Phytoplankton biomass#

%load_ext autoreload
%autoreload 2

import xarray as xr

from dask.distributed import Client

import catalog
import util

xr.set_options(keep_attrs=True)

/glade/work/kristenk/miniconda/envs/cesm-exp/lib/python3.7/site-packages/dask_jobqueue/core.py:20: FutureWarning: tmpfile is deprecated and will be removed in a future release. Please use dask.utils.tmpfile instead.
  from distributed.utils import tmpfile

<xarray.core.options.set_options at 0x2aca4bccfc10>

import matplotlib.pyplot as plt
import cartopy
import cartopy.crs as ccrs
import pop_tools

ds_grid = pop_tools.get_grid('POP_gx1v7')
lons=ds_grid.TLONG
lats=ds_grid.TLAT

Parameters#

casename = 'g.e22a06.G1850ECOIAF_JRA_PHYS_DEV.TL319_g17.scope_v1'
component = 'pop'
stream = 'h'

cluster_scheduler_address = None

# Parameters
casename = "g.e22.GOMIPECOIAF_JRA-1p4-2018.TL319_g17.4p2z.001branch"
component = "pop"
stream = "h"
cluster_scheduler_address = "tcp://10.12.206.3:35506"

assert component in ['pop']
assert stream in ['h', 'h.ecosys.nday1']

Connect to cluster#

if cluster_scheduler_address is None:
    cluster, client = util.get_ClusterClient()
    cluster.scale(12)
else:
    client = Client(cluster_scheduler_address)
client

Client

Client-e30da450-9356-11ed-9501-3cecef1acc46

Connection method: Direct
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/8787/status

Scheduler Info

Scheduler

Scheduler-7b28f886-17c1-40f8-ae24-3360603786e8

Comm: tcp://10.12.206.3:35506	Workers: 32
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/8787/status	Total threads: 32
Started: 13 minutes ago	Total memory: 744.96 GiB

Workers

Worker: PBSCluster-0

Comm: tcp://10.12.206.60:40381	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/37473/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.60:43642
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-she593m8
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 0.0%	Last seen: Just now
Memory usage: 291.93 MiB	Spilled bytes: 0 B
Read bytes: 219.43 MiB	Write bytes: 144.36 kiB

Worker: PBSCluster-1

Comm: tcp://10.12.206.57:34913	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/43168/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.57:40520
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-ais4w5nl
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 4.0%	Last seen: Just now
Memory usage: 452.27 MiB	Spilled bytes: 0 B
Read bytes: 32.30 MiB	Write bytes: 26.21 kiB

Worker: PBSCluster-10

Comm: tcp://10.12.206.55:40610	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/41580/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.55:41770
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-24q12p4a
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 452.43 MiB	Spilled bytes: 0 B
Read bytes: 26.50 kiB	Write bytes: 16.21 kiB

Worker: PBSCluster-11

Comm: tcp://10.12.206.35:36760	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/34231/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.35:39163
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-tm589a2g
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 0.0%	Last seen: Just now
Memory usage: 384.21 MiB	Spilled bytes: 0 B
Read bytes: 32.86 kiB	Write bytes: 15.10 kiB

Worker: PBSCluster-12

Comm: tcp://10.12.206.42:46667	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/44609/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.42:43503
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-63bl396p
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 459.02 MiB	Spilled bytes: 0 B
Read bytes: 40.03 kiB	Write bytes: 25.18 kiB

Worker: PBSCluster-13

Comm: tcp://10.12.206.55:34741	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/41987/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.55:39933
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-3taktpky
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 397.91 MiB	Spilled bytes: 0 B
Read bytes: 26.68 kiB	Write bytes: 11.49 kiB

Worker: PBSCluster-14

Comm: tcp://10.12.206.42:44723	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/38884/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.42:37139
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-btgwv71o
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 419.00 MiB	Spilled bytes: 0 B
Read bytes: 40.15 kiB	Write bytes: 28.41 kiB

Worker: PBSCluster-15

Comm: tcp://10.12.206.60:34840	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/36356/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.60:36517
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-s50upym9
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 0.0%	Last seen: Just now
Memory usage: 411.21 MiB	Spilled bytes: 0 B
Read bytes: 221.07 MiB	Write bytes: 145.31 kiB

