#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x0000000129be645f, pid=28190, tid=0x000000000000eb07
#
# JRE version: Java(TM) SE Runtime Environment (8.0_144-b01) (build 1.8.0_144-b01)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.144-b01 mixed mode bsd-amd64 compressed oops)
# Problematic frame:
# C [libawt_lwawt.dylib+0x1c45f] OGLSD_SetScratchSurface+0x49
#
# 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 (0x00007fb7d6a28000): JavaThread "Java2D Queue Flusher" daemon [_thread_in_native, id=60167, stack(0x000070000a322000,0x000070000a422000)]
siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x0000000000000002
Registers:
RAX=0x0000000129c06d0e, RBX=0x0000000000000002, RCX=0x0000000000000047, RDX=0x0000000129c07258
RSP=0x000070000a421730, RBP=0x000070000a421750, RSI=0x00007fb7dc2381e0, RDI=0x00007fb7d6a281f8
R8 =0x00000000000002d5, R9 =0x000000000190822f, R10=0x000000010e0ee8f8, R11=0x000000010e6e8100
R12=0x0000000000000000, R13=0x000070000a4218e8, R14=0x00007fb7d6a281f8, R15=0x00007fb7d6a28000
RIP=0x0000000129be645f, EFLAGS=0x0000000000010202, ERR=0x0000000000000004
TRAPNO=0x000000000000000e
Top of Stack: (sp=0x000070000a421730)
0x000070000a421730: 00007fb7dc2381e0 0000000000000000
0x000070000a421740: 00007fb7d6a5d610 00007fb7d6a28000
0x000070000a421750: 000070000a4217d0 0000000129c06d36
0x000070000a421760: 00007fb7d648b700 0000000200000001
0x000070000a421770: 0000000000000000 000070000a421800
0x000070000a421780: 0000000000000000 0000000000000000
0x000070000a421790: 000070000a4217d0 00007fb7d6a5d620
0x000070000a4217a0: 00000000005effd0 00007fb7d6a281f8
0x000070000a4217b0: 000000016d2bc370 0000000000000000
0x000070000a4217c0: 000070000a421968 00007fb7d6a28000
0x000070000a4217d0: 000070000a421820 000000010e0ee96a
0x000070000a4217e0: 00000006c00a3af8 000000010d138a00
0x000070000a4217f0: 0000000000000064 0000000000000000
0x000070000a421800: 0000000000000064 00007fb7d648b1e8
0x000070000a421810: 000070000a421870 000000010cf501e8
0x000070000a421820: 000070000a421940 000000010e6e86fc
0x000070000a421830: 0000000000000001 00007fb7d648bea0
0x000070000a421840: 00000006c00a3b00 00007fb7d6a28000
0x000070000a421850: 00007fb7d6a28000 00000001258fda00
0x000070000a421860: 000070000a421968 00007fb7d6a28000
0x000070000a421870: 000070000a4218c0 000000010e2f2968
0x000070000a421880: 00000006c00a3af8 000000010e5aafe6
0x000070000a421890: 000070000a421940 000000010e6e815c
0x000070000a4218a0: 000000012f278bb4 000070000a4218e8
0x000070000a4218b0: 000000012f278c30 0000000000000000
0x000070000a4218c0: 000070000a421940 000000010dbaf2bd
0x000070000a4218d0: 000070000a421940 000000010dbaf2bd
0x000070000a4218e0: 000000010dbaf2bd 00000006c00a3af8
0x000070000a4218f0: 0000000000000001 00000006c00a3b80
0x000070000a421900: 000070000a4218f0 000000012e64d689
0x000070000a421910: 000070000a421968 000000012e64d820
0x000070000a421920: 0000000000000000 000000012e64d790
Instructions: (pc=0x0000000129be645f)
0x0000000129be643f: c0 e9 82 00 00 00 48 8b 5e 10 48 85 db 75 0e bf
0x0000000129be644f: 01 00 00 00 48 8d 15 67 7b 03 00 eb d6 49 89 fe
0x0000000129be645f: 4c 8b 3b 30 c0 e8 21 a6 02 00 49 8b 3f 49 89 c4
0x0000000129be646f: 48 8b 35 aa 02 06 00 30 c0 e8 51 a7 02 00 48 85
Register to memory mapping:
RAX=0x0000000129c06d0e: Java_sun_java2d_opengl_OGLRenderQueue_flushBuffer+0x612 in /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libawt_lwawt.dylib at 0x0000000129bca000
RBX=0x0000000000000002 is an unknown value
RCX=0x0000000000000047 is an unknown value
RDX=0x0000000129c07258: Java_sun_java2d_opengl_OGLRenderQueue_flushBuffer+0xb5c in /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libawt_lwawt.dylib at 0x0000000129bca000
RSP=0x000070000a421730 is pointing into the stack for thread: 0x00007fb7d6a28000
RBP=0x000070000a421750 is pointing into the stack for thread: 0x00007fb7d6a28000
RSI=0x00007fb7dc2381e0 is an unknown value
RDI=0x00007fb7d6a281f8 is an unknown value
