%matplotlib inline
import pandas as pd
import socket
host = socket.getfqdn()
from core import load, zoom, calc, save,plots,monitor
#reload funcs after updating ./core/*.py
import importlib
importlib.reload(load)
importlib.reload(zoom)
importlib.reload(calc)
importlib.reload(save)
importlib.reload(plots)
importlib.reload(monitor)
<module 'core.monitor' from '/ccc/work/cont003/gen7420/odakatin/monitor-sedna/notebook/core/monitor.py'>
If you submit the job with job scheduler; below are list of enviroment variable one can pass
local : if True run dask local cluster, if not true, put number of workers setted in the 'local' if no 'local ' given, local will be setted automatically to 'True'
%env ychunk='2', #%env tchunk='2'
controls chunk. 'False' sets no modification from original netcdf file's chunk.
ychunk=10 will group the original netcdf file to 10 by 10
tchunk=1 will chunk the time coordinate one by one
%env file_exp=
'file_exp': Which 'experiment' name is it? this corresopnds to intake catalog name without path and .yaml
#%env year=
for Validation, this correspoinds to path/year/month 's year for monitoring, this corresponids to 'date' having means do all files in the monitoring directory setting it as 0[0-9] &1[0-9]& [2-3][0-9], the job can be separated in three lots. For DELTA experiment, year corresponds to really 'year'
%env month=
for monitoring this corresponds to file path path-XIOS.{month}/
For DELTA experiment, year corresponds to really 'month'
proceed saving? True or False , Default is setted as True
proceed plotting? True or False , Default is setted as True
proceed computation? or just load computed result? True or False , Default is setted as True
save output file used for plotting
using kerchunked file -> False, not using kerhcunk -> True
name of control file to be used for computation/plots/save/ We have number of M_xxx.csv
Monitor.sh calls M_MLD_2D
and AWTD.sh, Fluxnet.sh, Siconc.sh, IceClim.sh, FWC_SSH.sh, Integrals.sh , Sections.sh
M_AWTMD
M_Fluxnet
M_Ice_quantities
M_IceClim M_IceConce M_IceThick
M_FWC_2D M_FWC_integrals M_FWC_SSH M_SSH_anomaly
M_Mean_temp_velo M_Mooring
M_Sectionx M_Sectiony
%%time
# 'savefig': Do we save output in html? or not. keep it true.
savefig=True
client,cluster,control,catalog_url,month,year,daskreport,outputpath = load.set_control(host)
!mkdir -p $outputpath
!mkdir -p $daskreport
client
local True using host= irene4050.c-irene.mg1.tgcc.ccc.cea.fr starting dask cluster on local= True workers 16 10000000000 rome local cluster starting This code is running on irene4050.c-irene.mg1.tgcc.ccc.cea.fr using SEDNA_DELTA_MONITOR file experiment, read from ../lib/SEDNA_DELTA_MONITOR.yaml on year= 2012 on month= 04 outputpath= ../results/SEDNA_DELTA_MONITOR/ daskreport= ../results/dask/6419622irene4050.c-irene.mg1.tgcc.ccc.cea.fr_SEDNA_DELTA_MONITOR_04M_Sectionx/ CPU times: user 509 ms, sys: 134 ms, total: 644 ms Wall time: 21 s
Client-377689dc-13e6-11ed-9fb0-080038c2124d
Connection method: Cluster object | Cluster type: distributed.LocalCluster |
Dashboard: http://127.0.0.1:8787/status |
0ecd267e
Dashboard: http://127.0.0.1:8787/status | Workers: 16 |
Total threads: 128 | Total memory: 251.06 GiB |
Status: running | Using processes: True |
Scheduler-283a17c3-025f-49a2-bb81-a27dce59bbe6
