The CM-5 operates on a timesharing system which allows several users to use the system simultaneously. Each user process executes only on one partition and is given access to all the nodes in the partition during execution. Processes executing on different partitions may communicate with each other. Each control processor in the CM-5 runs the CMOST operating system which is an enhanced version of UNIX. Each processing node runs a micro-kernel of CMOST.
The following is an important artifact of the CM-5 operating system. Once a program has been loaded on a partition of the CM-5, it remains in the primary memory of the processing nodes until completion even if it is idle during someone else's time slice. Therefore, the amount of memory available at any time depends on all the programs loaded on the processing node at that time. This can affect both the scheduling and the performance of programs.