After checking catalina.sh (for windows use the .bat versions of everything mentioned below)
# Do not set the variables in this script. Instead put them into a script
# setenv.sh in CATALINA_BASE/bin to keep your customizations separate.
# CATALINA_OPTS (Optional) Java runtime options used when the "start",
# "run" or "debug" command is executed.
# Include here and not in JAVA_OPTS all options, that should
# only be used by Tomcat itself, not by the stop process,
# the version command etc.
# Examples are heap size, GC logging, JMX ports etc
So create a setenv.sh under CATALINA_BASE/bin (same dir where the catalina.sh resides). Edit the file and set the arguments to CATALINA_OPTS
For e.g. the file would look like this if you wanted to change the heap size
Or in your case since you're using windows setenv.bat would be
set CATALINA_OPTS=-agentpath:C:\calltracer\jvmti\calltracer5.dll=traceFile-C:\calltracer\call.trace,filterFile-C:\calltracer\filters.txt,outputType-xml,usage-uncontrolled -Djava.library.path=C:\calltracer\jvmti -Dcalltracerlib=calltracer5
To clear the added options later just delete setenv.bat/sh