Worker: PBSCluster-16

Comm: tcp://10.12.206.55:33480	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/44604/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.55:34515
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-20gqvxq8
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 386.36 MiB	Spilled bytes: 0 B
Read bytes: 26.50 kiB	Write bytes: 15.41 kiB

Worker: PBSCluster-17

Comm: tcp://10.12.206.42:46005	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/44117/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.42:32947
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-18iilri4
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 297.92 MiB	Spilled bytes: 0 B
Read bytes: 40.01 kiB	Write bytes: 27.59 kiB

Worker: PBSCluster-18

Comm: tcp://10.12.206.60:33226	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/42773/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.60:46337
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-8qq6z3y3
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 0.0%	Last seen: Just now
Memory usage: 405.38 MiB	Spilled bytes: 0 B
Read bytes: 217.51 MiB	Write bytes: 143.51 kiB

Worker: PBSCluster-19

Comm: tcp://10.12.206.36:36934	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/38605/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.36:40345
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-0wibvgh_
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 4.0%	Last seen: Just now
Memory usage: 337.22 MiB	Spilled bytes: 0 B
Read bytes: 95.67 kiB	Write bytes: 81.99 kiB

Worker: PBSCluster-2

Comm: tcp://10.12.206.42:35532	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/37233/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.42:38029
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-tvn8qi89
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 0.0%	Last seen: Just now
Memory usage: 400.52 MiB	Spilled bytes: 0 B
Read bytes: 40.08 kiB	Write bytes: 26.02 kiB

Worker: PBSCluster-20

Comm: tcp://10.12.206.57:44618	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/35828/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.57:39590
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-j87b3i6z
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 0.0%	Last seen: Just now
Memory usage: 410.20 MiB	Spilled bytes: 0 B
Read bytes: 32.27 MiB	Write bytes: 24.58 kiB

Worker: PBSCluster-21

Comm: tcp://10.12.206.42:36146	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/42013/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.42:42567
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-te65hpsa
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 410.47 MiB	Spilled bytes: 0 B
Read bytes: 40.74 kiB	Write bytes: 31.30 kiB

Worker: PBSCluster-22

Comm: tcp://10.12.206.37:45266	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/41617/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.37:46778
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-6zjl_rf2
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 410.84 MiB	Spilled bytes: 0 B
Read bytes: 9.09 MiB	Write bytes: 132.72 kiB

Worker: PBSCluster-23

Comm: tcp://10.12.206.57:36646	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/33282/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.57:39220
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-tedt0oqb
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 439.96 MiB	Spilled bytes: 0 B
Read bytes: 32.28 MiB	Write bytes: 25.39 kiB

Worker: PBSCluster-24

Comm: tcp://10.12.206.35:43781	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/41280/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.35:41682
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-oenmf7ye
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 298.23 MiB	Spilled bytes: 0 B
Read bytes: 33.11 kiB	Write bytes: 17.65 kiB

Worker: PBSCluster-25

Comm: tcp://10.12.206.42:38958	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/45762/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.42:41096
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-r999w54s
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 301.61 MiB	Spilled bytes: 0 B
Read bytes: 40.17 kiB	Write bytes: 28.42 kiB

Worker: PBSCluster-26

Comm: tcp://10.12.206.35:41019	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/46197/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.35:41093
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-n8z_ugpj
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 330.75 MiB	Spilled bytes: 0 B
Read bytes: 33.12 kiB	Write bytes: 17.66 kiB

Worker: PBSCluster-27

Comm: tcp://10.12.206.40:37756	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/34868/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.40:46061
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-ah4h4uwy
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 351.82 MiB	Spilled bytes: 0 B
Read bytes: 26.35 kiB	Write bytes: 13.25 kiB

Worker: PBSCluster-28

Comm: tcp://10.12.206.55:40536	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/40763/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.55:43688
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-mqh1_swd
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 0.0%	Last seen: Just now
Memory usage: 378.38 MiB	Spilled bytes: 0 B
Read bytes: 23.86 kiB	Write bytes: 17.58 kiB

Worker: PBSCluster-29

Comm: tcp://10.12.206.35:43010	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/45869/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.35:38155
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-0zp2yifw
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 307.01 MiB	Spilled bytes: 0 B
Read bytes: 32.87 kiB	Write bytes: 15.11 kiB

