Any progress with Force Atlas 2 and Dynamic Layout?

Evolution and dynamics on networks in Gephi: UI, data formats, algorithms...
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francis_flavin
Posts: 68
Joined: 21 Jan 2012 18:34
Location: Washington, DC, USA

Any progress with Force Atlas 2 and Dynamic Layout?

Post by francis_flavin » 26 Aug 2014 19:48

Hi all,

Has there been any progress in resolving the bug that causes Force Atlas 2 to hang with Dynamic Layouts?

The problem has been mentioned here:

https://forum.gephi.org/viewtopic.php?t=2424&p=8387

and here:

https://github.com/gephi/gephi/issues/736

The problem was stated rather well as follows:
When I play a dynamic graph while the force atlas (or force atlas 2) is running it hangs about 75% of the time. When this happens the graph continues to change according to the dynamic timeline, but the vertices no longer respond to the layout algorithm. Also the layout algorithm shows that it is running and can't be stopped (hitting the stop button does nothing). The only way to restore normal behavior is to quit the entire application.

This happens for me with every dynamic graph I've tried in gexf format, and also if I use "File > Generate > Dynamic Graph Example..." from the menu. It happens with version 0.8.1-beta, 0.8.2-beta, and 0.9-snapshot, on Ubuntu Linux, and with 0.8.2-beta on OS X.
I have the problem with Gephi 0.8.2 on two different Windows 7 machines, both of which are sufficiently powerful to handle the layouts. And, I get the problem even if I use "File > Generate > Dynamic Graph Example..." from the drop-down menu. I have had the problem on a MacBook Pro with Retina Display running the latest version of OS X, too.

I have successfully used Force Atlas 2 and dynamic layouts in the past, so I'm reasonably confident I'm setting up the data and the dynamic layout correctly. However, the Force Atlas 2 layout freezes quite frequently (although the timeline continues to function properly). It appears that Force Atlas 2 freezes more frequently now than in the past; although I am using different data sets. My data sets have dynamic nodes and dynamic edges.

One poster had suggested that turning "Prevent Overlap" off would solve the problem. Unfortunately, for me that is not the case.

Any guidance or updates would be appreciated.

Thanks!

Francis

francis_flavin
Posts: 68
Joined: 21 Jan 2012 18:34
Location: Washington, DC, USA

Re: Any progress with Force Atlas 2 and Dynamic Layout?

Post by francis_flavin » 11 Oct 2014 01:48

Okay, I restored my dynamic layout capability.

I got it working again by doing a "clean" installation of Gephi (and, of course, pointing Gephi to Java 6).

Here's what I suggest you do:
  • 1. Delete your old Gephi.app package, which is presumably in your Applications folder.
  • 2. Delete the residual Gephi files from your OS in the Users folder. These are hidden files, so you'll have to un-hide them first. You can un-hide the files by opening a terminal window and typing

    Code: Select all

    chflags nohidden ~/Library/
    Then, navigate to you Users folder, then to /Library/Application Support/ and look for the gephi folder. Delete it. (You can hide the /Library/ folder again if you want.
  • 4. Install Gephi 0.8.2 again either via you old .dmg file or a via a fresh download from the Gephi website. Presumably, you'll put the Gephi.app package in your Applications folder.
  • 5. Edit the Gephi configuration file to use Java 6 rather than Java 7. This file will likely be here: /Applications/Gephi.app/Contents/Resources/gephi/etc/gephi.conf. You can use TextEdit or some other editor to edit the file.
  • 6. Edit the file to include this command to point Gephi to your Java 6 environment:

    Code: Select all

    jdkhome="/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/"
    and save the updated gephi.conf file. You might want to re-open the file to see that your changes saved.
  • 7. Launch Gephi. It should work. To check that Gephi is using Java 6, go to the pull-down menu and click gephi->About. In the pop-up window, you should see this line Java: 1.6.0_65; Java HotSpot(TM) 64-Bit Server VM 20.65-b04-466.1 or something indicating that the Java 1.6.0 virtual machine is running.
It might be the case that a plug-in was causing the problem with freezes during a dynamic layout and that a clean installation simply wiped out any reference to a problematic plug-in. I haven't put all the plug-ins back yet, so we'll see what happens.

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