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Assert valid neighbors before stitching
This turned out to be a red herring but it's a good idea in general.
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src/mesh/unstructured_mesh.C

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@@ -1773,6 +1773,11 @@ void UnstructuredMesh::stitching_helper (const MeshBase * other_mesh,
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bool enforce_all_nodes_match_on_boundaries,
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bool skip_find_neighbors)
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{
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#ifdef DEBUG
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// We rely on neighbor links here
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MeshTools::libmesh_assert_valid_neighbors(*this);
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#endif
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// FIXME: make distributed mesh support efficient.
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// Yes, we currently suck.
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MeshSerializer serialize(*this);

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