add grace calculator, clarify gpu/cpu fixes #408 #426

alinelena · 2025-02-14T16:25:00Z

No description provided.

ElliottKasoar

Looks good so far.

Which bits are the gpu/cpu fixes?

pyproject.toml

janus_core/helpers/mlip_calculators.py

tests/test_mlip_calculators.py

janus_core/helpers/mlip_calculators.py

pyproject.toml

ElliottKasoar · 2025-02-14T18:02:25Z

Also to do:

Update README (dependencies, features)
Update docs (getting_started)

alinelena · 2025-02-15T00:11:54Z

Looks good so far.

Which bits are the gpu/cpu fixes?

exactly... I did not see an obvious way to select use of cpu/gpu via python

ElliottKasoar · 2025-02-19T19:22:50Z

Looks good so far.
Which bits are the gpu/cpu fixes?

exactly... I did not see an obvious way to select use of cpu/gpu via python

I suppose similar to dpa3?

alinelena · 2025-02-19T19:27:12Z

Looks good so far.
Which bits are the gpu/cpu fixes?

exactly... I did not see an obvious way to select use of cpu/gpu via python

I suppose similar to dpa3?

i suspect is tensorflow specific https://www.tensorflow.org/guide/gpu

ElliottKasoar · 2025-03-14T16:52:56Z

A shorter way to trigger the test failures is (with grace and mace installed):

pytest -vvv tests/test_single_point.py::test_extras tests/test_neb_cli.py::test_neb --pdb results in:

Traceback (most recent call last):
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/main.py", line 283, in wrap_session
    session.exitstatus = doit(config, session) or 0
                         ^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/main.py", line 337, in _main
    config.hook.pytest_runtestloop(session=session)
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_hooks.py", line 513, in __call__
    return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_manager.py", line 120, in _hookexec
    return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 139, in _multicall
    raise exception.with_traceback(exception.__traceback__)
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 122, in _multicall
    teardown.throw(exception)  # type: ignore[union-attr]
    ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/logging.py", line 803, in pytest_runtestloop
    return (yield)  # Run all the tests.
            ^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 122, in _multicall
    teardown.throw(exception)  # type: ignore[union-attr]
    ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/terminal.py", line 673, in pytest_runtestloop
    result = yield
             ^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 103, in _multicall
    res = hook_impl.function(*args)
          ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/main.py", line 362, in pytest_runtestloop
    item.config.hook.pytest_runtest_protocol(item=item, nextitem=nextitem)
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_hooks.py", line 513, in __call__
    return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_manager.py", line 120, in _hookexec
    return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 139, in _multicall
    raise exception.with_traceback(exception.__traceback__)
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 122, in _multicall
    teardown.throw(exception)  # type: ignore[union-attr]
    ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/warnings.py", line 112, in pytest_runtest_protocol
    return (yield)
            ^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 122, in _multicall
    teardown.throw(exception)  # type: ignore[union-attr]
    ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/assertion/__init__.py", line 176, in pytest_runtest_protocol
    return (yield)
            ^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 122, in _multicall
    teardown.throw(exception)  # type: ignore[union-attr]
    ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/unittest.py", line 429, in pytest_runtest_protocol
    res = yield
          ^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 122, in _multicall
    teardown.throw(exception)  # type: ignore[union-attr]
    ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/faulthandler.py", line 88, in pytest_runtest_protocol
    return (yield)
            ^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 103, in _multicall
    res = hook_impl.function(*args)
          ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/runner.py", line 113, in pytest_runtest_protocol
    runtestprotocol(item, nextitem=nextitem)
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/runner.py", line 132, in runtestprotocol
    reports.append(call_and_report(item, "call", log))
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/runner.py", line 248, in call_and_report
    ihook.pytest_exception_interact(node=item, call=call, report=report)
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_hooks.py", line 513, in __call__
    return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_manager.py", line 120, in _hookexec
    return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 139, in _multicall
    raise exception.with_traceback(exception.__traceback__)
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 103, in _multicall
    res = hook_impl.function(*args)
          ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/debugging.py", line 286, in pytest_exception_interact
    out, err = capman.read_global_capture()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 801, in read_global_capture
    return self._global_capturing.readouterr()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 705, in readouterr
    err = self.err.snap() if self.err else ""
          ^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 589, in snap
    self.tmpfile.seek(0)
ValueError: I/O operation on closed file.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/main.py", line 303, in wrap_session
    config.notify_exception(excinfo, config.option)
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py", line 1173, in notify_exception
    res = self.hook.pytest_internalerror(excrepr=excrepr, excinfo=excinfo)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_hooks.py", line 513, in __call__
    return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_manager.py", line 120, in _hookexec
    return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 139, in _multicall
    raise exception.with_traceback(exception.__traceback__)
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 103, in _multicall
    res = hook_impl.function(*args)
          ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 911, in pytest_internalerror
    self.stop_global_capturing()
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 776, in stop_global_capturing
    self._global_capturing.pop_outerr_to_orig()
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 657, in pop_outerr_to_orig
    out, err = self.readouterr()
               ^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 705, in readouterr
    err = self.err.snap() if self.err else ""
          ^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 589, in snap
    self.tmpfile.seek(0)
ValueError: I/O operation on closed file.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/bin/pytest", line 10, in <module>
    sys.exit(console_main())
             ^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py", line 201, in console_main
    code = main()
           ^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py", line 175, in main
    ret: ExitCode | int = config.hook.pytest_cmdline_main(config=config)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_hooks.py", line 513, in __call__
    return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_manager.py", line 120, in _hookexec
    return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 139, in _multicall
    raise exception.with_traceback(exception.__traceback__)
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 103, in _multicall
    res = hook_impl.function(*args)
          ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/main.py", line 330, in pytest_cmdline_main
    return wrap_session(config, _main)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/main.py", line 325, in wrap_session
    config._ensure_unconfigure()
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py", line 1127, in _ensure_unconfigure
    fin()
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 776, in stop_global_capturing
    self._global_capturing.pop_outerr_to_orig()
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 657, in pop_outerr_to_orig
    out, err = self.readouterr()
               ^^^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 705, in readouterr
    err = self.err.snap() if self.err else ""
          ^^^^^^^^^^^^^^^
  File "/Users/elliottkasoar/Documents/PSDI/janus-core/.venv/lib/python3.12/site-packages/_pytest/capture.py", line 589, in snap
    self.tmpfile.seek(0)
ValueError: I/O operation on closed file.

