JVM crash on loading network.dat using r5

I am working with a library named R5. It has a main method com.conveyal.r5.R5Main to start it as service. It works perfectly fine. But when i try to use it in my application as library and call the same flow, JVM crashes and following traces prints on the console.

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fd2945622d4, pid=20894, tid=0x00007fd29595b700
#
# JRE version: Java(TM) SE Runtime Environment (8.0_131-b11) (build 1.8.0_131-b11)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.131-b11 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# V  [libjvm.so+0x7fe2d4]
#
# 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/user/workspace/r5-project/hs_err_pid20894.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.java.com/bugreport/crash.jsp
#

My project pom.xml is:

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<groupId>org.playground.r5</groupId>
<artifactId>r5-project</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>

<name>r5-project</name>
<url>http://maven.apache.org</url>

<properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>

  <repositories>
    <repository>
        <id>jitpack.io</id>
        <url>https://jitpack.io</url>
    </repository>
  </repositories>

  <dependencies>
    <dependency>
    <groupId>com.conveyal</groupId>
    <artifactId>r5</artifactId>
    <version>2.1.1</version>
    </dependency>
  </dependencies>
</project>

And code that crashes is:

String dir = "/home/user/r5/portland";
File file = new File(dir, "network.dat");
TransportNetwork transportNetwork = TransportNetwork.read(file);

And the content of file hs_err_pid20894.log that it mentions are:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fd2945622d4, pid=20894, tid=0x00007fd29595b700
#
# JRE version: Java(TM) SE Runtime Environment (8.0_131-b11) (build 1.8.0_131-b11)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.131-b11 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# V  [libjvm.so+0x7fe2d4]
#
# 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
#

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

Current thread (0x00007fd28c013800):  JavaThread "main" [_thread_in_vm, id=20901, stack(0x00007fd29585b000,0x00007fd29595c000)]

siginfo: si_signo: 11 (SIGSEGV), si_code: 2 (SEGV_ACCERR), si_addr: 0x00007fd22c021000

Registers:
RAX=0x00007fd2840a6264, RBX=0x00007fd28c013800, RCX=0x00000006db82e378, RDX=0xfffffffff4fef5b4
RSP=0x00007fd295959eb8, RBP=0x00007fd295959f10, RSI=0x0000000000000000, RDI=0x00007fd229a8ed0c
R8 =0x000000002d30bab3, R9 =0x0000000000000010, R10=0x00007fd27d01fc78, R11=0x00007fd294729190
R12=0x0000000000000000, R13=0x00007fd295959fe8, R14=0x00007fd294d25f40, R15=0x00007fd294d2acc0
RIP=0x00007fd2945622d4, EFLAGS=0x0000000000010286, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
  TRAPNO=0x000000000000000e

Top of Stack: (sp=0x00007fd295959eb8)
0x00007fd295959eb8:   00007fd2947ff2af 0000000000000010
0x00007fd295959ec8:   00007fd229a8ed0c 00007fd28c013800
0x00007fd295959ed8:   00007fd200000000 00007fd295959fa8
0x00007fd295959ee8:   00007fd272880dc8 0000000000000000
0x00007fd295959ef8:   00007fd272880dc8 00007fd29595a008
0x00007fd295959f08:   00007fd28c013800 00007fd295959fa8
0x00007fd295959f18:   00007fd27d01fca4 000000005a617566
0x00007fd295959f28:   00007fd295959f80 00007fd28c013800
0x00007fd295959f38:   00007fd295959f90 00007fd272880dc8
0x00007fd295959f48:   0000000000000000 00007fd295959fa8
0x00007fd295959f58:   00007fd27d01f8bb 00007fd27d01f879
0x00007fd295959f68:   00007fd295959f68 00007fd272880dc8
0x00007fd295959f78:   00007fd29595a008 00007fd2728aed80
0x00007fd295959f88:   0000000000000000 00007fd272880dc8
0x00007fd295959f98:   0000000000000000 00007fd295959fc8
0x00007fd295959fa8:   00007fd29595a050 00007fd27d00833d
0x00007fd295959fb8:   0000000000000000 00007fd27d016478
0x00007fd295959fc8:   000000005a617566 00007fd29595a050
0x00007fd295959fd8:   0000000000000010 00000007559d0c70
0x00007fd295959fe8:   0000000681216e10 00007fd229a8ed0c
0x00007fd295959ff8:   00007fd27d018dd2 0000000000000000
0x00007fd29595a008:   00000007594b3ee0 00007fd29595a010
0x00007fd29595a018:   00007fd272e0c106 00007fd29595a0a8
0x00007fd29595a028:   00007fd272e0db08 0000000000000000
0x00007fd29595a038:   00007fd272e0c198 00007fd295959fc8
0x00007fd29595a048:   00007fd29595a070 00007fd29595a0f0
0x00007fd29595a058:   00007fd27d00833d 0000000000000000
0x00007fd29595a068:   00000007559d0c70 000000005a617566
0x00007fd29595a078:   00007fd200000000 0000000001b8ed0c
0x00007fd29595a088:   0000000000000000 0000000000000000
0x00007fd29595a098:   00007fd27d018dd2 00000007559d0c70
0x00007fd29595a0a8:   0000000759487a20 00007fd29595a0b0 