Worker: PBSCluster-3

Comm: tcp://10.12.206.55:43243	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/45154/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.55:40506
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-d77lpe1m
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 4.0%	Last seen: Just now
Memory usage: 292.34 MiB	Spilled bytes: 0 B
Read bytes: 26.68 kiB	Write bytes: 11.49 kiB

Worker: PBSCluster-30

Comm: tcp://10.12.206.42:40059	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/38562/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.42:35150
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-s1j98ibm
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 0.0%	Last seen: Just now
Memory usage: 401.30 MiB	Spilled bytes: 0 B
Read bytes: 40.03 kiB	Write bytes: 25.18 kiB

Worker: PBSCluster-31

Comm: tcp://10.12.206.55:40509	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/46123/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.55:42505
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-0193oowl
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 369.57 MiB	Spilled bytes: 0 B
Read bytes: 26.67 kiB	Write bytes: 14.71 kiB

Worker: PBSCluster-4

Comm: tcp://10.12.206.60:33761	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/38547/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.60:43086
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-go_20xsh
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 464.43 MiB	Spilled bytes: 0 B
Read bytes: 217.73 MiB	Write bytes: 143.89 kiB

Worker: PBSCluster-5

Comm: tcp://10.12.206.56:36183	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/39960/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.56:36523
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-ak_et0qx
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 308.13 MiB	Spilled bytes: 0 B
Read bytes: 80.86 MiB	Write bytes: 32.85 kiB

Worker: PBSCluster-6

Comm: tcp://10.12.206.55:42418	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/43316/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.55:35755
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-w069mt42
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 299.44 MiB	Spilled bytes: 0 B
Read bytes: 26.51 kiB	Write bytes: 15.41 kiB

Worker: PBSCluster-7

Comm: tcp://10.12.206.42:38064	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/33959/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.42:37237
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-8g92ok8a
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 301.73 MiB	Spilled bytes: 0 B
Read bytes: 40.57 kiB	Write bytes: 30.36 kiB

Worker: PBSCluster-8

Comm: tcp://10.12.206.35:46716	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/38950/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.35:46823
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-t0bj5mka
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 364.84 MiB	Spilled bytes: 0 B
Read bytes: 32.75 kiB	Write bytes: 15.01 kiB

Worker: PBSCluster-9

Comm: tcp://10.12.206.55:36074	Total threads: 1
Dashboard: https://jupyterhub.hpc.ucar.edu/stable/user/kristenk/proxy/41381/status	Memory: 23.28 GiB
Nanny: tcp://10.12.206.55:35112
Local directory: /glade/scratch/kristenk/dask-workers/dask-worker-space/worker-vzrt3wyj
Tasks executing: 0	Tasks in memory: 0
Tasks ready: 0	Tasks in flight: 0
CPU usage: 2.0%	Last seen: Just now
Memory usage: 464.30 MiB	Spilled bytes: 0 B
Read bytes: 26.61 kiB	Write bytes: 11.46 kiB

Load the data#

dsets = catalog.to_dataset_dict(
    case=casename,
    component=component,
    stream=stream,
)
dsets.keys()

g.e22.GOMIPECOIAF_JRA-1p4-2018.TL319_g17.4p2z.001branch pop h /glade/scratch/kristenk/archive

dict_keys(['g.e22.GOMIPECOIAF_JRA-1p4-2018.TL319_g17.4p2z.001branch.pop.h'])

Compute long-term mean and plot#

ds = dsets[f'{casename}.{component}.{stream}']

Variable list#

variables =['diatC', 'coccoC','spC','diazC']

keep_vars=['z_t','z_t_150m','dz','time_bound','TAREA','TLAT','TLONG'] + variables
ds = ds.drop([v for v in ds.variables if v not in keep_vars])

ds.coccoC.isel(time=0,z_t_150m=0).plot()

<matplotlib.collections.QuadMesh at 0x2aca4ea48d10>

ds.coccoC.isel(time=6,z_t_150m=0).plot()

