A periodic checkpoint means that the job will checkpoint itself, but then it will immediately continue running after the checkpoint has completed. condor_vacate, on the other hand, will result in the job exiting (vacating) after it checkpoints.
If the job being checkpointed is running in the Standard Universe, the job is checkpointed and then just continues running on the same machine. If the job is running in the Vanilla Universe, or there is currently no Condor job running on that host, then condor_checkpoint has no effect.
Normally there is no need for the user or administrator to explicitly run condor_checkpoint. Checkpointing a running condor job is normally handled automatically by Condor by following the policies stated in Condor's configuration files.
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See the Condor Version 6.0 Manual for additional notices.