R8 =0x00000000000002d5 is an unknown value
R9 =0x000000000190822f is an unknown value
R10=0x000000010e0ee8f8 is at entry_point+56 in (nmethod*)0x000000010e0ee750
R11=0x000000010e6e8100 is at entry_point+0 in (nmethod*)0x000000010e6e7f90
R12=0x0000000000000000 is an unknown value
R13=0x000070000a4218e8 is pointing into the stack for thread: 0x00007fb7d6a28000
R14=0x00007fb7d6a281f8 is an unknown value
R15=0x00007fb7d6a28000 is a thread
Stack: [0x000070000a322000,0x000070000a422000], sp=0x000070000a421730, free space=1021k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [libawt_lwawt.dylib+0x1c45f] OGLSD_SetScratchSurface+0x49
C [libawt_lwawt.dylib+0x3cd36] Java_sun_java2d_opengl_OGLRenderQueue_flushBuffer+0x63a
J 4748 sun.java2d.opengl.OGLRenderQueue.flushBuffer(JI)V (0 bytes) @ 0x000000010e0ee96a [0x000000010e0ee8c0+0xaa]
J 3668 C1 sun.java2d.opengl.OGLRenderQueue.flushBuffer()V (41 bytes) @ 0x000000010e6e86fc [0x000000010e6e84a0+0x25c]
J 3667 C1 sun.java2d.opengl.OGLRenderQueue.access$100(Lsun/java2d/opengl/OGLRenderQueue;)V (5 bytes) @ 0x000000010e6e815c [0x000000010e6e8100+0x5c]
j sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run()V+81
v ~StubRoutines::call_stub
V [libjvm.dylib+0x2ee70a]
V [libjvm.dylib+0x2eeeae]
V [libjvm.dylib+0x2ef05a]
V [libjvm.dylib+0x3497b1]
V [libjvm.dylib+0x56c0b3]
V [libjvm.dylib+0x56d7a0]
V [libjvm.dylib+0x48baee]
C [libsystem_pthread.dylib+0x393b] _pthread_body+0xb4
C [libsystem_pthread.dylib+0x3887] _pthread_body+0x0
C [libsystem_pthread.dylib+0x308d] thread_start+0xd
C 0x0000000000000000
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
J 4748 sun.java2d.opengl.OGLRenderQueue.flushBuffer(JI)V (0 bytes) @ 0x000000010e0ee8f8 [0x000000010e0ee8c0+0x38]
J 3668 C1 sun.java2d.opengl.OGLRenderQueue.flushBuffer()V (41 bytes) @ 0x000000010e6e86fc [0x000000010e6e84a0+0x25c]
J 3667 C1 sun.java2d.opengl.OGLRenderQueue.access$100(Lsun/java2d/opengl/OGLRenderQueue;)V (5 bytes) @ 0x000000010e6e815c [0x000000010e6e8100+0x5c]
j sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run()V+81
v ~StubRoutines::call_stub
--------------- P R O C E S S ---------------
Java Threads: ( => current thread )
0x00007fb7d92c2000 JavaThread "class jalview.workers.ConservationThread" [_thread_in_Java, id=84243, stack(0x000070000acc0000,0x000070000adc0000)]
0x00007fb7d6c86000 JavaThread "Image Fetcher 0" daemon [_thread_blocked, id=46819, stack(0x000070000abbd000,0x000070000acbd000)]
0x00007fb7d6996800 JavaThread "LoadFileThread" [_thread_blocked, id=71699, stack(0x000070000aaba000,0x000070000abba000)]
0x00007fb7d935c800 JavaThread "TimerQueue" daemon [_thread_blocked, id=81411, stack(0x000070000b14f000,0x000070000b24f000)]
0x00007fb7d6bc7800 JavaThread "DestroyJavaVM" [_thread_blocked, id=7171, stack(0x0000700008b54000,0x0000700008c54000)]
0x00007fb7d9213800 JavaThread "pool-1-thread-1" [_thread_blocked, id=70863, stack(0x000070000a934000,0x000070000aa34000)]
0x00007fb7d7389000 JavaThread "ConsoleTextAppendThread" daemon [_thread_blocked, id=69379, stack(0x000070000a831000,0x000070000a931000)]
0x00007fb7d7388000 JavaThread "ConsoleReader2Thread" daemon [_thread_blocked, id=68867, stack(0x000070000a72e000,0x000070000a82e000)]
0x00007fb7d7387800 JavaThread "ConsoleReader1Thread" daemon [_thread_blocked, id=68363, stack(0x000070000a62b000,0x000070000a72b000)]
0x00007fb7d7344800 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=62987, stack(0x000070000a528000,0x000070000a628000)]
0x00007fb7d7313800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=62479, stack(0x000070000a425000,0x000070000a525000)]
=>0x00007fb7d6a28000 JavaThread "Java2D Queue Flusher" daemon [_thread_in_native, id=60167, stack(0x000070000a322000,0x000070000a422000)]
0x00007fb7da830800 JavaThread "AWT-Shutdown" [_thread_blocked, id=32287, stack(0x0000700009f10000,0x000070000a010000)]
