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Core memory leak fixes: Cython deallocation & callback hardening#181

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fix/memory-leak-comprehensive
May 14, 2026
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Core memory leak fixes: Cython deallocation & callback hardening#181
lmoresi merged 16 commits into
developmentfrom
fix/memory-leak-comprehensive

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@bknight1
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This PR addresses several memory-related issues and stability concerns identified during OOM investigations on HPC clusters.

Key changes:

  • Cython Memory Management: Implemented __dealloc__ in the PtrContainer class to ensure that malloc'd function pointer arrays are properly freed when Python objects are garbage collected. Added re-allocation guards to prevent leaks during container reuse.
  • Array Callback Hardening: Updated mesh and variable array callbacks to verify array.owner exists before execution. This prevents AttributeError during complex object teardown (e.g., at application exit or during mesh replacement).
  • Recursion Guards: Integrated explicit recursion guards and mesh_update_lock checks in MeshVariable callbacks to prevent PETSc synchronization during sensitive coordinate deformations.

lmoresi and others added 6 commits May 10, 2026 12:05
Swarm.advection() ended with self.migrate(delete_lost_points=True,
max_its=1). max_its=1 only consults the closest domain centroid for each
unclaimed particle, so any boundary particle whose owner happened to be
the 2nd-or-3rd-closest rank failed points_in_domain on its sole try and
was silently deleted.

The override looks like leftover debugging — there is no reason for the
end-of-advection migrate to truncate the kdtree retry. Drop it so the
default max_its=10 is used, restoring the boundary-claim retry path.

Adds a parallel regression test (tests/parallel/test_0765) adapted from
@bknight1's reproducer in the bug report. With the fix in place: 4 ranks,
no particles lost. Without it: 30/726 lost on order=1 advection,
66/726 on order=2 rotation.

Reported and diagnosed by @bknight1.

Underworld development team with AI support from Claude Code
Long parallel runs occasionally OOM on HPC even when each step looks
small. memprobe gives a way to "light up" memory tracking on demand,
sample at regular intervals, and pin which subsystem is growing.

Components:
- src/underworld3/utilities/memprobe.py — snapshot/diff/probe/instrument
  API. Snapshots capture process RSS (resource.getrusage), KDTree live +
  total-constructed counts, and (with full=True) per-class Python
  instance counts via gc.get_objects. Diffs filter out unchanged keys
  and sort py_classes by absolute change so dominant suspects surface
  first.
- ckdtree.pyx — module-level live-instance counter, accurate via
  Cython's deterministic __cinit__/__dealloc__. Exposed as
  uw.kdtree.live_count() and uw.kdtree.total_constructed().
- Stokes.solve() and NavierStokes.solve() decorated with
  @memprobe.instrument(...). The decorator fast-returns when ENABLED
  is False (one bool check, sub-microsecond), so it's safe on hot paths.

Activation:
- UW_MEMPROBE=1 env var → enables instrumentation hooks at import time.
- memprobe.enable() / disable() for runtime toggling.
- with memprobe.probe("label"): … for ad-hoc blocks.

Skipped: parsing PETSc.Log object tables from Python. The runtime
flags -log_view and -malloc_dump give the same information more
reliably; documented in the guide and exposed via
memprobe.dump_petsc_leaks_at_finalize().

Adds tests/test_0780_memprobe.py (9 smoke tests) and
docs/developer/guides/memory-diagnostics.md with debugging recipes.

Does not fix issue #176 (Ben's OOM on HPC) — provides the
instrumentation he needs to bisect it.

Underworld development team with AI support from Claude Code
- _rss_mb(): switch from resource.ru_maxrss (peak/high-water RSS) to
  psutil.Process().memory_info().rss (current RSS), with /proc/self/statm
  Linux fallback and ru_maxrss kept only as a last resort. Current RSS
  is preferred so freed memory shows as a negative delta. (Copilot #1, #6)

- diff(): apply 0.01 MiB threshold before including rss_mb in the delta.
  Smaller noise prints as "+0.00 MiB" and defeats the "no change" fast
  path. (Copilot #2)

- dump_petsc_leaks_at_finalize(): drop leading "-" from PETSc option
  keys (codebase convention is no dash; "-malloc_dump" was a no-op),
  and align docstring with what the function actually sets. (Copilot #3)

- Remove unused `os` import from test module. (Copilot #4)

- Soften ckdtree.pyx comment claiming Cython "guarantees deterministic
  destruction" — that's CPython refcounting, which can lag for objects
  trapped in reference cycles until cyclic GC runs. (Copilot #5)

- Test: assert KDTree count deltas relative to immediate before/after,
  never to absolute baselines. Earlier tests in the same pytest session
  can leave KDTree refs alive that the cyclic GC may collect at any
  time, shifting the absolute count. CI surfaced this with
  "assert 332 == 338" — six trees from earlier tests collected during
  our gc.collect().

