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Exception Access Violation in JRE
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acather96
Oct 2, 2016, 8:00:21 AM10/2/16
to beast-users
Hi,
I installed Beagle and Beast today and so far have not been able to complete a successful run. Whilst I can convert my FASTA file to xml using BEAUti, when I run it in BEAST it fails. A file called "hs_err_pid1936.log" is created, which contains the text I've posted below. Two blank files (filename.log.txt and filename.trees.txt) are also created. Any ideas? I'm on Windows 10 x64, AMD A4-5000 APU. My Java is Version 8 Update 101 build 1.8.0_101-b13. Any ideas?
#
# A fatal error has been detected by the Java Runtime Environment:
#
# EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x4c36b6c0, pid=1936, tid=7916
#
# JRE version: Java(TM) SE Runtime Environment (8.0_71-b15) (build 1.8.0_71-b15)
# Java VM: Java HotSpot(TM) Client VM (25.71-b15 mixed mode windows-x86 )
# Problematic frame:
# C [hmsbeagle-cpu-sse32-21.DLL+0xb6c0]
#
# Failed to write core dump. Minidumps are not enabled by default on client versions of Windows
#
# 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 (0x4d086000): JavaThread "pool-1-thread-1" [_thread_in_native, id=7916, stack(0x4c3e0000,0x4c430000)]
siginfo: ExceptionCode=0xc0000005, reading address 0xffffffff
Registers:
EAX=0x00000060, EBX=0x4c42f2f0, ECX=0x00000000, EDX=0x4a99bc68
ESP=0x4c42f130, EBP=0x4c42f2e0, ESI=0x00000000, EDI=0x4a993850
EIP=0x4c36b6c0, EFLAGS=0x00010216
Top of Stack: (sp=0x4c42f130)
0x4c42f130: 4a99bc68 492fb440 ffffffff 00000000
0x4c42f140: 00000155 4a931660 493dd0c8 492fb440
0x4c42f150: 11981236 3fefd0dd cd87d380 3f5797fe
0x4c42f160: 9ab70880 3f678aef cd87d380 3f5797fe
0x4c42f170: cd36c280 3f5797fe 119811f9 3fefd0dd
0x4c42f180: cd36c280 3f5797fe 9a663300 3f678aef
0x4c42f190: 9ab70880 3f678aef cd87d380 3f5797fe
0x4c42f1a0: 11981236 3fefd0dd cd87d380 3f5797fe
Instructions: (pc=0x4c36b6c0)
0x4c36b6a0: 66 0f 59 c5 66 0f 58 c8 66 0f 28 85 80 fe ff ff
0x4c36b6b0: c1 e0 05 66 0f 59 c3 66 0f 59 8c 05 30 ff ff ff
0x4c36b6c0: 66 0f 29 0a 66 0f 28 8d a0 fe ff ff 66 0f 59 cc
0x4c36b6d0: 66 0f 58 c8 66 0f 28 85 c0 fe ff ff 66 0f 59 c2
Register to memory mapping:
EAX=0x00000060 is an unknown value
EBX=0x4c42f2f0 is pointing into the stack for thread: 0x4d086000
ECX=0x00000000 is an unknown value
EDX=0x4a99bc68 is an unknown value
ESP=0x4c42f130 is pointing into the stack for thread: 0x4d086000
EBP=0x4c42f2e0 is pointing into the stack for thread: 0x4d086000
ESI=0x00000000 is an unknown value
EDI=0x4a993850 is an unknown value
Stack: [0x4c3e0000,0x4c430000], sp=0x4c42f130, free space=316k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [hmsbeagle-cpu-sse32-21.DLL+0xb6c0]
C [hmsbeagle-cpu-sse32-21.DLL+0x113bc]
C [hmsbeagle32.dll+0x693e]
C [hmsbeagle32.dll+0x7679]
j beagle.BeagleJNIWrapper.updatePartials(I[III)I+0
j beagle.BeagleJNIImpl.updatePartials([III)V+10
j dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood()D+489
j dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood()D+9
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Double;+8
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Object;+1
j java.util.concurrent.FutureTask.run()V+42
j java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j java.lang.Thread.run()V+11
v ~StubRoutines::call_stub
V [jvm.dll+0x158bf5]
V [jvm.dll+0x21e0be]
V [jvm.dll+0x158c8e]
V [jvm.dll+0x158e16]
V [jvm.dll+0x158e87]
V [jvm.dll+0xfd68f]
V [jvm.dll+0x17c03c]
V [jvm.dll+0x17c12a]
V [jvm.dll+0x1c0636]
C [msvcr100.dll+0x5c556]
C [msvcr100.dll+0x5c600]
C [KERNEL32.DLL+0x162c4]
C [ntdll.dll+0x60609]
C [ntdll.dll+0x605d4]
C 0x00000000
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j beagle.BeagleJNIWrapper.updatePartials(I[III)I+0
j beagle.BeagleJNIImpl.updatePartials([III)V+10
j dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood()D+489
j dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood()D+9
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Double;+8
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Object;+1
j java.util.concurrent.FutureTask.run()V+42
j java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j java.lang.Thread.run()V+11
v ~StubRoutines::call_stub
--------------- P R O C E S S ---------------
Java Threads: ( => current thread )
0x4d086800 JavaThread "pool-1-thread-2" [_thread_blocked, id=7920, stack(0x4da80000,0x4dad0000)]
=>0x4d086000 JavaThread "pool-1-thread-1" [_thread_in_native, id=7916, stack(0x4c3e0000,0x4c430000)]
0x4649c000 JavaThread "TimerQueue" daemon [_thread_blocked, id=6152, stack(0x49430000,0x49480000)]
0x46465000 JavaThread "D3D Screen Updater" daemon [_thread_blocked, id=3044, stack(0x4a2c0000,0x4a310000)]
0x46457c00 JavaThread "Thread-3" [_thread_blocked, id=6724, stack(0x4a130000,0x4a180000)]
0x46457800 JavaThread "Thread-2" [_thread_blocked, id=7600, stack(0x4a0a0000,0x4a0f0000)]
0x459cc000 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=7484, stack(0x49940000,0x49990000)]
0x45982800 JavaThread "AWT-Windows" daemon [_thread_in_native, id=4716, stack(0x46100000,0x46150000)]
0x45982000 JavaThread "AWT-Shutdown" [_thread_blocked, id=5912, stack(0x46070000,0x460c0000)]
0x45981800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=7236, stack(0x45fe0000,0x46030000)]
0x457fb800 JavaThread "Service Thread" daemon [_thread_blocked, id=5524, stack(0x45dd0000,0x45e20000)]
0x457f3800 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=940, stack(0x45d40000,0x45d90000)]
0x457fd800 JavaThread "Attach Listener" daemon [_thread_blocked, id=5620, stack(0x45cb0000,0x45d00000)]
0x457fc800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=5404, stack(0x45c20000,0x45c70000)]
0x457d6400 JavaThread "Finalizer" daemon [_thread_blocked, id=5540, stack(0x45aa0000,0x45af0000)]
0x457d1400 JavaThread "Reference Handler" daemon [_thread_blocked, id=5688, stack(0x45a10000,0x45a60000)]
0x02e5b800 JavaThread "main" [_thread_blocked, id=4848, stack(0x02d50000,0x02da0000)]
Other Threads:
0x02f5b400 VMThread [stack: 0x04fa0000,0x04ff0000] [id=1700]
0x45825400 WatcherThread [stack: 0x45e60000,0x45eb0000] [id=5528]
VM state:not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: None
Heap:
def new generation total 78720K, used 9950K [0x05000000, 0x0a560000, 0x1a550000)
eden space 70016K, 14% used [0x05000000, 0x059b7808, 0x09460000)
from space 8704K, 0% used [0x09460000, 0x09460000, 0x09ce0000)
to space 8704K, 0% used [0x09ce0000, 0x09ce0000, 0x0a560000)
tenured generation total 174784K, used 9672K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 5% used [0x1a550000, 0x1aec2358, 0x1aec2400, 0x25000000)
Metaspace used 13354K, capacity 13561K, committed 13696K, reserved 13696K
Card table byte_map: [0x45000000,0x45210000] byte_map_base: 0x44fd8000
Polling page: 0x02da0000
CodeCache: size=32768Kb used=1798Kb max_used=1800Kb free=30969Kb
bounds [0x02f60000, 0x03128000, 0x04f60000]
total_blobs=1155 nmethods=861 adapters=224
compilation: enabled
Compilation events (10 events):
Event: 58.132 Thread 0x457f3800 863 dr.xml.XMLObject::getRawChild (9 bytes)
Event: 58.133 Thread 0x457f3800 nmethod 863 0x03120148 code [0x03120260, 0x0312050c]
Event: 58.133 Thread 0x457f3800 864 dr.xml.XMLObject::getChild (56 bytes)
Event: 58.135 Thread 0x457f3800 nmethod 864 0x03120808 code [0x03120930, 0x03120cbc]
Event: 58.163 Thread 0x457f3800 865 ! java.util.zip.Inflater::setInput (74 bytes)
Event: 58.164 Thread 0x457f3800 nmethod 865 0x03121388 code [0x031214a0, 0x031217c8]
Event: 58.189 Thread 0x457f3800 866 javax.swing.text.GapContent::findSortIndex (128 bytes)
Event: 58.191 Thread 0x457f3800 nmethod 866 0x03121c08 code [0x03121d30, 0x03121f78]
Event: 58.195 Thread 0x457f3800 867 sun.font.GlyphList::usePositions (5 bytes)
Event: 58.195 Thread 0x457f3800 nmethod 867 0x03122248 code [0x03122340, 0x031223c0]
GC Heap History (2 events):
Event: 55.715 GC heap before
{Heap before GC invocations=0 (full 0):
def new generation total 78656K, used 54605K [0x05000000, 0x0a550000, 0x1a550000)
eden space 69952K, 78% used [0x05000000, 0x085534d0, 0x09450000)
from space 8704K, 0% used [0x09450000, 0x09450000, 0x09cd0000)
to space 8704K, 0% used [0x09cd0000, 0x09cd0000, 0x0a550000)
tenured generation total 174784K, used 0K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 0% used [0x1a550000, 0x1a550000, 0x1a550200, 0x25000000)
Metaspace used 11992K, capacity 12185K, committed 12288K, reserved 12672K
Event: 55.868 GC heap after
Heap after GC invocations=1 (full 1):
def new generation total 78720K, used 0K [0x05000000, 0x0a560000, 0x1a550000)
eden space 70016K, 0% used [0x05000000, 0x05000000, 0x09460000)
from space 8704K, 0% used [0x09460000, 0x09460000, 0x09ce0000)
to space 8704K, 0% used [0x09ce0000, 0x09ce0000, 0x0a560000)
tenured generation total 174784K, used 9672K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 5% used [0x1a550000, 0x1aec2358, 0x1aec2400, 0x25000000)
Metaspace used 11992K, capacity 12185K, committed 12288K, reserved 12672K
}
Deoptimization events (0 events):
No events
Internal exceptions (10 events):
Event: 0.233 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.defineClass(Ljava/lang/String;[BII)Ljava/lang/Class; name or signature does not match> (0x0500b960) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vðŸ$Ò³ÖÍ?
Event: 0.233 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.prefetchRead(Ljava/lang/Object;J)V name or signature does not match> (0x0500bc30) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, l÷*ì¨ûàâ?
