Gitools unresponsive on OSX10.9 with Java 7v51

[Vasilios Zachariadis]

Hi, 

Currently I can't get v2.0.1 of Gitools to run for more than a few seconds on OSX 10.9 - it then becomes unresponsive and has to be force quit. 

Sometimes it freezes at loading of files, sometimes when exploring a heat map, sometimes directly at startup. 

This is true of the web launch version, running it locally and even compiling and running 2.1.0 devel. 

Java version: 

java version "1.7.0_51"

Java(TM) SE Runtime Environment (build 1.7.0_51-b13)

Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)

Any known issues (and possible solutions) with Gitools/Java/Mac right now? 

Other java apps, like IGV, seem to run without issue. 

Thanks,

Vasilios

[Michael P Schroeder]

Hi,

Thanks for the report and all the checks you have already performed. Currently we are not aware of any freezing problem similar to what you describe.

Nevertheless, we have update a library on which Gitools depends for the development version since it had issues with the mentioned Java version. Please download the latest snapshot at http://bg.upf.edu/gitools-snapshots/ and check if the problem persists. Is there any unusual output from Gitools when you run it from the terminal? If there is any error messages in the terminal, these could be helpful.

Also we have tried the Java 7v51 in Linux systems where it runs well. We will try to get our hands on a Mac computer with the versions you describe. 

Best,

Michael

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[Michael P Schroeder]

Hi Vasilios,

Were you able to check if problem persist?

Thanks for reporting,

Michael

[Vasilios Zachariadis]

Hi,

Yes sorry, it ran fine when I used it on a colleauges mac osx 10.9 (but newer laptop and only webstart), with what I think was the same java version. I removed and reinstalled java on my own laptop, still the same issue. Since other java programs seem to work fine, I'm not sure what's going on. It doesn't seem to be a memory issue, since it shows just 50-60mb used in gitools status bar. Any ideas?

V.

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[Michael P Schroeder]

We are not sure. One think it could be is the Look and Feel or some 3D options for Java or the OS. So you could try two things, described below to get to know what the problem may be. Without error messages it's difficult to know where the error lies.

1. You could try to add the line "-Dsun.java2d.d3d=false" in the file bin/gitools64.vmoptions

2. If you'd like you could try if Gitools 1.8 is also freezing. This version uses a different Look and Feel than the current versions. Gitools 1.8 can be downloaded from here http://www.gitools.org/downloads/gitools-1.8.0-bin.zip

Terminal errors: When you start Gitools from a terminal, there is some output written, especially when things go wrong. Please copy the output of the terminal after the freeze happens. 

 Java crash file: Serious Java crashes generate a .log with information about the problem. Maybe you could check that when you start Gitools from your Computer, if there is a .log file in your gitools or gitools/bin folder. If yes this would be very helpful. Also not that there

Screenshot: Could you also send us a screenshot of Gitools when it freezes?

Thanks very much for your help! If smething of what I explained above is not all clear, do not hesitate to ask

Michael

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