2 # A fatal error has been detected by the Java Runtime Environment:
4 # SIGSEGV (0xb) at pc=0x0000000129be645f, pid=28190, tid=0x000000000000eb07
6 # JRE version: Java(TM) SE Runtime Environment (8.0_144-b01) (build 1.8.0_144-b01)
7 # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.144-b01 mixed mode bsd-amd64 compressed oops)
9 # C [libawt_lwawt.dylib+0x1c45f] OGLSD_SetScratchSurface+0x49
11 # Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
13 # If you would like to submit a bug report, please visit:
14 # http://bugreport.java.com/bugreport/crash.jsp
15 # The crash happened outside the Java Virtual Machine in native code.
16 # See problematic frame for where to report the bug.
19 --------------- T H R E A D ---------------
21 Current thread (0x00007fb7d6a28000): JavaThread "Java2D Queue Flusher" daemon [_thread_in_native, id=60167, stack(0x000070000a322000,0x000070000a422000)]
23 siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x0000000000000002
26 RAX=0x0000000129c06d0e, RBX=0x0000000000000002, RCX=0x0000000000000047, RDX=0x0000000129c07258
27 RSP=0x000070000a421730, RBP=0x000070000a421750, RSI=0x00007fb7dc2381e0, RDI=0x00007fb7d6a281f8
28 R8 =0x00000000000002d5, R9 =0x000000000190822f, R10=0x000000010e0ee8f8, R11=0x000000010e6e8100
29 R12=0x0000000000000000, R13=0x000070000a4218e8, R14=0x00007fb7d6a281f8, R15=0x00007fb7d6a28000
30 RIP=0x0000000129be645f, EFLAGS=0x0000000000010202, ERR=0x0000000000000004
31 TRAPNO=0x000000000000000e
33 Top of Stack: (sp=0x000070000a421730)
34 0x000070000a421730: 00007fb7dc2381e0 0000000000000000
35 0x000070000a421740: 00007fb7d6a5d610 00007fb7d6a28000
36 0x000070000a421750: 000070000a4217d0 0000000129c06d36
37 0x000070000a421760: 00007fb7d648b700 0000000200000001
38 0x000070000a421770: 0000000000000000 000070000a421800
39 0x000070000a421780: 0000000000000000 0000000000000000
40 0x000070000a421790: 000070000a4217d0 00007fb7d6a5d620
41 0x000070000a4217a0: 00000000005effd0 00007fb7d6a281f8
42 0x000070000a4217b0: 000000016d2bc370 0000000000000000
43 0x000070000a4217c0: 000070000a421968 00007fb7d6a28000
44 0x000070000a4217d0: 000070000a421820 000000010e0ee96a
45 0x000070000a4217e0: 00000006c00a3af8 000000010d138a00
46 0x000070000a4217f0: 0000000000000064 0000000000000000
47 0x000070000a421800: 0000000000000064 00007fb7d648b1e8
48 0x000070000a421810: 000070000a421870 000000010cf501e8
49 0x000070000a421820: 000070000a421940 000000010e6e86fc
50 0x000070000a421830: 0000000000000001 00007fb7d648bea0
51 0x000070000a421840: 00000006c00a3b00 00007fb7d6a28000
52 0x000070000a421850: 00007fb7d6a28000 00000001258fda00
53 0x000070000a421860: 000070000a421968 00007fb7d6a28000
54 0x000070000a421870: 000070000a4218c0 000000010e2f2968
55 0x000070000a421880: 00000006c00a3af8 000000010e5aafe6
56 0x000070000a421890: 000070000a421940 000000010e6e815c
57 0x000070000a4218a0: 000000012f278bb4 000070000a4218e8
58 0x000070000a4218b0: 000000012f278c30 0000000000000000
59 0x000070000a4218c0: 000070000a421940 000000010dbaf2bd
60 0x000070000a4218d0: 000070000a421940 000000010dbaf2bd
61 0x000070000a4218e0: 000000010dbaf2bd 00000006c00a3af8
62 0x000070000a4218f0: 0000000000000001 00000006c00a3b80
63 0x000070000a421900: 000070000a4218f0 000000012e64d689
64 0x000070000a421910: 000070000a421968 000000012e64d820
65 0x000070000a421920: 0000000000000000 000000012e64d790
67 Instructions: (pc=0x0000000129be645f)
68 0x0000000129be643f: c0 e9 82 00 00 00 48 8b 5e 10 48 85 db 75 0e bf
69 0x0000000129be644f: 01 00 00 00 48 8d 15 67 7b 03 00 eb d6 49 89 fe
70 0x0000000129be645f: 4c 8b 3b 30 c0 e8 21 a6 02 00 49 8b 3f 49 89 c4
71 0x0000000129be646f: 48 8b 35 aa 02 06 00 30 c0 e8 51 a7 02 00 48 85
73 Register to memory mapping:
75 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
76 RBX=0x0000000000000002 is an unknown value
77 RCX=0x0000000000000047 is an unknown value
78 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
79 RSP=0x000070000a421730 is pointing into the stack for thread: 0x00007fb7d6a28000
80 RBP=0x000070000a421750 is pointing into the stack for thread: 0x00007fb7d6a28000
81 RSI=0x00007fb7dc2381e0 is an unknown value
82 RDI=0x00007fb7d6a281f8 is an unknown value
83 R8 =0x00000000000002d5 is an unknown value
84 R9 =0x000000000190822f is an unknown value
85 R10=0x000000010e0ee8f8 is at entry_point+56 in (nmethod*)0x000000010e0ee750
86 R11=0x000000010e6e8100 is at entry_point+0 in (nmethod*)0x000000010e6e7f90
87 R12=0x0000000000000000 is an unknown value
88 R13=0x000070000a4218e8 is pointing into the stack for thread: 0x00007fb7d6a28000
89 R14=0x00007fb7d6a281f8 is an unknown value
90 R15=0x00007fb7d6a28000 is a thread
93 Stack: [0x000070000a322000,0x000070000a422000], sp=0x000070000a421730, free space=1021k
94 Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
95 C [libawt_lwawt.dylib+0x1c45f] OGLSD_SetScratchSurface+0x49
96 C [libawt_lwawt.dylib+0x3cd36] Java_sun_java2d_opengl_OGLRenderQueue_flushBuffer+0x63a
97 J 4748 sun.java2d.opengl.OGLRenderQueue.flushBuffer(JI)V (0 bytes) @ 0x000000010e0ee96a [0x000000010e0ee8c0+0xaa]
98 J 3668 C1 sun.java2d.opengl.OGLRenderQueue.flushBuffer()V (41 bytes) @ 0x000000010e6e86fc [0x000000010e6e84a0+0x25c]
99 J 3667 C1 sun.java2d.opengl.OGLRenderQueue.access$100(Lsun/java2d/opengl/OGLRenderQueue;)V (5 bytes) @ 0x000000010e6e815c [0x000000010e6e8100+0x5c]
100 j sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run()V+81
101 v ~StubRoutines::call_stub
102 V [libjvm.dylib+0x2ee70a]
103 V [libjvm.dylib+0x2eeeae]
104 V [libjvm.dylib+0x2ef05a]
105 V [libjvm.dylib+0x3497b1]
106 V [libjvm.dylib+0x56c0b3]
107 V [libjvm.dylib+0x56d7a0]
108 V [libjvm.dylib+0x48baee]
109 C [libsystem_pthread.dylib+0x393b] _pthread_body+0xb4