Event: 0.590 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e1a50) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.590 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e1c50) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.593 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e5a38) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.593 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e5c38) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.630 Thread 0x02e5b800 Exception <a 'java/io/FileNotFoundException'> (0x050e9e98) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, line 709]
Event: 0.767 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x05460368) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\methodHandles.cpp, line 1146]
Event: 0.772 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x0546c508) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\methodHandles.cpp, line 1146]
Event: 1.017 Thread 0x02e5b800 Exception <a 'java/io/FileNotFoundException'> (0x0556f8a0) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, line 709]
Events (10 events):
Event: 58.188 Thread 0x4d086800 Thread added: 0x4d086800
Event: 58.189 loading class dr/app/beagle/evomodel/substmodel/EigenDecomposition
Event: 58.190 loading class dr/app/beagle/evomodel/substmodel/EigenDecomposition done
Event: 58.190 Executing VM operation: RevokeBias
Event: 58.191 Executing VM operation: RevokeBias done
Event: 58.192 loading class dr/app/beagle/evomodel/branchmodel/BranchModel$1
Event: 58.192 loading class dr/app/beagle/evomodel/branchmodel/BranchModel$1 done
Event: 58.192 Executing VM operation: RevokeBias
Event: 58.193 Executing VM operation: RevokeBias done
Event: 58.195 Thread 0x457f3800 flushing nmethod 0x03081b48
Dynamic libraries:
0x00b40000 - 0x00b73000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\javaw.exe
0x77bc0000 - 0x77d42000 C:\WINDOWS\SYSTEM32\ntdll.dll
0x746a0000 - 0x74780000 C:\WINDOWS\System32\KERNEL32.DLL
0x75160000 - 0x75301000 C:\WINDOWS\System32\KERNELBASE.dll
0x76f50000 - 0x76fc7000 C:\WINDOWS\System32\ADVAPI32.dll
0x75090000 - 0x7514e000 C:\WINDOWS\System32\msvcrt.dll
0x74dc0000 - 0x74e01000 C:\WINDOWS\System32\sechost.dll
0x771e0000 - 0x772a1000 C:\WINDOWS\System32\RPCRT4.dll
0x74680000 - 0x7469e000 C:\WINDOWS\System32\SspiCli.dll
0x74670000 - 0x7467a000 C:\WINDOWS\System32\CRYPTBASE.dll
0x776f0000 - 0x7774a000 C:\WINDOWS\System32\bcryptPrimitives.dll
0x77020000 - 0x7717f000 C:\WINDOWS\System32\USER32.dll
0x75320000 - 0x75335000 C:\WINDOWS\System32\win32u.dll
0x74d90000 - 0x74dbb000 C:\WINDOWS\System32\GDI32.dll
0x749a0000 - 0x74afb000 C:\WINDOWS\System32\gdi32full.dll
0x6a6e0000 - 0x6a8ea000 C:\WINDOWS\WinSxS\x86_microsoft.windows.common-controls_6595b64144ccf1df_6.0.14393.0_none_74bc87d3d22d9abe\COMCTL32.dll
0x74780000 - 0x74991000 C:\WINDOWS\System32\combase.dll
0x74e10000 - 0x74ef0000 C:\WINDOWS\System32\ucrtbase.dll
0x75060000 - 0x75085000 C:\WINDOWS\System32\IMM32.DLL
0x59fe0000 - 0x5a09f000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\msvcr100.dll
0x59c10000 - 0x59fd8000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\client\jvm.dll
0x75150000 - 0x75156000 C:\WINDOWS\System32\PSAPI.DLL
0x70d10000 - 0x70d18000 C:\WINDOWS\SYSTEM32\WSOCK32.dll
0x71690000 - 0x716b4000 C:\WINDOWS\SYSTEM32\WINMM.dll
0x73fc0000 - 0x73fc8000 C:\WINDOWS\SYSTEM32\VERSION.dll
0x71660000 - 0x71683000 C:\WINDOWS\SYSTEM32\WINMMBASE.dll
0x77400000 - 0x77436000 C:\WINDOWS\System32\cfgmgr32.dll
0x74d20000 - 0x74d83000 C:\WINDOWS\System32\WS2_32.dll
0x5e8d0000 - 0x5e8dc000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\verify.dll
0x5e050000 - 0x5e071000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\java.dll
0x5e230000 - 0x5e243000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\zip.dll
0x758b0000 - 0x76c87000 C:\WINDOWS\System32\SHELL32.dll
0x75340000 - 0x758ae000 C:\WINDOWS\System32\windows.storage.dll
0x76ca0000 - 0x76ce5000 C:\WINDOWS\System32\powrprof.dll
0x76fd0000 - 0x77016000 C:\WINDOWS\System32\shlwapi.dll
0x74d10000 - 0x74d1d000 C:\WINDOWS\System32\kernel.appcore.dll
0x775e0000 - 0x77668000 C:\WINDOWS\System32\shcore.dll
0x772b0000 - 0x772bf000 C:\WINDOWS\System32\profapi.dll
0x59ac0000 - 0x59c05000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\awt.dll
0x77530000 - 0x775c4000 C:\WINDOWS\System32\OLEAUT32.dll
0x77670000 - 0x776eb000 C:\WINDOWS\System32\msvcp_win.dll
0x598d0000 - 0x59962000 C:\WINDOWS\SYSTEM32\apphelp.dll
0x69d30000 - 0x69da5000 C:\WINDOWS\system32\uxtheme.dll
0x772c0000 - 0x773f6000 C:\WINDOWS\System32\MSCTF.dll
0x6b7d0000 - 0x6b7ef000 C:\WINDOWS\system32\dwmapi.dll
0x77440000 - 0x7752a000 C:\WINDOWS\System32\ole32.dll
0x60280000 - 0x603df000 C:\WINDOWS\system32\d3d9.dll
0x5fc40000 - 0x5fd6f000 C:\WINDOWS\SYSTEM32\aticfx32.dll
0x5dc50000 - 0x5dc6c000 C:\WINDOWS\SYSTEM32\atiu9pag.dll
0x59010000 - 0x598c1000 C:\WINDOWS\SYSTEM32\atiumdag.dll
0x58850000 - 0x5900f000 C:\WINDOWS\SYSTEM32\atiumdva.dll
0x59a80000 - 0x59ab9000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\fontmanager.dll
0x76ec0000 - 0x76f44000 C:\WINDOWS\System32\clbcatq.dll
0x5ed60000 - 0x5eece000 C:\WINDOWS\SYSTEM32\WindowsCodecs.dll
0x5f150000 - 0x5f194000 C:\WINDOWS\system32\dataexchange.dll
0x5f030000 - 0x5f143000 C:\WINDOWS\system32\dcomp.dll
0x69590000 - 0x697c0000 C:\WINDOWS\system32\d3d11.dll
0x697c0000 - 0x69844000 C:\WINDOWS\system32\dxgi.dll
0x5ef30000 - 0x5f021000 C:\WINDOWS\system32\twinapi.appcore.dll
0x74110000 - 0x7412b000 C:\WINDOWS\system32\bcrypt.dll
0x59a60000 - 0x59a76000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\net.dll
0x70ca0000 - 0x70cee000 C:\WINDOWS\system32\mswsock.dll
0x5dc40000 - 0x5dc4f000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\nio.dll
0x58820000 - 0x58850000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\t2k.dll
0x74ef0000 - 0x74fd5000 C:\WINDOWS\System32\COMDLG32.dll
0x587a0000 - 0x5881b000 C:\Program Files (x86)\Common Files\microsoft shared\ink\tiptsf.dll
0x58760000 - 0x5879d000 C:\WINDOWS\SYSTEM32\edputil.dll
0x58710000 - 0x58753000 C:\Windows\System32\thumbcache.dll
0x673b0000 - 0x674ff000 C:\WINDOWS\system32\propsys.dll
0x672e0000 - 0x673a1000 C:\WINDOWS\SYSTEM32\ntshrui.dll
0x68a70000 - 0x68a8c000 C:\WINDOWS\SYSTEM32\srvcli.dll
0x6b930000 - 0x6b93f000 C:\WINDOWS\SYSTEM32\cscapi.dll
0x58680000 - 0x58705000 C:\WINDOWS\System32\StructuredQuery.dll
0x58640000 - 0x5867f000 C:\WINDOWS\SYSTEM32\policymanager.dll
0x585d0000 - 0x58637000 C:\WINDOWS\SYSTEM32\msvcp110_win.dll
0x58520000 - 0x585cf000 C:\WINDOWS\system32\Windows.Storage.Search.dll
0x584e0000 - 0x58518000 C:\Program Files (x86)\Dropbox\Client\DropboxExt.65536.dll
0x58350000 - 0x584d8000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\FileSyncShell.dll
0x580b0000 - 0x58121000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\MSVCP120.dll
0x58180000 - 0x5826e000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\MSVCR120.dll
0x58130000 - 0x5817d000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\Telemetry.dll
0x6f610000 - 0x6f83e000 C:\WINDOWS\SYSTEM32\WININET.dll
0x58320000 - 0x58347000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\LoggingPlatform.DLL
0x58270000 - 0x58318000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\ClientTelemetry.dll
0x6f840000 - 0x6f86f000 C:\WINDOWS\SYSTEM32\IPHLPAPI.DLL
0x68be0000 - 0x68c01000 C:\WINDOWS\SYSTEM32\Cabinet.dll
0x74560000 - 0x745ff000 C:\WINDOWS\SYSTEM32\WINHTTP.dll
0x58090000 - 0x580a2000 C:\WINDOWS\system32\mssprxy.dll
0x46220000 - 0x46256000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle32.dll
0x46270000 - 0x462ad000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-cpu32-21.DLL
0x4c8d0000 - 0x4ce3e000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-opencl32-21.DLL
0x57ec0000 - 0x57ed3000 C:\WINDOWS\SYSTEM32\OpenCL.dll
0x556e0000 - 0x57eb2000 C:\WINDOWS\SYSTEM32\amdocl.dll
0x777b0000 - 0x77bbb000 C:\WINDOWS\System32\SETUPAPI.dll
0x6c320000 - 0x6c465000 C:\WINDOWS\SYSTEM32\dbghelp.dll
0x55600000 - 0x556e0000 C:\WINDOWS\SYSTEM32\OPENGL32.dll
0x554e0000 - 0x55505000 C:\WINDOWS\SYSTEM32\GLU32.dll
0x55510000 - 0x555fd000 C:\WINDOWS\SYSTEM32\DDRAW.dll
0x5dba0000 - 0x5dba7000 C:\WINDOWS\SYSTEM32\DCIMAN32.dll
0x553e0000 - 0x554d5000 C:\WINDOWS\SYSTEM32\atiadlxy.DLL
0x74600000 - 0x7460f000 C:\WINDOWS\SYSTEM32\WTSAPI32.dll
0x74530000 - 0x7454a000 C:\WINDOWS\SYSTEM32\USERENV.dll
0x6f980000 - 0x6f9a2000 C:\WINDOWS\SYSTEM32\DEVOBJ.dll
0x76cf0000 - 0x76d34000 C:\WINDOWS\System32\WINTRUST.dll
0x75310000 - 0x7531e000 C:\WINDOWS\System32\MSASN1.dll
0x76d40000 - 0x76ebd000 C:\WINDOWS\System32\CRYPT32.dll
0x53e30000 - 0x553d8000 C:\WINDOWS\SYSTEM32\amdocl12cl.dll
0x53e00000 - 0x53e27000 C:\WINDOWS\SYSTEM32\atigktxx.dll
0x4c360000 - 0x4c39c000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-cpu-sse32-21.DLL
VM Arguments:
jvm_args: -Xms256m -Xmx1024m
java_command: C:\Users\Andrew\Documents\BEAST v1.8.3\BEAST v1.8.3.exe -window -working -options
java_class_path (initial): C:\Users\Andrew\Documents\BEAST v1.8.3\BEAST v1.8.3.exe
Launcher Type: SUN_STANDARD
Environment Variables:
PATH=C:\Program Files (x86)\Common Files\libhmsbeagle\;C:\ProgramData\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Windows Live\Shared;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program Files (x86)\Skype\Phone\;C:\Program Files\MATLAB\R2013a\bin;C:\Program Files (x86)\FAHClient;C:\Users\Andrew\AppData\Local\Microsoft\WindowsApps;;C:\Program Files (x86)\Java\jre1.8.0_71\bin
USERNAME=Andrew
OS=Windows_NT
