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Last active May 18, 2019 05:42
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Kubernetes Cluster Setup

Started from https://zero-to-jupyterhub.readthedocs.io/en/latest/amazon/step-zero-aws-eks.html

Notes from each step:

Step 1: EKS Service Role

Step 2: EKS Cluster

Steps 3-5 nothing to add

Step 6 This was a bit confusing because the zero-to-jupyterhub guide makes me think I need to update ~/.kube/config but it looks like that file is generated completely by the aws cli correctly when you run:

aws eks --region {region} update-kubeconfig --name {cluster_name}

per AWS instructions

Steps 7-10 Nothing to add

Deploying Helm

Now using https://docs.dask.org/en/latest/setup/kubernetes.html

helm repo update 
helm install stable/dask
helm upgrade --force --recreate-pods --devel singed-sabertooth stable/dask -f dask_config.yml

See dask_config.yml in this gist.

AWS EKS Cluster

  • 3 m4.2xlarge ec2 instances

Other references

Other notes (can ignore)

  • When runninng ./3_deploy_helm.sh got the error:

    Error: priorityclasses.scheduling.k8s.io "pangeohub-default-priority" is forbidden: User "system:serviceaccount:kube-system:default" cannot delete priorityclasses.scheduling.k8s.io at the cluster scope

    This might be because of the instruction https://zero-to-jupyterhub.readthedocs.io/en/latest/amazon/step-zero-aws-eks.html to use

    kubectl create clusterrolebinding cluster-system-anonymous --clusterrole=cluster-admin --user=system:anonymous

    I googled the error and ran these commands and it seems to have resolved itself. I can now run ./3_deploy_helm.sh without error.