110 C [libsystem_pthread.dylib+0x3887] _pthread_body+0x0
111 C [libsystem_pthread.dylib+0x308d] thread_start+0xd
114 Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
115 J 4748 sun.java2d.opengl.OGLRenderQueue.flushBuffer(JI)V (0 bytes) @ 0x000000010e0ee8f8 [0x000000010e0ee8c0+0x38]
116 J 3668 C1 sun.java2d.opengl.OGLRenderQueue.flushBuffer()V (41 bytes) @ 0x000000010e6e86fc [0x000000010e6e84a0+0x25c]
117 J 3667 C1 sun.java2d.opengl.OGLRenderQueue.access$100(Lsun/java2d/opengl/OGLRenderQueue;)V (5 bytes) @ 0x000000010e6e815c [0x000000010e6e8100+0x5c]
118 j sun.java2d.opengl.OGLRenderQueue$QueueFlusher.run()V+81
119 v ~StubRoutines::call_stub
121 --------------- P R O C E S S ---------------
123 Java Threads: ( => current thread )
124 0x00007fb7d92c2000 JavaThread "class jalview.workers.ConservationThread" [_thread_in_Java, id=84243, stack(0x000070000acc0000,0x000070000adc0000)]
125 0x00007fb7d6c86000 JavaThread "Image Fetcher 0" daemon [_thread_blocked, id=46819, stack(0x000070000abbd000,0x000070000acbd000)]
126 0x00007fb7d6996800 JavaThread "LoadFileThread" [_thread_blocked, id=71699, stack(0x000070000aaba000,0x000070000abba000)]
127 0x00007fb7d935c800 JavaThread "TimerQueue" daemon [_thread_blocked, id=81411, stack(0x000070000b14f000,0x000070000b24f000)]
128 0x00007fb7d6bc7800 JavaThread "DestroyJavaVM" [_thread_blocked, id=7171, stack(0x0000700008b54000,0x0000700008c54000)]
129 0x00007fb7d9213800 JavaThread "pool-1-thread-1" [_thread_blocked, id=70863, stack(0x000070000a934000,0x000070000aa34000)]
130 0x00007fb7d7389000 JavaThread "ConsoleTextAppendThread" daemon [_thread_blocked, id=69379, stack(0x000070000a831000,0x000070000a931000)]
131 0x00007fb7d7388000 JavaThread "ConsoleReader2Thread" daemon [_thread_blocked, id=68867, stack(0x000070000a72e000,0x000070000a82e000)]
132 0x00007fb7d7387800 JavaThread "ConsoleReader1Thread" daemon [_thread_blocked, id=68363, stack(0x000070000a62b000,0x000070000a72b000)]
133 0x00007fb7d7344800 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=62987, stack(0x000070000a528000,0x000070000a628000)]
134 0x00007fb7d7313800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=62479, stack(0x000070000a425000,0x000070000a525000)]
135 =>0x00007fb7d6a28000 JavaThread "Java2D Queue Flusher" daemon [_thread_in_native, id=60167, stack(0x000070000a322000,0x000070000a422000)]
136 0x00007fb7da830800 JavaThread "AWT-Shutdown" [_thread_blocked, id=32287, stack(0x0000700009f10000,0x000070000a010000)]
137 0x00007fb7d69c8800 JavaThread "AppKit Thread" daemon [_thread_in_native, id=775, stack(0x00007fff54a39000,0x00007fff55239000)]
138 0x00007fb7d8065800 JavaThread "Service Thread" daemon [_thread_blocked, id=20995, stack(0x0000700009c87000,0x0000700009d87000)]
139 0x00007fb7d6800800 JavaThread "C1 CompilerThread3" daemon [_thread_blocked, id=20483, stack(0x0000700009b84000,0x0000700009c84000)]
140 0x00007fb7d8044800 JavaThread "C2 CompilerThread2" daemon [_thread_blocked, id=19971, stack(0x0000700009a81000,0x0000700009b81000)]
141 0x00007fb7d7044000 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=19459, stack(0x000070000997e000,0x0000700009a7e000)]
142 0x00007fb7d7011000 JavaThread "C2 CompilerThread0" daemon [_thread_in_native, id=18947, stack(0x000070000987b000,0x000070000997b000)]
143 0x00007fb7d702a800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=18435, stack(0x0000700009778000,0x0000700009878000)]
144 0x00007fb7d802a000 JavaThread "Finalizer" daemon [_thread_blocked, id=14595, stack(0x0000700009675000,0x0000700009775000)]
145 0x00007fb7d8027000 JavaThread "Reference Handler" daemon [_thread_blocked, id=14083, stack(0x0000700009572000,0x0000700009672000)]
148 0x00007fb7d9012800 VMThread [stack: 0x000070000946f000,0x000070000956f000] [id=13571]
149 0x00007fb7d8076000 WatcherThread [stack: 0x0000700009d8a000,0x0000700009e8a000] [id=21507]
151 VM state:not at safepoint (normal execution)
153 VM Mutex/Monitor currently owned by a thread: None
156 PSYoungGen total 86528K, used 20241K [0x000000076ab00000, 0x0000000774800000, 0x00000007c0000000)
157 eden space 75776K, 15% used [0x000000076ab00000,0x000000076b683258,0x000000076f500000)
158 from space 10752K, 78% used [0x000000076f600000,0x000000076fe413f8,0x0000000770080000)
159 to space 42496K, 0% used [0x0000000771e80000,0x0000000771e80000,0x0000000774800000)
160 ParOldGen total 209920K, used 31492K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
161 object space 209920K, 15% used [0x00000006c0000000,0x00000006c1ec11e8,0x00000006ccd00000)
162 Metaspace used 37085K, capacity 37796K, committed 38016K, reserved 1083392K
163 class space used 4752K, capacity 4927K, committed 4992K, reserved 1048576K
165 Card table byte_map: [0x000000010ae5a000,0x000000010b65b000] byte_map_base: 0x000000010785a000
167 Marking Bits: (ParMarkBitMap*) 0x000000010d4f35d0
168 Begin Bits: [0x000000011d0fd000, 0x00000001210fd000)
169 End Bits: [0x00000001210fd000, 0x00000001250fd000)
171 Polling page: 0x000000010aa87000
173 CodeCache: size=245760Kb used=15978Kb max_used=15978Kb free=229781Kb
174 bounds [0x000000010dba7000, 0x000000010eb57000, 0x000000011cba7000]
175 total_blobs=5726 nmethods=5006 adapters=631
178 Compilation events (10 events):
179 Event: 1054.326 Thread 0x00007fb7d8044800 nmethod 5621 0x000000010eb34b10 code [0x000000010eb34c60, 0x000000010eb34cd8]
180 Event: 1054.327 Thread 0x00007fb7d6800800 5622 3 javax.swing.DefaultButtonModel::isArmed (15 bytes)
181 Event: 1054.327 Thread 0x00007fb7d6800800 nmethod 5622 0x000000010eb343d0 code [0x000000010eb34540, 0x000000010eb346f0]
182 Event: 1054.346 Thread 0x00007fb7d6800800 5623 % 3 jalview.schemes.ResidueProperties::buildAmbiguityCodonSet @ 657 (878 bytes)