PROCESSOR_IDENTIFIER=AMD64 Family 22 Model 0 Stepping 1, AuthenticAMD
--------------- S Y S T E M ---------------
OS: Windows 10.0 , 64 bit Build 14393 (10.0.14393.0)
CPU:total 4 (4 cores per cpu, 1 threads per core) family 22 model 0 stepping 1, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, aes, clmul, mmxext, 3dnowpref, lzcnt, sse4a, tsc, tscinvbit, tscinv, bmi1
Memory: 4k page, physical 7827400k(5485404k free), swap 9072584k(6535724k free)
vm_info: Java HotSpot(TM) Client VM (25.71-b15) for windows-x86 JRE (1.8.0_71-b15), built on Dec 22 2015 17:22:59 by "java_re" with MS VC++ 10.0 (VS2010)
time: Sun Oct 02 11:57:43 2016
elapsed time: 58 seconds (0d 0h 0m 58s)
#
# A fatal error has been detected by the Java Runtime Environment:
#
# EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x4c36b6c0, pid=1936, tid=7916
#
# JRE version: Java(TM) SE Runtime Environment (8.0_71-b15) (build 1.8.0_71-b15)
# Java VM: Java HotSpot(TM) Client VM (25.71-b15 mixed mode windows-x86 )
# Problematic frame:
# C [hmsbeagle-cpu-sse32-21.DLL+0xb6c0]
#
# Failed to write core dump. Minidumps are not enabled by default on client versions of Windows
#
# 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 (0x4d086000): JavaThread "pool-1-thread-1" [_thread_in_native, id=7916, stack(0x4c3e0000,0x4c430000)]
siginfo: ExceptionCode=0xc0000005, reading address 0xffffffff
Registers:
EAX=0x00000060, EBX=0x4c42f2f0, ECX=0x00000000, EDX=0x4a99bc68
ESP=0x4c42f130, EBP=0x4c42f2e0, ESI=0x00000000, EDI=0x4a993850
EIP=0x4c36b6c0, EFLAGS=0x00010216
Top of Stack: (sp=0x4c42f130)
0x4c42f130: 4a99bc68 492fb440 ffffffff 00000000
0x4c42f140: 00000155 4a931660 493dd0c8 492fb440
0x4c42f150: 11981236 3fefd0dd cd87d380 3f5797fe
0x4c42f160: 9ab70880 3f678aef cd87d380 3f5797fe
0x4c42f170: cd36c280 3f5797fe 119811f9 3fefd0dd
0x4c42f180: cd36c280 3f5797fe 9a663300 3f678aef
0x4c42f190: 9ab70880 3f678aef cd87d380 3f5797fe
0x4c42f1a0: 11981236 3fefd0dd cd87d380 3f5797fe
Instructions: (pc=0x4c36b6c0)
0x4c36b6a0: 66 0f 59 c5 66 0f 58 c8 66 0f 28 85 80 fe ff ff
0x4c36b6b0: c1 e0 05 66 0f 59 c3 66 0f 59 8c 05 30 ff ff ff
0x4c36b6c0: 66 0f 29 0a 66 0f 28 8d a0 fe ff ff 66 0f 59 cc
0x4c36b6d0: 66 0f 58 c8 66 0f 28 85 c0 fe ff ff 66 0f 59 c2
Register to memory mapping:
EAX=0x00000060 is an unknown value
EBX=0x4c42f2f0 is pointing into the stack for thread: 0x4d086000
ECX=0x00000000 is an unknown value
EDX=0x4a99bc68 is an unknown value
ESP=0x4c42f130 is pointing into the stack for thread: 0x4d086000
EBP=0x4c42f2e0 is pointing into the stack for thread: 0x4d086000
ESI=0x00000000 is an unknown value
EDI=0x4a993850 is an unknown value
Stack: [0x4c3e0000,0x4c430000], sp=0x4c42f130, free space=316k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [hmsbeagle-cpu-sse32-21.DLL+0xb6c0]
C [hmsbeagle-cpu-sse32-21.DLL+0x113bc]
C [hmsbeagle32.dll+0x693e]
C [hmsbeagle32.dll+0x7679]
j beagle.BeagleJNIWrapper.updatePartials(I[III)I+0
j beagle.BeagleJNIImpl.updatePartials([III)V+10
j dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood()D+489
j dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood()D+9
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Double;+8
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Object;+1
j java.util.concurrent.FutureTask.run()V+42
j java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j java.lang.Thread.run()V+11
v ~StubRoutines::call_stub
V [jvm.dll+0x158bf5]
V [jvm.dll+0x21e0be]
V [jvm.dll+0x158c8e]
V [jvm.dll+0x158e16]
V [jvm.dll+0x158e87]
V [jvm.dll+0xfd68f]
V [jvm.dll+0x17c03c]
V [jvm.dll+0x17c12a]
V [jvm.dll+0x1c0636]
C [msvcr100.dll+0x5c556]
C [msvcr100.dll+0x5c600]
C [KERNEL32.DLL+0x162c4]
C [ntdll.dll+0x60609]
C [ntdll.dll+0x605d4]
C 0x00000000
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j beagle.BeagleJNIWrapper.updatePartials(I[III)I+0
j beagle.BeagleJNIImpl.updatePartials([III)V+10
j dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood()D+489
j dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood()D+9
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Double;+8
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Object;+1
j java.util.concurrent.FutureTask.run()V+42
j java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j java.lang.Thread.run()V+11
v ~StubRoutines::call_stub
--------------- P R O C E S S ---------------
Java Threads: ( => current thread )
0x4d086800 JavaThread "pool-1-thread-2" [_thread_blocked, id=7920, stack(0x4da80000,0x4dad0000)]
=>0x4d086000 JavaThread "pool-1-thread-1" [_thread_in_native, id=7916, stack(0x4c3e0000,0x4c430000)]
0x4649c000 JavaThread "TimerQueue" daemon [_thread_blocked, id=6152, stack(0x49430000,0x49480000)]
0x46465000 JavaThread "D3D Screen Updater" daemon [_thread_blocked, id=3044, stack(0x4a2c0000,0x4a310000)]
0x46457c00 JavaThread "Thread-3" [_thread_blocked, id=6724, stack(0x4a130000,0x4a180000)]
0x46457800 JavaThread "Thread-2" [_thread_blocked, id=7600, stack(0x4a0a0000,0x4a0f0000)]
0x459cc000 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=7484, stack(0x49940000,0x49990000)]
0x45982800 JavaThread "AWT-Windows" daemon [_thread_in_native, id=4716, stack(0x46100000,0x46150000)]
0x45982000 JavaThread "AWT-Shutdown" [_thread_blocked, id=5912, stack(0x46070000,0x460c0000)]
0x45981800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=7236, stack(0x45fe0000,0x46030000)]
0x457fb800 JavaThread "Service Thread" daemon [_thread_blocked, id=5524, stack(0x45dd0000,0x45e20000)]
0x457f3800 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=940, stack(0x45d40000,0x45d90000)]
0x457fd800 JavaThread "Attach Listener" daemon [_thread_blocked, id=5620, stack(0x45cb0000,0x45d00000)]
0x457fc800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=5404, stack(0x45c20000,0x45c70000)]
0x457d6400 JavaThread "Finalizer" daemon [_thread_blocked, id=5540, stack(0x45aa0000,0x45af0000)]
0x457d1400 JavaThread "Reference Handler" daemon [_thread_blocked, id=5688, stack(0x45a10000,0x45a60000)]
0x02e5b800 JavaThread "main" [_thread_blocked, id=4848, stack(0x02d50000,0x02da0000)]
Other Threads:
0x02f5b400 VMThread [stack: 0x04fa0000,0x04ff0000] [id=1700]
0x45825400 WatcherThread [stack: 0x45e60000,0x45eb0000] [id=5528]
VM state:not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: None
Heap:
def new generation total 78720K, used 9950K [0x05000000, 0x0a560000, 0x1a550000)
eden space 70016K, 14% used [0x05000000, 0x059b7808, 0x09460000)
from space 8704K, 0% used [0x09460000, 0x09460000, 0x09ce0000)
to space 8704K, 0% used [0x09ce0000, 0x09ce0000, 0x0a560000)
tenured generation total 174784K, used 9672K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 5% used [0x1a550000, 0x1aec2358, 0x1aec2400, 0x25000000)
Metaspace used 13354K, capacity 13561K, committed 13696K, reserved 13696K
Card table byte_map: [0x45000000,0x45210000] byte_map_base: 0x44fd8000
Polling page: 0x02da0000
CodeCache: size=32768Kb used=1798Kb max_used=1800Kb free=30969Kb
bounds [0x02f60000, 0x03128000, 0x04f60000]
total_blobs=1155 nmethods=861 adapters=224
compilation: enabled
Compilation events (10 events):
Event: 58.132 Thread 0x457f3800 863 dr.xml.XMLObject::getRawChild (9 bytes)
Event: 58.133 Thread 0x457f3800 nmethod 863 0x03120148 code [0x03120260, 0x0312050c]
Event: 58.133 Thread 0x457f3800 864 dr.xml.XMLObject::getChild (56 bytes)
Event: 58.135 Thread 0x457f3800 nmethod 864 0x03120808 code [0x03120930, 0x03120cbc]
Event: 58.163 Thread 0x457f3800 865 ! java.util.zip.Inflater::setInput (74 bytes)
Event: 58.164 Thread 0x457f3800 nmethod 865 0x03121388 code [0x031214a0, 0x031217c8]
Event: 58.189 Thread 0x457f3800 866 javax.swing.text.GapContent::findSortIndex (128 bytes)
Event: 58.191 Thread 0x457f3800 nmethod 866 0x03121c08 code [0x03121d30, 0x03121f78]
Event: 58.195 Thread 0x457f3800 867 sun.font.GlyphList::usePositions (5 bytes)
Event: 58.195 Thread 0x457f3800 nmethod 867 0x03122248 code [0x03122340, 0x031223c0]
GC Heap History (2 events):
Event: 55.715 GC heap before
{Heap before GC invocations=0 (full 0):
def new generation total 78656K, used 54605K [0x05000000, 0x0a550000, 0x1a550000)
eden space 69952K, 78% used [0x05000000, 0x085534d0, 0x09450000)
from space 8704K, 0% used [0x09450000, 0x09450000, 0x09cd0000)
to space 8704K, 0% used [0x09cd0000, 0x09cd0000, 0x0a550000)
tenured generation total 174784K, used 0K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 0% used [0x1a550000, 0x1a550000, 0x1a550200, 0x25000000)
Metaspace used 11992K, capacity 12185K, committed 12288K, reserved 12672K
Event: 55.868 GC heap after
Heap after GC invocations=1 (full 1):
def new generation total 78720K, used 0K [0x05000000, 0x0a560000, 0x1a550000)
eden space 70016K, 0% used [0x05000000, 0x05000000, 0x09460000)
from space 8704K, 0% used [0x09460000, 0x09460000, 0x09ce0000)
to space 8704K, 0% used [0x09ce0000, 0x09ce0000, 0x0a560000)
tenured generation total 174784K, used 9672K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 5% used [0x1a550000, 0x1aec2358, 0x1aec2400, 0x25000000)
Metaspace used 11992K, capacity 12185K, committed 12288K, reserved 12672K
}
Deoptimization events (0 events):
No events
Internal exceptions (10 events):
Event: 0.233 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.defineClass(Ljava/lang/String;[BII)Ljava/lang/Class; name or signature does not match> (0x0500b960) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vðŸ$Ò³ÖÍ?
Event: 0.233 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.prefetchRead(Ljava/lang/Object;J)V name or signature does not match> (0x0500bc30) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, l÷*ì¨ûàâ?
