Synonym for "utilize" that means "to use without waste"
Two options are exploit and harness:
exploit NOAD
make full use of and derive benefit from (a resource):
500 companies sprang up to exploit this new technologyharness Macmillan
utilize:
harness the computer's potential
Both words, especially exploit, fit your bill:
The program exploited/harnessed the supercomputer's resources.
You could go with exhaust or deplete.