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.
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. 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. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-------------- next part -------------- A non-text attachment was scrubbed... Name: test.pdf Type: application/pdf Size: 7445 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20150703/23571280/attachment.pdf>
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. >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >-- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universit?t Berlin Email loris.bennett at fu-berlin.de