PyLib.stopPython() generates a memory core with java 8 #77

pabloa · 2016-12-19T22:34:12Z

I executed this test with java 1.8.111, Scala 2.11 and jpy 0.9-SNAPSHOT (SHA1 4a8a43c) and it hangs the JVM when the test tries to stop the python engine.

import org.jpy.{PyLib, PyModule, PyObject}
import org.junit.Test
import org.junit.Assert._

/**
  * Tests of invoking from java python code.
  */
class PythonInvocationTest {

  def before(): Unit = {
    System.setProperty("jpy.debug", "true")
    System.setProperty("jpy.config", "/usr/local/lib/python2.7/dist-packages/jpyconfig.properties")
    if (!PyLib.isPythonRunning) {
      val pythonPathEnv = System.getenv("PYTHONPATH")
      val morePhythonPath = "/home/pablo/develop/my/python/stuff:/home/pablo/develop/my/other/stuff"
      println(s"$pythonPathEnv:$morePhythonPath")
      PyLib.startPython((pythonPathEnv + ":" + morePhythonPath).split(":").array: _*)
    }
  }

  def after(): Unit = {
    if (PyLib.isPythonRunning) {
      PyLib.stopPython()  // <-- this line hangs the JVM
    }
  }

  @Test
  def executeSomePython(): Unit = {
    before()
    PyLib.execScript("print 'this is from python'")
    after()
  }
}

The output is:

org.jpy.PyLib: entered static initializer
org.jpy.PyLibConfig: entered static initializer
org.jpy.PyLibConfig: trying to use C libraries from jar file.
org.jpy.PyLibConfig: about to read configuration.
org.jpy.PyLibConfig: loading configuration file /usr/local/lib/python2.7/dist-packages/jpyconfig.properties
org.jpy.PyLibConfig: exited static initializer
org.jpy.PyLib: DL.dlopen("/usr/lib/x86_64-linux-gnu/libpython2.7.so", DL.RTLD_GLOBAL + DL.RTLD_LAZY
org.jpy.PyLib: System.load("/home/pablo/borrar/borrar1/jpy/build/lib.linux-x86_64-2.7/jpy.so")
org.jpy.PyLib: exited static initializer

org.jpy.PyLib: Starting Python with 8 extra module path(s):
org.jpy.PyLib:   /home/pablo/borrar/borrar1/jpy/build/lib.linux-x86_64-2.7
org.jpy.PyLib:   /home/pablo/src/bin
org.jpy.PyLib:   /home/pablo/src/bin/build
org.jpy.PyLib:   /home/pablo/pyModules
org.jpy.PyLib:   /home/pablo/develop
PyLib_startPython: entered: jenv=0x7efcf80119f8, pyInit=0, JPy_Module=(nil)
PyLib_startPython: global Python interpreter information:
  Py_GetProgramName()     = "python"
  Py_GetPrefix()          = "/usr"
  Py_GetExecPrefix()      = "/usr"
  Py_GetProgramFullPath() = "/usr/bin/python"
  Py_GetPath()            = "/all/the/paths/above:/usr/lib/python2.7/:/usr/lib/python2.7/plat-x86_64-linux-gnu:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-old:/usr/lib/python2.7/lib-dynload"
  Py_GetPythonHome()      = "(null)"
  Py_GetVersion()         = "2.7.6 (default, Oct 26 2016, 20:33:43) 
[GCC 4.8.4]"
  Py_GetPlatform()        = "linux2"
  Py_GetCompiler()        = "
[GCC 4.8.4]"
  Py_GetBuildInfo()       = "default, Oct 26 2016, 20:33:43"
PyLib_startPython: exiting: jenv=0x7efcf80119f8, pyInit=1, JPy_Module=0x7efce152c948
Java_org_jpy_PyLib_execScript: script='print 'this is from python''
this is from python
Java_org_jpy_PyLib_stopPython: entered: JPy_Module=0x7efce152c948
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007efce1df57b8, pid=14716, tid=0x00007efd01a05700
#
# JRE version: Java(TM) SE Runtime Environment (8.0_111-b14) (build 1.8.0_111-b14)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.111-b14 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libpython2.7.so+0x15b7b8]  Py_Finalize+0x28
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/pablo/develop/my/test/hs_err_pid14716.log
#
# 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.
#
Process finished with exit code 0

This is the content of hs_err_pid14716.log file:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007efce1df57b8, pid=14716, tid=0x00007efd01a05700
#
# JRE version: Java(TM) SE Runtime Environment (8.0_111-b14) (build 1.8.0_111-b14)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.111-b14 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  [libpython2.7.so+0x15b7b8]  Py_Finalize+0x28
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

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

Current thread (0x00007efcf8011800):  JavaThread "main" [_thread_in_native, id=14717, stack(0x00007efd01905000,0x00007efd01a06000)]

siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x0000000000000008

Registers:
RAX=0x0000000000000000, RBX=0x00007efce1860680, RCX=0x00007efd00ef572d, RDX=0x0000000000000000
RSP=0x00007efd01a038c0, RBP=0x00007efce21f0f70, RSI=0x00007efce1ef544b, RDI=0x0000000000000000
R8 =0x00007efd01a05700, R9 =0x50706f74735f6269, R10=0x00007efd01a036a0, R11=0x00007efce1df5790
R12=0x0000000000000000, R13=0x00007efcfce96f58, R14=0x00007efd01a03948, R15=0x00007efcf8011800
RIP=0x00007efce1df57b8, EFLAGS=0x0000000000010206, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
  TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00007efd01a038c0)
0x00007efd01a038c0:   50706f74735f6269 00007efce1860680
0x00007efd01a038d0:   00007efd01a03930 00007efce1655a35
0x00007efd01a038e0:   00007efcfce96f58 00007efce9017a34
0x00007efd01a038f0:   00007efd01a038f0 00007efcfce96f58
0x00007efd01a03900:   00007efd01a03948 00007efcfce99290
0x00007efd01a03910:   0000000000000000 00007efcfce96f58
0x00007efd01a03920:   0000000000000000 00007efd01a03950
0x00007efd01a03930:   00007efd01a03990 00007efce90082bd
0x00007efd01a03940:   000000076e09ceb8 00007efce9011538
0x00007efd01a03950:   00007efd01a03950 00007efcfce3ae9e
0x00007efd01a03960:   00007efd01a039a0 00007efcfce50478
0x00007efd01a03970:   0000000000000000 00007efcfce3aeb8
0x00007efd01a03980:   00007efd01a03950 00007efd01a039a0
0x00007efd01a03990:   00007efd01a039e8 00007efce90082bd
0x00007efd01a039a0:   000000076e02f2d8 00007efd01a039a8
0x00007efd01a039b0:   00007efcfce3af63 00007efd01a039f8
0x00007efd01a039c0:   00007efcfce50478 0000000000000000
0x00007efd01a039d0:   00007efcfce3af88 00007efd01a039a0
0x00007efd01a039e0:   00007efd01a039f8 00007efd01a03a60
0x00007efd01a039f0:   00007efce90007a7 000000076e02f2d8
0x00007efd01a03a00:   0000000000001fa0 00007efcf8011318
0x00007efd01a03a10:   00007efcf8011800 00007efd01a03ae0
0x00007efd01a03a20:   00007efd01a03df0 00007efd01a03aa0
0x00007efd01a03a30:   00007efd01a03aa0 00007efd01a03df8
0x00007efd01a03a40:   00007efd0000000a 00007efcfce3af88
0x00007efd01a03a50:   00007efce9012c80 00007efd01a03ce8
0x00007efd01a03a60:   00007efd01a03bd0 00007efd004aa206
0x00007efd01a03a70:   00007efd00000001 00007efcf8011800
0x00007efd01a03a80:   00007efd01a03ce0 00007efd01a03df0
0x00007efd01a03a90:   00007efce9012c80 00007efd0000000a
0x00007efd01a03aa0:   00007efcf8011800 00007efcf8089250
0x00007efd01a03ab0:   00007efcfce3af88 000000076e02f2d8 

