%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= irene5169.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 irene5169.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/6419619irene5169.c-irene.mg1.tgcc.ccc.cea.fr_SEDNA_DELTA_MONITOR_04M_Mooring/ CPU times: user 546 ms, sys: 140 ms, total: 686 ms Wall time: 19.9 s
Client-1ca05a79-13e5-11ed-8b5c-080038b93e07
Connection method: Cluster object | Cluster type: distributed.LocalCluster |
Dashboard: http://127.0.0.1:8787/status |
e557e0c4
Dashboard: http://127.0.0.1:8787/status | Workers: 16 |
Total threads: 128 | Total memory: 251.06 GiB |
Status: running | Using processes: True |
Scheduler-efdd9c6e-c1c1-4d19-b41a-95de5a97a183
Comm: tcp://127.0.0.1:41327 | Workers: 16 |
Dashboard: http://127.0.0.1:8787/status | Total threads: 128 |
Started: Just now | Total memory: 251.06 GiB |
Comm: tcp://127.0.0.1:42581 | Total threads: 8 |
Dashboard: http://127.0.0.1:40187/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:38404 | |
Local directory: /tmp/dask-worker-space/worker-7myxvnbt |
Comm: tcp://127.0.0.1:34860 | Total threads: 8 |
Dashboard: http://127.0.0.1:38256/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:46005 | |
Local directory: /tmp/dask-worker-space/worker-_i6fy3nn |
Comm: tcp://127.0.0.1:42466 | Total threads: 8 |
Dashboard: http://127.0.0.1:37587/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:43780 | |
Local directory: /tmp/dask-worker-space/worker-efcbu_s7 |
Comm: tcp://127.0.0.1:39132 | Total threads: 8 |
Dashboard: http://127.0.0.1:40097/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:35059 | |
Local directory: /tmp/dask-worker-space/worker-b1tulipy |
Comm: tcp://127.0.0.1:33922 | Total threads: 8 |
Dashboard: http://127.0.0.1:39036/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:36150 | |
Local directory: /tmp/dask-worker-space/worker-cfu_hhl5 |
Comm: tcp://127.0.0.1:41267 | Total threads: 8 |
Dashboard: http://127.0.0.1:45717/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:43297 | |
Local directory: /tmp/dask-worker-space/worker-a458z8p3 |
Comm: tcp://127.0.0.1:34637 | Total threads: 8 |
Dashboard: http://127.0.0.1:45099/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:37781 | |
Local directory: /tmp/dask-worker-space/worker-rhn16qaf |
Comm: tcp://127.0.0.1:35759 | Total threads: 8 |
Dashboard: http://127.0.0.1:34799/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:39545 | |
Local directory: /tmp/dask-worker-space/worker-l1fxs1n7 |
Comm: tcp://127.0.0.1:45309 | Total threads: 8 |
Dashboard: http://127.0.0.1:43799/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:45872 | |
Local directory: /tmp/dask-worker-space/worker-h9xrs5v0 |
Comm: tcp://127.0.0.1:40518 | Total threads: 8 |
Dashboard: http://127.0.0.1:40694/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:44059 | |
Local directory: /tmp/dask-worker-space/worker-ltczjp2o |
Comm: tcp://127.0.0.1:37983 | Total threads: 8 |
Dashboard: http://127.0.0.1:34309/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:41080 | |
Local directory: /tmp/dask-worker-space/worker-vz2w1o6h |
Comm: tcp://127.0.0.1:40905 | Total threads: 8 |
Dashboard: http://127.0.0.1:46298/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:35572 | |
Local directory: /tmp/dask-worker-space/worker-76z05ifp |
Comm: tcp://127.0.0.1:34391 | Total threads: 8 |
Dashboard: http://127.0.0.1:40787/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:45772 | |
Local directory: /tmp/dask-worker-space/worker-17x6qmno |
Comm: tcp://127.0.0.1:33847 | Total threads: 8 |
Dashboard: http://127.0.0.1:45200/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:35163 | |
Local directory: /tmp/dask-worker-space/worker-isccnrdw |
Comm: tcp://127.0.0.1:38161 | Total threads: 8 |
Dashboard: http://127.0.0.1:46636/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:40164 | |
Local directory: /tmp/dask-worker-space/worker-_7so1b0l |
Comm: tcp://127.0.0.1:44377 | Total threads: 8 |
Dashboard: http://127.0.0.1:36296/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:40555 | |
Local directory: /tmp/dask-worker-space/worker-_4w88jc9 |
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 | |
---|---|---|---|---|---|---|---|---|---|---|
Mooring_Arc_B | gridS.vosaline,gridT.votemper,param.depth,para... | data | Arc_B | Mooring | rainbow | {'vosaline': (28.0,34.4), 'votemper': (-2.0,2.0)} | None | x | ||