183 Event: 1054.350 Thread 0x00007fb7d6800800 nmethod 5623% 0x000000010eb34d90 code [0x000000010eb357e0, 0x000000010eb3e3f8]
184 Event: 1054.351 Thread 0x00007fb7d6800800 5624 3 jalview.schemes.ResidueProperties::buildAmbiguityCodonSet (878 bytes)
185 Event: 1054.363 Thread 0x00007fb7d6800800 nmethod 5624 0x000000010eb45590 code [0x000000010eb45fc0, 0x000000010eb4e878]
186 Event: 1054.363 Thread 0x00007fb7d6800800 5625 3 java.io.FileInputStream::finalize (22 bytes)
187 Event: 1054.363 Thread 0x00007fb7d6800800 nmethod 5625 0x000000010eb33f50 code [0x000000010eb340c0, 0x000000010eb34348]
188 Event: 1054.364 Thread 0x00007fb7d7011000 5626 % 4 jalview.schemes.ResidueProperties::buildAmbiguityCodonSet @ 575 (878 bytes)
190 GC Heap History (10 events):
191 Event: 8.499 GC heap before
192 {Heap before GC invocations=3 (full 1):
193 PSYoungGen total 76288K, used 65536K [0x000000076ab00000, 0x0000000770000000, 0x00000007c0000000)
194 eden space 65536K, 100% used [0x000000076ab00000,0x000000076eb00000,0x000000076eb00000)
195 from space 10752K, 0% used [0x000000076eb00000,0x000000076eb00000,0x000000076f580000)
196 to space 10752K, 0% used [0x000000076f580000,0x000000076f580000,0x0000000770000000)
197 ParOldGen total 121856K, used 7919K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
198 object space 121856K, 6% used [0x00000006c0000000,0x00000006c07bbd10,0x00000006c7700000)
199 Metaspace used 32188K, capacity 32772K, committed 33024K, reserved 1077248K
200 class space used 4214K, capacity 4351K, committed 4352K, reserved 1048576K
201 Event: 8.510 GC heap after
202 Heap after GC invocations=3 (full 1):
203 PSYoungGen total 76288K, used 10746K [0x000000076ab00000, 0x0000000770d80000, 0x00000007c0000000)
204 eden space 65536K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076eb00000)
205 from space 10752K, 99% used [0x000000076f580000,0x000000076fffe850,0x0000000770000000)
206 to space 10752K, 0% used [0x000000076eb00000,0x000000076eb00000,0x000000076f580000)
207 ParOldGen total 121856K, used 24160K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
208 object space 121856K, 19% used [0x00000006c0000000,0x00000006c17980a8,0x00000006c7700000)
209 Metaspace used 32188K, capacity 32772K, committed 33024K, reserved 1077248K
210 class space used 4214K, capacity 4351K, committed 4352K, reserved 1048576K
212 Event: 28.095 GC heap before
213 {Heap before GC invocations=4 (full 1):
214 PSYoungGen total 76288K, used 76282K [0x000000076ab00000, 0x0000000770d80000, 0x00000007c0000000)
215 eden space 65536K, 100% used [0x000000076ab00000,0x000000076eb00000,0x000000076eb00000)
216 from space 10752K, 99% used [0x000000076f580000,0x000000076fffe850,0x0000000770000000)
217 to space 10752K, 0% used [0x000000076eb00000,0x000000076eb00000,0x000000076f580000)
218 ParOldGen total 121856K, used 24160K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
219 object space 121856K, 19% used [0x00000006c0000000,0x00000006c17980a8,0x00000006c7700000)
220 Metaspace used 34471K, capacity 35178K, committed 35456K, reserved 1079296K
221 class space used 4439K, capacity 4626K, committed 4736K, reserved 1048576K
222 Event: 28.111 GC heap after
223 Heap after GC invocations=4 (full 1):
224 PSYoungGen total 76288K, used 10746K [0x000000076ab00000, 0x0000000770b00000, 0x00000007c0000000)
225 eden space 65536K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076eb00000)
226 from space 10752K, 99% used [0x000000076eb00000,0x000000076f57e870,0x000000076f580000)
227 to space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
228 ParOldGen total 121856K, used 49145K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
229 object space 121856K, 40% used [0x00000006c0000000,0x00000006c2ffe560,0x00000006c7700000)
230 Metaspace used 34471K, capacity 35178K, committed 35456K, reserved 1079296K
231 class space used 4439K, capacity 4626K, committed 4736K, reserved 1048576K
233 Event: 28.286 GC heap before
234 {Heap before GC invocations=5 (full 1):
235 PSYoungGen total 76288K, used 21665K [0x000000076ab00000, 0x0000000770b00000, 0x00000007c0000000)
236 eden space 65536K, 16% used [0x000000076ab00000,0x000000076b5a9db8,0x000000076eb00000)
237 from space 10752K, 99% used [0x000000076eb00000,0x000000076f57e870,0x000000076f580000)
238 to space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
239 ParOldGen total 121856K, used 49145K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
240 object space 121856K, 40% used [0x00000006c0000000,0x00000006c2ffe560,0x00000006c7700000)
241 Metaspace used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
242 class space used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
243 Event: 28.293 GC heap after
244 Heap after GC invocations=5 (full 1):
245 PSYoungGen total 87552K, used 10724K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
246 eden space 76800K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f600000)
247 from space 10752K, 99% used [0x0000000770080000,0x0000000770af9260,0x0000000770b00000)
248 to space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
249 ParOldGen total 121856K, used 50465K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
250 object space 121856K, 41% used [0x00000006c0000000,0x00000006c3148700,0x00000006c7700000)
251 Metaspace used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
252 class space used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
254 Event: 28.293 GC heap before
255 {Heap before GC invocations=6 (full 2):
256 PSYoungGen total 87552K, used 10724K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
257 eden space 76800K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f600000)
