I'm trying to run yt's clump_find function directly on a Parthenon .rhdf file, but it crashes as soon as it starts generating the first contours. Has anyone run into this with native Parthenon data, and is there a way to fix it without regridding? Regridding avoids the crash, but it also reduces the resolution and loses detail.
2 Answers
This sounds like a possible edge case in yt’s contour-linking code rather than a problem with clump finding itself. The crash appears to occur in link_node_contours, possibly inside construct_boundary_relationships, where contour bounds, joins between objects, or the calculated contour count could be going wrong. Try rebuilding the relevant Cython code with optimization disabled, such as -O0, so bounds and indexing checks can expose the exact failure. A traceback showing the precise Cython line would help distinguish a bounds issue from a bad contour relationship.
Regridding can work around it, but it’s definitely not ideal when preserving the native resolution matters. I’d investigate the contour-linking routine first instead of treating the regridded result as the real fix.
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