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Gephi won't close on OS X #728

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nalice opened this Issue Jan 24, 2013 · 17 comments

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nalice commented Jan 24, 2013

Any time I quit Gephi (whether explicitly or as part of an automatic restart after a plugin update), all of the windows close, but the program never terminates. Eventually it shows up as "not responding" in the Activity Monitor. It doesn't appear to be using any CPU cycles or reading from or writing to the disk. This behavior just started after updating to 0.8.2.

OS: OS X 10.8.2
Java Version: 1.7.0_09, 64-bit
Gephi: 0.8.2

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alves Feb 5, 2013

Confirm the behaviour after installing version 0.8.2. Os version is the same but Java is 1.7.0_13 (64 bit).

In addition to the inability to quit Gephi (have to force quit every time), Gephi becomes unresponsive when selecting any elements of the GUI (Overview, Data Laboratory or Preview) - the menus are inaccessible and Force quit lists its process as unresponsive.

This is a show stopper for using Gephi on OS X and would be very grateful for some guidance on what to correct this error (is a Java preference that needs to be changed?)

alves commented Feb 5, 2013

Confirm the behaviour after installing version 0.8.2. Os version is the same but Java is 1.7.0_13 (64 bit).

In addition to the inability to quit Gephi (have to force quit every time), Gephi becomes unresponsive when selecting any elements of the GUI (Overview, Data Laboratory or Preview) - the menus are inaccessible and Force quit lists its process as unresponsive.

This is a show stopper for using Gephi on OS X and would be very grateful for some guidance on what to correct this error (is a Java preference that needs to be changed?)

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mhct Feb 6, 2013

I also confirm the behaviour of Gephi 0.8.2.
The software starts up correctly and show an initial File Wizard.
After selecting a simple graph to open, gephi shows some options on how to import the graph. It simply freezes
after confirming the graph options. The UI becomes unresponsive, it doesn't display any graph, and nothing else happens.

I also would like to add that gephi 0.8.1 works perfectly on the same environment.

OS: OS X 10.7.5
Java version: 1.7.0_11, 64-bit
Gephi: 0.8.2 (The exact downloaded filename is gephi-0.8.2-beta.dmg)

mhct commented Feb 6, 2013

I also confirm the behaviour of Gephi 0.8.2.
The software starts up correctly and show an initial File Wizard.
After selecting a simple graph to open, gephi shows some options on how to import the graph. It simply freezes
after confirming the graph options. The UI becomes unresponsive, it doesn't display any graph, and nothing else happens.

I also would like to add that gephi 0.8.1 works perfectly on the same environment.

OS: OS X 10.7.5
Java version: 1.7.0_11, 64-bit
Gephi: 0.8.2 (The exact downloaded filename is gephi-0.8.2-beta.dmg)

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fedosov Mar 1, 2013

Same here.

OS: OS X 10.8.2
Java version: 1.7.0_07, 64-bit
Gephi: 0.8.2

fedosov commented Mar 1, 2013

Same here.

OS: OS X 10.8.2
Java version: 1.7.0_07, 64-bit
Gephi: 0.8.2

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cearley Mar 10, 2013

I also confirmed this; the freezing, unresponsiveness, ..., (all of the above)

OSX 10.8.2
Java 1.7.0_15 64-Bit
Gephi: 0.8.2

I removed Gephi 0.8.2 and installed 0.8.1 and that version works fine.

cearley commented Mar 10, 2013

I also confirmed this; the freezing, unresponsiveness, ..., (all of the above)

OSX 10.8.2
Java 1.7.0_15 64-Bit
Gephi: 0.8.2

I removed Gephi 0.8.2 and installed 0.8.1 and that version works fine.

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madgpap Mar 12, 2013

same here for OSX Mountain Lion and Gephi 0.8.2

madgpap commented Mar 12, 2013

same here for OSX Mountain Lion and Gephi 0.8.2

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mmohsen Mar 30, 2013

Same behavior. In addition, it doesn't load data files.

OSX 10.8.2
Java 1.7.0
Gephi 0.8.1 and 0.8.2

mmohsen commented Mar 30, 2013

Same behavior. In addition, it doesn't load data files.

