Hello all,
A few days ago our locally installed Jira on Windows Server 64 bit stopped functioning (can't load the site). The last log that was written has the error: java.util.zip.zipexception: error in opening zip file.
I have backed up our old database, uninstalled and deleted Jira's folder then reinstalled Jira. If Jira uses the newly created database, Jira will load and try to set everything up normally. If i replace the new empty database with our original database, I get the same java error as before.
I have attempted to launch Jira with all of of the plugins disabled as per the troubleshooting instructions but then i get in command prompt "The Catalina_Home environment is not defined correctly".
I have found this link that says i need to set Catalina_Home but doesn't really explain what to do other than "Edit setenv.sh and set your CATALINA_HOME accordingly.". https://community.atlassian.com/t5/Off-topic-questions/The-CATALINA-HOME-environment-variable-is-not-defined-correctly/qaq-p/398487
This is the point where I am stuck. Am I on the right path? Seems like an odd thing to just stop functioning one day.
Kind regards,
Mo
Thank you for the reply Moses.
I have updated dbconfig.xml to use my admin credentials but still no luck. I get the same page error as before.
I have stopped and started the server.
I am using the the localhost:8080 to access the database which is on the local C drive so there shouldn't be any firewall issues.
Is there anything else i should try?
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@Cory Bond What i meant by user credentials( that original credentials that was running the original data base) and do you have dabase server on the same host or another server ? could you verify that the database is up and running?
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The original credentials would have been my credentials as well as I installed Jira in the beginning.
The entirety of Jira is located on 1 VM so it is not accessing any other server for anything besides maybe DNS.
I am unsure what you are asking in "could you verify that the database is up and running?". That is basically my issue, I can't get the Jira to access the DB. How would I know if the DB is running vs not running?
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@Cory Bond Ok so have you installed any SQL server on the VM ? if not it means that you are using the H2 embedded db. To check if database is running by typing services.msc on Windows Run
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Yes it is an H2 db.
When you say check if it is running, do you mean the Atlassian Jira service? If so I have started and stopped the service multiple times.
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The next is to go back to the "CATALINA_HOME" environment variable is not set correctly. i.e is the path the same with the installation directory?
and 'CATALINA_HOME" should be the full path for the JIRA installation directory
it should look like this C:\Program Files\Atlassian\JIRA"
so make sure it is the same and then start Jira service. You can also check environment variables in Windows.
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I am not seeing Catalina_Home in setenv.bat.
I have added the setenv.bat below. What am I supposed to change?
rem --------------------------------------------------------------------------
rem Note: If running JIRA as a Service, settings in this file have no
rem effect. See http://confluence.atlassian.com/display/JIRA/Increasing+JIRA+memory
rem
rem --------------------------------------------------------------------------
rem --------------------------------------------------------------------------
rem
rem One way to set the JIRA HOME path is here via this variable. Simply uncomment it and set a valid path like c:\jira\home. You can of course set it outside in the command terminal. That will also work.
rem
rem JIRA_HOME=""
rem --------------------------------------------------------------------------
rem --------------------------------------------------------------------------
rem
rem Occasionally Atlassian Support may recommend that you set some specific JVM arguments. You can use this variable below to do that.
rem
rem --------------------------------------------------------------------------
set JVM_SUPPORT_RECOMMENDED_ARGS=
rem --------------------------------------------------------------------------
rem
rem You can use variable below to modify garbage collector settings.
rem For Java 8 we recommend default settings
rem For Java 11 and relatively small heaps we recommend: -XX:+UseParallelGC
rem For Java 11 and larger heaps we recommend: -XX:+UseG1GC -XX:+ExplicitGCInvokesConcurrent
rem
rem --------------------------------------------------------------------------
set JVM_GC_ARGS=-XX:+ExplicitGCInvokesConcurrent
rem --------------------------------------------------------------------------
rem
rem The following 2 settings control the minimum and maximum given to the JIRA Java virtual machine. In larger JIRA instances, the maximum amount will need to be increased.
rem
rem --------------------------------------------------------------------------
set JVM_MINIMUM_MEMORY=384m
set JVM_MAXIMUM_MEMORY=2048m
rem --------------------------------------------------------------------------
rem
rem The following setting configures the size of JVM code cache. A high value of reserved size allows Jira to work with more installed apps.
rem
rem --------------------------------------------------------------------------
set JVM_CODE_CACHE_ARGS=-XX:InitialCodeCacheSize=32m -XX:ReservedCodeCacheSize=512m
rem --------------------------------------------------------------------------
rem
rem The following are the required arguments for JIRA.
