atlas-run A fatal error with Java Runtime Environment simplebp

[Joshua Kacen]

Following the instructions on https://developer.atlassian.com/server/confluence/write-a-simple-confluence-blueprint-plugin/ on a new server installation get a fatal error detected by the Java Runtime Environment whilst running atlas-run

#
# A fatal error has been detected by the Java Runtime Environment:
#
# EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x74693722, pid=580, tid=9904
#
# JRE version: Java(TM) SE Runtime Environment (8.0_51-b16) (build 1.8.0_51-b16)
# Java VM: Java HotSpot(TM) Client VM (25.51-b03 mixed mode windows-x86 )
# Problematic frame:
# V [jvm.dll+0x93722]
#
# 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
#

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

Current thread (0x02b3e800): VMThread [stack: 0x25460000,0x254b0000] [id=9904]

siginfo: ExceptionCode=0xc0000005, reading address 0x000000c1

Registers:
EAX=0x07f15c70, EBX=0x254af1b0, ECX=0x07f2d658, EDX=0x00000005
ESP=0x254aef38, EBP=0x254aef54, ESI=0x02a46824, EDI=0x02a466a8
EIP=0x74693722, EFLAGS=0x00010246

Top of Stack: (sp=0x254aef38)
0x254aef38: 07f15c70 254af1b0 07f15c70 02a466a8
0x254aef48: 07f15c70 02a466a8 07f15c70 254aef64
0x254aef58: 74694450 00000000 097447f0 254aef80
0x254aef68: 7469450a 07f15c73 30edc36c 254af1b0
0x254aef78: 00000142 02a466a8 254aef94 746946e6
0x254aef88: 07f15c70 254af1b0 30edc364 254aefac
0x254aef98: 7464c240 30edc36c 254af1b0 02a43c28
0x254aefa8: 00000000 254aefc0 7464c306 254af1b0

Instructions: (pc=0x74693722)
0x74693702: f8 89 46 10 8b 45 fc eb 0a 8b 4e 1c 48 89 46 10
0x74693712: 8b 04 81 8b 48 04 8b 9f 78 01 00 00 8b 11 53 50
0x74693722: 8b 82 bc 00 00 00 ff d0 83 bf 98 01 00 00 00 0f
0x74693732: 85 6a ff ff ff 5e 5b 5f 8b e5 5d c3 cc cc 55 8b

Register to memory mapping:

EAX=0x07f15c70 is pointing into object: 0x07f15ac0

[error occurred during error reporting (printing register info), id 0xc0000005]

Stack: [0x25460000,0x254b0000], sp=0x254aef38, free space=315k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V [jvm.dll+0x93722]
V [jvm.dll+0x94450]
V [jvm.dll+0x9450a]
V [jvm.dll+0x946e6]
V [jvm.dll+0x4c240]
V [jvm.dll+0x4c306]
V [jvm.dll+0xa36e7]
V [jvm.dll+0x96e9b]
V [jvm.dll+0x98157]
V [jvm.dll+0x94089]
V [jvm.dll+0x97d25]
V [jvm.dll+0x91d75]
V [jvm.dll+0x1b3b06]
V [jvm.dll+0x17e37b]
V [jvm.dll+0x17d791]
V [jvm.dll+0x17dba7]
V [jvm.dll+0x17dda2]
V [jvm.dll+0x1bd7b6]
C [msvcr100.dll+0x5c556]
C [msvcr100.dll+0x5c600]
C [KERNEL32.DLL+0x1fe09]
C [ntdll.dll+0x6607d]
C [ntdll.dll+0x6604d]

VM_Operation (0x37a4e4f0): GenCollectForAllocation, mode: safepoint, requested by thread 0x2d3f6400

Other Threads:
=>0x02b3e800 VMThread [stack: 0x25460000,0x254b0000] [id=9904]
0x25269000 WatcherThread [stack: 0x25850000,0x258a0000] [id=9484]

VM state:at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
[0x02b6c9d0] Threads_lock - owner thread: 0x02b3e800
[0x02b6be08] Heap_lock - owner thread: 0x2d3f6400

Heap:
def new generation total 157248K, used 139776K [0x04c00000, 0x0f6a0000, 0x0f6a0000)
eden space 139776K, 100% used [0x04c00000, 0x0d480000, 0x0d480000)
from space 17472K, 0% used [0x0d480000, 0x0d480000, 0x0e590000)
to space 17472K, 13% used [0x0e590000, 0x0e7d4a50, 0x0f6a0000)
tenured generation total 349568K, used 306812K [0x0f6a0000, 0x24c00000, 0x24c00000)
the space 349568K, 87% used [0x0f6a0000, 0x2223f058, 0x2223f200, 0x24c00000)
Metaspace used 134582K, capacity 143081K, committed 143104K, reserved 143744K

