EXCEPTION_ACCESS_VIOLATION

[orena1]

Hi,
I'm getting an error when I'm loading data to ImageJ using something like this:

    import imagej
    ij = imagej.init(headless=False)
    ij.ui().showUI()
    loaded_data = np.array(x)
    print(loaded_data.shape) # -> (928, 7, 1, 512, 796)
    print(loaded_data.dtype) # -> dtype('uint16')
    ij.ui().show(file_path, ij.py.to_java(loaded_data))

The load is working, but after some browsing, I get this error:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x0000009ad46349d2, pid=20700, tid=10588
#
# JRE version: OpenJDK Runtime Environment Zulu11.43+55-CA (11.0.9.1+1) (build 11.0.9.1+1-LTS)
# Java VM: OpenJDK 64-Bit Server VM Zulu11.43+55-CA (11.0.9.1+1-LTS, mixed mode, tiered, compressed oops, g1 gc, windows-am
d64)
# Problematic frame:
# J 5326 c2 net.imglib2.display.projector.IterableIntervalProjector2D.map()V (552 bytes) @ 0x0000009ad46349d2 [0x0000009ad4
633700+0x00000000000012d2]
#
# Core dump will be written. Default location: C:\Users\....\hs_err_pid20700.mdmp
#
# An error report file with more information is saved as:
# C:\Users\....\hs_err_pid20700.log
Compiled method (c2)   17742 5326       4       net.imglib2.display.projector.IterableIntervalProjector2D::map (552 bytes)
 total in heap  [0x0000009ad4633310,0x0000009ad4637b48] = 18488
 relocation     [0x0000009ad4633488,0x0000009ad46336e8] = 608
 main code      [0x0000009ad4633700,0x0000009ad4635da0] = 9888
 stub code      [0x0000009ad4635da0,0x0000009ad4635e88] = 232
 oops           [0x0000009ad4635e88,0x0000009ad4635ea0] = 24
 metadata       [0x0000009ad4635ea0,0x0000009ad4636060] = 448
 scopes data    [0x0000009ad4636060,0x0000009ad4636ec8] = 3688
 scopes pcs     [0x0000009ad4636ec8,0x0000009ad4637708] = 2112
 dependencies   [0x0000009ad4637708,0x0000009ad4637750] = 72
 handler table  [0x0000009ad4637750,0x0000009ad4637960] = 528
 nul chk table  [0x0000009ad4637960,0x0000009ad4637b48] = 488
Could not load hsdis-amd64.dll; library not loadable; PrintAssembly is disabled
#
# If you would like to submit a bug report, please visit:
#   http://www.azulsystems.com/support/
#

here is hs_err_pid20700

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x0000009ad46349d2, pid=20700, tid=10588
#
# JRE version: OpenJDK Runtime Environment Zulu11.43+55-CA (11.0.9.1+1) (build 11.0.9.1+1-LTS)
# Java VM: OpenJDK 64-Bit Server VM Zulu11.43+55-CA (11.0.9.1+1-LTS, mixed mode, tiered, compressed oops, g1 gc, windows-amd64)
# Problematic frame:
# J 5326 c2 net.imglib2.display.projector.IterableIntervalProjector2D.map()V (552 bytes) @ 0x0000009ad46349d2 [0x0000009ad4633700+0x00000000000012d2]
#
# Core dump will be written. Default location: C:\Users\oamsalem\Projects\sbx2imagej\hs_err_pid20700.mdmp
#
# If you would like to submit a bug report, please visit:
#   http://www.azulsystems.com/support/
#

---------------  S U M M A R Y ------------

Command Line: 

Host: Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz, 56 cores, 511G,  Windows Server 2012 R2 , 64 bit Build 9600 (6.3.9600.19843)
Time: Thu Apr 22 17:09:14 2021 Eastern Daylight Time elapsed time: 17.733269 seconds (0d 0h 0m 17s)

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

Current thread (0x0000009b30273000):  JavaThread "zSelector" [_thread_in_Java, id=10588, stack(0x0000009b32550000,0x0000009b32740000)]

Stack: [0x0000009b32550000,0x0000009b32740000],  sp=0x0000009b3273f030,  free space=1980k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  0x0000009ad46349d2


siginfo: EXCEPTION_ACCESS_VIOLATION (0xc0000005), reading address 0x000000a20b5a4040


Register to memory mapping:

RIP=0x0000009ad46349d2 is at entry_point+4818 in (nmethod*)0x0000009ad4633310
RAX=0x0000009b32264be0 is pointing into metadata
RBX=0x0000000086e55c30 is an oop: net.imglib2.type.numeric.integer.UnsignedShortType 
{0x0000000086e55c30} - klass: 'net/imglib2/type/numeric/integer/UnsignedShortType'
RCX=0x000000a20b5a4040 is an unknown value
RDX=6110176 is a compressed pointer to class: 0x00000008005d3be0
net.imglib2.converter.readwrite.longaccess.UnsignedShortLongAccessTypeUnsignedShortTypeConverter$ConvertedAccess {0x00000008005d3be8}
RSP=0x0000009b3273f030 is pointing into the stack for thread: 0x0000009b30273000
RBP=0x0000000086e550f8 is an oop: net.imglib2.display.projector.IterableIntervalProjector2D 
{0x0000000086e550f8} - klass: 'net/imglib2/display/projector/IterableIntervalProjector2D'
RSI=879392 is a compressed pointer to class: 0x00000008000d6b20
net.imglib2.img.basictypelongaccess.unsafe.ShortUnsafe {0x00000008000d6b28}
RDI=0x0 is NULL
R8 =0x0000000086e55bf0 is an oop: net.imglib2.img.array.ArrayCursor 
{0x0000000086e55bf0} - klass: 'net/imglib2/img/array/ArrayCursor'
R9 =0x0000000086e55cd0 is an oop: net.imglib2.converter.readwrite.WriteConvertedRandomAccess 
{0x0000000086e55cd0} - klass: 'net/imglib2/converter/readwrite/WriteConvertedRandomAccess'
R10=0x000000a20b5a4040 is an unknown value
R11=0xffffffff89271000 is an unknown value
R12=0x0 is NULL
R13=0x000000000000031c is an unknown value
R14=0x0000000000000200 is an unknown value
R15=0x0000009b30273000 is a thread


Registers:
RAX=0x0000009b32264be0, RBX=0x0000000086e55c30, RCX=0x000000a20b5a4040, RDX=0x00000000005d3be0
RSP=0x0000009b3273f030, RBP=0x0000000086e550f8, RSI=0x00000000000d6b20, RDI=0x0000000000000000
R8 =0x0000000086e55bf0, R9 =0x0000000086e55cd0, R10=0x000000a20b5a4040, R11=0xffffffff89271000
R12=0x0000000000000000, R13=0x000000000000031c, R14=0x0000000000000200, R15=0x0000009b30273000
RIP=0x0000009ad46349d2, EFLAGS=0x0000000000010203

Top of Stack: (sp=0x0000009b3273f030)
0x0000009b3273f030:   0000009b3273f048 0000009b3273f0a8
0x0000009b3273f040:   0000009acc779dec 0000000000000004
0x0000009b3273f050:   0000000086e550f8 0000000086e55bf0
0x0000009b3273f060:   0000000086e55cd0 000000000000031c
0x0000009b3273f070:   000000000000031c 0000000000000005
0x0000009b3273f080:   0000000000000000 0000000011129c73
0x0000009b3273f090:   fffffffffffffce4 0000000000000000
0x0000009b3273f0a0:   0000009adb360000 0000009b3273f128
0x0000009b3273f0b0:   0000009acc779da7 0000000000000003
0x0000009b3273f0c0:   0000009b3273f128 0000009acc779da7
0x0000009b3273f0d0:   0000009acc779da7 0000000086e550f8
0x0000009b3273f0e0:   0000009b3273f0e0 0000009b3215208f
0x0000009b3273f0f0:   0000009b3273f158 0000009b32157f60
0x0000009b3273f100:   0000000000000000 0000000088920d90
0x0000009b3273f110:   0000009b321520e0 0000009b3273f0d8
0x0000009b3273f120:   0000009b3273f140 0000009b3273f1a8 

