Mac OS Freeze/Hang

[Simounawind]

EDIT: If you're experiencing a hang/freeze on Mac OS, please fill this short questionnaire. Thank you!

Expected Behavior

I'm using the Gephi 0.95 and 0.96, but after trying these two versions, I found that sometimes it may go crashing with the rainbow circle running all the time, so I have to reopen it. Il doesn't hit me all the time but occasionally. Also, there is always nothing showing in "preview" even if i have tried to presse the refresh bottom.

Current Behavior

Crash

Possible Solution

Maybe the version is not compatible with the new MacOS monterey 12.4 ?
Idk too

Steps to Reproduce

1. Open the software
2. Load a existing program
3. Crash

Context

These 2 issues existes ever since i start using this software, about 7 days before.

Your Environment

• Version used: Gephi 0.9.5
• Operating System: MacOS Monterey 12.4

Here is the report :
report.txt

[jumingKaigua]

I got the same problem, I tried the older version but still got rainbel circle

[mbastian]

Hi, thanks for the report. There is no known problem on Monterey 12.4. I'm curious if you're running M1 processors by any chance?

[Simounawind]

Hi, yes I'm actually running on M1Pro. Btw thanks for this amazing software, we talked a lot about it on class !

[jumingKaigua]

When strat Gephi, I need to open another window above it. And the rainbow circle never come back. I'm running on M1Pro too.

[teddyPA]

what exactly do you mean - open another window above it?? I'm running OS 12.4, M1, 16G ram, and Gephi 9.5

[jumingKaigua]

when you launch Gephi, you open About this Mac and let About this Mac window above the Gephi launch interface.

[dhosterman]

Hello. I'm having the same issue on 12.4 on an M1 Mac, though I was able to run Gephi on this M1 Mac in the past without issue.

[mbastian]

Hi, unfortunately so far I'm not able to reproduce this issue. The report provided says that it hang but not much other details. I would need some more help to investigate, potentially even having a Zoom call with someone so I can see it "live". Otherwise, any clues on the following would help:

1. When does it hang exactly? After the spash screen? When the graph window is initatializing?
2. Has this issue appeared when you moved from Mac OS 12.3 to 12.4?
3. Does version 0.9.3 work? and 0.9.2?
4. Attach the content of the messages.log so I can see the application logs
5. Try launching it from a terminal /Applications/Gephi.app/Contents/MacOS/gephi and provide any logs if any
6. Open the Applications > Console and see if you have any gephi/netbeans/java crash or spin reports. Attach those as well.

Much appreciated

[dhosterman]

I'd be happy to do a Zoom meeting with you! In the meanwhile, I'll try to answer the questions you've asked.

1. I make it through the splash screen and it seems to hang when the Graph window is initializing.
2. It's hard to say exactly when this issue started occurring, but I was able to successfully use Gephi in the past and this issue is new. It might have been after the upgrade from 12.3 to 12.4 as I don't think I've used Gephi after that upgrade, but I can't say for certain.
3. 0.9.3 seems to have the same issue. 0.9.2 DOES seem to load correctly.
4. messages.log
5. Starting from the terminal did not provide any stderr output.
6. Not seeing anything in crash or spin reports.

Edit: I know the messages.log file says I'm on x86_64, but I'm assuming that's because it is running through Rosetta. I am running on an M1 Mac.

[ineffyble]

I seem to have same problem, 12.3, M1 Pro, Gephi 0.9.6

[sudame]

I had the same problem, but I found @jumingKaigua 's comment is a work around.

When strat Gephi, I need to open another window above it. And the rainbow circle never come back. I'm running on M1Pro too.
#2546 (comment)

1. Launch Gphi.
2. Quickly launch "About this Mac" from Apple icon in the Mac menu bar.
3. If the "About this Mac" window overlay the Gephi launch splash, Gephi will work.

OS: macOS 12.4
CPU: M1 Max
Gephi version: 0.9.5, 0.9.6

[jeremyreffin]

I encountered the rotating beachball crash problem this morning and found a fix / work-around.

I navigated to the user config files at /Users/username/Library/Application\ Support/gephi and I deleted them.

Gephi then launched fine.

(My config: Mac OSX, macOS Big Sur, intel CPU).
I had both 0.92 and 0.9 folders in there.