Instructions: (pc=0x00007fd2945622d4)
0x00007fd2945622b4:   74 47 fe 66 89 71 08 c3 0f 1f 40 00 48 8b 74 d0
0x00007fd2945622c4:   e8 48 89 74 d1 e8 48 8b 74 d0 f0 48 89 74 d1 f0
0x00007fd2945622d4:   48 8b 74 d0 f8 48 89 74 d1 f8 48 8b 34 d0 48 89
0x00007fd2945622e4:   34 d1 48 83 c2 04 7e d4 48 83 ea 04 7c 93 eb a1 

Register to memory mapping:

RAX=0x00007fd2840a6264 is an unknown value
RBX=0x00007fd28c013800 is a thread
RCX=0x00000006db82e378 is pointing into object: 0x0000000681216e10
[B 
 - klass: {type array byte}
 - length: 1516336486
RDX=0xfffffffff4fef5b4 is an unknown value
RSP=0x00007fd295959eb8 is pointing into the stack for thread: 0x00007fd28c013800
RBP=0x00007fd295959f10 is pointing into the stack for thread: 0x00007fd28c013800
RSI=0x0000000000000000 is an unknown value
RDI=0x00007fd229a8ed0c is an unknown value
R8 =0x000000002d30bab3 is an unknown value
R9 =0x0000000000000010 is an unknown value
R10=0x00007fd27d01fc78 is at code_begin+1528 in an Interpreter codelet
method entry point (kind = native)  [0x00007fd27d01f680, 0x00007fd27d0205c0]  3904 bytes
R11=0x00007fd294729190: <offset 0x9c5190> in /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so at 0x00007fd293d64000
R12=0x0000000000000000 is an unknown value
R13=0x00007fd295959fe8 is pointing into the stack for thread: 0x00007fd28c013800
R14=0x00007fd294d25f40: <offset 0xfc1f40> in /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so at 0x00007fd293d64000
R15=0x00007fd294d2acc0: <offset 0xfc6cc0> in /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so at 0x00007fd293d64000