rem
rem --------------------------------------------------------------------------
set JVM_REQUIRED_ARGS=-Djava.awt.headless=true -Datlassian.standalone=JIRA -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
rem --------------------------------------------------------------------------
rem Uncomment this setting if you want to import data without notifications
rem
rem --------------------------------------------------------------------------
rem set DISABLE_NOTIFICATIONS= -Datlassian.mail.senddisabled=true -Datlassian.mail.fetchdisabled=true -Datlassian.mail.popdisabled=true
rem --------------------------------------------------------------------------
rem
rem In general don't make changes below here
rem
rem --------------------------------------------------------------------------
rem --------------------------------------------------------------------------
rem Prevents the JVM from suppressing stack traces
rem if a given type of exception occurs frequently,
rem which could make it harder for support to diagnose a problem.
rem --------------------------------------------------------------------------
set JVM_EXTRA_ARGS=-XX:-OmitStackTraceInFastThrow -Djava.locale.providers=COMPAT
set _PRG_DIR=%~dp0
type "%_PRG_DIR%\jirabanner.txt"
set JIRA_HOME_MINUSD=
IF "x%JIRA_HOME%x" == "xx" GOTO NOJIRAHOME
set JIRA_HOME_MINUSD=-Djira.home="%JIRA_HOME%"
:NOJIRAHOME
set JAVA_OPTS=%JAVA_OPTS% -Xms%JVM_MINIMUM_MEMORY% -Xmx%JVM_MAXIMUM_MEMORY% %JVM_CODE_CACHE_ARGS% %JVM_REQUIRED_ARGS% %DISABLE_NOTIFICATIONS% %JVM_SUPPORT_RECOMMENDED_ARGS% %JVM_EXTRA_ARGS% %JIRA_HOME_MINUSD% %START_JIRA_JAVA_OPTS%
rem Checks if the JAVA_HOME has a space in it (can cause issues)
SET _marker="x%JAVA_HOME%"
SET _marker=%_marker: =%
IF NOT %_marker% == "x%JAVA_HOME%" ECHO JAVA_HOME "%JAVA_HOME%" contains spaces. Please change to a location without spaces if this causes problems.
rem DO NOT remove the following line
SET "JAVA_HOME=C:\Program Files\Atlassian\JIRA\jre\"
echo.
echo If you encounter issues starting or stopping JIRA, please see the Troubleshooting guide at https://docs.atlassian.com/jira/jadm-docs-085/Troubleshooting+installation
echo.
IF "x%JIRA_HOME%x" == "xx" GOTO NOJIRAHOME2
echo Using JIRA_HOME: %JIRA_HOME%
:NOJIRAHOME2
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@Cory Bond Sorry the file looks OK, nothing should be change here please show the result of the environment variables in
when we fixed this you should be fine!
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Yes could you scroll down to check whether there is JAVA_HOME or JRE_HOME set in the system variables.
for the setenv.bat " it says JAVA_HOME=C:\Program Files\Atlassian\JIRA\jre\
because i think you install JIRA via the atlassxx.bin file so JAVA is packed together
JIRA need java_home/jre_home to be set in the environment variables for it to run.
check the right path to verify whether the path C:\Program Files\Atlassian\JIRA\jre\ exist and scroll down to check whether there is JAVA_HOME or JRE_HOME set in the system variables. if you don't have it then add new
variable name : JAVA_HOME
variable value: C:\Program Files\Atlassian\JIRA\jre\
if the path exist then edit to verify the path is correct.
Setting the JAVA_HOME Variable in Windows
Please try and give feed back.
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I have made the change in Enviorment Variables, stopped and started the Jira service, but am still having the same "Jira had problems starting" page.
Are there any logs you would like to see that may help?
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@Cory Bond Does this path truly exist ? if yes what do you get when you
from the command prompt type
echo %JAVA_HOME%
you should get the path, if not try restart host
then check again if it doesn't work then please provide logs in <jira_home_folder>/logs/
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@Cory Bond The path is not updated please see my previous comment
Try restart the whole jira server(machine)
Try again check java home if it appear then restart service (Jira)
If it doesn't work I need to see logs in logs in <jira_home_folder>/logs/
Also show the service.bat file
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I have restarted the VM, now the Java_Home shows up. However still no luck.
What in the logs do you need?
Service.bat
@[deleted] off
rem Licensed to the Apache Software Foundation (ASF) under one or more
rem contributor license agreements. See the NOTICE file distributed with
rem this work for additional information regarding copyright ownership.
rem The ASF licenses this file to You under the Apache License, Version 2.0
rem (the "License"); you may not use this file except in compliance with
rem the License. You may obtain a copy of the License at
rem
rem http://www.apache.org/licenses/LICENSE-2.0
rem
rem Unless required by applicable law or agreed to in writing, software
rem distributed under the License is distributed on an "AS IS" BASIS,
rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
rem See the License for the specific language governing permissions and
rem limitations under the License.
rem ---------------------------------------------------------------------------
rem NT Service Install/Uninstall script
rem
rem Options
rem install Install the service using Tomcat8 as service name.
rem Service is installed using default settings.
rem remove Remove the service from the System.