258 from space 10752K, 99% used [0x0000000770080000,0x0000000770af9260,0x0000000770b00000)
259 to space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
260 ParOldGen total 121856K, used 50465K [0x00000006c0000000, 0x00000006c7700000, 0x000000076ab00000)
261 object space 121856K, 41% used [0x00000006c0000000,0x00000006c3148700,0x00000006c7700000)
262 Metaspace used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
263 class space used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
264 Event: 28.336 GC heap after
265 Heap after GC invocations=6 (full 2):
266 PSYoungGen total 87552K, used 0K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
267 eden space 76800K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f600000)
268 from space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
269 to space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
270 ParOldGen total 209920K, used 22383K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
271 object space 209920K, 10% used [0x00000006c0000000,0x00000006c15dbcc8,0x00000006ccd00000)
272 Metaspace used 34701K, capacity 35362K, committed 35456K, reserved 1079296K
273 class space used 4482K, capacity 4662K, committed 4736K, reserved 1048576K
275 Event: 1054.355 GC heap before
276 {Heap before GC invocations=7 (full 2):
277 PSYoungGen total 87552K, used 76800K [0x000000076ab00000, 0x0000000772080000, 0x00000007c0000000)
278 eden space 76800K, 100% used [0x000000076ab00000,0x000000076f600000,0x000000076f600000)
279 from space 10752K, 0% used [0x0000000770080000,0x0000000770080000,0x0000000770b00000)
280 to space 10752K, 0% used [0x000000076f600000,0x000000076f600000,0x0000000770080000)
281 ParOldGen total 209920K, used 22383K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
282 object space 209920K, 10% used [0x00000006c0000000,0x00000006c15dbcc8,0x00000006ccd00000)
283 Metaspace used 37084K, capacity 37796K, committed 38016K, reserved 1083392K
284 class space used 4752K, capacity 4927K, committed 4992K, reserved 1048576K
285 Event: 1054.361 GC heap after
286 Heap after GC invocations=7 (full 2):
287 PSYoungGen total 86528K, used 8452K [0x000000076ab00000, 0x0000000774800000, 0x00000007c0000000)
288 eden space 75776K, 0% used [0x000000076ab00000,0x000000076ab00000,0x000000076f500000)
289 from space 10752K, 78% used [0x000000076f600000,0x000000076fe413f8,0x0000000770080000)
290 to space 42496K, 0% used [0x0000000771e80000,0x0000000771e80000,0x0000000774800000)
291 ParOldGen total 209920K, used 31492K [0x00000006c0000000, 0x00000006ccd00000, 0x000000076ab00000)
292 object space 209920K, 15% used [0x00000006c0000000,0x00000006c1ec11e8,0x00000006ccd00000)
293 Metaspace used 37084K, capacity 37796K, committed 38016K, reserved 1083392K
294 class space used 4752K, capacity 4927K, committed 4992K, reserved 1048576K
297 Deoptimization events (10 events):
298 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
299 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
300 Event: 1054.165 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010dd0ceac method=java.awt.EventQueue.setCurrentEventAndMostRecentTimeImpl(Ljava/awt/AWTEvent;)V @ 16
301 Event: 1054.205 Thread 0x00007fb7d6996800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010e197614 method=java.util.regex.Matcher.search(I)Z @ 86
302 Event: 1054.205 Thread 0x00007fb7d6996800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000010e197614 method=java.util.regex.Matcher.search(I)Z @ 86
303 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
304 Event: 1054.306 Thread 0x00007fb7d6996800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000010e19b9d4 method=java.awt.Component.isShowing()Z @ 20
305 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
306 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
307 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
309 Internal exceptions (10 events):
310 Event: 23.206 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': com/sun/org/glassfish/hk2/osgiresourcelocator/ServiceLoader> (0x000000076e381ed8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
311 Event: 23.208 Thread 0x00007fb7d98fb800 Exception <a 'java/io/FileNotFoundException'> (0x000000076e3d4c68) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/prims/jni.cpp, line 709]
312 Event: 23.492 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': com/sun/org/glassfish/hk2/osgiresourcelocator/ServiceLoader> (0x000000076e616378) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
313 Event: 23.495 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': javax/servlet/ServletContext> (0x000000076e69f500) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
314 Event: 23.718 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': com/sun/org/glassfish/hk2/osgiresourcelocator/ServiceLoader> (0x000000076e722190) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
315 Event: 23.719 Thread 0x00007fb7d98fb800 Exception <a 'java/io/FileNotFoundException'> (0x000000076e772ab8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/prims/jni.cpp, line 709]
316 Event: 23.847 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': com/sun/org/glassfish/hk2/osgiresourcelocator/ServiceLoader> (0x000000076e9b3cd8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cp
317 Event: 23.850 Thread 0x00007fb7d98fb800 Exception <a 'java/lang/ClassNotFoundException': javax/servlet/ServletContext> (0x000000076ea3ab10) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
318 Event: 28.222 Thread 0x00007fb7d68ba800 Exception <a 'java/io/FileNotFoundException'> (0x000000076b08b318) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u144/9417/hotspot/src/share/vm/prims/jni.cpp, line 709]
