Diagnosis
　　To assess whether the service is still running， run ps -A | grep jira.
　　Resolution
　　To kill the java process and stop JIRA，
　　Pass the -force parameter to catalina.sh as:
　　catalina.sh stop -force
　　Still not shutting down properly?
　　1、If the above results in an error， such as:
　　Kill failed: $CATALINA_PID not set
　　Add the following line of code to the top of your <JIRA-Installation-Directory>/bin/setenv.sh file (Standalone instance):
　　CATALINA_PID="<Change this to your preferred location>/id.pid"
　　export CATALINA_PID
　　Tomcat will automatically write its process id to id.pid in your specified path and kill its process with the -force parameter.
　　2、In addition to the above， you can try a custom script that runs shutdown.sh first before forcing Tomcat to shutdown. This script will sleep 60 seconds then look inside ./id.pid to check if Tomcat is still running. If Tomcat is still running， it will issue a catalina.sh stop -force.
　　3、Also， here you can find a script which forces JIRA to shutdown and deletes the lock file in the JIRA Home directory. It will look inside ./id.pid for the process ID and run catalina.sh stop -forcefor that process.
　　(info) Both scripts need to be saved in <JIRA install>/bin and assume id.pid is located in the same location.
　　Lets start by making sure there is no JIRA instance running. In order to do it so， please run the following command from your Terminal:
ps aux | grep jira
// as the output， you will find something similar to:
rafael           9176  24.6  2.2  3799364 182160 s001  U     5:14PM   0:06.10 /Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home/bin/java -Djava.util.logging.config.file=/<jira-home>/jira-6.2.4/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -XX:MaxPermSize=384m -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:+PrintGCDateStamps -XX:-OmitStackTraceInFastThrow -Djira.home=/var/www/ATLASSIAN/data/jira-6.2.4 -Djava.endorsed.dirs=/<jira-home>/jira-6.2.4/endorsed -classpath /<jira-home>/jira-6.2.4/bin/bootstrap.jar:/<jira-home>/jira-6.2.4/bin/tomcat-juli.jar -Dcatalina.base=/<jira-home>/jira-6.2.4 -Dcatalina.home=/<jira-home>/jira-6.2.4 -Djava.io.tmpdir=/<jira-home>/jira-6.2.4/temp org.apache.catalina.startup.Bootstrap start
rafael           9233   0.0  0.0  2432784    600 s001  S+    5:14PM   0:00.00 grep jira
// Please， kill the process as per following:
kill -9 9176
// where 9176 is the processID to my JIRA instance， in the example above mentioned
　　According to the above mentioned， your JAVA_HOME is pointing to JAVA JRE instead of JAVA JDK. Please， review where your Java JDK6 or JDK7 is installed and setup your JAVA_HOME as per Installing Java documentation.
　　After you have done that， go to <jira-home> directory and run the following from your terminal:
　　./bin/start-jira.sh
　　In case you continue on experiencing difficulties on starting up your JIRA instance， I would kindly advise you to open a Support ticket under (https://support.atlassian.com)
　　Kind regards，
　　Rafael