Jira not starting

[ENSO ORIGINS]

Hello,

We recently updated our Jira Server to lateste version.

It was working really good until today, when we inspect catalina.out we found lots of errors like:

'Exception in thread "main" java.lang.OutOfMemoryError: unable to create new native thread'

Our server is a VPS with 8G RAM memory, Centos 7 with all yum updates done.

As we looked into memory resources we think it shouldn't a problem..

Here follows the full output of /opt/atlassian/jira2/logs/catalina.out:

13-Mar-2019 16:19:53.091 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause
13-Mar-2019 16:19:53.091 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
13-Mar-2019 16:19:53.091 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira2
13-Mar-2019 16:19:53.091 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira2
13-Mar-2019 16:19:53.091 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira2/temp
13-Mar-2019 16:19:53.092 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: [/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
13-Mar-2019 16:19:53.226 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-6969"]
13-Mar-2019 16:19:53.291 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 661 ms
13-Mar-2019 16:19:53.301 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
13-Mar-2019 16:19:53.378 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.35

2019-03-13 16:19:57,103 localhost-startStop-1 INFO [c.a.jira.startup.JiraHomeStartupCheck] The jira.home directory '/var/atlassian/application-data/jira2' is validated and locked for exclusive use by this instance.

2019-03-13 16:19:57,339 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

****************
JIRA starting...
****************

2019-03-13 16:19:57,457 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

___ Environment _____________________________

JIRA Build : 8.0.1#800009-sha1:f5186e157f3e26c0180673ce49d51cb56d8f7579
Build Date : Wed Feb 20 00:00:00 GMT 2019
JIRA Installation Type : Standalone
Application Server : Apache Tomcat/8.5.35 - Servlet API 3.1
Java Version : 1.8.0_181 - Oracle Corporation
Current Working Directory : /opt/atlassian/jira2
Maximum Allowable Memory : 1820MB
Total Memory : 1323MB
Free Memory : 1276MB
Used Memory : 47MB
Memory Pool: Code Cache : Code Cache: init = 33554432(32768K) used = 9795648(9566K) committed = 33554432(32768K) max = 536870912(524288K)
Memory Pool: Metaspace : Metaspace: init = 0(0K) used = 21981456(21466K) committed = 22675456(22144K) max = -1(-1K)
Memory Pool: Compressed Class Space : Compressed Class Space: init = 0(0K) used = 2545536(2485K) committed = 2752512(2688K) max = 1073741824(1048576K)
Memory Pool: PS Eden Space : PS Eden Space: init = 268435456(262144K) used = 27708744(27059K) committed = 626524160(611840K) max = 626524160(611840K)
Memory Pool: PS Survivor Space : PS Survivor Space: init = 44564480(43520K) used = 0(0K) committed = 44564480(43520K) max = 44564480(43520K)
Memory Pool: PS Old Gen : PS Old Gen: init = 716177408(699392K) used = 21130600(20635K) committed = 716177408(699392K) max = 1431830528(1398272K)
JVM Input Arguments : -Djava.util.logging.config.file=/opt/atlassian/jira2/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms1024m -Xmx2048m -XX:InitialCodeCacheSize=32m -XX:ReservedCodeCacheSize=512m -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 -Djava.locale.providers=COMPAT -Datlassian.plugins.startup.options= -Djdk.tls.ephemeralDHKeySize=2048 -Djava.protocol.handler.pkgs=org.apache.catalina.webresources -Dorg.apache.catalina.security.SecurityListener.UMASK=0027 -Xloggc:/opt/atlassian/jira2/logs/atlassian-jira-gc-%t.log -XX:+UseGCLogFileRotation -XX:NumberOfGCLogFiles=5 -XX:GCLogFileSize=20M -XX:+PrintGCDetails -XX:+PrintGCDateStamps -XX:+PrintGCTimeStamps -XX:+PrintGCCause -Dignore.endorsed.dirs= -Dcatalina.base=/opt/atlassian/jira2 -Dcatalina.home=/opt/atlassian/jira2 -Djava.io.tmpdir=/opt/atlassian/jira2/temp
Java Compatibility Information : JIRA version = 8.0.1, Java Version = 1.8.0_181

