moi curvilinear `pset_execute_2d` and `pset_execute_3d` benchmark failure

[fluidnumericsJoe]

Parcels version

Parcels-code/Parcels@32bcf93 (v4-dev branch)

Steps to reproduce

pixi run asv run

Error message

Example error message shown below for the time_pset_execute_3d benchmark

[100.00%] ··· ============== =============
              --             chunk / npart
              -------------- -------------
               interpolator   256 / 10000 
              ============== =============
                 XLinear         failed   
              ============== =============
              For parameters: 'XLinear', 256, 10000
              Traceback (most recent call last):
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/server.py", line 179, in _run_server
                  _run(run_args)
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/run.py", line 72, in _run
                  result = benchmark.do_run()
                           ^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/_base.py", line 661, in do_run
                  return self.run(*self._current_params)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/time.py", line 165, in run
                  samples, number = self.benchmark_timing(
                                    ^^^^^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/time.py", line 258, in benchmark_timing
                  timing = timer.timeit(number)
                           ^^^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/timeit.py", line 180, in timeit
                  timing = self.inner(it, self.timer)
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "<timeit-src>", line 6, in inner
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/time.py", line 90, in func
                  self.func(*param)
                File "/group/tdgs/joe/parcels-benchmarks/benchmarks/moi_curvilinear.py", line 102, in time_pset_execute_3d
                  self.pset_execute_3d(interpolator,chunk,npart)
                File "/group/tdgs/joe/parcels-benchmarks/benchmarks/moi_curvilinear.py", line 84, in pset_execute_3d
                  U = parcels.Field("U", ds["U"], grid, interp_method=interp_method)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/parcels/_core/field.py", line 119, in __init__
                  raise e
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/parcels/_core/field.py", line 114, in __init__
                  self.time_interval = _get_time_interval(data)
                                       ^^^^^^^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/parcels/_core/field.py", line 448, in _get_time_interval
                  return TimeInterval(data.time.values[0], data.time.values[-1])
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/parcels/_core/utils/time.py", line 42, in __init__
                  raise ValueError(f"Expected left to be strictly less than right, got left={left} and right={right}.")
              ValueError: Expected left to be strictly less than right, got left=2025-01-03T12:00:00.000000000 and right=2025-01-01T12:00:00.000000000.
              Error getting time interval for field 'U'. Are you sure that the time dimension on the xarray dataset is stored as timedelta, datetime or cftime datetime objects?

[VeckoTheGecko]

Hi Joe, I tried recreating this - but I don't know which branch of parcels-benchmarks you're working from :/ . I don't get the same errors

Working from main I got the following errors.

   ImportError: cannot import name 'UxPiecewiseConstantFace' from 'parcels.interpolators' (/private/tmp/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/parcels/interpolators/__init__.py)

   ImportError: cannot import name 'Geographic' from 'parcels' (/private/tmp/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/parcels/__init__.py)

I've resolved these in vecko/33, and now am running into

                  UV = parcels.VectorField("UV", U, V)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/private/tmp/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/parcels/_core/field.py", line 251, in __init__
                  raise ValueError("vector_interp_method must be provided for VectorField initialization.")
              ValueError: vector_interp_method must be provided for VectorField initialization.

I should have fixed this fixed this in the week when I had more time for a back and forth, as I have to go now (and I'm away next week) . I'll take a look when I'm back in Utrecht.

[fluidnumericsJoe]

Yeah, the error you're showing is in #32 and I've gotten that mostly worked out. I'll be spending more time on this one next week.

[fluidnumericsJoe]

The parcels version I'm using is referenced in the issue description

[VeckoTheGecko]

I still get the "AttributeError: module 'parcels' has no attribute 'GeographicPolar'" error in pset_execute_3d as I saw in #33 (comment) .

logs

[91.67%] ··· moi_curvilinear.MOICurvilinear.time_load_data_3d                                        ok
[91.67%] ··· ============== =============
             --             chunk / npart
             -------------- -------------
              interpolator   256 / 10000
             ============== =============
                XLinear       43.3±0.2s
             ============== =============

