraph libigraph-dev
> > >
> > > Does it work for you? If not, what's the error message?
> > >
> > > --
> > > Tamas
> > >
> > >
> > > _______________________________________________
> > > 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
>
>
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/igraph-help
>
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Message: 11
Date: Fri, 15 Jan 2010 09:36:52 -0500
From: zhengjun chen <zhjchen.sa@gmail.com>
Subject: Re: [igraph] Question about vector
To: Help for igraph users <address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="iso-8859-1"
Hi
Got it. Thanks.
On Fri, Jan 15, 2010 at 5:30 AM, Tamas Nepusz <address@hidden> wrote:
> Hi,
>
> Please send a full code that reproduces the error. It might have
> happened that your membership vector is not initialized properly for
> instance. By the way, there is an easier way to treat a C array as an
> igraph_vector_t, see:
>
> http://igraph.sourceforge.net/doc-0.5/html/ch06s02s05.html
>
> Make sure that you neither modify nor destroy vectors created this way.
> Modifying the underlying array is fine.
>
> --
> Tamas
>
>
> > vector. The code is in the following:
> >
> > int member[12000] ;
> > ..........
> > for(j=0; j<nodes; j++) // nodes is the number of nodes in the graph
> > {
> > igraph_vector_set( &membership, j, (double) member [j] ); //
> member
> > array stores the membership of vertices
> > printf( "%f\n", (double)VECTOR(membership)[j] );
> > }
> > igraph_modularity( &graph, &membership, &modu, NULL );
> >
> > The vector membership is initialized correctly. But when running
> > igraph_modularity() function, it reports the following errors:
> >
> > *** glibc detected *** ./modularity: malloc(): memory corruption (fast):
> > 0x08084318 ***
> > ======= Backtrace: =========
> > /lib/i686/nosegneg/libc.so.6[0x45dbfc6e]
> > /lib/i686/nosegneg/libc.so.6(__libc_calloc+0x94)[0x45dc0874]
> > /usr/local/lib/libigraph.so.0(igraph_vector_init+0x33)[0xeb1143]
> > /usr/local/lib/libigraph.so.0(igraph_modularity+0x5f)[0xf0600f]
> > ./modularity[0x8048980]
> > /lib/i686/nosegneg/libc.so.6(__libc_start_main+0xdc)[0x45d6ddec]
> > ./modularity[0x8048691]
> >
> > So, I am a bit confused. Where is wrong?
> > --
> > Thanks
> > zhengjun
> >
> > Graduate research assistant
> > Dept of Computer Science and Engineering
> > Lehigh University
>
> > _______________________________________________
> > 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
>
--
Thanks
zhengjun
Graduate research assistant
Dept of Computer Science and Engineering
Lehigh University
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Message: 12
Date: Fri, 15 Jan 2010 09:49:42 -0500
From: zhengjun chen <zhjchen.sa@gmail.com>
Subject: [igraph] edge_betweenness community detection
To: Help for igraph users <address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I run igraph_community_edge_betweenness () on my dataset. The dataset
consists of 12,000 nodes and 222,156 edges.
The program has been running the whole night. It still does not finish.
In contrast, fastgreedy community detection can finish in much less time.
So, could anyone can tell me a rough time that the edge_betweenness() needs
to detect community?
--
Thanks
zhengjun
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Message: 13
Date: Fri, 15 Jan 2010 15:55:05 +0100
From: G?bor Cs?rdi <address@hidden>
Subject: Re: [igraph] edge_betweenness community detection
To: Help for igraph users <address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
how should we know that? It depends on your computer and on your graph.
But you can try to estimate it yourself. Try running a simple edge
betweenness calculation and measure the running time (T). The running
time for the community detection will be 1/2 n * T, where n is the
number of vertices in the graph. This is just a rough estimate.
To get a better estimate, run the community detection on smaller
graphs with similar density and degree distribution, for graph with
(say) 50, 100, 200, 500, 1000 vertices and extrapolate from that.
Best,
Gabor
On Fri, Jan 15, 2010 at 3:49 PM, zhengjun chen <zhjchen.sa@gmail.com> wrote:
> Hi,
> I run igraph_community_edge_betweenness () on my dataset. The dataset
> consists of 12,000 nodes and 222,156 edges.
> The program has been running the whole night. It still does not finish.
> In contrast, fastgreedy community detection can finish in much less time.
> So, could anyone can tell me a rough time that the edge_betweenness() needs
> to detect community?
> --
> Thanks
> zhengjun
>
>
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/igraph-help
>
>
--
Gabor Csardi <address@hidden> UNIL DGM
------------------------------
Message: 14
Date: Fri, 15 Jan 2010 14:56:33 +0000
From: Tamas Nepusz <address@hidden>
Subject: Re: [igraph] edge_betweenness community detection
To: Help for igraph users <address@hidden>
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii
> I run igraph_community_edge_betweenness () on my dataset. The dataset
> consists of 12,000 nodes and 222,156 edges.
> The program has been running the whole night. It still does not finish.
> In contrast, fastgreedy community detection can finish in much less time.
> So, could anyone can tell me a rough time that the edge_betweenness() needs
> to detect community?
A rough estimate is something like "a LOT". :)
The edge betweenness method calculates the betweennesses of ALL the
edges in EVERY step of the algorithm. The algorithm will take 222.156
steps since it removes edges one by one. So, a quick estimate can be
given by doing the following:
1. Measure the time it takes to calculate all the edge betweennesses
(222.156 edges) in the network.
