Yourkit & Tomcat webapp on Fedora

Yourkit is a great tool for profiling Java applications.  I'm using it to do some profiling on our webapp that is deployed in a Tomcat on a remote server (virtual machine on Rackspace).  I've found that Yourkit is really simple and intuitive to use and set up, for the most part.

The only issue I've had was getting it set up on the remote server to hook my local GUI to.  Theoretically, it is a very simple process.  Download yourkit to the remote server, start up tomcat, and type the following at the command prompt:

/bin/yjp.sh -integrate

I've downloaded & installed the linux version into my /opt/ folder on my remote server.  My remote server is Fedora 14 64bit.  When I run the above command, I get the following prompts:

And here is where I run into a problem. Where is the tomcat startup.sh?? I do a search on the remote machine for the file and come up empty handed. I sift around online and come up empty handed.  Finally after trial and error, I find that the file that is used on Fedora for starting up tomcat is called:

/usr/sbin/tomcat6

I would have thought this would be the end of it.  Unfortunately, it looks the -integrate command munges the startup.sh to add an additional JAVA_OPTS to create the hooks for Yourkit.  And of course /usr/sbin/tomcat6 is not formatted how Yourkit is expecting the startup.sh to be formatted.  So no go.

The next option is to manually add the JAVA_OPTS to the file.  What I've done is add the following:

-agentpath:/opt/yjp-9.5.6/bin/linux-x86-64/libyjpagent.so=port=10001

after the {JAVA_OPTS} in the start block of the /usr/sbin/tomcat6 script (around line 30):

if [ "$1" = "start" ]; then
  ${JAVACMD} $JAVA_OPTS -agentpath:/opt/yjp-9.5.6/bin/linux-x86-64/libyjpagent.so=port=10001 $CATALINA_OPTS \
    -classpath "$CLASSPATH" \
    -Dcatalina.base="$CATALINA_BASE" \
    -Dcatalina.home="$CATALINA_HOME" \
    -Djava.endorsed.dirs="$JAVA_ENDORSED_DIRS" \
    -Djava.io.tmpdir="$CATALINA_TMPDIR" \
    -Djava.util.logging.config.file="${CATALINA_BASE}/conf/logging.properties" \
    -Djava.util.logging.manager="org.apache.juli.ClassLoaderLogManager" \
    org.apache.catalina.startup.Bootstrap start \
    >> ${CATALINA_BASE}/logs/catalina.out 2>&1 &
    if [ ! -z "$CATALINA_PID" ]; then
      echo $! > $CATALINA_PID
    fi

I have added an additional startup option to this, specifying the port to use.  Pay close attention when inserting this option and be sure that is a space between $JAVA_OPTS and [agentpath] as well as a space between [agentpath] and $CATALINA_OPTS.  Because I will not always want the agent attached (overhead and performance reasons), I created two copies of the tomcat6, a tomcat6_yourkit & tomcat6_orig (original tomcat6 file) that I copy to tomcat6 as needed to swap the configurations.

Finally, the last thing that needs to be done is to open up the port in the iptables file on the remote server to allow the connection to be made.

Summary:

1. Download the correct distribution for the remote server's platform to /opt/.
   
   (In my case I need the Linux distribution)

   [root@bakeYourkit opt]# wget http://www.yourkit.com/download/yjp-9.5.6-linux.tar.bz2

2. Extract the file.
   
   (In my case it is a tar.bz2, which I always forget how to do).
3. Make a copy of /usr/sbin/tomcat6 as /usr/sbin/tomcat6_orig
   

   [root@bakeYourkit ~]# cp /usr/sbin/tomcat6 /usr/sbin/tomcat6_orig

4. Edit /usr/sbin/tomcat6, save, and make a copy as /usr/sbin/tomcat6_yourkit
   

   [root@bakeYourkit ~]# vim /usr/sbin/tomcat6
   [root@bakeYourkit ~]# cp /usr/sbin/tomcat6 /usr/sbin/tomcat6_yourkit
   

5. Edit the iptables to listen to the port specified in the startup option above (in my example here, port number 10001).  See this post for information about editing the iptables file.
6. Restart tomcat to pick up the options.
7. On your local machine, start up yourkit and connect to the remote server:
   

Ta-da!  That's all.  Now if you want to switch off the agent, copy the original /usr/sbin/tomcat6_orig over the /usr/sbin/tomcat6 file.  There is definitely a nicer way to this, possibly by adding some environment variable and setting it to.  But this works for me.