Instructions: (pc=0x0000009ad46349d2)
0x0000009ad46348d2:   0c 4d 8b 97 08 01 00 00 48 83 c7 01 41 85 02 49
0x0000009ad46348e2:   3b fd 0f 8d a9 fd ff ff c4 e1 f9 7e c3 c4 c1 f9
0x0000009ad46348f2:   7e ca 48 8b 6c 24 20 8b 75 28 4c 8b 4c 24 30 41
0x0000009ad4634902:   8b 49 18 4c 8b 44 24 28 45 8b 58 20 41 8b 54 f4
0x0000009ad4634912:   08 81 fa 40 6c 5f 00 0f 84 3a 01 00 00 81 fa 40
0x0000009ad4634922:   68 5f 00 0f 85 bd 03 00 00 41 8b 74 cc 08 81 fe
0x0000009ad4634932:   80 e0 0d 00 0f 85 80 0e 00 00 48 c1 e1 03 43 8b
0x0000009ad4634942:   74 dc 08 81 fe 80 e0 0d 00 0f 85 ab 0e 00 00 8b
0x0000009ad4634952:   71 14 8b 49 0c 41 8b 54 f4 08 c4 c1 f9 6e ca c4
0x0000009ad4634962:   e1 f9 6e c3 4d 8d 14 f4 4b 8d 1c dc 81 fa e0 3b
0x0000009ad4634972:   5d 00 74 2a 81 fa 98 2d 0d 00 0f 85 32 06 00 00
0x0000009ad4634982:   41 8b 72 0c 45 8b 5c f4 0c 41 3b cb 0f 83 d0 05
0x0000009ad4634992:   00 00 4d 8d 14 f4 45 0f bf 54 4a 10 eb 36 41 8b
0x0000009ad46349a2:   72 0c 45 8b 54 f4 18 4d 8b 5c f4 10 43 8b 74 d4
0x0000009ad46349b2:   08 81 fe 20 6b 0d 00 0f 85 55 05 00 00 49 c1 e2
0x0000009ad46349c2:   03 49 63 4a 0c 49 0f af cb 49 03 4a 18 4c 8b d1
0x0000009ad46349d2:   45 0f bf 12 44 8b 5b 14 8b 73 0c 43 8b 4c dc 08
0x0000009ad46349e2:   4b 8d 1c dc 81 f9 e0 3b 5d 00 74 2c 81 f9 98 2d
0x0000009ad46349f2:   0d 00 0f 85 5a 06 00 00 44 8b 5b 0c 43 8b 4c dc
0x0000009ad4634a02:   0c 3b f1 0f 83 f9 05 00 00 49 c1 e3 03 66 45 89
0x0000009ad4634a12:   54 73 10 e9 29 fe ff ff 8b 4b 0c 41 8b 74 cc 18
0x0000009ad4634a22:   4d 8b 5c cc 10 41 8b 4c f4 08 81 f9 20 6b 0d 00
0x0000009ad4634a32:   0f 85 8c 04 00 00 49 8d 0c f4 8b 71 0c 48 8b 49
0x0000009ad4634a42:   18 48 63 de 49 0f af db 48 03 d9 4c 8b db 66 45
0x0000009ad4634a52:   89 13 e9 ea fd ff ff 41 8b 74 cc 08 81 fe 80 e0
0x0000009ad4634a62:   0d 00 0f 85 de 0d 00 00 48 c1 e1 03 43 8b 54 dc
0x0000009ad4634a72:   08 81 fa 80 e0 0d 00 0f 85 09 0e 00 00 49 c1 e3
0x0000009ad4634a82:   03 41 8b 73 14 45 8b 5b 0c 41 8b 54 f4 08 c4 c1
0x0000009ad4634a92:   f9 6e ca c4 e1 f9 6e c3 4d 8d 14 f4 81 fa e0 3b
0x0000009ad4634aa2:   5d 00 74 2d 81 fa 98 2d 0d 00 0f 85 22 03 00 00
0x0000009ad4634ab2:   41 8b 72 0c 41 8b 54 f4 0c 44 3b da 0f 83 c0 02
0x0000009ad4634ac2:   00 00 4d 8d 14 f4 47 0f bf 54 5a 10 e9 f4 fc ff 


Stack slot to memory mapping:
stack at sp + 0 slots: 0x0000009b3273f048 is pointing into the stack for thread: 0x0000009b30273000
stack at sp + 1 slots: 0x0000009b3273f0a8 is pointing into the stack for thread: 0x0000009b30273000
stack at sp + 2 slots: 0x0000009acc779dec is at code_begin+2412 in an Interpreter codelet
invoke return entry points  [0x0000009acc779480, 0x0000009acc779e80]  2560 bytes
stack at sp + 3 slots: 0x0000000000000004 is an unknown value
stack at sp + 4 slots: 0x0000000086e550f8 is an oop: net.imglib2.display.projector.IterableIntervalProjector2D 
{0x0000000086e550f8} - klass: 'net/imglib2/display/projector/IterableIntervalProjector2D'
stack at sp + 5 slots: 0x0000000086e55bf0 is an oop: net.imglib2.img.array.ArrayCursor 
{0x0000000086e55bf0} - klass: 'net/imglib2/img/array/ArrayCursor'
stack at sp + 6 slots: 0x0000000086e55cd0 is an oop: net.imglib2.converter.readwrite.WriteConvertedRandomAccess 
{0x0000000086e55cd0} - klass: 'net/imglib2/converter/readwrite/WriteConvertedRandomAccess'
stack at sp + 7 slots: 0x000000000000031c is an unknown value



---------------  P R O C E S S  ---------------

Threads class SMR info:
_java_thread_list=0x0000009b20cff210, length=21, elements={
0x0000009291207800, 0x0000009291205000, 0x0000009291208800, 0x0000009291209000,
0x000000929120a000, 0x0000009284924800, 0x000000928492b800, 0x000000928492c000,
0x000000928492d000, 0x000000928492a800, 0x000000928492f800, 0x0000009284932000,
0x0000009284937800, 0x0000009284935000, 0x0000009284938800, 0x0000009284936000,
0x0000009b2e936000, 0x0000009b3027c000, 0x0000009b3027f000, 0x0000009b30273000,
0x0000009b30273800
}

Java Threads: ( => current thread )
  0x0000009291207800 JavaThread "main" [_thread_blocked, id=23236, stack(0x000000928d4c0000,0x000000928d6b0000)]
  0x0000009291205000 JavaThread "Reference Handler" daemon [_thread_blocked, id=21004, stack(0x0000009299250000,0x0000009299440000)]
  0x0000009291208800 JavaThread "Finalizer" daemon [_thread_blocked, id=19112, stack(0x0000009299440000,0x0000009299630000)]
  0x0000009291209000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=12376, stack(0x0000009299630000,0x0000009299820000)]
  0x000000929120a000 JavaThread "Attach Listener" daemon [_thread_blocked, id=16872, stack(0x0000009299820000,0x0000009299a10000)]
  0x0000009284924800 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=11112, stack(0x0000009299a10000,0x0000009299c00000)]
  0x000000928492b800 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=15776, stack(0x0000009299c00000,0x0000009299df0000)]
  0x000000928492c000 JavaThread "Sweeper thread" daemon [_thread_blocked, id=5000, stack(0x0000009299df0000,0x0000009299fe0000)]
  0x000000928492d000 JavaThread "Service Thread" daemon [_thread_blocked, id=13816, stack(0x000000929a1d0000,0x000000929a3c0000)]
  0x000000928492a800 JavaThread "Common-Cleaner" daemon [_thread_blocked, id=14628, stack(0x000000929a5b0000,0x000000929a7a0000)]
  0x000000928492f800 JavaThread "Python Reference Queue" daemon [_thread_blocked, id=16100, stack(0x000000929ab80000,0x000000929ad70000)]
  0x0000009284932000 JavaThread "SciJava-d4602a-Thread-0" [_thread_blocked, id=17732, stack(0x0000009b28330000,0x0000009b28520000)]
  0x0000009284937800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=17736, stack(0x0000009b2c3f0000,0x0000009b2c5e0000)]
  0x0000009284935000 JavaThread "AWT-Shutdown" [_thread_blocked, id=16748, stack(0x0000009b2c5e0000,0x0000009b2c7d0000)]
  0x0000009284938800 JavaThread "AWT-Windows" daemon [_thread_in_native, id=10484, stack(0x0000009b2c7d0000,0x0000009b2c9c0000)]
  0x0000009284936000 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=5924, stack(0x0000009b30f90000,0x0000009b31180000)]
  0x0000009b2e936000 JavaThread "SciJava-d4602a-Thread-1" [_thread_blocked, id=23248, stack(0x0000009b31f50000,0x0000009b32140000)]
  0x0000009b3027c000 JavaThread "SciJava-d4602a-Thread-58" [_thread_blocked, id=20300, stack(0x0000009b2bdf0000,0x0000009b2bfe0000)]
  0x0000009b3027f000 JavaThread "SciJava-d4602a-Thread-59" [_thread_blocked, id=17164, stack(0x0000009b2bfe0000,0x0000009b2c1d0000)]
=>0x0000009b30273000 JavaThread "zSelector" [_thread_in_Java, id=10588, stack(0x0000009b32550000,0x0000009b32740000)]
  0x0000009b30273800 JavaThread "C1 CompilerThread1" daemon [_thread_blocked, id=22192, stack(0x0000009299fe0000,0x000000929a1d0000)]

