Jira installation

[Eric Seibert]

I'm trying to install Jira, in fact I've tried to install Jira core, Jira software and Jira service desk on VMware Rhel7.4 with jdk1.8 on a machine that has 8 cpus 16 gb or memory plenty of disk space. From what I've read it has more than enough resources to run one of these and confluence, bamboo, crucible and fisheye. 

That however seems to be not to be the case. I try installing and its painstakingly forever slow, and then starting it is just as slow if it starts to complete the install. I tried 7.11 I'm about to install 7.12 and see if that changes anything but I can't even get through the setup to even start doing something with it.

What I am looking for advice on and my goal is how and should I install core, software and service desk on the same server with any of these other applications. or do I need to install them on separate servers, and what kinda of resources should I be aiming for since 8 cpus and 32 GB seem to make no difference over 2 cpus and 4 gb mem. I'm only trying to install a test instance at the moment so I am looking at less than 10 users and maybe 4 or 5 test projects to evaluate the needs when we scale up.

Since I haven't got it installed any of them I don't even know how to go about adding the other applications (core and software for instance)

I've uninstalled Jira software, and when I try to install the newest version or any version for that matter its taking well over 2-3 hours to install and if it starts the set up to get everything loaded. 

[Tom Lister]

Hi @Eric Seibert

I’m not sure what your issue could be but I can tell you I’m running core/software/service desk/mysql on my MacBook Pro with far less resources than you have. So I don’t think your hardware capability is the issue. 

Do you have log files? 

There may be clues there as to what part of the process is slow running.

[Eric Seibert]

got the furthest this time

it seems to be something with the plugins :

SYSTEM PLUGINS FAILED TO START: WE HAVEN'T BEEN ABLE TO START ALL THE REQUIRED SYSTEM PLUGINS
We couldn't start the following plugins:

Gadget Directory Plugin (com.atlassian.gadgets.directory)
Atlassian Jira - Plugins - Global Issue Navigator (com.atlassian.jira.jira-issue-nav-plugin)

the logs are huge but in a condensed form

12-Nov-2018 16:27:28.070 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause
12-Nov-2018 16:27:28.070 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
12-Nov-2018 16:27:28.070 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira
12-Nov-2018 16:27:28.070 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira
12-Nov-2018 16:27:28.070 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
12-Nov-2018 16:27:28.070 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]
12-Nov-2018 16:27:34.654 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
12-Nov-2018 16:27:35.017 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 17834 ms
12-Nov-2018 16:27:35.073 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
12-Nov-2018 16:27:35.074 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.32

2018-11-12 16:29:40,597 localhost-startStop-1 INFO [c.a.jira.startup.JiraHomeStartupCheck] The jira.home directory '/var/atlassian/application-data/jira' is validated and locked for exclusive use by this instance.
2018-11-12 16:29:41,321 localhost-startStop-1 WARN [o.a.catalina.util.SessionIdGeneratorBase] Creation of SecureRandom instance for session ID generation using [SHA1PRNG] took [703] milliseconds.
2018-11-12 16:29:45,271 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

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

2018-11-12 16:29:50,033 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

___ Environment _____________________________

JIRA Build : 7.12.3#712004-sha1:5ef91d760d7124da5ebec5c16a948a4a807698df
Build Date : Fri Oct 12 00:00:00 EDT 2018
JIRA Installation Type : Standalone
Application Server : Apache Tomcat/8.5.32 - Servlet API 3.1
Java Version : 1.8.0_181 - Oracle Corporation
Current Working Directory : /opt/atlassian/jira/logs
Maximum Allowable Memory : 683MB
Total Memory : 462MB
Free Memory : 415MB
Used Memory : 47MB
Memory Pool: Code Cache : Code Cache: init = 2555904(2496K) used = 8676736(8473K) committed = 8716288(8512K) max = 251658240(245760K)
Memory Pool: Metaspace : Metaspace: init = 0(0K) used = 21792224(21281K) committed = 22593536(22064K) max = -1(-1K)
Memory Pool: Compressed Class Space : Compressed Class Space: init = 0(0K) used = 2554336(2494K) committed = 2752512(2688K) max = 1073741824(1048576K)
Memory Pool: PS Eden Space : PS Eden Space: init = 100663296(98304K) used = 31092880(30364K) committed = 207618048(202752K) max = 228589568(223232K)
Memory Pool: PS Survivor Space : PS Survivor Space: init = 16777216(16384K) used = 0(0K) committed = 8912896(8704K) max = 8912896(8704K)
Memory Pool: PS Old Gen : PS Old Gen: init = 268435456(262144K) used = 20724496(20238K) committed = 268435456(262144K) max = 536870912(524288K)
JVM Input Arguments : -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms384m -Xmx768m -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 -Djdk.tls.ephemeralDHKeySize=2048 -Djava.protocol.handler.pkgs=org.apache.catalina.webresources -Dorg.apache.catalina.security.SecurityListener.UMASK=0027 -Xloggc:/opt/atlassian/jira/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/jira -Dcatalina.home=/opt/atlassian/jira -Djava.io.tmpdir=/opt/atlassian/jira/temp
Java Compatibility Information : JIRA version = 7.12.3, Java Version = 1.8.0_181