0x00007fb7d69c8800 JavaThread "AppKit Thread" daemon [_thread_in_native, id=775, stack(0x00007fff54a39000,0x00007fff55239000)]
0x00007fb7d8065800 JavaThread "Service Thread" daemon [_thread_blocked, id=20995, stack(0x0000700009c87000,0x0000700009d87000)]
0x00007fb7d6800800 JavaThread "C1 CompilerThread3" daemon [_thread_blocked, id=20483, stack(0x0000700009b84000,0x0000700009c84000)]
0x00007fb7d8044800 JavaThread "C2 CompilerThread2" daemon [_thread_blocked, id=19971, stack(0x0000700009a81000,0x0000700009b81000)]
0x00007fb7d7044000 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=19459, stack(0x000070000997e000,0x0000700009a7e000)]
0x00007fb7d7011000 JavaThread "C2 CompilerThread0" daemon [_thread_in_native, id=18947, stack(0x000070000987b000,0x000070000997b000)]
0x00007fb7d702a800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=18435, stack(0x0000700009778000,0x0000700009878000)]
0x00007fb7d802a000 JavaThread "Finalizer" daemon [_thread_blocked, id=14595, stack(0x0000700009675000,0x0000700009775000)]
0x00007fb7d8027000 JavaThread "Reference Handler" daemon [_thread_blocked, id=14083, stack(0x0000700009572000,0x0000700009672000)]
Other Threads:
0x00007fb7d9012800 VMThread [stack: 0x000070000946f000,0x000070000956f000] [id=13571]
0x00007fb7d8076000 WatcherThread [stack: 0x0000700009d8a000,0x0000700009e8a000] [id=21507]
VM state:not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: None
Heap:
PSYoungGen total 86528K, used 20241K [0x000000076ab00000, 0x0000000774800000, 0x00000007c0000000)
eden space 75776K, 15% used [0x000000076ab00000,0x000000076b683258,0x000000076f500000)
from space 10752K, 78% used [0x000000076f600000,0x000000076fe413f8,0x0000000770080000)
to space 42496K, 0% used [0x0000000771e80000,0x0000000771e80000,0x0000000774800000)
ParOldGen total 209920K, used 31492K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
object space 209920K, 15% used [0x00000006c0000000,0x00000006c1ec11e8,0x00000006ccd00000)
Metaspace used 37085K, capacity 37796K, committed 38016K, reserved 1083392K
class space used 4752K, capacity 4927K, committed 4992K, reserved 1048576K
Card table byte_map: [0x000000010ae5a000,0x000000010b65b000] byte_map_base: 0x000000010785a000
Marking Bits: (ParMarkBitMap*) 0x000000010d4f35d0
Begin Bits: [0x000000011d0fd000, 0x00000001210fd000)
End Bits: [0x00000001210fd000, 0x00000001250fd000)
Polling page: 0x000000010aa87000
CodeCache: size=245760Kb used=15978Kb max_used=15978Kb free=229781Kb
bounds [0x000000010dba7000, 0x000000010eb57000, 0x000000011cba7000]
total_blobs=5726 nmethods=5006 adapters=631
compilation: enabled
Compilation events (10 events):
Event: 1054.326 Thread 0x00007fb7d8044800 nmethod 5621 0x000000010eb34b10 code [0x000000010eb34c60, 0x000000010eb34cd8]
Event: 1054.327 Thread 0x00007fb7d6800800 5622 3 javax.swing.DefaultButtonModel::isArmed (15 bytes)
Event: 1054.327 Thread 0x00007fb7d6800800 nmethod 5622 0x000000010eb343d0 code [0x000000010eb34540, 0x000000010eb346f0]
Event: 1054.346 Thread 0x00007fb7d6800800 5623 % 3 jalview.schemes.ResidueProperties::buildAmbiguityCodonSet @ 657 (878 bytes)
Event: 1054.350 Thread 0x00007fb7d6800800 nmethod 5623% 0x000000010eb34d90 code [0x000000010eb357e0, 0x000000010eb3e3f8]
Event: 1054.351 Thread 0x00007fb7d6800800 5624 3 jalview.schemes.ResidueProperties::buildAmbiguityCodonSet (878 bytes)
Event: 1054.363 Thread 0x00007fb7d6800800 nmethod 5624 0x000000010eb45590 code [0x000000010eb45fc0, 0x000000010eb4e878]
Event: 1054.363 Thread 0x00007fb7d6800800 5625 3 java.io.FileInputStream::finalize (22 bytes)
Event: 1054.363 Thread 0x00007fb7d6800800 nmethod 5625 0x000000010eb33f50 code [0x000000010eb340c0, 0x000000010eb34348]
Event: 1054.364 Thread 0x00007fb7d7011000 5626 % 4 jalview.schemes.ResidueProperties::buildAmbiguityCodonSet @ 575 (878 bytes)
GC Heap History (10 events):
Event: 8.499 GC heap before
{Heap before GC invocations=3 (full 1):
PSYoungGen total 76288K, used 65536K [0x000000076ab00000, 0x0000000770000000, 0x00000007c0000000)