Other Threads:
  0x00000092848b4800 VMThread "VM Thread" [stack: 0x0000009299060000,0x0000009299250000] [id=21256]
  0x0000009280d1a000 WatcherThread [stack: 0x000000929a3c0000,0x000000929a5b0000] [id=22520]
  0x000000928416d000 GCTaskThread "GC Thread#0" [stack: 0x00000092839a0000,0x0000009283b90000] [id=13876]
  0x0000009b1f102800 GCTaskThread "GC Thread#1" [stack: 0x0000009b20df0000,0x0000009b20fe0000] [id=17032]
  0x0000009b1f103800 GCTaskThread "GC Thread#2" [stack: 0x0000009b20fe0000,0x0000009b211d0000] [id=7284]
  0x0000009b1eec7000 GCTaskThread "GC Thread#3" [stack: 0x0000009b211d0000,0x0000009b213c0000] [id=4360]
  0x0000009b1eec8000 GCTaskThread "GC Thread#4" [stack: 0x0000009b213c0000,0x0000009b215b0000] [id=15516]
  0x0000009b1fa2d800 GCTaskThread "GC Thread#5" [stack: 0x0000009b215b0000,0x0000009b217a0000] [id=15820]
  0x0000009b1fa2e000 GCTaskThread "GC Thread#6" [stack: 0x0000009b217a0000,0x0000009b21990000] [id=22408]
  0x0000009b1fa2e800 GCTaskThread "GC Thread#7" [stack: 0x0000009b21990000,0x0000009b21b80000] [id=22644]
  0x000000928fc8b800 GCTaskThread "GC Thread#8" [stack: 0x0000009b21b80000,0x0000009b21d70000] [id=21108]
  0x000000928fc8c800 GCTaskThread "GC Thread#9" [stack: 0x0000009b21d70000,0x0000009b21f60000] [id=22800]
  0x000000928fc8c000 GCTaskThread "GC Thread#10" [stack: 0x0000009b21f60000,0x0000009b22150000] [id=23288]
  0x000000928fc8a000 GCTaskThread "GC Thread#11" [stack: 0x0000009b22150000,0x0000009b22340000] [id=15080]
  0x000000928fc8e000 GCTaskThread "GC Thread#12" [stack: 0x0000009b22340000,0x0000009b22530000] [id=21160]
  0x000000928fc8d800 GCTaskThread "GC Thread#13" [stack: 0x0000009b22530000,0x0000009b22720000] [id=22948]
  0x0000009b1fead800 GCTaskThread "GC Thread#14" [stack: 0x0000009b22720000,0x0000009b22910000] [id=22676]
  0x0000009b1feab800 GCTaskThread "GC Thread#15" [stack: 0x0000009b22910000,0x0000009b22b00000] [id=23524]
  0x0000009b1feae000 GCTaskThread "GC Thread#16" [stack: 0x0000009b22b00000,0x0000009b22cf0000] [id=23252]
  0x0000009b1feac800 GCTaskThread "GC Thread#17" [stack: 0x0000009b22cf0000,0x0000009b22ee0000] [id=17088]
  0x0000009b1feac000 GCTaskThread "GC Thread#18" [stack: 0x0000009b22ee0000,0x0000009b230d0000] [id=21304]
  0x0000009b1feaf000 GCTaskThread "GC Thread#19" [stack: 0x0000009b230d0000,0x0000009b232c0000] [id=21824]
  0x0000009b1feb0800 GCTaskThread "GC Thread#20" [stack: 0x0000009b232c0000,0x0000009b234b0000] [id=20216]
  0x0000009b1feb2800 GCTaskThread "GC Thread#21" [stack: 0x0000009b234b0000,0x0000009b236a0000] [id=15648]
  0x0000009b1feaf800 GCTaskThread "GC Thread#22" [stack: 0x0000009b236a0000,0x0000009b23890000] [id=22512]
  0x0000009b1feb4000 GCTaskThread "GC Thread#23" [stack: 0x0000009b23890000,0x0000009b23a80000] [id=20756]
  0x0000009b1feb3000 GCTaskThread "GC Thread#24" [stack: 0x0000009b23a80000,0x0000009b23c70000] [id=22744]
  0x0000009b1feb2000 GCTaskThread "GC Thread#25" [stack: 0x0000009b23c70000,0x0000009b23e60000] [id=17996]
  0x0000009b1feb1000 GCTaskThread "GC Thread#26" [stack: 0x0000009b23e60000,0x0000009b24050000] [id=19608]
  0x0000009b1feb7000 GCTaskThread "GC Thread#27" [stack: 0x0000009b24050000,0x0000009b24240000] [id=22028]
  0x0000009b1feb7800 GCTaskThread "GC Thread#28" [stack: 0x0000009b24240000,0x0000009b24430000] [id=13788]
  0x0000009b1feb4800 GCTaskThread "GC Thread#29" [stack: 0x0000009b24430000,0x0000009b24620000] [id=6068]
  0x0000009b1feb8800 GCTaskThread "GC Thread#30" [stack: 0x0000009b24620000,0x0000009b24810000] [id=23108]
  0x0000009b1feb5800 GCTaskThread "GC Thread#31" [stack: 0x0000009b24810000,0x0000009b24a00000] [id=19768]
  0x0000009b1feb9000 GCTaskThread "GC Thread#32" [stack: 0x0000009b24a00000,0x0000009b24bf0000] [id=22904]
  0x0000009b1feb6000 GCTaskThread "GC Thread#33" [stack: 0x0000009b24bf0000,0x0000009b24de0000] [id=11716]
  0x0000009b1feb9800 GCTaskThread "GC Thread#34" [stack: 0x0000009b24de0000,0x0000009b24fd0000] [id=23208]
  0x0000009b1feba800 GCTaskThread "GC Thread#35" [stack: 0x0000009b24fd0000,0x0000009b251c0000] [id=4196]
  0x0000009b1fe31000 GCTaskThread "GC Thread#36" [stack: 0x0000009b251c0000,0x0000009b253b0000] [id=10820]
  0x0000009b1fe31800 GCTaskThread "GC Thread#37" [stack: 0x0000009b253b0000,0x0000009b255a0000] [id=9060]
  0x00000092842ca800 ConcurrentGCThread "G1 Main Marker" [stack: 0x000000928b920000,0x000000928bb10000] [id=17252]
  0x00000092842cb800 ConcurrentGCThread "G1 Conc#0" [stack: 0x000000928bb10000,0x000000928bd00000] [id=20884]
  0x0000009b1fe32800 ConcurrentGCThread "G1 Conc#1" [stack: 0x0000009b29ab0000,0x0000009b29ca0000] [id=17264]
  0x0000009b1fe33000 ConcurrentGCThread "G1 Conc#2" [stack: 0x0000009b29ca0000,0x0000009b29e90000] [id=10116]
  0x0000009b1fe30800 ConcurrentGCThread "G1 Conc#3" [stack: 0x0000009b29e90000,0x0000009b2a080000] [id=18032]
  0x0000009b1fe34000 ConcurrentGCThread "G1 Conc#4" [stack: 0x0000009b2a080000,0x0000009b2a270000] [id=19440]
  0x0000009b1fe35800 ConcurrentGCThread "G1 Conc#5" [stack: 0x0000009b2a270000,0x0000009b2a460000] [id=22900]
  0x0000009b1fe37800 ConcurrentGCThread "G1 Conc#6" [stack: 0x0000009b2a460000,0x0000009b2a650000] [id=19716]
  0x0000009b1fe34800 ConcurrentGCThread "G1 Conc#7" [stack: 0x0000009b2a650000,0x0000009b2a840000] [id=22960]
  0x0000009b1fe38000 ConcurrentGCThread "G1 Conc#8" [stack: 0x0000009b2a840000,0x0000009b2aa30000] [id=22924]
  0x0000009b1fe39000 ConcurrentGCThread "G1 Conc#9" [stack: 0x0000009b2aa30000,0x0000009b2ac20000] [id=13988]
  0x0000009284727800 ConcurrentGCThread "G1 Refine#0" [stack: 0x00000092981b0000,0x00000092983a0000] [id=12728]
  0x000000928472c800 ConcurrentGCThread "G1 Young RemSet Sampling" [stack: 0x0000009298670000,0x0000009298860000] [id=22440]

Threads with active compile tasks:

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap address: 0x0000000082000000, size: 30688 MB, Compressed Oops mode: Zero based, Oop shift amount: 3
Narrow klass base: 0x0000000800000000, Narrow klass shift: 0
Compressed class space size: 1073741824 Address: 0x0000000800000000