rem
rem name (optional) If the second argument is present it is considered
rem to be new service name
rem ---------------------------------------------------------------------------
setlocal
set "SELF=%~dp0%service.bat"
set "BIN_DIR=%~dp0"
set CATALINA_HOME=C:\Program Files\Atlassian\JIRA
set JIRA_HOME=C:\Program Files\Atlassian\Application Data\JIRA
set "CURRENT_DIR=%cd%"
if not "%CATALINA_HOME%" == "" goto gotHome
set "CATALINA_HOME=%cd%"
if exist "%CATALINA_HOME%\bin\tomcat8.exe" goto okHome
rem CD to the upper dir
cd ..
set "CATALINA_HOME=%cd%"
:gotHome
if exist "%CATALINA_HOME%\bin\tomcat8.exe" goto okHome
echo The tomcat8.exe was not found...
echo The CATALINA_HOME environment variable is not defined correctly.
echo This environment variable is needed to run this program
goto end
:okHome
rem Make sure prerequisite environment variables are set
rem if not "%JAVA_HOME%" == "" goto gotJdkHome
if not "%JRE_HOME%" == "" goto gotJreHome
echo Neither the JAVA_HOME nor the JRE_HOME environment variable is defined
echo Service will use the bundled JRE.
echo Failing that, service will try to guess them from the registry.
set "JRE_HOME=%BIN_DIR%\..\jre"
goto okJavaHome
:gotJreHome
if not exist "%JRE_HOME%\bin\java.exe" goto noJavaHome
goto okJavaHome
:gotJdkHome
if not exist "%JAVA_HOME%\bin\javac.exe" goto noJavaHome
rem Java 9 has a different directory structure
if exist "%JAVA_HOME%\jre\bin\java.exe" goto preJava9Layout
if not exist "%JAVA_HOME%\bin\java.exe" goto noJavaHome
if not "%JRE_HOME%" == "" goto okJavaHome
set "JRE_HOME=%JAVA_HOME%"
goto okJavaHome
:preJava9Layout
if not "%JRE_HOME%" == "" goto okJavaHome
set "JRE_HOME=%JAVA_HOME%\jre"
goto okJavaHome
:noJavaHome
echo The JAVA_HOME environment variable is not defined correctly
echo This environment variable is needed to run this program
echo NB: JAVA_HOME should point to a JDK not a JRE
goto end
:okJavaHome
if not "%CATALINA_BASE%" == "" goto gotBase
set "CATALINA_BASE=%CATALINA_HOME%"
:gotBase
set "EXECUTABLE=%CATALINA_HOME%\bin\tomcat8.exe.x64"
rem Set default Service name
set SERVICE_NAME=JIRASoftware260520105329
set DISPLAYNAME=Atlassian JIRA
rem Java 9 no longer supports the java.endorsed.dirs
rem system property. Only try to use it if
rem JAVA_ENDORSED_DIRS was explicitly set
rem or CATALINA_HOME/endorsed exists.
set ENDORSED_PROP=ignore.endorsed.dirs
if "%JAVA_ENDORSED_DIRS%" == "" goto noEndorsedVar
set ENDORSED_PROP=java.endorsed.dirs
goto doneEndorsed
:noEndorsedVar
if not exist "%CATALINA_HOME%\endorsed" goto doneEndorsed
set ENDORSED_PROP=java.endorsed.dirs
:doneEndorsed
if "x%1x" == "xx" goto displayUsage
set SERVICE_CMD=%1
shift
if "x%1x" == "xx" goto checkServiceCmd
:checkUser
if "x%1x" == "x/userx" goto runAsUser
if "x%1x" == "x--userx" goto runAsUser
set SERVICE_NAME=JIRASoftware260520105329
set DISPLAYNAME=Atlassian JIRA
shift
if "x%1x" == "xx" goto checkServiceCmd
goto checkUser
:runAsUser
shift
if "x%1x" == "xx" goto displayUsage
set SERVICE_USER=%1
shift
runas /env /savecred /user:%SERVICE_USER% "%COMSPEC% /K \"%SELF%\" %SERVICE_CMD% %SERVICE_NAME%"
goto end
:checkServiceCmd
if /i %SERVICE_CMD% == install goto doInstall
if /i %SERVICE_CMD% == remove goto doRemove
if /i %SERVICE_CMD% == uninstall goto doRemove
echo Unknown parameter "%SERVICE_CMD%"
:displayUsage
echo.
echo Usage: service.bat install/remove [service_name] [/user username]
goto end
:doRemove
rem Remove the service
echo Removing the service '%SERVICE_NAME%' ...
echo Using CATALINA_BASE: "%CATALINA_BASE%"
"%EXECUTABLE%" //DS//%SERVICE_NAME% ^
--LogPath "%CATALINA_BASE%\logs"
if not errorlevel 1 goto removed
echo Failed removing '%SERVICE_NAME%' service
goto end
:removed
echo The service '%SERVICE_NAME%' has been removed
goto end
:doInstall
echo.
