Closing 3D window makes Icy crash

[Antoine Le Gall]

Hi everyone, 

when I open a 3D stack and vizualize it in 3D with Icy, as soon as I close the window Icy freezes. Then there's no alternative than forcing Icy to close through windows task manager.

I'm using Icy 1.5.3.1 and windows 7 64-bit. I tried reinstalling Icy which solved the problem for a little while and then started crashing again.

Anyone has experienced the same problem?

Antoine

[Stephane]

Hi Antoine,

I never encountered this problem and what is strange is that reinstalling Icy fixed the problem for a bit of time...
Can you give us more informations about the hardware configuration you are using ?
Also do you use a 64 bits java ? You can check it in the output console of Icy.
Thanks !

- Stephane

[Antoine Le Gall]

Hi Stephane,

I just checked the info from the output consol and updated with the 64bits version of Java (I was using 32bits) but the problem persists. The consol reads:

Java(TM) SE Runtime Environment 1.7.0_67-b01 (64 bit)

Running on Windows 7 6.1 (amd64)

Number of processors : 8

System total memory : 8115.5 MB

System available memory : 4746.0 MB

Max java memory : 910.5 MB

VTK library successfully loaded...

Icy Version 1.5.3.1 started !

java.net.ConnectException: Connection timed out: connect

Cannot connect to chat.

If you use a proxy, verify you have valid SOCKS settings.

Antoine.

[Stephane]

Hi Antoine,

Thanks for the informations ! Now you upgraded to 64 bits java, can you just try to increase the maximum memory allocated to Icy ? Usually 3D view require a lot of memory so raising it to 4 GB could help (in Icy preferences). Still usually low memory makes VTK to completely crash and not freeze on exit...
Does the crash occurs whatever is the 3D dataset you intent to view ?

- Stephane

[Antoine Le Gall]

Stephane,

I increased the memory to 4Gb as you suggested but it didn't help.

The data that I load shouldn't require too much memory as I make some relatively small ROI (100x50x15, <50kb). I tested different data files but Icy still systematically freezes as I close the 3D view...

Antoine.

[Stephane]

Ok, something else you can try : instead of closing the 3D view, you turn it back to 2D. Do the freeze happens as well ? or it only happens when you close the view while it uses the 3D rendering ?
From this last info i will try to identify what can cause the freeze (of course it would be better to be able to reproduce it here).
Thanks !

- Stephane

[Antoine Le Gall]

it still freezes as I turn back to 2D...

Now that I think of it (I should have started with that, I'm sorry) it started crashing with some updates of Icy a few month ago. Among those updates there was the 3D grid, axes and box I believe.

I tried un-ticking those options before leaving the 3D view but it's not helping...

Antoine

[Stephane]

That is an helpful information. We upgraded to VTK 6.1 library and at same time we rewrote the VTK canvas in Icy so almost everything changed, but good to know old version was ok about it...
I guess now it goes to sort of death lock when exiting VTK canvas for some reason, we will investigate the problem.
Also it would be nice to know if you meet the same problem on another computer :) Thanks.

- Stephane

[Antoine Le Gall]

Thanks a lot for helping me with this!

So I checked Icy 3D viewer on 2 other computers, both have the same following configuration (32bit) and none of them crashed:

Java(TM) SE Runtime Environment 1.7.0_67-b01 (32 bit)

Running on Windows 7 6.1 (x86)

Number of processors : 4

System total memory : 2048.0 MB

System available memory : 1034.8 MB

Max java memory : 897.1 MB

Class 'plugins.tprovoost.Microscopy.CalibratorPixelSize.CalibrationPainter' cannot be loaded :

Required class 'plugins.tprovoost.Microscopy.MicroManagerForIcy.painters.MicroscopePainter' not found.

The following plugin(s) has been correctly installed:

Active Cells SDK 2.2.0.0

VTK library successfully loaded...

Icy Version 1.5.3.1 started !

java.net.ConnectException: Connection timed out: connect

Cannot connect to chat.

If you use a proxy, verify you have valid SOCKS settings.

Class 'plugins.tprovoost.Microscopy.CalibratorPixelSize.CalibrationPainter' cannot be loaded :

Required class 'plugins.tprovoost.Microscopy.MicroManagerForIcy.painters.MicroscopePainter' not found.

The following plugin(s) has been correctly installed:

Active Contours 3.1.5.0

Active Cells 3D 2.3.0.1

Unfortunatly I don't have any other 64bits windows computer to check whether the problem comes from the Windows version.

Antoine.

[Stephane]

Ok, thanks for the tests !
So it is definitely related to your specific computer as we are working here with both windows 7 and windows 8 in 64 bits and never observed this problem, Still can you test this :
- Download the following file : http://www.icy.bioimageanalysis.org/downloadIcy/temp/icy.jar
- Overwrite the icy.jar file located in your icy folder by this one (don't forget to backup the old one just in case).
- Test with this new core to see if that make any difference (i changed some things on VTK shutdown process).

Best,

- Stephane

[Antoine Le Gall]

I did replace the .jar file but it still freezes when closing directly the 3D viewer BUT now I can go from 3D to 2D viewer and then close the window!!! This workaround is already helpful for me as I can now screen several data file without restarting Icy too often.

One thing that I also noticed (never checked before with the previsous .jar file): Icy doesn't crash when I close the 3D elevation map viewer... Doesn't it use VTK as well?

Antoine.

[Stephane]

Hi Antoine,

Good to know the changes already improved the situation (even if still not perfect). Indeed the Elevation canvas also uses VTK but anyway, the fact that modifying the code made it working better definitely show there is something to do on our side.
The problem is that VTK is not thread safe, even worse it requires some tasks to be done in the EDT (graphics thread) which make the application less responsive, laggy... we are using a custom event system for the 3D VTK Canvas to deal with that and make the application as smooth as possible but i believe in some situation we fall in a "deadlock" case (as when you close the window on your system). We will continue to investigate, thanks for testing and reporting the changes !

- Stephane

[Antoine Le Gall]

Hi Stephane,

I do realize that solving an issue that you cannot reproduce on your side is probably very tricky.

I'll let you know if I find anything new on this issue.

thanks a lot for your help! 

Antoine.

[Stephane]

Yeah it is always tricky when we are not able to reproduce bug here, but already the freeze thing was an indication, as we deal a lot with the EDT in the 3D VTK Canvas, a deadlock is possible and so i modified the code to be safer on that. Still that is not enough to eradicate your problem but we can continue to investigate in that scope. Of course if you have more informations it can help us to resolve it but we already have somewhere to look at !

Best,

- Stephane

Le mardi 12 août 2014 11:02:48 UTC+2, Antoine Le Gall a écrit :

Hi Stephane,