Analyzing the National Water Model with Xarray, Dask, and Coiled

This example was adapted from this notebook by Deepak Cherian, Kevin Sampson, and Matthew Rocklin.

You can download this jupyter notebook to follow along.

The National Water Model Dataset

In this example, we’ll perform a county-wise aggregation of output from the National Water Model (NWM) available on the AWS Open Data Registry. You can read more on the NWM from the Office of Water Prediction.

Problem description

Datasets with high spatio-temporal resolution can get large quickly, vastly exceeding the resources you may have on your laptop. Dask integrates with Xarray to support parallel computing and you can use Coiled to scale to the cloud.

We’ll calculate the mean depth to soil saturation for each US county:

  • Years: 2020

  • Temporal resolution: 3-hourly land surface output

  • Spatial resolution: 250 m grid

  • 6 TB

This example relies on a few tools:

  • dask + coiled process the dataset in parallel in the cloud

  • xarray + flox to work with the multi-dimensional Zarr datset and aggregate to county-level means from the 250m grid.

Before you start

You’ll first need to install the necessary packages. For the purposes of this example, we’ll do this in a new virtual environment, but you could also install them in whatever environment you’re already using for your project.

conda create -n coiled-xarray -c conda-forge python=3.10 coiled dask xarray flox rioxarray zarr s3fs geopandas geoviews matplotlib
conda activate coiled-xarray

You also could use pip for everything, or any other package manager you prefer; conda isn’t required.

When you later create a Coiled cluster, your local coiled-xarray environment will be automatically replicated on your cluster.

Start a Coiled cluster

To demonstrate calculation on a cloud-available dataset, we will use Coiled to set up a dask cluster in AWS us-east-1.

import coiled

cluster = coiled.Cluster(
    name="xarray-nwm",
    region="us-east-1", # close to dataset, avoid egress charges
    n_workers=10,
    tags={"project": "nwm"},
    scheduler_vm_types="r7g.xlarge", # memory optimized AWS EC2 instances
    worker_vm_types="r7g.2xlarge"
)

client = cluster.get_client()

cluster.adapt(minimum=10, maximum=50)

Setup

import flox  # make sure its available
import fsspec
import numpy as np
import rioxarray
import xarray as xr

xr.set_options( # display options for xarray objects
    display_expand_attrs=False,
    display_expand_coords=False,
    display_expand_data=True,
)

Load NWM data

ds = xr.open_zarr(
    fsspec.get_mapper("s3://noaa-nwm-retrospective-2-1-zarr-pds/rtout.zarr", anon=True),
    consolidated=True,
    chunks={"time": 896, "x": 350, "y": 350}
)
ds
<xarray.Dataset>
Dimensions:       (time: 122479, y: 15360, x: 18432)
Coordinates: (3)
Data variables:
    crs           |S1 ...
    sfcheadsubrt  (time, y, x) float64 dask.array<chunksize=(896, 350, 350), meta=np.ndarray>
    zwattablrt    (time, y, x) float64 dask.array<chunksize=(896, 350, 350), meta=np.ndarray>
Attributes: (7)

Each field in this dataset is big!

ds.zwattablrt
<xarray.DataArray 'zwattablrt' (time: 122479, y: 15360, x: 18432)>
dask.array<open_dataset-zwattablrt, shape=(122479, 15360, 18432), dtype=float64, chunksize=(896, 350, 350), chunktype=numpy.ndarray>
Coordinates: (3)
Attributes: (4)

Subset to a single year subset for demo purposes

subset = ds.zwattablrt.sel(time=slice("2020-01-01", "2020-12-31"))
subset
<xarray.DataArray 'zwattablrt' (time: 2928, y: 15360, x: 18432)>
dask.array<getitem, shape=(2928, 15360, 18432), dtype=float64, chunksize=(896, 350, 350), chunktype=numpy.ndarray>
Coordinates: (3)
Attributes: (4)

Load county raster for grouping

Load a raster TIFF file identifying counties by unique integer with rioxarray.

import fsspec
import rioxarray

fs = fsspec.filesystem("s3", requester_pays=True)

counties = rioxarray.open_rasterio(
    fs.open("s3://nwm-250m-us-counties/Counties_on_250m_grid.tif"), chunks="auto"
).squeeze()

# remove any small floating point error in coordinate locations
_, counties_aligned = xr.align(subset, counties, join="override")

counties_aligned
<xarray.DataArray (y: 15360, x: 18432)>
dask.array<getitem, shape=(15360, 18432), dtype=int32, chunksize=(1820, 18432), chunktype=numpy.ndarray>
Coordinates: (4)
Attributes: (9)

We’ll need the unique county IDs later, calculate that now.

county_id = np.unique(counties_aligned.data).compute()
county_id = county_id[county_id != 0]
print(f"There are {len(county_id)} counties!")
There are 3108 counties!

