Without seeing the code, the advice can only be general:
You should investigate on which line of the 100MB-file your script fails. Using 100% of the CPU is an indication that the program enters an "endless" loop. Once you know the last line the script processed normally - and, more importantly, the line where you script hangs - you can investigate why it hangs... and implement countemeasures.
If you want the help of us monks, this information is essential (which line won't be processed, which code do you use to process that file)
All the best, Rata
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