Mooring_Eur_B | gridS.vosaline,gridT.votemper,param.depth,para... | data | Eur_B | Mooring | rainbow | {'vosaline': (32.0,35.0), 'votemper': (-2.0,3.0)} | None | x |
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 622 µs, sys: 0 ns, total: 622 µs Wall time: 548 µs
0
%%time
monitor.auto(df,data,savefig,daskreport,outputpath,file_exp='SEDNA'
)
#calc= False #save= False #plot= True Value='Mooring_Arc_B' Zone='Arc_B' Plot='Mooring' cmap='rainbow' clabel='None' clim= {'vosaline': (28.0, 34.4), 'votemper': (-2.0, 2.0)} outputpath='../results/SEDNA_DELTA_MONITOR/' nc_outputpath='../nc_results/SEDNA_DELTA_MONITOR/' filename='SEDNA_Mooring_Arc_B_Mooring_Arc_B' #3 no computing , loading starts data=save.load_data(plot=Plot,path=nc_outputpath,filename=filename) start saving data load 1Dnc file from ../nc_results/SEDNA_DELTA_MONITOR/../*/SEDNA_Mooring_Arc_B_Mooring_Arc_B*.nc load computed data completed
<xarray.Dataset> Dimensions: (t: 120, z: 102) Coordinates: time_centered (t) object dask.array<chunksize=(31,), meta=np.ndarray> * t (t) object 2012-01-01 12:00:00 ... 2012-04-30 12:00:00 y int64 ... x int64 ... * z (z) int64 1 2 3 4 5 6 7 8 9 ... 94 95 96 97 98 99 100 101 102 mask2d int8 ... depth (z) float32 dask.array<chunksize=(102,), meta=np.ndarray> nav_lon float32 ... nav_lat float32 ... mask (z) int8 dask.array<chunksize=(102,), meta=np.ndarray> Data variables: vosaline (t, z) float32 dask.array<chunksize=(31, 102), meta=np.ndarray> votemper (t, z) float32 dask.array<chunksize=(31, 102), 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-17 19:00:16 GMT title: ocean T grid variables uuid: d8db76f6-a436-451a-9ab1-72dc892753af
#5 Plotting filename= plots.Mooring(data,path=outputpath,filename=filename,save=savefig,cmap=cmap,clim=clim,clabel=clabel)
WARNING:param.QuadMeshPlot02054: 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.QuadMeshPlot02054: 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.QuadMeshPlot02054: 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_Mooring_Arc_B_Mooring_Arc_B_20120101-20120430.html starts plotting
WARNING:param.QuadMeshPlot02069: 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.QuadMeshPlot02069: 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.QuadMeshPlot02069: 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_Mooring_Arc_B_Mooring_Arc_B_20120101-20120430.html created
Value='Mooring_Eur_B' Zone='Eur_B' Plot='Mooring' cmap='rainbow' clabel='None' clim= {'vosaline': (32.0, 35.0), 'votemper': (-2.0, 3.0)} outputpath='../results/SEDNA_DELTA_MONITOR/' nc_outputpath='../nc_results/SEDNA_DELTA_MONITOR/' filename='SEDNA_Mooring_Eur_B_Mooring_Eur_B' #3 no computing , loading starts data=save.load_data(plot=Plot,path=nc_outputpath,filename=filename) start saving data load 1Dnc file from ../nc_results/SEDNA_DELTA_MONITOR/../*/SEDNA_Mooring_Eur_B_Mooring_Eur_B*.nc load computed data completed
<xarray.Dataset> Dimensions: (t: 120, z: 102) Coordinates: time_centered (t) object dask.array<chunksize=(31,), meta=np.ndarray> * t (t) object 2012-01-01 12:00:00 ... 2012-04-30 12:00:00 y int64 ... x int64 ... * z (z) int64 1 2 3 4 5 6 7 8 9 ... 94 95 96 97 98 99 100 101 102 mask2d int8 ... depth (z) float32 dask.array<chunksize=(102,), meta=np.ndarray> nav_lon float32 ... nav_lat float32 ... mask (z) int8 dask.array<chunksize=(102,), meta=np.ndarray> Data variables: vosaline (t, z) float32 dask.array<chunksize=(31, 102), meta=np.ndarray> votemper (t, z) float32 dask.array<chunksize=(31, 102), 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-17 19:00:16 GMT title: ocean T grid variables uuid: d8db76f6-a436-451a-9ab1-72dc892753af
#5 Plotting filename= plots.Mooring(data,path=outputpath,filename=filename,save=savefig,cmap=cmap,clim=clim,clabel=clabel)
WARNING:param.QuadMeshPlot104916: 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.QuadMeshPlot104916: 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_Mooring_Eur_B_Mooring_Eur_B_20120101-20120430.html starts plotting
WARNING:param.QuadMeshPlot104916: 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.QuadMeshPlot104931: 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.QuadMeshPlot104931: 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.QuadMeshPlot104931: 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_Mooring_Eur_B_Mooring_Eur_B_20120101-20120430.html created
CPU times: user 2min 8s, sys: 2.37 s, total: 2min 10s Wall time: 2min 23s