Heap:
 garbage-first heap   total 122880K, used 63397K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 10 young (40960K), 0 survivors (0K)
 Metaspace       used 45454K, capacity 46304K, committed 46424K, reserved 1089536K
  class space    used 5865K, capacity 6184K, committed 6272K, reserved 1048576K
Heap Regions: E=young(eden), S=young(survivor), O=old, HS=humongous(starts), HC=humongous(continues), CS=collection set, F=free, A=archive, TAMS=top-at-mark-start (previous, next)
|   0|0x0000000082000000, 0x0000000082400000, 0x0000000082400000|100%| O|  |TAMS 0x0000000082000000, 0x0000000082000000| Untracked 
|   1|0x0000000082400000, 0x00000000827fffc8, 0x0000000082800000| 99%| O|  |TAMS 0x0000000082400000, 0x0000000082400000| Untracked 
|   2|0x0000000082800000, 0x0000000082bfff10, 0x0000000082c00000| 99%| O|  |TAMS 0x0000000082800000, 0x0000000082800000| Untracked 
|   3|0x0000000082c00000, 0x0000000082ffa0f8, 0x0000000083000000| 99%| O|  |TAMS 0x0000000082c00000, 0x0000000082c00000| Untracked 
|   4|0x0000000083000000, 0x000000008331c710, 0x0000000083400000| 77%| O|  |TAMS 0x0000000083000000, 0x0000000083000000| Untracked 
|   5|0x0000000083400000, 0x00000000837fdbd8, 0x0000000083800000| 99%| O|  |TAMS 0x0000000083400000, 0x0000000083400000| Untracked 
|   6|0x0000000083800000, 0x00000000839a25e0, 0x0000000083c00000| 40%| O|  |TAMS 0x0000000083800000, 0x0000000083800000| Untracked 
|   7|0x0000000083c00000, 0x0000000083c00000, 0x0000000084000000|  0%| F|  |TAMS 0x0000000083c00000, 0x0000000083c00000| Untracked 
|   8|0x0000000084000000, 0x0000000084000000, 0x0000000084400000|  0%| F|  |TAMS 0x0000000084000000, 0x0000000084000000| Untracked 
|   9|0x0000000084400000, 0x0000000084400000, 0x0000000084800000|  0%| F|  |TAMS 0x0000000084400000, 0x0000000084400000| Untracked 
|  10|0x0000000084800000, 0x0000000084800000, 0x0000000084c00000|  0%| F|  |TAMS 0x0000000084800000, 0x0000000084800000| Untracked 
|  11|0x0000000084c00000, 0x0000000084c00000, 0x0000000085000000|  0%| F|  |TAMS 0x0000000084c00000, 0x0000000084c00000| Untracked 
|  12|0x0000000085000000, 0x0000000085000000, 0x0000000085400000|  0%| F|  |TAMS 0x0000000085000000, 0x0000000085000000| Untracked 
|  13|0x0000000085400000, 0x0000000085400000, 0x0000000085800000|  0%| F|  |TAMS 0x0000000085400000, 0x0000000085400000| Untracked 
|  14|0x0000000085800000, 0x0000000085b93288, 0x0000000085c00000| 89%| O|  |TAMS 0x0000000085800000, 0x0000000085800000| Untracked 
|  15|0x0000000085c00000, 0x0000000085c00000, 0x0000000086000000|  0%| F|  |TAMS 0x0000000085c00000, 0x0000000085c00000| Untracked 
|  16|0x0000000086000000, 0x0000000086000000, 0x0000000086400000|  0%| F|  |TAMS 0x0000000086000000, 0x0000000086000000| Untracked 
|  17|0x0000000086400000, 0x0000000086400000, 0x0000000086800000|  0%| F|  |TAMS 0x0000000086400000, 0x0000000086400000| Untracked 
|  18|0x0000000086800000, 0x0000000086800000, 0x0000000086c00000|  0%| F|  |TAMS 0x0000000086800000, 0x0000000086800000| Untracked 
|  19|0x0000000086c00000, 0x0000000086e5ce30, 0x0000000087000000| 59%| E|  |TAMS 0x0000000086c00000, 0x0000000086c00000| Complete 
|  20|0x0000000087000000, 0x0000000087400000, 0x0000000087400000|100%| E|CS|TAMS 0x0000000087000000, 0x0000000087000000| Complete 
|  21|0x0000000087400000, 0x0000000087800000, 0x0000000087800000|100%| E|CS|TAMS 0x0000000087400000, 0x0000000087400000| Complete 
|  22|0x0000000087800000, 0x0000000087b9f888, 0x0000000087c00000| 90%| E|  |TAMS 0x0000000087800000, 0x0000000087800000| Complete 
|  23|0x0000000087c00000, 0x0000000088000000, 0x0000000088000000|100%| E|CS|TAMS 0x0000000087c00000, 0x0000000087c00000| Complete 
|  24|0x0000000088000000, 0x0000000088400000, 0x0000000088400000|100%| E|CS|TAMS 0x0000000088000000, 0x0000000088000000| Complete 
|  25|0x0000000088400000, 0x0000000088800000, 0x0000000088800000|100%| E|CS|TAMS 0x0000000088400000, 0x0000000088400000| Complete 
|  26|0x0000000088800000, 0x0000000088c00000, 0x0000000088c00000|100%| E|CS|TAMS 0x0000000088800000, 0x0000000088800000| Complete 
|  27|0x0000000088c00000, 0x0000000088d9fc90, 0x0000000089000000| 40%| O|  |TAMS 0x0000000088c00000, 0x0000000088c00000| Untracked 
|  28|0x0000000089000000, 0x0000000089400000, 0x0000000089400000|100%| E|CS|TAMS 0x0000000089000000, 0x0000000089000000| Complete 
|  29|0x0000000089400000, 0x0000000089800000, 0x0000000089800000|100%| E|CS|TAMS 0x0000000089400000, 0x0000000089400000| Complete 

Card table byte_map: [0x0000009adb770000,0x0000009adf360000] _byte_map_base: 0x0000009adb360000

Marking Bits (Prev, Next): (CMBitMap*) 0x0000009280f88ce0, (CMBitMap*) 0x0000009280f88ca8
 Prev Bits: [0x0000009b00ed0000, 0x0000009b1ee50000)
 Next Bits: [0x0000009ae2f50000, 0x0000009b00ed0000)

Polling page: 0x0000009283790000

Metaspace:

Usage:
  Non-class:     39.18 MB capacity,    38.66 MB ( 99%) used,   436.60 KB (  1%) free+waste,    94.56 KB ( <1%) overhead. 
      Class:      6.04 MB capacity,     5.73 MB ( 95%) used,   273.27 KB (  4%) free+waste,    45.50 KB ( <1%) overhead. 
       Both:     45.22 MB capacity,    44.39 MB ( 98%) used,   709.88 KB (  2%) free+waste,   140.06 KB ( <1%) overhead. 

Virtual space:
  Non-class space:       40.00 MB reserved,      39.21 MB ( 98%) committed 
      Class space:        1.00 GB reserved,       6.13 MB ( <1%) committed 
             Both:        1.04 GB reserved,      45.34 MB (  4%) committed 

Chunk freelists:
   Non-Class:  32.00 KB
       Class:  24.00 KB
        Both:  56.00 KB

MaxMetaspaceSize: 17179869184.00 GB
CompressedClassSpaceSize: 1.00 GB

CodeHeap 'non-profiled nmethods': size=118912Kb used=3634Kb max_used=3645Kb free=115278Kb
 bounds [0x0000009ad4350000, 0x0000009ad46f0000, 0x0000009adb770000]
CodeHeap 'profiled nmethods': size=118848Kb used=9711Kb max_used=9711Kb free=109136Kb
 bounds [0x0000009accf40000, 0x0000009acd8d0000, 0x0000009ad4350000]
CodeHeap 'non-nmethods': size=8000Kb used=1885Kb max_used=3613Kb free=6115Kb
 bounds [0x0000009acc770000, 0x0000009accb00000, 0x0000009accf40000]
 total_blobs=5270 nmethods=4530 adapters=648
 compilation: enabled
              stopped_count=0, restarted_count=0
 full_count=0

Compilation events (20 events):
Event: 17.679 Thread 0x000000928492b800 nmethod 5514 0x0000009acd8cb590 code [0x0000009acd8cb800, 0x0000009acd8cc4e8]
Event: 17.702 Thread 0x0000009b30273800 5516       3       java.awt.Rectangle::getBounds (24 bytes)
Event: 17.703 Thread 0x0000009b30273800 nmethod 5516 0x0000009acd89b290 code [0x0000009acd89b460, 0x0000009acd89b778]
Event: 17.704 Thread 0x000000928492b800 5517       3       sun.java2d.pipe.PixelToParallelogramConverter::len (37 bytes)
Event: 17.704 Thread 0x000000928492b800 nmethod 5517 0x0000009acd8a3810 code [0x0000009acd8a39e0, 0x0000009acd8a3c38]
Event: 17.704 Thread 0x0000009b30273800 5518       3       java.awt.LightweightDispatcher::dispatchEvent (73 bytes)
Event: 17.705 Thread 0x0000009b30273800 nmethod 5518 0x0000009acd8a2c90 code [0x0000009acd8a2ea0, 0x0000009acd8a3648]
Event: 17.711 Thread 0x0000009284924800 nmethod 5493 0x0000009ad46df510 code [0x0000009ad46dfa40, 0x0000009ad46e6b18]
Event: 17.711 Thread 0x0000009284924800 5500       4       java.util.AbstractList::listIterator (6 bytes)
Event: 17.713 Thread 0x0000009284924800 nmethod 5500 0x0000009ad4605210 code [0x0000009ad46053c0, 0x0000009ad46055d8]
Event: 17.713 Thread 0x0000009284924800 5504       4       java.lang.Double::isNaN (12 bytes)
Event: 17.714 Thread 0x0000009284924800 nmethod 5504 0x0000009ad4501b10 code [0x0000009ad4501ca0, 0x0000009ad4501cf8]
Event: 17.714 Thread 0x0000009284924800 5515       4       sun.awt.windows.WComponentPeer::preprocessPostEvent (1 bytes)
Event: 17.714 Thread 0x0000009284924800 nmethod 5515 0x0000009ad4560410 code [0x0000009ad45605a0, 0x0000009ad45605f8]
Event: 17.715 Thread 0x000000928492b800 5519       1       sun.awt.windows.WCanvasPeer::shouldClearRectBeforePaint (5 bytes)
Event: 17.715 Thread 0x000000928492b800 nmethod 5519 0x0000009ad4626210 code [0x0000009ad46263c0, 0x0000009ad4626478]
Event: 17.723 Thread 0x0000009b30273800 5520       3       net.imglib2.type.numeric.integer.UnsignedShortLongAccessType::duplicateTypeOnSameNativeImg (5 bytes)
Event: 17.723 Thread 0x000000928492b800 5521       3       net.imglib2.converter.readwrite.WriteConvertedIterableRandomAccessibleInterval$$Lambda$273/0x00000008004fd840::get (8 bytes)
Event: 17.723 Thread 0x000000928492b800 nmethod 5521 0x0000009acd89ae90 code [0x0000009acd89b040, 0x0000009acd89b198]
Event: 17.723 Thread 0x000000928492b800 5522       3       net.imglib2.converter.readwrite.WriteConvertedIterableRandomAccessibleInterval::lambda$new$0 (2 bytes)