___ Java System Properties _________________

atlassian.plugins.startup.options :
atlassian.standalone : JIRA
awt.toolkit : sun.awt.X11.XToolkit
catalina.base : /opt/atlassian/jira2
catalina.home : /opt/atlassian/jira2
catalina.useNaming : true
common.loader : "${catalina.base}/lib",
"${catalina.base}/lib/*.jar",
"${catalina.home}/lib",
"${catalina.home}/lib/*.jar"
file.encoding : ANSI_X3.4-1968
file.encoding.pkg : sun.io
ignore.endorsed.dirs :
java.awt.graphicsenv : sun.awt.X11GraphicsEnvironment
java.awt.headless : true
java.awt.printerjob : sun.print.PSPrinterJob
java.class.version : 52.0
java.home : /opt/atlassian/jira2/jre
java.io.tmpdir : /opt/atlassian/jira2/temp
java.locale.providers : COMPAT
java.naming.factory.initial : org.apache.naming.java.javaURLContextFactory
java.naming.factory.url.pkgs : org.apache.naming
java.protocol.handler.pkgs : org.apache.catalina.webresources
java.runtime.name : Java(TM) SE Runtime Environment
java.runtime.version : 1.8.0_181-b13
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 : /opt/atlassian/jira2/conf/logging.properties
java.util.logging.manager : org.apache.juli.ClassLoaderLogManager
java.vendor : Oracle Corporation
java.vendor.url : http://java.oracle.com/
java.vendor.url.bug : http://bugreport.sun.com/bugreport/
java.version : 1.8.0_181
java.vm.info : mixed mode
java.vm.name : Java HotSpot(TM) 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 : 25.181-b13
jdk.tls.ephemeralDHKeySize : 2048
mail.mime.decodeparameters : true
org.apache.catalina.security.SecurityListener.UMASK : 0027
org.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER : true
org.dom4j.factory : com.atlassian.core.xml.InterningDocumentFactory
os.arch : amd64
os.name : Linux
os.version : 2.6.32-042stab127.2
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 : /opt/atlassian/jira2/jre/lib/amd64
sun.cpu.endian : little
sun.cpu.isalist :
sun.io.unicode.encoding : UnicodeLittle
sun.java.command : org.apache.catalina.startup.Bootstrap start
sun.java.launcher : SUN_STANDARD
sun.jnu.encoding : ANSI_X3.4-1968
sun.management.compiler : HotSpot 64-Bit Tiered Compilers
sun.os.patch.level : unknown
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-en.jar,
tomcat-i18n-es.jar,
tomcat-i18n-fr.jar,
tomcat-i18n-ja.jar,
tomcat-i18n-ru.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 : /opt/atlassian/jira2
user.home : /home/jira
user.language : en
user.name : jira
user.timezone : GMT

2019-03-13 16:19:57,628 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira2/dbconfig.xml
2019-03-13 16:19:57,918 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Running JIRA startup checks.
2019-03-13 16:19:58,009 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] JIRA pre-database startup checks completed successfully.
2019-03-13 16:19:58,189 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira2/dbconfig.xml
13-Mar-2019 16:19:58.445 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-6969"]
13-Mar-2019 16:19:58.605 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
Exception in thread "main" java.lang.OutOfMemoryError: unable to create new native thread

We would appreciate some help solving this problem.

Best Regards,

Pedro Marques

[ENSO ORIGINS · Accepted solution]

Hello everyone,

Thanks in advance for helping me out!

The problem is finally solved and had not much to do with Jira, but with our VPS provider.

