%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= irene4945.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 irene4945.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/6476218irene4945.c-irene.mg1.tgcc.ccc.cea.fr_SEDNA_DELTA_MONITOR_06M_Sectiony/ CPU times: user 561 ms, sys: 139 ms, total: 700 ms Wall time: 19.7 s
Client-6a57bfaf-1970-11ed-a0df-080038b93bbf
| Connection method: Cluster object | Cluster type: distributed.LocalCluster |
| Dashboard: http://127.0.0.1:8787/status |
4cd0a6f3
| Dashboard: http://127.0.0.1:8787/status | Workers: 16 |
| Total threads: 128 | Total memory: 251.06 GiB |
| Status: running | Using processes: True |
Scheduler-8a8201d2-9b53-4a9f-8cf3-cea561efb4a0
| Comm: tcp://127.0.0.1:45463 | Workers: 16 |
| Dashboard: http://127.0.0.1:8787/status | Total threads: 128 |
| Started: Just now | Total memory: 251.06 GiB |
| Comm: tcp://127.0.0.1:33338 | Total threads: 8 |
| Dashboard: http://127.0.0.1:42967/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:43438 | |
| Local directory: /tmp/dask-worker-space/worker-ulse4cqw | |
| Comm: tcp://127.0.0.1:33386 | Total threads: 8 |
| Dashboard: http://127.0.0.1:42211/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:36736 | |
| Local directory: /tmp/dask-worker-space/worker-m4ed_nfl | |
| Comm: tcp://127.0.0.1:37351 | Total threads: 8 |
| Dashboard: http://127.0.0.1:38191/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:38345 | |
| Local directory: /tmp/dask-worker-space/worker-myimxil8 | |
| Comm: tcp://127.0.0.1:37974 | Total threads: 8 |
| Dashboard: http://127.0.0.1:39523/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:40830 | |
| Local directory: /tmp/dask-worker-space/worker-loq0k9c1 | |
| Comm: tcp://127.0.0.1:38577 | Total threads: 8 |
| Dashboard: http://127.0.0.1:44178/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:36789 | |
| Local directory: /tmp/dask-worker-space/worker-rgz6akn6 | |
| Comm: tcp://127.0.0.1:42552 | Total threads: 8 |
| Dashboard: http://127.0.0.1:37332/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:40755 | |
| Local directory: /tmp/dask-worker-space/worker-rsjx9_4k | |
| Comm: tcp://127.0.0.1:33575 | Total threads: 8 |
| Dashboard: http://127.0.0.1:33411/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:41956 | |
| Local directory: /tmp/dask-worker-space/worker-vours49c | |
| Comm: tcp://127.0.0.1:42627 | Total threads: 8 |
| Dashboard: http://127.0.0.1:40835/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:45989 | |
| Local directory: /tmp/dask-worker-space/worker-bitadvzm | |
| Comm: tcp://127.0.0.1:43190 | Total threads: 8 |
| Dashboard: http://127.0.0.1:36415/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:39605 | |
| Local directory: /tmp/dask-worker-space/worker-ktx2u8ef | |
| Comm: tcp://127.0.0.1:33049 | Total threads: 8 |
| Dashboard: http://127.0.0.1:46211/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:35660 | |
| Local directory: /tmp/dask-worker-space/worker-sntrv2f9 | |
| Comm: tcp://127.0.0.1:42910 | Total threads: 8 |
| Dashboard: http://127.0.0.1:39039/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:35824 | |
| Local directory: /tmp/dask-worker-space/worker-8h1hm2c3 | |
| Comm: tcp://127.0.0.1:39645 | Total threads: 8 |
| Dashboard: http://127.0.0.1:46460/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:37131 | |
| Local directory: /tmp/dask-worker-space/worker-i3v567p4 | |
| Comm: tcp://127.0.0.1:34920 | Total threads: 8 |
| Dashboard: http://127.0.0.1:36650/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:39224 | |
| Local directory: /tmp/dask-worker-space/worker-e19wyq41 | |
| Comm: tcp://127.0.0.1:42980 | Total threads: 8 |
| Dashboard: http://127.0.0.1:33387/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:45073 | |
| Local directory: /tmp/dask-worker-space/worker-c_33i9p4 | |
| Comm: tcp://127.0.0.1:44372 | Total threads: 8 |
| Dashboard: http://127.0.0.1:35552/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:46785 | |
| Local directory: /tmp/dask-worker-space/worker-u4nphflz | |
| Comm: tcp://127.0.0.1:45372 | Total threads: 8 |
| Dashboard: http://127.0.0.1:41710/status | Memory: 15.69 GiB |
| Nanny: tcp://127.0.0.1:44238 | |
| Local directory: /tmp/dask-worker-space/worker-gmp8e77z | |
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,gridV.vomecrty,p... | data.unify_chunks().persist() | FramS | section | None | {'vosaline': (33,36.2), 'votemper': (-2,6), 'v... | None | S-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= False df.Inputs != nothing True lazy= False CPU times: user 376 µs, sys: 0 ns, total: 376 µs Wall time: 372 µs
0
%%time
monitor.auto(df,data,savefig,daskreport,outputpath,file_exp='SEDNA'
)
#calc= False
#save= False
#plot= True
Value='Section'
Zone='FramS'
Plot='section'
cmap='None'
clabel='None'
clim= {'vosaline': (33, 36.2), 'votemper': (-2, 6), 'vomecrty': (-0.05, 0.05)}
outputpath='../results/SEDNA_DELTA_MONITOR/'
nc_outputpath='../nc_results/SEDNA_DELTA_MONITOR/'
filename='SEDNA_section_FramS_Section'
#3 no computing , loading starts
data=save.load_data(plot=Plot,path=nc_outputpath,filename=filename)
start loading data
filename= ../nc_results/SEDNA_DELTA_MONITOR/SEDNA_section_FramS_Section/t_*.nc dim t
load computed data completed
<xarray.Dataset>
Dimensions: (t: 122, z: 150, x: 601)
Coordinates:
* t (t) object 2012-03-01 12:00:00 ... 2012-06-30 12:00:00
y int64 ...
* x (x) int64 3734 3735 3736 3737 3738 ... 4330 4331 4332 4333 4334
* z (z) int64 1 2 3 4 5 6 7 8 9 ... 143 144 145 146 147 148 149 150
depth (z, x) float32 dask.array<chunksize=(150, 601), meta=np.ndarray>
mask2d (x) bool dask.array<chunksize=(601,), meta=np.ndarray>
nav_lat (x) float32 dask.array<chunksize=(601,), meta=np.ndarray>
mask (z, x) bool dask.array<chunksize=(150, 601), meta=np.ndarray>
nav_lon (x) float32 dask.array<chunksize=(601,), meta=np.ndarray>
Data variables:
vosaline (t, z, x) float32 dask.array<chunksize=(1, 150, 601), meta=np.ndarray>
votemper (t, z, x) float32 dask.array<chunksize=(1, 150, 601), meta=np.ndarray>
vomecrty (t, z, x) float32 dask.array<chunksize=(1, 150, 601), 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_FramS_Section_20120301-20120630.html starts plotting ../results/SEDNA_DELTA_MONITOR/SEDNA_section_FramS_Section_20120301-20120630.html created
CPU times: user 1min 19s, sys: 12.1 s, total: 1min 31s Wall time: 4min 13s