GC Heap History (20 events):
Event: 2.652 GC heap before
{Heap before GC invocations=18 (full 11):
 garbage-first heap   total 110592K, used 85560K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 14 young (57344K), 0 survivors (0K)
 Metaspace       used 20258K, capacity 20582K, committed 20864K, reserved 1067008K
  class space    used 2513K, capacity 2632K, committed 2688K, reserved 1048576K
}
Event: 2.660 GC heap after
{Heap after GC invocations=19 (full 11):
 garbage-first heap   total 110592K, used 34927K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 2 young (8192K), 2 survivors (8192K)
 Metaspace       used 20258K, capacity 20582K, committed 20864K, reserved 1067008K
  class space    used 2513K, capacity 2632K, committed 2688K, reserved 1048576K
}
Event: 2.704 GC heap before
{Heap before GC invocations=19 (full 11):
 garbage-first heap   total 110592K, used 67695K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 11 young (45056K), 2 survivors (8192K)
 Metaspace       used 20258K, capacity 20582K, committed 20864K, reserved 1067008K
  class space    used 2513K, capacity 2632K, committed 2688K, reserved 1048576K
}
Event: 2.776 GC heap after
{Heap after GC invocations=20 (full 12):
 garbage-first heap   total 110592K, used 43528K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 0 young (0K), 0 survivors (0K)
 Metaspace       used 20258K, capacity 20582K, committed 20864K, reserved 1067008K
  class space    used 2513K, capacity 2632K, committed 2688K, reserved 1048576K
}
Event: 2.872 GC heap before
{Heap before GC invocations=20 (full 12):
 garbage-first heap   total 110592K, used 88584K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 11 young (45056K), 0 survivors (0K)
 Metaspace       used 20264K, capacity 20582K, committed 20864K, reserved 1067008K
  class space    used 2513K, capacity 2632K, committed 2688K, reserved 1048576K
}
Event: 2.891 GC heap after
{Heap after GC invocations=21 (full 12):
 garbage-first heap   total 110592K, used 62912K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 2 young (8192K), 2 survivors (8192K)
 Metaspace       used 20264K, capacity 20582K, committed 20864K, reserved 1067008K
  class space    used 2513K, capacity 2632K, committed 2688K, reserved 1048576K
}
Event: 2.909 GC heap before
{Heap before GC invocations=21 (full 12):
 garbage-first heap   total 110592K, used 75200K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 5 young (20480K), 2 survivors (8192K)
 Metaspace       used 20264K, capacity 20582K, committed 20864K, reserved 1067008K
  class space    used 2513K, capacity 2632K, committed 2688K, reserved 1048576K
}
Event: 2.917 GC heap after
{Heap after GC invocations=22 (full 12):
 garbage-first heap   total 110592K, used 64721K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 1 young (4096K), 1 survivors (4096K)
 Metaspace       used 20264K, capacity 20582K, committed 20864K, reserved 1067008K
  class space    used 2513K, capacity 2632K, committed 2688K, reserved 1048576K
}
Event: 2.935 GC heap before
{Heap before GC invocations=22 (full 12):
 garbage-first heap   total 110592K, used 68817K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 3 young (12288K), 1 survivors (4096K)
 Metaspace       used 20264K, capacity 20582K, committed 20864K, reserved 1067008K
  class space    used 2513K, capacity 2632K, committed 2688K, reserved 1048576K
}
Event: 3.010 GC heap after
{Heap after GC invocations=23 (full 13):
 garbage-first heap   total 110592K, used 47423K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 0 young (0K), 0 survivors (0K)
 Metaspace       used 20264K, capacity 20582K, committed 20864K, reserved 1067008K
  class space    used 2513K, capacity 2632K, committed 2688K, reserved 1048576K
}
Event: 3.177 GC heap before
{Heap before GC invocations=23 (full 13):
 garbage-first heap   total 110592K, used 67903K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 5 young (20480K), 0 survivors (0K)
 Metaspace       used 21127K, capacity 21389K, committed 21504K, reserved 1069056K
  class space    used 2589K, capacity 2710K, committed 2816K, reserved 1048576K
}
Event: 3.184 GC heap after
{Heap after GC invocations=24 (full 13):
 garbage-first heap   total 1105920K, used 47818K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 1 young (4096K), 1 survivors (4096K)
 Metaspace       used 21127K, capacity 21389K, committed 21504K, reserved 1069056K
  class space    used 2589K, capacity 2710K, committed 2816K, reserved 1048576K
}
Event: 3.915 GC heap before
{Heap before GC invocations=24 (full 13):
 garbage-first heap   total 1105920K, used 88778K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 12 young (49152K), 1 survivors (4096K)
 Metaspace       used 33907K, capacity 34549K, committed 34776K, reserved 1079296K
  class space    used 4073K, capacity 4339K, committed 4352K, reserved 1048576K
}
Event: 3.922 GC heap after
{Heap after GC invocations=25 (full 13):
 garbage-first heap   total 1105920K, used 51824K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 2 young (8192K), 2 survivors (8192K)
 Metaspace       used 33907K, capacity 34549K, committed 34776K, reserved 1079296K
  class space    used 4073K, capacity 4339K, committed 4352K, reserved 1048576K
}
Event: 3.962 GC heap before
{Heap before GC invocations=26 (full 13):
 garbage-first heap   total 1105920K, used 43632K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 3 young (12288K), 2 survivors (8192K)
 Metaspace       used 34166K, capacity 34775K, committed 34904K, reserved 1079296K
  class space    used 4161K, capacity 4436K, committed 4480K, reserved 1048576K
}
Event: 3.995 GC heap after
{Heap after GC invocations=27 (full 14):
 garbage-first heap   total 163840K, used 23556K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 0 young (0K), 0 survivors (0K)
 Metaspace       used 34166K, capacity 34775K, committed 34904K, reserved 1079296K
  class space    used 4161K, capacity 4436K, committed 4480K, reserved 1048576K
}
Event: 4.815 GC heap before
{Heap before GC invocations=27 (full 14):
 garbage-first heap   total 163840K, used 72708K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 13 young (53248K), 0 survivors (0K)
 Metaspace       used 43725K, capacity 44533K, committed 44632K, reserved 1087488K
  class space    used 5699K, capacity 5999K, committed 6016K, reserved 1048576K
}
Event: 4.817 GC heap after
{Heap after GC invocations=28 (full 14):
 garbage-first heap   total 163840K, used 29415K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 2 young (8192K), 2 survivors (8192K)
 Metaspace       used 43725K, capacity 44533K, committed 44632K, reserved 1087488K
  class space    used 5699K, capacity 5999K, committed 6016K, reserved 1048576K
}
Event: 4.864 GC heap before
{Heap before GC invocations=28 (full 14):
 garbage-first heap   total 163840K, used 37607K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 5 young (20480K), 2 survivors (8192K)
 Metaspace       used 43846K, capacity 44667K, committed 44888K, reserved 1087488K
  class space    used 5708K, capacity 6001K, committed 6016K, reserved 1048576K
}
Event: 4.899 GC heap after
{Heap after GC invocations=29 (full 15):
 garbage-first heap   total 122880K, used 30629K [0x0000000082000000, 0x0000000800000000)
  region size 4096K, 0 young (0K), 0 survivors (0K)
 Metaspace       used 43846K, capacity 44667K, committed 44888K, reserved 1087488K
  class space    used 5708K, capacity 6001K, committed 6016K, reserved 1048576K
}

Deoptimization events (20 events):
Event: 11.475 Thread 0x0000009b30273000 Uncommon trap: trap_request=0xffffffde fr.pc=0x0000009ad44640a4 relative=0x0000000000001304
Event: 11.475 Thread 0x0000009b30273000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x0000009ad44640a4 method=net.imglib2.display.projector.IterableIntervalProjector2D.map()V @ 378 c2
Event: 11.475 Thread 0x0000009b30273000 DEOPT PACKING pc=0x0000009ad44640a4 sp=0x0000009b3273f110
Event: 11.475 Thread 0x0000009b30273000 DEOPT UNPACKING pc=0x0000009acc79772f sp=0x0000009b3273f098 mode 2
Event: 12.071 Thread 0x0000009b30273000 Uncommon trap: trap_request=0xffffffde fr.pc=0x0000009ad44640a4 relative=0x0000000000001304
Event: 12.071 Thread 0x0000009b30273000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x0000009ad44640a4 method=net.imglib2.display.projector.IterableIntervalProjector2D.map()V @ 378 c2
Event: 12.071 Thread 0x0000009b30273000 DEOPT PACKING pc=0x0000009ad44640a4 sp=0x0000009b3273f110
Event: 12.071 Thread 0x0000009b30273000 DEOPT UNPACKING pc=0x0000009acc79772f sp=0x0000009b3273f098 mode 2
Event: 13.110 Thread 0x0000009b30273000 Uncommon trap: trap_request=0xffffffde fr.pc=0x0000009ad44640a4 relative=0x0000000000001304
Event: 13.110 Thread 0x0000009b30273000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x0000009ad44640a4 method=net.imglib2.display.projector.IterableIntervalProjector2D.map()V @ 378 c2
Event: 13.110 Thread 0x0000009b30273000 DEOPT PACKING pc=0x0000009ad44640a4 sp=0x0000009b3273f110
Event: 13.110 Thread 0x0000009b30273000 DEOPT UNPACKING pc=0x0000009acc79772f sp=0x0000009b3273f098 mode 2
Event: 13.496 Thread 0x0000009b30273000 Uncommon trap: trap_request=0xffffffde fr.pc=0x0000009ad44640a4 relative=0x0000000000001304
Event: 13.496 Thread 0x0000009b30273000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x0000009ad44640a4 method=net.imglib2.display.projector.IterableIntervalProjector2D.map()V @ 378 c2
Event: 13.496 Thread 0x0000009b30273000 DEOPT PACKING pc=0x0000009ad44640a4 sp=0x0000009b3273f110
Event: 13.496 Thread 0x0000009b30273000 DEOPT UNPACKING pc=0x0000009acc79772f sp=0x0000009b3273f098 mode 2
Event: 17.541 Thread 0x0000009b30273000 Uncommon trap: trap_request=0xffffff4d fr.pc=0x0000009ad44af974 relative=0x00000000000001b4
Event: 17.541 Thread 0x0000009b30273000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000009ad44af974 method=java.util.concurrent.locks.ReentrantLock$Sync.nonfairTryAcquire(I)Z @ 19 c2
Event: 17.541 Thread 0x0000009b30273000 DEOPT PACKING pc=0x0000009ad44af974 sp=0x0000009b3273ef30
Event: 17.541 Thread 0x0000009b30273000 DEOPT UNPACKING pc=0x0000009acc79772f sp=0x0000009b3273ed98 mode 2

