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I am experiencing massive unreliability with my gephi install after it complained about being out of memory and tried to reset the memory limit itself. That didn't work and the VM wouldn't start, so I manually reset the memory to 1024, which didn't work, then to 512, by editing the config file accessed via my start menu.

The system is now hugely unreliable. Freezes and crashes every time I try to work with it. I tried abandoning my project (which is not huge - 11k nodes) in case the project file had gotten corrupted, and tried round tripping a checkpoint, reading in edge and node lists to a blank project from a "just in case of disaster" csv edge and node list export I did. It read the node list ok, but wouldn't read the edge list and froze up again. The logfile contains lots of warnings about deprecated netbeans usages and then a final "SEVERE" warning about a java array index out of bounds. Which doesn't sound to me like something I can do anything about....but hope springs eternal.

In addition to wiping it all out and doing a reinstall, are there any practical tips anyone can offer to help keep gephi happy?

I am on XP SP3 with up to date Java, dual core and 2 gig of RAM.

The config file I edited was on a different system path from the logfile messages. Config file was a general path, and the logfile was specific to me as a user. Which I think is as it should be far as I can tell from the docs - but is something that could be potentially suspicious. I am wondering if my memory allowance reset might not actually have taken effect properly. But I don't know how to inspect this except via the config.

I really really really like Gephi - when it works right. (But to do what I need to do today, I'm going to need to go back to R...)

thanks!

Heather Stark
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  • What exactly happened when you tried to reset the memory to 1024? – Robin Green Nov 30 '13 at 13:55
  • VM failed to initialise. So as per docset, I assumed Gephi's guess was too high and went for a lower figure, 512. – Heather Stark Nov 30 '13 at 20:35
  • I'm having similar problems with a much smaller graph (~1k nodes) on a similar HW/SW setup to what you have. I got a little more stability (and a lot better performance) by pointing the config at a specific JDK installation and adding -J-server to the command line. Memory usage doesn't appear to be a problem, because the process isn't growing to max heap. I suspect it's a mix of an old, weak graphics card with old drivers, and old OS making JOGL hang, but don't have any solid evidence of that yet. – Erik Engbrecht Jan 18 '14 at 17:08

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A few tips when you are absolutely memory starved: - minimize the number of attributes to your nodes and edges. Ideally, you'd have none. - fine tune the Gephi RAM settings. The Gephi installation page says:

On computers with 2GB of memory, you can set -Xmx1400 to get maximum performance.

If 1024 was too high for your machine, and 512 is too low, try intermediary values? and of course, kill any unnecessary process running on your machine.

seinecle
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