%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/talandel/TOOLS/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= irene4338.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 irene4338.c-irene.mg1.tgcc.ccc.cea.fr using SEDNA_DELTA_MONITOR file experiment, read from ../lib/SEDNA_DELTA_MONITOR.yaml on year= 2015 on month= 12 outputpath= ../results/SEDNA_DELTA_MONITOR/ daskreport= ../results/dask/7449100irene4338.c-irene.mg1.tgcc.ccc.cea.fr_SEDNA_DELTA_MONITOR_12M_Fluxnet/ CPU times: user 473 ms, sys: 126 ms, total: 599 ms Wall time: 17.8 s
Client-bca49973-6f43-11ed-a01a-080038b9355b
Connection method: Cluster object | Cluster type: distributed.LocalCluster |
Dashboard: http://127.0.0.1:8787/status |
e3f3b38f
Dashboard: http://127.0.0.1:8787/status | Workers: 16 |
Total threads: 128 | Total memory: 221.88 GiB |
Status: running | Using processes: True |
Scheduler-e79aa34b-95d7-46ae-88fc-785f8fc5e663
Comm: tcp://127.0.0.1:37311 | Workers: 16 |
Dashboard: http://127.0.0.1:8787/status | Total threads: 128 |
Started: Just now | Total memory: 221.88 GiB |
Comm: tcp://127.0.0.1:41228 | Total threads: 8 |
Dashboard: http://127.0.0.1:43944/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:45773 | |
Local directory: /tmp/dask-worker-space/worker-ctl_86v8 |
Comm: tcp://127.0.0.1:44276 | Total threads: 8 |
Dashboard: http://127.0.0.1:37057/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:39768 | |
Local directory: /tmp/dask-worker-space/worker-76yj04rf |
Comm: tcp://127.0.0.1:34234 | Total threads: 8 |
Dashboard: http://127.0.0.1:43057/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:43815 | |
Local directory: /tmp/dask-worker-space/worker-aa_op3we |
Comm: tcp://127.0.0.1:42171 | Total threads: 8 |
Dashboard: http://127.0.0.1:46348/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:33676 | |
Local directory: /tmp/dask-worker-space/worker-j2in0gm6 |
Comm: tcp://127.0.0.1:36249 | Total threads: 8 |
Dashboard: http://127.0.0.1:41343/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:42970 | |
Local directory: /tmp/dask-worker-space/worker-memdmbzi |
Comm: tcp://127.0.0.1:41120 | Total threads: 8 |
Dashboard: http://127.0.0.1:41920/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:45715 | |
Local directory: /tmp/dask-worker-space/worker-1fvg047a |
Comm: tcp://127.0.0.1:46006 | Total threads: 8 |
Dashboard: http://127.0.0.1:34444/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:35421 | |
Local directory: /tmp/dask-worker-space/worker-0h56z1pz |
Comm: tcp://127.0.0.1:41225 | Total threads: 8 |
Dashboard: http://127.0.0.1:46315/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:45791 | |
Local directory: /tmp/dask-worker-space/worker-ymd63une |
Comm: tcp://127.0.0.1:36555 | Total threads: 8 |
Dashboard: http://127.0.0.1:41865/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:45286 | |
Local directory: /tmp/dask-worker-space/worker-qtkf0t8r |
Comm: tcp://127.0.0.1:41078 | Total threads: 8 |
Dashboard: http://127.0.0.1:45775/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:36841 | |
Local directory: /tmp/dask-worker-space/worker-q29ip7tt |
Comm: tcp://127.0.0.1:35381 | Total threads: 8 |
Dashboard: http://127.0.0.1:40992/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:42950 | |
Local directory: /tmp/dask-worker-space/worker-16njp421 |
Comm: tcp://127.0.0.1:34033 | Total threads: 8 |
Dashboard: http://127.0.0.1:33575/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:37883 | |
Local directory: /tmp/dask-worker-space/worker-ujsj4nod |
Comm: tcp://127.0.0.1:42050 | Total threads: 8 |
Dashboard: http://127.0.0.1:38791/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:43825 | |
Local directory: /tmp/dask-worker-space/worker-36hdmc1u |
Comm: tcp://127.0.0.1:42176 | Total threads: 8 |
