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Enabling GPU-native analytics with Xarray and kvikIO

Tuesday, August 30th, 2022 (28 days ago)



TLDR#

We demonstrate registering an Xarray backend that reads data from a Zarr store directly to GPU memory as CuPy arrays using the new kvikIO library and GPU Direct Storage technology. This allows direct-to-GPU reads and GPU-native analytics on existing pipelines 🎉 😱 🤯 🥳.

Background#

What is GPU Direct Storage?#

Quoting this nVIDIA blogpost

Diagram showing standard path between GPU memory and CPU memory on the left, versus a direct data path between GPU memory and storage on the right

What is kvikIO?#

For Xarray, the key bit is that kvikIO exposes a a zarr store called GDSStore that does all the hard work for us. Since Xarray knows how to read Zarr stores, we can adapt it to create a new storage backend that uses kvikio. And thanks to recent work funded by the Chan Zuckerberg Initiative, creating and registering a new backend is quite easy!

Integrating with Xarray#

Getting all these pieces to work together requires using three in-progress pull requests that

  1. Teach Zarr to handle alternative array classes
  2. Rewrite a small bit of Xarray to not cast all data to a numpy array after read from disk
  3. Make a backend that connects Xarray to kvikIO

Writing the backend for Xarray was relatively easy with most of the code copied over or inherited from the existing Zarr backend. We did have to ensure that dimension coordinates (for example, a time dimension with timestamps for a timeseries dataset) could be read in directly to host memory (RAM) without raising an error (by default kvikIO loads all data to device memory). This is required because Xarrays creates pandas.Index objects for such variables. In the future, we could consider using cudf.Index instead to allow a fully GPU-backed Xarray object.

Usage#

Assuming you have all the pieces together (see Appendix I and Appendix II for step-by-step instructions), then using all this cool technology only requires adding engine="kvikio" to your open_dataset line (!)

1import xarray as xr
2
3ds = xr.open_dataset("file.zarr", engine="kvikio", consolidated=False)
4

Notice that importing cupy_xarray was not needed. cupy_xarray uses entrypoints to register the kvikIO backend with Xarray.

With this ds.load() will load directly to GPU memory and ds will now contain CuPy arrays. At present there are a few limitations:

  1. Zarr stores cannot be read with consolidated metadata, and
  2. compression is unsupported by the kvikIO backend.

Quick demo#

First create an example uncompressed dataset to read from

1import xarray as xr
2
3store = "./air-temperature.zarr"
4
5airt = xr.tutorial.open_dataset("air_temperature", engine="netcdf4")
6
7for var in airt.variables:
8    airt[var].encoding["compressor"] = None
9airt.to_zarr(store, mode="w", consolidated=True)
10

Now read

1# consolidated must be False
2ds = xr.open_dataset(store, engine="kvikio", consolidated=False)
3ds.air
4
1<xarray.DataArray 'air' (time: 2920, lat: 25, lon: 53)>
2[3869000 values with dtype=float32]
3Coordinates:
4  * lat      (lat) float32 75.0 72.5 70.0 67.5 65.0 ... 25.0 22.5 20.0 17.5 15.0
5  * lon      (lon) float32 200.0 202.5 205.0 207.5 ... 322.5 325.0 327.5 330.0
6  * time     (time) datetime64[ns] 2013-01-01 ... 2014-12-31T18:00:00
7Attributes:
8    GRIB_id:       11
9    GRIB_name:     TMP
10    actual_range:  [185.16000366210938, 322.1000061035156]
11    dataset:       NMC Reanalysis
12    level_desc:    Surface
13    long_name:     4xDaily Air temperature at sigma level 995
14    parent_stat:   Other
15    precision:     2
16    statistic:     Individual Obs
17    units:         degK
18    var_desc:      Air temperature
19

Note that we get Xarray's lazy backend arrays by default, and that dimension coordinate variables lat, lon, time were read. At this point this looks identical to what we get with a standard xr.open_dataset(store, engine="zarr") command.

Now load a small subset

1type(ds["air"].isel(time=0, lat=10).load().data)
2
cupy._core.core.ndarray

Success! 🎉 😱 🤯 🥳

Xarray integrates decently well with CuPy arrays so you should be able to test out existing analysis pipelines pretty easily.

Cool demo#

See above! 😆 We don't have a more extensive analysis demo yet but are looking to develop one very soon! The limiting step here is access to capable hardware.

Reach out on the Pangeo discourse forum or over at cupy-xarray if you have ideas. We would love to hear from you.

Summary#

We demonstrate integrating the kvikIO library using Xarray's new backend entrypoints. With everything set up, simply adding engine="kvikio" enables direct-to-GPU reads from disk or over the network.

Acknowledgments#

This experiment was supported by funding from NASA-OSTFL 80NSSC22K0345 "Enhancing analysis of NASA data with the open-source Python Xarray Library".

Appendix I : Step-by-step install instructions#

Wei Ji Leong helpfully provided steps to get started on your machine:

1# May need to install nvidia-gds first
2# https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html#ubuntu-installation-common
3sudo apt install nvidia-gds
4
5git clone https://github.com/dcherian/cupy-xarray.git
6cd cupy-xarray
7
8mamba create --name cupy-xarray python=3.9 cupy=11.0 rapidsai-nightly::kvikio=22.10 jupyterlab=3.4.5 pooch=1.6.0 netcdf4=1.6.0 watermark=2.3.1
9mamba activate cupy-xarray
10python -m ipykernel install --user --name cupy-xarray
11
12# https://github.com/pydata/xarray/pull/6874
13pip install git+https://github.com/dcherian/xarray.git@kvikio
14# https://github.com/zarr-developers/zarr-python/pull/934
15pip install git+https://github.com/madsbk/zarr-python.git@cupy_support
16# https://github.com/xarray-contrib/cupy-xarray/pull/10
17git switch kvikio-entrypoint
18pip install --editable=.
19
20# Start jupyter lab
21jupyter lab --no-browser
22# Then open the docs/kvikio.ipynb notebook
23

Appendix II : making sure GDS is working#

Scott Henderson pointed out that running python kvikio/python/benchmarks/single-node-io.py prints nice diagnostic information that lets you check whether GDS is set up. Note that on our system, we have "compatibility mode" enabled. So we don't see the benefits now but this was enough to wire everything up.

----------------------------------
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   WARNING - KvikIO compat mode
      libcufile.so not used
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
GPU               | Quadro GP100 (dev #0)
GPU Memory Total  | 16.00 GiB
BAR1 Memory Total | 256.00 MiB
GDS driver        | N/A (Compatibility Mode)
GDS config.json   | /etc/cufile.json
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