Event: 0.590 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e1a50) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.590 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e1c50) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.593 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e5a38) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.593 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e5c38) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.630 Thread 0x02e5b800 Exception <a 'java/io/FileNotFoundException'> (0x050e9e98) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, line 709]
Event: 0.767 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x05460368) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\methodHandles.cpp, line 1146]
Event: 0.772 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x0546c508) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\methodHandles.cpp, line 1146]
Event: 1.017 Thread 0x02e5b800 Exception <a 'java/io/FileNotFoundException'> (0x0556f8a0) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, line 709]
Events (10 events):
Event: 58.188 Thread 0x4d086800 Thread added: 0x4d086800
Event: 58.189 loading class dr/app/beagle/evomodel/substmodel/EigenDecomposition
Event: 58.190 loading class dr/app/beagle/evomodel/substmodel/EigenDecomposition done
Event: 58.190 Executing VM operation: RevokeBias
Event: 58.191 Executing VM operation: RevokeBias done
Event: 58.192 loading class dr/app/beagle/evomodel/branchmodel/BranchModel$1
Event: 58.192 loading class dr/app/beagle/evomodel/branchmodel/BranchModel$1 done
Event: 58.192 Executing VM operation: RevokeBias
Event: 58.193 Executing VM operation: RevokeBias done
Event: 58.195 Thread 0x457f3800 flushing nmethod 0x03081b48
Dynamic libraries:
0x00b40000 - 0x00b73000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\javaw.exe
0x77bc0000 - 0x77d42000 C:\WINDOWS\SYSTEM32\ntdll.dll
0x746a0000 - 0x74780000 C:\WINDOWS\System32\KERNEL32.DLL
0x75160000 - 0x75301000 C:\WINDOWS\System32\KERNELBASE.dll
0x76f50000 - 0x76fc7000 C:\WINDOWS\System32\ADVAPI32.dll
0x75090000 - 0x7514e000 C:\WINDOWS\System32\msvcrt.dll
0x74dc0000 - 0x74e01000 C:\WINDOWS\System32\sechost.dll
0x771e0000 - 0x772a1000 C:\WINDOWS\System32\RPCRT4.dll
0x74680000 - 0x7469e000 C:\WINDOWS\System32\SspiCli.dll
0x74670000 - 0x7467a000 C:\WINDOWS\System32\CRYPTBASE.dll
0x776f0000 - 0x7774a000 C:\WINDOWS\System32\bcryptPrimitives.dll
0x77020000 - 0x7717f000 C:\WINDOWS\System32\USER32.dll
0x75320000 - 0x75335000 C:\WINDOWS\System32\win32u.dll
0x74d90000 - 0x74dbb000 C:\WINDOWS\System32\GDI32.dll
0x749a0000 - 0x74afb000 C:\WINDOWS\System32\gdi32full.dll
0x6a6e0000 - 0x6a8ea000 C:\WINDOWS\WinSxS\x86_microsoft.windows.common-controls_6595b64144ccf1df_6.0.14393.0_none_74bc87d3d22d9abe\COMCTL32.dll
0x74780000 - 0x74991000 C:\WINDOWS\System32\combase.dll
0x74e10000 - 0x74ef0000 C:\WINDOWS\System32\ucrtbase.dll
0x75060000 - 0x75085000 C:\WINDOWS\System32\IMM32.DLL
0x59fe0000 - 0x5a09f000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\msvcr100.dll
0x59c10000 - 0x59fd8000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\client\jvm.dll
0x75150000 - 0x75156000 C:\WINDOWS\System32\PSAPI.DLL
0x70d10000 - 0x70d18000 C:\WINDOWS\SYSTEM32\WSOCK32.dll
0x71690000 - 0x716b4000 C:\WINDOWS\SYSTEM32\WINMM.dll
0x73fc0000 - 0x73fc8000 C:\WINDOWS\SYSTEM32\VERSION.dll
0x71660000 - 0x71683000 C:\WINDOWS\SYSTEM32\WINMMBASE.dll
0x77400000 - 0x77436000 C:\WINDOWS\System32\cfgmgr32.dll
0x74d20000 - 0x74d83000 C:\WINDOWS\System32\WS2_32.dll
0x5e8d0000 - 0x5e8dc000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\verify.dll
0x5e050000 - 0x5e071000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\java.dll
0x5e230000 - 0x5e243000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\zip.dll
0x758b0000 - 0x76c87000 C:\WINDOWS\System32\SHELL32.dll
0x75340000 - 0x758ae000 C:\WINDOWS\System32\windows.storage.dll
0x76ca0000 - 0x76ce5000 C:\WINDOWS\System32\powrprof.dll
0x76fd0000 - 0x77016000 C:\WINDOWS\System32\shlwapi.dll
0x74d10000 - 0x74d1d000 C:\WINDOWS\System32\kernel.appcore.dll
0x775e0000 - 0x77668000 C:\WINDOWS\System32\shcore.dll
0x772b0000 - 0x772bf000 C:\WINDOWS\System32\profapi.dll
0x59ac0000 - 0x59c05000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\awt.dll
0x77530000 - 0x775c4000 C:\WINDOWS\System32\OLEAUT32.dll
0x77670000 - 0x776eb000 C:\WINDOWS\System32\msvcp_win.dll
0x598d0000 - 0x59962000 C:\WINDOWS\SYSTEM32\apphelp.dll
0x69d30000 - 0x69da5000 C:\WINDOWS\system32\uxtheme.dll
0x772c0000 - 0x773f6000 C:\WINDOWS\System32\MSCTF.dll
0x6b7d0000 - 0x6b7ef000 C:\WINDOWS\system32\dwmapi.dll
0x77440000 - 0x7752a000 C:\WINDOWS\System32\ole32.dll
0x60280000 - 0x603df000 C:\WINDOWS\system32\d3d9.dll
0x5fc40000 - 0x5fd6f000 C:\WINDOWS\SYSTEM32\aticfx32.dll
0x5dc50000 - 0x5dc6c000 C:\WINDOWS\SYSTEM32\atiu9pag.dll
0x59010000 - 0x598c1000 C:\WINDOWS\SYSTEM32\atiumdag.dll
0x58850000 - 0x5900f000 C:\WINDOWS\SYSTEM32\atiumdva.dll
0x59a80000 - 0x59ab9000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\fontmanager.dll
0x76ec0000 - 0x76f44000 C:\WINDOWS\System32\clbcatq.dll
0x5ed60000 - 0x5eece000 C:\WINDOWS\SYSTEM32\WindowsCodecs.dll
0x5f150000 - 0x5f194000 C:\WINDOWS\system32\dataexchange.dll
0x5f030000 - 0x5f143000 C:\WINDOWS\system32\dcomp.dll
0x69590000 - 0x697c0000 C:\WINDOWS\system32\d3d11.dll
0x697c0000 - 0x69844000 C:\WINDOWS\system32\dxgi.dll
0x5ef30000 - 0x5f021000 C:\WINDOWS\system32\twinapi.appcore.dll
0x74110000 - 0x7412b000 C:\WINDOWS\system32\bcrypt.dll
0x59a60000 - 0x59a76000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\net.dll
0x70ca0000 - 0x70cee000 C:\WINDOWS\system32\mswsock.dll
0x5dc40000 - 0x5dc4f000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\nio.dll
0x58820000 - 0x58850000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\t2k.dll
0x74ef0000 - 0x74fd5000 C:\WINDOWS\System32\COMDLG32.dll
0x587a0000 - 0x5881b000 C:\Program Files (x86)\Common Files\microsoft shared\ink\tiptsf.dll
0x58760000 - 0x5879d000 C:\WINDOWS\SYSTEM32\edputil.dll
0x58710000 - 0x58753000 C:\Windows\System32\thumbcache.dll
0x673b0000 - 0x674ff000 C:\WINDOWS\system32\propsys.dll
0x672e0000 - 0x673a1000 C:\WINDOWS\SYSTEM32\ntshrui.dll
0x68a70000 - 0x68a8c000 C:\WINDOWS\SYSTEM32\srvcli.dll
0x6b930000 - 0x6b93f000 C:\WINDOWS\SYSTEM32\cscapi.dll
0x58680000 - 0x58705000 C:\WINDOWS\System32\StructuredQuery.dll
0x58640000 - 0x5867f000 C:\WINDOWS\SYSTEM32\policymanager.dll
0x585d0000 - 0x58637000 C:\WINDOWS\SYSTEM32\msvcp110_win.dll
0x58520000 - 0x585cf000 C:\WINDOWS\system32\Windows.Storage.Search.dll
0x584e0000 - 0x58518000 C:\Program Files (x86)\Dropbox\Client\DropboxExt.65536.dll
0x58350000 - 0x584d8000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\FileSyncShell.dll
0x580b0000 - 0x58121000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\MSVCP120.dll
0x58180000 - 0x5826e000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\MSVCR120.dll
0x58130000 - 0x5817d000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\Telemetry.dll
0x6f610000 - 0x6f83e000 C:\WINDOWS\SYSTEM32\WININET.dll
0x58320000 - 0x58347000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\LoggingPlatform.DLL
0x58270000 - 0x58318000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\ClientTelemetry.dll
0x6f840000 - 0x6f86f000 C:\WINDOWS\SYSTEM32\IPHLPAPI.DLL
0x68be0000 - 0x68c01000 C:\WINDOWS\SYSTEM32\Cabinet.dll
0x74560000 - 0x745ff000 C:\WINDOWS\SYSTEM32\WINHTTP.dll
0x58090000 - 0x580a2000 C:\WINDOWS\system32\mssprxy.dll
0x46220000 - 0x46256000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle32.dll
0x46270000 - 0x462ad000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-cpu32-21.DLL
0x4c8d0000 - 0x4ce3e000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-opencl32-21.DLL
0x57ec0000 - 0x57ed3000 C:\WINDOWS\SYSTEM32\OpenCL.dll
0x556e0000 - 0x57eb2000 C:\WINDOWS\SYSTEM32\amdocl.dll
0x777b0000 - 0x77bbb000 C:\WINDOWS\System32\SETUPAPI.dll
0x6c320000 - 0x6c465000 C:\WINDOWS\SYSTEM32\dbghelp.dll
0x55600000 - 0x556e0000 C:\WINDOWS\SYSTEM32\OPENGL32.dll
0x554e0000 - 0x55505000 C:\WINDOWS\SYSTEM32\GLU32.dll
0x55510000 - 0x555fd000 C:\WINDOWS\SYSTEM32\DDRAW.dll
0x5dba0000 - 0x5dba7000 C:\WINDOWS\SYSTEM32\DCIMAN32.dll
0x553e0000 - 0x554d5000 C:\WINDOWS\SYSTEM32\atiadlxy.DLL
0x74600000 - 0x7460f000 C:\WINDOWS\SYSTEM32\WTSAPI32.dll
0x74530000 - 0x7454a000 C:\WINDOWS\SYSTEM32\USERENV.dll
0x6f980000 - 0x6f9a2000 C:\WINDOWS\SYSTEM32\DEVOBJ.dll
0x76cf0000 - 0x76d34000 C:\WINDOWS\System32\WINTRUST.dll
0x75310000 - 0x7531e000 C:\WINDOWS\System32\MSASN1.dll
0x76d40000 - 0x76ebd000 C:\WINDOWS\System32\CRYPT32.dll
0x53e30000 - 0x553d8000 C:\WINDOWS\SYSTEM32\amdocl12cl.dll
0x53e00000 - 0x53e27000 C:\WINDOWS\SYSTEM32\atigktxx.dll
0x4c360000 - 0x4c39c000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-cpu-sse32-21.DLL
VM Arguments:
jvm_args: -Xms256m -Xmx1024m
java_command: C:\Users\Andrew\Documents\BEAST v1.8.3\BEAST v1.8.3.exe -window -working -options
java_class_path (initial): C:\Users\Andrew\Documents\BEAST v1.8.3\BEAST v1.8.3.exe
Launcher Type: SUN_STANDARD
Environment Variables:
PATH=C:\Program Files (x86)\Common Files\libhmsbeagle\;C:\ProgramData\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Windows Live\Shared;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program Files (x86)\Skype\Phone\;C:\Program Files\MATLAB\R2013a\bin;C:\Program Files (x86)\FAHClient;C:\Users\Andrew\AppData\Local\Microsoft\WindowsApps;;C:\Program Files (x86)\Java\jre1.8.0_71\bin
USERNAME=Andrew
OS=Windows_NT
PROCESSOR_IDENTIFIER=AMD64 Family 22 Model 0 Stepping 1, AuthenticAMD
--------------- S Y S T E M ---------------
OS: Windows 10.0 , 64 bit Build 14393 (10.0.14393.0)
CPU:total 4 (4 cores per cpu, 1 threads per core) family 22 model 0 stepping 1, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, aes, clmul, mmxext, 3dnowpref, lzcnt, sse4a, tsc, tscinvbit, tscinv, bmi1
Memory: 4k page, physical 7827400k(5485404k free), swap 9072584k(6535724k free)
vm_info: Java HotSpot(TM) Client VM (25.71-b15) for windows-x86 JRE (1.8.0_71-b15), built on Dec 22 2015 17:22:59 by "java_re" with MS VC++ 10.0 (VS2010)
time: Sun Oct 02 11:57:43 2016
elapsed time: 58 seconds (0d 0h 0m 58s)
Thanks,
Andrew
I installed Beagle and Beast today and so far have not been able to complete a successful run. Whilst I can convert my FASTA file to xml using BEAUti, when I run it in BEAST it fails. A file called "hs_err_pid1936.log" is created, which contains the text I've posted below. Two blank files (filename.log.txt and filename.trees.txt) are also created. Any ideas? I'm on Windows 10 x64, AMD A4-5000 APU. My Java is Version 8 Update 101 build 1.8.0_101-b13. Any ideas?
