How do I install JIRA

[Richard Luciano]

I am trying to install JIRA on my hosted Linux Centos 7.9 server.  I found a variety of installation instructions but when I tried to run it, JIRA would never start up.  I have literally been trying this for weeks and am very frustrated at this point because our projects are being held up.

Do you have any documentation that shows how I can install this on my server either in WHM/CPanel, etc?  Why is this software so difficult to install I don't understand it, it makes no sense.  It goes against any other software I've loaded on my server.

If you can please give me some direction with how to do this it would be most appreciated, thank you!

[Nic Brough -Adaptavist-]

You should be trying to install Jira from the command line, it's far easier than trying to do it through something like cpanel.

First create an empty database for it to use, then, from the command line, download the installer, run it, answer the questions it asks about file locations, and leave it for a few minutes, and you're done.  

I did this last week for a customer, took 10 minutes, then another 2-3 to use the ui to run the last bits of the new config.  

I think the question has to be "where are you stuck?".  I suspect the answer is that you're not using a standard simple install process for it.

[Richard Luciano]

I did do it from the command line, I did install it with no problem.  However, I was unclear where to make the database.  Also, I couldn't get JIRA to run no matter what I did.  I did install on a different port than 8080, but again, no matter what I did it wouldn't start.

Also, I couldn't get the server to install because I was too apprehensive to screw up anything on my server.  There are other sites running on my server so I don't want to risk screwing up the database that runs on the server already.

What confuses me is why I can't just install this under a domain like every other piece of software I've ever installed.  Why can't we do that, it makes no sense.

[Nic Brough -Adaptavist-]

Because it's not a domain service, it's a fully fledged server in its own right.

"Where to make the database" - you'll need to provision a database for it to use somewhere.  It has the flexibility to be used on a range of databases, see https://confluence.atlassian.com/adminjiraserver/connecting-jira-applications-to-a-database-938846850.html for the details of how to commission a database for it.  (This is generally not complicated - in the one I did the other day, it was "install postgresql as a standard CentOS package, then run the command to create an empty database and a user for Jira to connect as")

"I couldn't get Jira to run" - what goes wrong when you ran "start-jira.sh"?  Does that give you an error message?  If not, then you should have a running Jira, and if you don't, then you'll want to read the <jira home>/log/atlassian-jira.log file to find out what is not starting up.

[Richard Luciano]

Oooooh, I think I missed that, typically when a software solution says it runs server site, that just means it runs in your environment/server.  I didn't know it was it's own full fledged server, yikes!

Actually, you know what, I'll just go through the documentation and see if I can get this to work.  Bare with me.

[Richard Luciano]

So here's my question, I'm going to try and install it again.  Maybe you can help me as I walk through it.

I just uninstalled everything from my past install, now I"m installing a fresh version.

atlassian-jira-core-8.14.0-x64.bin

[Richard Luciano]

Okay, I just reinstalled via command line, everything said it went perfectly.  It then gave me the link to JIRA, however, it's not coming up, it's saying the connection has timed out.

Just as a note, this is a Linux dedicated server I use to host websites, you're sure this will run off of this server?

[Richard Luciano]

Oh also, does JIRA have to be connected to the database for it to run?  maybe that's the issue with why it's not coming up.

[Nic Brough -Adaptavist-]

Ah, I'm not an Atlassian - you're in a wider community of people with an interest in Atlassian for some reason.

The Server package really is a compound of several things - the simplest version is a Tomcat Server, a bundled Java, and a Jira (Core) application built on top of it.    That can be deployed on any operating system that can run Java.  You don't deploy it on other server platforms, it already is a server.  (In the ancient mists of time, you used to be able to get a package that could be deployed on any Java application server - I had some good experiences running Jira on Orion instead of Tomcat for example)

Anyway, Server is going away in a couple of years, so I wouldn't be looking at it anyway.  If you have a need for a large, heavy use instance (let's say you're starting with at least 500 users) or have worries about compliance and regulation that mean you can't got ot the Cloud, you should be looking towards Data Centre versions.  If you're smaller and not so concerned with the data location, then Cloud is definitely a good option.

If you do decide to go to Cloud, then yes, get in touch with atlassian's billing support, and they'll be able to convert your payment for a server licence into a credit against your Cloud subscription (I think it's in full if you've got more than 10 months left on it)

[Richard Luciano]

Thanks so much for the feedback, much appreciated.