319 Event: 1047.684 Thread 0x00007fb7d7344800 Implicit null exception at 0x000000010dd0e2c2 to 0x000000010dd0e48d
322 Event: 1054.333 loading class jalview/schemes/RNAHelicesColour
323 Event: 1054.333 loading class jalview/schemes/RNAHelicesColour done
324 Event: 1054.334 loading class jalview/schemes/TCoffeeColourScheme
325 Event: 1054.334 loading class jalview/schemes/TCoffeeColourScheme done
326 Event: 1054.335 loading class jalview/schemes/Consensus
327 Event: 1054.335 loading class jalview/schemes/Consensus done
328 Event: 1054.335 loading class jalview/api/analysis/PairwiseScoreModelI
329 Event: 1054.335 loading class jalview/api/analysis/PairwiseScoreModelI done
330 Event: 1054.355 Executing VM operation: ParallelGCFailedAllocation
331 Event: 1054.361 Executing VM operation: ParallelGCFailedAllocation done
335 0x000000004dd98000 /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
336 0x000000004dd98000 /System/Library/Frameworks/Security.framework/Versions/A/Security
337 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
338 0x000000004dd98000 /usr/lib/libz.1.dylib
339 0x000000004dd98000 /usr/lib/libSystem.B.dylib
340 0x000000004dd98000 /usr/lib/libobjc.A.dylib
341 0x000000004dd98000 /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
342 0x000000004dd98000 /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
343 0x000000004dd98000 /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
344 0x000000004dd98000 /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
345 0x000000004dd98000 /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
346 0x000000004dd98000 /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
347 0x000000004dd98000 /System/Library/PrivateFrameworks/DFRFoundation.framework/Versions/A/DFRFoundation
348 0x000000004dd98000 /usr/lib/libenergytrace.dylib
349 0x000000004dd98000 /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
350 0x000000004dd98000 /System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
351 0x000000004dd98000 /usr/lib/libScreenReader.dylib
352 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
353 0x000000004dd98000 /System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
354 0x000000004dd98000 /System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
355 0x000000004dd98000 /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
356 0x000000004dd98000 /System/Library/PrivateFrameworks/DataDetectorsCore.framework/Versions/A/DataDetectorsCore
357 0x000000004dd98000 /System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
358 0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
359 0x000000004dd98000 /usr/lib/libicucore.A.dylib
360 0x000000004dd98000 /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
361 0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition
362 0x000000004dd98000 /usr/lib/libauto.dylib
363 0x000000004dd98000 /usr/lib/libxml2.2.dylib
364 0x000000004dd98000 /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI
365 0x000000004dd98000 /System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
366 0x000000004dd98000 /System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
367 0x000000004dd98000 /usr/lib/liblangid.dylib
368 0x000000004dd98000 /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
369 0x000000004dd98000 /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
370 0x000000004dd98000 /usr/lib/libDiagnosticMessagesClient.dylib
371 0x000000004dd98000 /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
372 0x000000004dd98000 /System/Library/PrivateFrameworks/PerformanceAnalysis.framework/Versions/A/PerformanceAnalysis
373 0x000000004dd98000 /System/Library/PrivateFrameworks/GenerationalStorage.framework/Versions/A/GenerationalStorage
374 0x000000004dd98000 /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
375 0x000000004dd98000 /System/Library/Frameworks/CoreImage.framework/Versions/A/CoreImage
376 0x000000004dd98000 /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText
377 0x000000004dd98000 /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
378 0x000000004dd98000 /System/Library/PrivateFrameworks/Backup.framework/Versions/A/Backup
379 0x000000004dd98000 /usr/lib/libarchive.2.dylib
380 0x000000004dd98000 /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
381 0x000000004dd98000 /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
382 0x000000004dd98000 /usr/lib/libCRFSuite.dylib
383 0x000000004dd98000 /usr/lib/libc++.1.dylib
384 0x000000004dd98000 /usr/lib/libc++abi.dylib
385 0x000000004dd98000 /usr/lib/system/libcache.dylib
386 0x000000004dd98000 /usr/lib/system/libcommonCrypto.dylib
387 0x000000004dd98000 /usr/lib/system/libcompiler_rt.dylib
388 0x000000004dd98000 /usr/lib/system/libcopyfile.dylib
389 0x000000004dd98000 /usr/lib/system/libcorecrypto.dylib
390 0x000000004dd98000 /usr/lib/system/libdispatch.dylib
391 0x000000004dd98000 /usr/lib/system/libdyld.dylib
392 0x000000004dd98000 /usr/lib/system/libkeymgr.dylib
393 0x000000004dd98000 /usr/lib/system/liblaunch.dylib
394 0x000000004dd98000 /usr/lib/system/libmacho.dylib
395 0x000000004dd98000 /usr/lib/system/libquarantine.dylib
396 0x000000004dd98000 /usr/lib/system/libremovefile.dylib
397 0x000000004dd98000 /usr/lib/system/libsystem_asl.dylib
398 0x000000004dd98000 /usr/lib/system/libsystem_blocks.dylib
399 0x000000004dd98000 /usr/lib/system/libsystem_c.dylib
400 0x000000004dd98000 /usr/lib/system/libsystem_configuration.dylib
401 0x000000004dd98000 /usr/lib/system/libsystem_coreservices.dylib
402 0x000000004dd98000 /usr/lib/system/libsystem_coretls.dylib
403 0x000000004dd98000 /usr/lib/system/libsystem_dnssd.dylib
404 0x000000004dd98000 /usr/lib/system/libsystem_info.dylib