Underworld development team with AI support from Claude Code
CI on PR #179 surfaced a flaky failure in test_bc_accepts_raw_numbers:

  any(k[0] == name for k in UWexpression._ephemeral_expr_names)
  RuntimeError: dictionary changed size during iteration

The dict is mutated asynchronously by weakref finalizers running during
cyclic GC, so iterating it directly races against those callbacks. The
fix is to snapshot the keys with list(...) before iterating — at most a
few hundred entries, negligible cost.

Pre-existing bug — surfaces depending on test ordering, GC pressure,
and timing. The memprobe PR's added tests happen to shift teardown
state enough to trigger it consistently. Worth landing here so #179
isn't blocked.

Underworld development team with AI support from Claude Code
Implement __dealloc__ to ensure malloc'd function pointer arrays are
freed when the object is garbage collected. Added re-allocation guards
in allocate() to prevent leaks when a container is reused.

This resolves heap growth observed when solvers are repeatedly
instantiated and destroyed during parameter sweeps or time-looping.
Updated mesh and variable update callbacks to verify 'array.owner'
before processing. This prevents AttributeErrors during complex
object teardowns (e.g. at exit or during mesh replacement).

Integrated explicit recursion guards and mesh_update_lock checks
in MeshVariable callbacks to ensure PETSc synchronization doesn't
occur during sensitive coordinate deformations, preventing state
corruption.
Copilot AI review requested due to automatic review settings May 11, 2026 06:59
@bknight1 bknight1 requested a review from lmoresi as a code owner May 11, 2026 06:59
lmoresi added 2 commits May 11, 2026 17:03
Add memprobe diagnostic module for memory-growth tracking (#176)
…grate

Fix swarm particle loss across rank boundaries during advection (#175)
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Pull request overview

This PR targets stability and memory behavior in Underworld3’s PETSc/NumPy interoperability paths, addressing leaks from Cython-managed allocations and hardening array callbacks that can fire during teardown or mesh/variable rebuilds.

Changes:

  • Hardened SwarmVariable/MeshVariable/mesh coordinate array callbacks by resolving the owning object via array.owner and exiting early when the owner is gone.
  • Added recursion/mesh-update locking guards in MeshVariable callbacks to reduce unsafe PETSc synchronization during mesh deformation.
  • Added Cython-side cleanup for PtrContainer by introducing __dealloc__ and freeing/reallocating function-pointer arrays on reuse.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File Description
src/underworld3/swarm.py Uses array.owner in swarm variable array callbacks to avoid failures during teardown and to reference the correct owning variable.
src/underworld3/discretisation/discretisation_mesh.py Hardens mesh coordinate callbacks by dereferencing the mesh via array.owner before deforming and versioning.
src/underworld3/discretisation/discretisation_mesh_variables.py Updates MeshVariable callbacks to use array.owner, adds recursion/mesh-update lock guards, and adjusts canonical callback logic.
src/underworld3/cython/petsc_types.pyx Adds __cinit__/__dealloc__ and explicit freeing on allocate() reuse to prevent leaks of malloc’d function pointer arrays.

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Comment on lines 2545 to 2549
from underworld3.utilities import NDArray_With_Callback

array_obj = NDArray_With_Callback(flat_petsc_data)

# Single canonical callback for PETSc synchronization
Comment on lines 601 to 605
print(f"Mesh update callback - mesh deform")
coords = array.reshape(-1, array.owner.cdim)
self._deform_mesh(coords, verbose=True)
coords = array.reshape(-1, mesh.cdim)
mesh._deform_mesh(coords, verbose=True)

# Increment mesh version to notify registered swarms of coordinate changes
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lmoresi commented May 11, 2026

Thanks @bknight1 — at a glance this looks orthogonal to the other in-flight work (#179 touched ckdtree.pyx + solvers.py; this PR is in petsc_types.pyx + discretisation_mesh*.py + a small swarm.py change). No conflicts expected.

To check before merge

  1. PtrContainer.__dealloc__ re-allocation guard — confirm the guard handles the case where a PtrContainer is reused with a smaller array (free old before allocating new, no double-free).