[100.00%] ··· moi_curvilinear.MOICurvilinear.time_pset_execute_3d                                 failed
[100.00%] ··· ============== =============
              --             chunk / npart
              -------------- -------------
               interpolator   256 / 10000
              ============== =============
                 XLinear         failed
              ============== =============
              For parameters: 'XLinear', 256, 10000
              /Users/Hodgs004/coding/repos/parcels-benchmarks/benchmarks/moi_curvilinear.py:5: UserWarning: This is an alpha version of Parcels v4. The API is not stable and may change without deprecation warnings.
                import parcels
              /Users/Hodgs004/coding/repos/parcels-benchmarks/benchmarks/moi_curvilinear.py:33: FutureWarning: In a future version of xarray the default value for join will change from join='outer' to join='exact'. This change will result in the following ValueError: cannot be aligned with join='exact' because index/labels/sizes are not equal along these coordinates (dimensions): 'time_counter' ('time_counter',) The recommendation is to set join explicitly for this case.
                ds = xr.merge([ds_u, ds_v, ds_depth, ds_mesh], compat="identical")
              Traceback (most recent call last):
                File "/Users/Hodgs004/coding/repos/parcels-benchmarks/.pixi/envs/default/lib/python3.12/site-packages/asv/benchmark.py", line 99, in <module>
                  main()
                File "/Users/Hodgs004/coding/repos/parcels-benchmarks/.pixi/envs/default/lib/python3.12/site-packages/asv/benchmark.py", line 91, in main
                  commands[mode](args)
                File "/Users/Hodgs004/coding/repos/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/run.py", line 72, in _run
                  result = benchmark.do_run()
                           ^^^^^^^^^^^^^^^^^^
                File "/Users/Hodgs004/coding/repos/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/_base.py", line 661, in do_run
                  return self.run(*self._current_params)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/Users/Hodgs004/coding/repos/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/time.py", line 165, in run
                  samples, number = self.benchmark_timing(
                                    ^^^^^^^^^^^^^^^^^^^^^^
                File "/Users/Hodgs004/coding/repos/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/time.py", line 258, in benchmark_timing
                  timing = timer.timeit(number)
                           ^^^^^^^^^^^^^^^^^^^^
                File "/Users/Hodgs004/coding/repos/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/timeit.py", line 180, in timeit
                  timing = self.inner(it, self.timer)
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "<timeit-src>", line 6, in inner
                File "/Users/Hodgs004/coding/repos/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/time.py", line 90, in func
                  self.func(*param)
                File "/Users/Hodgs004/coding/repos/parcels-benchmarks/benchmarks/moi_curvilinear.py", line 102, in time_pset_execute_3d
                  self.pset_execute_3d(interpolator,chunk,npart)
                File "/Users/Hodgs004/coding/repos/parcels-benchmarks/benchmarks/moi_curvilinear.py", line 86, in pset_execute_3d
                  U.units = parcels.GeographicPolar()
                            ^^^^^^^^^^^^^^^^^^^^^^^
              AttributeError: module 'parcels' has no attribute 'GeographicPolar'

Maybe your error is only occuring on your machine @fluidnumerics-joe ?

But this does mean that we need to update main to bring into line with parcels v4-dev

[fluidnumericsJoe]

@VeckoTheGecko - from our screen share...
we tracked this down to an issue with glob

"Whether or not the results are sorted depends on the file system"
Python glob docs

On my system, the files were not sorted and the time_counter dimension was in the wrong order. To fix this problem, we need to wrap glob calls at https://github.com/Parcels-code/parcels-benchmarks/blob/main/benchmarks/moi_curvilinear.py#L17 in sorted().

Alas, this results in another error:

[100.00%] ··· moi_curvilinear.MOICurvilinear.time_pset_execute_3d                                                                                       failed
[100.00%] ··· ============== =============
              --             chunk / npart
              -------------- -------------
               interpolator   256 / 10000 
              ============== =============
                 XLinear         failed   
              ============== =============
              For parameters: 'XLinear', 256, 10000
              Traceback (most recent call last):
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/server.py", line 179, in _run_server
                  _run(run_args)
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/run.py", line 72, in _run
                  result = benchmark.do_run()
                           ^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/_base.py", line 661, in do_run
                  return self.run(*self._current_params)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/time.py", line 165, in run
                  samples, number = self.benchmark_timing(
                                    ^^^^^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/time.py", line 258, in benchmark_timing
                  timing = timer.timeit(number)
                           ^^^^^^^^^^^^^^^^^^^^
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/timeit.py", line 180, in timeit
                  timing = self.inner(it, self.timer)
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "<timeit-src>", line 6, in inner
                File "/group/tdgs/joe/parcels-benchmarks/.asv/env/b54e0339d4ce929e91168b1373f7b02b/lib/python3.12/site-packages/asv_runner/benchmarks/time.py", line 90, in func
                  self.func(*param)
                File "/group/tdgs/joe/parcels-benchmarks/benchmarks/moi_curvilinear.py", line 102, in time_pset_execute_3d
                  self.pset_execute_3d(interpolator,chunk,npart)
                File "/group/tdgs/joe/parcels-benchmarks/benchmarks/moi_curvilinear.py", line 86, in pset_execute_3d
                  U.units = parcels.GeographicPolar()
                            ^^^^^^^^^^^^^^^^^^^^^^^
              AttributeError: module 'parcels' has no attribute 'GeographicPolar'

Perhaps we need to change the fieldset loader to use the new convert/from_sgrid methodology

[VeckoTheGecko]

I can reproduce this error - I'm happy to work on this from here. Thanks @fluidnumerics-joe