Connection to MySQL database randomly stopped working

[Chris Anderson]

My instance has worked fine for months - and suddenly, on Friday, it stopped connecting to the database.  The Jira instance and the DB are on the same PC, so its not a port issue (using localhost).  I have confirmed credentials - and all other applications that use that database are working fine.  There have been no maintenance events or any other abnormal processing on the machine.  The dbconfig.xml file remains unchanged from my original installation in 2017.  I do not have the ability to do an NMAP command - as the PC is on a Windows 7 computer (this is my test instance as I am getting production hardware prepared for migration).  I do not know what else I can check to confirm why JIRA suddenly stopped talking to the database. I followed the tutorial to check on everything, but still can't determine 

EDIT: Here are some of the logs: 

atlassian-jira-gc-2018-11-26_22-42-25.log.0

2018-11-26T22:43:06.626-0600: 41.644: [GC (Allocation Failure) [PSYoungGen: 65536K->10747K(76288K)] 65536K->12168K(251392K), 0.0118435 secs] [Times: user=0.03 sys=0.02, real=0.02 secs]
2018-11-26T22:43:07.359-0600: 42.367: [GC (Allocation Failure) [PSYoungGen: 76283K->9361K(76288K)] 77704K->10790K(251392K), 0.0065582 secs] [Times: user=0.00 sys=0.00, real=0.00 secs]
2018-11-26T22:43:10.152-0600: 45.158: [GC (Allocation Failure) [PSYoungGen: 74897K->10739K(76288K)] 76326K->17432K(251392K), 0.0130445 secs] [Times: user=0.00 sys=0.00, real=0.00 secs]
20

.... and so on for a long time... 

2019-01-21T22:50:08.785-0600: 4838630.050: [GC (Allocation Failure) [PSYoungGen: 248064K->1792K(251904K)] 671708K->427220K(770560K), 0.0155784 secs] [Times: user=0.06 sys=0.00, real=0.02 secs]
2019-01-21T22:50:11.927-0600: 4838633.192: [GC (System.gc()) [PSYoungGen: 27685K->350K(253952K)] 453113K->426842K(772608K), 0.0195552 secs] [Times: user=0.05 sys=0.00, real=0.02 secs]

2019-01-21T22:50:11.943-0600: 4838633.212: [Full GC (System.gc()) [PSYoungGen: 350K->0K(253952K)] [ParOldGen: 426492K->169608K(518656K)] 426842K->169608K(772608K), [Metaspace: 249820K->229244K(1298432K)], 8.6272455 secs] [Times: user=1.53 sys=0.00, real=8.63 secs]
Heap
PSYoungGen total 253952K, used 20931K [0x00000000f0000000, 0x0000000100000000, 0x0000000100000000)
eden space 246784K, 8% used [0x00000000f0000000,0x00000000f1470ef0,0x00000000ff100000)
from space 7168K, 0% used [0x00000000ff900000,0x00000000ff900000,0x0000000100000000)
to space 7680K, 0% used [0x00000000ff100000,0x00000000ff100000,0x00000000ff880000)
ParOldGen total 518656K, used 169608K [0x00000000d0000000, 0x00000000efa80000, 0x00000000f0000000)
object space 518656K, 32% used [0x00000000d0000000,0x00000000da5a23a8,0x00000000efa80000)
Metaspace used 229341K, capacity 243287K, committed 288532K, reserved 1298432K
class space used 29763K, capacity 33225K, committed 39956K, reserved 1048576K

and then from 

jirasoftware040817140315-stdout.2019-01-21

... things running normally until: 

2019-01-21 22:57:08,142 JIRA-Bootstrap INFO [o.o.c.entity.jdbc.DatabaseUtil] Created function based indices for entity "IssueSecurityScheme"
2019-01-21 22:57:08,142 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigurationManagerImpl] The database is configured. Now running Database Checklist Launcher
2019-01-21 22:57:08,158 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseChecklistLauncher] JIRA database startup checks completed successfully.

2019-01-21 22:57:08,158 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigurationManagerImpl] The database is configured. Now running Post database-configuration launchers
2019-01-21 22:57:11,098 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from C:\Program Files\Atlassian\Application Data\JIRA\dbconfig.xml
2019-01-21 22:57:12,670 JIRA-Bootstrap INFO [c.a.j.c.embedded.ofbiz.OfBizUserDao] Using full user cache
2019-01-21 22:57:22,481 JIRA-Bootstrap ERROR [c.a.jira.startup.ComponentContainerLauncher] A fatal error occurred during initialisation. JIRA has been locked.
com.atlassian.plugin.osgi.container.OsgiContainerException: Unable to clean the cache directory: C:\Program Files\Atlassian\Application Data\JIRA\plugins\.osgi-plugins\felix
at com.atlassian.plugin.osgi.container.impl.DefaultOsgiPersistentCache.validate(DefaultOsgiPersistentCache.java:81)
at com.atlassian.plugin.osgi.container.impl.DefaultOsgiPersistentCache.<init>(DefaultOsgiPersistentCache.java:38)
at com.atlassian.jira.plugin.PluginPath$JiraHomeAdapter.<init>(PluginPath.java:135)

[Tom Lister]

Hi

could you check the Atlassian-Jira.log files for errors and post then here?