Classes redefined (0 events):
No events

Internal exceptions (20 events):
Event: 3.600 Thread 0x0000009291207800 Exception <a 'java/lang/NoSuchMethodError'{0x00000000c4129a68}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, int, int, int, int)'> (0x00000000c4129a68) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 3.600 Thread 0x0000009291207800 Exception <a 'java/lang/NoSuchMethodError'{0x00000000c412cb90}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeStaticInit(java.lang.Object, int, int, int, int)'> (0x00000000c412cb90) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 3.653 Thread 0x0000009291207800 Exception <a 'java/lang/NoSuchMethodError'{0x00000000c41475d8}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, java.lang.Object, int, int, int, int)'> (0x00000000c41475d8) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 3.653 Thread 0x0000009291207800 Exception <a 'java/lang/NoSuchMethodError'{0x00000000c414a930}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeStaticInit(java.lang.Object, java.lang.Object, int, int, int, int)'> (0x00000000c414a930) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 3.698 Thread 0x0000009291207800 Exception <a 'java/lang/NoSuchMethodError'{0x00000000c42d58f8}: 'int java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object)'> (0x00000000c42d58f8) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 3.808 Thread 0x0000009291207800 Implicit null exception at 0x0000009ad4449ccc to 0x0000009ad4449ec4
Event: 3.808 Thread 0x0000009291207800 Implicit null exception at 0x0000009ad441becc to 0x0000009ad441c0c4
Event: 3.958 Thread 0x0000009291207800 Exception <a 'java/lang/NoClassDefFoundError'{0x00000000c55affa8}: jupyter/Displayer> (0x00000000c55affa8) thrown at [./src/hotspot/share/classfile/systemDictionary.cpp, line 223]
Event: 4.098 Thread 0x0000009291207800 Exception <a 'java/lang/NoSuchMethodError'{0x000000008b9d5d78}: 'void java.lang.invoke.DirectMethodHandle$Holder.invokeStaticInit(java.lang.Object)'> (0x000000008b9d5d78) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 4.104 Thread 0x0000009291207800 Exception <a 'java/lang/NoSuchMethodError'{0x000000008bad7848}: 'java.lang.Object java.lang.invoke.Invokers$Holder.linkToTargetMethod(java.lang.Object, int, java.lang.Object)'> (0x000000008bad7848) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 4.110 Thread 0x0000009291207800 Exception <a 'java/lang/ClassNotFoundException'{0x000000008baeaaa8}: sun/awt/windows/spi/awtLocalizationProvider> (0x000000008baeaaa8) thrown at [./src/hotspot/share/classfile/systemDictionary.cpp, line 234]
Event: 4.140 Thread 0x0000009284938800 Implicit null exception at 0x0000009ad466880b to 0x0000009ad46688f8
Event: 4.261 Thread 0x0000009291207800 Implicit null exception at 0x0000009ad43c7674 to 0x0000009ad43c78a0
Event: 4.354 Thread 0x0000009291207800 Exception <a 'java/lang/NoSuchMethodError'{0x000000008b3a6e98}: 'void java.lang.invoke.DirectMethodHandle$Holder.invokeSpecial(java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object)'> (0x000000008b3a6e98) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 4.367 Thread 0x0000009291207800 Exception <a 'java/lang/NoSuchMethodError'{0x000000008ac6ed10}: 'void java.lang.invoke.DirectMethodHandle$Holder.invokeVirtual(java.lang.Object, java.lang.Object)'> (0x000000008ac6ed10) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 5.017 Thread 0x0000009284936000 Exception <a 'java/lang/NoSuchMethodError'{0x00000000888d26d0}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeVirtual(java.lang.Object, java.lang.Object, int)'> (0x00000000888d26d0) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 5.019 Thread 0x0000009284936000 Exception <a 'java/lang/NoSuchMethodError'{0x00000000888e7070}: 'java.lang.Object java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, java.lang.Object, java.lang.Object, int)'> (0x00000000888e7070) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 5.026 Thread 0x0000009284936000 Exception <a 'java/lang/IncompatibleClassChangeError'{0x000000008896b410}: Found class java.lang.Object, but interface was expected> (0x000000008896b410) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 839]
Event: 5.028 Thread 0x0000009284936000 Exception <a 'java/lang/NoSuchMethodError'{0x0000000088971818}: 'long java.lang.invoke.DirectMethodHandle$Holder.invokeStatic(java.lang.Object, long, long)'> (0x0000000088971818) thrown at [./src/hotspot/share/interpreter/linkResolver.cpp, line 773]
Event: 5.080 Thread 0x0000009284936000 Exception <a 'java/lang/ClassCastException'{0x0000000088b94c78}: class java.awt.MenuItem cannot be cast to class java.awt.CheckboxMenuItem (java.awt.MenuItem and java.awt.CheckboxMenuItem are in module java.desktop of loader 'bootstrap')> (0x0000000088b94c78) thrown at [./src/hotspot/share/interpreter/interpreterRuntime.cpp, line 474]

Events (20 events):
Event: 11.513 loading class ij/plugin/frame/ThresholdAdjuster done
Event: 11.515 loading class ij/plugin/frame/PlugInDialog
Event: 11.515 loading class ij/plugin/frame/PlugInDialog done
Event: 11.515 loading class ij/plugin/frame/ThresholdPlot
Event: 11.515 loading class ij/plugin/frame/ThresholdPlot done
Event: 11.516 loading class ij/gui/TrimmedButton
Event: 11.516 loading class ij/gui/TrimmedButton done
Event: 11.517 loading class ij/process/AutoThresholder
Event: 11.517 loading class ij/process/AutoThresholder done
Event: 11.518 loading class ij/process/AutoThresholder$Method
Event: 11.518 loading class ij/process/AutoThresholder$Method done
Event: 12.430 loading class sun/awt/windows/WScrollbarPeer$2
Event: 12.430 loading class sun/awt/windows/WScrollbarPeer$2 done
Event: 13.092 Thread 0x000000928492e000 Thread exited: 0x000000928492e000
Event: 13.147 Thread 0x0000009284929800 Thread exited: 0x0000009284929800
Event: 14.945 loading class sun/awt/image/OffScreenImage
Event: 14.945 loading class sun/awt/image/OffScreenImage done
Event: 14.959 Thread 0x0000009b30273800 Thread added: 0x0000009b30273800
Event: 14.960 Thread 0x0000009b30271000 Thread added: 0x0000009b30271000
Event: 17.539 Thread 0x0000009b30271000 Thread exited: 0x0000009b30271000


