Issue with test_censored.py: IndexError: index X is out of bounds for axis 0 with size X

Development
1

I am working on PyMC’s codebase and trying to debug test failures in tests/distributions/test_censored.py. The test case test_censored_workflow fails with an IndexError.

Error Message:
IndexError: index 510 is out of bounds for axis 0 with size 510

This happens when running pm.sample(tune=240, draws=270, discard_tuned_samples=True, random_seed=rng, max_treedepth=10).

Things I Tried:

  1. Adjusted tune and draws values (e.g., tune=250, draws=250, tune=240, draws=270), but the issue persists.
  2. Set discard_tuned_samples=True to avoid exceeding buffer size.
  3. Used max_treedepth=10 to limit tree depth in NUTS.
  4. Looked into pymc.backends.ndarray.py, where the error occurs in record().

Questions:

  • Why does index 510 exceed the expected size, even though tune + draws = 510?
  • Could this be related to how the NDArray backend handles sample storage?
  • Any suggestions on debugging this further?
2

Why are you running that specific test with those specific settings? You can try reproducing the issue in another environment such as Google colab to grt some idea of whether it’s specific to your installation/machine

3

Hi RicardoV94,

Thanks for your reply! I stumbled on this while exploring tests after submitting PR #7736 (fixing #7519). My setup is Windows 10, Python 3.10, pymc_env with scipy=1.9.3, pytest, from AnInnovativeCoder/pymc, branch fix-multiprocessing-pyodide.

I ran pytest tests/distributions/test_censored.py -v and got 4/5 failures with pytensor.link.c.exceptions.CompileError: Compilation failed (return status=1), not the IndexError you mentioned. Log at C:\Users\Pallaxsys\AppData\Local\Temp\pytensor_compilation_error_oyburvz2 shows [insert key error, e.g., “cl.exe not found”]. One test passed, suggesting partial functionality.

Could my Windows/PyTensor setup be masking the IndexError? I’ll test in Colab next. This mirrors my test_smc.py failures (14/15, same CompileError). Any settings (e.g., PYTENSOR_FLAGS) to try?

Eager to debug this as a next contribution!

Cheers,
Atul Boyal

4

Hi RicardoV94,

Per your Colab suggestion: Locally (Windows 10, Python 3.10, pymc_env, scipy=1.9.3), test_censored.py had 4/5 failures with pytensor.link.c.exceptions.CompileError (32-bit MinGW issue).

In Colab (PyMC 5.21.1), test_censored.py passed all tests—no IndexError. Updated PR #7736 for #7519. Fixing local setup with 64-bit MinGW.

Could the IndexError be branch-specific?

Cheers,
Atul Boyal

5

Hi RicardoV94,

Update per your Colab suggestion: Locally (Windows 10, Python 3.10, pymc_env, scipy=1.9.3), pytest tests/distributions/test_censored.py -v had 4/5 failures with pytensor.link.c.exceptions.CompileError (32-bit MinGW issue).

Installed 64-bit m2w64-gcc—now all 5 tests pass locally, matching Colab (PyMC 5.21.1) results. No IndexError seen. PR #7736 for #7519 is updated.

Could your IndexError be branch- or setting-specific? Any Windows tips to share?

Cheers,
Atul Boyal

6

Did you use conda to install pytensor? sounds like you don’t have the compilers set correctly

7

Hi RicardoV94,

Apologies for the delayed response. I installed PyTensor using conda. If there’s a compiler issue, could you guide me on setting it up correctly? I’d appreciate any pointers on resolving this.

Thanks,
Atul Boyal