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Alerting system for Munin

I am very satisfied with munin as a monitoring tool (as I only have a simple 2-server setup) but its alerting system is very annoying as you can only configure it to send an e-mail upon every check ...
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How to monitor and alert on a program's resource usage Server 2008?

We have a program that at various times utilizes very high CPU and memory. I would like to create a collection of performance logs of this particular application to see a historical trend over time ...