Stack: [0x00007fd29585b000,0x00007fd29595c000],  sp=0x00007fd295959eb8,  free space=1019k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V  [libjvm.so+0x7fe2d4]
j  sun.misc.Unsafe.copyMemory(Ljava/lang/Object;JLjava/lang/Object;JJ)V+0
j  org.nustaq.offheap.bytez.malloc.MallocBytez.copyTo(Lorg/nustaq/offheap/bytez/BasicBytez;JJJ)V+38
j  com.conveyal.r5.util.ExpandingMMFBytez.copyTo(Lorg/nustaq/offheap/bytez/BasicBytez;JJJ)V+20
j  org.nustaq.serialization.coders.FSTBytezDecoder.readStringAsc()Ljava/lang/String;+60
j  org.nustaq.serialization.FSTClazzNameRegistry.decodeClass(Lorg/nustaq/serialization/FSTDecoder;Lorg/nustaq/serialization/FSTConfiguration;)Lorg/nustaq/serialization/FSTClazzInfo;+28
j  org.nustaq.serialization.coders.FSTBytezDecoder.readClass()Lorg/nustaq/serialization/FSTClazzInfo;+9
j  org.nustaq.serialization.FSTObjectInput.readClass()Lorg/nustaq/serialization/FSTClazzInfo;+4
j  org.nustaq.serialization.FSTObjectInput.readObjectWithHeader(Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;)Ljava/lang/Object;+28
j  org.nustaq.serialization.FSTObjectInput.readObjectFields(Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;Lorg/nustaq/serialization/FSTClazzInfo;[Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;Ljava/lang/Object;II)V+491
j  org.nustaq.serialization.FSTObjectInput.instantiateAndReadNoSer(Ljava/lang/Class;Lorg/nustaq/serialization/FSTClazzInfo;Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;I)Ljava/lang/Object;+266
j  org.nustaq.serialization.FSTObjectInput.readObjectWithHeader(Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;)Ljava/lang/Object;+172
j  org.nustaq.serialization.FSTObjectInput.readObjectFields(Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;Lorg/nustaq/serialization/FSTClazzInfo;[Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;Ljava/lang/Object;II)V+491
j  org.nustaq.serialization.FSTObjectInput.instantiateAndReadNoSer(Ljava/lang/Class;Lorg/nustaq/serialization/FSTClazzInfo;Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;I)Ljava/lang/Object;+266
j  org.nustaq.serialization.FSTObjectInput.readObjectWithHeader(Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;)Ljava/lang/Object;+172
j  org.nustaq.serialization.FSTObjectInput.readObjectInternal([Ljava/lang/Class;)Ljava/lang/Object;+38
j  org.nustaq.serialization.FSTObjectInput.readObject([Ljava/lang/Class;)Ljava/lang/Object;+63
j  com.conveyal.r5.util.ExpandingMMFBytez.readObjectFromFile(Ljava/io/File;)Ljava/lang/Object;+38
j  com.conveyal.r5.transit.TransportNetwork.read(Ljava/io/File;)Lcom/conveyal/r5/transit/TransportNetwork;+11
j  org.playground.otp.otp.R5App.main([Ljava/lang/String;)V+15
v  ~StubRoutines::call_stub
V  [libjvm.so+0x691d16]
V  [libjvm.so+0x6d3132]
V  [libjvm.so+0x6ef99a]
C  [libjli.so+0x7bdf]  JavaMain+0x81f
C  [libpthread.so.0+0x76ba]  start_thread+0xca

