As I found out "on my own skin", setting fs.file-max in /etc/sysctl.conf is a BAD idea. It can render your system useless in one step. Please don't do it! If you did it, use the recovery mode to roll back the change. Also, currently I would only recommend doubling the limit (ie going from 1024 to 2048 or from 2048 to 4096) not going to the maximum value.
JProfiler is a great tool, however under 32 bit Ubuntu you can run into the problem of having a too low limit for open filehandles. This is a problem for JProfiler because it uses temporary files to work around the address-space limitation created by 32 bit (yeah, I know, I should upgrade to 64 bit - but 32 bit works great for now...)
To raise the maximum filehandle limit, do the following:
sudo gedit /etc/security/limits.conf # add the following two lines before the # End of file marker # yes, the initial star is also part of line, and you should add it * hard nofile 4096 * soft nofile 4096 sudo gedit /etc/sysctl.conf # restart your system
You can check if the changes were successful by using the ulimit command:
ulimit -n # it should print out 4096