issues: 859218255
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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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859218255 | MDU6SXNzdWU4NTkyMTgyNTU= | 5165 | Poor memory management with dask=2021.4.0 | 39069044 | closed | 0 | 4 | 2021-04-15T20:19:05Z | 2021-04-21T12:16:31Z | 2021-04-21T10:17:40Z | CONTRIBUTOR | What happened:
With the latest dask release What you expected to happen:
Dask would intelligently manage chunks and not fill up memory. This works fine in Minimal Complete Verifiable Example: Generate a synthetic dataset with time/lat/lon variable and associated climatology stored to disk, then calculate the anomaly: ```python import xarray as xr import pandas as pd import numpy as np import dask.array as da dates = pd.date_range('1980-01-01', '2019-12-31', freq='D') ds = xr.Dataset( data_vars = { 'x':( ('time', 'lat', 'lon'), da.random.random(size=(dates.size, 360, 720), chunks=(1, -1, -1))), 'clim':( ('dayofyear', 'lat', 'lon'), da.random.random(size=(366, 360, 720), chunks=(1, -1, -1))), }, coords = { 'time': dates, 'dayofyear': np.arange(1, 367, 1), 'lat': np.arange(-90, 90, .5), 'lon': np.arange(-180, 180, .5), } ) My original use case was pulling this data from disk, but it doesn't actually seem to matterds.to_zarr('test-data', mode='w') ds = xr.open_zarr('test-data') ds['anom'] = ds.x.groupby('time.dayofyear') - ds.clim ds[['anom']].to_zarr('test-anom', mode='w') ``` Anything else we need to know?: Distributed vs local scheduler and file backend e.g. zarr vs netcdf don't seem to affect this. Dask graphs look the same for both 2021.3.0:
Environment: Output of <tt>xr.show_versions()</tt>INSTALLED VERSIONS ------------------ commit: None python: 3.8.6 | packaged by conda-forge | (default, Dec 26 2020, 05:05:16) [GCC 9.3.0] python-bits: 64 OS: Linux OS-release: 5.8.0-48-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8 libhdf5: 1.10.6 libnetcdf: 4.7.4 xarray: 0.17.1.dev52+ge5690588 pandas: 1.2.1 numpy: 1.19.5 scipy: 1.6.0 netCDF4: 1.5.5.1 pydap: None h5netcdf: 0.8.1 h5py: 2.10.0 Nio: None zarr: 2.6.1 cftime: 1.3.1 nc_time_axis: 1.2.0 PseudoNetCDF: None rasterio: 1.1.8 cfgrib: 0.9.8.5 iris: None bottleneck: 1.3.2 dask: 2021.04.0 distributed: 2021.04.0 matplotlib: 3.3.3 cartopy: 0.18.0 seaborn: None numbagg: None pint: 0.16.1 setuptools: 49.6.0.post20210108 pip: 20.3.3 conda: None pytest: None IPython: 7.20.0 sphinx: None |
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completed | 13221727 | issue |