@mbastian - Mathieu, I think it must be something to do with these configs getting a bit messed up. Possibly the look-and-feel settings or something to do with handling of the separate little graph windows etc. It was hanging this morning before being able to render the small graph window that invites you to open a recent file etc etc. Obviously this will be hard to re-produce without knowing what's in a person's config files.

[For gephi 0.92 I had been using the "Metal" look-and-feel in order to get around the bug in 0.92 which would lead to hanging in certain circumstances with "OS-X" look-and-feel. When I first installed 0.96 it ran fine and invited me to bring in settings from 0.92 - I note that "Metal" no longer exists as a look-and-feel so am speculating as to whether that caused a problem.]

Once the beachball hang was created, both re-installing 0.96 or installing 0.93 didn't fix it. 0.92 re-installed and ran fine. As mentioned above, deleting user configs fixed the problem for an installed version of 0.96

[mbastian]

Thanks @jeremyreffin that's helpful. It's an interesting hypothesis this could be caused by 0.9.2 configuration being imported. I'll see if I can reproduce that. In the meantime, if you still have these two user folders in your Bin I would love to have them for investigation!

[jeremyreffin]

0.9.zip
0.9.2.zip

Hi @mbastian - Sorry for the slow reply (annual holiday and email backlog indigestion). I attach those user folders in case they are useful! All best, Jeremy

[brianckeegan]

I used @jeremyreffin's suggestion, but still have a hang on load and exit. The workaround mentioned by @sudame continues to work for me. Force quitting brings up a netbeans error reporting tool. Gephi 0.9.7 on Mac OS 12.5.1 + M1.

[francescoragazzi]

Hi I was wondering if there is an update on the problems with Macos Monterrey, or a consensus on how to solve them. In my case, the freezing happens when switching from overview to data lab. I tried deleting the user settings folder, but the problem persists. @mbastian I'm happy to send all necessary logs or make a video recording of the issue if it can be helpful. Thanks! (For info, this is my setup Mac M1 Max, 32GB RAM, Macos Monterrey 12.5.1.)

[mbastian]

Hi @francescoragazzi no despite by efforts I've never being able to reproduce this issue locally. Root cause is unknown.

Given the issue being not systematic, it could be related to some threading issue. When the application is freezing, could someone run this command to obtain a dump of the application's thread:

jcmd PID Thread.print

The PID can be found in the Activity Monitor. Just search for Gephi and find the PID column. That's the number you put instead of PID in the command above. For instance,

Attach the output here so I can investigate. Thanks!

[francescoragazzi]

@mbastian Sorry for the long delay, had a crazy week. Here is the file with the thread info. Very curious to see what you find!

Frozen GEPHI PID Thread.txt

[mbastian]

Thanks @francescoragazzi the thread dump helped provide some leads on what might be happening. Still, not an issue I've been able to reproduce myself yet.

In order to confirm some hypothesis I would need some help if you don't mind (you, or anyone else on this thread).

Here is a patched version where I disabled some initialization code that might be causing the trouble.

• https://oss.sonatype.org/content/repositories/snapshots/org/gephi/gephi/0.9.8-SNAPSHOT/gephi-0.9.8-20221104.192046-12-macos-x64.dmg

Please let me know if that changes anything.

[francescoragazzi]

Hi @mbastian sorry again for the delayed response. I will try this asap and let you know what happens. Thanks!!

[francescoragazzi]

Hi @mbastian no luck I'm afraid. Here is the new dump. As soon as I opened a file it froze again. (Also, I promise to be more responsive from now on! :)
Full thread dump OpenJDK.txt

[mbastian]

Thanks @francescoragazzi much appreciated. Let's try something else, what about this version: https://oss.sonatype.org/content/repositories/snapshots/org/gephi/gephi/0.9.8-SNAPSHOT/gephi-0.9.8-20221121.201741-14-macos-x64.dmg

This version has a patched version for JOGL, the OpenGL library we use. This patch is quite experimental and comes from the community, but seem to address some "hanging" issue on similar applications. I haven't investigated very deeply but it could be the same issue.

[iyzg]

Just wanted to bump with the same issue. I've tried the solutions in this thread, but none of them have worked.