#
# A fatal error has been detected by the Java Runtime Environment:
#
# EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x4c36b6c0, pid=1936, tid=7916
#
# JRE version: Java(TM) SE Runtime Environment (8.0_71-b15) (build 1.8.0_71-b15)
# Java VM: Java HotSpot(TM) Client VM (25.71-b15 mixed mode windows-x86 )
# Problematic frame:
# C [hmsbeagle-cpu-sse32-21.DLL+0xb6c0]
#
# Failed to write core dump. Minidumps are not enabled by default on client versions of Windows
#
# 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 (0x4d086000): JavaThread "pool-1-thread-1" [_thread_in_native, id=7916, stack(0x4c3e0000,0x4c430000)]
siginfo: ExceptionCode=0xc0000005, reading address 0xffffffff
Registers:
EAX=0x00000060, EBX=0x4c42f2f0, ECX=0x00000000, EDX=0x4a99bc68
ESP=0x4c42f130, EBP=0x4c42f2e0, ESI=0x00000000, EDI=0x4a993850
EIP=0x4c36b6c0, EFLAGS=0x00010216
Top of Stack: (sp=0x4c42f130)
0x4c42f130: 4a99bc68 492fb440 ffffffff 00000000
0x4c42f140: 00000155 4a931660 493dd0c8 492fb440
0x4c42f150: 11981236 3fefd0dd cd87d380 3f5797fe
0x4c42f160: 9ab70880 3f678aef cd87d380 3f5797fe
0x4c42f170: cd36c280 3f5797fe 119811f9 3fefd0dd
0x4c42f180: cd36c280 3f5797fe 9a663300 3f678aef
0x4c42f190: 9ab70880 3f678aef cd87d380 3f5797fe
0x4c42f1a0: 11981236 3fefd0dd cd87d380 3f5797fe
Instructions: (pc=0x4c36b6c0)
0x4c36b6a0: 66 0f 59 c5 66 0f 58 c8 66 0f 28 85 80 fe ff ff
0x4c36b6b0: c1 e0 05 66 0f 59 c3 66 0f 59 8c 05 30 ff ff ff
0x4c36b6c0: 66 0f 29 0a 66 0f 28 8d a0 fe ff ff 66 0f 59 cc
0x4c36b6d0: 66 0f 58 c8 66 0f 28 85 c0 fe ff ff 66 0f 59 c2
Register to memory mapping:
EAX=0x00000060 is an unknown value
EBX=0x4c42f2f0 is pointing into the stack for thread: 0x4d086000
ECX=0x00000000 is an unknown value
EDX=0x4a99bc68 is an unknown value
ESP=0x4c42f130 is pointing into the stack for thread: 0x4d086000
EBP=0x4c42f2e0 is pointing into the stack for thread: 0x4d086000
ESI=0x00000000 is an unknown value
EDI=0x4a993850 is an unknown value
Stack: [0x4c3e0000,0x4c430000], sp=0x4c42f130, free space=316k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [hmsbeagle-cpu-sse32-21.DLL+0xb6c0]
C [hmsbeagle-cpu-sse32-21.DLL+0x113bc]
C [hmsbeagle32.dll+0x693e]
C [hmsbeagle32.dll+0x7679]
j beagle.BeagleJNIWrapper.updatePartials(I[III)I+0
j beagle.BeagleJNIImpl.updatePartials([III)V+10
j dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood()D+489
j dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood()D+9
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Double;+8
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Object;+1
j java.util.concurrent.FutureTask.run()V+42
j java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j java.lang.Thread.run()V+11
v ~StubRoutines::call_stub
V [jvm.dll+0x158bf5]
V [jvm.dll+0x21e0be]
V [jvm.dll+0x158c8e]
V [jvm.dll+0x158e16]
V [jvm.dll+0x158e87]
V [jvm.dll+0xfd68f]
V [jvm.dll+0x17c03c]
V [jvm.dll+0x17c12a]
V [jvm.dll+0x1c0636]
C [msvcr100.dll+0x5c556]
C [msvcr100.dll+0x5c600]
C [KERNEL32.DLL+0x162c4]
C [ntdll.dll+0x60609]
C [ntdll.dll+0x605d4]
C 0x00000000
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j beagle.BeagleJNIWrapper.updatePartials(I[III)I+0
j beagle.BeagleJNIImpl.updatePartials([III)V+10
j dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood()D+489
j dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood()D+9
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Double;+8
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Object;+1
j java.util.concurrent.FutureTask.run()V+42
j java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j java.lang.Thread.run()V+11
v ~StubRoutines::call_stub
--------------- P R O C E S S ---------------
Java Threads: ( => current thread )
0x4d086800 JavaThread "pool-1-thread-2" [_thread_blocked, id=7920, stack(0x4da80000,0x4dad0000)]
=>0x4d086000 JavaThread "pool-1-thread-1" [_thread_in_native, id=7916, stack(0x4c3e0000,0x4c430000)]
0x4649c000 JavaThread "TimerQueue" daemon [_thread_blocked, id=6152, stack(0x49430000,0x49480000)]
0x46465000 JavaThread "D3D Screen Updater" daemon [_thread_blocked, id=3044, stack(0x4a2c0000,0x4a310000)]
0x46457c00 JavaThread "Thread-3" [_thread_blocked, id=6724, stack(0x4a130000,0x4a180000)]
0x46457800 JavaThread "Thread-2" [_thread_blocked, id=7600, stack(0x4a0a0000,0x4a0f0000)]
0x459cc000 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=7484, stack(0x49940000,0x49990000)]
0x45982800 JavaThread "AWT-Windows" daemon [_thread_in_native, id=4716, stack(0x46100000,0x46150000)]
0x45982000 JavaThread "AWT-Shutdown" [_thread_blocked, id=5912, stack(0x46070000,0x460c0000)]
0x45981800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=7236, stack(0x45fe0000,0x46030000)]
0x457fb800 JavaThread "Service Thread" daemon [_thread_blocked, id=5524, stack(0x45dd0000,0x45e20000)]
0x457f3800 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=940, stack(0x45d40000,0x45d90000)]
0x457fd800 JavaThread "Attach Listener" daemon [_thread_blocked, id=5620, stack(0x45cb0000,0x45d00000)]
0x457fc800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=5404, stack(0x45c20000,0x45c70000)]
0x457d6400 JavaThread "Finalizer" daemon [_thread_blocked, id=5540, stack(0x45aa0000,0x45af0000)]
0x457d1400 JavaThread "Reference Handler" daemon [_thread_blocked, id=5688, stack(0x45a10000,0x45a60000)]
0x02e5b800 JavaThread "main" [_thread_blocked, id=4848, stack(0x02d50000,0x02da0000)]
Other Threads:
0x02f5b400 VMThread [stack: 0x04fa0000,0x04ff0000] [id=1700]
0x45825400 WatcherThread [stack: 0x45e60000,0x45eb0000] [id=5528]
VM state:not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: None
Heap:
def new generation total 78720K, used 9950K [0x05000000, 0x0a560000, 0x1a550000)
eden space 70016K, 14% used [0x05000000, 0x059b7808, 0x09460000)
from space 8704K, 0% used [0x09460000, 0x09460000, 0x09ce0000)
to space 8704K, 0% used [0x09ce0000, 0x09ce0000, 0x0a560000)
tenured generation total 174784K, used 9672K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 5% used [0x1a550000, 0x1aec2358, 0x1aec2400, 0x25000000)
Metaspace used 13354K, capacity 13561K, committed 13696K, reserved 13696K
Card table byte_map: [0x45000000,0x45210000] byte_map_base: 0x44fd8000
Polling page: 0x02da0000
CodeCache: size=32768Kb used=1798Kb max_used=1800Kb free=30969Kb
bounds [0x02f60000, 0x03128000, 0x04f60000]
total_blobs=1155 nmethods=861 adapters=224
compilation: enabled
Compilation events (10 events):
Event: 58.132 Thread 0x457f3800 863 dr.xml.XMLObject::getRawChild (9 bytes)
Event: 58.133 Thread 0x457f3800 nmethod 863 0x03120148 code [0x03120260, 0x0312050c]
Event: 58.133 Thread 0x457f3800 864 dr.xml.XMLObject::getChild (56 bytes)
Event: 58.135 Thread 0x457f3800 nmethod 864 0x03120808 code [0x03120930, 0x03120cbc]
Event: 58.163 Thread 0x457f3800 865 ! java.util.zip.Inflater::setInput (74 bytes)
Event: 58.164 Thread 0x457f3800 nmethod 865 0x03121388 code [0x031214a0, 0x031217c8]
Event: 58.189 Thread 0x457f3800 866 javax.swing.text.GapContent::findSortIndex (128 bytes)
Event: 58.191 Thread 0x457f3800 nmethod 866 0x03121c08 code [0x03121d30, 0x03121f78]
Event: 58.195 Thread 0x457f3800 867 sun.font.GlyphList::usePositions (5 bytes)
Event: 58.195 Thread 0x457f3800 nmethod 867 0x03122248 code [0x03122340, 0x031223c0]
GC Heap History (2 events):
Event: 55.715 GC heap before
{Heap before GC invocations=0 (full 0):
def new generation total 78656K, used 54605K [0x05000000, 0x0a550000, 0x1a550000)
eden space 69952K, 78% used [0x05000000, 0x085534d0, 0x09450000)
from space 8704K, 0% used [0x09450000, 0x09450000, 0x09cd0000)
to space 8704K, 0% used [0x09cd0000, 0x09cd0000, 0x0a550000)
tenured generation total 174784K, used 0K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 0% used [0x1a550000, 0x1a550000, 0x1a550200, 0x25000000)
Metaspace used 11992K, capacity 12185K, committed 12288K, reserved 12672K
Event: 55.868 GC heap after
Heap after GC invocations=1 (full 1):
def new generation total 78720K, used 0K [0x05000000, 0x0a560000, 0x1a550000)
eden space 70016K, 0% used [0x05000000, 0x05000000, 0x09460000)
from space 8704K, 0% used [0x09460000, 0x09460000, 0x09ce0000)
to space 8704K, 0% used [0x09ce0000, 0x09ce0000, 0x0a560000)
tenured generation total 174784K, used 9672K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 5% used [0x1a550000, 0x1aec2358, 0x1aec2400, 0x25000000)
Metaspace used 11992K, capacity 12185K, committed 12288K, reserved 12672K
}
Deoptimization events (0 events):
No events
Internal exceptions (10 events):
Event: 0.233 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.defineClass(Ljava/lang/String;[BII)Ljava/lang/Class; name or signature does not match> (0x0500b960) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vðŸ$Ò³ÖÍ?
Event: 0.233 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.prefetchRead(Ljava/lang/Object;J)V name or signature does not match> (0x0500bc30) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, l÷*ì¨ûàâ?
