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Add rechunking example #47

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merged 3 commits into from
May 23, 2024
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Add rechunking example #47

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b6a1376
Add rechunking example
jrbourbeau May 15, 2024
0ccfa8e
add rechunking example to xarray example
mrocklin May 23, 2024
78928c2
remove rechunk notebook
mrocklin May 23, 2024
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119 changes: 76 additions & 43 deletions xarray.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,34 @@
"This is a national water model: https://registry.opendata.aws/nwm-archive/"
]
},
{
"cell_type": "markdown",
"id": "8185966d-6659-482b-bcbb-826b8f30b1e3",
"metadata": {
"tags": []
},
"source": [
"## Load NWM data"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e8b1749a-0d64-4278-823c-892120bf1a5b",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"import xarray as xr\n",
"\n",
"ds = xr.open_zarr(\n",
" \"s3://noaa-nwm-retrospective-2-1-zarr-pds/rtout.zarr\",\n",
" consolidated=True,\n",
").drop_encoding()\n",
"ds"
]
},
{
"cell_type": "markdown",
"id": "5dd71599-465f-4c97-baaa-19d900d2a070",
Expand All @@ -39,107 +67,112 @@
"import coiled\n",
"\n",
"cluster = coiled.Cluster(\n",
" n_workers=40,\n",
" n_workers=100,\n",
" region=\"us-east-1\",\n",
")\n",
"client = cluster.get_client()"
]
},
{
"cell_type": "markdown",
"id": "8185966d-6659-482b-bcbb-826b8f30b1e3",
"metadata": {},
"id": "0911fb96-7c08-4ca6-a35a-22e2a5a908cd",
"metadata": {
"tags": []
},
"source": [
"## Load NWM data"
"## Compute average over space"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e8b1749a-0d64-4278-823c-892120bf1a5b",
"id": "2a6fb91d-6a02-4afc-8d8a-ec3529f805f4",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"import xarray as xr\n",
"\n",
"ds = xr.open_zarr(\n",
" \"s3://noaa-nwm-retrospective-2-1-zarr-pds/rtout.zarr\",\n",
" consolidated=True,\n",
")\n",
"ds"
"subset = ds.zwattablrt.sel(time=slice(\"2001-01-01\", \"2001-03-31\"))\n",
"subset"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2147fc5c-60ee-4409-8c22-69c5e68a4c63",
"id": "8ae07b31-383c-4cc9-b94a-cbbb68369746",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"ds.nbytes / 1e12 # half-petabyte"
"avg = subset.mean(dim=[\"x\", \"y\"]).compute()\n",
"avg.plot()"
]
},
{
"cell_type": "markdown",
"id": "0911fb96-7c08-4ca6-a35a-22e2a5a908cd",
"metadata": {
"tags": []
},
"id": "b237d221-a2db-44fb-924d-6003cd73f933",
"metadata": {},
"source": [
"## Compute average over space"
"## Rechunk"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2a6fb91d-6a02-4afc-8d8a-ec3529f805f4",
"metadata": {
"tags": []
},
"id": "da1eca49-8362-42c6-aea7-ac986df36ef3",
"metadata": {},
"outputs": [],
"source": [
"subset = ds.zwattablrt.sel(time=slice(\"2001-01-01\", \"2001-12-31\"))\n",
"subset"
"import dask\n",
"\n",
"dask.config.set({\n",
" \"array.rechunk.method\": \"p2p\",\n",
" \"optimization.fuse.active\": False,\n",
"});"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8ae07b31-383c-4cc9-b94a-cbbb68369746",
"metadata": {
"tags": []
},
"id": "8ac6e24d-24d6-445d-a532-438b9d3a13f9",
"metadata": {},
"outputs": [],
"source": [
"avg = subset.mean(dim=[\"x\", \"y\"]).persist()"
"result = subset.chunk({\"time\": \"auto\", \"x\": -1, \"y\": \"auto\"})\n",
"result"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c42ef712-c60c-4049-816f-fcbd115a27a5",
"metadata": {
"tags": []
},
"id": "657ce639-b644-42ea-b98b-b70c2cb3170a",
"metadata": {},
"outputs": [],
"source": [
"cluster.scale(300)"
"%%time\n",
"\n",
"result.to_zarr(\"s3://oss-scratch-space/nwm-x-optimized.zarr\", mode=\"w\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "fdb5ac6f-48c3-4457-bf80-aab4336598f3",
"metadata": {
"tags": []
},
"id": "1d615e48-29dc-48b8-a185-c2fd20c3fdda",
"metadata": {},
"outputs": [],
"source": [
"avg.compute().plot()"
"result.chunk("
]
},
{
"cell_type": "markdown",
"id": "268ccde2-7e83-4e97-9fb7-4887a52adbe6",
"metadata": {},
"source": [
"## Cleanup if you like\n",
"\n",
"(but we'll clean up automatically eventually)"
]
},
{
Expand All @@ -155,9 +188,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python [conda env:deepak]",
"display_name": "Python [conda env:coiled]",
"language": "python",
"name": "conda-env-deepak-py"
"name": "conda-env-coiled-py"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -169,7 +202,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.3"
"version": "3.11.8"
}
},
"nbformat": 4,
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