___ Java System Properties _________________

atlassian.standalone : JIRA
awt.toolkit : sun.awt.X11.XToolkit
catalina.base : /opt/atlassian/jira
catalina.home : /opt/atlassian/jira
catalina.useNaming : true
common.loader : "${catalina.base}/lib",
"${catalina.base}/lib/*.jar",
"${catalina.home}/lib",
"${catalina.home}/lib/*.jar"
file.encoding : UTF-8
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/jira/jre
java.io.tmpdir : /opt/atlassian/jira/temp
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/jira/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 : 3.10.0-693.11.6.el7.x86_64
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/jira/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 : UTF-8
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-web*.jar,
log4j-taglib*.jar,
log4javascript*.jar,
slf4j-taglib*.jar
tomcat.util.scan.StandardJarScanFilter.jarsToSkip : bootstrap.jar,
commons-daemon.jar,
tomcat-juli.jar,
annotations-api.jar,
el-api.jar,
jsp-api.jar,
servlet-api.jar,
websocket-api.jar,
jaspic-api.jar,
catalina.jar,
catalina-ant.jar,
catalina-ha.jar,
catalina-storeconfig.jar,
catalina-tribes.jar,
jasper.jar,
jasper-el.jar,
ecj-*.jar,
tomcat-api.jar,
tomcat-util.jar,
tomcat-util-scan.jar,
tomcat-coyote.jar,
tomcat-dbcp.jar,
tomcat-jni.jar,
tomcat-websocket.jar,
tomcat-i18n-en.jar,
tomcat-i18n-es.jar,
tomcat-i18n-fr.jar,
tomcat-i18n-ja.jar,
tomcat-juli-adapters.jar,
catalina-jmx-remote.jar,
catalina-ws.jar,
tomcat-jdbc.jar,
tools.jar,
commons-beanutils*.jar,
commons-codec*.jar,
commons-collections*.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,
jstl.jar,
taglibs-standard-spec-*.jar,
geronimo-spec-jaxrpc*.jar,
wsdl4j*.jar,
ant.jar,
ant-junit*.jar,
aspectj*.jar,
jmx.jar,
h2*.jar,
hibernate*.jar,
httpclient*.jar,
jmx-tools.jar,
jta*.jar,
log4j*.jar,
mail*.jar,
slf4j*.jar,
xercesImpl.jar,
xmlParserAPIs.jar,
xml-apis.jar,
junit.jar,
junit-*.jar,
hamcrest-*.jar,
easymock-*.jar,
cglib-*.jar,
objenesis-*.jar,
ant-launcher.jar,
cobertura-*.jar,
asm-*.jar,
dom4j-*.jar,
icu4j-*.jar,
jaxen-*.jar,
jdom-*.jar,
jetty-*.jar,
oro-*.jar,
servlet-api-*.jar,
tagsoup-*.jar,
xmlParserAPIs-*.jar,
xom-*.jar
user.country : US
user.dir : /opt/atlassian/jira/logs
user.home : /root
user.language : en
user.name : root
user.timezone : America/New_York

...