OSX 10.8.2
Java 1.7.0
Gephi 0.8.1 and 0.8.2

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neil-rubens May 21, 2013

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Same here.

OS: OS X 10.8.3
Java version: 1.7.0_12
Gephi: 0.8.2

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neil-rubens commented May 21, 2013

Same here.

OS: OS X 10.8.3
Java version: 1.7.0_12
Gephi: 0.8.2

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mmohsen May 21, 2013

I downgraded to Java 1.6 and it worked back fine

mmohsen commented May 21, 2013

I downgraded to Java 1.6 and it worked back fine

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neil-rubens May 28, 2013

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@mmohsen thanks for pointing out a fix; worked for me.

Here are details for a quick workaround for the OSX issue:

edit the /Applications/gephi_0.8.2-beta.app/Contents/Resources/gephi/bin/gephi
and add the following line towards the top of the file

jdkhome="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"

p.s. you might have different versions of jdk installed; but it should be something like 1.6.*

p.p.s. @alves thanks for pointing out line omission

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neil-rubens commented May 28, 2013

@mmohsen thanks for pointing out a fix; worked for me.

Here are details for a quick workaround for the OSX issue:

edit the /Applications/gephi_0.8.2-beta.app/Contents/Resources/gephi/bin/gephi
and add the following line towards the top of the file

jdkhome="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"

p.s. you might have different versions of jdk installed; but it should be something like 1.6.*

p.p.s. @alves thanks for pointing out line omission

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alves May 28, 2013

Sorry Neils, something seems to be missing: that is the line we need to add to the gephi file?

alves commented May 28, 2013

Sorry Neils, something seems to be missing: that is the line we need to add to the gephi file?

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alves May 28, 2013

Perfect! It works - even though funnily enough I have version 1.7.0_21 installed in "/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java". Any reference for understanding Java installations would be appreciated!

alves commented May 28, 2013

Perfect! It works - even though funnily enough I have version 1.7.0_21 installed in "/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java". Any reference for understanding Java installations would be appreciated!

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qiaoshun8888 Dec 24, 2013

@neil-rubens Thanks. It fixed my problem.

qiaoshun8888 commented Dec 24, 2013

@neil-rubens Thanks. It fixed my problem.

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oztalha Feb 21, 2014

@neil-rubens Thanks ! I had tried jenv (https://github.com/gcuisinier/jenv) but did not work for me.

oztalha commented Feb 21, 2014

@neil-rubens Thanks ! I had tried jenv (https://github.com/gcuisinier/jenv) but did not work for me.

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neil-rubens Feb 21, 2014

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@oztalha Did you add the proper JDK path in the /Applications/gephi_0.8.2-beta.app/Contents/Resources/gephi/bin/gephi

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neil-rubens commented Feb 21, 2014

@oztalha Did you add the proper JDK path in the /Applications/gephi_0.8.2-beta.app/Contents/Resources/gephi/bin/gephi

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oztalha Feb 21, 2014

@neil-rubens your suggestion worked well. jenv method did not work.

oztalha commented Feb 21, 2014

@neil-rubens your suggestion worked well. jenv method did not work.

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shongololo Jun 15, 2014

Exactly same issues here. The solution works. Thanks.

shongololo commented Jun 15, 2014

Exactly same issues here. The solution works. Thanks.

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eduramiba Aug 26, 2015

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Duplicate of #748

Gephi does not work in Mac OS sine Java 7 and Windows since Java 8.
It's due to problems with old JOGL version and is going to be updated in next version.

Please check https://forum.gephi.org/viewtopic.php?f=3&t=3580&p=10712#p10712 for help about running Gephi with Java 6.

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eduramiba commented Aug 26, 2015

Duplicate of #748

Gephi does not work in Mac OS sine Java 7 and Windows since Java 8.
It's due to problems with old JOGL version and is going to be updated in next version.

Please check https://forum.gephi.org/viewtopic.php?f=3&t=3580&p=10712#p10712 for help about running Gephi with Java 6.

@eduramiba eduramiba closed this Aug 26, 2015

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