Card table byte_map: [0x24c00000,0x24d10000] byte_map_base: 0x24bda000

Polling page: 0x01150000

CodeCache: size=32768Kb used=7050Kb max_used=10106Kb free=25717Kb
bounds [0x02b70000, 0x03588000, 0x04b70000]
total_blobs=3488 nmethods=3141 adapters=277
compilation: enabled

Compilation events (10 events):
Event: 404.602 Thread 0x25251800 27535 com.sun.jna.Structure::calculateSize (7 bytes)
Event: 404.603 Thread 0x25251800 nmethod 27535 0x03301848 code [0x03301940, 0x033019dc]
Event: 404.905 Thread 0x25251800 27536 java.util.HashMap$EntrySet::iterator (12 bytes)
Event: 404.905 Thread 0x25251800 nmethod 27536 0x02d041c8 code [0x02d042d0, 0x02d043bc]
Event: 404.958 Thread 0x25251800 27537 java.math.BigDecimal::add (189 bytes)
Event: 404.959 Thread 0x25251800 nmethod 27537 0x02c334c8 code [0x02c336a0, 0x02c33bdc]
Event: 404.961 Thread 0x25251800 27538 java.math.BigDecimal::add (42 bytes)
Event: 404.961 Thread 0x25251800 nmethod 27538 0x02dc8a48 code [0x02dc8b70, 0x02dc8d58]
Event: 404.961 Thread 0x25251800 27539 java.math.BigDecimal::add (26 bytes)
Event: 404.962 Thread 0x25251800 nmethod 27539 0x02d2d548 code [0x02d2d640, 0x02d2d700]

Events (10 events):
Event: 404.961 Thread 0x25251800 flushing nmethod 0x033af608
Event: 404.961 Thread 0x25251800 flushing nmethod 0x033af848
Event: 404.961 Thread 0x25251800 flushing nmethod 0x033bd8c8
Event: 404.961 Thread 0x25251800 flushing nmethod 0x033bdb08
Event: 404.961 Thread 0x25251800 flushing nmethod 0x033bdd88
Event: 404.961 Thread 0x25251800 flushing nmethod 0x033be308
Event: 404.961 Thread 0x25251800 flushing nmethod 0x033be548
Event: 404.961 Thread 0x25251800 flushing nmethod 0x0340d548
Event: 404.961 Thread 0x25251800 flushing nmethod 0x03554b88
Event: 405.034 Executing VM operation: GenCollectForAllocation

VM Arguments:
jvm_args: -Xmx512m -Xms128m -Dbaseurl=http://CONFLUENCE:1990/confluence -Dplugin.root.directories=C:\Users\Administrator\Plugins\simplebp -Dcargo.servlet.uriencoding=UTF-8 -Dconfluence.home=C:\Users\Administrator\Plugins\simplebp\target\confluence\home -Dplugin.resource.directories=C:\Users\Administrator\Plugins\simplebp\src\main\resources -Datlassian.dev.mode=true -Djava.awt.headless=true -Datlassian.sdk.version=6.3.21 -Dcatalina.home=C:\Users\Administrator\Plugins\simplebp\target\container\tomcat9x\apache-tomcat-9.0.11 -Dcatalina.base=C:\Users\Administrator\Plugins\simplebp\target\container\tomcat9x\cargo-confluence-home -Djava.io.tmpdir=C:\Users\Administrator\Plugins\simplebp\target\container\tomcat9x\cargo-confluence-home\temp -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.util.logging.config.file=C:\Users\Administrator\Plugins\simplebp\target\container\tomcat9x\cargo-confluence-home\conf/logging.properties
java_command: org.apache.catalina.startup.Bootstrap start
java_class_path (initial): C:\Users\Administrator\Plugins\simplebp\target\container\tomcat9x\apache-tomcat-9.0.11\bin\tomcat-juli.jar;C:\Users\Administrator\Plugins\simplebp\target\container\tomcat9x\apache-tomcat-9.0.11\bin\bootstrap.jar
Launcher Type: SUN_STANDARD

Environment Variables:
JAVA_HOME=C:\Applications\Atlassian\atlassian-plugin-sdk-6.3.12\jre
PATH=C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\Users\Administrator\AppData\Local\Microsoft\WindowsApps;;C:\Applications\Atlassian\atlassian-plugin-sdk-6.3.12\bin
USERNAME=Administrator
OS=Windows_NT
PROCESSOR_IDENTIFIER=Intel64 Family 6 Model 85 Stepping 4, GenuineIntel

