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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:1.9.1.9pre) Gecko/20100217 Lightning/1.0b1 Shredder/3.0.3pre |
Hi,
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.
gr2<read.table("base/test");
g2<-graph.data.frame(gr2);
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?
Best,
pms.
- [igraph] Critically slow read.graph(), non-linear completion time,
Przemek Grabowicz <=