<matplotlib.collections.QuadMesh at 0x2aca4ffb0e50>

ds

<xarray.Dataset>
Dimensions:     (time: 120, d2: 2, z_t: 60, z_t_150m: 15, nlat: 384, nlon: 320)
Coordinates:
  * z_t         (z_t) float32 500.0 1.5e+03 2.5e+03 ... 5.125e+05 5.375e+05
  * z_t_150m    (z_t_150m) float32 500.0 1.5e+03 2.5e+03 ... 1.35e+04 1.45e+04
    TLONG       (nlat, nlon) float64 dask.array<chunksize=(384, 320), meta=np.ndarray>
    TLAT        (nlat, nlon) float64 dask.array<chunksize=(384, 320), meta=np.ndarray>
    TAREA       (nlat, nlon) float64 dask.array<chunksize=(384, 320), meta=np.ndarray>
Dimensions without coordinates: time, d2, nlat, nlon
Data variables:
    time_bound  (time, d2) float64 dask.array<chunksize=(1, 2), meta=np.ndarray>
    dz          (time, z_t) float32 dask.array<chunksize=(1, 60), meta=np.ndarray>
    spC         (time, z_t_150m, nlat, nlon) float32 dask.array<chunksize=(1, 15, 384, 320), meta=np.ndarray>
    diatC       (time, z_t_150m, nlat, nlon) float32 dask.array<chunksize=(1, 15, 384, 320), meta=np.ndarray>
    diazC       (time, z_t_150m, nlat, nlon) float32 dask.array<chunksize=(1, 15, 384, 320), meta=np.ndarray>
    coccoC      (time, z_t_150m, nlat, nlon) float32 dask.array<chunksize=(1, 15, 384, 320), meta=np.ndarray>
Attributes:
    title:             g.e22.GOMIPECOIAF_JRA-1p4-2018.TL319_g17.4p2z.001branch
    history:           none
    Conventions:       CF-1.0; http://www.cgd.ucar.edu/cms/eaton/netcdf/CF-cu...
    time_period_freq:  month_1
    model_doi_url:     https://doi.org/10.5065/D67H1H0V
    contents:          Diagnostic and Prognostic Variables
    source:            CCSM POP2, the CCSM Ocean Component
    revision:          $Id$
    calendar:          All years have exactly  365 days.
    start_time:        This dataset was created on 2022-09-27 at 10:32:16.2
    cell_methods:      cell_methods = time: mean ==> the variable values are ...

dt_wgt = ds.time_bound.diff('d2').squeeze()
dt_wgt /= dt_wgt.sum()
dt_wgt

<xarray.DataArray 'time_bound' (time: 120)>
dask.array<truediv, shape=(120,), dtype=float64, chunksize=(1,), chunktype=numpy.ndarray>
Dimensions without coordinates: time
Attributes:
    long_name:  boundaries for time-averaging interval
    units:      days since 0000-01-01 00:00:00

ds = ds.weighted(dt_wgt).mean('time')

ds['spC'].isel(z_t_150m=0).plot()

<matplotlib.collections.QuadMesh at 0x2aca60155410>

Phytoplankton biomass at the surface#

###### 
fig = plt.figure(figsize=(8,10))

ax = fig.add_subplot(4,1,1, projection=ccrs.Robinson(central_longitude=305.0))
ax.set_title('spC at surface', fontsize=12)
lon, lat, field = util.adjust_pop_grid(lons, lats,  ds.spC.isel(z_t_150m=0))
pc=ax.pcolormesh(lon, lat, field, cmap='jet',vmin=0,vmax=2,transform=ccrs.PlateCarree())
cbar1 = fig.colorbar(pc, ax=ax,extend='max',label='spC (mmol m$^{-3}$)')


ax = fig.add_subplot(4,1,2, projection=ccrs.Robinson(central_longitude=305.0))
ax.set_title('diatC at surface', fontsize=12)
lon, lat, field = util.adjust_pop_grid(lons, lats,  ds.diatC.isel(z_t_150m=0))
pc=ax.pcolormesh(lon, lat, field, cmap='jet',vmin=0,vmax=4,transform=ccrs.PlateCarree())
cbar1 = fig.colorbar(pc, ax=ax,extend='max',label='diatC (mmol m$^{-3}$)')


ax = fig.add_subplot(4,1,3, projection=ccrs.Robinson(central_longitude=305.0))
ax.set_title('coccoC at surface', fontsize=12)
lon, lat, field = util.adjust_pop_grid(lons, lats,  ds.coccoC.isel(z_t_150m=0))
pc=ax.pcolormesh(lon, lat, field, cmap='jet',vmin=0,vmax=2,transform=ccrs.PlateCarree())
cbar1 = fig.colorbar(pc, ax=ax,extend='max',label='coccoC (mmol m$^{-3}$)')