Device: M1 Macbook Pro
macOS: 14.4.1 (23E224)
Gephi V: 0.10.1

[tophee]

Solution: In Gephi 0.9.5, I've found that if I open Gephi and then immediately switch to a different application or desktop, Gephi can load successfully in the background and then runs just fine.

I can confirm that this works for me on a MacBook Pro M1 on Sonoma 14.4.1 and Gephi 0.10.1. Thanks a lot for sharing!

Edit: unfortunately, even though the workaround prevents the hang at startup, the app is still unusable, as it still hangs at a later point, e.g. when switching to data lab or so.

I also tried 0.10.2 but here not even the workaround worked, apparently because the app now forces itself into the foreground while starting. So I went back to 0.10.1 but I just can't get it to work.

Given that this issue has existed for some time now, I suppse this means that Gephi for Mac is dead for the time being. Can anyone recommend any altermatives?

[tophee]

I'm wondering how people are handling this situation. Is anybody using Gephi on Mac (if so, what's the trick?) or is everybody just switching to Windows? This bug has cost me so much time and I'm wondering whether I'm just trying to get something to work that simply wont work. But I'm having a hard time believing that all Mac users just gave up on Gephi. Or is this just happening on some Mac Systems?

I am having a hard time even locating what the actual problem is because the behavious is so weird, I've never seen anything like it. For example, during the phases when Gephi actually runs, the View menu is is dead (no menu unfolding when clicked). At one point, I believe, Gephi even case other the View menu in other apps to die. I have no idea how this is possible, but I assume that Gephi crashed some system service related to the view menu.

Another weird behaviour is that when I install a new (or old) version of Gephi, it usually works on first try (provided I use the trick of switching to a different app while Gephi loads, as described above), but when it then crashes/freezes, it will sometimes start again but then fail to load the project file 4% into loading, or it will (most of the time) be completely dead, i.e. crash before even the splash screen appears (the app bounces a couple of times in the dock and then stops).

I have tried the version 11.0 snapshot but (almost) no difference. I seem to remember that the first start worked without switching to a different app (though I had to manually specify the path to the javasdk because, apparently it comes with java11 included but requires java 17), but after it froze again, the behavious was the same as in version 10.

I also tried 9.7 but no luck there either.

What seems to work best for me at the moment (fingers crossed) is to install java version 17 and point Gephi 10.1 to it in the config file. It still crashes sometimes but what seems to fix it then is to reinstall java, which is also weird, I think. Can a java app break you java installation?

Perhaps it's not the actual installation that breaks but some component of java that crashes and that gets restarted when I reinstall? Perhaps a virtual machine? I have no idea how java apps work, but I thought that the javasdk obly provides libraries and is not running any services in the background, independent of the java apps. So, again: weird.

The other day I got this:

It says that I force quit java, which probably means that I force quit the java app Gephi, but I'm not even sure I actually did force quit it in that situation. I often do, when it hangs, but I seem to remember that it crashed by itself in this situation. Usually, when I force quit Gephi, no such message appears. So, somehow, there seem to be different levels at which it hangs or crashes. Maybe sometimes it is the gephi app itself, sometimes it is java, and sometimes it might be some system service related to the view menu (which, taken by itself, I would have a hard time believing, but given that the freezes can be prevented by foregrounding another app, it kinda makes sense.

Edit: Oh, and, yes, I also sometimes get the message that "org.netbeans.Main" was killed, like someone reported above. So, yet another level of crashing ;-)

And yet another detail that I just discovered when I actually tried to quitting Gephi (Haven't had to do that so often in the past because it mostly crashes): I saved the project before quitting. And even though I had just saved, it asked me whether I wanted to save. I said no (because it previously crashed when I said save, so I wanted to try what happens if I say don't save). It seemed to close fine, but then I saw that it actually didn't fully quit (it still had a dot under the icon in the dock). So, I actually can't close Gephi in any regular way. I have to force quit it.

[wonheecho]

I think this problem is hard to pinpoint because replicating the problem is so...unpredictable. As I said before, when I had gephi as the only third party app on my Mac, it worked fine. But then at some point it got messed up. And that's the problem - I cannot simply pinpoint what app is causing the problem.

The solution for me right now is almost crazy - I have Parallels as a VM and use Gephi in Windows. The more recent Mac (I have an M3 Mac) seem to be powerful enough to handle this problem.