Instructions: (pc=0x00007efce1df57b8)
0x00007efce1df5798:   75 06 f3 c3 0f 1f 40 00 55 48 8d 35 a3 fc 0f 00
0x00007efce1df57a8:   53 48 83 ec 08 48 8b 2d 8c 16 38 00 48 8b 45 00
0x00007efce1df57b8:   48 8b 40 08 48 8b 78 10 e8 9b 9f fc ff 48 85 c0
0x00007efce1df57c8:   48 89 c3 0f 84 ae 01 00 00 48 8d 15 02 47 08 00 

Register to memory mapping:

RAX=0x0000000000000000 is an unknown value
RBX=0x00007efce1860680: JPy_DiagFlags+0 in /home/pablo/borrar/borrar1/jpy/build/lib.linux-x86_64-2.7/jpy.so at 0x00007efce1642000
RCX=0x00007efd00ef572d: __write+0x2d in /lib/x86_64-linux-gnu/libc.so.6 at 0x00007efd00e0a000
RDX=0x0000000000000000 is an unknown value
RSP=0x00007efd01a038c0 is pointing into the stack for thread: 0x00007efcf8011800
RBP=0x00007efce21f0f70: _PyThreadState_Current+0 in /usr/lib/x86_64-linux-gnu/libpython2.7.so at 0x00007efce1c9a000
RSI=0x00007efce1ef544b: <offset 0x25b44b> in /usr/lib/x86_64-linux-gnu/libpython2.7.so at 0x00007efce1c9a000
RDI=0x0000000000000000 is an unknown value
R8 =0x00007efd01a05700 is pointing into the stack for thread: 0x00007efcf8011800
R9 =0x50706f74735f6269 is an unknown value
R10=0x00007efd01a036a0 is pointing into the stack for thread: 0x00007efcf8011800
R11=0x00007efce1df5790: Py_Finalize+0 in /usr/lib/x86_64-linux-gnu/libpython2.7.so at 0x00007efce1c9a000
R12=0x0000000000000000 is an unknown value
R13={method} {0x00007efcfce96f58} 'stopPython' '()V' in 'org/jpy/PyLib'
R14=0x00007efd01a03948 is pointing into the stack for thread: 0x00007efcf8011800
R15=0x00007efcf8011800 is a thread


Stack: [0x00007efd01905000,0x00007efd01a06000],  sp=0x00007efd01a038c0,  free space=1018k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [libpython2.7.so+0x15b7b8]  Py_Finalize+0x28

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  org.jpy.PyLib.stopPython()V+0
j  com.physiosigns.python.PythonInvocationTest.after()V+6
j  com.physiosigns.python.PythonInvocationTest.executeSomePython()V+11
v  ~StubRoutines::call_stub
j  sun.reflect.NativeMethodAccessorImpl.invoke0(Ljava/lang/reflect/Method;Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;+0
j  sun.reflect.NativeMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;+100
j  sun.reflect.DelegatingMethodAccessorImpl.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;+6
j  java.lang.reflect.Method.invoke(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;+56
j  org.junit.runners.model.FrameworkMethod$1.runReflectiveCall()Ljava/lang/Object;+15
j  org.junit.internal.runners.model.ReflectiveCallable.run()Ljava/lang/Object;+1
j  org.junit.runners.model.FrameworkMethod.invokeExplosively(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;+10
j  org.junit.internal.runners.statements.InvokeMethod.evaluate()V+12
j  org.junit.runners.ParentRunner.runLeaf(Lorg/junit/runners/model/Statement;Lorg/junit/runner/Description;Lorg/junit/runner/notification/RunNotifier;)V+17
j  org.junit.runners.BlockJUnit4ClassRunner.runChild(Lorg/junit/runners/model/FrameworkMethod;Lorg/junit/runner/notification/RunNotifier;)V+30
j  org.junit.runners.BlockJUnit4ClassRunner.runChild(Ljava/lang/Object;Lorg/junit/runner/notification/RunNotifier;)V+6
j  org.junit.runners.ParentRunner$3.run()V+12
j  org.junit.runners.ParentRunner$1.schedule(Ljava/lang/Runnable;)V+1
j  org.junit.runners.ParentRunner.runChildren(Lorg/junit/runner/notification/RunNotifier;)V+44
j  org.junit.runners.ParentRunner.access$000(Lorg/junit/runners/ParentRunner;Lorg/junit/runner/notification/RunNotifier;)V+2
j  org.junit.runners.ParentRunner$2.evaluate()V+8
j  org.junit.runners.ParentRunner.run(Lorg/junit/runner/notification/RunNotifier;)V+20
j  org.junit.runner.JUnitCore.run(Lorg/junit/runner/Runner;)Lorg/junit/runner/Result;+37
j  com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs([Ljava/lang/String;Ljava/lang/String;IZ)I+146
j  com.intellij.rt.execution.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(Lcom/intellij/rt/execution/junit/IdeaTestRunner;[Ljava/lang/String;Ljava/util/ArrayList;Ljava/lang/String;IZ)I+20
j  com.intellij.rt.execution.junit.JUnitForkedStarter.main([Ljava/lang/String;)V+148
v  ~StubRoutines::call_stub

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

Java Threads: ( => current thread )
  0x00007efcf80d3000 JavaThread "Service Thread" daemon [_thread_blocked, id=14737, stack(0x00007efce2b10000,0x00007efce2c11000)]
  0x00007efcf80cf800 JavaThread "C1 CompilerThread3" daemon [_thread_blocked, id=14736, stack(0x00007efce2c11000,0x00007efce2d12000)]
  0x00007efcf80cd800 JavaThread "C2 CompilerThread2" daemon [_thread_blocked, id=14735, stack(0x00007efce2d12000,0x00007efce2e13000)]
  0x00007efcf80cb800 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=14734, stack(0x00007efce2e13000,0x00007efce2f14000)]
  0x00007efcf80c8800 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=14733, stack(0x00007efce2f14000,0x00007efce3015000)]
  0x00007efcf80c7000 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=14732, stack(0x00007efce3015000,0x00007efce3116000)]
  0x00007efcf8094000 JavaThread "Finalizer" daemon [_thread_blocked, id=14731, stack(0x00007efce37f8000,0x00007efce38f9000)]
  0x00007efcf808f800 JavaThread "Reference Handler" daemon [_thread_blocked, id=14730, stack(0x00007efce38f9000,0x00007efce39fa000)]
=>0x00007efcf8011800 JavaThread "main" [_thread_in_native, id=14717, stack(0x00007efd01905000,0x00007efd01a06000)]