405 0x000000004dd98000 /usr/lib/system/libsystem_kernel.dylib
406 0x000000004dd98000 /usr/lib/system/libsystem_m.dylib
407 0x000000004dd98000 /usr/lib/system/libsystem_malloc.dylib
408 0x000000004dd98000 /usr/lib/system/libsystem_network.dylib
409 0x000000004dd98000 /usr/lib/system/libsystem_networkextension.dylib
410 0x000000004dd98000 /usr/lib/system/libsystem_notify.dylib
411 0x000000004dd98000 /usr/lib/system/libsystem_platform.dylib
412 0x000000004dd98000 /usr/lib/system/libsystem_pthread.dylib
413 0x000000004dd98000 /usr/lib/system/libsystem_sandbox.dylib
414 0x000000004dd98000 /usr/lib/system/libsystem_secinit.dylib
415 0x000000004dd98000 /usr/lib/system/libsystem_symptoms.dylib
416 0x000000004dd98000 /usr/lib/system/libsystem_trace.dylib
417 0x000000004dd98000 /usr/lib/system/libunwind.dylib
418 0x000000004dd98000 /usr/lib/system/libxpc.dylib
419 0x000000004dd98000 /usr/lib/libbsm.0.dylib
420 0x000000004dd98000 /usr/lib/system/libkxld.dylib
421 0x000000004dd98000 /usr/lib/libcoretls.dylib
422 0x000000004dd98000 /usr/lib/libcoretls_cfhelpers.dylib
423 0x000000004dd98000 /usr/lib/libOpenScriptingUtil.dylib
424 0x000000004dd98000 /usr/lib/libpam.2.dylib
425 0x000000004dd98000 /usr/lib/libsqlite3.dylib
426 0x000000004dd98000 /usr/lib/libxar.1.dylib
427 0x000000004dd98000 /usr/lib/libbz2.1.0.dylib
428 0x000000004dd98000 /usr/lib/liblzma.5.dylib
429 0x000000004dd98000 /usr/lib/libnetwork.dylib
430 0x000000004dd98000 /usr/lib/libpcap.A.dylib
431 0x000000004dd98000 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/FSEvents.framework/Versions/A/FSEvents
432 0x000000004dd98000 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore
433 0x000000004dd98000 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
434 0x000000004dd98000 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
435 0x000000004dd98000 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/SearchKit
436 0x000000004dd98000 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
437 0x000000004dd98000 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
438 0x000000004dd98000 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices
439 0x000000004dd98000 /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList
440 0x000000004dd98000 /System/Library/Frameworks/NetFS.framework/Versions/A/NetFS
441 0x000000004dd98000 /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth
442 0x000000004dd98000 /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
443 0x000000004dd98000 /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
444 0x000000004dd98000 /usr/lib/libmecabra.dylib
445 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
446 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
447 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
448 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
449 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore
450 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
451 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
452 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
453 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
454 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
455 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBNNS.dylib
456 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libQuadrature.dylib
457 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
458 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
459 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
460 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib
461 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib
462 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
463 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
464 0x000000004dd98000 /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
465 0x000000004dd98000 /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
466 0x000000004dd98000 /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
467 0x000000004dd98000 /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
468 0x000000004dd98000 /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
469 0x000000004dd98000 /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
470 0x000000004dd98000 /usr/lib/libcompression.dylib
471 0x000000004dd98000 /System/Library/PrivateFrameworks/AppleJPEG.framework/Versions/A/AppleJPEG
472 0x000000004dd98000 /usr/lib/libcups.2.dylib
473 0x000000004dd98000 /System/Library/Frameworks/Kerberos.framework/Versions/A/Kerberos
474 0x000000004dd98000 /System/Library/Frameworks/GSS.framework/Versions/A/GSS
475 0x000000004dd98000 /usr/lib/libresolv.9.dylib
476 0x000000004dd98000 /usr/lib/libiconv.2.dylib
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478 0x000000004dd98000 /usr/lib/libheimdal-asn1.dylib
479 0x000000004dd98000 /System/Library/Frameworks/OpenDirectory.framework/Versions/A/OpenDirectory
480 0x000000004dd98000 /System/Library/PrivateFrameworks/CommonAuth.framework/Versions/A/CommonAuth
481 0x000000004dd98000 /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
482 0x000000004dd98000 /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation
483 0x000000004dd98000 /System/Library/PrivateFrameworks/LanguageModeling.framework/Versions/A/LanguageModeling
484 0x000000004dd98000 /usr/lib/libmarisa.dylib
485 0x000000004dd98000 /usr/lib/libChineseTokenizer.dylib
486 0x000000004dd98000 /usr/lib/libcmph.dylib
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488 0x000000004dd98000 /System/Library/Frameworks/ServiceManagement.framework/Versions/A/ServiceManagement
489 0x000000004dd98000 /usr/lib/libxslt.1.dylib
490 0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
