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[igraph] Critically slow read.graph(), non-linear completion time

From: Przemek Grabowicz
Subject: [igraph] Critically slow read.graph(), non-linear completion time
Date: Thu, 08 Jul 2010 16:57:24 +0200
User-agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv: Gecko/20100217 Lightning/1.0b1 Shredder/3.0.3pre


I've encountered this when I moved to another workplace. Before I was running
$ uname -a
Darwin alice 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

Now I'm running
$ uname -a
Linux bob 2.6.24-27-server #1 SMP Wed Jan 27 23:39:33 UTC 2010 x86_64 GNU/Linux

Now, when I try to run simple command
> system.time(g2 <- read.graph("base/test", format="edgelist", directed=TRUE))

I get it done much slower on the new platform. By much slower I mean, that the completion time of this task is not growing linearly in case of Linux, and it is growing linearly for Darwin. Because of this reading big graphs (2.5m nodes) is not possible at all (takes more than a day to do this...).
This is independent of formats (I used edgelist and ncol).

There is a way to avoid it with simple trick, by separating file-loading and graph-creation, e.g.
Then again completion time is almost growing linearly and it's possible to load big graphs.

Do you have any ideas what may be a source of this problem?


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