After opening a ticket on our host provider explaining that the VPS was giving errors like:

fork: Cannot allocate memory

java.lang.OutOfMemoryError: unable to create new native thread

They solved the problem on their side and asked us to test again.

I started Jira and no errors were found this time since it is working correctly again.

Best Regards,

Pedro Marques

[Sid]

@ENSO ORIGINS , check this out - https://confluence.atlassian.com/jirakb/jira-applications-crash-due-to-outofmemoryerror-unable-to-create-new-native-thread-224397455.html

[Alexis Robert]

Hi @ENSO ORIGINS , 

I see from the logs that you have the following settings in your setenv.sh file for the JVM memory:

-Xms1024m -Xmx2048m

You should try increasing this as the logs clearly say that the JVM is too small for your workload. You could set it to:

-Xms4096m -Xmx4096m

 You VM has 8GB RAM so you should be OK with this, if you don't have any other atlassian products running on it or something like a database for example.

Let me know how if it works, 

--Alexis

[ENSO ORIGINS]

Hello @Alexis Robert ,

I proceeded with your changes but unfortunatly still getting the error:

___ Starting the JIRA Plugin System _________________

ERROR: Bundle org.eclipse.gemini.blueprint.extender [14] Error starting file:/opt/atlassian/jira2/atlassian-jira/WEB-INF/osgi-framework-bundles/gemini-blueprint-extender-3.0.0.M01.jar (org.osgi.framework.BundleException: Activator start error in bundle org.eclipse.gemini.blueprint.extender [14].)
java.lang.OutOfMemoryError: unable to create new native thread

Best Regards,

Pedro Marques

[Sid]

@ENSO ORIGINS , check this out - https://confluence.atlassian.com/jirakb/jira-applications-crash-due-to-outofmemoryerror-unable-to-create-new-native-thread-224397455.html

[Taranjeet Singh]

@ENSO ORIGINS Please find this KB article from Atlassian that you can use to diagnose and resolve your issue: https://confluence.atlassian.com/jirakb/jira-applications-crash-due-to-outofmemoryerror-unable-to-create-new-native-thread-224397455.html

Hope it helps !

[ENSO ORIGINS]

Hello @Taranjeet Singh ,

I tried your suggestion and it starts Jira till the page:

"Jira had problems starting up"
SYSTEM PLUGINS FAILED TO START: WE HAVEN'T BEEN ABLE TO START ALL THE REQUIRED SYSTEM PLUGINS

We couldn't start the following plugins:

Jira Projects Plugin (com.atlassian.jira.jira-projects-plugin)
Atlassian OAuth Consumer Plugin (com.atlassian.oauth.consumer)
Atlassian Navigation Links Plugin (com.atlassian.plugins.atlassian-nav-links-plugin)
Atlassian Jira - Plugins - OAuth Service Provider SPI (com.atlassian.jira.oauth.serviceprovider)
Atlassian Jira - Plugins - Project Config Plugin (com.atlassian.jira.jira-project-config-plugin)
Applinks - Plugin - Core (com.atlassian.applinks.applinks-plugin)
Atlassian OAuth Service Provider Plugin (com.atlassian.oauth.serviceprovider)
jira-webresources-plugin (jira.webresources)
Embedded Gadgets Plugin (com.atlassian.gadgets.embedded)
Gadget Directory Plugin (com.atlassian.gadgets.directory)
Atlassian Jira - Plugins - Gadgets Plugin (com.atlassian.jira.gadgets)
Atlassian Jira - Plugins - Global Issue Navigator (com.atlassian.jira.jira-issue-nav-plugin)
Atlassian JIRA - Plugins - File viewer plugin (com.atlassian.jira.jira-fileviewer-plugin)
Atlassian Pretty URLs Plugin (com.atlassian.prettyurls.atlassian-pretty-urls-plugin)
jira-ui (com.atlassian.jira.plugins.jira-ui)
Atlassian JIRA - Plugins - Quick Edit Plugin (com.atlassian.jira.jira-quick-edit-plugin)
Atlassian OAuth Admin Plugin (com.atlassian.oauth.admin)
Atlassian REST - Module Types (com.atlassian.plugins.rest.atlassian-rest-module)
Atlassian Jira - Plugins - REST Plugin (com.atlassian.jira.rest)
Opensocial Plugin (com.atlassian.gadgets.opensocial)
atlassian-servlet-plugin (com.atlassian.web.atlassian-servlet-plugin)
Atlassian Jira - Plugins - Look And Feel Logo Upload Plugin (com.atlassian.jira.lookandfeel)
Gadget Spec Publisher Plugin (com.atlassian.gadgets.publisher)
Atlassian Jira - Plugins - OAuth Consumer SPI (com.atlassian.jira.oauth.consumer)
Atlassian Jira - Plugins - SAL Plugin (com.atlassian.sal.jira)
Gadget Dashboard Plugin (com.atlassian.gadgets.dashboard)

