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Currently the incremental root stage has a low threshold, because it accumulates lots of data in memory and cannot process large ranges at once. When the number of blocks we need to catch up exceeds this threshold, we do a clean merkle root calculation, which is often slower than if we had run the incremental stage.
The incremental stage branch is here
reth/crates/stages/stages/src/stages/merkle.rs
Lines 253 to 266 in 5c64d59
We could instead do this in a loop with a fixed range each time, until we catch up. This way we could avoid doing the clean merkle stage
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