Other Threads:
  0x00007efcf8087800 VMThread [stack: 0x00007efce39fa000,0x00007efce3afb000] [id=14729]
  0x00007efcf80d6000 WatcherThread [stack: 0x00007efce2a0f000,0x00007efce2b10000] [id=14738]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap:
 PSYoungGen      total 74752K, used 30967K [0x000000076cd80000, 0x0000000772080000, 0x00000007c0000000)
  eden space 64512K, 48% used [0x000000076cd80000,0x000000076ebbdeb0,0x0000000770c80000)
  from space 10240K, 0% used [0x0000000771680000,0x0000000771680000,0x0000000772080000)
  to   space 10240K, 0% used [0x0000000770c80000,0x0000000770c80000,0x0000000771680000)
 ParOldGen       total 171008K, used 0K [0x00000006c6800000, 0x00000006d0f00000, 0x000000076cd80000)
  object space 171008K, 0% used [0x00000006c6800000,0x00000006c6800000,0x00000006d0f00000)
 Metaspace       used 6871K, capacity 7014K, committed 7168K, reserved 1056768K
  class space    used 943K, capacity 977K, committed 1024K, reserved 1048576K

Card table byte_map: [0x00007efcfe72a000,0x00007efcfeef7000] byte_map_base: 0x00007efcfb0f6000

Marking Bits: (ParMarkBitMap*) 0x00007efd00ddd220
 Begin Bits: [0x00007efcb4340000, 0x00007efcb81a0000)
 End Bits:   [0x00007efcb81a0000, 0x00007efcbc000000)

Polling page: 0x00007efd01a26000

CodeCache: size=245760Kb used=2396Kb max_used=2396Kb free=243363Kb
 bounds [0x00007efce9000000, 0x00007efce9270000, 0x00007efcf8000000]
 total_blobs=757 nmethods=473 adapters=198
 compilation: enabled

Compilation events (10 events):
Event: 0.542 Thread 0x00007efcf80cf800  469       3       java.lang.ClassLoader::compareCerts (149 bytes)
Event: 0.542 Thread 0x00007efcf80cf800 nmethod 469 0x00007efce9255810 code [0x00007efce92559e0, 0x00007efce9256298]
Event: 0.560 Thread 0x00007efcf80cf800  470       3       java.io.File::getAbsolutePath (8 bytes)
Event: 0.561 Thread 0x00007efcf80cf800 nmethod 470 0x00007efce9256990 code [0x00007efce9256b60, 0x00007efce9257198]
Event: 0.561 Thread 0x00007efcf80cf800  471       3       java.util.regex.Pattern$Single::isSatisfiedBy (14 bytes)
Event: 0.561 Thread 0x00007efcf80cf800 nmethod 471 0x00007efce9257490 code [0x00007efce9257600, 0x00007efce92577b0]
Event: 0.561 Thread 0x00007efcf80cf800  472       3       java.util.regex.Pattern$Ctype::isSatisfiedBy (24 bytes)
Event: 0.561 Thread 0x00007efcf80cf800 nmethod 472 0x00007efce9257810 code [0x00007efce92579a0, 0x00007efce9257d30]
Event: 0.561 Thread 0x00007efcf80cf800  473       3       java.nio.ByteBuffer::arrayOffset (35 bytes)
Event: 0.562 Thread 0x00007efcf80cf800 nmethod 473 0x00007efce9257ed0 code [0x00007efce9258060, 0x00007efce9258378]

GC Heap History (0 events):
No events

Deoptimization events (3 events):
Event: 0.112 Thread 0x00007efcf8011800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007efce9100058 method=java.lang.String.hashCode()I @ 14
Event: 0.145 Thread 0x00007efcf8011800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007efce911c6bc method=java.lang.String.indexOf(II)I @ 49
Event: 0.379 Thread 0x00007efcf8011800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007efce917f9d8 method=java.lang.String.indexOf([CII[CIII)I @ 3

Internal exceptions (10 events):
Event: 0.156 Thread 0x00007efcf8011800 Exception <a 'java/security/PrivilegedActionException'> (0x000000076d1bf2a0) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u111/7883/hotspot/src/share/vm/prims/jvm.cpp, line 1386]
Event: 0.156 Thread 0x00007efcf8011800 Exception <a 'java/security/PrivilegedActionException'> (0x000000076d1bf4b0) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u111/7883/hotspot/src/share/vm/prims/jvm.cpp, line 1386]
Event: 0.156 Thread 0x00007efcf8011800 Exception <a 'java/security/PrivilegedActionException'> (0x000000076d1c0430) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u111/7883/hotspot/src/share/vm/prims/jvm.cpp, line 1386]
Event: 0.156 Thread 0x00007efcf8011800 Exception <a 'java/security/PrivilegedActionException'> (0x000000076d1c0640) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u111/7883/hotspot/src/share/vm/prims/jvm.cpp, line 1386]
Event: 0.156 Thread 0x00007efcf8011800 Exception <a 'java/security/PrivilegedActionException'> (0x000000076d1c14b0) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u111/7883/hotspot/src/share/vm/prims/jvm.cpp, line 1386]
Event: 0.156 Thread 0x00007efcf8011800 Exception <a 'java/security/PrivilegedActionException'> (0x000000076d1c16c0) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u111/7883/hotspot/src/share/vm/prims/jvm.cpp, line 1386]
Event: 0.182 Thread 0x00007efcf8011800 Exception <a 'java/security/PrivilegedActionException'> (0x000000076d355758) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u111/7883/hotspot/src/share/vm/prims/jvm.cpp, line 1386]
Event: 0.182 Thread 0x00007efcf8011800 Exception <a 'java/security/PrivilegedActionException'> (0x000000076d355968) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u111/7883/hotspot/src/share/vm/prims/jvm.cpp, line 1386]
Event: 0.182 Thread 0x00007efcf8011800 Exception <a 'java/security/PrivilegedActionException'> (0x000000076d357da8) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u111/7883/hotspot/src/share/vm/prims/jvm.cpp, line 1386]
Event: 0.182 Thread 0x00007efcf8011800 Exception <a 'java/security/PrivilegedActionException'> (0x000000076d357fb8) thrown at [/HUDSON3/workspace/8-2-build-linux-amd64/jdk8u111/7883/hotspot/src/share/vm/prims/jvm.cpp, line 1386]

Events (10 events):
Event: 0.560 loading class java/util/ArrayList$SubList$1
Event: 0.560 loading class java/util/ArrayList$SubList$1 done
Event: 0.561 loading class org/jpy/PyLib$Diag
Event: 0.561 loading class org/jpy/PyLib$Diag done
Event: 0.613 loading class org/jpy/PyObject
Event: 0.613 loading class org/jpy/PyObject done
Event: 0.614 loading class java/lang/IllegalStateException
Event: 0.614 loading class java/lang/IllegalStateException done
Event: 0.614 loading class org/jpy/PyModule
Event: 0.614 loading class org/jpy/PyModule done