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  sun.misc.Unsafe.copyMemory(Ljava/lang/Object;JLjava/lang/Object;JJ)V+0
j  org.nustaq.offheap.bytez.malloc.MallocBytez.copyTo(Lorg/nustaq/offheap/bytez/BasicBytez;JJJ)V+38
j  com.conveyal.r5.util.ExpandingMMFBytez.copyTo(Lorg/nustaq/offheap/bytez/BasicBytez;JJJ)V+20
j  org.nustaq.serialization.coders.FSTBytezDecoder.readStringAsc()Ljava/lang/String;+60
j  org.nustaq.serialization.FSTClazzNameRegistry.decodeClass(Lorg/nustaq/serialization/FSTDecoder;Lorg/nustaq/serialization/FSTConfiguration;)Lorg/nustaq/serialization/FSTClazzInfo;+28
j  org.nustaq.serialization.coders.FSTBytezDecoder.readClass()Lorg/nustaq/serialization/FSTClazzInfo;+9
j  org.nustaq.serialization.FSTObjectInput.readClass()Lorg/nustaq/serialization/FSTClazzInfo;+4
j  org.nustaq.serialization.FSTObjectInput.readObjectWithHeader(Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;)Ljava/lang/Object;+28
j  org.nustaq.serialization.FSTObjectInput.readObjectFields(Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;Lorg/nustaq/serialization/FSTClazzInfo;[Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;Ljava/lang/Object;II)V+491
j  org.nustaq.serialization.FSTObjectInput.instantiateAndReadNoSer(Ljava/lang/Class;Lorg/nustaq/serialization/FSTClazzInfo;Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;I)Ljava/lang/Object;+266
j  org.nustaq.serialization.FSTObjectInput.readObjectWithHeader(Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;)Ljava/lang/Object;+172
j  org.nustaq.serialization.FSTObjectInput.readObjectFields(Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;Lorg/nustaq/serialization/FSTClazzInfo;[Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;Ljava/lang/Object;II)V+491
j  org.nustaq.serialization.FSTObjectInput.instantiateAndReadNoSer(Ljava/lang/Class;Lorg/nustaq/serialization/FSTClazzInfo;Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;I)Ljava/lang/Object;+266
j  org.nustaq.serialization.FSTObjectInput.readObjectWithHeader(Lorg/nustaq/serialization/FSTClazzInfo$FSTFieldInfo;)Ljava/lang/Object;+172
j  org.nustaq.serialization.FSTObjectInput.readObjectInternal([Ljava/lang/Class;)Ljava/lang/Object;+38
j  org.nustaq.serialization.FSTObjectInput.readObject([Ljava/lang/Class;)Ljava/lang/Object;+63
j  com.conveyal.r5.util.ExpandingMMFBytez.readObjectFromFile(Ljava/io/File;)Ljava/lang/Object;+38
j  com.conveyal.r5.transit.TransportNetwork.read(Ljava/io/File;)Lcom/conveyal/r5/transit/TransportNetwork;+11
j  org.playground.otp.otp.R5App.main([Ljava/lang/String;)V+15
v  ~StubRoutines::call_stub

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

Java Threads: ( => current thread )
  0x00007fd28c0f8000 JavaThread "Service Thread" daemon [_thread_blocked, id=20924, stack(0x00007fd2708b4000,0x00007fd2709b5000)]
  0x00007fd28c0da800 JavaThread "C1 CompilerThread2" daemon [_thread_blocked, id=20923, stack(0x00007fd2709b5000,0x00007fd270ab6000)]
  0x00007fd28c0d8800 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=20922, stack(0x00007fd270ab6000,0x00007fd270bb7000)]
  0x00007fd28c0d5800 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=20921, stack(0x00007fd270bb7000,0x00007fd270cb8000)]
  0x00007fd250001000 JavaThread "JDWP Command Reader" daemon [_thread_in_native, id=20917, stack(0x00007fd270cb8000,0x00007fd270db9000)]
  0x00007fd28c0d3800 JavaThread "JDWP Event Helper Thread" daemon [_thread_blocked, id=20916, stack(0x00007fd270db9000,0x00007fd270eba000)]
  0x00007fd28c0d0000 JavaThread "JDWP Transport Listener: dt_socket" daemon [_thread_blocked, id=20915, stack(0x00007fd270eba000,0x00007fd270fbb000)]
  0x00007fd28c0bf800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=20911, stack(0x00007fd2711bf000,0x00007fd2712c0000)]
  0x00007fd28c08d800 JavaThread "Finalizer" daemon [_thread_blocked, id=20908, stack(0x00007fd2712c0000,0x00007fd2713c1000)]
  0x00007fd28c089000 JavaThread "Reference Handler" daemon [_thread_blocked, id=20907, stack(0x00007fd2713c1000,0x00007fd2714c2000)]
=>0x00007fd28c013800 JavaThread "main" [_thread_in_vm, id=20901, stack(0x00007fd29585b000,0x00007fd29595c000)]

