Force Atlas hangs during dynamic #736

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lynchs61 opened this Issue Jan 30, 2013 · 8 comments

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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.

Owner

mbastian commented Feb 12, 2013

Hi Sean, thanks for your report.

I'm trying to think what could be the issue. Its somehow weird because that sounds like something pretty common and tested so I don't expect big issues like this. Before digging into the code, what is your Java version? If you're using OpenJDK you may want to try using the Oracle JVM. The way threads are implemented might differ and cause issues on some platform and not on others.

The issue might be related to some sort of locking mechanism. What tells me that is the freeze issue that you're describing. Once the application is freezed due to a lock, it would be normal that the Layout run button won't turn off.

One question thought, once the application hangs, can you still manipulate other parts of the UI (like menus at the top etc)? If no, your issue might be rather related to a graphic driver crash. Manipulating the timeline would force a lot of visual objects changes and stress the OpenGL rendering engine in a way that it cause a crash and freeze. That happens a lot more on Linux because of unstable drivers so as you run on Ubuntu it might be worth checking if you can update your graphic card to the proprietary drivers.

One last thing, can you attach the message.log file so I can see if something fails there? Thanks. The file should be located at /home/username/.gephi/0.8.2/dev/var/log.

My java version is Oracle 7

Yes, when the application hangs I CAN still manipulate the enter UI. Everything works as normal except for the fact that I can't turn off the layout.

The message.log file is here:
https://gist.github.com/lynchs61/4832171

I deleted the old logs and then started the application fresh. Then I caused the hang so what you see in the log is what happened during that time.
I don't really know what I'm looking for but it doesn't seem to have anything related to the hung layout.

I have the same problem and it happens also with Force Atlas and Fruchterman-Reingold. Does anyone know how to solve the problem? Otherwise it becomes impossible to visualize a dynamic evolution of data :)

I'm experiencing this problem as well. I could provide more detail, but it seems to be a pretty common problem.

Has anyone found a fix? Can others duplicate?

Hi, same for me. Easy to generate, impossible to avoid.

For me it seems to relate to the time-window passing of periods with no nodes/edges.

Bug is rather crucial for me, at the moment we're visualizing dynamic financial networks.

Thanks on beforehand to anyone finding the time/priority/courage to tackle this bug.

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

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

mbastian self-assigned this Oct 8, 2015

Owner

mbastian commented Feb 9, 2016

This should have been fixed with Gephi 0.9.0. Please try again and reopen if it still doesn't work.

mbastian closed this Feb 9, 2016

Will do!


Van: Mathieu Bastianmailto:notifications@github.com
Verzonden: ‎9-‎2-‎2016 11:39
Aan: gephi/gephimailto:gephi@noreply.github.com
CC: Richard Heuvermailto:richardheuver@hotmail.nl
Onderwerp: Re: [gephi] Force Atlas hangs during dynamic (#736)

This should have been fixed with Gephi 0.9.0. Please try again and reopen if it still doesn't work.


Reply to this email directly or view it on GitHub:
#736 (comment)

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