Event: 0.590 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e1a50) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.590 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e1c50) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.593 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e5a38) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.593 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e5c38) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.630 Thread 0x02e5b800 Exception <a 'java/io/FileNotFoundException'> (0x050e9e98) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, line 709]
Event: 0.767 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x05460368) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\methodHandles.cpp, line 1146]
Event: 0.772 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x0546c508) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\methodHandles.cpp, line 1146]
Event: 1.017 Thread 0x02e5b800 Exception <a 'java/io/FileNotFoundException'> (0x0556f8a0) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, line 709]
Events (10 events):
Event: 58.188 Thread 0x4d086800 Thread added: 0x4d086800
Event: 58.189 loading class dr/app/beagle/evomodel/substmodel/EigenDecomposition
Event: 58.190 loading class dr/app/beagle/evomodel/substmodel/EigenDecomposition done
Event: 58.190 Executing VM operation: RevokeBias
Event: 58.191 Executing VM operation: RevokeBias done
Event: 58.192 loading class dr/app/beagle/evomodel/branchmodel/BranchModel$1
Event: 58.192 loading class dr/app/beagle/evomodel/branchmodel/BranchModel$1 done
Event: 58.192 Executing VM operation: RevokeBias
Event: 58.193 Executing VM operation: RevokeBias done
Event: 58.195 Thread 0x457f3800 flushing nmethod 0x03081b48
Dynamic libraries:
0x00b40000 - 0x00b73000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\javaw.exe
0x77bc0000 - 0x77d42000 C:\WINDOWS\SYSTEM32\ntdll.dll
0x746a0000 - 0x74780000 C:\WINDOWS\System32\KERNEL32.DLL
0x75160000 - 0x75301000 C:\WINDOWS\System32\KERNELBASE.dll
0x76f50000 - 0x76fc7000 C:\WINDOWS\System32\ADVAPI32.dll
0x75090000 - 0x7514e000 C:\WINDOWS\System32\msvcrt.dll
0x74dc0000 - 0x74e01000 C:\WINDOWS\System32\sechost.dll
0x771e0000 - 0x772a1000 C:\WINDOWS\System32\RPCRT4.dll
0x74680000 - 0x7469e000 C:\WINDOWS\System32\SspiCli.dll
0x74670000 - 0x7467a000 C:\WINDOWS\System32\CRYPTBASE.dll
0x776f0000 - 0x7774a000 C:\WINDOWS\System32\bcryptPrimitives.dll
0x77020000 - 0x7717f000 C:\WINDOWS\System32\USER32.dll
0x75320000 - 0x75335000 C:\WINDOWS\System32\win32u.dll
0x74d90000 - 0x74dbb000 C:\WINDOWS\System32\GDI32.dll
0x749a0000 - 0x74afb000 C:\WINDOWS\System32\gdi32full.dll
0x6a6e0000 - 0x6a8ea000 C:\WINDOWS\WinSxS\x86_microsoft.windows.common-controls_6595b64144ccf1df_6.0.14393.0_none_74bc87d3d22d9abe\COMCTL32.dll
0x74780000 - 0x74991000 C:\WINDOWS\System32\combase.dll
0x74e10000 - 0x74ef0000 C:\WINDOWS\System32\ucrtbase.dll
0x75060000 - 0x75085000 C:\WINDOWS\System32\IMM32.DLL
0x59fe0000 - 0x5a09f000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\msvcr100.dll
0x59c10000 - 0x59fd8000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\client\jvm.dll
0x75150000 - 0x75156000 C:\WINDOWS\System32\PSAPI.DLL
0x70d10000 - 0x70d18000 C:\WINDOWS\SYSTEM32\WSOCK32.dll
0x71690000 - 0x716b4000 C:\WINDOWS\SYSTEM32\WINMM.dll
0x73fc0000 - 0x73fc8000 C:\WINDOWS\SYSTEM32\VERSION.dll
0x71660000 - 0x71683000 C:\WINDOWS\SYSTEM32\WINMMBASE.dll
0x77400000 - 0x77436000 C:\WINDOWS\System32\cfgmgr32.dll
0x74d20000 - 0x74d83000 C:\WINDOWS\System32\WS2_32.dll
0x5e8d0000 - 0x5e8dc000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\verify.dll
0x5e050000 - 0x5e071000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\java.dll
0x5e230000 - 0x5e243000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\zip.dll
0x758b0000 - 0x76c87000 C:\WINDOWS\System32\SHELL32.dll
0x75340000 - 0x758ae000 C:\WINDOWS\System32\windows.storage.dll
0x76ca0000 - 0x76ce5000 C:\WINDOWS\System32\powrprof.dll
0x76fd0000 - 0x77016000 C:\WINDOWS\System32\shlwapi.dll
0x74d10000 - 0x74d1d000 C:\WINDOWS\System32\kernel.appcore.dll
0x775e0000 - 0x77668000 C:\WINDOWS\System32\shcore.dll
0x772b0000 - 0x772bf000 C:\WINDOWS\System32\profapi.dll
0x59ac0000 - 0x59c05000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\awt.dll
0x77530000 - 0x775c4000 C:\WINDOWS\System32\OLEAUT32.dll
0x77670000 - 0x776eb000 C:\WINDOWS\System32\msvcp_win.dll
0x598d0000 - 0x59962000 C:\WINDOWS\SYSTEM32\apphelp.dll
0x69d30000 - 0x69da5000 C:\WINDOWS\system32\uxtheme.dll
0x772c0000 - 0x773f6000 C:\WINDOWS\System32\MSCTF.dll
0x6b7d0000 - 0x6b7ef000 C:\WINDOWS\system32\dwmapi.dll
0x77440000 - 0x7752a000 C:\WINDOWS\System32\ole32.dll
0x60280000 - 0x603df000 C:\WINDOWS\system32\d3d9.dll
0x5fc40000 - 0x5fd6f000 C:\WINDOWS\SYSTEM32\aticfx32.dll
0x5dc50000 - 0x5dc6c000 C:\WINDOWS\SYSTEM32\atiu9pag.dll
0x59010000 - 0x598c1000 C:\WINDOWS\SYSTEM32\atiumdag.dll
0x58850000 - 0x5900f000 C:\WINDOWS\SYSTEM32\atiumdva.dll
0x59a80000 - 0x59ab9000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\fontmanager.dll
0x76ec0000 - 0x76f44000 C:\WINDOWS\System32\clbcatq.dll
0x5ed60000 - 0x5eece000 C:\WINDOWS\SYSTEM32\WindowsCodecs.dll
0x5f150000 - 0x5f194000 C:\WINDOWS\system32\dataexchange.dll
0x5f030000 - 0x5f143000 C:\WINDOWS\system32\dcomp.dll
0x69590000 - 0x697c0000 C:\WINDOWS\system32\d3d11.dll
0x697c0000 - 0x69844000 C:\WINDOWS\system32\dxgi.dll
0x5ef30000 - 0x5f021000 C:\WINDOWS\system32\twinapi.appcore.dll
0x74110000 - 0x7412b000 C:\WINDOWS\system32\bcrypt.dll
0x59a60000 - 0x59a76000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\net.dll
0x70ca0000 - 0x70cee000 C:\WINDOWS\system32\mswsock.dll
0x5dc40000 - 0x5dc4f000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\nio.dll
0x58820000 - 0x58850000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\t2k.dll
0x74ef0000 - 0x74fd5000 C:\WINDOWS\System32\COMDLG32.dll
0x587a0000 - 0x5881b000 C:\Program Files (x86)\Common Files\microsoft shared\ink\tiptsf.dll
0x58760000 - 0x5879d000 C:\WINDOWS\SYSTEM32\edputil.dll
0x58710000 - 0x58753000 C:\Windows\System32\thumbcache.dll
0x673b0000 - 0x674ff000 C:\WINDOWS\system32\propsys.dll
0x672e0000 - 0x673a1000 C:\WINDOWS\SYSTEM32\ntshrui.dll
0x68a70000 - 0x68a8c000 C:\WINDOWS\SYSTEM32\srvcli.dll
0x6b930000 - 0x6b93f000 C:\WINDOWS\SYSTEM32\cscapi.dll
0x58680000 - 0x58705000 C:\WINDOWS\System32\StructuredQuery.dll
0x58640000 - 0x5867f000 C:\WINDOWS\SYSTEM32\policymanager.dll
0x585d0000 - 0x58637000 C:\WINDOWS\SYSTEM32\msvcp110_win.dll
0x58520000 - 0x585cf000 C:\WINDOWS\system32\Windows.Storage.Search.dll
0x584e0000 - 0x58518000 C:\Program Files (x86)\Dropbox\Client\DropboxExt.65536.dll
0x58350000 - 0x584d8000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\FileSyncShell.dll
0x580b0000 - 0x58121000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\MSVCP120.dll
0x58180000 - 0x5826e000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\MSVCR120.dll
0x58130000 - 0x5817d000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\Telemetry.dll
0x6f610000 - 0x6f83e000 C:\WINDOWS\SYSTEM32\WININET.dll
0x58320000 - 0x58347000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\LoggingPlatform.DLL
0x58270000 - 0x58318000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\ClientTelemetry.dll
0x6f840000 - 0x6f86f000 C:\WINDOWS\SYSTEM32\IPHLPAPI.DLL
0x68be0000 - 0x68c01000 C:\WINDOWS\SYSTEM32\Cabinet.dll
0x74560000 - 0x745ff000 C:\WINDOWS\SYSTEM32\WINHTTP.dll
0x58090000 - 0x580a2000 C:\WINDOWS\system32\mssprxy.dll
0x46220000 - 0x46256000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle32.dll
0x46270000 - 0x462ad000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-cpu32-21.DLL
0x4c8d0000 - 0x4ce3e000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-opencl32-21.DLL
0x57ec0000 - 0x57ed3000 C:\WINDOWS\SYSTEM32\OpenCL.dll
0x556e0000 - 0x57eb2000 C:\WINDOWS\SYSTEM32\amdocl.dll
0x777b0000 - 0x77bbb000 C:\WINDOWS\System32\SETUPAPI.dll
0x6c320000 - 0x6c465000 C:\WINDOWS\SYSTEM32\dbghelp.dll
0x55600000 - 0x556e0000 C:\WINDOWS\SYSTEM32\OPENGL32.dll
0x554e0000 - 0x55505000 C:\WINDOWS\SYSTEM32\GLU32.dll
0x55510000 - 0x555fd000 C:\WINDOWS\SYSTEM32\DDRAW.dll
0x5dba0000 - 0x5dba7000 C:\WINDOWS\SYSTEM32\DCIMAN32.dll
0x553e0000 - 0x554d5000 C:\WINDOWS\SYSTEM32\atiadlxy.DLL
0x74600000 - 0x7460f000 C:\WINDOWS\SYSTEM32\WTSAPI32.dll
0x74530000 - 0x7454a000 C:\WINDOWS\SYSTEM32\USERENV.dll
0x6f980000 - 0x6f9a2000 C:\WINDOWS\SYSTEM32\DEVOBJ.dll
0x76cf0000 - 0x76d34000 C:\WINDOWS\System32\WINTRUST.dll
0x75310000 - 0x7531e000 C:\WINDOWS\System32\MSASN1.dll
0x76d40000 - 0x76ebd000 C:\WINDOWS\System32\CRYPT32.dll
0x53e30000 - 0x553d8000 C:\WINDOWS\SYSTEM32\amdocl12cl.dll
0x53e00000 - 0x53e27000 C:\WINDOWS\SYSTEM32\atigktxx.dll
0x4c360000 - 0x4c39c000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-cpu-sse32-21.DLL
VM Arguments:
jvm_args: -Xms256m -Xmx1024m
java_command: C:\Users\Andrew\Documents\BEAST v1.8.3\BEAST v1.8.3.exe -window -working -options
java_class_path (initial): C:\Users\Andrew\Documents\BEAST v1.8.3\BEAST v1.8.3.exe
Launcher Type: SUN_STANDARD
Environment Variables:
PATH=C:\Program Files (x86)\Common Files\libhmsbeagle\;C:\ProgramData\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Windows Live\Shared;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program Files (x86)\Skype\Phone\;C:\Program Files\MATLAB\R2013a\bin;C:\Program Files (x86)\FAHClient;C:\Users\Andrew\AppData\Local\Microsoft\WindowsApps;;C:\Program Files (x86)\Java\jre1.8.0_71\bin
USERNAME=Andrew
OS=Windows_NT
PROCESSOR_IDENTIFIER=AMD64 Family 22 Model 0 Stepping 1, AuthenticAMD
--------------- S Y S T E M ---------------
