Code

Parallel interpolation#108

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johnomotani merged 101 commits intomasterboutproject/xBOUT:masterfrom parallel-interpolationboutproject/xBOUT:parallel-interpolationCopy head branch name to clipboardAug 29, 2020

+1,684-406

Commits

Commits on Mar 21, 2020

• Chunk grid file after removing upper boundary points

  Show description for 1277532
  johnomotani

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  1277532

• Methods for parallel interpolation of variables

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  bd0e88d

• Caching argument for getHighParallelResRegion

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• Cache high-res variables in Region, not in Dataset

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• Move highParallelResRegion to BoutDataArray from BoutDataset

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  f84d919

• When interpolating, extrapolate at the boundaries if necessary

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  ae50094

• Remove uses of dx and dy in highParallelResRegion

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• Method to create high resolutions of a variable for all regions

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  2e63880

• Remove caching of high-resolution variables

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  9213bff

• Update definition of y_fine used for parallel interpolation

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  845e2eb

• Update metadata of high-resolution variable

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• Rename setupParallelInterp to resetParallelInterpFactor

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  a74f325

• BoutDataArray.highParallelRes returns a Dataset

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• Update default to n=8 in highParallelResRegion

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• Remove regions attr when creating high-res interpolated variable

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• Workaround for combine_by_coords not keeping attrs

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  67a2939

• Allow geometries to be re-applied to a Dataset

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• Fix applying s-alpha geometry

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  15dfe81

• Add dy to interpolated DataArray as a coordinate

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  4b4999a

• Create new Dataset of high-parallel resolution variables

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• Only select toroidal_points if variable has z-dimension

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• Test for _update_metadata_increased_resolution()

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• Test for BoutDataSet.resetParallelInterpFactor()

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• import numpy.testing as npt instead of importing assert_allclose

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• Tests for BoutDataArray.highParallelResRegion()

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• Drop attrs that do not belong in Dataset in BoutDataArray.to_dataset()

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• Define global 1d coordinates in apply_geometry()

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  d8f8d54

• Fix the coordinate calculations in Region.__init__()

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• Add 'direction_y' attrs to test data

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  c804396

• Fix region coordinate limits at boundaries

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• Set up connections in Region constructor

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  a180248

• Don't drop 'x' when creating 'r' for s-alpha geometry

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  c155d70

• Include 'dy' in all inputs for tests

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• Test for BoutDataArray.highParallelResRegion() in single-null topology

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• Test for highParallelResRegion with different enhancement factors

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• Test for BoutDataArray.highParallelRes()

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  05fd4cd

• Test for BoutDataset.getHghParallelResVars()

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• Remove region attribute from result in BoutDataArray.highParallelRes()

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  fda57ea

• Fix merge of Datasets in BoutDataset.getHighParallelResVars()

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  c69f81e

• Reduce grid sizes to speed up parallel interpolation tests

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  8487f3f

• Test toroidal_points argument for highParallelRes, highParallelResRegion

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  73fe457

• Fix for when toroidal_points does not divide nz exactly

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  f772530

• Add pytest.mark.long to disable long tests by default

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• Return DataArray by default from BoutDataArray.highParallelRes()

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  6ff08f8

• Merge branch 'rfft' into parallel-interpolation

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• Mark most permutations of to/fromFieldAligned tests as 'long'

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• Merge branch 'rfft' into parallel-interpolation

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• PEP8 fixes

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Commits on Mar 23, 2020

• Move Region creation out into a dict of functions

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  8db119d

• Just use dict, not OrderedDict, in region.py

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  ffb5bd5

• Use more f-strings

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• Merge branch 'regions' into parallel-interpolation

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  2d04255

• Fix merge of 'regions' branch

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  4aab6fe

• Rename highParallelResRegion and highParallelRes to interpolate_parallel

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  bd7a824

• Rename resetParallelInterpFactor to set_parallel_interpolation_factor

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  f9cdbda

• Better test for whether ds has a 'geometry' attribute

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  c5686c9

• Rename getHighParallelResVars() to interpolate_parallel()

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  f3a652a

• Merge branch 'regions' into parallel-interpolation

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• Remove accidentally-committed print statements

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• More f-strings

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Commits on Mar 24, 2020

• Fix merge of test_toFieldAligned from regions

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  55b7fb9

• Add Ellipsis option for 'variables' arg BoutDataset.interpolate_parallel

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  8c2ff03

• Extra test for interpolate_parallel

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  d06e38f

• Fix update of jyseps to higher resolution

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  50af753

• Add t_array as the t-coordinate in apply_geometry()

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• PEP8 fixes

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  ac41588

Commits on Mar 25, 2020

• Merge branch 'regions' into parallel-interpolation

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  8e989b5

• Update to incorporate variable and argument name changes from regions

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  6a7a748

Commits on Mar 26, 2020

• Fix merge of regions

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  fafe7ae

Commits on Apr 4, 2020

• Refactor fine_interpolation_factor as a @Property

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• Small tidy-up

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  c81a143

• Still need to use .values() to get DataArrays instead of names

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Commits on Apr 9, 2020

• Fix use of fine_interpolation_factor in tests

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  37d1220

Commits on Apr 20, 2020

• Always check if dy is in variables in BoutDataset.interpolate_parallel

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  acad60d

• Simplify BoutDataset.interpolate_parallel()

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  a316fb2

• Convert tuple to list if passed to BoutDataset.interpolate_parallel()

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  c74b941

• Check dimensions of variables to interpolate

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  2e49738

• Add test of ... arg: TestBoutDatasetMethods.test_interpolate_parallel

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  5f300ea

• PEP8 fixes

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Commits on Apr 21, 2020

• Assign DataArray to Dataset member instead of using merge()

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  c95f194

• Avoid errors if regions were not created

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  2acb61d

• Better support for generic x and y in poloidal plots

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  1e4d47a

Commits on Apr 23, 2020

• Merge branch 'master' into parallel-interpolation

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  10fda87

Commits on Jul 29, 2020

• Merge branch 'master' into parallel-interpolation

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  46e30d2

• Require xarray-0.16.0, fix merging attrs in interpolate_parallel()

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  b642545

• Check for xcoord in updated_ds not ds

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  f313bc1

• More consistent attrs on coordinates

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  d062fa9

Commits on Jul 30, 2020

• Fix performance regression in BoutDataArray.interpolate_parallel()

  Show description for 56a597c
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  56a597c

• Update Travis config for minimum versions to xarray-0.16.0

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  ed27def

• Update minimum dask to minimum version supported by xarray-0.16.0

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  dfab775

• Better fix, BoutDataArray.interpolate_parallel() performance regression

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  ccf1017

• Clean up merge - remove duplicated code adding 1d coordinates

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  ff1bc30

• Update coord attrs in _update_metadata_increased_resolution()

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  66b286a

Commits on Aug 1, 2020

• Add checks for cell_location in toFieldAligned and fromFieldAligned

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  629aacf

• Add staggered zShift variables as coordinates if they exist

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• set_coords() raises ValueError not KeyError when variable not present

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Commits on Aug 16, 2020

• Allow toFieldAligned and fromFieldAligned when no cell_location attr

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  324179a

• Add cell_location attr to variables in unit test Datasets

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Commits on Aug 17, 2020

• Remove drop('x') from add_s_alpha_geometry_coords()

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  585330f

• Drop cell_location attr from Dataset in BoutDataArray.to_dataset()

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• Add fsspec to PIP_PACKAGES in minimum versions Travis test

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