Database connection failing after upgrading Jira
After upgrading to 8.20 from 8.7 the same database connection that we used to have does not work anymore. The MYSQL version is 5.7 and it's still supported by Jira Core 8.20. We are using the exact same connection driver also 5.1 which should be good.
We also tried removing the dbconfig.xml file and to setup the connection through the starting menu of Jira, but it now shows this error when trying to connect to the same database:
Error connecting to database
Communications link failure The last packet successfully received from the server was 17 milliseconds ago. The last packet sent successfully to the server was 11 milliseconds ago. No appropriate protocol (protocol is disabled or cipher suites are inappropriate)
And after trying to modify the /etc/mysql/my.cnf file and to restart the mysql service is it still shows the same error
After we stopped the mysql service then we got this:
Error connecting to database
Communications link failure The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server. Connection refused (Connection refused)
This is our dbconfig.xml file:
<?xml version="1.0" encoding="UTF-8"?>
<jira-database-config>
<name>defaultDS</name>
<delegator-name>default</delegator-name>
<database-type>mysql</database-type>
<jdbc-datasource>
<url>jdbc:mysql://localhost:3306/amc_servicedesk_jira?useUnicode=true&characterEncoding=UTF8&sessionVariables=default_storage_engine=InnoDB</url>
<driver-class>com.mysql.jdbc.Driver</driver-class>
<username>amcdesk</username>
<password>***</password>
<pool-min-size>20</pool-min-size>
<pool-max-size>20</pool-max-size>
<pool-max-wait>30000</pool-max-wait>
<validation-query>select 1</validation-query>
<min-evictable-idle-time-millis>60000</min-evictable-idle-time-millis>
<time-between-eviction-runs-millis>300000</time-between-eviction-runs-millis>
<pool-max-idle>20</pool-max-idle>
<pool-remove-abandoned>true</pool-remove-abandoned>
<pool-remove-abandoned-timeout>300</pool-remove-abandoned-timeout>
<pool-test-on-borrow>false</pool-test-on-borrow>
<pool-test-while-idle>true</pool-test-while-idle>
<validation-query-timeout>3</validation-query-timeout>
</jdbc-datasource>
</jira-database-config>
And this is our Catalina.out file:
NOTE: Picked up JDK_JAVA_OPTIONS: --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent=ALL-UNNAMED --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
30-Nov-2021 14:07:16.257 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/8.5.65
30-Nov-2021 14:07:16.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Mar 30 2021 12:28:40 UTC
30-Nov-2021 14:07:16.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 8.5.65.0
30-Nov-2021 14:07:16.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
30-Nov-2021 14:07:16.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 5.4.0-1031-azure
30-Nov-2021 14:07:16.270 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
30-Nov-2021 14:07:16.276 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /opt/atlassian/jira/jre
30-Nov-2021 14:07:16.276 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 11.0.11+9
30-Nov-2021 14:07:16.276 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: AdoptOpenJDK
30-Nov-2021 14:07:16.277 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /opt/atlassian/jira
30-Nov-2021 14:07:16.277 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /opt/atlassian/jira
30-Nov-2021 14:07:16.277 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.lang=ALL-UNNAMED
30-Nov-2021 14:07:16.278 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.io=ALL-UNNAMED
30-Nov-2021 14:07:16.278 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.util=ALL-UNNAMED
30-Nov-2021 14:07:16.278 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.base/java.util.concurrent=ALL-UNNAMED
30-Nov-2021 14:07:16.278 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
30-Nov-2021 14:07:16.279 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties
30-Nov-2021 14:07:16.280 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
30-Nov-2021 14:07:16.280 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms384m
30-Nov-2021 14:07:16.280 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx2048m
30-Nov-2021 14:07:16.281 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:InitialCodeCacheSize=32m
30-Nov-2021 14:07:16.281 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:ReservedCodeCacheSize=512m