OS: Windows 10.0 , 64 bit Build 14393 (10.0.14393.0)
CPU:total 4 (4 cores per cpu, 1 threads per core) family 22 model 0 stepping 1, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, aes, clmul, mmxext, 3dnowpref, lzcnt, sse4a, tsc, tscinvbit, tscinv, bmi1
Memory: 4k page, physical 7827400k(5485404k free), swap 9072584k(6535724k free)
vm_info: Java HotSpot(TM) Client VM (25.71-b15) for windows-x86 JRE (1.8.0_71-b15), built on Dec 22 2015 17:22:59 by "java_re" with MS VC++ 10.0 (VS2010)
time: Sun Oct 02 11:57:43 2016
elapsed time: 58 seconds (0d 0h 0m 58s)
#
# A fatal error has been detected by the Java Runtime Environment:
#
# EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x4c36b6c0, pid=1936, tid=7916
#
# JRE version: Java(TM) SE Runtime Environment (8.0_71-b15) (build 1.8.0_71-b15)
# Java VM: Java HotSpot(TM) Client VM (25.71-b15 mixed mode windows-x86 )
# Problematic frame:
# C [hmsbeagle-cpu-sse32-21.DLL+0xb6c0]
#
# Failed to write core dump. Minidumps are not enabled by default on client versions of Windows
#
# 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 (0x4d086000): JavaThread "pool-1-thread-1" [_thread_in_native, id=7916, stack(0x4c3e0000,0x4c430000)]
siginfo: ExceptionCode=0xc0000005, reading address 0xffffffff
Registers:
EAX=0x00000060, EBX=0x4c42f2f0, ECX=0x00000000, EDX=0x4a99bc68
ESP=0x4c42f130, EBP=0x4c42f2e0, ESI=0x00000000, EDI=0x4a993850
EIP=0x4c36b6c0, EFLAGS=0x00010216
Top of Stack: (sp=0x4c42f130)
0x4c42f130: 4a99bc68 492fb440 ffffffff 00000000
0x4c42f140: 00000155 4a931660 493dd0c8 492fb440
0x4c42f150: 11981236 3fefd0dd cd87d380 3f5797fe
0x4c42f160: 9ab70880 3f678aef cd87d380 3f5797fe
0x4c42f170: cd36c280 3f5797fe 119811f9 3fefd0dd
0x4c42f180: cd36c280 3f5797fe 9a663300 3f678aef
0x4c42f190: 9ab70880 3f678aef cd87d380 3f5797fe
0x4c42f1a0: 11981236 3fefd0dd cd87d380 3f5797fe
Instructions: (pc=0x4c36b6c0)
0x4c36b6a0: 66 0f 59 c5 66 0f 58 c8 66 0f 28 85 80 fe ff ff
0x4c36b6b0: c1 e0 05 66 0f 59 c3 66 0f 59 8c 05 30 ff ff ff
0x4c36b6c0: 66 0f 29 0a 66 0f 28 8d a0 fe ff ff 66 0f 59 cc
0x4c36b6d0: 66 0f 58 c8 66 0f 28 85 c0 fe ff ff 66 0f 59 c2
Register to memory mapping:
EAX=0x00000060 is an unknown value
EBX=0x4c42f2f0 is pointing into the stack for thread: 0x4d086000
ECX=0x00000000 is an unknown value
EDX=0x4a99bc68 is an unknown value
ESP=0x4c42f130 is pointing into the stack for thread: 0x4d086000
EBP=0x4c42f2e0 is pointing into the stack for thread: 0x4d086000
ESI=0x00000000 is an unknown value
EDI=0x4a993850 is an unknown value
Stack: [0x4c3e0000,0x4c430000], sp=0x4c42f130, free space=316k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [hmsbeagle-cpu-sse32-21.DLL+0xb6c0]
C [hmsbeagle-cpu-sse32-21.DLL+0x113bc]
C [hmsbeagle32.dll+0x693e]
C [hmsbeagle32.dll+0x7679]
j beagle.BeagleJNIWrapper.updatePartials(I[III)I+0
j beagle.BeagleJNIImpl.updatePartials([III)V+10
j dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood()D+489
j dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood()D+9
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Double;+8
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Object;+1
j java.util.concurrent.FutureTask.run()V+42
j java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j java.lang.Thread.run()V+11
v ~StubRoutines::call_stub
V [jvm.dll+0x158bf5]
V [jvm.dll+0x21e0be]
V [jvm.dll+0x158c8e]
V [jvm.dll+0x158e16]
V [jvm.dll+0x158e87]
V [jvm.dll+0xfd68f]
V [jvm.dll+0x17c03c]
V [jvm.dll+0x17c12a]
V [jvm.dll+0x1c0636]
C [msvcr100.dll+0x5c556]
C [msvcr100.dll+0x5c600]
C [KERNEL32.DLL+0x162c4]
C [ntdll.dll+0x60609]
C [ntdll.dll+0x605d4]
C 0x00000000
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j beagle.BeagleJNIWrapper.updatePartials(I[III)I+0
j beagle.BeagleJNIImpl.updatePartials([III)V+10
j dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.calculateLogLikelihood()D+489
j dr.app.beagle.evomodel.treelikelihood.AbstractTreeLikelihood.getLogLikelihood()D+9
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Double;+8
j dr.inference.model.CompoundLikelihood$LikelihoodCaller.call()Ljava/lang/Object;+1
j java.util.concurrent.FutureTask.run()V+42
j java.util.concurrent.ThreadPoolExecutor.runWorker(Ljava/util/concurrent/ThreadPoolExecutor$Worker;)V+95
j java.util.concurrent.ThreadPoolExecutor$Worker.run()V+5
j java.lang.Thread.run()V+11
v ~StubRoutines::call_stub
--------------- P R O C E S S ---------------
Java Threads: ( => current thread )
0x4d086800 JavaThread "pool-1-thread-2" [_thread_blocked, id=7920, stack(0x4da80000,0x4dad0000)]
=>0x4d086000 JavaThread "pool-1-thread-1" [_thread_in_native, id=7916, stack(0x4c3e0000,0x4c430000)]
0x4649c000 JavaThread "TimerQueue" daemon [_thread_blocked, id=6152, stack(0x49430000,0x49480000)]
0x46465000 JavaThread "D3D Screen Updater" daemon [_thread_blocked, id=3044, stack(0x4a2c0000,0x4a310000)]
0x46457c00 JavaThread "Thread-3" [_thread_blocked, id=6724, stack(0x4a130000,0x4a180000)]
0x46457800 JavaThread "Thread-2" [_thread_blocked, id=7600, stack(0x4a0a0000,0x4a0f0000)]
0x459cc000 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=7484, stack(0x49940000,0x49990000)]
0x45982800 JavaThread "AWT-Windows" daemon [_thread_in_native, id=4716, stack(0x46100000,0x46150000)]
0x45982000 JavaThread "AWT-Shutdown" [_thread_blocked, id=5912, stack(0x46070000,0x460c0000)]
0x45981800 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=7236, stack(0x45fe0000,0x46030000)]
0x457fb800 JavaThread "Service Thread" daemon [_thread_blocked, id=5524, stack(0x45dd0000,0x45e20000)]
0x457f3800 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=940, stack(0x45d40000,0x45d90000)]
0x457fd800 JavaThread "Attach Listener" daemon [_thread_blocked, id=5620, stack(0x45cb0000,0x45d00000)]
0x457fc800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=5404, stack(0x45c20000,0x45c70000)]
0x457d6400 JavaThread "Finalizer" daemon [_thread_blocked, id=5540, stack(0x45aa0000,0x45af0000)]
0x457d1400 JavaThread "Reference Handler" daemon [_thread_blocked, id=5688, stack(0x45a10000,0x45a60000)]
0x02e5b800 JavaThread "main" [_thread_blocked, id=4848, stack(0x02d50000,0x02da0000)]
Other Threads:
0x02f5b400 VMThread [stack: 0x04fa0000,0x04ff0000] [id=1700]
0x45825400 WatcherThread [stack: 0x45e60000,0x45eb0000] [id=5528]
VM state:not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: None
Heap:
def new generation total 78720K, used 9950K [0x05000000, 0x0a560000, 0x1a550000)
eden space 70016K, 14% used [0x05000000, 0x059b7808, 0x09460000)
from space 8704K, 0% used [0x09460000, 0x09460000, 0x09ce0000)
to space 8704K, 0% used [0x09ce0000, 0x09ce0000, 0x0a560000)
tenured generation total 174784K, used 9672K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 5% used [0x1a550000, 0x1aec2358, 0x1aec2400, 0x25000000)
Metaspace used 13354K, capacity 13561K, committed 13696K, reserved 13696K
Card table byte_map: [0x45000000,0x45210000] byte_map_base: 0x44fd8000
Polling page: 0x02da0000
CodeCache: size=32768Kb used=1798Kb max_used=1800Kb free=30969Kb
bounds [0x02f60000, 0x03128000, 0x04f60000]
total_blobs=1155 nmethods=861 adapters=224
compilation: enabled
Compilation events (10 events):
Event: 58.132 Thread 0x457f3800 863 dr.xml.XMLObject::getRawChild (9 bytes)
Event: 58.133 Thread 0x457f3800 nmethod 863 0x03120148 code [0x03120260, 0x0312050c]
Event: 58.133 Thread 0x457f3800 864 dr.xml.XMLObject::getChild (56 bytes)
Event: 58.135 Thread 0x457f3800 nmethod 864 0x03120808 code [0x03120930, 0x03120cbc]
Event: 58.163 Thread 0x457f3800 865 ! java.util.zip.Inflater::setInput (74 bytes)
Event: 58.164 Thread 0x457f3800 nmethod 865 0x03121388 code [0x031214a0, 0x031217c8]
Event: 58.189 Thread 0x457f3800 866 javax.swing.text.GapContent::findSortIndex (128 bytes)
Event: 58.191 Thread 0x457f3800 nmethod 866 0x03121c08 code [0x03121d30, 0x03121f78]
Event: 58.195 Thread 0x457f3800 867 sun.font.GlyphList::usePositions (5 bytes)
Event: 58.195 Thread 0x457f3800 nmethod 867 0x03122248 code [0x03122340, 0x031223c0]
GC Heap History (2 events):
Event: 55.715 GC heap before
{Heap before GC invocations=0 (full 0):
def new generation total 78656K, used 54605K [0x05000000, 0x0a550000, 0x1a550000)
eden space 69952K, 78% used [0x05000000, 0x085534d0, 0x09450000)
from space 8704K, 0% used [0x09450000, 0x09450000, 0x09cd0000)
to space 8704K, 0% used [0x09cd0000, 0x09cd0000, 0x0a550000)
tenured generation total 174784K, used 0K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 0% used [0x1a550000, 0x1a550000, 0x1a550200, 0x25000000)
Metaspace used 11992K, capacity 12185K, committed 12288K, reserved 12672K
Event: 55.868 GC heap after
Heap after GC invocations=1 (full 1):
def new generation total 78720K, used 0K [0x05000000, 0x0a560000, 0x1a550000)
eden space 70016K, 0% used [0x05000000, 0x05000000, 0x09460000)
from space 8704K, 0% used [0x09460000, 0x09460000, 0x09ce0000)
to space 8704K, 0% used [0x09ce0000, 0x09ce0000, 0x0a560000)
tenured generation total 174784K, used 9672K [0x1a550000, 0x25000000, 0x45000000)
the space 174784K, 5% used [0x1a550000, 0x1aec2358, 0x1aec2400, 0x25000000)
Metaspace used 11992K, capacity 12185K, committed 12288K, reserved 12672K
}
Deoptimization events (0 events):
No events
Internal exceptions (10 events):
Event: 0.233 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.defineClass(Ljava/lang/String;[BII)Ljava/lang/Class; name or signature does not match> (0x0500b960) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vðŸ$Ò³ÖÍ?
Event: 0.233 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchMethodError': Method sun.misc.Unsafe.prefetchRead(Ljava/lang/Object;J)V name or signature does not match> (0x0500bc30) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, l÷*ì¨ûàâ?
