Fiji crashes upon opening large files

[Thorsten Mielke]

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.: [phone]
Fax: [phone]
E-mail: [hidden email]


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

[Ignacio Arganda-Carreras-2]

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.: [phone]
> Fax: [phone]
> 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 : [phone]
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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