eden space 65536K, 100% used [0x000000076ab00000,0x000000076eb00000,0x000000076eb00000)
from space 10752K, 0% used [0x000000076eb00000,0x000000076eb00000,0x000000076f580000)
to space 10752K, 0% used [0x000000076f580000,0x000000076f580000,0x0000000770000000)
ParOldGen total 121856K, used 7919K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
object space 121856K, 6% used [0x00000006c0000000,0x00000006c07bbd10,0x00000006c7700000)
Metaspace used 32188K, capacity 32772K, committed 33024K, reserved 1077248K
class space used 4214K, capacity 4351K, committed 4352K, reserved 1048576K
Event: 8.510 GC heap after
Heap after GC invocations=3 (full 1):
PSYoungGen total 76288K, used 10746K [0x000000076ab00000, 0x0000000770d80000, 0x00000007c0000000)
eden space 65536K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076eb00000)
from space 10752K, 99% used [0x000000076f580000,0x000000076fffe850,0x0000000770000000)
to space 10752K, 0% used [0x000000076eb00000,0x000000076eb00000,0x000000076f580000)
ParOldGen total 121856K, used 24160K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
object space 121856K, 19% used [0x00000006c0000000,0x00000006c17980a8,0x00000006c7700000)
Metaspace used 32188K, capacity 32772K, committed 33024K, reserved 1077248K
class space used 4214K, capacity 4351K, committed 4352K, reserved 1048576K
}
Event: 28.095 GC heap before
{Heap before GC invocations=4 (full 1):
PSYoungGen total 76288K, used 76282K [0x000000076ab00000, 0x0000000770d80000, 0x00000007c0000000)
eden space 65536K, 100% used [0x000000076ab00000,0x000000076eb00000,0x000000076eb00000)
from space 10752K, 99% used [0x000000076f580000,0x000000076fffe850,0x0000000770000000)
to space 10752K, 0% used [0x000000076eb00000,0x000000076eb00000,0x000000076f580000)
ParOldGen total 121856K, used 24160K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
object space 121856K, 19% used [0x00000006c0000000,0x00000006c17980a8,0x00000006c7700000)
Metaspace used 34471K, capacity 35178K, committed 35456K, reserved 1079296K
class space used 4439K, capacity 4626K, committed 4736K, reserved 1048576K
Event: 28.111 GC heap after
Heap after GC invocations=4 (full 1):
PSYoungGen total 76288K, used 10746K [0x000000076ab00000, 0x0000000770b00000, 0x00000007c0000000)
eden space 65536K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076eb00000)
from space 10752K, 99% used [0x000000076eb00000,0x000000076f57e870,0x000000076f580000)
to space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
ParOldGen total 121856K, used 49145K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
object space 121856K, 40% used [0x00000006c0000000,0x00000006c2ffe560,0x00000006c7700000)
Metaspace used 34471K, capacity 35178K, committed 35456K, reserved 1079296K
class space used 4439K, capacity 4626K, committed 4736K, reserved 1048576K
}
Event: 28.286 GC heap before
{Heap before GC invocations=5 (full 1):
PSYoungGen total 76288K, used 21665K [0x000000076ab00000, 0x0000000770b00000, 0x00000007c0000000)
eden space 65536K, 16% used [0x000000076ab00000,0x000000076b5a9db8,0x000000076eb00000)
from space 10752K, 99% used [0x000000076eb00000,0x000000076f57e870,0x000000076f580000)
to space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
ParOldGen total 121856K, used 49145K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
object space 121856K, 40% used [0x00000006c0000000,0x00000006c2ffe560,0x00000006c7700000)
Metaspace used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
class space used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
Event: 28.293 GC heap after
Heap after GC invocations=5 (full 1):
PSYoungGen total 87552K, used 10724K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
eden space 76800K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f600000)
from space 10752K, 99% used [0x0000000770080000,0x0000000770af9260,0x0000000770b00000)
to space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
