monitor cpu usage while app is running (windows cygwin)

I am working on a parallel processing server/client app with a multi-threaded server and several data processing clients, each their own process. I am trying to optimize some of the parameters, such as the size of the chunks that are read, processed, and output, and also some of the timeout values and such. I can track the time to finish a given task well enough, but it would be really nice to be able to track the cpu use. When CPU use is near 100% (on all cores) for the entire run, that is a good sign. I have noticed that with some combinations of parameters, CPU drops quite a bit for long stretches, which is not such a good sign. This app process large input files (2.5GB-65GB so far) and needs to be stable for long periods of time.

Other than sitting and staring at the task manager all day, is there a good way to track/log the CPU usage over runs that take many hours? I know that there are some apps like Everest that chart CPU use, but it would be nice to have something that would write to the same log file I am already using for other program output.

Suggestions would be appreciated.

LMHmedchem