[Richard Luciano]

Hey Nic, so I reinstalled the software on my server, everything went fine, the software started.  However, when I run it the page doesn't load and then I get an error.  The error is:  The connection has timed out.  The server at MYIP is taking too long to respond.

Any idea's with why this is happening and how can I fix it?

[Nic Brough -Adaptavist-]

That sounds like Tomcat is running, but has not started Jira.  It can take a while to load up a Jira system, even a new empty one, so leave it a few minutes.  If it is failing to start, then you're into reading the application and possibly application server logs to see what the errors are.  The application log is <jira home>/log/atlassian-jira.log (given your description, I'd expect to see the error in there, you shouldn't need to resort to looking at <jira installation>/log/catalina.out )

[Richard Luciano]

Hi Nic, this is the log from "atlassian-jira-gc-2021-01-04_01-46-49.log.0.current"

OpenJDK 64-Bit Server VM (25.202-b08) for linux-amd64 JRE (1.8.0_202-b08), built on Jan 22 2019 13:35:07 by "jenkins" with gcc 4.8.2 20140120 (Red Hat 4.8.2-15)
Memory: 4k page, physical 65257188k(2607756k free), swap 6143996k(5990440k free)
CommandLine flags: -XX:+ExplicitGCInvokesConcurrent -XX:GCLogFileSize=20971520 -XX:InitialCodeCacheSize=33554432 -XX:InitialHeapSize=402653184 -XX:MaxHeapSize=2147483648 -XX:NumberOfGCLogFiles=5 -XX:-OmitStackTraceInFastThrow -XX:+PrintGC -XX:+PrintGCCause -XX:+PrintGCDateStamps -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:ReservedCodeCacheSize=536870912 -XX:+UseCompressedClassPointers -XX:+UseCompressedOops -XX:+UseGCLogFileRotation -XX:+UseParallelGC
2021-01-04T01:46:50.264-0500: 0.645: [GC (Allocation Failure) [PSYoungGen: 98304K->13850K(114688K)] 98304K->13938K(376832K), 0.0081655 secs] [Times: user=0.05 sys=0.00, real=0.01 secs]
2021-01-04T01:46:50.613-0500: 0.994: [GC (Allocation Failure) [PSYoungGen: 112154K->13656K(212992K)] 112242K->13752K(475136K), 0.0078396 secs] [Times: user=0.04 sys=0.01, real=0.01 secs]
2021-01-04T01:46:50.893-0500: 1.274: [GC (Allocation Failure) [PSYoungGen: 210264K->15665K(212992K)] 210360K->15833K(475136K), 0.0103353 secs] [Times: user=0.03 sys=0.03, real=0.01 secs]
2021-01-04T01:46:51.151-0500: 1.532: [GC (Allocation Failure) [PSYoungGen: 212273K->16373K(409600K)] 212441K->16921K(671744K), 0.0120356 secs] [Times: user=0.07 sys=0.01, real=0.01 secs]
2021-01-04T01:46:51.597-0500: 1.978: [GC (Allocation Failure) [PSYoungGen: 409589K->16364K(409600K)] 410137K->21372K(671744K), 0.0127480 secs] [Times: user=0.06 sys=0.01, real=0.01 secs]
2021-01-04T01:46:52.199-0500: 2.580: [GC (Allocation Failure) [PSYoungGen: 409580K->20982K(667648K)] 414588K->31271K(929792K), 0.0144769 secs] [Times: user=0.07 sys=0.00, real=0.02 secs]
2021-01-04T01:46:52.473-0500: 2.854: [GC (Metadata GC Threshold) [PSYoungGen: 187845K->8834K(655872K)] 198135K->29727K(918016K), 0.0122221 secs] [Times: user=0.06 sys=0.01, real=0.01 secs]
2021-01-04T01:46:52.486-0500: 2.867: [Full GC (Metadata GC Threshold) [PSYoungGen: 8834K->0K(655872K)] [ParOldGen: 20892K->19369K(262144K)] 29727K->19369K(918016K), [Metaspace: 20721K->20721K(1069056K)], 0.0496056 secs] [Times: user=0.30 sys=0.00, real=0.05 secs]
2021-01-04T01:46:53.664-0500: 4.046: [GC (Allocation Failure) [PSYoungGen: 646656K->20011K(671744K)] 666025K->39389K(933888K), 0.0113460 secs] [Times: user=0.05 sys=0.00, real=0.01 secs]
2021-01-04T01:46:54.153-0500: 4.534: [GC (Metadata GC Threshold) [PSYoungGen: 241124K->13652K(658432K)] 260502K->33037K(920576K), 0.0059913 secs] [Times: user=0.03 sys=0.00, real=0.00 secs]
2021-01-04T01:46:54.159-0500: 4.540: [Full GC (Metadata GC Threshold) [PSYoungGen: 13652K->0K(658432K)] [ParOldGen: 19385K->30484K(262144K)] 33037K->30484K(920576K), [Metaspace: 34514K->34514K(1081344K)], 0.0550291 secs] [Times: user=0.34 sys=0.00, real=0.06 secs]
2021-01-04T01:46:56.706-0500: 7.087: [GC (Allocation Failure) [PSYoungGen: 644608K->26613K(665088K)] 675092K->59627K(927232K), 0.0106770 secs] [Times: user=0.05 sys=0.00, real=0.01 secs]
2021-01-04T19:08:54.626-0500: 62525.981: [GC (Allocation Failure) [PSYoungGen: 665077K->2591K(641536K)] 698091K->52258K(903680K), 0.0110040 secs] [Times: user=0.07 sys=0.01, real=0.02 secs]