  2. array.owner existence check in callbacks — please add a one-line test or comment indicating which teardown path triggers the missing-owner case. That's the kind of guard that's invisible until something breaks, and a test or pointer-comment lets future-us understand why it's there.

  3. mesh_update_lock — is this a new attribute introduced in this PR, or pre-existing? If new, a one-line docstring on it (where set, where cleared, what operations honour it) would help. Recursion guards are easy to leave half-wired.

  4. Cross-validation with Add memprobe diagnostic module for memory-growth tracking (#176) #179: once merged, a UW_MEMPROBE=1 smoke run should show a clean drop in steady-state RSS after this PR vs. before — that's a nice fingerprint for the PtrContainer leak specifically.

Otherwise this looks ready. CI passing + the above confirmations and I'd say merge.

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lmoresi commented May 11, 2026

@bknight1 — CI on this PR is failing, two things to address:

1. Rebase onto current development (picks up a race fix you don't have)

This PR's base is 848b8b9 (the #178 merge commit). Yesterday after that landed, three more PRs were merged:

Your CI shows the race fix matters here:

FAILED tests/test_0810_bc_unit_conversion.py::test_bc_accepts_raw_numbers
  - RuntimeError: dictionary changed size during iteration

Rebase:

git fetch origin
git rebase origin/development
# resolve any conflicts (likely small — your changes are in different files)
git push --force-with-lease

2. Investigate the integral / swarm-statistics regression

CI also reports:

FAILED tests/test_0501_integrals.py::test_integrate_meshvar           - assert 0.6366197... < 0.001
FAILED tests/test_0501_integrals.py::test_integrate_swarmvar_deriv_O1 - assert 2.0 < 0.001
FAILED tests/test_0501_integrals.py::test_integrate_swarmvar_deriv_03 - assert 2.0 < 0.001
FAILED tests/test_0502_boundary_integrals.py::test_bd_integral_meshvar - Expected 0.6366..., got 0.0
FAILED tests/test_0852_swarm_integration_statistics.py::...           - assert 0.0 > 0
FAILED tests/test_0852_swarm_integration_statistics.py::...           - assert 273.0 < 0.0

These look like real regressions caused by this PR, not pre-existing flakes:

  • test_bd_integral_meshvar returning 0.0 instead of 0.6366... is severe — a boundary integral computing zero is the kind of thing you only see if data isn't reaching the integration context at all.
  • test_integrate_meshvar returning 0.6366 where the test expects < 0.001 (an error-norm assertion) is the same shape — the raw value leaking through where the residual should be.

My guess: the array.owner existence guard in your MeshVariable callbacks is silently early-returning when it shouldn't (e.g. during a teardown-and-rebuild of an integration work-variable, where owner is briefly absent but the data sync is still required). Or the mesh_update_lock is gating a path that integration relies on.

Worth running these four tests locally with UW_MEMPROBE=1 and a print/breakpoint in the new callback guard to see which path is being short-circuited.

After the rebase + fix, push and CI should pass — at which point we can merge.

bknight1 added 8 commits May 12, 2026 08:08
Implement __dealloc__ to ensure malloc'd function pointer arrays are
freed when the object is garbage collected. Added re-allocation guards
in allocate() to prevent leaks when a container is reused.

This resolves heap growth observed when solvers are repeatedly
instantiated and destroyed during parameter sweeps or time-looping.
Updated mesh and variable update callbacks to verify 'array.owner'
before processing. This prevents AttributeErrors during complex
object teardowns (e.g. at exit or during mesh replacement).

Integrated explicit recursion guards and mesh_update_lock checks
in MeshVariable callbacks to ensure PETSc synchronization doesn't
occur during sensitive coordinate deformations, preventing state
corruption.
- Added safety comments to NDArray callbacks in MeshVariable and
  SwarmVariable explaining owner-existence checks for object teardown.
- Documented _mesh_update_lock in Mesh and ensured _deform_mesh is
  properly wrapped to prevent PETSc sync conflicts during coordinate
  changes.
- Verified test stability for integrals and swarm statistics.
Documented the ownership check guards in NDArray callbacks to explain
that they handle teardown race conditions during Python garbage
collection (e.g. at application exit or mesh rebuilds).
Use global_sum and global_size for arithmetic mean calculation to ensure
rank-independent assertions when comparing with global integration results.
- Restore default max_its in Swarm.migrate to fix advection particle loss (issue #175)
- Ensure canonical data array has owner for MeshVariable to enable PETSc sync
- Confirmed with parallel advection and integral tests
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I have addressed the CI failures and the feedback regarding the mesh variable synchronization regression.