ParOldGen total 121856K, used 50465K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
object space 121856K, 41% used [0x00000006c0000000,0x00000006c3148700,0x00000006c7700000)
Metaspace used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
class space used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
}
Event: 28.293 GC heap before
{Heap before GC invocations=6 (full 2):
PSYoungGen total 87552K, used 10724K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
eden space 76800K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f600000)
from space 10752K, 99% used [0x0000000770080000,0x0000000770af9260,0x0000000770b00000)
to space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
ParOldGen total 121856K, used 50465K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
object space 121856K, 41% used [0x00000006c0000000,0x00000006c3148700,0x00000006c7700000)
Metaspace used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
class space used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
Event: 28.336 GC heap after
Heap after GC invocations=6 (full 2):
PSYoungGen total 87552K, used 0K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
eden space 76800K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f600000)
from space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
to space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
ParOldGen total 209920K, used 22383K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
object space 209920K, 10% used [0x00000006c0000000,0x00000006c15dbcc8,0x00000006ccd00000)
Metaspace used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
class space used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
}
Event: 1054.355 GC heap before
{Heap before GC invocations=7 (full 2):
PSYoungGen total 87552K, used 76800K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
eden space 76800K, 100% used [0x000000076ab00000,0x000000076f600000,0x000000076f600000)
from space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
to space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
ParOldGen total 209920K, used 22383K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
object space 209920K, 10% used [0x00000006c0000000,0x00000006c15dbcc8,0x00000006ccd00000)
Metaspace used 37084K, capacity 37796K, committed 38016K, reserved 1083392K
class space used 4752K, capacity 4927K, committed 4992K, reserved 1048576K
Event: 1054.361 GC heap after
Heap after GC invocations=7 (full 2):
PSYoungGen total 86528K, used 8452K [0x000000076ab00000, 0x0000000774800000, 0x00000007c0000000)
eden space 75776K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f500000)
from space 10752K, 78% used [0x000000076f600000,0x000000076fe413f8,0x0000000770080000)
to space 42496K, 0% used [0x0000000771e80000,0x0000000771e80000,0x0000000774800000)
ParOldGen total 209920K, used 31492K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
object space 209920K, 15% used [0x00000006c0000000,0x00000006c1ec11e8,0x00000006ccd00000)
Metaspace used 37084K, capacity 37796K, committed 38016K, reserved 1083392K
class space used 4752K, capacity 4927K, committed 4992K, reserved 1048576K
}
Deoptimization events (10 events):
Event: 1012.924 Thread 0x00007fb7d7344800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010e9f3390 method=java.awt.LightweightDispatcher.processMouseEvent(Ljava/awt/event/MouseEvent;)Z @ 52
Event: 1047.684 Thread 0x00007fb7d7344800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010dd0e4a4 method=java.awt.font.FontRenderContext.equals(Ljava/awt/font/FontRenderContext;)Z @ 53
Event: 1054.165 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010dd0ceac method=java.awt.EventQueue.setCurrentEventAndMostRecentTimeImpl(Ljava/awt/AWTEvent;)V @ 16
Event: 1054.205 Thread 0x00007fb7d6996800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010e197614 method=java.util.regex.Matcher.search(I)Z @ 86