Here is the log for "catalina.2021-01-04.log"

04-Jan-2021 01:46:06.929 INFO [main] org.apache.catalina.core.StandardServer.await A valid shutdown command was received via the shutdown port. Stopping the Server instance.
04-Jan-2021 01:46:06.929 INFO [main] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8081"]
04-Jan-2021 01:46:06.936 INFO [main] org.apache.catalina.core.StandardService.stopInternal Stopping service [Catalina]
04-Jan-2021 01:46:06.971 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [plugin-transaction-0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
sun.misc.Unsafe.park(Native Method)
java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:2078)
java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1093)
java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1074)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1134)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
java.lang.Thread.run(Thread.java:748)
04-Jan-2021 01:46:06.976 INFO [main] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8081"]
04-Jan-2021 01:46:06.977 INFO [main] org.apache.coyote.AbstractProtocol.destroy Destroying ProtocolHandler ["http-nio-8081"]
04-Jan-2021 01:46:49.960 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/8.5.57
04-Jan-2021 01:46:49.961 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jun 30 2020 21:49:10 UTC
04-Jan-2021 01:46:49.961 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 8.5.57.0
04-Jan-2021 01:46:49.961 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
04-Jan-2021 01:46:49.961 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 3.10.0-1160.11.1.el7.x86_64
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/atlassian/jira/jre
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_202-b08
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /opt/atlassian/jira
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /opt/atlassian/jira
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx2048m
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:InitialCodeCacheSize=32m
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:ReservedCodeCacheSize=512m
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
04-Jan-2021 01:46:49.962 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.locale.providers=COMPAT
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xloggc:/opt/atlassian/jira/logs/atlassian-jira-gc-%t.log
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseGCLogFileRotation
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:NumberOfGCLogFiles=5
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:GCLogFileSize=20M
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDetails
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCDateStamps
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCTimeStamps
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+PrintGCCause
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+ExplicitGCInvokesConcurrent
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
04-Jan-2021 01:46:49.963 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The Apache Tomcat Native library which allows using OpenSSL wasnot found on the java.library.path: [/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib]
04-Jan-2021 01:46:50.022 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8081"]
04-Jan-2021 01:46:50.033 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 287 ms
04-Jan-2021 01:46:50.039 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
04-Jan-2021 01:46:50.039 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet Engine: Apache Tomcat/8.5.57
04-Jan-2021 01:46:52.635 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8081"]
04-Jan-2021 01:46:52.639 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
04-Jan-2021 01:46:52.647 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 2614 ms

Any ideas?

[Richard Luciano]

If you could please help me get JIRA running, I desperately need this application, I have projects that need this work flow.

[Nic Brough -Adaptavist-]

GC Allocation failures means there's something wrong with the memory setup.  Often, this is "not enough memory to work with".  Generally, I'd start by trying to give it more (maximum heap size).  Probably increment in 1/4Gb steps

[Richard Luciano]

How would I do that?  How do I increase the heap size?

[Nic Brough -Adaptavist-]

Find and edit the setenv.sh file, it should be in <jira install>/bin

You should check that the XXMaxHeapSize you've got in your log above changes to match any new setting