Fiji crashes UI on Ubuntu (all recent versions)

[Mario Emmenlauer-3]

Dear Developers,

since more than a year I'm plagued by an issue with Fiji that I never
reported in the hope it would be fixed by updates to my system or to Fiji
over time. However the issue never resolved: Fiji crashes my user interface,
on all recent versions of Ubuntu with all recent versions of Fiji for the
last year or more. The error is triggered simply by zooming into an image
using the "+" (plus) key.

The crash shows no error message, it looks like a "logout", all programs
close instantly and the login manager appears after a second or two. The
only error message I could find is in syslog:
Nov 19 13:51:23 wasabi gnome-session[3626]: Gdk-WARNING: gnome-session: Fatal IO
error 11 (Resource temporarily unavailable) on X server :0.#012

I'm using the binary starter fiji-linux64 without arguments, and I'm
guessing this uses the Fiji-supplied Java in java/linux-amd64/jdk1.6.0_24.
I did not try other Java versions.

My hardware is a Lenovo Thinkpad X220 with built-in Intel Graphics,
Integrated Graphics Chipset: Intel(R) HD Graphics 3000, using the standard
Xorg intel_drv.so driver.

Is this a known error? Would any logfiles help, anything I can try?

All the best,

    Mario

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Mario,

On Tue, 19 Nov 2013, Mario Emmenlauer wrote:

> since more than a year I'm plagued by an issue with Fiji that I never
> reported in the hope it would be fixed by updates to my system or to Fiji
> over time.

Good that you found the time to report the bug; as you know (being a
software maintainer yourself): you cannot fix bugs you do not even know
exist.

However, you unfortunately hit a very busy time here: I am in the middle
of a hackathon.

But given that you already waited a year, maybe I can ask you to wait
just half a week more and nudge me again?

Thank you,
Johannes

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Robert Lockwood]

FWIW I'm running FIJI on Ubuntu 12.04 both 64 bit and 32 bit on an old HP
notebook and a custom machine (32 bit)  with no problems. Not sure what the
video board is ...

Nate


On Tue, Nov 19, 2013 at 10:03 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Mario,
>
> On Tue, 19 Nov 2013, Mario Emmenlauer wrote:
>
> > since more than a year I'm plagued by an issue with Fiji that I never
> > reported in the hope it would be fixed by updates to my system or to Fiji
> > over time.
>
> Good that you found the time to report the bug; as you know (being a
> software maintainer yourself): you cannot fix bugs you do not even know
> exist.
>
> However, you unfortunately hit a very busy time here: I am in the middle
> of a hackathon.
>
> But given that you already waited a year, maybe I can ask you to wait
> just half a week more and nudge me again?
>
> Thank you,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
When I was 12 I thought I would live forever.
So far, so good.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mario Emmenlauer-3]

Hi,

On 19.11.2013 19:17, Robert Lockwood wrote:
> FWIW I'm running FIJI on Ubuntu 12.04 both 64 bit and 32 bit on an old HP
> notebook and a custom machine (32 bit)  with no problems. Not sure what the
> video board is ...

Thanks to both of you for the quick responses! I should maybe add that
I did not have any other UI problems or crashes whatsoever except for
this Fiji-related crash in the last year. Also, I can reproduce the
issue in 100% percent of the cases. Fiji killed my UI every time I tried
pressing "+" for zooming (I did not try more than a few times). Last not
least, it might be relevant that zooming via the menu seems to work. I
did not try that too often either, but at least it never crashed the
few times I tried.

So to summarize: I'm pretty sure its not a problem with my hardware, and
I'm pretty sure its related to what the "+" key does compared to what the
"Zoom" menu entry does.

Hope this helps to isolate the issue... :-)

All the best,

    Mario

> On Tue, Nov 19, 2013 at 10:03 AM, Johannes Schindelin <
> [hidden email]> wrote:
>
>> Hi Mario,
>>
>> On Tue, 19 Nov 2013, Mario Emmenlauer wrote:
>>
>>> since more than a year I'm plagued by an issue with Fiji that I never
>>> reported in the hope it would be fixed by updates to my system or to Fiji
>>> over time.
>>
>> Good that you found the time to report the bug; as you know (being a
>> software maintainer yourself): you cannot fix bugs you do not even know
>> exist.
>>
>> However, you unfortunately hit a very busy time here: I am in the middle
>> of a hackathon.
>>
>> But given that you already waited a year, maybe I can ask you to wait
>> just half a week more and nudge me again?
>>
>> Thank you,
>> Johannes
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Mario,

> I can reproduce the issue in 100% percent of the cases. Fiji killed my
> UI every time I tried pressing "+" for zooming

Should be pretty easy to test out a few things then, to get some more
information!

Try with different versions of Java: java-7-openjdk vs. java-6-openjdk vs.
Oracle's Java 6 or Java 7? Does it happen with all of them? 32-bit mode vs.
64-bit mode (with/without the -d32 flag)? What about with -Xint (no JIT)?
Would be good to find out exactly which scenarios cause the problem.

If you run:
    ./ImageJ-linux64 --dry-run

It will spit out the command you would need to run to launch Fiji is a
similar (not quite identical) way to what the launcher does. You can then
tweak which "java" executable is used, to control the JVM. (The ImageJ
launcher might also respect JAVA_HOME; haven't tested this in a while
personally though, and have had problems at some points in the past.)

Regards,
Curtis


On Tue, Nov 19, 2013 at 12:32 PM, Mario Emmenlauer <[hidden email]>wrote:

> Hi,
>
> On 19.11.2013 19:17, Robert Lockwood wrote:
> > FWIW I'm running FIJI on Ubuntu 12.04 both 64 bit and 32 bit on an old HP
> > notebook and a custom machine (32 bit)  with no problems. Not sure what
> the
> > video board is ...
>
> Thanks to both of you for the quick responses! I should maybe add that
> I did not have any other UI problems or crashes whatsoever except for
> this Fiji-related crash in the last year. Also, I can reproduce the
> issue in 100% percent of the cases. Fiji killed my UI every time I tried
> pressing "+" for zooming (I did not try more than a few times). Last not
> least, it might be relevant that zooming via the menu seems to work. I
> did not try that too often either, but at least it never crashed the
> few times I tried.
>
> So to summarize: I'm pretty sure its not a problem with my hardware, and
> I'm pretty sure its related to what the "+" key does compared to what the
> "Zoom" menu entry does.
>
> Hope this helps to isolate the issue... :-)
>
> All the best,
>
>     Mario
>
>
> > On Tue, Nov 19, 2013 at 10:03 AM, Johannes Schindelin <
> > [hidden email]> wrote:
> >
> >> Hi Mario,
> >>
> >> On Tue, 19 Nov 2013, Mario Emmenlauer wrote:
> >>
> >>> since more than a year I'm plagued by an issue with Fiji that I never
> >>> reported in the hope it would be fixed by updates to my system or to
> Fiji
> >>> over time.
> >>
> >> Good that you found the time to report the bug; as you know (being a
> >> software maintainer yourself): you cannot fix bugs you do not even know
> >> exist.
> >>
> >> However, you unfortunately hit a very busy time here: I am in the middle
> >> of a hackathon.
> >>
> >> But given that you already waited a year, maybe I can ask you to wait
> >> just half a week more and nudge me again?
> >>
> >> Thank you,
> >> Johannes
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> >
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html