echo Granting full access for Network Service to the Jira home directory '%JIRA_HOME%'
icacls "%JIRA_HOME%" /grant "NT AUTHORITY\NetworkService":(OI)(CI)(F)
echo.
echo Granting read and execute access for Network Service to the Jira installation directory '%CATALINA_HOME%'
icacls "%CATALINA_HOME%" /grant "NT AUTHORITY\NetworkService":(OI)(CI)(RX)
echo.
echo Granting full access for Network Service to the work, temp and logs subdirectories of Jira installation directory '%CATALINA_HOME%'
icacls "%CATALINA_HOME%/work" /grant "NT AUTHORITY\NetworkService":(OI)(CI)(F)
icacls "%CATALINA_HOME%/temp" /grant "NT AUTHORITY\NetworkService":(OI)(CI)(F)
icacls "%CATALINA_HOME%/logs" /grant "NT AUTHORITY\NetworkService":(OI)(CI)(F)
setlocal enabledelayedexpansion
echo.
echo Granting read and execute access for Network Service for parent directories of the Jira home directory '%JIRA_HOME%'.
echo They're required to make Java native IO operations work, which are required e.g. when starting up the plugin system.
call :setPermissionsForAllParentDirectories "%JIRA_HOME%"
echo.
echo Granting read and execute access for Network Service for parent directories of the Jira installation directory '%CATALINA_HOME%'.
echo They're required to make Java native IO operations work, which are required e.g. when starting up the plugin system.
call :setPermissionsForAllParentDirectories "%CATALINA_HOME%"
rem Skip the block of code below, as it was already called with parameters earlier. The regular way of using `goto :eof` will not work,
rem because that would actually move to the end of the file and the service would not be installed.
goto :afterSetPermissionsForAllParentDirectories
rem Navigates parents of the passed-in directory one by one and sets read an execute permissions to Network Service
:setPermissionsForAllParentDirectories
set dirname=%~1\
echo Starting to walk up from: "!dirname!"
:doLoop
for %%A in ("!dirname!") do (
set currentPath=%%~dpA
set onlyPath=%%~pA
if NOT "!onlyPath!"=="\" (
echo.
echo Checking permissions of !currentPath! [!dirname!]
icacls "!currentPath!." | find "NT AUTHORITY\NETWORK SERVICE" | find "" /v /c > last_check
for /f "delims=" %%x in (last_check) do set permission_count=%%x
if not !permission_count! geq 1 (
if not "!currentPath!" == "" (
echo Granting read and execute access for Network Service to !currentPath!
icacls "!currentPath!." /grant "NT AUTHORITY\NETWORK SERVICE:(RX)"
)
)
set dirname=!dirname!..\
goto doLoop
)
)
echo end
goto :eof
:afterSetPermissionsForAllParentDirectories
rem Install the service
echo Installing the service '%SERVICE_NAME%' ...
echo Using CATALINA_HOME: "%CATALINA_HOME%"
echo Using CATALINA_BASE: "%CATALINA_BASE%"
echo Ignoring JAVA_HOME: "%JAVA_HOME%"
echo Using JRE_HOME: "%JRE_HOME%"
rem Try to use the server jvm
set "JVM=%JRE_HOME%\bin\server\jvm.dll"
if exist "%JVM%" goto foundJvm
rem Try to use the client jvm
set "JVM=%JRE_HOME%\bin\client\jvm.dll"
if exist "%JVM%" goto foundJvm
echo Warning: Neither 'server' nor 'client' jvm.dll was found at JRE_HOME.
