Gephi out of memory, how to increase it?

[yannis]

After some 24 hours on processing by Force Atlas 2 my graph (16k vertices, 39k edges), I got the same error message as some other user of this forum in October:

The project file couldn't be opened. Please check the file has .gephi extension.

ArrayIndexOutOfBoundsException - 0

Gephi said something about memory being too low (505 MB) and also that it can be increased to 2193MB on my system. Then it said "Increase memory and restart Gephi? Your data will be saved", I clicked on OK, but Gephi did not restart and my data was not saved: in fact the *.gephi file of the project was corrupted, I unzipped it and the XML data end abruptly…

Can I recover that file?

It is really a pity that Gephi stops after 24 hours of steady work. Is there no way to save the file periodically so that the next time I do not lose everything again?

Last question: how can I increase memory allocated to Gephi, so that the same problem does not occur again?

How can I (even roughly) calculate in advance the amount of memory needed so that I can prevent the crash?

Your answers will be very appreciated, that graph is very important for a paper i'm preparing, and the deadline is in the mid of January…

Thanks in advance and season's greetings

[eduramiba]

Hi,
It is possible that Gephi has tried to modify the configuration file to increase memory but did not have file permissions (this is usual in windows 7 program files folder).

But you can increase manually the memory by editing the etc/gephi.conf file placed where your gephi is installed. Check this https://gephi.org/users/install/#memory for more info.

Unfortunately, if the xml ends abruptly it will not be possible to recover the information after it ends.

Eduardo

[katjah]

I got exactly the same problem as described above by "yannis". The memory run out and the .gephi file got corrupted in the process. I now receive 'ArrayIndexOutOfBoundsException when trying to open the file. I used ForceAtlas2 layout and the newest Gephi version (0.8.1 beta) on Ubuntu. My configuration was already set to use the maximum amount of memory available (1 GB) and my data set is not very big (approx 100+ nodes with 200 edges). I'd have a couple of questions in this regard.

1. Am I right to suppose that there must be a bug causing memory leakage? Is there anything reported around this issue already? When I look at the Gephi system requirements, processing such a number of nodes should not need more than 1GB of memory. Is this correct?

2. I also wonder if you might have any hints on how to recover the data from the XML file inside .gephi. I can see that most of the data is still there, but I have not found a straightforward way to extract it. Considering its not thousands of nodes (luckily), should I just re-enter it all manually?

Many thanks for your time in advance.

Katja

[Cloudman]

Hi,
I tried editing the xmx value by increasing to 1400MB on my 16GB machine.But when I tried to increase it further to 2000MB,it doesn't work i.e. Gephi doesn't even open when double clicked.
I would like to understand how to increase the xmx value so as to import large volumes of data in to gephi.

[eduramiba]

Hi, make sure your Java is 64 bit and not 32 bit.