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.

[chrisji]

Similar hanging problem here (v0.10.1, Mac M1).

I've found that I can consistently trigger a hang by interacting with Gephi on boot (e.g. attempting to open a recent project) while the "Initialising..." message shows on the Graph window.

[aelkholy]

Yeah I'm on a Mac M1 and I tried your snapshots and the latest on the site, and I tried them on my older intel silicon mac as well, but nothing worked, still froze on startup.

[mbastian]

Hi folks, I've got an update to share

JOGL, the OpenGL library we use got updated to the 2.4.0 version. This might be a game changer with regard to this issue as I was able to switch to NEWT on Mac OS as well (this is the default on Windows and Linux). NEWT has a different (and better) threading model than the default GLCanvas we were using previosuly. The 2.4.0 release fixed a number of issues that preventing us to use NEWT in the past.

My hope is that using NEWT completely eliminates this issue. And doesn't create new ones of course. I would love to hear from you on whether you still experience this issue and/or other crashes.

Please download/install the snapshot versions for testing:

• gephi-0.10.2-SNAPSHOT-macos-x64.dmg (Mac OS X)

• gephi-0.10.2-SNAPSHOT-macos-aarch64.dmg (Mac OS X Silicon)

[epageperron]

@mbastian I'm trying your snapshot now and as soon as I open Gephi I get the rainbow beachball, still. On a Mac Intel with Ventura.

[alex-roc]

@mbastian I'm trying your snapshot now and as soon as I open Gephi I get the rainbow beachball, still. On a Mac Intel with Ventura.

Same here, with an iMac M1, Monterey.

[vladUng]

@mbastian It kinda works for me. I opened an older project, and close&open Gephi x3 with the Overview as the last tab used and Gephi didn't freeze. However, if I interact with Gephi while the Overview tab still says "Initialising..." the application freezes.

As I stated in the comment above I experienced less problems if I switch to a different mode from "Overview" to "Data Laboratory" when closing Gephi. Somehow, this helps the initialisation of the "Overview"

It also feels faster. Thank you for the hard work!

My config: MacBook Pro Intel (2018), Ventura 13.12.1.

Hi,

Thanks for all the work done on this issue. I've tried 0.10.0-Spanshot and it didn't solved the problem for me so I switched back to the normal 0.10.0. However, I might have found a workaround which so far worked for me (MacBook Pro 15" - 2018):

1. Open Gephi
2. Don’t interact with Gephi until the “Initialising..” message from the top left corner of the Graph window disappears (this takes a few seconds)
3. Close the welcome dialog once the init message disappears (the Graph window is white - which probably is the background colour)
4. Switch to the Data Laboratory tab
5. Open your project and wait until the data appears in the table
6. Switch to the Overview tab and it should work.

This works for me with Gephi 0.10 and tried it several times.

Maybe a potential quick fix will be to always show first the Data Laboratory tab regardless of the user's previous state?

[carloalbertobono]

hi @mbastian and thank you

I can confirm a beachball on opening Gephi (M1 Max, Ventura) when trying to interact with the splash screen (eg. load file) while the pane in the background shows "Initializing..."

Not getting the beachball while switching panes (overview / data) for now!
Now it looks like it's briefly "redrawing" the whole application window when switching.

But I did get an unseen behaviour in which the application: it basically gets stuck redrawing again and again the graph in overview. It seems to me that it occurs when closing a tab (eg. a GEXF file) when multiple tabs are opened.

[markpedretti]

Hi @mbastian and thanks for all of your hard work on this. I'm having the same problem as everyone else: spinning beachball of death on launch in 0.10.1 on a MacBook Pro M1Pro running Monterey 12.6.3 (filled out the questionnaire). I tried deleting ~/Application Support/gephi/0.10 but no joy. And then I tried something else: I disconnected my external monitor and ran from the built-in screen. Eureka! Gephi launches just fine. I can even plug the external monitor back in once Gephi is launched and it continues to work. But I'm still having frequent hangs while working in the program (e.g., clicking the Preview tab), so this is by no means a full workaround — but it's another piece of the puzzle I though I should share.

[mbastian]

Hi folks,

I've discovered that the hang might be mitigated by calling revalidate() right after we add the graph canvas to the panel. It would be great if I could get feedback based on the development version. Has anything changed compared to previous versions?

Please download/install the snapshot versions for testing:

gephi-0.10.2-SNAPSHOT-macos-x64.dmg (Mac OS X)

gephi-0.10.2-SNAPSHOT-macos-aarch64.dmg (Mac OS X Silicon)

[carloalbertobono]

hi @mbastian,

kudos as always.

previous version and also this one look stable, about the issue of beachball while switching panes.
just did quick tests on this one but still looks good (M1 Max, Ventura)

in my case they still both suffer from the "beachball hang if opening a file on program load, when the 'Initializing' message is still on screen"

but apart from this, it is working fine also with "big" graphs.