Event: 1054.205 Thread 0x00007fb7d6996800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010e197614 method=java.util.regex.Matcher.search(I)Z @ 86
Event: 1054.298 Thread 0x00007fb7d6996800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010eacccb4 method=sun.java2d.loops.SurfaceType.pixelFor(ILjava/awt/image/ColorModel;)I @ 6
Event: 1054.306 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010e19b9d4 method=java.awt.Component.isShowing()Z @ 20
Event: 1054.306 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010ea97958 method=javax.swing.RepaintManager.addDirtyRegion0(Ljava/awt/Container;IIII)V @ 53
Event: 1054.306 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010ea60790 method=javax.swing.RepaintManager.addDirtyRegion0(Ljava/awt/Container;IIII)V @ 53
Event: 1054.306 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010ea46b30 method=javax.swing.RepaintManager.addDirtyRegion0(Ljava/awt/Container;IIII)V @ 53
Internal exceptions (10 events):
Event: 23.206 Thread 0x00007fb7d98fb800 Exception (0x000000076e381ed8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
Event: 23.208 Thread 0x00007fb7d98fb800 Exception (0x000000076e3d4c68) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/prims/jni.cpp, line 709]
Event: 23.492 Thread 0x00007fb7d98fb800 Exception (0x000000076e616378) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
Event: 23.495 Thread 0x00007fb7d98fb800 Exception (0x000000076e69f500) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
Event: 23.718 Thread 0x00007fb7d98fb800 Exception (0x000000076e722190) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
Event: 23.719 Thread 0x00007fb7d98fb800 Exception (0x000000076e772ab8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/prims/jni.cpp, line 709]
Event: 23.847 Thread 0x00007fb7d98fb800 Exception (0x000000076e9b3cd8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
Event: 23.850 Thread 0x00007fb7d98fb800 Exception (0x000000076ea3ab10) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
Event: 28.222 Thread 0x00007fb7d68ba800 Exception (0x000000076b08b318) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/prims/jni.cpp, line 709]
Event: 1047.684 Thread 0x00007fb7d7344800 Implicit null exception at 0x000000010dd0e2c2 to 0x000000010dd0e48d
Events (10 events):
Event: 1054.333 loading class jalview/schemes/RNAHelicesColour
Event: 1054.333 loading class jalview/schemes/RNAHelicesColour done
Event: 1054.334 loading class jalview/schemes/TCoffeeColourScheme
Event: 1054.334 loading class jalview/schemes/TCoffeeColourScheme done
Event: 1054.335 loading class jalview/schemes/Consensus
Event: 1054.335 loading class jalview/schemes/Consensus done
Event: 1054.335 loading class jalview/api/analysis/PairwiseScoreModelI
Event: 1054.335 loading class jalview/api/analysis/PairwiseScoreModelI done
Event: 1054.355 Executing VM operation: ParallelGCFailedAllocation
Event: 1054.361 Executing VM operation: ParallelGCFailedAllocation done
Dynamic libraries:
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0x0000000127bc4000 /System/Library/PrivateFrameworks/JavaLaunching.framework/Versions/A/JavaLaunching
0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels
0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help
0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
0x0000000129a56000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libawt.dylib
0x0000000129afe000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/./libmlib_image.dylib
0x0000000129bca000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libawt_lwawt.dylib
0x0000000129c81000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/./libosxapp.dylib
0x000000004dd98000 /System/Library/Frameworks/ExceptionHandling.framework/Versions/A/ExceptionHandling
0x000000004dd98000 /System/Library/PrivateFrameworks/CoreServicesInternal.framework/Versions/A/CoreServicesInternal
