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id | node_id | number | title | user | state | locked | assignee | milestone | comments | created_at | updated_at ▲ | closed_at | author_association | active_lock_reason | draft | pull_request | body | reactions | performed_via_github_app | state_reason | repo | type |
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659129613 | MDU6SXNzdWU2NTkxMjk2MTM= | 4234 | Add ability to change underlying array type | jacobtomlinson 1610850 | open | 0 | 12 | 2020-07-17T10:37:34Z | 2021-04-19T03:21:54Z | CONTRIBUTOR | Is your feature request related to a problem? Please describe. In order to use Xarray with alternative array types like Right now I'm doing something like this. ```python import xarray as xr import cupy as cp ds = xr.tutorial.load_dataset("air_temperature") ds.air.data = cp.asarray(ds.air.data) ``` However this will become burdensome when there are many data arrays and feels brittle and prone to errors. As I see it a conversion could instead be done in a couple of places; on load, or as a utility method. Currently Xarray supports NumPy and Dask array well. Numpy is the defrault and the way you specify whether a Dask array should be used is to give the Side note: There are a few places where the Dask array API bleeds into Xarray in order to have compatibility, the Describe the solution you'd like For other array types I would like to propose the addition of an This would result in something like the following. ```python import xarray as xr import cupy as cp ds = xr.open_mfdataset("/path/to/files/*.nc", asarray=cp.ndarray) ords = xr.open_mfdataset("/path/to/files/*.nc") gds = ds.asarray(cp.ndarray) ``` These operations would convert all data arrays to It is still unclear what to do about index variables, which are currently of type Describe alternatives you've considered Instead of an Another option would be to go more high level with it. For example a Additional context Related to #4212. I'm keen to start implementing this. But would like some discussion/feedback before I dive in here. |
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654135405 | MDU6SXNzdWU2NTQxMzU0MDU= | 4212 | Add cupy support | jacobtomlinson 1610850 | open | 0 | 7 | 2020-07-09T15:06:37Z | 2021-02-08T16:50:38Z | CONTRIBUTOR | I'm intending on working on cupy support in xarray along with @quasiben. Thanks for the warm welcome in the xarray dev meeting yesterday! I'd like to use this issue to track cupy support and discuss certain design decisions. I appreciate there are also issues such as #4208, #3484 and #3232 which are related to cupy support, but maybe this could represent an umbrella issue for cupy specifically. The main goal here is to improve support for array types other than numpy and dask in general. However, it is likely there will need to be some cupy specific compatibility code in xarray. (@andersy005 raised issues with calling I would love to hear from folks wanting to use cupy with xarray to help build up some use cases for us to develop against. We have some ideas but more are welcome. My first steps here will be to add some tests which use cupy. These will skip in the main CI but we will also look at running xarray tests on some GPU CI too as we develop. A few limited experiments that I've run seem to work, so I'll start with tests which reproduce those. |
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xarray 13221727 | issue | ||||||||
658361860 | MDU6SXNzdWU2NTgzNjE4NjA= | 4231 | as_shared_dtype coerces scalars into numpy regardless of other array types | jacobtomlinson 1610850 | closed | 0 | 0 | 2020-07-16T16:36:19Z | 2020-07-24T20:38:57Z | 2020-07-24T20:38:57Z | CONTRIBUTOR | Related to #4212 When trying to get the Calculating Seasonal Averages from Timeseries of Monthly Means example from the documentation to work with I dug through this with @quasiben and it seems to be related to the What happened: Running the MCVE below results in However Cupy is then passed this numpy array to it's where function which does raises the exception. What you expected to happen: The Therefore a few things could be done here: 1. Xarray could not convert the int/float to a numpy array 1. It could convert it to a cupy array 1. Cupy could be modified to accept a numpy scalar. We thew together a quick fix for option 2, which I'll put in a draft PR. But happy to discuss the alternatives. Minimal Complete Verifiable Example: ```python import numpy as np import pandas as pd import xarray as xr import matplotlib.pyplot as plt import cupy as cp Load datads = xr.tutorial.open_dataset("rasm").load() Move data to GPUds.Tair.data = cp.asarray(ds.Tair.data) ds_unweighted = ds.groupby("time.season").mean("time") Calculate the weights by grouping by 'time.season'.month_length = ds.time.dt.days_in_month weights = ( month_length.groupby("time.season") / month_length.groupby("time.season").sum() ) Test that the sum of the weights for each season is 1.0np.testing.assert_allclose(weights.groupby("time.season").sum().values, np.ones(4)) Move weights to GPUweights.data = cp.asarray(weights.data) Calculate the weighted averageds_weighted = ds * weights ds_weighted = ds_weighted.groupby("time.season") ds_weighted = ds_weighted.sum(dim="time") ``` Traceback```python-traceback Traceback (most recent call last): File "/home/jacob/miniconda3/envs/dask/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/home/jacob/miniconda3/envs/dask/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/jacob/.vscode-server/extensions/ms-python.python-2020.6.91350/pythonFiles/lib/python/debugpy/__main__.py", line 45, in <module> cli.main() File "/home/jacob/.vscode-server/extensions/ms-python.python-2020.6.91350/pythonFiles/lib/python/debugpy/../debugpy/server/cli.py", line 430, in main run() File "/home/jacob/.vscode-server/extensions/ms-python.python-2020.6.91350/pythonFiles/lib/python/debugpy/../debugpy/server/cli.py", line 267, in run_file runpy.run_path(options.target, run_name=compat.force_str("__main__")) File "/home/jacob/miniconda3/envs/dask/lib/python3.7/runpy.py", line 263, in run_path pkg_name=pkg_name, script_name=fname) File "/home/jacob/miniconda3/envs/dask/lib/python3.7/runpy.py", line 96, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File "/home/jacob/miniconda3/envs/dask/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/jacob/Projects/pydata/xarray/test_seasonal_averages.py", line 32, in <module> ds_weighted = ds_weighted.sum(dim="time") File "/home/jacob/Projects/pydata/xarray/xarray/core/common.py", line 84, in wrapped_func func, dim, skipna=skipna, numeric_only=numeric_only, **kwargs File "/home/jacob/Projects/pydata/xarray/xarray/core/groupby.py", line 994, in reduce return self.map(reduce_dataset) File "/home/jacob/Projects/pydata/xarray/xarray/core/groupby.py", line 923, in map return self._combine(applied) File "/home/jacob/Projects/pydata/xarray/xarray/core/groupby.py", line 943, in _combine applied_example, applied = peek_at(applied) File "/home/jacob/Projects/pydata/xarray/xarray/core/utils.py", line 183, in peek_at peek = next(gen) File "/home/jacob/Projects/pydata/xarray/xarray/core/groupby.py", line 922, in <genexpr> applied = (func(ds, *args, **kwargs) for ds in self._iter_grouped()) File "/home/jacob/Projects/pydata/xarray/xarray/core/groupby.py", line 990, in reduce_dataset return ds.reduce(func, dim, keep_attrs, **kwargs) File "/home/jacob/Projects/pydata/xarray/xarray/core/dataset.py", line 4313, in reduce **kwargs, File "/home/jacob/Projects/pydata/xarray/xarray/core/variable.py", line 1591, in reduce data = func(input_data, axis=axis, **kwargs) File "/home/jacob/Projects/pydata/xarray/xarray/core/duck_array_ops.py", line 324, in f return func(values, axis=axis, **kwargs) File "/home/jacob/Projects/pydata/xarray/xarray/core/nanops.py", line 111, in nansum a, mask = _replace_nan(a, 0) File "/home/jacob/Projects/pydata/xarray/xarray/core/nanops.py", line 21, in _replace_nan return where_method(val, mask, a), mask File "/home/jacob/Projects/pydata/xarray/xarray/core/duck_array_ops.py", line 274, in where_method return where(cond, data, other) File "/home/jacob/Projects/pydata/xarray/xarray/core/duck_array_ops.py", line 268, in where return _where(condition, *as_shared_dtype([x, y])) File "/home/jacob/Projects/pydata/xarray/xarray/core/duck_array_ops.py", line 56, in f return wrapped(*args, **kwargs) File "<__array_function__ internals>", line 6, in where File "cupy/core/core.pyx", line 1343, in cupy.core.core.ndarray.__array_function__ File "/home/jacob/miniconda3/envs/dask/lib/python3.7/site-packages/cupy/sorting/search.py", line 211, in where return _where_ufunc(condition.astype('?'), x, y) File "cupy/core/_kernel.pyx", line 906, in cupy.core._kernel.ufunc.__call__ File "cupy/core/_kernel.pyx", line 90, in cupy.core._kernel._preprocess_args TypeError: Unsupported type <class 'numpy.ndarray'> ```Anything else we need to know?: Environment: Output of <tt>xr.show_versions()</tt>INSTALLED VERSIONS ------------------ commit: 52043bc57f20438e8923790bca90b646c82442ad python: 3.7.6 | packaged by conda-forge | (default, Jun 1 2020, 18:57:50) [GCC 7.5.0] python-bits: 64 OS: Linux OS-release: 5.3.0-62-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_GB.UTF-8 LOCALE: en_GB.UTF-8 libhdf5: None libnetcdf: None xarray: 0.15.1 pandas: 0.25.3 numpy: 1.18.5 scipy: 1.5.0 netCDF4: None pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.2.0 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: 0.9.8.3 iris: None bottleneck: None dask: 2.20.0 distributed: 2.20.0 matplotlib: 3.2.2 cartopy: 0.17.0 seaborn: 0.10.1 numbagg: None pint: None setuptools: 49.1.0.post20200704 pip: 20.1.1 conda: None pytest: 5.4.3 IPython: 7.16.1 sphinx: None |
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346525275 | MDU6SXNzdWUzNDY1MjUyNzU= | 2335 | Spurious "Zarr requires uniform chunk sizes excpet for final chunk." | jacobtomlinson 1610850 | closed | 0 | 3 | 2018-08-01T09:43:06Z | 2018-08-14T17:15:02Z | 2018-08-14T17:15:01Z | CONTRIBUTOR | Problem descriptionUsing xarray 0.10.7 I'm getting the following error when trying to write out a zarr.
Those chunks look fine to me, only one has an inconsistent chunking and it's the final chunk in the second index. Seems related to #2225. |
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completed | xarray 13221727 | issue |
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