Summary 

On many occasions, JIRA is not able to run properly due to file or directory permission error

Environment

Any version of Jira installed in a Linux environment

Diagnosis

• Manually checking Jira's Home and Installation directory show that the ownership of some files/directories is not of the expected Jira user, and also lacking some read/write/execute permissions

• Errors in the logs will vary, for example an errors like below may show in the logs:

  JIRA couldn't create the jira.home directory

  java.lang.IllegalStateException: java.io.IOException: Permission denied
  Caused by: java.io.IOException: Permission denied
  java.io.FileNotFoundException: atlassian-jira.log (Permission denied)
  org.apache.catalina.startup.HostConfig.beforeStart Unable to create directory for deployment: [path to the directory]

Cause

Jira was likely started with a different user (commonly root) at some point, causing the ownership of the necessary files/directories to be changed.

Even if you specify a user to start Jira in user.sh, this will only be enforced if Jira is started using start-jira.sh. If Jira was started with startup.sh, Jira will run as the user who executed the script, thus possibly causing the ownership of files/directories to be changed.

Solution

There are two options to fix the issue.

Option 1: (Preferred)

Fix the permissions on a case by case basis

1. You will first need to find out the user who installed JIRA. There are 3 methods to do this :

   1. From The System Info page on your JIRA instance :
      
      
      
   2. From the Support Zip ( application.xml file ) search for <JIRA_USER>
      
      
   3. From the $JIRA_HOME/log/atlassian-jira.log, search for 'user.name'
      
      

2. You will also need to know the group the user belongs to run JIRA and most of the time the group name is the same as the username that runs JIRA.  

   If you're unsure of what these permissions should be, please consult with your System Administrator and the user who installed JIRA.

   If you are the user who installed Jira, you can see these details by running these commands:

   	whoami (this will tell your exact username)
   	id -g -n (this will tell your group name)

3. Next, depending on the actual path in the error, execute the 2 lines below to fix the permission of the JIRA Home & Installation directory

   sudo chown -R jirauser:jiragroup /path/referenced/in/the/error
   sudo chmod -R u=rwx,o-rwx /path/referenced/in/the/error

   You may also want to create particular directories manually instead of granting the access on the upper directories, i.e.:

   mkdir -p /path/referenced/in/the/error

   Substitute Jira with the correct user that installed JIRA and the path with the correct path to the respective directory 

4. Restart JIRA and check the logs ($JIRA_INST/logs/catalina.out), $JIRA_HOME/logs/atlassian-jira.log) for any other permission denied errors and repeat steps 3 and 4 above until Jira is fully operational
   

Option 2: 

Disclaimer: The following steps suggest to fix the permissions on all Jira sub directories at once.

1. Follow Steps 1 to 2 to identify the user running Jira

2. Next, execute the following commands to fix the permissions on all Jira folders:

   sudo chown -R jirauser:jiragroup /path/to/jira-local-home
   sudo chown -R jirauser:jiragroup /path/to/jira-install
   sudo chown -R jirauser:jiragroup /path/to/jira-shared-home
   
   
   chmod -R u=rwx,go-rwx,o-rwx /path/to/jira-local-home
   chmod -R u=rwx,go-rwx,o-rwx /path/to/jira-install
   chmod -R u=rwx,go-rwx,o-rwx /path/to/jira-shared-home

Caveat 

Jira might still fail to start even if the permissions are correct after running the commands to fix the permission of the JIRA Home & Installation directory.

The following error will be present:

Setup: JIRA couldn't create the jira.home directory
Ensure JIRA has permission to create and write to the jira.home directory /jira-home.
Review our documentation for more information on setting your JIRA home.

Solution

This can be caused by a symbolic link hidden in the JIRA Home directory.

Follow the Resolution in Symbolic Link in JIRA Home during upgrading using Installer will throw 'java.lang.OutOfMemoryError: GC overhead limit exceeded'.