Making a simple map of a variable - Ocean Biogeochemistry Cookbook

Overview¶

Take the data we read in in the previous notebook, and learn how to make a simple map of a few different variables.

Spin up a Dask cluster and load the data
Super quick plot
Two nicer plots on a map projection

Prerequisites¶

Concepts	Importance	Notes
Matplotlib	Necessary
Intro to Cartopy	Necessary
Dask Cookbook	Helpful
Intro to Xarray	Helpful

Time to learn: 10 min

Imports¶

import xarray as xr
from dask.distributed import LocalCluster
import glob
import numpy as np
import matplotlib.pyplot as plt
import cartopy
import cartopy.crs as ccrs
import pop_tools
import s3fs

from module import adjust_pop_grid
from display_source import display_source

/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/pop_tools/__init__.py:4: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import DistributionNotFound, get_distribution

Connect to cluster¶

Since we’re doing a little more processing in this notebook, we spin up a local Dask cluster. See the Dask Cookbook or Dask tutorial to learn more about this!

cluster = LocalCluster()
client = cluster.get_client()

/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/node.py:187: UserWarning: Port 8787 is already in use.
Perhaps you already have a cluster running?
Hosting the HTTP server on port 45485 instead
  warnings.warn(

Load the data¶

jetstream_url = 'https://js2.jetstream-cloud.org:8001/'

s3 = s3fs.S3FileSystem(anon=True, client_kwargs=dict(endpoint_url=jetstream_url))

# Generate a list of all files in CESM folder
s3path = 's3://pythia/ocean-bgc/cesm/g.e22.GOMIPECOIAF_JRA-1p4-2018.TL319_g17.4p2z.002branch/ocn/proc/tseries/month_1/*'
remote_files = s3.glob(s3path)
s3.invalidate_cache()

# Open all files from folder
fileset = [s3.open(file) for file in remote_files]

# Open with xarray
ds = xr.open_mfdataset(fileset, data_vars="minimal", coords='minimal', compat="override", parallel=True,
                       drop_variables=["transport_components", "transport_regions", 'moc_components'], decode_times=True)

ds

Fetching long content....

2025-09-03 01:42:13,907 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:          (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT             (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG            (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time             (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12...
Dimensions without coordinates: nlat, nlon
Data variables:
    photoC_TOT_zint  (time, nlat, nlon) float32 59MB dask.array<chunksize=(120, 384, 320), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:13,946 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:                    (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT                       (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG                      (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time                       (time) object 960B 2010-01-16 12:00:00 ... 201...
Dimensions without coordinates: nlat, nlon
Data variables:
    sp_P_lim_Cweight_avg_100m  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:13,980 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:          (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT             (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG            (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time             (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12...
Dimensions without coordinates: nlat, nlon
Data variables:
    diat_P_lim_surf  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:13,955 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 4GB
Dimensions:  (time: 120, z_t: 60, nlat: 384, nlon: 320)
Coordinates:
    TLAT     (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG    (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time     (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:00:00
  * z_t      (z_t) float32 240B 500.0 1.5e+03 2.5e+03 ... 5.125e+05 5.375e+05
Dimensions without coordinates: nlat, nlon
Data variables:
    TEMP     (time, z_t, nlat, nlon) float32 4GB dask.array<chunksize=(30, 15, 96, 80), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,011 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7fa9d7c92c20>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,060 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:          (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT             (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG            (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time             (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12...
Dimensions without coordinates: nlat, nlon
Data variables:
    diat_N_lim_surf  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,050 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7fa9dc2a6ce0>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,026 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:                       (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT                          (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG                         (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time                          (time) object 960B 2010-01-16 12:00:00 ... ...
Dimensions without coordinates: nlat, nlon
Data variables:
    diaz_Fe_lim_Cweight_avg_100m  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,083 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7fab495646a0>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled

2025-09-03 01:42:14,118 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:           (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT              (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG             (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time              (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 1...
Dimensions without coordinates: nlat, nlon
Data variables:
    diat_Fe_lim_surf  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,133 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 4GB
Dimensions:  (time: 120, z_t: 60, nlat: 384, nlon: 320)
Coordinates:
    TLAT     (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG    (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time     (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:00:00
  * z_t      (z_t) float32 240B 500.0 1.5e+03 2.5e+03 ... 5.125e+05 5.375e+05
Dimensions without coordinates: nlat, nlon
Data variables:
    SALT     (time, z_t, nlat, nlon) float32 4GB dask.array<chunksize=(30, 15, 96, 80), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,143 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 887MB
Dimensions:   (time: 120, z_t_150m: 15, nlat: 384, nlon: 320)
Coordinates:
    TLAT      (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG     (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time      (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:00:00
  * z_t_150m  (z_t_150m) float32 60B 500.0 1.5e+03 2.5e+03 ... 1.35e+04 1.45e+04
Dimensions without coordinates: nlat, nlon
Data variables:
    diatC     (time, z_t_150m, nlat, nlon) float32 885MB dask.array<chunksize=(40, 5, 128, 107), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,208 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7fab49a116c0>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,204 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:                      (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT                         (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG                        (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time                         (time) object 960B 2010-01-16 12:00:00 ... 2...
Dimensions without coordinates: nlat, nlon
Data variables:
    diat_P_lim_Cweight_avg_100m  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,217 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7f44efd7fb80>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,282 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:                      (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT                         (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG                        (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time                         (time) object 960B 2010-01-16 12:00:00 ... 2...
Dimensions without coordinates: nlat, nlon
Data variables:
    diaz_P_lim_Cweight_avg_100m  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,283 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:                       (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT                          (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG                         (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time                          (time) object 960B 2010-01-16 12:00:00 ... ...
Dimensions without coordinates: nlat, nlon
Data variables:
    diat_Fe_lim_Cweight_avg_100m  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,369 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7fa9d77a0d00>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled

2025-09-03 01:42:14,342 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:          (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT             (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG            (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time             (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12...
Dimensions without coordinates: nlat, nlon
Data variables:
    diaz_P_lim_surf  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,396 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7f44effd9420>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,399 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:                        (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT                           (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG                          (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time                           (time) object 960B 2010-01-16 12:00:00 ......
Dimensions without coordinates: nlat, nlon
Data variables:
    cocco_Fe_lim_Cweight_avg_100m  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,458 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:           (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT              (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG             (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time              (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 1...
Dimensions without coordinates: nlat, nlon
Data variables:
    photoC_diaz_zint  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,445 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:                       (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT                          (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG                         (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time                          (time) object 960B 2010-01-16 12:00:00 ... ...
Dimensions without coordinates: nlat, nlon
Data variables:
    cocco_N_lim_Cweight_avg_100m  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,494 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:            (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT               (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG              (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time               (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 ...
Dimensions without coordinates: nlat, nlon
Data variables:
    cocco_Fe_lim_surf  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,519 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7f44eff7a800>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,536 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7f44ef868fa0>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,542 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7fab49cdb9a0>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,564 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7f44eff12500>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,522 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 887MB
Dimensions:   (time: 120, z_t_150m: 15, nlat: 384, nlon: 320)
Coordinates:
    TLAT      (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG     (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time      (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:00:00
  * z_t_150m  (z_t_150m) float32 60B 500.0 1.5e+03 2.5e+03 ... 1.35e+04 1.45e+04
Dimensions without coordinates: nlat, nlon
Data variables:
    spC       (time, z_t_150m, nlat, nlon) float32 885MB dask.array<chunksize=(40, 5, 128, 107), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled

2025-09-03 01:42:14,615 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7fa9d7e0ec20>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,662 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7f44f42585e0>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,595 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 4GB
Dimensions:  (time: 120, z_t: 60, nlat: 384, nlon: 320)
Coordinates:
    TLAT     (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG    (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time     (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:00:00
  * z_t      (z_t) float32 240B 500.0 1.5e+03 2.5e+03 ... 5.125e+05 5.375e+05
Dimensions without coordinates: nlat, nlon
Data variables:
    NO3      (time, z_t, nlat, nlon) float32 4GB dask.array<chunksize=(30, 15, 96, 80), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,656 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7fa9d780ba00>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,733 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7fa9ce68b520>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,729 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:           (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT              (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG             (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time              (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 1...
Dimensions without coordinates: nlat, nlon
Data variables:
    photoC_diat_zint  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,750 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 887MB
Dimensions:   (time: 120, z_t_150m: 15, nlat: 384, nlon: 320)
Coordinates:
    TLAT      (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG     (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time      (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:00:00
  * z_t_150m  (z_t_150m) float32 60B 500.0 1.5e+03 2.5e+03 ... 1.35e+04 1.45e+04
Dimensions without coordinates: nlat, nlon
Data variables:
    mesozooC  (time, z_t_150m, nlat, nlon) float32 885MB dask.array<chunksize=(40, 5, 128, 107), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,828 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7fa9dc1bb3a0>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled

2025-09-03 01:42:14,862 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:         (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT            (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG           (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time            (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:...
Dimensions without coordinates: nlat, nlon
Data variables:
    photoC_sp_zint  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,844 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 887MB
Dimensions:   (time: 120, z_t_150m: 15, nlat: 384, nlon: 320)
Coordinates:
    TLAT      (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG     (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time      (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:00:00
  * z_t_150m  (z_t_150m) float32 60B 500.0 1.5e+03 2.5e+03 ... 1.35e+04 1.45e+04
Dimensions without coordinates: nlat, nlon
Data variables:
    diazC     (time, z_t_150m, nlat, nlon) float32 885MB dask.array<chunksize=(40, 5, 128, 107), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,886 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 887MB
Dimensions:    (time: 120, z_t_150m: 15, nlat: 384, nlon: 320)
Coordinates:
    TLAT       (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG      (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time       (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:00:00
  * z_t_150m   (z_t_150m) float32 60B 500.0 1.5e+03 ... 1.35e+04 1.45e+04
Dimensions without coordinates: nlat, nlon
Data variables:
    microzooC  (time, z_t_150m, nlat, nlon) float32 885MB dask.array<chunksize=(40, 5, 128, 107), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:14,986 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:                         (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT                            (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG                           (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time                            (time) object 960B 2010-01-16 12:00:00 .....
Dimensions without coordinates: nlat, nlon
Data variables:
    diat_SiO3_lim_Cweight_avg_100m  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:15,083 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 61MB
Dimensions:                       (time: 120, nlat: 384, nlon: 320)
Coordinates:
    TLAT                          (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG                         (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time                          (time) object 960B 2010-01-16 12:00:00 ... ...
Dimensions without coordinates: nlat, nlon
Data variables:
    cocco_C_lim_Cweight_avg_100m  (time, nlat, nlon) float32 59MB dask.array<chunksize=(60, 192, 160), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled

2025-09-03 01:42:14,970 - distributed.protocol.pickle - ERROR - Failed to serialize <bound method H5NetCDFStore.close of <xarray.backends.h5netcdf_.H5NetCDFStore object at 0x7f44efd06140>>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:15,152 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 4GB
Dimensions:  (time: 120, z_t: 60, nlat: 384, nlon: 320)
Coordinates:
    TLAT     (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG    (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time     (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:00:00
  * z_t      (z_t) float32 240B 500.0 1.5e+03 2.5e+03 ... 5.125e+05 5.375e+05
Dimensions without coordinates: nlat, nlon
Data variables:
    PO4      (time, z_t, nlat, nlon) float32 4GB dask.array<chunksize=(30, 15, 96, 80), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled
2025-09-03 01:42:15,240 - distributed.protocol.pickle - ERROR - Failed to serialize <xarray.Dataset> Size: 887MB
Dimensions:   (time: 120, z_t_150m: 15, nlat: 384, nlon: 320)
Coordinates:
    TLAT      (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLONG     (nlat, nlon) float64 983kB dask.array<chunksize=(384, 320), meta=np.ndarray>
  * time      (time) object 960B 2010-01-16 12:00:00 ... 2019-12-16 12:00:00
  * z_t_150m  (z_t_150m) float32 60B 500.0 1.5e+03 2.5e+03 ... 1.35e+04 1.45e+04
Dimensions without coordinates: nlat, nlon
Data variables:
    coccoC    (time, z_t_150m, nlat, nlon) float32 885MB dask.array<chunksize=(40, 5, 128, 107), meta=np.ndarray>.
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled

2025-09-03 01:42:15,546 - distributed.protocol.core - CRITICAL - Failed to deserialize
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/core.py", line 175, in loads
    return msgpack.loads(
           ~~~~~~~~~~~~~^
        frames[0], object_hook=_decode_default, use_list=False, **msgpack_opts
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "msgpack/_unpacker.pyx", line 194, in msgpack._cmsgpack.unpackb
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/core.py", line 159, in _decode_default
    return merge_and_deserialize(
        sub_header, sub_frames, deserializers=deserializers
    )
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/contextlib.py", line 85, in inner
    return func(*args, **kwds)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/serialize.py", line 525, in merge_and_deserialize
    return deserialize(header, merged_frames, deserializers=deserializers)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/serialize.py", line 452, in deserialize
    return loads(header, frames)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/serialize.py", line 195, in serialization_error_loads
    raise TypeError(msg)
TypeError: Could not serialize object of type method
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/serialize.py", line 366, in serialize
    header, frames = dumps(x, context=context) if wants_context else dumps(x)
                     ~~~~~^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/serialize.py", line 78, in pickle_dumps
    frames[0] = pickle.dumps(
                ~~~~~~~~~~~~^
        x,
        ^^
        buffer_callback=buffer_callback,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        protocol=context.get("pickle-protocol", None) if context else None,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[3], line 14
     11 fileset = [s3.open(file) for file in remote_files]
     13 # Open with xarray
---> 14 ds = xr.open_mfdataset(fileset, data_vars="minimal", coords='minimal', compat="override", parallel=True,
     15                        drop_variables=["transport_components", "transport_regions", 'moc_components'], decode_times=True)
     17 ds

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/xarray/backends/api.py:1802, in open_mfdataset(paths, chunks, concat_dim, compat, preprocess, engine, data_vars, coords, combine, parallel, join, attrs_file, combine_attrs, errors, **kwargs)
   1797     datasets = [preprocess(ds) for ds in datasets]
   1799 if parallel:
   1800     # calling compute here will return the datasets/file_objs lists,
   1801     # the underlying datasets will still be stored as dask arrays
-> 1802     datasets, closers = dask.compute(datasets, closers)
   1804 # Combine all datasets, closing them in case of a ValueError
   1805 try:

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/dask/base.py:681, in compute(traverse, optimize_graph, scheduler, get, *args, **kwargs)
    678     expr = expr.optimize()
    679     keys = list(flatten(expr.__dask_keys__()))
--> 681     results = schedule(expr, keys, **kwargs)
    683 return repack(results)

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/utils_comm.py:416, in retry_operation(coro, operation, *args, **kwargs)
    410 retry_delay_min = parse_timedelta(
    411     dask.config.get("distributed.comm.retry.delay.min"), default="s"
    412 )
    413 retry_delay_max = parse_timedelta(
    414     dask.config.get("distributed.comm.retry.delay.max"), default="s"
    415 )
--> 416 return await retry(
    417     partial(coro, *args, **kwargs),
    418     count=retry_count,
    419     delay_min=retry_delay_min,
    420     delay_max=retry_delay_max,
    421     operation=operation,
    422 )

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/utils_comm.py:395, in retry(coro, count, delay_min, delay_max, jitter_fraction, retry_on_exceptions, operation)
    393             delay *= 1 + random.random() * jitter_fraction
    394         await asyncio.sleep(delay)
--> 395 return await coro()