Other Threads:
  0x00007fd28c081800 VMThread [stack: 0x00007fd2714c2000,0x00007fd2715c3000] [id=20906]
  0x00007fd28c10b000 WatcherThread [stack: 0x00007fd2707b3000,0x00007fd2708b4000] [id=20925]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap:
 PSYoungGen      total 74752K, used 27738K [0x0000000755580000, 0x000000075a880000, 0x00000007c0000000)
  eden space 64512K, 27% used [0x0000000755580000,0x000000075669c2f0,0x0000000759480000)
  from space 10240K, 99% used [0x0000000759480000,0x0000000759e7a740,0x0000000759e80000)
  to   space 10240K, 0% used [0x0000000759e80000,0x0000000759e80000,0x000000075a880000)
 ParOldGen       total 1652224K, used 1499320K [0x0000000680000000, 0x00000006e4d80000, 0x0000000755580000)
  object space 1652224K, 90% used [0x0000000680000000,0x00000006db82e388,0x00000006e4d80000)
 Metaspace       used 9358K, capacity 9604K, committed 9728K, reserved 1058816K
  class space    used 1133K, capacity 1210K, committed 1280K, reserved 1048576K

Card table byte_map: [0x00007fd2914e7000,0x00007fd291ee8000] byte_map_base: 0x00007fd28e0e7000

Marking Bits: (ParMarkBitMap*) 0x00007fd294d29f60
 Begin Bits: [0x00007fd273000000, 0x00007fd278000000)
 End Bits:   [0x00007fd278000000, 0x00007fd27d000000)

Polling page: 0x00007fd295979000

CodeCache: size=245760Kb used=1803Kb max_used=1803Kb free=243956Kb
 bounds [0x00007fd27d000000, 0x00007fd27d270000, 0x00007fd28c000000]
 total_blobs=590 nmethods=255 adapters=257
 compilation: enabled

Compilation events (10 events):
Event: 143.796 Thread 0x00007fd28c0da800  252       3       java.lang.ref.Finalizer::hasBeenFinalized (14 bytes)
Event: 143.796 Thread 0x00007fd28c0da800 nmethod 252 0x00007fd27d1c0690 code [0x00007fd27d1c0800, 0x00007fd27d1c09b0]
Event: 143.796 Thread 0x00007fd28c0da800  253   !   3       java.lang.ref.Finalizer::remove (94 bytes)
Event: 143.797 Thread 0x00007fd28c0da800 nmethod 253 0x00007fd27d1c0a10 code [0x00007fd27d1c0ba0, 0x00007fd27d1c10b0]
Event: 143.797 Thread 0x00007fd28c0da800  254       3       java.lang.System$2::invokeFinalize (5 bytes)
Event: 143.800 Thread 0x00007fd28c0da800 nmethod 254 0x00007fd27d1c1250 code [0x00007fd27d1c13c0, 0x00007fd27d1c15e8]
Event: 143.800 Thread 0x00007fd28c0da800  240   !   3       java.lang.ref.Reference::tryHandlePending (115 bytes)
Event: 143.800 Thread 0x00007fd28c0da800 nmethod 240 0x00007fd27d1c1690 code [0x00007fd27d1c18c0, 0x00007fd27d1c25c8]
Event: 143.800 Thread 0x00007fd28c0da800  241   !   3       java.lang.ref.ReferenceQueue::enqueue (119 bytes)
Event: 143.801 Thread 0x00007fd28c0da800 nmethod 241 0x00007fd27d1c2b10 code [0x00007fd27d1c2cc0, 0x00007fd27d1c34a8]

GC Heap History (2 events):
Event: 143.757 GC heap before
{Heap before GC invocations=1 (full 0):
 PSYoungGen      total 74752K, used 63191K [0x0000000755580000, 0x000000075a880000, 0x00000007c0000000)
  eden space 64512K, 97% used [0x0000000755580000,0x0000000759335f58,0x0000000759480000)
  from space 10240K, 0% used [0x0000000759e80000,0x0000000759e80000,0x000000075a880000)
  to   space 10240K, 0% used [0x0000000759480000,0x0000000759480000,0x0000000759e80000)
 ParOldGen       total 171008K, used 0K [0x0000000680000000, 0x000000068a700000, 0x0000000755580000)
  object space 171008K, 0% used [0x0000000680000000,0x0000000680000000,0x000000068a700000)
 Metaspace       used 9283K, capacity 9540K, committed 9728K, reserved 1058816K
  class space    used 1124K, capacity 1210K, committed 1280K, reserved 1048576K
Event: 143.789 GC heap after
Heap after GC invocations=1 (full 0):
 PSYoungGen      total 74752K, used 10217K [0x0000000755580000, 0x000000075a880000, 0x00000007c0000000)
  eden space 64512K, 0% used [0x0000000755580000,0x0000000755580000,0x0000000759480000)
  from space 10240K, 99% used [0x0000000759480000,0x0000000759e7a740,0x0000000759e80000)
  to   space 10240K, 0% used [0x0000000759e80000,0x0000000759e80000,0x000000075a880000)
 ParOldGen       total 171008K, used 18523K [0x0000000680000000, 0x000000068a700000, 0x0000000755580000)
  object space 171008K, 10% used [0x0000000680000000,0x0000000681216e10,0x000000068a700000)
 Metaspace       used 9283K, capacity 9540K, committed 9728K, reserved 1058816K
  class space    used 1124K, capacity 1210K, committed 1280K, reserved 1048576K
}