Comm: tcp://127.0.0.1:44217 | Workers: 16 |
Dashboard: http://127.0.0.1:8787/status | Total threads: 128 |
Started: Just now | Total memory: 251.06 GiB |
Comm: tcp://127.0.0.1:45754 | Total threads: 8 |
Dashboard: http://127.0.0.1:41277/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:46634 | |
Local directory: /tmp/dask-worker-space/worker-d3ssfp99 |
Comm: tcp://127.0.0.1:42960 | Total threads: 8 |
Dashboard: http://127.0.0.1:37020/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:40904 | |
Local directory: /tmp/dask-worker-space/worker-0olwzckb |
Comm: tcp://127.0.0.1:41008 | Total threads: 8 |
Dashboard: http://127.0.0.1:42848/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:46043 | |
Local directory: /tmp/dask-worker-space/worker-xy8afnk6 |
Comm: tcp://127.0.0.1:36347 | Total threads: 8 |
Dashboard: http://127.0.0.1:38120/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:35339 | |
Local directory: /tmp/dask-worker-space/worker-k3k1cgv4 |
Comm: tcp://127.0.0.1:38816 | Total threads: 8 |
Dashboard: http://127.0.0.1:39552/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:45416 | |
Local directory: /tmp/dask-worker-space/worker-aazu7p3g |
Comm: tcp://127.0.0.1:34497 | Total threads: 8 |
Dashboard: http://127.0.0.1:38588/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:35119 | |
Local directory: /tmp/dask-worker-space/worker-b723dcl9 |
Comm: tcp://127.0.0.1:43532 | Total threads: 8 |
Dashboard: http://127.0.0.1:36707/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:45729 | |
Local directory: /tmp/dask-worker-space/worker-crk1kgtd |
Comm: tcp://127.0.0.1:33102 | Total threads: 8 |
Dashboard: http://127.0.0.1:36035/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:41455 | |
Local directory: /tmp/dask-worker-space/worker-15nmpdkr |
Comm: tcp://127.0.0.1:42279 | Total threads: 8 |
Dashboard: http://127.0.0.1:35031/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:42583 | |
Local directory: /tmp/dask-worker-space/worker-6ybk7gfx |
Comm: tcp://127.0.0.1:38410 | Total threads: 8 |
Dashboard: http://127.0.0.1:42984/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:45873 | |
Local directory: /tmp/dask-worker-space/worker-vj176bi3 |
Comm: tcp://127.0.0.1:35436 | Total threads: 8 |
Dashboard: http://127.0.0.1:35302/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:35630 | |
Local directory: /tmp/dask-worker-space/worker-4rsmpz32 |
Comm: tcp://127.0.0.1:41550 | Total threads: 8 |
Dashboard: http://127.0.0.1:40848/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:38760 | |
Local directory: /tmp/dask-worker-space/worker-w_d78dea |
Comm: tcp://127.0.0.1:44398 | Total threads: 8 |
Dashboard: http://127.0.0.1:35796/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:41347 | |
Local directory: /tmp/dask-worker-space/worker-kujakurt |
Comm: tcp://127.0.0.1:39528 | Total threads: 8 |
Dashboard: http://127.0.0.1:35408/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:43514 | |
Local directory: /tmp/dask-worker-space/worker-p_0ehq8a |
Comm: tcp://127.0.0.1:46523 | Total threads: 8 |
Dashboard: http://127.0.0.1:43119/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:38181 | |
Local directory: /tmp/dask-worker-space/worker-sa4wxc5w |
Comm: tcp://127.0.0.1:37857 | Total threads: 8 |