Dynamic libraries:
00400000-00401000 r-xp 00000000 00:11 12240858                           /usr/lib/jvm/java-8-oracle/bin/java
00600000-00601000 rw-p 00000000 00:11 12240858                           /usr/lib/jvm/java-8-oracle/bin/java
01c39000-01c5a000 rw-p 00000000 00:00 0                                  [heap]
6c6800000-6d0f00000 rw-p 00000000 00:00 0 
6d0f00000-76cd80000 ---p 00000000 00:00 0 
76cd80000-772080000 rw-p 00000000 00:00 0 
772080000-7c0000000 ---p 00000000 00:00 0 
7c0000000-7c0100000 rw-p 00000000 00:00 0 
7c0100000-800000000 ---p 00000000 00:00 0 
7efc90000000-7efc90021000 rw-p 00000000 00:00 0 
7efc90021000-7efc94000000 ---p 00000000 00:00 0 
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7efce292a000-7efce2976000 r--s 00411000 00:11 14344694                   /home/pablo/.m2/repository/org/scala-lang/scala-reflect/2.11.8/scala-reflect-2.11.8.jar
7efce2976000-7efce29cf000 r--s 00522000 00:11 14344508                   /home/pablo/.m2/repository/org/scala-lang/scala-library/2.11.8/scala-library-2.11.8.jar
7efce29cf000-7efce29e2000 r--s 00345000 00:11 12241166                   /usr/lib/jvm/java-8-oracle/jre/lib/resources.jar
7efce29e2000-7efce29f4000 r--s 000d6000 00:11 12241165                   /usr/lib/jvm/java-8-oracle/jre/lib/plugin.jar
7efce29f4000-7efce2a0f000 r--s 00208000 00:11 12241050                   /usr/lib/jvm/java-8-oracle/jre/lib/deploy.jar
7efce2a0f000-7efce2a10000 ---p 00000000 00:00 0 
7efce2a10000-7efce2b10000 rw-p 00000000 00:00 0                          [stack:14738]
7efce2b10000-7efce2b13000 ---p 00000000 00:00 0 
7efce2b13000-7efce2c11000 rw-p 00000000 00:00 0                          [stack:14737]
7efce2c11000-7efce2c14000 ---p 00000000 00:00 0 
7efce2c14000-7efce2d12000 rw-p 00000000 00:00 0                          [stack:14736]
7efce2d12000-7efce2d15000 ---p 00000000 00:00 0 
7efce2d15000-7efce2e13000 rw-p 00000000 00:00 0                          [stack:14735]
7efce2e13000-7efce2e16000 ---p 00000000 00:00 0 
7efce2e16000-7efce2f14000 rw-p 00000000 00:00 0                          [stack:14734]
7efce2f14000-7efce2f17000 ---p 00000000 00:00 0 
7efce2f17000-7efce3015000 rw-p 00000000 00:00 0                          [stack:14733]
7efce3015000-7efce3018000 ---p 00000000 00:00 0 
7efce3018000-7efce3116000 rw-p 00000000 00:00 0                          [stack:14732]
7efce3116000-7efce37f8000 r--p 00000000 00:11 18371                      /usr/lib/locale/locale-archive
7efce37f8000-7efce37fb000 ---p 00000000 00:00 0 
7efce37fb000-7efce38f9000 rw-p 00000000 00:00 0                          [stack:14731]
7efce38f9000-7efce38fc000 ---p 00000000 00:00 0 
7efce38fc000-7efce39fa000 rw-p 00000000 00:00 0                          [stack:14730]
7efce39fa000-7efce39fb000 ---p 00000000 00:00 0 
7efce39fb000-7efce4000000 rw-p 00000000 00:00 0                          [stack:14729]
7efce4000000-7efce4021000 rw-p 00000000 00:00 0 
7efce4021000-7efce8000000 ---p 00000000 00:00 0 
7efce8000000-7efce8006000 r--s 0004d000 00:11 30058942                   /home/pablo/.m2/repository/com/orientechnologies/orientdb-graphdb/2.2.10/orientdb-graphdb-2.2.10.jar
7efce8006000-7efce8008000 r--s 0000c000 00:11 30058940                   /home/pablo/.m2/repository/org/ow2/asm/asm/5.1/asm-5.1.jar
7efce8008000-7efce800a000 r--s 00006000 00:11 30058937                   /home/pablo/.m2/repository/org/ow2/asm/asm-tree/5.1/asm-tree-5.1.jar
7efce800a000-7efce9000000 rw-p 00000000 00:00 0 
7efce9000000-7efce9270000 rwxp 00000000 00:00 0 
7efce9270000-7efcf8000000 ---p 00000000 00:00 0 
7efcf8000000-7efcf8c5b000 rw-p 00000000 00:00 0 
7efcf8c5b000-7efcfc000000 ---p 00000000 00:00 0 
7efcfc000000-7efcfc001000 r--s 00003000 00:11 30058998                   /home/pablo/.m2/repository/com/github/haifengl/smile-graph/1.2.0/smile-graph-1.2.0.jar
7efcfc001000-7efcfc003000 r--s 0000a000 00:11 30058938                   /home/pablo/.m2/repository/org/ow2/asm/asm-commons/5.1/asm-commons-5.1.jar
7efcfc003000-7efcfc77a000 rw-p 00000000 00:00 0 
7efcfc77a000-7efcfc952000 r--s 03d2a000 00:11 12240934                   /usr/lib/jvm/java-8-oracle/jre/lib/rt.jar
7efcfc952000-7efcfd023000 rw-p 00000000 00:00 0 
7efcfd023000-7efcfd223000 ---p 00000000 00:00 0 
7efcfd223000-7efcfd9ef000 rw-p 00000000 00:00 0 
7efcfd9ef000-7efcfd9f0000 ---p 00000000 00:00 0 
7efcfd9f0000-7efcfdaf0000 rw-p 00000000 00:00 0                          [stack:14728]
7efcfdaf0000-7efcfdaf1000 ---p 00000000 00:00 0 
7efcfdaf1000-7efcfdbf1000 rw-p 00000000 00:00 0                          [stack:14727]
7efcfdbf1000-7efcfdbf2000 ---p 00000000 00:00 0 
7efcfdbf2000-7efcfdcf2000 rw-p 00000000 00:00 0                          [stack:14726]
7efcfdcf2000-7efcfdcf3000 ---p 00000000 00:00 0 
7efcfdcf3000-7efcfddf3000 rw-p 00000000 00:00 0                          [stack:14725]
7efcfddf3000-7efcfddf4000 ---p 00000000 00:00 0 
7efcfddf4000-7efcfdef4000 rw-p 00000000 00:00 0                          [stack:14724]
7efcfdef4000-7efcfdef5000 ---p 00000000 00:00 0 
7efcfdef5000-7efcfdff5000 rw-p 00000000 00:00 0                          [stack:14723]
7efcfdff5000-7efcfdff6000 ---p 00000000 00:00 0 
7efcfdff6000-7efcfe0f6000 rw-p 00000000 00:00 0                          [stack:14722]
7efcfe0f6000-7efcfe0f7000 ---p 00000000 00:00 0 
7efcfe0f7000-7efcfe24b000 rw-p 00000000 00:00 0                          [stack:14721]
7efcfe24b000-7efcfe72a000 ---p 00000000 00:00 0 
7efcfe72a000-7efcfe77e000 rw-p 00000000 00:00 0 
7efcfe77e000-7efcfec5c000 ---p 00000000 00:00 0 
7efcfec5c000-7efcfec87000 rw-p 00000000 00:00 0 
7efcfec87000-7efcfeef6000 ---p 00000000 00:00 0 
7efcfeef6000-7efcfef01000 rw-p 00000000 00:00 0 
7efcfef01000-7efcff2b7000 ---p 00000000 00:00 0 
7efcff2b7000-7efcff2d1000 r-xp 00000000 00:11 12240965                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libzip.so
7efcff2d1000-7efcff4d1000 ---p 0001a000 00:11 12240965                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libzip.so
7efcff4d1000-7efcff4d2000 rw-p 0001a000 00:11 12240965                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libzip.so
7efcff4d2000-7efcff4fd000 r-xp 00000000 00:11 12240992                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libjava.so
7efcff4fd000-7efcff6fc000 ---p 0002b000 00:11 12240992                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libjava.so
7efcff6fc000-7efcff6fe000 rw-p 0002a000 00:11 12240992                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libjava.so
7efcff6fe000-7efcff70b000 r-xp 00000000 00:11 12240943                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libverify.so
7efcff70b000-7efcff90a000 ---p 0000d000 00:11 12240943                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libverify.so
7efcff90a000-7efcff90c000 rw-p 0000c000 00:11 12240943                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/libverify.so
7efcff90c000-7efcff913000 r-xp 00000000 00:11 8317859                    /lib/x86_64-linux-gnu/librt-2.19.so
7efcff913000-7efcffb12000 ---p 00007000 00:11 8317859                    /lib/x86_64-linux-gnu/librt-2.19.so
7efcffb12000-7efcffb13000 r--p 00006000 00:11 8317859                    /lib/x86_64-linux-gnu/librt-2.19.so
7efcffb13000-7efcffb14000 rw-p 00007000 00:11 8317859                    /lib/x86_64-linux-gnu/librt-2.19.so
7efcffb14000-7efcffc19000 r-xp 00000000 00:11 8317845                    /lib/x86_64-linux-gnu/libm-2.19.so
7efcffc19000-7efcffe18000 ---p 00105000 00:11 8317845                    /lib/x86_64-linux-gnu/libm-2.19.so
7efcffe18000-7efcffe19000 r--p 00104000 00:11 8317845                    /lib/x86_64-linux-gnu/libm-2.19.so
7efcffe19000-7efcffe1a000 rw-p 00105000 00:11 8317845                    /lib/x86_64-linux-gnu/libm-2.19.so
7efcffe1a000-7efd00ae7000 r-xp 00000000 00:11 12240996                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so
7efd00ae7000-7efd00ce6000 ---p 00ccd000 00:11 12240996                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so
7efd00ce6000-7efd00dbf000 rw-p 00ccc000 00:11 12240996                   /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so
7efd00dbf000-7efd00e0a000 rw-p 00000000 00:00 0 
7efd00e0a000-7efd00fc4000 r-xp 00000000 00:11 8317860                    /lib/x86_64-linux-gnu/libc-2.19.so
7efd00fc4000-7efd011c4000 ---p 001ba000 00:11 8317860                    /lib/x86_64-linux-gnu/libc-2.19.so
7efd011c4000-7efd011c8000 r--p 001ba000 00:11 8317860                    /lib/x86_64-linux-gnu/libc-2.19.so
7efd011c8000-7efd011ca000 rw-p 001be000 00:11 8317860                    /lib/x86_64-linux-gnu/libc-2.19.so
7efd011ca000-7efd011cf000 rw-p 00000000 00:00 0 
7efd011cf000-7efd011d2000 r-xp 00000000 00:11 8317847                    /lib/x86_64-linux-gnu/libdl-2.19.so
7efd011d2000-7efd013d1000 ---p 00003000 00:11 8317847                    /lib/x86_64-linux-gnu/libdl-2.19.so
7efd013d1000-7efd013d2000 r--p 00002000 00:11 8317847                    /lib/x86_64-linux-gnu/libdl-2.19.so
7efd013d2000-7efd013d3000 rw-p 00003000 00:11 8317847                    /lib/x86_64-linux-gnu/libdl-2.19.so
7efd013d3000-7efd013e8000 r-xp 00000000 00:11 12240077                   /usr/lib/jvm/java-8-oracle/lib/amd64/jli/libjli.so
7efd013e8000-7efd015e8000 ---p 00015000 00:11 12240077                   /usr/lib/jvm/java-8-oracle/lib/amd64/jli/libjli.so
7efd015e8000-7efd015e9000 rw-p 00015000 00:11 12240077                   /usr/lib/jvm/java-8-oracle/lib/amd64/jli/libjli.so
7efd015e9000-7efd01602000 r-xp 00000000 00:11 8317852                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7efd01602000-7efd01801000 ---p 00019000 00:11 8317852                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7efd01801000-7efd01802000 r--p 00018000 00:11 8317852                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7efd01802000-7efd01803000 rw-p 00019000 00:11 8317852                    /lib/x86_64-linux-gnu/libpthread-2.19.so
7efd01803000-7efd01807000 rw-p 00000000 00:00 0 
7efd01807000-7efd0182a000 r-xp 00000000 00:11 8317853                    /lib/x86_64-linux-gnu/ld-2.19.so
7efd0182a000-7efd0182b000 r--s 00000000 00:11 12241013                   /usr/lib/jvm/java-8-oracle/jre/lib/management-agent.jar
7efd0182b000-7efd0182f000 r--s 00097000 00:11 12240886                   /usr/lib/jvm/java-8-oracle/jre/lib/jsse.jar
7efd0182f000-7efd01831000 r--s 00007000 00:11 12241007                   /usr/lib/jvm/java-8-oracle/jre/lib/jfxswt.jar
7efd01831000-7efd01836000 r--s 00084000 00:11 12241041                   /usr/lib/jvm/java-8-oracle/jre/lib/jfr.jar
7efd01836000-7efd01839000 r--s 0001a000 00:11 12241196                   /usr/lib/jvm/java-8-oracle/jre/lib/jce.jar
7efd01839000-7efd018d0000 rw-p 00000000 00:00 0 
7efd018d0000-7efd01905000 r--s 00000000 00:11 460131                     /var/cache/nscd/passwd
7efd01905000-7efd01908000 ---p 00000000 00:00 0 
7efd01908000-7efd01a0a000 rw-p 00000000 00:00 0                          [stack:14717]
7efd01a0a000-7efd01a14000 r--s 0006c000 00:11 12241049                   /usr/lib/jvm/java-8-oracle/jre/lib/javaws.jar
7efd01a14000-7efd01a19000 r--s 002f9000 00:11 12240887                   /usr/lib/jvm/java-8-oracle/jre/lib/charsets.jar
7efd01a19000-7efd01a1b000 r--s 0001d000 00:11 31757170                   /home/pablo/myProgs/idea-IU-163.7743.44/plugins/junit/lib/junit-rt.jar
7efd01a1b000-7efd01a1d000 r--s 00019000 00:11 31757800                   /home/pablo/myProgs/idea-IU-163.7743.44/lib/idea_rt.jar
7efd01a1d000-7efd01a25000 rw-s 00000000 00:11 12699552                   /tmp/hsperfdata_pablo/14716
7efd01a25000-7efd01a26000 rw-p 00000000 00:00 0 
7efd01a26000-7efd01a27000 r--p 00000000 00:00 0 
7efd01a27000-7efd01a29000 rw-p 00000000 00:00 0 
7efd01a29000-7efd01a2a000 r--p 00022000 00:11 8317853                    /lib/x86_64-linux-gnu/ld-2.19.so
7efd01a2a000-7efd01a2b000 rw-p 00023000 00:11 8317853                    /lib/x86_64-linux-gnu/ld-2.19.so
7efd01a2b000-7efd01a2c000 rw-p 00000000 00:00 0 
7fffbc82f000-7fffbc855000 rw-p 00000000 00:00 0                          [stack]
7fffbc871000-7fffbc873000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

