I finally got the track length application working. Turns out it runs fine removing the database calls from the C application. These are replaced with a wrapper script written in Python (the first time I've used Python in such a way). The script makes all the database calls then uses fork-exec to run the length application. It seems to be working fine and is currently running in a screen session on one of STAR's machines.
You can view the Python script here. I will get onto packaging the rest of the source for your viewing some point in the near future.
EDIT: Full source code can be obtained here. Also, the application seems to use 100% CPU. I might want to put a sleep call in somewhere.
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