30-Nov-2021 14:07:16.281 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
30-Nov-2021 14:07:16.281 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.standalone=JIRA
30-Nov-2021 14:07:16.281 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.jasper.runtime.BodyContentImpl.LIMIT_BUFFER=true
30-Nov-2021 14:07:16.283 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dmail.mime.decodeparameters=true
30-Nov-2021 14:07:16.284 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.dom4j.factory=com.atlassian.core.xml.InterningDocumentFactory
30-Nov-2021 14:07:16.284 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:-OmitStackTraceInFastThrow
30-Nov-2021 14:07:16.284 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.locale.providers=COMPAT
30-Nov-2021 14:07:16.284 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Datlassian.plugins.startup.options=
30-Nov-2021 14:07:16.284 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
30-Nov-2021 14:07:16.284 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
30-Nov-2021 14:07:16.285 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
30-Nov-2021 14:07:16.285 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xlog:gc*:file=/opt/atlassian/jira/logs/atlassian-jira-gc-%t.log:tags,time,uptime,level:filecount=5,filesize=20M
30-Nov-2021 14:07:16.286 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+ExplicitGCInvokesConcurrent
30-Nov-2021 14:07:16.286 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
30-Nov-2021 14:07:16.286 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/opt/atlassian/jira
30-Nov-2021 14:07:16.287 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/opt/atlassian/jira
30-Nov-2021 14:07:16.287 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/opt/atlassian/jira/temp
30-Nov-2021 14:07:16.289 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The Apache Tomcat Native library which allows using OpenSSL was not found on the java.library.path: [/home/amc/atlassian-jira-core-8.20.0-x64.bin.13671.dir/user::/usr/java/packages/lib:/usr/lib64:/lib64:/lib:/usr/lib]
30-Nov-2021 14:07:16.741 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
30-Nov-2021 14:07:16.771 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 1607 ms
30-Nov-2021 14:07:16.872 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
30-Nov-2021 14:07:16.872 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/8.5.65]
30-Nov-2021 14:07:16.887 SEVERE [Catalina-startStop-1] org.apache.catalina.startup.HostConfig.beforeStart Unable to create directory for deployment: [/opt/atlassian/jira/conf/Catalina/localhost]
2021-11-30 14:07:23,931+0000 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.
2021-11-30 14:07:24,146+0000 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]
****************
Jira starting...
****************
2021-11-30 14:07:24,413+0000 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]
___ Environment _____________________________
JIRA Build : 8.20.0#820000-sha1:12d32736019f23930cfd2092dd230e869932e04a
Build Date : Tue Oct 19 00:00:00 UTC 2021
JIRA Installation Type : Standalone
Application Server : Apache Tomcat/8.5.65 - Servlet API 3.1
Java Version : 11.0.11 - AdoptOpenJDK
Current Working Directory : /opt/atlassian/jira/bin
Maximum Allowable Memory : 2048MB
Total Memory : 384MB
Free Memory : 230MB
Used Memory : 154MB
Memory Pool: CodeHeap 'non-nmethods' : CodeHeap 'non-nmethods': init = 5828608(5692K) used = 1173760(1146K) committed = 5828608(5692K) max = 5828608(5692K)
Memory Pool: Metaspace : Metaspace: init = 0(0K) used = 28305704(27642K) committed = 29278208(28592K) max = -1(-1K)
Memory Pool: CodeHeap 'profiled nmethods' : CodeHeap 'profiled nmethods': init = 33554432(32768K) used = 8092800(7903K) committed = 33554432(32768K) max = 265519104(259296K)
Memory Pool: Compressed Class Space : Compressed Class Space: init = 0(0K) used = 3081776(3009K) committed = 3407872(3328K) max = 1073741824(1048576K)
Memory Pool: G1 Eden Space : G1 Eden Space: init = 20971520(20480K) used = 122683392(119808K) committed = 236978176(231424K) max = -1(-1K)
Memory Pool: G1 Old Gen : G1 Old Gen: init = 381681664(372736K) used = 22036480(21520K) committed = 148897792(145408K) max = 2147483648(2097152K)
Memory Pool: G1 Survivor Space : G1 Survivor Space: init = 0(0K) used = 16777216(16384K) committed = 16777216(16384K) max = -1(-1K)