I'm wondering how people are handling this situation. Is anybody using Gephi on Mac (if so, what's the trick?) or is everybody just switching to Windows? This bug has cost me so much time and I'm wondering whether I'm just trying to get something to work that simply wont work. But I'm having a hard time believing that all Mac users just gave up on Gephi. Or is this just happening on some Mac Systems?

I am having a hard time even locating what the actual problem is because the behavious is so weird, I've never seen anything like it. For example, during the phases when Gephi actually runs, the View menu is is dead (no menu unfolding when clicked). At one point, I believe, Gephi even case other the View menu in other apps to die. I have no idea how this is possible, but I assume that Gephi crashed some system service related to the view menu.

Another weird behaviour is that when I install a new (or old) version of Gephi, it usually works on first try (provided I use the trick of switching to a different app while Gephi loads, as described above), but when it then crashes/freezes, it will sometimes start again but then fail to load the project file 4% into loading, or it will (most of the time) be completely dead, i.e. crash before even the splash screen appears (the app bounces a couple of times in the dock and then stops).

I have tried the version 11.0 snapshot but (almost) no difference. I seem to remember that the first start worked without switching to a different app (though I had to manually specify the path to the javasdk because, apparently it comes with java11 included but requires java 17), but after it froze again, the behavious was the same as in version 10.

I also tried 9.7 but no luck there either.

What seems to work best for me at the moment (fingers crossed) is to install java version 17 and point Gephi 10.1 to it in the config file. It still crashes sometimes but what seems to fix it then is to reinstall java, which is also weird, I think. Can a java app break you java installation?

Perhaps it's not the actual installation that breaks but some component of java that crashes and that gets restarted when I reinstall? Perhaps a virtual machine? I have no idea how java apps work, but I thought that the javasdk obly provides libraries and is not running any services in the background, independent of the java apps. So, again: weird.

The other day I got this:

It says that I force quit java, which probably means that I force quit the java app Gephi, but I'm not even sure I actually did force quit it in that situation. I often do, when it hangs, but I seem to remember that it crashed by itself in this situation. Usually, when I force quit Gephi, no such message appears. So, somehow, there seem to be different levels at which it hangs or crashes. Maybe sometimes it is the gephi app itself, sometimes it is java, and sometimes it might be some system service related to the view menu (which, taken by itself, I would have a hard time believing, but given that the freezes can be prevented by foregrounding another app, it kinda makes sense.

Edit: Oh, and, yes, I also sometimes get the message that "org.netbeans.Main" was killed, like someone reported above. So, yet another level of crashing ;-)

And yet another detail that I just discovered when I actually tried to quitting Gephi (Haven't had to do that so often in the past because it mostly crashes): I saved the project before quitting. And even though I had just saved, it asked me whether I wanted to save. I said no (because it previously crashed when I said save, so I wanted to try what happens if I say don't save). It seemed to close fine, but then I saw that it actually didn't fully quit (it still had a dot under the icon in the dock). So, I actually can't close Gephi in any regular way. I have to force quit it.

[tophee]

Thanks for sharing your workaround. Parallels has quite a price tag, but if that's the only way, maybe that's the way to go. Edit: Oh, and a windows license is needed on top of that. Yea, that is crazy.

Adding some more observations (still hoping this can be solved on Mac):

I can confirm that it is not sufficient to restart the computer. I need to re-install Java in order to get Gephi running again after a (certain kind of) crash. Not all crashes require a reinstall, only the ones where Gephi will crash immediately after starting (no splash screen). Actually, when I say crash, I mean hang + force quit.

I just had another "org.netbeans.Main" force-quit. After that, Gephi started "normally", so no java-reinstall needed.

[vladUng]

Hi @tophee and everyone, for me the solution is to simply do nothing (such as mouse or keyboard input) while the Graph tab from the Overview is loading; i.e., when switching to view the network. This approach works consistently for me. Also, I switch to the Data Laboratory tab before closing Gephi, ensuring that upon reopening, I don’t accidentally move the mouse or press any keys when it is using the graph intialisation. I assume the issue might be related to the initialization process for the graph view 🤷.

I hope this helps.

Specs: Gephi 0.10, MacBook Pro (Intel), macOS 14.5

[hbruch]

Hi, I'm running into the same issue, starting 0.11-SNAPSHOT 86903b4 from IntelliJ on Apple M3 Max (arm), macOS 14.5.