Deoptimization events (2 events):
Event: 0.158 Thread 0x00007fd28c013800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007fd27d10af68 method=java.lang.String.hashCode()I @ 14
Event: 0.191 Thread 0x00007fd28c013800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007fd27d136898 method=java.lang.String.indexOf(II)I @ 49

Internal exceptions (10 events):
Event: 87.524 Thread 0x00007fd28c013800 Exception <a 'java/lang/ClassNotFoundException': ch/qos/logback/core/encoder/LayoutWrappingEncoderCustomizer> (0x0000000756625c88) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u131/8869/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 2
Event: 87.531 Thread 0x00007fd28c013800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 68> (0x00000007566296c0) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u131/8869/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
Event: 87.534 Thread 0x00007fd28c013800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 35> (0x000000075662d420) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u131/8869/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
Event: 87.535 Thread 0x00007fd28c013800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 6> (0x000000075662eed8) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u131/8869/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
Event: 87.536 Thread 0x00007fd28c013800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 36> (0x0000000756631058) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u131/8869/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
Event: 87.596 Thread 0x00007fd28c013800 Exception <a 'java/lang/ClassNotFoundException': ch/qos/logback/core/pattern/PatternLayoutEncoderBaseCustomizer> (0x00000007566644e0) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u131/8869/hotspot/src/share/vm/classfile/systemDictionary.cpp, lin
Event: 87.603 Thread 0x00007fd28c013800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 78> (0x0000000756667e10) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u131/8869/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
Event: 87.605 Thread 0x00007fd28c013800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 36> (0x000000075666a4b8) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u131/8869/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
Event: 87.671 Thread 0x00007fd28c013800 Exception <a 'java/lang/ClassNotFoundException': ch/qos/logback/classic/encoder/PatternLayoutEncoderCustomizer> (0x00000007566a24f8) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u131/8869/hotspot/src/share/vm/classfile/systemDictionary.cpp, line
Event: 87.678 Thread 0x00007fd28c013800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': 98> (0x00000007566a5890) thrown at [/HUDSON/workspace/8-2-build-linux-amd64/jdk8u131/8869/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]

Events (10 events):
Event: 148.930 loading class gnu/trove/list/array/TShortArrayList
Event: 148.930 loading class gnu/trove/list/array/TShortArrayList done
Event: 148.932 loading class gnu/trove/list/array/TShortArrayList$1
Event: 148.932 loading class gnu/trove/list/array/TShortArrayList$1 done
Event: 148.933 loading class gnu/trove/iterator/TShortIterator
Event: 148.933 loading class gnu/trove/iterator/TShortIterator done
Event: 148.934 loading class gnu/trove/procedure/TShortProcedure
Event: 148.934 loading class gnu/trove/procedure/TShortProcedure done
Event: 148.935 loading class gnu/trove/function/TShortFunction
Event: 148.935 loading class gnu/trove/function/TShortFunction done
....

The problem mostly encounter due to version miss match of current r5 API and available network.dat file that was generated with some earlier version of r5. To solve the issue delete network.dat and regenerate using current version. This will solve the issue.

R5 don't validate network.dat before loading, and api throw exception while loading.