set JVM=auto
:foundJvm
echo Using JVM: "%JVM%"
set "CLASSPATH=%CATALINA_HOME%\bin\bootstrap.jar;%CATALINA_BASE%\bin\tomcat-juli.jar"
if not "%CATALINA_HOME%" == "%CATALINA_BASE%" set "CLASSPATH=%CLASSPATH%;%CATALINA_HOME%\bin\tomcat-juli.jar"
if "%SERVICE_STARTUP_MODE%" == "" set SERVICE_STARTUP_MODE=auto
if "%JvmMs%" == "" set JvmMs=384
if "%JvmMx%" == "" set JvmMx=2048
call "%CATALINA_HOME%\bin\set-gc-params-service"
if errorlevel 1 exit /b 1
"%EXECUTABLE%" //IS//%SERVICE_NAME% ^
--Description "Atlassian JIRA 8.5.4" ^
--DisplayName "%DISPLAYNAME%" ^
--Install "%EXECUTABLE%" ^
--LogPath "%CATALINA_BASE%\logs" ^
--StdOutput auto ^
--StdError auto ^
--Classpath "%CLASSPATH%" ^
--Jvm "%JVM%" ^
--StartMode jvm ^
--StopMode jvm ^
--StartPath "%CATALINA_HOME%" ^
--StopPath "%CATALINA_HOME%" ^
--StartClass org.apache.catalina.startup.Bootstrap ^
--StopClass org.apache.catalina.startup.Bootstrap ^
--StartParams start ^
--StopParams stop ^
--JvmOptions "-Djava.awt.headless=true;-Datlassian.standalone=JIRA;-Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true;-Dmail.mime.decodeparameters=true;-Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory;-XX:-OmitStackTraceInFastThrow;%GC_JVM_PARAMETERS%;-XX:InitialCodeCacheSize=32m;-XX:ReservedCodeCacheSize=512m;-Dcatalina.home=%CATALINA_HOME%;-Dcatalina.base=%CATALINA_BASE%;-D%ENDORSED_PROP%=%CATALINA_HOME%\endorsed;-Djava.io.tmpdir=%CATALINA_BASE%\temp;-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager;-Djava.util.logging.config.file=%CATALINA_BASE%\conf\logging.properties;%JvmArgs%" ^
--JvmOptions9 "--add-opens=java.base/java.lang=ALL-UNNAMED#--add-opens=java.base/java.io=ALL-UNNAMED#--add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED" ^
--Startup "%SERVICE_STARTUP_MODE%" ^
--JvmMs "%JvmMs%" ^
--JvmMx "%JvmMx%" ^
--ServiceUser "NT AUTHORITY\NetworkService"
if not errorlevel 1 goto installed
echo Failed installing '%SERVICE_NAME%' service
goto end
:installed
echo The service '%SERVICE_NAME%' has been installed.
:end
cd "%CURRENT_DIR%"
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@Cory Bond There should be logs in this folder C:\Program Files\Atlassian\Application Data\JIRA\log\atlassian-jira.log
Please provide this logs, there could be valuable info there
Kind regards,
Mo
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I'm unable to post the entire log as it's too big but here is the portion just for today.
2020-05-29 11:16:56,006-0500 localhost-startStop-2 INFO [c.a.jira.startup.DefaultJiraLauncher] Stopping launchers
2020-05-29 11:16:56,022-0500 localhost-startStop-2 ERROR [o.a.c.c.C.[Catalina].[localhost].[/]] Exception sending context destroyed event to listener instance of class [com.atlassian.jira.startup.LauncherContextListener]
java.lang.NullPointerException
at com.atlassian.jira.startup.ClusteringLauncher.stop(ClusteringLauncher.java:49)
at com.atlassian.jira.startup.DefaultJiraLauncher.stop(DefaultJiraLauncher.java:200)
at com.atlassian.jira.startup.LauncherContextListener.contextDestroyed(LauncherContextListener.java:211)
at org.apache.catalina.core.StandardContext.listenerStop(StandardContext.java:4817)
at org.apache.catalina.core.StandardContext.stopInternal(StandardContext.java:5474)
... 3 filtered
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
2020-05-29 11:17:03,553-0500 localhost-startStop-1 INFO [c.a.jira.startup.JiraHomeStartupCheck] The jira.home directory 'C:\Program Files\Atlassian\Application Data\JIRA' is validated and locked for exclusive use by this instance.
2020-05-29 11:17:03,616-0500 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]
****************
JIRA starting...
****************
2020-05-29 11:17:03,834-0500 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]
___ Environment _____________________________
JIRA Build : 8.5.4#805004-sha1:0444eab799707f9ad7b248d69f858774aadfd250
Build Date : Thu Mar 19 00:00:00 CDT 2020
JIRA Installation Type : Standalone
Application Server : Apache Tomcat/8.5.42 - Servlet API 3.1
Java Version : 1.8.0_202 - AdoptOpenJdk
Current Working Directory : C:\Program Files\Atlassian\JIRA
Maximum Allowable Memory : 1820MB
Total Memory : 655MB
Free Memory : 494MB