Starting gephi with remote debugging, I see this stack when Gephi is not responding:

wait:-1, Object (java.lang)
wait:338, Object (java.lang)
RunOnMainThread:318, OSXUtil (jogamp.nativewindow.macosx)
CreateNSWindow:161, OSXUtil (jogamp.nativewindow.macosx)
create:29, OSXDummyUpstreamSurfaceHook (jogamp.nativewindow.macosx)
createNotify:101, ProxySurfaceImpl (jogamp.nativewindow)
setRealized:181, GLDrawableImpl (jogamp.opengl)
getOrCreateSharedResourceImpl:263, MacOSXCGLDrawableFactory (jogamp.opengl.macosx.cgl)
getOrCreateSharedResourceImpl:85, MacOSXCGLDrawableFactory (jogamp.opengl.macosx.cgl)
getOrCreateSharedResource:188, GLDrawableFactoryImpl (jogamp.opengl)
createSharedResourceImpl:217, GLDrawableFactoryImpl (jogamp.opengl)
createSharedResource:385, GLDrawableFactory (com.jogamp.opengl)
initProfilesForDeviceCritical:1938, GLProfile (com.jogamp.opengl)
initProfilesForDevice:1895, GLProfile (com.jogamp.opengl)
initProfilesForDefaultDevices:1862, GLProfile (com.jogamp.opengl)
access$000:80, GLProfile (com.jogamp.opengl)
run:239, GLProfile$1 (com.jogamp.opengl)
doPrivileged:80, SecurityUtil (com.jogamp.common.util)
initSingleton:225, GLProfile (com.jogamp.opengl)
getProfileMap:2334, GLProfile (com.jogamp.opengl)
get:1009, GLProfile (com.jogamp.opengl)
get:1025, GLProfile (com.jogamp.opengl)
getCaps:179, GLAbstractListener (org.gephi.visualization.swing)
initDrawable:69, NewtGraphCanvas (org.gephi.visualization.swing)
getGraphComponent:548, GLAbstractListener (org.gephi.visualization.swing)
lambda$run$1:131, GraphTopComponent$1 (org.gephi.visualization.component)
run:-1, GraphTopComponent$1$$Lambda$388/0x000000016f227270 (org.gephi.visualization.component)
dispatch:308, InvocationEvent (java.awt.event)
dispatchEventImpl:771, EventQueue (java.awt)
run:722, EventQueue$4 (java.awt)
run:716, EventQueue$4 (java.awt)
executePrivileged:776, AccessController (java.security)
doPrivileged:399, AccessController (java.security)
doIntersectionPrivilege:86, ProtectionDomain$JavaSecurityAccessImpl (java.security)
dispatchEvent:741, EventQueue (java.awt)
dispatchEvent:136, TimableEventQueue (org.netbeans.core)
pumpOneEventForFilters:203, EventDispatchThread (java.awt)
pumpEventsForFilter:124, EventDispatchThread (java.awt)
pumpEventsForHierarchy:113, EventDispatchThread (java.awt)
pumpEvents:109, EventDispatchThread (java.awt)
pumpEvents:101, EventDispatchThread (java.awt)
run:90, EventDispatchThread (java.awt)

This JOGL discussion might be related

[wonheecho]

Hi, so for what is worth, a clean reinstall of macOS Sonoma without restoring anything fixed the Gephi issue for me.

Note it was the same computer (MacBook Pro M3 Max), same OS (Sonoma) that had screwed me up for such a long time. Previously, whenever (for whatever reason) I reinstalled my OS or moved to a new device, I fully utilized TM backup or Migration Assistant provided by MacOS, but this time I simply reinstalled every single app, and simply synced my files via dropbox, and...gephi works.

I hate to say that I don't know the exact reason why this occurred and how to fix it, but I think it would be worth sharing this experience.

[tophee]

@wonheecho so you reinstalled every single app you had on your previous system? No exception?

[wonheecho]

"Most" but not every single app. I wasn't diligent enough to keep a list of the previous setting.

@wonheecho so you reinstalled every single app you had on your previous system? No exception?

