Fiji crashes on ubuntu when opening large tiff files

Hi,

Fiji running on Ubuntu 16.04 always crashes when I try to open large (2,2GB) 16-bit gray scale tif files. The PC has 128 GB of RAM and ImageJ memory is set to 64 GB.

Fiji running on Windows on another machine has no problems in opening the very same files.

Does anybody have an idea how to solve this?

Thank you.
best regards,

Harald

Harald

Do you get any error message?

No, Fiji just closes. I cannot find an error log file within the Fiji folder.

Could you please follow the instructions on https://imagej.net/Troubleshooting#If_ImageJ_crashes, i.e. start Fiji from the terminal, and get back to us with the output from the terminal?

Ok, like this a get an error log:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f5c34758110, pid=17730, tid=140032697100032
#
# 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
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  T H R E A D  ---------------

Current thread (0x0000000003ec3800):  JavaThread "AWT-EventQueue-0" [_thread_in_native, id=17784, stack(0x00007f5be71ae000,0x00007f5be72af000)]

siginfo: si_signo: 11 (SIGSEGV), si_code: 2 (SEGV_ACCERR), si_addr: 0x00007f5bdc06b000

Registers:
RAX=0x00000000ff9b9b9b, RBX=0x0000000000008000, RCX=0x0000000000000000, RDX=0x0000000000008000
RSP=0x00007f5be72aaf88, RBP=0x00007f5be72aaf90, RSI=0x00000000000059d8, RDI=0x00007f5d63990948
R8 =0x0000000000000000, R9 =0x00007f5be72aaff0, R10=0x00007f5bdc0548a0, R11=0x00007f5ce328ad00
R12=0x00007f5bdc0636f0, R13=0x00007f5bdc064e90, R14=0x00007f5c349adb00, R15=0x00007f5be72aaff0
RIP=0x00007f5c34758110, EFLAGS=0x0000000000010287, CSGSFS=0x002b000000000033, ERR=0x0000000000000006
  TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00007f5be72aaf88)
0x00007f5be72aaf88:   0000000003ec39f8 00007f5be72ab1b0
0x00007f5be72aaf98:   00007f5c34734a75 00007f5c349adb00
0x00007f5be72aafa8:   00007f5be72ab170 0000000000000300
0x00007f5be72aafb8:   00007f5be72ab170 00007f5be72ab090
0x00007f5be72aafc8:   00007f5be72ab130 00007f5be72ab160
0x00007f5be72aafd8:   00007f5be72ab2b8 0000000000000000
0x00007f5be72aafe8:   0000000000000000 0000000000000000
0x00007f5be72aaff8:   0000800000008000 00007f5bdc0548a0
0x00007f5be72ab008:   0000000400000000 0000000000020000
0x00007f5be72ab018:   0000000000000000 0000000000000000
0x00007f5be72ab028:   0000000000000000 0000000000000000
0x00007f5be72ab038:   0000000000000000 0000000000000000
0x00007f5be72ab048:   0000000200000002 00007f5bdc065080
0x00007f5be72ab058:   0000000000000000 00007f5be7c30a00
0x00007f5be72ab068:   0000000003ec3800 0000000003760e80
0x00007f5be72ab078:   00007f5c08001350 00007f5c08001360
0x00007f5be72ab088:   00007f5c08001738 0000000000000000
0x00007f5be72ab098:   0000800000008000 00007f5d63990948
0x00007f5be72ab0a8:   0000000100000000 0000010000008000
0x00007f5be72ab0b8:   00007f5ce328ad00 0000000000000000
0x00007f5be72ab0c8:   0000000000000000 0000000000000000
0x00007f5be72ab0d8:   0000000000000000 00007f5be7c30a00
0x00007f5be72ab0e8:   00007f5b00000005 00007f5d63990948
0x00007f5be72ab0f8:   00007f5ce328ad00 0000000000000000
0x00007f5be72ab108:   0000000003ec3800 00007f5be72ab1a0
0x00007f5be72ab118:   00007f6c036a9d6f 00007f5be7c30a00
0x00007f5be72ab128:   0000000003ec3800 0000000000000000
0x00007f5be72ab138:   0000800000008000 00007f5b00000000
0x00007f5be72ab148:   0000000000000000 0000000000000001
0x00007f5be72ab158:   0000000000000000 0000000000000000
0x00007f5be72ab168:   0000800000008000 0000000003ec3800
0x00007f5be72ab178:   0000000003fca970 00007f5be72ab1c0 

Instructions: (pc=0x00007f5c34758110)
0x00007f5c347580f0:   f0 83 ea 01 48 83 c2 01 48 63 c9 4c 63 c0 66 90
0x00007f5c34758100:   31 f6 66 0f 1f 44 00 00 0f b6 04 37 41 8b 04 83
0x00007f5c34758110:   41 89 04 b2 48 83 c6 01 48 39 d6 75 eb 83 eb 01
0x00007f5c34758120:   74 16 48 8d 04 0a 48 01 c7 49 8d 04 90 49 01 c2 

Register to memory mapping:

RAX=0x00000000ff9b9b9b is an unknown value
RBX=0x0000000000008000 is an unknown value
RCX=0x0000000000000000 is an unknown value
RDX=0x0000000000008000 is an unknown value
RSP=0x00007f5be72aaf88 is pointing into the stack for thread: 0x0000000003ec3800
RBP=0x00007f5be72aaf90 is pointing into the stack for thread: 0x0000000003ec3800
RSI=0x00000000000059d8 is an unknown value
RDI=0x00007f5d63990948 is pointing into object: 0x00007f5d63990930
[B 
 - klass: {type array byte}
 - length: 1073741824
R8 =0x0000000000000000 is an unknown value
R9 =0x00007f5be72aaff0 is pointing into the stack for thread: 0x0000000003ec3800
R10=0x00007f5bdc0548a0 is an unknown value
R11=0x00007f5ce328ad00 is pointing into object: 0x00007f5ce328ace8
[I 
 - klass: {type array int}
 - length: 256
R12=0x00007f5bdc0636f0 is an unknown value
R13=0x00007f5bdc064e90 is an unknown value
R14=0x00007f5c349adb00: IntRgbPrimitives+0x1c0 in /home/hhausen/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/amd64/libawt.so at 0x00007f5c34704000
R15=0x00007f5be72aaff0 is pointing into the stack for thread: 0x0000000003ec3800


Stack: [0x00007f5be71ae000,0x00007f5be72af000],  sp=0x00007f5be72aaf88,  free space=1011k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [libawt.so+0x54110]  ByteIndexedToIntArgbConvert+0x40
C  [libawt.so+0x30a75]  Java_sun_java2d_loops_Blit_Blit+0x315
j  sun.java2d.loops.Blit.Blit(Lsun/java2d/SurfaceData;Lsun/java2d/SurfaceData;Ljava/awt/Composite;Lsun/java2d/pipe/Region;IIIIII)V+0
j  sun.java2d.xr.XRPMBlitLoops.cacheToTmpSurface(Lsun/java2d/SurfaceData;Lsun/java2d/xr/XRSurfaceData;IIII)Lsun/java2d/xr/XRSurfaceData;+176
j  sun.java2d.xr.XrSwToPMTransformedBlit.Transform(Lsun/java2d/SurfaceData;Lsun/java2d/SurfaceData;Ljava/awt/Composite;Lsun/java2d/pipe/Region;Ljava/awt/geom/AffineTransform;IIIIIII)V+16
j  sun.java2d.xr.XRDrawImage.renderImageXform(Lsun/java2d/SunGraphics2D;Ljava/awt/Image;Ljava/awt/geom/AffineTransform;IIIIILjava/awt/Color;)V+156
j  sun.java2d.pipe.DrawImage.transformImage(Lsun/java2d/SunGraphics2D;Ljava/awt/Image;Ljava/awt/geom/AffineTransform;IIIIILjava/awt/Color;)V+120
j  sun.java2d.pipe.DrawImage.scaleImage(Lsun/java2d/SunGraphics2D;Ljava/awt/Image;IIIIIIIILjava/awt/Color;)Z+467
j  sun.java2d.pipe.DrawImage.scaleImage(Lsun/java2d/SunGraphics2D;Ljava/awt/Image;IIIIIIIILjava/awt/Color;Ljava/awt/image/ImageObserver;)Z+27
j  sun.java2d.pipe.ValidatePipe.scaleImage(Lsun/java2d/SunGraphics2D;Ljava/awt/Image;IIIIIIIILjava/awt/Color;Ljava/awt/image/ImageObserver;)Z+33
j  sun.java2d.SunGraphics2D.drawImage(Ljava/awt/Image;IIIIIIIILjava/awt/Color;Ljava/awt/image/ImageObserver;)Z+214
j  sun.java2d.SunGraphics2D.drawImage(Ljava/awt/Image;IIIIIIIILjava/awt/image/ImageObserver;)Z+19
j  ij.gui.ImageCanvas.paint(Ljava/awt/Graphics;)V+224
j  ij.gui.ImageCanvas.update(Ljava/awt/Graphics;)V+2
j  sun.awt.RepaintArea.updateComponent(Ljava/awt/Component;Ljava/awt/Graphics;)V+6
j  sun.awt.X11.XRepaintArea.updateComponent(Ljava/awt/Component;Ljava/awt/Graphics;)V+7
j  sun.awt.RepaintArea.paint(Ljava/lang/Object;Z)V+263
j  sun.awt.X11.XComponentPeer.handleEvent(Ljava/awt/AWTEvent;)V+224
J 4210 C1 java.awt.Component.dispatchEventImpl(Ljava/awt/AWTEvent;)V (883 bytes) @ 0x00007f6bf47d8b5c [0x00007f6bf47d18a0+0x72bc]
J 4013 C1 java.awt.EventQueue.dispatchEventImpl(Ljava/awt/AWTEvent;Ljava/lang/Object;)V (149 bytes) @ 0x00007f6bf469fb8c [0x00007f6bf469e300+0x188c]
J 3907 C1 java.awt.EventQueue$3.run()Ljava/lang/Void; (60 bytes) @ 0x00007f6bf4663504 [0x00007f6bf4663300+0x204]
J 3906 C1 java.awt.EventQueue$3.run()Ljava/lang/Object; (5 bytes) @ 0x00007f6bf465accc [0x00007f6bf465ac40+0x8c]
v  ~StubRoutines::call_stub
V  [libjvm.so+0x68bc46]

Bad error :-/ Maybe you should check if there are any memory problems on your machine using memtest?