VM Arguments:
jvm_args: -ea -Didea.launcher.port=7532 -Didea.launcher.bin.path=/home/pablo/myProgs/idea-IU-163.7743.44/bin 
java_command: com.intellij.rt.execution.junit.JUnitForkedStarter com.physiosigns.python.PythonInvocationTest,executeSomePython com.intellij.junit4.JUnit4IdeaTestRunner
java_class_path (initial): /home/pablo/myProgs/idea-IU-163.7743.44/lib/idea_rt.jar:/home/pablo/myProgs/idea-IU-163.7743.44/plugins/junit/lib/junit-rt.jar:/usr/lib/jvm/java-8-oracle/jre/lib/charsets.jar:/usr/lib/jvm/java-8-oracle/jre/lib/deploy.jar:/usr/lib/jvm/java-8-oracle/jre/lib/ext/cldrdata.jar:/usr/lib/jvm/java-8-oracle/jre/lib/ext/dnsns.jar:/usr/lib/jvm/java-8-oracle/jre/lib/ext/jaccess.jar:/usr/lib/jvm/java-8-oracle/jre/lib/ext/jfxrt.jar:/usr/lib/jvm/java-8-oracle/jre/lib/ext/localedata.jar:/usr/lib/jvm/java-8-oracle/jre/lib/ext/nashorn.jar:/usr/lib/jvm/java-8-oracle/jre/lib/ext/sunec.jar:/usr/lib/jvm/java-8-oracle/jre/lib/ext/sunjce_provider.jar:/usr/lib/jvm/java-8-oracle/jre/lib/ext/sunpkcs11.jar:/usr/lib/jvm/java-8-oracle/jre/lib/ext/zipfs.jar:/usr/lib/jvm/java-8-oracle/jre/lib/javaws.jar:/usr/lib/jvm/java-8-oracle/jre/lib/jce.jar:/usr/lib/jvm/java-8-oracle/jre/lib/jfr.jar:/usr/lib/jvm/java-8-oracle/jre/lib/jfxswt.jar:/usr/lib/jvm/java-8-oracle/jre/lib/jsse.jar:/usr/lib/jvm/java-8-oracle/jre/lib/management-agent.jar:/usr/lib/jvm/java-8-oracle/jre/lib/plugin.jar:/usr/lib/jvm/java-8-oracle/jre/lib/resources.jar:/usr/lib/jvm/java-8-oracle/jre/lib/rt.jar:/home/pablo/develop/physiosigns/livebetter/lb/featureSystem/target/test-classes:/home/pablo/develop/physiosigns/livebetter/lb/featureSystem/target/classes:/home/pablo/.m2/repository/org/scala-lang/scala-library/2.11.8/scala-library-2.11.8.jar:/home/pablo/.m2/repository/org/scala-lang/scala-reflect/2.11.8/scala-reflect-2.11.8.jar:/home/pablo/.m2/repository/org/ow2/asm/asm-commons/5.1/asm-commons-5.1.jar:/home/pablo/.m2/repository/org/ow2/asm/asm-tree/5.1/asm-tree-5.1.jar:/home/pablo/.m2/repository/org/ow2/asm/asm/5.1/asm-5.1.jar:/home/pablo/.m2/repository/com/orientechnologies/orientdb-graphdb/2.2.10/orientdb-graphdb-2.2.10.jar:/home/pablo/.m2/repository/com/orientechnologies/orientdb-server/2.2.10/orientdb-server-2.2.10.jar:/home/pablo/.m2/repository/com/orientechnologies/orientdb-client/2.2.10/orientdb-clie
Launcher Type: SUN_STANDARD