2019-03-13 17:18:07,746 JIRA-Bootstrap ERROR [c.a.jira.startup.SystemPluginsEnabledHealthCheck] We couldn't start the following plugins:
- Jira Projects Plugin (com.atlassian.jira.jira-projects-plugin)
- Atlassian OAuth Consumer Plugin (com.atlassian.oauth.consumer)
- Atlassian Navigation Links Plugin (com.atlassian.plugins.atlassian-nav-links-plugin)
- Atlassian Jira - Plugins - OAuth Service Provider SPI (com.atlassian.jira.oauth.serviceprovider)
- Atlassian Jira - Plugins - Project Config Plugin (com.atlassian.jira.jira-project-config-plugin)
- Applinks - Plugin - Core (com.atlassian.applinks.applinks-plugin)
- Atlassian OAuth Service Provider Plugin (com.atlassian.oauth.serviceprovider)
- jira-webresources-plugin (jira.webresources)
- Embedded Gadgets Plugin (com.atlassian.gadgets.embedded)
- Gadget Directory Plugin (com.atlassian.gadgets.directory)
- Atlassian Jira - Plugins - Gadgets Plugin (com.atlassian.jira.gadgets)
- Atlassian Jira - Plugins - Global Issue Navigator (com.atlassian.jira.jira-issue-nav-plugin)
- Atlassian JIRA - Plugins - File viewer plugin (com.atlassian.jira.jira-fileviewer-plugin)
- Atlassian Pretty URLs Plugin (com.atlassian.prettyurls.atlassian-pretty-urls-plugin)
- jira-ui (com.atlassian.jira.plugins.jira-ui)
- Atlassian JIRA - Plugins - Quick Edit Plugin (com.atlassian.jira.jira-quick-edit-plugin)
- Atlassian OAuth Admin Plugin (com.atlassian.oauth.admin)
- Atlassian REST - Module Types (com.atlassian.plugins.rest.atlassian-rest-module)
- Atlassian Jira - Plugins - REST Plugin (com.atlassian.jira.rest)
- Opensocial Plugin (com.atlassian.gadgets.opensocial)
- atlassian-servlet-plugin (com.atlassian.web.atlassian-servlet-plugin)
- Atlassian Jira - Plugins - Look And Feel Logo Upload Plugin (com.atlassian.jira.lookandfeel)
- Gadget Spec Publisher Plugin (com.atlassian.gadgets.publisher)
- Atlassian Jira - Plugins - OAuth Consumer SPI (com.atlassian.jira.oauth.consumer)
- Atlassian Jira - Plugins - SAL Plugin (com.atlassian.sal.jira)
- Gadget Dashboard Plugin (com.atlassian.gadgets.dashboard)

