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Test suite failure on 32bit architectures #133

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avalentino opened this issue Aug 14, 2022 · 6 comments · Fixed by #136
Closed

Test suite failure on 32bit architectures #133

avalentino opened this issue Aug 14, 2022 · 6 comments · Fixed by #136
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@avalentino
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=== python3.10 ===
============================= test session starts ==============================
platform linux -- Python 3.10.5, pytest-7.1.2, pluggy-1.0.0+repack
rootdir: /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src, configfile: pyproject.toml
collected 8429 items / 48 deselected / 8381 selected

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=================================== FAILURES ===================================
_______ test_groupby_reduce_nans[flox-2-groups0-expected_shape0-chunks1] _______
../build.D7c/src/tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:287: in assert_eq
    raise AssertionError(f"a and b have different dtypes: (a: {adt}, b: {bdt})")
E   AssertionError: a and b have different dtypes: (a: int32, b: int64)
_____ test_groupby_reduce_nans[flox-None-groups1-expected_shape1-chunks1] ______
../build.D7c/src/tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:287: in assert_eq
    raise AssertionError(f"a and b have different dtypes: (a: {adt}, b: {bdt})")
E   AssertionError: a and b have different dtypes: (a: int32, b: int64)
_____ test_groupby_reduce_nans[flox-None-groups2-expected_shape2-chunks1] ______
../build.D7c/src/tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:287: in assert_eq
    raise AssertionError(f"a and b have different dtypes: (a: {adt}, b: {bdt})")
E   AssertionError: a and b have different dtypes: (a: int32, b: int64)
______ test_groupby_reduce_nans[numpy-2-groups0-expected_shape0-chunks1] _______
../build.D7c/src/tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:287: in assert_eq
    raise AssertionError(f"a and b have different dtypes: (a: {adt}, b: {bdt})")
E   AssertionError: a and b have different dtypes: (a: int32, b: int64)
_____ test_groupby_reduce_nans[numpy-None-groups1-expected_shape1-chunks1] _____
../build.D7c/src/tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:287: in assert_eq
    raise AssertionError(f"a and b have different dtypes: (a: {adt}, b: {bdt})")
E   AssertionError: a and b have different dtypes: (a: int32, b: int64)
_____ test_groupby_reduce_nans[numpy-None-groups2-expected_shape2-chunks1] _____
../build.D7c/src/tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:287: in assert_eq
    raise AssertionError(f"a and b have different dtypes: (a: {adt}, b: {bdt})")
E   AssertionError: a and b have different dtypes: (a: int32, b: int64)
=============================== warnings summary ===============================
../build.D7c/src/tests/__init__.py:3
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/tests/__init__.py:3: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
    from distutils import version

../../../../usr/lib/python3/dist-packages/numpy_groupies/utils_numpy.py:101
  /usr/lib/python3/dist-packages/numpy_groupies/utils_numpy.py:101: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe. 
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    'array': np.object,

tests/test_core.py: 1800 warnings
  /usr/lib/python3/dist-packages/dask/array/core.py:1593: FutureWarning: The `numpy.expand_dims` function is not implemented by Dask array. You may want to use the da.map_blocks function or something similar to silence this warning. Your code may stop working in a future release.
    warnings.warn(

tests/test_core.py: 12 warnings
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/tests/test_core.py:182: RuntimeWarning: Mean of empty slice
    expected = getattr(np, func)(array[..., ~nanmask], axis=-1, **kwargs)

tests/test_core.py: 15 warnings
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/flox/aggregate_flox.py:105: RuntimeWarning: invalid value encountered in true_divide
    out /= nanlen(group_idx, array, size=size, axis=axis, fill_value=0)

tests/test_core.py: 82 warnings
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/flox/aggregations.py:258: RuntimeWarning: invalid value encountered in true_divide
    finalize=lambda sum_, count: sum_ / count,

tests/test_core.py: 12 warnings
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/tests/test_core.py:182: RuntimeWarning: Degrees of freedom <= 0 for slice.
    expected = getattr(np, func)(array[..., ~nanmask], axis=-1, **kwargs)

tests/test_core.py: 292 warnings
  /usr/lib/python3/dist-packages/numpy_groupies/aggregate_numpy.py:156: RuntimeWarning: invalid value encountered in true_divide
    means = sums.astype(dtype) / counts

tests/test_core.py: 264 warnings
  /usr/lib/python3/dist-packages/numpy_groupies/aggregate_numpy.py:157: RuntimeWarning: invalid value encountered in true_divide
    ret = np.bincount(group_idx, (a - means[group_idx]) ** 2,

tests/test_core.py: 216 warnings
  /usr/lib/python3/dist-packages/dask/array/numpy_compat.py:40: RuntimeWarning: invalid value encountered in true_divide
    x = np.divide(x1, x2, out)

tests/test_core.py: 400 warnings
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/flox/aggregations.py:267: RuntimeWarning: invalid value encountered in true_divide
    result = (sumsq - (sum_**2 / count)) / (count - ddof)