Environment Variables:
JAVA_HOME=/usr/lib/jvm/java-8-oracle
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin
LD_LIBRARY_PATH=/home/pablo/myProgs/idea-IU-163.7743.44/bin:/home/pablo/myProgs/idea-IU-163.7743.44/bin:
SHELL=/bin/bash
DISPLAY=:0

Signal Handlers:
SIGSEGV: [libjvm.so+0xac64b0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGBUS: [libjvm.so+0xac64b0], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGFPE: [libjvm.so+0x91f950], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGPIPE: SIG_IGN, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
SIGXFSZ: SIG_IGN, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
SIGILL: [libjvm.so+0x91f950], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
SIGUSR2: [libjvm.so+0x920f80], sa_mask[0]=00100000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
SIGHUP: SIG_IGN, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
SIGINT: [libjvm.so+0x922380], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGTERM: [libjvm.so+0x922380], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO
SIGQUIT: [libjvm.so+0x922380], sa_mask[0]=11111111011111111101111111111110, sa_flags=SA_RESTART|SA_SIGINFO


---------------  S Y S T E M  ---------------

OS:DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=14.04
DISTRIB_CODENAME=trusty
DISTRIB_DESCRIPTION="Ubuntu 14.04.5 LTS"

uname:Linux 3.13.0-106-generic #153-Ubuntu SMP Tue Dec 6 15:44:32 UTC 2016 x86_64
libc:glibc 2.19 NPTL 2.19 
rlimit: STACK 8192k, CORE 0k, NPROC 126733, NOFILE 4096, AS infinity
load average:1.24 1.43 1.56

/proc/meminfo:
MemTotal:       16344220 kB
MemFree:          156744 kB
Buffers:              76 kB
Cached:          1816736 kB
SwapCached:       247596 kB
Active:         13739756 kB
Inactive:        1852764 kB
Active(anon):   13579112 kB
Inactive(anon):  1669692 kB
Active(file):     160644 kB
Inactive(file):   183072 kB
Unevictable:         208 kB
Mlocked:             208 kB
SwapTotal:      15999996 kB
SwapFree:       12658164 kB
Dirty:             13964 kB
Writeback:             0 kB
AnonPages:      13612212 kB
Mapped:           878080 kB
Shmem:           1471408 kB
Slab:             205972 kB
SReclaimable:      95824 kB
SUnreclaim:       110148 kB
KernelStack:       14800 kB
PageTables:       171032 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:    24172104 kB
Committed_AS:   38960340 kB
VmallocTotal:   34359738367 kB
VmallocUsed:      598684 kB
VmallocChunk:   34359099756 kB
HardwareCorrupted:     0 kB
AnonHugePages:   2312192 kB
HugePages_Total:       0
HugePages_Free:        0
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB
DirectMap4k:      150272 kB
DirectMap2M:     5003264 kB
DirectMap1G:    11534336 kB


CPU:total 8 (4 cores per cpu, 2 threads per core) family 6 model 60 stepping 3, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2