2019-03-13 17:18:09,980 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira2/dbconfig.xml
2019-03-13 17:18:11,219 JIRA-Bootstrap ERROR [c.a.jira.startup.DefaultJiraLauncher] JIRA has failed to start because of the following errors: [(Event: Level = (EventLevel: fatal) , Key = (EventType: system-plugins) , Desc = We haven't been able to start all the required system plugins , Exception = We couldn't start the following plugins:<br/><ul><li>Jira Projects Plugin (com.atlassian.jira.jira-projects-plugin)</li><li>Atlassian OAuth Consumer Plugin (com.atlassian.oauth.consumer)</li><li>Atlassian Navigation Links Plugin (com.atlassian.plugins.atlassian-nav-links-plugin)</li><li>Atlassian Jira - Plugins - OAuth Service Provider SPI (com.atlassian.jira.oauth.serviceprovider)</li><li>Atlassian Jira - Plugins - Project Config Plugin (com.atlassian.jira.jira-project-config-plugin)</li><li>Applinks - Plugin - Core (com.atlassian.applinks.applinks-plugin)</li><li>Atlassian OAuth Service Provider Plugin (com.atlassian.oauth.serviceprovider)</li><li>jira-webresources-plugin (jira.webresources)</li><li>Embedded Gadgets Plugin (com.atlassian.gadgets.embedded)</li><li>Gadget Directory Plugin (com.atlassian.gadgets.directory)</li><li>Atlassian Jira - Plugins - Gadgets Plugin (com.atlassian.jira.gadgets)</li><li>Atlassian Jira - Plugins - Global Issue Navigator (com.atlassian.jira.jira-issue-nav-plugin)</li><li>Atlassian JIRA - Plugins - File viewer plugin (com.atlassian.jira.jira-fileviewer-plugin)</li><li>Atlassian Pretty URLs Plugin (com.atlassian.prettyurls.atlassian-pretty-urls-plugin)</li><li>jira-ui (com.atlassian.jira.plugins.jira-ui)</li><li>Atlassian JIRA - Plugins - Quick Edit Plugin (com.atlassian.jira.jira-quick-edit-plugin)</li><li>Atlassian OAuth Admin Plugin (com.atlassian.oauth.admin)</li><li>Atlassian REST - Module Types (com.atlassian.plugins.rest.atlassian-rest-module)</li><li>Atlassian Jira - Plugins - REST Plugin (com.atlassian.jira.rest)</li><li>Opensocial Plugin (com.atlassian.gadgets.opensocial)</li><li>atlassian-servlet-plugin (com.atlassian.web.atlassian-servlet-plugin)</li><li>Atlassian Jira - Plugins - Look And Feel Logo Upload Plugin (com.atlassian.jira.lookandfeel)</li><li>Gadget Spec Publisher Plugin (com.atlassian.gadgets.publisher)</li><li>Atlassian Jira - Plugins - OAuth Consumer SPI (com.atlassian.jira.oauth.consumer)</li><li>Atlassian Jira - Plugins - SAL Plugin (com.atlassian.sal.jira)</li><li>Gadget Dashboard Plugin (com.atlassian.gadgets.dashboard)</li></ul>)]
2019-03-13 17:18:11,235 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 839 MiB. Committed: 3926 MiB. Max: 4016 MiB
Non-heap memory : Used: 123 MiB. Committed: 130 MiB. Max: 1536 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 962 MiB. Committed: 4055 MiB. Max: 5552 MiB
---------------------------------------------------------------------------------

Any idea?

Best Regards,

Pedro Marques

[Taranjeet Singh]

@ENSO ORIGINS Please refer the below Community post for the similar issue as well as the KB article that provides workaround and permanent resolution of the issue: https://community.atlassian.com/t5/Jira-Software-questions/jira-start-up-error/qaq-p/719330

https://confluence.atlassian.com/jirakb/jira-applications-system-plugin-timeout-while-waiting-for-add-ons-to-enable-212173447.html?_ga=2.93653918.2020062517.1552315738-1671602508.1532093427

Try the workaround for now and plan for permanent resolution in near future, since it seems that your JIRA application has too much data and the host resources are not enough for that.