GroupBy with flox

We could run the computation as:

subset.groupby(counties_aligned).mean()

This would use flox in the background, however, it would also load counties_aligned into memory. To avoid egress charges, you can use flox.xarray which allows you to lazily groupby a Dask array (here counties_aligned) as long as you pass in the expected group labels in expected_groups. See the flox documentation.

import flox.xarray

county_mean = flox.xarray.xarray_reduce(
    subset,
    counties_aligned.rename("county"),
    func="mean",
    expected_groups=(county_id,),
)

county_mean
<xarray.DataArray 'zwattablrt' (time: 2928, county: 3108)>
dask.array<groupby_nanmean, shape=(2928, 3108), dtype=float64, chunksize=(896, 3108), chunktype=numpy.ndarray>
Coordinates: (4)
Attributes: (4)
county_mean.load()
<xarray.DataArray 'zwattablrt' (time: 2928, county: 3108)>
array([[1.6148426 , 1.77337928, 1.64958168, ..., 1.96216723, 1.88654191,
        1.66249746],
       [1.61630079, 1.7736926 , 1.65047253, ..., 1.9620833 , 1.88661932,
        1.66218315],
       [1.6158894 , 1.77379078, 1.65159624, ..., 1.96205491, 1.88628079,
        1.66221987],
       ...,
       [1.65066191, 1.73475125, 1.52970677, ..., 1.97500157, 1.96858928,
        1.95776549],
       [1.65242966, 1.73532446, 1.53078175, ..., 1.97483371, 1.96860777,
        1.95795127],
       [1.652059  , 1.73476713, 1.52733207, ..., 1.97489542, 1.96873255,
        1.95791995]])
Coordinates: (4)
Attributes: (4)

Cleanup

# since our dataset is much smaller now, we no longer need cloud resources
cluster.shutdown()

Visualize

Data prep

# Read county shapefile, combo of state FIPS code and county FIPS code as multi-index
import geopandas as gpd

counties = gpd.read_file(
    "https://www2.census.gov/geo/tiger/GENZ2020/shp/cb_2020_us_county_20m.zip"
).to_crs("EPSG:3395")
counties["STATEFP"] = counties.STATEFP.astype(int)
counties["COUNTYFP"] = counties.COUNTYFP.astype(int)
continental = counties[~counties["STATEFP"].isin([2, 15, 72])].set_index(["STATEFP", "COUNTYFP"]) # drop Alaska, Hawaii, Puerto Rico

# Interpret `county` as combo of state FIPS code and county FIPS code. Set multi-index:
yearly_mean = county_mean.mean("time")
yearly_mean.coords["STATEFP"] = (yearly_mean.county // 1000).astype(int)
yearly_mean.coords["COUNTYFP"] = np.mod(yearly_mean.county, 1000).astype(int)
yearly_mean = yearly_mean.drop_vars("county").set_index(county=["STATEFP", "COUNTYFP"])

# join
continental["zwattablrt"] = yearly_mean.to_dataframe()["zwattablrt"]

Plot

import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable

fig, ax = plt.subplots(1, 1, figsize=(7.68, 4.32))

ax.set_axis_off()

divider = make_axes_locatable(ax)
cax = divider.append_axes("bottom", size='5%', pad=0.1)

cax.tick_params(labelsize=8)
cax.set_title("Average depth (in meters) of the water table in 2020", fontsize=8)

continental.plot(
    column="zwattablrt",
    cmap="BrBG_r",
    vmin=0,
    vmax=2,
    legend=True,
    ax=ax,
    cax=cax,
    legend_kwds={
        "orientation": "horizontal",
        "ticks": [0,0.5,1,1.5,2],
        }
)

plt.text(0, 1, "6 TB processed, ~$1 in cloud costs", transform=ax.transAxes, size=9)
plt.show()
../_images/04c1fa53b919eca40e47a31e664c04b9f7e763ea02c5680e07b42b3e89a7a820.png