Used Memory : 161MB
Memory Pool: Code Cache : Code Cache: init = 33554432(32768K) used = 11129024(10868K) committed = 33554432(32768K) max = 536870912(524288K)
Memory Pool: Metaspace : Metaspace: init = 0(0K) used = 20933768(20443K) committed = 21626880(21120K) max = -1(-1K)
Memory Pool: Compressed Class Space : Compressed Class Space: init = 0(0K) used = 2336184(2281K) committed = 2490368(2432K) max = 1073741824(1048576K)
Memory Pool: PS Eden Space : PS Eden Space: init = 100663296(98304K) used = 139241872(135978K) committed = 400556032(391168K) max = 677904384(662016K)
Memory Pool: PS Survivor Space : PS Survivor Space: init = 16777216(16384K) used = 17276656(16871K) committed = 18350080(17920K) max = 18350080(17920K)
Memory Pool: PS Old Gen : PS Old Gen: init = 268435456(262144K) used = 12112952(11829K) committed = 268435456(262144K) max = 1431830528(1398272K)
JVM Input Arguments : -Djava.awt.headless=true -Datlassian.standalone=JIRA -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true -Dmail.mime.decodeparameters=true -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory -XX:-OmitStackTraceInFastThrow -XX:+ExplicitGCInvokesConcurrent -XX:+PrintGCDetails -XX:+PrintGCDateStamps -XX:+PrintGCTimeStamps -XX:+PrintGCCause -XX:+UseGCLogFileRotation -XX:NumberOfGCLogFiles=5 -XX:GCLogFileSize=20M -Xloggc:C:\Program Files\Atlassian\JIRA\logs\atlassian-jira-gc-%t.log -XX:InitialCodeCacheSize=32m -XX:ReservedCodeCacheSize=512m -Dcatalina.home=C:\Program Files\Atlassian\JIRA -Dcatalina.base=C:\Program Files\Atlassian\JIRA -Dignore.endorsed.dirs=C:\Program Files\Atlassian\JIRA\endorsed -Djava.io.tmpdir=C:\Program Files\Atlassian\JIRA\temp -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Djava.util.logging.config.file=C:\Program Files\Atlassian\JIRA\conf\logging.properties exit abort -Xms384m -Xmx2048m
Java Compatibility Information : JIRA version = 8.5.4, Java Version = 1.8.0_202
___ Java System Properties ________________
atlassian.standalone : JIRA
awt.toolkit : sun.awt.windows.WToolkit
catalina.base : C:\Program Files\Atlassian\JIRA
catalina.home : C:\Program Files\Atlassian\JIRA
catalina.useNaming : true
common.loader : "${catalina.base}/lib",
"${catalina.base}/lib/*.jar",
"${catalina.home}/lib",
"${catalina.home}/lib/*.jar"
file.encoding : Cp1252
file.encoding.pkg : sun.io
ignore.endorsed.dirs : C:\Program Files\Atlassian\JIRA\endorsed
java.awt.graphicsenv : sun.awt.Win32GraphicsEnvironment
java.awt.headless : true
java.awt.printerjob : sun.awt.windows.WPrinterJob
java.class.version : 52.0
java.home : C:\PROGRA~1\ATLASS~1\JIRA\jre
java.io.tmpdir : C:\Program Files\Atlassian\JIRA\temp
java.naming.factory.initial : org.apache.naming.java.javaURLContextFactory
java.naming.factory.url.pkgs : org.apache.naming
java.runtime.name : OpenJDK Runtime Environment
java.runtime.version : 1.8.0_202-b08
java.specification.name : Java Platform API Specification
java.specification.vendor : Oracle Corporation
java.specification.version : 1.8
java.util.concurrent.ForkJoinPool.common.threadFactory : org.apache.catalina.startup.SafeForkJoinWorkerThreadFactory
java.util.logging.config.file : C:\Program Files\Atlassian\JIRA\conf\logging.properties
java.util.logging.manager : org.apache.juli.ClassLoaderLogManager
java.vendor : AdoptOpenJdk
java.vendor.url : https://adoptopenjdk.net/
java.vendor.url.bug : https://github.com/AdoptOpenJDK/openjdk-build/issues
java.version : 1.8.0_202
java.vm.info : mixed mode
java.vm.name : OpenJDK 64-Bit Server VM
java.vm.specification.name : Java Virtual Machine Specification
java.vm.specification.vendor : Oracle Corporation
java.vm.specification.version : 1.8
java.vm.vendor : Oracle Corporation
java.vm.version : 25.202-b08
mail.mime.decodeparameters : true
org.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER : true
org.dom4j.factory : com.atlassian.core.xml.InterningDocumentFactory
os.arch : amd64
os.name : Windows Server 2016
os.version : 10.0
package.access : sun.,
org.apache.catalina.,
org.apache.coyote.,
org.apache.jasper.,
org.apache.tomcat.
package.definition : sun.,
java.,
org.apache.catalina.,
org.apache.coyote.,
org.apache.jasper.,
org.apache.naming.,
org.apache.tomcat.