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/core.py:1259, in PooledRPCCall.__getattr__.<locals>.send_recv_from_rpc(**kwargs)
   1257 prev_name, comm.name = comm.name, "ConnectionPool." + key
   1258 try:
-> 1259     return await send_recv(comm=comm, op=key, **kwargs)
   1260 finally:
   1261     self.pool.reuse(self.addr, comm)

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/core.py:1018, in send_recv(comm, reply, serializers, deserializers, **kwargs)
   1016 await comm.write(msg, serializers=serializers, on_error="raise")
   1017 if reply:
-> 1018     response = await comm.read(deserializers=deserializers)
   1019 else:
   1020     response = None

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/comm/tcp.py:248, in TCP.read(self, deserializers)
    246 else:
    247     try:
--> 248         msg = await from_frames(
    249             frames,
    250             deserialize=self.deserialize,
    251             deserializers=deserializers,
    252             allow_offload=self.allow_offload,
    253         )
    254     except EOFError:
    255         # Frames possibly garbled or truncated by communication error
    256         self.abort()

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/comm/utils.py:78, in from_frames(frames, deserialize, deserializers, allow_offload)
     76     res = await offload(_from_frames)
     77 else:
---> 78     res = _from_frames()
     80 return res

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/comm/utils.py:61, in from_frames.<locals>._from_frames()
     59 def _from_frames():
     60     try:
---> 61         return protocol.loads(
     62             frames, deserialize=deserialize, deserializers=deserializers
     63         )
     64     except EOFError:
     65         if size > 1000:

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/core.py:175, in loads(frames, deserialize, deserializers)
    172             return pickle.loads(sub_header["pickled-obj"], buffers=sub_frames)
    173         return msgpack_decode_default(obj)
--> 175     return msgpack.loads(
    176         frames[0], object_hook=_decode_default, use_list=False, **msgpack_opts
    177     )
    179 except Exception:
    180     logger.critical("Failed to deserialize", exc_info=True)

File msgpack/_unpacker.pyx:194, in msgpack._cmsgpack.unpackb()

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/core.py:159, in loads.<locals>._decode_default(obj)
    157     if "compression" in sub_header:
    158         sub_frames = decompress(sub_header, sub_frames)
--> 159     return merge_and_deserialize(
    160         sub_header, sub_frames, deserializers=deserializers
    161     )
    162 else:
    163     return Serialized(sub_header, sub_frames)

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/contextlib.py:85, in ContextDecorator.__call__.<locals>.inner(*args, **kwds)
     82 @wraps(func)
     83 def inner(*args, **kwds):
     84     with self._recreate_cm():
---> 85         return func(*args, **kwds)

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/serialize.py:525, in merge_and_deserialize(header, frames, deserializers)
    521             merged = host_array_from_buffers(subframes)
    523         merged_frames.append(merged)
--> 525 return deserialize(header, merged_frames, deserializers=deserializers)

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/serialize.py:452, in deserialize(header, frames, deserializers)
    447     raise TypeError(
    448         "Data serialized with %s but only able to deserialize "
    449         "data with %s" % (name, str(list(deserializers)))
    450     )
    451 dumps, loads, wants_context = families[name]
--> 452 return loads(header, frames)

File ~/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/serialize.py:195, in serialization_error_loads(header, frames)
    193 def serialization_error_loads(header, frames):
    194     msg = "\n".join([codecs.decode(frame, "utf8") for frame in frames])
--> 195     raise TypeError(msg)

TypeError: Could not serialize object of type method
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
    ~~~~~~~~~~~~^^^
TypeError: cannot pickle 'module' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/serialize.py", line 366, in serialize
    header, frames = dumps(x, context=context) if wants_context else dumps(x)
                     ~~~~~^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/serialize.py", line 78, in pickle_dumps
    frames[0] = pickle.dumps(
                ~~~~~~~~~~~~^
        x,
        ^^
        buffer_callback=buffer_callback,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        protocol=context.get("pickle-protocol", None) if context else None,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/distributed/protocol/pickle.py", line 80, in dumps
    result = cloudpickle.dumps(x, **dump_kwargs)
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1537, in dumps
    cp.dump(obj)
    ~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/cloudpickle/cloudpickle.py", line 1303, in dump
    return super().dump(obj)
           ~~~~~~~~~~~~^^^^^
  File "/home/runner/micromamba/envs/ocean-bgc-cookbook-dev/lib/python3.13/site-packages/h5py/_hl/base.py", line 369, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled

Super quick plot¶

We use xarray’s isel() (select by index) function to grab the first entry in time and vertical coordinate available in our data set. Note that our dataset has some metadata associated with it, so xarray knows that the units are in degrees Celsius without us manually specifying. Xarray’s plot() function is great for looking at data quickly to make sure things look right before diving into more involved analysis or plotting.

We arbitrarily choose to plot temperature, but there are lots of options for variables to plot!

ds["TEMP"].isel(time=0, z_t=0).plot()

Making a plot on a nicer map projection¶

Bringing in some POP grid tools¶

This version of CESM uses POP2 (the Parallel Ocean Program) as its ocean model. All of the ocean variable output is on the POP grid, which requires some extra wrangling to get it to work properly with standard mapping utilities.

ds_grid = pop_tools.get_grid('POP_gx1v7')
lons = ds_grid.TLONG
lats = ds_grid.TLAT
depths = ds_grid.z_t * 0.01

In this Cookbook, we have written a function for adjusting the POP2 grid. For better code reuse, we have moved this code into a module called module.py that is imported into every notebook within this Cookbook. The content of module.py is:

display_source(adjust_pop_grid)

Making the map¶

fig = plt.figure(figsize=(8,6))
ax = fig.add_subplot(1,1,1, projection=ccrs.Robinson(central_longitude=305.0))

# Using the utilities we added above to process our data, and plotting it
lon, lat, field = adjust_pop_grid(lons, lats, ds["TEMP"].isel(time=0, z_t=0))
pc1=ax.pcolormesh(lon, lat,field, cmap='plasma',
                  vmin=0, vmax=30,
                 transform=ccrs.PlateCarree())

# Adding the land features
land = cartopy.feature.NaturalEarthFeature('physical', 'land', scale='110m', edgecolor='k', facecolor='white', linewidth=0.5)
ax.add_feature(land)

# Adding colorbar and title
cbar1 = fig.colorbar(pc1, ax=ax,extend='max',label=ds["TEMP"].units)
ax.set_title('CESM Surface Temperature', fontsize=10)

plt.show()

Let’s try the same thing with another variable, salinity (SALT). We replace which variable we’re extracting from ds in the adjust_pop_grid() function, where we preprocess the data. If you’re trying this on your own, some other good ones to try looking at are dissolved inorganic carbon (DIC), oxygen (O2), or pH (PH).

fig = plt.figure(figsize=(8,6))
ax = fig.add_subplot(1,1,1, projection=ccrs.Robinson(central_longitude=305.0))

# Using the utilities we added above to process our data, and plotting it
lon, lat, field = adjust_pop_grid(lons, lats, ds['SALT'].isel(time=0, z_t=0))

# Pick a different colorscheme from the plot above so we can distinguish them more easily
pc1=ax.pcolormesh(lon, lat,field, cmap='cividis',
                  vmin=32, vmax=38,
                 transform=ccrs.PlateCarree())

# Adding the land features
land = cartopy.feature.NaturalEarthFeature('physical', 'land', scale='110m', edgecolor='k', facecolor='white', linewidth=0.5)
ax.add_feature(land)

# Adding colorbar and title
cbar1 = fig.colorbar(pc1, ax=ax,extend='both',label=ds["SALT"].units)
ax.set_title('CESM Surface Salinity', fontsize=10)

plt.show()

Close the Dask cluster we spun up at the beginning.

cluster.close()

Summary¶

You’ve learned how to make simple plots of CESM output.

Resources and references¶

Dask tutorial

Intro

Reading in CESM output

Nutrients

Ocean macronutrients