0x000000004dd98000 /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libTrueTypeScaler.dylib
0x000000012bcdb000 /System/Library/Frameworks/OpenGL.framework/Resources/GLEngine.bundle/GLEngine
0x000000004dd98000 /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x000000012bec0000 /System/Library/Extensions/AppleIntelHD5000GraphicsGLDriver.bundle/Contents/MacOS/AppleIntelHD5000GraphicsGLDriver
0x000000004dd98000 /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib
0x000000004dd98000 /System/Library/Extensions/GeForceGLDriver.bundle/Contents/MacOS/GeForceGLDriver
0x000000004dd98000 /System/Library/Extensions/GeForceGLDriver.bundle/Contents/MacOS/libclh.dylib
0x000000012a6a7000 /System/Library/Frameworks/OpenGL.framework/Resources//GLRendererFloat.bundle/GLRendererFloat
0x000000004dd98000 /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libcldcpuengine.dylib
0x000000004dd98000 /usr/lib/libcrypto.0.9.8.dylib
0x000000004dd98000 /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x000000004dd98000 /System/Library/Extensions/GeForceMTLDriver.bundle/Contents/MacOS/GeForceMTLDriver
0x000000012c642000 /System/Library/Extensions/AppleIntelHD5000GraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelHD5000GraphicsMTLDriver
0x000000004dd98000 /System/Library/PrivateFrameworks/FamilyControls.framework/Versions/A/FamilyControls
0x000000004dd98000 /System/Library/PrivateFrameworks/CommerceKit.framework/Versions/A/Frameworks/CommerceCore.framework/Versions/A/CommerceCore
0x000000004dd98000 /System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration
0x000000004dd98000 /System/Library/PrivateFrameworks/AppContainer.framework/Versions/A/AppContainer
0x000000004dd98000 /System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper
0x000000004dd98000 /System/Library/Frameworks/DirectoryService.framework/Versions/A/DirectoryService
0x000000004dd98000 /System/Library/PrivateFrameworks/DiskImages.framework/Versions/A/DiskImages
0x000000004dd98000 /System/Library/PrivateFrameworks/LoginUIKit.framework/Versions/A/Frameworks/LoginUICore.framework/Versions/A/LoginUICore
0x000000004dd98000 /usr/lib/libCoreStorage.dylib
0x000000004dd98000 /usr/lib/libcsfde.dylib
0x000000004dd98000 /usr/lib/libodfde.dylib
0x000000004dd98000 /System/Library/Frameworks/DiscRecording.framework/Versions/A/DiscRecording
0x000000004dd98000 /usr/lib/libcurl.4.dylib
0x000000004dd98000 /System/Library/PrivateFrameworks/MediaKit.framework/Versions/A/MediaKit
0x000000004dd98000 /System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage
0x000000004dd98000 /System/Library/PrivateFrameworks/EFILogin.framework/Versions/A/EFILogin
0x000000004dd98000 /usr/lib/libutil.dylib
0x000000004dd98000 /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP
0x000000004dd98000 /usr/lib/libsasl2.2.dylib
0x000000004dd98000 /System/Library/PrivateFrameworks/CoreDaemon.framework/Versions/B/CoreDaemon
0x000000004dd98000 /System/Library/PrivateFrameworks/AppleSRP.framework/Versions/A/AppleSRP
0x000000004dd98000 /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS
0x000000012da1c000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libfontmanager.dylib
0x00000001297a9000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libosxui.dylib
0x000000004dd98000 /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x000000004dd98000 /System/Library/PrivateFrameworks/XPCService.framework/Versions/A/XPCService
0x000000004dd98000 /System/Library/PrivateFrameworks/AppSandbox.framework/Versions/A/AppSandbox
0x000000004dd98000 /usr/lib/libsandbox.1.dylib
0x000000004dd98000 /usr/lib/libMatch.1.dylib
0x000000012f42b000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libnet.dylib
0x000000012f47f000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libnio.dylib
0x0000000166784000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libdcpr.dylib
0x00000001667b2000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libsunec.dylib
