You observation is correct. In the current implementation, we do not aggregate past data. For example, suppose the current time is 15:20. The server receives a measurement report with data having timestamps from the 13:00 hour. We will persist those metrics, but they won't get aggregated. That's the bad news. The good news is that we will handle this in RHQ 4.12. The changes are described at https://docs.jboss.org/author/display/RHQ/Aggregation+Schema+Changes.
Does it have some sort of performance impact if this happens? I'm wondering if I have late collections (all the time) for a schedule that it may make aggregation take longer. I'm guessing not, but just confirming.
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The late collections will make the aggregation take longer simply because this data would not have been aggregated at all previously. We only aggregate the late data for those measurement schedules reporting late data. The performance impact therefore depends on the number of measurement schedules having late data.