Crash on window resize

Hi,

I'm running Jalview 2.5.1 on Ubuntu Linux. Sometimes Jalview crashes
when I resize the window. I can only replicate this sometimes, not all
the time, by doing the following:

1. Open FASTA alignment in Jalview.
2. Maximize the alignment window.
3. Resize the Jalview app window to make it smaller.

I saved output.txt from the last time this happened, but it's about 3
MB. Please let me know if I should send it to this list or somewhere
else. The main thing I see in this file is a bunch of
java.net.UnknownHostExceptions about my proxy server. But that server
is currently disabled.

If needed, I can also send a FASTA alignment that often causes this crash.

I did modify Jalview to increase the memory, per the InstallAnywhere
Linux instructions at <http://www.jalview.org/jvmmemoryparams.html>.

Thanks,
Jeremy
UT Southwestern, Dallas TX

Hi there Jeremy. Thanks for taking the time to investigate the problem!

If you could register at the jalview bug tracker (issues.jalview.org), you should be able to create a new bug under the Jalview project, and then upload the file.

Alternately, you could trim down the console text to a managable size and send it to to me directly. I suspect that of the 3MB of text, the only relevant bit of the console output is the first 5 lines (containing the version/platform info) and the last 100k or so - which most likely contain the last set of exceptions, and the JVM's stack dump which was generated when the crash occured.

Jim.

···

On 18/07/2010 18:20, Jeremy Semeiks wrote:

Hi,

I'm running Jalview 2.5.1 on Ubuntu Linux. Sometimes Jalview crashes
when I resize the window. I can only replicate this sometimes, not all
the time, by doing the following:

1. Open FASTA alignment in Jalview.
2. Maximize the alignment window.
3. Resize the Jalview app window to make it smaller.

I saved output.txt from the last time this happened, but it's about 3
MB. Please let me know if I should send it to this list or somewhere
else. The main thing I see in this file is a bunch of
java.net.UnknownHostExceptions about my proxy server. But that server
is currently disabled.

If needed, I can also send a FASTA alignment that often causes this crash.

I did modify Jalview to increase the memory, per the InstallAnywhere
Linux instructions at<http://www.jalview.org/jvmmemoryparams.html>.

Thanks,
Jeremy
UT Southwestern, Dallas TX
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

Bug created, file uploaded.

- Jeremy

···

On Mon, Jul 19, 2010 at 4:34 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

Hi there Jeremy. Thanks for taking the time to investigate the problem!

If you could register at the jalview bug tracker (issues.jalview.org),
you should be able to create a new bug under the Jalview project, and
then upload the file.

Alternately, you could trim down the console text to a managable size
and send it to to me directly. I suspect that of the 3MB of text, the
only relevant bit of the console output is the first 5 lines (containing
the version/platform info) and the last 100k or so - which most likely
contain the last set of exceptions, and the JVM's stack dump which was
generated when the crash occured.

Jim.

On 18/07/2010 18:20, Jeremy Semeiks wrote:

Hi,

I'm running Jalview 2.5.1 on Ubuntu Linux. Sometimes Jalview crashes
when I resize the window. I can only replicate this sometimes, not all
the time, by doing the following:

1. Open FASTA alignment in Jalview.
2. Maximize the alignment window.
3. Resize the Jalview app window to make it smaller.

I saved output.txt from the last time this happened, but it's about 3
MB. Please let me know if I should send it to this list or somewhere
else. The main thing I see in this file is a bunch of
java.net.UnknownHostExceptions about my proxy server. But that server
is currently disabled.

If needed, I can also send a FASTA alignment that often causes this crash.

I did modify Jalview to increase the memory, per the InstallAnywhere
Linux instructions at<http://www.jalview.org/jvmmemoryparams.html>.

Thanks,
Jeremy
UT Southwestern, Dallas TX
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
-------------------------------------------------------------------
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

Hi Jeremy.

I took a look at your bug report (http://issues.jalview.org/browse/JAL-603) and realised that you are using openJDK, which doesn't fully support Jalview's GUI, so I won't be fixing this bug anytime soon (probably because its a bug in the open JDK, rather than in Jalview).

The workaround for you is to either install the InstallAnywhere version of Jalview 2.5.1 - making sure you use the installation package that includes the JVM, or install a Sun JDK on your machine. Either way, it's unlikely that you'll see this problem on the 'Official' Java 1.6 runtime.

Thanks for filing the bug report - I'll keep it open for anyone interested in resolving the issue.
Jim.