Knime 1.3.5 unstable in Linux ?

KNIME Analytics Platform
1

Dear KNIMErs,

I have played around with KNIME a little in Linux using Xming and I have found - unfortunately - that KNIME crashes quite regularly with the following error message:

Quote:
The program 'KNIME' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadWindow (invalid Window parameter)'.
(Details: serial 250085 error_code 3 request_code 15 minor_code 0)
(Note to programmers: normally, X errors are reported asynchronously;
that is, you will receive the error a while after causing it.
To debug your program, run it with the --sync command line
option to change this behavior. You can then get a meaningful
backtrace from your debugger if you break on the gdk_x_error() function.)

Can anybody help me with this?

Many Thanks,

Phil.

2

Hi mixmaxx,

can you please check whether you've run into a problem with eclipse/ssh "Crash in Xming & Eclipse 3.1 GTK"?

The cause of the problem relates to ssh, which should be called with the '-Y' argument instead of '-X' (details are in the eclipse bug report above).

Please let us know if it helps.
Bernd

3

Here the Linux version of KNIME also crashed very often.
The error message is like the one you've posted.
But its not everytime the same error here.

The error comes here only if I setup nodes using the ConfigurationDialog.
Especially if you open a FileDialog or if you show a MessageBox and so on.

Greetings,
imax.

4

Are you also using Xming (or another sort of remote X connection)? (Which?)
Did you do any modifications to the product (for instance removed the JRE directory or upgraded the underlying eclipse)?

5

Hi wiswedel.

No the problem was "there" since I tried the first time KNIME.
I don't have modified anything. The default installation of KNIME crashes too under Linux here.

Tested under Kubuntu 8.04 and SuSE 10.x.
Both are very unstable if you configure the Nodes. But its not 100% reproducable. Its very randomized. Say: 1 of 3 trys will crash here :)

Greetings,
imax.

EDIT:
I don't use anything special here. It's a default Kubuntu installation.

6

That comes as a surprise now. I've been using KNIME on SuSE 10.3 myself (and that heavily). Just to confirm: You don't use a remote X connection?

What window manager are you using? Gnome, KDE, ...? Can you send a sample log file and possibly the error message that is printed to the console (if any)?

1 out of 3 sounds very reproducible (and unusable). Anyone else out there who has similar problems?

7

Hi again.

I've tried right now to reproduce it. But like a curse it won't crash now :D
I will collect now every crash log for you and will post them if it occurs the next time.

And yes I don't use remote X connection or something like that. I use a 100% default Kubuntu KDE3 system.

EDIT:

The program 'Eclipse' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadWindow (invalid Window parameter)'.
  (Details: serial 95391 error_code 3 request_code 20 minor_code 0)
  (Note to programmers: normally, X errors are reported asynchronously;
   that is, you will receive the error a while after causing it.
   To debug your program, run it with the --sync command line
   option to change this behavior. You can then get a meaningful
   backtrace from your debugger if you break on the gdk_x_error() function.)

Here is a crashlog :)
It crashed right now where I selected a File using the Mol2 Reader Node.

8

Thanks for the error output. I'll try to reproduce the problem by installing "Kubuntu 8.04.1 (Hardy Heron)" in a virtual box (please correct me if you used another version).

9

Hi imax,

I installed Kubuntu and played with KNIME 1.3.5 for about 30mins but it didn't crash (I'll keep trying). I tested in particular the file reader dialog with the popups that you get when clicking the column headers of the preview table (which is a message box on top of a dialog).

Another user reported that he has been working on Ubuntu 8.04 (GNOME) extensively ... no problems.

Do you use any fancy window settings? (I saw that Compiz is pretty easy to install.) You also mentioned that you had similar problems on SuSE 10.x. Is it the same machine (same hardware?). Are the KDE settings the same? Sorry for bothering but we have absolutely no idea.

10

Hi wiswedel.

You don't bother me. ;)

I use here at home Kubuntu 8.04 with KDE 3.
No Compiz at all (I don't like too much eyecandy :P)
A default Xserver.
At work I have a SuSE 10.x System also KDE 3.
Both PCs have a Nvidia Graphics.
It's very strange that both systems crash.