0x000000004dd98000 /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x000000004dd98000 /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
VM Arguments:
jvm_args: -Dfile.encoding=UTF-8
java_command: jalview.bin.Jalview
java_class_path (initial): /Users/kjvanderheide/Documents/Jalview development/classes:/Users/kjvanderheide/Documents/Jalview development/lib/activation.jar:/Users/kjvanderheide/Documents/Jalview development/lib/axis.jar:/Users/kjvanderheide/Documents/Jalview development/lib/commons-discovery.jar:/Users/kjvanderheide/Documents/Jalview development/lib/jaxrpc.jar:/Users/kjvanderheide/Documents/Jalview development/lib/jhall.jar:/Users/kjvanderheide/Documents/Jalview development/lib/mail.jar:/Users/kjvanderheide/Documents/Jalview development/lib/regex.jar:/Users/kjvanderheide/Documents/Jalview development/lib/saaj.jar:/Users/kjvanderheide/Documents/Jalview development/lib/wsdl4j.jar:/Users/kjvanderheide/Documents/Jalview development/lib/xercesImpl.jar:/Users/kjvanderheide/Documents/Jalview development/lib/castor-1.1-cycle-xml.jar:/Users/kjvanderheide/Documents/Jalview development/lib/JGoogleAnalytics_0.3.jar:/Users/kjvanderheide/Documents/Jalview development/lib/vamsas-client.jar:/Users/kjvanderheide/Documents/Jalview development/lib/commons-logging-1.1.1.jar:/Users/kjvanderheide/Documents/Jalview development/lib/apache-mime4j-0.6.jar:/Users/kjvanderheide/Documents/Jalview development/lib/httpclient-4.0.3.jar:/Users/kjvanderheide/Documents/Jalview development/lib/httpcore-4.0.1.jar:/Users/kjvanderheide/Documents/Jalview development/lib/httpmime-4.0.3.jar:/Users/kjvanderheide/Documents/Jalview development/lib/miglayout-4.0-swing.jar:/Users/kjvanderheide/Documents/Jalview development/lib/jswingreader-0.3.jar:/Users/kjvanderheide/Documents/Jalview development/lib/commons-codec-1.3.jar:/Users/kjvanderheide/Documents/Jalview development/lib/jdas-1.0.4.jar:/Users/kjvanderheide/Documents/Jalview development/lib/spring-core-3.0.5.RELEASE.jar:/Users/kjvanderheide/Documents/Jalview development/lib/spring-web-3.0.5.RELEASE.jar:/Users/kjvanderheide/Documents/Jalview development/lib:/Users/kjvanderheide/Documents/Jalview development/lib/jabaws-min-client-2.2.0.jar:/Users/kjvanderhe
Launcher Type: SUN_STANDARD
Environment Variables:
PATH=/usr/bin:/bin:/usr/sbin:/sbin
SHELL=/bin/bash
Signal Handlers:
SIGSEGV: [libjvm.dylib+0x5b26e5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_ONSTACK|SA_RESTART|SA_SIGINFO
SIGBUS: [libjvm.dylib+0x5b26e5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
SIGFPE: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
SIGPIPE: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
SIGXFSZ: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
SIGILL: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
SIGUSR2: [libjvm.dylib+0x488c1e], sa_mask[0]=00100000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
SIGHUP: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
SIGINT: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
SIGTERM: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
SIGQUIT: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
--------------- S Y S T E M ---------------
OS:Bsduname:Darwin 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64
rlimit: STACK 8192k, CORE 0k, NPROC 709, NOFILE 10240, AS infinity
load average:1.63 2.07 2.13
CPU:total 8 (initial active 8) (4 cores per cpu, 2 threads per core) family 6 model 70 stepping 1, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, rtm, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2
Memory: 4k page, physical 16777216k(1152628k free)
/proc/meminfo:
vm_info: Java HotSpot(TM) 64-Bit Server VM (25.144-b01) for bsd-amd64 JRE (1.8.0_144-b01), built on Jul 21 2017 22:07:42 by "java_re" with gcc 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
time: Wed Nov 15 14:06:19 2017
elapsed time: 1054 seconds (0d 0h 17m 34s)