tests/test_core.py: 12 warnings
  /usr/lib/python3/dist-packages/numpy/lib/nanfunctions.py:1670: RuntimeWarning: Degrees of freedom <= 0 for slice.
    var = nanvar(a, axis=axis, dtype=dtype, out=out, ddof=ddof,

tests/test_core.py: 38 warnings
  /usr/lib/python3/dist-packages/dask/array/reductions.py:567: RuntimeWarning: All-NaN slice encountered
    return np.nanmax(x_chunk, axis=axis, keepdims=keepdims)

tests/test_core.py: 24 warnings
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/tests/test_core.py:182: RuntimeWarning: All-NaN slice encountered
    expected = getattr(np, func)(array[..., ~nanmask], axis=-1, **kwargs)

tests/test_core.py: 140 warnings
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/flox/core.py:816: RuntimeWarning: All-NaN slice encountered
    result = getattr(np, combine)(array, axis=axis[:-1] + (DUMMY_AXIS,), keepdims=True)

tests/test_core.py: 38 warnings
  /usr/lib/python3/dist-packages/dask/array/reductions.py:538: RuntimeWarning: All-NaN slice encountered
    return np.nanmin(x_chunk, axis=axis, keepdims=keepdims)

tests/test_core.py: 22 warnings
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/flox/aggregate_flox.py:96: RuntimeWarning: divide by zero encountered in true_divide
    out /= nanlen(group_idx, array, size=size, axis=axis, fill_value=0)

tests/test_core.py: 46 warnings
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/flox/aggregations.py:249: RuntimeWarning: invalid value encountered in true_divide
    finalize=lambda sum_, count: sum_ / count,

tests/test_core.py: 22 warnings
  /tmp/autopkgtest-lxc.86e5wyro/downtmp/build.D7c/src/flox/aggregate_flox.py:105: RuntimeWarning: divide by zero encountered in true_divide
    out /= nanlen(group_idx, array, size=size, axis=axis, fill_value=0)

tests/test_core.py: 20 warnings
  /usr/lib/python3/dist-packages/dask/array/reductions.py:991: RuntimeWarning: All-NaN slice encountered
    vals = func(x, axis=arg_axis, keepdims=True)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED ../build.D7c/src/tests/test_core.py::test_groupby_reduce_nans[flox-2-groups0-expected_shape0-chunks1]
FAILED ../build.D7c/src/tests/test_core.py::test_groupby_reduce_nans[flox-None-groups1-expected_shape1-chunks1]
FAILED ../build.D7c/src/tests/test_core.py::test_groupby_reduce_nans[flox-None-groups2-expected_shape2-chunks1]
FAILED ../build.D7c/src/tests/test_core.py::test_groupby_reduce_nans[numpy-2-groups0-expected_shape0-chunks1]
FAILED ../build.D7c/src/tests/test_core.py::test_groupby_reduce_nans[numpy-None-groups1-expected_shape1-chunks1]
FAILED ../build.D7c/src/tests/test_core.py::test_groupby_reduce_nans[numpy-None-groups2-expected_shape2-chunks1]
= 6 failed, 4164 passed, 1735 skipped, 48 deselected, 2475 xfailed, 1 xpassed, 3457 warnings in 307.36s (0:05:07) =
@dcherian
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Thanks for the bug report @avalentino

can you change intp to int64 here and try the tests again please?

flox/flox/aggregations.py

Lines 229 to 230 in e405517

dtypes=np.intp,
final_dtype=np.intp,

If that works, a pull request with that change would be very welcome

@dcherian dcherian added the bug Something isn't working label Aug 15, 2022
@avalentino
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Dear @dcherian, unfortunately it still does not work, but th error seems to be a little bit different now:

$ python3 -m pytest -k test_groupby_reduce_nans
=========================================================== test session starts ===========================================================
platform linux -- Python 3.10.6, pytest-7.1.2, pluggy-1.0.0+repack
rootdir: /home/antonio/debian/git/flox, configfile: pyproject.toml
collected 8429 items / 8411 deselected / 18 selected                                                                                      

tests/test_core.py .F.F.F.F.F.Fxxxxxx                                                                                               [100%]

