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Re: Fiji crashes upon opening large files

Posted by Ignacio Arganda-Carreras-2 on Sep 28, 2016; 3:11pm
URL: http://imagej.273.s1.nabble.com/Fiji-crashes-upon-opening-large-files-tp5017213p5017252.html

How did you create your TIFF file?

My Fiji installation crashes as well when opening your file but it has no
problems with larger TIFF files I created. Is it compressed? What is its
size?

I recommend you to post your questions as well in the ImageJ forum:
http://forum.imagej.net/

Best,

On Tue, Sep 20, 2016 at 3:20 PM, Thorsten Mielke <[hidden email]>
wrote:

> Dear ImageJ/Fiji developers,
>
> I recently installed Fiji/ImageJ version 1.51 (ImageJ 2.0.0-rc-49/1.51f;
> Java 1.8.0_66) and do observe a strange behavior when opening large
> tif-files (> 1 GB). When open, the image window is just blank. In many but
> not all cases, Fiji crashes giving an error message:
>
> # A fatal error has been detected by the Java Runtime Environment:
> #
> #  SIGSEGV (0xb) at pc=0x00007f4d8b982110, pid=9080, tid=139971012933376
> #
> # JRE version: Java(TM) SE Runtime Environment (8.0_66-b17) (build
> 1.8.0_66-b17)
> # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.66-b17 mixed mode
> linux-amd64 )
> # Problematic frame:
> # C  [libawt.so+0x54110]  ByteIndexedToIntArgbConvert+0x40
> #
> # Failed to write core dump. Core dumps have been disabled. To enable core
> dumping, try "ulimit -c unlimited" before starting Java again
> #
> # An error report file with more information is saved as:
> # /package/em/software/hs_err_pid9080.log
> #
> # If you would like to submit a bug report, please visit:
> #   http://bugreport.java.com/bugreport/crash.jsp
> #
>
> I submitted a java bug report without any response until today. Our IT
> tried different Java Versions (java 8.0u12 or java 8.0u101) instead of the
> bundled version 8.0u66 as well as usingthe Hotspot VM from openJDK instead
> of Oracle .... the same.
>
> I can open (and work with) the same files using an older Fiji version
> (ImageJ 2.0.0-rc-30/1.49s; Java 1.6.0_24 [64-bit]) on the same workstation
> and OS (linux). Smaller tif files (100-300 MB) are opened and displayed
> correctly, though. Thus it feels like the new Fiji/ImageJ version is having
> a memory problem, but I unfortunately can not pin it down further.
>
> In case you will need a file for testing, I uploaded one of the tif-files
> which crash to
>
> http://owww.molgen.mpg.de/~mielke/7923589/
>
> It is part of a montage of > 2000 TEM images showing basically background
> ...
>
> Best,
>
> Thorsten
>
>
> --
> *******************************************
> Dr. Thorsten Mielke
> - Head Microscopy & Cryo Electron Microscopy Group -
>
> Max Planck Institute for Molecular Genetics
> Ihnestr. 63-73
> D-14195 Berlin
>                            Tel.: +49-(0)30 8413-1644
> Fax: +49-(0)30 8413-1385
> E-mail: [hidden email]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencia de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain

Phone : +34 943 01 73 25
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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