/proc/cpuinfo:
processor	: 0
vendor_id	: GenuineIntel
cpu family	: 6
model		: 60
model name	: Intel(R) Core(TM) i7-4700HQ CPU @ 2.40GHz
stepping	: 3
microcode	: 0x1a
cpu MHz		: 2401.000
cache size	: 6144 KB
physical id	: 0
siblings	: 8
core id		: 0
cpu cores	: 4
apicid		: 0
initial apicid	: 0
fpu		: yes
fpu_exception	: yes
cpuid level	: 13
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid
bogomips	: 4788.93
clflush size	: 64
cache_alignment	: 64
address sizes	: 39 bits physical, 48 bits virtual
power management:

processor	: 1
vendor_id	: GenuineIntel
cpu family	: 6
model		: 60
model name	: Intel(R) Core(TM) i7-4700HQ CPU @ 2.40GHz
stepping	: 3
microcode	: 0x1a
cpu MHz		: 1700.000
cache size	: 6144 KB
physical id	: 0
siblings	: 8
core id		: 0
cpu cores	: 4
apicid		: 1
initial apicid	: 1
fpu		: yes
fpu_exception	: yes
cpuid level	: 13
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid
bogomips	: 4788.93
clflush size	: 64
cache_alignment	: 64
address sizes	: 39 bits physical, 48 bits virtual
power management:

processor	: 2
vendor_id	: GenuineIntel
cpu family	: 6
model		: 60
model name	: Intel(R) Core(TM) i7-4700HQ CPU @ 2.40GHz
stepping	: 3
microcode	: 0x1a
cpu MHz		: 800.000
cache size	: 6144 KB
physical id	: 0
siblings	: 8
core id		: 1
cpu cores	: 4
apicid		: 2
initial apicid	: 2
fpu		: yes
fpu_exception	: yes
cpuid level	: 13
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid
bogomips	: 4788.93
clflush size	: 64
cache_alignment	: 64
address sizes	: 39 bits physical, 48 bits virtual
power management:

processor	: 3
vendor_id	: GenuineIntel
cpu family	: 6
model		: 60
model name	: Intel(R) Core(TM) i7-4700HQ CPU @ 2.40GHz
stepping	: 3
microcode	: 0x1a
cpu MHz		: 2401.000
cache size	: 6144 KB
physical id	: 0
siblings	: 8
core id		: 1
cpu cores	: 4
apicid		: 3
initial apicid	: 3
fpu		: yes
fpu_exception	: yes
cpuid level	: 13
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid
bogomips	: 4788.93
clflush size	: 64
cache_alignment	: 64
address sizes	: 39 bits physical, 48 bits virtual
power management:

processor	: 4
vendor_id	: GenuineIntel
cpu family	: 6
model		: 60
model name	: Intel(R) Core(TM) i7-4700HQ CPU @ 2.40GHz
stepping	: 3
microcode	: 0x1a
cpu MHz		: 1800.000
cache size	: 6144 KB
physical id	: 0
siblings	: 8
core id		: 2
cpu cores	: 4
apicid		: 4
initial apicid	: 4
fpu		: yes
fpu_exception	: yes
cpuid level	: 13
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid
bogomips	: 4788.93
clflush size	: 64
cache_alignment	: 64
address sizes	: 39 bits physical, 48 bits virtual
power management:

processor	: 5
vendor_id	: GenuineIntel
cpu family	: 6
model		: 60
model name	: Intel(R) Core(TM) i7-4700HQ CPU @ 2.40GHz
stepping	: 3
microcode	: 0x1a
cpu MHz		: 1900.000
cache size	: 6144 KB
physical id	: 0
siblings	: 8
core id		: 2
cpu cores	: 4
apicid		: 5
initial apicid	: 5
fpu		: yes
fpu_exception	: yes
cpuid level	: 13
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid
bogomips	: 4788.93
clflush size	: 64
cache_alignment	: 64
address sizes	: 39 bits physical, 48 bits virtual
power management:

processor	: 6
vendor_id	: GenuineIntel
cpu family	: 6
model		: 60
model name	: Intel(R) Core(TM) i7-4700HQ CPU @ 2.40GHz
stepping	: 3
microcode	: 0x1a
cpu MHz		: 2401.000
cache size	: 6144 KB
physical id	: 0
siblings	: 8
core id		: 3
cpu cores	: 4
apicid		: 6
initial apicid	: 6
fpu		: yes
fpu_exception	: yes
cpuid level	: 13
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid
bogomips	: 4788.93
clflush size	: 64
cache_alignment	: 64
address sizes	: 39 bits physical, 48 bits virtual
power management:

processor	: 7
vendor_id	: GenuineIntel
cpu family	: 6
model		: 60
model name	: Intel(R) Core(TM) i7-4700HQ CPU @ 2.40GHz
stepping	: 3
microcode	: 0x1a
cpu MHz		: 800.000
cache size	: 6144 KB
physical id	: 0
siblings	: 8
core id		: 3
cpu cores	: 4
apicid		: 7
initial apicid	: 7
fpu		: yes
fpu_exception	: yes
cpuid level	: 13
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid
bogomips	: 4788.93
clflush size	: 64
cache_alignment	: 64
address sizes	: 39 bits physical, 48 bits virtual
power management:



Memory: 4k page, physical 16344220k(156744k free), swap 15999996k(12658164k free)

vm_info: Java HotSpot(TM) 64-Bit Server VM (25.111-b14) for linux-amd64 JRE (1.8.0_111-b14), built on Sep 22 2016 16:14:03 by "java_re" with gcc 4.3.0 20080428 (Red Hat 4.3.0-8)

time: Mon Dec 19 14:35:04 2016
elapsed time: 0 seconds (0d 0h 0m 0s)

The text was updated successfully, but these errors were encountered:

voutilad · 2017-02-21T14:26:53Z

@pabloa I'm curious if you have tried the same logic in plain Java on your machine using the libraries you built from that snapshot of JPY. Are you able to try a similar JUnit case in plain java?

I resolved a similar issue when using Java 8 (see #71) and I'll see if I can reproduce this in Scala on my machine.

voutilad · 2017-02-21T22:35:17Z

I just tried this on my local machine with the latest build of master and it seems to work. It's a slightly different environment (macOS, Python 2.7.13) but it seems to work at its most basic:

$scala -classpath "./lib/*"
Welcome to Scala 2.12.1 (Java HotSpot(TM) 64-Bit Server VM, Java 1.8.0_112).
Type in expressions for evaluation. Or try :help.

scala> import org.jpy.{PyLib, PyModule, PyObject}
import org.jpy.{PyLib, PyModule, PyObject}

scala>     System.setProperty("jpy.debug", "true")
res0: String = null

scala> System.setProperty("jpy.config", "/Users/dave/src/jpy/build/lib.macosx-10.12-x86_64-2.7/jpyconfig.properties")
res1: String = null

scala> PyLib.startPython()
org.jpy.PyLib: entered static initializer
org.jpy.PyLibConfig: entered static initializer
org.jpy.PyLibConfig: loading configuration file /Users/dave/src/jpy/build/lib.macosx-10.12-x86_64-2.7/jpyconfig.properties
org.jpy.PyLibConfig: exited static initializer
org.jpy.PyLib: DL.dlopen("/usr/local/opt/python/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib", DL.RTLD_GLOBAL + DL.RTLD_LAZY
org.jpy.PyLib: System.load("/Users/dave/src/jpy/build/lib.macosx-10.12-x86_64-2.7/jpy.so")
org.jpy.PyLib: exited static initializer
org.jpy.PyLib: Starting Python with 1 extra module path(s):
org.jpy.PyLib:   /Users/dave/src/jpy/build/lib.macosx-10.12-x86_64-2.7
PyLib_startPython: entered: jenv=0x7fca7d0019f8, pyInit=0, JPy_Module=0x0
PyLib_startPython: global Python interpreter information:
  Py_GetProgramName()     = "python"
  Py_GetPrefix()          = "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7"
  Py_GetExecPrefix()      = "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7"
  Py_GetProgramFullPath() = "/Library/Java/JavaVirtualMachines/jdk1.8.0_112.jdk/Contents/Home//bin/java"
  Py_GetPath()            = "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python27.zip:/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7:/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin:/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac:/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages:/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk:/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old:/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload"
  Py_GetPythonHome()      = "(null)"
  Py_GetVersion()         = "2.7.13 (default, Dec 18 2016, 07:03:39)
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)]"
  Py_GetPlatform()        = "darwin"
  Py_GetCompiler()        = "
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.42.1)]"
  Py_GetBuildInfo()       = "default, Dec 18 2016, 07:03:39"
PyLib_startPython: exiting: jenv=0x7fca7d0019f8, pyInit=1, JPy_Module=0x10a6e21d8