  • When running kubectl commands, always need to add --namespace pangeo

  • Using kubectl logs is critical, worker logs will not show up in jupyter

jupyter:
name: jupyter
env:
- name: EXTRA_CONDA_PACKAGES
value: numpy zarr netCDF4 xarray s3fs -c conda-forge --yes
- name: AWS_ACCESS_KEY_ID
value: xxx
- name: AWS_SECRET_ACCESS_KEY
value: xxx
worker:
name: worker
env:
- name: EXTRA_CONDA_PACKAGES
value: numpy zarr netCDF4 xarray s3fs -c conda-forge --yes
- name: AWS_ACCESS_KEY_ID
value: xxx
- name: AWS_SECRET_ACCESS_KEY
value: xxx
scheduler:
name: scheduler
env:
- name: EXTRA_CONDA_PACKAGES
value: numpy zarr netCDF4 xarray s3fs -c conda-forge --yes
- name: AWS_ACCESS_KEY_ID
value: xxx
- name: AWS_SECRET_ACCESS_KEY
value: xxx
Display the source blob
Display the rendered blob
Raw
{
"cells": [
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table style=\"border: 2px solid white;\">\n",
"<tr>\n",
"<td style=\"vertical-align: top; border: 0px solid white\">\n",
"<h3>Client</h3>\n",
"<ul>\n",
" <li><b>Scheduler: </b>tcp://singed-sabertooth-dask-scheduler:8786\n",
" <li><b>Dashboard: </b><a href='http://singed-sabertooth-dask-scheduler:8787/status' target='_blank'>http://singed-sabertooth-dask-scheduler:8787/status</a>\n",
"</ul>\n",
"</td>\n",
"<td style=\"vertical-align: top; border: 0px solid white\">\n",
"<h3>Cluster</h3>\n",
"<ul>\n",
" <li><b>Workers: </b>3</li>\n",
" <li><b>Cores: </b>24</li>\n",
" <li><b>Memory: </b>101.19 GB</li>\n",
"</ul>\n",
"</td>\n",
"</tr>\n",
"</table>"
],
"text/plain": [
"<Client: scheduler='tcp://192.168.64.237:8786' processes=3 cores=24>"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import xarray as xr\n",
"import zarr\n",
"from dask.distributed import Client\n",
"client = Client()\n",
"client.get_versions(check=True)\n",
"client"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [],
"source": [
"sst_netcdf = 'https://podaac-opendap.jpl.nasa.gov:443/opendap/allData/ghrsst/data/GDS2/L4/GLOB/JPL/MUR/v4.1/2002/152/20020601090000-JPL-L4_GHRSST-SSTfnd-MUR-GLOB-v02.0-fv04.1.nc'\n",
"files = [ sst_netcdf ]\n",
"ds = xr.open_dataset(files[0], chunks={'time': 366, 'lat': 250, 'lon': 500})"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
"compressor = zarr.Blosc(cname='zstd', clevel=5, shuffle=zarr.Blosc.AUTOSHUFFLE)\n",
"encoding = {v: {'compressor': compressor} for v in ds.data_vars}"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"ename": "ValueError",
"evalue": "array not found at path 'analysed_sst'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-18-cd92f12cb6a8>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mds\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mto_zarr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'gmet.zarr'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmode\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'w'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mencoding\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mencoding\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mconsolidated\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/xarray/core/dataset.py\u001b[0m in \u001b[0;36mto_zarr\u001b[0;34m(self, store, mode, synchronizer, group, encoding, compute, consolidated)\u001b[0m\n\u001b[1;32m 1366\u001b[0m return to_zarr(self, store=store, mode=mode, synchronizer=synchronizer,\n\u001b[1;32m 1367\u001b[0m \u001b[0mgroup\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mgroup\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mencoding\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mencoding\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcompute\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcompute\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1368\u001b[0;31m consolidated=consolidated)\n\u001b[0m\u001b[1;32m 1369\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1370\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m__repr__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/xarray/backends/api.py\u001b[0m in \u001b[0;36mto_zarr\u001b[0;34m(dataset, store, mode, synchronizer, group, encoding, compute, consolidated)\u001b[0m\n\u001b[1;32m 975\u001b[0m \u001b[0;31m# TODO: figure out how to properly handle unlimited_dims\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 976\u001b[0m \u001b[0mdump_to_store\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdataset\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mzstore\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mwriter\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mencoding\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mencoding\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 977\u001b[0;31m \u001b[0mwrites\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mwriter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msync\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcompute\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcompute\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 978\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 979\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mcompute\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/xarray/backends/common.py\u001b[0m in \u001b[0;36msync\u001b[0;34m(self, compute)\u001b[0m\n\u001b[1;32m 176\u001b[0m delayed_store = da.store(self.sources, self.targets,\n\u001b[1;32m 177\u001b[0m \u001b[0mlock\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlock\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcompute\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcompute\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 178\u001b[0;31m flush=True)\n\u001b[0m\u001b[1;32m 179\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msources\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 180\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtargets\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/dask/array/core.py\u001b[0m in \u001b[0;36mstore\u001b[0;34m(sources, targets, lock, regions, compute, return_stored, **kwargs)\u001b[0m\n\u001b[1;32m 769\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 770\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mcompute\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 771\u001b[0;31m \u001b[0mresult\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompute\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 772\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 773\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/dask/base.py\u001b[0m in \u001b[0;36mcompute\u001b[0;34m(self, **kwargs)\u001b[0m\n\u001b[1;32m 154\u001b[0m \u001b[0mdask\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbase\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcompute\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 155\u001b[0m \"\"\"\n\u001b[0;32m--> 156\u001b[0;31m \u001b[0;34m(\u001b[0m\u001b[0mresult\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcompute\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtraverse\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 157\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 158\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/dask/base.py\u001b[0m in \u001b[0;36mcompute\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 396\u001b[0m \u001b[0mkeys\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__dask_keys__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mcollections\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 397\u001b[0m \u001b[0mpostcomputes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__dask_postcompute__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mcollections\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 