[R] igraph plot slowness

[Loris Bennett]

Hi Jim,

jim holtman <jholtman at gmail.com> writes:

> Here is what it does locally on my PC:
>
>> library("igraph")
>>  topo_data <- read.table(text = "ibcore01        ibswitch01
> +  ibcore01        ibswitch02
> +  ibcore01        ibswitch03
> +  ibcore02        ibswitch01
> +  ibcore02        ibswitch02
> +  ibcore02        ibswitch03
> +  ibswitch01      node001
> +  ibswitch01      node002
> +  ibswitch01      node003
> +  ibswitch02      node004
> +  ibswitch02      node005
> +  ibswitch02      node006
> +  ibswitch03      node007
> +  ibswitch03      node008
> +  ibswitch03      node009" ,head=FALSE)
>>  system.time({
> +  network_data <-graph.data.frame(topo_data, directed=F)
> +  plot(network_data)
> + })
>    user  system elapsed
>    0.01    0.01    0.03
>>
>>
>
> Does not seem too slow.  Creating a PDF file takes a little longer:
>
>> library("igraph")
>>  topo_data <- read.table(text = "ibcore01        ibswitch01
> +  ibcore01        ibswitch02
> +  ibcore01        ibswitch03
> +  ibcore02        ibswitch01
> +  ibcore02        ibswitch02
> +  ibcore02        ibswitch03
> +  ibswitch01      node001
> +  ibswitch01      node002
> +  ibswitch01      node003
> +  ibswitch02      node004
> +  ibswitch02      node005
> +  ibswitch02      node006
> +  ibswitch03      node007
> +  ibswitch03      node008
> +  ibswitch03      node009" ,head=FALSE)
>>  system.time({
> +  network_data <-graph.data.frame(topo_data, directed=F)
> +  pdf('test.pdf')
> +  plot(network_data)
> +  dev.off()
> + })
>    user  system elapsed
>    0.09    0.00    0.16
>
> The PDF file is attached.  So maybe it is something with your remote
> connection.

You're right.  Running locally even the plot of complete network takes
less than 0.2 seconds via the X11 device.  I'll have a closer look at
the connection.

Thanks,

Loris

> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
> Tell me what you want to do, not how you want to do it.
>
> On Fri, Jul 3, 2015 at 3:21 AM, Loris Bennett <loris.bennett at fu-berlin.de>
> wrote:
>
>> Hi,
>>
>> With the following data
>>
>> ibcore01        ibswitch01
>> ibcore01        ibswitch02
>> ibcore01        ibswitch03
>> ibcore02        ibswitch01
>> ibcore02        ibswitch02
>> ibcore02        ibswitch03
>> ibswitch01      node001
>> ibswitch01      node002
>> ibswitch01      node003
>> ibswitch02      node004
>> ibswitch02      node005
>> ibswitch02      node006
>> ibswitch03      node007
>> ibswitch03      node008
>> ibswitch03      node009
>>
>> in the file "topology.txt"
>>
>> and the following code:
>>
>> library("igraph")
>> topo_data <- read.csv(file="topology.txt",head=FALSE,sep="\t")
>> network_data <-graph.data.frame(topo_data, directed=F)
>> plot(network_data)
>>
>> it takes about 5 seconds for the plot to be drawn with R 3.2.0 on a
>> 12-core 2.67 GHz Xeon X5650 server with no other CPU-intensive processes
>> running.
>>
>> This strikes me as rather slow, particularly as my full network has over
>> 120 components and the plot takes around 50 seconds.
>>
>> Am I doing anything wrong?
>>
>> (I am working over an ssh connection with X forwarding, but plotting to
>> a PDF file on the server does not seem to be faster.)
>>
>> Cheers,
>>
>> Loris
>>
>> --
>> This signature is currently under construction.
>>
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>

-- 
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin         Email loris.bennett at fu-berlin.de