Memory Pool: CodeHeap 'non-profiled nmethods' : CodeHeap 'non-profiled nmethods': init = 33554432(32768K) used = 1790080(1748K) committed = 33554432(32768K) max = 265523200(259300K)
JVM Input Arguments : --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent=ALL-UNNAMED --add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED -Djava.util.logging.config.file=/opt/atlassian/jira/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms384m -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 -Xlog:gc*:file=/opt/atlassian/jira/logs/atlassian-jira-gc-%t.log:tags,time,uptime,level:filecount=5,filesize=20M -XX:+ExplicitGCInvokesConcurrent -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 = 8.20.0, Java Version = 11.0.11
___ Java System Properties _________________
atlassian.plugins.startup.options :
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
ignore.endorsed.dirs :
java.awt.graphicsenv : sun.awt.X11GraphicsEnvironment
java.awt.headless : true
java.awt.printerjob : sun.print.PSPrinterJob
java.class.version : 55.0
java.home : /opt/atlassian/jira/jre
java.io.tmpdir : /opt/atlassian/jira/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 : OpenJDK Runtime Environment
java.runtime.version : 11.0.11+9
java.specification.name : Java Platform API Specification
java.specification.vendor : Oracle Corporation
java.specification.version : 11
java.util.logging.config.file : /opt/atlassian/jira/conf/logging.properties
java.util.logging.manager : org.apache.juli.ClassLoaderLogManager
java.vendor : AdoptOpenJDK
java.vendor.url : https://adoptopenjdk.net/
java.vendor.url.bug : https://github.com/AdoptOpenJDK/openjdk-support/issues
java.vendor.version : AdoptOpenJDK-11.0.11+9
java.version : 11.0.11
java.version.date : 2021-04-20
java.vm.compressedOopsMode : 32-bit
java.vm.info : mixed mode
java.vm.name : OpenJDK 64-Bit Server VM
java.vm.specification.name : Java Virtual Machine Specification
java.vm.specification.vendor : Oracle Corporation
java.vm.specification.version : 11
java.vm.vendor : AdoptOpenJDK
java.vm.version : 11.0.11+9
jdk.debug : release
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 : 5.4.0-1031-azure
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
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-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-*.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.dir : /opt/atlassian/jira/bin
user.home : /home/jira
user.language : en
user.name : jira
user.timezone : Etc/UTC
30-Nov-2021 14:07:24.731 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
30-Nov-2021 14:07:24.745 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
2021-11-30 14:07:24,963+0000 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira/dbconfig.xml
30-Nov-2021 14:07:24.973 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 8201 ms
2021-11-30 14:07:25,063+0000 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Trying to get encrypted password from xml and decrypt it
2021-11-30 14:07:25,073+0000 JIRA-Bootstrap INFO [c.a.j.config.database.DatabaseConfigHandler] Database password decryption not performed.
Tue Nov 30 14:07:25 UTC 2021 WARN: Establishing SSL connection without server's identity verification is not recommended. According to MySQL 5.5.45+, 5.6.26+ and 5.7.6+ requirements SSL connection must be established by default if explicit option isn't set. For compliance with existing applications not using SSL the verifyServerCertificate property is set to 'false'. You need either to explicitly disable SSL by setting useSSL=false, or set useSSL=true and provide truststore for server certificate verification.
2021-11-30 14:07:25,954+0000 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Running Jira startup checks.
2021-11-30 14:07:25,954+0000 JIRA-Bootstrap FATAL [c.a.jira.startup.JiraStartupLogger] Startup check failed. Jira will be locked.
2021-11-30 14:07:26,062+0000 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Startup is complete. Jira is ready to serve.
2021-11-30 14:07:26,067+0000 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 66 MiB. Committed: 451 MiB. Max: 2048 MiB
Non-heap memory : Used: 52 MiB. Committed: 112 MiB. Max: 1536 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 118 MiB. Committed: 563 MiB. Max: 3584 MiB
---------------------------------------------------------------------------------