server.loader :
shared.loader :
sun.arch.data.model : 64
sun.boot.library.path : C:\PROGRA~1\ATLASS~1\JIRA\jre\bin
sun.cpu.endian : little
sun.cpu.isalist : amd64
sun.desktop : windows
sun.io.unicode.encoding : UnicodeLittle
sun.jnu.encoding : Cp1252
sun.management.compiler : HotSpot 64-Bit Tiered Compilers
sun.os.patch.level :
tomcat.util.buf.StringCache.byte.enabled : true
tomcat.util.scan.StandardJarScanFilter.jarsToScan : log4j-taglib*.jar,
log4j-web*.jar,
log4javascript*.jar,
slf4j-taglib*.jar
tomcat.util.scan.StandardJarScanFilter.jarsToSkip : annotations-api.jar,
ant-junit*.jar,
ant-launcher.jar,
ant.jar,
asm-*.jar,
aspectj*.jar,
bootstrap.jar,
catalina-ant.jar,
catalina-ha.jar,
catalina-jmx-remote.jar,
catalina-storeconfig.jar,
catalina-tribes.jar,
catalina-ws.jar,
catalina.jar,
cglib-*.jar,
cobertura-*.jar,
commons-beanutils*.jar,
commons-codec*.jar,
commons-collections*.jar,
commons-daemon.jar,
commons-dbcp*.jar,
commons-digester*.jar,
commons-fileupload*.jar,
commons-httpclient*.jar,
commons-io*.jar,
commons-lang*.jar,
commons-logging*.jar,
commons-math*.jar,
commons-pool*.jar,
dom4j-*.jar,
easymock-*.jar,
ecj-*.jar,
el-api.jar,
geronimo-spec-jaxrpc*.jar,
h2*.jar,
hamcrest-*.jar,
hibernate*.jar,
httpclient*.jar,
icu4j-*.jar,
jasper-el.jar,
jasper.jar,
jaspic-api.jar,
jaxb-*.jar,
jaxen-*.jar,
jdom-*.jar,
jetty-*.jar,
jmx-tools.jar,
jmx.jar,
jsp-api.jar,
jstl.jar,
jta*.jar,
junit-*.jar,
junit.jar,
log4j*.jar,
mail*.jar,
objenesis-*.jar,
oraclepki.jar,
oro-*.jar,
servlet-api-*.jar,
servlet-api.jar,
slf4j*.jar,
taglibs-standard-spec-*.jar,
tagsoup-*.jar,
tomcat-api.jar,
tomcat-coyote.jar,
tomcat-dbcp.jar,
tomcat-i18n-*.jar,
tomcat-jdbc.jar,
tomcat-jni.jar,
tomcat-juli-adapters.jar,
tomcat-juli.jar,
tomcat-util-scan.jar,
tomcat-util.jar,
tomcat-websocket.jar,
tools.jar,
websocket-api.jar,
wsdl4j*.jar,
xercesImpl.jar,
xml-apis.jar,
xmlParserAPIs-*.jar,
xmlParserAPIs.jar,
xom-*.jar
user.country : US
user.dir : C:\Program Files\Atlassian\JIRA
user.home : C:\Windows\ServiceProfiles\NetworkService
user.language : en
user.name : 999750-UI$
user.script :
user.timezone : America/Chicago
user.variant :
2020-05-29 11:17:04,147-0500 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from C:\Program Files\Atlassian\Application Data\JIRA\dbconfig.xml
2020-05-29 11:17:04,194-0500 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Trying to get encrypted password from xml and decrypt it
2020-05-29 11:17:04,209-0500 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Database password decryption not performed.
2020-05-29 11:17:04,537-0500 JIRA-Bootstrap ERROR [c.a.config.bootstrap.DefaultAtlassianBootstrapManager] Could not successfully test your database:
org.h2.jdbc.JdbcSQLException: File corrupted while reading record: "C:/Program Files/Atlassian/Application Data/JIRA/database/h2db.mv.db". Possible solution: use the recovery tool [90030-185]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:345)
at org.h2.message.DbException.get(DbException.java:168)
at org.h2.mvstore.db.MVTableEngine.init(MVTableEngine.java:116)
at org.h2.engine.Database.getPageStore(Database.java:2379)
at org.h2.engine.Database.open(Database.java:666)
at org.h2.engine.Database.openDatabase(Database.java:266)
at org.h2.engine.Database.<init>(Database.java:260)
at org.h2.engine.Engine.openSession(Engine.java:60)
at org.h2.engine.Engine.openSession(Engine.java:167)
at org.h2.engine.Engine.createSessionAndValidate(Engine.java:145)
at org.h2.engine.Engine.createSession(Engine.java:128)
at org.h2.engine.Engine.createSession(Engine.java:26)
at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:347)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:108)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:92)
at org.h2.Driver.connect(Driver.java:72)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:247)
at com.atlassian.config.bootstrap.DefaultAtlassianBootstrapManager.getTestDatabaseConnection(DefaultAtlassianBootstrapManager.java:347)
at com.atlassian.jira.config.database.JdbcDatasource.getConnection(JdbcDatasource.java:219)
at com.atlassian.jira.config.database.DatabaseConfig.testConnection(DatabaseConfig.java:88)
at com.atlassian.jira.health.checks.DbConfigurationAndConnectionCheck.doPerform(DbConfigurationAndConnectionCheck.java:60)
at com.atlassian.jira.health.HealthCheckTemplate.perform(HealthCheckTemplate.java:23)
at com.atlassian.jira.health.DefaultHealthCheckExecutor.runCheck(DefaultHealthCheckExecutor.java:74)
at com.atlassian.jira.health.DefaultHealthCheckExecutor.lambda$applyAndCollectExceptions$1(DefaultHealthCheckExecutor.java:53)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at com.atlassian.jira.health.DefaultHealthCheckExecutor.applyAndCollectExceptions(DefaultHealthCheckExecutor.java:53)
at com.atlassian.jira.health.DefaultHealthCheckExecutor.performHealthChecks(DefaultHealthCheckExecutor.java:42)
at com.atlassian.jira.health.HealthChecks.executeChecksAndRecordResults(HealthChecks.java:164)
