TST: interpolate: mark rbf chunking tests as slow

[ev-br]

Reference issue

closes gh-16136

What does this implement/fix?

Mark RBFInterpolator chunking tests as slow, because:

$ python dev.py -t scipy.interpolate.tests.test_rbfinterp -- --durations=10
ninja: Entering directory `build'
[2/2] Generating scipy/generate-config with a custom command
Build OK
Installing, see meson-install.log...
Installation OK
Running tests for scipy version:1.9.0.dev0+1994.c166a9b, installed at:/home/br/repos/scipy/scipy/build-install/lib/python3.8/site-packages/scipy
=========================================================================================== test session starts ===========================================================================================
platform linux -- Python 3.8.10, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/br/repos/scipy/scipy, configfile: pytest.ini
collected 185 items                                                                                                                                                                                       

scipy/interpolate/tests/test_rbfinterp.py ......................................................................................................................................................... [ 82%]
................................                                                                                                                                                                    [100%]

========================================================================================== slowest 10 durations ===========================================================================================
20.90s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighborsInf::test_chunking
10.48s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighbors20::test_chunking
2.11s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighborsNone::test_chunking
0.48s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighborsInf::test_smoothing_misfit[thin_plate_spline]
0.47s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighborsInf::test_smoothing_misfit[linear]
0.36s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[cubic]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[quintic]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[thin_plate_spline]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[gaussian]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[linear]
========================================================================================== 185 passed in 40.77s ===========================================================================================

[ev-br]

@segasai maybe you could think of a way to excercise the chunking functionality in a smaller/shorter test instead?

[rgommers]

@ev-br given the comment on gh-16136, does setting OPENBLAS_NUM_THREADS=1 help, and if so how many threads does your machine default to to give results like you reported above?

[ev-br]

It does seem to be sensitive to the OpenBLAS defaults; the default seems to be oversubscribing indeed (8 processes seen in htop); setting OPENBLAS_NUM_THREADS to 1 does limit the number of threads and lowers the test time; but no, even with a single thread it is still not very reasonable (33 sec is better than 41 sec but still). Not sure what it would be on other linalg implementations (unlikely to be more reasonable).

Openblas does its default:

$ python dev.py -t scipy.interpolate.tests.test_rbfinterp -- --durations=10
ninja: Entering directory `build'
[2/2] Generating scipy/generate-config with a custom command
Build OK
Installing, see meson-install.log...
Installation OK
Running tests for scipy version:1.9.0.dev0+2002.168046f, installed at:/home/br/repos/scipy/scipy/build-install/lib/python3.8/site-packages/scipy
=========================================================================================== test session starts ===========================================================================================
platform linux -- Python 3.8.10, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/br/repos/scipy/scipy, configfile: pytest.ini
collected 185 items                                                                                                                                                                                       

scipy/interpolate/tests/test_rbfinterp.py ......................................................................................................................................................... [ 82%]
................................                                                                                                                                                                    [100%]

========================================================================================== slowest 10 durations ===========================================================================================
20.51s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighborsInf::test_chunking
10.23s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighbors20::test_chunking
2.20s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighborsNone::test_chunking
0.59s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighborsInf::test_smoothing_misfit[linear]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[cubic]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[quintic]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[thin_plate_spline]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[gaussian]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[multiquadric]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[linear]
========================================================================================== 185 passed in 41.07s ===========================================================================================

Setting OPENBLAS_NUM_THREADS:

$ export OPENBLAS_NUM_THREADS=1; python dev.py -t scipy.interpolate.tests.test_rbfinterp -- --durations=10
ninja: Entering directory `build'
[2/2] Generating scipy/generate-config with a custom command
Build OK
Installing, see meson-install.log...
Installation OK
Running tests for scipy version:1.9.0.dev0+2002.168046f, installed at:/home/br/repos/scipy/scipy/build-install/lib/python3.8/site-packages/scipy
=========================================================================================== test session starts ===========================================================================================
platform linux -- Python 3.8.10, pytest-7.1.2, pluggy-1.0.0
rootdir: /home/br/repos/scipy/scipy, configfile: pytest.ini
collected 185 items                                                                                                                                                                                       

scipy/interpolate/tests/test_rbfinterp.py ......................................................................................................................................................... [ 82%]
................................                                                                                                                                                                    [100%]

========================================================================================== slowest 10 durations ===========================================================================================
19.10s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighborsInf::test_chunking
8.73s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighbors20::test_chunking
1.41s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::TestRBFInterpolatorNeighborsNone::test_chunking
0.39s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[quintic]
0.37s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[multiquadric]
0.36s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[thin_plate_spline]
0.36s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[cubic]
0.36s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[inverse_quadratic]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[linear]
0.35s call     build-install/lib/python3.8/site-packages/scipy/interpolate/tests/test_rbfinterp.py::test_conditionally_positive_definite[inverse_multiquadric]
========================================================================================== 185 passed in 33.34s ===========================================================================================```

[rgommers]

Hmm yes that's way too slow, not sure how that was missed in previous PR reviews. In it goes, thanks @ev-br

[ev-br]

not sure how that was missed in previous PR reviews.

That was me as well :-). Not sure how to systematically check it other than running --durations=N manually of each PR. Would be happy to hear suggestions.

[rgommers]

For big new feature PRs I do indeed check manually.

[tupui]

Now we can have job summaries with actions: https://github.blog/2022-05-09-supercharging-github-actions-with-job-summaries/. Maybe we could add such things (also thinking about benchmarks) as summary.

[ev-br]

For big new feature PRs I do indeed check manually.

Point taken, thanks for confirming the workflow.

Re job summaries: would be great if it could show stats about what changed in the PR specifically (total CI time etc are available).

[tupui]

Re job summaries: would be great if it could show stats about what changed in the PR specifically (total CI time etc are available).

In the end it's a matter of computing what we want and saving this to an env variable.