PDF export seems to fail with very large networks

[Axel Bruns]

Hi,

this is going to be a bug which will be very hard to reproduce, unfortunately: I have a very large network (150,000 nodes) which renders just fine in both the Overview and Preview tabs (on a Windows 7 64bit machine with 24GB RAM and a Xeon 8-core CPU).

However, I seem to be unable to export the network as a PDF - Gephi simply sits there and chews up 100% of processing time on one of the CPU cores, but doesn't do anything, and the Gephi user interface no longer responds to any mouse clicks. I've been able to export slightly smaller networks (around 60,000 nodes) relatively quickly (within 15 minutes or so) without any trouble, but with the 150,000 node network it seems that nothing happens even if I keep Gephi running for several days.

To simplify things, I've even tried to export the network with edges and node labels turned off - no difference. The maximum memory setting in the Gephi config file is set to -J-Xmx20000m (but only around 16GB RAM is actually used).

I realise this is an extreme case, but I hope there might eb a simple solution (perhaps just a maximum memory setting in the PDF export function that's set too low ?). I'd be happy to share the .gephi file of the network graph - but it's about 160MB in size...

Many thanks,

Axel Bruns

[Axel Bruns (a-bruns)]

Hi,

One further addition: saving as SVG also times out. The progress bar goes as far as 28%, and then gets stuck - and processor activity drops down to almost 0%.

Axel

[Mathieu Bastian (mathieu.bastian)]

I don't see any reason the process can't finish, and memory starvation is probably the problem here.

One thing Java is not good at is detecting when it runs out of memory and crash. It will actually try to optimize current memory, sometimes for a very long time before giving up.

Question: What is the status of the progress bar when your export start not responding?

[Axel Bruns (a-bruns)]

Hi Mathieu,

OK, this is weird: I just tried the PDF export again, and this time it worked ! I have no idea why, and I didn't do anything differently from the other times - and I tried a good dozen times before, without any success...

When starting the export, the progress bar actually takes quite a while to appear in the first place - after I click OK to export, Gephi just sits there without any indication that it's doing something (but the Windows task manager shows that there's a significant load across all CPU cores). At times, the Gephi window itself is also unresponsive. Previously, the progress bar then appeared, and got stuck at some point. This time around, it appeared only very briefly, and then the export was finished. Very odd.

SVG export behaves differently again: the SVG exporter shows the progress bar the got stuck at 28% last time I tried.

As for the Java issue: are there any Java settings I can experiment with, to see if it makes any difference ?

Sorry about this. I still think there's an issue (and if there's anything about the PDF export that can be further optimised, that would be great), but I can't reproduce it now. Very strange.

Axel

[Sébastien Heymann (sebastien.heymann)]

I mark this bug as Incomplete until we are able to reproduce it.