How can we kill and restart one partition without killing the second partition on the same server?
This is one of the drawbacks of running partitioned servers on Windows 2000. Windows 2000 is not designed for domaining, LPARs, etc., the way Unix is. Often a crash will leave orphan processes that cannot be killed, and it also does not release memory. Usually you will wind up rebooting the entire server to get back online.
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