2. Multiply it by, say, half the number of edges. This gives you a rough
estimate.
--
Tamas
------------------------------
Message: 15
Date: Fri, 15 Jan 2010 16:02:15 +0100
From: G?bor Cs?rdi <address@hidden>
Subject: Re: [igraph] edge_betweenness community detection
To: Help for igraph users <address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset=ISO-8859-1
On Fri, Jan 15, 2010 at 3:55 PM, Gábor Csárdi <address@hidden> wrote:
> Hi,
>
> how should we know that? It depends on your computer and on your graph.
>
> But you can try to estimate it yourself. Try running a simple edge
> betweenness calculation and measure the running time (T). The running
> time for the community detection will be 1/2 n * T, where n is the
> number of vertices in the graph. This is just a rough estimate.
Ooops, Tamas is right of course, n is the number of edges in this formula....
G.
> To get a better estimate, run the community detection on smaller
> graphs with similar density and degree distribution, for graph with
> (say) 50, 100, 200, 500, 1000 vertices and extrapolate from that.
>
> Best,
> Gabor
>
> On Fri, Jan 15, 2010 at 3:49 PM, zhengjun chen <zhjchen.sa@gmail.com> wrote:
>> Hi,
>> I run igraph_community_edge_betweenness () on my dataset. The dataset
>> consists of 12,000 nodes and 222,156 edges.
>> The program has been running the whole night. It still does not finish.
>> In contrast, fastgreedy community detection can finish in much less time.
>> So, could anyone can tell me a rough time that the edge_betweenness() needs
>> to detect community?
>> --
>> Thanks
>> zhengjun
>>
>>
>>
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>
>>
>
>
>
> --
> Gabor Csardi <address@hidden> UNIL DGM
>
--
Gabor Csardi <address@hidden> UNIL DGM
------------------------------
Message: 16
Date: Fri, 15 Jan 2010 21:28:15 +0530
From: Vijaykumar Muley <address@hidden>
Subject: [igraph] Query regarding modularity calculations
To: address@hidden
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="iso-8859-1"
Dear all,
I tried to run modularity calculations for a graph which has 4000 nodes and
60,000 interactions. I performed these calculations using modularity
function of the igraph packages the R code is as follow
x is a graph
b <- edge.betweenness.community( x )
comm <- community.to.membership( x, b$merges, steps=10)
modularity=modularity(x, comm$membership)
but I am getting negative values for modularity moreover it took around 5
days.
am I doing anything wrong ? can you suggests me where I am going wrong and
the estimated time to perform these calculations ?
is there alternate ways to calculate modularity ?
Please, do help me to overcome this problem.
Thanks and Regards
--
Vijaykumar Yogesh Muley
Senior Research Fellow,
Dr. Akash Ranjan's Group,
Computational and Functional Genomics Laboratory (CFG),
Centre for DNA Fingerprinting and Diagnostics (CDFD),
Bldg.7, Gruhakalpa
5-4-399/B, Nampally
Hyderabad- 500001
India
Ph.No: +91 9441189013
E-mail : address@hidden
Life : A journey from Cell to Cell
----------------------------------------------
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Message: 17
Date: Fri, 15 Jan 2010 17:04:06 +0100
From: G?bor Cs?rdi <address@hidden>
Subject: Re: [igraph] Query regarding modularity calculations
To: Help for igraph users <address@hidden>
Message-ID:
<address@hidden>
Content-Type: text/plain; charset=ISO-8859-1
Dear Vijaykumar Yogesh Muley,
On Fri, Jan 15, 2010 at 4:58 PM, Vijaykumar Muley <address@hidden> wrote:
> Dear all,
>
> I tried to run modularity calculations for a graph which has 4000 nodes and
> 60,000 interactions. I performed these calculations using modularity
> function of the igraph packages the R code is as follow
>
> x is a graph
>
> b <- edge.betweenness.community( x )
> comm <- community.to.membership( x, b$merges, steps=10)
> modularity=modularity(x, comm$membership)
>
> but I am getting negative values for modularity moreover it took around 5
> days.
as I already wrote you, it is not the modularity calculation that
takes a long time, but the edge-betweenness based community structure
detection. The modularity calculation should be fast.
Moreover, the negative value is normal, modularity is not necessarily
positive. If you just take 10 merges in such a big graph, as you did,
then you will have very poor communities and the modularity score will
be negative.
Best Regards,
Gabor
> am I doing anything wrong ? can you suggests me where I am going wrong and
> the estimated time to perform these calculations ?
> is there alternate ways to calculate modularity ?
> Please, do help me to overcome this problem.
>
>
> Thanks and Regards
>
>
> --
> Vijaykumar Yogesh Muley
>
> Senior Research Fellow,
> Dr. Akash Ranjan's Group,
> Computational and Functional Genomics Laboratory (CFG),
> Centre for DNA Fingerprinting and Diagnostics (CDFD),
> Bldg.7, Gruhakalpa
> 5-4-399/B, Nampally
> Hyderabad- 500001
> India
>
> Ph.No: +91 9441189013
> E-mail : address@hidden
>
> Life : A journey from Cell to Cell
> ----------------------------------------------
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/igraph-help
>
>
--
Gabor Csardi <address@hidden> UNIL DGM
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End of igraph-help Digest, Vol 42, Issue 11
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