Dynamic libraries:
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0x00007ffd3ee10000 - 0x00007ffd3ee1a000 	C:\Windows\SYSTEM32\VERSION.dll
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0x00007ffd3a0f0000 - 0x00007ffd3a0f4000 	C:\ProgramData\Anaconda3\api-ms-win-crt-string-l1-1-0.dll
0x00007ffd3a0e0000 - 0x00007ffd3a0e4000 	C:\ProgramData\Anaconda3\api-ms-win-crt-convert-l1-1-0.dll
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0x00007ffd3a0c0000 - 0x00007ffd3a0c3000 	C:\ProgramData\Anaconda3\api-ms-win-crt-environment-l1-1-0.dll
0x00007ffd35ef0000 - 0x00007ffd35ef3000 	C:\ProgramData\Anaconda3\api-ms-win-crt-process-l1-1-0.dll
0x00007ffd35ee0000 - 0x00007ffd35ee3000 	C:\ProgramData\Anaconda3\api-ms-win-crt-conio-l1-1-0.dll
0x00007ffd351d0000 - 0x00007ffd351d3000 	C:\ProgramData\Anaconda3\api-ms-win-crt-filesystem-l1-1-0.dll
0x00007ffd456d0000 - 0x00007ffd4577a000 	C:\Windows\system32\msvcrt.dll
0x00007ffd45780000 - 0x00007ffd45991000 	C:\Windows\SYSTEM32\combase.dll
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0x00007ffd45120000 - 0x00007ffd4525f000 	C:\Windows\system32\RPCRT4.dll
0x00007ffd47a40000 - 0x00007ffd47a98000 	C:\Windows\SYSTEM32\sechost.dll
0x00007ffd31de0000 - 0x00007ffd31ed4000 	C:\ProgramData\Anaconda3\ucrtbase.DLL
0x00007ffd44f20000 - 0x00007ffd44f4e000 	C:\Windows\system32\SspiCli.dll
0x00007ffd453e0000 - 0x00007ffd45416000 	C:\Windows\system32\IMM32.DLL
0x00007ffd459a0000 - 0x00007ffd45af1000 	C:\Windows\system32\MSCTF.dll
0x00007ffd443d0000 - 0x00007ffd443f0000 	C:\Windows\SYSTEM32\CRYPTSP.dll
0x00007ffd44050000 - 0x00007ffd44086000 	C:\Windows\system32\rsaenh.dll
0x00007ffd44700000 - 0x00007ffd44726000 	C:\Windows\SYSTEM32\bcrypt.dll
0x00007ffd44a90000 - 0x00007ffd44a9b000 	C:\Windows\SYSTEM32\CRYPTBASE.dll
0x00007ffd44a20000 - 0x00007ffd44a83000 	C:\Windows\SYSTEM32\bcryptPrimitives.dll
0x00007ffd351c0000 - 0x00007ffd351cf000 	C:\ProgramData\Anaconda3\python3.DLL
0x00007ffcca190000 - 0x00007ffcca618000 	C:\ProgramData\Anaconda3\lib\site-packages\PyQt5\QtWidgets.pyd
0x00007ffccd960000 - 0x00007ffccdeb5000 	C:\ProgramData\Anaconda3\Library\bin\Qt5Widgets_conda.dll
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0x00007ffd45b60000 - 0x00007ffd45cf5000 	C:\Windows\system32\ole32.dll
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0x0000000000490000 - 0x000000000053b000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\liblsoda-f2.M3IWPPNXINBZ5SXPFCCGERCLVR6WHEPC.gfortran-win_amd64.dll
0x0000000000540000 - 0x000000000067b000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\libmvndst.Z2J7WCKWUL7BF3EY5COJGYWW5ABC56T7.gfortran-win_amd64.dll
0x0000000061a00000 - 0x0000000061a88000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\libnnls.CIPXREFDQXW5IC3B54ATLDPIDPDER25X.gfortran-win_amd64.dll
0x000000006d180000 - 0x000000006d1d9000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\libslsqp_op.LI3JXMZVXHIOTDMMB67NX3NO2MRTBPRU.gfortran-win_amd64.dll
0x0000000069bc0000 - 0x0000000069d39000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\libspecfun.Q33DPELISCZFCXFLNAYXILA5IGW5LOG7.gfortran-win_amd64.dll
0x0000000000680000 - 0x0000000000766000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\libvode-f2p.4E57NPHO2MA2REO3J4NBI2SU25IRYJNE.gfortran-win_amd64.dll
0x0000000070e00000 - 0x0000000070e26000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\libwrap_g77.IYQB4HJFNDDENYBLCL52NM5ZBX67SYI6.gfortran-win_amd64.dll
0x0000000062680000 - 0x00000000626ba000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\libwrap_g77.LZD3DQNKLAWECVHO6OOIWWS4RVBM4V6B.gfortran-win_amd64.dll
0x000000006bec0000 - 0x000000006c059000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\lib_arpack-.OTIAT2MCBSAO5P4Z5KD4BT6CVP5JFXUR.gfortran-win_amd64.dll
0x000000006ee80000 - 0x000000006eeb4000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\lib_blas_su.3IESECTNEJ6AD23B2LNDZLLI6H23LK6C.gfortran-win_amd64.dll
0x000000006f500000 - 0x000000006f5a3000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\lib_dop-f2p.YEMONBCO23YHB3BB4NP5S52BSU5GFDEA.gfortran-win_amd64.dll
0x0000000069380000 - 0x0000000069402000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\.libs\lib_test_fo.4XAR4HZBYUDUUMLVXXYLWXLONYNLTO4M.gfortran-win_amd64.dll
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0x00007ffcecfa0000 - 0x00007ffced01f000 	C:\ProgramData\Anaconda3\lib\site-packages\scipy\sparse\_csparsetools.cp38-win_amd64.pyd

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Environment Variables:
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USERNAME=oamsalem
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---------------  S Y S T E M  ---------------

OS: Windows Server 2012 R2 , 64 bit Build 9600 (6.3.9600.19843)
OS uptime: 6 days 22:52 hours
HyperV virtualization detected

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current process commit charge ("private bytes"): 33974M, peak: 67122M

vm_info: OpenJDK 64-Bit Server VM (11.0.9.1+1-LTS) for windows-amd64 JRE (Zulu11.43+55-CA) (11.0.9.1+1-LTS), built on Nov  5 2020 09:18:55 by "zulu_re" with MS VC++ 15.9 (VS2017)

END.

I get similar errors both in Linux and in Windows.
Any tips?
Thanks

[elevans]

@orena1 Hello!

I just tried to reproduce your error but I was unable to do so. A couple of questions:

1. How did you load your data into pyimagej? I used ij.io().open(path) to get a test file into pyimagej (returns a net.imagej.DefaultDataset) and then used ij.py.from_java(data) to get an xarray.DataArray object which wraps a numpy array.
2. The shape of your data is pretty interesting, does it normally display well in Fiji/ImageJ?

All together my code snippet that works looks like this:

import imagej

# start imagej and show UI
ij = imagej.init(headless=False)
ij.ui().showUI()

# open test image
path = "path/to/image.tif"
img = ij.io().open(path)

# convert to xarray (fancy numpy array)
img_py = ij.py.from_java(img)

# show in UI
ij.ui().show(path, ij.py.to_java(img_py))

[orena1]

thanks @elevans,
I managed to create a simple code that replicates it, I actually think its a measure of the image size (Above 4GB maybe?)

import imagej
import numpy as np
# start imagej and show UI
ij = imagej.init(headless=False)
ij.ui().showUI()

#generate random data
loaded_data = np.ones(shape=(1000,3,2,512,796)).astype(np.uint16)

# show in UI
ij.ui().show('ones', ij.py.to_java(loaded_data))

See here:

[elevans]

@orena1 Woah okay yeah this one gave me the same error you got.

# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007efeb33b2577, pid=4925, tid=0x00007efea052f700
#
# JRE version: OpenJDK Runtime Environment (Zulu 8.52.0.23-CA-linux64) (8.0_282-b08) (build 1.8.0_282-b08)
# Java VM: OpenJDK 64-Bit Server VM (25.282-b08 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# J 4670 C2 net.imglib2.display.projector.IterableIntervalProjector2D.map()V (552 bytes) @ 0x00007efeb33b2577 [0x00007efeb33b18c0+0xcb7]
#
# 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:
# /home/edward/hs_err_pid4925.log
#
# If you would like to submit a bug report, please visit:
#   http://www.azulsystems.com/support/
#
Aborted (core dumped)

Like your demonstration, I had to scroll a little bit trigger the bug.

@ctrueden Have you seen something like this before?

[elevans]

@orena1 As you noted this crash is happening when trying to access slices above a 4GB limit. Passing this array and slicing to the last slice, 880, crashes the JVM.

data = np.ones(shape=(880,3,2,512,796)).astype(np.uint16)

This traces back to a Numpy conversion in imglib2-imglyb. I'm doing some debugging and will update when I get more information.

[elevans]

Okay here's some more info on this bug and some additional poking I've done. I'll take any and all ideas!

The general process of testing was the following:

1. Perform the test condition (i.e. whats listed under Task).
2. Open the image (either large > 4GB or small < 4GB) and scrub to end of file.
3. Record result -- crash or stable?

I used 2 test files. The first is a small 2.7 GB .tif file of live microscopy data. The second is a large 8.0 GB file that I concatenated together in Fiji from other microscopy data I had and saved as a .tif file.

Here are the results:

Task	Result
Try openjdk 11.5 < 4GB	stable
Try openjdk 11.5 > 4GB	crash
Try other dtypes < 4GB	stable
Try other dtypes > 4GB	crash
Reduce numpy array dimensions to 1 channel < 4GB	stable
Reduce numpy array dimensions to 1 channel > 4GB	crash
Open > 4GB image (do not convert to DataArray)	stable
Open < 4GB image (do not convert to DataArray)	stable
Open < 4GB image and convert to DataArray (ij.py.from_java)	stable
Open > 4GB image and convert to DataArray (ij.py.from_java)	crash

The last conditions indicate to me that the issue is in numpy and not in other places I was concerned about like jpype. The JVM crash can be triggered without interacting with it by converting > 4GB data to a DataArray.

import scyjava as sj
import imagej

# start imagej
sj.config.add_option('-Xmx20g')
ij = imagej.init('sc.fiji:fiji:2.1.1', headless=False)

# get convert service and dataset class
ConvertService = ij.get('org.scijava.convert.ConvertService')
Dataset = sj.jimport('net.imagej.Dataset')
IJ = sj.jimport('ij.IJ')

# get test image
imp = IJ.openImage('img/large.tif')
img = ConvertService.convert(imp, Dataset)
img_xr = ij.py.from_java(img) # > 4GB crashes here
img_ds = ij.py.to_dataset(img_xr)

# show image
ij.ui().show(img_ds)

Thoughts?

[Thrameos]

The JVM installs signal handlers which intercept the standard core dump process and redirect so the Java can add the state to output. Unfortunately this has the side effect that a Python crash in numpy will end up dumped as a Java like error leading to confusion about the source.