at com.atlassian.jira.health.HealthChecks.runHealthChecks(HealthChecks.java:154)
at com.atlassian.jira.health.HealthChecks.runHealthChecks(HealthChecks.java:66)
at com.atlassian.jira.startup.BootstrapContainerLauncher.start(BootstrapContainerLauncher.java:48)
at com.atlassian.jira.startup.DefaultJiraLauncher.preDbLaunch(DefaultJiraLauncher.java:117)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$0(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:102)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:154)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.IllegalStateException: File corrupted in chunk 2926553, expected page length =< 1024, got 761885485 [1.4.185/6]
at org.h2.mvstore.DataUtils.newIllegalStateException(DataUtils.java:773)
at org.h2.mvstore.Page.read(Page.java:640)
at org.h2.mvstore.Page.read(Page.java:194)
at org.h2.mvstore.MVStore.readPage(MVStore.java:1830)
at org.h2.mvstore.MVMap.readPage(MVMap.java:736)
at org.h2.mvstore.Cursor.fetchNext(Cursor.java:150)
at org.h2.mvstore.Cursor.next(Cursor.java:50)
at org.h2.mvstore.MVStore.readFileHeader(MVStore.java:696)
at org.h2.mvstore.MVStore.<init>(MVStore.java:357)
at org.h2.mvstore.MVStore$Builder.open(MVStore.java:2769)
at org.h2.mvstore.db.MVTableEngine$Store.<init>(MVTableEngine.java:162)
at org.h2.mvstore.db.MVTableEngine.init(MVTableEngine.java:98)
... 44 more
2020-05-29 11:17:04,553-0500 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] JIRA couldn't connect to your database
2020-05-29 11:17:04,553-0500 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] JIRA failed to establish a connection to your database.
This could be because:
- Your database isn't running
- The configuration of your dbconfig.xml file is incorrect (user, password, or database URL etc.)
- There is a network issue between JIRA and your database (e.g. firewall, database doesn't allow remote access etc.)
There are several other solutions you can try, review our documentation and see what works for you.
2020-05-29 11:17:04,569-0500 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Running JIRA startup checks.
2020-05-29 11:17:04,569-0500 JIRA-Bootstrap FATAL [c.a.jira.startup.JiraStartupLogger] Startup check failed. JIRA will be locked.
2020-05-29 11:17:04,631-0500 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 278 MiB. Committed: 919 MiB. Max: 2029 MiB
Non-heap memory : Used: 39 MiB. Committed: 63 MiB. Max: 1536 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 318 MiB. Committed: 982 MiB. Max: 3565 MiB
---------------------------------------------------------------------------------
2020-05-29 11:17:05,709-0500 http-nio-8080-exec-1 WARN anonymous 677x1x1 - 10.242.2.6 /secure/johnson/data [c.a.j.config.properties.ApplicationPropertiesStore] Exception getting property 'jira.filters.encoding.enforcer.excluded.mimes' from database. Using default
2020-05-29 11:17:05,741-0500 http-nio-8080-exec-1 WARN anonymous 677x1x1 - 10.242.2.6 /secure/johnson/data [c.a.j.config.properties.ApplicationPropertiesStore] Exception getting property 'jira.filters.encoding.enforcer.excluded.paths' from database. Using default
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@Cory Bond After going through the logs i found this.
[c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from C:\Program Files\Atlassian\Application Data\JIRA\dbconfig.xml
2020-05-29 11:17:04,194-0500 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Trying to get encrypted password from xml and decrypt it
2020-05-29 11:17:04,209-0500 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Database password decryption not performed.
2020-05-29 11:17:04,537-0500 JIRA-Bootstrap ERROR [c.a.config.bootstrap.DefaultAtlassianBootstrapManager] Could not successfully test your database:
org.h2.jdbc.JdbcSQLException: File corrupted while reading record: "C:/Program Files/Atlassian/Application Data/JIRA/database/h2db.mv.db". Possible solution: use the recovery tool [90030-185]
It is clear that the H2.db (database) file is corrupted. I have not used the recovery tool before there is an official documentation from the site. Using the Recover Tool
before using the recovery tool try to check C:\Program Files\Atlassian\Application Data\JIRA\export to see whether you have back up before this issue, then use the one in the backup, so there will be no need to use the recovering tool.
Best regards,
Mo
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Thank you for your help Moses. I did not have any backups and didn't have any luck with the recovery tool. Ultimately I'm just going to give up and start over again.
Thanks again.
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@Cory Bond OK let me advice further more , it is time to use your own DB (Msql, or Postgres sql or MS SQL ) instead of the h2 embedded db. This will help avoid such situations i.e stability.
Kind regards,
Mo.
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