398\u001b[0;31m \u001b[0mresults\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mschedule\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdsk\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkeys\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 399\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mrepack\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0ma\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mzip\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresults\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpostcomputes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 400\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/distributed/client.py\u001b[0m in \u001b[0;36mget\u001b[0;34m(self, dsk, keys, restrictions, loose_restrictions, resources, sync, asynchronous, direct, retries, priority, fifo_timeout, actors, **kwargs)\u001b[0m\n\u001b[1;32m 2336\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2337\u001b[0m results = self.gather(packed, asynchronous=asynchronous,\n\u001b[0;32m-> 2338\u001b[0;31m direct=direct)\n\u001b[0m\u001b[1;32m 2339\u001b[0m \u001b[0;32mfinally\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2340\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mf\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mfutures\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/tornado/gen.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1139\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mexc_info\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1140\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1141\u001b[0;31m \u001b[0myielded\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgen\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mthrow\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mexc_info\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1142\u001b[0m \u001b[0;32mfinally\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1143\u001b[0m \u001b[0;31m# Break up a reference to itself\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/distributed/client.py\u001b[0m in \u001b[0;36m_gather\u001b[0;34m(self, futures, errors, direct, local_worker)\u001b[0m\n\u001b[1;32m 1501\u001b[0m six.reraise(type(exception),\n\u001b[1;32m 1502\u001b[0m \u001b[0mexception\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1503\u001b[0;31m traceback)\n\u001b[0m\u001b[1;32m 1504\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0merrors\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'skip'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1505\u001b[0m \u001b[0mbad_keys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/six.py\u001b[0m in \u001b[0;36mreraise\u001b[0;34m(tp, value, tb)\u001b[0m\n\u001b[1;32m 690\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtp\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 691\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__traceback__\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mtb\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 692\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwith_traceback\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 693\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 694\u001b[0m \u001b[0;32mfinally\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/distributed/protocol/pickle.py\u001b[0m in \u001b[0;36mloads\u001b[0;34m()\u001b[0m\n\u001b[1;32m 57\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mloads\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 58\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 59\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mpickle\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloads\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 60\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mException\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 61\u001b[0m \u001b[0mlogger\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minfo\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Failed to deserialize %s\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m10000\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mexc_info\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/zarr/core.py\u001b[0m in \u001b[0;36m__setstate__\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1941\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1942\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m__setstate__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstate\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1943\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mstate\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1944\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1945\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_synchronized_op\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/zarr/core.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m()\u001b[0m\n\u001b[1;32m 122\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 123\u001b[0m \u001b[0;31m# initialize metadata\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 124\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_load_metadata\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 125\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 126\u001b[0m \u001b[0;31m# initialize attributes\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/zarr/core.py\u001b[0m in \u001b[0;36m_load_metadata\u001b[0;34m()\u001b[0m\n\u001b[1;32m 139\u001b[0m \u001b[0;34m\"\"\"(Re)load metadata from store.\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 140\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_synchronizer\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 141\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_load_metadata_nosync\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 142\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 143\u001b[0m \u001b[0mmkey\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_key_prefix\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0marray_meta_key\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/zarr/core.py\u001b[0m in \u001b[0;36m_load_metadata_nosync\u001b[0;34m()\u001b[0m\n\u001b[1;32m 150\u001b[0m \u001b[0mmeta_bytes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_store\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mmkey\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 151\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 152\u001b[0;31m \u001b[0merr_array_not_found\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_path\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 153\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 154\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/zarr/errors.py\u001b[0m in \u001b[0;36merr_array_not_found\u001b[0;34m()\u001b[0m\n\u001b[1;32m 23\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 24\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0merr_array_not_found\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 25\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'array not found at path %r'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mpath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 26\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 27\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mValueError\u001b[0m: array not found at path 'analysed_sst'"
]
}
],
"source": [
"ds.to_zarr('gmet.zarr', mode='w', encoding=encoding, consolidated=True)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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