Dashboard: http://127.0.0.1:37378/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:40042 | |
Local directory: /tmp/dask-worker-space/worker-a9zdti4s |
Comm: tcp://127.0.0.1:38525 | Total threads: 8 |
Dashboard: http://127.0.0.1:41650/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:36844 | |
Local directory: /tmp/dask-worker-space/worker-x37w_3eo |
Comm: tcp://127.0.0.1:43609 | Total threads: 8 |
Dashboard: http://127.0.0.1:45658/status | Memory: 13.87 GiB |
Nanny: tcp://127.0.0.1:45650 | |
Local directory: /tmp/dask-worker-space/worker-ek1x1qzf |
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 | |
---|---|---|---|---|---|---|---|---|---|---|
Fluxnet | gridV.vomecrty,param.e3v_0,param.e1v,param.mas... | calc.Fluxnet(data) | FramS_All | Fluxnet_integrals | None | ((-10,10),(-10,50) ,(-150,50),(-25,5) ) | (Sv,TW, mSv,10^-2 Sv) | I-6 | ||
Fluxnet | gridV.vomecrty,param.e3v_0,param.e1v,param.mas... | calc.Fluxnet(data) | Davis | Fluxnet_integrals | None | ((-5.0,5.0),(-25,27) ,(-200,50),(-9,5) ) | (Sv,TW, mSv,10^-2 Sv) | I-6 | ||
Fluxnet | gridV.vomecrty,param.e3v_0,param.e1v,param.mas... | calc.Fluxnet(data) | Bering | Fluxnet_integrals | None | ((-2,2),(-10,50) ,(-150,50),(-2,4) ) | (Sv,TW, mSv,10^-2 Sv) | I-6 |
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 428 µs, sys: 63 µs, total: 491 µs Wall time: 472 µs
0
%%time
monitor.auto(df,data,savefig,daskreport,outputpath,file_exp='SEDNA'
)
#calc= False #save= False #plot= True Value='Fluxnet' Zone='FramS_All' Plot='Fluxnet_integrals' cmap='None' clabel='(Sv,TW, mSv,10^-2 Sv)' clim= ((-10, 10), (-10, 50), (-150, 50), (-25, 5)) outputpath='../results/SEDNA_DELTA_MONITOR/' nc_outputpath='../nc_results/SEDNA_DELTA_MONITOR/' filename='SEDNA_Fluxnet_integrals_FramS_All_Fluxnet' #3 no computing , loading starts data=save.load_data(plot=Plot,path=nc_outputpath,filename=filename) start loading data load 1Dnc file from ../nc_results/SEDNA_DELTA_MONITOR/../*/SEDNA_Fluxnet_integrals_FramS_All_Fluxnet*.nc load computed data completed
<xarray.Dataset> Dimensions: (t: 365) Coordinates: * t (t) object 2015-01-01 12:00:00 ... 2015-12-31 12:0... y int64 ... Data variables: Volume flux Net (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Volume flux Northward (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Heat flux Net (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Heat flux Northward (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Freshwater Net (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Freshwater Northward (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Ice export (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Volume flux South (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Heat flux South (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Freshwater South (t) float64 dask.array<chunksize=(31,), meta=np.ndarray>
#5 Plotting filename= plots.Fluxnet_integrals(data,path=outputpath,filename=filename,save=savefig,cmap=cmap,clim=clim,clabel=clabel)
WARNING:param.CurvePlot02240: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot02241: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot02242: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot02266: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot02267: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot02268: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend.
../results/SEDNA_DELTA_MONITOR/SEDNA_Fluxnet_integrals_FramS_All_Fluxnet_20150101-20151231.html starts plotting
WARNING:param.CurvePlot02290: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot02291: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot02292: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot02299: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend.