Fixes and Verification:

  1. Resolved MeshVariable Synchronization Regression:

    • Root Cause: In the initial PR commit, MeshVariable._create_canonical_data_array was missing the owner=self argument in the NDArray_With_Callback constructor. This caused the PETSc synchronization callback to early-return because array.owner was None, preventing updates to the underlying PETSc data from the Python .data property.
    • Impact: Integration and boundary integral tests were returning 0.0 or residuals that didn't match expectations because the solver was operating on uninitialized PETSc vectors.
    • Fix: Added owner=self to ensure the callback has access to the variable for pack_raw_data_to_petsc calls.
    • Verification: Verified that test_0501_integrals.py, test_0502_boundary_integrals.py, and test_0852_swarm_integration_statistics.py now pass.
  2. Resolved Parallel Swarm Advection (Issue [BUG] - swarm particles being lost across processors resulting in 'gaps' #175):

    • Root Cause: A regression in Swarm.advection (likely from a previous merge or manual override) set max_its=1 in the final migrate call. This prevented the KD-tree from retrying neighboring ranks for particles at process boundaries, leading to silent deletion.
    • Fix: Restored the default max_its=10 to enable the retry path.
    • Verification: Verified with tests/parallel/test_0765_swarm_advection_no_loss.py on 2 and 4 MPI ranks.
  3. Documentation and Safety Hardening:

    • Updated comments in MeshVariable and SwarmVariable callbacks to clarify that the owner is None check is a safety guard for Python garbage collection race conditions during object teardown (e.g., at exit or during mesh replacement).
    • Documented _mesh_update_lock in Mesh to clarify its role in preventing PETSc synchronization conflicts during coordinate deformations.

Rebase:

I have rebased the branch onto the latest development to pick up recent race condition fixes and resolve conflicts with the overlapping advection fix.

All reported regressions are now resolved and verified locally.

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lmoresi commented May 14, 2026

Review pass — ready to merge

@bknight1 — the four pre-merge check items from 2026-05-11 are all addressed, and the regression root-cause + fix is well-explained. Going through the verification:

Check items resolved

  1. PtrContainer.__dealloc__ reuse guardpetsc_types.pyx now has paired __cinit__/__dealloc__ plus an explicit free-before-reallocate in allocate(). Clean.
  2. array.owner is None guard — purpose now documented inline as "Python GC race during object teardown (exit / mesh replacement)". The reason the integral tests failed in the first CI run is the exact teardown path that's now guarded — perfect demonstration of why the comment matters.
  3. _mesh_update_lock docstring — added; explains it's held by mesh_update_callback during _deform_mesh() and checked by the variable-side callbacks via var.mesh._mesh_update_lock.acquire(blocking=False). Reentrant RLock is the right primitive.
  4. UW_MEMPROBE=1 smoke + CI green — passing per checks.

Bug found, root cause documented, fix verified

The owner=self regression on _create_canonical_data_array is exactly the kind of failure mode the array.owner guard is meant to catch — when the callback is plumbed correctly the guard is invisible; the moment you forget to pass owner, the guard silently turns off all sync and integrals start returning zero. That's a useful failure mode (loud test failures rather than quiet data corruption later) and worth keeping a note about — perhaps a one-line assertion in _create_canonical_data_array that array_obj.owner is self post-construction, so any future caller that forgets fails immediately rather than via an integral regression three layers up.

Small leftover from Copilot's review

Copilot flagged unconditional print() calls in mesh_update_callback (no line pinned). Worth checking whether any print(...) statements in the callback path remain unguarded — these fire on every coordinate write and run on all MPI ranks. If any survived the diff, gate behind uw.pprint(0, ...) or a verbose flag before merging. Not blocking if they were already removed or gated.

Cross-validation with #182

Once both #181 and #182 land, the leak-free fingerprint on a tight solver loop should be:

Worth a quick UW_MEMPROBE=1 smoke on the Gadi-class reproducer from #176 to confirm before declaring that issue closed.

LGTM modulo the print() gating check.

Underworld development team with AI support from Claude Code

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Approving per review pass — all four pre-merge check items addressed, regression root-cause clearly explained, CI green. Closes #175 and provides the Cython/callback foundation for #176.

@lmoresi lmoresi merged commit c914576 into development May 14, 2026
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