%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= irene4281.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 irene4281.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= 06 outputpath= ../results/SEDNA_DELTA_MONITOR/ daskreport= ../results/dask/6476247irene4281.c-irene.mg1.tgcc.ccc.cea.fr_SEDNA_DELTA_MONITOR_06M_FWC_integrals/ CPU times: user 543 ms, sys: 139 ms, total: 681 ms Wall time: 21 s
Client-8f13fc45-197a-11ed-84ea-080038b932d7
Connection method: Cluster object | Cluster type: distributed.LocalCluster |
Dashboard: http://127.0.0.1:8787/status |
79d131a9
Dashboard: http://127.0.0.1:8787/status | Workers: 16 |
Total threads: 128 | Total memory: 251.06 GiB |
Status: running | Using processes: True |
Scheduler-0f978b91-61df-4b6a-a331-dc61586b5ea5
Comm: tcp://127.0.0.1:41277 | Workers: 16 |
Dashboard: http://127.0.0.1:8787/status | Total threads: 128 |
Started: Just now | Total memory: 251.06 GiB |
Comm: tcp://127.0.0.1:40364 | Total threads: 8 |
Dashboard: http://127.0.0.1:36173/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:40395 | |
Local directory: /tmp/dask-worker-space/worker-76z5_z7y |
Comm: tcp://127.0.0.1:37899 | Total threads: 8 |
Dashboard: http://127.0.0.1:39691/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:35103 | |
Local directory: /tmp/dask-worker-space/worker-g0qly2mu |
Comm: tcp://127.0.0.1:41901 | Total threads: 8 |
Dashboard: http://127.0.0.1:34786/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:33089 | |
Local directory: /tmp/dask-worker-space/worker-kn2aa_r1 |
Comm: tcp://127.0.0.1:33794 | Total threads: 8 |
Dashboard: http://127.0.0.1:34241/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:34340 | |
Local directory: /tmp/dask-worker-space/worker-7kx5scro |
Comm: tcp://127.0.0.1:46577 | Total threads: 8 |
Dashboard: http://127.0.0.1:37965/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:35432 | |
Local directory: /tmp/dask-worker-space/worker-3uuu7zjp |
Comm: tcp://127.0.0.1:38466 | Total threads: 8 |
Dashboard: http://127.0.0.1:42959/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:33012 | |
Local directory: /tmp/dask-worker-space/worker-5xypj7hg |
Comm: tcp://127.0.0.1:37348 | Total threads: 8 |
Dashboard: http://127.0.0.1:45036/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:33514 | |
Local directory: /tmp/dask-worker-space/worker-8lnzis9j |
Comm: tcp://127.0.0.1:36969 | Total threads: 8 |
Dashboard: http://127.0.0.1:42838/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:36396 | |
Local directory: /tmp/dask-worker-space/worker-rua5qhs2 |
Comm: tcp://127.0.0.1:39112 | Total threads: 8 |
Dashboard: http://127.0.0.1:41795/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:41517 | |
Local directory: /tmp/dask-worker-space/worker-9a7jc_s5 |
Comm: tcp://127.0.0.1:41847 | Total threads: 8 |
Dashboard: http://127.0.0.1:43102/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:37871 | |
Local directory: /tmp/dask-worker-space/worker-_io5a1d9 |
Comm: tcp://127.0.0.1:37433 | Total threads: 8 |
Dashboard: http://127.0.0.1:37898/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:44696 | |
Local directory: /tmp/dask-worker-space/worker-vo9g960f |
Comm: tcp://127.0.0.1:35243 | Total threads: 8 |
Dashboard: http://127.0.0.1:41935/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:38580 | |
Local directory: /tmp/dask-worker-space/worker-s17k0kbl |
Comm: tcp://127.0.0.1:38152 | Total threads: 8 |
Dashboard: http://127.0.0.1:35614/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:38776 | |
Local directory: /tmp/dask-worker-space/worker-7s1093vm |
Comm: tcp://127.0.0.1:38636 | Total threads: 8 |
Dashboard: http://127.0.0.1:36500/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:33914 | |
Local directory: /tmp/dask-worker-space/worker-9q9916m9 |
Comm: tcp://127.0.0.1:41624 | Total threads: 8 |
Dashboard: http://127.0.0.1:38845/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:42599 | |
Local directory: /tmp/dask-worker-space/worker-cf7ckc5l |
Comm: tcp://127.0.0.1:39117 | Total threads: 8 |
Dashboard: http://127.0.0.1:35177/status | Memory: 15.69 GiB |
Nanny: tcp://127.0.0.1:39638 | |
Local directory: /tmp/dask-worker-space/worker-6922kvxs |
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 | |
---|---|---|---|---|---|---|---|---|---|---|
FWC_integrals | calc.FWC_load_integrals(data,nc_outputpath) | BBFG | FWC_integrals | (12000,24000) | Km^3 | I-1 |
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= True df.Inputs != nothing False lazy= False CPU times: user 345 µs, sys: 56 µs, total: 401 µs Wall time: 385 µs
0
%%time
monitor.auto(df,data,savefig,daskreport,outputpath,file_exp='SEDNA'
)
#calc= True #save= True #plot= False Value='FWC_integrals' Zone='BBFG' Plot='FWC_integrals' cmap='' clabel='Km^3' clim= (12000, 24000) outputpath='../results/SEDNA_DELTA_MONITOR/' nc_outputpath='../nc_results/SEDNA_DELTA_MONITOR/' filename='SEDNA_FWC_integrals_BBFG_FWC_integrals' #3 Start computing data= calc.FWC_load_integrals(data,nc_outputpath) monitor.optimize_dataset(data) start loading data filename= ../nc_results/SEDNA_DELTA_MONITOR/SEDNA_maps_BBFG_FWC_2D/t_*/y_*/x_*.nc dim ('x', 'y', 't') load computed data completed add optimise here once otimise can recognise
<xarray.Dataset> Dimensions: (t: 122) Coordinates: * t (t) object 2012-03-01 12:00:00 ... 2012-06-30 12:00:00 Data variables: FWC_Arctic (t) float64 dask.array<chunksize=(1,), meta=np.ndarray> FWC_CRF (t) float64 dask.array<chunksize=(1,), meta=np.ndarray>
#4 Saving SEDNA_FWC_integrals_BBFG_FWC_integrals data=save.datas(data,plot=Plot,path=nc_outputpath,filename=filename) start saving data saving data in a csv file ../nc_results/SEDNA_DELTA_MONITOR/SEDNA_FWC_integrals_BBFG_FWC_integrals2012-03-01_2012-06-30.nc save computed data at ../nc_results/SEDNA_DELTA_MONITOR/SEDNA_FWC_integrals_BBFG_FWC_integrals2012-03-01_2012-06-30.nc completed CPU times: user 58.6 s, sys: 6.35 s, total: 1min 4s Wall time: 1min 35s