ElliottKasoar · 2025-04-01T19:36:28Z

A shorter way to trigger the test failures is (with grace and mace installed):

pytest -vvv tests/test_single_point.py::test_extras tests/test_neb_cli.py::test_neb --pdb results in:

The exact causes of this remain a bit unclear, given that it's dependent on the order/combination of tests, but it's some form of known pytest error, with tensorflow (which calls sys.stdout.close() and sys.stderr.close()) and/or the typer/click runner.

Most of the Python solutions seemed to involve clearing/disabling logging at various points, but we already do that to some extent, and there didn't seem to be a solution that resolves this for us.

What I've gone with for now is a wrapper blocking stderr/stdout being closed, which seems to work:

sys.stderr.close = lambda *args: None
sys.stdout.close = lambda *args: None

If we're not happy with that, the main other alternatives are:

Always run with --capture=no, but I'm not a fan of potential failures based on the options we pass to pytest
Don't use the typer/click runner, and use something like subprocess.run instead, which from initial testing also seems to fix this, but would mean changing a huge number of tests

ElliottKasoar · 2025-04-04T15:42:09Z

Looks like there are a few compatibility issues relating to one of tensorflow's dependencies and Windows: tensorflow/io#2087.

Should be fixable, but if it's too painful, we could also not explicitly support it.

alinelena · 2025-04-04T15:45:02Z

given tensorflow is not most used in the wild I would not waste the time... just make it clear we did not test it for windows and we do not plan to do so since we like our sanity

ElliottKasoar

Needs another approval but I'm happy, assuming the tests all pass.

harveydevereux

All seems to be in order

alinelena requested a review from ElliottKasoar February 14, 2025 16:25

alinelena self-assigned this Feb 14, 2025

ElliottKasoar reviewed Feb 14, 2025

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ElliottKasoar linked an issue Feb 14, 2025 that may be closed by this pull request

add support for grace #408

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ElliottKasoar added the enhancement New/improved feature or request label Feb 14, 2025

ElliottKasoar force-pushed the grace branch from 51a5da4 to d81c11e Compare February 19, 2025 19:19

ElliottKasoar force-pushed the grace branch from d81c11e to 7455b08 Compare March 14, 2025 16:36

ElliottKasoar force-pushed the grace branch from 7455b08 to 89c2ee9 Compare April 1, 2025 19:12

ElliottKasoar requested a review from oerc0122 April 1, 2025 19:36

ElliottKasoar force-pushed the grace branch from 89c2ee9 to ee3991e Compare April 4, 2025 15:08

ElliottKasoar requested a review from harveydevereux April 4, 2025 15:08

alinelena and others added 11 commits April 4, 2025 16:20

add grace calculator, clarify gpu/cpu

dfe1727

Update docs for GRACE

213ccff

Fix tensorflow installation

5934ff9

Set GRACE default model consistently

23ba166

Fix and add GRACE tests

6590f5f

Fix grace test

f6c5007

Fix skipping grace tests

b016b6b

Update grace

1f6738e

Tidy dependencies

fbe3cf7

Fix CLI tests

ec5d006

Fix test errors

9f7b576

ElliottKasoar added 2 commits April 4, 2025 16:20

Add explanation for test fix

8e43d04

Fix grace for Windows

94a5a6e

ElliottKasoar force-pushed the grace branch from ee3991e to 94a5a6e Compare April 4, 2025 15:52

ElliottKasoar approved these changes Apr 4, 2025

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harveydevereux approved these changes Apr 7, 2025

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ElliottKasoar merged commit f83394d into stfc:main Apr 7, 2025
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add grace calculator, clarify gpu/cpu fixes #408 #426

add grace calculator, clarify gpu/cpu fixes #408 #426

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add grace calculator, clarify gpu/cpu fixes #408 #426

add grace calculator, clarify gpu/cpu fixes #408 #426

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