Event: 0.590 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e1a50) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.590 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e1c50) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.593 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e5a38) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.593 Thread 0x02e5b800 Exception <a 'java/security/PrivilegedActionException'> (0x050e5c38) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jvm.cpp, line 1386]
Event: 0.630 Thread 0x02e5b800 Exception <a 'java/io/FileNotFoundException'> (0x050e9e98) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, line 709]
Event: 0.767 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x05460368) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\methodHandles.cpp, line 1146]
Event: 0.772 Thread 0x02e5b800 Exception <a 'java/lang/NoSuchFieldError': method resolution failed> (0x0546c508) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\methodHandles.cpp, line 1146]
Event: 1.017 Thread 0x02e5b800 Exception <a 'java/io/FileNotFoundException'> (0x0556f8a0) thrown at [C:\re\workspace\8-2-build-windows-i586-cygwin\jdk8u71\5731\hotspot\src\share\vm\prims\jni.cpp, line 709]
Events (10 events):
Event: 58.188 Thread 0x4d086800 Thread added: 0x4d086800
Event: 58.189 loading class dr/app/beagle/evomodel/substmodel/EigenDecomposition
Event: 58.190 loading class dr/app/beagle/evomodel/substmodel/EigenDecomposition done
Event: 58.190 Executing VM operation: RevokeBias
Event: 58.191 Executing VM operation: RevokeBias done
Event: 58.192 loading class dr/app/beagle/evomodel/branchmodel/BranchModel$1
Event: 58.192 loading class dr/app/beagle/evomodel/branchmodel/BranchModel$1 done
Event: 58.192 Executing VM operation: RevokeBias
Event: 58.193 Executing VM operation: RevokeBias done
Event: 58.195 Thread 0x457f3800 flushing nmethod 0x03081b48
Dynamic libraries:
0x00b40000 - 0x00b73000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\javaw.exe
0x77bc0000 - 0x77d42000 C:\WINDOWS\SYSTEM32\ntdll.dll
0x746a0000 - 0x74780000 C:\WINDOWS\System32\KERNEL32.DLL
0x75160000 - 0x75301000 C:\WINDOWS\System32\KERNELBASE.dll
0x76f50000 - 0x76fc7000 C:\WINDOWS\System32\ADVAPI32.dll
0x75090000 - 0x7514e000 C:\WINDOWS\System32\msvcrt.dll
0x74dc0000 - 0x74e01000 C:\WINDOWS\System32\sechost.dll
0x771e0000 - 0x772a1000 C:\WINDOWS\System32\RPCRT4.dll
0x74680000 - 0x7469e000 C:\WINDOWS\System32\SspiCli.dll
0x74670000 - 0x7467a000 C:\WINDOWS\System32\CRYPTBASE.dll
0x776f0000 - 0x7774a000 C:\WINDOWS\System32\bcryptPrimitives.dll
0x77020000 - 0x7717f000 C:\WINDOWS\System32\USER32.dll
0x75320000 - 0x75335000 C:\WINDOWS\System32\win32u.dll
0x74d90000 - 0x74dbb000 C:\WINDOWS\System32\GDI32.dll
0x749a0000 - 0x74afb000 C:\WINDOWS\System32\gdi32full.dll
0x6a6e0000 - 0x6a8ea000 C:\WINDOWS\WinSxS\x86_microsoft.windows.common-controls_6595b64144ccf1df_6.0.14393.0_none_74bc87d3d22d9abe\COMCTL32.dll
0x74780000 - 0x74991000 C:\WINDOWS\System32\combase.dll
0x74e10000 - 0x74ef0000 C:\WINDOWS\System32\ucrtbase.dll
0x75060000 - 0x75085000 C:\WINDOWS\System32\IMM32.DLL
0x59fe0000 - 0x5a09f000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\msvcr100.dll
0x59c10000 - 0x59fd8000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\client\jvm.dll
0x75150000 - 0x75156000 C:\WINDOWS\System32\PSAPI.DLL
0x70d10000 - 0x70d18000 C:\WINDOWS\SYSTEM32\WSOCK32.dll
0x71690000 - 0x716b4000 C:\WINDOWS\SYSTEM32\WINMM.dll
0x73fc0000 - 0x73fc8000 C:\WINDOWS\SYSTEM32\VERSION.dll
0x71660000 - 0x71683000 C:\WINDOWS\SYSTEM32\WINMMBASE.dll
0x77400000 - 0x77436000 C:\WINDOWS\System32\cfgmgr32.dll
0x74d20000 - 0x74d83000 C:\WINDOWS\System32\WS2_32.dll
0x5e8d0000 - 0x5e8dc000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\verify.dll
0x5e050000 - 0x5e071000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\java.dll
0x5e230000 - 0x5e243000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\zip.dll
0x758b0000 - 0x76c87000 C:\WINDOWS\System32\SHELL32.dll
0x75340000 - 0x758ae000 C:\WINDOWS\System32\windows.storage.dll
0x76ca0000 - 0x76ce5000 C:\WINDOWS\System32\powrprof.dll
0x76fd0000 - 0x77016000 C:\WINDOWS\System32\shlwapi.dll
0x74d10000 - 0x74d1d000 C:\WINDOWS\System32\kernel.appcore.dll
0x775e0000 - 0x77668000 C:\WINDOWS\System32\shcore.dll
0x772b0000 - 0x772bf000 C:\WINDOWS\System32\profapi.dll
0x59ac0000 - 0x59c05000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\awt.dll
0x77530000 - 0x775c4000 C:\WINDOWS\System32\OLEAUT32.dll
0x77670000 - 0x776eb000 C:\WINDOWS\System32\msvcp_win.dll
0x598d0000 - 0x59962000 C:\WINDOWS\SYSTEM32\apphelp.dll
0x69d30000 - 0x69da5000 C:\WINDOWS\system32\uxtheme.dll
0x772c0000 - 0x773f6000 C:\WINDOWS\System32\MSCTF.dll
0x6b7d0000 - 0x6b7ef000 C:\WINDOWS\system32\dwmapi.dll
0x77440000 - 0x7752a000 C:\WINDOWS\System32\ole32.dll
0x60280000 - 0x603df000 C:\WINDOWS\system32\d3d9.dll
0x5fc40000 - 0x5fd6f000 C:\WINDOWS\SYSTEM32\aticfx32.dll
0x5dc50000 - 0x5dc6c000 C:\WINDOWS\SYSTEM32\atiu9pag.dll
0x59010000 - 0x598c1000 C:\WINDOWS\SYSTEM32\atiumdag.dll
0x58850000 - 0x5900f000 C:\WINDOWS\SYSTEM32\atiumdva.dll
0x59a80000 - 0x59ab9000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\fontmanager.dll
0x76ec0000 - 0x76f44000 C:\WINDOWS\System32\clbcatq.dll
0x5ed60000 - 0x5eece000 C:\WINDOWS\SYSTEM32\WindowsCodecs.dll
0x5f150000 - 0x5f194000 C:\WINDOWS\system32\dataexchange.dll
0x5f030000 - 0x5f143000 C:\WINDOWS\system32\dcomp.dll
0x69590000 - 0x697c0000 C:\WINDOWS\system32\d3d11.dll
0x697c0000 - 0x69844000 C:\WINDOWS\system32\dxgi.dll
0x5ef30000 - 0x5f021000 C:\WINDOWS\system32\twinapi.appcore.dll
0x74110000 - 0x7412b000 C:\WINDOWS\system32\bcrypt.dll
0x59a60000 - 0x59a76000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\net.dll
0x70ca0000 - 0x70cee000 C:\WINDOWS\system32\mswsock.dll
0x5dc40000 - 0x5dc4f000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\nio.dll
0x58820000 - 0x58850000 C:\Program Files (x86)\Java\jre1.8.0_71\bin\t2k.dll
0x74ef0000 - 0x74fd5000 C:\WINDOWS\System32\COMDLG32.dll
0x587a0000 - 0x5881b000 C:\Program Files (x86)\Common Files\microsoft shared\ink\tiptsf.dll
0x58760000 - 0x5879d000 C:\WINDOWS\SYSTEM32\edputil.dll
0x58710000 - 0x58753000 C:\Windows\System32\thumbcache.dll
0x673b0000 - 0x674ff000 C:\WINDOWS\system32\propsys.dll
0x672e0000 - 0x673a1000 C:\WINDOWS\SYSTEM32\ntshrui.dll
0x68a70000 - 0x68a8c000 C:\WINDOWS\SYSTEM32\srvcli.dll
0x6b930000 - 0x6b93f000 C:\WINDOWS\SYSTEM32\cscapi.dll
0x58680000 - 0x58705000 C:\WINDOWS\System32\StructuredQuery.dll
0x58640000 - 0x5867f000 C:\WINDOWS\SYSTEM32\policymanager.dll
0x585d0000 - 0x58637000 C:\WINDOWS\SYSTEM32\msvcp110_win.dll
0x58520000 - 0x585cf000 C:\WINDOWS\system32\Windows.Storage.Search.dll
0x584e0000 - 0x58518000 C:\Program Files (x86)\Dropbox\Client\DropboxExt.65536.dll
0x58350000 - 0x584d8000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\FileSyncShell.dll
0x580b0000 - 0x58121000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\MSVCP120.dll
0x58180000 - 0x5826e000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\MSVCR120.dll
0x58130000 - 0x5817d000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\Telemetry.dll
0x6f610000 - 0x6f83e000 C:\WINDOWS\SYSTEM32\WININET.dll
0x58320000 - 0x58347000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\LoggingPlatform.DLL
0x58270000 - 0x58318000 C:\Users\Andrew\AppData\Local\Microsoft\OneDrive\17.3.6381.0405\ClientTelemetry.dll
0x6f840000 - 0x6f86f000 C:\WINDOWS\SYSTEM32\IPHLPAPI.DLL
0x68be0000 - 0x68c01000 C:\WINDOWS\SYSTEM32\Cabinet.dll
0x74560000 - 0x745ff000 C:\WINDOWS\SYSTEM32\WINHTTP.dll
0x58090000 - 0x580a2000 C:\WINDOWS\system32\mssprxy.dll
0x46220000 - 0x46256000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle32.dll
0x46270000 - 0x462ad000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-cpu32-21.DLL
0x4c8d0000 - 0x4ce3e000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-opencl32-21.DLL
0x57ec0000 - 0x57ed3000 C:\WINDOWS\SYSTEM32\OpenCL.dll
0x556e0000 - 0x57eb2000 C:\WINDOWS\SYSTEM32\amdocl.dll
0x777b0000 - 0x77bbb000 C:\WINDOWS\System32\SETUPAPI.dll
0x6c320000 - 0x6c465000 C:\WINDOWS\SYSTEM32\dbghelp.dll
0x55600000 - 0x556e0000 C:\WINDOWS\SYSTEM32\OPENGL32.dll
0x554e0000 - 0x55505000 C:\WINDOWS\SYSTEM32\GLU32.dll
0x55510000 - 0x555fd000 C:\WINDOWS\SYSTEM32\DDRAW.dll
0x5dba0000 - 0x5dba7000 C:\WINDOWS\SYSTEM32\DCIMAN32.dll
0x553e0000 - 0x554d5000 C:\WINDOWS\SYSTEM32\atiadlxy.DLL
0x74600000 - 0x7460f000 C:\WINDOWS\SYSTEM32\WTSAPI32.dll
0x74530000 - 0x7454a000 C:\WINDOWS\SYSTEM32\USERENV.dll
0x6f980000 - 0x6f9a2000 C:\WINDOWS\SYSTEM32\DEVOBJ.dll
0x76cf0000 - 0x76d34000 C:\WINDOWS\System32\WINTRUST.dll
0x75310000 - 0x7531e000 C:\WINDOWS\System32\MSASN1.dll
0x76d40000 - 0x76ebd000 C:\WINDOWS\System32\CRYPT32.dll
0x53e30000 - 0x553d8000 C:\WINDOWS\SYSTEM32\amdocl12cl.dll
0x53e00000 - 0x53e27000 C:\WINDOWS\SYSTEM32\atigktxx.dll
0x4c360000 - 0x4c39c000 C:\Program Files (x86)\Common Files\libhmsbeagle\hmsbeagle-cpu-sse32-21.DLL
VM Arguments:
jvm_args: -Xms256m -Xmx1024m
java_command: C:\Users\Andrew\Documents\BEAST v1.8.3\BEAST v1.8.3.exe -window -working -options
java_class_path (initial): C:\Users\Andrew\Documents\BEAST v1.8.3\BEAST v1.8.3.exe
Launcher Type: SUN_STANDARD
Environment Variables:
PATH=C:\Program Files (x86)\Common Files\libhmsbeagle\;C:\ProgramData\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Windows Live\Shared;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-Static;C:\Program Files (x86)\Skype\Phone\;C:\Program Files\MATLAB\R2013a\bin;C:\Program Files (x86)\FAHClient;C:\Users\Andrew\AppData\Local\Microsoft\WindowsApps;;C:\Program Files (x86)\Java\jre1.8.0_71\bin
USERNAME=Andrew
OS=Windows_NT
PROCESSOR_IDENTIFIER=AMD64 Family 22 Model 0 Stepping 1, AuthenticAMD
--------------- S Y S T E M ---------------
OS: Windows 10.0 , 64 bit Build 14393 (10.0.14393.0)
CPU:total 4 (4 cores per cpu, 1 threads per core) family 22 model 0 stepping 1, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, aes, clmul, mmxext, 3dnowpref, lzcnt, sse4a, tsc, tscinvbit, tscinv, bmi1
Memory: 4k page, physical 7827400k(5485404k free), swap 9072584k(6535724k free)
vm_info: Java HotSpot(TM) Client VM (25.71-b15) for windows-x86 JRE (1.8.0_71-b15), built on Dec 22 2015 17:22:59 by "java_re" with MS VC++ 10.0 (VS2010)
time: Sun Oct 02 11:57:43 2016
elapsed time: 58 seconds (0d 0h 0m 58s)
Thanks,
Andrew
Marc Suchard
Oct 2, 2016, 10:59:50 AM10/2/16
to beast-users
32-bit Java installs no longer work under Windows 10. Upgrade to a 64-bit Java install.
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