================================================================ FAILURES =================================================================
____________________________________ test_groupby_reduce_nans[flox-2-groups0-expected_shape0-chunks1] _____________________________________
tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:282: in assert_eq
    a, adt, a_meta, a_computed = _get_dt_meta_computed(
/usr/lib/python3/dist-packages/dask/array/utils.py:244: in _get_dt_meta_computed
    x = _check_chunks(x)
/usr/lib/python3/dist-packages/dask/array/utils.py:225: in _check_chunks
    assert chunk.dtype == x.dtype
E   AssertionError
___________________________________ test_groupby_reduce_nans[flox-None-groups1-expected_shape1-chunks1] ___________________________________
tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:282: in assert_eq
    a, adt, a_meta, a_computed = _get_dt_meta_computed(
/usr/lib/python3/dist-packages/dask/array/utils.py:244: in _get_dt_meta_computed
    x = _check_chunks(x)
/usr/lib/python3/dist-packages/dask/array/utils.py:225: in _check_chunks
    assert chunk.dtype == x.dtype
E   AssertionError
___________________________________ test_groupby_reduce_nans[flox-None-groups2-expected_shape2-chunks1] ___________________________________
tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:282: in assert_eq
    a, adt, a_meta, a_computed = _get_dt_meta_computed(
/usr/lib/python3/dist-packages/dask/array/utils.py:244: in _get_dt_meta_computed
    x = _check_chunks(x)
/usr/lib/python3/dist-packages/dask/array/utils.py:225: in _check_chunks
    assert chunk.dtype == x.dtype
E   AssertionError
____________________________________ test_groupby_reduce_nans[numpy-2-groups0-expected_shape0-chunks1] ____________________________________
tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:282: in assert_eq
    a, adt, a_meta, a_computed = _get_dt_meta_computed(
/usr/lib/python3/dist-packages/dask/array/utils.py:244: in _get_dt_meta_computed
    x = _check_chunks(x)
/usr/lib/python3/dist-packages/dask/array/utils.py:225: in _check_chunks
    assert chunk.dtype == x.dtype
E   AssertionError
__________________________________ test_groupby_reduce_nans[numpy-None-groups1-expected_shape1-chunks1] ___________________________________
tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:282: in assert_eq
    a, adt, a_meta, a_computed = _get_dt_meta_computed(
/usr/lib/python3/dist-packages/dask/array/utils.py:244: in _get_dt_meta_computed
    x = _check_chunks(x)
/usr/lib/python3/dist-packages/dask/array/utils.py:225: in _check_chunks
    assert chunk.dtype == x.dtype
E   AssertionError
__________________________________ test_groupby_reduce_nans[numpy-None-groups2-expected_shape2-chunks1] ___________________________________
tests/test_core.py:507: in test_groupby_reduce_nans
    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
/usr/lib/python3/dist-packages/dask/array/utils.py:282: in assert_eq
    a, adt, a_meta, a_computed = _get_dt_meta_computed(
/usr/lib/python3/dist-packages/dask/array/utils.py:244: in _get_dt_meta_computed
    x = _check_chunks(x)
/usr/lib/python3/dist-packages/dask/array/utils.py:225: in _check_chunks
    assert chunk.dtype == x.dtype
E   AssertionError
============================================================ warnings summary =============================================================
tests/__init__.py:3
  /home/antonio/debian/git/flox/tests/__init__.py:3: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
    from distutils import version

../../../../../usr/lib/python3/dist-packages/numpy_groupies/utils_numpy.py:101
  /usr/lib/python3/dist-packages/numpy_groupies/utils_numpy.py:101: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe. 
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    'array': np.object,

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================================================= short test summary info =========================================================
FAILED tests/test_core.py::test_groupby_reduce_nans[flox-2-groups0-expected_shape0-chunks1] - AssertionError
FAILED tests/test_core.py::test_groupby_reduce_nans[flox-None-groups1-expected_shape1-chunks1] - AssertionError
FAILED tests/test_core.py::test_groupby_reduce_nans[flox-None-groups2-expected_shape2-chunks1] - AssertionError
FAILED tests/test_core.py::test_groupby_reduce_nans[numpy-2-groups0-expected_shape0-chunks1] - AssertionError
FAILED tests/test_core.py::test_groupby_reduce_nans[numpy-None-groups1-expected_shape1-chunks1] - AssertionError
FAILED tests/test_core.py::test_groupby_reduce_nans[numpy-None-groups2-expected_shape2-chunks1] - AssertionError
=================================== 6 failed, 6 passed, 8411 deselected, 6 xfailed, 2 warnings in 1.55s ===================================

@dcherian
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dcherian commented Aug 15, 2022 •
edited
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What is the dtype of np.sum([True, False]) on your platform? np.int32?

I've consistently used np.intp in the code (aggregations.py) except in the tests. So maybe the solution is to find-replace int64 with intp in the tests.

@avalentino
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Yes, this is the way to go:

diff --git a/tests/test_core.py b/tests/test_core.py
index 9c0bd6a..c70ae83 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -504,7 +504,7 @@ def test_groupby_reduce_nans(chunks, axis, groups, expected_shape, engine):
         fill_value=0,
         engine=engine,
     )
-    assert_equal(result, np.zeros(expected_shape, dtype=np.int64))
+    assert_equal(result, np.zeros(expected_shape, dtype=np.intp))
 
     # now when subsets are NaN
     # labels = np.array([0, 0, 1, 1, 1], dtype=float)

@dcherian
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OK can you send in a PR so you get credit for it?

avalentino added a commit to avalentino/flox that referenced this issue Aug 16, 2022
@avalentino
Fix test failure on 32bit architectures
324e152 
Closes xarray-contrib#133.
@avalentino avalentino mentioned this issue Aug 16, 2022
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@avalentino
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Done: #136.

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Fix test failure on 32bit architectures avalentino/flox
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@avalentino @dcherian