I'm trying to parallelize the running of the test inputs

Is it possible to run the test cases in parallel when using ‘ctest’?

ctest -jN where N is the number of threads to use.

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This seems to run N tests at once for N threads. Is it possible to use N threads for each test case?

Not at the moment; however, no test job should be long enough such that it would sufficiently benefit from threading.

If you want to use as many processors as your computer has available:

ctest -j`getconf _NPROCESSORS_ONLN`
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Some of the test cases do a little bit of disk I/O. Running a large number of them at once on a machine might actually slow things down if the different test jobs start fighting for the disk.