[markpedretti]

Hi @mbastian, about the same result here: cleared out the Application Support files and the snapshot version launched just fine, no hang; open a project, fiddled a bit, quit Gephi; on relaunch, spinning beachball of death with "Initializing," as before.

[epageperron]

@mbastian I'm trying your snapshot now and as soon as I open Gephi I get the rainbow beachball, still. On a Mac Intel with Ventura.

I just tried Gephi again, I'm on 0.10.2 snapshot and now it works normally without any issue. I haven't done anything special except keep my OS up to date.

[nabsiddiqui]

M1 Max Pro here. I am not able to go past the welcome screen even after deleted Application support files and using the 0.10.2 version.

[epageperron]

@mbastian I'm trying your snapshot now and as soon as I open Gephi I get the rainbow beachball, still. On a Mac Intel with Ventura.

I just tried Gephi again, I'm on 0.10.2 snapshot and now it works normally without any issue. I haven't done anything special except keep my OS up to date.

And now again I haven't updated, still using the snapshot, and i get initializing forever... :( I did install some plugins and they worked but the next time opening Gephi and all subsequent times I get stuck on initializing.

[exaos]

Same issue here.

• OS: 13.5.1
• MacBook Pro M2
• Gephi 0.10.1

[WuHuiCHN]

Same

macOS: Ventura 13.5.1
Chip: Apple M1 Pro
Memory: 16GB
Gephi: 0.10.1

[rcgonzalezf]

I'm still experiencing the issue, I added the thread dump here:

https://gist.github.com/rcgonzalezf/707d90380602734f5fcd0531b44a84d5

I hope it helps, adding a screenshot because it immediately hangs after opening the app:

[nabsiddiqui]

Is there any update on this?

[abbeythorpe]

I have had a similar issue running on mac and found a consistent (dumb) solution, so going to add details here. Not sure if it's the exact issue that others are having though.

Device: MacBook Pro 13-in 2019
macOS: Ventura 13.6.1
Gephi versions: 0.10.1, 0.9.5

Problem: On opening Gephi, the main window and load project windows open, but the spinning wait cursor (aka rainbow wheel of death) appears if you try to select a project or click in any Gephi window. This wait hangs forever (I've tried waiting 2-3 hours) and the app never crashes, so as far as I can tell no error log or crash file is generated. I can only exit the app via the Force Quit menu.

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. It does occasionally get stuck if I switch between preview and data laboratory too quickly, or otherwise don't give each new change time to load, but it's mostly usable now. I recommend frequent saving though as it's prone to crashing.

I have no idea why loading in the background works, I've never observed this behavior with any other application in 10+ years as a mac user. But after much uninstalling & trying different versions of Gephi, this has consistently worked with Gephi 0.9.5 for the last few days. I haven't taken the time to reinstall Gephi 0.10.1 and try it yet.

Hope this information helps someone.

[roolio]

Your method works for me, too! Thanks @abbeythorpe !

Device: MacBook Pro / M2 Max
macOS: Sonoma 14.2.1
Gephi versions: 0.10.1

[mediapathic]

Hi, new user here, trying Gephi for the first time on MacOS 12.2.1 (Apple silicon), Gephi 0.10.2, and I get freeze and beachball on startup every time. I've tried swapping to other apps immediately as mentioned above, as well as launching from command line. No matter what I do, it sits at "initializing" forever.

It may be worth noting that when I force quit, the dialogue button says I've killed "org.netbeans.Main", not Gephi. But I'm assuming you already know that.

Happy to provide any additional information if there's anything useful I can.

[wonheecho]

I've discovered that there must be some kind of conflict with MacOS and other apps. Previously, I used a MacBook 2019 (the last intel version) and suspected that maybe there was an issue with intel chip. It was seemingly confirmed when I got a new M3Max Macbook, and when I first installed gephi everything was fine!

However, after I installed a few more apps, gephi started to go into the eternal "initializing" error again. Knowing that I needed to use Gephi, immediately, I made a separate partition in my Mac with no other apps and...Gephi worked again.

So Gephi freezing is not a chip problem. It must be some kind conflict with other apps. I'll keep experiment on my end, but would ask others to see if they can find anything.

[wonheecho]

So, I've kept digging into this, and I think I know what's causing the problem - homebrew (https://brew.sh/). My "clean" slate mac kept running Gephi fine, even after numerous app installs, but then stopped working after I installed homebrew via terminal.

I wonder (if anyone is still paying attention) if anyone can verify - if you are having the Gephi freeze issue, have you installed homebrew via the terminal script?

(FWIW, even after I've uninstalled homebrew I still can run Gephi. Hmmm). @mbastian Can you help?

edit - I think I spoke to fast. My gephi only partition ran fine even after installing homebrew. Dang this is so annoying.

[vladUng]

Thanks for debugging @wonheecho. I also have homebrew installed via terminal and the Gephi freeze issue.

(This is on an Intel MacBook)

[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?