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gephi 0.9.1 freezes for dynamical graphs #1633

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frbkrm opened this issue Dec 14, 2016 · 12 comments
Closed

gephi 0.9.1 freezes for dynamical graphs #1633

frbkrm opened this issue Dec 14, 2016 · 12 comments
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@eduramiba
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Awaiting for response Confirmed Critical Fix Committed
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0.9.2

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@frbkrm
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frbkrm commented Dec 14, 2016

Hi!

No matter which machine I use, gephi freezes when I try to work with dynamical graph (e.g. running modularity, layout etc.). I read somewhere that gephi 0.9.1 does not support gexf 1.2. Is that true? If that is the case, I don't find a proper link to download gexf 1.3. It seems that gephi 0.9 for dynamical graphs are still very buggy and there are not enough documentations to get around this problem.

Any help appreciated.
@eduramiba
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Hi,
It supports all versions of gexf, but it's true that there are some stability problems with dynamic graphs in Gephi 0.9.1.

You can try 0.9.2-SNAPSHOT nightly build, it may work better.

Also, can you provide a file and steps to reproduce?

@eduramiba eduramiba self-assigned this Dec 14, 2016
@frbkrm
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frbkrm commented Dec 14, 2016

Here is the gexf file that I want to use in gephi:
graph_w_time.gexf.zip

@eduramiba
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Hi,
I am able to load that graph and run Force Atlas 2 and the timeline at the same time in Gephi 0.9.1 (with updates installed).

Modularity also works.

@frbkrm
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frbkrm commented Dec 14, 2016 •
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could you also try noverlap, enable the time line and colour the nodes based on the modularity. That is usually where my gephi freezes. thanks :)

@eduramiba
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Right, there seems to be a deadlock sometimes. We need to investigate the problem.

@eduramiba eduramiba added this to the 0.9.2 milestone Dec 14, 2016
@eduramiba
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eduramiba commented Dec 14, 2016 •
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Please try again with new 0.9.2-SNAPSHOT nightly build as soon as the travis job ends

eduramiba added a commit that referenced this issue Dec 14, 2016
@eduramiba
Fix #1633 Gephi 0.9.1 freezes for dynamical graphs
64b1f7d
eduramiba added a commit that referenced this issue Dec 14, 2016
@eduramiba
Fix #1633 Gephi 0.9.1 freezes for dynamical graphs
f556986
@eduramiba
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Did it work?

@eduramiba eduramiba mentioned this issue Dec 19, 2016
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eduramiba added a commit that referenced this issue Dec 30, 2016
@eduramiba
Uploading hotfix updates for 0.9.1:
1a3bc4a 
Based on commit 6b041a4

#1526 NullPointerException on Modularity Statistics with gexf with kind / parallel nodes
#1633 Gephi 0.9.1 freezes for dynamical graphs
#1636 Ranking operation not working (node color and size)
#1640 taken screenshot will be overwritten
#1454 Suddenly not importing all of my edges
#1489 CSV import error: found rows with empty source or target columns
#1251 Multiple edges won't be merged
@frbkrm
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frbkrm commented Jan 5, 2017

Sorry for late reply.
I downloaded the latest nightly build gephi. Right now my problem is to run the gephi. When I run "$ ./bin/gephi --jdkhome /usr/lib/jvm/java-7-oracle" in the terminal, I get a lengthy java error and my knowledge is not enough to figure out the problem :S

@eduramiba
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Can you post the full error?

@frbkrm
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frbkrm commented Jan 7, 2017

In my other linux machine where I haven't messed up the java, the gephi nightly build is working! I can now work with dynamical networks without it crashes or freezes. Great!
To run the gephi in terminal I write: $ LIBGL_ALWAYS_SOFTWARE=1 ./bin/gephi
Are the changes now implemented in the official release of the Gephi?

@eduramiba
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Yes, just install latest updates in your Gephi 0.9.1 (Help - Check for Updates)

eduramiba added a commit that referenced this issue Jun 30, 2017
@eduramiba
#1633 Trying to improve performance
1dd46d1
@fabian-rudolf
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Gephi still appears to freeze in version 0.9.2 for dynamic graphs with timeset intervals, a calculated modularity and while running OpenOrd for example.

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