2018-11-12 16:46:39,562 JIRA-Bootstrap INFO [c.a.plugin.manager.DefaultPluginManager] Plugin system earlyStartup ended
2018-11-12 16:46:41,901 JIRA-Bootstrap ERROR [c.a.jira.startup.SystemPluginsEnabledHealthCheck] We couldn't start the following plugins:
- Gadget Directory Plugin (com.atlassian.gadgets.directory)
- Atlassian Jira - Plugins - Global Issue Navigator (com.atlassian.jira.jira-issue-nav-plugin)

2018-11-12 16:46:41,925 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] We haven't been able to start all the required system plugins
2018-11-12 16:46:41,925 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] We couldn't start the following plugins:
- Gadget Directory Plugin (com.atlassian.gadgets.directory)
- Atlassian Jira - Plugins - Global Issue Navigator (com.atlassian.jira.jira-issue-nav-plugin)

2018-11-12 16:46:47,332 http-nio-8080-exec-15 WARN anonymous 1006x4x1 11df98a 10.249.18.228 /secure/errors.jsp [c.a.jira.security.JiraSecurityFilter] Rejecting security-sensitive request that bypassed Johnson filter: /secure/errors.jsp
2018-11-12 16:46:47,850 JIRA-Bootstrap INFO [c.a.j.c.cache.pauser.NonClusteredReplicationPauserManager] Non-clustered mode: ReplicationPauserManager implemented by NonClusteredReplicationPauserManager
2018-11-12 16:46:52,873 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira/dbconfig.xml
2018-11-12 16:46:52,888 JIRA-Bootstrap INFO [c.a.j.instrumentation.external.DatabaseExternalGauges] Installing DBCP monitoring instruments: DatabaseExternalGauges.JiraDbcpInstruments[instruments=[DBCP_MAX, DBCP_ACTIVE, DBCP_IDLE],objectName=com.atlassian.jira:name=BasicDataSource]
2018-11-12 16:46:59,597 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>Gadget Directory Plugin (com.atlassian.gadgets.directory)</li><li>Atlassian Jira - Plugins - Global Issue Navigator (com.atlassian.jira.jira-issue-nav-plugin)</li></ul>)]
2018-11-12 16:46:59,617 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 341 MiB. Committed: 669 MiB. Max: 721 MiB
Non-heap memory : Used: 226 MiB. Committed: 247 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 568 MiB. Committed: 916 MiB. Max: 1985 MiB
---------------------------------------------------------------------------------

[Tom Lister]

Hi @Eric Seibert

no smoking guns in those snippets, I.e. what is holding up the plugins.

our servers quite often fail to start after a server reboot but are usually ok if then restarted manually.

are you able to post the whole log to https://pastebin.com ?

Is there a separate error log as well.

did you get the ‘Jira failed to start’ page in your browser listing it’s errors

See

https://confluence.atlassian.com/jirakb/troubleshooting-jira-startup-failed-error-394464512.html

I usually up the plugin wait timeout on servers

also you could increase the memory usage since you have oodles of it

Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms384m -Xmx768m -

[Eric Seibert]

So I've done that and I added the timeout and tried anywhere from 300 -1000 and it still times out on 

[c.a.plugin.manager.PluginEnabler] Unable to start the following plugins due to timeout while waiting for plugin to enable: com.pyxis.greenhopper.jira.

I've checked the IO on the disks and I suspect that it might be what's making things lag so much and really gumming up the process. I don't suspect that its a network issue, although I know there are speed issues on that particular segment.

I'm not sure how to approach the disk IO on VMware but it really shouldn't take the better part of 35 minutes to start Jira core.

[Eric Seibert]

this is the same result I've gotten with multiple changes to the setenv.sh



2018-11-13 15:20:21,084 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 Jira - Plugins - Project Config Plugin (com.atlassian.jira.jira-project-config-plugin)</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 - Quick Edit Plugin (com.atlassian.jira.jira-quick-edit-plugin)</li><li>Atlassian Jira - Plugins - REST Plugin (com.atlassian.jira.rest)</li><li>Gadget Dashboard Plugin (com.atlassian.gadgets.dashboard)</li></ul>)]
2018-11-13 15:20:22,543 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 307 MiB. Committed: 672 MiB. Max: 733 MiB
Non-heap memory : Used: 199 MiB. Committed: 217 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 507 MiB. Committed: 889 MiB. Max: 1997 MiB
---------------------------------------------------------------------------------

[Tom Lister]

Hi Eric

I guess that is the status list at the end of the startup

are there any more detailed errors earlier on for each plugin fail.

To be honest this seems to be system events outside of Jira  my expertise but happy to keep reading the logs for clues