Please let me now if you need some more information.
Do you need SSH\VNC on my home machine? Let me know.

Greetings,
imax.

EDIT:
The Hardware is very different on both machines. My home machine is more "hightek" than the one on the work. Only thing which theyve equal is that the Graphiccard is from Nvidia. Greetings.

EDIT 2:
Again a crash:

The error was 'BadMatch (invalid parameter attributes)'.
  (Details: serial 7491 error_code 8 request_code 147 minor_code 4)
  (Note to programmers: normally, X errors are reported asynchronously;
   that is, you will receive the error a while after causing it.
   To debug your program, run it with the --sync command line
   option to change this behavior. You can then get a meaningful
   backtrace from your debugger if you break on the gdk_x_error() function.)

EDIT 3:
One last thing i must tell. Sorry that i dont mention it befor.
This error primary occures here if I start KNIME using the Developer Version of KNIME. For Example if I want to start my Node using the "PlayButton" from Eclipse. You have then a "sandboxed" version of the "user" version from KNIME. I think you know what I mean :). I don't have tested the "user" version of KNIME in Linux.
This scenario works under windows w\o problems. (Also if i don't like windows :P)

11

The two error messages seem to differ. One was on 'BadWindow', the other (from your above post) was on 'BadMatch'.

The latter one may be related to this eclipse bug: SWT_AWT bridge sometimes crashes on Linux (which has been fixed in the meantime).

Would you be willing to try to install our KNIME plugins (using the update site) into a "fresh" eclipse 3.3.2, available here, and try to reproduce the problem? (Please don't use eclipse 3.4, ganymede). You'll also need to install GEF (prerequisite for KNIME), see details on our web page.

If that's too complicated or you miss some dependency, we can also do that and provide you with a ready-to-run version (which we will need some time for to setup).

Thanks
Bernd

PS: The KNIME product version (not developer version) is available at http://www.knime.org/download/linux/knime-1.3.5-linux.gtk.x86.tar.gz

12

Quote:
Would you be willing to try to install our KNIME plugins (using the update site) into a "fresh" eclipse 3.3.2, available here, and try to reproduce the problem? (Please don't use eclipse 3.4, ganymede). You'll also need to install GEF (prerequisite for KNIME), see details on our web page.

Allright.
I'm going to test it today. I'll report you the results here.

Greetings,
imax.

13

Hi Guys.

Sorry for my late response,
I was very busy with learning and coding for university and work.

I've tried to create a KNIME from an unmodified Eclipse like you've said.

KNIME installed well using the UpdateManager.
I've also installed GEF.

But if I open a new KNIME workflow it shows me an "Error Page":

Error opening the editor.
An error occurred while automatically activating bundle org.knime.workbench.editor (158).

What should I do? :)

Greetings,
imax.

14

imax wrote:
But if I open a new KNIME workflow it shows me an "Error Page":
Error opening the editor.
An error occurred while automatically activating bundle org.knime.workbench.editor (158).

What should I do? :)


Have you looked at /.metadata/.log? Maybe there is more information in it.

Thorsten

15

Hi.
Here is my .metadata/.log

I've installed every KNIME feature from the update site.

http://rafb.net/p/w3bTXt40.html

Greetings,
imax.

16

Sorry, my mistake: I could have anticipated that installing KNIME plugins does not work with newer versions of eclipse (as also reported in another thread).

Maybe we can put this discussion offline as you are apparently the only one (that we know of) who has problems with KNIME on Linux. We have some power linux users in the group (including myself) and also the KNIME partners mainly depend on linux, whose QAs (and customers) have not (yet) reported such problems on linux. (Which is good for us but bad for you.)

And then of course there is the community - of which we don't really know how many linux users there are (and if they have problems with KNIME on Linux). If they do - please report them!

I'll contact you by Email, ok? If we find anything useful, we post it here.

17

After exchanging few Emails and testing different setups, we can conclude that:

  • The problem does not occur in the product version of KNIME
  • If it occurs in the developer version, it can be fixed by upgrading eclipse to 3.2.2 using the update manager
Regards, Bernd (& imax)[/]