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. https://github.com/gephi/gephi/issues/2546#issuecomment-1159396919

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.

[francescoragazzi]

Hi @mbastian thanks for all your efforts! Still no luck I'm afraid :( Gephi still hanging. - dump attached. 2022-11-25 Thread Dump.txt

[mbastian]

Thanks @francescoragazzi I continue my investigation. The attached dumps help as I can see whether it's the same issue everytime or some variation of it. Can you try this one? https://oss.sonatype.org/content/repositories/snapshots/org/gephi/gephi/0.9.8-SNAPSHOT/gephi-0.9.8-20221125.203902-16-macos-x64.dmg

Here the perspective control is disabled so Gephi will open blank. You'll need to go to the Window Menu and then Graph to open the graph window. I would like to know when things would freeze. Thanks!

[francescoragazzi]

Hi @mbastian - still hanging. 2022-11-25 Thread Dump v2.txt

[mbastian]

Hi @mbastian - still hanging. 2022-11-25 Thread Dump v2.txt

@francescoragazzi At start or when you opened the graph window? Thx

[francescoragazzi]

When I opened it was fine, but as soon as I switch from data lab to graph it hangs. The hanging generally happens when switching from one to the other On 26 Nov 2022, 08:18 +0100, Mathieu Bastian @.***>, wrote:

Hi @mbastian - still hanging. 2022-11-25 Thread Dump v2.txt @francescoragazzi At start or when you opened the graph window? Thx — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

[mbastian]

Hi all, this back-n-forth is not doing much progress. As often, without the ability to reproduce a bug and inspect it's almost impossible to fix it. So let's try a different approach and try for me to understand on what exact environment this bug appears. Once I have that information, I will be able to make progress again (hopefully).

To all: Please please please, fill this questionnaire about this issue. Much appreciated!

[francescoragazzi]

@mbastian Makes sense! Thanks for all the work and for the exchange.

[kl-thamm]

Hi, I am having the same issue - came out of nowhere and used to work fine before the weekend. Just filled the questionaire.