ax = fig.add_subplot(4,1,4, projection=ccrs.Robinson(central_longitude=305.0))
ax.set_title('diazC at surface', fontsize=12)
lon, lat, field = util.adjust_pop_grid(lons, lats,  ds.diazC.isel(z_t_150m=0))
pc=ax.pcolormesh(lon, lat, field, cmap='jet',vmin=0,vmax=1,transform=ccrs.PlateCarree())
cbar1 = fig.colorbar(pc, ax=ax,extend='max',label='diazC (mmol m$^{-3}$)')

Phytoplankton biomass at 100m#

###### 
fig = plt.figure(figsize=(8,10))


ax = fig.add_subplot(4,1,1, projection=ccrs.Robinson(central_longitude=305.0))
ax.set_title('spC at 100m', fontsize=12)
lon, lat, field = util.adjust_pop_grid(lons, lats,  ds.spC.isel(z_t_150m=9))
pc=ax.pcolormesh(lon, lat, field, cmap='jet',vmin=0,vmax=0.4,transform=ccrs.PlateCarree())
cbar1 = fig.colorbar(pc, ax=ax,extend='max',label='spC (mmol m$^{-3}$)')

ax = fig.add_subplot(4,1,2, projection=ccrs.Robinson(central_longitude=305.0))
ax.set_title('diatC at 100m', fontsize=12)
lon, lat, field = util.adjust_pop_grid(lons, lats,  ds.diatC.isel(z_t_150m=9))
pc=ax.pcolormesh(lon, lat, field, cmap='jet',vmin=0,vmax=0.4,transform=ccrs.PlateCarree())
cbar1 = fig.colorbar(pc, ax=ax,extend='max',label='diatC (mmol m$^{-3}$)')

ax = fig.add_subplot(4,1,3, projection=ccrs.Robinson(central_longitude=305.0))
ax.set_title('coccoC at 100m', fontsize=12)
lon, lat, field = util.adjust_pop_grid(lons, lats,  ds.coccoC.isel(z_t_150m=9))
pc=ax.pcolormesh(lon, lat, field, cmap='jet',vmin=0,vmax=0.2,transform=ccrs.PlateCarree())
cbar1 = fig.colorbar(pc, ax=ax,extend='max',label='coccoC (mmol m$^{-3}$)')

ax = fig.add_subplot(4,1,4, projection=ccrs.Robinson(central_longitude=305.0))
ax.set_title('diazC at 100m', fontsize=12)
lon, lat, field = util.adjust_pop_grid(lons, lats,  ds.diazC.isel(z_t_150m=9))
pc=ax.pcolormesh(lon, lat, field, cmap='jet',vmin=0,vmax=0.1,transform=ccrs.PlateCarree())

cbar1 = fig.colorbar(pc, ax=ax,extend='max',label='diazC (mmol m$^{-3}$)')

My CESM Experiment

Phytoplankton biomass

Contents

Phytoplankton biomass#

Parameters#

Connect to cluster#

Client

Scheduler Info

Scheduler

Workers

Worker: PBSCluster-0

Worker: PBSCluster-1

Worker: PBSCluster-10

Worker: PBSCluster-11

Worker: PBSCluster-12

Worker: PBSCluster-13

Worker: PBSCluster-14

Worker: PBSCluster-15

Worker: PBSCluster-16

Worker: PBSCluster-17

Worker: PBSCluster-18

Worker: PBSCluster-19

Worker: PBSCluster-2

Worker: PBSCluster-20

Worker: PBSCluster-21

Worker: PBSCluster-22

Worker: PBSCluster-23

Worker: PBSCluster-24

Worker: PBSCluster-25

Worker: PBSCluster-26

Worker: PBSCluster-27

Worker: PBSCluster-28

Worker: PBSCluster-29

Worker: PBSCluster-3

Worker: PBSCluster-30

Worker: PBSCluster-31

Worker: PBSCluster-4

Worker: PBSCluster-5

Worker: PBSCluster-6

Worker: PBSCluster-7

Worker: PBSCluster-8

Worker: PBSCluster-9

Load the data#

Compute long-term mean and plot#

Variable list#

Phytoplankton biomass at the surface#

Phytoplankton biomass at 100m#