To set JAVA_OPTS options which you want to set additionally while running the tomcat should be set inside set <tomcat home>/bin$setenv.sh if this file is not present then create one and set variable JAVA_OPTS="-Dsomething $JAVA_OPTS". If you have to set some variables while only starting the tomcat then you need to set those variables to CATALINA_OPTS rather than JAVA_OPTS.
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