scala> PyLib.execScript("print('this is from python')")
<console>:13: warning: method execScript in object PyLib is deprecated: see corresponding Javadoc for more information.
       PyLib.execScript("print('this is from python')")
             ^
Java_org_jpy_PyLib_execScript: script='print('this is from python')'
this is from python
res3: Int = 0

scala> PyLib.isPythonRunning
res4: Boolean = true

scala> PyLib.stopPython()
Java_org_jpy_PyLib_stopPython: entered: JPy_Module=0x10a6e21d8
JPy_free: freeing module data...
JPy_free: done freeing module data
Java_org_jpy_PyLib_stopPython: exiting: JPy_Module=0x0

scala> PyLib.isPythonRunning
res6: Boolean = false

Looking at the source for Python 2.7.6 and 2.7.13 there's very minimal difference between their Py_Finalize(void) functions. The difference just has to do 2.7.13 having a call (_PyRandom_Fini(void)) for closing or release anything being held related to the OS's random number generation capabilities for the Python random functions.

Can you try a similar Scala repl test like I performed above? Don't add any extra modules or libs to the Python or Java (class)paths and make sure you set jpy.config to the generated jpyconfig.properties file from your local jpy project.

voutilad · 2017-02-22T00:47:59Z

I also just tested with Scala 2.12.1 and Python 2.7.6 on Ubuntu 14.04.5. My JPY debug details on start:

scala> PyLib.startPython()
org.jpy.PyLib: entered static initializer
org.jpy.PyLibConfig: entered static initializer
org.jpy.PyLibConfig: loading configuration file /home/vagrant/jpy/build/lib.linux-x86_64-2.7/jpyconfig.properties
org.jpy.PyLibConfig: exited static initializer
org.jpy.PyLib: DL.dlopen("/usr/lib/x86_64-linux-gnu/libpython2.7.so", DL.RTLD_GLOBAL + DL.RTLD_LAZY
org.jpy.PyLib: System.load("/home/vagrant/jpy/build/lib.linux-x86_64-2.7/jpy.so")
org.jpy.PyLib: exited static initializer
org.jpy.PyLib: Starting Python with 1 extra module path(s):
org.jpy.PyLib:   /home/vagrant/jpy/build/lib.linux-x86_64-2.7
PyLib_startPython: entered: jenv=0x7fa61400a1f8, pyInit=0, JPy_Module=(nil)
PyLib_startPython: global Python interpreter information:
  Py_GetProgramName()     = "python"
  Py_GetPrefix()          = "/usr"
  Py_GetExecPrefix()      = "/usr"
  Py_GetProgramFullPath() = "/usr/bin/python"
  Py_GetPath()            = "/usr/lib/python2.7/:/usr/lib/python2.7/plat-x86_64-linux-gnu:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-old:/usr/lib/python2.7/lib-dynload"
  Py_GetPythonHome()      = "(null)"
  Py_GetVersion()         = "2.7.6 (default, Oct 26 2016, 20:33:43)
[GCC 4.8.4]"
  Py_GetPlatform()        = "linux2"
  Py_GetCompiler()        = "
[GCC 4.8.4]"
  Py_GetBuildInfo()       = "default, Oct 26 2016, 20:33:43"
PyLib_startPython: exiting: jenv=0x7fa61400a1f8, pyInit=1, JPy_Module=0x7fa6000b54e8

Treydone · 2017-02-23T13:17:23Z

Hi, I have the same error on a Windows 7.1 Java 1.8.25 Python 2.7.13 (Anaconda 4.3.0) 64-bit: the PyLib.stopPython() generates a JVM crash with a EXCEPTION_ACCESS_VIOLATION

voutilad · 2017-02-23T13:32:55Z

@Treydone are you building JPY from the master branch or installing from PyPI?

Also, I believe there are some potential issues with versions of Java 8 prior to update 60 according to issue #56.

pabloa · 2017-02-23T18:32:35Z

Hello @voutilad, I used scala 2.11.8
I will update the JVM to the current last one and I will try again.

Treydone · 2017-02-23T21:38:08Z

@voutilad Yes I was using the master branch. I'll give a try tomorrow with a more recent JDK.

Treydone · 2017-02-27T10:54:28Z

@voutilad I've got the same error using the latest JDK (Java(TM) SE Runtime Environment (8.0_121-b13) (build 1.8.0_121-b13))

voutilad · 2017-02-28T12:49:30Z

@Treydone and @pabloa I'm still struggling to reproduce the same error using the code in the master branch.

When we fixed some issues with the PyLib.stopPython() call, a unit test was introduced called org.jpy.LifeCycleTest. You should be able to run it directly via Maven by executing:

mvn -Dtest=org.jpy.LifeCycleTest test -Djpy.config=/Users/dave/src/python/jpy/build/lib.macosx-10.12-x86_64-2.7/jpyconfig.properties

Replace /Users/dave/src/python/jpy/build/lib.macosx-10.12-x86_64-2.7/jpyconfig.properties with the path to your jpyconfig.properties from the build/directory for JPY.

You should get 1 test run without errors. If it fails, then either you aren't running master (commit has e20cea6) or haven't built the Python libs with python setup.py bdist_wheel. If you've properly built the libs and it's still failing, it's possibly an issue with JPY and your Python version. In that case, if you have multiple versions installed, I recommend trying again with a Python virtualenv to make sure you can isolate the version.

If this test works, but your code does not, it could be few issues:

pointing jpy.jpyLib/jpy.jdlLibto the wrong or old instances of the JPY libraries.
using a different Python version/instance than used to build JPY (are you using virtualenvs?)
something absolutely funky with our inability to get the GIL lock to safely shutdown the interpreter

If it's the GIL lock issue, it could be related to what you're doing with your Python code. In that case it might be worth taking this into a private discussion for a bit to see if we can isolate what could be the cause.

Sorry for the long winded message! I really want to help get to the bottom of this. If your project can be shared publicly, please let me know and I can take a look at how you've implemented JPY.

forman · 2017-05-22T08:00:51Z

It seems, the issue remains merely on Windows. AppVeyor builds still crash with unit-level tests that call PyLib.startPython() / stopPython() a second time.

forman added the bug label May 3, 2017

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PyLib.stopPython() generates a memory core with java 8 #77

PyLib.stopPython() generates a memory core with java 8 #77

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forman commented May 22, 2017

PyLib.stopPython() generates a memory core with java 8 #77

PyLib.stopPython() generates a memory core with java 8 #77

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