[tophee]

In that case, it would seem plausible to assume that one of the apps you didn’t reinstall might be the “perpetrator”, right? If you remember any of them, please let us know. If any of them turns out to be on other affected conputers, that would give us a chance to check what happens once we uninstall them.

[wonheecho]

Okay, so there seems to be one app that I didn't expect, but does seem to be one of the potential "perpetrators." - Can you see if you (anyone with this problem?) is using contexts, the alternative alt-tab app switcher app (https://contexts.co)?

update - also tried it on my MacOS VM. No apps installed, install gephi and contexts - gephi freezes, uninstall contexts, gephi works fine.

One very very specific and reliable way of replicating the freeze found. What next can I help to solve this?

In that case, it would seem plausible to assume that one of the apps you didn’t reinstall might be the “perpetrator”, right? If you remember any of them, please let us know. If any of them turns out to be on other affected conputers, that would give us a chance to check what happens once we uninstall them.

[tophee]

Wow, that sounds like a significant discovery!

I believe I tried Contexts on my Mac mini some time ago, but I don't have it installed on my MacBook, which means that Contexts is not the only app causing the issue.

I have no idea what in Contexts might be the root cause but since I am using AltTab, I'm going to try removing that...

Update: uninstalling AltTab didn't help. It was worth a try, but now we need someone with some programming knowlegde who can tell us (a) in what way Contexts might differ from many other apps and (b) what other apps might be similar to Contexts in that respect.

[wonheecho]

Just wanted to say that I used AltTab with no issues. My hunch is that Contexts being a relatively old app (and not really updated?) might have something to do with this.

[tophee]

@wonheecho Since Contexts is an app that usually runs in the background, could you confirm whether quitting it suffices to let Gephi run without issues or whether it needs to be uninstalled?

[wonheecho]

Nice suggestion! It seems that Contexts running in the background seems to be the issue. Gephi installed, Contexts installed, "Quitting Contexts" - Gephi doesn't freeze.

Even though I had Contexts disabled/hidden, Contexts has the persistent "sidebar" thingy. And knowing that some people have suggested the quickly switching to another app helping, maybe the "sidebar" has something to do with this? FWIW, I have Yonik, Fresh all installed on my main machine that works fine.

@wonheecho Since Contexts is an app that usually runs in the background, could you confirm whether quitting it suffices to let Gephi run without issues or whether it needs to be uninstalled?

[nabsiddiqui]

@wonheecho I honestly had almost no hope that something like Contexts being closed would make a difference, but it does! I am now able to use Gephi again after almost three years!

@tophee I think you are correct that it isn't specific to Contexts, but whatever library, etc. that Contexts uses, seems to be the root of the problem

[mediapathic]

I am no longer actively trying to solve this issue, but I can confirm that I was also using Contexts when the problem occurred for me.

[nabsiddiqui]

I am surprised so many people use Contexts. I honestly have never met another person that uses it, but it is good to see that there is some hope in the horizon.

[vladUng]

Hi I am using Magnet instead of Contexts app and when I quit Magnet I don't have any freezing problems with Gephi!

[wonheecho]

Thanks for the input! I also can confirm that Magnet causes Gephi to freeze, and quitting Magnet solves the problem. So some of these third party utility apps seem to have problem.

Hi I am using Magnet instead of Contexts app and when I quit Magnet I don't have any freezing problems with Gephi!

[tophee]

Wow! We're finally getting this sorted out. I went through most of my background apps that are always running and identified Timing as the app that causes the freeze in my case. Yay (for finally being able to use Gephi), but what a bummer for not being able to consistently use the timing app.

In case you're puzzled how a time tracking app is similar to those window management apps: I believe Timing is accessing (or trying to access) the title of the active window (as well as the name of its application and possibly the path of the document shown). So, my hunch is that there are certain states or phases in the Gephi runtime where it does not like to be queried for one or more of these things. In fact, it may be the case that this vulnerability only exists during the start process, because I restarted Timing after Gephi was up and running and it doesn't seem to freeze despite Timing running.

And here is another lead: remember how we usually/often are told that it was something called Netbeans that crashed or was force closed? Well, Timing lists Netbeans as possibly compatible on its website:

I'm curious whether this might be of any help to @mbastian to narrow down what is going on and perhaps make Gephi more resilient against interference from apps that query window related data. (Disclaimer: I have no idea whether this is a weakness in Gephi or in Netbeans or perhaps in how those perpetrator apps interact with Gephi/ Java. I'm just thinking aloud.)