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

OS: Windows 10.0 , 64 bit Build 17763 (10.0.17763.1)

CPU:total 1 (1 cores per cpu, 1 threads per core) family 6 model 85 stepping 4, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, rtm, 3dnowpref, lzcnt, tsc, bmi1, bmi2, adx

Memory: 4k page, physical 4193304k(481000k free), swap 7010564k(1094100k free)

vm_info: Java HotSpot(TM) Client VM (25.51-b03) for windows-x86 JRE (1.8.0_51-b16), built on Jun 8 2015 18:00:23 by "java_re" with MS VC++ 10.0 (VS2010)

time: Fri Nov 30 14:20:05 2018
elapsed time: 405 seconds (0d 0h 6m 45s)

[807528895]

I'm facing the same problem now, is there any solution? Thanks very much.

[Daniel Eads]

Hi Joshua,

Welcome to the Community! First things first, I see you're running Java 8 u51. While I don't know offhand if this is the source of the startup error, I do know that's a pretty old build in the Java lifecycle. Would you be up for installing a more recent build like u191?

If that's something you're able to do on your machine, I'd recommend uninstalling the JDK that's already on your machine before getting the most recent update. At that point try going through the setup guide again and seeing if we get a different error (or hopefully it just runs)!

Cheers,
Daniel

[Joshua Kacen]

Hi Daniel,

Thanks for the reply.

I installed Confluence server fresh from the Windows Installer which is supposed to come packaged with the appropriate version of JDK.

I'm happy to try uninstall it and manually install the updated version of JDK and report back, however you might want to update your Windows Installer if it is currently packaged with an old build of Java.

Are you able to point me to some instructions as to how to uninstall / update the JDK that comes packaged with the Windows Installer?

Regards,

Josh

[Daniel Eads]

Hey Josh,

We did a bit of testing with the latest installer and weren't able to find a bundled JDK. I'm following the documentation here:

https://developer.atlassian.com/server/framework/atlassian-sdk/install-the-atlassian-sdk-on-a-windows-system/

Can you let me know if you happened to download from a different link than that document points to or if you are using a different document for installation? I'd love to get any incorrect links/documentation updated!

For updating, let's do a remove/reinstall:

Uninstalling Java - Windows 10

1. Click Start
2. Select Settings
3. Select System
4. Select Apps & features
5. Select the JDK to uninstall and then click its Uninstall button.
6. Respond to the prompts to complete the uninstall

Installing a fresher JDK

The latest JDK 8 update is available here.

Setting path variables (copied from the Atlassian SDK install guide linked at the top of this reply)

The JAVA_HOME environment variable specifies the location of the JDK on your system. For Windows users, the default directory is C:\Program Files\Java\jdk1.8.x_y , where x_y is the Java JDK 8 version you have installed. 

To set these environment variables:

1. Browse to the C:\Program Files\Java\jdk1.8.x_y folder on your system and copy the path to the folder.
2. Open Control Panel > System>Advanced System Settings.
3. On the Advanced tab click Environment Variables.
4. Locate the System variables section and click New.
5. Enter JAVA_HOME in the Variable name field and paste the folder path you copied into the Variable value field.
6. Click OK to close the dialog.
7. Click on Path variable in the System variables  section and click Edit. 
8. Click New and type %JAVA_HOME%\binin the available space.
9. Close all dialog windows.

10. Open a new  Command Prompt window, and run the following command:
    

    C:\Users\manthony>javac -version javac 1.8.0_91
    javac 1.8.0_91

     verify that your output is similar to what appears above.

Let me know how that goes!

Thanks,
Daniel

[Joshua Kacen]

Hi,

The JDK in question is bundled with Confluence not the SDK. It was installed via the link https://www.atlassian.com/software/confluence/download.

According to this page https://confluence.atlassian.com/doc/installing-java-for-confluence-144212101.html If you install Confluence via the installer, which is what I did you don't need to install Java manually.

If you can please test and advise.

With regards to your instructions to uninstall; JDK doesn't show up in the Apps & features list? I suspect it is because it was installed bundled up with the Confluence Installer.

[Joshua Kacen]

Hi,

I've installed the JDK as requested and re-run atlas-run

The script no longer stops on the error previously advised, however now seems to go into an endless loop around these lines of code.

All these issues are not feeling me with confidence about the product.