Segfault on large multi-column Iceberg upserts

pyiceberg.table.upsert_util.create_match_filter から開始し、iceberg_upsert_segfault_repro.py を実行して複数列 upsert のクラッシュを再現し、pyiceberg-stacktrace.txt を使って正規化パスを確認します。完全一致を維持したままキーのタプルをより少ない選言にまとめ、その後、合成した低カーディナリティのケースで segfault が発生しなくなったことを検証し、高カーディナリティに関する注意点を確認します。

Apache Iceberg version

0.11.0 (latest release)

Please describe the bug 🐞

When upserting into an Iceberg table, PyIceberg first scans the target table to
find which existing rows match the source rows' key columns. It builds that
"matching" predicate in pyiceberg.table.upsert_util.create_match_filter:

• For a single join column it emits one flat In(col, [v1, v2, ...]).
  PyArrow lowers this to a single is_in compute node, no matter how many
  values it contains — so single-column upserts of huge tables are fine.

• For a multi-column key it instead emits one disjunct per distinct key
  tuple::

  Or(And(c1 == v1, c2 == w1),
     And(c1 == v2, c2 == w2),
     ...)                          # ONE disjunct PER ROW
  

PyIceberg builds that Or as a balanced tree, so the Python side copes.
But when the expression is handed to PyArrow's dataset scanner as a filter, the
C++ expression engine canonicalises it: Dataset::GetFragments calls
SimplifyWithGuarantee → Canonicalize, which flattens the associative
or_kleene chain and then recurses over it. With tens of thousands of
disjuncts that recursion overflows the C++ call stack and the process
segfaults (SIGSEGV) — typically after several minutes of work, with a
backtrace full of arrow::compute::Canonicalize / ModifyExpression
frames.

Reference: https://github.com/apache/iceberg-python/issues/3272

Note that apache/iceberg-python#3448 addresses a different upsert segfault (a
per-batch Acero re-filter in _task_to_record_batches, mostly observed on
Apple Silicon). It does not touch the GetFragments canonicalisation path
exercised here, so it does not help with this crash.

The fix

Produce a predicate that matches exactly the same rows, but with far fewer
disjuncts. Group the key tuples and emit a single In over whichever column
collapses to the fewest distinct "prefix" combinations (choosing that column
makes the result independent of the caller's column ordering)::

Or(And(c1 == v1, c2 IN [w, x, y]),
   And(c1 == v2, c2 IN [z]),
   ...)                            # one disjunct per distinct PREFIX

The disjunct count drops from "number of rows" to "number of distinct prefix
values". In the synthetic data below there are 50 000 unique ids spread over
just 50 group values, so the predicate shrinks from 50 000 disjuncts to 50 —
shallow enough that PyArrow's canonicaliser no longer overflows.

Caveat

This helps whenever at least one key column is low-cardinality (or, equivalently,
one column is near-unique and can be folded into the In). A genuinely
high-cardinality composite key — where every column is near-unique and all of
them are needed to identify a row — still produces roughly one disjunct per row
even after grouping, and can still overflow. For that pathological case the
only robust option is to upsert in smaller batches.

pyiceberg-stacktrace.txt

iceberg_upsert_segfault_repro.py

Willingness to contribute

• I can contribute a fix for this bug independently
• I would be willing to contribute a fix for this bug with guidance from the Iceberg community
• I cannot contribute a fix for this bug at this time