plotting ../results/SEDNA_DELTA_MONITOR/SEDNA_Fluxnet_integrals_FramS_All_Fluxnet_20150101-20151231.html ../results/SEDNA_DELTA_MONITOR/SEDNA_Fluxnet_integrals_FramS_All_Fluxnet_20150101-20151231.html created
Value='Fluxnet' Zone='Davis' Plot='Fluxnet_integrals' cmap='None' clabel='(Sv,TW, mSv,10^-2 Sv)' clim= ((-5.0, 5.0), (-25, 27), (-200, 50), (-9, 5)) outputpath='../results/SEDNA_DELTA_MONITOR/' nc_outputpath='../nc_results/SEDNA_DELTA_MONITOR/' filename='SEDNA_Fluxnet_integrals_Davis_Fluxnet' #3 no computing , loading starts data=save.load_data(plot=Plot,path=nc_outputpath,filename=filename) start loading data load 1Dnc file from ../nc_results/SEDNA_DELTA_MONITOR/../*/SEDNA_Fluxnet_integrals_Davis_Fluxnet*.nc load computed data completed
<xarray.Dataset> Dimensions: (t: 365) Coordinates: * t (t) object 2015-01-01 12:00:00 ... 2015-12-31 12:0... y int64 ... Data variables: Volume flux Net (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Volume flux Northward (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Heat flux Net (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Heat flux Northward (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Freshwater Net (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Freshwater Northward (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Ice export (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Volume flux South (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Heat flux South (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Freshwater South (t) float64 dask.array<chunksize=(31,), meta=np.ndarray>
#5 Plotting filename= plots.Fluxnet_integrals(data,path=outputpath,filename=filename,save=savefig,cmap=cmap,clim=clim,clabel=clabel)
WARNING:param.CurvePlot03176: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot03177: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot03178: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot03202: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot03203: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot03204: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend.
../results/SEDNA_DELTA_MONITOR/SEDNA_Fluxnet_integrals_Davis_Fluxnet_20150101-20151231.html starts plotting
WARNING:param.CurvePlot03226: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot03227: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot03228: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot03235: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend.
plotting ../results/SEDNA_DELTA_MONITOR/SEDNA_Fluxnet_integrals_Davis_Fluxnet_20150101-20151231.html ../results/SEDNA_DELTA_MONITOR/SEDNA_Fluxnet_integrals_Davis_Fluxnet_20150101-20151231.html created
Value='Fluxnet' Zone='Bering' Plot='Fluxnet_integrals' cmap='None' clabel='(Sv,TW, mSv,10^-2 Sv)' clim= ((-2, 2), (-10, 50), (-150, 50), (-2, 4)) outputpath='../results/SEDNA_DELTA_MONITOR/' nc_outputpath='../nc_results/SEDNA_DELTA_MONITOR/' filename='SEDNA_Fluxnet_integrals_Bering_Fluxnet' #3 no computing , loading starts data=save.load_data(plot=Plot,path=nc_outputpath,filename=filename) start loading data load 1Dnc file from ../nc_results/SEDNA_DELTA_MONITOR/../*/SEDNA_Fluxnet_integrals_Bering_Fluxnet*.nc load computed data completed
<xarray.Dataset> Dimensions: (t: 365) Coordinates: * t (t) object 2015-01-01 12:00:00 ... 2015-12-31 12:0... y int64 ... Data variables: Volume flux Net (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Volume flux Northward (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Heat flux Net (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Heat flux Northward (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Freshwater Net (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Freshwater Northward (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Ice export (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Volume flux South (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Heat flux South (t) float64 dask.array<chunksize=(31,), meta=np.ndarray> Freshwater South (t) float64 dask.array<chunksize=(31,), meta=np.ndarray>
#5 Plotting filename= plots.Fluxnet_integrals(data,path=outputpath,filename=filename,save=savefig,cmap=cmap,clim=clim,clabel=clabel)
WARNING:param.CurvePlot04112: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot04113: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot04114: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot04138: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot04139: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot04140: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend.
../results/SEDNA_DELTA_MONITOR/SEDNA_Fluxnet_integrals_Bering_Fluxnet_20150101-20151231.html starts plotting
WARNING:param.CurvePlot04162: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot04163: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot04164: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend. WARNING:param.CurvePlot04171: Converting cftime.datetime from a non-standard calendar (noleap) to a standard calendar for plotting. This may lead to subtle errors in formatting dates, for accurate tick formatting switch to the matplotlib backend.
plotting ../results/SEDNA_DELTA_MONITOR/SEDNA_Fluxnet_integrals_Bering_Fluxnet_20150101-20151231.html ../results/SEDNA_DELTA_MONITOR/SEDNA_Fluxnet_integrals_Bering_Fluxnet_20150101-20151231.html created
CPU times: user 7.08 s, sys: 884 ms, total: 7.97 s Wall time: 17.4 s