Wow, very impressive!
You are absolutely right that in S5R3 we've started splitting the sky and each WU doing only one sky-patch, while in S5R2 each WU was "all-sky". We also think this is what caused the run-time variations as you suspected, and we're currently looking into how to best deal with that: either by adjusting the credits correctly to the actual runtime for a given skypatch, or by eliminating the run-time fluctuations.
Your visualization tool definitely looks very nice, and I'm happy to see it's been released under the GPL. A little how-to on how you produced those plots would be interesting indeed.

Visualization of S5R2 / S5R3 difference
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Apps which use the "old checkpointing" (all official Apps except Windows) keep an intermediate version of the (uncompressed) ASCII file in their slot directory while computing. Should be easy to copy it on-the-fly.
For Apps with the new checkpointing this information is stored in the (binary format) checkpoint file. I'll contact you privately, you're probably able to write a conversion tool faster than me (at least in Java).
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RE: What candidates may be
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It's impossible to tell from a single value. The last column just describes a significance value, not e.g. the strength of a GW. Furthermore candidates returned from the HierarchicalSearch code only describe a region in the sky, not a single pulsar. In any case needs further analysis of the returned results (not only one btw.) to tell.
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The higher the frequency
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The higher the frequency band, the finer we need to make the grid of templates. As by design each workunit has basically the same number of templates, in higher frequency bands there aren't enough to span a whole circle, so it's no wonder the most significant candidates of some workunits are limited to a certain area.
Whether such a spot actually is significant can only be told if taking the results of the adjacent workunits into comparison.
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RE: so still no reason to
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No, not at all. The are other possible reasons for sucha spot, even if it should come out statistically significant: It can be an instrumental artifact (harmonics of 60Hz are pretty noisy, for obvious reasons), or a fake signal we injected into the data to validate the analysis (yes we do).
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RE: I've found that
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You mean the classic server rain?
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