491 0x000000004dd98000 /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO
492 0x000000004dd98000 /System/Library/Frameworks/Metal.framework/Versions/A/Metal
493 0x000000004dd98000 /usr/lib/libate.dylib
494 0x000000004dd98000 /System/Library/PrivateFrameworks/GPUCompiler.framework/libmetal_timestamp.dylib
495 0x000000004dd98000 /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
496 0x000000004dd98000 /System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator
497 0x000000004dd98000 /System/Library/Frameworks/CoreVideo.framework/Versions/A/CoreVideo
498 0x000000004dd98000 /usr/lib/libFosl_dynamic.dylib
499 0x000000004dd98000 /System/Library/PrivateFrameworks/MetalPerformanceShaders.framework/Versions/A/MetalPerformanceShaders
500 0x000000004dd98000 /System/Library/PrivateFrameworks/FaceCore.framework/Versions/A/FaceCore
501 0x000000004dd98000 /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
502 0x000000004dd98000 /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
503 0x000000004dd98000 /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
504 0x000000004dd98000 /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
505 0x000000004dd98000 /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
506 0x000000004dd98000 /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
507 0x000000004dd98000 /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
508 0x000000004dd98000 /System/Library/PrivateFrameworks/CrashReporterSupport.framework/Versions/A/CrashReporterSupport
509 0x000000004dd98000 /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
510 0x000000004dd98000 /System/Library/PrivateFrameworks/IconServices.framework/Versions/A/IconServices
511 0x000000004dd98000 /System/Library/PrivateFrameworks/ProtocolBuffer.framework/Versions/A/ProtocolBuffer
512 0x000000004dd98000 /System/Library/PrivateFrameworks/Apple80211.framework/Versions/A/Apple80211
513 0x000000004dd98000 /System/Library/Frameworks/CoreWLAN.framework/Versions/A/CoreWLAN
514 0x000000004dd98000 /System/Library/PrivateFrameworks/CoreUtils.framework/Versions/A/CoreUtils
515 0x000000004dd98000 /System/Library/Frameworks/IOBluetooth.framework/Versions/A/IOBluetooth
516 0x000000004dd98000 /System/Library/PrivateFrameworks/CoreWiFi.framework/Versions/A/CoreWiFi
517 0x000000004dd98000 /System/Library/Frameworks/CoreBluetooth.framework/Versions/A/CoreBluetooth
518 0x000000004dd98000 /System/Library/Frameworks/CoreDisplay.framework/Versions/A/CoreDisplay
519 0x000000004dd98000 /System/Library/PrivateFrameworks/IOPresentment.framework/Versions/A/IOPresentment
520 0x000000004dd98000 /System/Library/PrivateFrameworks/DSExternalDisplay.framework/Versions/A/DSExternalDisplay
521 0x000000004dd98000 /System/Library/PrivateFrameworks/DebugSymbols.framework/Versions/A/DebugSymbols
522 0x000000004dd98000 /System/Library/PrivateFrameworks/CoreSymbolication.framework/Versions/A/CoreSymbolication
523 0x000000004dd98000 /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
524 0x000000004dd98000 /System/Library/PrivateFrameworks/AppleFSCompression.framework/Versions/A/AppleFSCompression
525 0x000000004dd98000 /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore
526 0x000000004dd98000 /System/Library/PrivateFrameworks/ChunkingLibrary.framework/Versions/A/ChunkingLibrary
527 0x000000010cc00000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server/libjvm.dylib
528 0x000000004dd98000 /usr/lib/libstdc++.6.dylib
529 0x000000010aa44000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libverify.dylib
530 0x000000010aa52000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libjava.dylib
531 0x000000010aa91000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libzip.dylib
532 0x0000000127b9d000 /System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/JavaRuntimeSupport
533 0x000000010bbea000 /System/Library/Frameworks/JavaVM.framework/Versions/A/Frameworks/JavaNativeFoundation.framework/Versions/A/JavaNativeFoundation
534 0x0000000127bb7000 /System/Library/Frameworks/JavaVM.framework/Versions/A/JavaVM
535 0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
536 0x0000000127bc4000 /System/Library/PrivateFrameworks/JavaLaunching.framework/Versions/A/JavaLaunching
537 0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels
538 0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Help.framework/Versions/A/Help
539 0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
540 0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
541 0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
542 0x000000004dd98000 /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
543 0x0000000129a56000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libawt.dylib
544 0x0000000129afe000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/./libmlib_image.dylib
545 0x0000000129bca000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libawt_lwawt.dylib
546 0x0000000129c81000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/./libosxapp.dylib
547 0x000000004dd98000 /System/Library/Frameworks/ExceptionHandling.framework/Versions/A/ExceptionHandling
548 0x000000004dd98000 /System/Library/PrivateFrameworks/CoreServicesInternal.framework/Versions/A/CoreServicesInternal
549 0x000000004dd98000 /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
550 0x000000004dd98000 /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
551 0x000000004dd98000 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libTrueTypeScaler.dylib
552 0x000000012bcdb000 /System/Library/Frameworks/OpenGL.framework/Resources/GLEngine.bundle/GLEngine
553 0x000000004dd98000 /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