The best solution I have had for this is to use the gdb debugging line in jpype/doc/develguide.rst and run Python with it. The reason for the special line is that Java deliberately causes a segmentation fault when starting to make sure its handler is installed. So you need to start the gdb to ignore the first segfault. It will then stop at the second segmentation fault and you can get a backtrace with origin of the problem. If the backtrace is in Java land then you can look over the Java log to see what frame and such. Otherwise, if it is in Python or some Python library you should see it backtrace.

Java internally only uses int for array addressing so it definitely has limits for very large images and maybe feeding bad data back so jpype may not be ruled out as a source.

I hope this helps with resolving this problem.

[ctrueden]

@elevans Could you please post the Python script we developed today? I'd like to continue whittling it down to as minimal as possible, and also play with some multithreaded access patterns on it.

[elevans]

@ctrueden Yup! Sorry I got distracted after our meeting with some other stuff. Here's the script we worked on today:

import imagej
import numpy as np
import time

# start fiji
ij = imagej.init("/home/edward/Documents/software/fiji/", headless=False)
print(f"imagej: {ij.getVersion()}")

# create data
print("creating array...")
np_data = np.ones(shape=(3,16,512,512,512), dtype=np.uint8)
pt = np_data.ctypes.data
print(f"array size: {np_data.nbytes}")
print(f"address:{pt}")

# set array values
print("setting array values...")
np_data[0, 0, 0, 0, 0] = 3
np_data[-1, -1, -1, -1, -1] = 15

# offset
g1 = (1024*1024*1024*1)
g2 = (1024*1024*1024*2)
g3 = (1024*1024*1024*3)
g4 = (1024*1024*1024*4)
offset = g4
#offset = (g2 + 3 * g1//4)
# offset = offset - 1

data = ij.py.to_dataset(np_data)
ij.ui().showUI()
ij.ui().show(data)
time.sleep(1)

# script
script = """
#@ Long pt
#@ Long offset

import java.lang.reflect.Field;
import java.security.AccessController;
import java.security.PrivilegedExceptionAction;

import sun.misc.Unsafe;

PrivilegedExceptionAction< Unsafe > action = () -> {
    final Field field = Unsafe.class.getDeclaredField( "theUnsafe" );
    field.setAccessible( true );
    return ( Unsafe ) field.get( null );
};

UNSAFE = AccessController.doPrivileged( action );

prev = -1
for(i = offset; i<offset+100; i++){
	thing = UNSAFE.getByte(pt + i)
	//if (i%2==1){
	//	if (thing != 0){
	//		println("unexpected value: " + thing + " at offset: " + i)
	//	}
	//}else{
		if (thing != prev){
			println(i+" : "+ thing)
			prev=thing
		}
	//}
}
"""

print("running script...")
ij.py.run_script("groovy", script, {"pt":pt, "offset":np_data.nbytes - 100})

time.sleep(9999999)

Just to recap I have tried to use gdb in the develguide.rst as noted by @Thrameos but it was unable to catch any meaningful traces. @ctrueden and @hinerm both helped create this more minimal example of the crash. Interacting with the numpy object from java doesn't cause a crash (i.e. reading the first and last bits of >4GB array). Wrapping it with ij.py.to_dataset(), showing it and attempting to access data beyond ~4GB crashes the JVM. Potentially this could be a result of a multi-threading issue.

[ctrueden]

I solved it. imglib/imglib2-unsafe@aa7c994

Here is a script to reproduce the problem headless:

crash.py

import os, random, time
import numpy as np
import imagej, scyjava
import imglyb

# enable remote debugging
scyjava.config.add_option('-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=localhost:8000')

# start fiji
home = os.path.expanduser("~")
ij = imagej.init(os.path.join(home, "Applications", "Fiji.app"), headless=True)
print(f"imagej: {ij.getVersion()}")

# create data
print("creating array...")
np_data = np.ones(shape=(3,16,512,512,512), dtype=np.uint8)
address = np_data.ctypes.data
address_end = address + np_data.nbytes
print(f"array size: {np_data.nbytes}")
print(f"addresses: {address} until {address_end}")

# set array values
print("setting array values...")
np_data[0, 0, 0, 0, 0] = 3
np_data[-1, -1, -1, -1, -1] = 15
print(f'First slice -> {np_data[:,0,0,0,0]}')
print(f'Final slice -> {np_data[:,-1,-1,-1,-1]}')

# offset
g1 = 1024*1024*1024
g2 = 2*g1
g3 = 3*g1
g4 = 4*g1
offset = g4

data = imglyb.to_imglib(np_data)

#data = ij.py.to_dataset(np_data)
#print(type(data.firstElement()))
#imgPlus = data.getImgPlus()
#print(type(imgPlus.firstElement()))
#img = imgPlus.getImg()
#print(type(img.firstElement()))

Intervals = scyjava.jimport('net.imglib2.util.Intervals')
dims = Intervals.dimensionsAsLongArray(data)
pos = dims.clone()

for i in range(10000000):
    for d in range(len(dims)):
        pos[d] = random.randint(0, dims[d] - 1)
    value = data.getAt(pos)
    if i == 0: print(f'{value.getClass().getName()}')
    if i % 100000 == 0: print(f'{pos} == {value}')

Here is a patch to imglib2-unsafe I used while I was digging:

git diff

diff --git a/src/main/java/net/imglib2/img/basictypelongaccess/unsafe/ByteUnsafe.java b/src/main/java/net/imglib2/img/basictypelongaccess/unsafe/ByteUnsafe.java
index 44fa976..b28b2ad 100644
--- a/src/main/java/net/imglib2/img/basictypelongaccess/unsafe/ByteUnsafe.java
+++ b/src/main/java/net/imglib2/img/basictypelongaccess/unsafe/ByteUnsafe.java
@@ -36,6 +36,7 @@ public class ByteUnsafe implements ByteLongAccess, VolatileByteAccess
        private static final boolean DEFAULT_IS_VALID = true;
 
        private final long address;
+       private long numElements = -1;
 
        private final Object ownerReference;
 
@@ -46,6 +47,12 @@ public class ByteUnsafe implements ByteLongAccess, VolatileByteAccess
                this( address, null );
        }
 
+       public ByteUnsafe( final long address, final long numElements )
+       {
+               this( address, null );
+               this.numElements = numElements;
+       }
+
        public ByteUnsafe( final long address, final boolean isValid )
        {
                this( address, null, isValid );
@@ -79,6 +86,11 @@ public class ByteUnsafe implements ByteLongAccess, VolatileByteAccess
        @Override
        public byte getValue( final long index )
        {
+               if (index < 0 || index >= numElements) {
+                       new Exception("[ByteUnsafe] " + index + " OUT OF BOUNDS [0, " + numElements + "]").printStackTrace();
+                       return 0;
+               }
+
                return UnsafeUtil.UNSAFE.getByte( address + index );
        }
 
diff --git a/src/main/java/net/imglib2/type/numeric/integer/GenericByteLongAccessType.java b/src/main/java/net/imglib2/type/numeric/integer/GenericByteLongAccessType.java
index 1d67b57..ccbce3c 100644
--- a/src/main/java/net/imglib2/type/numeric/integer/GenericByteLongAccessType.java
+++ b/src/main/java/net/imglib2/type/numeric/integer/GenericByteLongAccessType.java
@@ -196,6 +196,9 @@ public abstract class GenericByteLongAccessType< T extends GenericByteLongAccess
        @Override
        public void updateIndex( final long index )
        {
+               if (index < 0) {
+                       new Exception("WTF").printStackTrace();
+               }
                i = index;
        }

And then in NumpyToImgLibConversions in imglib2-imglyb, pass numElements accordingly.

Then set imglib2-unsafe and imglib2-imglyb to version 999 and mvn installed them, and copied them into my local Fiji.app/jars folder. Then in a local clone of fiji/fiji, I added dependencies on imglib2-unsafe and imglib2-imglyb at version 999.

Then I added the following line to the Python script:

scyjava.config.add_option('-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=localhost:8000')

Then in Eclipse, I imported my fiji/fiji, opened GenericByteLongAccessType.class and ByteUnsafe.class via ctrl+shift+T, navigated to the new Exception lines I added, set breakpoints there. Then right-clicked fiji in the Project Explorer, Debug As..., Debug Configurations, Remote Java Application, clicked the new/plus icon on the toolbar, named it "fiji [Remote]", leaving everything else default but don't close the dialog box.

Then on the command line, launched crash.py and it starts going, but waits upon JVM startup for Eclipse to connect. Jump back to Eclipse, click the Debug button from the Debug Configurations dialog box. It connects.

In my case, it then paused a thread due to a ClassNotFoundException, so I had to click the green pause/play icon on the toolbar once to move past that, at which point, I started hitting the new Exception breakpoints and could inspect the state of the program. This led me to understand that the problem was in UnsafeRandomAccess.

[orena1]

Thanks for the fix @ctrueden, any idea when I can use it in production (upgrade using pip install?).

[imagejan]

@orena1 as far as I can tell, the following steps are required:

• cut a new release 0.4.1 of imglib2-unsafe,
• in imglib2-imglyb, bump the imglib2-unsafe dependency version to that newly released version (ideally via a version update in the parent POM, pom-scijava),
• cut a new release 1.0.1 of imglib2-imglyb
• in imglyb, bump the imglib2-imglyb dependency version to that newly released version, and finally
• use that new imglyb version in pyimagej.

[orena1]

Thanks, so 6 months ;-)