So, just to give a summary of apps that have been identified as causing the freeze:

• Contexts
• Magnet
• Timing

Apps that don't seem to cause the freeze (at least not for me):

• AltTab
• PopClick
• BetterTouchTool
• ICE
• Moom
• Grammarly
• LanguageTool

[tophee]

OK, here is another update. I believe there are at least two different freezes/hangs in Gephi, only one of which can be avoided by quitting the above mentioned apps. That is the freeze/hang that occurs when Gephi starts and while using Gephi (when switching tabs or so). The other is related to closing Gephi/saving the current project and I described it briefly above. This second type of hang/freeze remains. I'm not sure whether this should be dealt with in a separate issue, but I'll leave it here for now.

Here is a more detailed description of the behaviour:

1. Open a .gephi file
2. Make some change <-- you'd think this is necessary for the saving to be triggered, but apparently it's not.
3. Quite Gephi. You will be asked whether you want to save:
   
4. It doesn't matter whether you click "Save" or "Don't save", either way everything looks as expected at first (the modal and the Gephi window disappear) but then they magically reappear. Trying to access them gives you the beach ball.

Now, what is even weirder is that when I force-quit Gephi it will now freeze also when starting (from what I can see, indistinguishable from the starting freeze caused by vartious apps.

And to make it completely incomprehensible, when I force quit Gephi again and start it again, it will start again without freezing. Problem fixed. Or is it? Because if I now try to reopen my gephi file, Gephi freezes after loading 4 percent or so.

If I then kill Gephi, start again and try to open the file once more, it works. Now it's fixed. - Unless I try to save the gephi project. Then the cycle starts anew...

[nabsiddiqui]

@tophee I am unable to replicate the issue that you are having. Granted, I'm on an older version of Mac OS X, and I'm on the stable 10.1 Gephi.

When I make a change and save it, the program closes properly, etc. The only time I get an issue is when opening the program. I need it to load fully before interacting with it. I think this is all related to much of the same issue.

If @mbastian is willing to take a look at this, I think there is a good chance that these background apps are what are causing the majority of issues.

[markpedretti]

For what it's worth, I think I can add another application switcher to the list of culprits: Witch from Many Tricks. I was having the spinning beach ball of death with Gephi 10.2; I just turned off the Witch daemon (it runs as a preference pane), and voilà, no hang. Turn it back on, beach ball again. Tested on both an Intel iMac (2017) running Ventura 13.6.7 and a M1 Pro MacBook Pro running Sonoma 14.5 with the same results. Thanks to everyone who is working to figure this out!

[wonheecho]

Hi, I can add the following background(?) apps that don't affect Gephi (and again, it seems regardless with the MacOS - had been using Sonoma, recently updated to Sequoia public beta)

• Alt-Tab
• Moom
• Bartender 5
• Fresh
• Yonik
• Default Folder X
• Hazel
• Shottr

I think this is about all that I can add based on my usage. Still miss contexts, once loved Witch, but can live without them.

[tophee]

Here is an update for Timing users: when I contacted the Timing developer, he provided me with a link that changed some (hidden) preference for the app and once I applied that, Timing no longer interfered with Gephi. If you’re in the same situation, please contact him at [email protected].

To be more precise: the changed setting is that Timing should not talk Gephi via the accessibility API. To be even more precise: when we originally told Timing not to use the API for Gephi, it did not work. Only when Java more broadly (i.e. netbeans) was excluded from the API, it worked.

What remains now, for me, are the hangs that reliably occur when closing Gephi…

[nabsiddiqui]

Here is an update for Timing users: when I contacted the Timing developer, he provided me with a link that changed some (hidden) preference for the app and once I applied that, Timing no longer interfered with Gephi. If you’re in the same situation, please contact him at [email protected].

To be more precise: the changed setting is that Timing should not talk Gephi via the accessibility API. To be even more precise: when we originally told Timing not to use the API for Gephi, it did not work. Only when Java more broadly (i.e. netbeans) was excluded from the API, it worked.

What remains now, for me, are the hangs that reliably occur when closing Gephi…

This is probably the root of all the issues in this thread.