Dashboard: http://127.0.0.1:43653/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:38415 | |
Local directory: /tmp/dask-worker-space/worker-omkit9jy |
df=load.controlfile(control)
#Take out 'later' tagged computations
#df=df[~df['Value'].str.contains('later')]
df
Value | Inputs | Equation | Zone | Plot | Colourmap | MinMax | Unit | Oldname | Unnamed: 10 | |
---|---|---|---|---|---|---|---|---|---|---|
Section | gridT.votemper,gridS.vosaline,gridU.vozocrtx,p... | data.chunk({'y':-1}).unify_chunks().persist() | BFGS | section | None | {'vosaline': (28,35), 'votemper': (-2,2), 'voz... | None | S-2 |
Each computation consists of
%%time
import os
calcswitch=os.environ.get('calc', 'True')
lazy=os.environ.get('lazy','False' )
loaddata=((df.Inputs != '').any())
print('calcswitch=',calcswitch,'df.Inputs != nothing',loaddata, 'lazy=',lazy)
data = load.datas(catalog_url,df.Inputs,month,year,daskreport,lazy=lazy) if ((calcswitch=='True' )*loaddata) else 0
data
calcswitch= False df.Inputs != nothing True lazy= False CPU times: user 426 µs, sys: 0 ns, total: 426 µs Wall time: 374 µs
0
%%time
monitor.auto(df,data,savefig,daskreport,outputpath,file_exp='SEDNA'
)
#calc= False #save= False #plot= True Value='Section' Zone='BFGS' Plot='section' cmap='None' clabel='None' clim= {'vosaline': (28, 35), 'votemper': (-2, 2), 'vozocrtx': (-0.05, 0.05)} outputpath='../results/SEDNA_DELTA_MONITOR/' nc_outputpath='../nc_results/SEDNA_DELTA_MONITOR/' filename='SEDNA_section_BFGS_Section' #3 no computing , loading starts data=save.load_data(plot=Plot,path=nc_outputpath,filename=filename) start saving data filename= ../nc_results/SEDNA_DELTA_MONITOR/SEDNA_section_BFGS_Section/t_*.nc load computed data completed
<xarray.Dataset> Dimensions: (t: 61, z: 95, y: 2384) Coordinates: time_centered (t) object dask.array<chunksize=(1,), meta=np.ndarray> * t (t) object 2012-03-01 12:00:00 ... 2012-04-30 12:00:00 * y (y) int64 3494 3495 3496 3497 3498 ... 5910 5911 5912 5913 x int64 ... * z (z) int64 1 2 3 4 5 6 7 8 9 10 ... 87 88 89 90 91 92 93 94 95 mask (z, y) bool dask.array<chunksize=(95, 2384), meta=np.ndarray> nav_lon (y) float32 dask.array<chunksize=(2384,), meta=np.ndarray> mask2d (y) bool dask.array<chunksize=(2384,), meta=np.ndarray> nav_lat (y) float32 dask.array<chunksize=(2384,), meta=np.ndarray> depth (z, y) float32 dask.array<chunksize=(95, 2384), meta=np.ndarray> Data variables: vosaline (t, z, y) float32 dask.array<chunksize=(1, 95, 2384), meta=np.ndarray> votemper (t, z, y) float32 dask.array<chunksize=(1, 95, 2384), meta=np.ndarray> vozocrtx (t, z, y) float32 dask.array<chunksize=(1, 95, 2384), meta=np.ndarray> Attributes: (12/26) CASE: DELTA CONFIG: SEDNA Conventions: CF-1.6 DOMAIN_dimensions_ids: [2 3] DOMAIN_halo_size_end: [0 0] DOMAIN_halo_size_start: [0 0] ... ... nj: 13 output_frequency: 1d start_date: 20090101 timeStamp: 2022-Jan-19 12:40:34 GMT title: ocean T grid variables uuid: b2000bef-0e1f-4f0d-ae2a-b9429429b7a2
#5 Plotting filename= plots.section(data,path=outputpath,filename=filename,save=savefig,cmap=cmap,clim=clim,clabel=clabel) ../results/SEDNA_DELTA_MONITOR/SEDNA_section_BFGS_Section_20120301-20120430.html starts plotting ../results/SEDNA_DELTA_MONITOR/SEDNA_section_BFGS_Section_20120301-20120430.html created
CPU times: user 43.9 s, sys: 7.46 s, total: 51.4 s Wall time: 3min 15s