554 0x000000012bec0000 /System/Library/Extensions/AppleIntelHD5000GraphicsGLDriver.bundle/Contents/MacOS/AppleIntelHD5000GraphicsGLDriver
555 0x000000004dd98000 /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib
556 0x000000004dd98000 /System/Library/Extensions/GeForceGLDriver.bundle/Contents/MacOS/GeForceGLDriver
557 0x000000004dd98000 /System/Library/Extensions/GeForceGLDriver.bundle/Contents/MacOS/libclh.dylib
558 0x000000012a6a7000 /System/Library/Frameworks/OpenGL.framework/Resources//GLRendererFloat.bundle/GLRendererFloat
559 0x000000004dd98000 /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libcldcpuengine.dylib
560 0x000000004dd98000 /usr/lib/libcrypto.0.9.8.dylib
561 0x000000004dd98000 /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
562 0x000000004dd98000 /System/Library/Extensions/GeForceMTLDriver.bundle/Contents/MacOS/GeForceMTLDriver
563 0x000000012c642000 /System/Library/Extensions/AppleIntelHD5000GraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelHD5000GraphicsMTLDriver
564 0x000000004dd98000 /System/Library/PrivateFrameworks/FamilyControls.framework/Versions/A/FamilyControls
565 0x000000004dd98000 /System/Library/PrivateFrameworks/CommerceKit.framework/Versions/A/Frameworks/CommerceCore.framework/Versions/A/CommerceCore
566 0x000000004dd98000 /System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration
567 0x000000004dd98000 /System/Library/PrivateFrameworks/AppContainer.framework/Versions/A/AppContainer
568 0x000000004dd98000 /System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper
569 0x000000004dd98000 /System/Library/Frameworks/DirectoryService.framework/Versions/A/DirectoryService
570 0x000000004dd98000 /System/Library/PrivateFrameworks/DiskImages.framework/Versions/A/DiskImages
571 0x000000004dd98000 /System/Library/PrivateFrameworks/LoginUIKit.framework/Versions/A/Frameworks/LoginUICore.framework/Versions/A/LoginUICore
572 0x000000004dd98000 /usr/lib/libCoreStorage.dylib
573 0x000000004dd98000 /usr/lib/libcsfde.dylib
574 0x000000004dd98000 /usr/lib/libodfde.dylib
575 0x000000004dd98000 /System/Library/Frameworks/DiscRecording.framework/Versions/A/DiscRecording
576 0x000000004dd98000 /usr/lib/libcurl.4.dylib
577 0x000000004dd98000 /System/Library/PrivateFrameworks/MediaKit.framework/Versions/A/MediaKit
578 0x000000004dd98000 /System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage
579 0x000000004dd98000 /System/Library/PrivateFrameworks/EFILogin.framework/Versions/A/EFILogin
580 0x000000004dd98000 /usr/lib/libutil.dylib
581 0x000000004dd98000 /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP
582 0x000000004dd98000 /usr/lib/libsasl2.2.dylib
583 0x000000004dd98000 /System/Library/PrivateFrameworks/CoreDaemon.framework/Versions/B/CoreDaemon
584 0x000000004dd98000 /System/Library/PrivateFrameworks/AppleSRP.framework/Versions/A/AppleSRP
585 0x000000004dd98000 /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS
586 0x000000012da1c000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libfontmanager.dylib
587 0x00000001297a9000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libosxui.dylib
588 0x000000004dd98000 /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
589 0x000000004dd98000 /System/Library/PrivateFrameworks/XPCService.framework/Versions/A/XPCService
590 0x000000004dd98000 /System/Library/PrivateFrameworks/AppSandbox.framework/Versions/A/AppSandbox
591 0x000000004dd98000 /usr/lib/libsandbox.1.dylib
592 0x000000004dd98000 /usr/lib/libMatch.1.dylib
593 0x000000012f42b000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libnet.dylib
594 0x000000012f47f000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libnio.dylib
595 0x0000000166784000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libdcpr.dylib
596 0x00000001667b2000 /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libsunec.dylib
597 0x000000004dd98000 /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
598 0x000000004dd98000 /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
601 jvm_args: -Dfile.encoding=UTF-8
602 java_command: jalview.bin.Jalview
603 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
604 Launcher Type: SUN_STANDARD
606 Environment Variables:
607 PATH=/usr/bin:/bin:/usr/sbin:/sbin
611 SIGSEGV: [libjvm.dylib+0x5b26e5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_ONSTACK|SA_RESTART|SA_SIGINFO
612 SIGBUS: [libjvm.dylib+0x5b26e5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
613 SIGFPE: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
614 SIGPIPE: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
615 SIGXFSZ: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
616 SIGILL: [libjvm.dylib+0x489100], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
617 SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
618 SIGUSR2: [libjvm.dylib+0x488c1e], sa_mask[0]=00100000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
619 SIGHUP: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
620 SIGINT: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
621 SIGTERM: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
622 SIGQUIT: [libjvm.dylib+0x4871f5], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
625 --------------- S Y S T E M ---------------
627 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
628 rlimit: STACK 8192k, CORE 0k, NPROC 709, NOFILE 10240, AS infinity
629 load average:1.63 2.07 2.13
631 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
633 Memory: 4k page, physical 16777216k(1152628k free)
638 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)
640 time: Wed Nov 15 14:06:19 2017
641 elapsed time: 1054 seconds (0d 0h 17m 34s)
git://source.jalview.org / jalview.git / blob